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https://f1000research.com/articles/13-263/v1
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12 Apr 24
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{
"type": "Research Article",
"title": "Minimal clinically important difference in physical activity in patients with stroke",
"authors": [
"Shogo Hiragami",
"Keishi Yoshida",
"Tsunehiro Otsuka",
"Yu Inoue",
"Keishi Yoshida",
"Tsunehiro Otsuka",
"Yu Inoue"
],
"abstract": "Background Estimates of the minimal clinically important difference (MCID) for stroke-related outcomes are needed, but the MCID for physical activity is unknown.\n\nObjective To provide an anchor-based estimate of the MCID for physical activity in patients with stroke.\n\nMethods This study included 31 patients with stroke admitted to a hospital and discharged home. Physical activity, including the daily number of steps and metabolic equivalents (METs), was evaluated shortly after informed consent was obtained following admission (baseline) and discharge using an Active-style Pro HJA-750C with a triaxial accelerometer. We calculated the number of steps and time rate (%) of sedentary behavior (SB), light-intensity physical activity (LPA), and moderate-to-vigorous physical activity (MVPA) per day. After discharge, the physical therapist rated each participant’s perceived amount of physical activity recovery on the Global Rating of Change scale (GRC). The mean change in each physical activity data point from baseline to after discharge in the group of participants who answered “a little better, meaningful” in the GRC was considered the MCID.\n\nResults Eighteen participants were included in the analysis. Participants’ physical function improved from baseline to at discharge during hospitalization, although mild motor paralysis persisted. MCID values for the step activity, SB, LPA, and MVPA were 1828 steps, -11.2%, 6.9%, 4.3% per day, respectively.\n\nConclusion For researchers and clinicians, this study’s MCIDs provide a benchmark for interpreting changes in the effects of intervention studies, and specific guidelines for interventions in clinical practice. Further research with larger sample sizes is required to confirm these findings.",
"keywords": [
"stroke",
"minimal clinically important difference",
"physical activity",
"global rating of change scale",
"rehabilitation"
],
"content": "Introduction\n\nThe number of people living with stroke worldwide has increased by 84% between 1990 and 2010. Stroke is the third leading cause of disability (Feigin et al., 2015). Notably, 50% of patients with ischemic stroke continually have hemiplegia for 6 months after onset (Kelly-Hayes et al., 2003), and a significant number of patients have activity limitations due to impaired extremities (Flynn, MacWalter and Doney, 2008). A low level of physical activity, often resulting from activity limitations, poses a significant risk factor for stroke (McDonnell et al., 2014). Engaging in regular physical activity and exercise, as recommended to enhance overall health, functionality, and daily independence (Belfiore, Miele, Gallè, and Liguori, 2018; Gordon et al., 2004; Lynch et al., 2018), is crucial for individuals recovering from stroke. However, it is observed that patients with stroke often lead sedentary lifestyles across various post-stroke stages (Bernhardt, Dewey, Thrift and Donnan, 2004; Field et al., 2013; Fini et al., 2017; Lacroix et al., 2016). Therefore, promoting physical activity stands as a critical intervention for patients with stroke.\n\nSeveral longitudinal observational studies have examined changes in patients’ physical activity after stroke onset. These studies have revealed that the number of steps, walking time, and standing time in patients with stroke increase over time after stroke onset with decreasing sitting/lying time (Kerr, Rowe, Esson and Barber, 2016; Kunkel, Fitton, Burnett and Ashburn, 2015; Moore et al., 2013; Simpson et al., 2018). Interventional studies on physical activity in patients with stroke have examined the effects of step activity (Danks, Pohlig and Reisman, 2016; Lynch et al., 2018), activity intensity (Askim et al. Stroke, 2018), and sitting time (English et al, 2016b). Notably, the results of these studies are crucial when considering interventions in clinical practice; however, it is also necessary to interpret data on changes in physical activity regarding patient-centered outcomes based on minimally clinically important differences (MCID), defined as “the smallest difference in scores in the domain of interest which patients perceive as beneficial” (Jaeschke, Singer and Guyatt, 1989). For researchers and clinicians, understanding MCID of physical activity in patients with stroke can help determine whether a change in outcome scores due to an intervention is clinically important (Revicki, Hays, Cella and Sloan, 2008). However, there is no knowledge of the MCID in physical activity, such as the number of steps and activity intensity, in patients with stroke. Therefore, this study aimed to estimate the anchor-based MCID for physical activity in patients with stroke.\n\n\nMethods\n\nThis study was approved by the Institutional Review Board of Hyogo Medical University (approval number: 4311), and all procedures followed the ethical standards of the Declaration of Helsinki. Written informed consent was obtained from all the participants.\n\nThis prospective observational study included 31 patients with stroke who were admitted to a hospital in Japan and discharged home between April 2019 and December 2022. No studies exist on the MCID in physical activity in patients with stroke; therefore, this study’s sample size was set at the minimum number of participants based on previous studies that examined the MCID in stroke-related outcomes (Bohannon, Andrews and Glenney, 2013; See et al., 2013). The inclusion criteria were 1) first stroke (ischemic or hemorrhagic) and stable medical condition after stroke onset, 2) no significant cognitive impairments and ability to have daily conversations to provide informed consent, and 3) no other disease influencing the physical activity. The participants underwent a rehabilitation program during hospitalization, including conventional physiotherapy, occupational therapy, and speech therapy (if needed) for approximately 150 min/day.\n\nInformation about participant characteristics such as age, sex, time since stroke onset, stroke type, side of paralysis, the severity of paralysis (assessed using the Brunnstrom recovery stage [BRS]), and functional performance (assessed using the Functional Independence Measure [FIM]) was extracted from each participant’s medical records after informed consent (baseline) and at discharge.\n\nGait ability and physical activity of the participants, including the number of steps and energy expenditure, were evaluated at baseline and after discharge from the hospital (average 42.1 ± 9.7 days, range: 32–62 days).\n\nA physical therapist assessed gait ability using the Functional Ambulation Category (FAC); the assessment after discharge was conducted through a telephone interview. Based on the physical support required, the FAC classifies walking ability into six categories, with score ranging from 0 (nonfunctional ambulator) to 5 (ambulator, independent) (Holden et al., 1984).\n\nPhysical activity was evaluated at baseline and after discharge using an Active-style Pro HJA-750C with a triaxial accelerometer (OMRON, Kyoto, Japan). The device can estimate step counts and metabolic equivalents (METs) every 10 seconds. The validity and accuracy of the device have been confirmed (Ohkawara et al., 2011; Oshima et al., 2010; Shimizu, Hashidate, Ota and Saito, 2018), and the device was used in a recent intervention study (Matsushita et al., 2022). The measurement method using this device was based on a previous study (Fini, Burge, Bernhardt and Holland, 2019; Troiano et al., 2008). All participants wore the device on a waist belt on their paretic side for 7 consecutive days. The participants were blinded to their step counts or activity intensity during the collection period by setting the device to avoid displaying step counts or activity intensity on the device screen. Participants were instructed to perform their usual physical activities. We extracted 12 hours of collected activity data between 8:00 am and 8:00 pm to analyze the data. An individual’s data were considered if there were ≥2 days of data with >10 h (600 min) of device-wearing time. Non-wearing of the device was defined as no counts for over 60 consecutive min in the daily measurement data. Sedentary behavior (SB) was defined as ≤1.5 estimated METs, light-intensity physical activity (LPA) as 1.6–2.9 estimated METs, and moderate-to-vigorous physical activity (MVPA) as ≥3 estimated METs (Ainsworth et al., 2011; Strath et al., 2013). We calculated the average number of steps and time rate (%) of SB, LPA, and MVPA (time for each intensity of physical activity divided by the wearing time of the device) daily for each participant. For measurement after discharge, the device was mailed to the participants’ homes. Subsequently, participants were asked by the physical therapist via telephone to wear the device and return it after the measurements were completed.\n\nIn a telephone interview conducted by the physical therapist after discharge, participants were asked about the extent to which they subjectively perceived a significant change in their physical activity from baseline to after discharge (at the time of the interview). For the assessment, we used the 7-point Global Rating of Change Scale (GRC) (Copay et al., 2007; Lang, Edwards, Birkenmeier and Dromerick, 2008). The participants were asked to answer the following question: “How much did your daily physical activity change compared with the time in the hospital?” using the GRC. Participants responded based on the following scores: 1 = much better; 2 = a little better, meaningful; 3 = a little better, not meaningful; 4 = approximately the same; 5 = a little worse, not meaningful; 6 = a little worse, meaningful; and 7 = much worse. The criterion validity and test-retest reliability of the GRC assessment has been confirmed in patients with stroke (Hiragami et al., 2012).\n\nFor the analysis, we first confirmed the participants’ cognitive function during hospitalization, using the mini-mental state examination scores ≥21 (Folstein, Folstein and McHugh, 1975) or FIM-cognitive scores ≥25 (Manuel et al., 2002; Tokunaga et al., 2014), and participants who did not meet these criteria were excluded from the analysis. Data were reported as mean and standard deviation (SD) or median and frequency (percentage). Two-sample t-tests or Wilcoxon rank tests were used to compare the participants’ characteristics between baseline and at discharge or after discharge. ANOVA or Kruskal–Wallis tests and Fisher’s exact tests were performed to compare the participants’ characteristics between the groups, classified by GRC score.\n\nThe MCID was calculated using anchor-based approaches. Following previous studies (Copay et al., 2007; Lang, Edwards, Birkenmeier and Dromerick, 2008), participants with a GRC score of 2 (a little better, meaningful) were assigned to the MCID group. The mean changes in the average number of steps and time rate (%) of SB, LPA, and MVPA per day in the MCID group between baseline and after discharge were considered the estimated MCID values. Two-sample t-tests or Wilcoxon rank tests, along with effect size calculations, were used to compare the average number of steps and the time rate (%) of SB, LPA, and MVPA at baseline and after discharge. The effect size (r) was calculated using the following formula:\n\nThe effect size values were interpreted as 0.1 for small, 0.3 for medium, and 0.5 for large (Cohen, 1992). Statistical significance was set at p < 0.05. All statistical analyses were conducted using IBM SPSS Statistics software (version 27).\n\n\nResults\n\nThirty-one participants consented to participate in this study. Eleven subjects had insufficient physical activity data for analysis (2, urgent discharge; 3, incomplete physical activity data after discharge; 1, refusal of measurements; and 5, no response to phone calls after discharge). Two participants had physical activity data for <2 days. Therefore, 18 participants were included in the analysis (Figure 1). Participants wore the device for an average of 5.4 ± 2.1 days at baseline and 4.2 ± 1.8 days after discharge. Participants’ average daily device wearing time was 706.3 ± 26.4 min/day at baseline and 682.3 ± 32.0 min/day after discharge. Four participants had missing step-count data at baseline or after discharge; these participants were excluded from the analysis of step-count data.\n\nOf 31 enrolled participants, 13 were excluded from the analysis and 18 were included in the final analysis.\n\nThe participants’ characteristics are summarized in Table 1. The average participant age was 72.8 ± 8.6 years, and the average number of days since stroke onset was 41.9 ± 19.2 days at baseline and 146.9 ± 49.1 days after discharge. The participants’ physical function, gait ability, and functional performance improved from baseline to at discharge during hospitalization, although mild motor paralysis remained.\n\n* Wilcoxon rank test.\n\nTable 2 summarizes participant characteristics based on GRC scores. The GRC response distribution was as follows: 1 (much better), n = 5; 2 (a little better, meaningful), n = 8; 4 (approximately the same), n = 5, 3, and 5-7: n = 0. There were no significant differences in participant characteristics, gait ability, and functional performance between the GRC score-classified groups except for physical function. There were significant differences in BRS; motor paralysis of upper and lower limb was more severe in the group with a GRC score of 4.\n\na Kruskal–Wallis test.\n\nb Fisher’s exact test.\n\nTable 3 summarizes the average number of steps and time rate (%) of SB, LPA, and MVPA and their changes from baseline to after discharge. For all participants and MCID group, MVPA% increased significantly after discharge compared to baseline, and there were no significant changes in other indicators of physical activity.\n\n* Wilcoxon rank test.\n\nThe mean changes in the average number of steps and time rate (%) of SB, LPA, and MVPA in the MCID group (GRC=2) between baseline and after discharge were 1828 steps/day, -11.2%/day, 6.9%/day, and 4.3%/day, respectively.\n\n\nDiscussion\n\nA novel finding of our study was that the MCIDs of physical activity were estimated using the stroke patient-centered outcome measure (GRC) as an anchor. We evaluated the physical activity of patients with stroke during hospitalization and after discharge to estimate the MCID. MVPA% increased significantly after discharge compared to baseline in all participants and MCID group, and there were no significant changes in the number of steps, SB%, and LPA%. As the results of these statistical analyses may have been influenced by the small sample size, we examined the changes using effect sizes. The effect sizes for changes in the number of steps and time rate (%) of SB, LPA, and MVPA from baseline to after discharge ranged from small to large for all participants. These results are consistent with those of previous studies. A previous study that investigated changes in the number of steps in patients with stroke with a similar number of days since stroke onset and walking ability as our study participants found a significant increase (at hospital: average 1872 steps/day and at home after discharge: 2596 steps/day; mean difference: 725 steps/day) (Simpson et al., 2018). The study also reported that sitting time decreased significantly (at the hospital: average 648 min/day; at home after discharge: 624 min/day, Mean Difference: - 45 min/day). Our study also showed a decrease in SB%/day; the SB time from baseline to after discharge, calculated using the average daily wearing time of the device after discharge (682 min), had reduced from 505 min/day to 480 min/day, with a difference of -26 min.\n\nBased on the data from previous studies, the physical activity levels of patients with stroke in our study remained low even after returning to the community. A systematic review of physical activity in people with stroke living in the community showed that the number of steps ranged from 1389 to 7379 steps/day, compared with 6294 to 14730 steps/day in healthy older adults (English, Manns, Tucak and Bernhardt, 2014). Community-dwelling patients with stroke spent 206 min in LPA and 5 min in MVPA and had significantly lower levels of LPA and MVPA than healthy controls (English et al, 2016a).\n\nTo our knowledge, this is the first study to estimate the MCID for physical activity in patients with stroke. Therefore, there are no data to compare with our results. The validity of the MCID estimated in our study can be examined using effect size as an external criterion (Copay et al., 2007). In this study, SB% decreased and the step activity, LPA%, and MVPA% increased; and the effect sizes of these changes were medium to large in the MCID group (GRC=2). Therefore, it was appropriate to use data from the group to estimate the MCID. The MCID is a more appropriate benchmark than statistical significance for determining the importance or effectiveness of change scores (Hsieh et al., 2007). The P-value is influenced by the magnitude of change and the study’s sample size and group variance (Crosby, Kolotkin and Williams et al., 2003). Therefore, if the physical activity data in a group of patients with stroke similar to those in our study exceeded the MCID, the change could be interpreted as meaningful. Conversely, if the physical activity is lower than the MCID, the change should not be regarded as meaningful, even if the amount of change reaches a statistically significant level. We believe that for researchers and clinicians, this study’s MCID provides a benchmark for interpreting changes in longitudinal studies, the effects of intervention studies, and specific guidelines for interventions for patients with stroke during hospitalization and after discharge to promote physical activity in patients.\n\nAccording to Tudor-Locke et al. (2011), the recommended number of steps for patients with chronic diseases, including stroke, is between 6,500 and 8,500 steps daily. Physical activity to prevent recurrent mild ischemic stroke is also aimed at achieving 6025 steps/day (Kono et al., 2015). Regarding the physical activity intensity, according to the World Health Organization (De Camargo and Añez, 2020), adults living with disabilities should engage in at least 150-300 min of moderate-intensity aerobic physical activity, or at least 75-150 min of vigorous-intensity aerobic physical activity throughout the week, or a combination of both, to achieve substantial health benefits. In our study, the duration of MVPA was calculated using the average daily wearing time of the device (682 min) after discharge in the MCID group (GRC=2), and MVPA was 37 min/day. Comparing our data with the indices presented in previous studies (De Camargo and Añez, 2020; Kono et al., 2015; Tudor-Locke et al., 2011), the number of steps taken in our study were considerably lower in the MCID group after discharge. Therefore, if health aspects are the main outcomes, changes in the number of steps taken in patients with stroke may need to be well above our study’s MCID.\n\nThis study has some limitations. First, the MCID estimation method was limited. The estimation of MCID for a specific patient-reported outcome measure should be based on multiple approaches (e.g., receiver operating characteristic curves) (Arya, Verma and Garg, 2011; Page, Fulk and Boyne, 2012). This study could not use the method due to its small sample size. Second, this study could not robustly align the time since the stroke onset, the degree of paralysis, walking ability, or individual factors of the participant. Third, during the survey period of our study, participants’ physical activities could have been altered due to the coronavirus 2019 pandemic. The MCID may vary by population and context. Therefore, future studies with a larger sample size should analyze MCID by including participants’ functional levels and individual factors.\n\n\nConclusions\n\nThe MCID values for the step activity, SB, LPA, and MVPA were 1828 steps/day, -11.2%/day, 6.9%/day, and 4.3%/day for patients with stroke with mild motor paralysis who were hospitalized and discharged home. These findings may be useful for clinical interpretation of physical activity data. Further research with larger sample sizes is required to confirm these estimates.",
"appendix": "Data availability\n\nFigshare: Dataset of minimal clinically important difference in physical activity in patients with stroke. https://doi.org/10.6084/m9.figshare.25471156.v1 (Hiragami, 2024).\n\nThis project contains the following underlying data:\n\n• Dataset of minimal clinically important difference in physical activity in patients with stroke.csv\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 are grateful to all individuals who gave their time to participate in this study.\n\n\nReferences\n\nAinsworth BE, Haskell WL, Herrmann SD, et al.: 2011 Compendium of physical activities: a second update of codes and MET values. Med. Sci. Sports Exerc. 2011; 43: 1575–1581. Publisher Full Text\n\nArya KN, Verma R, Garg RK: Estimating the minimal clinically important difference of an upper extremity recovery measure in subacute stroke patients. Top. Stroke Rehabil. 2011; 18: 599–610. 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}
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[
{
"id": "304216",
"date": "06 Aug 2024",
"name": "Joachim Liepert",
"expertise": [
"Reviewer Expertise Neurorehabilitation",
"plasticity",
"motor functions"
],
"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 paper attempts to identify the minimal clinically important difference in physical activity in stroke patients by assessing the number of steps and time rates of 3 different behaviors (sedentary behavior, light-intensity physical activity, and moderate-to-vigorous physical activity) and attributing them to results obtained from the Global Rating of Change Scale (GRC). According to the GRC results, 18 stroke patients could be assigned to 3 groups (“much better“ (n=5), “a little better, meaningful“ (n=8) and “approximately the same“ (n=5)). The patients that evaluated their change as “a little better, meaningful“ (n=8) were chosen as those that represent the minimal clinically important difference. Changes in the number of steps and behavioral time rates were calculated and presented.\nThe idea of this study is highly important and clinically relevant. However, I have several concerns and questions. My main concern relates to the number of subjects on which the data is based. Eight stroke patients do not seem to be a representative number on which conclusions and recommendations can be based. I am aware of the fact that the prerequisites for a power analysis are not fulfilled due to lack of pre-existing data on this topic. Nevertheless, eight patients are not sufficient to establish cut off values. Another concern relates to the question the patients were asked (“How much did your daily physical activity change compared with the time in the hospital“). As far as I understood the protocol, patients stayed in the rehab hospital for about 7 weeks. During this time, physical activity should have changed considerably. However, the question does not specify whether patients should consider the beginning or the end of their inpatient stay. As mentioned above, it is most unlikely that patients can estimate a “mean value“ because of the changes in performance and activity level that usually occur during rehabilitation. Please provide a more detailed description of how “metabolic equivalents“ (page 4) are calculated. Please provide information about the time patients had already spent at home when they were asked to wear the Active-style Pro HJA-750C device. Please define more precisely when the baseline evaluation was done – how many days after admission to the hospital? Please provide explanations for the letters “Z“ and “N“ used in the formula (page 4). To my knowledge, Cohen´s d is interpreted as being large if it exceeds 0.8 (and not 0.5, as stated in the manuscript on page 4). Why was the FAC not assessed at discharge?\nIn conclusion, I acknowledge that the authors have listed the limitations of their study (page 7) and agree on this paragraph. However, my concern regarding the group size still persists.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-263
|
https://f1000research.com/articles/12-560/v1
|
30 May 23
|
{
"type": "Research Article",
"title": "Indoor environmental quality in schools: NOTECH solution vs. standard solution",
"authors": [
"Carlo Volf",
"Klaus Martiny",
"Mathias Andersen",
"Bodil Engberg Pallesen",
"Klaus Martiny",
"Mathias Andersen",
"Bodil Engberg Pallesen"
],
"abstract": "Background: In many Danish schools, the indoor environmental quality (IEQ) is challenging and studies document a poor IEQ in a majority of existing schools. Municipalities cannot afford comprehensive renovations and expensive mechanical ventilation solutions, hence public schools often suffer from poor indoor environment conditions. This study tests a new façade based, demand-controlled ventilation solution called NOTECH in the renovation of school. The study tests NOTECH vs. existing mechanical ventilation solution, comparing performance of both solutions at Skovbrynet Skole in Denmark. Methods: The project implements and investigates the effect of the NOTECH solution in a primary school classroom, comparing it to a similar classroom with conventional, mechanical ventilation. Methodically, indoor environmental quality and energy performance is monitored in the two identical classrooms during one school year 2018 - 2019. Results: The results show that both systems keep the conditions within acceptable limits and CO2 levels below 1000 ppm, which is the requirement according to the Danish Building Regulations. In terms of costs, the NOTECH system has a lower overall cost than the mechanical ventilation system, with total estimated costs for installation, heating, electricity and maintenance amounting to approximately 35% of the mechanical system’s costs. Finally, the results show that the NOTECH solution has a smaller embedded CO2 footprint for building materials, reducing the estimated carbon load by 95% compared to the mechanical ventilation solution. Conclusions: The performance of the two systems roughly is the same in relation to the indoor environmental quality, temperature, CO2 levels, humidity and noise level. Costs for implementation, energy consumption for heating and CO2 footprint for building materials however, are significantly lower for the NOTECH solution, compared to the mechanical solution.",
"keywords": [
"Natural ventilation – indoor environmental quality (IEQ) – schools – mechanical ventilation – energy performance"
],
"content": "Introduction\n\nWhen it comes to establishing and maintaining a good indoor climate, schools have always been of particular interest. Historically, a good, balanced indoor climate was established in a very low-tech manner; pupils typically spending 45 minutes in each lesson, in high-ceilinged classrooms, often followed by 15 minutes of venting during breaks, in empty classrooms and with children outdoor in the school yard year-round. This meant that in most cases, natural ventilation - which most schools were fully based on until the mid1960s – probably did meet the requirement of CO2 < 1.000 ppm, based on natural air-intake from windows and doors,1 the buildings at that time not being air-tight as today.2,3 However, the situation and teaching philosophy is different today. First of all, schoolchildren spend more time inside the buildings. According to a report from Organization for Economic Cooperation and Development, OECD (2016),4 Danish pupils spend a total of 10,960 hours on school education, which is considerably more time than the European average of 7,540 hours. Secondly, lessons tend to have a longer duration today, the children often having 2-period lessons corresponding to 1.5 hours. Thirdly, the architecture of the schools has changed. Together with energy renovation and air-tight mechanically ventilated buildings, new types of classrooms have been introduced, such as project space schools and open-plan schools. Older schools however, built before 1995, still have traditional classrooms based on natural ventilation through the windows. These schools make up 90% of all schools in Denmark and often suffer from a poor indoor environmental quality. A Danish study from 2016 by Toftum and Wargocki5 showed that more than half of the existing schools in Denmark (1,300) suffer from a poor indoor air quality. Only 40-44% of schools in Denmark had a “good” indoor air quality (CO2 below 1.000 ppm).\n\nA few years later, a study with 234 Danish schools and 709 classrooms found that 53% of the classes had higher CO2-concentration levels than the allowed threshold of 1000 ppm (Toftum, Clausen and Christensen, 2022) (25). This study showed largely the same result as the earlier study from 2016, despite a number of initiatives to correct the inadequate ventilation. Even though slightly more classes than before had a ventilation system, the air quality did not improve significantly. Based on measurements in 60 Danish schools, with a total of 245 classrooms, the researchers found that ventilation had a positive effect on sick leave among teachers. The study also showed that generally increased air change per hour resulted in students’ performance improving by9%. Furthermore, lowering the temperature from 25 °C to 21 °C resulted in an 8% improvement in student performance. However, 91% of 245 classrooms in Denmark exceeded the recommended upper limit of 1.000 ppm CO2 in some periods during the school hours. On average, the 1.000 ppm CO2 limit was exceeded during 47% of the school hours during the heating season (November – April) and 12% during the summer season (May - October). The results also indicated that general noise levels were too high (above 65 dB(A)) in the classrooms in 63% of the usage time.\n\nThese findings are supported by other studies by e.g. Heschong Mahone Group (1999),6 Tanner (2009)7 and Shendell et al., 2004,8 which suggested that a poor indoor climate often resulted in more noise in the classroom, reduced concentration ability and poorer learning. Better air quality and better light quality also have shown to increase students' concentration and performance in mathematics and reading, among other subjects (Barrett et al., 20159 and Grün and Susanne Urlaub, 2015).22\n\nA study (Kjeldsen et al. 2015)10 suggested a link between indoor climate parameters, such as room temperature (°C), CO2 levels (ppm), daylight (lux), relative humidity (%) and noise level (dB(A)), and performance, with these parameters having an effect on well-being, learning and general health of students. Economically, a Danish study in 201811 showed that maintaining a good indoor climate costs approximately 0.38-0.54 EUR per pupil per day, using conventional, mechanical ventilation, corresponding to approximately 2.100 – 3.000 EUR per class annually. This represents a heavy burden for schools and municipalities, and may be the reason why the renovation of schools is happening slowly in Denmark. Approximately 50% of Danish schools were built in the 1960s and 1970s, and so many schools need renovations. Only approximately 10% of all schools have been built according to the energy requirements in the Building Regulations 1995 and onwards, and only a fraction of these, approximately 5%, are built according to the energy requirements for buildings from 2006.10 In other words, more than half of the Danish schools face an urgent need for energy renovation and improvement of the indoor climate in order to meet the current requirements.\n\n\nMethods\n\nMethodically, the study monitored the performance of the NOTECH solution and compared it to a traditional mechanical ventilation (MechVent) solution. The systems were implemented in identical, east-facing classrooms at Skovbrynet Skole in Copenhagen. The school was built in 1968 and chosen as it was representative of typical Danish schools, which mostly were built in the 1960s. These schools were originally based on natural ventilation through façade windows, but today they are often being renovated to full mechanical ventilation. Inclusion criteria for the class were set to 4th – 5th grade pupils representing the median for a normal 9-10 years period of schooling. The NOTECH system included façade elements, windows, blinded windows, solar chimneys for supplementary air outlet, and louvres for air intake with eelgrass filtering of outdoor air. Intelligent demand-controlled outlets on the top of the classroom and intakes at the bottom of the classroom were continuously adjusting the NOTECH ventilation rates according to temperature and CO2 levels inside and weather conditions outside; see Figure 2. In comparison, the mechanical ventilation system included conventional air-tight construction and conventional materials such as mineral wool and wood. The mechanical ventilation system was controlled by a clock timer in the intelligent building system (IBS).\n\nFrom the village school (1910) to the aula school and an early example of the open plan school, up to the project school.\n\nTop: A solar chimney (E, D) provides under-pressure and IoT demand-controlled dampers (A) control fresh air-intake at the same time filtering the fresh air and reducing outside noise through special designed eelgrass filters (B). Bottom: Each classroom has two solar chimneys outside with air outlet above ceiling height.\n\nThe study was performed at Skovbrynet Skole. The public school was built in 1967 and renovated in 2002. Two east-facing classrooms were included in the study, both dimensioned for 24-28 pupils, each having a total of 16 pupils and 1-2 teachers. Both classrooms measured 9.5 x 8.6 m, with a net area of 81 m2. The classroom with the mechanical ventilation system had a recessed ceiling with a ceiling height of 2.7 m. The classroom with the NOTECH system had a total ceiling height of 3.2 m, with no recessed ceiling, since NOTECH was a façade-based ventilation system. Thus, the volumes were 220 m3 for the classroom with the mechanical system and 262 m3 for the test room with the NOTECH system.\n\nThe two classrooms had identical materials, structure and furniture, except for the façades. In the classroom with the NOTECH system, novel natural insulating materials (eelgrass) and clear glazing (g = 0.72) were introduced, while the reference classroom was based on conventional materials (mineral wool) and standard glazing (g = 0.60). The total glass-area of the classroom with the NOTECH solution was 14 m2 (glass-floor area ratio of 17.3%) whereas the total glass area of the MechVent solution was 16.1 m2 (glass-floor area ratio of 19.9%). Both classrooms had exterior yellow screens for solar protection and two openable windows.\n\nThe ventilation principles of the two classrooms were fundamentally different. The NOTECH system in the test classroom was a passive ventilation system, driven by thermal stack pressure, while the system in the reference classroom was driven by a central, mechanical ventilation unit. Both systems fulfilled the minimum requirements of 5 l/s/pupil and 0.35 l/s/m2 floor area. The ventilation in the reference classroom was similar to that of the rest of the school.\n\nThe MechVent solution\n\nThe existing mechanical ventilation system was based on a standard, central unit serving a number of other classrooms (28), driven by motors running at an installed power of 2x4 kilo-Watts and demand-controlled by a clock timer in the IBS system. Via a (IBS) timer, the system was set automatically to start ventilating the classroom at 7 am, one hour before the start of teaching and end at 5 pm. The capacity of the standard mechanical ventilation system was dimensioned for a maximum airflow of approximately 500 m3/h per classroom. During the experiment, the airflow was estimated to be running at 80% of the full capacity.\n\nThe NOTECH solution\n\nThe capacity of the NOTECH system was dimensioned to a maximum airflow of approximately 750 m3/h per classroom. The demand-control of the NOTECH system was controlled by being tuned to an estimated airflow of 50% of full capacity, based on the number of pupils. The NOTECH system was set to automatically ventilate from 07.30 am and end at 3 pm, since the demand-controlled system only ventilated during the usage hours. The tuning was regulated twice, on October 6th 2019 from 20 to 22°C and again the Dec 20th to 21.5°C. The later adjustments were based on a wish to optimize and balance the ventilation rate, at the same time making sure that no pupils nor teachers found the room too chilly. Adjustments only affected the setpoint of temperature, not the setpoint of timer.\n\nThe total outlet area of NOTECH was 0.7 m2 and had a maximum air velocity of approximately 0.3 m/s. The air intake was 2.1 m2, approximately three times larger than the outlet area, allowing lower airflow speed at high air change per hour (ACH), without the risk of draught. At the same time the NOTECH system was designed to reduce noise, using eelgrass as a noise-reducing, acoustic material. The NOTECH system also included two supplementary solar chimneys, enabling potentially higher ventilation rates during sunny days. The solar chimneys may potentially have an effect, especially on the summer ventilation, causing more passive cooling/ventilation during sunny days (Figure 2). This effect was not studied in this project.\n\nThe NOTECH system integrated three elements 1) natural ventilation 2) clear glazing and 3) natural materials, as described below.\n\nNatural ventilation\n\nNOTECH was based on passive, one-sided thermal ventilation; taking advantage of the solar heat radiation as a supplementing force to enhance the buoyancy effect. The solar chimney ventilation system was designed to reduce excessive temperatures in the classroom during summer periods. In most cases this system means that the original building physics can be maintained, so that recessed ceiling heights may be avoided and only windows replaced.\n\nClear glazing\n\nThe system introduced high-transmittance windows based on two-layered low-iron clear glass that provided more transmitted daylight in the form of UV, visible and IR light.12 The window allowed a clearer view out. It also allowed parts of UVB light to penetrate, which may have positive health effects such as enabling vitamin D formation,13 as well as germicidal effects and killing of bacteria/viruses.14 During winter periods, the NOTECH solution was designed to utilize to a higher degree solar light and heat, using high transmitting, clear glazing, with a higher g-value, thus facilitating a higher passive solar heat gain in the heating season.\n\nNatural materials\n\nThe system introduced traditional, vernacular materials such as eelgrass combined with natural ventilation using intelligent demand-control technology. Natural materials such as eelgrass are known to have a antimicrobial effects, because of its natural salt-content and antimicrobial secondary metabolites (Choi et al., 2009; Papazian et al., 2019) (22, 24). Traditionally, eelgrass was applied in mattresses and indoor furnishings, etc. When applied in larger quantities, these natural materials help maintain a higher, more natural, relative humidity, being a hygroscopic building material, absorbing and releasing moist.15 In this way, eelgrass helps balance the humidity, maintaining a relative humidity above 40% RH, which is a recommended minimum threshold value for a healthy environment.16,17\n\nMonitoring procedure and time plan\n\nData were collected continuously over one year and analyzed for representative 3-week periods during the summer and winter, respectively. Typical periods were chosen as 3-week periods with temperatures above 20 C during summer and 3-week periods with temperatures below 10 C during winter. This was in order represent a normal Danish summer and winter setting. Data were simultaneously collected for both classrooms (NOTECH and standard mechanical ventilation) using two identical Indoor Climate meters (IC-Meter Mobile (GSM), in each classroom, placed 1.8 m above the floor in each classroom. IC meters were placed at identical locations, in the center of both inner walls in the two classrooms. Indoor climate parameters CO2, temperature, relative humidity, and noise were measured and logged every 5 minutes. Data were extracted for representative weeks for the summer period and the winter period, week 35/37 in 2019 (26.08.19 – 15.09.19) and week 8/10 17.02.20 – 11.03.20) in 2020, respectively; these periods being the warmest and coldest periods. See Table 1.\n\nBaseline measures were not included in the results and only served as a baseline for the parallel health study to confirm that the two classrooms were identical before intervention.\n\nIndoor environmental quality\n\nHourly average values of CO2 concentration, relative humidity, noise and temperature were analyzed for the representative weeks, as averages, cumulated frequency of different CO2 levels, relative humidity (% RH), temperature and noise levels. Data on the two glass types used in the study document a higher transmittance of the NOTECH system’s glazing types (g = 0.72, visible light transmittance = 0.82) providing more transmitted daylight and solar heat compared to the mechanical system (g = 0.6, visible light transmittance = 0.74). Differences in daylight between the classrooms were not measured, since the focus of the study was on CO2 levels, relative humidity (% RH), temperature and noise levels.\n\nEnergy performance\n\nThe operation costs for electricity of both systems, excluding energy costs for lighting, were calculated as EUR per pupil per month in total estimated electricity consumption, based on a Danish national kWh price of 0.30 EUR (2019/2020), with an estimated average of 20 children in each classroom, 7 h per day, and the standard usage period of 25.2 days per month (corresponding to 200 days per year).\n\nOperation costs of both systems were based on measurements using digital Ista Oprimo III evaporation meters. The evaporation meters were installed directly in front of the radiators in each classroom 0.5 m above floor level. Installation was carried out at the same day and evaporation meters were monitored every 15 minutes during the heating season.\n\nTotal installation costs\n\nIn order to represent a realistic school setting, the calculations of energy performance for electricity and heating, together with the estimated installation costs, were based on a total of 10 classrooms for both systems. All operating costs for electricity, heating and maintenance together with installation costs were based on a 20-year lifetime, which is considered the lifetime of conventional, mechanical ventilation systems.\n\nCarbon footprint\n\nThe approximated life-cycle analysis (LCA) was based on the European ECO2 carbon footprint for materials and products with a focus on wooden building products.17 Material calculation for the mechanical system was based on data and description of materials from the suppliers. Material calculation for the mechanical system was based on one central, mechanical system, Danvent Combi Aggregate TC, with heat recovery running on 240 V, with galvanized steel ducts. Material calculation for the NOTECH system was based on 2 pcs IoT-controlled chain actuators (WMX 804) in steel and 4 pcs Klimatek dampers in aluminum, running on 24 V Belimo motors.\n\nParameters for intelligent demand-control\n\nThe NOTECH system was demand-controlled by three parameters: usage time, temperature levels and CO2 levels, taking into account the number of pupils. The standard mechanical system was controlled by one parameter: usage time, not taking into account the number of pupils in the classroom.\n\nAnalysis\n\nIndoor environmental quality parameters for a 3-week representative period during summer and winter, were represented in grouped in intervals in pie charts showing a percentage of the different ranges observed in order to compare the two systems across seasons.\n\n\nResults\n\nThe overall results of the indoor environmental quality (Volf, 2023) showed the following differences between the two systems.\n\nIndoor classroom CO2 levels were lower than 1.000 ppm for 100 % of school hours for the mechanical system and 95% of the school hours for the NOTECH system in the summer period 2019 and winter period 2020 (Figure 3). CO2 levels above 1.000 ppm were reached for the NOTECH system in short periods of 10-15 minutes, 5 % of the usage time, and only during the summer period (Figure 3). CO2 levels for the mechanical system generally were lower than for the NOTECH system (Figure 4). On average during the summer and winter period, the CO2 levels were 600 ppm for the mechanical vs. 800 ppm for the NOTECH system. Higher CO2 levels were reached during the summer period than during the winter period for the NOTECH.\n\nNOTECH and mechanical ventilation summer (above) and winter (below)\n\nTypical average hourly levels for NOTECH natural ventilation compared to mechanical ventilation (MechVent).\n\nNOTECH uses outside air directly without preheating, hence control of the indoor temperature (> 20°C) was a determining factor for the ventilation rates. MechVent, using preheated air, had higher air rates, which reduced the CO2 levels compared to natural ventilation. The indoor temperature for the NOTECH system was typically about 2-2.5 °C lower than the temperature for the mechanical system (MechVent) (Figure 5). For the NOTECH system, comfortable temperatures of 20-24°C were obtained 25.2% of the time in the summer period, with no hours with temperatures above 27°C. For the mechanical system, comfort temperatures of 20-24°C were obtained 15.3% of the time in summer, and the hours with temperatures above 27°C added up to 5% of the usage time (Figure 6).\n\nTypical hourly average levels for NOTECH natural ventilation compared to mechanical ventilation (MechVent). Because NOTECH uses cold “fresh” outside air, the indoor temperature is lower (20 °C) and the relative humidity (%) higher compared to mechanical ventilation.\n\nThe high-transmittance glazing types (g = 0.72) in the NOTECH system did not cause more hours with temperatures above 27°C during the summer period. Temperatures above 26°C were observed 18.5% of the time for the NOTECH system, compared to 21% of the time for the mechanical system, Figure 6.\n\nTemperatures during winter were generally colder for the NOTECH system, with the lowest temperatures recorded between 20 and 21°C, observed 16.8 % of the usage time, whereas no temperatures below 21°C were observed in the classroom with the mechanical system.\n\nDuring the summer period, the relative humidity was roughly the same for both systems, see Figure 7. This is despite the fact that the temperatures generally were higher for the classroom with the mechanical system. During the winter period, the relative humidity for the NOTECH system was between 35-45% RH 39.9% of the time, while a relative humidity between 35-45% was observed only 4.9% of the time for the mechanical system. The general indoor winter temperatures were however higher for the mechanical system during winter, thus lowering the relative humidity; see Figure 6.\n\nNoise levels dB(A) during the school hours showed no measurable difference between the two systems. Noise levels above 50 dB(A) are more frequent during the summer period for both systems (37.8% NOTECH system - 39.5% MechVent). Noise levels above 50 dB(A) are less frequent during the winter period (26.6% NOTECH system - 24.5% mechanical system), Figure 8.\n\nAverage daylight levels indoors were not measurably different between the systems, although more daylight was transmitted through the two layered low iron glazing of the NOTECH solution compared to that of the standard glazing in the room with the mechanical system. The glass area, on the other hand, was reduced in the NOTECH system.\n\nThe energy costs of electricity for both systems were estimated based on a total of 10 classrooms with 20 pupils 7 h per day, 25.2 days per month and kWh price set at 0.30 EUR. The estimated annual running cost for electricity was based on a 20 year lifetime. Estimated annual electricity consumption per classroom for the standard mechanical system was 305 kWh, amounting to 91 EUR annually per classroom. Estimated annual electricity consumption per classroom for the NOTECH system was 7 kWh, amounting to 2 EUR annually per classroom.\n\nEnergy consumption for heating was measured in the classrooms for NOTECH and the mechanical system, respectively. The energy for heating during the heating season (October-March), as measured by Ista evaporation meters, showed cumulated 693 units for the NOTECH system and 1,351 units for the mechanical system. Monitoring was carried out in two periods, the first period was for 2019 (15.08.2019-31.12.2019) and second period was for 2020 (01.01.2020-01.03.2020) (Figure 9).\n\nThe monitored data from evaporation meters monitoring each system during two periods. The first period is 15.08.2019-31.12.2019 and second period is 01.01.2020-01.03.2020. Source: Ista-meter 839, 891, 952, 072.\n\nBased on data from Gladsaxe Municipality, the degree day corrected total energy consumption for Skovbrynet Skole for heating October 2019 – April 2020 was 1,358 MWh for a gross heated area of 11,080 m2, giving the following average energy consumption for the two systems based on 81 m2 classrooms and 0.30 EUR per kWh. Based on Ista measurements, the energy consumption for the heating season 2019/2020 was 62,9 kWh/m2 per year for the NOTECH system and122,6 kWh/m2 per year for the mechanical system. Costs for heating per classroom in the heating season 2019/2020 amounted to1.540 EUR per year for the NOTECH system and 3.000 EUR per year for the mechanical system, based on 0.3 EUR/kWh.\n\nThe estimated total installation costs were calculated based on data from Skovbrynet Skole, based on information from suppliers of the NOTECH system (WindowMaster Ltd and Velfac Ltd) and the mechanical system (DanVent Ltd). All installation costs were based on 10 classrooms, each having 20 children for both systems and a lifespan of 20 years. The total installation costs for the NOTECH system were all in all 48.450 EUR and the total installation costs for the mechanical system were 147.800 EUR (40.300 EUR for the ventilation system and 107.500 EUR for ducts, fixtures, filters, etc.).\n\nThe total estimated costs for energy, installation, heating and maintenance per day per pupil (based on 20 pupils per classroom and 200 school days per year) was 1.06 EUR for the NOTECH system and 3.00 EUR for the conventional mechanical system. All in all, the total annual estimated costs of the NOTECH system amounted to 35% of the conventional, mechanical system; see Table 2.\n\nThe NOTECH solution was based on natural, bio-based materials, thus the CO2 footprint was smaller. The conventional mechanical solution spent 873 kg CO2, while the NOTECH solution spent 44 kg CO2. Thus, the NOTECH system reduced the embedded CO2 in the building materials by a total of 95%, compared to the mechanical ventilation system (Figure 10).\n\nEmbedded CO2 in the building materials is estimated for a standard life time period of 30 years. ECO2 data for materials used is standard values from Ruuska.18\n\n\nDiscussion\n\nThe aim of this study was to make a comparison between the NOTECH system and a conventional mechanical ventilation system. The classrooms in the study were representative for schools from the 1960s and 1970s and the results of this pilot study therefore should be seen as “a proof of concept” for this type of schools. The two rooms were alike though differing in volume due to the recessed ceiling height (0.5 m) in the classroom with the mechanical ventilation system – a difference which is considered representative for the solutions, since NOTECH as a façade solution, is not taking up ceiling space. The usage of the rooms were comparable, each hosting 16 fourth/fifth grade pupils.\n\nThe airflow in the mechanical system was controlled by a clock-timer, while the NOTECH system was demand-controlled by three parameters: usage time, temperature levels and CO2 levels. Except for short periods, both systems could keep the CO2 levels and temperatures within acceptable limits under the given conditions in the actual measurement periods.\n\nCO2 levels\n\nGenerally, higher values of CO2, temperature, humidity and noise tended to follow a higher activity and person load in the classrooms. Lower CO2 levels were generally observed during the summer period, compared to higher levels in the winter period. For both systems the summer period showed increased hours with low CO2 levels (below 500 ppm), indicating that the pupils were spending more time outdoor during summer – since inside activity at these periods would have shown an increase in the CO2 levels (above 500 ppm). However, higher CO2 levels were reached during the summer in the NOTECH solution. The natural, temperature gradient driven ventilation in NOTECH did not provide a constant air change per hour. The demand-control of the NOTECH system was tuned and slightly adjusted during the winter period, to provide a slightly higher air change during the winter period. We cannot tell if these adjustments caused lower CO2 levels in general during winter. Windows could be manually opened in both classrooms and other unknown factors were present.\n\nNormally the winter period is “the critical” period for natural ventilation systems, however, the demand-control of the NOTECH system in this pilot study seems to meet the requirements, providing sufficient fresh air in 95% of the usage time at a lower cost, during both the summer and winter periods being tested. However, it should be kept in mind that the winter 2019/2020 was mild compared to a normal Danish winter.\n\nTemperature\n\nThe difference in spatial volume between the systems is typical and representative for the two different systems. However, ceiling heights and room volumes may vary from building to building, and today´s mechanical systems may even have lower recessed ceilings. Increased ceiling height acts as a buffer reducing excessive temperatures. This may be another explanation for the higher frequency of temperatures above 26 °C in the classroom with the mechanical system, compared to the classroom with the NOTECH system.\n\nThe results show a lower number of hours with temperature above 26°C for the NOTECH system during the summer period, compared to the mechanical system (18.5% for NOTECH compared to 21% for mechanical ventilation) (Figure 6). The fact that the glass area in the NOTECH system was reduced by 13% compared to the standard mechanical system may explain these results. The higher frequency of hours with temperatures above 26 °C (21%) in the standard mechanical system may also be explained by the fact that the NOTECH system provides generally lower room temperatures, passively cooling during the morning and daytime. Difference in air volumes in the classrooms may also have influenced the temperatures. Increased ceiling height and thus greater air volume acts as a buffer, reducing excessive temperatures. Taken together, these factors may all add up to explain the differences between the two systems.\n\nRelative humidity\n\nDuring the winter period, the relative humidity generally tended to be higher for the NOTECH system. The lower limit <30% RH was reached more frequently for the mechanical system (37.1%) compared to the NOTECH system (9.8%) (Figure 7). This was partly caused by the general lower temperature in the classroom with natural ventilation. The heat recovery of the mechanical ventilation system together with differences in airflow – the NOTECH system being laminar and the mechanical system being turbulent airflow – may have had an influence on this, but the effects were not examined in detail in this study. In addition to a single-sided focus on set limits of CO2 concentrations, these results may suggest to include other parameters for a more satisfying indoor environmental quality, e.g. a better relative humidity.\n\nNoise levels\n\nThe measured average noise levels (dB(A)) were not significantly different between the systems. Generally, indoor noise levels exceeded outdoor noise levels. Levels above 50 dB (A) were more frequent during the summer period (37.8% of the usage time for the NOTECH system - 39.5% of the usage time for the mechanical system) and less frequent during the winter period (24.5% of the usage time for the mechanical system - 26.6% of the usage time for the NOTECH system).\n\nThis study reveals several differences between the two systems when it comes to energy performance and sustainability. The NOTECH system in general provides a sufficient air-change-per-hour at a lower estimated total annual cost. Estimated annual costs are 65% cheaper for the NOTECH system than for the mechanical system.\n\nThis study found that NOTECH saved energy for heating: 59.7 kWh/m2 per year compared to the standard system, corresponding to a reduction of 51% for heating. This was not expected, the NOTECH system being a passive system taking in cold, outside air directly without preheating. The energy consumption for heating is based on dynamic factors (such as solar heat gain, weather/wind/outdoor and indoor temperatures, etc.); the function of the NOTECH system needs to be investigated further, especially during cold winter periods. Generally, the NOTECH system had a lower air change per hour which may explain the lower energy consumption for heating compared to the mechanical system. The energy consumption for heating fluctuates from year to year and data in this study were collected empirically during one year and through a mild winter period. A cold winter period may result in colder indoor air-temperatures or in a higher general energy consumption for heating, and remains to be examined further during cold winter periods.\n\nOur estimated installation and running costs for the mechanically ventilated indoor climate system in this pilot study are in good agreement with a previous study.10 Based on 10 classrooms and 20 years lifetime, the installation cost for the NOTECH system is estimated to save 66%, compared to the conventional, mechanical ventilation system. The difference between the two systems in the estimated total capital expenditure (operating costs for electricity, heating, maintenance and installation costs) shows that the NOTECH system has a markedly lower cost compared to the mechanical system, costing only 35% of a mechanical ventilation system in total running costs. Based on a classroom with 20 pupils, the estimated total costs for the NOTECH are 1.06 EUR per day per pupil, while the costs for the mechanical ventilation system are 3.00 EUR per day per pupil.\n\nMore than half of the Danish schools face a need for energy renovation and improvement of the indoor climate in the form of optimized ventilation. In this respect, the results of this study show that systems such as the NOTECH can be an alternative to mechanical systems, resulting in fewer changes in existing architecture of the schools and less CO2 emissions and energy consumption.\n\nWith this background, the development of ventilation that merely relies on mechanical systems (Figure 1) should be questioned. Mechanical systems are not the only solutions and supplemented by intelligent, natural ventilation systems, a balanced indoor environment may be obtained, at a far cheaper price than only relaying on mechanical systems. Today, existing schools often cannot afford expensive mechanical ventilation systems. Intelligent systems like NOTECH can be an alternative, avoiding technical retrofit changes in existing architecture, suspended ceilings and ducts, etc. A system such as the NOTECH system will often be technically easier to implement than a mechanical system, both when it comes to existing and new building constructions. This includes the fact that lowering existing ceiling heights can be avoided, which means that the system uses fewer materials, at the same time maintaining more space, both in the form of more volume (which means increased buffer against excessive temperatures) as well as more area due to the need of fewer and smaller technical rooms.\n\nAccording to statistics in Denmark19 approximately 710,000 students are attending grades 0 – 10 in public schools, based on a recent 5-year period 2015 – 2020. Assuming that 50% of these students attend schools build in the 1960s and 1970s, there is a market of approximately 355,000 students. Assuming NOTECH is distributed in classrooms, corresponding to 25% of these 355,000 pupils, with savings of 1.98 EUR per pupil per day, this corresponds to a total reduction in national costs of 33.145.000 EUR per year, compared to conventional, mechanical ventilation solutions.\n\nThe approximated LCA analysis, based on the European ECO2 carbon footprint for building data for materials and products with focus on wooden building products, showed that the NOTECH system had a far smaller CO2 footprint, being only 5% of the CO2 footprint of the mechanical system (see Figure 10). In this respect, NOTECH is better in line with future sustainability requirements such as e.g. Level(s) in the European Commission and Denmark’s New Class of Sustainable Architecture.20 According to a recent study,21 waste and materials from the building industry today make up 50-83% of the emitted CO2 over a period of 80 years. Making an effort to reduce the carbon footprint of the building materials by 95% is a significant and valuable contribution to a more sustainable architecture and an important result of this pilot study of the NOTECH system.\n\n\nConclusion\n\nThis pilot study shows a proof-of-concept for the NOTECH system in typical school settings at Skovbrynet Skole built in 1967 and renovated in 2002. Further studies are needed to conclude that the demand-controlled system can also meet the acceptable levels under dimensioning conditions, i.e. with 24-28 students in the classrooms and during colder winter periods. The classrooms are representative for schools built in this period and the findings are only representative for similar cases. Likewise, the following conclusive points based on the specific case study are:\n\n• With the person load of the classrooms and considering that the NOTECH system was controlled by CO2 in the indoor air, both systems could keep both the CO2 level and temperature within acceptable limits. CO2 levels were on average lower for the mechanical system, compared to the NOTECH system.\n\n• The indoor room temperature was generally lower for the NOTECH system compared to the mechanical system. Having a lower set-point when compared to the mechanical system, the NOTECH system resulted in more hours with comfortable temperatures between 20-24°C compared to the mechanical system and fewer hours of temperatures above 27°C during the summer period when compared to the mechanical system.\n\n• The relative humidity was higher for the NOTECH system, corresponding to a generally lower indoor room temperature. The lower limit <30% RH was reached more frequently for the mechanical system (37.1%) compared to the NOTECH system (9.8%). Variations in temperature and relative humidity generally tended to follow high activity and person load in the classrooms.\n\n• Noise levels dB(A) measured during the school hours showed no measurable differences between the systems, indicating a similar activity level in the classrooms.\n\n• The estimated total costs for energy costs (energy consumption for electricity and heating) were lower for the NOTECH system compared to the mechanical system. The energy consumption for heating showed that the NOTECH system accounted for only 51% of the energy consumption, corresponding to 62.9 kWh/m2 per year compared to 122.6 kWh/m2 per year for the mechanical system, during the heating season tested (October 2019 - April 2020). Usage time between the two systems was different. Usage time for NOTECH was 07.30 – 14.30 and 07.00 – 17.00 for the mechanical system, and this accounts for some of the energy excess energy consumption of the mechanical system. Also, the setpoint for heating was lower for the NOTECH system (20.5 C) compared to the mechanical system (22 C). The test period was a mild winter period and this affected the energy consumption, however this was the case for both systems.\n\n• The total estimated installation costs for the NOTECH system amounts to 35% of the total installation costs of the conventional, mechanical system used in this study. However, the systems had a different start-time and end-time; NOTECH had a shorter operation time, 2.5 hours shorter than the mechanical system.\n\n• Over a period of 20 years, the estimated total running costs of the NOTECH system were 65% cheaper than the estimated total running costs of the mechanical system.\n\n• According to the life cycle assessment (LCA) over 30 years, the NOTECH system was estimated to reduce the carbon emissions of the building materials, the embedded CO2, by 95% compared to that of the mechanical ventilation system.\n\nSince the NOTECH system is a passive system, primarily using energy for heating, the winter period is decisive for the total energy balance of NOTECH. In this study, the results show that NOTECH reduced the energy consumption for heating during a mild winter period – which is contrary to what could be expected during a normal Danish winter. This needs to be further investigated.\n\nThis pilot-study challenges the current building requirements when it comes to demands for mechanical ventilation. Today, it is mandatory to use mechanical ventilation systems with heat recovery, thus hindering systems such as NOTECH in the planning of school classrooms in Denmark. The results indicate that intelligent control of passive, natural ventilation systems can be a sustainable solution, if not fully replacing a mechanical ventilation system then supplementing mechanical systems. The NOTECH system did have lower energy consumption, less impact on the architecture of the school, used fewer materials and therefore had a lower environmental impact. The results suggest that other types of buildings, with rooms having a lower person load than classrooms, can also benefit from demand-controlled natural ventilation systems such as NOTECH.\n\n\nEthical considerations\n\nThis study did not include any human participants.",
"appendix": "Data availability\n\nZenodo: Indoor Environmental Quality in Schools: Notech Solution vs. Standard Solution. https://doi.org/10.5281/zenodo.7821202 (Volf, 2023).\n\nThis project contains the following files:\n\n- IC-Meter-QR-Indoor-Outdoor-Hour-Data-Aug-2019_MECH_VENT_5X.csv (mechanical ventilation data for summer 2019)\n\n- IC-Meter-QR-Indoor-Outdoor-Hour-Data-Aug-2019_NOTECH_5Y.csv (NOTECH ventilation data for summer 2019)\n\n- IC-Meter-QR-Indoor-Outdoor-Hour-Data-Feb-2020_MECH_VENT_5X.csv (mechanical ventilation data for winter 2020)\n\n- IC-Meter-QR-Indoor-Outdoor-Hour-Data-Feb-2020_NOTECH_5Y.csv (NOTECH ventilation data for winter 2020)\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 WindowMaster for their aid developing and providing the demand control system, and Velfac, Region H, Gladsaxe Municipality, Skovbrynet Skole, Sustainable Build, and Advanced Nonwoven for their valuable contributions to the research project.\n\n\nReferences\n\nVolf C: Light, Air and Natural Surroundings - Different Hospital Typologies. Aarch 17 Conference Poceedings. 2017; p. 203 – 226.\n\nIn Denmark the first building requirements were introduced in March 1961. Ministry for Housing. Bygningsreglement for købestæderne og landet. Copenhagen 1961. http\n\nMinistry of Transport, Building and Housing, Copenhagen, 2018. Bygningsreglement.dk. xxx In English: BR18_Executive_order_on_building_regulations_2017.pdf. Reference Source\n\nEducation at a Glance 2016. Paris: OECD Indicators, OECD Publishing; Publisher Full Text\n\nClausen G, Toftum J, Bekö G, et al.: Indeklimaet I skoler. (Indoor climate in schools), Realdania. Copenhagen 2017. Masseundersøgelsen. The Technical University of Denmark (DTU) together with a study performed by DTU, based on 60 schools in Denmark.2016. Reference Source\n\nHeschong Mahone Group: Daylighting in schools: an investigation into the relationship between daylighting and human performance Illuminating engineering society.1999. Reference SourceReference Source\n\nTanner CK: Effects of school design on student outcomes. Journal of Educational Administration. 2009; 47(3): 381–399. Publisher Full Text\n\nShendel GS, Prill RJ: Association between class room CO2 concentrations and student attendance in Washington and Idaho. Indoor Air. 2004; 14(5): 333–341. Publisher Full Text\n\nBarret P, et al.: The impact of classroom design on pupils' learning: Final results of a holistic, multi-level analysis. Building and Environment. 2015; 89: 118–133. Publisher Full Text Reference Source\n\nKjeldsen J, Wargocki BU, Menå P, et al.: Association between classroom ventilation mode and learning outcome in Danish schools. Building and Environment. 2015; 92(2015): 494–503.\n\nAccording to a field study in Bornholm, Denmark.2018. Reference Source\n\nVolf C, Hagemann I, Martiny K, et al.: Accessed 14.09.2020. June 2015Reference Source\n\nMatusiak B, Kuhn T, Wirz-Justice A, et al.: Accessed 14.09.2020: Chapter 4 Daylight in the built environment in the \"Changing perspectives on daylight: Science, technology, and culture\" A Sponsored Supplement to Science.November 2017.\n\nBeck SE, Wright HB, Hargy TM, et al.: Action spectra for validation of pathogen disinfection in medium-pressure ultraviolet (UV) systems. Water Res. 2015 Mar 1; 70: 27–37. Epub 2014 Nov 28. PubMed Abstract | Publisher Full Text\n\nKlima EB: bolig og boformer. Momentum nr 1.2020; Pages 29 – 31. Reference Source\n\nSterling EM, Rundel A, Sterling TD: Criteria for Human Exposure to Humidity in Occupied Buildings. ASHRAE Transactions. 1985; 91, Part 1.\n\nWolkoff P, Kjærgaard SK: The dichotomy of relative humidity on indoor air quality. Environment International. August 2007; 33(6): 850–857. PubMed Abstract | Publisher Full Text Reference Source\n\nRuuska A: Carbon footprint for building products ECO2 data for materials and products with the focus on wooden building products. VTT technology 115, Espoo.2013. Reference Source\n\nhttp\n\nAccording to e.g. the EU-Commission initiative Level(s). Together with the Danish pendant. http http\n\nBirgisdottir H, et al.: ”SBI 2020:04 – Klimapåvirkning fra 60 bygninger – Muligheder for udformning af referenceværdier til LCA for bygninger”.2020. Reference Source\n\nVolf C: Indoor Environmental Quality in Schools: NOTECH Solution vs. Standard Solution - dataset (Version 01). [Dataset]. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "189717",
"date": "25 Jul 2023",
"name": "Asit Kumar Mishra",
"expertise": [
"Reviewer Expertise Indoor climate in low energy buildings",
"thermal comfort standards",
"HVAC"
],
"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 work investigates a noel passive ventilation system for classrooms and compares it with mechanical ventilation system. As expected, the passive system consumes less energy but it also provides similar indoor conditions and has lowers embedded carbon. These are good points in favour of the new system.\n\nMore information needs to be provided on the monitors used for indoor environment measurements and where they were positioned. Also, it would be greatly appreciated to have images and floor plans of the classrooms studied.\n\nLiterature discussed needs to cover more such studies and studies that have investigated similar systems for improving ventilation, using passive and/or low energy measures.\nComments to authors:\nAbstract - Results - \"keeps within acceptable limits\" - acceptable limits of what?\n\nAim for shorter sentences. A lot of sentences are getting long winded and losing their track.\n\nIntroduction - what is the meaning of balanced indoor climate?\n\nReference missing for pre-1995 schools making up 90% of all Danish schools\n\nSchool construction year - there is some discrepancy, sometimes authors use 1968 and sometimes 1967\n\nWhy specifically was eelgrass chosen for filters? This justification seems to be missing\n\nEquipment specs for indoor environmental monitors is missing\n\nOccupancy data for either classroom seems to be missing. There is value in energy cost estimates. But is this the occupancy though the entire study duration?\n\nCost estimates - why do a 10 classroom 20 year estimate - some justification would be appreciated?\n\nA section covering study limitations would be useful for this work. An important limitation as I see it is authors compare NOTECH to mechanical ventilation. And this is understood that there are logistic limitations. But, ideally we would want a comparison against the building as it is and maybe even include some existing passive ventilation systems to compare to the novel ventilation system.\nAlong the same lines, existing literature on similar passive measures for classrooms (ones involving solar chimneys, façade modifications for comfort and air quality control) should have been discussed more.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "10252",
"date": "02 Oct 2023",
"name": "Carlo Volf",
"role": "Author Response",
"response": "We have now added valuable informations to the article, also specifying what you have asked for. We will upload it shortly. Thanks a lot for you valuable input to the article."
},
{
"c_id": "11272",
"date": "12 Apr 2024",
"name": "Carlo Volf",
"role": "Author Response",
"response": "Dear Asit Kumar Mishra, Thanks a lot for you comments - I have revised the ms. according to your valluable input. Please find changes described below. A revised version 3 of the manuscript will be uploaded shortly in F1000Research.. My Best Regards Carlo Volf We have added drawings: Link to Figure xx Figure xx. In classroom 5x with mechanical ventilation (dark grey), indoor environmental quality was measured 1.6 m above floor level on wall, suing IC-Meter-911139. SBi-17, Box ID: 2DF19FEE. In classroom 5y with Notech ventilation (light grey). Indoor environmental quality also was measured 1.6 m above floor level on wall, using IC-Meter-4615. SBi-27, Box ID: 19FCA309. We have added more literature/references. We have elaborated your questions below and in the ms. Q: Abstract - Results - \"keeps within acceptable limits\" - acceptable limits of what? Acceptable limits according to National Building Regulations, BR18, stipulating that sufficient fresh air should be provided, so that CO² levels may not exceed 1.000 PPM. Q: School construction year - there is some discrepancy, sometimes authors use 1968 and sometimes 1967 The Skovbrynet School was constructed in 1968 Q: Why specifically was eelgrass chosen for filters? This justification seems to be missing Eelgrass was chosen since it is a vernacular material, originally known for being resistant to bacteria and weathering, etc. The material has been used traditionally in mattresses, etc. for hygienic reasons. Eelgrass also is known to have large biophilic surface with a natural salt content, absorbing and releasing humidity and hereby filtering the particles in the air. Finally the transmission loss is approximately 5 Pa, making it ideal for natural ventilation, since it is reducing risk of high draught rates, at the same time enabling an efficient airflow pr. hour. Q: Equipment specs for indoor environmental monitors is missing In the study we used IC-Meters, see spacs in Figure xx and https://www.ic-meter.com/uk/ Q: Occupancy data for either classroom seems to be missing. There is value in energy cost estimates. But is this the occupancy though the entire study duration? In the study, we did not collect occupancy data for each classroom, however, both classrooms had identical occupation scheme with a total of 24 children and 1-2 teachers. In both classrooms, the children were Fifth grade, corresponding to 11 – 12 years of age. Q: Cost estimates - why do a 10 classroom 20 year estimate - some justification would be appreciated? In the study, we chose a 20 year cost for maintenance and running costs. This estimate was chosen, since this represents a standard full lifespan of a mechanical ventilation system. In the cost estimates, in all 10 classrooms were chosen since this corresponded to the planned capacity of each section of the existing mechanical ventilation system. Each section consisted of two identical halfs, each having their own separate mechanical ventilation system. See plan drawing, Figure xx. Q: A section covering study limitations would be useful for this work. An important limitation as I see it is authors compare NOTECH to mechanical ventilation. And this is understood that there are logistic limitations. But, ideally we would want a comparison against the building as it is and maybe even include some existing passive ventilation systems to compare to the novel ventilation system. Thanks a lot for this comment. I agree. We have added limitations of the study ."
}
]
},
{
"id": "189714",
"date": "15 Aug 2023",
"name": "Alo Mikola",
"expertise": [
"Reviewer Expertise Hvac technology",
"energy efficiency of buildings",
"indoor climate of buildings"
],
"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 of this manuscript is novel and the paper has a practical value to give better overview of indoor air quality and ventilation systems in case of school buildings. The topic is particularly important in light of the spread of the coronavirus. At the same time, I have some questions and recommendations that should be taken into account before publishing the article.\nIt is hard to understand the methods and results of the measurements of sound pressure levels of studied ventilation systems. Is this possible to add more detailed description what are the required noise levels in Danish classrooms, how exactly the measurements were conducted, what was the measuring period in both case, were people in the classroom during the measurement period, which measuring instruments were used, what was the background noise level during the measuring period.\n\nThe required noise level should be compared to the measurements results. At the moment there are just the results brought out.\n\nAre the results of sound pressure level (corrected with A-filter) described in paper. If so, please use the correct terminology.\n\nIf the sound pressure level is above the permissible level for both systems how could such systems be accepted by the customer?\n\nIf the noise level where measured during the during the period of use, then the analyze do not show the noise from ventilation system and I'm not sure if the noise level should be analyzed in the article in such a case.\n\nThe description of the noise levels in paper should be added closer to the Figure 8. If the Figure 8 is far away from the analysis chapter, it is hard to read the paper.\n\nCan You describe what kind of measurements where done using “evaporation meter”, what is the main working principle of this device?\n\nPage 7 – “Operation costs of both systems were based on measurements using digital Ista Oprimo III evaporation meters.” This statement needs a detailed description how exactly the operational costs can be analysed according to the evaporation meter?\n\nThe heat recovery value of studied mechanical ventilation system is not described in paper.\n\nThe SFP values of fans of studied mechanical ventilation system is not described in paper.\n\nIt is hard to estimate the energy calculations, if these vales are not described.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "10253",
"date": "02 Oct 2023",
"name": "Carlo Volf",
"role": "Author Response",
"response": "We have now added valuable informations to the article, answering your questions and adressing your concerns. For your information, we have decided not to add data on noise levels, since it is not a primary outcome of the study. Like daylight, it is a very important element. However, for the ventilation we have chosen to focus only on air-quality and temperature. In this way we think, that the findings are more precise - especially since we did not find any significant differences in noise levels between the systems. We will upload shortly. Thanks a lot for your valuable feedback and comments."
}
]
}
] | 1
|
https://f1000research.com/articles/12-560
|
https://f1000research.com/articles/13-259/v1
|
11 Apr 24
|
{
"type": "Study Protocol",
"title": "Critical Thinking and Clinical Reasoning in Undergraduate Medical Course: A Mixed-Methods Study in a Medical College in Kolkata, West Bengal, India",
"authors": [
"Dipta Kanti Mukhopadhyay",
"Sonali G. Choudhari",
"Sonali G. Choudhari"
],
"abstract": "Critical thinking is considered as the essential set of skills for medical practice, particularly during emergencies. However, there is lack of conceptual clarity around it and it was not explicitly included in the undergraduate medical curriculum in India. The present study has been planned to assess the critical thinking disposition and clinical reasoning skills among medical undergraduate students in a medical college in West Bengal, India. The perceived definition and attributes of critical thinking in medical education will be explored and the contexts where application of critical thinking skills may be crucial for medical practice will be identified. The content validity index, test-retest agreement; internal consistency and construct validity of the Critical Thinking Disposition Assessment Questionnaire (CTDAQ) will be assessed through step-by-step procedure. CTDAQ and the case-based objective-type questions for the clinical reasoning skills will be applied to around 200 medical undergraduate students. Their perception and experience on critical thinking in medical education will be assessed with structured open-ended questions. In-depth interviews with medical teachers of the second and third phases of undergraduate medical curriculum will be conducted to assess their perception and experiences on critical thinking. The quantitative analysis will be conducted with MS excel and R software using the relevant packages. The qualitative data will be transcribed and translated in English, close to the participants’ verbatim. The thematic analysis will be conducted with inductive coding and memoing. The study will be conducted maintaining ethical standards for epidemiological studies. The present study, one of the first a few studies in India, will help to meet the conceptual gap in understanding the attributes of critical thinking, its association with clinical reasoning and the contexts of preferred application in medical practice.",
"keywords": [
"Critical thinking",
"Clinical reasoning",
"Medical Students",
"Education",
"Medical",
"Undergraduate"
],
"content": "Introduction\n\nCritical thinking, the ability to think clearly and rationally about what to do or what to believe, is essential for the practice of medicine.1 Although it is not a new concept in medical education, most of the published literature on critical thinking in the healthcare setting concerns nursing personnel.1\n\nAcquiring critical thinking skills is crucial for the practice of medicine. Doctors are supposed to make effective decisions in both well-defined and ill-defined emergencies. The inability to make appropriate decisions in ill-defined emergencies may lead to untoward incidents and affect the reputation of the healthcare facility and career of the individual doctor.2 When encountering an ill-defined emergency, one of the primary reasons for difficulties is the inability to think critically.3 Healthcare is prone to diagnostic and management errors.3 Knowledge and cognitive processing skills are interrelated and interdependent, which in turn are associated with conceptual understanding and metacognition.3 These skills, commonly referred as clinical reasoning skills, help in problem-solving based on the principles during unfamiliar and novel scenarios.3 Strict adherence to standard operating procedures will help minimize errors in data collection and decision making in well-defined medical problems, but is not an effective strategy to stimulate critical thinking and creativity in undefined, resource-constrained settings.3,4 Around one-third of problems in healthcare settings worldwide result from diagnostic errors.2\n\nTraining in clinical reasoning and critical thinking may provide a solution to this problem, at least in part. Critical thinking is not explicitly included within the ambits of core competency in medical curricula in most cases.1,2,5 Now, the time requires that teaching and learning critical thinking skills should be explicitly considered in the curriculum for medical undergraduates. However, critical thinking and its implications in undergraduate medical education suffer from a lack of conceptual clarity.6,7 There are certain questions that remain unresolved: what is meant by critical thinking to medical educators and students, where in the medical curriculum does it appear, when, and how can it be inculcated, particularly in resource-constrained setting?6,7\n\nThe Watson and Glaser Critical Thinking Appraisal and the California Critical Thinking Disposition Instrument are commonly used to assess critical thinking in different settings, primarily in Western culture.8 Several questionnaires were developed to assess critical thinking disposition among medical professionals in Asian cultures.8,9 Two of these are the 19-item Critical Thinking Disposition Assessment (CTDA) questionnaire in English and 27-item Yoon’s Critical Thinking Disposition (YCTD) Instrument. As there is transcultural variation in the meanings of different constructs, the questionnaire to be used needs to be validated in the Indian setting.8,9\n\nIn this background, the present study is planned in a Medical College in Kolkata, West Bengal, India, with the following objectives:\n\n1. To develop and validate a questionnaire to assess critical thinking disposition among undergraduate medical students\n\n2. To assess the critical thinking disposition among medical undergraduates at different levels of the course\n\n3. To assess the clinical reasoning skills among medical undergraduates at different levels of the course\n\n4. To find out the correlation between critical thinking and clinical reasoning among medical undergraduate students\n\n5. To explore the perceptions and experiences of undergraduate medical students regarding critical thinking in medical education\n\n6. To explore the perceptions and experiences of medical teachers regarding critical thinking in medical practice and education\n\n\nMethods\n\nThis will be a descriptive, cross-sectional study using mixed-methods approach. Mixed-methods research allows researchers the opportunity to gain a more meaningful understanding of the problems and answer questions that may have been partially answered had quantitative or qualitative data alone.10,11\n\nThe mixed-methods approach will help to triangulate different systematic measures through quantitative and qualitative approaches to provide a comprehensive scenario on critical thinking in medical education.12 Critical thinking disposition and clinical reasoning skills will be quantitatively measured. However, to enhance the critical thinking and clinical reasoning skills among undergraduate medical students, it is imperative to understand the perceptions and experiences about what is meant by critical thinking and what are its essential attributes, as well as where and how training on those skills be placed in the undergraduate medical curriculum. This will be explored using qualitative methods.\n\nThe collection of both quantitative and qualitative data will be conducted simultaneously.\n\nThe study will be conducted at a Medical College at the outskirts of the Kolkata Metropolitan area in the district of North 24 Parganas of West Bengal, India.\n\nThe total duration of the study will be ten months. First two months will be used for preparatory work including development and validation of tool. Next four months will be used for collection of data from study participants. The last four months will be utilized for data entry, analysis and report writing.\n\n\n\n1. The tool will be validated among undergraduate medical students (for objective-1)\n\n2. The students enrolled in the second and third phases of undergraduate medical course during the data collection period in the referred college (for objectives2-5)\n\n3. The Medical Teachers of the referred college who are imparting teaching during the second and third phases of undergraduate medical course (for objective 6)\n\nFor step-by-step validation of the questionnaire, the required sample size was as per the guidelines on educational research.13,14\n\nThe convenience sampling method will be used to approach all students (~ 125 per year-batch) enrolled in the second and third phases of MBBS at the College of Medicine and Sagore Dutta Hospital, Kolkata. Assuming a 20% non-response rate, the approximate number of respondents will be 200.\n\nAround 20-25 Medical Teachers, depending on data saturation, attached to various departments of the College of Medicine and Sagore Dutta Hospital, Kolkata, imparting teaching and training during the second and third phases of MBBS, will be included for in-depth interviews through purposive stratified sampling.\n\n\n\n1. A self-administered questionnaire with both closed- and open-ended questions will be administered to the students.\n\n2. Case vignettes with follow-up questions will be applied to the students\n\n3. Interview Guide for Medical Teachers of the second and third phases6,15\n\nThe first section of the questionnaire will contain an informed consent form. The students will respond to the next section only after providing their consent. The second section will consist of anonymous structured questions on the socio-demographic and individual characteristics of the students.\n\nThe third section will consist of questions on different domains of Critical Thinking Disposition (CTD) and a few open-ended questions.8,9,16 The open-ended questions will explore the perceptions and experiences of medical students regarding critical thinking skills in medical education. The validated questionnaire will be used to assess critical thinking among undergraduate medical students in different phases.\n\nThe fourth section will contain case vignettes with follow-up questions to assess clinical reasoning skills. With the involvement of subject material experts, a series of case vignettes will be prepared with a case scenario followed by some questions to assess the clinical reasoning skills from five broad clinical specialties (Internal Medicine, Community Medicine, General Surgery, Pediatrics and Gynecology & Obstetrics) of the undergraduate medical curriculum. These case vignettes with follow-up supply type objective questions will be applied to assess the clinical reasoning skills of the students in each selected subject.\n\nBoth the authors were trained in qualitative research techniques. After obtaining written informed consent, the first author will conduct in-depth interview with audio recording with medical teachers from the selected medical college in a place and time of mutual convenience, with the help of the interview guide. After collecting socio-demographic and individual information about the teacher, their perceptions and experiences of critical thinking skills in medical practice and education will be explored. They will be requested to identify the context in medical practice where critical thinking skills can play a crucial role.6,15\n\n\n\n1. Critical Thinking Disposition: It will be measured using the domain-wise score and the total score. A higher score reflects a higher critical thinking disposition of the students. Students will be categorized based on quartile values: those with scores greater than the third quartile value will be considered to have a high critical thinking disposition, those within the third and first quartiles will be considered to have an average, and those below the first quartile will be considered to have low critical thinking disposition.\n\n2. Clinical Reasoning Skills: It will be assessed using the total score obtained by the individual students from the case-based questions. A higher score reflects higher clinical reasoning skills. Students will be categorized based on quartile values: those with scores more than the third quartile value will be considered to have high clinical reasoning skills, those within the third and first quartiles will be considered to have average, and those below the first quartile will be considered to have low clinical reasoning skills.\n\n3. The perceptions and experiences of students and teachers on critical thinking skills in medical education and practice under\n\na) Conceptual definition of critical thinking\n\nb) The essential attributes of critical thinking\n\nc) The importance of critical thinking skills in medical practice\n\nd) Contexts in medical practice, where the application of critical thinking skills may be crucial in terms of outcomes\n\nThe Critical Thinking Disposition Assessment Questionnaire (CTDAQ) will be developed and tested for content validity with the help of experts from the field of Psychiatry, Psychology and Medical Education. Item-wise and total content validity indices will be calculated in MS Excel. It will first be applied to 25 first-year students twice, with a gap of three weeks to check test-retest agreement with weighted kappa statistics. It will then be applied to 150 MBBS students, other than the study population, to check internal consistency with Cronbach’s alpha and construct validity through exploratory principal component analysis with varimax rotation.13,14 All analysis will be conducted using different packages (kappaGUI, cronbach and prcomp) of open-source ‘R’ 4.3.1 software.17\n\nThe data gathered through the questionnaire survey will be entered into an MS Excel spreadsheet and tested for consistency. The individual items of the questionnaire will be rated on a five-point Likert scale, ranging from 1 (strong disagreement) to 5 (strong agreement). The scores of all items under a specific domain will be added to obtain the domain-wise score. Domain-wise median (IQR) scores will be calculated for each phase and compared. Case-based questions will be marked according to the protocol designed by subject material experts. All the marks attained collectively in all case vignettes will be added to obtain total marks. The central tendency and dispersion will be expressed as the median and IQR of the marks.\n\nSpearman correlation will be used to examine the relationship between the total scores of the critical thinking disposition assessment questionnaire and the total score from the test of clinical reasoning skills.\n\nIn-depth interviews will be transcribed from audio tape and field notes and then translated into English by the first author, close to verbatim within 48 hours of the interview. Participant confirmation will be ensured by Medical Teachers individually. The codes will be generated by two authors separately through inductive reasoning. They will be compared and contrasted, and discrepancies will be sorted out through discussion. Then, the codes will be collated with the help of memoing to generate categories and themes. The audit-trail of the analytic pathways will be maintained.\n\nThe study will strictly adhere to the Declaration of Helsinki and follow the standards of observational study. The study obtained approval from the Institutional Ethics Committee, College of Medicine and Sagore Dutta Hospital, Kolkata-700058 (Registration. No. ECR/1210/Inst/WB/2019/RR-22) with Approval No. CMSDH/IEC/107/12-2023; date: 04.12.2023.\n\nWritten informed consent will be obtained from each participant after explaining the purpose, procedure, and probable outcome of the study, ensuring confidentiality of data, voluntary participation, and right to withdraw at any point in time. The format was approved by the concerned Institutional Ethics Committee.\n\nThe transcripts will be kept under custody of the authors to maintain anonymity and confidentiality. The same principle will be applied to the quantitative and qualitative databases.\n\nThe study is planned as a dissertation for Masters in Health Professional Education (MHPE) and will be submitted to the university. The results of the study may be published in medical/health journals.\n\nThe study is yet to start.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nDr. Soumalya Ray and Dr. Kajari Bandyopadhyay of the College of Medicine and Sagore Dutta Hospital, West Bengal, India, for their intellectual inputs.\n\n\nReferences\n\nSharples JM, Oxman AD, Mahtani KR, et al.: Critical thinking in healthcare and education. Br. Med. J. 2017 [cited 2023 Mar 11]; 357: j2234. Publisher Full Text Reference Source\n\nZayapragassarazan Z, Menon V, Kar SS, et al.: Understanding Critical Thinking to Create Better Doctors. J. Adv. Med. Educ. Res. 2016; 1(3): 9–13.\n\nScott IA, Hubbard RE, Crock C, et al.: Developing critical thinking skills for delivering optimal care. Intern. Med. J. 2021; 51(4): 488–493. PubMed Abstract | Publisher Full Text\n\nSathyanarayana Rao TS, Radhakrishnan R, Andrade C: Standard Operating Procedures for Clinical Practice. Indian J. Psychiatry. 2011; 53(1): 1–3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMehrpour SR, Hoseini Shavoun A, Kheiltash A, et al.: Evaluating and comparing critical thinking skills of residents of Tehran University of Medical Sciences. BMC Med. Educ. 2023 Feb 27; 23(1): 1–13. Publisher Full Text\n\nKrupat E, Sprague JM, Wolpaw D, et al.: Thinking critically about critical thinking: ability, disposition or both? Med. Educ. 2011; 45: 625–635. Publisher Full Text\n\nBerg C, Philipp R, Taff SD: Scoping Review of Critical Thinking Literature in Healthcare Education. Occup. Ther. Health Care. 2023; 37(1): 18–39. Publisher Full Text\n\nYuan SP, Liao HC, Wang YH, et al.: Development of a scale to measure the critical thinking disposition of medical care professionals. Soc. Behav. Personal. 2014 Jan 15; 42(2): 303–311. Publisher Full Text\n\nShin H, Park CG, Kim H: Validation of Yoon’s Critical Thinking Disposition Instrument. Asian Nurs. Res. 2015 Dec 1; 9(4): 342–348. PubMed Abstract | Publisher Full Text\n\nHalcomb EJ, Hickman L: Faculty of Science, Medicine and Health: Papers- part A: Mixed methods research. Wollongong, Australia: 2015.\n\nOzawa S, Pongpirul K: 10 best resources on … mixed methods research in health systems. Health Policy Plan. 2014; 29(3): 323–327. PubMed Abstract | Publisher Full Text\n\nO’Cathain A, Murphy E, Nicholl J: The quality of mixed methods studies in health services research. J. Health Serv. Res. Policy. 2008 Apr; 13(2): 92–98. Publisher Full Text\n\nYusoff MSB, Arifin WN, Hadie SNH: ABC of Questionnaire Development and Validation for Survey Research. Educ. Med. J. 2021; 13(1): 97–108. Publisher Full Text\n\nde Winter JCF , Dodou D, Wieringa PA: Exploratory Factor Analysis With Small Sample Sizes. Multivar. Behav. Res. 2009; 44(2): 147–181. Publisher Full Text\n\nMulnix JW: Thinking critically about critical thinking. Educ. Philos. Theory. 2012; 44(5): 464–479. Publisher Full Text\n\nWade C: Using writing to develop and assess critical thinking. Teach. Psychol. 1995; 22(1): 24–28. Publisher Full Text\n\nDownload R-4.3.2 for Windows: The R-project for statistical computing.[cited 2023 Nov 14]. Reference Source\n\nZotero|Downloads: [cited 2023 Dec 11]. Reference Source"
}
|
[
{
"id": "271966",
"date": "09 May 2024",
"name": "Samy A Azer",
"expertise": [
"Reviewer Expertise I am professor of medical education for over 15 years. I have expertise in medical education",
"research methods",
"public health",
"and gastroenterology. I have over 120 published research in top journals and 5 textbooks."
],
"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\nCritical Thinking and Clinical Reasoning in Undergraduate Medical Course: A Mixed-Methods Study in a Medical College in Kolkata, West Bengal, India STUDY PROTOCOL Thank you for inviting me to review the above-titled manuscript. While the topic is intriguing, the manuscript is marred by a lack of focus, unclear research questions, and insufficient details. ABSTRACT- 1) Too many objectives. You must have a focus. 2) State your research question. 3) What did you use as a research method? What tools did you use? 4) We do not start methods by mentioning validity and reliability issues- We need to know what type of method was used to answer the research question and what tools were used. 5) What is \"test-retest agreement\"? \"construct validity\"- mentioned twice but never explained how these will be considered. 6) Who are the participants - include inclusion and exclusion criteria. 7) Which questionnaire data? Is this a validated questionnaire from the literature, or will the authors create it? 8) Statistical tests to be used is missing. English editing is required for the whole manuscript. INTRODUCTION- 1) Definition given is incomplete and not well addressed; please read the literature (first three lines). 2) \"well-defined and ill-defined emergencies\" - Why? and what do you mean? 3) Is this only about an emergency? Emergency has been repeated but not in the title or the abstract. Is critical thinking in medicine limited to Emergencies? 4) Define critical thinking, state its scope, and give examples. 5) Figure - \"In-depth interviews\". Why? Why not focus groups? You must explain and justify the purpose. Need to know where in the course and which subjects, what situations in small group learning students experience critical thinking. METHODS- 1) What do you mean by mixed methods - explain what will be qualitative and what will be quantitative, regarding research design, methods used, data collected, data analysis, etc. 2) Add citations and references to methods. 3) Study Population - Which tools? 3) What is the sample size and sample power? Explain the basis for your calculations, the equation to be used and give the exact number of sample sizes and sample types. 4) Several parts were not clearly written Plamn for data analysis- Should be edited, organised and focused. Avoid contradictions- Earlier, the author mentioned applying for ethical approval, then here they say, \"The study has obtained ethical approval.\" - which one should we believe? References - the authors should read and cite proper literature in Academic Medicine, Medical Education, Medical Teacher, BMC Medical Education, Teaching and Learning in Medicine, Journal of Surgical Education. Ref 16- too old Ref 17- Should be replaced Ref 18- Not a reference- Should be replaced\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? Not applicable",
"responses": []
},
{
"id": "271971",
"date": "15 May 2024",
"name": "Ananya Mandal",
"expertise": [
"Reviewer Expertise Pharmacology",
"Medical Education",
"Clinical trials",
"Drug utilization",
"Rational drug use",
"Antimicrobial sensitivity and 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\nI found this study proposal very intriguing. Moving head of rote learning that used to be the cornerstone of medical education critical thinking can allow students to be better prepared for their lives as doctors. This is however not constructively taught to the students. As the authors have mentioned an in depth look at the methodology of such training for medical undergraduates is essential. Their planning involves content validity index, test-retest agreement; internal consistency and construct validity of the Critical Thinking Disposition Assessment Questionnaire (CTDAQ). This will provide a scientifically backed method of development of the module that may help in future teaching. Also their suggestion of using case based scenarios for the student questionnaire seems appropriate for fulfilling their ultimate objective. Another good part of their methodology is the use of in depth interviews of the medical teachers to assess their perception and experiences on critical thinking. The primary stakeholders of the system being the students and teachers, this seems to be vital. As such the plan for analysis doesn’t warrant a comment as it is well thought out and detailed. Overall, the protocol seems to be well planned and thought out. The study has not been conducted yet so data is not available for review. As such study methodology appears to be complete and logical.\nComment: Approved\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": []
},
{
"id": "271974",
"date": "21 May 2024",
"name": "Sanhita Mukherjee",
"expertise": [
"Reviewer Expertise Medical Education"
],
"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\nAPPROVED. Critical thinking is an essential cognitive skill for every individual but is a crucial component for healthcare professionals such as doctors. This helps the medical students to analyze the information critically and then apply that to the existing information. Critical thinking skill is considered a cornerstone for teaching and training medical students so as to maintain clinical competence and medical professionalism. This study nicely tries to assess the the critical thinking disposition and clinical reasoning skills among medical undergraduate students. This is an excellent attempt to develop and validate a questionnaire to assess critical thinking skill. I found a flawless method by which they are trying to develop the Critical Thinking Disposition Assessment Questionnaire (CTDAQ). Traditionally, higher education is thought to produce career thinkers equipped with the knowledge and intellectual abilities. However, there is a growing awareness that many students do not have expected professional abilities. Therefore, the higher education system needs development of these thinking abilities in curriculum. Specially in medical field to reach correct diagnosis one should not only depend on knowledge but also on this CRT in order to reduce the pain and harassment of the patient. CRT should be taught and assessed in undergraduate medical students in order to make them competent before they start their clinical practice. This study is a visionary effort toward this direction which is very rare in Indian medical schools. Although CT is influenced by many educational and sociological parameters, curriculum is the most important parameter every student must deal with during academic studies. If a curriculum is based on CT skills, it directs learners toward disposition to CT. This study shows a crucial step towards inclusion of CRT in undergraduate medical curriculum in India. Perception of students on CRT will also help to understand student's point of view on it. Students of this era of social media and AI are more practical and tech savvy. The patients and their relatives are also open to the information domain. Previously in India ignorance of patient and patient party about medical science made the job of the clinicians easier. Nowadays in order to face well informed patient and to communicate with them CRT is essential.\nHence I approve this study.\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/13-259
|
https://f1000research.com/articles/12-1589/v1
|
14 Dec 23
|
{
"type": "Study Protocol",
"title": "Efficacy of Dashmool Vasti as an adjuvant therapy with the standard of care (modern + physiotherapy) in the rehabilitation of stroke as compared to standard of care – a clinical trial protocol",
"authors": [
"Punam Sawarkar",
"Vaishali Kuchewar",
"Gaurav Sawarkar",
"Irshad Qureshi",
"Vaishali Kuchewar",
"Gaurav Sawarkar",
"Irshad Qureshi"
],
"abstract": "Background Stroke is ischemia and neurological dysfunction caused by acute brain circulation loss. It causes acute localized neurological abnormalities such as weakness, sensory deficit, or language issues that require long-term treatment. These deficiencies harm the patient and their family psychologically, socially, and economically. Thus, combination treatment can rapidly rehabilitate such patients. Detoxification methods like Ayurvedic medicated enema help stroke pathophysiology. Physical modalities in physiotherapy have been shown to facilitate normal movement and function on the stroke patient’s affected side, increasing independence with everyday duties. A stroke patient may benefit from Dashmoola Niruha Vasti, Function Electrical Stimulation (FES), and Motor Relearning Programme (MRP).\n\nAim & Objectives This study compares the adjuvant role of Dashmoola Vasti with MRP and FES in stroke recovery. The main goals of this study are to assess and compare the adjuvant role of Dashmoola Vasti with standard control over sensorimotor function of lower extremities; static & dynamic balance in stroke patients; gait parameters; resistance experienced during passive range of motion; quality of life of patients; Barthel Index; Modified Ashworth Scale; and Fuglmeyer assessment, Single Limb Stance Test, Functional Reach Test.\n\nMethods A total of 40 patients will be enrolled and divided randomly into two equal groups. In Group A (control), standard treatment (modern + physiotherapy) will be prescribed for one month. In Group B (interventional group), Dashmoola Vasti will be added to the afore-said standard treatment for one month.\n\nExpected results Improvement in Fuglmeyer assessment, Single Limb Stance Test, Functional reach test, quality of life of patients, Barthel Index, Modified Ashworth scale and National Institute of Health (NIH) stroke-scale-score, will be observed and recorded.\n\nConclusions Results and conclusions will be derived according to the data collected in case record form and assessment sheets filled at baseline and follow-up visits.\n\nTrial registration\nCTRI/2021/10/037445 dated 21.10.2021.",
"keywords": [
"Stroke",
"Pakshaghata",
"Panchkarama",
"Niruha Vasti",
"Dashmoola",
"Adjuvant",
"Physiotherapy",
"MRP",
"FES"
],
"content": "Introduction\n\nIn clinical practice, stroke has been very notorious for impeding the continuity of life and day-to-day activities. It is the most common example of such a crippling disorder. On extensive review of contemporary literature, it is observed that, despite massive worldwide efforts in this science to rectify early results in reducing the risk of death or disability, it is disappointing.1 Partial recovery is obtained after a particularly long time. Moreover, it is observed that there are certain limitations, contra-indications, or side effects of currently established treatment modalities for stroke.2\n\nConsidering the complicated and critical nature of the disease, i.e., stroke, it becomes imperative to search for safe, promising and effective treatment modalities in alternative sciences for early rehabilitation purposes for stroke. Though most of the studies suggest that the individual use of Panchakarma therapy, especially external oleation (Bahya Snehana), sudation therapy (Swedana) along with medicated enema (Vasti) and conventional physiotherapy, i.e., Motor Relearning Programme (MRP), and the combination of electrical modality with Functional Electrical Stimulation (FES) shows promising results in the rehabilitation of patients with stroke.\n\nHowever, no study has been carried out to assess their combined effects on the therapeutic outcome of the rehabilitation of such patients. Moreover, the research is also required to determine the MRP and FES combined effect of supporting stroke patients for improving knee extension and gait parameters. Therefore, this study is proposed to generate clinical evidence showing excellent post-stroke recovery within a short time in restoring gross and fine movements to the maximum extent in a quicker manner.\n\nThe study’s goal is to analyze and compare the adjuvant role of Dashmoola Vasti with standard treatment in stroke rehabilitation. In addition, the efficacy of physiotherapy (MRP and FES) in the rehabilitation of stroke patients will be assessed. The study’s goal is to assess and compare the adjuvant role of Dashmoola Vasti with standard control over sensorimotor function of lower extremities in stroke patients using the Fugl-Meyer assessment, as well as to assess and compare the adjuvant role of Dashmoola Vasti with standard control over static and dynamic balance in stroke patients using the Single Limb Stance Test and Functional Reach Test, respectively. The secondary goal is to evaluate and compare the adjuvant role of Dashmoola Vasti with standard control over gait parameters (distance and time parameters), the Barthel Index, resistance experienced during passive range of motion based on the modified Ashworth scale, and the National Institute of Health (NIH) stroke-scale-score in stroke patients.\n\n\nMethods\n\nIEC clearance is taken from the Institutional Ethical Committee, Datta Meghe Institute of Higher Education and Research (DMIHER), Wardha. IEC certificate obtained: Ref No. DMIHER (DU)/IEC/2021/279 dated 15.04.2021. The project has been registered with Clinical Trials Registry India (CTRI) (registration number CTRI/2021/10/037445) dated 21.10.2021).\n\nWritten informed consent will be taken from the patient before starting the study. During the study, the confidentiality of each patient will be maintained.\n\nIt is an interventional study, it is a superiority clinical trial, i.e., randomized reference standard control open-labeled two-arm comparative clinical trial.\n\nDue to practical considerations such as cost, patient inconvenience, judgments not to proceed with an investigation or a lengthy study duration, the number of participants in the study is restricted. So for the phase-I trial, 20 sample size is considered for each group.3\n\nDaily visit to the stroke inpatient ward is planned at Acharya Vinoba Bhave Rural Hospital, and if the patient is willing to enroll in the said study can be recruited for the study after written informed consent. Patients will be added one at a time until the target sample size is reached.\n\nLocus of the study: out patient department and inpatient department of Panchakarma & Kayachikitsa department, Mahatma Gandhi Ayurveda College Hospital and Research Centre (MGACH&RC), Salod (Hirapur) Wardha, Maharashtra. & Department of Neuro physiotherapy, Ravi Nair Physiotherapy College, Sawangi, Wardha Maharashtra, Datta Meghe Institute of Higher Education and Research, Wardha, Maharashtra.\n\nStudy setting: The study will be conducted in Panchakarma OPD & IPD, Mahatma Gandhi Ayurveda College Hospital and Research Centre (MGACH&RC), Salod (Hirapur) Wardha, Maharashtra.\n\nPatients will be recruited after approval from Clinical Trials Registry- India (CTRI), and the exposure period for treatment will be one month. The follow-up will be conducted on the 60th and 90th day of treatment.\n\nCriteria for discontinuing or modifying: if patients are willing to quit in between they will be allowed to quit and will be replaced; if the patient develops an acute illness during the trial, which may hamper the study and withdrawn patients will be replaced.\n\nDiagnosed cases of stroke will be enrolled in the study with the computerized randomization method.\n\nThe inclusion criteria for the study are the patients with the first stroke diagnosed with CT/MRI (thrombolytic stroke only) without other neurological deficits but < six months of onset, patients diagnosed as stroke with ICD code 2020 ICD-10-CM Diagnosis Code I69.351 patients between 45 to 60 years of age irrespective of gender/occupation and socio-economic status. Patients with controlled hypertension and Noninsulin dependent Diabetes Mellitus (NIDDM). Patient with ankle dorsiflexors stage 1 to 2 and ankle plantar flexors spasticity 1+ on. Patients willing to give informed consent and ready to follow simple instructions.\n\nThe exclusion criteria for the study are the patients having thrombolytic stroke with onset for > than six months, subjects with complications such as uncontrolled metabolic disorders and severe systemic disorders, e.g., renal or cardiac failure, altered sensorium, or coma. Those who are on tube feeding or intravenous fluid therapy. The patients of stroke with a history of trauma (Abhighatajanya), onset due to intracranial space-occupying lesions, post-surgical or postpartum complication, degenerative disorders of the brain or intracranial infectious disease or hemorrhagic nature. The patients with specific medical and psychological contraindications for electrical stimulation Brooks,4 patients with visual or auditory difficulties, anti-anxiolytic treatments. Pregnant women and lactating mothers will also excludedbe. Patients contraindicated for Vasti & Swedana therapy and patients with fixed ankle or foot contracture, pacemaker, and a metal plate in the lower limb will be excluded.\n\nFor group A, standard control modern treatment (Anti-thrombotic treatment, e.g. Tab. Ecosprin 75/150 mg OD and Tab. Notropril 800mg TDS) will be given along with physiotherapy. The physiotherapy sitting for motor relearning program and functional stimulation will be given for 55 mins per sitting, five days weekly for one month.\n\nFor group B, standard control modern treatment will be given along with Ayurveda Panchakarma and physiotherapy. In this case, gentle massage with Dashmoola Taila + Nadi Sweda with Dashmoola Qwath + medicated enema (alternate regime of Dashamoola Niruha Vasti with Anuvasana Vasti with Dashmoola Taila will be prescribed for the treatment. The alternative regime of medicated enema i.e., Anuvasana Vasti (oil enema) and Dashamoola Niruha Vasti (decoction enema) will be given on odd and even days respectively for one month, and physiotherapy for five days weekly for one month.\n\nThe methodology of the study is mentioned in Table 1 and the flowchart of the study design or methodology is given in Figure 1.\n\n\n\n• Same as group A+ Dashmoola Vasti Details of Dashmoola Vasti Are as follows:\n\n• Local Snehana-10 mins\n\n• Local Swedana-10 mins or till attainment of Samyak Swinna Lakshana, whichever is earlier.\n\n\n\n• Panchakarma for complete one month (Day 1st – Day 30th)\n\n• Physiotherapy for Five days weekly for one month\n\n* FES – Function Electrical Stimulation, MRP – Motor Relearning Programme.\n\n*FES – Function Electrical Stimulation, MRP – Motor Relearning Programme, NIH – National Institutes of Health.\n\nThe assessment criteria will be the Fugl-Meyer assessment, one-leg stance test, gait parameters (distance and time parameters), modified Ashworth scale, functional reach test, quality of life scale, Barthel index, NIH stroke scale score (NIHSS)5,6\n\nImprovements in the following assessment variables are expected as primary outcomes: Fugl-Meyer assessment for sensori-motor function of lower extremities, one-leg stance test, functional reach test for static and dynamic balance in patients, quality of life scale and Barthel index independent living of patients with Stroke, resistance experienced during passive range of motion based measured on Modified Ashworth scale NIHSS for improvements in clinical features of stroke are expected to be measured.7\n\n\n\n• For physiotherapy (five days weekly for one month)\n\n• Karma Vasti (alternate regime of Niruha Vasti with Dashmoola Qwath and Anuvasana Vasti with Dashamoola oil for complete one month, i.e., Day 1st–Day 30th)\n\nTime schedule of enrolment: Patients with the first Stroke diagnosed with CT/MRI (thrombolytic Stroke only) without other neurological deficits but <6 months of onset will be enrolled for the study.\n\nInterventions (including any run-ins and washouts): There are no washout periods; the intervention of Panchakarma treatment and Physiotherapy sitting for 30 days.\n\nAssessments and visits for participants: Assessment will be carried out at baseline level and after the intervention, i.e., on the 30th day, then followup visits on the 60th and 90th day.\n\nPatients will be recruited by simple randomization through the computer-generated table. The principal investigator (PI) and co-investigator (CO-I) will allocate and enroll the patient.\n\nUsing computer-generated random numbers, the researcher creates random allocation cards. He will keep the original random allocation sequences in a secure third location and work with an alternate copy. A researcher will enroll the patients.\n\nThe envelopes will be marked with serial numbers on the outside. The date, time, patient ID, post-procedure results, and other required details will be on the envelope.\n\nFor retention of patients, appointment reminders will be scheduled, and question-answering sessions will be planned. The complete followup will be mentioned in the patient file, and if patients are required to withdraw or discontinue, the patient file will be closed and maintained for the record purposes.\n\nObservations will be made after the completion of the study, according to the data collected with the help of the following:\n\nI. Case registration form with detailed history and examinations\n\nII. Follow-up assessment proforma\n\nData monitoring and coding will be done by the principal investigator and co-investigator. Data entry will be done in soft copy and case record form in hard copy. The values will be verified twice before submission in soft copy. Each file of the patient is secured with a specific patient code.\n\nThe data obtained will be calculated using the Student’s Paired ‘t-test and Unpaired ‘t’ test for objective variables with SPSS statistical software.\n\nTo verify the significance of the results\n\nImprovements in Fugl-Meyer assessment-35%, one leg stance test-20%, functional reach test-35%, quality of life scale-25%, Barthel index-25% and NIH stroke-scale-score-20% will be considered as significant.\n\n\nDiscussion\n\nCerebrovascular accidents (CVA) can be correlated with Pakshaghata in Ayurveda. Its pathophysiology evolves in Shira (head). In Ayurveda, Panchakarma is considered the most effective regime to break the pathogenesis of the disease from the root and avoid its recurrence. Snehana, Swedana, including Vasti, is the ultimate treatment modality for Pakshaghata. Acharya Sushruta stated that Vasti is half of the entire management of diseases having chronic and deeply rooted pathology, primarily for conditions originating from the morbid Vata Dosha.8,9 It is the most important as it drastically expels the vitiated Vata responsible for the movements of all Dosha, Dhatu, and Mala within the body. Niruha Vasti serves the purpose of the elimination of vitiated Vata Dosha. As Shosha of Sira and Snayu, which is the most critical event in the Samprapti of Pakshaghata, the Bruhana effect induced by Anuvasana Vasti, which pacifies Vata. Being an obstinate Vata disorder, Pakshaghata demands a pioneering treatment of Vata, i.e., Vasti, especially Shodhana or Bruhana Vasti, for a more extended period. Therefore, Vasti is considered one of the foremost treatments for Pakshaghata, capable of eliminating Doshas from the body.10,11 It sustains life by maintaining the harmony between Dosha, Dhatu, and Mala in the body.12,13\n\nAmong various types of Niruha Vasti Dravyas, Dashamula, i.e., a combination of the 10 drugs, is the best Tridoshahara, especially has Vatahara property; therefore, it is highly efficacious for Vata predominant disorders. Dashmoola Niruha Vasti & Anuvasana Vasti with Dashmoola Oil are considered very effective, providing additional benefits of Shodhana and Rasayana, which are expected in Pakshaghata.14–16\n\nDue to this devastating and refractory nature of Pakshaghata, a minimum course of three months of appropriate treatment is recommended. Therefore, among detoxification procedures, Karma Vasti (course of 30 Vasti having a regime of alternate 18 Anuvasana Vasti and 12 Niruha Vasti) with Snehana and Swedana are selected for this study.17–20\n\nLocal Snehana and Swedana is the mandatory pre-procedural protocol before administering both Niruha and Anuvasana Vasti that is helpful to achieve expected proper procedural symptoms (i.e., Samyak Niruha and Anuvasana Vasti Lakshana). Moreover, it also increases the therapeutic outcome of these therapies by improving blood circulation in that local region.\n\nAs local massage nourishes the muscular tissue and fomentation with Dashmool decoction, massage quickly relieves the extremities’ stiffness, especially muscular tissues. Both these procedures also play an important role in enhancing the speed of rehabilitation of the stroke, resulting in a speedy recovery in cognitive functions hampered in it. According to Ayurveda, vitiation of Vata is the most important factor responsible for inducing impairment of cognitive functions and musculoskeletal movements. Both procedures were done by using Dashmoola oil and Dashmoola decoction, respectively, to pacify vitiated Vata due to their Snigdha & Ushna Guna. Moreover, both improve the gait of the patient & reduce the dependency of the affected individual on relatives.21,22 Local massage and fomentation with Vata pacifying medicines improve the patient’s quality of life by building confidence and contributing to induce expected positive outcomes.23\n\nOn the other hand, the efficacy of physiotherapy, especially of the “Motor Relearning Program” (MRP) and “Functional Electrical Stimulation” (FES) in the early rehabilitation of the stroke can be justified as follows:\n\nMotor learning theory underpins the Motor Relearning Programme (MRP). Carr and Shepherd claimed that motor control training necessitates anticipatory acts as well as continuing exercise. The motor relearning program is useful for improving a group of post-stroke patients’ balance function and functional performance. It consists of four distinct steps, i.e., to analyze the task and practice the missing component and task with a transference of training. Eight studies suggested that MRP planned for five weeks showed better improvement in functional performance on self-care, instrumental activities of daily living, and integration into the community hospital.24\n\nThe FES is based on electrical stimulation to the peripheral nerves that innervate the paralyzed muscle to generate action potentials in motor neurons, propagating towards the power, and causing its contraction. According to John E.R. 1999 et al. and Niu et al., 2019, it is an excellent recovery tool for motor functions hampered in post-stroke conditions.\n\nBoth MRP and FES are quite useful to regain full mobility in such patients, enhance muscle strength and endurance, expand movement capacity, reduce atrophy, increase walking speed, reduce spasticity, and relieve pain. This technique is quite effective to improve the swing phase of the gait, correct a foot drop and decrease the energy expenditure during walking by restoring ankle dorsiflexion affected in the patient with stroke.25,26\n\nIn a nutshell, all-composite treatment modalities induce restoration of gross and fine movements, increase gait speed to the maximum extent quicker, decrease falls, and improve he patient’s quality of life.\n\n\nConclusion\n\nShreds of evidence generated from the current study may prove the positive benefits of the use of integrative approach of Dashamool Niruha Vasti in Panchakarma added with MRP and FES in physiotherapy, to improve gait and speed of movement, decrease the rate of fall while standing or walking, and improves quality of life of patients having stroke. This treatment protocol may become an effective tool in the rehabilitation of such patients, which may broaden the scope of Ayurveda in neurology.\n\nAbhighatajanya – Trauma\n\nAnuvasana Vasti – Oil enema\n\nBahya Snehana – Especially external oleation\n\nDashmool – Combination of 10 Ayurveda drugs\n\nDhatu – Body tissues\n\nDosha – Bio-humours\n\nKarma Vasti – Alternate regime of decoction enema & medicated oil enema for complete one month\n\nKayachikitsa department – Medicine department\n\nMala – Body toxins\n\nNiruha Vasti – Decoction enema\n\nNiruha Vasti Dravyas – Decoction enema content\n\nPakshaghata – Paralysis\n\nPanchakarma department – Purification Putative treatment department\n\nPanchkarama – Purification putative treatment\n\nRasayana – Rejuvenation\n\nSamprapti – Pathophysiology\n\nShira – Head\n\nShodhana – Purification\n\nSnigdha Guna – Unctuousness quality\n\nSwedana – Sudation therapy\n\nTridoshahara – Bio-humour enhancer\n\nUshna Guna – Hot quality\n\nVasti – Medicated Enema\n\nVata Dosha – Air entity in the body\n\nVatahara – Air entity pacifier",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: SPIRIT checklist for ‘Efficacy of Dashmool Vasti as an adjuvant therapy with the standard of care (modern + physiotherapy) in the rehabilitation of stroke as compared to standard of care – a clinical trial protocol’. https://doi.org/10.6084/m9.figshare.24488059.\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\nPatel J, et al.: A non-randomized observational clinical study on ayurvedic treatment in Pakshaghata. J. Biol. Sci. Opin. 2015; 3(5): 230–234. Publisher Full Text\n\nAcharya JT, editor. Agnivesha: Charaka samhitha, Chaukambha Orientalia. 5th Edition.Varanasi: 2001; pp. 738. page no: 500.\n\nPourhoseingholi MA, Vahedi M, Rahimzadeh M: Sample size calculation in medical studies. Gastroenterol Hepatol Bed Bench. 2013 Winter ; 6(1): 14–17. PubMed Abstract | Free Full Text\n\nFrenette J, Lam T, Mackay-Lyons M: Electrophysical agents: Contraindications and precautions. Canadá. Physiother. Can. 2010.\n\nNiu CM, Bao Y, Zhuang C, et al.: Synergy-based FES for post-stroke rehabilitation of upper-limb motor functions. IEEE Trans. Neural Syst. Rehabil. Eng. 2019 Feb 8; 27(2): 256–264. PubMed Abstract | Publisher Full Text\n\nEraifej J, Clark W, France B, et al.: Effectiveness of upper limb functional electrical stimulation after Stroke to improve activities of daily living and motor function: a systematic review and meta-analysis. Syst. Rev. 2017 Dec 1; 6(1): 40. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee KB, Lim SH, Kim KH, et al.: Six-month functional recovery of stroke patients: a multi-time-point study. Int. J. Rehabil. Res. 2015 Jun; 38(2): 173–180. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAcharaya JT, editor. Sushruta Samhita of Sushruta, reprint 2003 Chaukamba Sura Bharati Prakashan Varanasi.2003; pp. 824. page no:525.\n\nA Clinical Study To Evaluate The Efficacy Of Dwi-Panchamula Niruha yesVasti In Pakshaghata”PG Thesis Submitted By Dr. Prakash Paltye, Department Of Panchakarma, SDMCA Udupi. In Rajiv Gandhi University Of Health Sciences, Karnataka, Bangalore, 2010-11.\n\nSamhita AC, editor. Jadavji Trikamji Acharya,5th edition Chaukamba publication Varanasi.2001; pp. 738. page no: 619.\n\nSena V, Samhita VS: edited by Kavivar Sri Saligramaji Vaishya Dec-2003, Kaumarajsri Krishna Das Prakashan Mumbi. pp. 1069. page no: 983.\n\nDr.Kaur Mandeep: A clinical study on the effect of Panchaprasritiki Niruha yesVasti in Pakshaghata Dept of Panchakarma SDMCA Udupi, RGUHS, Bangalore in 2007-2008.\n\nDr.Upadhyaya Asha: A clinical study on the effect of Upanaha Sweda in Pakshaghata, Dept of Panchakarma SDMCA Udupi, RGUHS Bangalore in 2007.\n\nAgnivesha CS, editor. Jadavji Trikamji Acharya reprint 2007 Chaukamba orientalia Golgahar Varabnasi.2007; pp. 738. page no: 619\n\nManish K, Kumudini K, Mala K: B.B. Conceptual And Therapeutic Study Of Pakshaghata. Int. J. Appl. Ayurved Res. 2017; 3(1): 48–56.\n\nPatel J, et al.: A non-randomized observational clinical study on ayurvedic treatment in pakshaghata. Journal of biological & scientific opinion 2015; 3(5): 230–234. Publisher Full Text\n\nAgnivesha: Charaka samhitha, Acharya Jadavji Trikamji, edited by Chaukambha Orientalia. 5th Edition 2001, Varanasi. pp. 738. page no: 500.\n\nDr.Patanjali: A clinical study on the effect of Agni chikitsa in Pakshaghata, Dept of Panchakarma SDMCA Udupi, RGUHS Bangalore in 2006.\n\nDr.Devagirikar Vaishali panduranga: A comparative study of the effect of samshodhana and Samshamana in Pakshaghata Dept of kayachikitsa SDMCA Udupi, RGUHS, Bangalore in 2004.\n\nDr.U Shreekanth: “studies on some systematic effect of yesVasti with special reference to Gridhrasi, Viswachi and Pakshavadha” undertaken at IPGT&R, Gujarat Ayurveda University – Jamnagar in 1984. L-1416.\n\nSawarkar G, Sawarkar P: Management Of Ardita (Bell’s Palsy) Through Ayurveda- A Case Study. Int. J. Recent Sci. Res. April, 2019; 10(04): 32040–32043.\n\nSingh N, Dubey S: Evaluate The Efficacy Of Shashtik-Shali Pinda Sweda And Abhyanga In Management Of Pakshaghata Along With Virechana Wsr To Hemiplegia. Int. J. Ayurveda Pharma. Res. 2020 Jul 12; 1–2. Publisher Full Text\n\nKumar DR: The role of Panchakarma therapy in musculoskeletal disorders with special reference to vatavyadhi. Global Journal of Research on Medicinal Plants & Indigenous Medicine. 2013; 2(1): 23.\n\nKrutulyte G, Kimtys A, Krisciūnas A: The effectiveness of physical therapy methods (Bobath and motor relearning program) in the rehabilitation of stroke patients. Medicine (Kaunas, Lithuania). 2003; 39(9): 889–895.\n\nNiu CM, Bao Y, Zhuang C, et al.: Synergy-based FES for post-stroke rehabilitation of upper-limb motor functions. IEEE Trans. Neural Syst. Rehabil. Eng. 2019 Feb 8; 27(2): 256–264. PubMed Abstract | Publisher Full Text\n\nEraifej J, Clark W, France B, et al.: Effectiveness of upper limb functional electrical stimulation after Stroke to improve activities of daily living and motor function: a systematic review and meta-analysis. Syst. Rev. 2017 Dec 1; 6(1): 40. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "231867",
"date": "22 Jan 2024",
"name": "Neha Tank",
"expertise": [
"Reviewer Expertise Panchakarma",
"Autoimmune diseases",
"Neurological diseases",
"Osteomuscular diseases",
"degenerative diseases",
"Stress and allergies"
],
"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\ngrammatical corrections required. Spell check e.g. Kwatha not Quath Basti not Vasti Non English words (Sanskrit) may be in Italic\n\nAssessment criteria is not submitted, study results in terms of demographic data, clinical data, blood report changes and statistical analysis are not submitted. duration of basti is too long for any stroke patient. Any findings related to adverse effect/complication of Basti? study details regarding effect of Basti is not submitted\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": "11048",
"date": "13 Apr 2024",
"name": "punam sawarkar",
"role": "Author Response",
"response": "Dear Madam, The updated version of the manuscript incorporates helpful comments, including correcting grammatical errors; all Ayurveda terms are made italic, Kwatha and Basti's spelling has been corrected, and Assessment criteria are specified in the text. Because the current manuscript is a PROTOCOL instead of an original article, so some suggestions of respected reviewers can not be incorporated. (For example, study results regarding demographic data, clinical data, blood report changes, and statistical analysis are not submitted, any findings relating to adverse effects/complications of Basti?, and study details addressing the effect of Basti are not submitted.) According to reviewers, the duration of Basti is too long for any stroke patient; nonetheless, the author submits that due to the devastating and refractory character of Pakshaghata, a minimum term of three months of proper treatment is advised. As a result, Karma Basti (a 30-day detoxification regimen consisting of 18 Anuvasana Basti and 12 Niruha Basti) with Snehana and Swedana was chosen for this study."
}
]
}
] | 1
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https://f1000research.com/articles/12-1589
|
https://f1000research.com/articles/12-956/v1
|
09 Aug 23
|
{
"type": "Data Note",
"title": "Identification of high-performing antibodies for amyloid-beta precursor protein for use in Western Blot, immunoprecipitation and immunofluorescence",
"authors": [
"Riham Ayoubi",
"Maryam Fotouhi",
"Donovan Worrall",
"Kathleen Southern",
"Carl Laflamme",
"NeuroSGC/YCharOS/EDDU collaborative group",
"ABIF consortium",
"Riham Ayoubi",
"Maryam Fotouhi",
"Donovan Worrall",
"Kathleen Southern"
],
"abstract": "The amyloid-beta precursor protein is a transmembrane protein expressed in many tissues and highly concentrated in the brain. The protein is of significant interest due to its involvement in the generation of amyloidogenic β-amyloid peptides, prone to plaque formation that is characteristic of Alzheimer’s Disease. The scientific community would benefit from the availability of high-quality anti-amyloid-beta precursor protein antibodies to enhance reproducible research on this target. In this study, we characterized eleven amyloid-beta precursor protein 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 P05067",
"APP",
"Amyloid-beta precursor protein",
"antibody characterization",
"antibody validation",
"Western Blot",
"immunoprecipitation",
"immunofluorescence"
],
"content": "Introduction\n\nThe amyloid-beta precursor protein, encoded by the APP gene, is a transmembrane protein with a single transmembrane domain, a large extracellular ectodomain and a short cytoplasmic tail.1 Although ubiquitously expressed, amyloid-beta precursor protein is predominantly found on the surface of neurons, where it promotes neurite growth, neuronal adhesion and axonogenesis.2\n\nDiscovered and isolated in the 1980’s, amyloid-beta precursor protein has become a significant area of interest as its proteolytic cleavage can give rise to amyloid β-proteins (Aβ).1,3,4 Aβ are small 40-42 amino acid-long peptides related to the pathogenesis of Alzheimer’s Disease as their accumulation can result in the formation of senile amyloid plaques.1,5 Further research is required to elucidate the pathway underlying the proteolytic processing of amyloid-beta precursor protein and in turn determine its potential as a diagnostic marker or therapeutic target to prevent degenerative brain progression. Mechanistic studies would be greatly facilitated with the availability of high-quality antibodies.\n\nIn this study, we compared the performance of a range of commercially available antibodies for amyloid-beta precursor protein and identified high-performing antibodies for Western blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of amyloid-beta precursor protein’s properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells.6–16 The first step was to identify a cell line(s) that expresses sufficient levels of a given protein to generate a measurable signal. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available HAP1 cells expressed the amyloid-beta precursor protein transcript at RNA levels above the average range of cancer cells analyzed. Parental and APP KO HAP1 cells were obtained from Horizon Discovery (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and APP KO cell extracts and probed them side-by-side with all antibodies in parallel (Figure 1).7–16\n\nLysates of HAP1 (WT and APP KO) were prepared and 50 μg of protein were processed for Western Blot with the indicated Amyloid-beta precursor protein 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. Exceptions were given for antibodies ab126732**, 29765** and 76600** which were all titrated to 1/500, as the signals were too weak when following the supplier’s recommendations. Antibody dilution used: ab126732** at 1/500, ab252814** at 1/500, ab252816** at 1/500, ARP33075 at 1/500, ARP34012 at 1/500, 29765** at 1/500, 76600** at 1/500, 25524-1-AP at 1/500, 13-0200* at 1/200, 14-9749-80* at 1/500, MA5-35187** at 1/500. Predicted band size: 87 kDa. *Monoclonal antibody, **Recombinant antibody.\n\nFor immunoprecipitation experiments, we used the antibodies to immunopurify amyloid-beta precursor protein from HAP1 cell extracts. The performance of each antibody was evaluated by detecting amyloid-beta precursor protein protein in extracts, in the immunodepleted extracts and in the immunoprecipitates (Figure 2).7–16\n\nHAP1 lysates were prepared, and IP was performed using 2.0 μg of the indicated Amyloid-beta precursor protein antibodies pre-coupled to Dynabeads protein G or protein A. Samples were washed and processed for Western Blot with the indicated Amyloid-beta precursor protein antibodies. For Western Blot, MA5-35187** and ab252816** were used at 1/500. The Ponceau stained transfers of each blot are shown for similar reasons as in Figure 1. SM=4% starting material; UB=4% unbound fraction; IP=immunoprecipitate, *Monoclonal antibody, **Recombinant antibody.\n\nFor immunofluorescence, antibodies were screened using a mosaic strategy.17 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\nHAP1 WT and APP 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 in a 96-well plate with an optically clear flat-bottom. Cells were stained with the indicated Amyloid-beta precursor protein 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 green and magenta dashed line, respectively. When the concentration was not indicated by the supplier, we tested antibodies at 1/100 and 1/500. At these concentrations, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: ab126732** at 1/500, ab252814** at 1/500, ab252816** at 1/500, ARP33075 at 1/500, ARP34012 at 1/500, 29765** at 1/100, 76600** at 1/50, 25524-1-AP at 1/500, 13-0200* at 1/500, 14-9749-80* at 1/500, MA5-35187** at 1/1000. *Monoclonal antibody, **Recombinant antibody, Bars=10 μm.\n\nIn conclusion, we have screened eleven amyloid-beta precursor protein commercial antibodies by Western blot, immunoprecipitation and immunofluorescence and identified several high-quality antibodies under our standardized experimental conditions. The underlying data can be found on the Zenodo open access repository.18,19\n\n\nMethods\n\nAll amyloid-beta precursor protein antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly.20 Peroxidase-conjugated goat anti-mouse, anti-mouse and anti-rat antibodies are from Thermo Fisher Scientific (cat. number 62-6520, 65-6120 and 31470, respectively). Alexa-555-conjugated goat anti-mouse and anti-rabbit secondary antibodies are from Thermo Fisher Scientific (cat. number A21424 and A21429).\n\n* Monoclonal antibody.\n\n** Recombinant antibody.\n\n1 Refers to RRID recently added to the Antibody Registry (in May 2023), they will be available on the Registry website in coming weeks.\n\nBoth HAP1 WT and APP KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.21 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.22 HAP1 WT and APP 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) supplemented with 1× protease inhibitor cocktail mix (MilliporeSigma, cat. number 78429). 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 precast midi 4-20% Tris-Glycine polyacrylamide gels (Thermo Fisher Scientific, cat. number WXP42012BOX) ran with Tris/Glycine/SDS buffer (bio-Rad, cat. number 1610772), loaded in Laemmli loading sample buffer (Thermo Fisher Scientific, cat. number AAJ61337AD) and transferred on nitrocellulose membranes. Proteins on the blots were visualized with Ponceau S staining (Thermo Fisher Scientific, cat. number BP103-10) which was scanned to show together with individual Western blot. Blots were blocked with 5% milk for 1 h, and antibodies were incubated overnight at 4°C with 5% milk 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 h 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 iBright CL1500 Imaging System (Thermo Fisher Scientific, cat. number A44240).\n\nImmunoprecipitation was performed as described in our standard operating procedure.23 Antibody-bead conjugates were prepared by adding 2 μg or 20 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 and rat antibodies) (Thermo Fisher Scientific, cat. number 10002D and 10004D, respectively). Tubes were rocked for ~2 h at 4°C followed by two washes to remove unbound antibodies.\n\nHAP1 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 for 30 min at 4°C and spun at 110,000 × g for 15 min at 4°C. 0.5 mL aliquots at 2.0 mg/mL of lysate were incubated with an antibody-bead conjugate for ~2 h 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 precast midi 4-20% Tris-Glycine polyacrylamide gels.\n\nImmunofluorescence was performed as described in our standard operating procedure.7–17 HAP1 WT and APP KO were labelled with a green and a deep 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 37°C, 5% CO2. Cells were fixed in 4% paraformaldehyde (PFA) (Beantown chemical, cat. number 140770-10ml) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL) for 15 min at room temperature and then washed three times with PBS. 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% bovine serum albumin (BSA) (Wisent, cat. number 800-095), 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 Amyloid-beta precursor protein 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 h at room temperature with DAPI. Cells were washed 3 × 10 min with IF buffer and once with PBS.\n\nImages were acquired on an ImageXpress micro widefield high-content microscopy system (Molecular Devices), using a 20x/0.95 NA water objective lens and scientific CMOS camera (16-bit, 1.97 mm field of view), equipped with 395, 475, 555 and 635 nm solid state LED lights (Lumencor Aura III light engine) and bandpass emission filters (432/36 nm, 520/35 nm, 600/37 nm and 692/40 nm) to excite and capture fluorescence emission for DAPI, CellTrackerTM Green, Alexa fluor 555 and CellTrackerTM Red, respectively. Images had pixel sizes of 0.68 × 0.68 microns. Exposure time was set with maximal (relevant) pixel intensity ~80% of dynamic range and verified on multiple wells before acquisition. Since the IF staining varied depending on the primary antibody used, the exposure time was set using the most intensely stained well as reference. Frequently, the focal plane varied slightly within a single field of view. To remedy this issue, a stack of three images per channel was acquired at a z-interval of 4 microns per field and best focus projections were generated during the acquisition (MetaExpress v6.7.1, Molecular Devices). Segmentation was carried out on the projections of CellTrackerTM channels using CellPose v1.0 on green (WT) and far-red (KO) channels, using as parameters the ‘cyto’ model to detect whole cells, and using an estimated diameter tested for each cell type, between 15 and 20 microns.24 Masks were used to generate cell outlines for intensity quantification. 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 Amyloid-beta precursor protein, https://doi.org/10.5281/zenodo.7971926. 18\n\nThis project contains the following underlying data;\n\n- Amyloid-beta precursor protein_APP_YCharOS report.pdf\n\nZenodo: Dataset for the Amyloid-beta precursor protein antibody screening study, https://doi.org/10.5281/zenodo.8140410. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe would like to thank the NeuroSGC/YCharOS/EDDU 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. We would also like to thank the Advanced BioImaging Facility (ABIF) consortium for their image analysis pipeline development and conduction (RRID:SCR_017697). Members of each group can be found below.\n\nNeuroSGC/YCharOS/EDDU collaborative group: Riham Ayoubi, Thomas M. Durcan, Aled M. Edwards, Carl Laflamme, Peter S. McPherson, Chetan Raina, Wolfgang Reintsch, Kathleen Southern and Donovan Worrall.\n\nABIF consortium: Claire M. Brown and Joel Ryan.\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 article can be found on Zenodo (doi: 10.5281/zenodo.7971926)\n\n\nReferences\n\nMüller UC, Zheng H: Physiological functions of APP family proteins. Cold Spring Harb. Perspect. Med. 2012; 2(2): a006288. PubMed Abstract | Publisher Full Text\n\nBaumkötter F, Schmidt N, Vargas C, et al.: Amyloid precursor protein dimerization and synaptogenic function depend on copper binding to the growth factor-like domain. J. Neurosci. 2014; 34(33): 11159–11172. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGlenner GG, Wong CW: Alzheimer’s disease: initial report of the purification and characterization of a novel cerebrovascular amyloid protein. Biochem. Biophys. Res. Commun. 1984; 120(3): 885–890. PubMed Abstract | Publisher Full Text\n\nKang J, Lemaire HG, Unterbeck A, et al.: The precursor of Alzheimer’s disease amyloid A4 protein resembles a cell-surface receptor. Nature. 1987; 325(6106): 733–736. Publisher Full Text\n\nZheng H, Koo EH: Biology and pathophysiology of the amyloid precursor protein. Mol. Neurodegener. 2011; 6(1): 1–16.\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\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\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\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. Publisher Full Text\n\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence.2021.\n\nAyoubi R, Fotouhi M, Ryan J, et al.: Antibody Characterization Report for Amyloid-beta precursor protein.2023. Publisher Full Text\n\nSouthern K: Dataset for the Amyloid-beta precursor protein antibody screening study. 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. 2022; 51: D358–D367. Publisher 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.\n\nStringer C, Wang T, Michaelos M, et al.: Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods. 2021; 18(1): 100–106. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "237217",
"date": "24 Jan 2024",
"name": "Amal Kaddoumi",
"expertise": [
"Reviewer Expertise Neuropharmacology",
"Alzheimer's disease",
"CAA",
"blood-brain barrier"
],
"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 report, the authors compared eleven APP commercial antibodies for Western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol using HAP1-APP expressing cells (WT) and HAP1-APP KO cells. This report could be useful if the authors elaborated more on their recommendations based on their findings. I have the following comments:\nThe authors should comment on the findings by clearly presenting their recommendations for which antibodies proved useful and for which assay. Also, they should comment on whether any of these antibodies could be used for the 3 assays, i.e., Western blot, immunoprecipitation, and immunofluorescence, or whether each assay requires one antibody but not the other. It’s unclear how many times each antibody was tested for validation/consistency. Is one time run/test enough to conclude? Each antibody specificity and species cross-reactivity should be reported. The antibodies showed 2 bands. Please comment on these 2 bands. Figure 3 presented binding in gray color; why is that? showing the images in their original staining colors (red, green, and blue for DAPI) would better clarify the binding. As presented, binding is not clear. Also, based on the results, which antibodies are recommended? As shown, the conclusions from Figure 3 are not clear.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and materials provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "11360",
"date": "13 Apr 2024",
"name": "Kathleen Southern",
"role": "Author Response",
"response": "Thank you Amal Kaddoumi for your comprehensive review of this study. A new version of this article has been submitted, to ensure transparency and prevent further misinterpretations. We trust that the refinements made meet your expectations, enhance comprehensibility and address any concerns you might have had. Please see our responses to your specific comments below. To your first comment regarding providing antibody recommendations for each application, we’d like to clarify that the aim of the YCharOS initiative is not to recommend antibodies based on their performance under our standardized protocol. Furthermore, given that this article is formatted as a Data Note, it does not require the results to be discussed nor concluded. YCharOS is a public-private organization whose mission is to characterize antibodies for every human protein and deliver the research as a collective good for the scientific community. This study is to be used as a guide to help researchers, interested in studying amyloid-beta precursor protein or amyloid-beta proteins, select high-quality antibodies to enhance their experiments and prevent reproducibility and financial issues that occur when purchasing antibodies that don’t bind their target of interest properly. Moreover, as the antibodies are tested under one specific set of conditions, summarizing the performance of the antibodies or providing recommendations for each application would be valid only under the precise experimental setup and cell line used. That being said, we understand how the intention of our initiative may be misinterpreted. A new version has been submitted, to include modifications to the title, introduction and results&discussion section that ensure the authors goals are aligned and defined to all readers. To your second comment, the antibodies are tested in each application once. The amount of antibody provided by our industry partners (usually 100 µl) is enough to perform each application once. Furthermore, all antibodies tested per human protein are evaluated side-by-side under the same experimental set-up providing more transparency and accuracy of results, even when subjected to the experiment only once. For the same reasoning as in our reply to the first comment, the authors do not report antibody specificity or cross-reactivity. That being said, the following article written by Ayoubi et al., referenced in this article, describes the antibody performance criteria (Box 1) which may provide insights on the specificity of antibodies evaluated in this article (1) In response to your fourth comment, according to the antibody manufacturer catalogs, all antibodies tested in this study are designed to target the amyloid-beta precursor protein. According to literature, amyloid-beta precursor protein undergoes post-translational proteolytic cleavage that gives rise to amyloid beta peptides via proteases (2-4). The appearance of two bands in Western blot and immunoprecipitation may be attributed to post-translation activity, although this was not confirmed and is outside the scope of this study. Further experiments by experts in the amyloid beta protein family is required, using the high-quality antibodies that can be identified in this study. As described in the Figure legend of Figure 3, representative images are in gray due to the merged blue and red channel which generates a grayscale. The blue channel represents the nuclei stained with DAPI while the red channel represents the primary antibody staining. Therefore, the gray represents where the antibody is binding in the cell. Images of each channel can be found in the Dataset created for this study, in the Underlying data section. Ayoubi, R., et al. (2023). \"Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications.\" eLife 12: RP91645 Müller UC, Zheng H: Physiological functions of APP family proteins. Cold Spring Harb. Perspect. Med.2012;2(2):a006288. 22355794 10.1101/cshperspect.a006288 Glenner GG, Wong CW: Alzheimer’s disease: initial report of the purification and characterization of a novel cerebrovascular amyloid protein. Biochem. Biophys. Res. Commun. 1984;120(3):885–890. 6375662 10.1016/S0006-291X(84)80190- Kang J, Lemaire HG, Unterbeck A, et al.: The precursor of Alzheimer’s disease amyloid A4 protein resembles a cell-surface receptor. Nature. 1987;325(6106):733–736. 10.1038/325733a0"
}
]
},
{
"id": "237210",
"date": "13 Feb 2024",
"name": "Jens-Ulrich Rahfeld",
"expertise": [
"Reviewer Expertise protein chemistry",
"antibody discovery",
"drug discovery",
"preclinical research",
"neurodegenerative 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\nThis manuscript \"Identification of high-performing antibodies for amyloid-beta precursor protein for use in Western Blot, immunoprecipitation and immunofluorescence\" fulfils the criteria for publication as a Data Note. The scientific topic - the immunological detection of the amyloid precursor protein APP in mammalian cells - is of current interest. On the one hand, this is based on research into the processes of neuronal development, homeostasis and interneuronal transmission and their connection to neurodegenerative diseases such as Alzheimer's disease. On the other hand, there are clear indications of increased expression of APP in malignant cells of various cancers.\nIn this context, it is very important to have appropriate, carefully characterized tools for the detection of the APP protein.\nThe manuscript contains a very impressive and well-designed overview and a head-to-head comparison of the performance of 11 commercially available antibodies from 5 different suppliers. It thus provides clear guidance for the selection of antibodies for a particular scientific or analytical question.\nTwo defined and well-characterized cell lines were used for the analysis, whose characteristics with regard to APP expression were clearly confirmed in the course of the work.\nMinor Remark: In this manuscript, the authors do not evaluate the individual antibodies in terms of their different performance in the results section. It would be helpful for the reader to be provided with such a summary or an overview of the results obtained for each antibody. This could be provided in the form of an additional table, or as a supplement in Table 2 in additional columns.\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": []
}
] | 1
|
https://f1000research.com/articles/12-956
|
https://f1000research.com/articles/13-111/v1
|
19 Feb 24
|
{
"type": "Case Study",
"title": "Prediction of Bioethanol from Production of Lignocellulosic Biomass Waste from Agriculture and Livestock Using Regression Analysis Model",
"authors": [
"Dini Dwi Ludfiani",
"Forita Dyah Arianti",
"Agung Prabowo",
"Bambang Haryanto",
"Megawati Megawati",
"Nugroho Adi Sasongko",
"Dini Dwi Ludfiani",
"Agung Prabowo",
"Bambang Haryanto",
"Megawati Megawati",
"Nugroho Adi Sasongko"
],
"abstract": "Background Every year, the food supply must need to increase to accommodate population growth and food consumption increases. It causes the production of lignocellulosic biomass waste (LBW) in Indonesia from sector of agriculture and livestock also increase. Contrast to energy supply, energy demand increases but energy supply from fossil fuel become limit. More than 80% of LBW is dumped or burned, whereas the LBW has the potential as raw material of sustainable bioenergy, especially bioethanol to replace or mix with fossil fuel. This study aimed to predict the bioethanol production from potential of LBW to optimize its utilization. Potential of LBW production is estimated based on production of LBW lignocellulose component (cellulose, hemicellulose, and lignin). The novelty of this study is obtained predicted values for bioethanol production based on LBW production using a regression analysis model.\n\nMethods The data of LBW production is calculated based on converting waste of the crops production (for agriculture sector) and animal unit (AU) (for livestock sector). The data of LBW consist of rice straw, corn stover, sugarcane bagasse, cassava peel, paunch content, and feces. This study use linear regression analysis model to predict bioethanol production from LBW.\n\nResults Estimation average LBW lignocellulose production in Indonesia is around 104.47 million tons, and can produce around 59.98 billion gallons (227.01 billion liters) of bioethanol. The regression model based on lignocellulose production (R2) was 0.9925 (cellulose), 0.9848 (hemicellulose), and 0.9294 (lignin). Production of LBW in Indonesia is highest in Southeast Asia and has increased 2.07% per year because crops production, ruminant population, and ruminants slaughtered increase. This value will continue to increase, same with bioethanol production from LBW production.\n\nConclusions Overall, Indonesia has potential to produce bioethanol from LBW. Using the entire the LBW for bioethanol make it possible to meet domestic energy demands in a sustainable.",
"keywords": [
"Bioethanol",
"biofuel",
"biomass",
"regression"
],
"content": "Introduction\n\nAsia is the largest of the world’s continents by both land area and population. Asia used about 54% of total land area for agriculture and Indonesia has an agricultural land of 62.30 million ha (FAO, 2022). The primary crop in Asia is paddy (rice), because rice is a staple food. Secondary crops in Indonesia named palawija like as maize, cassava, and sorghum. Paddy is planted during the rainy season and palawija are planted during the dry season. Every year, the food consumption in Indonesia continuously increases, linear with population growth and economic development. Since 2020 until 2021, the crops production, ruminant population, and ruminant slaughtered increase of 1.38%. This increasing number shows that every year food supplies increase to meet food demand.\n\nThe energy demand continuously increases, linear with increasing food demand. The type of the most consumed energy is fossil fuel, but the fossil fuel has an impact on environmental pollution (emission) and has a depletion issue. International Energy Agency (IEA) reported that energy demand is increase 5% and carbon emissions is increase 3.5% in 2022. United States Environmental Protection Agency (US EPA) reported that fossil fuel has contribute to greenhouse gas (CO2) emissions of 65%. Currently, alternative energy sources (bioenergy) are being explored and developed with the aim of reducing emissions and meet increasing energy demand.\n\nContinuously increasing of crops production, population of ruminants and ruminants slaughtered to meet food demand causes the lignocellulose biomass waste (LBW) production increase especially agricultural residue such as straw, peel, husk, etc., and livestock waste such as feces, and paunch content waste. The LBW has not been used optimally yet (Fitri et al., 2020). Only 10-20% the LBW is used as fertilizer and feed, but 80-90% is disposed, burned, piled, or used as mulch for the following crop (Hanafi et al., 2012; Vasić et al., 2021). Burning of LBW is low-cost method for disposal, but this method causes pollution, reduce air quality, and effect on health. The LBW has significant potential as raw material for biofuel or biomass energy (Alrikabi, 2014). The advantages of LBW are inexpensive resource (Rosado et al., 2022; Yang and Wyman, 2008), low value, renewable, rich in carbohydrate content (Canilha et al., 2012), high sugar content (Rijal, 2020), carbon-neutral nature (Wang et al., 2021), abundant (Novia et al., 2019) and eco-friendly (Krishnan et al., 2020). Lignocellulose has the capacity to be converted into biofuels such as bioethanol (Dahman et al., 2019). The advantage of biofuel is reduced greenhouse gas emission (Sindhu et al., 2019).\n\nBiofuel derived from biomass has the potential to be a sustainable transportation fuel and can replace gasoline or fossil fuel (Kim & Dale, 2004). Biofuel is produced from different converting technologies (biological and physicochemical methods) (Azeez & Al-Zuhairi, 2020). Bioethanol (C2H5OH) is the one of biofuel which the promising biofuel to resolve energy crisis and can meet energy demand by full utilizing bioethanol as fuel (Wang & Lü, 2021). Bioethanol has advantages based on characteristic such as eco-fuel, sustainable, and renewable (Halder et al., 2018). Bioethanol as biofuel also plays an important role in reducing crude oil consumption and environmental pollution. Bioethanol is produced from carbohydrate substrate such as sugar, starch, lignocellulose, etc. through alcoholic fermentation process by microorganisms (Mohd Azhar et al., 2017). Characteristic of bioethanol are a liquid, burn cleanly with a bluish flame color (Log & Moi, 2018). According to Tanwar et al. (2023) bioethanol has higher octane rating and heat evaporation than gasoline, and can reduce carbon monoxide gas emission up to 25%.\n\nThe value of biomass conversion into biofuel can be determined through several experiments in the laboratory and in the field, but this process certainly takes time to get optimal results. In calculating the conversion of biomass into bioethanol are usually based on fermentation parameters such as volume of the starting culture and volume of the gas produced during fermentation; and carbohydrate value such as monosaccharides C5 and C6. The novelty of this study is the use of a regression analysis model to prediction of bioethanol production from LBW based on production of lignocellulose component (cellulose, hemicellulose, and lignin). The aim of this study is to predict the bioethanol, production from potential of LBW to optimize its utilization.\n\n\nMethods\n\nThe data of crops production, ruminant population, and ruminant slaughtered in Indonesia are collected from FAO for prediction of LBW. The calculation of the number of LBW is carried out by considering the proportion of crops: LBW (for agriculture sector) (Kim & Dale, 2004; Ntelok, 2017) and based on animal unit (AU) (for livestock sector) (Felisberto et al., 2011). The values obtained are converted to the production of LBW lignocellulose component (cellulose, hemicellulose, and lignin). One AU equal to 1 cattle weight 450 kg.\n\nThis study use linear regression analysis model to predict bioethanol production. This model is used to predict bioethanol production from the annual amount of LBW based on production of lignocellulose component include cellulose, hemicellulose, and lignin. This approach is in line with Núñez et al. (2011) method, which prioritize the use of regression model to predict and effect estimation. The following equation describes the linear regression model:\n\nWhere y is the dependent variable, x is the independent or explanatory variable, a is the intercept, b is the slope of the line, and ε is error or residue.\n\n\nResults and Discussion\n\nEvery year, crops production, population of ruminant, and ruminant slaughtered in Indonesia increases. It is linear with increasing LBW production (Table 1). Every year, the average crops production increase 1.99%, population of ruminant 2.85%, ruminant slaughtered 2.23%, and LBW production 2.07%. Indonesian crops consist of 2 types, primary crops (paddy) and secondary crops (maize, cassava, sorghum, and sugarcane). Sorghum is only grown in certain areas in Indonesia.\n\n* Source: FAO; 1,2,4estimated LBW are 1.4 from rice production, 1.0 from maize (corn) production, 0.6 from sugarcane production (Kim & Dale, 2004); 3estimated LBW 20% from total cassava weight (Ntelok, 2017); 5estimated LBW are 13% BW for buffalo and cattle; 8% BW for goat and sheep (Felisberto et al., 2011); 6estimated LBW is 7% BW for 1 AU per year (365 day).\n\nIndonesia has various types of ruminants, such as beef cattle, goat, sheep, and buffalo. Every day, ruminants are slaughtered in slaughterhouse (abattoir) to meet food demand (especially meat). One of the most common types of waste produced in large amount from slaughterhouses is paunch content waste. According to Pancapalaga et al. (2021) the paunch content waste is incompletely digested of feed consumed and has still nutrient content that can be used by microbes in the gastrointestinal tract. During raising ruminants, they produce feces and urine every day while abattoir produce paunch content. According to Gupta et al. (2016) ratio of feces and urine is 3:1. Feces and paunch content waste contain nutrients such as fiber or lignocellulose.\n\nMaize (corn) is composed of 38% grain, 7% cobs, 12% husks, 13% leaves, and 30% stalk (Ludfiani, 2016). So, the potency of LBW production from maize is around 62%. Compare to cassava, the LBW production from cassava is around 20% of the total cassava weight, specifically cassava peel (Ntelok, 2017). Indonesia also high LBW production in palm oil because palm oil production increase every year and it is potential to be used as biofuel (high potential for biodiesel). In this study is not discussed further about palm oil because in Southeast Asia has only Indonesia and Malaysia produce palm oil.\n\nBPS-Statistic Indonesia reported palm oil production is 44.75 million tons in 2020, 45.12 million tons in 2021, and 45.58 million tons in 2022. FAO reported that Indonesia is the top 1 producer of palm oil in the world and production in 2021 is around 44.75 million tons of palm oil, 10.17 million tons of palm kernel, 253.31 million tons oil of palm fruit, 4.44 million tons of oil of palm kernel. According to Mahlia et al. (2019) palm oil tree biomass can be converted into biofuels and biopower. About 5% of the biodiesel produced from palm oil can be mixed with petroleum diesel as fuel (Hassan et al., 2011). Palm oil plantation residues and residues from the palm oil industry are quite high and also potential to be used fuel. Palm oil empty fruit brunch can produce one third of the power from a direct combustion compare to methane gas for electricity (Kaniapan et al., 2021).\n\nBased on the data in Table 1, the largest amount of LBW production is from livestock sector. Compare to LBW production in Southeast Asia, LBW production in Indonesia is in 1st position in Southeast Asia from sector of agricultural and livestock (Figure 1). FAO reported that Indonesia is in 3rd position in the world (after China and India) for rice production, and it is in 8th position in the world for maize and sugar cane production. This indicates that Indonesia has great potential in producing abundant LBW, and has potential to be used as biofuel such as bioethanol.\n\n(A) Production of LBW from agricultural crops; (B) production of LBW from livestock sector.\n\nThe LBW from agriculture (agricultural residue) and livestock (feces and paunch content) contain nutrients that can be utilized into value-added products. The LBW contain high fiber (80 to 95%) (Shrotri et al., 2017). The main components of fiber or lignocellulose of LBW are cellulose, hemicellulose, and lignin. The fiber value of LBW depend on management factor and the part of plant. According to Gummert et al. (2019) variations in fiber content of biomass depend on various factors such as the type or part of the plant, species, type of tissue, growth stage, and growth condition.\n\nTable 2 show the potency of LBW production from sector of agriculture and livestock based on lignocellulose component. The average of LBW lignocellulose contents from various types of LBW such as rice straw, corn stover, sugarcane, bagasse, cassava peel, paunch content, and feces are 29.36% of cellulose, 23.76% of hemicellulose, and 16.17% of lignin. Based on these contents, production lignocellulose of LBW can reach 136.99 million tons of cellulose, 112.33 million tons of hemicellulose, and 64.09 million tons of lignin. Feces and rice straw produce higher amount of LBW than other.\n\n* Estimated calculation based on lignocellulose content.\n\nCellulose is the largest fraction in LBW. According to Vasić et al. (2021) forages and agricultural waste contain lignin around 10-30%. Compare to palm oil tree residue, this value is lower. Palm oil tree residue such as palm oil frond, palm oil empty fruit bunch, and palm oil trunk have chemical composition arranged 34.40-40.70% cellulose, 26.10-31.80% hemicellulose, and 12.45-26.20% lignin (Kaniapan et al., 2021).\n\nCellulose and hemicellulose are carbohydrate which is the main feedstock for producing energy (Kim & Dale, 2004; Zeinaly et al., 2017). Both of them are unavailable carbohydrate (Paxton, 2020). The LBW contain carbohydrate structure which can be used as an energy source (Zeinaly et al., 2017). To optimize the pre-treatment process and expand the usability value of LBW, it is necessary to be evaluated through proximate analysis and energy content (Kaniapan et al., 2021). Cellulose can be synthesized by bacteria and fungi (Vasić et al., 2021), and hemicellulose is an important component and it used in biofuels and various bioproducts (Huang et al., 2021).\n\nBased on the data in Table 2, lignocellulose content of paunch content is in the middle value. The paunch content contains groups of microbes and lignocellulose derived from feed which are being degraded by rumen microbes and enzymes in the gastrointestinal tract during the digestion process. This is a factor that affect the chemical content of paunch content because the lignocellulose value is obtained not only from feed, but also from rumen microbes. According to Elfaki & Abdelatti (2015) and Sarteshnizi et al. (2018) paunch content contain various components, such as saliva, anaerobic microbes (fungi, protozoa, and bacteria), nutrient content (cellulose, hemicellulose, protein, fat, carbohydrates, minerals, and vitamins), and enzymes. It also contain volatile fatty acids (VFAs) such as acetate, propionate, and butyrate (Gleason et al., 2022; Koppolu & Clements, 2004).\n\nAccording to Partama (2019) ruminant can consume 3.21% of dry matter, and digestibility level of feed is a maximum of 70%. Feed of ruminant consist 60-70% of carbohydrates (cellulose, hemicellulose) and almost 50% of the lignocellulose component is digested by rumen microbes. According to Fasake and Dashora (2020) around 10.86% undigested feed from ruminant feces. The average total digestibility nutrient of fiber from forage is 40-65% in ruminant, so the undigested nutrient will be excreted through the feces (Hartadi, 2019). Feces is the undigested residue of feed consumed and contain nutrients content, microbes, or enzyme (Santoso et al., 2015). Digestibility of buffalo is higher (2-3%) than cattle (Prihantoro et al., 2012).\n\nBioethanol production can predict using linear regression model with production factor of lignocellulose LBW (Table 3). The analysis result show the regression model based on production of cellulose show bioethanol production (R2) of 0.9925, while based on hemicellulose production of 0.9848, and model based on lignin production of 0.9294. Regression analysis can estimate the correlation between the dependent variable and the independent variable. Linear regression is used to predict the linear correlation between predictors (Maulud & Abdulazeez, 2020). Linear regression in this study to learn more the variables that affect bioethanol production.\n\nPrediction of bioethanol production from lignocellulose LBW production show in Table 4. Average production of lignocellulose LBW in Indonesia in 2021 can reach 104.47 million tons and has potential to bioethanol produce of 59.98 billion gallons (227.01 billion liters). This value is quite high than bioethanol production from grain (1G bioethanol). United State produces 15.25 billion gallons of bioethanol from corn (Mohanty & Swain, 2019). The major producer of bioethanol in the world is the United State (55%) and followed Brazil (27%) in 2021 (Broda et al., 2022). United State produces ethanol from corn (grain) and Brazil from sugarcane (Kim & Dale, 2004). Bioethanol has the potential to become a prime candidate for gasoline substitution (Halder et al., 2018). This is because the energy content of bioethanol is higher than gasoline, and it can be blended with gasoline about 5-24% (Sánchez & Cardona, 2008).\n\nBased on Figure 1, Indonesia, Thailand, and Viet Nam have high potential to LBW production. If we calculate the prediction of bioethanol production based on lignocellulose LBW production, Indonesia, Thailand, and Viet Nam have significant potential to produce quite high amount of bioethanol. Currently, Thailand has been producing bioethanol from corn (1G bioethanol) and it is around 1% (over 1,02 million liters) of worldwide bioethanol production. Indonesia has also produced bioethanol (from sugarcane) but in small quantities and has not been able to supply domestic demand yet. Ministry of Energy and Mineral Resources Indonesia reported that bioethanol production just reached 40 million liters, but bioethanol fuel demand in Indonesia reaches 696 million liters.\n\nBased on Table 4, the prediction of bioethanol production from lignocellulose LBW production can meet domestic bioethanol demand. This value is expected to continuously increase every year linear with food demand and LBW production. From the analysis result, the predictive value bioethanol production based on lignin production is predicted to reach the highest. It is suspected that the process of breaking down of lignin can contribute quite high fermented sugar than fermented sugar obtained from only breaking down of cellulose and hemicellulose. According to Zhong et al. (2021) lignin is the main contributor to the structure of roughage, but lignin can be broken down or degrades by rumen fungi (Vahidi et al., 2021).\n\n\nConclusion\n\nUsing the regression analysis model can predict bioethanol production from LBW based on the production of lignocellulose components (cellulose, hemicellulose, and lignin). Indonesia has the potential to bioethanol production from LBW from sector of agricultural and livestock with production of lignocellulose LBW can reach significant amount 136.99 million tons cellulose, 112.33 million tons hemicellulose, and 64.09 million tons lignin. The estimated average bioethanol production from lignocellulose LBW production can reach 59.98 billion gallons (227.01 billion liters). Using the entire the LBW for bioethanol, Indonesia has great potential to meet domestic energy demand.\n\n\nAuthorship contribution statement\n\nDini Dwi Ludfiani: Conceptualization, Methodology, Formal analysis, Resoures, Writing-original draft, Visualization.\n\nForita Dyah Arianti: Conceptualization, Methodology, Resoures, Writing-original draft, Writing-review & editing, Supervision.\n\nAgung Prabowo: Conceptualization, Methodology, Formal analysis, Visualization, Writing-review & editing.\n\nBambang Haryanto: Conceptualization, Methodology, Writing-review & editing, Resouces.\n\nMegawati Megawati: Formal analysis, Visualization, Writing-original draft, Writing-review & editing.\n\nNugroho Adi Sasongko: Resouces, Visualization, Writing-original draft, Writing-review & editing.",
"appendix": "Data availability\n\nFigshare: Prediction of Bioethanol from Production of Lignocellulosic Biomass Waste from Agriculture and Livestock Using Regression Analysis Model, https://doi.org/10.5281/zenodo.10212631.\n\nThis project contains the following underlying data:\n\n• Calculated.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAcknowledgments\n\nThis study was supported by the Postdoctoral Program at National Research and Innovation Agency (BRIN) Indonesia (2023-2024).\n\n\nReferences\n\nAlrikabi NKMA: Renewable Energy Types. J. Clean Energy Technol. 2014; 2(1): 61–64. Publisher Full Text\n\nAzeez RA, Al-Zuhairi FK: Biofuels (Bioethanol, Biodiesel,and Biogas) from Lignocellulosic Biomass:A Review. J. Univ. Babylon Eng. Sci. 2020; 28: 2020.\n\nBroda M, Yelle DJ, Serwańska K: Bioethanol Production from Lignocellulosic Biomass—Challenges and Solutions. Molecules. 2022; 27(24). 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PubMed Abstract | Publisher Full Text\n\nSantoso SAB, Puspitasari G, Muktiani A, et al.: A study on the use of fecal characteristics for feed digestibility determination in Goat. J. Indones. Trop. Anim. Agric. 2015; 40(1): 59–67. Publisher Full Text\n\nSarteshnizi FR, Seifdavati J, Abdi-benemar H, et al.: The potential of rumen fluid waste from slaughterhouses as an environmentally friendly source of enzyme additives for ruminant feedstuffs. J. Clean. Prod. 2018; 195: 1026–1031. Publisher Full Text\n\nShrotri A, Kobayashi H, Fukuoka A: Catalytic Conversion of Structural Carbohydrates and Lignin to Chemicals. Advances in Catalysis. 1st ed. Vol. 60. . Elsevier Inc.; 2017. Publisher Full Text\n\nSindhu R, Binod P, Pandey A, et al.: Biofuel production from biomass: Toward sustainable development. Current Developments in Biotechnology and Bioengineering: Waste Treatment Processes for Energy Generation. Elsevier B.V; 2019. 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Publisher Full Text\n\nWilliams GA, Akinola OS, Adeleye TM, et al.: Influence of Processed Cassava Peel-leaf Blend as Replacement for Maize on Growth Performance and Serum Parameters of Growing Pigs. Asian J. Dairy Food Res. 2023; 42(2): 161–167. Publisher Full Text\n\nYang B, Wyman CE: Pretreatment: the key to unlocking low-cost cellulosic ethanol. Biofuels Bioprod. Biorefin. 2008; 2: 26–40. Publisher Full Text\n\nZeinaly F, Saraeian A, Gabov K, et al.: Determination of Carbohydrates in Sugarcane Bagasse Pulp in Different Tcf Bleaching Sequences. Cellul. Chem. Technol. 2017; 51(2): 45–53.\n\nZhong H, Zhou J, Abdelrahman M, et al.: The effect of lignin composition on ruminal fiber fractions degradation from different roughage sources in water buffalo (Bubalus bubalis). Agriculture (Switzerland). 2021; 11(10). Publisher Full Text"
}
|
[
{
"id": "251956",
"date": "18 Mar 2024",
"name": "Gabriel Salierno",
"expertise": [
"Reviewer Expertise Clean energy technology"
],
"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 suggest that Indonesia possesses remarkable potential for bioethanol production by utilizing LBW. This approach offers a sustainable solution to address the nation's energy needs while reducing dependence on fossil fuels and their associated environmental consequences.\nWhile the study presents promising findings regarding the abundance of lignocellulosic biomass waste (LBW) and its estimated bioethanol yield, crucial aspects of the employed model warrant further clarification.\nFirstly, the utilized model lacks transparency. The authors fail to provide a clear definition of the output variables, hindering a comprehensive understanding of the model's function. Additionally, the absence of interpretation for the model parameters limits the reader's grasp of their influence on the predicted bioethanol yield.\nSecondly, the sole presentation of the R-squared value (coefficient of determination) is insufficient. While it indicates a good fit between the model and the data, a more thorough analysis encompassing the interpretation of the model's coefficients and their significance levels is necessary.\nFurthermore, the terminology employed requires refinement. The phrase \"Potency of LBW production\" seems imprecise. A more accurate term would be \"Potential of LBW production,\" signifying the inherent capability of LBW to be converted into bioethanol.\nWhile the research holds promise, it suffers from a lack of clarity in several crucial aspects. Model Opacity: A significant concern lies in the obscurity surrounding the employed model. The authors fail to provide a clear definition or detailed explanation of the model, hindering a comprehensive understanding of its function and underlying assumptions. Uncertain Output Variables: Furthermore, the research neglects to define how bioethanol production is calculated. This ambiguity raises questions about the data's validity. It remains unclear whether the provided data, presumably from the Food and Agriculture Organization (FAO), has actually undergone any conversion process to yield bioethanol. Missing Process Information: A critical shortcoming lies in the complete absence of information regarding the conversion process itself. The research fails to mention crucial details such as whether separate steps for saccharification and fermentation are employed, or if a combined approach is utilized. Limited Model Interpretation: The analysis solely reports the R-squared value, which signifies the model's goodness-of-fit. However, it disregards the interpretation of the model's parameters, which are essential for understanding the influence of individual variables on bioethanol production. Language Considerations: The manuscript requires thorough language polishing to enhance clarity and conciseness. Several instances require correction:\n\"Potency of LBW production\" should be replaced with \"Potential of LBW production\". \"Bioethanol production can predict using linear regression model with production factor of lignocellulose LBW\" can be rephrased as \"A linear regression model can be used to predict bioethanol production based on the lignocellulose content of LBW\". \"Prediction of bioethanol production from lignocellulose LBW production show in Table 4\" can be improved as \"Table 4 presents the predicted bioethanol production based on the lignocellulose content of LBW\". \"Linear regression in this study to learn more the variables that affect bioethanol production\" should be revised to \"This study employs linear regression to identify factors influencing bioethanol production\".\nRecommendations for Improvement: To strengthen the research, the authors should provide:\nA clear description of the utilized model, including its purpose and underlying assumptions. A definition of the bioethanol production calculation method and clarification regarding the conversion process of the FAO data (if any). Detailed information about the conversion process, specifying whether separate or combined saccharification and fermentation steps are involved. An in-depth interpretation of the model parameters beyond just the R-squared value. Addressing the identified grammatical errors and awkward phrasing throughout the manuscript.\nBy incorporating these recommendations, the research can achieve greater clarity, address the identified limitations, and contribute more effectively to the field of bioethanol production from LBW.\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? Partly\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\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? No",
"responses": [
{
"c_id": "11374",
"date": "19 Jun 2024",
"name": "dini dwi ludfiani",
"role": "Author Response",
"response": "Recommendations for Improvement from reviewer: A clear description of the utilized model, including its purpose and underlying assumptions Response: We have done this. A definition of the bioethanol production calculation method and clarification regarding the conversion process of the FAO data (if any). Response: Bioethanol production calculations are obtained based on FAO data conversion. The calculations have been described below in Table 1. Raw data can be seen in \"data availability\". Detailed information about the conversion process, specifying whether separate or combined saccharification and fermentation steps are involved. Response: The conversion process is enzymatic saccharification, and already described in the manuscript. An in-depth interpretation of the model parameters beyond just the R-squared value. Response: Interpretation of the model parameter has been explained in the results and discussion section. Addressing the identified grammatical errors and awkward phrasing throughout the manuscript. Response: We have done this"
}
]
}
] | 1
|
https://f1000research.com/articles/13-111
|
https://f1000research.com/articles/12-105/v1
|
27 Jan 23
|
{
"type": "Research Article",
"title": "Modeling document labels using Latent Dirichlet allocation for archived documents in Integrated Quality Assurance System (IQAS)",
"authors": [
"Freddie Prianes",
"Thelma Palaoag"
],
"abstract": "Background: As part of the transition of every higher education institution into an intelligent campus here in the Philippines, the Commission of Higher Education has launched a program for the development of smart campuses for state universities and colleges to improve operational efficiency in the country. With regards to the commitment of Camarines Sur Polytechnic Colleges in improving the accreditation operation and to resolve the evident problems in the accreditation process, the researchers propose this study as part of an Integrated Quality Assurance System that aims to develop an intelligent model that will be used in categorizing and automating tagging of archived documents used during accreditation. Methods: As a guide in modeling the study, the researchers use an agile method as it promotes flexibility, speed, and, most importantly, continuous improvement in developing, testing, documenting, and even after delivery of the software. This method helped the researchers in designing the prototype with the implementation of the said model to aid the process in file searching and label tagging. Moreover, a computational analysis is also included to further understand the result from the devised model. Results: As a result, from the processed sample corpus, the document labels are faculty, activities, library, research, and materials. The labels generated are based on the total relative frequencies which are 0.009884, 0.008825, 0.007413, 0.007413, 0.006354, respectively, that have been computed between the ratio on how many times the term was used in the document and the total word count of the whole document. Conclusions: The devised model and prototype support the organization in file storing and categorization of accreditation documents. Through this, it is easier to retrieve and classify the data, which is the main problem for the task group. Further, other patterns in clustering, modeling, and text classification can be integrated in the prototype.",
"keywords": [
"Latent Dirichlet allocation",
"document labels",
"natural language processing",
"accreditation",
"quality assurance",
"Intelligent model",
"CSPC"
],
"content": "Introduction\n\nThe creation of a smart campus is a step toward the creation of a smart city. Teaching and learning will be more difficult in the future as a result of the rapid advancements in information and communication technology (Kwok, 2015). With this rapid advancement, there is already a shift from the “smart” era to the “intelligent” era. A “smart phone”, “smart building” or “smart home” is one that is capable of adapting to changing conditions. The term “intelligent,” on the other hand, refers to more than just being smart; rather, it refers to having the ability to think, reason, and understand, as well as being able to adapt to changing conditions. If you apply this to a device example, “smart devices” can perform tricks, but “intelligent devices” can learn new tricks in response to their changing surroundings (Ng et al., 2010).\n\nAs part of the transition of every Higher Educational Institution (HEI) to being an intelligent campus, the Commission of Higher Education (CHED) has launched a program under CHED Memorandum Order No. 9 s. 2020 for the development of smart campuses for State Universities and Colleges (SUCs). In fact, CHED releases a budget to assist SUCs in the development of smart campuses in which HEIs use next-generation digital technologies woven seamlessly within a well-architected infrastructure in developing tools to enhance teaching and learning, research, and extension as well as to improve operational efficiency. On the other hand, as a requirement by CHED and maintaining the quality of education in HEIs, CHED gives the accountability and responsibility to the accrediting body, such as the Accrediting Agency of Chartered Colleges and Universities of the Philippines (AACCUP), Philippines Association of Colleges and Universities Commission on Accreditation (PACU-COA), Philippine Accrediting Association of Schools, Colleges, and Universities (PAASCU), and many others to assess and provide certifications of quality education in the accredited program/institution as stated in the CHED Memorandum Order No. 1 s. 200.\n\nAchieving a smart/intelligent campus requires consideration of different areas by the institution. Based on the study of Ng et al., there are six main areas of intelligence, namely (1) iLearning, (2) iManagement, (3) iGovernance, (4) iSocial, (5) iHealth, and (6) iGreen. The accreditation process alone will fall under iManagement, however that entire aspect and purpose of accreditation falls in all the areas.\n\nCamarines Sur Polytechnic Colleges (CSPC) as a state college will be one of the settings for the initial implementation of the system. As part of the goal of CSPC to be the center for development and center of excellence, the institution opted to go along with the launch of the CHED program to become one of the smart campuses in the region. In connection to this, the institution also undergoes continuous accreditation through AACUP, as depicted in Figure 1, and ISO quality assurance to achieve the goal and gain the university status as the Polytechnic University of Bicol.\n\nThe accreditation process, as shown in Figure 1, passes through various phases or actions: (a) Application: An educational institution submits an application to AACCUP for accreditation. (b) Institutional self-survey: After the application has been approved, the applicant institution is expected to conduct an internal evaluation by its internal accreditors to evaluate whether the program is ready for an external review. (c) Preliminary survey visit: This is when external accreditors evaluate the program for the first time. The program is eligible to receive a Candidate status that is good for two years after passing the assessment. (d) The first formal survey visit reviews the program that has obtained Candidate status, and if it has met a higher standard of excellence, it is given a Level I Accredited status, which is valid for three years. (e) The second survey visit entails evaluating an accredited program, and if it has met the standards for a greater degree of quality than the survey visit that came before it, the program may be eligible to get a Level II Re-accreditation status that is valid for five years. (f) During the third survey visit, the accreditation level is completed by a program after five years of holding Level II Re-accreditation status. The program is reviewed and must perform exceptionally in four categories, namely instruction and extension, which are essential; and two other areas, which must be selected from among research, performance in licensure exams, faculty development, and links. (g) The fourth survey visit is a more difficult level that, if passed, may grant the organization institutional accreditation status.\n\nAccompanied with the tedious accreditation process are many documents that needs to be produced. For most experiences in the current accreditation undertakings in CSPC, the majority of the tasks have been done manually. Though there are tools available for cloud storage and automation like Google Drive, Dropbox, etc., problems such as repetition of work, invalid instruments, inefficient resource utilization, and inefficient monitoring before, during, and after the accreditation are still experienced by the personnel. With this perceived problem, an integrated system dedicated to quality assurance processes is a must.\n\nUpon the CSPC’s goal of becoming a university and becoming a smart/intelligent campus, the researchers propose a centralized system that will cater to the needs of the institution in the process of accreditation, which is part of quality assurance. Through this study, CSPC will benefit from being a smart/intelligent campus by means of utilization of the system in the iManagement area and, at the same time, it addresses the problems encountered during the accreditation processes.\n\nBased on the problems identified and the commitment of the institution to be a smart/intelligent campus, the researchers propose this study as a component in the Integrated Quality Assurance System (IQAS) (RRID:SCR_023146). The study focuses on the documents archive needed for the accreditation process. The system will have a document repository of archived documents and these documents will be analyzed by the system through the use of intelligent modeling. Through the use of this, the documents will be categorized by means of the extracted labels.\n\nIn general, the study aims to create a model in support of the categorization and automated tagging of the archived documents used during accreditation.\n\n\nRelated works\n\nUnstructured data make it more difficult and time-consuming to find a relevant document due to the exponential growth of electronic documents. Text document classification, which organizes unstructured documents into pre-defined classifications, is crucial to information processing and retrieval (Akhter et al., 2020). The text documents provide a number of difficult problems for data processing in order to retrieve the pertinent data. One of the well-liked methods for information retrieval based on themes from biomedical documents is topic modeling. Finding the correct subjects from the biological documents is a difficult task in topic modeling. Additionally, redundancy in biomedical text documents has a detrimental effect on text mining quality. As a result, the exponential rise of unstructured documents necessitates the development of topic modeling machine learning approaches (Rashid et al., 2019). In the framework of document categorization, they have conducted a comparative analysis of three models for a feature representation of text documents. The most popular family of bag-of-words models, the recently suggested continuous space models Word2Vec and Doc2Vec, and the model based on the representation of text documents as language networks are all taken into consideration in detail (Martinčić-Ipšić et al., 2019).\n\nIn this study, word representation techniques were used to analyze how the similarity between English words is calculated. This work used the Word2Vec paradigm to express words as vectors. The 320,000 English Wikipedia articles included in this study’s model served as the corpus, and the similarity value was calculated using the cosine similarity calculation method (Jatnika et al., 2019). Real-world text categorization problems frequently involve a multitude of closely related categories arranged in a taxonomy or hierarchical structure. When processing huge sets of closely related categories, hierarchical multi-label text categorization has grown more difficult (Ma et al., 2021). A popular technique for clustering functional data is the functional k-means clustering algorithm. The derivative information is not further taken into account by this approach when determining how similar two functional samples are to one another. In actuality, the derivative information is crucial for spotting variances in trend characteristics among functional data. By including their derivative information, we establish a novel distance in this paper that is utilized to compare functional samples (Meng et al., 2018). Due to its capacity to analyze data from numerous sources or views, multi-view clustering has drawn a growing amount of interest in recent years. In the research, they presented a unique multi-view clustering method called Two-level Weighted Collaborative k-means (TW-Co-k-means) to simultaneously address the issues on consistency across different views and weighing the views for the improvement of cluster results. For multi-view clustering, a new objective function has been developed that leverages the unique information in each view while also cooperatively utilizing the complementarity and consistency between various views (Zhang et al., 2018). The various pattern matching algorithms are used to locate every instance of a constrained set of patterns inside an input text or input document in order to examine the content of the documents. This research utilized four string matching techniques that are now in use: the Brute Force approach, the Knuth–Morris–Pratt algorithm (KMP), the Boyer–Moore algorithm, and the Rabin–Karp algorithm (Bhagya Sri et al., 2018). All the literature listed has similarity in text clustering, modeling, and classification, and serves as a proof that the study is feasible, and the proposed intelligent model can be integrated to further assist in the accreditation process of CSPC.\n\n\nMethods\n\nAs a guide in modeling the study, the researchers used the agile method (https://dx.doi.org/10.17504/protocols.io.n2bvj82mxgk5/v2) as it promotes flexibility, speed, and, most importantly, continuous improvement in developing, testing, documenting, and even after delivery of the software. Since the phases of this model are light, the teams are not bound by a rigid systematic-based process on pre-set constraints and restrictions as some other models, like the waterfall model, and can adjust changes whenever they are needed. This flexibility on every stage propagates creativity and freedom within processes. Furthermore, development teams can modify and re-prioritize the backlog, allowing for speedy implementation (Trivedi, 2021).\n\nFollowing the agile methodology, the researchers adapted the stages, as presented in Figure 2. These are: (1) Plan: the researchers collected previous documents involved in the accreditation process, such as compliance reports under the areas of student, faculty, facility, library, and administration. Also, understanding of the existing problems in tracking, tagging, and duplication of these documents during the accreditation process. (2) Design: the requirement specifications in this stage were identified in relation to the existing problem of the HEI in tracking, tagging, and duplication of the documents for accreditation and quality assurance. Along with this, the researchers also created the process of the intelligent model, which will be the basis of document labelling. (3) Develop: this stage is intended on the creation of the prototype, which involves the processing of the documents in order to identify the proper label for each document. (4) Deploy: the prototype undergoes a test run during this stage. (5) Review: the researchers conduct a checklist function review to check if each component is running properly. Lastly, (6) launch: wherein the prototype is embedded to the local system of the HEI.\n\n\nResults and discussion\n\nThe results from this intelligent model are used for visualization in the super word vector and histogram. The super word vector is presented in a cloud map word to visualize the frequency of the words in the corpus, and the histogram is used to present the relationship of the words per sentence in the form of line graphs. The extracted labels and generated word vector and histogram are tagged and linked to the uploaded document, as patterned in the process shown in Figure 3. This model is implemented in the IQAS to assist in categorization and searching in the file repository of accreditation documents.\n\nThe design prototype presented in this section is focused on the label extraction feature for automatic tagging of the archive documents used in accreditation.\n\nUpload and clean\n\nAs shown in Figure 4, this phase allows the user to upload and clean the document through tokenization. Once uploaded, the user may set the configuration in cleaning the document. The options are removing numbers, symbols, and duplicates, adding and uploading additional stopwords, and showing and downloading the pre-processed data. There are other useful features particularly in managing the stopwords, such as showing the list of default stopwords and deleting the added and uploaded stopwords.\n\nSetting up parameters\n\nPhase II is intended for setting up the parameters for topic modeling, as presented in Figure 5. Right after uploading and cleaning the document, the user can set the topic modeling parameters that will be use in identifying and extracting the labels. The parameters included are the desired number of topics, frequency of iteration, the number of words per topic to be generated, optimization interval, and the model’s name. These parameters are primarily the factors in modeling the topics and label identification for automatic tagging.\n\nExtract label\n\nThis phase, as shown in Figure 6, provides the result of the processed corpus from the processing of the pre-processed document and the parameters that have been set up from the previous phase. This shows the number of documents uploaded, the total number of words in the document, the number of unique words, vocabulary density, readability index, average words per sentence, and most importantly the frequent words in the corpus. These frequently used words are extracted to be the label for automatic tagging later on. The user can also set the items to be shown in the most frequent word.\n\nWord cloud\n\nAlong with the results of phase III, a word cloud is also generated. Phase IV, as depicted in Figure 7, is a super word vector view of the frequent words in the processed corpus. The most evident words in the word cloud are the frequently used words from the previous phase, which are faculty, activities, library, research, and materials. The font size of the word is based on how many times this word is used in the corpus.\n\nLDA visualization\n\nWith the result generated during phase III, this phase provides the histogram presentation of the sample processed corpus with the support of the LDA visualization, as shown in Figure 8. The line graph provides the relative frequencies of each generated label per document segment.\n\nAuto-tagging to uploaded document\n\nAfter the five phases, automatic tagging of the generated labels takes place, as shown in Figure 9. The document is then stored in the file repository of the IQAS. The uploaded document will have corresponding metadata such as filename, file size, user, date created, tags, and the link of the processed model. The filename can also be updated, and adding and removing tags is also possible.\n\nComputational analysis\n\nFor better understanding, this section provides the computational analysis of the actual result based on the processed document.\n\nIn reference to the results of phase III, there are four significant results evident in Figure 6. Vocabulary density is the ratio between the total number of words present in the corpus and the unique words. To obtain the vocabulary density, the total number of unique words is divided by the total number of words; for the sample computation see Equation 1.\n\nEquation 1. Vocabulary density computation.\n\nThe vocabulary density of the processed corpus is 0.254, which implies that the corpus contains complex text with many unique words. Moreover, the readability index and average word per sentence uses Java break iteration, which is a local sensitive class that has an imaginary cursor that points to the current boundary in a string of natural language text. This contains different kinds of boundaries such as for text character, words, sentence instance, and potential line breaks. These boundaries are the basis for the readability index and average words per sentence, which are 16.106 and 21.5, respectively. Frequently used words are identified based on the number counts of the word used in the processed corpus.\n\nThe LDA visualization is presented through the correlation of the relative frequency of the word per document segmentation, as shown in Figure 8. To identify the relative frequency, it is necessary to decide the number of document segmentations. For the purpose of this study, the researchers used 10 segments for the document. The grouping of words per segment is based on the total word count. The prototype now determines how many times a particular word is used per segment. Upon determination, the identified number of counts is divided into the total word count. For the sample computation, see Equations 2 and 3.\n\n* First seven segments contain 283 words while the last three segments contain 284 words.\n\nEquation 2. Words per segment computation.\n\nEquation 3. Sample computation for relative frequency (Word: research|2nd Segment).\n\nFor the overall results of the histogram, Tables 1 and 2 present the tabular representation of the relative frequency per label and per segment.\n\n\nConclusions\n\nCSPC is in an exploratory phase when it comes to solving this particular problem involving accreditation. It is evident that there are problems encountered by the organization pertaining to the accreditation process. Therefore, the researchers devised a model that supports the organization for accreditation. In addition, the researchers also designed a prototype with the implementation of the model to help the organization through the process. As a result, it is easier to retrieve and classify the data, which is the main problem of the task group. Furthermore, other text classification patterns may also be integrated into the system and the results compared with given parameters.\n\n\nSoftware availability\n\nSoftware available from: https://github.com/CraigList056/iqas/tree/v1.0.0-alpha\n\nSource code available from: https://github.com/CraigList056/iqas\n\nArchived source code at time of publication: https://www.doi.org/10.5281/zenodo.7507492\n\nLicense: MIT License",
"appendix": "Acknowledgements\n\nWe would like to express our great appreciation to our colleagues and friends for their undeniable support and for uplifting our spirits to make this research paper possible. We would like to also extend our appreciation to our respective institutions (Camarines Sur Polytechnic Colleges and University of the Cordilleras), which have been our second home and witness of our efforts during the research process.\n\n\nReferences\n\nAkhter MP, Jiangbin Z, Naqvi IR, et al.: Document-Level Text Classification Using Single-Layer Multisize Filters Convolutional Neural Network. IEEE Access. 2020; 8(Ml): 42689–42707. Publisher Full Text\n\nBhagya Sri M, Bhavsar R, Narooka P: String Matching Algorithms. International Journal Of Engineering And Computer Science. 2018; 7(03): 23769–23772. Publisher Full Text\n\nCraigList056: CraigList056/iqas: Initial Release (v1.0.0-alpha). Zenodo. 2023. Publisher Full Text\n\nTrivedi D: Agile Methodologies. International Journal of Computer Science & Communication. 2021; 12(2): 91–100.\n\nJatnika D, Bijaksana MA, Suryani AA: Word2vec model analysis for semantic similarities in English words. Procedia Computer Science. 2019; 157: 160–167. Publisher Full Text\n\nKwok L: A vision for the development of i-campus. Smart Learning Environments. 2015; 2(1): 1–12. Publisher Full Text\n\nMa Y, Liu X, Zhao L, et al.: Hybrid embedding-based text representation for hierarchical multi-label text classification. Expert Systems with Applications. 2021; 187(July 2020): 115905. Publisher Full Text\n\nMartinčić-Ipšić S, Miličić T, Todorovski L: The influence of feature representation of text on the performance of document classification. Applied Sciences (Switzerland). 2019; 9(4). Publisher Full Text\n\nMeng Y, Liang J, Cao F, et al.: A new distance with derivative information for functional k-means clustering algorithm. Information Sciences. 2018; 463-464: 166–185. Publisher Full Text\n\nNg JWP, Azarmi N, Leida M, et al.: The intelligent campus (iCampus): End-to-end learning lifecycle of a knowledge ecosystem. Proceedings - 2010 6th International Conference on Intelligent Environments, IE 2010. 2010; 332–337. Publisher Full Text\n\nRashid J, Adnan Shah SM, Irtaza A, et al.: Topic Modeling Technique for Text Mining over Biomedical Text Corpora through Hybrid Inverse Documents Frequency and Fuzzy K-Means Clustering. IEEE Access. 2019; 7: 146070–146080. Publisher Full Text\n\nZhang GY, Wang CD, Huang D, et al.: TW-Co-k-means: Two-level weighted collaborative k-means for multi-view clustering. Knowledge-Based Systems. 2018; 150: 127–138. Publisher Full Text"
}
|
[
{
"id": "165836",
"date": "29 Mar 2023",
"name": "Shahid Naseem",
"expertise": [
"Reviewer Expertise Artificial Intelligence",
"Machine Learning",
"and Deep learning for analyzing healthcare data"
],
"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\nBy looking at paper overall structure, presentation and above all the provided contents, I would say the authors of the paper requires minor changes to accept it for indexing.\n\nIn this study, the indexing of the tagging/titles, sub-titles is missing.\n\nNumber of sentences and grammar mistakes in different sections of the paper.\n\nIn result section, number of students studied in the batch to be accredited, financial statement, and infrastructure must also be included because these documents are also required in accreditation process.\n\nIn related work, there should be structured or labelled data instead of f pre-defined data items.\n\nIn second paragraph of related work, the authors defined four types of machine learning techniques, but didn’t explain for what purpose, these four techniques were used in this study.\n\nIn figure 2, there should be one more step i.e. maintenance included.\n\nAll the equations used in this study must be numbering.\n\nIn equation 1, explain the procedure to calculate VD, from where we get the used valued to calculate VD.\n\nNumbers of references used to validate this study are too short. There must be some more literature review to authenticate this study be used in 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?\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": [
{
"c_id": "10895",
"date": "13 Apr 2024",
"name": "Freddie Prianes",
"role": "Author Response",
"response": "We would like to express our sincere appreciation for reviewing our paper. Your comments and suggestions are utmost valued. These are our response: 1. In this study, the indexing of the tagging/titles, sub-titles is missing. This is somehow unclear to us. But if this is pertaining to the generated tags/titles or sub-titles for the indexing of the documents, it’s been mentioned on Fig. 9 – Phase VI. 2. Number of sentences and grammar mistakes in different sections of the paper. Accomplished 3. In result section, number of students studied in the batch to be accredited, financial statement, and infrastructure must also be included because these documents are also required in accreditation process. Since the study is in exploratory analysis, we focused first on the area of Faculty and Library. But upon implementation of the prototype, we will include the other areas i.e. Students, Finance, and Infrastructure. 4. In related work, there should be structured or labelled data instead of f pre-defined data items. Accomplished 5. In second paragraph of related work, the authors defined four types of machine learning techniques, but didn’t explain for what purpose, these four techniques were used in this study. Accomplished 6. In figure 2, there should be one more step i.e. maintenance included. Actually we include maintenance as a sub-phase of launch. We did not elaborate on this phase because we are doing another research on prototype testing and implementation which we will touch the maintenance procedure. 7. All the equations used in this study must be numbering. We believe that all the equations in this study has values and have been numbered. 8. In equation 1, explain the procedure to calculate VD, from where we get the used valued to calculate VD. Accomplished 9. Numbers of references used to validate this study are too short. There must be some more literature review to authenticate this study be used in this research. Accomplished We already made another a submission for the version 2 of our paper. Thank you."
}
]
}
] | 1
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https://f1000research.com/articles/12-105
|
https://f1000research.com/articles/12-1434/v1
|
06 Nov 23
|
{
"type": "Research Article",
"title": "The role and interplay of institutions in water governance in the Central Rift Valley of Ethiopia",
"authors": [
"Endalew Jibat",
"Feyera Senbeta",
"Tesfaye Zeleke",
"Fitsum Hagos",
"Feyera Senbeta",
"Tesfaye Zeleke",
"Fitsum Hagos"
],
"abstract": "Background Institutions can play a key role in coordinating how natural resources are effectively managed and used without over-exploitation. Institutions are laws, policies, and organizational arrangements that permit, forbid or regulate human action. This study aimed to look into the roles of formal and informal institutions, and their interactions in water resources governance in the Central Rift Valley (CRV), Ethiopia.\n\nMethods Key informant interviews, focus group discussions, and secondary data sources were employed to collect relevant data.\n\nResults The result of the study indicated that the influence of informal institutions on formal institutions or vice versa was insignificant, and unable to change the actions of water users in the CRV. Other limitations observed in water resources governance in the CRV include a lack of actors’ clear roles and responsibilities, absence of meaningful decentralization, limited engagement of key actors in policy development, lack of synergy between the institutions, and absence of enforcement mechanisms.\n\nConclusion Considering the local contexts and community’s traditional knowledge of water governance in water-related policy, rules, and regulations, and enhancing the capacity of local-level institutions, strong interplay among all institutions involved in water governance, and meaningful actors’ engagement were recommended to advance the role of institutions in water resources governance in the CRV and in the country.",
"keywords": [
"Institutions",
"Governance",
"Role of Institution",
"Institutional Interplay",
"Water Users"
],
"content": "Introduction\n\nInstitutions can shape natural resource users' actions and encourage efficient resource use (Medase et al. 2023). The term ‘institution’ is referred to multiple times in development literature such as specific organizations, human relationships in a society, and rules that individuals use to shape specific relationships with others (Pradhan et al. 2022). Institutions are also laws, policies, and organizational arrangements that societies develop to allow, prohibit, or regulate certain human actions (Chopra and Ramachandran 2021).\n\nWater management is a mix of formal and informal institutions in many countries in the world (Yeboah-Assiamah et al. 2017). Formal institutions are related to the official channels of the governmental system, and enforced by lawful procedures, while informal institutions refer to socially shared rules such as social or cultural norms and reflect local people’s views (Gilmore et al. 2022). Both formal and informal institutions are shared, enforced, and long-lived (Hassenforder and Barone 2019). Empirical studies, e.g., Yami et al. (2009) indicate that both formal and informal institutions played a great role in natural resources governance.\n\nInstitutional diversity can enhance the capacity of a certain community by educating multiple ways of responding to challenges (Pellowe and Leslie 2020). For instance, Yami et al. (2009) revealed that informal institutions contributed to sustainable Common Pool Resources (CPR) management in Sub-Saharan Africa through common decisions, reducing costs for CPR users, taking advantage of local knowledge, and implementing locally agreed rules. Institutional measures such as enforced formal laws, informal norms, and standards shared among communities help to govern the individual actions of resource users (Medase et al. 2023).\n\nSeveral studies indicate that the interaction of formal and informal institutions results in positive effects on natural resources governance. For instance, Yeboah-Assiamah et al. (2017) reported that informal institutions were harmonized with formal and synergistically improved the viability of the natural resources in Ghana. Similarly, both formal and informal institutions have shaped fishing practices in Mexico (Pellowe and Leslie 2020). In some cases, informal institutions gradually become part of formal institutions, and formal also take informal forms in governing resources such as water resources (Nhundu et al. 2015). Hence, scholars, for instance, Tinoco (2012) suggested the need to consider both formal and informal water institutions to operate and enforce them at different levels based on local reality.\n\nProductive interactions between formal and informal institutions could be facilitated when shared experiences exist between diverse actors. Mechanisms designed to enable shared learning, feedback, and adaptation experiences between both institutions can facilitate positive management development, and encourage institutional interplay (June et al. 2019). It is also important to devise intervention mechanisms to enhance the capacity of the informal systems to manage water resources because both institutions can draw lessons from each other (Nhundu et al. 2015).\n\nOn the other hand, there is also a situation where formal and informal institutional conflicts have notably compromised water service delivery and water security (Muok and Onyango 2020), as a result of poor planning, unable to align national and regional strategies, and political intervention. In a similar manner, the informal institution of the ancient caste system in India hindered the effectiveness of formal institutions (Haider 2017).\n\nThe effectiveness of institutions depends on the nature of institutions and their enforcement mechanisms (Yeboah-Assiamah et al. 2021). The strength of the governance system, planning, and financial adequacy can be factors affecting the effectiveness of institutions and are essential for sound water governance (Tortajada 2010b). Institutional ineffectiveness may be caused because of inadequate consideration of the human element and its failure to take into account the need for awareness of future uncertainty to adapt to changes (Akamani 2016).\n\nIn this paper, institutions are defined as formal and informal institutions, which concern what and how actors are playing their roles in water resources governance actions. Formal institutions include rules and regulations decreed to use and conserve water resources in the country, the role of state structures engaged in water decisions and actions, the contribution of development partners and irrigation water user associations in water resources governance practices in the Central Rift Valley (CRV) of Ethiopia. Informal institutions include traditions and customs practiced in water uses and conservation activities in the CRV of Ethiopia. The interplay of institutions is the interaction of these institutions (whether they overlap/are similar or conflict) on the grassroots level in irrigation water resources collective actions in the study area. Hence, the main aim of this study was to assess the roles of formal and informal institutions and their interplay in water resources governance in the CRV of Ethiopia.\n\n\nMethods\n\nThe ethical clearance letter of this study No/0035/2023 was signed by Teshome Tefesse (PhD), Chairperson of the institutional review board of the College of Development Studies at Addis Ababa University, Ethiopia. The proposal was defended in February 2021, and during that time providing an ethical approval letter was not started at the College. The proposal for the research was reviewed and approved by the committee of the institutional review board. Written informed consent was also obtained from all participants who allowed the publishing and publicizing of the data. During data collection, participants were informed that the data would be used for the PhD dissertation of the corresponding author and could be published.\n\nThe Central Rift Valley (CRV) of Ethiopia is part of the African Great Rift Valley, and it is located between 38°00’-39°30’ east longitude and 7°00’- 8°30’ north latitude (Pascual-Ferrer and Candela 2015). The altitude of the CRV ranges from 1500m – 4000m above sea level. The climate is semi-arid, and the mean annual temperature is around 20°C in the valley. The rainfall in the CRV is erratic and high rainfall intensity and extreme spatial and temporal variability were the experiences of the area (Pascual-Ferrer and Candela 2015). The average annual rainfall ranges from 650 mm on the rift floor to 1150mm in the highlands (Tafesse Matewos & Tewodros Tefera 2019). The study area (Figure 1) covered large areas and was found in two different administrative boundaries, Oromia Regional State and South Nation Nationalities and Peoples Region.\n\nThe majority of the population relied on subsistence farming and small landholding size (Vilalta 2010). The major farming system in the CRV was a small mixed rain-fed production system consisting of grain crops and livestock farming. The main livestock productions in CRV were cattle, sheep, and goats; and donkeys, mules, and horses were kept for transportation (Vilalta 2010).\n\nFood security issues and access to health facilities were the major concern in CRV, and there were few opportunities to engage in income-generating activities (Vilalta 2010). During the disaster and stress period, cultivators developed several survival strategies such as seasonal out-migration, engagement in off-farm activities, leasing out of farmland, and selling livestock.\n\nThe main source of irrigation was from surface water (44% is by river diversion and 31% from Lake Dembel/Ziway), and 25% was from groundwater (Pascual-Ferrer and Candela 2015). Agricultural production and its related activities were the main sources of the economy. About 67% of the CRV's Gross Domestic Product (GDP) was from agriculture, which includes crops, livestock, fisheries, and forestry while industry and service sectors accounted for 10% and 23% respectively (Pascual-Ferrer and Candela 2015).\n\nThis study employed a survey design and qualitative research approach. A survey is any activity that collects information in an organized and methodological manner from some or all units of a population using well-defined methods and procedures (Creswell 2014). A survey has benefits including generalizing from a sample to a population. The rationales for selecting a sample survey for this study were cost implication and timeliness to produce the result of the report.\n\nThe study employed a multi-stage sampling technique. The study covered wider areas (both site and beyond the site). In this study, the CRV was categorized into three catchments (upper, middle, and lower catchments). From each of the categories, one Woreda was selected using a simple random sample method. From each selected Woreda, two Kebeles were purposely selected based on long-term experiences of irrigation activities to get sufficient data for the study. Accordingly, East Meskan, Dugda, and Adami Tullu Jiddo Kombolcha were the selected Woredas from the upper, middle, and lower catchments respectively. The sampling frame included individual farmers or households, who are economically active (from age 18-64) and involved in cultivating crop/vegetable/fruit and livestock production.\n\nThe study used key informants’ interviews, focus group discussions, and a review of policy documents and literature to collect relevant data. The study involved various government tiers: federal, regional, District, and Kebele (which is the smallest administrative unit in the country). A total of 36 key informants were interviewed. Key informants were selected from government organizations, Irrigation Water Users Associations (IWUAs), fishery associations, farmers, local elders, development partners, researchers, and representatives of informal institutions (from age 18-64). Semi-structured guiding questions were prepared for data collection. The interview guide was prepared and discussed in detail with supervisors before field data collection.\n\nIn addition, four focus group discussions (FGD) were held. The participants were selected from farmers, IWUAs members and local elders considering gender, age, occupation, experiences on irrigation activities, and accessibility to information. The total participants of focus group discussion were 28 people; 8 people in each group of 1 and 2, and 6 people in each group of 3 and 4. Participants were categorized based on the selection criteria mentioned in this paragraph. Five main guiding questions were prepared, and explained by moderator for the participants.\n\nThe data was collected at the workplace, and on field through face-to-face personal contact interviews and group discussions, and only the researcher and participants were presented. The data collection was assisted by audio recording based on the full consent of participants. The field note was made during the interview and focus group discussion and was revised using the audio recorded. The start and end time of the interview and focus group discussion duration was recorded. Key informant interviews and focus group discussion activities were conducted until data saturation was reached. The data collection was carried out using local languages (Afan Oromo and Amharic) and translated to English later on. The data were transcribed, organized, and used for analysis. Data were collected in March and May 2021.\n\nRegarding secondary data, different laws and water policy-related documents including the Constitution of the Federal Democratic Republic of Ethiopia (FDRE 1995), Environmental Policy of Ethiopia (FDRE 1997), Water Resources Management Proclamation (FDRE 2000), Water Resources Management Regulation (FDRE 2005), Ethiopian Water Sector Strategy (FDRE 2001), Power and Duty of Ministry of Water and Energy, and Power and Duty of Ministry of Agriculture (FDRE 2018a), Irrigation Water Users Association (FDRE 2014), Power and Duty of the Basin Development Authority (FDRE 2018b), National Water Policy and Strategy (FDRE 2020), and other related policy documents were analyzed.\n\nData collected through interviews and focus group discussions were transcribed and documented using Word documents. The transcribed data were coded and organized under sub-themes of the study by carefully reading the transcribed data. The backgrounds of the respondents were organized separately using Excel Sheets. Following data organization; the data were imported into NVivo 11 software for coding and analysis purposes. In a similar manner, different water policies and strategies, proclamations, regulations, and related PDF documents were imported into NVivo 11.\n\nAfter importing all the necessary information into the NVivo 11 software application major themes and sub-themes were created using the software. As Zamawe (2015) stated, NVivo helps in the analysis of qualitative data by facilitating the tasks of managing data and ideas, modeling visually, and reporting. Following this procedure, all the imported data were carefully read and coded under each of the major themes and sub-themes, and qualitative analysis was carried out using a thematic approach. The study was organized and analyzed under major themes such as the role of formal and informal institutions, and the interplay between institutions.\n\n\nResults\n\nFederal and two regional governments were engaged in managing water resources in the CRV of Ethiopia. At the federal level, various organizations such as the Ministry of Water and Energy, Ministry of Agriculture, Ministry of Irrigation and Lowland Development, and Rift Valley Basin Development Office were established and involved in water resources governance in the study area (FDRE Proc. No. 1097/2018; FDRE Proc. No. 841/2014). The two regional states have also arranged similar water-related organizations, and engaged in various activities related to water resources governance including at the District level. In addition, at the Kebele level (the lowest administrative unit in Ethiopia) Development Agents (DAs) and other natural resources experts were assigned to support the development by providing extension services and advice on crop and livestock production, and natural resources conservation activities including water resources.\n\nThe federal Constitution (Art 52/3 (d)) granted regional governments to administer natural resources in accordance with federal laws. The existing institutional arrangements indicate that agencies established at regional and lower levels were engaged in water resources governance activities in the area. The Constitutional provision promotes decentralization of authority to the lower administrative levels. However, evidence from this study indicates that there was a lack of alignment between the constitutional provisions and the implementation of rules and regulations on the ground. For instance, one of the key informants (KI-1) mentioned that:\n\n“Alignment between Constitutional provisions and implementation are lacking when going down from federal to region, District, and Kebele levels. Integration is lacking among respective sectors; the agriculture sector is not worrying about water efficiency and buffer zone areas while doing irrigation activities; the industry sector is not worrying about water pollution. Water sectors were not integrated (they have no common plan), and each of the institutions ran their duties independently without considering water saving and conservation contrary to the rules and regulations.”\n\nInstitutional arrangements were established at all levels; however, their coordination and integration were weak to improve water resources governance due to a lack of enforcement mechanisms of the existing rules and regulations, and a lack of systematized monitoring and evaluation in the study area.\n\nEmpowering the local level institutions and decentralization were tried to be implemented in the study area. However, there was a capacity gap among water resource users, particularly farmers and public institutions that are supposed to support and enforce the implementation of improved water governance in the area. One of the key informants (KI-2) stated that “Water sectors do not have equivalent capacity in terms of finance, logistics, knowledge, technology, and human resources. Only roles were decentralized to the lower levels without capacitating them with finance, knowledge, expertise, and other essential resources.” Another key informant (KI-8) also added that clear rules, regulations, directives, and guidelines that enable lower-level administration were not fully decentralized to manage water for sustainable uses in the study area.\n\nData and information collected for this study show that required institutional arrangements were established and in place at all levels. However, implementation limitations were observed. One of the key informants (KI-29) stated that:\n\n“All structures of water sectors exist. However, the institutions were not implementing the policy and regulation of water resources management on the ground. There is no problem regarding structure, but limitations on implementation. This may be caused by a lack of capacity to implement their mandate and a lack of monitoring and evaluation from respective Regional and Federal level water sectors. The local government agencies should be capacitated by required knowledge and resources.”\n\nIn addition to government institutional arrangements, there were also community-based institutions (for instance, Irrigation Water Users Associations/IWUAs) that were engaged in water resources governance in the CRV. The government recognized the role of these institutions in improving water use efficiency and protecting the environment. To strengthen these institutions, the federal government decreed IWUA’s proclamation (FDRE Procl. No. 841/2014, FDRE Regulation 441/2018) with the objectives: to manage and operate an irrigation and drainage system; to provide water equitably to its members for agricultural purposes; to maintain, and rejuvenate and improve the irrigation and drainage system; and to maintain and operate irrigation equipment.\n\nThe proclamation also stated that the IWUAs shall be guided by principles of fairness and equity in decision-making and allocation of irrigation water; preventing wastage and pollution of water; protecting and administering irrigation and drainage system within the operation area; and complying with a system of cost recovery and efficient use of resources. The associations have also developed their own rules (agreements) that address how to distribute water for the members, how to undertake scheme maintenance and impose sanctions on non-compliance, and the way they conduct monitoring and evaluation. The performance of the associations varied from association to association due to factors such as financial capacity, the commitment of the IWUAs committee, and support from the district office.\n\nIn addition, development partners and NGOs were also involved in water resources matters, particularly in protection and conservation activities in the CRV of Ethiopia. Data obtained from key informants (e.g.KI-19 and KI-26) shows that development partners and NGOs were supporting farmers and IWUAs in awareness creation, material support, and providing capacity building training. An informant added that gap was observed among government institutions and community-based organizations in taking the responsibility of sustaining projects initiated by development partners and NGOs when their projects were phased out.\n\nThe government of Ethiopia adopted various water policies, rules, and regulations to improve water resources governance in the country. Information from secondary data (FDRE 1995; FDRE 2001; FDRE 2005) shows that the policy documents advocate the necessity of building and strengthening the capacity of water institutions, institutional stability, and user-based management of irrigation systems. In addition, the rules and regulations promote the development of appropriate institutional structures as well as decentralization to the lowest level of governance for better and more efficient management of water resources. Various public institutions were also established to play their roles in the implementation of these policies and regulations. For instance, water-related sectors such as the Water and Energy Ministry, Basin Development Office, Ministry of Agriculture, Ministry of Irrigation and Lowland Development, Environment Protection Authority, and others were established at the federal level to effectively manage water resources.\n\nOne of the roles of public institutions in improving water resources governance is undertaking studies and collecting relevant and updated water-related information. In this regard, one of the key informant (KI-7) expressed that some of the institutions (e.g. Rift Valley Basin Development Office/RVBDO) have conducted the study, and the study addressed water use sustainability, current and future demand for water, the potential of available water resources, and the government development plan in the area. An informant added that identifying present and future demand could help to allocate water resources for domestic, livestock, environment, agriculture, and industry, and also for catchment-based water allocation. Another key informant (KI-26) mentioned that the RVBDO was playing its role by working with respective Districts’ implementing agencies on conservation activities such as terrace and watershed development at the upper catchment to protect Lake Dembel. The informant also stated that RVBDO was educating/consulting individuals and companies polluting water resources although taking measures was not its mandate.\n\nRegional water sectors such as Water and Energy, Agriculture, and Environmental Protection have also tried to exchange data and coordinate horizontally at the District level. They were exerting efforts to contribute to improved water governance in terms of awareness creation, capacity-building training, supporting irrigation equipment, and providing extension services through Development Agents (DA’s) at the Kebele level. One of the key informants (KI-11) mentioned that:\n\nGovernment institutions have played roles in irrigation water supply, and conservation activities by building a check dam at the upper catchment, mobilizing the community to plant grasses and trees to protect siltation from Dembel Lake, developing and maintaining irrigation schemes, registering and organizing IWUAs, providing irrigation water services, supporting women and economically poor people during IWUAs registration by providing pump, motor, and technical training and advice for farmers.”\n\nData and information obtained for this study shows that public institutions have supported Irrigation Water User Associations to enhance their capacity to manage irrigation schemes and use the resources in a sustainable manner. Data obtained from participants of focus group discussion (FGD1) shows that public institutions have attempted to improve the efficiency of irrigation water uses (i.e. water saving, protecting wastage, implementing crop-water requirement technique, etc) by enhancing the awareness of the local water users to bring behavioral changes and improve water use practices. The discussants explained that institutions have contributed in terms of supplying irrigation equipment, providing technical advice related to cropping and water use, and mobilizing the local community to protect the environment in the CRV. The data indicates that the institutions conducted various capacity-building training, monitoring, and evaluation of the implementation of water sector policy and strategy, supporting IWUAs to strengthen community-based institutions for better water resources governance.\n\nEven though these public institutions have played roles in improving water resources governance in the CRV, this study pointed out some limitations of the institutions. These institutions were not coordinated and systematically not managing the resources by sharing roles and responsibilities. For instance, RVBDO was educating polluters while the Environmental Protection Authority (EPA) was mandated to take measures on polluters. However, there was no clear linkage between these two organizations to exchange data to make informed decisions. One of the key informants (KI-8) stated that:\n\n“There is a license called the so-called ‘treat and release water license’. The license is given by the Regional Water and Energy Bureau (WEB). Any company that has this type of license must treat wastewater before releasing it to water bodies. Due to lack of strong coordination between WEB and EPA, and absence of enforcement mechanisms, significant measures were not taken on polluters.”\n\nAnother observation of this study was related to the capacity of public institutions which were supposed to play a great role in improving water governance in the study area. Data and information obtained for this study show that public institutions operating at lower levels (at Kebele and District) were not fully capacitated by human resources skills, required facilities, logistics, budget, and decision-making mandates. One of the key informants (KI-13) mentioned that “Licenses were provided by Region or Zone where relatively better capacity exists based on the study conducted by District experts where capacity is relatively low.” Public institutions at regional and zonal levels have not played expected roles in terms of capacitating lower-level institutions by knowledgeable experts, finance, technology, logistics, etc to improve water resources governance. In addition, water sectors at the District level were not empowered to take corrective measures for non-compliance with water rules and regulations in the CRV of Ethiopia.\n\nRespective sectors are expected to conduct a detailed study before providing licenses related to water projects. In the case of CRV, water projects were designed either at the Zone or Region level without detailed study. One of the key informants (KI-13) mentioned that:\n\n“Decisions such as license for projects are made at Region and Zone. The projects are not supported by a detailed study that shows the availability of water (what quantity of water is available, how much quantity of water the project needs, how much quantity of water remains for the environment, etc) are not studied by project owners either government or private. Similarly, the Agriculture Office organizes IWUAs by simply observing the availability of water resources (without a detailed study of the availability of water resources, environmental flow requirements, irrigable land size and volume of water demanded, amount of water required for irrigation discharging, etc).”\n\nMoreover, projects designed at the upper catchment were not supported by a detailed study such as the amount of water discharged throughout the year, the number of populations whose livelihoods depend on the river at the lower catchment, the quantity of water could be diverted at upper and need to flow for the lower catchment. Irrigation projects at the upper catchment were implemented without considering these data and information.\n\nAs a result, water resource degradation still continued in the study area. For instance, over-abstraction and waste of water resources were continued. Irrigation water practices were not in the saving approach on the field, and users were not protecting the resource from exploitation. The lack of enforcement mechanisms and the absence of clear roles and responsibilities of water sector institutions were among the causes of the failure to implement the promulgated and decreed policies and regulations. Water resources management policies, rules, and regulations were not adequately implemented. As a result, the behavior and misuse of water users were not significantly changed in the CRV. One of the key informants of the study (KI-22) stated that:\n\n“The behavior of water users' was not changed, and a majority of users did not understand the impact of current water over-abstraction and malpractices because a majority of water users and implementing agencies did not understand well the severe water scarcity unfolding in the area.”\n\nAccording to data and information obtained, a lack of monitoring and evaluation system, an absence of institutional performance evaluation, a lack of coordination and integration among water sectors, a low level of public organizations’ capacity and community awareness, and a lack of implementation capacity at a local level were the factors affecting the effectiveness of public institutions in the CRV. One of the key informants (KI-23) mentioned that low policy awareness of implementers and lack of integrated plans and actions among water sectors contributed to the inefficiency of formal institutions in water governance in the CRV of Ethiopia.\n\nData obtained from the focus group discussions (FGD2) indicated that there was a committee established from various sectors to mobilize the community for specific water resources management and environmental conservation activities in the CRV. However, the efforts were not systematically assessed, and its implementation lacked continuity and consistency. Participants have also addressed that insufficient budget and logistics to reach farmers in remote areas, and lack of knowledgeable experts on water resources management and governance hindered the role of these institutions in water resources governance water in the study area.\n\nIn addition to government institutions, there are community-based institutions that have developed local rules/agreements by members of the IWUAs and are involved in water governance in the CRV of Ethiopia. Informants (e.g. KI-29 and KI-30) stated that IWUAs have contributed by developing local rules which address issues such as an irrigation water distribution schedule, sanction on non-compliance, annual fee contribution, conflict resolution mechanisms, and protecting water and scheme equipment from wastage and damages.\n\nParticipants of focus group discussion (FGD2) discussed that according to the IWUAs’ rules, any member of the IWUAs who violates the local regulations would be sanctioned according to their agreements. According to the discussants explanation, members of the IWUAs were expected to contribute to the sustainability of the irrigation system by developing and cleaning irrigation canals, developing soil and water conservation terraces, and removing harmful plants. In this regard, community members and the IWUAs committee have attempted to play roles to minimize irrigation water wastage and reduce conflicts in the CRV. However, the behavior and practices of water users were not significantly changed in terms of protecting and saving water resources in the study area.\n\nThe major factors attributed to the low performance of IWUAs in terms of improving water resources governance in the CRV were related to financial limitations, skill gaps, and low implementation capacity. For instance, the report of the Agriculture Office of Adami Tullu Jido Kombolcha District indicates that out of 70 active IWUAs in the District, about 87% of them have no offices and documentation facilities, 55% have no local regulations, and 19% are not legally registered and certified (Adami Tullu Jido Kombolcha District Agricultural Office, 2020). Moreover, the local regulations decreed by the associations were not adequately practiced among irrigation water users in the study area. Information obtained from key informant interviews (e.g. KI-28) indicates that the main factors attributed to the inefficiency of IWUAs were the failure of public institutions' support and lack of continuous monitoring and evaluation systems, lack of capacity, low financial and technical capacity to undertake scheme operation and maintenance. Participants of the focus group discussion (FGD-3) also mentioned that lack of awareness and mistrust among some members, particularly on financial management, were factors attributed to the inefficiency of the associations in the study area.\n\nIn addition to IWUAs, there were also various development partners and NGOs who were exerting their efforts to improve water resources governance in the CRV of Ethiopia. For instance, Farm Africa, International Water Management Institute, Sustainable Environment and Development Agency, SOS Sahel Ethiopia, and Population and Health Consortium Ethiopia have been playing roles in terms of awareness creation on the effects of cutting trees and high water abstraction on irrigation sustainability, capacity-building training, and providing water-saving technologies, e.g. pumps, promoting catchment management practices in the CRV of Ethiopia. The main purpose of their engagement was to protect Lakes Dembel, Langano, and Abijata-Shalla which were under pressure due degradation of natural resources at the upper and middle catchments. The degradation was caused by soil erosion (siltation), excessive chemical use in irrigation, population pressure, and high-density rainfall (erratic nature). Moreover, Wetland International was also working on watershed management at the upper catchment, buffer zone development, and wetland management in the study area.\n\nIn addition to formal institutions, there were also informal institutions contributing to water resources governance in the CRV of Ethiopia. When disputes and conflicts occurred because of disagreements between water users, elders mediated and resolved the disputes at the local level. There was a group of elders – very respected and known individuals, the so-called ‘Tulama’, who could resolve the disputes, particularly in Dugda Woreda. According to the statement of a key informant (KI-13), “Any individual who ignores the decision made by the ‘Tulama’ would be socially sanctioned.” The ‘Tulama’ is a broad informal institution that manages various issues including disagreements between individuals on irrigation water use in Dugda Woreda. The role of this institution in resolving problems was great, and it is also recognized by the District Administration.\n\nTraditionally, the community members were protecting water sources from pollution and maintaining their cleanliness. One of the key informants (KI-5) stated that there were social norms that encouraged the purity of water sources by saying “Malkaa gubbaatti hin fincaa’iin ykn hin bobba’iin”, which means never urine or defecate at the head of water sources. Similarly, another key informant (KI-13) mentioned that “the communities were protecting lands surrounding water bodies by protecting lands from cultivation/farming, which was previously covered by water bodies, instead they have planted trees.”\n\nSources of this study indicate that the opportunity of implementing informal rules is greater than the governments in some areas because community members trust the local elders more than others. One of the key informants (KI-29) mentioned that “Community members have contributed a lot to the environment by involving forestation, watershed management, soil and water conservation, optimizing fertilizers, etc.” Moreover, another source of this study (KI-19) pointed out that the local social norms, traditions, customs, and practices were used as a source for IWUA's rules and agreements. The informant added that informal institutions could be more fruitful if the government institutions supported them in terms of providing extension services and technical advice without interfering in their local agreements.\n\nEven though informal institutions have played a great role in the governance of water resources in the CRV, various factors have hindered its effectiveness. One of the major factors was the lack of strong support from policy direction. The majority of water-related rules and regulations decreed by the country have not addressed the roles and means of informal institutions' engagement in water resources governance. In the Ethiopian Water Sector Strategy (FDRE 2001), there is an article that promotes the involvement of religious and customary organizations in water source selection, public awareness, and environmental education. However, there were no clear enforcement mechanisms devised to implement the provisions in practice. In other water resources policy documents, the issue was partially or completely untouched.\n\nOn the other hand, the existing traditional practices and norms that had been used in earlier times in water governance at the local level were replaced with formal institutions such as IWUAs and farmers’ cooperatives. One of the key informants (KI-13) mentioned that in earlier times elders were educating children and younger by saying that “Making open defecation at the head of water sources is forbidden and unethical.” This was how the community members were protecting water sources traditionally from pollution in the area. However, nowadays such traditional advice and practices are not observed in a wider manner in the community. The informant associated this with the effect of the modern supply of water resources by pipelines, pumps, and water points for drinking water as it minimized interaction with open water sources partially or completely. In addition, informal institutions may lack data so that formal institutions may have to make informed decisions. The informant added that in recent times farmers were cultivating closer to water bodies due to population pressures and economic factors such as meeting current production and benefits.\n\nMoreover, these informal institutions lacked capacity-building support to play more roles in the governance of water resources in the CRV of Ethiopia. One of the key informants (KI-31) mentioned that District and kebele-level public institutions and other partners had not provided sufficient support and capacitated them to enhance the capacity of informal institutions at the local level. The informant addresses that giving priority to formal institutions and losing attention to informal institutions from public organizations negatively affected the role of informal institutions in water resources governance in the study area.\n\nUnderstanding the types of institutions and their interplay can indicate how the resource users engage in their common-pool resources governance (Etiegni et al. 2017). In the case of CRV, rules decreed by the government and the traditional practices advocated by elders such as ‘Tulama’ in Dugda District were similar and overlapped in many aspects of the governance of water resources. For instance, both formal and informal institutions promote efficient water use and equitable distribution of water resources among water users. Both institutions also discourage the over-abstraction of water resources and impose sanctions on non-compliance. These institutions were interacting with one another to improve water resources governance in the area.\n\nAlthough the rules and procedures of formal and traditional practices of informal institutions involved in water resources governance were supporting one another, the practices of water users contradicted the rules and traditional customs. Both formal and informal institutions promote saving irrigation water use, environmental conservation, and equitable and fair distribution of irrigation water. However, irrigation water users were practicing over-abstraction, flooding excessive quantities of water on their farms, and degrading water resources in the CRV of Ethiopia. One of the key informants (KI-11) mentioned this:\n\n“Farmers assume that they are more productive by flooding more water on their farming, which is opposite to what public (formal) institutions were advocating in that excessive irrigation of crops negatively affects the quantity of water, increases the cost of fuels of pumping, causes erosion of soil and agro-chemical inputs, reduce productivity, consume more time of the farmers, disturb the schedule of other irrigators and negatively affects water efficiency.”\n\nOn the other hand, the local community believes that every member of the community should benefit from the available water resources and projects related to water in the area. One of the key informants (KI-5) states that “The society in the CRV believes that ‘water is for all’, ‘malkaan kan hundaati’. The government constructed irrigation schemes benefiting farmers who have irrigation land in the irrigation compound. Farmers who do not have irrigation land in the identified irrigation compound were not benefiting from the schemes though the budget used to construct the schemes was public funds, which should equally benefit all the community members in the area.” In this case, the public institutions' action, which is benefiting those who have a plot of land in an irrigation compound, contradicts the society’s belief that ‘water is for all’. Hence, there should be some mechanisms that benefit all community members either devising rotation or cost recovery of the public budget that was used for the scheme construction. If the gap in the economy between the scheme users and non-users is widening, it may be a source of conflicts in the future.\n\nIn general, various organizations were involved in different aspects of water resource matters such as its management and uses in the CRV. These organizations include government organizations (both federal and regional States), community water user associations, individual water users (farmers and private companies), development organizations, and NGOs. However, interlinks among the institutions were weak to positively influence one another to improve water resources governance in the CRV of Ethiopia. For instance, to improve water resources governance and other resources in the area, committees were organized from different water sectors at District levels. However, the established committee was not inclusive; the committee did not include representatives from the community, development partners, NGOs, individual investors, fishery associations, and other private companies who were very decisive for sustainable water resources in the study area.\n\n\nDiscussion\n\nThe Constitution of the Federal Democratic Republic of Ethiopia recognizes the need to enact laws for the utilization and conservation of land and other natural resources. Following the Constitution, several water-related policies, rules, and regulations were promulgated and decreed by federal and regional governments. These rules and regulations advocate the necessity of building and strengthening water sector institutions in terms of facilities, human resources, finance, system, and institutional stability. The rules and regulations also promote users-based-management of irrigation systems, appropriate institutional structures, as well as decentralization to the lowest level of governance for better and more efficient management of water resources. Following the rules and regulations, public institutions were established and arranged to implement and enforce the policies, rules, and regulations at all scales.\n\nThe result of this study revealed that public institutions have attempted to play their roles to improve water resources governance through awareness creation about water saving and environmental protection, supporting irrigation equipment, and providing technical advice to irrigator farmers on how to use scarce water resources in a sustainable manner. In addition, the government organizations have conducted various capacity-building training, monitoring and evaluation, and support local institutions to strengthen community-level institutions for better water resources governance. The institutions have also attempted to decentralize water resources governance to the lower administration levels.\n\nAlthough public institutions have played immense roles in improving water governance in the study area, the efforts were setback by different causes. For instance, the absence of clear roles and responsibilities for every actor, lack of harmonized integration, lack of skilled human resources at lower administrative levels, insufficient budget and logistics, and lack of full decentralization were the majors. The result agreed with the arguments reported in previous studies which state that lack of clarity on roles and responsibilities, and poor implementation capacity at a lower scale can constrain the success of decentralization in water resources governance (Stoa 2014; Hegga et al. 2020).\n\nThe lower level of water institutions in the CRV lacked the capacity to make effective the rules and regulations of water resources management. The institutions lacked skilled experts to make assessments of water resources availability and collect relevant data, process data and disseminate information. At a lower administrative level, funds for operation and maintenance were not available in the study area. The existing local water institutions were not capacitated with the required facilities to identify specific characteristics and requirements regarding the water resources situation and devise operational strategies to implement water rules and regulations in the CRV of Ethiopia.\n\nWater sector rules and regulations promulgated at different levels set obligations that irrigators must comply with when using water resources. For instance: efficiency of water use, preventing wastage and pollution of water, fairness and equity in water distribution, and protecting and administering irrigation and drainage systems can be mentioned as an example. However, these commitments were not attained in the CRV of Ethiopia. The higher water demand and inefficient use of water resources for irrigation were leading to over-abstraction and water resource degradation in the study area. Moreover, excessive water losses, discharging of untreated wastewater to water bodies, overuse of agrochemical inputs, and farming buffer zone areas were continued by water users in the CRV, contrary to the decreed rules and regulations. Public institutions could not place an accountability system on non-compliance by bringing them to the court system or other comparable mechanisms. These limitations, exacerbated by water hyacinth invasion, put the resource under serious stress and a fragile situation. This implies that public institutions engaged in water resources governance have not achieved results associated with their roles in the study area.\n\nIn addition to public organizations, there were also other institutions such as IWUAs, Development Partners, and NGOs engaged in water resources governance in the CRV of Ethiopia. IWUAs have attempted to contribute to water resources governance in irrigation water distribution, conflict resolution, protecting irrigation schemes and equipment from damage, and collecting annual fees for maintenance and operation. In addition, various development partners and NGOs have also exerted their efforts via awareness creation, capacity building training, watershed management, wetland management, and providing irrigation technologies to improve water resources governance in the CRV of Ethiopia. These development partners and NGOs also contributed to activities such as integrated natural resources management (reforestation, conservation, etc).\n\nHowever, the efforts of these institutions were not systematically integrated and coordinated. The efforts of these organizations were not interlinked with public institutions and with other similar institutions to boost the contribution of the institutions. There was no strong platform that could bring all actors to plan, act, and evaluate together to intervene in the problem systematically. In addition, many works have been done by different development partners and NGOs were slid back due to a lack of an institutionalized system that sustains the initiatives designed by development partners and NGOs when their projects were phased out.\n\nIn addition to formal institutions, informal institutions such as local institutions, traditional practices, customs, and norms have been positively contributing to water resources governance in the CRV. For instance, traditional practices of the so-called ‘Tulama’ in Dugda District have been contributing positively to water resources governance in terms of equitable distribution of irrigation water, and resolving disputes and conflicts. A ‘Tulama’ is a local institution established by a group of respected and well-known elders who resolve various disputes including water conflicts in the Dugda District. These respected elders mediate among disputants after understanding the cause of their conflicts. The ‘Tulama’ made a decision that the disputants would accept. If any of the disputant parties refused the decision made by ‘Tulama’, the individual/s would be socially sanctioned. The District Administration has also recognized the role of ‘Tulama’ in conflict resolution. This type of institution was also reported from a study conducted in the Borena Zone of Oromia which indicates ‘Abbaa konfi’ who first excavated the pond and the ponds were administered by respected local elders (Edossa et al. 2007). There were also the community’s customary practices such as developing terraces for soil and water conservation, planting trees in their home garden, and arranging irrigation schedules considering priority for women and elders in the study area.\n\nSeveral studies also show that informal institutions could play significant roles in natural resource governance in many parts of the world (Pellowe and Leslie 2020). For instance, a study conducted in northern Ethiopia, in Zimbabwe, and in India reported that informal institutions have contributed to positive outcomes in resource governance including water resources (Degefa 2010; Nhundu et al. 2015; Haider 2017). This positive influence of informal institutions on resource governance implies that the rural community set up in most developing countries including Ethiopia has greater values for local leaders and respected individuals such as elders and religious leaders, and they were playing great roles in resource governance.\n\nAlthough informal institutions were contributing to improving water resources governance in the CRV, different factors were setting back its effectiveness in the area. The major factors attributing to the lower efficiency of these institutions in the study area were: a lack of technical and financial capacity and a lack of organized working environment and facilities can be mentioned as an example. Similar to this finding Tortajada (2010a) mentioned that even though informal institutions have played key roles in the governance of commons like water bodies, many of these institutions were challenged due to a lack of support, limitation of funds, and lack of capacities. This study also revealed that the informal institutions were hampered due to a lack of policy support and limited support from public agencies. Previous studies argued that informal institutions can contribute positively to resource governance if they are considered during policy formulation, and interlinked with the existing formal governance system (Anaba 2016). Hence, it is important to consider the role of informal institutions when policies, rules and regulations are drafted, as well as when public agencies are established for the management of water resources.\n\nUnderstanding the types of institutions and their interplay can indicate how the resource users engage in their common-pool resources governance (Ostrom 2011; Etiegni et al. 2017). There were instances where institutions conflicted or overlapped with one another. These conflicts were the results of incongruence between the objectives of formal institutions and the practices of water users or the rules of informal institutions (Pellowe and Leslie 2020). In the case of CRV, the objectives and roles of both formal and informal institutions were overlapping in many aspects. For instance, monitoring and evaluation techniques, conflict resolution mechanisms, means of irrigation water distribution, and conservation activities of water resources were some of the overlapping roles and operating mechanisms of formal and informal institutions in water governance efforts in the study area.\n\nOn the other hand, the interplay between formal and informal institutions was weak and not systematically coordinated. Water institutions engaged in the CRV were not well interlinked horizontally and vertically at all scales. The organizations lacked an integrated plan and missed the opportunity of collaboratively operating to efficiently use the available resources that enable better water sector performance. Organizations engaged in water resources governance were failed to engage and coordinate all relevant water-related institutions operating in the study area, and were unable to establish a common stakeholders' platform. Fragmented efforts were the common feature of institutions in water resources governance in the study area. This finding is similar to Jacobi et al.(2014) reports, which addressed that major challenges related to water institutions are a lack of integrated planning, a lack of coordination among key actors, and missing management mechanisms that may fit local conditions.\n\nMoreover, the interplay between water institutions engaged at the federal, regional, Woreda, and local level were not strong enough to advance the efforts towards improving water resources governance in the CRV of Ethiopia. Hence, identifying the types of institutions involved in the governance of water resources, understanding how the existing institutions interact, and considering an integrated view of these institutions to shape water users' behavior is essential to improve water resources governance and sustainable uses of water resources, particularly in the CRV of Ethiopia.\n\n\nConclusion and Recommendation\n\nThere were various formal and informal institutions engaged in water resources governance in the CRV of Ethiopia. The formal institutions have played significant roles in terms of providing training for water users and agencies, supporting irrigation equipment, and providing technical advice to irrigators about cropping, water use, and how to protect the environment. In a similar manner, informal institutions were also contributing to water resources governance in terms of awareness creation, conflict resolution, and environmental conservation in the CRV. The roles of these institutions overlapped in many aspects. However, the interplay between the institutions was weak in water resources governance in the CRV. There were also instances where both types of institutions failed to harmonize in improving water resource governance due to the absence of equal attention for both types of institutions; particularly, a lack of clear supporting policy for informal institutions. Lack of strong monitoring and evaluation, lack of incentives, and low level of capacity at lower administrative scales were the main factors contributing to the low performance of water institutions in the study area. These limitations were also associated with weak interlinks between both formal and informal institutions, which emanated from a lack of consideration in policy formulation. As a result, actions undertaken via both institutions did not significantly change the behavior and practices of water users, and were unable to improve water resources governance in the CRV. As a consequence, water resources degradation was continued in the study area, which was in turn affecting the livelihoods of the community, stressing the sustainability of irrigation activities, and degrading the environment. Hence, revisiting how formal and informal institutions could be synergistically embedded, and reconsidering the role of informal institutions in water policy, rules, and regulations are essential. It is also very important to reconsider customary and traditional practices, and socially constructed values, and respected elders could engage in managing water resources. Moreover, developing strategies and techniques to strengthen the interplay among all institutions involved in water governance at different scales, meaningful decentralization and key stakeholders engagement, and horizontal and vertical institutional integrations of water sectors need greater attention to enhance the role of institutions, and to improve water governance in the country in general and in the CRV in particular.",
"appendix": "Data availability\n\nOSF: Underlying data for “The Role and Interplay of Institutions in Water Governance in the Central Rift Valley of Ethiopia” OSF Storage in The Role and Interplay of Institutions. https://doi.org/10.17605/OSF.IO/AP8HT (Jibat et al., 2023)\n\nThis project contains the following underlying data:\n\n- Transcribed data for the role of institutions\n\nOSF: Underlying data for “The Role and Interplay of Institutions in Water Governance in the Central Rift Valley of Ethiopia” OSF Storage in The Role and Interplay of Institutions. https://doi.org/10.17605/OSF.IO/AP8HT (Jibat et al., 2023)\n\nThis project contains the following extended data:\n\n- Interview guide for key informant interviews and focus group discussions\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n“Adami Tullu Jido Kombolcha District Agricultural Office Annual Report (2020)” is an unpublished hardcopy report document that the corresponding author (EJ) obtained by providing a support letter from the university. A reader or reviewer may apply for access to the report by contacting the Adami Tullu Jido Kombolcha District Agricultural Office via phone (+251)0464413479.\n\n\nAcknowledgments\n\nThe authors are grateful to government officials, public sector officers, researchers, NGOs, and development partner representatives throughout the CRV and beyond for taking their time to be part of this study. The authors also would like to thank the International Water Management Institute for technical support, and Farm Africa and Ethiopian American Foundation (EAF) 2022-23 round STEM Award for funding this research.\n\nThe previous version abstract of this manuscript was submitted to present at the ICW 2023 International Conference on Water (Berlin, Germany) and can be accessed at https://publications.waset.org/abstracts/155986/pdf. The manuscript was not peer-reviewed.\n\n\nReferences\n\nAkamani K: Adaptive Water Governance: Integrating the Human Dimensions into Water Resource Governance. Journal of Contemporary Water Research & Education. 2016; 158: 2–18. Publisher Full Text\n\nAdami Tullu Jido Kombolcha District Agricultural Office: Agriculture Office Annual Report, unpublished report.2020.\n\nAnaba JA: Institutional Analysis of Irrigation Water Management: A Case of the Via Irrigation Scheme in Ghana, Master’s Thesis (MSc) in Natural Resources Management, Specializing in Geography at Norwegian University of Science and Technology.2016. Reference Source\n\nChopra A, Ramachandran P: Understanding water institutions and their impact on the performance of the water sector in India. Water Policy. 2021; 23(2021): 466–486. Publisher Full Text\n\nCreswell JW: Research design: qualitative, quantitative, and mixed methods approaches. 4th ed. John W. Creswell; 2014.\n\nDegefa MY: How Informal Institutions Strengthen Sustainable Management of Common Pool Resources in Tigray, Ethiopia? [Doctoral thesis, University of Natural Resources and Applied Life Sciences, Vienna].2010. retrieved on May 20, 2023. Reference Source\n\nEdossa DC, Awulachew SB, Namara RE, et al.: Indigenous Systems of Conflict Resolution in Oromia, Ethiopia.van Koppen B , Giordano M, Butterworth J, editors. Community-based water law and water resource management reform in developing countries. Wallingford, UK: CABI; 2007; pp.146–157. (Comprehensive Assessment of Water Management in Agriculture Series 5). Reference Source\n\nEtiegni CA, Irvine K, Kooy M: Playing by whose rules? Community norms and fisheries rules in selected beaches within Lake Victoria (Kenya) co-management. Environ. Dev. Sustain. 2017; 19: 1557–1575. Publisher Full Text\n\nFDRE: Constitution of the Federal Democratic Republic of Ethiopia, Proclamation No. 1/1995.1995.\n\nFDRE: Ethiopian Water Sector Strategy.2001. accessed on November 25, 2021. Reference Source\n\nFDRE: Irrigation Water Users' Associations, Proclamation No. 841/2014.2014.\n\nFederal Democratic Republic of Ethiopia: Environmental Policy of Ethiopia.1997. Reference Source\n\nFederal Democratic Republic of Ethiopia: Ethiopian Water Resources Management Proclamation, No. 197/2000.2000.\n\nFederal Democratic Republic of Ethiopia: Ethiopian Water Resources Management Regulations No. 115/2005.2005.\n\nFederal Democratic Republic of Ethiopia: Power and Duty of the Basin Development Authority (Regulation 441/2018).2018a.\n\nFederal Democratic Republic of Ethiopia: Power and Duty of Ministry of Water and Energy, and Ministry of Agriculture. No. 441/2018.2018b. Reference Source\n\nFederal Democratic Republic of Ethiopia: National Water Policy and Strategy.2020. Reference Source\n\nGilmore S, Cosens B, Griffith DL, et al.: Adapting to Socio-Environmental Change: Institutional Analysis of the Adaptive Capacity of Interacting Formal and Informal Cooperative Water Governance. Sustainability. 2022; 14(14): 10394. Publisher Full Text\n\nHaider A: Role of Informal Institutions in Explaining Water Governance Performance: A Case of Inequality and Corruption in Megacity Delhi, India.2017. accessed on November 23, 2021. Reference Source\n\nHassenforder E, Barone S: Institutional arrangements for water governance. International Journal of Water Resources Development. 2019; 35(5): 783–807. Publisher Full Text\n\nHegga S, Kunamwene I, Ziervogel G: Local participation in decentralized water governance: insights from north-central Namibia. Reg. Environ. Chang. 2020; 20: 105. Publisher Full Text\n\nDe Jacobi PR , Stefano L, López-Gunn E, et al.: Reforming water governance structures: Water for Food and Wellbeing in Latin America and the Caribbean. Social and Environmental Implications for a Globalized Economy. Oxon and New York: Routledge; 2014; pp. 286–315.\n\nJibat E, Senbeta F, Zeleke T, et al.: The role and Interplay of Institutions in Water Governance in the Central Rift Valley of Ethiopia. [Dataset]. OSF. 2023. Publisher Full Text\n\nMedase SK, Ahali AY, Belitski M: Natural resources, quality of institutions and entrepreneurship activity. Res. Policy. 2023; 83(2023): 103592. Publisher Full Text\n\nMuok BO, Onyango OD: Impacts of Conflicting, Institutional Mandates on Water Security: Pathways for Water Sector Development in Turkana County, Kenya. Science, Technology & Public Policy. 2020; 4(2): 44–53. Publisher Full Text\n\nNhundu K, Mushunje A, Aghdasi F: Nature and Role of Water Institutions — Implications to Irrigation Water Management in Zimbabwe. InTech; 2015. Publisher Full Text\n\nOstrom E: Understanding Institutional Diversity. Princeton and Oxford: Princeton University Press; 2011.\n\nPascual-Ferrer J, Candela L: Water Balance on the Central Rift Valley, in case studies for developing globally responsible engineers. GDEE; 2015.\n\nPellowe KE, Leslie HM: The interplay between formal and informal institutions and the potential for co-management in a Mexican small-scale fishery. Mar. Policy. 2020; 121(2020): 104179. Publisher Full Text\n\nPradhan P, Khadka M, Raj KGC, et al.: Community institutions in water governance for sustainable livelihoods. Waterlines. 2022; 41(3): 1–14. Publisher Full Text\n\nStoa R: Subsidiarity in Principle: Decentralization of Water Resources Management.2014; 10(2). (May) 2014|URN:NBN:NL:UI:10-1-115815. Reference Source\n\nMatewos T, Tefera T: Local level rainfall and temperature variability in drought-prone districts of rural Sidama, central rift valley region of Ethiopia. Phys. Geogr. 2019; 41: 36–53. Publisher Full Text\n\nTinoco CAB: Governance of the Drinking Water Supply Service: A Case Study of Three Mexican Communities [Doctoral thesis, University of East Anglia].2012. and retrieved on October 27, 2020. Reference Source\n\nTortajada C: Water Governance: Some Critical Issues. International Journal of Water Resources Development. 2010a; 26(2): 297–307. Publisher Full Text\n\nTortajada C: Water governance: A research agenda. International Journal of Water Resources Development. 2010b; 26(2): 309–316. Publisher Full Text\n\nVilalta RE: Water Resources Management in the Central Rift Valley of Ethiopia [MSc Thesis in Civil Engineering, Universitat Politècnica de Catalunya].2010. accessed on August 11, 2020. Reference Source\n\nYami M, Vogl C, Hauser M: Comparing the Effectiveness of Informal and Formal Institutions in Sustainable Common Pool Resources Management in Sub-Saharan Africa. Conserv. Soc. 2009; 7(3): 153–164. Publisher Full Text\n\nYeboah-Assiamah E, Muller K, Domfeh KA: Institutional assessment in natural resource governance: A conceptual overview. Forest Policy Econ. 2017; 74(2017): 1–12. Publisher Full Text\n\nYeboah-Assiamah E, Muller K, Domfeh KA: ‘Complex crisis’ and the rise of collaborative natural resource governance: Institutional trajectory of a wildlife governance experience in Ghana. Environ. Dev. Sustain. 2021; 20(5): 2205–2224.\n\nZamawe FC: The Implication of Using NVivo Software in Qualitative Data Analysis: Evidence-Based Reflections. Malawi. Med. J. 2015 Mar; 27(1): 13–15. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "227329",
"date": "15 Feb 2024",
"name": "Samwel J Kabote",
"expertise": [
"Reviewer Expertise Development Studies with research interest in water governance"
],
"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 dwell on a critical and pressing issue of water governance. It is well written but needs minor improvement in the following areas:\n1. On page 4, the author should a bit improve description about context of the study area by including water bodies available in Ethiopia particularly in the Central Rift Valley of Ethiopia. 2. On page 7, third paragraph, it looks the author used secondary data. However, detailed information about sources of data, types of data and how data were analyzed is missing. This should be improved. 3. When making quotation from a key informant, the author should indicate date, place of interview and title of the key informant 4. The sub-titles used in the results section and in the discussion section are almost similar. This brings confusion and so needs improvement to avoid repetition\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": [
{
"c_id": "11323",
"date": "13 Apr 2024",
"name": "Endalew Jibat",
"role": "Author Response",
"response": "Amendments from Version 1 We added a definition of water management. The order of keywords was also arranged in chronological order. We added institutional theories and frameworks used. The study considered various theories and approaches and used some components to analyze the roles and interplay of water institutions in the study area. We added water resources available in the CRV of Ethiopia."
}
]
},
{
"id": "239502",
"date": "05 Mar 2024",
"name": "Mekonnen Bogale",
"expertise": [
"Reviewer Expertise my area of research is management and governance"
],
"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 examines the role of institutions in ensuring water governance in Ethiopia, with a focus on the Central Refit Valley. The premise of the article is that institutions' interactive intervention can be crucial in coordinating the efficient management and responsible use of natural resources without going overboard with exploitation. Laws, regulations, and organizational structures that allow, prohibit, or control human behavior are known as institutions. Methodologically, qualitative research approach was used, which I feel the correct choice to examine such types of research.\n\nThe study's findings showed that there was little to no impact of informal institutions on formal institutions or vice versa, and that these institutions were unable to alter the behavior of water management within the Central Rift Valley. Unclear roles and responsibilities among them, insignificant power decentralization, lack of integrating policies and other enforcement measures are issues that create loose performance linkage among the institutions. The study is helpful in informing those who develop water management policies and legal frameworks about the importance of taking into account the integrative performance of various institutions, both formal and informal, to ensure water utilization governance in the particular context. It will also help academics gain an empirical understanding of the problems.\n\nWith all the above general qualities of the article, it has the following minor and major flaws to be improved .\nMinor comments\n\nThe novelty of the study is not mentioned. The abstract will be better if the authors show the uniqueness of the study in a few words at the end of the abstract. Keywords are not arranged in alphabetical order The definition of water management in the first line of paragraph two of the introduction part needs rewriting in a way that shows 'water management' is a process\n\nMajor comments\n\nThe knowledge gap this study intended to fill is not mentioned at the end of the introduction part. Please revisit and clearly show this to the readers or scientific community. It could be methodological, conceptual, or study period gaps that you identified from the prior studies to fill as a gap. You should review theoretical literatures that emphasize how formal and informal institutions interact to ensure resource governance in order to provide a solid foundation for your article..\n\nIn the research design part of the study, the authors have mentioned survey design and sample survey to generalize about population based on the sample. Do you think that such a design is appropriate for your study, which applied Key informant interviewand focus group discussion to collect qualitative information? The key informants you mentioned as data sources are not coincident with this frame. Please revisit and correct this.\n\nLine 6/7 of sampling technique paragraph is about sampling frame of farmers, which is best fit for selecting representative farmers for statistical analysis using systematic sampling technique. However, yours is qualitative which was relied on households/farmers which were purposely selected for Focus Group Discussion/Key informant interview. Please check this also. As a result Paragraphs 1, 2, and 3 of the sampling technique part has been abet confusing and need improvement and alignment with each other. The purposively selected Kebeles from each Woreda\n\n(districts) are not mentioned. The first part of the discussion part (Role of formal institutions in water governance in the CRV of Ethiopia) lacks supportive latest empirical studies conducted in similar settings. You have used only one. Please revisit and support this by similar empirical 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": []
}
] | 1
|
https://f1000research.com/articles/12-1434
|
https://f1000research.com/articles/11-1191/v1
|
18 Oct 22
|
{
"type": "Software Tool Article",
"title": "HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones",
"authors": [
"Ryland T. Giebelhaus",
"Lauren A.E. Erland",
"Susan J. Murch",
"Ryland T. Giebelhaus",
"Lauren A.E. Erland"
],
"abstract": "Background: Metabolomics is the simultaneous determination of all metabolites in a system. Despite significant advances in the field, compound identification remains a challenge. Prior knowledge of the compound classes of interest can improve metabolite identification. Hormones are a small signaling molecules, which function in coordination to direct all aspects of development, function and reproduction in living systems and which also pose challenges as environmental contaminants. Hormones are inherently present at low levels in tissues, stored in many forms and mobilized rapidly in response to a stimulus making them difficult to measure, identify and quantify.\n\nMethods: An in-depth literature review was performed for known hormones, their precursors, metabolites and conjugates in plants to generate the database and an RShiny App developed to enable web-based searches against the database. An accompanying liquid chromatography – mass spectrometry (LC-MS) protocol was developed with retention time prediction in Retip. A meta-analysis of 14 plant metabolomics studies was used for validation.\n\nResults: We developed HormonomicsDB, a tool which can be used to query an untargeted mass spectrometry (MS) dataset against a database of more than 200 known hormones, their precursors and metabolites. The protocol encompasses sample preparation, analysis, data processing and hormone annotation and is designed to minimize degradation of labile hormones. The plant system is used a model to illustrate the workflow and data acquisition and interpretation. Analytical conditions were standardized to a 30 min analysis time using a common solvent system to allow for easy transfer by a researcher with basic knowledge of MS. Incorporation of synthetic biotransformations enables prediction of novel metabolites.\n\nConclusions: HormonomicsDB is suitable for use on any LC-MS based system with compatible column and buffer system, enables the characterization of the known hormonome across a diversity of samples, and hypothesis generation to reveal knew insights into hormone signaling networks.",
"keywords": [
"Plant metabolomics",
"phytohormones",
"synthetic biotransformations",
"hormonomics"
],
"content": "Introduction\n\nWith the growth of interest in metabolomics studies has come an explosion in the development of tools and databases for the annotation, analysis and interpretation of untargeted datasets. Fundamental to the ability to appropriately identify and annotate features in a dataset is the development of libraries and databases as the economics of purchasing standards to validate feature identification in these datasets is not feasible. While many tools and databases have been developed to assist in identification of metabolites from untargeted mass spectrometry (MS), much of the focus has been on capturing the largest possible depth and breadth of metabolites in a system.1 While this increases the likelihood of matches often times identification using large databases, particularly for mass to charge (m/z) and retention time (RT) data or identification to level three confidence,2 it also often leads to large numbers of improbable identities. This has led to calls for more specific databases, for example by sample type of metabolite class of interest which can improve the quality of matches and simplify the process.3 The ability to search a dataset against a smaller, more focused database can therefore be helpful in identification of biologically relevant features within a dataset.\n\nHormonomics is a subset of metabolomics which has been defined as the study of the full spectrum of hormones, their conjugates and precursors in a living system.4,5 The first hormonomics experiment is reported in Simura et al. 2018, where a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed to rapidly profile 101 phytohormones in plant tissues, including the bioactive forms of the hormones, their precursors, and their catabolites, allowing for a quantitative view of the state of the hormonome in the tissue being sampled.5 This approach was then expanded and adapted to an untargeted metabolomics work flow.4,6 Hormones are not however exclusive to plants and in fact are best studied in mammalian systems having been defined as “substance [s] which, being produced in any one part of the organism, is transferred to another part and there influence a specific physiological process”.7 Hormones are often hard to quantify due to their labile nature and presence at low concentrations. Additionally, hormones, and phytohormones particularly are known to undergo diverse biotransformations, many of which remain uncharacterized, but which may play essential roles in their biological activity.4,8 To avoid undesired induction of signaling cascade during storage or transport phytohormones are modified or conjugated to deactivate the compounds, while also allowing for the rapid release of these compounds when needed. To gain a full understanding of the hormonome of a sample all these possible forms must be considered.\n\nWe have developed a protocol using a standard buffer system, gradient and column which can be adopted for any LC-MS platform in coordination with the HormonomicsDB platform to specifically characterize the hormonome of a desired sample while also enabling discovery of novel phytohormone metabolites which may have physiological relevance. The inhouse hormonomics dataset described by Erland et al 2020a, b has been expanded and moved to a publicly accessible RShiny based web-tool “HormonomicsDB” (http://hormonomicsDB.com) which allows for the putative identification of phytohormones, their precursors, metabolites, conjugates in untargeted datasets. We also performed a meta-analysis of data from 14 plant metabolomics studies archived on the Metabolomics Workbench using the HormonomicsDB web-tool to demonstrate the utility of the approach in exploring the plant hormonome.9 Our previously developed synthetic biotransformations algorithms10,11 are additionally integrated into the tool to allow for prediction and discovery of novel metabolites from MS metabolomics data using m/z and RT for compound ID.\n\n\nMethods\n\nThe HormonomicsDB web-tool is available at http://hormonomicsdb.com/ (Figure 1). The code was written using R (https://www.r-project.org) and RStudio (https://rstudio.com). To run the app, the RShiny package was utilized (https://www.shiny.rstudio.com). The code of the current version 1.4 reported in this manuscript is archived on GitHub.com: https://github.com/plantSMART-UBC/HormonomicsDB.\n\nA list of 249 plant phytohormones of interest was catalogued in a csv file, along with the class, monoisotopic mass, and M+H, m/z, InChI and SMILES terms. The list was expanded from those previously published in Erland et al. 2020 and Simura et al. 2018.4,5 For each database entry, 7 common adducts and 27 synthetic biotransformations (Table 1) are calculated.4,12\n\nUser data is supplied via file upload as a comma separated value (CSV) file. A standard format is used for uploading data to HormonomicsDB, with m/z in the first column, RT in the second column, and sample intensities populating the remaining columns.\n\nThe maximum file size for HormonomicsDB has been set to 10 Mb for the web tool, however, this can be increased as desired when running locally in R by editing the source code manually. To demonstrate the features of the app, example data is provided on the app’s website, of which the details of the data can be found elsewhere 11. Prior to data upload, the user selects the databases that they wish to search against; PGR Monoisotopic, PGR M+H, PGR Adducts, or PGR Biotransformations (Table 1) and mass tolerance. The user can then view the data in the “Screener Output” tab on the app or downloaded as a CSV onto the user’s computer by clicking the “Download Results” on the “m/z Screener” tab.\n\nHormonomicsDB custom search The HormonomicsDB code was modified to create the “Custom Database Search” feature which allows users to use the existing search algorithm and user interface to search against a user uploaded database rather than the internal list of compounds. To use this feature, the user first makes their own database of compounds in a CSV using the same standard format as the “m/z screener”.\n\nHormonomicsDB putatively identifies metabolites on both m/z as well as RT. The query algorithm developed for HormonomicsDB first searches on m/z, selecting features that match to PGRs within the user specified search tolerance. Next these putatively identified PGRs are sorted on % RT match, calculating how close the experimental RT for the feature is to the predicted RT for the putatively identified PGR. HormonomicsDB putatively identifies metabolites to the metabolomics standards initiative (MSI) level 3, as two physicochemical properties, m/z and RT, are used to annotate compounds, without comparison to a chemical reference standard but which do not yield unambiguous matches.2\n\nAn extraction protocol previously established for the extraction of phytohormones for LC-MS analysis was adapted for untargeted hormonomics.12–15 For extraction, multiple different extraction solvents can be utilized to achieve the desired extraction. This includes water for polar extractions, as well as methanol for nonpolar extractions. Additionally, two extraction buffers used in previously published LC-MS protocols are recommended. The two extraction buffers are 0.5 N trichloroacetic acid (Fischer Scientific, Ottawa, ON, Canada) in 80% methanol (Optima, Fisher Scientific) and 50% methanol (MS Grade, Fisher Scientific, Canada; MeOH) and 4% acetic acid (glacial, Fisher Scientific, Canada) in Milli-Q water.\n\nAll sample preparation is performed in a reduced light environment, under a red light. Approximately 100 mg of plant tissue was weighed into a 1.5 mL microcentrifuge tube (Figure 2) and immediately stored on ice or in liquid nitrogen. Extraction buffer was added to the sample in a 3:1 volume (μL): mass (mg) ratio then homogenized on ice using a disposable tissue grinder (Kontes Pellet Pestle; Fisher). The resulting homogenate was vortexed for 30 seconds (Lab Dancer ©, VWR) then centrifuged for 3 minutes at 13,000 rpm (VWR Galaxy 16DH centrifuge). The supernatant was filtered using a 400 μL microcentrifuge filter (0.2 μm PVDF Ultrafree Centrifuge filter; Millipore, Etobicoke, ON, Canada) and centrifuged for 3 minutes at 13,000 rpm. If the sample matrix was complex, the filtrate could be further diluted with ultrapure water up to 1:10 filtrate: water. The filtrate was then aliquoted into an amber glass autosampler vial and stored at 4 °C prior to analysis.\n\nAn untargeted metabolomics method previously established in Brown et al. 2012 was developed with slight modifications.11,10,15,16 Separation was optimized for use with Waters Acquity UPLC BEH C18 column (2.1 × 150 mm × 1.7 μm) at a temperature of 30 °C. A volume of 5 μL was injected onto the column at the start of the gradient. The elution was performed using eluents consisting of 0.25% formic acid (Sigma) in ultrapure water (Eluent A); 100% acetonitrile (Eluent B) was used with the following gradient: 0.0-10.0 min, 95:5-5:95 v/v, 10.0-15.0 min, 5:95 v/v, 15.0-20.0min, 5:95-95:5 v/v, 20.025.0min, 95:5 v/v. The needle wash solvent and purge solvent were both 10:90% water: acetonitrile (v/v). A pre-inject wash of 5 seconds was performed, followed by a 10 second post-injection wash. The total runtime was 25 minutes and a flow rate of 0.25 mL/min was used. The method should be compatible with most mass spectrometry platforms. For acquisition of MS data we have tested data acquire on a Waters LCT Premier to good success using positive electrospray ionization and positive ion detection, with capillary voltage of 2.9 kV, cone voltage 60 V, source temperature 120 °C, desolvation temperature 250 °C, mass range of 100–1000 amu and a scan time of 0.1 s.\n\nUsing the validated method, a mixture of 46 known analytes were weighed then dissolved in the 0.5 N trichloroacetic acid and 80% methanol extraction buffer (Table 2), each with a concentration of approximately 100 ng/mL were injected and eluted. Using the predicted M+H m/z for each analyte, extracted ion chromatograms were generated to determine the retention time of these analytes. These RTs were then catalogued in an ExcelTM document.\n\nAll RTs and ∆ RT given in minutes.\n\nSeparation was performed according to the standardized protocol described above on a Waters Acquity I-Class ultra performance liquid chromatography system. Detection was on a Waters Xevo TQ-S in full scan mode (ESI+) using the following optimized settings: Mass range: 75.01100.0 m/z; capillary: 3.5 kV; cone voltage: 30.0 V; Source offset: 60.0 V; Source temperature: 150 °C; desolvation temperature: 400 °C; cone gas flow: 150 L/Hr; desolvation gas flow: 550 L/Hr; collision gas flow: 0.00 mL/min; nebulizer gas flow: 7.00 Bar. In addition to the injected samples, extraction solvent blanks and standards were injected between blocks of samples for quality control and to prevent carryover. In silico RT prediction was performed using the Retip package in the R environment.17 The package used the in-house RT database as a training set and testing set for up to five ML methods; Random Forest (RF), bidirectional recurrent neural networks (BRNN), XGBoost, lightGBM, and Keras. Of these five models, two worked and were tested; RF and BRNN. The RF ML model was selected as the model to predict RTs for HormonomicsDB. Validation was performed by comparing the predicted RTs to experimental values of known compounds.\n\nTo test and validate the tool, a previously published untargeted metabolomics dataset generated using the same chromatographic parameters as described above was analyzed using HormonomicsDB.15 The purpose of testing and validating was to assess the tools querying ability to ensure fit for purpose, while processing a large dataset. Additionally, we wanted to compare HormonomicDBs outputs to a previously published list of putative metabolites to determine if the tool returning the desired outputs.\n\nThis dataset was analyzed through HormonomicsDB using the ‘M+H’ database and a search tolerance of ± 0.02 Da. The putative hits from HormonomicsDB were then exported as a CSV, duplicate hits were removed, yielding a list of putatively identified metabolites. This list was then compared to the putatively identified analytes from Brown et al. 2012 to determine if ‘HormonomicsDB’ has any major bugs which cause issues in querying.\n\nTo demonstrate the utility of the HormonomicsDB webtool, we performed untargeted hormonomics analysis on all LC-MS the plant studies present on Metabolomics Workbench (Figure 3).9 First, studies with the study organism “PLANT” were selected, which as of June 2022 returned 58 studies. From these, studies which incorrectly returned a plant species, or used nuclear magnetic resonance (NMR), gas chromatography mass spectrometry (GC-MS), separation techniques such as hydrophilic layer interaction chromatography (HILIC), or reversed phase LC techniques with detection methods other than high resolution MS were excluded, leaving 34 studies. Of these, a number of studies had named peak tables, incomplete peak tables, or only raw, unaligned data. These were excluded further narrowing the number of studies to 14 (Table 3). There were 13 studies, with 10 unique species, with peak tables acquired in ESI+ mode, and 8 studies with 5 unique species in ESI- mode. All these peak tables were formatted for HormonomicsDB and queued against the’M+H’ adduct with a mass tolerance of ±0.02 Da. The output from HormonomicsDB was sorted by RT match. For studies with the same gradient and column used to construct the in silico RT prediction training set, compounds with an RT match >70% were retained. If the gradient and column were different compounds with a match >50% were retained. For studies where the gradient was not provided, RTs >1 minute and before column re-equilibration were retained. If direct injection was used, all compounds were selected. Duplicate compound hits were then removed and the compounds were binned by class.\n\n\nResults and discussion\n\nThe HormonomicsDB web-tool is an open source web tool developed using RShiny allowing users to perform compound annotation of untargeted metabolomics datasets using retention time and accurate mass matching (Figure 1). The database includes 249 hormones which were originally assembled from the plant science perspective. In addition to matching to monoisotopic mass the database allows for matching to common adducts as well as predicted metabolites through the synthetic biotransformations approach (Figure 2; Table 1). Data is uploaded in.csv format and results can be viewed either on the web or downloaded as a .csv file. The search functionality may also be used to search any two datasets given they contain m/z.RT data.\n\nBy comparing the putatively identified phytohormones from Brown et al. 2012 to the output of HormonomicsDB we determined the tool was fit for purpose.15 The match rate was 104.5%, and was considered acceptable as our algorithm matches first on m/z then on RT, therefore, two or more isobaric phytohormones may return for a given m/z (Table 4).\n\nIn order to facilitate high confidence compound identification, a standardized and easily adapted LC-MS method was developed that accounts for the low concentration, labile nature of hormones and also accounts for the differential polarity of some phytohormones (Figure 2). The method is derived from established protocols and uses equipment and solvents already present in most biology, chemistry and analytical labs and is outlined in Figure 4.13,18,14 Special consideration was applied to extraction conditions as phytohormones represent unique challenges as analytes. First, in sample preparation, keeping samples on ice in a low light environment helps to prevent the degradation of labile phytohormones such as melatonin and auxin.13,19,20 Typically, degradation of analytes during sample preparation is negligible for quantitative work, however, hormones often occur at levels approaches detection limits, particularly in untargeted studies making extraction losses a significant concern. Another concern is the potential for reactions during the extraction process which may lead to modification of structures and potentially loss of the biologically relevant forms or bias in the forms observed in the dataset. The use of methanol and water in the extraction solution encourages the extraction of both polar and non-polar analytes. Acidification of the extraction buffer with acetic acid or trichloroacetic (TCA) acid helps to acidify the solution to increase the solubility of phytohormones and protonation increase ionization efficiency in ESI+. TCA also precipitates proteins, and provides ion paring to reduce ion suppression in the mass analyzer.21\n\nThe databased includes 249 metabolites which are established hormones or precursors or metabolites thereof. Classes of hormones include both naturally occurring and synthetic hormones with broad class coverage of: catecholamines, indolamines, auxins, jasmonates, salicylates, cytokinins, gibberellins, polyamines, butenolids (karrikins and strigolactones), steroids and abscisic acid. While development of the initial database has been from a plant hormone perspective, it also represents good coverage of the overall hormone landscape across Kingdoms. Only known metabolites have been included in the database, though the capacity to predict novel metabolites is built into the predictive biotransformations functionality. Inclusion of molecular formula, SMILES and InChI terms facilitates interoperability between database search results and classification tools such as MetaboAnalyst, ChemRich or ClassyFire. Accurate mass and molecular formula are available for all database entries, predicted retention time is also included for all entries and was predicted for the standardized method using the Retip App17 to allow for compound identification to MSI Level 3 as the presence of isobars within the database leads to the possibility for non-unique matches even with integration of retention time.2 The complete database is available in .csv format in Supplementary File 1.\n\nThe advent of machine learning algorithms has led to several important tools which facilitate compound identification. We have applied the ReTip app to allow for retention time prediction within the database, given users have uploaded data generated from the standard separation protocol or one similar. The random forest model for retention time prediction showed the best fit to the training data with an R2 = 0.92 (Table 5). Both the standard error (1.1 min) and the 95% confidence interval (± 1.17 min) were lowest of the models tested and were considered acceptable for the purpose. Manual plotting of predicted vs experimental retention time showed a highly linear relationship with R2 > 0.9 and slope of 1.39. We anticipate that the predictions will be robust for LC-MS based systems running the standard separation protocol.\n\nBRNN; Bidirectional recurrent neural networks. CI; Confidence interval.\n\nOne of the fundamental challenges which exists within the field of metabolomics is the scale of unknown unknowns within datasets. The average plant leaf has been estimated to contain >70,000 metabolites and with only a fraction of these having been characterized this leaves a vast chemical space for compound discovery as well as a significant challenge.10 One advantage to living systems is that metabolites are generally not independent and are the result of enzymatic reactions, meaning there are a finite number of reactions that can occur.10 While the vast number of potential novel metabolites is almost infinite, the number of basic reactions is more finite. In the synthetic biotransformations or logical algorithms approach developed in our group we use common chemical reactions such as (de) methylation, oxidation, reduction, (de) hydroxylation, (de) glycosylation, (de) carboxylation and apply these to a select subset of metabolites of interest to predict new pathways and metabolites in a sample based on a known starting point.4,6,11,10 This approach uses the predicted change in monoisotopic mass of a specific metabolite by the addition or removal of a common moiety which can then be mined in the metabolomics dataset.\n\nThe synthetic biotransformations approach can also be used for the annotation of unknown knowns in a sample. This approach is particularly relevant for hormones as due to their biological activity at low concentrations, a common strategy is activation/deactivation of metabolites through simple reactions. It is possible that the active form is present at levels well below detection limits but a storage or deactivated form for transport is present at detectable levels and may still provide interesting biological context. Similarly, as the compounds are generally labile, a biologically active form of a hormone may be absent in a sample due to degradation during sample preparation or ionization but a modified form may be present. One of the best described examples of this is the classical phytohormone auxin which may be stored/deactivated/transported through methylation, glycosylation, and conjugation to amino acids among for example.8,22,23 Phytohormones activity in some instances may also be enhanced or modified through conjugation or biotransformation as is the case for jasmonic acid, where the active form is jasmonic acid isoleucine,24 or serotonin where phenolic conjugates such as feruloylserotonin are important in response to wounding, pathogen challenge and insect feeding.25,26 A proof of concept of the application of synthetic biotransformations was performed on the pathway responsible for melatonin biosynthesis in plants using known conjugates (Figure 5). In this proof of concept, two glycosylated metabolites are present, tryptophan-N-glycoside, and serotonin 5-O-β-glycoside.27 These glycosylated forms may serve as inactive storage or transport forms of their parent molecule. Furthermore, the serotonin conjugates N-coumaroyl-serotonin and N-feruloyl-serotonin (Figure 5, Table 5) have been found in several plant species where they serve important functions as defensive molecules.28 There are potentially many more conjugates in this pathway that are yet to be identified, such as melatonin glycosides or N-coumaroyl-melatonin. The logic can also be performed in reverse, in the absence of a match for the parent compound melatonin the presence of for example while feruloyl-serotonin is not identified in the example cranberry dataset both a hydroxylated version and an aminated version are possible (Table 6).\n\nThe molecules in blue represent identified conjugates of these main metabolites in the pathway.\n\nNote that while the web-tool provides a predicted retention time this is for the parent compound not the transformed metabolite.\n\nMeta-analysis of previous studies Tryptophan metabolism had the most hits of all the classes, across both ionization modes. This is not unexpected as tryptophan is involved in both primary and secondary metabolism, and tryptophan metabolites also make up the largest class in HormonomicsDB, with 75 tryptophan metabolites catalogued in HormonomicsDB (Figure 6). Cytokinins and melatonin conjugates are the next two most abundant classes, respectively, however unlike tryptophan metabolism where the abundance is high across the species and experiments, these classes have a varying range in abundance across species. This demonstrates the sensitive nature of plant hormones, particularly with melatonin conjugates which are prone to degradation under light and oxidative conditions.18\n\n(a) Electrospray ionization (ESI) positive peak tables, and (b) ESI negative peak tables.\n\nIn species where there is an increase in tryptophan metabolism metabolites, an increase in melatonin conjugates and cytokinins is observed (Figure 6). Increases in tryptophan have been observed to increase auxin and indolamine levels in Hypericum perforatum L.29 Additionally, there is evidence suggesting auxin mediates indolamine biosynthesis in plants.29 These mechanisms are not yet well understood and require further investigation. These empirical observations of increased tryptophan, auxin, and melatonin conjugate biosynthesis through the HormonomicsDB meta-analysis reveals the usefulness of the HormonomicsDB approach and how it could be applied to better understand how auxins interact with indolamine biosynthesis in plants.\n\nUnlike the other -omics fields, particularly transcriptomics and genomics, variation between metabolomics experimental conditions, including extraction conditions, column chemistry, mobile phase composition, and ionization voltages makes meta-analyses challenging the data is not easily normalized and aligned (Supplementary File 2).30 Our demonstration of a metabolomics meta-analysis through HormonomicsDB demonstrates the utility of having a standardized untargeted hormonomics protocol, which not only allows for the HormonomicsDB web-tool to be utilized for putative identification, but permits other researchers to analyze multiple metabolomics datasets without the need to account for variation between experiments.\n\n\nConclusions\n\nPhytohormones are an important class of metabolites as they regulate most physiological responses in plants, including reproduction, growth and development, stress response, and secondary metabolism. Our goal was to develop a tool that can putatively identify phytohormones from untargeted metabolomics datasets, as well as predicted phytohormone conjugates, to assist in the development of novel hypotheses about plant physiology. The putative identification of phytohormones from untargeted LC-MS metabolomics experiments provides valuable insight into plant physiology. We developed an easy to use and freely available webtool which allows users to mine their untargeted metabolomics data for phytohormones and potential conjugates. The web tool and accompanying standardized LC-MS protocol is unique in its specific focus on phytohormones and allows for compound identification up to MSI level 3 through incorporation of RT prediction.\n\nThe discovery of new hormone derived metabolites can generate novel hypotheses about plant physiology and signalling mechanisms. The synthetic biotransformations approach which is integrated into the tool could be applied to future studies to discover new bioactive secondary metabolites to explore how plants metabolize synthetic compounds including pesticides.4,10 It is important to recognize that while the biotransformations approaches has significant power in annotation of unknowns it also has significant limitations and it should be used as a hypothesis generating tool rather than a confirmatory tool. For example, searching the same cranberry dataset15 finds dozens of potential biotransformations which must be critically assessed for plausibility and feasibility, for example a compound which is not glycosylated cannot lose a sugar moiety. Additionally, as the biotransformations are predicted features, retention time prediction is not feasible for these compounds emphasizing the low confidence as a compound identification strategy alone. The ability to generate novel hypotheses for metabolite metabolism is also the strength of this approach. While some computational work and development is still necessary to implement this at larger scale, at the single metabolite or pathway level it can be a powerful approach to investigate and predict novel medicinal compounds,10,12 understand metabolism of synthetic herbicides,6 investigate regulation of morphogenesis4,31 or microbiome interactions.32 Additionally, our meta-analysis of 14 plant metabolomics experiments highlights the utility of using standardized metabolomics protocols, which allows for more comprehensive metabolomics meta-analyses.\n\nAlthough this approach was designed to study phytohormones, there is significant overlap between phytohormones and endogenous human hormones. This approach can be used to explore small molecule hormones in animal samples as well, including in human tissues and bodily fluids. There is significant overlap between phytohormones and endogenous human hormones. As an example, serotonin, melatonin, and IAA are both phytohormones and endogenously produced hormones in humans. Aside from the role melatonin plays in regulating circadian rhythm in humans, it has been investigated for its role in reducing the impact that coronavirus disease 2019 (COVID-19) plays in supressing the damage caused by the virus SARS-CoV-2.33,34 Serotonin metabolism is also altered in breast cancer cells leading to resistance in serotonin induced apoptosis and the serotonin conjugate, N-(p-coumaroyl) serotonin has been observed to induce apoptosis in breast cancer cells.35,36 This highlights the multidisciplinary functionality of this approach to explore hormone biosynthesis in humans, plants and beyond.\n\n\nAuthor contributions\n\nRTG: Conceptualization, Data curation, formal analysis, investigation, methodology, software, validation, visualization, writing original draft, writing review and editing, formal analysis; LAEE: Conceptualization, Data curation, visualization, writing original draft, writing review and editing, methodology; SJM: Conceptualization, data curation, funding acquisition, supervision, writing review and editing.\n\n\nData and software availability\n\nHormonomicsDB is free to use and accessible at HormonomicsDB.com. The code used to develop HormonomicsDB is available at https://github.com/plantSMART-UBC/HormonomicsDB. Formatting instructions, sample data, and output descriptions are available at HormonomicsDB.com and in the GitHub repository.\n\nBorealis. Supporting information for “HormonomicsDB: A novel workflow for the untargeted analysis of plant growth regulators and hormones”. DOI: https://doi.org/10.5683/SP3/SIGTUN.37\n\nThis project contains the following underlying data:\n\n- Supporting information, consisting of a list of all phytohormones catalogued in HormonomicsDB and their accompanying chemical information (Supplementary File 1) and additional information regarding the studies assessed in the meta-analyses (Supplementary File 2)\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\nWe are grateful to Olivier Dube (Research Computing, University of British Columbia, Canada) for his assistance in setting up the HormonomicsDB server.\n\n\nReferences\n\nMisra BB: New software tools, databases, and resources in metabolomics: Updates from 2020. Metabolomics. 2021; 17(5): 1–24.\n\nBlaženovi´c I, Kind T, Ji J, et al.: Software tools and approaches for compound identification of lc-ms/ms data in metabolomics. Meta. 8(2): 31–2018.\n\nReisdorph NA, Walmsley S, Reisdorph R: A perspective and framework for developing sample type specific databases for lc/ms-based clinical metabolomics. Meta. 2019; 10(1): 8. Publisher Full Text\n\nErland LAE, Turi CE, Saxena PK, et al.: Metabolomics and hormonomics to crack the code of filbert growth. Metabolomics. 2020; 16(5): 1–15. Publisher Full Text\n\nŠimura J, Antoniadi I, Široká J, et al.: Plant hormonomics: multiple phytohormone profiling by targeted metabolomics. Plant Physiol. 2018; 177(2): 476–489. PubMed Abstract | Publisher Full Text\n\nErland LAE, Giebelhaus RT, Victor JMR, et al.: The morphoregulatory role of thidiazuron: Metabolomics-guided hypothesis generation for mechanisms of activity. Biomolecules. 2020; 10(9): 1253. PubMed Abstract | Publisher Full Text\n\nWent FW, Thimann KV, et al.: Phytohormones. Phytohormones. 1937.\n\nLudwig-Müller J: Auxin conjugates: their role for plant development and in the evolution of land plants. J. Exp. Bot. 2011; 62(6): 1757–1773. PubMed Abstract | Publisher Full Text\n\nSud M, Fahy E, Cotter D, et al.: Metabolomics workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleicacidsresearch. 2016; 44(D1): D463–D470.\n\nTuri CE, Finley J, Shipley PR, et al.: Metabolomics for phytochemical discovery: development of statistical approaches using a cranberry model system. J. Nat. Prod. 2015; 78(4): 953–966. PubMed Abstract | Publisher Full Text\n\nTuri CE, Murch SJ: Targeted and untargeted phytochemistry of ligusticum canbyi: indoleamines, phthalides, antioxidant potential, and use of metabolomics as a hypothesis-generating technique for compound discovery. Planta Med. 2013; 79(14): 1370–1379. PubMed Abstract | Publisher Full Text\n\nTuri CE, Axwik KE, Murch SJ: In vitro conservation, phytochemistry, and medicinal activity of artemisia tridentata nutt.: metabolomics as a hypothesis-generating tool for plant tissue culture. Plant Growth Regul. 2014; 74(3): 239–250. Publisher Full Text\n\nErland LAE, Chattopadhyay A, Jones AMP, et al.: Melatonin in plants and plant culture systems: Variability, stability and efficient quantification. Front. Plant Sci. 2016; 7: 1721.\n\nSaremba BM, Tymm FJM, Baethke K, et al.: Plant signals during beetle (scolytus multistriatus) feeding in american elm (ulmus americana planch). Plant Signal. Behav. 2017; 12: e1296997. PubMed Abstract | Publisher Full Text\n\nBrown PN, Turi CE, Shipley PR, et al.: Comparisons of large (vaccinium macrocarpon ait.) and small (vaccinium oxycoccos l., vaccinium vitis-idaea l.) cranberry in british columbia by phytochemical determination, antioxidant potential, and metabolomic profiling with chemometric analysis. Planta Med. 2012; 78(06): 630–640. PubMed Abstract | Publisher Full Text\n\nBrown PN, Murch SJ, Shipley P: Phytochemical diversity of cranberry (vaccinium macrocarpon aiton) cultivars by anthocyanin determination and metabolomic profiling with chemometric analysis. J. Agric. Food Chem. 2012; 60(1): 261–271. Publisher Full Text\n\nBonini P, Kind T, Tsugawa H, et al.: Retip: retention time prediction for compound annotation in untargeted metabolomics. Anal. Chem. 2020; 92(11): 7515–7522. PubMed Abstract | Publisher Full Text\n\nErland LAE, Shukla MR, Glover W, et al.: A simple and efficient method for analysis of plant growth regulators: a new tool in the chest to combat recalcitrance in plant tissue culture. Plant Cell Tissue Organ Cult. 2017; 131(3): 459–470. Publisher Full Text\n\nYamakawa T, Kurahashi O, Ishida K, et al.: Stability of indole-3-acetic acid to autoclaving, aeration and light illumination. Agric. Biol. Chem. 1979; 43(4): 879–880. Publisher Full Text\n\nDaya S, Walker RB, Glass BD, et al.: The effect of variations in ph and temperature on stability of melatonin in aqueous solution. J. Pineal Res. 2001; 31(2): 155–158. PubMed Abstract | Publisher Full Text\n\nJiang L, He L, Fountoulakis M: Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J. Chromatogr. A. 2004; 1023(2): 317–320. Publisher Full Text\n\nKorasick DA, Enders TA, Strader LC: Auxin biosynthesis and storage forms. J. Exp. Bot. 2013; 64(9): 2541–2555. PubMed Abstract | Publisher Full Text\n\nOstrowski M, Jakubowska A: Udpglycosyltransferases of plant hormones. Med. J. Cell Biol. 2014; 4(1): 43–60. Publisher Full Text\n\nStaswick PE, Tiryaki I: The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in arabidopsis. Plant Cell. 2004; 16(8): 2117–2127. PubMed Abstract | Publisher Full Text\n\nIshihara A, Hashimoto Y, Tanaka C, et al.: The tryptophan pathway is involved in the defense responses of rice against pathogenic infection via serotonin production. Plant J. 2008; 54(3): 481–495. PubMed Abstract | Publisher Full Text\n\nKang K, Kang S, Lee K, et al.: Enzymatic features of serotonin biosynthetic enzymes and serotonin biosynthesis in plants. Plant Signal. Behav. 2008; 3(6): 389–390. PubMed Abstract | Publisher Full Text\n\nServillo L, Giovane A, Casale R, et al.: Glucosylated forms of serotonin and tryptophan in green coffee beans. LWT. 2016; 73: 117–122. Publisher Full Text\n\nErland LAE, Turi CE, Saxena PK: Serotonin in plants: origin, functions, and implications. Serotonin. 2019: 23–46. Publisher Full Text\n\nLauren AE: Erland and Praveen Saxena. Auxin driven indoleamine biosynthesis and the role of tryptophan as an inductive signal in hypericum perforatum (l.). PLoS One. 2019; 14(10): e0223878. Publisher Full Text\n\nZeggini E, Ioannidis JPA: Meta-analysis in genome-wide association studies.2009.\n\nRaspor M, Motyka V, Ninković S, et al.: Endogenous levels of cytokinins, indole-3-acetic acid and abscisic acid in in vitro grown potato: A contribution to potato hormonomics. Sci. Rep. 2020; 10(1): 1–13.\n\nYe J, Erland LAE, Gill SK, et al.: Metabolomics-guided hypothesis generation for mechanisms of intestinal protection by live biotherapeutic products. Biomolecules. 2021; 11(5). 2218-273X. PubMed Abstract | Publisher Full Text Reference Source\n\nAcuña-Castroviejo D, Escames G, Figueira JC, et al.: Clinical trial to test the efficacy of melatonin in covid-19. J. Pineal Res. 69(3): e12683–e12020. Publisher Full Text\n\nAnderson G, Reiter RJ: Covid-19 pathophysiology: Interactions of gut microbiome, melatonin, vitamin d, stress, kynurenine and the alpha 7 nicotinic receptor: Treatment implications. Melatonin Res. 2020; 3(3): 322–345. Publisher Full Text\n\nLazari D, Alexiou GA, Markopoulos GS, et al.: Entela Hodaj, Ieremias Chousidis, Ioannis Leonardos, Vasiliki Galani, and Athanasios P Kyritsis. N-(p-coumaroyl) serotonin inhibits glioblastoma cells growth through triggering s-phase arrest and apoptosis. J. Neuro-Oncol. 2017; 132(3): 373–381. PubMed Abstract | Publisher Full Text\n\nPai VP, Marshall AM, Hernandez LL, et al.: Altered serotonin physiology in human breast cancers favors paradoxical growth and cell survival. Breast Cancer Res. 2009; 11(6): 1–17. Publisher Full Text\n\nGiebelhaus R, Erland L, Murch S: “Supporting information for “HormonomicsDB: A novel workflow for the untargeted analysis of plant growth regulators and hormones””,[dataset].2022. Borealis, V1, UNF:6:3zWc0kOHv3aEilUA2UbrAQ== [fileUNF]. Publisher Full Text"
}
|
[
{
"id": "153643",
"date": "08 Nov 2022",
"name": "Ainsely Lewis",
"expertise": [
"Reviewer Expertise Mass spectrometry-based metabolomics",
"phytohormone profiling",
"chemometrics"
],
"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 by Ainsely Lewis, Ph.D., and Professor RJ Neil Emery\n\nGood points/Strengths of article:\n\nHormonomicsDB undoubtedly is a needed comprehensive tool to screen metabolites/phytohormones and plant growth regulators putatively. This tool is no doubt a novel tool that will aid researchers using mass spectrometry-based metabolomics for hormones in either plant or animal systems.\n\nMaking choices of what classes or types of compounds to search for is particularly difficult. Therefore, this is a particularly helpful tool for narrowing metabolomics studies into a search for signaling molecules. It offers a focused study on a higher level in that it can uncover important compounds that have wider reaching or pleiotropic effects.\n\nThis is especially good for screening for these hormones especially if they are not known to be present in a given system of study.\n\nKnowing putative compounds in an extraction procedure with various factors (extraction buffer used, solvents, using SPE or not), can really aid in targeted analysis, or to help develop a method to maximize extraction of hormones/phytohormones of interest.\n\nThis manuscript is quite an undertaking! This is a well written and well-done manuscript, that is scientifically sound.\n\nIntroduction was well done and nicely sets the pace for readers. Methodology was thorough and straightforward. Results and discussion section was thorough. Liked the COVID angle in the conclusions. The grammar and word choices used in the manuscript was good as well.\nApproved with reservations. Minor adjustments/revisions needed.\nMinor suggestions - Things for clarification for other users/readers with commentary.\n\nThese are suggestions that we believe can aid in improving the manuscript:\nNot everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers.\n\nWe suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a high-resolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments.\n\nHaving being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards.\n\nAlthough the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc).\n\nIn the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading.\n\nWe tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other open-source tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool.\n\nWhile not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more.\n\nWhen do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit?\n\nLetting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful.\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": "10878",
"date": "08 Apr 2024",
"name": "Susan Murch",
"role": "Author Response",
"response": "We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which we believe will strengthen our manuscript and metabolomics tool. Below we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. Comment #2: We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a highresolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Author Response to Comment: We have chosen to address comment #1 and #2 together since they are closely related. We have added a Supplemental Information (SI) file to address this issue regarding mass tolerance in Da and ppm. We have added the following to the SI under the heading “Selecting Mass Tolerance”. Reference has been made to this section in the SI on page 4 in the manuscript under the section “Data inputs and outputs”: We have also updated HormonomicsDB to include an option to use ppm for mass tolerance. “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below (https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Comment #3: Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Comment #4: Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). Author Response to Comment: We are going to address comments #3 and #4 together as they discuss similar concerns. We will add a mention of the RT and gradient used on the landing page for HormonomicsDB. Additionally, we will add a link to this manuscript there so users can refer to the paper before using the tool. We feel that this should address the concerns in comment #3. We have added the following statement to the manuscript to the section “Retention time prediction” in the Result and discussion: “While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient”. Comment #5: In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. Author Response to Comment: We appreciate these great suggestions for the database content. The synthetic compounds provide some useful and comparatively inexpensive standards to train the chromatography model and are useful for the analytical method but not necessarily the biological question. We are working on software updates will incorporate a tool to distinguish between synthetics and naturally occurring compounds in a future version. Comment #6: We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other opensource tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. Author Response to Comment: This is an important point that is often understated in the literature, since many analysts do not consider how raw data files are converted into a peak table, or the “X” block for putative ID or statistical analysis. To address this, we added the following to the section “Data input and output”: “Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst (metaboanalyst.com), mzMine (mzmine.github.io), and Metaboseek (metaboseek.com).” Comment #7: While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. Author Response to Comment: To emphasize the utility of the HormonomicsDB custom search function we have changed this section from a sub section to its own section in the manuscript (in the methods), and discussed the utility of this function by adding the following to the Results and discussion section “HormonomicsDB web-tool functionality and interface”: “Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment.” Comment #8: When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Comment #9: Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Author Response to Comment: Comments #8 and #9 are related, so we will address them together. We added the following to the end of the section in methods “Data input and output”: “The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. In ESI-LC-MS, the most common adduct is M+H in ESI positive mode and M-H in ESI negative mode. To queue for molecular ions only in the untargeted dataset, users should select the “PGR M+H” or “PGR M-H” databases, depending on their ionization mode. Adducts are often encountered in ESI-LC-MS, especially in ESI positive mode, as metal ions tend to form cations in aqueous solution. If the intensity for a particular PGR is decreased, or the PGR is absent when searching for molecular ion, the user can search for the common adducts of the PGRs in HormonomicsDB by queueing against the “PGR Adducts” database. Searching for the molecular ion and adducts at the same time is permissible in HormonomicsDB and allows the user to detect PGRs present in both forms. Biotransformations allow the user to search for modified forms of PGRs in their metabolomics dataset. This is useful when the goal is to identify conjugates and metabolites of PGRs in plants. The “PGR Biotransformations” database can be searched concurrently with the “PGR M+H” database, to identify PGRs in their native state and as conjugates. This approach can lead to the generation of new hypotheses in plant physiology and metabolism.”"
}
]
},
{
"id": "174935",
"date": "12 Jun 2023",
"name": "Jian You Wang",
"expertise": [
"Reviewer Expertise Analytical biochemistry",
"Plant hormones",
"Strigolactones",
"Plant growth regulators"
],
"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\nHormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content.\nWhat is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm.\n\nPlease include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users.\n\nIt is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds?\n\nAs a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful.\n\nWhat is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise?\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\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? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "10879",
"date": "08 Apr 2024",
"name": "Susan Murch",
"role": "Author Response",
"response": "We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. Author Response to Comment: We appreciate that reviewer #2 has also identified the need for metabolomics approaches specifically tailored to the identification of phytohormones, specifically due to their labile and sensitive nature, as addressed in our manuscript. Comment #2: What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Author Response to Comment: This was a comment also brought up by reviewer #1, and we have revised the manuscript to address this concern. Regarding mass tolerance, we updated HormonomicsDB to include an option to use ppm for mass tolerance. We have also added the following to the supplemental information: “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below (https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Regarding isomers/isoforms, it is often challenging in LC-MS to separate isomers as they can have relatively similar retention times. Additionally, MS/MS fragmentation often struggles to differentiate isomers. Ion mobility spectrometry – mass spectrometry (IMS-MS) is a relatively new technique which has been deployed to separate isomers in time based on their collisional cross section (CCS). This is an emerging technology and we expect that IMS will play an important role in future hormonomics studies. However, in silico CCS predictions are still in their infancy and IMS-MS capable instruments are still fairly inaccessible. Given these hurdles we cannot include IMS-MS in this current version of HormonomicsDB, however as these technologies become more accessible we will work toward including IMS-MS data in HormonomicsDB. Comment #3: Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. Author Response to Comment: To address any ambiguity to these terms we have added the following to the Methods section “Plant growth regulators”: “PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts (Table 1), and PGR biotransformations contains 27 common biotransformations (Table 1) as M+H adducts.” Comment #4: It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? Author Response to Comment: We have updated table 4 and 6 to include more decimal points for both the experimental and library match m/z. Additionally, we have included the ppm difference, as HormonomicsDB now computes this. The data in Brown et al. was acquired on a TOF, therefore an uncertainty of 3-5 ppm is expected. We have added the following to the methods section discussing this: “The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm.” Comment #5: As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. Author Response to Comment: We understand that MS/MS is an important tool for discovering and identifying phytohormones in untargeted studies, however, we found that current tools for in silico prediction of low energy MS/MS spectra often provide incorrect predictions, we felt it would be inappropriate to add MS/MS to HormonomicsDB in this publication. But, as in silico MS/MS prediction tools improve and more phytohormone standards become accessible, we hope to release another version of HormonomicsDB with MS/MS searching capabilities. Comment #5: What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Author Response to Comment: Since HormonomicsDB takes aligned peak tables, the signal to noise (S/N) cut-off would have been determined during the alignment process, as this is the most common approach vendor software currently use for selecting chemical features prior to alignment. Additionally, some software outputs the aligned peak table with relative intensities. To address this concern we added the following to the Methods: “HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step.”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1191
|
https://f1000research.com/articles/12-335/v1
|
24 Mar 23
|
{
"type": "Research Article",
"title": "Effects of Ashwagandha (Withania somnifera) standardized root extract on physical endurance and VO2max in healthy adults preforming resistance training: An eight-week, prospective, randomized, double-blind, placebo-controlled study",
"authors": [
"Narsingh Verma",
"Sandeep Kumar Gupta",
"Sayali Patil",
"Shashank Tiwari",
"Ashok Kumar Mishra",
"Narsingh Verma",
"Sandeep Kumar Gupta",
"Shashank Tiwari",
"Ashok Kumar Mishra"
],
"abstract": "Background: Ashwagandha is a well-known Ayurvedic herb used for youthful vigor and wellbeing. This study investigated the effects of 300 mg standardized root extract (>5% withanolides) of Ashwagandha (Withania somnifera) on muscle mass, strength and cardiorespiratory endurance following resistance training. Methods: In this eight-week, parallel-group, multicenter, randomized, double-blind, placebo-controlled clinical study, 80 healthy male and female participants aged 18-45 years, who engaged in regular physical activity were randomly allocated in a 1:1 ratio to receive Ashwagandha (AG, n=40) 300 mg capsules twice daily for eight weeks, or identical placebo (PB, n=40). Seven (3 AG, 4 PB) participants were excluded due to poor compliance. All participants conducted eight-week resistance training. Study outcomes included muscle strength (1RM bench press and leg extension), muscle size (circumference of arm, chest and upper thigh) and cardio-respiratory endurance (VO2max) assessed at baseline and at eight weeks. Analysis of covariance (ANCOVA) was used to estimate adjusted differences based on sex, BMI and chest circumference at baseline. Results: AG caused greater improvement in chest press (males: p = 0.0084; females: p = 0.0005), leg press (males: p = 0.0049; females: p = 0.018) and endurance (males: p <0.0001; females: p <0.0001) as compared to PB. Also, greater improvements in muscle girth for arm, chest and thigh were seen in both male and female participants with AG. No adverse events were reported in the study. Conclusions: Eight weeks of AG root extract supplementation along with resistance training is effective in improving muscle strength, growth, endurance and recovery in both male and female participants. AG root extract could be a safer, effective and low-cost alternative for athletes to improve muscle endurance.",
"keywords": [
"Muscle strength",
"Cardiorespiratory endurance",
"Muscle girth",
"Resistance training"
],
"content": "Introduction\n\nResistance training is a specific conditioning technique in which an individual works against a broad spectrum of resistive loads to enhance general health, fitness and performance.1 A resistance training program comprises a set of well-organized exercises and aids in rhythmic muscular contraction and relaxation against external resistance. The repetition of actions allows the human body to adapt to such resistance and induces strength and endurance over time.2–4 In addition to strength development, resistance training improves immunity, bone and muscle health and overall function of all organs.5 Furthermore, regular exercise alters biochemical and physiological processes. Biochemical assessments reveal that individuals who regularly participate in endurance exercise have significantly higher creatine kinase levels, which peak approximately 48 hours after the exercise.6\n\nA major component of physical fitness and resistance training is cardiorespiratory endurance. Maximal oxygen consumption (VO2max) refers to the maximum amount of oxygen that an individual can utilize during an intense exercise session and is considered a valid measure to estimate cardiovascular fitness.7 Studies suggest that resistance training enhances VO2max by improving heart-muscle function, increased blood volume and increased oxygen-carrying capacity.8\n\nAlongside resistance training and exercises, diet plays a key role in attaining physical and mental fitness and improving overall health. Traditionally, herbs and their extracts have been considered important dietary supplements with multiple health benefits.9 Several studies have shown multifaceted efficacy of herbs as they can diminish recovery time, improve performance, enhance muscle mass and reduce fat levels.10,11 This has resulted in a growing demand for safe and effective herbal supplements to improve endurance and strength performance among athletes and those with an active lifestyle.12 Withania somnifera, popularly known as Ashwagandha (AG), is a plant that belongs to the Solanaceae family and grows in arid or semi-arid regions. AG is one of the most frequently used medicinal plants in the Ayurvedic system of complementary medicine for a varied range of ailments. It has been used to treat musculoskeletal conditions and improve general vitality and quality of life.13–15 Pharmacologically, AG has been explored extensively for its potential as a versatile health supplement.13\n\nSandhu et al. (2010) studied the impact of 500 mg of AG supplementation for eight weeks on aerobic exercise performance and the activity of associated muscles in healthy young adults. There was a significant increase in VO2max and muscular power.16 In another study, Raut et al. (2012) explored the safety, tolerability and activity of 750 mg to 1250 mg of AG in healthy volunteers for 30 days and found that AG supplementation increased muscle strength, improved sleep quality and reduced lipid concentrations.17 Wankhede et al. (2012) also demonstrated that as in adjunction to a resistance training program, 600 mg of AG supplementation for eight weeks increased muscle strength in untrained male adults.18 Looking at these previous studies, the current study was based on a hypothesis that AG will lead to a significant improvement in muscle strength, muscle growth and cardio-respiratory endurance in the study participants.\n\nAlthough preliminary studies mentioned above have been conducted, robust human clinical trials evaluating the performance-enhancing effects of standardized AG root extract are still limited. A previously published study evaluating muscle strength focused only on male participants.18 Physical endurance is considered higher in males owing it to the testosterone hormone. Therefore, this randomized, double-blind, placebo-controlled study aims to examine the effects of a standardized AG root extract (as a complement to a resistance training program) on changes in muscle strength, muscle growth and cardio-respiratory endurance in active, healthy participants of either sex.\n\n\nMethods\n\nThe study was approved by the Institutional Ethics Committees of both King George Medical University (Reference number. #202/IEC/R.Cell-18) and M. V. Hospital and Research (Reference number #IEC/01/28/18) and it was prospectively registered with the Clinical Trials Registry of India (Registration# CTRI/2018/07/014969).\n\nThis was a parallel-group=eight-week, multicenter, randomized, double-blind, PB-controlled study. The study was approved by respective Institutional Ethics Committees (IECs) from both study sites – King George Medical University (Reference no. #202/IEC/R.Cell-18) and M. V. Hospital and Research (Reference no. #IEC/01/28/18). It was also prospectively registered with the Clinical Trial Registry of India (Registration #CTRI/2018/07/014969; on 19/07/2018). In addition, it was conducted in compliance with the Declaration of Helsinki guidelines, the New Drugs and Clinical trials rules 2019 and the Indian Council of Medical Research (ICMR) ethical guidelines for biomedical research on human subjects.\n\nThe recruitment of participants was performed by circulating printed fliers in the purlieu of a gymnasium which served as the site for the training program. This brochure was approved by both institutional ethics committees. Recruitment of participants started on 11 September, 2018 (first visit of first participant) and ended on 28 March, 2019 (last visit of last participant). Subjects were randomly and equally allocated to two groups in 1:1 ratio using stratified randomization (male and female) to receive either an AG capsule standardized root extract (n=40), or PB which looked identical to AG capsule (n=40). The randomization was computer-generated through randomly permuted blocks of 20. Within each block, the number of participants assigned to each of the two treatment arms was equal. The AG and PB capsules were manufactured and packed in identical containers and labeled equivalently, along with unique serial numbers to ensure blinding. The study centers received numbered and sealed envelopes that contained no information about treatment allocation.\n\nAll participants read and signed an informed consent form before final selection and enrollment in this study. Healthy adults of either sex aged between 18 to 45 years engaging in regular physical activity (gymnasium/strength training exercise at least three months before screening for this study) were considered eligible. Sex of the participants was defined based on self-reporting. Participants agreed to engage in the same exercise schedule and diet regime for the study period as prescribed in the study protocol and if of child-bearing age, agreed to use barrier birth control measures. Participants were excluded if they were taking any nutritional supplements, medications, or steroids used to enhance physical performance. Those with a history of drug abuse, who smoked more than 10 cigarettes a day, or were habitually consuming more than 14 grams of alcohol per day were also excluded. Other exclusion criteria were: any planned participation in any sporting event during the study period; a weight loss of >5 kg in the previous three months; a history of any orthopedic injury or surgery in the past six months; any known hypersensitivity to AG; participation in any clinical study in the past three months; a history of heart disease, diabetes, depression, stroke or neurological disorder. Participants were also excluded if they were taking anti-hypertensive drugs, beta-blockers, beta-agonists, hormonal contraceptives, corticosteroids, or psychotropic substances over the previous three months.\n\nCapsules containing either 300 mg of AG standardized root extract (KSM-66, Ixoreal Biomed, CA, US) or 300 mg starch (Shri Kartikeya Pharma, Hyderabad, India) were used for AG and PB groups respectively. Both the AG and PB formulations were cellulose-based hard capsules and identical in appearance, weight, texture and color. Participants were required to take one capsule twice daily with milk or water.\n\nThe AG root extract is a light yellowish powder extracted using a proprietary process. The green extraction process is devoid of any alcohol or similar solvents, hence maintaining the standards as recommended by traditional Ayurveda. The product, KSM-66 Ashwagandha, contains a high concentration of root extract of this herb and more than 5% of total withanolides as standardized by high-performance liquid chromatography. The batch number of product used was KSM/VG/18/1020. The chemical profile of the study product was confirmed by Shri Kartikeya Pharma, Hyderabad, India.\n\nThe target sample size was estimated using G*Power (Version 3.1.9.3). It was based on a previously published randomized controlled clinical study evaluating the effect of an AG root extract on muscle strength and recovery.18 A recently published systematic review on AG also supported this kind of improvement (effect size of 0.67) in physical performance.19 Considering the previous study, we hypothesized that AG treatment is better than PB by an effect size of 0.6 with regards to change in the one-repetition maximum (1 RM) chest press exercise after eight weeks. To detect an effect size of 0.6 in a two-parallel-group design (1:1) using independent Student t-test, with a 5% risk of type 1 error (alpha) and 80% power, 40 subjects per group were required while considering a 10% drop-out rate. Thus, 80 healthy male and female subjects were recruited in the study.\n\nThe resistance training regimen used in this study was focused on improving muscle strength, increasing muscle mass and enhancing cardiorespiratory endurance. Various resistance exercises were chosen with the objective of training targeted muscle groups. Such training programs target the upper and lower body and consist of a series of exercises with suitable resistance, grouped into multiple sets and repetitions as per the National Strength and Conditioning Association’s (NSCA) regulations and guidelines.20 Each participant was required to complete the training session every alternate day with a one-day complete rest per week. Therefore, participants were training three days per week. Each training session started with a warm-up of low intensity aerobic exercise. Participants were instructed to perform the maximum repetitions possible for each set until exhaustion. The exercise program is detailed in Figure 1, comprising exercises for week 1, week 2 and remainder of the study (weeks 3 to 8).\n\nData for this study is available in the online repository ‘Figshare’ under the dataset named ‘Ashwagandha_Muscle study’ (Underlying data).34\n\nPrimary outcome measures\n\nMuscle strength\n\nChanges in upper and lower body muscular strength were the primary efficacy assessment of this study. As per common practice in sports medicine, muscle strength was assessed by one-repetition maximum (1RM) for bench press and leg press. 1RM testing was performed using NSCA’s protocol.20 1 RM refers to the maximal load lifted by a participant for one cycle of the exercise. Muscle strength measurements were conducted at baseline (first day of training) and end of the study (after the completion of eight weeks of training and supplementation). The equipment used was a Bench Press (SL7028) manufactured by Impulse and a Leg extension (GCEC340) manufactured by Body Solid Inc.\n\nSecondary outcome measures\n\nMuscle girth\n\nMuscle size was measured at three sites - arm (flexed mid-upper arm), chest (sternum at mid-tidal volume) and upper thigh (just inferior to gluteal fold) of each participant. Measurements were undertaken on the first day of training (baseline) and at end of the study (day 56). Maximal cross-sectional area (CSA) was measured for thigh and arm using the Moritani-DeVries method,21 whereas, for chest measurement, girth was measured at the level of middle of the sternum by passing a measuring tape under both arms at the end of normal expiration.\n\nCardiorespiratory endurance (maximum rate of oxygen consumption)\n\nResistance training and endurance are highly correlated.22,23 Cardiorespiratory endurance measures overall body performance during high-intensity exercises. Studies indicate that resistance training induces an increase in the maximal rate of oxygen consumption (VO2max).22,23 VO2max is measured during incremental exercise, most typically on a motorized treadmill. Bruce protocol was used to assess the treadmill test outcomes of all participants. Test score was considered as time taken for the test in minutes and it was converted to estimate a VO2max score as per the Bruce protocol.22\n\nSafety assessment and adverse events\n\nClinical safety was assessed based on the frequency of adverse events reported by the participants. In addition to this subjective report, standard biochemistry tests were also performed along with measurement of vital signs.\n\nData was entered in Microsoft Excel spreadsheet using manual double-entry method to ensure data accuracy. Statistical analyses were done using MedCalc (version 20.011). Efficacy analysis was done on the modified intention to treat (ITT) dataset (n=73), and safety analysis was done on the whole dataset (n=80). Data for continuous variables are presented as means with standard deviation (SD), whereas categorical and discrete data are presented as counts with percentages. Unpaired t-test was used to assess between-group differences. Change in values form baseline to eight weeks were computed from and compared between the two groups using unpaired t-test. Effects of sex, BMI and chest circumference on different parameters were analyzed using analysis of covariance (ANCOVA). Adjusted means with 95% confidence intervals (CI) and effect size (Cohen’s d) were presented for change from baseline. Criteria for effect sizes were based on the standard criteria (<0.2, trivial; 0.2–0.6, small; 0.6–1.2, moderate; 1.2–2.0, large; 2.0–4.0, very large; and >4.0, nearly perfect).24\n\nNormality assumptions were checked on all variables using a one-sample Shapiro-Wilk test. A p-value lower than 0.05 was considered the threshold to claim statistical significance.\n\n\nResults\n\nA total of 92 people were screened for participation in the study, of which 80 met the inclusion criteria and were enrolled in the study (Figure 2). All enrolled participants completed the eight-week follow-up. However, four subjects (3 males and 1 female) in the PB and three subjects (3 males) in the AG group did not consume supplementation after their second visit. These participants were documented as having poor compliance to treatment and were excluded from the efficacy analysis. Reasons for premature medication discontinuation were reported as unintentional forgetfulness due to travel and other personal issues by these seven subjects. Baseline demographic characteristics and vital signs are detailed in Table 1 and indicate that the study population was homogenous with no significant differences between the treatment and control groups. Baseline parameters across both the groups are displayed in Table 2.\n\nChanges in 1 RM bench press and leg press across both treatment groups throughout the eight-week trial period are detailed in Table 3. There were significant differences between the groups in both 1 RM bench press (males: effect size, 0.91; p=0.0084; females: effect size, 1.56; p=0.0005; total: effect size, 1.14; p<0.0001) and 1 RM Leg press (males: effect size, 1.22; p=0.0049; females: effect size, 0.63; p=0.018; total: effect size, 1.11; p=0.0005). A within-group analysis in AG group demonstrated a significant (p<0.0001) increase of 23.5 % and 22.8% in 1 RM bench press and an increase of 15% and 9.9% in 1 RM leg press over time and in both male and female participants respectively. Table 4 presents the comparison of AG and PB for change (unadjusted and adjusted for baseline values) in 1 RM leg press and 1 RM bench press from baseline to eight weeks.\n\nChanges in muscle size across the two treatment groups during the study period are detailed in Table 3. At the end of the study, there was a significant increase in both chest circumference (Total participants: p=0.019) and arm circumference (Total participants: p<0.0001), among the participants in AG group as compared to the PB group. However, no improvement was seen in thigh circumference when compared to PB group. A within-group analysis in AG group demonstrated a significant increase in the chest circumference (males: p<0.0001; females: p<0.0001), mid-arm circumference (males: p<0.0001; females: p<0.0001) and thigh circumference (males: p=0.0003; females: p<0.0001). Table 4 presents the comparison of AG and PB for change (unadjusted and adjusted for baseline values) for mid-arm, thigh and chest circumference from baseline to eight weeks.\n\nChanges in the VO2max across the two treatment groups throughout the eight-week trial period are detailed in Table 3. At the end of the study, there was a statistically significant between-group difference in VO2max values (males: p<0.0001; females: p=0.0001), when compared with the PB group. In the AG group=a statistically significant 9.5% and 7% increase were observed over time in both males (p<0.0001) and females (p<0.0001), respectively. Table 4 presents the comparison of AG and PB for change (unadjusted and adjusted for baseline values) in VO2max from baseline to eight weeks. The analysis for VO2max yielded 100% power and greater changes were observed with AG as compared to placebo (effect size, 1.034, p<0.0001).\n\nFigures 3 and 4 depict changes across all the parameters between the two study groups.\n\nThe participants did not report any adverse events during the study period. Additionally, we conducted an array of routine clinical tests such as hematology, renal function, liver function and thyroid function tests to evaluate the safety and tolerability of AG root extract supplementation in participants. Physical examination and vital signs were collected as well. At the screening visit, all tested parameters were within the normal ranges. None of the parameters in the study samples showed any abnormal changes at the end of the intervention.\n\n\nDiscussion\n\nThe present study assessed the impact of AG root extract supplementation on resistance training adaptations such as muscle strength and endurance in healthy and active adults. The primary findings of the study are that significantly greater improvements in muscle strength for both lower body (1 RM Leg press) and upper body (1 RM Chest press) occurred in participants consuming AG as compared to PB. In addition, AG supplementation significantly increased muscle size and endurance. However, there were no differences in thigh muscle size (male) and body composition (body fat) between the two groups.\n\nThe impact of resistance exercise training on increasing muscular strength was better (p <0.05) with AG (23%) versus PB (8%). Similarly, a previous study by Wankhede et al. (2012) reported significant improvements in both bench press and leg extension after eight weeks of the AG supplement in healthy adult males.18 However, these improvements were greater in comparison to the current study, which could be due to the fact that experiment was conducted on inexperienced individuals in the previous study versus resistance-trained adults in the current investigation. Earlier studies recommended that along with strength and muscle growth, factors such as human growth hormone and testosterone were found higher in males compared to females.25 Our study also measured the muscular strength of male and female participants (1 RM bench press and leg press), and a significantly greater outcome was found in males than female participants with an exception of 1 RM bench press in females, both before and after the resistance training program. Furthermore, due to resistance training, general development from the baseline parameters was observed for all the participants. This suggests that the improvement was of clinical relevance (effect size, 0.9, indicating larger effect) which is an improvement over the meta-analysis conducted by Bonilla et al. (2021)19 that analyzed twelve clinical trials of AG on physical performance; however, only two trials were relevant for muscular strength.\n\nThe percentage of adults whose chest, thigh and mid-arm muscle size increased differed significantly between the two study groups, although men’s thigh size remained similar in both groups. Furthermore, endurance measured by VO2max also increased significantly in AG group which suggests that the effect, although small in magnitude (8%), might be clinically relevant. This observation is lower compared to a previous study by Tiwari et al.,26 which reported a 16% improvement in VO2max. Similarly, another study by Choudhary et al.27 observed 13% increase in VO2max after eight weeks of AG supplementation. Therefore, the current improvement is comparable and consistent with literature review.\n\nNo significant benefit was seen with respect to body fat (Figure 3), as assessed by the body composition monitor. Slight improvement was seen in AG group, but there was no significant difference between the two groups. However, the study was not powered enough to assess the change in body fat.\n\nAG was well tolerated by the subjects and no serious side effects were reported. This finding is consistent with previously published studies on AG (Withania somnifera) root extract in healthy volunteers, which also advocated the herb’s tolerance.17,18,28,29 Thus, it could be a safer alternative to improve and maintain physical performance.\n\nIncreased levels of anabolic hormone (serum testosterone) may be the cause of improved muscular strength, which could be associated with its structural similarities to withanolides (major constituents of AG root extract).30 Most of the studies included in the meta-analysis by Bonilla et al., which involved muscle strength, endurance and recovery might be owed to the antioxidant properties of this plant.19 In addition, as previously shown, AG alleviates stress, improves sleep and physical performance,14,31–33 even though these were not measured in this study.\n\nOur trial had certain strengths, including enrollment of resistance-trained adult men and women, adequate sample size, a double-blind, PB-controlled design, excellent participant retention and use of standardized AG extract. However, one noteworthy drawback was the lack of quantitative data on the subjects’ food intake. They were, however, instructed not to change and follow the specified diet for entire length of the trial. Although the subjects claimed to have followed the instructions (as per subject’s diary), we were unable to determine if these factors influenced the effect of AG due to a lack of reliable detailed quantitative information on daily calorie and protein intake. Another limitation is that our research focused on resistance-trained adults for eight weeks, so extrapolating results to other groups for a longer duration should be done with caution. As a result, in future studies, we advocate a comprehensive dietary analysis of participants' daily calorie and protein consumption, as well as a longer-term follow-up with diverse populations.\n\n\nConclusions\n\nIn conclusion, eight weeks of AG root extract supplementation in combination with resistance training is effective in promoting muscle strength, muscle growth and can also improve endurance in both male and female participants. The study also indicated that the participants have tolerated the AG root extract well. Thus, AG root extract could probably represent a safer low-cost alternative for athletes.\n\n\nAuthor contributions\n\nAll the authors of this study contributed to the project equally. NV supervised the study at the KGMU hospital and led the study. SKG supervised the study at MV hospital. SP worked on review and editing of the article. ST helped in data collection and analysis. AKM conceptualized the study, helped in data analysis and writing the manuscript. All the authors participated in study designing and implementation and all the authors have gone through the final article and approved it for submission. Every author actively participated in drafting the manuscript and approved the final version of the article.",
"appendix": "Data availability\n\nFigshare: Ashwagandha_Muscle study, https://doi.org/10.6084/m9.figshare.22081895.v3. 34\n\nThe project contains the following underlying data:\n\n- Ashwagandha_Muscle study_Raw data.csv\n\n- Ashwagandha_Muscle study_Raw data.xlsx\n\n- Filled consort checklist\n\n- Study protocol\n\nFigshare: CONSORT checklist for ‘Effects of Ashwagandha (Withania somnifera) standardized root extract on physical endurance and VO2max in healthy adults preforming resistance training: An eight-week, prospective, randomized, double-blind, placebo-controlled study’. https://doi.org/10.6084/m9.figshare.22081895.v3. 34\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\nThe authors thank Ixoreal BioMed Inc., Los Angeles, California, USA, for supplying the AG high concentration root extract used in this study.\n\n\nReferences\n\nLloyd RS, Faigenbaum AD, Stone MH, et al.: Position statement on youth resistance training: the 2014 International Consensus. Br J Sports Med. 2014 Apr; 48(7): 498–505. PubMed Abstract | Publisher Full Text\n\nKraemer WJ, Ratamess NA: Fundamentals of Resistance Training: Progression and Exercise Prescription. Med Sci Sport Exerc. 2004 Apr; 36(4): 674–688. PubMed Abstract | Publisher Full Text Reference Source\n\nStaron RS, Karapondo DL, Kraemer WJ, et al.: Skeletal muscle adaptations during early phase of heavy-resistance training in men and women. J Appl Physiol. 1994 Mar 1; 76(3): 1247–1255. PubMed Abstract | Publisher Full Text\n\nSale DG: Neural adaptation to resistance training. Med Sci Sport Exerc. 1988 Oct; 20(Sup 1): S135–S145. Publisher Full Text Reference Source\n\nNieman DC, Wentz LM: The compelling link between physical activity and the body’s defense system. J Sport Heal Sci. 2019 May; 8(3): 201–217. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nTotsuka M, Nakaji S, Suzuki K, et al.: Break point of serum creatine kinase release after endurance exercise. J Appl Physiol. 2002 Oct 1; 93(4): 1280–1286. PubMed Abstract | Publisher Full Text\n\nJones GL, Killian KJ, Summers E, et al.: Inspiratory muscle forces and endurance in maximum resistive loading. J Appl Physiol. 1985 May 1; 58(5): 1608–1615. PubMed Abstract | Publisher Full Text\n\nHellsten Y, Nyberg M: Cardiovascular Adaptations to Exercise Training. Comprehensive Physiology. Wiley; 2015; pp. 1–32. Publisher Full Text\n\nProbst YC, Guan VX, Kent K: Dietary phytochemical intake from foods and health outcomes: a systematic review protocol and preliminary scoping. BMJ Open. 2017 Feb 15; 7(2): e013337. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKonda MR, Alluri KV, Janardhanan PK, et al.: Combined extracts of Garcinia mangostana fruit rind and Cinnamomum tamala leaf supplementation enhances muscle strength and endurance in resistance trained males. J Int Soc Sports Nutr. 2018 Jan 5; 15(1): 50. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen CK, Muhamad AS, Ooi FK: Herbs in exercise and sports. J Physiol Anthropol. 2012 Dec 8; 31(1): 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilliams MH: Dietary Supplements and Sports Performance: Introduction and Vitamins. J Int Soc Sports Nutr. 2004 Dec 1; 1(2): 1–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMishra LC, Singh BB, Dagenais S: Scientific basis for the therapeutic use of Withania somnifera (ashwagandha): a review. Altern Med Rev. 2000 Aug; 5(4): 334–346. PubMed Abstract\n\nChandrasekhar K, Kapoor J, Anishetty S: A Prospective, Randomized Double-Blind, Placebo-Controlled Study of Safety and Efficacy of a High-Concentration Full-Spectrum Extract of Ashwagandha Root in Reducing Stress and Anxiety in Adults. Indian J Psychol Med. 2012 Jul 1; 34(3): 255–262. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArchana R, Namasivayam A: Antistressor effect of Withania somnifera. J Ethnopharmacol. 1998 Jan; 64(1): 91–93. PubMed Abstract | Publisher Full Text Reference Source\n\nSandhu J, Shah B, Shenoy S, et al.: Effects of Withania somnifera (Ashwagandha) and Terminalia arjuna (Arjuna) on physical performance and cardiorespiratory endurance in healthy young adults. Int J Ayurveda Res. 2010; 1(3): 144–149. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRaut A, Rege N, Shirolkar S, et al.: Exploratory study to evaluate tolerability, safety, and activity of Ashwagandha (Withania somnifera) in healthy volunteers. J Ayurveda Integr Med. 2012; 3(3): 111–114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWankhede S, Langade D, Joshi K, et al.: Examining the effect of Withania somnifera supplementation on muscle strength and recovery: a randomized controlled trial. J Int Soc Sports Nutr. 2015 Oct 20; 12(1): 43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBonilla DA, Moreno Y, Gho C, et al.: Effects of Ashwagandha (Withania somnifera) on Physical Performance: Systematic Review and Bayesian Meta-Analysis. J Funct Morphol Kinesiol. 2021 Feb 11; 6(1): 20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaff G, Triplett N: Essentials of strength training and conditioning. 4th ed.United States, Champaign, IL: Human Kinetics; 2016; pp. 264–470.\n\nDeFreitas JM, Beck TW, Stock MS, et al.: A Comparison of Techniques for Estimating Training-Induced Changes in Muscle Cross-Sectional Area. J Strength Cond Res. 2010 Sep; 24(9): 2383–2389. PubMed Abstract | Publisher Full Text Reference Source\n\nGäbler M, Prieske O, Hortobágyi T, et al.: The Effects of Concurrent Strength and Endurance Training on Physical Fitness and Athletic Performance in Youth: A Systematic Review and Meta-Analysis. Front Physiol. 2018 Aug 7; 9. Publisher Full Text\n\nHughes DC, Ellefsen S, Baar K: Adaptations to Endurance and Strength Training. Cold Spring Harb Perspect Med. 2018 Jun; 8(6): a029769. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCohen J: Statistical Power Analysis for the Behavioral Sciences. Elsevier; 1977. Reference Source\n\nKraemer W, Gordon S, Fleck S, et al.: Endogenous Anabolic Hormonal and Growth Factor Responses to Heavy Resistance Exercise in Males and Females. Int J Sports Med. 1991 Apr 14; 12(02): 228–235. PubMed Abstract | Publisher Full Text\n\nTiwari S, Gupta SK, Pathak AK: A double-blind, randomized, placebo-controlled trial on the effect of Ashwagandha (Withania somnifera dunal.) root extract in improving cardiorespiratory endurance and recovery in healthy athletic adults. J Ethnopharmacol. 2021 May; 272: 113929. PubMed Abstract | Publisher Full Text Reference Source\n\nChoudhary B, Shetty A, Langade D: Efficacy of Ashwagandha (Withania somnifera [L.] Dunal) in improving cardiorespiratory endurance in healthy athletic adults. AYU (An Int Q J Res Ayurveda). 2015; 36(1): 63. Reference Source\n\nLopresti AL, Drummond PD, Smith SJ: A Randomized, Double-Blind, Placebo-Controlled, Crossover Study Examining the Hormonal and Vitality Effects of Ashwagandha (Withania somnifera) in Aging, Overweight Males. Am J Mens Health. 2019 Mar 10; 13(2): 155798831983598. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKuchewar V, Borkar M, Nisargandha M: Evaluation of antioxidant potential of Rasayana drugs in healthy human volunteers. AYU (An Int Q J Res Ayurveda). 2014; 35(1): 46–49. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMirjalili M, Moyano E, Bonfill M, et al.: Steroidal Lactones from Withania somnifera, an Ancient Plant for Novel Medicine. Molecules. 2009 Jul 3; 14(7): 2373–2393. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalve J, Pate S, Debnath K, et al.: Adaptogenic and Anxiolytic Effects of Ashwagandha Root Extract in Healthy Adults: A Double-blind, Randomized, Placebo-controlled Clinical Study. Cureus. 2019 Dec 25; 11: e6466. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLangade D, Kanchi S, Salve J, et al.: Efficacy and Safety of Ashwagandha (Withania somnifera) Root Extract in Insomnia and Anxiety: A Double-blind, Randomized, Placebo-controlled Study. Cureus. 2019 Sep 28; 11: e5797. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLangade D, Thakare V, Kanchi S, et al.: Clinical evaluation of the pharmacological impact of ashwagandha root extract on sleep in healthy volunteers and insomnia patients: A double-blind, randomized, parallel-group, placebo-controlled study. J Ethnopharmacol. 2021 Jan; 264: 113276. PubMed Abstract | Publisher Full Text Reference Source\n\nVerma N, Gupta SK, Patil S, et al.: Ashwagandha_Muscle study. Dataset. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "219543",
"date": "13 Nov 2023",
"name": "Mark E. T. Willems",
"expertise": [
"Reviewer Expertise Exercise Physiology",
"Training",
"Sports Nutrition"
],
"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 the title, change “preforming”.\nPlease clarify In the background section of the abstract that 600 mg was used.\nPlease revise in the background of the abstract that muscle mass was not measured. An indirect measurement of cross sectional area seems to have been measured.\nPlease have specific conclusions. There are no measurements of recovery. Please revise the conclusion in the abstract.\nThe introduction does not provide justification for the need to examine the effects in females. Please provide that justification.\nP3, Does we need the statement supported by reference 6. It is very misleading and has nothing to do with the study.\nP3. Just linking physical endurance in males with testosterone is an extreme simplification of all the factors and determinants of physical endurance. Please revise.\nThere is repeat in the method section regarding ethical approval. Please revise.\nThe methods indicate that participants could take the capsules with milk. Please provide the number of participants in each group that consumed the capsules with milk. Milk intake may enhance protein synthesis and may have affected some of the parameters of interest. This needs to be discussed and probably acknowledged as a limitation of the study.\nThe sample size calculation is confusing. It seems 40 participants were required in each group and with consideration of 10% drop-out, 44-45 participants should have been in each group. Please clarify.\nOn P5 is mentioned “standard biochemistry tests”. Please provide more information.\nTable 1. I suggest to provide values without decimal places.\nTable 2. Do you need to express values with two decimal places? Please reconsider.\nPlease be consistent with terminology. Is the bench press the same as the chest press?\nTable 3. Are you allowed to express the differences with three decimal places? For example, with circumference changes expressed with 3 decimal places indicates a measurement to the nearest 0.001 cm. I am sure that was not done.\nThe p-values in the text in the result section does not match with the information provided in the Tables. For example “There were significant differences between the groups in both 1 RM bench press (males: effect size, 0.91; p=0.0084; females: effect size, 1.56; p=0.0005; total: effect size, 1.14; p<0.0001)”. Please ensure that text information matches table information.\nFigs 3 and 4 has data that is communicated as well in Table 3. Please avoid duplication. I suggest to delete Figs 3 and 4 as it does not present new information.\nP10. Please provide the outcome of the clinical tests.\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?\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? No",
"responses": [
{
"c_id": "11362",
"date": "08 Apr 2024",
"name": "sayali patil",
"role": "Author Response",
"response": "Dear Mark E. T. Willems, Thank you for your time and valuable feedback on our manuscript. We have carefully reviewed your comments. As suggested, we provide a point-by-point response as below: In the title, change “preforming”. Correction from “preforming” to “performing” in the title has been made for version 2 of the article. Please clarify in the background section of the abstract that 600 mg was used. Correction from 300mg to 600mg of Ashwagandha has been made for version 2 of the article. [page 1, paragraph 1] Please revise in the background of the abstract that muscle mass was not measured. An indirect measurement of cross-sectional area seems to have been measured. As suggested “muscle mass” in abstract is replaced with “muscle size” in the version-2 of the article. (page 1, paragraph 1; page 3, paragraph 3; page 4, paragraph 6) Please have specific conclusions. There are no measurements of recovery. Please revise the conclusion in the abstract. We acknowledge that there were no measurements of recovery. Revision has been made for version 2 of the article. [page 2, paragraph 2] The introduction does not provide justification for the need to examine the effects in females. Please provide that justification. “Since gender is an important factor affecting serum hormone levels (and subsequent response to effects of exercise) due to physiological factors, this study focussed on testing the responses in both the genders who are regularly active exercising. There is scarcity of data in previously published literature.” This above statement has been added in the paragraph 5 on page 3. P3, do we need the statement supported by reference 6. It is very misleading and has nothing to do with the study. “Biochemical assessments reveal that individuals who regularly participate in endurance exercise have significantly higher creatine kinase levels, which peak approximately 48 hours after the exercise.” This statement on page-3 is rephrased to improve clarity as below: “Serum creatine kinase is raised in individuals who regularly participate in endurance exercise, with peak levels seen 48 hours after the exercise.” P3. Just linking physical endurance in males with testosterone is an extreme simplification of all the factors and determinants of physical endurance. Please revise. “A previously published study evaluating muscle strength focused only on male participants.18 Physical endurance is considered higher in males owing it to the testosterone hormone.” The sentences are revised as below: “A previously published study evaluating muscle strength focused only on male participants.18 However, data on muscle strength and endurance in female participants is scarce.” There is repeat in the method section regarding ethical approval. Please revise. We have removed the repetition and ethical approval details are mentioned only in the “ethical approval” section under Methods. The methods indicate that participants could take the capsules with milk. Please provide the number of participants in each group that consumed the capsules with milk. Milk intake may enhance protein synthesis and may have affected some of the parameters of interest. This needs to be discussed and probably acknowledged as a limitation of the study. Two males and one female consumed capsules with milk in AG group, whereas 3 males and one female in PB group consumed capsules with milk. This information has been included in the “Interventions” section of the article (version 2). The same has been included as a limitation of the study as suggested. The sample size calculation is confusing. It seems 40 participants were required in each group and with consideration of 10% drop-out, 44-45 participants should have been in each group. Please clarify. Since it was expected that the study participants were highly motivated adults performing regular exercises, we had not anticipated data loss due to lost to follow-up. However, we had data loss not due to lost to follow-up, but due to poor compliance (3 participants in AG and 4 in PB group). We failed to anticipate this possibility during study planning. However, we estimated the effect size (1.14 and 1.11 for 1-RM bench press and 1-RM leg press respectively) for the primary outcomes, to derive our conclusions. On P5 is mentioned “standard biochemistry tests”. Please provide more information. Please find the outcomes of the “standard biochemistry tests” as clinical tests (hematology, renal function, liver function and thyroid function tests) included in the article’s Data Availability section as “Extended data”. Table 1. I suggest to provide values without decimal places. All 3 tables in the article uniformly have values with a single decimal place in the version-2 of this article. Table 2. Do you need to express values with two decimal places? Please reconsider. All 3 tables in the article uniformly have values with a single decimal place in the version-2 of this article. Please be consistent with terminology. Is the bench press the same as the chest press? We have made changes and kept the terminology as “bench press” throughout the article in the version 2. Table 3. Are you allowed to express the differences with three decimal places? For example, with circumference changes expressed with 3 decimal places indicates a measurement to the nearest 0.001 cm. I am sure that was not done. Thank you for the observation. All 3 tables in the article uniformly have values with a single decimal place in the version-2 of this article. The p-values in the text in the result section does not match with the information provided in the Tables. For example, “There were significant differences between the groups in both 1 RM bench press (males: effect size, 0.91; p=0.0084; females: effect size, 1.56; p=0.0005; total: effect size, 1.14; p<0.0001)”. Please ensure that text information matches table information. Kindly note that in the result section (page 8, paragraph 1), p-values in the text are with respect to the effect size whereas p-values in tables are with respect to the comparison of means (t-test). Figs 3 and 4 has data that is communicated as well in Table 3. Please avoid duplication. I suggest to delete Figs 3 and 4 as it does not present new information. Thank you for the observation. We have removed Figures 3 and 4 for the version 2 of the article. P10. Please provide the outcome of the clinical tests. Please find the outcomes of the clinical tests (hematology, renal function, liver function and thyroid function tests) included in the article’s Data Availability section as “Extended data”."
}
]
},
{
"id": "200814",
"date": "27 Nov 2023",
"name": "Nawab John Dar",
"expertise": [
"Reviewer Expertise Neuropharmacology"
],
"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 entitled \" Effects of Ashwagandha (Withania somnifera) standardized root extract on physical endurance and VO2max in healthy adults preforming resistance training: An eight-week, prospective, randomized, double-blind, placebo-controlled study by Verma et al, is well designed and conducted, however, I have few queries before it is approved for indexing:\nThe authors did not mention about the habits of the volunteers, what about their smoking habits and sleep cycle?\n\nWho manufactured the AG capsules and how did they made sure Quality of the capsules (QC&QA), why would they buy the control and AG from different companies?\n\nI would love to know what happened to the endurance once the study is over and the volunteers stopped taking AG?\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? Partly",
"responses": [
{
"c_id": "11363",
"date": "08 Apr 2024",
"name": "sayali patil",
"role": "Author Response",
"response": "Dear Nawab John Dar, Thank you for your time and valuable feedback on our manuscript. We have carefully reviewed your comments. As suggested, we provide a point-by-point response as below: The authors did not mention about the habits of the volunteers, what about their smoking habits and sleep cycle? The two groups were similar with respect to the personal history and habits. A statement to that effect is added in the “subjects” section of the article (version 2). Who manufactured the AG capsules and how did they made sure Quality of the capsules (QC&QA), why would they buy the control and AG from different companies? Control capsules were manufactured specifically for the study purpose and hence, it was outsourced to third party manufacturing. However, the study capsules (AG) were provided to manufacturer to match (identical placebo) the control (PB) capsules with AG. I would love to know what happened to the endurance once the study is over and the volunteers stopped taking AG? Follow-up was not a part of the study plan and we did not assess this."
}
]
}
] | 1
|
https://f1000research.com/articles/12-335
|
https://f1000research.com/articles/13-37/v1
|
08 Jan 24
|
{
"type": "Review",
"title": "A BRIEF EXPLORATION OF ARTIFICIAL INTELLIGENCE IN DENTAL HEALTHCARE: A Narrative review",
"authors": [
"Prakrati Kamath",
"Prathvi Kamath",
"Sharon J R Saldanha",
"Thilak B Shetty",
"Shobha J Rodrigues",
"Mahesh M",
"Umesh Y Pai",
"Puneeth K Hegde",
"Prashant Bajantri",
"Sandipan Mukherjee",
"Prakrati Kamath",
"Prathvi Kamath",
"Thilak B Shetty",
"Shobha J Rodrigues",
"Mahesh M",
"Umesh Y Pai",
"Puneeth K Hegde",
"Prashant Bajantri",
"Sandipan Mukherjee"
],
"abstract": "Artificial intelligence is a computer system which can replicate human behavior and largely supports human actions and interpretation, but not replace human responses. Over the past few decades, the field of artificial intelligence (AI) has experienced phenomenal development and expansion. We are surrounded by several instances of AI. The most typical examples include Chat GPT, Alexa, Google Maps, autocorrect and text editors, e-payments, virtual travel booking agent, social media monitoring, gaming, including chess matches involving computers versus human chess masters, self driving cars, adaptive cruise control, parking assistance, and facial recognition for biometrics such as retinal scans and fingerprint scans. AI has applications in different branches of Dentistry. This review article attempts to highlight these points and lays an emphasis on how AI is driving dentistry in the present and will improve dental care in the future. A total of 59 papers from an electronic search using Google Scholar and PubMed were used to create this narrative review. Artificial intelligence can be utilised for diagnosis, decision-making, treatment planning, early detection and prevention of oral disease, and finally result prediction by utilising cutting-edge technology in imaging. It shows how dentists can use it as a useful tool at various phases of clinical cases. The future of AI in dentistry appears to be outstanding with advancements in full artificial intelligence technology, dental assistance, and dental instructional tools. In order to help dental professionals better grasp AI as a tool to assist their work with enhanced efficiency, investigations need to be done to uncover patterns and foresee future related to oral health concerns.",
"keywords": [
"Artificial intelligence",
"Dental Health",
"Health",
"Wellness"
],
"content": "Introduction\n\nThe field of artificial intelligence (AI) has seen development & growth over past few decades. There are multiple examples of AI, most common would be Chat GPT, Alexa, google maps, autocorrect and text editors, search engine recommendation algorithms, e-payments, virtual travel booking agent, social media monitoring, gaming, self-driving cars, adaptive cruise control, parking assistance, retinal scans and fingerprint scans for biometrics. The purpose of this article is to provide information about the application of artificial intelligence in the field of dentistry that is currently available.1\n\nThe phrase “artificial intelligence” was first used by John McCarthy in 1955.2 AI is a branch of applied computer science that endows machines with the ability to mimic intelligent human behaviour.3 An alternate paradigm of limited AI in healthcare, augmented intelligence (AuI), was introduced by the American Medical Association (2018),4 emphasising its support and supplementary function to medical professionals. AuI is increasingly being employed in the dental industry to support clinical and administrative tasks, as a tool to help the clinician complete a task.5\n\nThe U.S. Food and Drug Administration (FDA) certified the first robotic surgery system in the country, known as “Yomi,” for dental implant surgery in 2017. Administrative workflows, image analysis, robotic surgery, virtual assistants, and clinical decision support will be the most important AI and AuI applications in the healthcare sector, according to Forbes.6 A 2018 report by Accenture, also included cybersecurity, dose error reduction, and connected machinery. The important domains being connected, according to a 2019 McKinsey report, include cognitive devices, targeted and personalised medicine, robotics-assisted surgery, and electroceuticals The laboratory side of dentistry has been utilising AI/AuI technology for the past 20 years, with the development of chairside scanning along with chairside design and milling of final restorations.7\n\nPhysical and virtual AI are both available for the delivery of general healthcare. Physical applications include automatic robotic arms or sophisticated robots.8 Most AI uses are virtual, such software-like algorithms that assist dentists in making clinical decisions. The two main categories of virtual AI approaches are knowledge-based AI and data-driven AI.9\n\nAI is built vertically from self-disclosed concepts used by people to solve problems in an effort to mimic human understanding.\n\nThe starting point for machine learning (ML), also known as data-driven AI, is the training of mathematical models utilising data generated by human actions. IBM defines ML as a branch of AI and computer science which focuses on the use of data and algorithms to imitate the way that humans learn, gradually and automatically improving its accuracy.10\n\nThere are three types of data-driven learning: supervised, unsupervised, and semisupervised. On the supervised platform, algorithms learn the correlations between data instances and labels using manually labelled training data sets, producing the desired and known results. In Supervised learning, ML algorithms used are Support vector machines (SVMs), decision tree (DT), random forest (RF), and artificial neural networks (ANNs).11\n\nAlgorithms are given unlabeled data in unsupervised learning, where they must recognise hidden data patterns that researchers may not have thought of as yet, producing unknown results. Principal component analysis and k-means clustering are common methods used in unsupervised learning.12\n\nSemisupervised learning creates the predictive model by learning from a sizable set of unlabeled training examples and a constrained set of labelled training examples.13\n\nDeep learning (DL), also known as Deep Neural Networks, is a subset of Machine Learning. Image classification, detection, and segmentation have all been accomplished using deep learning. In a medical setting, function of DL might take a variety of clinical data as input and return proof for a certain medical condition.11\n\nSo far the most popular and successful DL architecture in dentistry is convolutional neural networks (CNN) for image analysis. They combine spatial data and picture configuration from 2D and 3D photos. CNNs are frequently employed in medical applications, such as drug research, diagnosis, treatment, and related procedures.14\n\nIntelligent document processing (IDP) and natural language processing (NLP) use AI/AuI to recognise concepts in written and spoken language, record these concepts as digital data elements, and interact with system users in natural language. The term “cognitive computing” describes the practise of simulating human thought processes using computer technology. Deep learning is used by computer vision to identify patterns in images and videos.\n\nClinical decision support (CDS) tools and technologies assist clinical teams by taking over some tedious activities, alerting them to potential issues, or making recommendations that the clinical team and patient should take into account. Typically, a training dataset consists of a number of dental pictures, such as intraoral radiographs.15\n\nValidation datasets are obtained by testing against a dataset of test cases, that serve as the industry's gold standard. After an algorithm is created using the training dataset and validation dataset, the testing dataset may be used to verify the algorithm’s ability to perform on new data. For supervised learning approaches, the accuracy of the training set's classification is referred to as ground truth (also known as gold standard classification). This is used to support or refute research hypotheses in statistical models. Accuracy of measurement and comprehensiveness are dependent on the expertise, instruments, and timing of the clinician.\n\n\nMethods\n\nA total of 59 papers from an electronic search using Google Scholar and PubMed were used to create this narrative review.\n\n\nResults\n\nA clinician's evaluation of a patient's symptoms, results of diagnostic tests, and other data are used to make a diagnosis for a particular ailment. The clinical outcomes will be more precise and effective with the integration of AI into the current dentistry clinical workflow.16 Computerised interpretations may be based only on radiologic image analysis or may integrate data from past, present, and future laboratory and clinical findings.\n\nThe type I data, such as radiographic results or cytopathologic images, is the focus of the prospective clinical use of AI/AuI in dentomaxillofacial radiologic imaging.\n\nAI's clinical promise depends on its capacity to identify important anatomical structures by labelling and/or segmenting them. The parotid gland, mandibular canal, interdigitated tongue muscles, and nerves are a few examples. While the discrepancy between expert measurement of anatomic location and AI-based segmentation is only in the millimetre range,17 it is nonetheless significant in case of structures like neurovascular canals,if missed could result in serious surgical difficulties.\n\nAccording to Yilmaz et al18 SVM in cone beam computed tomography (CBCT) has demonstrated accuracy in separating periapical cysts from keratocystic odontogenic tumours. Interpreting radiologic disease signs, such as calculus identification, marginal discrepancies, apical periodontal inflammation, detection of odontogenic cysts, tumours, as well as screening for possible diseases including osteoporosis.\n\nIt has also been demonstrated that AI/AuI techniques can help with early oral cancer identification.19 The benefit is that it may contribute to lowering the mortality rate linked to delayed or missed diagnosis. ML-based predictive models including all patient performance variables,for oral cancer prognosis have been developed, A brush biopsy and cytology-based risk classification model created using ML techniques like SVM and RF. In order to predict occult nodal metastases, decision forest, SVM, and gradient boosting algorithms were used.20 Of the algorithms DT, SVM, decision forest, and naive Bayes in predicting loco regional recurrence of squamous cell carcinoma; these algorithms beat a current clinical model that solely relied on tumour invasion depth.21 Moreoral robotic surgery has gathered a lot of attention for oropharyngeal cancer surgery.22\n\nClinical data-driven decision trees assist in deciding which imaging test is best to perform in order to determine whether surgery is necessary, the type of surgery that should be performed, and the results of the operation, for example in orthognathic surgery situations. After the removal of impacted mandibular third teeth, the ANN was successful in predicting facial edema. (Zhang et al. 2018).23\n\nIn order to improve the speech comprehension of oral surgery patients during postoperative rehabilitation, an ML-based voice conversion technique has been used.24 In order to enhance results following a cleft lip operation, Microsoft and Operation Smile are developing a tool that leverages AI to standardise patient before-and-after pictures.\n\nAlthough there are currently just a few uses of AI/AuI in oral and maxillofacial surgery, this may change in the future.\n\nBy including patient complaints, clinical and biochemical markers, and objective radiomic properties in training data sets and accumulating larger samples of the aforementioned data sets, a computer-assisted diagnosis technique is necessary to improve diagnostic accuracy of temporomandibular joint disorders (TMD). It is possible to identify TMD’s based on a patient's complaint and medical background. A model based on natural language processing was successful in distinguishing between diseases that mimic TMDs and actual TMDs based on the amount of words used in the patient's primary complaint and the size of the mouth opening.25 According to Shukri et al. (2019), classification of condylar morphology showed conformity using ANNs based on CBCT. Internal derangements can be correctly predicted using AI/AuI-assisted imaging. The design of nightguards employing AI/AuI-based technology in conjunction with intraoral scanning ensures that the patient bites properly.\n\nSince 1980, dental implants have been widely utilised to restore lost teeth. In order to identify the implant type in periapical and panoramic radiographs, numerous AI/augmented intelligence models have been constructed. Three AI models using panoramic and radiographic images have been proposed as trustworthy methods for assessing the success of osteointegration, as well as for optimising dental implant design and for spotting fractured dental implants.26 On most dental design software, a digital AI-based wax-up can be finished in a matter of seconds. It can help with the creation of occlusal guards and surgical guides. The chairside use of CAD/CAM is enhanced by AI integration.27 The most recent AI/AuI-based laboratory technology includes automated margin marking, case routing, and scoring.\n\nAn ablation system integrating robotics and a picosecond laser has been developed for abutment tooth preparation. The average linear ablation errors of this technology, according to in vitro studies, were just 0.06 mm for wax resin and 0.05 mm for dentin.28 However, the 3.5-hour dentin ablation time prevented its use in clinical settings. In the field of fixed prosthodontics, research on an autonomous robotic system is still in its infancy. A clinical decision support model for removable prosthodontics that uses ontology and case-based reasoning was able to suggest a design for customised removable partial dentures.29\n\nImaging combined with several AI/AuI technologies is already assisting with morphological studies, OSA classification, screening, and automated landmark documentation.6 Future applications could involve better risk detection, remote monitoring, and choosing the patient's best course of treatment.\n\nPeriodontitis varies in its distribution and severity. A periodontal probe and radiographic images are frequently used to collect information in order to establish the diagnosis, prognosis as well as the available treatment options. Radiographic bone level and clinical attachment levels (CAL) have been calculated using AI/AuI evolutions.30 The alveolar bone level on panoramic or intraoral radiographs has been measured in research using deep learning techniques. Current radiography pictures might not be sensitive enough to detect the earliest stage of bone loss, even if they are of high quality.\n\nAlthough the relationship between immunologic responses, microbial composition and the aetiology of periodontitis has not yet been fully clarified, artificial intelligence-based classifiers can distinguish between aggressive and chronic periodontitis. An SVM that focuses on the relative bacterial load is one example, as is a multilayer perceptron neural network that concentrates on leukocytes, interleukins, and IgG antibody titers.31 A validated periodontal diagnosis is aided by artificial intelligence by including conventional symptoms, immunologic, and microbiological components.\n\nA great amount of research has been done in the field of orthodontics on growth evaluation, a crucial component in choosing the best course of treatment. The use of hand-wrist radiographs and the cervical vertebrae maturation (CVM) detected on the lateral cephalogram are currently two of the most popular techniques for measuring growth.32 The classification of cervical vertebral maturation stage and vertebral body shape by ANN and DT, respectively, produced the best results.33 Using ML techniques such ANN, SVM, RF, and DT, a diagnostic model based on lateral cephalometric radiographs was developed to measure cervical vertebral maturation.34\n\nConvoluted Neural Network powered AI/AuI system analysis showed a tracing accuracy of over 90% and came to the conclusion that automated identification was more trustworthy than manual identification.35 In the future, more precise and accurate automated cephalometric analysis should be possible thanks to hybrid methodologies that combine ML and knowledge-based algorithms.\n\nAI/AuI technologies for facial analysis increase the precision of diagnosis, case formulation, and treatment planning. By identifying certain face characteristics, CNNs were able to estimate apparent age and score attractiveness.36 Scans, model design, and retainer manufacture are three areas where AI/AuI assisted technologies are revolutionising orthodontic office therapy and care practises.\n\nIn the diagnosis of orthodontic treatment needs, the Bayesian network had excellent agreement with orthodontists.37 The two potential uses of AI in orthodontics are result grading and treatment need assessment.38\n\nThe detection and diagnosis of signs including caries are frequent in dentistry. Early enamel caries detection may improve minimally invasive methods for treating early caries. From a clinical perspective, Imaging techniques such radiograph, optical coherence tomography, quantitative light-induced fluorescence, intraoral scanning, or near-infrared light transillumination are used in addition to visual-tactile detection. Dental X-rays or images from near-infrared light transillumination can be utilised to diagnose caries using deep learning and convolutional neural networks (CNNs). From near-infrared transillumination images, DL found proximal carious lesions.39 When applied to assess patient demographic, nutritional, lifestyle, and clinical data, SVM performed at its peak level.40 Predictive models based on ML methods like SVM, RF, and k-nearest neighbours were used to pinpoint those who are more prone to develop dental surface loss and root cavities.\n\nAccording to a study from 2021,41 AI-enabled sensitivity was shown to be present in enamel caries, but not in early or advanced dentin lesions. None of the dental imaging methods that are now available can tell the difference between active and halted caries. Based on an encoder-decoder architecture (U-Net), DL divided CBCT voxels into categories such as “lesion,” “tooth structure,” “bone,” “restorative materials,” and “background,” producing results that were comparable to those of medical professionals in the diagnosis of periapical lesions.42 DL with CNN has supplanted other AI components in cariology and endodontic diagnostics due to its capacity for automated lesion segmentation.43\n\nThe ability to offer unbiased baseline and follow-up measurements for remineralization is an attractive prospect for AI/AuI. AI/AuI's capability to calculate the percentage of demineralization and look at patterns may help demonstrate the validity of longitudinal data assessment over time as opposed to a one-time, cross-sectional examination. Additionally, when employing clinical pictures as a potential machine-readable source of information for diagnostic purposes, additional pathological features, such as developmental flaws or dental restorations, must also be taken into account.\n\nFor diagnosis of radiolucent jaw lesions like apical periodontitis, which affects around 75% of endodontic patients panoramic and intraoral periapical radiographs are employed.44 Dental history, clinical data, and sociodemographic information, for example, can all be connected using AI. Digital radiography, cone beam computed tomography, computer-aided diagnostics (CAD), 3D printing, and guided endodontics are the various diagnostic methods utilised in endodontics.\n\nUsing 83 features from the “Endodontic Case Difficulty Assessment Form” of the American Association of Endodontists as input, SVM and ANN were able to predict the degree of difficulty of cases requiring root canal therapy with >90% accuracy.4 This demonstrated how ML might potentially help general dentists make better decisions when referring patients to endodontists.45\n\nProbabilistic neural networks (PNN), Convoluted Neural Network and Machine Learning systems appear to be the focus of recent breakthroughs in the use of AI/AuI systems in endodontics.46 Identification - A diagnostic aid that aids in the identification of periapical lesions, crown and root fractures, the apical foramen, and the efficacy of an existing root canal filling. It is utilised to provide information on the morphology of the root and root canal systems as well as the degree of canal curvature.\n\nThree commonly used methods for evaluating root canal length are hand sensation, radiological determination, and use of an electronic apex locator. Modern technologies for locating the apical foramen include CBCT and computerised apex locators. Due to its capability to do automatic lesion segmentation, the DL with CNN has grown to be the most popular AI component utilised in endodontic diagnostics. The DL system of AI is also used to assess the root canal morphology. The ANN diagnosis method results in a better radiographic estimation of working length and helps to enhance diagnosis. Both intact and non-intact teeth, that have undergone endodontic treatment can benefit from the use of CBCT in the diagnosis of vertical root fractures (VRF). Campo et al47 described the case-based reasoning (CBR) paradigm to reasonably estimate nonsurgical endodontic retreatment outcomes and the advantages and dangers. AI is being utilised to forecast stem cell viability and the results of endodontic retreatment.\n\nIn order to distinguish oral lichen planus from other white lesions of the oral mucosa,48 found that the expression of the inflammatory cytokine genes ANN, SVM, and RF can be used. By spotting steatosis (i.e., abnormal retention of lipids) of the salivary gland parenchyma in ultrasound pictures, ANN was found to be more effective at differentiating between people with xerostomia and those with true Sjögren's syndrome.49\n\nClinical assessments, patient dental histories, and interpretation of diagnostic radiographs are used for preventive restoration treatment. The intention is to discover and measure the radiographic extent of caries in order to possibly establish the least invasive and most efficient course of treatment. It can also help in the early discovery of issues such as dental impaction, congenitally missing teeth, ectopic eruption, ankylosis of a primary tooth, loss of space inside the dental arch, and other atypical dental morphology.\n\nClassifier and predictive AI models, which explore connections between clinical symptom-related features and patient data, assist in identifying risk factors and forecasting long-term consequences of dental illnesse. A patient list that comprises the patient's ongoing needs and health details can be scheduled by AI. If patient records are made public, it could be able to anticipate patient-specific drug problems. AI could aid in diagnosis, staging, and outcome prediction.6\n\nA multilayer perceptron neural network successfully predicted tooth mobility and the durability of resin composite restorations based on the characteristics of the patients. According to Yamaguchi et al50 CNNs were successful in accurately predicting the likelihood of de-bonding of CAD/CAM resin composite crowns. A prediction model combining ANN could be used in the future to assess regenerative dentistry methods in a simulated inflammatory microenvironment. Great sensitivity in detecting oral malignant (93%) and high-grade prospective malignant (73%) lesions by using CNN to score the malignancy of cytology pictures acquired from a telemedicine platform.9\n\nApplications of virtual AI hold enormous promise for streamlining clinical procedures. They have been instrumental in the growth of precision dentistry.\n\n\nLimitations of Artificial Intelligence in Dentistry\n\nThe inability to represent internal decision-making processes, the limitations of classical computing, the disregard for moral principles in the design of AI frameworks, the lack of data curation, sharing, and readability are all potential obstacles that could prevent the routine implementation of AI.\n\nLimitations such inadequate data sharing and curation,51 a lack of knowledge about data processing, measurement, and validation.52\n\nInterpretability is significant for two reasons. First, check to see if the algorithm makes sense in terms of how humans and technology interact. Second, because there is a lack of transparency and interpretability, it is difficult to predict failures and generalise specific techniques for situations that are comparable.53\n\nProcessing power must always be upgraded for AI applications. In comparison to conventional methods, quantum computing processes are tenfold faster.54 Quantum computing is a great platform for accelerating ML,55 from algorithms to data collecting and modelling due to its capacity to process data concurrently from widely diverse data sets.\n\nAccording to Currie G,56 the doctor is responsible for each patient and how the data is used. AI is not accountable whether it is deployed in a supervised or unsupervised environment. Determining legal obligation raises an ethical dilemma. When the distinction between human responsibility and AI-based diagnosis based on chatbots is becoming increasingly blurry, it is irrational to impose the same social and ethical criteria that apply to people.57 Ethical contradictions show the need for clear guidelines on how AI should be applied in healthcare settings.\n\nWhen AI/AuI technologies are integrated into EDR, other criteria, including security, privacy, trust, quality, safety, and data standardisation, will ultimately determine the validity and utility of these dental technologies. Additionally, consumers should anticipate having access to their EDR digital data, including images, in the near future as required by the federal laws regarding information blocking included in the 21st Century Cures Act.\n\nThere are questions over whether AI will ever replace dentists.\n\nThe knowledge of dentists is required for higher-level comprehension since machines cannot provide clinical intuition, intangible perception, or empathy, which are necessary for providing customised healthcare and professionalism. Modern AI excels in two areas: the utilisation of codified knowledge and the extraction of understanding from vast amounts of data.6 It cannot build associations, though, and in a therapeutic situation, it is only partially capable of making complex decisions. It is impossible to directly transform the most exciting part of human-to-human conversation into computer language.\n\nThe development of AI and dental education should go hand in hand. When patients cannot access quick dental care, teledentistry offers a more modern technique that could help them manage oral problems.58 Images taken on cellphones are helpful tools when information are gathered through distant dialogues or internet platforms to assess the clinical conditions. Furthermore, a lot of dental clinics have digital records of their patients, and these already-existing photos might help the physician with diagnosis and treatment planning. It may also be used to keep track of treatment compliance and development.\n\nImage quality and quality analysis are predicted to significantly increase as a result of artefact reduction, low-dose imaging, and automated analysis of 2D and 3D image datasets to identify artefacts and technical errors and less radiation exposure. Over time, the suppliers' selections of visualisations, designs, or essential tools will evolve. It is advantageous for the laboratory industry to integrate AI/AUI based technology into their ecosystem because of the benefits of consistency, repeatability, cost savings, time, and enhanced intelligence.\n\nBy developing a comprehensive open-access standard data set that contains information on demographics, clinical trials, and treatments, thereby increasing the amount, quality, and readability of data by standardising data curation and reporting technique, Dental professionals will have access to more organised documentation alternatives and evidence-based guidelines.\n\n\nConclusions\n\nAI is quickly evolving and has applications in diagnosis, therapy, and prognosis. AI could be used as an augmentation tool by dental practitioners to assist them in performing more valuable tasks, such as integrating patient data and improving professional interactions.59 AI is recognised as a useful tool for dentists, despite the difficulties that must be overcome in terms of data collecting, interpretation, computing capacity, and ethical issues.\n\nWith careful design and extensive clinical validation, AI may be user-friendly, transparent, repeatable, and impartial. Future AI development should continue to put the needs of people first while enhancing its capacity to handle massive amounts of data.\n\nIn order to support human-technology rapport and ensure AI'S affirmative development, which will revolutionise dentistry practise, it is imperative to have a proactive attitude towards AI.",
"appendix": "Data availability\n\nReporting guidelines\n\nFigshare. A BRIEF EXPLORATION OF ARTIFICIAL INTELLIGENCE IN DENTAL HEALTHCARE.xlsx\n\nDOI: https://doi.org/10.6084/m9.figshare.23803026\n\nThis project contains the following underlying data\n\n• A BRIEF EXPLORATION OF ARTIFICIAL INTELLIGENCE IN DENTAL HEALTHCARE.xlsx (Details of included studies in the present narrative review)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 Public domain dedication).\n\n\nReferences\n\nAgrawal P, Nikhade P: Artificial Intelligence in Dentistry: Past, Present, and Future. Cureus. 2022 Jul 28; 14(7): e27405. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRajaraman V: JohnMcCarthy—Father of artificial intelligence. Resonance. 2014; 19: 198–207. Publisher Full Text\n\nXu Y, et al.: Artificial intelligence: A powerful paradigm for scientific research. 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}
|
[
{
"id": "253468",
"date": "27 Mar 2024",
"name": "Hao Ding",
"expertise": [
"Reviewer Expertise Digital Dentistry",
"Dental Materials"
],
"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,\nThe aim of this study is to provide readers with a general overview of the current state of artificial intelligence (AI) in dentistry. As AI is still rapidly evolving, an updated review on the subject matter is welcomed. The topic is interesting and will be useful for dental clinicians, computer engineers, and other interested parties. While the topic fits within the scope of the journal, there are some concerns that need to be addressed. Please see my comments below:\nGeneral Comments: 1. Given that there have been many review articles published in this field, I would suggest acknowledging existing review articles in the field and discussing the emphasis of the current review. 2. Consider combining some of the short paragraphs to improve the flow of the manuscript.\nAbstract: 1. Consider revising the Abstract. The first paragraph contains too much information that is not related to dental AI, while the third and fourth paragraphs about dental AI are too brief. 2. Move the sentence \"This review article attempts to highlight these points and lays emphasis on how AI is driving dentistry in the present and will improve dental care in the future\" to the end of the abstract.\nIntroduction: 1. In the third paragraph of the Introduction, it would be clearer if the authors can clarify that robotic surgery is not considered as AI, as they are two different concepts.\nMethods: 1. The Methods section appears to be too brief. I recommend adding information such as the keywords used, selection criteria employed, publication year range, and other relevant details when searching for reference articles.\nResults: 1. I personally think it would be more appropriate to change the subtitle from \"Results\" to \"Discussion\". As for a review paper, a discussion section is needed to synthesize all the information retrieved from the literature search into comprehensive paragraphs. This is where readers should find the information they are looking for in one location. 2. I suggest merging the \"Limitations of Artificial Intelligence in Dentistry\" section into the discussion part to simplify the structure of the manuscript. 3. I recommend including tables of information to make it easier for readers to access and understand the review. The tables can include specific AI tasks, input data types and dataset sizes, types of algorithms used, and results of the studies. 4. It would be beneficial to include studies on Generative AI in dentistry.\nThank you for considering these comments. I believe that addressing these concerns will strengthen the scientific quality of your manuscript.\nBest regards, Ding Hao\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? 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": []
}
] | 1
|
https://f1000research.com/articles/13-37
|
https://f1000research.com/articles/12-449/v1
|
27 Apr 23
|
{
"type": "Research Article",
"title": "The effect of canal curvature on cyclic fatigue resistance of rotary instruments using different irrigation materials (in vitro study)",
"authors": [
"Mohammed Hamoudi Alsunboli",
"Sally Saad Ali Ihsan",
"Duha Qais Sabah",
"Sally Saad Ali Ihsan",
"Duha Qais Sabah"
],
"abstract": "Background: The mechanical qualities of Ni-Ti is crucial because they give the files their flexibility and enable us to prepare curved and double-curved canals with more ease. It happens frequently for instruments to separate during canal preparation, and cyclic fatigue (metal fatigue) is a frequent cause. This study aimed to assess how irrigation affected the two rotary endodontic instruments' cyclic fatigue resistance. Methods: The Edge File and Fanta File rotary endodontic instrument groups were chosen. Each group (n = 42) was split into 3 subgroups (n = 14 each), one receiving NaOH, one Glycine, and one EDTA treatment. The number of cycles to failure (NCF) was determined after each subgroup underwent testing for cyclic fatigue resistance. Results: The result appeared different significant between the two group and sub-group with the different materials that used with it with the length of fractures and time that recorded in each group. Conclusion: NaOCl, glycine, and EDTA as chemical materials appeared to have considerably varied cycle fatigue resistance for various lengths of fractures and durations, according to the comparison between the two evaluated instruments.",
"keywords": [
"cyclic fatigue",
"rotation",
"fracture",
"M wire",
"autoclave",
"irrigation",
"curve canal"
],
"content": "Introduction\n\nThe success of endodontic therapy is associated with the cleansing and shape of the root system, which is impacted by mechanical elements such the preparation system and preparation process. The effectiveness of chemical agents with irrigation solutions in tissue solution, germination, and residue removal is covered next (Estrela et al., 2003).\n\nThe amount of flexing a rotary endodontic tool experiences when placed inside of an angulated root canal determines how long it will last before becoming fatigued. A torsional fracture occurs when the instrument shaft is still rotating when the endodontic file's tip or a piece of it is lodged inside a canal. In this case, the metal's elastic limits are exceeded, causing plastic deformation and finally fracture (Berutti et al., 2012a).\n\nIn contemporary endodontic, NiTi rotary devices are utilized without exception to shape root canals (Torabinejad and Walton, 2009). Compared to standard stainless steel files, they are more flexible and have better cutting efficiency (Schafer et al., 2004). Because of their extreme flexibility, producing the desired tapering root canal form is simple and has a lower tendency to cause canal transportation (Chen and Messer, 2002). Despite these benefits, NiTi instruments are prone to separation (Arens et al., 2003), which is primarily caused by wear and torsional shear forces (Varela-Patino et al., 2010; Berutti et al., 2012b). As would happen during rotating instrumentation in a curved canal, cyclic fatigue happens when an instrument is repeatedly subjected to cycles of compression and tension (Chen and Messer, 2002).\n\nOperational speed, metal surface treatment, and metallurgical characterization of the NiTi alloys are only a few of the variables that have been studied as potential influences on the fatigue resistance of NiTi rotary files (Gambarini et al., 2008).\n\nDue to flexural loads and cyclic fatigue, canal curvature is thought to be the main cause of instrument failure (Hulsmann et al., 2005). Corrosion that could happen in the presence of an irrigating solution is another issue that could reduce resistance to fatigue fracture (Sonntag and Heithecker, 2006). The current gold standard for tissue disintegration and disinfection is the irrigation of root canals with NaOCl and EDTA (Torabinejad and Walton, 2009). When NiTi instruments are used to instrument a root canal, they come into contact with irrigating solutions.\n\nAs a result, corrosion patterns that involve the selective removal of nickel from the surface can result in micro pitting, which compromises the instrument's structural integrity. Very little can be done by the clinician to stop or lessen such stresses (Berutti et al., 2012a). This study aims to assess the impact of irrigation on the two rotary endodontic devices' cyclic fatigue resistance.\n\n\nMethods\n\nThe Edge File (0.25/0.6) and Fanta file (0.25/0.6) groups of rotary endodontic instruments, respectively, were chosen. There were three subgroups total (n = 14) for each group (n = 42).\n\nSubgroup1 = treated with glycerin\n\nSubgroup2 = treated with EDTA\n\nSubgroup3 = treated with sodium hypochlorite.\n\nDue to the vast diversity of canal shapes present in real teeth, the cyclic fatigue test cannot be performed with natural teeth consistently.\n\nThis study was conducted in artificial canals made of tapered stainless steel that was created especially for the purpose. These synthetic canals have regular (60°) curvature angles and 5 mm radius of curvature and 1.5 mm width of coronal portion of canal gradually decrease to 1 mm at its end (Plotino and others, 2009).\n\nThe block was created in accordance with the files' specifications, and testing was done at the rotary system's manufacturer-recommended, according to fanta and edge system speed of 500 Rpm with a 2.5 N torque manipulating setting. The file tip, which has been set to its full working length, is now (Bhagabati et al., 2012) 7 mm from the center of the simulated curvature (19 mm). The working area is 25 mm long and the entire set of files is brand-new. The file was rotated freely during cyclic fatigue tests inside the artificial canal's tapered section, which produced a reproducible simulation of the file restrained in the canal's curved section (Schneider, 1971).\n\nTo make manipulating the hand-piece movement and the simple insertion of each file into the artificial canal possible, the dental hand-piece was mounted on a wooden block. This enabled uniform file depth placement and three-dimensional alignment. A transparent plastic sheet was placed over the artificial canal to stop the files from slipping out and to allow the researcher to observe the files as they were utilized and when a fracture developed. As a result, the fracture could be seen because the files could be seen through the transparent plastic sheet window (Plotino et al., 2010).\n\nIn the past, the wooden block was fastened to the stainless steel block in order to stop the wooden block from moving and to keep the relationship between the steel block and the hand-piece nearly constant (Yılmaz et al., 2017).\n\nTo reduce heat generation and friction, glycerin has been completely packed inside the artificial canal before each file was cut to the proper size (19 mm). Using the (ENDOMAX PLUS) cordless endodontic hand-piece, the files were triggered inside the canals. In order to improve productivity and reduce human mistake, video recording has been done concurrently (Bhagabati et al., 2012). Every file's (NCF) is described by this equation.\n\n“Number of cycles to failure NCF = Speed RPM X Time (T) to fracture in minute” The armamentarium used in this study are show in Figure 1.\n\nAfter being removed from the solutions, each file was rinsed with bi-distilled water to counteract the effects of NaOCl, dried, given an ID number, and stored in glass vials.\n\nThen, using a mechanical device created expressly for the job and capable of simulating the conditions of an instrument encased in a curved canal, instruments from all three groups and each brand were put through cyclic fatigue testing. (Grande et al. 2006; Plotino et al. 2009).\n\nThe apparatus was connected to the same dynamic immersion programs and motor set. This made it possible for the endodontic instruments to freely reciprocate and maintain constant pressure inside a stainless steel artificial channel. To make the artificial canal, the instrument's dimensions and taper were reproduced. When the file made contact with the canal walls in the simulated canal, a special high-flow synthetic lubricant (Super Oil; Singer Co Ltd, Elizabethport, NJ, USA) was sprayed into the canal to lessen friction. The time to fracture (TtF) for each instrument, measured in seconds from the start of the test until the point of breakage, was recorded and registered using a chronometer to the nearest whole number. The TtF was the dependent variable, whereas the type of files used and the immersion conditions were independent factors.\n\nThe Statistical Analysis System - SAS (2018) application was used to determine the effects of various factors on the research parameters. The least significant difference (LSD) test was used in this investigation to compare the means in a significant manner (ANOVA).\n\n\nResults\n\nDescriptive statistics of TtF for each file is summarized in Tables 1 and 2.\n\n* P ≤ 0.05.\n\n** P ≤ 0.01.\n\n** P ≤ 0.01.\n\nIn Table 1, we notice different significant differences in the effect of three materials on the edge file, which appeared a high significant differences for the material EDTA, then NaOH, then Glycerin in respectively, while there are no significant differences of the chemical materials on the Fanta file. While in Table 2 we notice very high significant differences between the effect of glycerin and the other two types of chemical materials, while appeared no significant differences between the two chemical materials when compared with each other on the two types of files.\n\nAverages that carry different letters in Tables 1 and 2 are significantly different, and averages that carry similar letters do not differ significantly. The highest average takes the letter A and so on downwards. If you find an average that takes two letters like ab, this is no different neither from the average that carries a nor from the average that carries b. as appeared in Figures 2 and 3.\n\n\nDiscussion\n\nDespite great improvements in NiTi instrument design and technology, the failure of NiTi instruments during root canal therapy continues to be a significant problem since these instruments are prone to fracture without visible symptoms of prior permanent distortion. Even with the creation of new endodontic instrument generations based on various manufacturing processes, instrument fracture is still a possibility.\n\nEvery file system must be disinfected for infection control before being used again, and while performing their functions, instruments are exposed to commonly used irrigants like NaOCl because the canals were filled with the irrigant during instrumentation. Even though various research has been conducted to assess the cyclic fatigue resistance of different file systems, autoclaving and exposure of file systems during operation may have varied effects on the properties of various file systems. As a result, in the current work, multiple file systems based on diverse manufacturing technologies have been contrasted for cyclic fatigue resistance after exposure to NaOCl, glycine, and EDTA.\n\nThe purpose of this study is to assess how irrigation affects the two rotary endodontic instruments' resistance to cyclic fatigue. A chemically active irrigation solution is used when clinically shaping curved root canals. Surface interactions between the file and canal walls during this process could lead to corrosion or surface roughness, which could then result in fissures and finally cyclic fatigue of the file (Hasegawa et al., 2014).\n\nSome researchers used the pre-immersion of NiTi files in an irrigation solution while others tested the files for cyclic fatigue in synthetic oil as a method of evaluating the fatigue failure process (Pedullà et al., 2014). The interaction between the file and the irrigation solutions while the file is rotating in the irrigation solution is not considered by this design. In additional studies, the files were evaluated in an irrigation solution bath (Elnaghy and Elsaka, 2017). However, the relationship between the file and the canal walls was not considered.\n\nThe files were tested while rotating in a curved glass tube filled with the irrigation fluid as part of the current study's specially created apparatus, which duplicates the clinical settings. To prevent galvanic corrosion from happening during testing in metal to or in contact with metal pins, as was stated in the previous research, a heat-resistant curved glass tube was employed (Shen et al., 2012). Glass tubes, which are not found in natural teeth, may have several drawbacks that come from chemical reactions with various irrigation solutions and should not be extrapolated clinically.\n\nTheoretically, employing aqueous media will allow the heat generated by friction to evaporate and gradually lengthen the fatigue lifetime of NiTi files. However, the current study's findings, which are in agreement with some reports (Shen et al., 2012; Hasegawa et al., 2014; Pedullà et al., 2011) and disagreement with others, show that the NCF of instruments tested in dry conditions without lubricant or coolant was significantly different from those tested in EDTA, Glycine, and NaOCl groups (Berutti et al., 2006; Elnaghy and Elsaka, 2017; Peters et al., 2007). These contradictory results could be the consequence of one of two factors.\n\nThe first is that these aqueous solutions may hurtan an adverse effect on cyclic fatigue due to their propensity to produce corrosion and the roughness of the NiTi alloy surface. As a result, the fatigue life did not improve. The second factor is that fatigue testing occurred in a location with minimal cyclic fatigue. Regarding the first factor, prior studies indicated that immersion in NaOCl and EDTA could result in file corrosion (Berutti et al., 2006; Peters et al., 2007).\n\nHowever, in these studies, the file and shank were fully submerged for a long period of time, which led to galvanic corrosion, which is clinically inapplicable. Recent studies, which concur with the present findings, have shown that immersion does not, on the other hand, promote corrosion (Shen et al., 2012; Pedullà et al., 2011) or exhibit any adverse impact on cyclic fatigue even with an increased surface roughness of the files.\n\nThe second theory appears more believable. The NCF in the existing configuration was in the low-cyclic fatigue range (Cheung et al., 2007; Tobushi et al., 1997). This amount of time is insufficient to demonstrate how the various circumstances interact. When the number of cycles fell within the low-cyclic fatigue life, Shen et al. (2012) showed no difference in NCF between the NCF of various files in dry conditions and a bath of irrigation solutions including Glycine, EDTA, and NaOCl. In contrast to dry conditions, liquid media has shown improvement in cycle fatigue in long fatigue life. In the landmark study by Tobushi et al. (1997), the researchers discovered that in areas of mild tiredness, there was no difference between wet and dry environments.\n\nSimilarly, to this, Pedullà et al. (2014) demonstrated that submerging NiTi files in EDTA and NaOCl had no detrimental effects on the NCF. On the other hand, testing WaveOne Gold in the air revealed better fatigue resistanceto fatigue compared to aqueous media, according to Elnaghy and Elsaka (2017). The methodology, instrument design, and type of motion employed may all be to fault for the inconsistent outcomes.\n\nThe degree of curvature is another element that could obscure the effect of irrigation solutions on cycle fatigue. It is understood that a file moving through a steep curve experiences a significant strain amplitude, hastening the failure process (Cheung et al., 2007). A 60° curvature was used in the existing configuration. As a result, there wasn't enough time to demonstrate how a different environment (a low-fatigue region) affected things.\n\nHasegawa et al. (2014) revealed that when evaluated in a 60° curved environment, three separate files examined in various conditions had similar NCF results. When the files were examined under a 30° arc of curvature, water increased the NFC of the files, but a different NFC was recorded. So, it stands to reason that aqueous solution performance would be greater with longer testing periods.\n\nIt's interesting to note that two fracture sites in the NaOCl group spread toward the file's center after being launched from opposing cutting edges. This might be connected to surface roughness, which could serve as a site for crack propagation. Thus, many cracks might account for the group's lower cycle count. The short testing period is the study's main drawback. The impact of irrigation solutions in areas with high cyclic fatigue should be evaluated. Additionally, analyzing the frictional forces that each solution generates and how they might affect the NCF may be helpful.\n\n\nConclusion\n\nThe comparison between the two instruments that were tested revealed that NaOCl, glycine, and EDTA as chemical materials appeared to have noticeably different cycle fatigue resistance for various lengths of fractures and timeframes. The cyclic fatigue of NiTi files may be impacted by the irrigation environment. Chemical materials enhanced file NCF. However, due to the brief testing period (low-cyclic fatigue region), all other settings did not demonstrate any differences. Since cyclic fatigue takes far longer to develop than it does to shape actual teeth, the results of this in vitro study should not be directly applied to clinical situations. So, it's important to proceed carefully when drawing clinical conclusions. However, further research is required to fully understand the various variables that can impact an instrument's cyclic fatigue resistance, fracture modes, and novel apparatus designs that share more properties with root dentine. Further research is therefore required to support the results of the current study.\n\n\nContributor role\n\nConceptualization: Mohammed Hamoudi Alsunboli\n\nData Curation: Sally Saad Ali Ihsan\n\nFormal Analysis: Sally Saad Ali Ihsan\n\nFunding Acquisition: Mohammed Hamoudi Alsunboli\n\nInvestigation: Duha Qais Sabah\n\nMethodology: Duha Qais Sabah\n\nProject Administration: Sally Saad Ali Ihsan\n\nResources: Mohammed Hamoudi Alsunboli\n\nSoftware: Duha Qais Sabah\n\nSupervision: Duha Qais Sabah\n\nValidation: Mohammed Hamoudi Alsunboli\n\nVisualization: all authors\n\nWriting – Original Draft Preparation: all authors\n\nWriting – Review & Editing: all authors",
"appendix": "Data availability\n\nZenodo. Basic data that show effect of irrigation on the cyclic fatigue resistance of the two rotary endodontic instruments. DOI: https://doi.org/10.5281/zenodo.7600416. (Alsunboli, 2023).\n\nThis project contains the following underlying data:\n\n‐ Edge file with glycerin\n\n‐ Edge file with EDTA\n\n‐ Edge file with sodium hypochlorite\n\n‐ Fanta file WITH glycerin\n\n‐ Fanta file with EDTA\n\n‐ Fanta file with sodium hypochlorite\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\nAlsunboli MH: Basic data that show effect of irrigation on the cyclic fatigue resistance of the two rotary endodontic instruments. Zenodo. 2023. Publisher Full Text\n\nArens FC, Hoen MM, Steiman HR, et al.: Evaluation of single-use rotary nickel-titanium instruments. J. Endod. 2003; 29: 664–666. PubMed Abstract | Publisher Full Text\n\nBerutti E, Angelini E, Rigolone M, et al.: Influence of sodium hypochlorite on fracture properties and corrosion of proTaper rotary instruments. Int. Endod. J. 2006; 39: 693–699. PubMed Abstract | Publisher Full Text\n\nBerutti E, Chiandussi G, Paolino DS, et al.: Canal shaping with WaveOne reciprocating files and Pro Taper system: a comparative study. J. Endod. 2012a; 38: 505–509. PubMed Abstract | Publisher Full Text\n\nBerutti E, Paolino DS, Chiandussi G, et al.: Root canal anatomy preservation of WaveOne reciprocating files with or without glyde path. J. Endod. 2012b; 38: 101–104.\n\nBhagabati N, Yadav S, Talwar S: An in vitro cyclic fatigue analysis of different endodontic nickel-titanium rotary instruments. J. Endod. 2012; 38: 515–518. PubMed Abstract | Publisher Full Text\n\nChen JL, Messer HH: A comparison of stainless steel hand and rotary nickel- titanium instrumentation using a silicone impression technique. Aust. Dent. J. 2002; 47: 12–20. PubMed Abstract | Publisher Full Text\n\nCheung G, Ko DH, Chung S, et al.: Fatigue testing of a NiTi rotary instrument. Part 2: Fractographic analysis. Int. Endod. J. 2007; 40: 619–625. PubMed Abstract | Publisher Full Text\n\nElnaghy AM, Elsaka SE: Effect of sodium hypochlorite and saline on cyclic fatigue resistance of WaveOne Gold and Reciproc reciprocating instruments. Int. Endod. J. 2017; 50: 991–998. PubMed Abstract | Publisher Full Text\n\nEstrela CR, Estrela C, Reis C, et al.: Control of microorganisms in vitro by endodontic irrigants. Braz. Dent. J. 2003; 14(3): 187–192. Publisher Full Text\n\nGambarini G, Grande NM, Plotino G, et al.: Fatigue resistance of engine-driven rotary nickel–titanium instruments produced by new manufacturing methods. J. Endod. 2008; 34: 1003–1005. PubMed Abstract | Publisher Full Text\n\nGrande NM, Plotino G, Pecci R, et al.: Cyclic fatigue resistance and three-dimensional analysis of instruments from two nickel-titanium rotary systems. Int. Endod. J. 2006; 39(10): 755–763. PubMed Abstract | Publisher Full Text\n\nHasegawa Y, Goto S, Ogura H: Effect of EDTA solution on corrosion fatigue of Ni-Ti files with different shapes. Dent. Mater. J. 2014; 33: 415–421. PubMed Abstract | Publisher Full Text\n\nHulsmann M, Peters OA, Dummer PMH: Mechanical preparation of root canals: shaping goals, techniques and means. Endod. Top. 2005; 10: 30–76. Publisher Full Text\n\nPedullà E, Franciosi G, Ounsi HF, et al.: Cyclic fatigue resistance of nickel-titanium instruments after immersion in irrigant solutions with or without surfactants. J. Endod. 2014; 40: 1245–1249. Publisher Full Text\n\nPedullà E, Grande NM, Plotino G, et al.: Cyclic fatigue resistance of three different nickel-titanium instruments after immersion in sodium hypochlorite. J. Endod. 2011; 37: 1139–1142. PubMed Abstract | Publisher Full Text\n\nPeters OA, Roehlike JO, Baumann MA: Effect of immersion in sodium hypochlorite on torque and fatigue resistance of nickel-titanium instruments. J. Endod. 2007; 33: 589–593. PubMed Abstract | Publisher Full Text\n\nPlotino G, Grande NM, Cordaro M, et al.: A review of cyclic fatigue testing of nickel-titanium rotary instruments. J. Endod. 2009; 35: 1469–1476. PubMed Abstract | Publisher Full Text\n\nPlotino G, Grande NM, Melo MC, et al.: Cyclic fatigue of NiTi rotary instruments in a simulated apical abrupt curvature. Int. Enndodont. J. 2010; 43: 226–230. PubMed Abstract | Publisher Full Text\n\nSAS: Statistical Analysis System, User's Guide. Statistical. Version 9. 1st ed.Cary. N.C. USA: SAS. Inst. Inc.; 2018.\n\nSchafer E, Schulz-Bongert U, Tulus G: Comparison of hand stainless steel and nickel titanium rotary instrumentation: a clinical study. J. Endod. 2004; 30: 432–435. PubMed Abstract | Publisher Full Text\n\nSchneider SW: A comparison of canal preparations in straight and curved root canals. Oral Surg. Oral Med. Oral Pathol. 1971; 32(2): 271–275. Publisher Full Text\n\nShen Y, Qian W, Abtin H, et al.: Effect of environment on fatigue failure of controlled memory wire nickel-titanium rotary instruments. J. Endod. 2012; 38: 376–380. PubMed Abstract | Publisher Full Text\n\nSonntag D, Heithecker K: Korrosion von Nickel-Titan-Instrumenten. Endodontie. 2006; 15: 23–30.\n\nTobushi H, Hachisuka T, Yamada S, et al.: Rotating-bending fatigue of a TiNi shape-memory alloy wire. Mech. Mater. 1997; 26: 35–42. Publisher Full Text\n\nTorabinejad M, Walton RE: Endodontics: principles and practice. 4th edn.St. Louis, Missouri; 2009.\n\nVarela-Patino P, Ibanez-Parraga A, Rivas-Mundina B, et al.: Alternating versus continuous rotation: a comparative study of the effect on instrument life. J. Endod. 2010; 36: 157–159. PubMed Abstract | Publisher Full Text\n\nYılmaz K, Uslu G, Özyürek T: In vitro comparison of the cyclic fatigue resistance of HyFlex EDM, One G, and ProGlider nickel titanium glide path instruments in single and double curvature canals. Restorative Dent. Endodont. 2017; 42: 282–289. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "208798",
"date": "13 Oct 2023",
"name": "Ahmed Sleibi Mustafa",
"expertise": [
"Reviewer Expertise Restorative",
"minimally invasive dentistry",
"root caries",
"endodontics",
"fixed prosthesis",
"dental materials",
"dental caries."
],
"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 effect of canal curvature on cyclic fatigue resistance of rotary instruments using different irrigation materials (in vitro study)\nThe subject of study is of clinical value in the field of endodontics since the strategy of root canal cleaning nowadays is a combination of both mechanical and chemical actions. Please find my comments:\nIntroduction\nThe 1st paragraph should be edited to highlight the rationality of the research. The references need to be updated.\n\nI am not sure why the authors mention the \"torsional fracture\" in the 2nd paragraph while the study assessed the cyclic fatigue? This is also the same for the next paragraph.\n\nIn the last, the sentence paragraph \"Very little can be done by the clinician to stop or lessen such stresses\" should be revised. The aim also needs to be expand to include types of rotary instrument, irrigation types and assessment method. Also, the words \"in curved canals\" should be added to the aim of the study.\n\nMethods\nThe sentence \"The Edge File (0.25/0.6) and Fanta file (0.25/0.6) groups of rotary endodontic instruments, respectively, were chosen. There were three subgroups total (n = 14) for each group (n = 42).\" should be changed to \" Two different types of rotary endodontic instruments in this study were assessed including Edge File (0.25/0.6) and Fanta file (0.25/0.6) (n=42 each). Each group was divided into 3 subgroups (n=14 each) with respect to irrigation type. Also, it is good to add a table showing the main features of rotary files including company details, speed, torque, .....etc. Please do the same for the irrigation solution.\n\nThe sentence “The file tip, which has been set to its full working length, is now (Bhagabati et al., 2012) 7 mm from the center of the simulated curvature (19 mm). The working area is 25 mm long and the entire set of files is brand-new. The file was rotated freely during cyclic fatigue tests inside the artificial canal's tapered section, which produced a reproducible simulation of the file restrained in the canal's curved section (Schneider, 1971).” need to be revised.\n\nThe sentence “In the past, the wooden block was fastened to the stainless steel block in order to stop the wooden block from moving and to keep the relationship between the steel block and the hand-piece nearly constant (Yılmaz et al., 2017).” Looks related to previous work. Please either connect to the present work or delete.\n\nIn the paragraph “To reduce heat generation and friction, glycerin ……..” the authors didn’t clarify whether they put glycerin for all groups or just the glycerin group.\nResults\nEdit the 1st line “Descriptive statistics of TtF for each file is summarized in Tables 1 and “ to include also the inferential statistics since the table contains LSD comparison.\n\nThe type of statistical analysis for the comparison between the three types of irrigation of each group is not clear. Please edit to clarify.\n\nThe sig difference between groups should be clarified to know which group is higher than the other.\n\nWhat does the author mean by “takes the letter A “ in the last paragraph of the result?\n\nDiscussion\n2nd paragraph, the “multiple file systems…” should be edited to “two different file systems…..”.\n\nIn the 3rd paragraph, its better to include a result summary of the current study instead of the previous study.\n\nThe 4th paragraph looks confusing, particularly the last two paragraphs, please edit to clarify.\n\nOverall, the discussion requires more critical appraisal in relation to the study outcomes.\n\nConclusion\nThe conclusion part needs to be edited to focus on the main outcomes. The sentence “Chemical materials enhanced file NCF” looks confusing.\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": "10965",
"date": "13 Apr 2024",
"name": "Susan F. K. Alsudani",
"role": "Author Response",
"response": "Thank you Dr.Ahmed Sleibi for yout time to this valuable notes i corrected as shown in highlighted. the effect of canal curvature on cyclic fatigue resistance of rotary instruments using different irrigation materials (in vitro study) The subject of study is of clinical value in the field of endodontics since the strategy of root canal cleaning nowadays is a combination of both mechanical and chemical actions. Please find my comments: Introduction comment 1: The 1st paragraph should be edited to highlight the rationality of the research. The references need to be updated. Answer / Nowadays, there is increased use of the term “modern endodontics” to refer to contemporary applied science and actual materials that have been introduced and invented in recent years. Diverse endodontic tools and technological devices have been designed to facilitate and enhance treatments(1) Wong, J.; Cheung, G.S.P.; Lee, A.H.C.; McGrath, C.; Neelakantan, P. PROMs following Root Canal Treatment and Surgical Endodontic Treatment. Int. Dent. J. 2023, 73, 28–41. Comment 2 : I am not sure why the authors mention the \"torsional fracture\" in the 2nd paragraph while the study assessed the cyclic fatigue? This is also the same for the next paragraph. Answer: this part is Change to A cyclic fatigue occurs when the instrument shaft is still rotating when the endodontic file's tip or a piece of it is lodged inside a canal. In this case, the metal's elastic limits are exceeded, causing plastic deformation and finally fracture (Berutti et al., 2012a). Comment 3: In the last, the sentence paragraph \"Very little can be done by the clinician to stop or lessen such stresses\" should be revised. The aim also needs to be expand to include types of rotary instrument, irrigation types and assessment method. Also, the words \"in curved canals\" should be added to the aim of the study. Answer \\ Aim of study: This study aimed to assess how irrigation affected the two rotary endodontic instruments' cyclic fatigue resistance in a curve canals . Methods Comment 1 : The sentence \"The Edge File (0.25/0.6) and Fanta file (0.25/0.6) groups of rotary endodontic instruments, respectively, were chosen. There were three subgroups total (n = 14) for each group (n = 42).\" should be changed to \" Two different types of rotary endodontic instruments in this study were assessed including Edge File (0.25/0.6) and Fanta file (0.25/0.6) (n=42 each). Each group was divided into 3 subgroups (n=14 each) with respect to irrigation type. Also, it is good to add a table showing the main features of rotary files including company details, speed, torque, .....etc. Please do the same for the irrigation solution. Answer \\ (The Edge File (0.25/0.6) and Fanta file (0.25/0.6) groups of rotary endodontic instruments, respectively, were chosen. There were three subgroups total (n = 14) for each group (n = 42).) Change to \" Two different types of rotary endodontic instruments in this study were assessed including Edge File (0.25/0.6) and Fanta file (0.25/0.6) (n=42 each). Each group was divided into 3 subgroups (n=14 each) with respect to irrigation type Comment 2: The sentence “The file tip, which has been set to its full working length, is now (Bhagabati et al., 2012) 7 mm from the center of the simulated curvature (19 mm). The working area is 25 mm long and the entire set of files is brand-new. The file was rotated freely during cyclic fatigue tests inside the artificial canal's tapered section, which produced a reproducible simulation of the file restrained in the canal's curved section (Schneider, 1971).” need to be revised. Answer \\ The sentence “The file tip, which has been set to its full working length, is now (Bhagabati et al., 2012) 7 mm from the center of the simulated curvature (19 mm). The file was rotated freely during cyclic fatigue tests inside the artificial canal's tapered section, which produced a reproducible simulation of the file restrained in the canal's curved section (Schneider, 1971) Comment 3: The sentence “In the past, the wooden block was fastened to the stainless steel block in order to stop the wooden block from moving and to keep the relationship between the steel block and the hand-piece nearly constant (Yılmaz et al., 2017).” Looks related to previous work. Please either connect to the present work or delete. A\\ it will be deleted Comment 4: In the paragraph “To reduce heat generation and friction, glycerin ……..” the authors didn’t clarify whether they put glycerin for all groups or just the glycerin group. Answer\\ To reduce heat generation and friction, glycerin has been completely packed inside the artificial canal before each file was cut to the proper size (19 mm). Using the (ENDOMAX PLUS) cordless endodontic hand-piece, the files were triggered inside the canals Change to Glycerin has been completely packed in the subgroup 1 for each type of file inside the artificial canal before each file was cut to the proper size (19 mm) To reduce heat generation and friction. Using the (ENDOMAX PLUS) cordless endodontic hand-piece, the files were triggered inside the canals Results Comment 1 : Edit the 1st line “Descriptive statistics of TtF for each file is summarized in Tables 1 and “ to include also the inferential statistics since the table contains LSD comparison. Answer \\ “Descriptive statistics of TtF for each file is summarized in Tables 1 and 2 “ Chane to Descriptive statistics and inferential statistics of TtF for each file is summarized in Tables 1 and 2 “ Comment 2 : The type of statistical analysis for the comparison between the three types of irrigation of each group is not clear. Please edit to clarify. Answer \\ it is shown in the figure 2 and 3 effect of three materials on the edge file, which appeared a high significant differences in the length of fracture for the material EDTA, then NaOH, then Glycerin in respectively, comment 3: The sig difference between groups should be clarified to know which group is higher than the other. we notice different significant differences in the effect of three materials on the edge file, which appeared a high significant differences for the material EDTA, then NaOH, then Glycerin in respectively, while there are no significant differences of the chemical materials on the Fanta file. While In the table (2), we notice very high significant differences between the effect of glycerin and the other two types of chemical materials, while appeared no significant differences between the two chemical materials when compared with each other on the two types of files. Comment 4 What does the author mean by “takes the letter A “ in the last paragraph of the result? Answer \\ Means with different big letters in the same column and small letters in the same row are significantly different , Discussion Comment 1 : 2nd paragraph, the “multiple file systems…” should be edited to “two different file systems…..”. Answer \\ even though various research has been conducted to assess the cyclic fatigue resistance of different file systems Cnange to even though various research has been conducted to assess the cyclic fatigue resistance of two different file systems comment 2: In the 3rd paragraph, its better to include a result summary of the current study instead of the previous study. answer : The purpose of this study is to assess how irrigation affects the two rotary endodontic instruments' resistance to cyclic fatigue. A chemically active irrigation …….. comment 3 : The 4th paragraph looks confusing, particularly the last two paragraphs, please edit to clarify. It's interesting to note that two fracture sites in the NaOCl group spread toward the file's center after being launched from opposing cutting edges. This might be connected to surface roughness, which could serve as a site for crack propagation. Thus, many cracks might account for the group's lower cycle count. The short testing period is the study's main drawback. The impact of irrigation solutions in areas with high cyclic fatigue should be evaluated. Additionally, analyzing the frictional forces that each solution generates and how they might affect the NCF may be helpful. The paragraph change to It's interesting to note that two fracture sites in the NaOCl group spread toward the file's center after being launched from opposing cutting edges. This might be connected to surface roughness, which could serve as a site for crack propagation. Thus, many cracks might account for the group's lower cycle count.. Additionally, analyzing the frictional forces that each solution generates and how they might affect the NCF may be helpful. Conclusion The conclusion part needs to be edited to focus on the main outcomes. The sentence “Chemical materials enhanced file NCF” looks confusing. It will change to : The comparison between the two instruments that were tested revealed that NaOCl, glycine, and EDTA as chemical materials appeared to have noticeably different cycle fatigue resistance for various lengths of fractures and timeframes. The cyclic fatigue of NiTi files may be impacted by the irrigation environment. Chemical materials enhanced file strength…."
}
]
},
{
"id": "223746",
"date": "23 Dec 2023",
"name": "Shehabeldin Saber",
"expertise": [
"Reviewer Expertise Endodontics",
"Cell culture"
],
"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- The manuscript need major language /grammar revision. - It is not clear if this was a static or a dynamic test. - limitations of the study should be added to the discussion section and should mention that the test was not done under oral temperatures and how would this affect the results (refer to Cyclic Fatigue Resistance of Three Heat-Treated Nickel-Titanium Instruments at Simulated Body Temperature. Saudi Endodontic Journal. 2020, 10(2), 131-136. 10.4103/sej.sej_122_19), and not having a dynamic model with simultaneous rotation and reciprocation (refer to https://doi.org/10.32067/GIE.2021.35.02.58) - The suggested articles are references for the limitations of the study that should be mentioned, which are\nThe test temperature The dynamic model\n\n- SEM examination of the fractured segments would give insights for the chemical effect of the used solutions on the metallurgic micro structure\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?\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": "11094",
"date": "08 May 2024",
"name": "Susan F. K. Alsudani",
"role": "Author Response",
"response": "thank you Dr. Shehabeldin Saber for these valuable comments its static test and I do it in a bath of 37 Cº I make grammar revisions for all articles and add your notes with highlighting thank you Abstract Background: The mechanical qualities of Ni Ti are crucial because they give the files their flexibility and enable us to prepare curved and double-curved canals with more ease. It happens frequently for instruments to separate during canal preparation, and cyclic fatigue (metal fatigue) is a frequent cause. Aim of study: This study aimed to assess how irrigation affected the two rotary endodontic instruments' cyclic fatigue resistance. Methods: The Edge File and Fanta File rotary endodontic instrument groups were chosen. Each group (n = 42) was split into 3 subgroups (n = 14 each), one receiving NaOH, one Glycine, and one EDTA treatment. The number of cycles to failure (NCF) was determined after each subgroup underwent testing for cyclic fatigue resistance. Results: The result appeared different significant between the two group and sub group with the different materials that used with it with the length of fractures and time that recorded in each group. Conclusion: NaOCl, glycine, and EDTA as chemical materials appeared to have considerably varied cycle fatigue resistance for various lengths of fractures and durations, according to the comparison between the two evaluated instruments. Keywords: cyclic fatigue, rotation, fracture, M wire, autoclave, irrigation, curve canal Introduction The success of endodontic therapy is associated with the cleansing and shape of the root system, which is impacted by mechanical elements such the preparation system and preparation process. The effectiveness of chemical agents with irrigation solutions in tissue solution, germination, and residue removal is covered next. (Estrela et al.,2003). The durability of a rotary endodontic tool inside an angulated root canal is determined by the extent of flexing it experiences, influencing its longevity before succumbing to fatigue. A torsional fracture arises when the instrument shaft still rotates with the endodontic file's tip, or a fragment of it, lodged within a canal. In such cases, the metal surpasses its elastic limits, resulting in plastic deformation and eventual fracture (Berutti et al., 2012). In modern endodontics, NiTi rotary devices universally shape root canals (Torabinejad and Walton, 2009). They exhibit superior flexibility and cutting efficiency compared to standard stainless steel files (Schafer et al., 2004). The remarkable flexibility simplifies achieving the desired tapering root canal form with a reduced risk of canal transportation (Chen and Messer, 2002). Despite these advantages, NiTi instruments are susceptible to separation (Arens et al., 2003), primarily due to wear and torsional shear forces (Varela-Patino et al., 2010; Berutti et al., 2012). Cyclic fatigue occurs during rotating instrumentation in a curved canal, subjecting the instrument to repeated cycles of compression and tension (Chen and Messer, 2002). Operational speed, metal surface treatment, and metallurgical characterization of NiTi alloys are among the variables studied for potential influences on the fatigue resistance of NiTi rotary files (Gambarini et al., 2008). Canal curvature, attributed to flexural loads and cyclic fatigue, is considered the primary cause of instrument failure (Hulsmann et al., 2005). Corrosion in the presence of an irrigating solution is another factor that may diminish resistance to fatigue fracture (Sonntag and Heithecker, 2006). The gold standard for tissue disintegration and disinfection involves irrigating root canals with NaOCl and EDTA (Torabinejad and Walton, 2009). NiTi instruments, when used in root canal instrumentation, come into contact with these irrigating solutions. Consequently, corrosion patterns, involving the selective removal of nickel from the surface, may lead to micro pitting, compromising the structural integrity of the instrument. Clinicians have limited options to mitigate such stresses (Berutti et al., 2012). This study aims to evaluate the impact of irrigation on the cyclic fatigue resistance of two rotary endodontic devices. Material and Methods For this study, the Edge File (0.25/0.6) and Fanta file (0.25/0.6) groups of rotary endodontic instruments were selected. Each group comprised three subgroups, resulting in a total of 42 samples (n = 42), with 14 samples in each subgroup. The subgroups were designated as follows: Subgroup 1: Treated with glycerin Subgroup 2: Treated with EDTA Subgroup 3: Treated with sodium hypochlorite Considering the diverse canal shapes found in natural teeth, conducting cyclic fatigue tests consistently with natural teeth is impractical. This study employed artificial canals constructed from fixed tapered stainless steel. These canals were placed in a water bath at 37ºC, specifically designed for this research. The synthetic canals featured regular (60º) curvature angles, a 5mm radius of curvature, and a gradual reduction in the width of the coronal portion from 1.5mm to 1mm at its end (Plotino and others, 2009). The testing followed the manufacturer-recommended settings for the rotary system (500 Rpm, 2.5 N torque) for both Fanta and Edge systems. The file tip, set to its full working length, was positioned 5-7mm from the center of the simulated curvature (19mm). The working area spanned 25mm, and all files were new. The cyclic fatigue tests involved rotating the file as static rest freely inside the tapered section of the artificial canal, simulating the file's restraint in the canal's curved section (Schneider, 1971). To facilitate hand-piece movement and file insertion, the dental hand-piece was mounted on a wooden block, ensuring uniform file depth placement and three-dimensional alignment. A transparent plastic sheet prevented file slippage and allowed researchers to observe file usage and fracture development. The wooden block was secured to the stainless steel block to minimize movement (Yılmaz et al., 2017). Glycerin was used to reduce heat and friction, packed inside the artificial canal before each file's insertion. The files were activated inside the canals using the cordless endodontic hand-piece (ENDOMAX PLUS), with concurrent video recording to enhance productivity and reduce errors (Bhagabati et al., 2012). The number of cycles to failure (NCF) was described by the equation: \"NCF = Speed (RPM) X Time (T) to fracture in minutes.\" The study's armamentarium is depicted in Fig(1) A B C Fig (1): The armamentarium used in this study After being removed from the solutions, each file was rinsed with bi-distilled water to counteract the effects of NaOCl, dried, given an ID number, and stored in glass vials. Then, using a mechanical device created expressly for the job and capable of simulating the conditions of an instrument encased in a curved canal, instruments from all three groups and each brand were put through cyclic fatigue testing. (Grande et al. 2006, Plotino et al. 2009). The apparatus was connected to the same dynamic immersion programs and motor set. This made it possible for the endodontic instruments to freely reciprocate and maintain constant pressure inside a stainless steel artificial channel. To make the artificial canal, the instrument's dimensions and taper were reproduced. When the file made contact with the canal walls in the simulated canal, a special high-flow synthetic lubricant (Super Oil; Singer Co Ltd, Elizabethport, NJ, USA) was sprayed into the canal to lessen friction. The time to fracture (TtF) for each instrument, measured in seconds from the start of the test until the point of breakage, was recorded and registered using a chronometer to the nearest whole number. The TtF was the dependent variable, whereas the type of files used and the immersion conditions were independent factors. Statistical Analysis: The Statistical Analysis System- SAS (2018) application was used to determine the effects of various factors on the research parameters. The least significant difference (LSD) test was used in this investigation to compare the means in a significant manner (ANOVA). Results Descriptive statistics of TtF for the each file are summarized in Table (1 and 2). Table 1: Effect of type of File and chemical materials in Length of Chemical materials Mean ± SE of Length of fracture LSD P-value Edge file Fanta file Glycerin 3.02 ±0.17 C b 3.65 ±0.16 A a 0.490 * 0.0136 EDTA 4.74 ±0.11 A a 3.45 ±0.09 A b 0.304 ** 0.0001 Sodium hypo-chloride 3.73 ±0.12 B a 3.28 ±0.16 A b 0.421 * 0.0371 LSD 0.397 ** 0.413 NS --- P-value 0.0001 0.199 Means with different big letters in the same column and small letters in the same row are significantly different , * (P≤0.05), ** (P≤0.01). Table 2: Effect of type of File and chemical materials in Time Chemical materials Mean ± SE of Time (sec.) LSD P-value Edge file Fanta file Glycerin 8.85 ±0.32 A a 4.48 ±0.14 A b 0.725 ** 0.0001 EDTA 5.61 ±0.29 B a 3.70 ±0.22 B b 0.764 ** 0.0001 Sodium hypo-chloride 5.45 ±0.09 B a 3.63 ±0.24 B b 0.543 ** 0.0001 LSD 0.741 ** 0.598 ** --- P-value 0.0001 0.010 Means with different big letters in the same column and small letters in the same row are significantly different , ** (P≤0.01). In the table (1), we notice different significant differences in the effect of three materials on the edge file, which appeared a high significant differences for the material EDTA, then NaOH, then Glycerin in respectively, while there are no significant differences of the chemical materials on the Fanta file. While In the table (2), we notice very high significant differences between the effect of glycerin and the other two types of chemical materials, while appeared no significant differences between the two chemical materials when compared with each other on the two types of files. Note:- Averages that carry different letters in table (1 and 2) are significantly different, and averages that carry similar letters do not differ significantly. The highest average takes the letter a and so on downwards. If you find an average that takes two letters like ab, this is no different neither from the average that carries a nor from the average that carries b. as appeared in figure (2 and 3) Link to Figure 2 Figure (2) the effect of types of file and chemical material on length of fractures Link to Figure 3 Figure (3) the effect of types of file and chemical material on time Discussion Despite considerable advancements in NiTi instrument design and technology, the persistence of NiTi instrument failure during root canal therapy remains a significant issue. These instruments are prone to fracture without apparent symptoms of permanent distortion. Even with the development of new endodontic instrument generations employing various manufacturing processes, the possibility of instrument fracture still exists. Every file system must undergo disinfection for infection control before reuse. While performing their functions, instruments are exposed to commonly used irrigants such as NaOCl, which fills the canals during instrumentation. Although various research efforts have assessed the cyclic fatigue resistance of different file systems, the effects of autoclaving and exposure during operation on various file systems' properties may vary. Consequently, this study contrasts multiple file systems, utilizing diverse manufacturing technologies, for cyclic fatigue resistance after exposure to NaOCl, glycine, and EDTA. The study aims to evaluate how irrigation affects the resistance to cyclic fatigue of two rotary endodontic instruments. Chemically active irrigation solutions are used during the clinical shaping of curved root canals. Surface interactions between the file and canal walls during this process could lead to corrosion or surface roughness, potentially resulting in fissures and cyclic fatigue of the file (Hasegawa et al., 2014). Various researchers have employed different methods, including pre-immersion of NiTi files in an irrigation solution or testing files for cyclic fatigue in synthetic oil, to evaluate the fatigue failure process (Pedulla et al., 2014). The interaction between the file and the irrigation solutions while the file is rotating in the irrigation solution is not taken into account by this design. In additional studies, the files were evaluated in an irrigation solution bath (Elnaghy and Elsaka, 2017). However, the relationship between the file and the canal walls was not taken into account. The files were tested while rotating in a curved glass tube filled with the irrigation fluid as part of the current study's specially created apparatus, which duplicates the clinical settings. To prevent galvanic corrosion from happening during testing in metal to or in contact with metal pins, as was stated in the previous research, a heat-resistant curved glass tube was employed (Shen et al., 2012). Glass tubes, which are not found in natural teeth, may have several drawbacks that come from chemical reactions with various irrigation solutions and should not be extrapolated clinically. Theoretically, employing aqueous media will allow the heat generated by friction to evaporate and gradually lengthen the fatigue lifetime of NiTi files. However, the current study's findings, which are in agreement with some reports (Shen et al., 2012; Hasegawa et al., 2014; Pedulla et al., 2011) and disagreement with others, show that the NCF of instruments tested in dry conditions without lubricant or coolant was significantly different from those tested in EDTA, Glycine, and NaOCl groups (Berutti et al., 2006; Elnaghy and Elsaka, 2017; Peters et al., 2007) These contradictory results could be the consequence of one of two factors. The first is that these aqueous solutions may hurtan an adverse effect on cyclic fatigue due to their propensity to produce corrosion and the roughness of the NiTi alloy surface. As a result, the fatigue life did not improve. The second factor is that fatigue testing occurred in a location with minimal cyclic fatigue. Regarding the first factor, prior studies indicated that immersion in NaOCl and EDTA could result in file corrosion (Berutti et al., 2006; Peter et al., 2007). However, in these studies, the file and shank were fully submerged for a long period of time, which led to galvanic corrosion, which is clinically inapplicable. Recent studies, which concur with the present findings, have shown that immersion does not, on the other hand, promote corrosion (Shen et al., 2012; Pedulla et al., 2011) or exhibit any adverse impact on cyclic fatigue even with an increased surface roughness of the files. The second theory appears more believable. The NCF in the existing configuration was in the low-cyclic fatigue range (Cheung et al., 2007; Tobushi et al., 1997). This amount of time is insufficient to demonstrate how the various circumstances interact. When the number of cycles fell within the low-cyclic fatigue life, Shen et al. (2012) showed no difference in NCF between the NCF of various files in dry conditions and a bath of irrigation solutions including Glycine, EDTA, and NaOCl. In contrast to dry conditions, liquid media has shown improvement in cycle fatigue in long fatigue life. In the landmark study by Tobushi et al. (1997), the researchers discovered that in areas of mild tiredness, there was no difference between wet and dry environments. Similarly to this, Pedullà et al. (2014) demonstrated that submerging NiTi files in EDTA and NaOCl had no detrimental effects on the NCF. On the other hand, testing WaveOne Gold in the air revealed better fatigue resistanceto fatigue compared to aqueous media, according to Elnaghy and Elsaka (2017). The methodology, instrument design, and type of motion employed may all be to fault for the inconsistent outcomes. The degree of curvature is another element that could obscure the effect of irrigation solutions on cycle fatigue. It is understood that a file moving through a steep curve experiences a significant strain amplitude, hastening the failure process (Cheung et al., 2007). A 60° curvature was used in the existing configuration. As a result, there wasn't enough time to demonstrate how a different environment (a low-fatigue region) affected things. Hasegawa et al. (2014) revealed that when evaluated in a 60° curved environment, three separate files examined in various conditions had similar NCF results. When the files were examined under a 30° arc of curvature, water increased the NFC of the files, but a different NFC was recorded. So it stands to reason that aqueous solution performance would be greater with longer testing periods. It's interesting to note that two fracture sites in the NaOCl group spread toward the file's center after being launched from opposing cutting edges. This might be connected to surface roughness, which could serve as a site for crack propagation. Thus, many cracks might account for the group's lower cycle count. The short testing period is the study's main drawback. The impact of irrigation solutions in areas with high cyclic fatigue should be evaluated. Additionally, analyzing the frictional forces that each solution generates and how they might affect the NCF may be helpful. Conclusion The comparison between the two instruments that were tested revealed that NaOCl, glycine, and EDTA, as chemical materials, exhibited noticeably different cyclic fatigue resistance for various lengths of fractures and timeframes. The cyclic fatigue of NiTi files may be influenced by the irrigation environment. Chemical materials enhanced the files' Number of Cycles to Failure (NCF). However, due to the brief testing period (in the low-cyclic fatigue region), all other settings did not show any differences. Since cyclic fatigue takes much longer to develop than shaping actual teeth, the results of this in vitro study should not be directly applied to clinical situations. Therefore, caution is essential when drawing clinical conclusions. Nevertheless, further research is necessary to fully understand the various variables that can impact an instrument's cyclic fatigue resistance, fracture modes, and novel apparatus designs that share more properties with root dentine. Additional research is, therefore, required to validate and support the results of the current study."
}
]
},
{
"id": "223743",
"date": "28 Dec 2023",
"name": "Mohamed Jamal",
"expertise": [
"Reviewer Expertise Instrument testing",
"stem cell research and CBCT in endodontics."
],
"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 revision needed\n\nIntroduction\nAdd short paragraphs describing the tested files: EdgeEndo and Fanta files. Methods: Needs major revisions as it not very clear how the experiments were conducted. Here are few comments: 1. Group designation and specimen preparation: It’s important to discuss the following: sample size calculation, how the instrument where submerged, the percentage of the irrigation solutions used, time of submerging the files in the solutions and temperature of the solutions. 2.Cyclic fatigue testing: Full explanation of the experimental device and method of recording the results. 3. The test was conducted in static mode rather than the recommended dynamic mode which is the model that is more similar to clinical conditions in which rotary files are used. 4. Unclear which method was used to calculate the results (NCF or TtF). It’s stated that the files were rotated and NCF calculated then files were used in reciprocation motion and TtF calculated. 5. Please add the name of the devices that were used to measure time and fracture fragment length.\n\nDiscussion Discuss the impact of the fracture fragment length and why it was investigated in the study.\n\nRevise language, grammar and syntax\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?\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": [
{
"c_id": "10966",
"date": "13 Apr 2024",
"name": "Susan F. K. Alsudani",
"role": "Author Response",
"response": "thank you Dr. Rashid ElAbed for these valuable comments I make grammar revisions for all articles and add your notes with highlighting thank you The effect of canal curvature on cyclic fatigue resistance of rotary instruments using different irrigation materials ( in vitro study) Mohammed Hamoudi Alsunboli1* , Sally Saad Ali Ihsan2* , Duha Qais Sabah3* *Al-Bayan University , College of Dentistry 1- m.hamoudi@albayan.edu.iq, 2- sally.saad@albayan.edu.iq,3- dhuha.q@albayan.edu.iq. Abstract Background: The mechanical qualities of Ni Ti are crucial because they give the files their flexibility and enable us to prepare curved and double-curved canals with more ease. It happens frequently for instruments to separate during canal preparation, and cyclic fatigue (metal fatigue) is a frequent cause. Aim of study: This study aimed to assess how irrigation affected the two rotary endodontic instruments' cyclic fatigue resistance. Methods: The Edge File and Fanta File rotary endodontic instrument groups were chosen. Each group (n = 42) was split into 3 subgroups (n = 14 each), one receiving NaOH, one Glycine, and one EDTA treatment. The number of cycles to failure (NCF) was determined after each subgroup underwent testing for cyclic fatigue resistance. Results: The result appeared different significant between the two group and sub group with the different materials that used with it with the length of fractures and time that recorded in each group. Conclusion: NaOCl, glycine, and EDTA as chemical materials appeared to have considerably varied cycle fatigue resistance for various lengths of fractures and durations, according to the comparison between the two evaluated instruments. Keywords: cyclic fatigue, rotation, fracture, M wire, autoclave, irrigation, curve canal Introduction The success of endodontic therapy is associated with the cleansing and shape of the root system, which is impacted by mechanical elements such the preparation system and preparation process. The effectiveness of chemical agents with irrigation solutions in tissue solution, germination, and residue removal is covered next. (Estrela et al.,2003). The durability of a rotary endodontic tool inside an angulated root canal is determined by the extent of flexing it experiences, influencing its longevity before succumbing to fatigue. A torsional fracture arises when the instrument shaft still rotates with the endodontic file's tip, or a fragment of it, lodged within a canal. In such cases, the metal surpasses its elastic limits, resulting in plastic deformation and eventual fracture (Berutti et al., 2012). In modern endodontics, NiTi rotary devices universally shape root canals (Torabinejad and Walton, 2009). They exhibit superior flexibility and cutting efficiency compared to standard stainless steel files (Schafer et al., 2004). The remarkable flexibility simplifies achieving the desired tapering root canal form with a reduced risk of canal transportation (Chen and Messer, 2002). Despite these advantages, NiTi instruments are susceptible to separation (Arens et al., 2003), primarily due to wear and torsional shear forces (Varela-Patino et al., 2010; Berutti et al., 2012). Cyclic fatigue occurs during rotating instrumentation in a curved canal, subjecting the instrument to repeated cycles of compression and tension (Chen and Messer, 2002). Operational speed, metal surface treatment, and metallurgical characterization of NiTi alloys are among the variables studied for potential influences on the fatigue resistance of NiTi rotary files (Gambarini et al., 2008). Canal curvature, attributed to flexural loads and cyclic fatigue, is considered the primary cause of instrument failure (Hulsmann et al., 2005). Corrosion in the presence of an irrigating solution is another factor that may diminish resistance to fatigue fracture (Sonntag and Heithecker, 2006). The gold standard for tissue disintegration and disinfection involves irrigating root canals with NaOCl and EDTA (Torabinejad and Walton, 2009). NiTi instruments, when used in root canal instrumentation, come into contact with these irrigating solutions. Consequently, corrosion patterns, involving the selective removal of nickel from the surface, may lead to micro pitting, compromising the structural integrity of the instrument. Clinicians have limited options to mitigate such stresses (Berutti et al., 2012). This study aims to evaluate the impact of irrigation on the cyclic fatigue resistance of two rotary endodontic devices. Material and Methods For this study, the Edge File (0.25/0.6) and Fanta file (0.25/0.6) groups of rotary endodontic instruments were selected. Each group comprised three subgroups, resulting in a total of 42 samples (n = 42), with 14 samples in each subgroup. The subgroups were designated as follows: Subgroup 1: Treated with glycerin Subgroup 2: Treated with EDTA Subgroup 3: Treated with sodium hypochlorite Considering the diverse canal shapes found in natural teeth, conducting cyclic fatigue tests consistently with natural teeth is impractical. This study employed artificial canals constructed from fixed tapered stainless steel. These canals were placed in a water bath at 37ºC, specifically designed for this research. The synthetic canals featured regular (60º) curvature angles, a 5mm radius of curvature, and a gradual reduction in the width of the coronal portion from 1.5mm to 1mm at its end (Plotino and others, 2009). The testing followed the manufacturer-recommended settings for the rotary system (500 Rpm, 2.5 N torque) for both Fanta and Edge systems. The file tip, set to its full working length, was positioned 5-7mm from the center of the simulated curvature (19mm). The working area spanned 25mm, and all files were new. The cyclic fatigue tests involved rotating the file as static rest freely inside the tapered section of the artificial canal, simulating the file's restraint in the canal's curved section (Schneider, 1971). To facilitate hand-piece movement and file insertion, the dental hand-piece was mounted on a wooden block, ensuring uniform file depth placement and three-dimensional alignment. A transparent plastic sheet prevented file slippage and allowed researchers to observe file usage and fracture development. The wooden block was secured to the stainless steel block to minimize movement (Yılmaz et al., 2017). Glycerin was used to reduce heat and friction, packed inside the artificial canal before each file's insertion. The files were activated inside the canals using the cordless endodontic hand-piece (ENDOMAX PLUS), with concurrent video recording to enhance productivity and reduce errors (Bhagabati et al., 2012). The number of cycles to failure (NCF) was described by the equation: \"NCF = Speed (RPM) X Time (T) to fracture in minutes.\" The study's armamentarium is depicted in Fig(1) Fig (1): The armamentarium used in this study After being removed from the solutions, each file was rinsed with bi-distilled water to counteract the effects of NaOCl, dried, given an ID number, and stored in glass vials. Then, using a mechanical device created expressly for the job and capable of simulating the conditions of an instrument encased in a curved canal, instruments from all three groups and each brand were put through cyclic fatigue testing. (Grande et al. 2006, Plotino et al. 2009). The apparatus was connected to the same dynamic immersion programs and motor set. This made it possible for the endodontic instruments to freely reciprocate and maintain constant pressure inside a stainless steel artificial channel. To make the artificial canal, the instrument's dimensions and taper were reproduced. When the file made contact with the canal walls in the simulated canal, a special high-flow synthetic lubricant (Super Oil; Singer Co Ltd, Elizabethport, NJ, USA) was sprayed into the canal to lessen friction. The time to fracture (TtF) for each instrument, measured in seconds from the start of the test until the point of breakage, was recorded and registered using a chronometer to the nearest whole number. The TtF was the dependent variable, whereas the type of files used and the immersion conditions were independent factors. Statistical Analysis: The Statistical Analysis System- SAS (2018) application was used to determine the effects of various factors on the research parameters. The least significant difference (LSD) test was used in this investigation to compare the means in a significant manner (ANOVA). Results Descriptive statistics of TtF for the each file are summarized in Table (1 and 2). Table 1: Effect of type of File and chemical materials in Length of Chemical materials Mean ± SE of Length of fracture LSD P-value Edge file Fanta file Glycerin 3.02 ±0.17 C b 3.65 ±0.16 A a 0.490 * 0.0136 EDTA 4.74 ±0.11 A a 3.45 ±0.09 A b 0.304 ** 0.0001 Sodium hypo-chloride 3.73 ±0.12 B a 3.28 ±0.16 A b 0.421 * 0.0371 LSD 0.397 ** 0.413 NS --- P-value 0.0001 0.199 Means with different big letters in the same column and small letters in the same row are significantly different , * (P≤0.05), ** (P≤0.01). Table 2: Effect of type of File and chemical materials in Time Chemical materials Mean ± SE of Time (sec.) LSD P-value Edge file Fanta file Glycerin 8.85 ±0.32 A a 4.48 ±0.14 A b 0.725 ** 0.0001 EDTA 5.61 ±0.29 B a 3.70 ±0.22 B b 0.764 ** 0.0001 Sodium hypo-chloride 5.45 ±0.09 B a 3.63 ±0.24 B b 0.543 ** 0.0001 LSD 0.741 ** 0.598 ** --- P-value 0.0001 0.010 Means with different big letters in the same column and small letters in the same row are significantly different , ** (P≤0.01). In the table (1), we notice different significant differences in the effect of three materials on the edge file, which appeared a high significant differences for the material EDTA, then NaOH, then Glycerin in respectively, while there are no significant differences of the chemical materials on the Fanta file. While In the table (2), we notice very high significant differences between the effect of glycerin and the other two types of chemical materials, while appeared no significant differences between the two chemical materials when compared with each other on the two types of files. Note:- Averages that carry different letters in table (1 and 2) are significantly different, and averages that carry similar letters do not differ significantly. The highest average takes the letter a and so on downwards. If you find an average that takes two letters like ab, this is no different neither from the average that carries a nor from the average that carries b. as appeared in figure (2 and 3) Figure (2) the effect of types of file and chemical material on length of fractures Figure (3) the effect of types of file and chemical material on time Discussion Despite considerable advancements in NiTi instrument design and technology, the persistence of NiTi instrument failure during root canal therapy remains a significant issue. These instruments are prone to fracture without apparent symptoms of permanent distortion. Even with the development of new endodontic instrument generations employing various manufacturing processes, the possibility of instrument fracture still exists. Every file system must undergo disinfection for infection control before reuse. While performing their functions, instruments are exposed to commonly used irrigants such as NaOCl, which fills the canals during instrumentation. Although various research efforts have assessed the cyclic fatigue resistance of different file systems, the effects of autoclaving and exposure during operation on various file systems' properties may vary. Consequently, this study contrasts multiple file systems, utilizing diverse manufacturing technologies, for cyclic fatigue resistance after exposure to NaOCl, glycine, and EDTA. The study aims to evaluate how irrigation affects the resistance to cyclic fatigue of two rotary endodontic instruments. Chemically active irrigation solutions are used during the clinical shaping of curved root canals. Surface interactions between the file and canal walls during this process could lead to corrosion or surface roughness, potentially resulting in fissures and cyclic fatigue of the file (Hasegawa et al., 2014). Various researchers have employed different methods, including pre-immersion of NiTi files in an irrigation solution or testing files for cyclic fatigue in synthetic oil, to evaluate the fatigue failure process (Pedulla et al., 2014). The interaction between the file and the irrigation solutions while the file is rotating in the irrigation solution is not taken into account by this design. In additional studies, the files were evaluated in an irrigation solution bath (Elnaghy and Elsaka, 2017). However, the relationship between the file and the canal walls was not taken into account. The files were tested while rotating in a curved glass tube filled with the irrigation fluid as part of the current study's specially created apparatus, which duplicates the clinical settings. To prevent galvanic corrosion from happening during testing in metal to or in contact with metal pins, as was stated in the previous research, a heat-resistant curved glass tube was employed (Shen et al., 2012). Glass tubes, which are not found in natural teeth, may have several drawbacks that come from chemical reactions with various irrigation solutions and should not be extrapolated clinically. Theoretically, employing aqueous media will allow the heat generated by friction to evaporate and gradually lengthen the fatigue lifetime of NiTi files. However, the current study's findings, which are in agreement with some reports (Shen et al., 2012; Hasegawa et al., 2014; Pedulla et al., 2011) and disagreement with others, show that the NCF of instruments tested in dry conditions without lubricant or coolant was significantly different from those tested in EDTA, Glycine, and NaOCl groups (Berutti et al., 2006; Elnaghy and Elsaka, 2017; Peters et al., 2007) These contradictory results could be the consequence of one of two factors. The first is that these aqueous solutions may hurtan an adverse effect on cyclic fatigue due to their propensity to produce corrosion and the roughness of the NiTi alloy surface. As a result, the fatigue life did not improve. The second factor is that fatigue testing occurred in a location with minimal cyclic fatigue. Regarding the first factor, prior studies indicated that immersion in NaOCl and EDTA could result in file corrosion (Berutti et al., 2006; Peter et al., 2007). However, in these studies, the file and shank were fully submerged for a long period of time, which led to galvanic corrosion, which is clinically inapplicable. Recent studies, which concur with the present findings, have shown that immersion does not, on the other hand, promote corrosion (Shen et al., 2012; Pedulla et al., 2011) or exhibit any adverse impact on cyclic fatigue even with an increased surface roughness of the files. The second theory appears more believable. The NCF in the existing configuration was in the low-cyclic fatigue range (Cheung et al., 2007; Tobushi et al., 1997). This amount of time is insufficient to demonstrate how the various circumstances interact. When the number of cycles fell within the low-cyclic fatigue life, Shen et al. (2012) showed no difference in NCF between the NCF of various files in dry conditions and a bath of irrigation solutions including Glycine, EDTA, and NaOCl. In contrast to dry conditions, liquid media has shown improvement in cycle fatigue in long fatigue life. In the landmark study by Tobushi et al. (1997), the researchers discovered that in areas of mild tiredness, there was no difference between wet and dry environments. Similarly to this, Pedullà et al. (2014) demonstrated that submerging NiTi files in EDTA and NaOCl had no detrimental effects on the NCF. On the other hand, testing WaveOne Gold in the air revealed better fatigue resistanceto fatigue compared to aqueous media, according to Elnaghy and Elsaka (2017). The methodology, instrument design, and type of motion employed may all be to fault for the inconsistent outcomes. The degree of curvature is another element that could obscure the effect of irrigation solutions on cycle fatigue. It is understood that a file moving through a steep curve experiences a significant strain amplitude, hastening the failure process (Cheung et al., 2007). A 60° curvature was used in the existing configuration. As a result, there wasn't enough time to demonstrate how a different environment (a low-fatigue region) affected things. Hasegawa et al. (2014) revealed that when evaluated in a 60° curved environment, three separate files examined in various conditions had similar NCF results. When the files were examined under a 30° arc of curvature, water increased the NFC of the files, but a different NFC was recorded. So it stands to reason that aqueous solution performance would be greater with longer testing periods. It's interesting to note that two fracture sites in the NaOCl group spread toward the file's center after being launched from opposing cutting edges. This might be connected to surface roughness, which could serve as a site for crack propagation. Thus, many cracks might account for the group's lower cycle count. The short testing period is the study's main drawback. The impact of irrigation solutions in areas with high cyclic fatigue should be evaluated. Additionally, analyzing the frictional forces that each solution generates and how they might affect the NCF may be helpful. Conclusion The comparison between the two instruments that were tested revealed that NaOCl, glycine, and EDTA, as chemical materials, exhibited noticeably different cyclic fatigue resistance for various lengths of fractures and timeframes. The cyclic fatigue of NiTi files may be influenced by the irrigation environment. Chemical materials enhanced the files' Number of Cycles to Failure (NCF). However, due to the brief testing period (in the low-cyclic fatigue region), all other settings did not show any differences. Since cyclic fatigue takes much longer to develop than shaping actual teeth, the results of this in vitro study should not be directly applied to clinical situations. Therefore, caution is essential when drawing clinical conclusions. Nevertheless, further research is necessary to fully understand the various variables that can impact an instrument's cyclic fatigue resistance, fracture modes, and novel apparatus designs that share more properties with root dentine. Additional research is, therefore, required to validate and support the results of the current study."
}
]
}
] | 1
|
https://f1000research.com/articles/12-449
|
https://f1000research.com/articles/12-727/v1
|
21 Jun 23
|
{
"type": "Research Article",
"title": "New insight on antioxidants and anti-obesity properties of two Indonesian seagrass Thalassia hemprichii and Zostera marina: an integrated molecular docking simulation with in vitro study",
"authors": [
"Billy Theodorus Wagey",
"William Ben Gunawan",
"Ridwan Lasabuda",
"Nelly Mayulu",
"Msy Firyal Nadya Al Mahira",
"Deogifta Graciani Lailossa",
"Fitra Riswanda",
"Elizabeth Levyna Berta",
"Putra Mahakarya Dewa",
"Dewangga Yudisthira",
"Darmawan Alisaputra",
"Astri Arnamalia",
"Nindy Sabrina",
"Nurpudji Astuti Taslim",
"Clarin Hayes",
"Fahrul Nurkolis",
"William Ben Gunawan",
"Ridwan Lasabuda",
"Nelly Mayulu",
"Msy Firyal Nadya Al Mahira",
"Deogifta Graciani Lailossa",
"Fitra Riswanda",
"Elizabeth Levyna Berta",
"Putra Mahakarya Dewa",
"Dewangga Yudisthira",
"Darmawan Alisaputra",
"Astri Arnamalia",
"Nindy Sabrina",
"Nurpudji Astuti Taslim",
"Clarin Hayes",
"Fahrul Nurkolis"
],
"abstract": "Background: The oceans are teeming with a diverse range of marine organisms that offer unique health benefits, such as seagrass which is one of many key marine products that have garnered attention for their potential therapeutic properties. However, until now there have been few successful reports of seagrass’s metabolites profile and biological activity. Therefore, this work aims to profile metabolites or chemical constituents and assess the potential antioxidants and anti-obesity effects of two Indonesian seagrasses, Thalassia hemprichii and Zostera marina. Methods: Once authenticated, T. hemprichii and Z. marina were extracted with two different solvents, polar (ethanol) and nonpolar (hexane). Metabolite profiling was performed using untargeted metabolomic profiling via liquid chromatography coupled to high-resolution tandem mass spectrometry method analysis, and then antioxidant and anti-obesity capabilities were assessed by molecular docking and in vitro studies on selected receptors. Results: A total of 9 and 11 metabolites were observed from T. hemprichii and Z. marina and continued molecular docking. Some of the observed compounds have promising potential as inhibitors of human inducible nitric oxide synthase, reactive oxygen species (ROS) 1 kinase, human pancreatic lipase, and fat mass and obesity-associated (FTO) proteins, including luteolin, 6-hydroxy compounds luteolin O-glucoside, luteolin-O-sulphate, Thalassiolin A, Thalassiolin C, kaempferol-7,4'-dimethylether-3-O-sulfate, apigenin, and diosmetin. T. hemprichii ethanol extract (THE) EC50 value shows antioxidant capabilities via ABTS radical scavenging activity of 76.00 μg/mL, a smaller value than standard antioxidant controls (Trolox, 76.54 μg/mL) and followed by EC50 of lipase inhibition activity by THE which has the same pattern (EC50 THE < EC50 Orlistat). Conclusions: This concludes that the two Indonesian seagrasses have promising biological activity as candidates for functional food and/or drugs in combating free radicals and obesity.",
"keywords": [
"Indonesian seagrass",
"marine resources",
"Thalassia hemprichii",
"Zostera marina",
"antioxidants",
"anti-obesity",
"combating free radicals",
"marine plant"
],
"content": "Introduction\n\nObesity is a complex problem being faced in almost every country in the world.1 In recent years, the obesity rate in the world has doubled since 1980, as one-third of the world’s population is overweight, and the same figure applidesto the Southeast Asian region.2 Obesity is a complex issue that can be treated with a variety of approaches. One is a biological approach that involves antioxidants, especially those derived from plants. Most natural antioxidant compounds in plants are divided into three types, namely polyphenols, carotenoids, and vitamins.3 Antioxidants work by inhibiting the oxidation of other compounds, and they have extensive benefits such as anti-inflammatory, neuroprotective, and cardioprotective properties. This means that antioxidants have a broad role in overcoming obesity and abnormalities of fat metabolism. Some of the antioxidants’ important roles include anti-inflammatory4 and inhibiting lipid anabolism in the body.5\n\nThe anti-inflammatory properties in antioxidant compounds serve to reduce obesity complications. This is because most complications stem from chronic low-grade systemic inflammation that often occurs in individuals with obesity. Such systemic inflammation can trigger insulin resistance, vascular endothelial remodeling, and other complications in obesity.6 While the inhibition of lipid anabolism is caused by the activation of (AMP)-activated protein kinase, AMPK reduces fat tissue formation which causes obesity. Antioxidants have also been shown to have an inhibitory effect on cholesterol formation through the inhibition of HMG-CoA reductase, thereby reducing the risk of dyslipidemia.7\n\nSeagrass is a flowering plant that can form vast seagrass meadows in temperate and tropical waters (marine environments) on all continents except Antarctica.8 Some types of seagrasses are widespread and invasive, such as the seagrass Halophila stipulacea, a type of tropical seagrass native to the Gulf of Aqaba (GoA; Northern Red Sea), which has invaded the eastern Mediterranean basin, south of the Adriatic, south of the Tyrrhenian Sea, the Atlantic Ocean, and even the French Riviera, far from its normal distribution.9 These plants can also dominate local species and potentially reduce ecosystem resilience, especially in areas that have been affected or changed due to human activities.10 However, seagrass has a lot of potential such as its high level of antioxidants.11 Apart from the potential waste and bioactive effects on the life of marine organisms, seagrass has several nutritional and pharmacological benefits that are sometimes overlooked. Seagrass is an important natural biological source of metabolites with diverse bioactivity. This plant has a biochemical composition (carbohydrates, proteins, ash, phenols, flavonoids, tannins, lipids) and photosynthetic pigments (chlorophyll A, chlorophyll B, and carotenoids) that function as nutrient-filled foodstuffs and have several medical effects on the body.12\n\nSeagrasses Thalassia hemprichii and Zostera marina contain substances including cinnamic esters of tartaric acid which are also contained in Halophila stipulacea.13,14 These metabolites are known to work as antioxidants through the mechanism of free radical scavenging. Free radical scavenging is the ability of the phenol group (-OH) to provide hydrogen ions or electrons that will form stable phenoxy radicals to reduce free radicals circulating in the body. In addition, structural modifications, especially the substitution of aromatic rings, can be carried out to increase antioxidant activity. This metabolite is also able to reduce body weight and angiotensin-converting enzyme (ACE) levels in serum.15 A decrease in ACE results in a decrease in the formation of angiotensin II and a decrease in bradykinin metabolism, which leads to systematic dilation of arteries and veins and a decrease in arterial blood pressure. Therefore, pancreatic lipase inhibitors are considered valuable therapeutic reagents for treating diet-induced obesity in humans because fats will not be absorbed by the body, and the inhibitors reduce the lipogenic effects which results in weight loss, observed in our study. In addition, cinnamic acid also plays a role in lowering leptin levels, a precursor to hunger, in the human body; leptin levels increasewith increased body weight.16 Therefore, it is strongly suspected that two Indonesian seagrasses – T. hemprichii and Z. marina – have promising antioxidant and anti-obesity activities that have not yet been reported.\n\nAnother substance found in the seagrasses T. hemprichii and Z. marina is flavone glycosides.13,17 The basic characteristics of flavonoids, such as polarity, solubility, and steric conformation, will affect their ability to bind to cell membranes. Compounds with hydrophilic groups that are more polar interacting with the membrane surface via hydrogen bonding will protect cell membranes from oxidative stress.18 In addition, flavonoids inhibit glucose digestion in the gut and glucose production in the liver, increase glucose uptake in skeletal muscle, and protect against pancreatic islet damage resulting in weight loss in obese patients.19 Judging from both seagrasses’ content (T. hemprichii and Z. marina), they have no less potential than H. stipulacea regarding antioxidant and anti-obesity.13,14,18 However, research discussing these two marine plants both in terms of metabolites and biological activity is still very limited and unfortunate considering their abundance and availability. Therefore, this study aims to provide new insights related to chemical constituents profiling and biological activity of two Indonesian seagrasses T. hemprichii and Z. marina in fighting free radicals and obesity via molecular docking and in vitro study.\n\n\nMethods\n\nThalassia hemprichii and Zostera marina L. were sourced from the Mantehage Island Waters situated in Manado, North Sulawesi Province, Indonesia (Coordinates: 1.728836, 124.783457). These were collected by a third party and then procured as part of this research. Upon acquisition, both seagrass samples underwent an immediate washing process using clean water to eliminate any impurities. The botanical species’ authentication and identification were conducted at Sam Ratulangi University, Indonesia. This process followed the reference outlined by the National Center for Biotechnology Information (NCBI) Taxonomy ID NCBI:txid55496 (T. hemprichii) and NCBI:txid29655 (Z. marina). To prepare the collected specimens, the entire body was thoroughly rinsed using distilled water, then subjected to drying using a hybrid hot water Goodle dryer (King Ston, Republic of Korea),20 and finally lyophilized using the Lyovapor™ L-200 equipment by BÜCHI Labortechnik AG (Flawil, Switzerland). The resulting dehydrated coarse powder was 0.5 mm in size. The fine simplica powder was carefully packed in aluminum foil and stored at a temperature of -20 °C until further use in subsequent experiments.\n\nTo prepare the seagrass extracts from Indonesia for analysis, a dark bottle was used to mix 1 kg of simplica powder obtained from each seagrass species (Thalassia hemprichii and Zostera marina) with 2,000 mL of 96% ethanol (EtOH) solvent in a ratio of 1:2. The residue was then soaked in fresh 96% ethanol (EtOH) solvent, repeating the process. Afterward, the mixture underwent sonication for 30 minutes at 40 °C using an ultrasound sonicator (400 W, Branson 2510 model; Danbury, CT, USA). The resulting extract was concentrated for 90 minutes using a rotary evaporator under low pressure (100 millibars) and evaporated in a 40 °C oven. Subsequently, the extract was partitioned into equal volumes using hexane solvents to yield a viscous extract. The extracts obtained included THE: Thalassia hemprichii—ethanol (polar), THH: Thalassia hemprichii—hexane (non-polar), ZME: Zostera marina—ethanol (polar), and ZMH: Zostera marina—hexane (non-polar), as referenced in previous studies (Figure 1).21,22\n\nProduced and created by Fahrul Nurkolis via Biorender Premium Licensed.\n\nTo analyze the compounds present in the samples of seagrass extracts, an untargeted metabolomic profiling test was conducted.23 For the analysis, 50 μL of each of the four samples was mixed with ethanol (96%) and vortexed 30 times. Subsequently, the mixture was centrifuged at 6000 rpm for 2 minutes. Before analysis, the supernatants were filtered using a 0.22 μm syringe filter. The liquid chromatography high-resolution mass spectrometry (LC-HRMS) system used in the test consisted of a Thermo Scientific Dionex Ultimate 3000 RSLC Nano high-performance liquid chromatography (HPLC) instrument and a micro flow meter. A Hypersil GOLD aQ 50 column (50 × 1 mm × 1.9 μ particle size) was employed, maintained at a temperature of 30 °C. Solvent A contained 0.1% formic acid in the water, while solvent B comprised acetonitrile. A linear gradient was employed for the separation process, with a flow rate of 40 μL/min for a duration of 30 minutes. Thermo Scientific Q Exact HRMS was utilized for full-scan resolution at 70,000 and data-dependent MS2 resolution at 17,500 in both positive and negative modes.\n\nThe ASUS Vivobook M413ia - Ek502t laptop, equipped with an AMD Ryzen 5 4500u processor running at 2.3 GHz, 8 GB DDR4 memory, a 512 GB SSD M.2 storage, and the Windows 10 Home operating system, was utilized in this study. The software tools employed included ChemDraw Ultra 12.0, AutoDock tools (version 4.2), and BIOVIA Discovery software. The Protein Data Bank website and the PubChem structure database were also accessed as resources. The molecular docking simulation protocols followed in this study were based on previous research.23\n\nThe seagrass extract profiles revealed some compounds, which were selected as test ligands. The 2D structure of these compounds was sketched using ChemDraw Ultra 12.0 and then converted to 3D and optimized using the MM2 algorithm. The target proteins chosen for the study were human inducible nitric oxide synthase (PDB ID: 3E7G), human reactive oxygen species 1 kinase (PDB ID: 3ZBF), human pancreatic lipase (PDB ID: 1LPB), and fat mass and obesity-associated protein (PDB ID: 3LFM). These protein structures were obtained from the Protein Data Bank.\n\nTo validate the molecular docking process, redocking was employed. AutoDock tools (version 4.2) were used to transfer the original ligand into the target binding pocket, utilizing specific grid coordinates. Following the redocking procedure, the root-mean-square deviation (RMSD) of the ligand position had to be less than 2.0 Å. The grid and docking parameters were adjusted based on the results of the docking validation. Each docking’s final conformation structure was recorded in a *dlg file, and the interaction between the ligands and receptors was analyzed using Discovery Studio 2016.\n\nThe antioxidant activity was assessed using the 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH radical, C18H12N5O6+) test, following the protocol of the previous study.21,24 In this test, THE, THH, ZME, ZMH, and Trolox were added to the DPPH reagent (3 mL) in the testing vial. The mixtures were then cooled to room temperature and left for 30 minutes. The change in DPPH concentration was observed by measuring the absorbance at 517 nm.\n\nThe scavenging activity of the 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS+, C18H24N6O6S4) or the diammonium salt radical cation was determined as follows. A mixture of potassium persulfate (K2S2O8; 2.4 mM) and ABTS (7 mM) was prepared at a 1:1 ratio, protected from light using aluminum foil, and allowed to react at 22 °C for 14 hours. The resulting stock solution was diluted by adding 1 mL of the stock solution to 60 mL of ethanol (EtOH, C2H6O) to obtain a working solution with an absorbance of 0.706 at 734 nm. A fresh working solution was prepared for each test. THE, THH, ZME, ZMH, and Trolox samples were diluted with the ABTS working solution. The absorbance was measured at 734 nm after 7 minutes.\n\nTo ensure data validity, each sample was tested in triplicate (n = 3) for both ABTS and DPPH assays. Trolox (C14H18O4), a known antioxidant molecule, was used as a positive control in both ABTS and DPPH tests. The half-maximal effective concentration ratio (EC50) was used to indicate the radical scavenging capability of all tested samples as well as Trolox. The EC50 represents the concentration of a sample that causes a 50% decrease in the initial radical concentration. The inhibition of DPPH and ABTS assays was expressed as a percentage and calculated using the formula described as follows. A0 represents the absorbance of the blank while A1 is the absorbance of the standard or sample.\n\nThe determination of the lipase inhibition potential of two Indonesian seagrasses was performed by adhering to previous studies.22,25 Initially, crude pig pancreatic lipase (PPL) at a concentration of 1 mg/mL was dissolved in a 50 mM phosphate buffer with a pH of 7. The solution was then centrifuged at 12,000× g to eliminate any insoluble components. To create an enzyme stock solution at a concentration of 0.1 mg/mL, the supernatant was diluted 10-fold with the buffer. The lipase inhibition potential was evaluated based on previous research. In a transparent 96-well microplate, 100 μL of THE, THH, ZME, ZMH, and Trolox were mixed with 20 μL of 10 mM p-nitrophenyl butyrate (pNPB) in a buffer and incubated at 37 °C for 10 minutes. The results were compared to Orlistat (C29H53NO5), a well-known inhibitor of PPL or lipase. Measurements were taken at 405 nm using a DR-200Bc ELISA microplate reader. The unit of activity was determined based on the rate of reaction, specifically the yield of 1 mol of p-nitrophenol (4-nitrophenol) per minute at 37 °C. To assess the lipase inhibition activity, the PPL activity in the test mixture was reduced by 50%. To ensure the reliability of the study results, each sample was tested in triplicate (n = 3). The inhibitory data were calculated using the equation as follows. A represents the activity without an inhibitor; B represents the activity with an inhibitor; Ac and Bc represent the negative control without and with the inhibitor, respectively.\n\nStatistical analyses for the data were conducted using the MacBook version of GraphPad Prism 9 Premium Software. The results are presented as mean values with their corresponding standard deviations (means ± SD). Multiple analysis of variance was performed to compare the lipase inhibition activity of THE, THH, ZME, ZMH, and Trolox at various concentrations. To analyze the EC50 values obtained from in vitro experiments, such as antioxidant inhibition of DPPH, ABTS, and anti-obesity assays (Lipase inhibition), a statistical analysis package called “non-linear regression (log [inhibitor] vs. normalized response)–variable slope” from GraphPad Premium was employed. All experiments were performed three times to ensure reliability and reproducibility.\n\n\nResults\n\nA total of 9 and 11 metabolites were detected from T. hemprichii and Z. marina, respectively. However, they were classified further based on the extraction solvent. Some of the detected compounds were in the form of acid. Table 1 highlights the observed selected metabolite compounds from both seagrasses. The metabolites that were successfully observed were then continued with studies in silico or molecular docking on selected receptors for antioxidants and obesity.\n\nAccording to Table 2, the molecular tethering assays focused on specific receptors such as human inducible nitric oxide synthase (iNOS), human reactive oxygen species (ROS) 1 kinase, human pancreatic lipase, and fat mass and obesity-associated (FTO) protein. All of these receptors were validated successfully with a judgment accuracy of less than 2 Å.\n\nBased on Table 3, the results of molecular docking on THE showed that 4 substances had higher ΔG values than orlistat (control) in terms of anti-obesity potential. Luteolin-O-sulphate and luteolin – which are known as beneficial-rich flavonoids – also have a ΔG value exceeding antioxidant control and, interestingly, have an almost threefold greater ΔG compared to Trolox ΔG. THH has substances whose ΔG values are higher than THE’s in general, with 4 substances having an ΔG value above all controls used in this study. In the sea seagrass Z. marina, there were 11 substances studied, with 6 substances coming from ZME and the rest being components of ZMH, all of which have a greater ΔG value than orlistat or, in other words, have better anti-obesity potential than orlistat. 2 substances from ZMH, namely apigenin and diosmetin, also have better ΔG values when compared to controls, meaning that seagrass’s substance quality can compete with Trolox and S-ibuprofen. By doing molecular docking to the 4 components of the control, it was proven that the compound components in T. hemprichii and Z. marina have the potential to have antioxidant and anti-obesity properties in silico.\n\nAmino acid interaction visualization of the active compounds of two Indonesian seagrasses against human pancreatic lipase, ROS1 Kinase, porcine pancreatic lipase, and FTO proteins can be found in Table S1.74 This subsequent part will present the results concerning the health-benefiting potential of the two Indonesian seagrasses based on in vitro biological assessment.\n\nFundamentally, oxidative stress from increased reactive oxygen species production can lead to various complications such as dyslipidemia and obesity.26 Therefore, this study assessed the antioxidant potential of T. hemprichii and Z. marina using in vitro DPPH and ABTS radical scavenging activity (Figure 2). From Figure 2A, it is seen that Trolox (control) had a lower EC50 value compared to the other groups in DPPH radical scavenging activity (EC50 Trolox = 83.85 μg/mL). From the data shown in Figure 2, it can be inferred that T. hemprichii and Z. marina have less potency in DPPH radical scavenging activity compared to the standard drug Trolox. However, between the two species, THE and THH had lower EC50 values (EC50 THE = 97.59 μg/mL, EC50 THH = 99.69 μg/mL) than ZMH and ZME (EC50 ZMH = 116.2 μg/mL, EC50 ZME = 117.7 μg/mL) meaning that T. hemprichii has better potency in radical scavenging activity than the species Z. marina with THE having the highest potency and ZME having the lowest potency respectively (Figure 2A).\n\nA. EC50 of Antioxidant capabilities via DPPH radical scavenging activity. B. EC50 of Antioxidant capabilities via ABTS radical scavenging activity. THE: Thalassia hemprichii—ethanol (polar); THH: Thalassia hemprichii—hexane (non-polar); ZME: Zostera marina—ethanol (polar); ZMH: Zostera marina—hexane (non-polar).\n\nAs for ABTS radical scavenging activity, ZME, THH, and ZMH showed higher EC50 values of 95.93 μg/mL, 94.00 μg/mL, and 85.91 μg/mL respectively, in comparison to Trolox EC50 value of 76.54 μg/mL meaning that THH, ZME, and ZMH performed less potency in radical scavenging activity compared to the standard drug Trolox. Interestingly, THE showed a lower EC50 value (EC50 THE = 76.00 μg/mL) than Trolox (EC50 THE = 76.54 μg/mL) meaning that THE has better potency in radical scavenging activity compared to the control. These results suggested that the ethanol (polar) extract of T. hemprichii (THE) has better antioxidant properties than the standard drug Trolox (Figure 2B).\n\nLipase inhibitory activity can determine the anti-obesity properties. It aims to confirm the potential of two seagrasses, T. hemprichii, and Z. marina, as functional food candidates to improve metabolic disorders, especially obesity. It was assessed in this study in a dose-dependent manner using in vitro lipase inhibitory activity (Figure 3B). It was shown that EC50 of T. hemprichii in polar extract (THE) has lower than EC50 of Orlistat, meaning that it has better potency than the positive control (Orlistat). Just as the polar extract, the non-polar extract of T. hemprichii (THH) is close to the EC50 value of Orlistat as a positive control, which suggests it has almost the same potency as the Orlistat. On the other hand, for both Z. marina samples, either extracted in polar (ZME) or non-polar (ZMH) solvent, the EC50 exceeded Orlistat as positive control; this shows that all samples have a lower potential for lipase inhibition activity than T. hemprichii. EC50 values from the smallest to largest values are THH, ZME, and ZMH are 69.97 μg/mL, 78.36 μg/mL, and 119.8 μg/mL respectively, in which Z. marina had larger EC50 than other samples.\n\nA. Differences in lipase inhibitory activity by Two Indonesian Seagrass compared to control (Orlistat) in different gradients concentration via MANOVA analysis. B. EC50 of lipase inhibition activity. THE: Thalassia hemprichii—ethanol (polar); THH: Thalassia hemprichii—hexane (non-polar); ZME: Zostera marina—ethanol (polar); ZMH: Zostera marina—hexane (non-polar). * p = 0.0417; ** p = 0.0066; **** p < 0.0001; ns p > 0.05 (not significant).\n\n\nDiscussion\n\nMarine products hold significant potential as a functional food and drug candidates due to their rich nutritional profiles and bioactive compounds. The oceans are teeming with a diverse range of marine organisms that offer unique health benefits. Fish, shellfish, seaweed, and microalgae are among the key marine products that have garnered attention for their potential therapeutic properties. Seagrasses are rich in essential nutrients, including vitamins, minerals, and dietary fibers. They also contain significant amounts of vitamins C, E, and folate, as well as minerals such as calcium, magnesium, and potassium.12 These nutrients are essential for maintaining optimal health and well-being and incorporating seagrass into the diet can contribute to meeting daily nutritional requirements. Beyond their nutritional value, seagrasses are assumed to contain bioactive compounds with potential health benefits. In this study, a total of 20 metabolites were successfully identified from various seagrass extracts.\n\nMolecular docking is a molecular-level approach to computationally assess the interactions of compounds that have been successfully explored from a natural product to proteins that in this case are disease receptors. In this work, we perform molecular docking on each compound of two Indonesian seagrass T. hemprichii and Z. marina that has the potential to have antioxidant and anti-obesity effects. The control we used to determine the ability of these compounds was to look for receptors from iNOS (3E7G) with ΔG -4.73 found in S-ibuprofen and ROS 1 kinase (3ZBF) with ΔG -5.36 found in Trolox as an antioxidant marker, as well as human pancreatic lipase (1LPB) with ΔG -2.38 and fat mass and obesity-associated protein (3LFM) with ΔG -3.71 used as substances that have anti-obesity effects. Excessive iNOS and ROS 1 kinases in the body have the effect of being free radicals that ultimately damage proteins and induce apoptosis in cells. So inhibition using substances that attach to receptors can provide antioxidant effects and reduce oxidative stress injury.27,28 Orlistat, which targets inhibition of human pancreatic lipase and FTO, is approved by the US Food and Drug Administration for its use as an anti-obesity substance due to its efficacy in reducing the absorption of 30% of fat consumed.29 On the other hand, the enzymatic activity of FTO plays a crucial role in maintaining energy and adipose tissue balance.30 However, when this activity is disrupted, it leads to the dysregulation of genes associated with energy metabolism, thereby affecting the homeostasis of energy and adipose tissue. Therefore, inhibition of FTO is relevant in preventing obesity-related conditions.\n\nSo far we have identified four main components of each of the polar and nonpolar extracts of T. hemprichii as well as the polar and non-polar extracts of Z. marina. The results of EC50 measurements provide promising results as the metabolites with potential anti-obesity properties from the two seagrasses have been reported. Of all the samples, only one type of extract, THE, had better EC50 results than Orlistat as a control. However, the entire samples had a much better lipase inhibition profile than the previous study (62.25 μg/mL to 119.8 μg/mL compared to up to 876.30 μg/mL in Ecklonia radiata.31 In addition, another study showed that with a concentration of 10 mg/mL extracts of Ascophyllum nodosum, Laminaria japonica, and Lessonia nigrescens could not even achieve pancreatic lipase inhibition by 40%.32 The comparison of the results of the study above shows Z. marina extract and T. hemprichii has superior lipase inhibition activity.\n\nOne of the resistance mechanisms to obesity is the inhibition of lipase enzymes or inhibitors. Exogenous fats obtained from outside the body must go through a hydrolysis process into monoglycerides, glycerol esters, and free fatty acids. This mechanism is mediated by the lipase enzyme found in the mouth, gaster, and pancreas with the pancreas as the main hydrolysate (50 – 70%). Human pancreatic lipase consists of 449 fatty acids with a catalytic center enclosed by an N-terminus. The bonding ability between substrate and lipase depends on the area of the hydrophobic area in the enzyme obtained from changes in lipase conformation. Lipase works together with the coenzyme co-lipase secreted by the pancreas. When co-lipase proteins combine with bile acids in the duodenum, lipase action is activated so that lipid absorption in the intestine is optimal.33 Departing from this concept, the anti-obesity approach using lipase enzyme inhibitors or lipase inhibitors is expected to reduce the number of lipids absorbed to minimize the accumulation of fatty acids, cholesterol, and lipoproteins in the blood and adipose tissue deposition in the body.34 Lipase inhibitors work by binding to residues located at the active binding site of pancreatic and gastric lipase so that the ability of triglycerides to bind to lipase becomes inhibited. Due to its selective nature, weak absorption rate, and low risk of systemic side effects, there is potential to develop lipase inhibitors further into mainstream anti-obesity.35\n\nA study suggests the potential use of H. stipulacea seagrass as an alternative to obesity therapy in extract form. The use of leaf and stalk extracts with hexane, ethyl acetate, and methanol as their solvents on zebrafish showed fat reduction activity in several extracts (EL, ML) with EC50 of 1.2-2.2 μg/mL based on the fat metabolism examination of Nile red zebrafish.36 These results are thought to be a result of the flavonoids cirsmarin (5-hydroxy-6,7-dimethoxy-2-[4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]chromen-4-one), N-acetyl-L-tyrosine, 2,4-dihydroxyheptadec-16-ynyl acetate, and 2,4-dihydroxyheptadec-16-ynyl acetate. Research using Halodule pinifolia extract has been conducted to understand the anti-inflammatory ability of the seagrass. By using ethyl acetal extract (EHP) and methanol (MHP) in vitro models of inflammation triggered by lipopolysaccharides, it was found that EHP has more anti-inflammatory abilities. With modern in vivo endotoxemia, EHP succeeded in reducing plasma IL-6 88.3%, TNF-α (78.2%), and IL-1β (74.5%). Similar results were also seen in carrageenan models of TNF-α edema (69.3%) and IL-1β (43.1%).37 Other studies showed antioxidant, antimicrobial, and antiproliferative properties. Another study observed sulfated polysaccharides from Cymodocea nodosa, finding the results of the examination of total antioxidants (59.03 mg ascorbic acid equivalent/g extract), reducing power (OD = 0.3), DPPH radical scavenging (EC50 = 1.22 mg/mL), and ABTS radical scavenging (EC50 = 1.14 mg/mL).38\n\nLipase inhibition holds an important key to preventing obesity because lipase inhibition will prevent the absorption of fat in the intestine so that it does not enter the bloodstream. If the amount of fat that enters the bloodstream is high continuously and for a long period, it will result in dysregulation of fat metabolism which will result in dyslipidemia.33 Besides its advantages as a lipase inhibitor, polar extract from T. hemprichii also has better antioxidant activity compared to Trolox as a control on ABTS assay. This makes the extract particularly valuable because it can work as a good antioxidant, where antioxidants are very important to prevent the emergence of obesity complications in people with metabolic syndrome. This is because most of the complications of obesity have a background of oxidative stress mechanisms such as pancreatic beta cell damage, insulin resistance, plaque formation in blood vessels, and endothelial damage to blood vessels.26 Oxidative stress has an important role in the pathophysiology of obesity such as by modifying the concentration of inflammatory mediators associated with the large number and size of adipocytes, promoting lipogenesis, stimulating the differentiation of preadipocytes into mature adipocytes, and regulating energy balance in hypothalamic neurons that control appetite. Fortunately, this can be countered by utilizing plants that have therapeutic antioxidant potential that can scavenge reactive oxygen species (ROS), such as in some types of seagrass plants.39,40\n\nLuteolin appears to show decreased lipogenesis activity, decreased ectopic fat deposits, increased fat thermogenesis, and increased systemic energy expenditure associated with improvements in obesity conditions.41 Betaine may prevent obesity through gut microbiota.42 Another study using experimental rats given oleamide showed a decrease in the incidence of obesity.43 Palmitoleic acid given to rats orally appears to induce satiety through the release of hormones.44 Rosmarinic acid, kaempferol, p-coumaric acid, apigenin, diosmetin, and azelaic acid also appear to be associated with a reduced incidence of obesity or a decrease in metabolic disorders due to obesity.45–50\n\nAntioxidants are one of the most important factors in reducing radical compounds in the body to reduce cell damage and ultimately prevent the occurrence of several diseases.51 Several other types of seagrass such as Enhalus acoroides, Halophila ovalis, Halophila major, and Halophila spinulosa contain flavonoids and phenolics which are commonly known as the largest phytochemical molecules and their antioxidant activity is stronger than vitamins C and E.52–54 Chrysoeriol, one type of flavonoid that is usually studied for its antioxidant effects and is often found in seagrass plants, has a significant effect on increased cell viability, reduced ROS formation, and increased occurrence of antioxidant molecules in H2O2. In addition, this compound has the ability to suppress peroxidation and has lipid interactions with peroxyl radicals.55,56 In phenolic compounds, antioxidant properties are obtained from the presence of hydroxyl groups in the benzene ring of the chemical element. The mechanism of antioxidant activity of this compound is obtained through the mechanism of hydrogen atom transfer by giving H atoms to the free radical substrate and producing non-radical substrate species (RH, ROH, or ROOH) and free radical antioxidants.57,58\n\nThere have not been many studies using DPPH substrate to evaluate the antioxidant potential of seagrass plants. Earlier studies used nitric oxide (NO), H2O2, catalase, and glutathione peroxidase to assess the antioxidant potential of this plant.59,60 DPPH can be used as a substrate to evaluate antioxidant activity because its stable nature can also form stable diamagnetic molecules.61 Previous research that has documented antioxidant potential through DPPH radical scavenging activity was obtained in a study that showed that H. ovalis methanol extract showed EC50 scavenging on DPPH radicals at 0.13 mg/mL.61 This was later validated by our in vitro study of DPPH radical scavenging activity in T. hemprichii and Z. marina which showed antioxidant potential as a therapy other than Trolox (Figure 2A).\n\nIn addition to the use of the DPPH method, an interesting discovery was found in measuring antioxidant capabilities using the ABTS radical scavenging activity method which showed that the potential of T. hemprichii in radical scavenging activity was better than the standard drug Trolox with a value of EC50 = 76.00 μg/mL. The results of this study complement the results of previous studies that assessed EC50 in T. hemprichii extracted 50% ethanol plus HCL 1 N at 60 oC with the DPPH method (EC50 = 83.48 μg/mL).62 Research by Jayaprakash et al. in 2017 also explained that compared to other seagrass species, T. hemprichii has the highest free radical flushing activity ability in its habitat.40 The discovery of EC50 values from DPPH and ABTS methods, as well as comparisons with Trolox as a standard antioxidant drug in this study confirm previous findings that have addressed the antioxidant capabilities of the seagrass T. hemprichii and provide comparisons in its potential use as a new antioxidant regimen option developed for humans. Furthermore, computational molecules of each compound showed the inhibition of free radicals by luteolin-O-sulphate, thalassiolin C, thalassiolin A, luteolin, apigenin, diosmetin, and other compounds (Table 3).\n\nLuteolin, kaempferol, and apigenin have previously demonstrated antioxidant activity using DPPH and ABTS methods, with superior antioxidant activity compared to the control (Vitamin C). Among these, luteolin and kaempferol exhibited the highest antioxidant capabilities, followed by apigenin with the lowest antioxidant ability.63 This can explain the antioxidant activity observed in THE, THH, ZME, and ZMH. In a study using radiation-induced liver damage in experimental mice, it was found that treatment with betaine, which was also identified in THE in this study, resulted in decreased oxidative stress, reduced CYP450 activity, increased glutathione levels, decreased caspase-3 activity, and a decrease in fibrotic markers, accompanied by improved kidney function.64 Other studies have also demonstrated the antioxidant abilities of oleamide metabolites in mitochondrial toxicity in experimental mice. The results showed a reduction in lipid oxidation and alterations in glutathione reduction or oxidation.65 Palmitoleic acid, one of the omega-7 fatty acids, found in ZME, appears to exhibit antioxidant activity in HaCaT cells.66 Rosmarinic acid, alpha-eleostearic acid, p-coumaric acid, myristic acid, diosmetin, and azelaic acid have also shown antioxidant activity based on several previous studies.67–72\n\nThis study is the first to successfully profile metabolites and perform molecular docking, and the results are promising for anti-obesity and antioxidant functional foods based on in vitro validation and molecular docking results. However, this still needs further research i.e., isolation and purification of each observed compound and continuing in vivo trials in animal models prior to human clinical trials.\n\n\nConclusion\n\nNew insights have been obtained from this reported study, ranging from the metabolites profile of chemical constituents of two Indonesian seagrasses T. hemprichii and Z. marina, and accompanied by molecular activity against obesity receptors and antioxidant potential via molecular docking simulation. Some of the compounds observed in two Indonesian seagrasses have promising potential as inhibitors of iNOS, ROS1 kinase, human pancreatic lipase, and FTO proteins. These compounds include luteolin observed from THE; 6-hydroxy compounds luteolin O-glucoside, luteolin-O-sulphate, Thalassiolin A, and Thalassiolin C from THH; kaempferol-7,4’-dimethylether-3-O-sulfate from ZME; and apigenin and diosmetin from ZMH. Interestingly, further tests of antioxidant and anti-obesity activity from two Indonesian seagrass extracts showed the same promising potential as the results of a molecular docking simulation. THE’s EC50 value shows antioxidant capabilities via ABTS radical scavenging activity of 76.00 μg/mL, a smaller value than standard antioxidant controls (Trolox, 76.54 μg/mL) and followed by EC50 of lipase inhibition activity by THE which has the same pattern (EC50 THE < EC50 Orlistat). This suggests that the two Indonesian seagrasses have promising biological activity as a candidate for functional food and/or drugs in fighting free radicals and their interlink to obesity. In vivo studies and clinical trials are certainly needed to see the sustained efficacy value of the two seagrasses, which are being planned in the future.\n\n\nAuthor contributions\n\nConceptualization and methodology: B.T.W., F.N., N.A.T. and N.M.; software, investigation, data curation, and visualization: F.N. and B.T.W.; validation, formal analysis and supervision: F.N., N.A.T. and N.M.; Writing, original draft preparation, review, and editing: B.T.W., F.N., W.B.G., M.F.N.A.M., D.G.L., F.R., E.L.B., P.M.D., D.Y.; Validation, Writing-revised-review, and editing: N.S., D.A., C.H., A.A. and R.L.; Molecular Docking Simulation and their visualization: D. A and A.A. All authors have read and agreed to the published version of the manuscript.",
"appendix": "Data availability statement\n\nfigshare: RAW data DPPH, ABTS, and Lipase of Seagrass “Antioxidants and Anti-Obesity Properties of Two Indonesian Seagrass Thalassia hemprichii and Zostera marina”, https://doi.org/10.6084/m9.figshare.22826048.v2. 73\n\nMetabolites data are provided in this manuscript, see Table 1.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nfigshare: Fully Visualization of Amino acid interaction of T. hemprichii and Z. marina metabolites against human inducible nitric oxide synthase (iNOS), human reactive oxygen species (ROS) 1 kinase, human pancreatic lipase, and fat mass and obesity-associated (FTO) protein. Available at: Figshare https://doi.org/10.6084/m9.figshare.22826078.v1. 74\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\nBlüher M: Obesity: global epidemiology and pathogenesis. Nat. Rev. Endocrinol. 2019; 15: 288–298. Publisher Full Text\n\nChooi YC, Ding C, Magkos F: The epidemiology of obesity. Metab. Clin. Exp. 2019; 92: 6–10. Publisher Full Text\n\nXu D-P, Li Y, Meng X, et al.: Natural Antioxidants in Foods and Medicinal Plants: Extraction, Assessment and Resources. Int. J. Mol. Sci. 2017; 18: 18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalehi B, Mishra AP, Nigam M, et al.: Resveratrol: A Double-Edged Sword in Health Benefits. Biomedicines. 2018; 6: 6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCheng C, Li Z, Zhao X, et al.: Natural alkaloid and polyphenol compounds targeting lipid metabolism: Treatment implications in metabolic diseases. 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}
|
[
{
"id": "180683",
"date": "26 Jun 2023",
"name": "Muhammad Iqhrammullah",
"expertise": [
"Reviewer Expertise natural product",
"medicinal chemistry",
"antioxidant",
"molecular docking"
],
"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 reviewing opportunity. Please find below my comments:\n“One is a biological approach that involves antioxidants..” The logical flow is somewhat missing. Before this explanation, the authors should firstly explain the oxidative stress in obese individuals, and how it contributes to the pathological condition.\n\nParagraph 1-2 can be combined with better logical flow.\n\n“In addition, structural modifications, especially the substitution of aromatic rings, can be carried out to increase antioxidant activity.” Not sure about the importance of this statement.\n\n“ A decrease in ACE results in….” I thought the authors wish to correlate this with systemic inflammation. Not sure what this “systematic dilation of arteries and veins and a decrease in arterial blood pressure.” has to do with bodyweight reduction? It may improve the complication, but not the body weight. Again, I think the authors should re-work the introduction for better logical flow.\n\n“…T. hemprichii and Z. marina is flavone glycosides” - the authors should explain why the two seagrass species are good sources for flavonoids. Note that flavonoids are common in plant secondary metabolites, what makes the plant or specimen special is the abundance of these compounds.\n\n“…using clean water” - do you mean deionized water?\n\n“fine simplica powder” - just ‘fine powder’… simplica is not an English word.\n\n“The molecular docking simulation protocols followed in this study were based on previous research” - which part of the protocol? Molecular docking protocol is complex and starts from protein and ligand preparation up to the visualization of the docking results. So, which one followed the previous study? Moreover, grid box dimensions usually are adjusted to the ligand size (the biggest ligand), this has to be clarifed.\n\nData about grid coordinates should be presented.\n\nCompounds library used for the untargeted metabolomic profiling should be stated.\n\nThe relative abundance should be included in Table 1.\n\nThe name of the native ligand should be presented in Table 2. Also, justification of choosing the native ligand (such as being reported as inhibitor) should be provided in the discussion.\n\nAnw, the presentation of Table 2 in the results is confusing. Better to move it to methods.\n\nEC50 was obtained based on the non-linear regression. This has to be declared in the caption.\n\nPictures of the molecular docking, especially from those with the best affinity should be presented.\n\nΔG has the unit of kcal/mol, please always present this unit whenever ΔG is presented in paragraph.\n\nPlease state that the in vitro results should be further validated in vivo since the studies do not consider the physiological response.\n\nDiscussion should be more concise and structured. The discussion structure ideally starts with the findings, comparison with previous research, general implications, and then future prospect.\n\n“There have not been many studies using DPPH substrate….” - I get the idea that the authors wish to stress the novelty of the study here. Nonetheless, it is unwise to underate nitric oxide (NO), H2O2, catalase, and glutathione peroxidase, especially because these molecules are most likely to be involved in regulating oxidative stress inside the body. I don’t think this paragraph is necessary.\n\nPlease discuss the molecular docking results based on whether the inhibition is competitive or non-competitive.\n\n“ The mechanism of antioxidant activity of this compound is obtained through the mechanism of hydrogen atom transfer by giving H atoms to the free radical substrate and producing non-radical substrate species (RH, ROH, or ROOH) and free radical antioxidants”. This is somewhat scientifically incorrect. It is always the electron that is transferred with or without the involvement of hydrogen. Moreover, what do you mean “…free radical antioxidants”?\n\nThe final sentence for the conclusion should answer whether the seagrass extracts have antioxidants and anti-obesity or not? Statements like this “…promising biological activity as a candidate for functional food and/or drugs in fighting free radicals and their interlink to obesity” is far-reaching.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "180684",
"date": "06 Jul 2023",
"name": "Sahar Abdelaziz",
"expertise": [
"Reviewer Expertise Natural products (Extraction",
"isolation",
"analysis and identification)",
"Chromatography",
"Site Directed Mutagenesis"
],
"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 so much for giving me this opportunity to review this interesting manuscript.\nFirst of all, I would like to thank the authors for their efforts in the practical work as well as in the preparation of this article. The topic is interesting and the study is very well designed and clearly written. In this article, the authors aimed to characterize the chemical constituents and evaluate the potential antioxidant and anti-obesity effects of two Indonesian seagrasses, Thalassia hemprichii and Zostera marina.\nIn general, the article follows the journal's guidelines. It is interesting and contributes to knowledge.\nI have a few minor comments:\n1 - English needs tightening throughout, please spell check and rephrase carefully to eliminate errors.\n2- The introduction:\na- The first paragraph second line correct the last word.\nb- The authors talked in two details paragraphs about obesity which is not compatible with the study aim which is the evaluation chemically and biologically of two sea grasses. I suggest starting the introduction with the information’s related to the two selected Seagrasses.\n3- Methods:\nAll the methods are adequately described and explained.\n4- Results:\nThey are clearly presented. I suggest providing the structures of the identified compounds either in the table or in a separate figure if applicable.\n5- Discussion:\nThe authors elaborate in describing the biological activities of different Seagrasses compared to those used in this study. I suggest summarizing the discussion part as there are too many details related to different reported seagrasses.\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": []
}
] | 1
|
https://f1000research.com/articles/12-727
|
https://f1000research.com/articles/12-1383/v1
|
20 Oct 23
|
{
"type": "Case Report",
"title": "Case Report: The role of Panchagavya and Panchakarma treatment in the management of radiotherapy and chemotherapy side effects in infiltrative ductal carcinoma",
"authors": [
"Punam Sawarkar",
"Gaurav Sawarkar",
"Nandini Bhojraj",
"Gaurav Sawarkar",
"Nandini Bhojraj"
],
"abstract": "The incidence rate of infiltrative ductal carcinoma of the breast is increasing worldwide. Chemo- and radiotherapy are commonly used after the surgical intervention for radical cure. The occurrence of various side-effects of these chemo-radiation therapies creates much discomfort to the patient. Therefore, the compliance rate of the patient towards their adoption becomes poor, or the patient is highly affected by their associated side effects in unavoidable circumstances. It is imperative to study the effect of safe, alternative options such as Panchakarma and Panchagavya treatment, which are widely used in clinical practice as an adjuvant therapy in various types of carcinoma. This report presents the case of a 31-year-old female patient diagnosed with right infiltrative ductal carcinoma of the breast, and who was advised to undergo chemo-radiation therapy after surgical intervention. However, as soon as she finished the first chemo cycle, she suffered from palpitations, loss of appetite, nausea, vomiting, severe restlessness, and hot flushes. She was rushed to the Kamdhenu Panchgavya Ayurvedic Clinic of Govigyan Anusandhan Kendra. Specific Panchagvya Chikitsa, along with Mrudu Shodhana based on Ayurvedic principles, was prescribed to her (Kamdhenu Gomutra Ark, Laghusutshekhar Ras, Panchagavya Ghrita, Panchatikta Kshir Vasti, Anuvasana Vasti with Panchgavya Ghrita) throughout her total rounds of chemo- and radiotherapy. After starting the above-said Ayurvedic treatment, the patient experienced significant relief in all symptoms. Her full six sittings of chemo- and radiotherapy were smoothly completed without causing any untoward effect. The selected combination of Ayurveda medicines gave relief in all symptoms induced by chemo- and radiotherapy therapy due to their Vatanulomak, Pittghna, Dahahara, Balya and Rasayana properties. The present case study shows that the Panchakarma and Panchagavya treatment is effective to subside the side effects induced by chemo- and radiotherapy, and improve the compliance rate of the patients towards these conventional therapies.",
"keywords": [
"Breast Carcinoma",
"Chemotherapy",
"Panchagavya",
"Panchakarma",
"Radiotherapy"
],
"content": "Introduction\n\nInfiltrating ductal carcinoma (IDC), also called invasive ductal carcinoma, is a carcinoma involving the milk duct. It is the most typical breast carcinoma (80 % of total incidences of breast carcinoma).1 Its spread takes place through the lymph nodes to other body tissues.2 The number of patients of this type of carcinoma of breast are increasing day by day, both globally and in India.3 Though the carcinoma of breast is considered as better compared to other cancers from a treatment and prognosis perspective, the recurrence of especially infiltrative ductal carcinoma is a common entity.4 Therefore, its radical cure treatment in the form of chemo- and radiotherapy is highly appreciated, preceded by surgical intervention. However, there are multiple side-effects of these chemo-radiation therapies such as body aches, nausea, vomiting, and a severe burning sensation, which is quite troublesome for the patient as these symptoms adversely affect the quality of life of the patient.5 As a result, many patients decline to undergo further courses and may be deprived of their total expected therapeutic outcome.6 In these circumstances, the pathogenesis of the primary disease may worsen or may even lead to the death of the patient due to further metastatic changes.\n\nMoreover, modern science is limited in preventing such complications; it is difficult to target cancer stem cells (CSCs), drug resistance properties of cancer stem cells make them immune to anticancer drugs, a lack of cancer epigenetic profiling and specificity of existing epi-drugs, problems associated with cancer diagnosis make it difficult to treat, a lack of effective biomarkers for cancer diagnosis and prognosis, and there are limitations of conventional chemotherapeutic agents.7 Therefore, it is the need of the hour to search for some safe alternative options in Ayurveda to manage these complications effectively. Panchagavya treatment and Mrudu Shodhana, sourced from Ayurveda medicine, seem to be a ray of hope for such patients which is demonstrated through this case report.\n\n\nCase report\n\nThe 31-year-old married female patient, housewife, with a diagnosis of right infiltrative ductal carcinoma of the breast, who had a mastectomy three weeks before her first chemotherapy session, approached Go-Anusandhana Chikitsasalaya, Nagpur, in February 2014. According to her history, she was experiencing issues such as palpitations, loss of appetite, nausea, and vomiting. These symptoms began after the first chemo session, and after the third session she additionally experienced hot flushes, constipation, burning micturition, and sensations of burning in the anal region. Thus, she was unable to consume any type of food. A detailed history of the patient is presented in Table 1. Upon examination at her first visit to the outpatient department, the general condition of the patient was fair, no icterus/swelling was found, mild pallor, palpable axillary lymphadenopathy, and blood pressure was 90/70 mm of Hg. Prakriti of patient was Vatapradhan Pittaj Prakriti. Ashatavidha Parikshana results are mentioned in Table 2.\n\nShe was given Ayurvedic medication as adjuvant therapy for infiltrative ductal cancer and to address these side effects of chemotherapy. The patient self-reported that the intensity of the above symptoms was controlled with the prescribed medicines: Kamdhenu Gomutra Ark (distilled cow urine) 10 ml twice a day with the dilution of 100 ml water on an empty stomach; Laghusutashekhar Rasa (comprising of Swarna gairika – purified red ochre, iron oxide; Shunthi – ginger rhizome, Zingiber officinalis; Nagavalli – betel leaf juice extract, piper betel) 125 mg tablets twice a day with clarified butter and candy sugar; Panchagavya Ghrita 10 ml twice a day with each meal when hungry; Panchatikta Kshir Vasti 50 ml before the day of chemotherapy and alternating three enemas sittings after three days of chemotherapy; Matra Vasti with Panchagavya Ghrita 60 ml once a week after food for six months.\n\nHowever, eight weeks after completing her third chemo round, she visited the out-patient department again suffering from additional symptoms such as severe hot flushes (all over the body), constipation, burning micturition and burning sensation in the anal region, and her quality of life was also severely affected. Therefore, specific Panchakarma (Mrudu Shodhana) of 60 ml Matra Basti with Panchagavya Ghrut was prescribed, which was continued throughout her chemo- and radiotherapy. After adding this, encouraging results were found in all signs and symptoms, and all sittings of chemo-radiotherapy were completed smoothly without any undue effect.\n\nThe patient first reported to the outpatient department with a pre-existing diagnosis of breast infiltrative ductal carcinoma. The oncologist did not determine the patient’s prognosis due to the unknown metastases in the body. Pathological investigations of the patient carried out for the diagnosis are described in Table 3.\n\nAfter the initial chemo treatments, the patient reported to the outpatient department with palpitation, lack of appetite, nausea, and vomiting. Kamdhenu Gomutra Ark, Laghusutshekhar, and Panchagavya Ghrit were prescribed for primary treatment. After 4 weeks between chemo rounds, the patient felt better. After 8 weeks, the third chemo session, the patient reported additional symptoms such hot flushes, constipation, burning micturition, and anal burning. Panchatikta Kshir Vasti was administered before chemo, three enemas three days after chemo, and Matra Vasti with Panchagavya Ghrita once a week after eating. After six months, the patient claimed improvement from palpitation, loss of appetite, nausea, vomiting, hot flushes, constipation, burning micturition, and anal burning.\n\nIn this therapeutic intervention, palliative treatment and purification were given: prescribed medicines: Kamdhenu Gomutra Ark (distilled cow urine) 10 ml twice a day with the dilution of 100 ml water on an empty stomach; Laghusutashekhar Rasa 3 125 mg tablets twice a day with clarified butter and candy sugar; Panchagavya Ghrita (Ghrit prepared from cow milk, curd, clarified butter, urine, and dung) 10 ml twice a day with each meal when hungry; Panchatikta Kshir Vasti (enema of cow milk treated with Azadirachta indica (stem bark), Tinospora cordifolia (stem), Adhatoda vasica (root), Solanum xanthocarpum (root) and Trichosanthes dioica (aerial parts)) 50 ml before the day of chemotherapy and alternating three enemas after three days of chemotherapy; Matra Vasti with Panchagavya Ghrita (medicated clarified butter enema with Panchagavya) 60 ml once a week after food for six months.\n\nPalliative treatment increases the quality of life of patients and their families who are dealing with the hardships of a life-threatening disease, and the purification method helps to detoxify the body for better improvement in quality of life. Details of the types of therapeutic intervention and administration of therapeutic intervention applied in this case are depicted in Table 4.\n\nAfter prescribing the above treatment plan compromising of Mrudu Shodhana (Ksheervasti +Anuvasana Vasti) with Panchagavya Chikitsa for 6 months, the patient felt significant relief in all side effects of the chemo- and radiotherapy and the conventional therapies were completed smoothly and successfully. Moreover, to date, there is no recurrence of the disease or any complication in the form of metastasis. The symptoms like palpitations, lack of appetite, nausea, vomiting, hot flushes, constipation, burning micturition, and burning sensation in the anal region reduced remarkably. Therapeutic outcomes observed in this patient are mentioned in Table 5.\n\n\nDiscussion\n\nKamdhenu Gomutra Arka (distilled cow urine) is one of the most effective medicines among Panchagavya formulations.8 Due to its highly concentrated nature as a result of the specific method of preparation and original properties of Gomutra, it is highly Kaphaghna and Agnidipaka in nature, which increases the patient’s appetite.9 According to the modern perspective, potassium in Gomutra Arka is responsible for its effect on appetite.9 Ruksha Guna decreases the excess Drava Guna of Pitta which results in relief of nausea. The sodium in Gomutra Arka relieves the hyperacidity. Mainly, Gomutra corrects the Kledak Kapha Dushti, which is the leading cause of Chhardi, i.e., vomiting. Due to its Kaphaghna properties, it is useful in Kapha-predominant conditions in Granthi and Arbuda. It is highly effective in various carcinomatous conditions due to the anti-cancer properties of Gomutra.10 Gomutra is diuretic in nature; it eliminates the excess Kleda (toxic materials induced by chemotherapeutic agents) and also decreases the burning sensation during urination.11 It also decreases hematological toxicities induced by chemo and radiation therapies.12,13\n\nGomutra plays a crucial role in immune modulation by enhancing the activity of macrophages, lymphocytes (both T and B cells), humoral cellular immunity, and cytokines (interleukin 1 and 2), and works as an adjuvant therapy with the conventional modalities.14 It also protects the cell from getting damaged by free radicals, which can cause tumor cell growth or recurrence.14\n\nLaghusutashekhar Rasa is the combination of herbs and minerals that consists of Gairik responsible for the Pitta Shamana effect due to its Shita Virya, which subsides the symptoms of Pitta Prakopaka such as Sarvang Daha (hot flushes), Mootra Daha and Guda Daha. It absorbs the excess Drava Guna of vitiated Pitta, which occurs due to Ushna Guna of the chemotherapeutic agent. Therefore, it decreases the sensation of nausea and reduces the frequency of vomiting15 and is highly recommended for acid peptic disease and lack of appetite. It also pacifies Vata due to its Madhura Rasa, Snigdha, and Madhur Vipaka.16 As it contains Go–Ghrita, which is Agnidipaka in nature, it results in increased appetite.17\n\nPanchagavya Ghrita (Ghrit prepared from cow milk, curd, clarified butter, urine, and dung) is the medicated Ghrita that pacifies the Pitta and Kapha.18 In this case, it was used in the forms of Shamana Snehapana and Matra Vasti. Shamana Snehapana, with Panchagavya Ghrita, acts as a carrier that can facilitate the drug or its pharmacological properties to get into the cells, enhancing the effects of Shamana drugs.19 It processes free radicals as a result of the anti-oxidant effects due to vitamins A, C, and E, and fatty acids present in it. It is especially recommended for liver disorders.20 It acts as the best immuno-modulator through its anti-oxidant properties.20 It also has anti-cancer properties and helps to remove the hematogenous toxins induced by chemotherapeutic agents.21–22 The neuroprotective action of Panchagvaya Ghrita is demonstrated by Sawarkar G et al. (2018), resulting in the relief in hot flushes.23\n\nMatra Vasti with Panchgavya Ghrita (enema of cow milk treated with Azadirachta indica (stem bark), Tinospora cordifolia (stem), Adhatoda vasica (root), Solanum xanthocarpum (root) and Trichosanthes dioica (aerial parts)) acts as a mild type of purification and can be adopted to induce harmony between the vitiated Dosha and Dhatu, which can normalize the Vata without causing any deterioration in the status of the person.24 While Shodhan Vasti is contraindicated in cancer treatment due to the complexity of the disease, Shaman Vasti can be used with cancer patients as it is a mild type of Vasti. Moreover, side effects induced by chemo- and radiotherapy mainly affect the Rasavaha, Annavaha and Pursihvaha Strotas by causing vitiation of Vata and Pitta primarily. Therefore, Panchagavya Ghrita, which mainly is Pitta Shamaka, also brings the Vatanulomama (especially ApanVayu) due to Snigdha Guna of Ghrita. As a result, it corrects the Saman Vayu and Pachak Pitta. It reverts the normalcy of Annavaha Strotas by improving appetite.25\n\nPanchtikta Kshir Vasti (medicated clarified butter enema with Panchagavya) is recommended for Pitta predominant and degenerative conditions due to its Pitta Shamaka, Kledahara, Balya, and Rasayan properties.26 In clinical practice, it has significant results in Amlapittta Daha, Astha-Majjagata Dushti Vikara, and Dhatukshayajanaya Vata Vyadhi.27 The Kaphaghna and Sukshma properties of Panchtikta (Guduchi, Patol, Kantakari, Nimba and Vasa) reduces the inflammation in gastric mucosa induced by chemotherapeutic agents due to their anti-inflammatory and anti-oxidant properties.28 At the same time, clarified butter and cow milk, in this enema preparation, induce a soothing effect due to their Pitta Shamaka nature.17\n\nThe combination of all Ayurveda medicines and Panchagavya therapies induces the Anulomana of Apana Vayu, which stimulates the Samana Vayu and corrects the vitiation of Kledka Kapha and Pachaka Pitta.24 Therefore, symptoms related to Amlapitta and Sarvanaga Daha (Pitta Prakopa) were completely subsided. Due to Kledahara and Agnidipaka properties, it removes the Rasa Dushti, resulting in the relief of heart palpitations. As a result, symptoms induced by chemo- and radiotherapy therapy will ease due to the correct combination of Panchakarma and Panchagavya formulations with their Vatanulomak, Pittghna, Dahahara, Balya, and Rasayana (immuno-modulators, anti-oxidant, bio-enhancing) properties. Because this is only a single case study, the patient should be treated according to suitable medical guidelines and under the supervision of specialists in the respective domains in the future.\n\n\nConclusion\n\nThe present case study shows that the Ayurvedic intervention based on Panchagavya and Panchakarma is effective in subsiding the side-effects induced by the chemo- and radiotherapy through their threefold effects of Shamana, Bruhana and Mrudu Shodhana. It is also helpful to increase the compliance rate of the patients towards conventional therapies like chemo-radiotherapy. Further multi-centric clinical trials with large sample sizes are encouraged to establish the significant and comprehensive role of Panchagavya Chikitsa with Panchakarma in Ayurveda. It will become a milestone for Ayurveda in oncology for its acceptance at a global level.\n\nThe patient is satisfied with the treatment protocol and desired outcomes.\n\nWritten informed consent was received from the patient for publishing this case study and the patient consented to the disclosure of her clinical details. The ethical clearance for the publication of this case study was taken from the local ethical committee at Mahatma Gandhi Ayurveda College, Hospital and Research Centre, Salod (H), Wardha with IRB No. MGAC/IEC/April/2023/102. All procedures and treatments advised and performed in this study were conducted by ethical standards mentioned in the 1964 Declaration of Helsinki, as revised in 2013.\n\n\n\n• Agnidipaka: increasing appetite\n\n• Amlapittta Daha: hyper acidity\n\n• Annavaha Strotas: gastro-intestinal channels\n\n• Anulomana- correct direction\n\n• Anuvasana Vasti with Panchgavya Ghrita: medicated clarified butter enema with Panchagavya\n\n• Apan Vayu: air entity below umbilicus\n\n• Ashatavidha Parikshana: eight-fold examination\n\n• Astha-Majjagata Dushti Vikara: disease that occurred due to vitiation of toxins at bone and bone marrow\n\n• Balya: nutritive\n\n• Bruhana: nutritive treatment\n\n• Chhardi: vomiting\n\n• Chikitsa: treatment\n\n• Dahahara: dispelling one’s burning sensation\n\n• Dhatu: body tissue\n\n• Dhatukshayajanaya Vata Vyadhi: diseases of air entity due to its depletion\n\n• Dosha: bio humour\n\n• Drava Guna of Pitta:liquid nature of fire/hot entity in body\n\n• Go–Ghrita: cow clarified butter\n\n• Gomutra: cow urine\n\n• Granthi and Arbuda: cyst\n\n• Guda Daha: burning sensation at the anus\n\n• Guduch: Tinospora cordifolia\n\n• Kamdhenu Gomutra Ark: distilled cow urine\n\n• Kantakari: Solanum xanthocarpum\n\n• Kapha: phlegm\n\n• Kaphaghna: anti-phlegm\n\n• Kledahara: hydrous conetent absorber\n\n• Kledak Kapha Dushti: vitiation of phlegm\n\n• Laghusutshekhar Ras: herbs-minerals Ayurveda drug combination\n\n• Matra Vasti: oil retention enema\n\n• Mootra Daha: burning micturition\n\n• Mrudu Shodhana: mild detoxification\n\n• Nimba: Azadirachta indica\n\n• Niruha Vasti: decoction enema\n\n• Pachak Pitta: fire/hot entity in abdomen\n\n• Panchagavya: a combination of cow milk, curd, clarified butter, urine, and dung\n\n• Panchagavya Ghrita: Ghrit prepared from cow milk, curd, clarified butter, urine, and dung\n\n• Panchakarma: putative therapy\n\n• Panchatikta Kshir Vasti: enema of cow milk treated with Azadirachta indica (stem bark), Tinospora cordifolia (stem), Adhatoda vasica (root), Solanum xanthocarpum (root), and Trichosanthes dioica (aerial parts)\n\n• Patol: Trichosanthes dioica\n\n• Pitta Dosha: fire entity or humor in the body\n\n• Pitta Prakopaka: Pitta dosha flare-up\n\n• Pitta Shamaka: pacification of Pitta dosha\n\n• Pittghna: anti-bilious\n\n• Pursihvaha Strotas: eliminitory channels\n\n• Ras Dushti: vitiation of circulatory tissues in the body\n\n• Rasavaha Strotas: the channels of the body which convey the first tissue formed from the nutritive juices\n\n• Rasayana: immuno-modulators, anti-oxidant, bio-enhancing\n\n• Ruksha Guna: dry property\n\n• Saman Vayu: air entity at the abdomen\n\n• Sarvanaga Daha:burning sensation in all over body\n\n• Sarvang Daha: hot flushes\n\n• Shamana: pacification treatment\n\n• Shamana Snehapana: palliative oleation\n\n• Shodhana: purification\n\n• Snigdha Guna: unctuous property\n\n• Strotas:circulatory channels\n\n• Sukshma: micro\n\n• Tikshana Shodhana:extreme putative therapy\n\n• Ushna Guna: thermal properties\n\n• Vamana: therpeutic emesis\n\n• Vasa: Adhatoda vasica\n\n• Vatanulomak: the drugs responsible for the change in direction of Vata Dosha i.e. Vata means to blow or to move like the wind. Containing the elements like air and space,\n\n• Vatanulomama: correct the direction of Vata Dosha\n\n• Vatapradhan Pittaj Prakriti: patient having predominantly air entity followed by fire entity\n\n• Virechana:therpeutic purgation",
"appendix": "References\n\nInvasive Breast Cancer (IDC/ILC): [cited 2022 Jul 19]. Reference Source\n\nDefinition of infiltrating ductal carcinoma - NCI Dictionary of Cancer Terms - NCI: 2011 [cited 2022 Jul 19]. Reference Source\n\nMehrotra R, Yadav K: Breast cancer in India: Present scenario and the challenges ahead. World J. Clin. Oncol. 2022 Mar 24; 13(3): 209–218. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee RJ, Vallow LA, McLaughlin SA, et al.: Ductal carcinoma in situ of the breast. Int. J. Surg. Oncol. 2012; 2012: 123549. Epub 2012 Jul 18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAltun İ, Sonkaya A: The Most Common Side Effects Experienced by Patients Were Receiving First Cycle of Chemotherapy. Iran. J. Public Health. 2018 Aug; 47(8): 1218–1219. PubMed Abstract | Free Full Text\n\nFrenkel M: Refusing treatment. Oncologist. 2013; 18(5): 634–636. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChakraborty S, Rahman T: The difficulties in cancer treatment. Ecancermedicalscience. 2012 Nov 14; 6: ed16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRandhawa GK, Sharma R: Chemotherapeutic potential of cow urine: A review. J. Intercult. Ethnopharmacol. 2015 Apr-Jun; 4(2): 180–186. Epub 2015 Mar 7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoyal R, Kaur M, Chandola HM: A clinical study on the role of Agnimanthadi compound in the management of Sthaulya (obesity). Ayu. 2011 Apr; 32(2): 241–249. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahajan SP, Chavan SA, Shinde SA, et al.: Miraculous Benefits of Cow Urine: A Review. JDDT. 15 Aug. 2020 [cited 2023 Jul 20]; 10(4-s): 275–281. Publisher Full Text Reference Source\n\nRandhawa GK: Cow urine distillate as bioenhancer. J. Ayurveda Integr. Med. 2010 Oct; 1(4): 240–241. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDr. Kalwar AK : Kamdhenu Urine (Fresh) Therapy in Cancer Patients: A Holistic Approach, Souvenir of Go Anusandhana Kendra. Rajasthan: Kamdhenu Urine Centre; 2018.\n\nDr. Varmudy SS : A clinical study on Gomutra for Stage IV Oro Pharyngeal Carcinoma Undergoes Complete Regression, Approach, Souvenir of Go Anusandhana Kendra. Rajasthan: Kamdhenu Urine Centre; 2018.\n\nHoh JM, Dhanashree B: Antifungal effect of cow’s urine distillate on Candida species. J. Ayurveda Integr. Med. 2017; 8(4): 233–237. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPatil SS, Khilare MC: Ayurvedic management of amlapitta with special reference to hyperacidity: A case study. World Journal of Advanced Research and Reviews. 2022; 16(2): 1022–1027. Publisher Full Text\n\nArchana K, Vaghela DB: Management of Migraine with Ayurvedic Intervention-A Case Report. European J. Med. Plants. 2020 Sep 3; 60–64. Publisher Full Text\n\nSawarkar PG, Prasad KS: Concept of Sadyasnehana-A review. J. Indian Syst. Med. 2017 Oct 1; 5(4): 292.\n\nSharma Prof. Priyavat, Charaka Samhita of Agnivesha, treatise refined and annotated by Charaka and redacted by Dridhbala, English translation, Volume II, Chikitsasthana, Verse 16,8 th edition, Varanasi, India: Chaukhamba Orientalia.2007; 237.\n\nhttp\n\nAchliya GS, Kotagale NR, Wadodkar SG, et al.: Hepatoprotective activity of panchagavya ghrita against carbontetrachloride induced hepatotoxicity in rats. Indian J. Pharm. 2003 Sep 1; 35(5): 308–311.\n\nJoshi R, Reeta KH, Sharma SK, et al.: Pharmacodynamic and pharmacokinetic interaction of Panchagavya Ghrita with phenytoin and carbamazepine in maximal electroshock induced seizures in rats. Ayu. 2015 Apr; 36(2): 196–202. PubMed Abstract | Publisher Full Text\n\nSawarka G, Sawarkar P: Management of Obsessive-Compulsive Disorder (OSD) Through Ayurveda. J. Indian Syst. Med. 2018 Jul 1; 6(3): 157.\n\nSawarkar G, Sawarkar P: Case Study of Avascular Necrosis of Femoral Head. J. Indian Syst. Med. 2016 Jan 1; 4(1): 46.\n\nBhojraj N, Sawarkar G: The effect of Panchagavya formulations in the case of CA Rectum. Int. J. Ayurvedic Med. 2020; 11(3): 572–574. Publisher Full Text\n\nKadambari PB, Dharmarajan P, Prathibha CK, et al.: A Critical Review on the Concept of Avapeedaka Snehapana, a Special Mode of Lipid Administration. J. Evid.-Based Integr. Med. 2018; 23: 23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLandge A, Sawarkar G, Sawarkar P: The role of Ayurveda in the management of Asthimajjagata Vata (Spondylosis): A Case Report. Drugs and Cell Therapies in Hematology. 2021; 10(1): 3324–3333.\n\nSawarkar P, Deshmukh M, Sawarkar G, et al.: A Comparative Efficacy Study of the Panchtikta Ghrita Matra Vasti and Panchtikta Ghrita Marsha Nasya in Cervical Spondylosis. Int. J. Ayurvedic Med. 2020; 11(2): 218–227. Publisher Full Text\n\nHarinarayanan CM, Kumar D, Geetha SP, et al.: The phytochemical composition and therapeutic efficacy of an Ayurvedic drug combination Panchatikta: A review. Med. Plants - Int. J. Phytomed. Relat. Ind. 2022; 14(3): 355–373. Publisher Full Text"
}
|
[
{
"id": "220496",
"date": "19 Dec 2023",
"name": "Amit Nakanekar",
"expertise": [
"Reviewer Expertise Ayurveda",
"Herbal 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\nThis Case report nicely describes the importance of Pangavya and Panchkarma treatment in infiltrative ductal carcinoma. I congratulate the authors for successfully treating this challenging case. The authors have nicely explained the case in detail. I suggest authors avoid the use of complicated Ayurvedic terminologies to increase the visibility and citation value of the article. Authors need to emphasise the concepts rather than medicines in the discussion section. Authors can compare their current study with previously published articles. Please mention the quality of life scales used for this case report. Provide all the reports as a supplementary material\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? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "11346",
"date": "19 Jun 2024",
"name": "Punam Sawarkar",
"role": "Author Response",
"response": "Concepts are more emphasized in the discussion section based on reviewer comments and comparisons to prior published papers. A scale for quality of life is employed. WHOQOL-SRPB: scoring and coding for the WHOQOL SRPB field-test instrument: Users Manual, 2012 version, WHO Reference Number: WHO/MSD/MER/Rev.2012.05. All the supporting reports are submitted as a supplementary material"
}
]
}
] | 1
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https://f1000research.com/articles/12-1383
|
https://f1000research.com/articles/12-1514/v1
|
27 Nov 23
|
{
"type": "Case Report",
"title": "Case Report: Leathery black plaque on the temple and scalp",
"authors": [
"Kaveri Rusia",
"Bhushan Madke",
"Soham Meghe",
"Yash Kashikar",
"Bhushan Madke",
"Soham Meghe",
"Yash Kashikar"
],
"abstract": "Background Epidermal nevus sebaceous, commonly known as the nevus sebaceous of Jadassohn, is a congenital sebaceous hamartoma. It typically manifests as a single yellowish plaque across the head and neck and is composed of sebaceous glands. It commonly occurs during infancy and grows during puberty. Usually, it follows a benign course; however, in a few cases, it can be malignant. This is the case of a 13-year-old child with verrucous plaques on the temple and scalp.\n\nCase report We report the case of a 13-year-old boy with a steadily developing hyperpigmented verrucous plaque on the scalp and ipsilateral side of his face. A dermoscopic examination revealed ridges and fissures in a cerebriform pattern with yellowish-gray globules and a papillary appearance. Physical examination and laboratory tests revealed no abnormalities. Biopsies were taken from the scalp and temple area, and the findings were consistent with the diagnosis of nevus sebaceous. The patient was referred to a plastic surgeon for a staged excision.\n\nConclusions We describe a unique example of a sebaceous nevus that affected the scalp and ipsilateral side of the face. As this hamartomatous growth carries the risk of cancer development, a dermatologist must identify the condition and begin treatment before malignant transformation occurs. This example of multiple verrucous plaques is an exception.",
"keywords": [
"hamartoma",
"nevus sebaceous",
"scalp",
"case report"
],
"content": "Introduction\n\nNevus sebaceous (NS), initially described by Jadassohn, is a complicated hamartoma that typically develops on the face or scalp and has an epithelial or adnexal origin.1\n\nIt can appear at birth or develop in infancy and increases during puberty, suggesting a hormonal influence. It can occasionally be found in other locations, such as the trunk or the oral or vaginal mucosa, although it mostly affects the scalp. Less frequently, it affects the preauricular area and neck.2\n\nNevus sebaceous of Jadassohn (NSJ) develops in three stages. It manifests as isolated, well-circumscribed, smooth, yellowish plaques without hair during the infantile period. It becomes more noticeable with a verrucous or mamillated appearance during puberty. The last stage is characterised by peripheral telangiectasias and a nodular or tumoral appearance.3\n\nMany neoplasms develop alongside NS as proliferative growth begins. Both benign and malignant tumors have been reported to grow in NS. NS can be a site of basal cell cancer, syringocystadenoma papilliferum, trichoblastoma, and hidradenoma.4\n\n\nCase report\n\nA 13-year-old boy visited the dermatology outpatient department on 8th September 2023 with a raised lesion on his scalp since birth and a lesion that had spread to the left side of the face over ten years. The ophthalmological, neurological, or cutaneous systems did not exhibit any abnormalities during physical examination. These skin lesions had not previously occurred in the family. The results of all laboratory tests, including the kidney function test, liver function test, urine examination, and complete blood count were within normal ranges. The patient had no other complaints.\n\nOn cutaneous examination, a well-demarcated hyperpigmented verrucous plaque with a size of 8 × 4 cm was present on the frontal area of the scalp extending down to involve the forehead and a 7 × 3 cm plaque was present on the temporoparietal area and left preauricular area [Figure 1]. Based on the patient’s medical history and physical examination, the possible differential diagnoses were identified as congenital melanocytic nevus, giant seborrhoeic keratoses, and verrucous epidermal nevus. However, a thorough examination through dermoscopy and histology conclusively ruled out these possibilities. On dermoscopic examination, ridges and fissures were present in a cerebriform pattern with yellowish-grey globules and a papillary appearance [Figure 2]. Histopathological examination revealed acanthosis, papillomatosis, and mild hyperkeratosis. There were immature and mature sebaceous glands with sebaceous hyperplasia and primitive hair follicles [Figure 3]. The diagnosis of nevus sebaceous was established based on clinical presentation, dermoscopic findings, and histological analysis. The patient was referred to a plastic surgeon on 8th September 2023 for a staged surgical excision of the nevus sebaceous. Our dermatology department does not offer plastic surgery services, hence the referral. Unfortunately, the patient was lost to follow-up after the referral, and we do not have any further information available.\n\n(Written informed consent for publication of their clinical details and clinical images was obtained from the relatives of the patient).\n\n\nDiscussion\n\nNevus sebaceous is a condition that appears at birth and increases in size with age. The exact cause of this condition is still uncertain, but recent studies have shown that it may be linked to women who have tested positive for the human papillomavirus or carry mutations in the PTCH gene.5,6\n\nNevus sebaceous can present as one of the manifestations of Epidermal Nevus Syndrome.7 There are some hereditary syndromes, including didymosis aplasticosebacea and SCALP (sebaceous nevus, central nervous system malformations, aplasia cutis congenita, limbal dermoid, and pigmented nevus) syndrome, that may present nevus sebaceous as a symptom. This condition typically appears as a smooth, yellowish-orange, round, oval, or linear plaque, mostly on the scalp, leading to alopecia.5\n\nA previous study found that nevus sebaceous can occur in multiple locations, similar to verrucous epidermal nevi.8 Nevus sebaceous is rarely reported in the literature to affect the scalp and ipsilateral side of the face.9 In our case, the scalp and the ipsilateral side of the face were affected.\n\nSeveral discussions have taken place regarding the emergence of secondary benign and malignant tumors inside the nevus sebaceous. While basal cell carcinoma development has been documented by multiple authors in adults, recent reports have also identified atypical malignant neoplasms such as eccrine porocarcinoma, sebaceous carcinoma, apocrine carcinoma, and squamous cell carcinoma developing inside the NS.10,11\n\nAlthough the timing of resection for nevus sebaceous therapy is debatable, most researchers feel that surgical excision is the preferred course of action. However, surgical excision to remove nevus sebaceous creates a linear scar. There are various therapeutic options, such as CO2 laser therapy, to reduce scarring. However, CO2 laser vaporization completely eradicates the sebaceous section of the nevus, which is located in the epidermis or papillary dermis.12\n\n\nConclusions\n\nThe primary take-away lesson from our case is as follows: We describe a unique example of a sebaceous nevus that affected the scalp and ipsilateral side of the face. As this hamartomatous growth carries the risk of cancer development, a dermatologist must identify the condition and begin treatment before malignant transformation occurs. This example of multiple verrucous plaques is an exception.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the relatives of 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\nLin HC, Lee JY, Shieh SJ, et al.: Large, papillomatous, and pedunculated nevus sebaceous. J. Dermatol. 2011 Feb; 38(2): 200–202. PubMed Abstract | Publisher Full Text\n\nKelati A, Baybay H, Gallouj S, et al.: Dermoscopic analysis of nevus sebaceus of Jadassohn: a study of 13 cases. Skin Appendage Disord. 2017 May 2; 3(2): 83–91. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSahu P, Lakra S, Dayal S: Nevus sebaceous on face: Histopathological and dermoscopic correlation. Indian Dermatol. Online J. 2020 Sep; 11(5): 878. Publisher Full Text\n\nAnkad BS, Beergouder SL, Domble V: Trichoscopy: the best auxiliary tool in the evaluation of nevus sebaceous. Int. J. Trichology. 2016 Jan; 8(1): 5–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoody MN, Landau JM, Goldberg LH: Nevus sebaceous revisited. Pediatr. Dermatol. 2012 Jan; 29(1): 15–23. PubMed Abstract | Publisher Full Text\n\nCarlson JA, Cribier B, Nuovo G, et al.: Epidermodysplasia verruciformis–associated and genital-mucosal high-risk human papillomavirus DNA are prevalent in nevus sebaceus of Jadassohn. J. Am. Acad. Dermatol. 2008 Aug 1; 59(2): 279–294. PubMed Abstract | Publisher Full Text\n\nHapple R: The group of epidermal nevus syndromes: Part I. Well defined phenotypes. J. Am. Acad. Dermatol. 2010 Jul 1; 63(1): 1–22. PubMed Abstract | Publisher Full Text\n\nCribier B, Scrivener Y, Grosshans E: Tumors arising in nevus sebaceus: a study of 596 cases. J. Am. Acad. Dermatol. 2000 Feb 1; 42(2): 263–268. PubMed Abstract | Publisher Full Text\n\nChi SG, Kim JY, Kim HY, et al.: Multiple nevus sebaceous occurring on the scalp and on the contralateral side of the face. Ann. Dermatol. 2011 Aug 1; 23(3): 389–391. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCorreale D, Ringpfeil F, Rogers M: Large, papillomatous, pedunculated nevus sebaceus: a new phenotype. Pediatr. Dermatol. 2008 May; 25(3): 355–358. PubMed Abstract | Publisher Full Text\n\nJadassohn J: Bemerkungen zur histology der systematisierten naevi und ubertigdrusen naevi. Arch. Dermatol. Syphilol. 1895; 33: 355–372. Publisher Full Text\n\nAshinoff R: Linear nevus sebaceus of Jadassohn treated with the carbon dioxide laser. Pediatr. Dermatol. 1993 Jun; 10(2): 189–191. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "241167",
"date": "23 Feb 2024",
"name": "Dipanjan Basu",
"expertise": [
"Reviewer Expertise Cell biology and therapeutic strategies of Large /giant congenital nevi and neurocutaneous melanocytosis."
],
"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\nNevus sebaceous of Jadassohn is known as a rare congenital malformation, grouped under hamartomas. Etiology is thought to be driven by somatic post-zygotic mutations in RAS genes among others. The clinical manifestation occurs as plaques and is commonly found on scalp and face, usually presenting with a verrucous appearance. The current study under review discusses a case of a 13-year-old child with verrucous plaques on the temple and scalp. The authors describe the case as Nevus sebaceous of Jadassohn based on clinical, dermoscopic and histological analysis. The case exhibits classic characteristics of a sebaceous nevus including hyperplasia of sebaceous glands. The incidence of nevus sebaceus is estimated approximately at 0.1% to 0.3% of all newborns without bias for sex or ethnicity. This case report is a valuable addition to previous reports to understand the nuances of this condition and would be a valuable source of knowledge for students and practicing clinicians. The authors described the background of the case’s history and progression in adequate detail including reference to current literature. However, the authors may include that RAS genes are also implicated in the development of this condition (See Ref [1],[2]. The authors describe in detail the process of diagnosis presenting appropriately labeled representative figures. However, it would be helpful for the readers if the histological images are presented with a scale bar of magnification. Overall, a well-presented case report to add to the existing knowledge on this congenital malformation.\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? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "11324",
"date": "13 Apr 2024",
"name": "Kaveri Rusia",
"role": "Author Response",
"response": "Thank you for your response."
}
]
},
{
"id": "251438",
"date": "28 Mar 2024",
"name": "Aswath Rajan",
"expertise": [
"Reviewer Expertise dermatology"
],
"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\nArticle is very well written. However here are following few suggestions/queries that could add more value to it. I had copied your statement mentioned in bold letters and its queries below it. here as follows,\n\n1. \"As this hamartomatous growth carries the risk of cancer development, a dermatologist must identify the condition and begin treatment before malignant transformation occurs\" Q: a) as the lesion is bigger, how did you confirmed that malignant transformation had not occurred in the lesion. what was the measures taken to identify malignancy change in the entire lesion.\n\nb) Was dermoscopy performed over the entire lesion! Was biopsy done on any suspicious part!\n2. \"The results of all laboratory tests, including the kidney function test, liver function test, urine examination, and complete blood count were within normal ranges.\" Q: what was the relevance and what laboratory abnormalities can be possibly expected in such cases.\n3. \"On dermoscopic examination, ridges and fissures were present in a cerebriform pattern with yellowish-grey globules and a papillary appearance\" Q: a) several dermoscopic features were missed out. Dermoscopy is the key factor in this case. As the biopsy cant be done over the entire lesion, dermoscopy can bridge the gap between clinical and histopathological findings. b) ridges and fissures seen in several other conditions like seborrheic keratosis, acanthosis nigricans, nevus. So What was the classical features in this case. c) mention about the clods/globules of different sizes and shapes d) several clods are black (indicates keratinous plug), bright black dots/globules indicates that it communicate with surface, whereas the dull black are intraepidermal one. e) was the biopsy performed on the same dermoscopic site. d) mention other close dermoscopic differential diagnosis and one or two points on its differentiation.\n\n4. \"Several discussions have taken place regarding the emergence of secondary benign and malignant tumors inside the nevus sebaceous\" Q: kindly mention for the readers, what are the possible clinical features that alerts the malignant change and its relevant investigations for early detection of local and systemic invasion with their likely management\n5.\" As this hamartomatous growth carries the risk of cancer development, a dermatologist must identify the condition and begin treatment before malignant transformation occurs\". Q: Malignant transformation was repeatedly emphasized in the article. So Mention the role of latest non-invasive skin imaging technique such as high-frequency ultrasound, multispectral imaging, optical coherence tomography, reflectance confocal microscopy etc. also mention a word on molecular/genetic study if reported earlier for early diagnosis of malignancy.\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? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "11349",
"date": "13 Apr 2024",
"name": "Kaveri Rusia",
"role": "Author Response",
"response": "Thank you for your comments. 1) We confirmed on clinical grounds that there were no clinical signs in the lesion to undergo a malignant transformation like ulceration, bleeding from the lesion or sudden increase in the size of the lesion. A dermoscopy was performed on the entire lesion and in the manuscript we have shown the characteristic features. On clinical examination, there were no suspicious parts to undergo malignant transformation so a biopsy was performed from a random site. 2) We performed the laboratory investigations since such cases may need surgical excision. 3) We have included the characteristic dermoscopic findings which were present in our case which is yellowish globules aggregated in clusters on a yellow background with cerebriform pattern of sulci and gyri. In seborrheic keratosis, other than ridges and fissures multiple milia and comedone-like openings will be there. In acanthosis nigricans, there will be papillary projections with hyperpigmented dots and perifollicular pigmentation. 4) The process of malignant degeneration is often accompanied by rapid morphological changes and other symptoms. Some of the morphological changes and symptoms include a change in the color of the skin, protruding mass, ulceration, change in size, and itching. Reflectance Confocal Microscopy can be performed to detect the malignant transformation. 5) The non-invasive techniques like High-frequency Ultrasound are used to visualize skin and skin appendages for accurate depth and lateral border detection for skin malignant and benign tumors. The reflectance confocal microscopy allows in vivo evaluation of lesion of the microscopic extension of lesion and shows both anatomical features and individual cells. The presence of PTCH deletion, HRAS, KRAS mutation leads to malignant transformation in the nevus sebaceous."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1514
|
https://f1000research.com/articles/11-1573/v1
|
23 Dec 22
|
{
"type": "Research Article",
"title": "Thickness and width of the menisci of adult knee joint: a descriptive cross-sectional observational study in cadavers",
"authors": [
"B.V. Murlimanju",
"S. Vikram",
"Vanishri Nayak",
"Nandini Bhat",
"Mangala M. Pai",
"Rajanigandha Vadgaonkar",
"Latha V. Prabhu",
"Sunil Nayak",
"B.V. Murlimanju",
"S. Vikram",
"Nandini Bhat",
"Mangala M. Pai",
"Rajanigandha Vadgaonkar",
"Latha V. Prabhu",
"Sunil Nayak"
],
"abstract": "Background: The goal was to determine the thickness and width of the knee joint meniscus at their different regions. The objective was to compare the dimensions at these regions and over the right- and left-sided specimens.\nMethods: The present study included 50 adult cadaveric knee joints, and 100 menisci (50 medial menisci and 50 lateral menisci) were studied. The meniscus was distributed into anterior, middle and posterior parts. Thickness and width at the mid-point of these three parts were determined by using the Vernier caliper.\nResults: The breadth of the medial meniscus was 8.38 ± 1.64 mm, 7.68 ± 1.92 mm and 13.93 ± 2.69 mm at the anterior, middle and posterior one-third regions. Same measurements for the lateral menisci at these regions were 9.84 ± 1.78 mm, 8.82 ± 2.01 mm and 10.18 ± 2.23 mm, respectively. The thickness of the medial meniscus was 4.49 ± 0.78 mm, 4.07 ± 0.81 mm and 4.79 ± 0.93 mm at these regions. The lateral meniscus thickness was 3.82 ± 0.69 mm, 4.43 ± 0.98 mm and 4.36 ± 0.8 mm, respectively.\nConclusion: It is believed that this data is enlightening to the arthroscopic surgeon during the meniscus transplantation either by using synthetic material or allograft as the proper sizing of the meniscus is important to prevent complications due to inaccurate sizing.",
"keywords": [
"allografts",
"arthroscopic meniscectomy",
"tibial meniscus",
"transplants"
],
"content": "Introduction\n\nThe investigation of intracapsular ligaments of knee joint is important in the clinical setup to make accurate diagnosis and surgical procedures of the knee joint. 1 There has been a substantial rise in the information about the arthroscopic management of the meniscal injuries. 2 The menisci can be easily injured and it is hard to repair them. 3 However, due to advanced technologies, the torn menisci can be repaired by arthroscopic surgery and the best modality of treatment available is the meniscal allograft transplantation, especially for the young symptomatic patients. 4 At present, arthroscopy can involve meniscal transplantation, scaffold implantation and insertion of healing substances at the torn area of the meniscus. 5 Meniscectomy can be performed arthroscopically and it is followed by synthetic or allograft meniscal transplantation as this prevents friction between the tibia and the femur. 6 It was opined that successful meniscus transplant surgery relies on the accuracy in the dimensions matching between the recipient and donor meniscus. 7 Precision of the measurements between the allograft and the recipient knee is important for successful function of the meniscus after the transplantation surgery. If the graft size is small, forces acting on the meniscus are increased, which may lead to misbalancing of the femoral condyles and compartment overload. 8 If the allograft is larger, there will be no load bearing and the forces will be increased over the articular cartilages of the knee joint, which causes degenerative changes in the knee joint. 7 It was reported that only 5-10% of the mismatch of the graft size is accepted. 9\n\nThe morphometric data of menisci will also assist the biomechanical research and hypothesis, which explores the functional relationships of the femoro-tibial articulation. 10 This has implications for tissue engineering of the meniscus and offering the normal joint function. There are clinical studies, which suggest that radiological measurements of the menisci need to be compared with the menisci from cadaveric specimens to confirm and make the radiological method as the gold standard. 7 The morphological information about the sizes of the meniscus can benefit in differentiating the normal meniscus from the discoid and tiny meniscus. 11 The bucket handle meniscal tear decreases the width, so it is important to differentiate the torn meniscus from the normal meniscus in the radio diagnosis. It was reported that, alterations in the width and thickness of meniscus can give clue to the type of its injury and impact. 12 Smillie 13 described that the thickness and width of the menisci are important to understand the possibility, location and type of meniscal injury. The morphological variability between the meniscus of medial and lateral compartment is important to understand the meniscal damage. 13\n\nThe operating surgeons should ask the tissue providing banks for the allograft, which matches with the dimension of the torn meniscus. 7 In this context, the normative data about the breadth and thickness of the menisci may help in choosing the accurate meniscal graft. Due to these clinical implications, the objective of the present research was to measure the breadth and depth of the meniscus in corpses and provide normative data of this sample population. The objective was to correlate the dimensions over the three different regions of meniscus and over the right- and left-sided specimens.\n\n\nMethods\n\nThis study was a descriptive cross-sectional observational research, performed at the department of anatomy of Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India. All the strobe guidelines for the cross-sectional study are met and the details are available at https://figshare.com/articles/dataset/Strobe_Checklist/21605694. The study participants were formalin fixed human adult cadaveric knee joints of unknown age and gender. Only embalmed undissected lower extremity specimens were included in this study. The specimens, which exhibited the visible pathological changes and congenital anomalies were excluded. The study duration was one year from 23.08.2021 to 23.08.2022. The sample size was 50 adult cadaveric knee joints; amongst them 25 were right- sided and 25 left-sided specimens. The sample size of this present study was calculated by the formula 'n = Zα2 x σ2/d2', where Zα= 1.96 at 95% confidence level, σ = standard deviation, d= 1% absolute precision with 95% confidence level and 80 % power with 1% absolute precision, the sample size comes to be 100. The reference article used to calculate the sample size was El-Aasar et al. 14\n\nIn total, 100 menisci were studied (50 medial menisci and 50 lateral menisci). The gender of the specimens were not taken into consideration. The cadaveric lower limbs were frozen, which were initially embalmed with 10% formalin. After dissecting the skin, fascia and muscles, a longitudinal cut was given on the medial and lateral sideways of the knee joint to open the capsule. The ligamentum patellae, tibial and fibular collateral ligaments were cut by giving a transverse incision. The knee capsule and cruciate ligaments were cut for better access to the menisci, while the femoral and tibial condyles were separated from the soft tissues, which exposed the whole menisci. The knee joints which showed pathological changes and were found damaged were excluded from the present study. The knee joints exhibiting congenital anomalies and tears of the menisci were also disqualified from the present research. This present research followed the guidelines of the international ethical standards as per Padulo et al. 15\n\nThe menisci were allocated into three parts by measuring with a thread and the points were marked. These three regions were named as the anterior, middle and posterior one third (Figure 1) and the measurements of thickness and width were performed at their middle parts. This was approximately corresponding to the 1 o clock, 3 o clock and 5 o clock positions. The measurements were performed with the vernier caliper of 0.02 mm accuracy. At the mid-point of each 1/3, the caliper was positioned between the outer and inner borders of the menisci to measure the width. The thickness was measured at the same points by placing the caliper between the upper and lower surfaces of the menisci at the outer edge only. All the dimensions were completed by the same researcher to avoid the inter observer variation and three readings were taken for each measurement to prevent the intra-observer error.\n\nThe data were tabulated in the microsoft excel (RRID:SCR_016137) document and presented as mean ± standard deviation. The online SPSS (RRID:SCR_002865) program (version number 25) was utilized for the analysis. The calculation of values and statistical analysis between the right versus left sides and medial versus lateral tibial partitions were done by using the paired samples ‘t’ test and repeated measures ANOVA (online software SPSS (RRID:SCR_002865), version number 25, https://www.ibm.com/products/spss-statistics-gradpack). The ‘p’ value less than 0.05 was considered as significant (α = 0.05). The protocol of this research is available online at https://www.protocols.io/view/thickness-and-width-of-the-menisci-of-adult-knee-j-cjh2uj8e.\n\n\nResults\n\nThe thickness and width of the medial meniscus at the 3 different regions are tabulated and compared among the right and left sides (Table 1). Table 2 shows the morphometric data and comparison of lateral meniscus among the left and right knee joints. The present study observed that there was no significance in this comparison for the thickness and width between the corresponding right and left knee menisci, in both medial and lateral compartments (p>0.05).\n\nThe medial and lateral menisci were compared to each other irrespective of their side and the comparison is given in Table 3. Related to the peripheral circumference thickness, the anterior one-third region of medial meniscus is thicker than the lateral (p<0.05). But in the middle and posterior third regions (Table 3), medial and lateral menisci are of relatively same thickness (p>0.05). In the anterior and middle third regions, the lateral meniscus has additional width than the medial (p<0.05). But in the posterior one-third region, medial meniscus was wider (p<0.05), than the lateral meniscus (Table 3).\n\n* p<0.05\n\nThe posterior one-third region of the medial meniscus is thicker (Figure 2) than its anterior and middle one-thirds (p<0.05). The middle and anterior one-third regions are of the same relative thickness (p>0.05). The posterior one-third region of the medial meniscus has greater width (Figure 2) than its own anterior and middle one-thirds (p<0.05). The anterior and middle one-third regions were of the same relative width (p>0.05).\n\nThe statistics did not reveal the differences (p>0.05) amongst the thicknesses of anterior, middle and posterior parts of lateral meniscus (Figure 3). However, the ventral and dorsal one-third regions of lateral meniscus (Figure 3) are of the same relative width (p>0.05) and they are greater than the middle one-third region (p<0.05).\n\nAfter taking the average from all the three regions, the breadth of medial and lateral meniscus was 9.69 ± 1.89 mm and 9.61 ± 1.77 mm, respectively. The average thickness of the medial and lateral meniscus was 4.39 ± 0.67 mm and 4.17 ± 0.58 mm, correspondingly. With respect to the average dimensions of width and thickness, the statistical significance was not observed (p>0.05) between the medial and lateral meniscus.\n\n\nDiscussion\n\nMeniscal damages are among the most frequent harms in the sports medicine, which can cause pain, functional disability and swelling around the knee joint. 16 The meniscal tears occur due to the bending forces and rotational knee injuries. They can also occur due to degeneration or spontaneously due to the progressive structural failure, which is known as the meniscal fatigue injury. 17 Knee arthroscopy is the gold standard investigation, which can simultaneously treat the meniscus disorders. 3 The graft sizing, precise positioning and fixation are the three prerequisites for successful allograft meniscal transplantation. 18 In allograft meniscal transplantation, which is performed for the torn menisci, inaccurate size of the graft can lead to its failure and cause complications like knee joint degeneration. Successful arthroscopic meniscal transplantation and regeneration depend on the accuracy in the shape and size of the allograft in comparison to the torn meniscus. This requires the morphometric data of the menisci as the mismatching leads to surgical failure and degenerative changes in the knee joint. 9 , 19 – 20 The normative data of dimensions of the meniscus are essential while planning the surgical interventions of the knee joint. This can help in differentiating the discoid meniscus from a normal one. The discoid meniscus is an anomaly and develops due to the variability in the morphogenesis. 21 It was reported that, variability in the thickness and width of menisci can lead to the meniscal injury. 12 Meniscectomy has long-term complications like joint degeneration, and it is advisable to do conservative surgery by repairing the torn meniscus, but for this, grafting is required. Accurate size of the meniscal allograft is required for the success of the arthroscopic surgery in terms of the joint function and healing. The correct sizing of the graft requires detailed knowledge about the dimensions of the menisci.\n\nIn this perspective, the present cadaveric study has provided normative data about the thickness and width of the meniscus in this sample population of Indians. The complete set of data of the present study was compared with the previous studies from other populations and is represented in Table 4. The observations of the present study agree with the findings of Didio, 22 Braz and Silva 23 that the posterior region was the broadest among all the three regions in the medial meniscus. In our previous study from fetal knee joints also, it was found that the posterior part was the wider of the medial meniscus. 24 In this research from Indian samples, significant difference was not obtained among the anterior and middle third widths. This was similar to our finding in the previous study in fetal medial meniscus. 24 However, Braz and Silva 23 stated that the mid body of the medial meniscus has greater width than the anterior one-third.\n\nAlmeida et al., 12 Braz and Silva 23 reported no statistical significance in the comparison of the width between the three regions of the lateral meniscus. We observed that the anterior and posterior one-third regions of lateral meniscus were of the same relative width. However, these two regions were wider than the middle one-third region. In the fetal lateral meniscus, it was a different observation, where the middle region was the widest. 24\n\nIn vivo radiological research by Bloecker et al. 10 revealed that medial meniscus has greater thickness than the lateral. However, there was no significance in the differences with respect to the breadth. Testut and Latarjet, 25 and Didio 22 reported that, meniscus of the medial side is wider than the lateral, when the average measurement was taken. Miller 26 also had the same observations in his study. However, the present study does not agree with these opinions as we didn’t find differences between the medial and lateral compartments, when the average was taken from all the three regions.\n\nFigueroa et al. 27 observed that, the anterior region of lateral meniscus is wider than the medial meniscus. In this study, dissimilarity was not observed between the medial and lateral meniscus, average widths. Dhananjaya et al. 28 reported the in vivo measurements of the menisci in south Indian population. In their study, it was obvious that the lateral meniscus had higher breadths at the anterior and middle regions than its counterpart. They also detected that the posterior region of the medial meniscus had higher width than the lateral meniscus in the same region. They noted that the medial and lateral menisci were wider at their posterior region than the anterior region. The middle one-third region was relatively lesser in width.\n\nHowever, the present study agrees with the finding of Braz and Silva 23 that the anterior region of the medial meniscus has greater thickness than that of the same part of the lateral meniscus. Our study agrees with the Bloecker et al. 10 that the thickness of the middle part of the medial and lateral menisci was the same. We further observed that the thickness of the dorsal part of the medial and lateral menisci was the same. This is not as per the findings of Bloecker et al., 10 where posterior region of medial meniscus was thicker than its counterpart. The study of fetal knee joints did not reveal statistically significant variance with respect to the thickness of the menisci of the medial and lateral compartments. 24 However, the lateral meniscus had greater width than its counterpart in the medial compartment in the fetal tibia.\n\nRico and Ayala 29 opined that the middle part of the medial menisci is prone to tears (51%), which is followed by the posterior one-third (39%). This was supported by the anatomical studies, and it was hypothesized that thicker region of the meniscus is more prone for tears. Braz and Silva 23 stated that, middle region of the medial meniscus was thicker, which is trailed by the posterior and anterior regions. Almeida et al. 12 published that the anterior end of medial meniscus was thicker, followed by the posterior and middle regions. The present study is not in agreement with this observation that, we found posterior one-third region of the medial meniscus is thicker than its anterior and middle one-thirds. This supports the clinical findings of Miller 26 that the longitudinal tears of the menisci were more common at the posterior region. The meniscal thickest region is prone to the friction between the condyles of femur and tibia. In the study by using the fetal knee joints, the anterior region of medial meniscus was thicker in comparison to the posterior and middle regions. 24\n\nMiller 26 reported that, middle part of the lateral meniscus is prone to radial tears. Braz and Silva 23 stated that, middle region of lateral meniscus was thicker, which is trailed by the posterior and anterior regions. Almeida et al. 12 also described the same observations as Braz and Silva. 23 The present study observed a different finding that the statistically significant difference was not observed between the thicknesses of the three regions of the lateral menisci. This is similar to the observations of our previous study from fetal specimens. 24\n\nIn this anatomical investigation, breadth and thickness measured at the three locations of lateral and medial menisci over the right and left knee joints did not show statistical significance. This confirms the opinion of Dargel et al. 30 that, there is a similarity in the dimensions of the right and left knees, even though they are asymmetrical. Hence, the contralateral radiological measurement of the corresponding meniscus may be considered while choosing the meniscus allograft. Prodromos et al. 31 suggested that, during the transplantation surgery, the contralateral meniscal dimensions measured by the magnetic resonance imaging can help in choosing the graft. The present study supports this opinion as there was no statistical significance observed between the comparison of these parameters.\n\n\nImplications and Limitations\n\nThe meniscal injuries are commonly observed as sports injuries like in soccer, cricket and baseball players. The arthroscopy is playing a paramount part in the treatment of these traumatic lesions. It is believed that the morphometric data of this research will be of help to the arthroscopic surgeons during the surgical repair of the torn meniscus and allograft meniscal transplantation. The data procured here can be of help in the manufacture of the artificial implants.\n\nThe limitation of the present study includes the smaller sample size, with respect to this group of Indian sample population. The age wise and gender-based comparison was also not performed in this study. The right and left embalmed knee joints were not from the same individual in this cadaveric research. For the paired test, the best would be to have the right and left samples from the same individual. This study utilized embalmed cadaveric specimens, in which formalin may alter the dimensions of the menisci and during the disarticulation of the femur and tibia, the anatomy of the menisci might have been disturbed, which may alter the width and thickness of the menisci.\n\n\nConclusion\n\nBest meniscal arthroscopic transplant surgeries depend on the correct sizing of the allografts or synthetic material. In this context, the present study has provided morphometric data of the menisci of the lateral and medial compartments in detail with respect to their width and thickness at the anterior, middle and posterior regions. We believe that these data are of help to the arthroscopic surgeon during the comparison of the radiological measurement with the cadaveric measurement and assessing the graft selection.\n\n\nEthical Approval\n\nThe ethics committee of our institution approved this research (Ethical Committee Name - Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee, Approval Number - IEC: 284/2021, dated 31.12.2021). Since this is a study from the cadaveric samples, the consent from the participants is not applicable. This was waived by our institutional ethics committee.\n\n\nConsent\n\nSince this is a cross-sectional study from the donated cadavers and did not reveal the identity of the body donor, the written informed consent was not taken from the body donor’s family for the use and publication of this research.",
"appendix": "Data availability\n\nFigshare: Medline database search strategy for ‘Thickness and width of the menisci of adult knee joint, a cadaveric study’ https://doi.org/10.6084/m9.figshare.21383763.v1. 32\n\nThe project contains the following underlying data:\n\n- (file name - master chart 6.xls).\n\nSupplementary figure is available at https://www.protocols.io/view/thickness-and-width-of-the-menisci-of-adult-knee-j-cjh2uj8e.\n\nFigshare: STROBE checklist for ‘[Thickness and width of the menisci of adult knee joint: a descriptive cross-sectional observational study in cadavers]’. https://figshare.com/articles/dataset/Strobe_Checklist/21605694\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\nKale A, Kopuz C, Edýzer M, et al.: Anatomic variations of the shape of the menisci: a neonatal cadaver study. Knee Surg. Sports Traumatol. Arthrosc. 2006; 14(10): 975–981. PubMed Abstract | Publisher Full Text\n\nLee AS, Kang RW, Kroin E, et al.: Allograft meniscus transplantation. Sports. Med. Arthrosc. 2012; 20(2): 106–114.\n\nVaquero J, Forriol F: Meniscus tear surgery and meniscus replacement. Muscles Ligaments Tendons J. 2016; 6(1): 71–89. PubMed Abstract | Publisher Full Text\n\nWang YJ, Yu JK, Luo H, et al.: An anatomical and histological study of human meniscal horn bony insertions and perimeniscal attachments as a basis for meniscal transplantation. Chin. Med. J. 2009; 122(5): 536–540. PubMed Abstract\n\nde Albornoz PM , Forriol F: The meniscal healing process. Muscles Ligaments Tendons J. 2012; 2(1): 10–18. PubMed Abstract\n\nElsner JJ, Portnoy S, Guilak F, et al.: MRI-based characterization of bone anatomy in the human knee for size matching of a medial meniscal implant. J. Biomech. Eng. 2010; 132(10): 101008. PubMed Abstract | Publisher Full Text\n\nKaleka CC, Netto AS, Silva JC, et al.: Which are the most reliable methods of predicting the meniscal size for transplantation?. Am. J. Sports Med. 2016; 44(11): 2876–2883. PubMed Abstract | Publisher Full Text\n\nNoyes FR, Heckmann TP, Barber-Westin SD: Meniscus repair and transplantation: a comprehensive update. J. Orthop. Sports Phys. Ther. 2012; 42(3): 274–290. PubMed Abstract | Publisher Full Text\n\nDienst M, Greis PE, Ellis BJ, et al.: Effect of lateral meniscal allograft sizing on contact mechanics of the lateral tibial plateau: an experimental study in human cadaveric knee joints. Am. J. Sports Med. 2007; 35(1): 34–42. PubMed Abstract | Publisher Full Text\n\nBloecker K, Wirth W, Hudelmaier M, et al.: Morphometric differences between the medial and lateral meniscus in healthy men - a three-dimensional analysis using magnetic resonance imaging. Cells Tissues Organs. 2012; 195(4): 353–364. PubMed Abstract | Publisher Full Text | Free Full Text\n\nErbagci H, Gumusburun E, Bayram M, et al.: The normal menisci: in vivo MRI measurements. Surg. Radiol. Anat. 2004; 26(1): 28–32.\n\nAlmeida SKS, Demoraes ASR, Tashiro T, et al.: Morphometric study of menisci of the knee joint. Int. J. Morphol. 2004; 22(3): 181–184.\n\nSmillie IS: Injuries of the knee Joint. London:Living Stone;4th ed1975; 79–84.\n\nEl-Aasar HM, Nasralla MM, Kamal HA, et al.: Anatomical and morphomertic study of the menisci of the knee joint in Egyptians. Med. J. Cairo Univ. 2018; 86(12): 4475–4494.\n\nPadulo J, Oliva F, Frizziero A, et al.: Muscles, Ligaments and Tendons Journal – Basic principles and recommendations in clinical and field Science Research: 2018 update. Muscles Ligaments Tendons J. 2018; 8(1): 305–307.\n\nFrizziero A, Ferrari R, Giannotti E, et al.: The meniscus tear. State of the art of rehabilitation protocols related to surgical procedures. Muscles Ligaments Tendons J. 2012; 2(4): 295–301. PubMed Abstract\n\nCamanho GL: Lesao meniscal por fadiga. Acta Ortopedica Brasileira. 2009; 17: 31–34. Publisher Full Text\n\nWajsfisz A, Meyer A, Makridis KG, et al.: A new arthroscopic technique for lateral meniscal allograft transplantation: cadaver feasibility study. Orthop. Traumatol. Surg. Res. 2013; 99(3): 299–304. PubMed Abstract | Publisher Full Text\n\nHaut TL, Hull ML, Howell SM: Use of roentgenography and magnetic resonance imaging to predict meniscal geometry determined with a three-dimensional coordinate digitizing system. J. Orthop. Res. 2000; 18(2): 228–237. PubMed Abstract | Publisher Full Text\n\nPollard ME, Kang Q, Berg EE: Radiographic sizing for meniscal transplantation. Arthroscopy. 1995; 11(6): 684–687. Publisher Full Text\n\nMurlimanju BV, Nair N, Ray B, et al.: Morphological variants of lateral meniscus of the knee: a cadaveric study in South Indian human fetuses. Anat. Sci. Int. 2011; 86(2): 63–68. PubMed Abstract | Publisher Full Text\n\nDidio LJA: Tratado de Anatomia Aplicada. São Paulo:Atheneu;2nd ed2002.\n\nBraz PRP, Silva WG: Meniscus morphometric study in humans. J. Morphol. Sci. 2010; 27(2): 62–66.\n\nMurlimanju BV, Nair N, Pai SR, et al.: Morphometric analysis of the menisci of the knee joint in south Indian human fetuses. Int. J. Morphol. 2010; 28(4): 1167–1171. Publisher Full Text\n\nTestut L, Latarjet A: Tratado de Anatomía Humana. Barcelona:Salvat;10th ed1975.\n\nIII Miller RH :Knee injuries.Canale ST, Beatty JH, editor. Campbell's Operative Orthopaedics. Philadelphia:Mosby Elsevier;2003; pp. 2182–2199.\n\nFigueroa M, Rios ALL, Narvaez C: Menisco discoid interno: presentacion de un caso y revision de la literatura. Rev. Colom. Ortop. Traumat. 1999; 13(2): 155–158.\n\nDhananjaya K, Murlimanju BV, Poornima V, et al.: In vivo morphometry of menisci of the knee in South Indians: A preliminary study. Biomed. J. 2014; 37(1): 14–17. PubMed Abstract | Publisher Full Text\n\nRico EGC, Ayala CEA: Localizacion de las rupturas meniscales en nuestro medio. Rev. Mex. Ortop. Traumatol. 1997; 11(1): 10–13.\n\nDargel J, Feiser J, Gotter M, et al.: Side differences in the anatomy of human knee joints. Knee Surg. Sports Traumatol. Arthrosc. 2009; 17: 1368–1376. Publisher Full Text\n\nProdromos CC, Joyce BT, Keller BL, et al.: Magnetic resonance imaging measurement of the contralateral normal meniscus is a more accurate method of determining meniscal allograft size than radiographic measurement of the recipient tibial plateau. Arthroscopy. 2007; 23(11): 1174–1179.e1. Publisher Full Text\n\nVanishri N: ‘Thickness and width of the menisci of adult knee joint, a cadaveric study’. xlsx. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "166822",
"date": "14 Jul 2023",
"name": "Narendra Pamidi",
"expertise": [
"Reviewer Expertise Clinical Anatomy"
],
"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 anthropometric study involves measuring the dimension of the menisci of the human knee joint. The sample size (50 cadavers) was good enough to derive statistically significant data to be useful for clinical evaluation. The data on measuring the menisci can help diagnose meniscal tears and determine the extent of the injury in preoperative planning, rehabilitation and in the prevention of Knee Osteoarthritis. The authors have used relevant literature to support their findings and appropriate statistical analysis to evaluate the data. Overall, I find this article is suitable for indexing and adds new information to the fields of anatomy and surgery.\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": "9913",
"date": "29 Nov 2023",
"name": "Vanishri Nayak",
"role": "Author Response",
"response": "We thank the reviewer for the expert comments. The morphometric data of this study are enlightening to the field of arthroscopic surgery. It has implications in analyzing the meniscal tears and discoid meniscus. The data can be used as morphological database for the Indian population."
}
]
},
{
"id": "243696",
"date": "28 Feb 2024",
"name": "C.S Ramesh Babu",
"expertise": [
"Reviewer Expertise Radiological Anatomy and Clinical Anatomy"
],
"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 adds morphometric data useful for selecting appropriate meniscal allograft transplant. Measurements of width and thickness of the menisci were done dividing the menisci into anterior, middle and posterior parts but authors failed to explain the exact method used nor provided any reference where such a method was described. Authors have also mentioned \"this was approximately corresponding to 1 o'clock, 3 o'clock and 5 o'clock positions\" but failed to add for which meniscus - lateral or medial / right side or left side. It is suggested that the exact method adopted by the authors to divide the menisci into three parts be added in the update. Coronal MRI images of the menisci appear triangular with a thick peripheral border and a thin inner border. How can the measurements made at MRI examination of normal knee joint of the recipient be used for selection of a cadaveric meniscal allograft?\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": []
}
] | 1
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https://f1000research.com/articles/11-1573
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https://f1000research.com/articles/12-745/v1
|
26 Jun 23
|
{
"type": "Data Note",
"title": "The identification of high-performing antibodies for RNA-binding protein TIA1 for use in Western Blot, immunoprecipitation and immunofluorescence",
"authors": [
"Maryam Fotouhi",
"Donovan Worrall",
"Riham Ayoubi",
"Kathleen Southern",
"Peter S. McPherson",
"Carl Laflamme",
"NeuroSGC/YCharOS/EDDU collaborative group",
"ABIF Consortium",
"Maryam Fotouhi",
"Donovan Worrall",
"Riham Ayoubi",
"Kathleen Southern",
"Peter S. McPherson"
],
"abstract": "A member of the RNA-binding protein family, T-cell intracellular antigen-1 (TIA1) regulates mRNA translation and splicing as well as cellular stress by promoting stress granule formation. Variants of the TIA1 gene have implications in neurogenerative disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Reproducible research on TIA1 would be enhanced with the availability of high-quality anti-TIA1 antibodies. In this study, we characterized twelve TIA1 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 P31483",
"TIA1",
"RNA-binding protein TIA1",
"antibody characterization",
"antibody validation",
"Western Blot",
"immunoprecipitation",
"immunofluorescence"
],
"content": "Introduction\n\nT-cell intracellular antigen 1, or TIA1, is a cytotoxic granule-associated RNA-binding protein involved in regulating alternative pre-mRNA splicing and mRNA translation when bound to 3’ uridine-rich RNA sequences.1–4 Suppressing translation in environmentally stressed cells and promoting stress granule formation, TIA1 modulates cellular response to stress and inflammation.5,6\n\nComparable to other RNA-binding proteins, disrupting the function of TIA1 can lead to various diseases including cancer, autoimmune diseases and neurodegenerative disorders. Studies have demonstrated that mutations to the TIA1 gene may delay the disassembly of stress granule, resulting in insoluble and immobile stress granules, a clinical feature of ALS and FTD.6,7 Significant efforts are required to further elucidate the relationship between dysregulated RNA metabolism and ALS/FTD pathogenesis which may lead to novel therapeutic discoveries.7,8\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 TIA1 and identified high-performing antibodies for Western Blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of TIA1 properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells.9–16 The first step was to identify a cell line(s) that expresses sufficient levels of TIA1 to generate a measurable signal. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available HAP1 cells expressed the TIA1 transcript at RNA levels above the average range of cancer cells analyzed. Parental and TIA1 KO HAP1 cells were obtained from Horizon Discovery (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and TIA1 KO cell extracts and probed them side-by-side with all antibodies in parallel (Figure 1).10–16\n\nLysates of HAP1 (WT and TIA1 KO) were prepared and 50 μg of protein were processed for Western Blot with the indicated TIA1 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. Antibody dilution used: ab140595** at 1/5000; ab263945** at 1/1000; A6237 at 1/1000; ARP40979 at 1/500; ARP40981 at 1/200; NBP2-53336* at 1/1000; NBP2-67203** at 1/1000; NBP3-13791** at 1/500; 86050** at 1/1000; GTX33545 at 1/500; MA5-26474* at 1/2000; and MA5-32615** at 1/500. Predicted band size: 43 kDa. *=monoclonal antibody, **=recombinant antibody.\n\nFor immunoprecipitation experiments, we used the antibodies to immunopurify TIA1 from HAP1 cell extracts. The performance of each antibody was evaluated by detecting the TIA1 protein in extracts, in the immunodepleted extracts and in the immunoprecipitates (Figure 2).10–16\n\nHAP1 lysates were prepared, and IP was performed using 1.0 μg of the indicated TIA1 antibodies pre-coupled to Dynabeads protein G or protein A. (A) Ability of the antibodies to capture TIA1 was assessed by comparing the level of protein available in the starting material to the level remaining in the unbound fraction. (B) The immunoprecipitates for antibodies which could immunocapture TIA1 in (A) are shown. For Western Blot, 86050** was used at 1/1000 in A) and B). The Ponceau stained transfers of each blot are shown. SM=4% starting material; UB=4% unbound fraction; IP=immunoprecipitate. *=monoclonal antibody, **=recombinant antibody.\n\nFor immunofluorescence, as described previously, antibodies were screened using a mosaic strategy.17 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\nHAP1 WT and TIA1 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 in a 96-well plate with optically clear flat-bottom. Cells were stained with the indicated TIA1 antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (identification of WT cells), red (antibody staining) and far-red (identification of KO cells) channels was performed. Representative images of the merged blue and red (grayscale) channels are shown. WT and KO cells are outlined with green and magenta dashed line, respectively. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Exceptions were given to antibodies ab140595**, A6237, NBP2-67203**, and GTX33545, which were titrated to their respective concentrations found bellow, as the signals were too weak when following the suppliers' recommendations. When the concentrations were not indicated by the supplier, which was the case for antibodies ab263945**, ARP40979, ARP40981, and NBP3-13791** we tested antibodies at 1/300, 1/500, 1/500 and 1/200, respectively. At these concentrations, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: ab140595** at 1/600; ab263945** at 1/300; A6237 at 1/1000; ARP40979 at 1/500; ARP40981 at 1/500; NBP2-53336* at 1/100; NBP2-67203** at 1/1000; NBP3-13791** at 1/200; 86050** at 1/100; GTX33545 at 1/800; MA5-26474* at 1/1000; and MA5-32615** at 1/100. Bars = 10 μm. *=monoclonal antibody, **=recombinant antibody.\n\nIn conclusion, we have screened TIA1 commercial antibodies by Western Blot, immunoprecipitation and immunofluorescence and identified several high-quality antibodies under our standardized experimental conditions. The underlying data can be found on Zenodo open access repository.18,19\n\n\nMethods\n\nAll tested TIA1 antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly.20 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).\n\n* = monoclonal antibody.\n\n** = recombinant antibody.\n\n1 refers to RRID recently added to the Antibody Registry (in February 2023), they will be available on their website in the coming weeks.\n\nBoth HAP1 WT and TIA1 KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.21 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.22 HAP1 WT and TIA1 KO were collected in RIPA buffer (25mM Tris-HCl pH 7.6, 150mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) (Thermo Fisher Scientific, cat. number 89901) supplemented with 1x protease inhibitor cocktail mix (MilliporeSigma, cat. number 78429). Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 x 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 from GeneDireX (cat. number PM008-0500) was used.\n\nWestern Blots were performed with precast midi 4-20% Tris-Glycine polyacrylamide gels from Thermo Fisher Scientific (cat. number WXP42012BOX) ran with Tris/Glycine/SDS buffer from Bio-Rad (cat. number 1610772), loaded in Laemmli loading sample buffer from Thermo Fisher Scientific (cat. number AAJ61337AD) and transferred onto 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 Blot. 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 from Thermo Fisher Scientific (cat. number 32106) prior to detection with the HyBlot CL autoradiography films from Denville (cat. number 1159T41).\n\nImmunoprecipitation was performed as described in our standard operating procedure.23 Antibody-bead conjugates were prepared by adding 1 μg to 500 μL of Pierce IP Lysis Buffer from 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) from Thermo Fisher Scientific (cat. number 10002D and 10004D, respectively). Tubes were rocked for ~1 hr at 4°C followed by two washes to remove unbound antibodies.\n\nHAP1 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 (Millipore Sigma, cat. number P8340). Lysates were rocked 30 min at 4°C and spun at 110,000 x g for 15 min at 4°C. 0.5 mL aliquots at 2.0 mg/mL of lysate were incubated with an antibody-bead conjugate for ~1 hr at 4°C. The unbound fractions were collected, and beads were subsequently washed three times with 1.0 mL of or IP lysis buffer and processed for SDS-PAGE and Western Blot on a precast midi 4-20% Tris-Glycine polyacrylamide gels. Prot-A: HRP (MilliporeSigma, cat. number P8651) was used as a secondary detection system at a dilution of 0.3 μg/mL for experiments where rabbit antibodies are used for both immunoprecipitation and its corresponding Western Blot.\n\nImmunofluorescence was performed as described in our standard operating procedure.10–17 HAP1 WT and TIA1 KO were labelled with a CellTrackerTM green (Thermo Fisher Scientific, cat. number C2925) or CellTrackerTM deep red (Thermo Fisher Scientific, cat. number C34565) fluorescence dye, respectively. The nuclei were labelled with DAPI (Thermo Fisher Scientific, cat. Number D3571) fluorescent stain. WT and KO cells were plated in 96-well plate with optically clear flat-bottom (Perkin Elmer, cat. number 6055300) 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 140770-10ml) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL) for 15 min at room temperature and then washed 3 times with PBS. 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 containing 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 TIA1 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.\n\nImages were acquired on an ImageXpress micro widefield high-content microscopy system (Molecular Devices), using a 20x/0.45 NA air objective lens and scientific CMOS camera (16-bit, 1.97mm field of view), equipped with 395, 475, 555 and 635 nm solid state LED lights (Lumencor Aura III light engine) and bandpass emission filters (432/36 nm, 520/35 nm, 600/37 nm and 692/40 nm) to excite and capture fluorescence emission for DAPI, CellTrackerTM green, Alexa fluor 555 and CellTrackerTM deep red, respectively. Images had pixel sizes of 0.68 x 0.68 microns. Exposure time was set with maximal (relevant) pixel intensity ~80% of dynamic range and verified on multiple wells before acquisition. Since the IF staining varied depending on the primary antibody used, the exposure time was set using the most intensely stained well as reference. Frequently, the focal plane varied slightly within a single field of view. To remedy this issue, a stack of three images per channel was acquired at a z-interval of 4 microns per field and best focus projections were generated during the acquisition (MetaExpress v6.7.1, Molecular Devices). Segmentation was carried out on the projections of CellTrackerTM channels using CellPose v1.0 on green (WT) and far-red (KO) channels, using as parameters the ‘cyto’ model to detect whole cells, and using an estimated diameter tested for each cell type, between 15 and 20 microns.24 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 TIA1, https://doi.org/10.5281/zenodo.7671718. 18\n\nZenodo: Dataset for the TIA1 antibody screening study, https://doi.org/10.5281/zenodo.7796012. 19\n\n\nAcknowledgment\n\nWe would like to thank the NeuroSGC/YCharOS/EDDU 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. We would also like to thank the Advanced BioImaging Facility (ABIF) consortium for their image analysis pipeline development and conduction (RRID:SCR_017697). Members of each group can be found below.\n\nNeuroSGC/YCharOS/EDDU collaborative group: Riham Ayoubi, Thomas M. Durcan, Aled M. Edwards, Carl Laflamme, Peter S. McPherson, Chetan Raina, Wolfgang Reintsch, Kathleen Southern and Donovan Worrall.\n\nABIF consortium: Claire M. Brown and Joel Ryan.\n\nAn earlier version of this of this article can be found on Zenodo (doi: 10.5281/zenodo.7671718)\n\n\nReferences\n\nDember LM, Kim ND, Liu KQ, et al.: Individual RNA recognition motifs of TIA-1 and TIAR have different RNA binding specificities. J. Biol. Chem. 1996; 271(5): 2783–2788. PubMed Abstract | Publisher Full Text\n\nFörch P, Puig O, Martínez C, et al.: The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5' splice sites. EMBO J. 2002; 21(24): 6882–6892. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFörch P, Puig O, Kedersha N, et al.: The apoptosis-promoting factor TIA-1 is a regulator of alternative pre-mRNA splicing. Mol. Cell. 2000; 6(5): 1089–1098. PubMed Abstract | Publisher Full Text\n\nIzquierdo JM, Valcárcel J: Two isoforms of the T-cell intracellular antigen 1 (TIA-1) splicing factor display distinct splicing regulation activities. Control of TIA-1 isoform ratio by TIA-1-related protein. J. Biol. Chem. 2007; 282(27): 19410–19417. PubMed Abstract | Publisher Full Text\n\nAnderson P, Kedersha N: Stressful initiations. J. Cell Sci. 2002; 115(16): 3227–3234. Publisher Full Text\n\nGilks N, Kedersha N, Ayodele M, et al.: Stress granule assembly is mediated by prion-like aggregation of TIA-1. Mol. Biol. Cell. 2004; 15(12): 5383–5398. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMackenzie IR, Nicholson AM, Sarkar M, et al.: TIA1 Mutations in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Promote Phase Separation and Alter Stress Granule Dynamics. Neuron. 2017; 95(4): 808–16.e9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhao M, Kim JR, van Bruggen R , et al.: RNA-Binding Proteins in Amyotrophic Lateral Sclerosis. Mol. Cells. 2018; 41(9): 818–829. PubMed Abstract | Publisher 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\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; 2023(12): 172.\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 [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 277. Publisher 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 [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 355. Publisher Full Text\n\nAyoubi R, Fotouhi M, Southern K, et al.: The identification of high-performing antibodies for transmembrane protein 106B (TMEM106B) for use in Western blot, immunoprecipitation, and immunofluorescence [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 308. 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\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\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence.2021.\n\nFotouhi M, Ryan J, Worrall D, et al.: Antibody Characterization Report for RNA-binding protein TIA1.2023.\n\nLaflamme C: Dataset for the TIA1 antibody screening study. [Data set]. Zenodo. 2023.\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.\n\nStringer C, Wang T, Michaelos M, et al.: Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods. 2021; 18(1): 100–106. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "195326",
"date": "07 Sep 2023",
"name": "Claudia Fallini",
"expertise": [
"Reviewer Expertise Cell biology",
"neurodegenerative research"
],
"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 manuscript, Fotouhi and colleagues characterized a panel of 12 antibodies for their ability to detect the RNA-binding protein TIA-1 in western blot, immunoprecipitation, and immunofluorescence assays. They selected the human cancer line HAP1 as model system as it produces high levels of the TIA-1 protein, and compared data to the isogenic TIA-1 KO line. The experimental procedures are well described and thorough, and the data are solidly presented. A couple of points that the authors could address are listed below:\n1. All experiments are performed on a human cell line. The authors should specify this limitation in their results and discussion section. Alternatively the authors could test the best performing antibodies on murine cells as well, as this would broaden the applicability of the study.\n\n2. A summary table ranking the antibodies tested based on their performance on the three different assays would be helpful.\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": "204755",
"date": "20 Mar 2024",
"name": "Jozsef Gal",
"expertise": [
"Reviewer Expertise Biochemistry",
"cell biology",
"neurodegeneration"
],
"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 by Fotouhi et al. describes the validation of 12 commercially available anti-TIA1 antibodies in immunoblotting, immunoprecipitation and immunofluorescence studies. The manuscript is well written. This is a very useful contribution to the field. It will certainly help researchers choose anti-TIA1 antibodies for future work. I only have minor issues and comments.\nGeneral issues:\nThe HAP1 cell line is of human origin. A lot of research employs murine models and cell lines. It would be very useful if the Authors could perform immunoblotting of a lysate from a murine cell line. I would recommend N2A/Neuro-2A cells. In my opinion, the antibodies that performed the best in HAP1 immunoblotting (ab140595, ab263945, NBP2-67203, 86050) would be sufficient.\n\nThe Authors present their findings in a rather raw format without much interpretation. It would be great if the Authors would summarize their findings after each technique. It would also be very useful to provide a summary paragraph about which antibodies the Authors consider overall the best.\nMinor comments:\nThe term “Western blot” is kind of colloquial. I recommend the term “immunoblotting”, but I would like to leave it up to the Authors.\n\nTIA-1 has a close homolog in human cells, TIAR. To me, one of the most valuable contributions of this work is the ability to see which tested antibodies may cross-react with TIAR. Based on the immunoblotting image, A6237, GTX33545, and MA5-26474 may cross-react with TIAR. I think that it would be useful if the Authors would touch on this issue.\n\nIn the Introduction: “... disrupting the function of TIA1 can lead to various diseases including cancer, autoimmune diseases and neurodegenerative disorders” – I recommend including further references in this paragraph for cancer and autoimmune diseases.\n\nCould you, please, check the molecular weight marker bands in Figure 1, A6237? The detected bands are a little lower than on several other immunoblotting images.\n\nIt would be useful to discuss the extra bands (ARP40981, NBP3-13791) and the unexpected band sizes (NBP2-53336) in immunoblotting.\n\nIn “Methods”, “Cell culture”: I believe that “2 mM L-glutamate (Wisent cat. number 609065)” is L-glutamine.\n\n“Methods”, “Antibody screening by Western Blot”: “... protease inhibitor cocktail mix (MilliporeSigma, cat. number 78429)”: I guess that you refer to the Halt™ Protease Inhibitor Cocktail, but that is a Thermo Fisher Scientific product.\n\nYou wrote that the lysates were cleared with 110,000 x g centrifugation. Could you, please, confirm that? That is an ultracentrifugation speed. Lysates are usually cleared with centrifugal forces about an order of magnitude lower for lysate preparation for immunoblotting and immunoprecipitation.\n\nI advise against using the wavy line “~” in a method paper. I believe that it reads “about” or “approximately”. Instead, please just state the numbers.\n\n“Methods”, “Antibody screening by immunoprecipitation”: please state the dilution of the P8340 protease inhibitor cocktail.\n\n“Methods”, “Antibody screening by immunoprecipitation”: please describe how you eluted the proteins from the immunoprecipitation beads.\n\n“Methods”, “Antibody screening by immunofluorescence”: the DAPI staining is mentioned early in the protocol, and then later again, when the secondary antibody staining is described (without stating the DAPI concentration). I would not mention DAPI before the plating step because it could confuse the readers that it was used alongside the CellTracker stains.\n\n“DAPI (Thermo Fisher Scientific, cat. Number D3571)”: that, however, is a Sigma-Aldrich product.\n\nNone of the TIA1 KO cells were completely dark in the immunofluorescence studies in Figure 3. It would be a good idea to point out that more stringent immunofluorescence conditions may be needed.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "11337",
"date": "13 Apr 2024",
"name": "Kathleen Southern",
"role": "Author Response",
"response": "Thank you to Jozsef Gal for your extensive review of this article. We have submitted a modified version of this manuscript, with the requested modifications the authors found appropriate. We trust that the refinements made meet your expectations, enhance comprehensibility and address any concerns you might have had. Please see our responses to your specific comments below. To address your general concerns, we’d first like to clarify that this study for TIA1 is part of a much larger collaborative initiative, seeking to characterize antibodies for all human proteins to address the antibody liability crisis. It would be very difficult to optimize every working parameter when in the process of trying to characterize antibodies for 20,000 proteins in the human proteome. That is why we have focused our initiative on testing antibodies in human cancer cell lines rather than murine models, but are well aware that many researchers employ these models. YCharOS presents the 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 to conduct further studies, including employing these high-performing antibodies on murine cell lines. Furthermore, the objective of this article, as well as the YCharOS initiative as a whole, is not to interpret the results nor summarize the performance of the antibodies tested. Given that it is formatted as a Data Note, it does not require the results to be discussed or concluded. WE’d like to re-iterate that YCharOS is a public-private organization whose mission is to characterize antibodies for every human protein and deliver the research as a collective good for the scientific community. That being said, we understand how this intention may be misinterpreted. A new version has been submitted, to include modifications to the title, and results&discussion section that ensure our goals are aligned and defined to all readers. Moreover, as the antibodies are tested under one specific set of conditions, summarizing the performance of the antibodies would be valid only under the precise experimental setup and cell line used. To address your minor comments, the authors have decided to stick with using the term Western blot to remain consistent with all other characterization reports. As for your concern regarding TIAR cross-reactivity, each commercial antibody tested was advertised on their respective catalogs as targeting TIA1, rather than TIAR. From what we’ve found in literature, TIAR is encoded by a different gene, being TIAL (1-3). For us to make accurate conclusions regarding the cross reactivity of the commercial antibodies, we would have had to prepare two KO cell lines; TIA1 and TIAL. In the newly submitted version of this article, additional references have been included to address TIA1’s role in various diseased states. The molecular weight marker has been confirmed the authors. Unlike other antibodies tested, A6237 recognizes bands in the WT cell line that do not disappear in the KO cell lines, indicating that it might not be properly targeting TIA1. When analyzing an antibody by Western blot, if it recognizes the target protein but produces extra bands as well, it is considered non-selective but specific. If it fails to recognize the target protein and produces unexpected bands, it is considered non-specific. Guidelines on how to analyze antibody characterization data can be found in an editorial by Biddle et al., featured on the YCharOS gateway (4). In the newly submitted version of this article, we will include this reference. The following responses address your concerns regarding the methods section: L-glutamate has been changed to L-glutamine. The MilliporeSigma protease inhibitor cocktail mentioned is the one used in our standardized protocol. In our efforts to be more accurate, we have removed the word “mix” in the manuscript to reflect how it is written in the catalog. WB: We found that ultra-centrifugation speed is required to pellet insoluble contaminants found in the lysates that would adhere to the bead-antibody conjugate, interfering with the detection of bound protein in Western blot. We’ve observed that Table-top centrifugation speeds do not adequately remove insoluble particles. IP: the concentration for the protease inhibitor cocktail mix as well as a statement describing how the protein of interest can be eluded using the antibody-bead conjugation protocol has been added. IF: we’ve relocated the mention of DAPI fluorescent stain to where secondary antibody conjugation is discussed to prevent confusion among readers. In this case, the DAPI stain was purchased from Thermo Fisher Scientific, which is why it is mentioned in the manuscript. Tian Q, Streuli M, Saito H, Schlossman SF, Anderson P. A polyadenylate binding protein localized to the granules of cytolytic lymphocytes induces DNA fragmentation in target cells. Cell. 1991 Nov 1;67(3):629-39. doi: 10.1016/0092-8674(91)90536-8. Velasco BR, Izquierdo JM. T-Cell Intracellular Antigen 1-Like Protein in Physiology and Pathology. Int J Mol Sci. 2022 Jul 16;23(14):7836. doi: 10.3390/ijms23147836. Beck AR, Medley QG, O'Brien S, Anderson P, Streuli M. Structure, tissue distribution and genomic organization of the murine RRM-type RNA binding proteins TIA-1 and TIAR. Nucleic Acids Res. 1996 Oct 1;24(19):3829-35. doi: 10.1093/nar/24.19.3829. Biddle MS and Virk HS. YCharOS open antibody characterisation data: Lessons learned and progress made [version 1; peer review: not peer reviewed]. F1000Research 2023, 12:1344 (https://doi.org/10.12688/f1000research.141719.1)"
}
]
}
] | 1
|
https://f1000research.com/articles/12-745
|
https://f1000research.com/articles/12-1580/v1
|
14 Dec 23
|
{
"type": "Brief Report",
"title": "Ex vivo precision-cut liver slices model disease phenotype and monitor therapeutic response for liver monogenic diseases",
"authors": [
"Dany Perocheau",
"Sonam Gurung",
"Loukia Touramanidou",
"Claire Duff",
"Garima Sharma",
"Neil Sebire",
"Patrick F Finn",
"Alex Cavedon",
"Summar Siddiqui",
"Lisa Rice",
"Paolo G.V. Martini",
"Andrea Frassetto",
"Julien Baruteau",
"Dany Perocheau",
"Sonam Gurung",
"Loukia Touramanidou",
"Claire Duff",
"Garima Sharma",
"Neil Sebire",
"Patrick F Finn",
"Alex Cavedon",
"Summar Siddiqui",
"Lisa Rice",
"Paolo G.V. Martini",
"Andrea Frassetto"
],
"abstract": "Background In academic research and the pharmaceutical industry, in vitro cell lines and in vivo animal models are considered as gold standards in modelling diseases and assessing therapeutic efficacy. However, both models have intrinsic limitations, whilst the use of precision-cut tissue slices can bridge the gap between these mainstream models. Precision-cut tissue slices combine the advantage of high reproducibility, studying all cell sub-types whilst preserving the tissue matrix and extracellular architecture, thereby closely mimicking a mini-organ. This approach can be used to replicate the biological phenotype of liver monogenic diseases using mouse models.\n\nMethods Here, we describe an optimised and easy-to-implement protocol for the culture of sections from mouse livers, enabling its use as a reliable ex-vivo model to assess the therapeutic screening of inherited metabolic diseases\n\nResults We show that precision-cut liver sections can be a reliable model for recapitulating the biological phenotype of inherited metabolic diseases, exemplified by common urea cycle defects such as citrullinemia type 1 and argininosuccinic aciduria, caused by argininosuccinic synthase (ASS1) and argininosuccinic lyase (ASL) deficiencies respectively.\n\nConclusions Therapeutic response to gene therapy such as messenger RNA replacement delivered via lipid nanoparticles can be monitored, demonstrating that precision-cut liver sections can be used as a preclinical screening tool to assess therapeutic response and toxicity in monogenic liver diseases.",
"keywords": [
"precision-cut tissue slices",
"vibratome",
"liver",
"urea cycle",
"Argininosuccinic aciduria",
"Citrullinemia type 1",
"lipid nanoparticle",
"mRNA"
],
"content": "Introduction\n\nIsolated primary cells and cell line cultures are usually models of choice for in vitro studies due to their easy access and low maintenance. However, limitations include the rapid loss of differentiation and lack of a tissue specific microenvironment.1,2 This can partially be overcome with three-dimensional systems such as spheroids3 and whole-organ bioreactors4; however, these techniques can be technically challenging and costly. Transgenic animals present their own limitations too i.e. high maintenance cost and experimental restrictions for ethical reasons. Precision-cut tissue slices (PCTS) fill a gap between such in vitro and in vivo models and mimic a mini-organ model whilst preserving the tissue architecture and extracellular matrix.5,6 The development of tissue slicers, e.g. vibratomes,7 has allowed the generation of thinner slices with better preserved structural integrity. They can be generated from a wide range of organs,8–11 tumours12,13 but also human surgical wastes.14,15 Also, one organ can generate multiple PCTS, thereby reducing drastically the number of animals but also limiting interindividual variations and off-target effects.\n\nDeveloping liver PCTS is an appealing strategy to model a disease phenotype such as chronic liver diseases and test preclinical therapeutic effect and potential toxicity.\n\nHere, we present an optimised and easy-to-implement method for the preparation and culture of precision-cut liver slice (PCLS) with survival of up to five days. As an appealing application for a model of chronic liver disease, we show that PCLS recapitulate key phenotypic aspects of two rare inherited metabolic diseases affecting the urea cycle, citrullinemia type 1 and argininosuccinic aciduria (ASA). We also show that PCLS effectively support the proof of concept of non-viral gene therapy by rescuing the ASA phenotype using hASL mRNA encapsulated in lipid nanoparticles.\n\n\nMethods\n\nAll animal work was approved following local ethical review by the University College London Animal Welfare and Ethical Review Board and performed under Home Office project license PP9223137 and in accordance with the Home Office (Animals) Scientific Procedures Act (1986). Individual Researchers were performing procedure under personal licences I3906A5FA and I42365670.\n\nAll efforts were made to limit harm to animals in accordance to standard practice at the Biological Services Unit at University College London. Animal procedures were performed under the UK Home Office licence PP9223137. Animal procedures were compliant with ARRIVE guidelines and The ARRIVE checklist is available on Open Science Framework, DOI: https://osf.io/vz4jp/.16\n\nThe transgenic mouse strains were purchased from Jackson Laboratory (Bar Harbor, ME): AslNeo/Neo (B6.129S7-Asltm1Brle/J) and Ass1fold (B6EiP-Ass1fold/GrsrJ). Mice were mated as heterozygous and a total of six mice per strain were used as parents to generate wild-type and homozygous littermate controls. A total of 15 littermates were used to generate the PCLS. Some of the remaining littermates were used as new breeders. Livers were harvested between the ages of day 12 and 19. All animal work was carried at the Biological Services Unit of University College London. Mice had free access to food and water, housed up to five per cages, in Individually ventilated cages with controlled temperature and humidity conditions and with a 12h light cycle.\n\nThe liver was excised from the mouse and in conditions as sterile as possible and stored in ice cold Krebs Buffer. All further steps were performed on ice at 4°C. Each lobe was isolated from the whole liver and all edges further trimmed to obtain a smaller more manageable lobe with straight edges. This helped remove some of the fibrous Glisson’s capsule to further facilitate sectioning. This was performed while keeping the liver surfaces wet into ice cold Krebs buffer (Figure 1A). One litre of Krebs (Merck, Cat. no K3753) buffer was prepared by dissolving one vial of Krebs powder into 1 L of ultrapure water and kept at 4°C before and during use. Each lobe section was embedded into 4% low melting agarose (ThermoFisher, Cat no 16520050).\n\n(A) Schematic summarising the protocol for generating PCLS. (B) Pre-cut liver lobe embedded in a low-melting agarose block. (C) Agarose block containing the mouse lobe ready for cutting onto vibratome filled with ice and ice-cold Krebs buffer. (D) PCLS following cutting and ready for culture. (E) A PCLS inside a transwell within a 12 well plate containing culture media.\n\nSlicing was performed using a vibratome (Leica, VT1000 S). The agarose blocks were glued, using standard cyanoacrylate glue, directly onto the platform (Figure 1B) and the tray filled with ice cold Krebs buffer to completely cover the agarose block. The blades (Agar Scientific, Cat no T569T) were placed onto the vibratome at an angle of 10 degree downwards and below horizontal (Figure 1C). The vibratome was set for cutting at a thickness of 250 μm and speed was set at 5 and frequency at 7. The cutting tray was cooled into the freezer before use and preserved cold with ice around it (Figure 1C). A spatula was used to collect the liver slices instead of forceps or brushes to avoid damaging the slices.\n\nWilliam’s Medium E with GlutaMAXTM (WME) slice incubation medium was prepared by adding 2 mM L-glutamine supplement (Gibco, Cat no 32551-020), 10% of dialysed FBS (ThermoFisher, Cat no 26400044), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco, Cat no 15750045), 10 μg/mL Gentamycin (Gibco, Cat no 15750045), 25 mM D-Glucose solution (Gibco, Cat no 15384895), 15 mM HEPES solution (Gibco, Cat no 15630), stored at 4°C. Slices were also cultured using porous 8 μm inserts to allow access to both faces of the slice (Strastedt, Cat no 83.3932.800). Media was also added to the well, enough to slightly cover the slices to create a liquid-air interface while shaking. Plates with slices were transferred into a humidified incubator set to 37°C, 5% carbon dioxide and 20% oxygen level while continuously shaking using an orbital shaker with a speed set at 130 rpm. Thereafter the media was changed every 48 h.\n\nThe slices were transferred into a 48 well plate containing 400 μl of prewarmed complete WME media and 80 μl of MTS (4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) reagent (Abcam, Cat no ab197010) was added. Following incubation for 1 h at 37°C, 5% CO2 onto a shaker, 200 μl of media was transferred into a 96 well plate and absorbance was measured at 490 nm.\n\nCodon optimized hASL encoding mRNA encapsulated in lipid nanoparticles (LNP-hASL mRNA) were provided by Moderna Therapeutics using their proprietary technology. A total of 2 μg of LNP-hASL in a 10 μL volume were added to the upper side of the slice.\n\nLiquid chromatography-Mass spectrometry (LC-MS/MS) was used from dried bloodspots using the hydrophilic interaction liquid chromatography (HILIC) separation of metabolites, method. Briefly, 40 μl of whole blood was spotted on Guthrie blood spot card, dried at room temperature for 24 h and stored in -20°C in a foil bag with desiccant. 3 mm blood spot punch was extracted in 100 μl methanol containing stable isotopes (2 nmol/l, L-citrulline-d7, CDN isotopes, Pomite-Claire, Quebec), used as internal standards, for 15 min in sonicating waterbath at room temperature. The supernatant was collected and dried using Eppendorf® Concentrator Plus and resuspended in 80 μl of 0.05 M HCl, topped with 280 μl of Solvent A (10 mM ammonium formiate+85% Acetonitrile (ACN)+0.15%Formic acid (FA)), centrifuged at 16,000 rpm for 5 min and supernatant taken for analysis.\n\nAcquity UltraPure Liquid Chromatography (UPLC)-system (Waters, Manchester, UK) using Acquity UPLC BEH Amide column (2.1×100 mm, 1.7 μm particle size) and Van GuardTM UPLC BEH Amide pre-column (2.1×5 mm, 1.7 μm particle size) (Waters Limited, UK) was used for amino acid chromatography. The mobile phases were (A) 10 mM ammonium formiate in 85% ACN and 0.15% FA and (B) 15 mM ammonium formiate containing 0.15% formic acid, pH 3.0. Detection was performed using a tandem mass spectrometer Xevo TQ-S (Waters, Manchester, UK) using multiple reaction monitoring in positive ion mode. The dwell time was set automatically with MRM-transition of 291.2>70.2, 273.2>70.2 and 176.1>159 respectively for ASA, ASA-anhydrides and L-citrulline. L-Citrulline-d7 (183.15>166.05) was used as internal standard control. Argininosuccinate data were analysed using Masslynx 4.2 software (Micromass UK Ltd, Cheshire, UK).\n\n20-30 mg of liver was homogenised in 400 μl of cold homogenising buffer (50 mM phosphate buffer pH 7.5 and 1x Roche EDTA-free protease inhibitor (Roche, Switzerland)) using Precellys homogeniser tube (VWR, UK) and Precellys 24 tissue homogeniser (Bertin Instruments, France), centrifuged at 10000 g for 20 min at 4°C and protein levels measured from the supernatant using BCA kit (Thermo Fisher Scientific, UK). 60 μg of protein lysate was incubated with 3.6 mM ASA in final volume of 50 μl, incubated at 37°C for 1h followed by reaction termination at 80°C for 20 min. The mixture was centrifuged at 10000 g for 5 min and 5 μl of the supernatant was used to measure fumarate levels per instruction from the commercial fumarate kit (Abcam, Cambridge, UK).\n\nGraphPad Prism 9.0 software (San Diego, CA, USA) was used for performing data analysis and generating graphs. The statistics for this research could be reproduced using the open-source graphical program for statistical analysis JASP.\n\n\nResults\n\nProtocols for PCLS preparation and culture vary significantly in the literature with a lack of standardisation, especially for slicing equipment, culture media, and engineering system. Optimisation is always key and varies noticeably depending on the tissue of interest. Here, we recapitulate a rapid and optimised protocol to generate PCLS (Figure 1). We observed that a minimal volume of culture medium was essential to sustain viability. A reduced volume in 24-well plate showed a significant reduction of viability (p=0.02) compared to 12-well and six-well plates (Figure 2A, Underlying data16). In agreement with others,17 the use of 12-well plates appears as the best option for optimal survival providing more nutrients and diluting toxic bile acid products. Approximately fifty percent reduction of PCLS viability was also observed without continuous shaking (Figure 2B, Underlying data16). Shaking creates a critical air-liquid interface, a constant flow, and combined with the use of transwells, increases access to nutrients and oxygen.\n\n(A) Effect of well size on cell viability (n=3). (B) Effect of shaking on cell viability (n=6 per condition). (C) MTS cell viability assay from liver sections from baseline until 6 days of incubation (n=5 per timepoint). OD: arbitrary unit of optical density, normalised to slice fresh weight. Graphs show mean±SD. Unpaired 2-tailed Student’s t test, ns=not significant, *p<0.05, **p<0.01. (D-G) Representative images of histology of liver PCTS following H&E staining (n=3). Scale bar=100 μM.\n\nWith these modifications, viability was assessed and remained constant before observing a significant decrease (p=0.05) at day six (Figure 2C, Underlying data16). The PCLS morphology showed no change of bile ducts and architecture up to five days post-incubation (Figures 2D–G). Only nuclear hyperchromasia, mild inflammatory infiltrates and vacuolisation were observed at day five (Figure 2G). Taken together, we showed that our optimised PCLS culture protocol enabled viability for five days.\n\nCitrullinemia type 1 and ASA are caused by deficiency of the hepatic urea cycle enzymes argininosuccinic synthetase (ASS1) and ASL, respectively (Figure 3A, Underlying data16). Patients suffering from these urea cycle disorders develop recurrent hyperammonaemia and subsequent neurological symptoms such as developmental delay, coma and death. Despite best-accepted standard of care combining ammonia scavenger drugs and protein-restricted diet, patients present with high rates of mortality and poor quality of life,18 highlighting high unmet needs. The ex vivo models rely on induced pluripotent stem cells (iPSC)-derived hepatocytes with a relative inaccuracy in modelling the disease phenotype partially due to sub-optimal differentiation.3 We therefore established a PCLS model using the hypomorphic mouse models Assfold/fold for citrullinemia type 1, and AslNeo/Neo recapitulating ASA. Both models reproduce the clinical phenotype, characterised by impaired growth, abnormal fur, hyperammonaemia and abnormal plasma amino acid profiles.19,20\n\n(A) ASL and ASS1 enzymes enable ammonia detoxification in the liver-based urea cycle. (B) Citrulline levels in media after 48 h of incubation in WT and ASS1-deficient PCLS. (C) Arginosuccininic acid levels in media after 48h of incubation in WT and ASS-deficient PCLS. (D) ASL western blot at 48 hours (cropped). (E) Quantification of ASL immunoblot normalised to GAPDH. (F) Liver ASL activity from WT, untreated ASLNeo/Neo and hASL mRNA. (G) Arginosuccininic acid levels in media after 48h of incubation in WT and ASS-deficient PCLS. (B-C) n=2 per group; (D-G) n=3 per group. Graphs show mean±SD. Unpaired 2-tailed Student’s t test, *p<0.05, **p<0.01, ***p<0.005.\n\nAs key biomarker for ASS deficiency, citrulline levels showed a significant eight-fold increase in the media of Assfold/fold PCLS compared to that of wild-type littermates (p = 0.01) (Figure 3B, Underlying data16). No significant difference was observed in argininosuccinate levels (Figure 3C, Underlying data16).\n\nmRNA encapsulated in lipid nanoparticles is an emerging therapeutic strategy for rare liver inherited metabolic diseases21,22 and PCLS present themselves as an attractive model to assess such therapies. PCLS generated from AslNeo/Neo mice were therefore treated with either hASL mRNA or phosphate buffer saline (PBS). We assessed efficacy by testing argininosuccinate levels in PCLS culture media, ASL protein expression and enzymatic function at 48h post-transfection. An eight-fold increase in ASL protein levels was observed in hASL mRNA-treated PCLS compared to untreated (Figures 3D, 3E, Underlying data16). ASL activity, assessed by fumarate production, was also restored in hASL mRNA versus PBS-treated PCLS to supraphysiological levels (Figure 3F, Underlying data16). Argininosuccinate levels were more than two-fold higher in the media of AslNeo/Neo PCLS that of WT controls and were corrected to that of WT levels after hASL mRNA incubation (Figure 3G, Underlying data16). Taken together, these results demonstrate that PCLS culture can replicate the disease phenotype and subsequently be used to assess therapeutic response to gene therapy.\n\n\nDiscussion\n\nWe demonstrate that PCLS can be an appealing ex vivo model to assess biological phenotype and therapeutic efficacy, whilst combining the advantage of respecting the complex liver architecture and reducing the use of animals.\n\nWhilst keeping a simple and easy set-up, our setting optimisation emphasizes key aspects to increase PCLS viability, such as volume of media, a dynamic system and agarose embedding for optimal cutting. Such models can be replicated in a standard cell culture laboratory, which has access to an animal facility and a vibratome. This optimisation allowed a viability maintained for 5 days, within the range of 48h to 10 days as previously described.23\n\nSome previously published protocols required complex settings whilst using oxygen concentration at a rate higher than 80% which theoretically should provide longer viability.8 However, such oxygen concentration is likely to generate toxic reactive oxygen species and subsequent antioxidant responses.24 Technical and safety limitations have also made it difficult to use oxygen-enriched media for culturing PCLS.24,25 Even if there is no consensus on the level of oxygen for culturing PCLS, a comparison between hyperoxic versus physiological models remains difficult.\n\nThe PCLS model is a relatively common model but has not been used previously in modelling liver monogenic diseases and assessing therapeutic response to gene therapy. Our work thereby expands the use of this model for these applications and replicates some key characteristics of Citrullinemia type 1 and ASA confirming the use of PCLS as an ex-vivo model for preclinical studies. Our approach could benefit other rare or common liver diseases, non-alcoholic fatty liver disease (NAFLD),26 liver cancer27 or even Fah-/- Rag2-/- Il2rg-/- (FRG) mice with a chimeric humanised liver.28 Whilst human material is difficult to obtain for technical and ethical reasons and additional variability due to genotyping i.e. residual activity and subsequent disease severity, quality of hepatocytes and age of patient at collection; makes such FRG mice, repopulated with primary human hepatocytes ideally from a single donor affected by the disease of interest, an ideal application as a preclinical human liver model for application of PCLS modelling. Such a model would also limit the mentioned variability of studying samples from human donors.\n\nThe main limitation associated with PCLS is the inability to maintain a sustained model longer than few days. The transduction of the therapeutic agent in inner cell layers of the PCLS has also been questioned.23 Additionally, the need for larger culture volume to increase PCLS viability is a trade-off for high-throughput screening. This variable also adds an important dilution factor and various biomarkers become below the limit of detection and/or quantification, even for accurate and sensitive methods such as tandem mass spectrometry.\n\nAlthough this warrants further validation, our experience shows that a target engagement with well-selected efficacy endpoints can be reliably tested in thin PCLS, thus enabling supraphysiological correction with potent therapeutic agents.\n\n\nConclusions\n\nTo conclude, we present key steps of a PCLS protocol to use as a reliable ex vivo model for liver monogenic diseases such as urea cycle defects. We show proof of concept that this model is successful in assessing therapeutic efficacy of gene therapy. We therefore believe this model should become a more recognised tool for preclinical studies in rare and common liver diseases.",
"appendix": "Data availability\n\nOpen Science Framework: Underlying data for ‘Ex vivo precision-cut liver slices model disease phenotype and monitor therapeutic response for liver monogenic diseases’, https://www.doi.org/osf.io/vz4jp. 16\n\nThis project contains the following underlying data:\n\n• ASA levels in ASL PCLS\n\n• ASL Activity\n\n• Citrulline and ASA levels in ASS PCLS\n\n• ASL Western blot quantification\n\n• MTA Assay data\n\n• Original Picture Western Blot\n\nOpen Science Framework: ARRIVE checklist for ‘Ex vivo precision-cut liver slices model disease phenotype and monitor therapeutic response for liver monogenic diseases’, https://www.doi.org/osf.io/vz4jp. 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 thank Mirabela Bandol, Samantha Richards, Louise Fisher, Rebecca Towns and the staff from UCL Biological Services for their help with breeding and maintenance of the animal colonies.\n\n\nReferences\n\nDong L, Hao H, Han W, et al.: The role of the microenvironment on the fate of adult stem cells. Sci. China Life Sci. 2015; 58: 639–648. Publisher Full Text\n\nFerguson LP, Diaz E, Reya T: The Role of the Microenvironment and Immune System in Regulating Stem Cell Fate in Cancer. Trends Cancer. 2021; 7: 624–634. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDuff C, Baruteau J: Modelling urea cycle disorders using iPSCs. NPJ Regen. Med. 2022; 7: 56. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLorvellec M, Pellegata AF, Maestri A, et al.: An in vitro Whole-Organ Liver Engineering for Testing of Genetic Therapies. iScience. 2020; 23: 101808. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMondonedo JR, Bartolak-Suki E, Bou Jawde S, et al.: A High-Throughput System for Cyclic Stretching of Precision-Cut Lung Slices During Acute Cigarette Smoke Extract Exposure. Front. Physiol. 2020; 11: 566. PubMed Abstract | Publisher Full Text | Free Full Text\n\nViana F, O’Kane CM, Schroeder GN: Precision-cut lung slices: A powerful ex vivo model to investigate respiratory infectious diseases. Mol. Microbiol. 2022; 117: 578–588. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIulianella A: Cutting Thick Sections Using a Vibratome. Cold Spring Harb. Protoc. 2017; 2017: pdb.prot094011. PubMed Abstract | Publisher Full Text\n\nPearen MA, Lim HK, Gratte FD, et al.: Murine Precision-Cut Liver Slices as an ex vivo Model of Liver Biology. J. Vis. Exp. 2020. PubMed Abstract | Publisher Full Text\n\nDe Kanter R, Monshouwer M, Draaisma AL, et al.: Prediction of whole-body metabolic clearance of drugs through the combined use of slices from rat liver, lung, kidney, small intestine and colon. Xenobiotica. 2004; 34: 229–241. PubMed Abstract | Publisher Full Text\n\nNogueira GO, Garcez PP, Bardy C, et al.: Modeling the Human Brain With ex vivo Slices and in vitro Organoids for Translational Neuroscience. Front. Neurosci. 2022; 16: 838594. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKlouda T, Kim H, Kim J, et al.: Precision Cut Lung Slices as an Efficient Tool for ex vivo Pulmonary Vessel Structure and Contractility Studies. J. Vis. Exp. 2021. Publisher Full Text\n\nZimmermann M, Armeanu S, Smirnow I, et al.: Human precision-cut liver tumor slices as a tumor patient-individual predictive test system for oncolytic measles vaccine viruses. Int. J. Oncol. 2009; 34: 1247–1256. PubMed Abstract\n\nPhilouze P, Gauthier A, Lauret A, et al.: CD44, gamma-H2AX, and p-ATM Expressions in Short-Term ex vivo Culture of Tumour Slices Predict the Treatment Response in Patients with Oral Squamous Cell Carcinoma. Int. J. Mol. Sci. 2022; 23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartin C: Human Lung Slices: New Uses for an Old Model. Am. J. Respir. Cell Mol. Biol. 2021; 65: 471–472. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSewald K, Danov O: Infection of Human Precision-Cut Lung Slices with the Influenza Virus. Methods Mol. Biol. 2022; 2506: 119–134. Publisher Full Text\n\nPerocheau D: Ex vivo precision-cut liver slices model disease phenotype and monitor therapeutic response for liver monogenic diseases. (Dataset). Open Science Framework. 2023. Reference Source\n\nvan de Kerkhof EG , de Graaf IA , de Jager MH , et al.: Characterization of rat small intestinal and colon precision-cut slices as an in vitro system for drug metabolism and induction studies. Drug Metab. Dispos. 2005; 33: 1613–1620. Publisher Full Text\n\nBaruteau J, Jameson E, Morris AA, et al.: Expanding the phenotype in argininosuccinic aciduria: need for new therapies. J. Inherit. Metab. Dis. 2017; 40: 357–368. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPerez CJ, Jaubert J, Guenet JL, et al.: Two hypomorphic alleles of mouse Ass1 as a new animal model of citrullinemia type I and other hyperammonemic syndromes. Am. J. Pathol. 2010; 177: 1958–1968. PubMed Abstract | Publisher Full Text | Free Full Text\n\nErez A, Nagamani SC, Shchelochkov OA, et al.: Requirement of argininosuccinate lyase for systemic nitric oxide production. Nat. Med. 2011; 17: 1619–1626. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartini PGV, Guey LT: A New Era for Rare Genetic Diseases: Messenger RNA Therapy. Hum. Gene Ther. 2019; 30: 1180–1189. PubMed Abstract | Publisher Full Text\n\nGurung S, Timmermand OV, Perocheau P, et al.: mRNA therapy restores ureagenesis and corrects glutathione metabolism in argininosuccinic aciduria. BioRxiv. 2022. Reference Source\n\nDewyse L, Reynaert H, van Grunsven LA : Best Practices and Progress in Precision-Cut Liver Slice Cultures. Int. J. Mol. Sci. 2021; 22. PubMed Abstract | Publisher Full Text | Free Full Text\n\nt Hart NA, van der Plaats A , Faber A, et al.: Oxygenation during hypothermic rat liver preservation: an in vitro slice study to demonstrate beneficial or toxic oxygenation effects. Liver Transpl. 2005; 11: 1403–1411. Publisher Full Text\n\nSzalowska E, Stoopen G, Rijk JC, et al.: Effect of oxygen concentration and selected protocol factors on viability and gene expression of mouse liver slices. Toxicol. In Vitro. 2013; 27: 1513–1524. PubMed Abstract | Publisher Full Text\n\nNagarajan P, Mahesh Kumar MJ, Venkatesan R, et al.: Genetically modified mouse models for the study of nonalcoholic fatty liver disease. World J. Gastroenterol. 2012; 18: 1141–1153. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPascale RM, Simile MM, Peitta G, et al.: Experimental Models to Define the Genetic Predisposition to Liver Cancer. Cancers (Basel). 2019; 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCabanes-Creus M, Hallwirth CV, Westhaus A, et al.: Restoring the natural tropism of AAV2 vectors for human liver. Sci. Transl. Med. 2020; 12. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "232090",
"date": "22 Jan 2024",
"name": "Tamir Rashid",
"expertise": [
"Reviewer Expertise Genetic liver diseases",
"disease 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\nThe authors describe an optimised and easy-to-implement protocol for the culture of precision-cut tissue slices (PCTS) from mouse liver, enabling its use as a reliable ex-vivo model to assess the therapeutic screening of inherited metabolic diseases.\nThey show that PCTS can be a reliable model for recapitulating some key aspects of the phenotype of two inherited metabolic diseases - citrullinemia type 1 and argininosuccinic aciduria, caused by argininosuccinic synthase (ASS1) and argininosuccinic lyase (ASL) deficiencies respectively.\nThey also provide ex vivo proof of concept data for the use of mRNA therapy in this context.\nOverall this is a simple, clear and helpful piece of work for people working in the field and expands the literature on PCTS.\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? 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",
"responses": [
{
"c_id": "11329",
"date": "13 Apr 2024",
"name": "Dany Perocheau",
"role": "Author Response",
"response": "We would like to thank the reviewer for the comments and for his time. Best wishes Dany Perocheau and co authors"
}
]
},
{
"id": "232092",
"date": "22 Jan 2024",
"name": "Vicente Rubio",
"expertise": [
"Reviewer Expertise Urea cycle disorders."
],
"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 is a technical report on the value on the use of precision-cut liver slices for the study of two urea cycle disorders and for the application of mRNA therapy for one of these two disorders (ASL deficiency). The paper is fine but there is a number of technical details that should be given to allow others reproduce the approach as well as for proper description and understanding. 1. The concept of liver excision requires indication of how was the animal at the time of excision, Presumably the excision was done on anesthetized animals and was followed by death of the animal by exsanguination or by other procedure. Alternatively, the animal could have been killed humanely and the liver excised. In the first case give full detail on the procedure and anesthetic drug. In the second also give killing procedure and the time from death when the liver was excised. 2. Data are referred to liver weight. Please indicate in the paper when were the slices weighted and how was the procedure performed to avoid heating them during weighting. In the eventuality that weighting was done at room temperature at the end of the entire procedure, it would be important to indicate this, and if possible please indicate if weight of the slice changes with days of incubation. In any case, it would be good to give, too the average or range of weights of the individual slices 3. In the figures data are given for days four and six, and since the data at six are inadequate and those at day 4 are found adequate, it is concluded that up to day five is fine. Please give data for day five too, to prove that these data were fine. 4. I am not a pathologist but from the size of the nuclei in the first slide and in the other slides, I think that the magnification is higher in the first slide (Fig. 2d) than in the other slides (Fig. 2e an subsequent ones). Therefore, please do review and correct the reference horizontal size bars. 5. On the same question, you mention the preservation of the liver architecture and also mention structural traits like biliary ducts and vacuoles. Please indicate all the traits mentioned using arrows pointing to the structures in the slides. 6. Also on the same subject, nuclei appear to be within a white non-stained vacuum that may be disrupted cytoplasm or a large aggregate of non-stainable material (glycogen?) Please explain in the figure caption. 7. Please give the amount of nanoparticles administered per gram of liver. 8, Please describe the mutations carried by the hypomorphic mice for the two diseases. 9. Please explain or at least discuss why the ASA levels are so low in the medium for the slices of the ASL deficiency mouse. 10. Please review the text for correctness as I have found some slips like missing particles or articles.\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? No\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11330",
"date": "13 Apr 2024",
"name": "Dany Perocheau",
"role": "Author Response",
"response": "We are grateful to the reviewer for his very helpful comments. Please find below specific answers to each of the comments. 1. The concept of liver excision requires indication of how was the animal at the time of excision, Presumably the excision was done on anesthetized animals and was followed by death of the animal by exsanguination or by other procedure. Alternatively, the animal could have been killed humanely and the liver excised. In the first case give full detail on the procedure and anesthetic drug. In the second also give killing procedure and the time from death when the liver was excised. We thank the reviewer for this comment. The mouse was euthanised by raising CO2 concentration and according to local procedures and the liver quickly excised and store in ice cold Krebs buffer. The liver should then be processed for cutting as quickly as possible and the time between harvest and culture shouldn’t exceed 3 hours but the shorter this time is, the better with regards to survival. We have updated the manuscript accordingly to make details regarding harvest of the liver more informative. 2. Data are referred to liver weight. Please indicate in the paper when were the slices weighted and how was the procedure performed to avoid heating them during weighting. In the eventuality that weighting was done at room temperature at the end of the entire procedure, it would be important to indicate this, and if possible please indicate if weight of the slice changes with days of incubation. In any case, it would be good to give, too the average or range of weights of the individual slices. We thank the reviewer for this comment. Indeed, the slices were weighted at the end of each experiment and following the MTS assay. We have updated the manuscript and also added the average range of weights of individual slices. 3. In the figures data are given for days four and six, and since the data at six are inadequate and those at day 4 are found adequate, it is concluded that up to day five is fine. Please give data for day five too, to prove that these data were fine. We thank the reviewer for this comment. We do not have data for day 5. When we refer to the slices surviving for 5 days, this refers to an experimental design from day 0 (day of animal harvest, organ slicing and first day of incubation) up to day 4 (5th day of incubation). 4. I am not a pathologist but from the size of the nuclei in the first slide and in the other slides, I think that the magnification is higher in the first slide (Fig. 2d) than in the other slides (Fig. 2e an subsequent ones). Therefore, please do review and correct the reference horizontal size bars. We thank the reviewer for this comment. We have checked the slices at day 0 and took new pictures and updated the horizontal size bar. The nuclei still appears relatively slightly large on average. We believe this could be an artefact following tissue fixation or staining. 5. On the same question, you mention the preservation of the liver architecture and also mention structural traits like biliary ducts and vacuoles. Please indicate all the traits mentioned using arrows pointing to the structures in the slides. We thank the reviewer for this comment. We have taken new pictures and more indicated in a clear manner with arrows as suggested the traits mentioned in figure 2. 6. Also on the same subject, nuclei appear to be within a white non-stained vacuum that may be disrupted cytoplasm or a large aggregate of non-stainable material (glycogen?) Please explain in the figure caption. We thank the reviewer for this comment. We have checked with our pathology department, and we believe this is an artefact due to fixation and processing. 7. Please give the amount of nanoparticles administered per gram of liver. We thank the reviewer for this comment. The amount of LNP per gram of liver averages to 0.19mg of LNP per gram of liver. We have updated the manuscript accordingly. 8, Please describe the mutations carried by the hypomorphic mice for the two diseases. We thank the reviewer for this comment. The model for citrullinemia type 1, Assfold/fold, contains a single base pair mutation within the ASS gene, and the model recapitulating Argininosuccinic aciduria (ASA), AslNeo/Neo, contains a neomycin (Neo) cassette inserted into the ASL gene and disrupting its transcription. We have amended the manuscript accordingly. 9. Please explain or at least discuss why the ASA levels are so low in the medium for the slices of the ASL deficiency mouse. We thank the reviewer for this comment. The levels of ASA does appear quite low compare to levels observed in patients. Based on the low thickness of 250 mm and the small superficie of about 0.14 cm2 within a relatively high volume of 700 ml, the rate of dilution for biomarkers such as ASA becomes quite high which explains why their levels seem low compare to patients for instance. We have amended the results section. 10. Please review the text for correctness as I have found some slips like missing particles or articles. We thank the reviewer for his comment. We have reviewed the manuscript and corrected it accordingly."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1580
|
https://f1000research.com/articles/13-254/v1
|
05 Apr 24
|
{
"type": "Genome Note",
"title": "Long-read datasets of Kayu Bawang (Azadirachta excelsa (Jack) Jacobs) from 3 different identified seed stands in Bengkulu (Sumatra), Indonesia and its phylogenetic relationships",
"authors": [
"Efratenta Katherina Depari",
"Nurheni Wijayanto",
"Lina Karlinasari",
"Mohamad Rafi",
"Iskandar Zulkarnaen Siregar",
"Efratenta Katherina Depari",
"Nurheni Wijayanto",
"Lina Karlinasari",
"Mohamad Rafi"
],
"abstract": "Abstract*\nAzadirachta excelsa (Jack) Jacobs, Kayu bawang (Meliaceae) is economically valuable and widely used by the local community in Bengkulu (Sumatra) as carpentry and construction wood because of its good durability class. However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa, Protium javanicum, and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbcL gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions.",
"keywords": [
"Azadirachta excelsa",
"chloroplast genome",
"identification",
"identified seed stand",
"long-reads",
"phylogenetics",
"gene marker"
],
"content": "Introduction\n\nAzadirachta excelsa (Jack) Jacobs or known as Kayu bawang (Meliaceae) is a main local wood in Bengkulu Province that is cultivated in private forests, mainly found in North Bengkulu and Central Bengkulu Districts (Depari et al. 2015; Siahaan & Sumadi 2015). Kayu bawang has been used for carpentry wood. Historically, this wood has been a favorite one of the local community as the primary material for building. In addition, the wood is also known for its resistance to attack by destructive organisms (Krisdianto et al. 2015). Despite kayu bawang is widely used for building wood and furniture, but some references are still ambiguous with respect to its scientific naming. Some references mentioned the naming of kayu bawang tree in Bengkulu as Protium javanicum Burm F (Adfa et al. 2013). In some other references, kayu bawang is named differently such as Dysoxylum mollissimum Blume (Ishiguri et al. 2016), Azadirachta excelsa (Jack) M Jacobs (Premono & Lestari 2014). In addition, in the identified seed stand (TBT) in Bengkulu as registered under No. 002/BPSMBK/SSB/2016, No. 001/BPTH.I-3/SSB/2016, and No. 006/P2STH/SSB/2018, kayu bawang is named respectively as Azadirachta exelsa, Dysoxylum molissimum, and Melia excelsa (synonym of Azadirachta excelsa). Based on morphological identification on Herbarium Bogoriense under National Research and Innovation Agency (BRIN), kayu bawang has been confirmed as Azadirachta excelsa (Jack) Jacobs. We used three specimens from different identified seed stands, namely TBT-A, TBT-K, and TBT-S, that were collected with the specimen numbers BO1991351 (TBT-A), BO1991352;1991353;1991354 (TBT- K), and BO1991350 (TBT-S) for genome sequencing using Oxford Nanopore Technologies. The objectives of the research were to assembly long-read DNA sequences and to construct a phylogeny for verifying species identification.\n\n\nMethods\n\nGenomic DNA was extracted from kayu bawang (Azadirachta excelsa) cambium samples which were taken from three different identified seed stands namely Talang Boseng (TBT-A, -3.66890°S, 102.292122°E), Batu Ampar (TBT-K, -4.394333°S, 103.138056°E), and Penyangkak (TBT-S, -3.531333°S, 102.252861°E) in Bengkulu Province, Indonesia. The modified CTAB (cetyl trimethyl ammonium bromide) method was used to extract the genomic DNA from each A. excelsa cambium (Doyle & Doyle 1987). The DNA extract buffer contained 200 μL of 10% CTAB (CAT NO. 194004, LOT NO. QR15741, MP Biomedicals, LLC), 100 μL of 1 M Tris-HCL, 280 μL of 5M NaCl, 40 μL of 0.5 M EDTA, 100 μL of 1% PVP, 280 μL of aquades. 0.1 g cambium mashed using mortar milling was put into a 2 mL tube, 1000 μL of DNA extract buffer that had been incubated at 65°C (60 min), 40 μL of 26% PVP, and 40 μL of β-Mercaptoethanol. The mixture was homogenized using a vortex and subsequently incubated at 65°C (60 min) with rehomogenization performed every 10 min by gently flipping the tube. The cooled mixture was centrifuged for 10 min, at 10,000 rpm. The supernatant was transferred to a 1.5 mL tube, and 500 μL of chloroform: isoamyl alcohol solution (24:1) and 10 μL of phenol were added and centrifuged for 10 min, at 10,000 rpm. Separation of the mixture was done again by adding 500 μL of chloroform: isoamyl alcohol solution (24:1). The obtained supernatant was put into a 1.5 mL tube, then 500 μL cold isopropanol and 250 μL NaCl were added. The mixture was stored in a freezer at 4°C for 1 day so that the DNA precipitation process occurring. After DNA precipitation, the mixture was centrifuged for 10 min, at 10,000 rpm. The mixture was removed gradually to retrieve the DNA pellet. DNA pellet washing using 500 μL of 70% ethanol, centrifuged for 10 min, at 10,000 rpm. The DNA pellet was separated from the mixture and dried in a desiccator containing silica gel (±20 min). 50 μL of TE RNAse buffer was added to dissolve the DNA pellet. The quality of extracted genomic DNA was evaluated using 1% agarose gel electrophoresis. The quality and quantity of the extracted genomic DNA were measured using NanoPhotometer® NP80 (IMPLEN) and Qubit 1.0 Fluorometer (Thermo Fisher Scientific) with the Qubit dsDNA BR assay kit. The library preparation of long-read sequencing was performed using Oxford Nanopore Technologies (ONT) manufactured protocol SQK-LSK109 version NBE_9065_v109_revZ_14Aug2019 with the MinION R9.4.1 flow cell (FLO-MIN106D, LOT 11001352) on a MinION Mk1C sequencer (Oxford Nanopore Technologies).\n\nThe chloroplast genome assembly for TBT-A, TBT-K, and TBT-S (Accession number DRA015537; https://ddbj.nig.ac.jp/resource/bioproject/PRJDB14301) (IPB University 2023) was performed using Galaxy Server (https://usegalaxy.eu/, RRID: SCR_006281, MIT License) v.23.1.1.dev0 following long-read data with some modifications (Wang et al. 2018). Long-read data for each sample was quality checked using NanoPlot (https://usegalaxy.eu/, RRID:SCR_024128, MIT License) v1.41.0 (De Coster et al. 2018). Those clean reads data were aligned with the reference NC_023792.1 (Azadirachta indica) using Minimap2 (https://usegalaxy.eu/, RRID:SCR_018550, MIT License) v.2.26 (Li 2018) and SAMTools (https://usegalaxy.eu/, RRID:SCR_002105, MIT License) v.2.05 (Li et al. 2009). Chloroplast reads were assembled using Canu Assembler (https://usegalaxy.eu/, RRID:SCR_015880, GPLv2 and others) v.2.1.1+galaxy0 (Koren et al. 2017) involving parameters such as technology Nanopore, estimated genome size 160k, and min read length 1000. Medaka Consensus Pipeline (https://usegalaxy.eu/, RRID:SCR_005857, Mozilla Public License 2.0) v1.7.2+galaxy1 was used to polish the assembly result (Oosterbroek et al. 2021). Geseq (https://chlorobox.mpimp-golm.mpg.de/geseq.html, RRID:SCR_017336, MIT License) (Tillich et al. 2017) was used to annotate the assembled chloroplast genome using all Meliaceae reference in NCBI RefSeq and visualized using OGDRaw (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html, RRID:SCR_017337, MIT License) in the CHLOROBOX (https://chlorobox.mpimp-golm.mpg.de/index.html, MIT License) (Greiner et al. 2019). Phylogenetic analysis was performed using MEGAX (https://www.megasoftware.net/, RRID:SCR_023471, MIT License) v10.2.2 (Kumar et al. 2018) with Maximum Likelihood method, Tamura-3 model and bootstrap value of 1000 replications. rbcL gene marker was used to construct the phylogenetic tree from TBT-A, TBT-K, and TBT-S samples (Owenia vernicocsa (DQ238063.1) as an outgroup) (Muellner et al. 2006).\n\n\nResults\n\nThe library yielded 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S. Based on the statistics, TBT-A has 3,339 bp of N50, 3,103 bp for TBT-K, and 3,882 bp for TBT-S (Figure 1). Chloroplast draft genomes of the TBT-A sample (36% GC content) produces 58,780 bp containing 14 tRNAs and 47 encoding genes, TBT-K sample (37% GC content) produced 142,139 bp containing 4 rRNAs, 24 tRNAs, and 78 encoding genes, also TBT-S sample (36% GC content) produced 84,906 bp containing 24 tRNAs and 53 encoding genes (Table 1). Based on the constructed phylogenetic tree, Azadirachta excelsa from three identified tree stands (TBT-A, TBT-K, and TBT-S) were placed in the same group with other Azadirachta excelsa accessions (Figure 2). We can confirm that all those samples belong to Azadirachta excelsa.\n\nd Gene duplication.\n\n* Single intron.\n\n** Double intron.\n\nGenBank accession numbers are listed beside the scientific name. The bootstrap value of 1000 replications is shown next to the nodes. Azadirachta excelsa (TBT-A, TBT-K, and TBT-S samples) are marked in coloring red.\n\n\nAuthor roles\n\nEfratenta Katherina Depari: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Visualization, Writing-Original Draft;\n\nNurheni Wijayanto: Investigation, Supervision, Writing-Review & Editing;\n\nLina Karlinasari: Supervision, Validation, Writing-Review & Editing;\n\nRafi M: Resources, Supervision, Writing-Review & Editing;\n\nIskandar Zulkarnaen Siregar: Conceptualization, Funding Acquisition, Methodology, Resources, Supervision, Validation, Writing-Review & Editing.",
"appendix": "Data availability\n\nDNA Data Bank of Japan (DDBJ): Characterization of kayu bawang in agroforestry system in Bengkulu: species name, wood quality, and metabolite profile. Accession number DRA015537; https://ddbj.nig.ac.jp/resource/bioproject/PRJDB14301 (IPB University 2023).\n\nThis project contains the following underlying data:\n\n• DRR437487 (TBT-A).\n\n• DRR437488 (TBT-K).\n\n• DRR437489 (TBT-S).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nSpecial thanks to the Forest Genetics and Molecular Forestry Laboratory, Department of Silviculture, Faculty of Forestry and Environment, IPB University and Molecular Science Laboratory, Advanced Research Laboratory, IPB University, Bogor, Indonesia, for providing lab facilities during this study.\n\n\nReferences\n\nAdfa M, Hattori Y, Ninomiya M, et al.: Chemical constituents of Indonesian plant Protium javanicum Burm. f. and their antifeedant activities against Coptotermes formosanus Shiraki. Nat. Prod. Res. 2013; 27(3): 270–273. PubMed Abstract | Publisher Full Text\n\nDe Coster W, D’Hert S, Schultz DT, et al.: NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018; 34(15): 2666–2669. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDepari EK, Wiryono W, Susatya A: Potensi tegakan kayu bawang (Dysoxylum mollissimum Blume) pada sistem agroforestri sederhana di Kabupaten Bengkulu Utara. Jurnal Hutan Tropis. 2015; 3(2).\n\nDoyle JJ, Doyle JL: A rapid DNA isolation prosedure for small quantities of fresh leaf tissue. Phytochemical Bulletin. 1987; 19(1): 11–15.\n\nGreiner S, Lehwark P, Bock R: OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47(W1): W59–W64. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIPB University: Characterization of kayu bawang in agroforestry system in Bengkulu: species name, wood quality, and metabolite profile. DDBJ Sequence Read Archive. 2023.\n\nIshiguri F, Aiso H, Hirano M, et al.: Effects of radial growth rate on anatomical characteristics and wood properties of 10-year-old (Dysoxylum mollissimum) trees planted in Bengkulu, Indonesia. Tropics. 2016; 25(1): 23–31. Publisher Full Text\n\nKoren S, Walenz BP, Berlin K, et al.: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017; 27(5): 722–736. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrisdianto, Dewi L, Muslich M: Analisis hasil pengujian kayu yang diserang penggerek kayu di laut dengan interpretasi gambar digital. Jurnal Penelitian Hasil Hutan. 2015; 33(1): 11–18. Publisher Full Text\n\nKumar S, Stecher G, Li M, et al.: MEGA X: molecular evolutionary genetics analysis across Computing Platforms. Mol. Biol. Evol. 2018; 35(6): 1547–1549. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi H: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34(18): 3094–3100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi H, Handsaker B, Wysoker A, et al.: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16): 2078–2079. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMuellner AN, Savolainen V, Samuel R, et al.: The mahogany family “out-of-Africa”: Divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity. Mol. Phylogenet. Evol. 2006; 40(1): 236–250. PubMed Abstract | Publisher Full Text\n\nOosterbroek S, Doorenspleet K, Nijland R, et al.: Decona: From demultiplexing to consensus for Nanopore amplicon data. ARPHA ARPHA Conf. Abstr. 2021; 4. Publisher Full Text\n\nPremono B, Lestari S: Karakteristik petani dan praktek silvikultur agroforestri kayu bawang (Azadirachta excelsa (Jack) M. Jacobs) di Kabupaten Bengkulu Utara. Jurnal Penelitian Hutan Tanaman. 2014; 11(3): 185–197. Publisher Full Text\n\nSiahaan H, Sumadi A: Site index prediction of smallholder plantations of kayu bawang (Disoxylum mollissimum Blume) in Bengkulu Province. Indones. J. For. Res. 2015; 2(2): 81–92. Publisher Full Text\n\nTillich M, Lehwark P, Pellizzer T, et al.: GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1): W6–W11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang W, Schalamun M, Morales-Suarez A, et al.: Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case. BMC Genomics. 2018; 19(1): 977. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "266729",
"date": "06 May 2024",
"name": "Hoang Dang Khoa Do",
"expertise": [
"Reviewer Expertise Genomics",
"Plant systematics."
],
"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, Thank you very much for adding new genomic data of Azadirachta excelsa (Jack) Jacobs, generated by long-read sequencing method of Oxford Nanopore Technologies. The content of the manuscript is suitable for F1000research. Please check my below comments. 1/ Why the chloroplast genomes of three samples were not completed? Please add some reason for this issue in the main text. 2/ There are several genes in the draft genomes. However, only rbcL was used for phylogenetic analysis. Please add the reason in the main text. 3/ In the Abstract, the authors mentioned that \"However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa, Protium javanicum, and Dysoxylum mollissimum.\". However, in the phylogenetic analysis, the authors used only \"Azadirachta excelsa\" for comparison. It is better if the authors add the data of Protium and Dysoxylum species to make a strong and reliable conclusion for the identification of three samples in this study. 4/ The draft genomes were constructed from three samples of one species. Therefore, the authors might add information about the pairwise identity of those genomes. Thank you.\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": []
},
{
"id": "269396",
"date": "09 May 2024",
"name": "Maria Stefanie Dwiyanti",
"expertise": [
"Reviewer Expertise My research area is plant genetics especially soybean and wild soybean",
"analysis of whole genome sequence",
"genotyping-by-sequencing",
"and SNP genotyping",
"GWAS and QTL analysis using SNP data."
],
"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 sequenced three samples of Kayu bawang (Azadirachta excelsa) obtained from three stands in Bengkulu Province, Indonesia. Since there is no genomic information about A. excelsa, this will help science community to use the information for sample authentication and further genetic analysis. The authors have provided detailed DNA extraction, sequencing and data analysis procedures to be replicated by others. Since the authors want to prove that Kayu bawang is indeed A. excelsa, I will suggest to add Protium and Dysoxylum rbcL sequences in the phylogenetic analysis to show that the difference between A. excelsa and the other two species. In addition, the chloroplast sequence sizes obtained from the three samples are different. If there is any estimated chloroplast genome sequence size for A. excelsa, or closely related species, the information can be added as estimation for the completeness of A. excelsa chloroplast genome sequences obtained in this study.\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/13-254
|
https://f1000research.com/articles/13-253/v1
|
05 Apr 24
|
{
"type": "Systematic Review",
"title": "The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review",
"authors": [
"José Arnaud",
"Henrique São Mamede",
"Frederico Branco",
"Henrique São Mamede",
"Frederico Branco"
],
"abstract": "Digital transformation has been one of the main trends in organizations in recent years, and digital literacy is a critical factor in the success of this transformation. Digital transformation involves the use of digital technologies to improve an organization’s processes, products, and services. For this transformation to be successful, it is necessary for employees to have knowledge of and skills in digital technologies. Digital literacy allows employees to understand technologies and their applications, know how to use them efficiently and safely, evaluate and select the most appropriate digital tools for each task, and be prepared to deal with problems and challenges that arise in the digital environment. Thus, this study is relevant because it seeks to understand how digital literacy can impact Digital Transformation in organizations and, through the construction of an explanatory model, allows the identification of variables that influence this relationship by developing strategies to improve the digital literacy of employees in organizations.",
"keywords": [
"Digital Literacy",
"Digital Transformation",
"Explanatory Models",
"Systematic Literature Review"
],
"content": "1. Introduction\n\nAccording to Datta (2020) and Blyznyuk et al. (2021), Digital Transformation (DT) positively impacts people’s daily lives and simplifies organizations, but for this to happen, people and organizations must be willing to change and restructure their attitudes towards DT and then the way they work. According to Ivanova and Putintseva (2020), DT allows for a change in society in terms of relationships with organizations. Currently, DT is a necessity for any organization, whether public or private, because of the vertiginous acceleration that digitization has had in society, which has meant that many organizations have not yet adapted to DT (Alvarenga et al., 2020). Although most organizations are already going through the DT process by incorporating digital technologies, many challenges must be overcome before fully embracing DT (Rupeika-Apoga et al., 2022; Zhou et al., 2023). According to Tanushev (2022), successful organizations in DT are more productive, efficient, technologically advanced, and therefore more competitive, digital technologies are quite broad (Schneider & Kokshagina, 2021).\n\nThe COVID-19 pandemic saw an acceleration of DT in organizations, helping lay the foundation for the implementation of this transformation (Gabryelczyk, 2020). The same author stated that the pandemic forced an acceleration in the expansion of Information Technology (IT) infrastructure, as it became clear that resources were scarce. As for Al-Alawi et al. (2023), COVID-19 made remote work the new normal, which meant that organizations had to ensure that their employees had the technology to carry out their professional activities. However, resistance to change is an important challenge in DT. COVID-19 has created a range of opportunities for innovation and transformation in organizations, associated with the use of Information and Communication Technologies (ICT) (Alam et al., 2022).\n\nDT adopts technology to transform services or business, replacing manual processes with digital processes, or upgrading existing technology with newer technology (Boban & Klaric, 2021; Park, Lee & Chung, 2022; Stoumpos et al., 2023). Most modern information technologies offer new opportunities for greater efficiency in the quality of service of organizations; however, the resulting benefits may not be guaranteed depending on several factors, such as accessibility, adaptability, and specialized personnel (Surnin et al., 2021).\n\nDuring DT, the main organizational processes are redesigned, new technological tools replace older tools, new capabilities are developed, and new ways of working are implemented (Pittaway & Montazemi, 2020; Scupola & Mergel, 2022). Organizational size is the first variable to consider when discussing organizational change (Tangi et al., 2020). DT requires organizations to adopt new strategies, organizational transformation, and new ways of implementing strategies (Rêgo et al., 2022), which are mainly driven by organizational flexibility (Sergei et al., 2023) thus improving their competitiveness (Yu et al., 2022) and increasing their productivity and efficiency (Balashov et al., 2020).\n\nAccording to Hanelt et al. (2021), DT can be defined as the organizational change triggered and shaped by the widespread diffusion of digital technologies. Thus, DT can be defined as “the most profound and accelerating transformation for business activities, processes, competencies, and models to leverage the changes of digital technology and their impact in a strategic and prioritized way” (Hamidi et al., 2018, p. 723).\n\nThe definition of DT can be broad, ranging from the profound transformation of organizational activities to the advanced use of digital technologies.\n\nDT will be a process of changing mindsets towards the use of technology, as people are at the center of DT and are responsible for its success. It is important, then, to make people part of the process, assuming them as a key factor of change; otherwise, people will not be part of the solution but part of the problem.\n\nPeople, processes, and technology are the three most important vectors in DT; however, if the digital literacy (DL) of the people involved is scarce, this could jeopardize this transformation. According to Fernández et al. (2023), people are the most essential part of an organization; therefore, it is very important to ensure their involvement and training when implementing DT. According to Nadkarni and Prügl (2020), all people who are part of an organization, regardless of their role or position, play a key role in the DT process, whether due to the simple need to acquire technical skills or the desirable involvement in taking advantage of all the potential of the adopted technologies, so that they can participate in the inevitable organizational transformation in these processes. The authors also refer to the problem of a possible division between older collaborators and less integration in the changes, in contrast with the new ones, which are more adapted to the technologies being adopted. The need to empower older people and adapt models and their usability are critical elements that need to be addressed for a better DT (Zanutto, 2021; Lee et al., 2022). According to Bykov and Medvedera (2021), DL among the younger population is generally present.\n\nCurrently, people are the most important resources in organizations because without them, organizations do not exist; however, to have quality and motivated employees, it is necessary to train them with the digital skills necessary to perform their work effectively (Glavas, Uroda & Mandic, 2021; Grgurevic et al., 2022; Galushi & Malatji, 2022; Jonathan et al., 2021). This need for digital skills was quite evident during the COVID-19 pandemic, as many people felt the need to find a new job or keep their current job, as organizations needed employees qualified in digital skills (Stofkova et al., 2022). The authors also add that some digital knowledge was optional a few years ago, was not considered important, and soon became critical.\n\nIt is necessary to reinforce the sharing of digital skills among employees during the DT process (Dee et al., 2019; Bousdekis & Kardaras, 2020). According to Shin and Rakhmatullayev (2019), Francisco et al. (2019), and Datta et al. (2020), the need for training is very important for those who do not have DL.\n\nThe most popular DL concept is that of Paul Gilster. Gilster (1997). He states that DL requires a profound change in the way we face the concept of literacy, and that it forces us to rethink the way we locate, evaluate, organize, read, and write information. Gilster defines DL as “the ability to understand and use information in multiple formats from a wide variety of sources when it is present via computers.” (Gilster, 1997, p.1). Tabusum et al. (2014) defined DL as the ability to locate, organize, understand, evaluate, and analyze information using technology. The same author states that having DL is not just knowing how to use the computer, but knowing how to use digital technologies to communicate. Walton (2016) defined DL as the ability to find, evaluate, use, share, and create content using the Internet and ICT. Based on these authors, we can say that DL is a vital competence in the knowledge society, but that, at the same time, it can constitute a barrier to personal development and social integration if it is absent or underdeveloped in the population.\n\nThe definition of DL changes according to different authors because new technologies and technological innovations change how people use technology and perform tasks. DL implies that the user can use information constructively.\n\nThis theme brings important reflections about DL because with technology and processes being transformed, the discussion on DL is very important.\n\nAccording to Feher and Szabo (2019), to digitally transform companies, they must transform their internal processes and their processes with their customers and business partners. The same authors also mentioned that company employees must be able to use technology and be digitally literate, as these skills are not just for the IT team. They add that organizations cannot transform overnight, and that the organizational culture itself and its employees cannot accept this type of DT.\n\nAl-Alawi et al. (2023) implemented well-established employee training and coaching as DT projects are subject to failure if employees adopt a passive position. This type of position on the part of employees can have consequences contrary to what was expected, that is, the relief of work that should exist with DT does not happen. Instead, we experience increased stress, increased workload, more time to process each case, and more demanding procedures (Kuhlmann & Heuberger, 2023). To create sustainable and meaningful DT, employees of organizations will have to play a critical role in the adoption and application of new technologies in different areas of the business (Ahn & Chen, 2022). According to Antunes (2022), it is essential to understand the relationship between knowledge and DT. DT has become a constant, opening countless possibilities to enrich the digital knowledge of employees in organizations, forcing them to continually update their digital skills, which is why DL is a prominent topic (Farias-Gaytan et al., 2022).\n\nDigitally transforming an organization may imply that people must be prepared and equipped with tools and, in this way, be the main drivers of this transformation. This makes it possible to rethink the processes associated with this transformation and use the added value of technology to carry out the respective implementations. Therefore, it is extremely important to reflect on the current state of digital skills in our society, more specifically, the digital skills of employees in organizations, and propose reforms and structural measures that are the true basis of sustainability.\n\nAn organization’s DT involves the implementation of digital technologies in all processes and business areas, which can lead to a significant change in the way activities are carried out and how teams collaborate. However, for DT to be successful, it is essential that the organization’s employees have an adequate level of DL, that is, skills and competencies to effectively use digital technologies in their work. Therefore, the development of an explanatory model that relates DT to the DL of employees is crucial for the organization to be able to plan and implement strategies for developing digital capabilities, ensuring that all employees can make the most of the technologies. digital implemented. This can lead to greater DT success and an overall improvement in the organization’s efficiency and productivity.\n\nKleinman et al. (1978) introduced the concept of the explanatory model and referred to the complex and culturally influenced process of interpretation that people make in relation to their own illness. This process includes giving meaning to symptoms, assigning causes to illnesses, and formulating expectations about treatment and outcomes. In summary, the explanatory model is a way in which everyone understands and explains their condition and health. Thus, explanatory models are simplified representations of reality that allow one to understand and explain the relationships between different variables that affect a phenomenon. Explanatory models are used to predict the behavior and outcome of a phenomenon and identify the variables that are most important for its occurrence. Several authors have addressed the concept of explanatory models in different areas of the study. According to Aznar-Díaz et al. (2020) and Romero-Rodríguez et al. (2022), explanatory models can provide information on aspects that can influence the development of good pedagogical practices.\n\nIn the area of technological innovation, there are also authors who address the concept of explanatory models, such as Ferreira and Torres (2017), who address the process of technological innovation in organizations and present different explanatory models to understand this process. The authors discuss important concepts, such as innovation, technology, explanatory models, and the relationship between them.\n\nThus, the importance of research and development of an explanatory model to understand the relationship between DT and DL of an organization’s employees is highlighted. It is critical that organizations understand how the DL of their employees can impact the organization’s DT, as this understanding can lead to more effective implementation and continuous improvement of DT. SLR is an important approach to identify and analyze relevant studies on DT and DL, and the description of these concepts can provide a solid basis for the development of an explanatory model. The scarcity of research investigating the relationship between these themes makes the need to conduct this research even more relevant.\n\nBy exploring the impact that DL can have on DT, an explanatory model can help organizations develop more effective strategies to improve the DL of their employees, thereby increasing the success of DT. This can lead to an increase in the efficiency, productivity, and competitiveness of organizations.\n\nThe remainder of this paper is organized as follows. In the next chapter, we present the methodology used for the Systematic Literature Review process. We then analyze the results obtained to answer the research questions and present some results obtained in relation to each of these questions, providing a more comprehensive understanding of the study. Finally, we discuss the theoretical and practical contributions before concluding the main findings and possible future research.\n\n\n2. Method\n\nIn this study, we followed Kitchenham’s guidelines (2004), involving several activities, as shown in Figure 1 and is grouped into three main phases: Planning, Execution and Reporting.\n\n• Planning phase: In planning phase, the objective to be achieved by the Systematic Literature Review (SLR) is defined, which includes formulating the research question and defining the inclusion and exclusion criteria for the studies to be selected. At this stage, it is also important to define the search terms and databases used in research. Finally, the quality of the retrieved papers was assessed.\n\n• Execution phase: In execution phase, a systematic search for relevant studies is carried out according to the inclusion and exclusion criteria defined in the planning phase. Documenting the study selection process to ensure review transparency and replicability is important. In this phase, the selected studies were evaluated for their quality and relevance to the research questions.\n\n• Reporting phase: In reporting phase, data are synthesized and analyzed to answer the research questions. This phase included extracting relevant data from selected studies, analyzing the data, and interpreting the results.\n\n\n3. Results\n\nThe research questions and their formulations must be chosen according to the focus and objective of the SLR. In this case, the research objective seeks to understand how DT impacts the DL of employees in local public administration, identifying the main factors that influence this relationship. This may include an analysis of the digital skills needed, the training and capacity building, and the barriers faced by employees in the use of digital technologies, among other relevant aspects. By proposing an explanatory model, this study aims to provide a solid theoretical framework that helps understand how DT affects the DL of employees in local public administration, thus enabling the development of more effective strategies to promote digital empowerment and the successful adoption of digital technologies in this specific context.\n\nTo assist in the construction of the research questions and their search for evidence, it was necessary to define five fundamental points, namely, Population, Intervention, Comparison, Outcome, and Context (PICOC), as shown in Table 1.\n\nTo begin the research, a strategy for searching articles was defined. Thus, in addition to the existence of other digital libraries used in an SLR, depending on the topic’s interdisciplinarity, the following are suggested:\n\n• Scopus – http://www.scopus.com\n\n• Science Direct – http://www.sciencedirect.com\n\n• IEEE – http://ieeexplore.ieee.org\n\n• Springer – http://link.springer.com\n\nWe structured the research questions using logically organized keywords. To this end, it was necessary to define search strings with the terms to be searched in a way that contemplates the research questions. The logical functions “AND” and “OR” were used to concatenate words, as digital libraries support this type of chaining. It is important to emphasize that the process of defining the search strings is iterative and involves several cycles of experimentation, checking the articles found, and adjusting the search strings. String adjustment is relevant to gain more robustness and retrieve the most relevant primary articles (Kitchenham and Charters, 2007).\n\nThe search strings used were as follows:\n\n• TITLE-ABS-KEY ((“explanatory models”) AND (“techniques” OR “methods” OR “approaches”)).\n\n• TITLE-ABS-KEY ((“digital transformation”) AND (“review” OR “survey”))\n\n• TITLE-ABS-KEY ((“digital literacy”) AND (“review” OR “survey”))\n\n• TITLE-ABS-KEY ((“digital transformation” AND “digital literacy”))\n\nThe main concepts of this research were Digital Transformation, Digital Literacy and Explanatory Models. Four digital libraries were used in view of the scope of the search terms’ results, and a significant number of articles were found through the search strings. Table 2 shows the research analysis model carried out on the main concepts during the months of March and April 2023.\n\nAfter the search strings were structured and validated, it was necessary to delimit the criteria used to exclude and include the articles that were found. The purpose of defining the criteria is to identify the primary studies that provide direct evidence for the research questions (Kitchenham & Charters, 2007).\n\nExclusion and inclusion criteria were applied to each article found in searches of digital library repositories, with some of the criteria defined based on practical issues of publications, such as the language in which it is written, type of publication, and year of publication. others. Secondary articles, summarized articles, technical reports, non-peer-reviewed publications, and redundant articles were excluded. If in the exclusion criteria it was enough for only the articles to be included in one of the criteria to be excluded from the review, in the inclusion criteria all the criteria had to be satisfied to be included in the final list of articles. For example, the timeframe entered in the search was delimited as an inclusion criterion. Another example of an inclusion criterion is the criterion of being only primary and peer-reviewed articles. The inclusion criteria are listed in Table 3.\n\n\n\n(1) Studies prior to 2018.\n\n(2) Duplicate studies.\n\n(3) Studies in any language other than English.\n\n(4) Studies in any language other than Portuguese.\n\n(5) Secondary or tertiary studies.\n\n(6) Literature such as manuals, reports, theses, dissertations.\n\n(7) Short papers (4 pages or less).\n\nTo obtain the final articles to be analyzed, the exclusion criteria were applied to 57.499 articles obtained initially. Table 4 shows the number of articles analyzed using selection filters. The number of articles in which the title and abstract were used, the number of articles in which the introduction and conclusion were used, and the number of articles in which there was full reading.\n\nThus, Figure 2 summarizes the excluded articles in the four digital libraries.\n\nAfter applying the exclusion criteria and defined criteria to assess the quality of the articles, it was found that 39 articles did not contain any criteria as defined, 22 articles contained some criteria as defined, and 32 articles met the defined criteria, as shown in Figure 3. In Figure 4, the year of publication of the articles selected for SLR was verified.\n\nAfter performing a quality assessment and obtaining a set of 54 articles valid for the SLR, it was necessary to collect data from these articles to answer the research questions.\n\nTo date, we have been able to identify 54 articles in the traditional review model and 93 articles in the snowballing model. The most cited article had all its references in English, and in one specific case, an article appeared as a result of three different strings.\n\nThese data, being an SLR, must be carefully extracted. It is important to extract and organize the most general data from the articles, such as the title of the article, authors of the article, year of publication of the article, country of the article, and type of publication of the article (for example, if it was published in a conference or if it is a chapter of a book), among others.\n\nThus, 54 articles have the essential criteria to be analysed for data extraction.\n\nAfter completing the search and selection of articles, a set of articles was selected, which served as the input for the next steps of the SLR protocol. One of the steps is the quality assessment of these articles, which is useful for increasing the accuracy of the data extraction results, thus enabling greater credibility of the results.\n\nKitchenham and Charters (2007) argued that the execution of the quality assessment of the included studies is critical for the following reasons:\n\n• Provide even more detail to apply exclusion/inclusion criteria.\n\n• Investigate whether quality differences explain differences in article results.\n\n• Quality assessment is a way to give more value to the importance of individual articles when the results are synthesized.\n\n• This step can guide the interpretation of results and determine the strength of inferences.\n\n• Can guide the recommendation of future work.\n\nIn an SLR, several criteria can be used to measure the quality of articles. Kitchenham and Charters (2007) referred to several sources that can help define the quality criteria that can be evaluated. These criteria are usually based on instruments containing checklists of factors, normally using a numerical scale that must be evaluated in each article. In this case, the scales of 0, 0.5, and 1. Scale 0 indicates that no criterion is in accordance with what was defined; the 0.5 scales to define that some criteria are in accordance with what was defined; and scale 1 indicates that the criteria are in accordance with what was defined.\n\nSeveral issues can be considered when assessing the quality of research articles. It is important to note that the relevance and weight assigned to each of these issues may vary depending on the context of the research and the specific criteria of the review. Some of the questions and their relevance are listed in Table 5.\n\nRegarding the exclusion of articles, during the review process, exclusion criteria can be established based on the specific aims and criteria of the research, with the value to be assigned being zero (0). Some common criteria may include direct relevance to the research questions, methodological quality, lack of relevant data or lack of significant contribution to the field of study. It is important to note that the assessment of the quality of articles is a subjective process, and that the final selection of articles should be made based on a combination of criteria and critical judgment.\n\nA total of 54 articles were selected for analysis and data extraction, as shown in Figure 5, the dispersion of articles analyzed on DT, DL and Explanatory Models, and most of the articles found (47 articles) refer to DT, eight articles refer to DL, and only two articles refer to Explanatory Models.\n\nAccording to Figure 6, the chronology of the selected articles on the research concepts is observed, as shown in Figure 7 percent of them.\n\nAfter analyzing the selected articles and applying the inclusion criteria using the defined scale to validate the quality of the articles, 54 articles were obtained. Table 6 presents the authors, year, and place of publication of the analyzed articles.\n\nThe number of citations of the articles analysed are those shown in Table 7.\n\nTo provide a more detailed answer to the request questions, additional articles had to be analyzed. Due to the relevance of the topic, articles prior to 2018 were considered, as well as other articles with some relevance. These articles are described in the corresponding tables.\n\nThis study is exploratory in nature. Thus, the investigation research will have the Research Questions (RQ):\n\n• RQ 1: Are there explanatory models that support DT, with a focus on DL?\n\nAlthough there are still no fully established explanatory models for the relationship between DT and DL, there are theoretical approaches that support DT with a focus on DL. Some of these approaches are listed in Table 8.\n\n• Dynamic Capabilities Model: This model emphasizes the importance of the culture of learning and innovation in the development of digital competencies. This suggests that organizations should adopt an iterative and experimental approach to develop digital skills, focusing on capabilities such as adaptability, innovation, and continuous learning.\n\n• Digital Skills Model: This model suggests that organizations should develop a digital skills management strategy to identify, measure, and develop the skills needed for DT. This emphasizes the importance of training and developing digital skills for employees and the need to align digital skills with the organization’s strategic objectives.\n\n• Digital Ecosystem Model: This model suggests that organizations should adopt a collaborative and open approach to DT, involving external partners, customers, and other stakeholders. It emphasizes the importance of the co-creation of value and collaboration in the development of digital competences and innovation.\n\nThese models can provide a useful starting point for organizations wishing to promote DL in their DT. However, it is important to remember that every organization is unique and may need to adapt these theoretical approaches to meet their specific needs.\n\nAs mentioned, there are still no established explanatory models that can explain the relationship between DT and DL, which means that research in this area is fundamental for organizations to better understand how DT affects DL and how they can promote DL in their daily tasks. The survey can help organizations develop effective strategies to improve DL among their employees and ensure that digital technologies are used in the best possible way to meet business needs. In summary, the relationship between DT and DL is crucial to the success of organizations in the digital age, and research is critical to better understand this relationship. I believe that the lack of established explanatory models can make it difficult to understand the impacts of DT on DL, as these models can help clarify how different variables and factors relate to each other and how DT can affect DL. They can also help predict the possible consequences of adopting digital technologies and identify areas in which DL needs to be improved.\n\n• RQ2: What methodologies support the implemented processes involving DT?\n\nDigital transformation has been one of the main trends in organizations in recent years. It involves the integration of digital technologies in all aspects of business, including internal processes, customer relationships, products, and services, among others. To implement this transformation successfully, it is essential to develop appropriate methodologies. Methodologies may vary depending on the context of the organization and its specific needs. In the literature, some authors specify these methodologies as understanding employee needs and developing employee-centric solutions, while others approach the methodology as iterative and incremental to develop solutions, which emphasizes collaboration and continuous delivery of value to the customer. There are also authors who advocate continuous process improvement, eliminating waste, and maximizing the value delivered to the customer. All of these approaches can be combined or adapted to meet the needs of organizations. It is important to have a clear and efficient process to manage DT and ensure its successful implementation.\n\nTable 9 shows some methodologies that can be used to support DT processes. It is important to remember that each organization is unique and may require different approaches, depending on its specific needs. Some methodologies are commonly used to support DT processes. The methodologies mentioned above are frequently used in DT projects because they have demonstrated success in a variety of situations. Each methodology has its own advantages and specific approaches; however, they all share the ability to support DT in different ways.\n\n• Agile: The agile methodology is often used in DT projects to enable an iterative and incremental approach to delivering results. This helps ensure that teams quickly adapt to changing business and market needs (Ionel, 2009).\n\n• Design Thinking: This approach focuses on the user and understanding their needs, priorities, and challenges. Teams can develop more user-centric solutions using a series of techniques and tools (Lewrick et al., 2020).\n\n• Lean: This methodology emphasizes eliminating waste and increasing efficiency, thereby making the DT process more agile and effective. It focuses on creating value for the customer and reducing the lead and cycle times (Staats & Upton, 2009).\n\n• Six Sigma: This methodology emphasizes the elimination of defects and continuous process improvement. It can be used to help organizations identify areas for improvement and implement changes to ensure more efficient and effective DT (Tjahjono et al., 2010).\n\nStudies on DT may not focus on a specific methodology but on a broader, integrated approach that combines several methodologies and strategies.\n\nDT is a continuous and dynamic process that allows organizations to meet ever-changing demands. However, successful adoption of these technologies depends on several factors, including the accessibility of the technology, adaptability of organizations to changes arising from the adoption of the technology, and availability of specialized personnel to implement and maintain the technology. If these factors are not properly considered, the expected benefits of adopting the technology may not be guaranteed and may even harm the organization. Therefore, it is important for organizations to carefully analyze the factors involved in the adoption of new technologies before making decisions.\n\nHowever, it is important to note that the size of an organization is not the only factor to consider when discussing organizational change. Other factors, such as organizational culture, financial resources, and the DL of employees can also play an important role in the success of DT. In addition, DT is not a single and continuous process, but a journey of evolution that requires constant monitoring, adjustments, and updates using the most appropriate methodology.\n\n• RQ3: What are the research perspectives on explanatory models involving DT and DL as the primary factors?\n\nThere are several research perspectives in the literature on the explanatory models of DT and DL. some of these perspectives are include in Table 10.\n\n• Models of technology adoption: These models examine why people do or do not adopt digital technologies and how DL can influence that process.\n\n• Digital empowerment models: These focus on people’s ability to understand, evaluate, and use digital information critically and effectively.\n\n• Digital governance models: These models examine how organizations manage and regulate the use of digital technologies, and how DL can affect these processes.\n\n• Digital innovation models: These models focus on how organizations can use DL to drive innovation and DT.\n\nAll these research perspectives on explanatory models involve DT and DL. This field is constantly evolving, and new research perspectives are emerging as technology and society continue to change.\n\nChallenges to overcome include resistance to change, which is one of the main obstacles facing DT. On the other hand, COVID-19 has also opened a range of opportunities for innovation and transformation in organizations, allowing them to take advantage of ICT to adapt to an increasingly digitized world. In addition, sharing digital skills between employees can contribute to the creation of a more collaborative and creative work environment in which new ideas and solutions are developed together.\n\nIn the era of DT, technology has become an integral part of business operations and the success of an organization depends on the ability of employees to use digital tools and processes. Digital transformation cannot be achieved overnight and requires cultural change within organizations as well as a change in the mindset of employees to accept and embrace this change. Therefore, education and training in digital skills are essential to help organizations and their employees face the challenges of DT and adapt to new ways of working. Digital Literacy is an essential skill for the success of DT and should be valued by organizations; however, employees may not be prepared for this change, making a careful and planned approach to DT essential.\n\nThus, DT involves a change in mindset towards the use of technology, and people are essential for the success of this process. It is important for organizations to provide their employees with the necessary resources and training so that they can adapt to technological changes and incorporate new tools into their work routines. In addition, cultural and organizational changes must be encouraged so that employees feel motivated to adopt new work practices. Digital transformation should not be seen only as a technological issue, but also as a holistic change that affects the culture, processes, and people within organizations.\n\nThe adoption of new technologies and methodologies in organizations can lead to the need to update the capabilities and skills of employees. Digital transformation has a significant impact on the way organizations operate, and for them to take full advantage of new technologies and methodologies, it is important that their employees are trained to work with them. As organizations digitally transform, employees must learn to use new digital tools and work with new systems and processes. This may require them to develop new capabilities, such as the ability to analyze data. Digital transformation can also create new opportunities for employees, such as working on new projects and in different areas of the organization. To ensure that employees are prepared for DT, organizations need to invest in training and education programs that help them develop the necessary skills and competencies. This should be ongoing and regularly updated to reflect changes in the ever-evolving digital environment.\n\nFinally, through a comparative analysis of all articles researched and selected, it appears that DL is a very important factor in organizations for the success of DT, being its crucial relationship within organizations.\n\n• RQ4: Which factors or variables impact the relationship between DT and DL among local public administration employees?\n\nStudies have addressed several factors and variables that influence the relationship between DT and DL among local public administration employees. These include access to technological resources and infrastructure, availability of training and capacity building in digital environments, organizational culture and leadership support, resistance to change, collaborative work environments, and policies and regulations related to digital technology. In addition, variables such as employees’ educational level, previous experience with digital technologies, level of DL, continuous training, technology adoption, job satisfaction, role, and age were also addressed.\n\nBy addressing these factors and variables, we hope to gain a deeper understanding of the factors that influence the relationship between local public administration employees’ DL and DT. Some factors that may impact the relationship between DT and the DL of local public administration employees are included in Table 11.\n\n• Access to resources and technological infrastructure: This refers to the availability of digital resources, such as computers, software, internet connectivity, and appropriate systems. Easy and reliable access to these resources facilitates employees’ DL, enabling them to effectively use digital technologies.\n\n• Training and capacity building in digital environments: The existence of training and capacity-building programs in digital environments is crucial for improving employees’ DL. Appropriate training provides the knowledge, skills, and practices necessary for employees to use digital technologies effectively in their daily tasks.\n\n• Organizational culture and leadership support: An organizational culture that values DT and provides support and guidance from leadership is essential. When organizational leaders demonstrate enthusiasm and support for DT, they positively influence employees’ DL, encouraging them to embrace and explore digital technologies.\n\n• Resistance to change: Employees’ resistance to change can negatively impact DL. An unwillingness to learn new technologies and adapt to digital processes can make it difficult to use digital tools effectively and affect employees’ DL.\n\n• Collaborative work environment: A work environment that promotes collaboration and digital knowledge sharing among employees is conducive to DL. The exchange of experience, questions, and mutual knowledge facilitates the acquisition and development of digital skills.\n\n• Policies and regulations related to digital technology: Policies and regulations that address data security, privacy, and the ethical use of digital technology can affect employees’ DL. Clear guidance and appropriate guidelines provide the context for the responsible use of digital technologies.\n\nSome variables that may impact the relationship between DT and the DL of local public administration employees are included in Table 12.\n\n• Digital literacy level: Refers to the ability of employees to effectively use digital technologies to perform their tasks and achieve organizational goals. A high DL level indicates proficiency and confidence in using digital tools.\n\n• Technology adoption: Reflects the degree to which employees adopt and incorporate digital technologies into their work routines and organizational processes. A high adoption rate indicated a positive relationship between DT and DL.\n\n• Job satisfaction: This relates to employee satisfaction with the use of digital technologies in the workplace. Employees who feel satisfied with the use of digital tools may indicate a positive relationship between DT and DL.\n\n• Age: Employees’ age can influence DL, with different levels of digital familiarity and skills between different age groups.\n\n• Previous experience: Employees’ prior experiences with digital technologies can affect their DL. Those with previous experience may have an advantage in adopting and using digital tools.\n\n• Educational level: Employees’ educational level can influence DL, and evidence suggests that people with higher educational levels tend to have better digital skills.\n\n• Role/Department: The role of department employees can affect their DL, as different departments may have specific digital needs and requirements.\n\n• Ongoing training: The availability of technology training opportunities can be an important factor in improving employees’ DL over time.\n\nIn addition to the factors and variables described above, other control variables can also be considered, such as the demographic and organizational characteristics of employees. These variables may influence the relationship between DT and DL. These additional factors and variables can provide a more comprehensive view of the elements that may influence the relationship between DT and DL among local public administration employees.\n\n\n4. Discussion\n\nThe relationship between DT and DL of local public administration employees was analyzed based on different factors and variables. The findings reveal important aspects that can influence employees’ DL and guide research in this field. One of the key factors is the access to technological resources and infrastructure. The availability of devices, Internet connectivity, and other adequate resources have been identified as elements that positively impact DL. On the other hand, a lack of access to these resources can hinder the development of necessary digital skills.\n\nTraining and capacity building in digital environments also play crucial roles in DL. Effective training and capacity-building programs have been associated with improvements in employee DL. However, the lack of learning and development opportunities is a significant barrier. Organizational culture and leadership support were identified as influential factors in DL. An organizational culture that values innovation, collaboration, and continuous learning encourages employee DL. Leadership support is key to promoting the adoption of digital technologies and the development of necessary skills.\n\nResistance to change has emerged as a challenge to overcome in improving the DL. Effective strategies to address resistance to change are needed to promote employee DL and ensure the successful adoption of digital technologies. A collaborative work environment has been highlighted as a facilitator of DL development. An environment that promotes knowledge exchange, collaboration, and cooperation among employees contributes to enhancing digital skills. Policies and regulations related to digital technology also affect employees’ DL. Clear policies and well-defined regulations are essential to provide guidance and establish guidelines for the use of digital technologies. A lack of adequate policies can create uncertainty and hinder DL development.\n\nThese findings highlight the importance of access to technological resources and infrastructure, adequate training and capacity building, favorable organizational culture, overcoming resistance to change, a collaborative work environment, and appropriate policies to promote the DL of local government employees. They provide insights into the factors that influence DL and highlight key areas that require further research.\n\nSeveral research directions can be explored in studying the relationship between DT and DL of local public administration employees.\n\n1. To assess the impact of individual variables such as age, previous experience, educational level, and function/department on the DL of local public administration employees.\n\n• How does employees’ age influence their willingness and ability to adopt digital technologies and develop DL?\n\n• Is there a correlation between employees’ previous experience with technology and their ability to adapt to DT and improve their DL?\n\n• What is the role of employees’ educational level in acquiring digital skills, and how does this affect DL?\n\n• Is there a difference in DL between different functions/departments in local public administration and how can this be addressed?\n\n2. To investigate the relationship between employees’ DL and technology adoption, job satisfaction, and current DL levels.\n\n• Is there a correlation between employees’ DL level and their job satisfaction?\n\n• How does employee DL influence their willingness to adopt new technologies and promote DT in their daily tasks and activities?\n\n• To what extent does the current level of employee DL affect the effectiveness of training and capacity-building initiatives in digital environments?\n\n3. Explore the influence of methodologies such as Agile, Design Thinking, Lean and Six Sigma in promoting DL and supporting DT in local public administration.\n\n• How can agile methodologies, such as agile, be applied to boost the DL of local public administration employees?\n\n• To what extent can the Design Thinking approach help identify employees’ DL needs and develop user-centered solutions?\n\n• How can Lean principles be used to optimize processes and improve employees’ DL?\n\n• What is the role of Six Sigma in continuously improving employee DL and reducing knowledge gaps?\n\n4. Investigate digital governance best practices in local public administration and how they affect employee DL. This research explores the following:\n\n• How do digital governance policies and regulations impact employees’ DL?\n\n• What are the best digital governance strategies that promote effective DL?\n\n• How can digital governance be aligned with DT initiatives to support the development of employee DL?\n\nThese research directions address key aspects of the relationship between DT and DL among local public administration employees, allowing for further analysis and providing relevant insights for research.\n\nSeveral open questions make this research on the relationship between DT and DL of local public administration employees highly relevant:\n\n1. What is the specific impact of DT on operational efficiency and public service delivery by the local public administration? It is important to investigate how DT affects the efficiency of processes and delivery of public services.\n\n2. What are the main challenges faced by local public administration when dealing with resistance to change during DT, and how can these challenges be overcome? Resistance to change is a common obstacle in DT. It is important to understand the specific challenges faced by local public administrations and to explore strategies to overcome resistance.\n\n3. What are the main obstacles and gaps that local public administration employees encounter when trying to improve their DL, and how can they be addressed? Identifying the obstacles and gaps in employee DL is essential for developing effective capacity-building strategies.\n\n4. What are the best strategies and approaches for providing effective training and capacity building in digital environments for local public administration employees? Identifying the best practices for training and capacity building is crucial for boosting employee DL.\n\nThese open questions highlight the relevance and importance of this study. By addressing these knowledge gaps, this research will contribute to a more comprehensive understanding of the relationship between DT and DL in local public administration, as well as provide practical guidance for improving operational efficiency, overcoming resistance to change, addressing barriers in DL, and developing effective training and capacity-building strategies.\n\n\n5. Conclusions and Future Research\n\nIn conclusion, SLR is carried out mainly to identify, evaluate, and interpret the studies carried out and published in the literature. Through SLR, we were able to collect evidence on the topic to be addressed, detect, and identify opportunities for research work. Therefore, it is extremely important to carry out an SLR before starting the research, as this way, it is possible to clearly assess the research area and how the research proposal can contribute to giving more value to what has already been published.\n\nThe scientific production of DT and DL in the context of organizations is a topic of interest in the scientific community. The results of this investigation clearly show that studies predominating DT are currently a topic with some relevance. DT and its impact on DL are topics of interest to organizations, as influencing processes imply proper functioning. In this investigation, interest in these concepts over the last five years is evident. The adoption of new technologies and methodologies in organizations impacts the digital training of their employees, as it requires them to develop new digital skills to be prepared for DT.\n\nTable 13 presents some of the main conclusions and results of the SLR for DT and DL.\n\nThis SLR research on the relationship between DT and DL, with the aim of creating an explanatory model, can stand out from previous reviews and add value for several reasons:\n\n• The emphasis on creating an explanatory model distinguishes reviews from traditional reviews that summarize and synthesize existing findings. An explanatory model can help clarify the causal relationships and complex interactions between the concepts of DT and DL.\n\n• This review can contribute to theory by developing a conceptual model that helps explain how DT affects DL and vice versa. This provides a solid theoretical framework for future research.\n\n• By creating an explanatory model, we can identify gaps in the literature where the relationship between DT and DL has not been sufficiently explored. These gaps can guide future research in this area.\n\n• The explanatory model has practical implications such as guidelines for organizations and adding a valuable practical component to the review.\n\n• This review explores the relationship between DT and DL in specific contexts, allowing for a more contextualized analysis of the implications and results.\n\n• In addition to developing an explanatory model, we expect to synthesize the existing evidence to support the relationships presented in the model. This will help to reinforce the conclusions and strengthen the validity of the model.\n\nTechnology has innovation as its main factor, having to adapt to its context and generate new learning. DT has had a systemic reach in organizations over the last five years, in which the development of employees’ digital skills contributes to the adoption of new technologies that support DT. It is important for organizations to generate strategies that guarantee systemic DT so that their services and processes evolve at a good pace. It is essential that the incorporation of technologies is accompanied by strategies that favor employees, thus promoting an increase in DL. This incorporation of technology has led organizations to rethink their processes, bearing in mind that technologies are a means of support and that their employees must be prepared for changes, especially digital changes.\n\nNo explanatory models have been found in the literature on the relationship between DT and DL, which makes research in this area even more relevant. Some authors, such as Eshet (2004), Jaeger et al. (2012), Cetindamar Kozanoglu, D., & Abedin, B. (2021), Sanders, C. K., & Scanlon, E. (2021), and Brown, N., & Brown, I. (2019) mention the relevance of this relationship. Eshet (2004) explored the key concepts of DL and the importance of survival skills in the digital age. Jaeger et al. (2012) discussed how digital inclusion and DL are fundamental to education and civic participation in the digital age. On the other hand, Cetindamar Kozanoglu D. and Abedin (2021) explore the importance of DL in the context of DT in organizations. Sanders K. and Scanlon (2021) investigated how DL affects digital inclusion, particularly among low-income populations. Finally, Brown N. and Brown (2019) examined the relationship between DT and digital skills including DL.\n\nIt is noteworthy that it was possible to answer the research questions, noting that DT is an emerging theme in organizations, especially in improving technology and adapting organizational processes, where DL is essential for improving and facilitating work. It is verified in the SLR that the concepts of DT and DL, as well as their relationship, allow a broad discussion on the subject, providing a deepening of the concepts related to each other, with the objective of strengthening their investigation.\n\nThus, there is a need to implement an explanatory model of the relationship between DT and DL. The methodological approach used in this study can serve as a model for other researchers investigating similar topics. The implementation of an explanatory model can be a crucial step in the current research and serves as a basis for future research. Some areas that could be explored in future research include the following.\n\n• Comparing Models: Explanatory models can vary in terms of complexity and emphasis on different variables. Future research could compare different models to determine the most effective in explaining the relationship between DT and DL.\n\n• Longitudinal Studies: Investigating how the relationship between DT and DL evolves over time can be an interesting area of research. Longitudinal studies can help identify the trends, changes, and factors that influence this relationship over time.\n\n• Case Analysis: Future research could focus on detailed case studies of local public administration organizations that have undergone successful digital transformation. This would allow for a deeper analysis of the practices and strategies that have led to positive DL results.\n\n• Effects of DL on Local Public Administration: In addition to understanding how DT affects DL, it is important to investigate how employee DL affects local public administration in terms of efficiency, quality of services, and innovation. This is an area that could be explored in future research.\n\n• Impact on Society: In addition to the effects on public administration, investigating how the relationship between DT and DL impacts society in general could be a relevant area of research. How does improving the DL of local public administration employees affect citizen participation and delivery of public services?\n\nThere are just a few suggestions for future research that can build on the explanatory model that will be developed. Each of these areas of research can contribute to a deeper understanding of the relationship between DT and DL, and offer valuable insights for local public administration.",
"appendix": "Data availability statement\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review. Extended data – Table 1-Search strategy for techniques or methods or approaches to explanatory models.docx. https://doi.org/10.6084/m9.figshare.25331788 (Arnaud et al., 2023a).\n\nFigshare: The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review. Extended data – Table 2-Search strategy for review or survey on digital transformation. https://doi.org/10.6084/m9.figshare.25331785 (Arnaud et al., 2023b).\n\nFigshare: Working title: The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review. Extended data – Table 3-Search strategy for review or survey on digital literacy.docx. https://doi.org/10.6084/m9.figshare.25331782 (Arnaud et al., 2023c).\n\nFigshare: The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review. Extended data – Table 4-Search strategy for digital transformation and digital literacy.docx. https://doi.org/10.6084/m9.figshare.25331791 (Arnaud et al., 2023d).\n\nFigshare: The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review. Extended data – PRISMA_2020_flow_diagram.docx. https://doi.org/10.6084/m9.figshare.25331863.v1 (Arnaud, 2024).\n\nFigshare: PRISMA checklist for ‘The relationship between digital transformation and digital literacy - an explanatory model: Systematic literature review’. https://doi.org/10.6084/m9.figshare.25331848 (Arnaud et al., 2023e).\n\nLICENCE CC0\n\n\nAcknowledgments\n\nWe would like to thank INESC TEC for their contributions during the whole project.\n\n\nReferences\n\nAarons GA, Hurlburt M, Horwitz SM: Advancing a conceptual model of evidence-based practice implementation in public service sectors. Adm. Policy Ment. Health Ment. Health Serv. Res. 2011; 38: 4–23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbd-Rabo A, Hashaikeh S: The digital transformation revolution. Int. J. Humanit. Educ. Res. 2021; 03(4): 124–128. Publisher Full Text\n\nAdner R, Kapoor R: Innovation ecosystems and the pace of substitution: Re-examining technology S-curves. Strateg. Manag. 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}
|
[
{
"id": "297239",
"date": "18 Jul 2024",
"name": "Silvia Farias-Gaytan",
"expertise": [
"Reviewer Expertise educational innovation",
"higher education",
"digital transformation"
],
"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\nEach section is well-organized and describes each phase and results in accordance with the objective and research questions. An aspect that can be included as part of the conclusion is about the limitations encountered during the study, in order to serve as a reference for other researchers. A suggestion, that the abstract be structured following IMRDC and that the methodology used be stated because it has not been included.\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.) Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-253
|
https://f1000research.com/articles/13-252/v1
|
05 Apr 24
|
{
"type": "Software Tool Article",
"title": "Improving Inventory Control Through a Web-Based System in a Retail Company",
"authors": [
"Cristhian Aguedo",
"José Espinoza",
"Alex Pacheco",
"José Espinoza",
"Alex Pacheco"
],
"abstract": "Background Currently, retail companies that fail to digitise their logistics processes experience difficulties in controlling stock, resulting in inaccuracies in the quantity of products and excess amounts in the warehouse. Consequently, the aim was to introduce a web-based system to enhance inventory control in retail firms within the city of Huaraz.\n\nMethods The Extreme Programming methodology was implemented in four phases. During the planning phase, roles and user stories were established. In the coding phase, Hypertext Preprocessor and JavaScript programming languages were utilised alongside the MySQL database management system. The testing phase involved evaluating each interface’s functionality to ensure that it was a part of the web system. The objective of this was to develop the web system and utilise it as an inventory control tool.\n\nResults The utilization of the web-based system within the logistics sector led to enhanced indicators, as seen through a 52.94% increase in inventory precision rate and 91.94% rise in the stock turnover rate.\n\nConclusions The web system facilitates the minimisation of input errors in product quantity records while also enabling visualisation of such data. It further provides an illustrated representation, in the form of a bar graph, of each product’s indicator behaviour.",
"keywords": [
"Web system",
"Inventory control",
"Inventory precision rate",
"Stock turnover rate",
"Logistics area."
],
"content": "1. Introduction\n\nCommercial companies in the retail sector now manage their product inventory through data analysis and visualization tools in the logistics field. Web-based systems have become a priority for organizations seeking valuable information about product characteristics, including quantity, name, brand, and supplier.1,2 The selected web-based system facilitates the management of data acquired during the execution of inventory control activities in the logistics field.3,4\n\nThe web system can efficiently manage data as it is stored on a web server, making it easily accessible rather than relying on local resources.5,6 The platform offers a versatile and adaptable framework that allows establishments to securely store significant quantities of data and access it from any point.7,8 The advantages of cloud technology include reduced costs, scalable resources that can be quickly accessed as required, and improved data accessibility, which facilitates the analysis and processing of large amounts of information.9,10\n\nIn this context, the web-based tool presents a compelling proposal for enhancing inventory management.11,12 The process involves visually depicting functions, data, statistical graphs, and tables, and presenting inventory precision and stock turnover rate indicators in a clear and understandable manner through user actions on web system interfaces that generate reports.13,14\n\nThe findings of Ref. 15 demonstrate that the laboratory company faced challenges in managing the inputs utilized in their activities, requiring implementation of an application to enhance data collection for logistical control of chemicals used in their operations. Furthermore, according to Ref. 16, proposes efficient techniques for storing pharmaceutical inventory control records in an internet-based platform to facilitate queries on the quantity of medication stocked at the logistics department. According to research conducted by Ref. 17, employees working in the logistics department of the medical consortium are responsible for managing the data related to their collected supplies from various suppliers. As a solution, they suggest implementing a web-based system to organize and improve accessibility of the data for the employees. Finally, a web-based system was developed by Ref. 18, and deployed on a web server to streamline communication of relevant material and merchandise data amongst departments of the construction company.\n\nThe above studies demonstrate the positive effect of implementing this tool in inventory control on key performance indicators, specifically the stock turnover rate and inventory precision rate; this facilitates comprehension of the results and enables informed decision-making within the chain of command.19,20\n\nHowever, it is imperative that the scientific community conducts research to demonstrate the latest inventory control features. This will ascertain how retail companies in the city of Huaraz can enhance their inventory control through the incorporation of a web-based system. The research should address security concerns, overcome interoperability challenges, and overcome the limitations inherent in the current technological infrastructure. Further research is necessary to determine the efficacy of the internet-based system in managing incoming and outgoing goods, given the significant volume of data that must be effectively managed via a database, while also enabling easy access to said data.\n\nThe current research aims to bridge the knowledge gap by presenting the advantages of implementing and executing a web system for inventory control. It analyses how this web system enhances the outcomes of the inventory control indicators mentioned earlier in the field of logistics.\n\nThus, the aim of this investigation was to implement and launch a web-based platform within the logistics sector of ROBLEPLAST S.A.C. in Huaraz. The platform would enable visualisation of outcomes acquired through the inventory precision rate and the stock rotation rate for every product within the logistics area.\n\nThis study is beneficial for inventory control, offering timely and pertinent data on each product’s quantity, frequency of restock, and percentage deviation from the amount recorded in the online system. Moreover, it aligns with Sustainable Development Goal 9, which emphasises sustainable technological advancement and enhanced labour productivity.\n\n\n2. Methods\n\nThis section outlines the components and use of the Extreme Programming approach incorporated in the creation of the inventory control system for the web.44\n\nA computer equipped with an Intel(R) Core (TM) i5-11400H processor, 8 gigabyte of double data rate type four synchronous dynamic random-access memory clocked at 3200 Megahertz, and a 1 terabyte non-volatile memory express M.2 solid-state drive was utilized. Programming was carried out in Hypertext Preprocessor21 and JavaScript within Visual Studio Code,22 with MySQL23 used as the database management system for web system development.\n\nThe web-based inventory control system was created following the Extreme Programming methodology, which involves four main phases: planning, designing, coding, and testing.24 In addition, the project utilised Hypertext Preprocessor as the programming language, HyperText Markup Language as the mark-up language, MySQL as the database manager, and cascading style sheets for visual development.\n\nFigure 1 illustrates the sequence of procedures devised within the methodology.\n\nPhase 1. Planning\n\nA set of criteria has been established.\n\n• Creation and identification of users. For each user to log in with their email and password to the web system to the respective interfaces according to their operational position.\n\n• Record and manage data about products and suppliers. Save data about products (name, brand, quantity) and suppliers (brand).\n\n• Calculate and represent in table and statistical graph the result of the inventory accuracy rate of each of the 50 products. Calculate by entering the start and end date to calculate the average of the results within the time interval; The percentage will then be plotted on a bar chart.\n\n• Calculate and represent in table the result of the stock turnover rate of each of the 50 products. Calculate by entering the start and end date to calculate the average of the results within the time interval; the percentage will then be plotted on a bar chart.\n\n• Enable the capability to retrieve data on a particular product through a query function.\n\n• Provide an instance to export the table into PDF format for report drafting. A button with its corresponding icon will be available to enable the screen table’s content’s exportation for report drafting.\n\nRoles were assigned for the software development project of “Web system for inventory control”. Table 1 shows the roles and the name of the person in charge.\n\nUser stories were developed as a fundamental basis for developing web system interfaces for inventory control.\n\nThe Table 2 provides a detailed user story for the development of an interface to calculate the inventory accuracy rate of each product.\n\nTable 3 outlines the user story to create an interface for computing the stock turnover rate of each product.\n\nFigure 2 shows the entity-relationship diagram made up of tables representing the entities and their attributes that together are part of the database structure.\n\nPhase 2. Design\n\nThe interface design was created utilizing cascading style sheets syntax within the Bootstrap25 framework. The development of the interface was further tested on the web browser, Brave.26\n\nFigure 3 shows the cascading style sheets syntax for the presentation of the dashboard interface.\n\nFigure 4 depicts the dashboard interface of the online inventory management system in the Brave browser, which displays statistical graphs of the inventory control indicators.\n\nPhase 3. Codification\n\nWe developed the Hypertext Preprocessor based coding in conjunction with JavaScript and structured query language syntax for inventory control operations, including stock turnover, inventory precision, product registration, supplier registration, and operator access data registration.\n\nFigure 5 shows the JavaScript code to confirm that all data in the “product” form is entered.\n\nFigure 6 illustrates the Hypertext Preprocessor code containing a structured query language statement for efficient registration of product-related data.\n\nPhase 4. Testing\n\nThe acceptance test was developed for each interface to be analysed, such as the interface called “inventory precision rate” and the corresponding “stock rotation” interface, where the result is acceptable for the interface to become part of the final software product.\n\nTable 4 gives details of the acceptance test to which the interface inventory precision rate was analysed.\n\nTable 5 gives details of the acceptance test to which the stock rotation rate interface was analysed.\n\nFurthermore, every interface was executed on a local server utilizing the XAMPP27 software, with each interface being programmed to provide an alert verifying the execution of actions.\n\nThe Figure 7 displays the interface of the XAMPP program operating on the Apache server, along with the MYSQL database manager.\n\nThe Figure 8 shows the interface where the result of the stock rotation rate on the product Ajicero is displayed within the period from 05/05/2023 to 07/07/2023. In section (a) you can see the notification confirming the successful filtering, so in each interface of the web system confirmation notifications have been implemented so that the user can see that his action was successful.\n\nThis web system is different from existing applications:\n\n• Focused on the logistics system: Our web-based system is designed for micro and macro companies in the retail sector and is adapted to the needs of the organisation’s management, enabling them to make decisions within the administrative management.\n\n• Customisation: Users can customise the reports they want to access and make product queries.\n\nA web-based system suitable for use in micro- and macro-enterprises in the commercial sector is presented and its features explained.\n\n\n3. Use case\n\nIn this section, we present the interfaces where you can see the scores that the products have obtained in terms of the inventory accuracy rate and inventory turnover rate indicators.\n\nFigure 9 illustrates the dashboard interface comprising two sections, (a) and (b). The first section presents bar charts representing the inventory precision rate, while the second section displays the stock turnover rate.\n\nInput: Accessing the Board view.\n\nOutput: Dashboard interface.\n\nFigure 10 displays the interface for registering the quantity of products entering the logistics region. The form requires the entry of the product name, quantity of entry, transaction code, and supplier details.\n\nInput: Access the Income view.\n\nOutput: Product entry form.\n\nFigure 11 displays the user interface of the form utilized to record the amount of merchandise exiting the logistics section and entering commercial premises. It entails input of the product name, order quantity, carrier name, and purpose of product withdrawal from the logistics area.\n\nInput: Access to the “Order” view.\n\nOutput: Order entry form.\n\nFigure 12 depicts the form interface which requires entry of the product description and the start and end dates, providing a display of the inventory precision rate achieved by the product.\n\nInput: Access to the view “Inventory Accuracy Rate - Consolidated”.\n\nOutput: Inventory Precision Rate Results Form.\n\nFigure 13 presents the interface of the form for inputting the product description alongside the start and end date of the specified period. This will subsequently filter and display the achieved stock rotation rate of the respective product.\n\nInput: Access to the “Stock Rotation Index” view.\n\nOutput: Stock Turnover Rate Results Form.\n\n\n5. Discussions\n\nFigure 9 presents the dashboard which displays essential data regarding the product quantity and its performance concerning all indicators in both sections (a and b); these indicators are depicted via bar graphs. Moreover, the dashboard provides a concise and up-to-date overview of processed data, facilitating the analysis of results for report generation and communication within the logistics department’s chain of command. This advantage is reinforced by Ref. 28 because considers that the dashboard gives a summary view, and you don’t need to be looking inside the system to get what is already in sight. Similarly, the dashboard data as per Ref. 29 provides a means to make informed decisions quickly based on the data presented. And finally Ref. 30, states that the dashboard is a source of strategic communication for employees to aim for the same goal to improve the outcome of the indicators.\n\nFigure 10 illustrates the digital system’s format to register product entries into the logistics zone, allowing for efficient data entry and minimizing errors on the completion of the form. This is reinforced by Ref. 31, as the digital tool is accessible from any internet-connected device and enables efficient time management when carrying out the activity. Furthermore Ref. 32, states that submitting the form digitally can result in savings on office supplies. Finally Ref. 33, believed that the digital form accelerates the registration process, enhancing the administrative relationship with suppliers who will then experience better quality services in receiving their products.\n\nFigure 11 displays the webpage form for recording product exits from the logistics area for onward transfer to the shopping centre. This facilitates the registration of the product quantity to enable tracking, which is critical for managing stock levels and placing appropriate orders with suppliers. This is corroborated by the statement from Ref. 34 says that the order process in a form involves data security as well as control over the quantity of products that are ordered. Furthermore, according to Ref. 35, the clarity of communication is heightened as all operators involved in product output are aware of the exact products being handled in real-time. Finally, according to Ref. 36, saving information in the web system form assigns responsibility to the operators for carrying out actions and tracking products to identify losses or thefts and take appropriate measures.\n\nFigure 12 displays an interface that enables users to filter the precision rate of inventory findings by product name and date. This functionality allows users to observe the product’s trend over time. In this regard, Ref. 37 asserts that implementing a filtering feature with date and product name options would facilitate result retrieval, allowing for clear insight into inventory management. Furthermore, as pointed out by Ref. 38, it is imperative to resolve any issues identified during the analysis of results to enhance the scheduling of product sourcing. Finally, according to Ref. 39, the results consistently indicate the need to take action to enhance the interoperability of employees for improved outcomes.\n\nFigure 13 displays an interface that permits the filtering of stock rotation rate outcomes by product name. In addition, one can enter dates as another filter option, thereby permitting an observation of trends in the frequency of product ordering and replenishing within the logistics domain. According to Ref. 40, the results presented enable the assessment of the efficacy of product ordering. Furthermore, according to Ref. 41, analysing trends enables the assessment of product demand. Conclusively, according to Ref. 42, the interface’s results enhance the market strategy for products exhibiting high and low performance within a particular duration.\n\n\n6. Conclusions\n\nThe study resulted in the creation of a web-based inventory management system with a focus on stock control, comprising both inbound and outbound movements of goods. The inventory of products within the logistics sector was closely examined, with special attention given to the indicators of precision and stock turnover rates. Data was collected on each product to determine its efficacy. In brief, the developed software application is aligned with inventory control optimisation as it allows for comparison of results on the same product and demonstrates improvement.\n\nFor future research, it is advisable to investigate alternative tools and methods for presenting and handling data related to additional indicators included in inventory control. This would enhance the web system’s functionality and augment its performance.",
"appendix": "Data availability statement\n\nThe data underlying this study can be found in the “database” directory, under the file name “almacent.sql”. Additionally, an archived version of the data is accessible on Zenodo, identified by the following DOI: https://doi.org/10.5281/zenodo.10815641. 43\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 extend our sincerest thanks to the management and personnel of Robleplast SA.C. for their cooperation during our research and for enabling us to obtain the presented findings.\n\n\nReferences\n\nVelásquez M, Cárcamo H, Aguirre J: Sistema web para el control de inventario y facturación de la distribuidora Villareyna utilizando la metodología SCRUM, en la ciudad de Estelí, segundo semestre 2019.,” Tesis de Pregrado, Universidad Nacional Autónoma de Nicaragua, Nicaragua.2020. Accessed: May 24, 2023. 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Publisher Full Text\n\nAguedo C, Espinoza J: Web System for Inventory Control in a Retail Store. Huaraz: Oct. 28, 2023. Accessed: Oct. 28, 2023. Publisher Full Text"
}
|
[
{
"id": "306135",
"date": "02 Aug 2024",
"name": "Muhammad Khan",
"expertise": [
"Reviewer Expertise Please see my ORCiD"
],
"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\nReviewer Comments:\nBased on my review of the paper, I would like to highlight the following points:\nStrengths: The paper provides a clear and detailed explanation of the developed web-based inventory management system, including its features, such as stock control and inventory accuracy.\nThe use of digital forms and dashboards for real-time data tracking is well-articulated, showcasing the system's practical utility.\nAreas for Improvement: The literature review could be expanded to include relevant studies, establishing a stronger theoretical foundation for the research. The methodology section should provide more details on the testing and evaluation criteria to assess the system's effectiveness. The conclusions could discuss the broader implications of the system and its potential limitations.\nRecommendation for Citations: The authors should consider citing the following relevant papers to strengthen the theoretical and practical background of their study: (https://doi.org/10.3390/su142416336) (https://doi.org/10.3390/logistics7020025) These papers provide insights into sustainable logistics and inventory management, which could enhance the discussion and relevance of the current study.\nOverall Impression:\nThe paper presents a practical and well-organized study on a web-based inventory management system. While the technical aspects are well-explained, additional context and references to existing literature would further enrich the paper's contributions.\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
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https://f1000research.com/articles/13-252
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https://f1000research.com/articles/13-250/v1
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04 Apr 24
|
{
"type": "Research Article",
"title": "Discrimination of persons with mental illness: testing the principles for the protection of persons with mental illness and the improvement of mental health care in Indonesia",
"authors": [
"Nelson Simanjuntak",
"Manotar Tampubolon",
"Favio Farinella",
"Nelson Simanjuntak",
"Favio Farinella"
],
"abstract": "Background Discriminatory acts against individual freedom rights in the context of human rights and dignity in Indonesia have been in the international spotlight due to human rights violations for years. Although the condition of individuals with mental disorders in Indonesia is quite worrying when viewed from the context of human rights; however, some basic mental health services are not available in most parts of the country.\n\nMethods This qualitative research uses secondary data such as health literature, social scientific, and national legal studies. The thematic analysis in this study concentrates on answering different research questions. However, this study encountered limited scope on two grounds; the first focuses on whether the National Mental Health Act (MHA) meets the basics set by the principles of CRPD. The second was the impact of other different rights on people with mental disorders.\n\nResults The results of this study on the number of cases of shackles and the differences between International Mental Health standards and the Indonesian Mental Health Act are also presented. A total of 23 studies have been used to determine the result from the analysis. It has been observed that adequate knowledge and awareness of people about mental retardation and health issues guide to the poor attitude as well as treatment of them. As per the report of Human Rights Watch in 2019, approximately 57,000 individuals with mental illness have been humiliated once in their overall lifetime in Indonesia.\n\nConclusions The tradition of shackles (pasung) has resulted in ongoing suffering due to ineffective actions that violate human freedom and are contrary to human values. The Indonesian government should provide proper facilities for individuals with mental disorders to protect and cure them the people who have mental disorders and structure its laws more strongly.",
"keywords": [
"shackles",
"pasung",
"mental illness",
"human freedom",
"discriminative treatment"
],
"content": "Introduction\n\nPopulations in most countries, including Indonesia, are facing mental illness struggles (Roberts, 2018). Nearly one billion people worldwide suffer from mental illnesses, and more than 75% of them do not receive adequate treatment (Kovacevic, 2021). According to Tang et al. (2022), suicide is the leading cause of death among people with mental illnesses because they do not receive timely and appropriate treatment. According to Hartini et al. (2018), 1.7% of Indonesia’s total population suffers from mental illness, which is often stigmatized by society. The proportion of people suffering from mental illness in 2022 was 3.7%, or 9.162,886 people, making Indonesia one of the countries with the highest number of people suffering from mental illness in the world (World Population Review, 2022), and it is expected to rise by 3.24 million before 2024 (Wolf, 2022). According to the Ministry of Health of the Republic of Indonesia’s Basic Health Research (Ministry of Health of the Republic of Indonesia, 2018), more than 19 and 12 million people over the age of 15 experience mental and emotional disorders, and depression, respectively. Furthermore, data on suicides show that 1,800 people per year, five per day, commit suicide, and 47.7% of suicide victims are aged 10-39 years, a group comprising teenagers and adults of productive age. The presented percentage of the suicide rate may be correct if no early efforts are made to slow the growth rate.\n\nGlobally, Ukraine has the highest number of depressed people according to their population at 6.30% followed by the United States of America and Australia at 5.90% each, and Brazil at 5.80%; whereas Laos and Nepal have the lowest proportion at 3.20% each (World Population Review, 2022). Further, Sweden, Germany, and Finland provide some of the best healthcare in the world because their governments promote psychological wellbeing including work-life balance and healthy work environments and allocate government spending to mental health care (CEO Magazine, 2022). Indonesia has the worst ratio of general medical practitioners to people worldwide, with only 0.22 medical practitioners for every 1,000 people (Clarkson, 2022). To overcome this problem, the Indonesian government imposed the National Mental Health Act (MHA). The aim of this act is to offer services regarding mental health for everyone and specify the rights of people with mental health problems (ODMK) are people who have physical, mental, social, growth and development problems and/or quality of life so they are at risk of experiencing mental disorders and people with mental health disorders (ODGJ) are people with personality disorders, where sufferers tend to have deviant thought patterns and deviant behavior. Although, it cannot be acquired optimally. The rights of ODGJ and ODMK individuals are sometimes ignored both legally and socially. There is still some stigma in society about people who have a mental illness, so families try to hide the existence of the members who have this issue. This sustains ODGJ and ODMK individuals’ access to adequate health services. Regulations and laws that are legally existing cannot comprehensively assist the fulfilment of ODGJ and ODMK rights.\n\nAlthough Indonesia has ratified the United Nations Convention on the Rights of Persons with Disabilities, and has rules that guarantee the rights of citizens with mental illness such as Act No. 18 of 2014 concerning Mental Disease, Act No. 19 of 2011 concerning the Ratification of Convention on the Rights of Persons with Disabilities, Act Number 18 of 2016 concerning Persons with Disabilities, and the Regulation of the Minister of Health of the Republic of Indonesia No. 54 of 2017 concerning the Completion of Increase in People with Mental Disorders (ODGJ), it often violates the rights of patients with mental illness (Edwards, 2014; Hartini et al., 2018; Widodo, 2019; Tampubolon, Silalahi, and Siagian, 2021; Wolf, 2022). Further, Indonesia must respect inherent dignity, individual autonomy including the freedom to make one’s own choices, and people’s independence (United Nations Office of Human Rights of the United Nations from the High Commissioner, 2006); further, there shall be no discrimination on the grounds of mental illness (United Nations of the Human Rights Office from the High Commissioner, 1991).\n\nHowever, problems arise when mental disorders are considered taboo, as they are in Indonesia (Subu et al., 2021; Puspitasari et al., 2020). In India, Kate et al. (2012) mentioned that mental disorders reflect abstract metaphysical entities; supernatural agents; witchcraft; disrespect for gods, teachers, or others; and excessive fear or excitement that causes mental shock and wrong bodily activity. These disorders are treated using herbs, ointments, mantras, prayers, and moral or emotional persuasion. In such situations, discrimination continues, causing the mental condition of the patient to worsen. To avoid the community’s taboo perception, previous practice in Indonesia stipulates that sufferers of mental diseases must be shackled by their feet so they cannot roam freely (Hidayat et al., 2020; World Health Organization Southeast Asia, 2021; Dahniar et al., 2022). To avoid being seen and so as not to disturb others, pasung (shackling) is enforced for sufferers of mental illnesses. Because of this method and inadequate health facilities, people’s health worsens, and they experience feelings of isolation and loneliness (Wang et al., 2017; Banerjee and Rai, 2020; McKenzie et al., 2022; Majmudar et al., 2022).\n\nIn the context of guaranteeing the rights of people with mental illness, the Indonesian government seems to be more focused on avoiding the practice of pasung than on treating people with mental illness by issuing regulations to eliminate the shackles that are so often used (Saputri, 2021). This has resulted in priorities that are detrimental to the rights of mentally ill individuals. In addition, the government’s lack of attention to building mental hospitals and the lack of psychiatrists available to treat patients with mental illnesses (Kokom, 2021) result in increasing feelings of isolation among patients and high suicide rates. This policy, which is not pro-mental health, not only hinders the right to access health facilities for people with mental illness but also causes them to lose their right to live due to depression and suicide.\n\nBased on these facts, this study focuses on a new problem with two driving questions: Is there a policy protecting the rights of persons with mental disabilities in accordance with the Convention on the Rights of Persons with Disabilities? What is the impact of discrimination on the rights of people with mental disabilities? The answer to the first question is no. Second, the protection of the rights of people with mental disabilities, misaligned with the Convention of the Rights of Persons with Disabilities (CRPD), is increasingly suffering and resulting in the harming of other rights. This specific study was presented at the EDI Conference, London 10–11 July 2023 as a Development Paper.\n\n\nMethods\n\nThis study critically evaluates the discrimination against people with mental illnesses in Indonesia and the inconsistency between mental health laws and the principles in the CRPD. Secondary research has been considered. It conceptually approaches human rights and legal studies approaches to overcome these issues and considers the fulfilment of human rights related to mental illness in Indonesia.\n\nFor this qualitative research, the author employs relevant national legal, social scientific, and health literature in its entirety, including international legal norms set by regulations. Secondary data were collected from articles selected from Google Scholar. All the studies were from 2002 to date; no studies were selected for qualitative data collection prior to 2002. This study evaluates Indonesian laws, and the Indonesian constitution regarding the health rights, operations, and structures of the “National Human Rights Commission”.\n\nMahendra (2023) considers that the government of Indonesia has a significant role in the development of the country that offers guarantees for decent and safe for citizens. The individual with disabilities as a citizen of Indonesia also has the same rights, similar to other general people. From the study of Eka and Daulima (2019), it has been found that mental illness stigma guides the abuse of human right and discrimination. To analyse the problem, primary sources such as MHA and CRDP records, as well as secondary data sources such as legal instruments, national and international literature, and reports by international organisations were required. Such a mix of approaches is ideal since it gives a solid foundation for exploring existing problems and finding more creative and liberating solutions.\n\nThis study begins with the MHA and the difficulties in its implementation as it has not fulfilled all the principles for the protection of persons with mental illness and the improvement of mental health care stipulated in the CRPD. The thematic analysis, as described below, focuses on answering the research questions: Does the MHA, which regulates the treatment of people with mental illnesses, fulfill their fundamental freedom and rights, and the provisions of the principles for the protection of persons with mental illness and the improvement of mental health care? Second, what is the impact on the other rights of people with mental illnesses? Different sources have been collected from Google Scholar, and later after analyzing every journal and article according to the study matter, relevant studies have been kept aside. From the selected studies, different themes have been established based on the subject.\n\nWe have limited the scope of this study to two areas. First, this study only focuses on whether the MHA meets the standards set by the CDRP principles of non-discrimination; therefore, no information is provided if the MHA is similar to other studies based on the studies (Praharso et al., 2020; Subu et al., 2023). Second, we used qualitative research to address the research problems, meaning that research on the same topic using quantitative analysis is outside the scope of this study. These are limited scopes, as this study only focused on these two aspects rather than other areas. The qualitative studies have been selected based on the study subject, which talks about laws and regulations regarding people with mental illness in Indonesia. Studies with quantitative analysis have been eliminated from this study, as it followed the qualitative data analysis method.\n\nTanaka et al. (2018) stated that the eligibility criteria for people with a mental health problem (PMHP) were categorised as epilepsy or “Diagnostic and Statistical Manual of Mental Disorders 5” (DSM 5). The main reason behind selecting people suffering from epilepsy as they are known to suffer discrimination and stigma. This study has observed that geographical barriers and stigma sometimes prevent patients from attending treatment till they are extremely unwell.\n\nThe dependent variable of this study is people with mental illness in Indonesia, and the independent variables are discrimination, certain mental illness-related acts, and human rights. From the selected articles and journals, all the necessary data have been determined and taken to complete the study. In case any particular data regarding mental illness in Indonesia has been taken, credit to the author has been provided there.\n\n\n\n• Secondary studies.\n\n• Articles published from 2002 to 2023.\n\n• Journals and articles focused on mental health issues.\n\n• Studies that mainly focused on discrimination towards people with mental illness.\n\n\n\n• Studies presenting quantitative data were avoided.\n\n• Articles published before 2002.\n\n• Articles and journals not focused on mental health issues.\n\n• Articles and journals not based on discrimination towards people suffering from mental illness.\n\nAll the qualitative data included in this study was gathered from reliable journals and articles from ScienceDirect, BMC Psychiatry, and PubMed. For further research and to test the authenticity of this study, the references have been added at the end of the paper. This study has used all the articles and journals that have online free access.\n\nThe Mental Health Act (Undang-Undang Kesehatan Jiwa) is intended to provide better protection for People with Mental Disorders (ODGJ), protect the human resources involved in handling ODGJ, and provide clarity regarding the authority and duties of each party that organizes health efforts (Hutomo & Sembiring, 2023). As stated in Article 3 of Act No. 18, 2014, the objectives of mental health efforts include the following:\n\na) Ensure that everyone can achieve a good quality of life; enjoy a healthy mental life; and be free from fear, pressure, and other disturbances that can interfere with mental health.\n\nb) Ensure that everyone can develop various intelligence potential.\n\nc) Provide protection and guaranteed mental health services for ODMK and ODGJ based on human rights (Dwisartika et al., 2023).\n\nd) Ensure the availability and availability of resources and power in Mental Health Efforts\n\ne) Improve the quality of Mental Health Efforts in accordance with scientific and technological advances\n\nf) Provide possibilities for ODMK and ODGJ to achieve rights as Indonesian citizens (Yunis & Afrita, 2023).\n\nHowever, this law cannot be properly implemented owing to several factors. First, psychiatrists and patients have different perspectives on mental illness and disorders (Bikker, Lesmana & Tiliopoulos, 2021). Indonesian people with mental illnesses (ODMK) are those who have physical, mental, social, growth, and developmental problems, and/or reduced quality of life, so they are at risk of experiencing mental disorders. Meanwhile, people with mental disorders (ODGJ) experience disturbances in thoughts, behavior, and feelings that manifest in the form of a set of symptoms and/or significant behavioral changes and can cause suffering and obstacles in carrying out people’s functions as human beings. What distinguishes the two disorders above is that mental illness is included in mental disorders; in other words, people who suffer from mental illness do not automatically suffer from mental disorders, whereas people who suffer from mental disorders definitely suffer from mental illness.\n\n\nResults\n\nIndonesians are still not concerned about the handling and treatment of people with mental illness or mental retardation. According to a 2022 Human Rights Watch (HRW) report in Indonesia, 57,000 people with certain mental health conditions have been in pasung at least once in their lifetime, and about 15,000 of them are still living in pasung. This difference in the perception of mental illness between Indonesians and World Health Organisation is shown in Table 1.\n\n\n\n- Embarrassing (Brogna et al., 2022).\n\n- Shameful (Rüsch and Kösters, 2021).\n\n- Taboo (The Jakarta Post, 2021).\n\n- Negative Perception (Puspitasari et al., 2020).\n\n\n\n1. Psychological and Medication (WHO, 2022).\n\n2. Limit the number of mental hospitals, build community mental health services, develop mental health services in general hospitals, integrate mental health services into primary health care, build informal community mental health services and promote self-care (WHO, 2023).\n\n\n\n1. Medical Treatment (Law No. 18 Year 2004).\n\n2. Shaman (Paranormal), Blackmagic.\n\n3. Spiritual healing (Anjara Brayne and Bortel, 2021; Subu et al., 2021).\n\n4. Shackling (Pasung), (World Health Organization SouthEast-Asia, Indonesia, 2021).\n\nIndonesia’s death rate due to ineffective mental health treatment is among the highest worldwide. According to the Village Potential Data (Podes) of the Central Statistics Agency (BPS) as cited by Firdaus (2022), there were 5,787 suicide victims and suicide attempts in 2021. A reason for this, according to Blignault et al. (2009) is that people with mental problems’ needs, such as receiving help from psychologists, are neglected. The government pays little attention to health facilities and psychiatric staff for people with mental illness; thus, the system struggles to cope with the increasing number of suicide victims among people with mental illness. Until 2021, the only available health facilities for people with mental illness are psychiatrists and, at most, 33 mental hospitals in Indonesia (Hidayat et al., 2023). This means that the state does not implement policies that can provide protection for people with mental illnesses and their struggles continue.\n\nFrom Table 2, it can be seen that fundamental freedoms and basic rights, protection of minors’ lives in society, health examinations, and confidentiality are partially implemented. The role of culture and community is taboo and discriminatory among the citizens of Indonesia. Care standard is adequate of care and there is a lack of treatment among the people who suffer from mental issues. Also, medication, treatment, notice rights, and treatment consent are partially implemented. There is an adequate of facilities regarding the conditions and rights within the mental health facilities. The admission principles, body review, and involuntary admission are all discriminatory in Indonesia. On the other hand, complaints, and opportunities of principles regarding facilities of mental health access are partially implemented. The basic rights and fundamental freedoms are partially implemented, whereas preserving the existing rights is discriminatory.\n\n\nDiscussion\n\nIt is undeniable that the Mental Health Law does not provide protection for people with mental disorders. This is due to the high number of ODGJ who are homeless or neglected because they do not have a place to live. Kementerian Kesehatan Republik Indonesia (Indonesian Ministry of Health, 2021) noted that in big cities in Indonesia, the number of homeless people with psychosis has increased by approximately 70%. In addition, the condition of individuals who have nothing, no one, or no support ultimately results in them living neglected or abandoned on the streets.\n\nSecond, mental illness is still socially stigmatized, leading families to hide the existence of family members who suffer from mental disorders. Furthermore, mental disorders and mental health in Indonesia are considered cursed diseases, so it is not unusual for family members who experience these problems to be hidden and placed in shackles. As such, some families choose to remain silent or hide, isolate, or shackle people with mental disorders (ODGJ). Many ODGJs wander the streets because they were abandoned by their families. This phenomenon occurs because of the stigma and discrimination that exists in society (Yu et al., 2023). Not only are ODGJs abandoned, but their families are ostracized by the surrounding social environment. This kind of behavior occurs because of a lack of access and information provided to the public; therefore, mental disorders are considered terrible.\n\nA lack of public awareness and knowledge about people with mental illness and mental retardation leads to the poor treatment of and attitudes towards them. This is due to culturally different perceptions of mental health (Choudhry et al., 2016). In most developed countries, people voluntarily seek help from professionals to treat mental health disorders. On the other hand, in other places such as Indonesia, mental disorders tend to be ignored; so, people are less enthusiastic about treating mental disorders.\n\nThird, mental illness is seen as a shameful family disgrace. Indonesian people think that mental disorders cannot be cured; so, suffering people deserve to be ostracized. The lack of knowledge about mental health disorders means that Indonesians believe that people with mental health disorders are different from those with physical illnesses that are also difficult to cure. Thus, labeling people with mental illness or mental health disorders as “strange creatures” can threaten their safety (Aulia, 2019).\n\nThe Western health model views mental disorders as problems that need to be cured. Thus, mental health services tend to be oriented only toward mental disorders that afflict the person and often ignore aspects related to the lives and welfare of the mentally ill (Choudhry et al., 2016). Therefore, in the Western world, those who suffer from mental illness receive special treatment without isolating them or putting them in shackles, as is the case in many areas of Indonesia.\n\nFourth, sanctuaries and shamans are considered treatments for mental illnesses. Indonesian society has several types of traditional and alternative medical practices, such as ‘smart people’, including shamans, Islamic religious leaders, religious teachers (kiyai or clerics), psychics, priests, and traditional Chinese medicine. In practice, ‘smart people’ use herbs, incantations, spells, inanimate objects, communication or spiritual guidance, and prayers as forms of healing. In contrast, the Western health model often ignores aspects related to religion while overcoming the impact of mental health illnesses on one’s life (Lucchetti, Koenig & Lucchetti, 2021; Harris, Edlund, & Larson, 2006).\n\nThe Indonesian government’s minimal efforts to save the lives of people with mental illness have catastrophic consequences for young people. These consequences are heightened in rural areas because they do not have access to healthcare. People are also reluctant to take those with mental illnesses to hospital because of the shame, exacerbating the situation. Statista (2022) notes that 19 million children under the age of 15 years suffer from mental illnesses and most live in rural areas far from medical facilities. Consequently, many people with mental illnesses die by suicide because they do not receive adequate treatment. Therefore, villagers are those most affected by government inattention. Apart from having minimal mental health facilities, they cannot afford the high cost of medical treatment.\n\nThe counter-shackle policy, the Issuance of Regulation of the Minister of Health Number 54 of 2017 Concerning Handling Detachment for People with Mental Disorders, instead of saving the lives of people with mental illness, wreaks havoc on them because it is not supported by health facilities. A recent independent survey by Statista (2022) predicts the number of people suffering from mental illness and related deaths will increase from 2,99 million in 2020 to 3, 24 million in 2024.\n\nAdditionally, the public’s reaction to mental illness impacts those struggling with mental health issues because it brings attention to their rights as human beings, including their rights to access treatment, obtain information, live, and be free from shackles. After the enactment of the Mental Health Law, the Indonesian government was deemed unable to protect the rights of people with mental illnesses. Further, the rights of people with mental disabilities are regulated under Article 42 of the Human Rights Law, which states:\n\n“Every citizen who is elderly, physically disabled and or mentally disabled has the right to receive special care, education, training and assistance at the expense of the state, to ensure a decent life in accordance with his human dignity, increase self-confidence, and the ability to participate in social life, nation and state.”\n\nThus, the confinement of people with mental illness, even if carried out by their families with the aim of keeping themselves and those around them safe, clearly violates human rights and can be categorized as the deprivation of the right to live properly.\n\nAlthough they may not be locked or shackled, the family cannot let someone suffering from mental illness roam freely. They might be charged under Article 491, point 1 of the Indonesian Criminal Code:\n\n“Threatened by a maximum fine of seven hundred and fifty rupiahs whoever is obliged to guard a mentally ill person who is dangerous to himself or to others, let that person roam unattended.”\n\nFinally, Article 10 of the Regulation concerning the insane in the State Gazette 97/54, February 4, 1897, stipulates that the immediate family of a mentally ill person has the authority to request the head of the district court to treat them in a mental care institution for the sake of peace and public order or for the sake of healing of the mentally ill person themself. However, in practice, it is difficult to trust the government’s ability to treat mentally ill persons.\n\nTo guarantee and fulfill the rights of people with mental illness, it is necessary to follow the principles of the treatment of people with mental illness and the improvement of health care, as stipulated by the United Nations Human Rights Office of the High Commissioner 1991. The question here is whether the system of treating people with mental illness and the improvement of mental healthcare in Indonesia meets these principles.\n\nMental illness tends to be avoided, in some countries namely Indonesia, due to this people here are not concerned about treating mental issues. The government of Indonesia puts minimum efforts into saving or curing people with mental disorders, which causes catastrophic results among young people. This study conceptually strategies human rights with legal perspectives to overcome these problems and contemplate the fulfilment of human rights regarding mental illness in Indonesia.\n\nSome individuals with mental disorders are restrained and confined within the community in a barbaric way. The mental health service quality in the majority of the hospitals is poor and protection regarding human rights for these patients is absent or weak. Custodial treatments govern within psychiatric hospitals, whereas involuntary treatment is basic although there are no such legal grounds for any involuntary admission. There is no guardianship arrangement or laws and no need for legal analysis for involuntary treatment as well as hospitalization. Irmansyah et al. (2009), opined that Article 27, of the health Law, 1992 states that the government of the country will offer a significant decree for the management of issues regarding people who have mental disorders. Article 29, 2004 based on Medical Practices retains the objectives of safeguarding patients and helathcare offerors, along with increasing the health service quality. Article 14, regarding the principles of government elections, eliminated the voting rights of the people who have mental issues. However, this law has been announced void from the newly developed legislation of the election by Law 10, 2008. Article 41, 2003, the provincial of Jakarta stated that individuals with mental disorders are sustained from being in different public areas. There is certainly no definite legislation regarding mental health provisions in Indonesia, that could serve to safeguard the rights of people who have mental disorders.\n\nHowever, Indonesia has reviewed related international domestic and covenants laws and offers a significant legal framework regarding the protection of human rights. There are some spaces that are unchallenged and unremarked regarding disabled people, those need to be highlighted to offer human rights to those people. The “National Human Rights Commission” recently engaged with the problem of protecting the definite rights of people who have mental illness. Eliminating abuses of human rights and positively safeguarding people’s rights with mental problems will need different strategies to be implemented. “Civil society organizations”, health professionals, and “The National Human Rights Commission”, have significant roles to comprehend. The crucial responsibilities underlie with district, national, and provincial governments of Indonesia. There is a need for basic need for protection of the people’s rights who have mental issues, this lies in the community and hospital health services that should meet nominal standards of quality, accessibility, and affordability. Definite legislation regarding mental health will clarify the people’s eights with mental disorders and will also offer substantial safeguarding of their basic rights. There is a lack of such legislation, although adequate basis regarding Indonesian principles and laws for safeguarding the people’s rights are there. Regardless of the safeguarding that is obtainable by law, and a human rights framework, violations of people’s rights with the mental disorder remain unnoticed and widespread. Non-governmental sectors do not authorize sufficiently on behalf of individuals who have mental issues. Also, health authorities and mental health experts do not properly safeguard the rights of those people or support them in asserting their definite rights. The governments should acknowledge that abuse of human rights is widespread, and they should initiate proper action to reduce systematic abuse.\n\nThe limitations of this research lie in two areas. The first area is that this study focuses specifically on whether the principles for the protection of persons with mental illness and the improvement of mental health care are appropriate in Indonesia. The second limitation is that the researcher chose a qualitative research method to review the principles for the protection of persons with mental illness and the improvement of mental health care, which is appropriate in Indonesia. This means that a more comprehensive view of the research topic based on primary quantitative analysis cannot be carried out.\n\n\nConclusions\n\nDiscrimination against people with mental illness occurs in Indonesia and the treatment offered does not align with the principles for the protection of people with mental illness and the improvement of mental health care. This policy discriminates against people with mental illnesses; not only are they shackled but they do not have adequate treatment facilities, resulting in high mortality rates. This is because treatment methods contradict these principles. In Indonesia, the recovery model for people with mental illnesses is a discriminatory policy that does not meet their needs and, further, violates human rights, especially the rights to life and health.\n\nTherefore, the government must provide adequate facilities for people with mental illnesses by referring to the principles of protecting them and improving their mental health services. To realize the effective and conducive recovery of people with mental disorders and the fulfillment of the rights of people with mental disorders, Law No. 18 of 2014 on Mental Health (Mental Health Law) must fulfill the principles and elements stipulated in the instrument for treatment of people with mental disorders and improvement of health services.",
"appendix": "Data availability\n\nThe data for this article consists of bibliographic references, which are included in the References section.\n\n\nReferences\n\nAnjara SG, Brayne C, Van Bortel T: Perceived Causes of Mental Illness and Views on Appropriate Care Pathways among Indonesians. Int. J. Ment. Heal. Syst. 2021; 15(74): 74. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAulia AC: Paradigma Kesehatan Mental. UNAIR News. 2019 October 10. Reference Source\n\nBanerjee D, Rai M: Social Isolation in Covid-19: The Impact of Loneliness. Int. J. Soc. Psychiatry. 2020; 66(6): 525–527. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBikker AP, Lesmana CBJ, Tiliopoulos N: The Indonesian Mental Health Act: Psychiatrists’ Views on the Act and its Implementation. Health Policy Plan. 2021; 36(2): 196–204. PubMed Abstract | Publisher Full Text\n\nBlignault I, Bunde-Birouste A, Ritchie J, et al.: Community perceptions of mental health needs: a qualitative study in the Solomon Islands. Int. J. Ment. Heal. Syst. 2009; 3(1): 6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrogna P, Brogna C, Santomassimo C, et al.: Shades of shame: Embarrassment as a covert marker of self-stigma in a sample case study of patients with schizophrenia. Schizophr. Res. 2022 Mar; 241: 10–11. PubMed Abstract | Publisher Full Text\n\nCEO Magazine: The Best Countries for Mental Wellbeing.2022. Reference Source\n\nChoudhry FR, Mani V, Ming LC, et al.: Beliefs and perception about mental health issues: a meta-synthesis. Neuropsychiatr. Dis. Treat. 2016; 12: 2807–2818. PubMed Abstract | Publisher Full Text | Free Full Text\n\nClarkson S: Which Countries have the Worst healthcare in the World in 2022?2022. Reference Source\n\nDahniar D, Asnurianti R, Amna N, et al.: Restraint and Confinement of Psychiatric Patients in Community: A Scoping Review of Pasung in Indonesia. Ment. Health Soc. Incl. 2022; 26(2): 134–143. Publisher Full Text\n\nDwisartika HA, Sidi R, Satria B: ANALYSIS ENHANCE OF SERVICE PEOPLES CONCERNING MENTAL HEALTH. Jurnal Ekonomi. 2023; 12(3): 780–783. Reference Source\n\nEdwards N: Disability Rights in Indonesia? Problems with Ratification of the United Nations Convention on the Rights of Persons with Disabilities. Aust. J. Asian Law. 2014; 15(1): 1–15. Reference Source\n\nEka AR, Daulima NH: Factors related to pasung on people with mental illness: A literature review. International Journal of Nursing and Health Services. 2019; 2(2): 36–41. Publisher Full Text\n\nFirdaus A: Kesehatan Mental dan Fenomena Tragedi Bunuh Diri, Antara, December 8.2022. Reference Source\n\nHarris KM, Edlund MJ, Larson SL: Religious Involvement and the Use of Mental Health Care. Health Serv. Res. 2006; 41(2): 395–410. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHartini N, Fardana NA, Ariana AD, et al.: Stigma Toward People with Mental Health Problems in Indonesia. Psychol. Res. Behav. Manag. 2018; 11: 535–541. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHidayat MT, Lawn S, Muir-Cochrane E, et al.: The Use of Pasung for People with Mental Illness: A Systematic Review and Narrative Synthesis. Int. J. Ment. Heal. Syst. 2020; 14(90): 90. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHidayat MT, Oster C, Muir-Cochrane E, et al.: Indonesia free from pasung: a policy analysis. Int. J. Ment. Heal. Syst. 2023; 17: 12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHutomo HM, Sembiring MSA: Legal Protection for People with Mental Illness as Victims and Perpetrators of Criminal Acts. ARRUS J. Soc. Sci. Hum. 2023; 3(4): 499–505. Publisher Full Text Reference Source\n\nIrmansyah I, Prasetyo YA, Minas H: Human rights of persons with mental illness in Indonesia: More than legislation is needed. Int. J. Ment. Health Syst. 2009; 3(1): 14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKate N, Grover S, Kulhara P, et al.: Supernatural Beliefs, Aetiological Models and Help Seeking Behaviour in Patients with Schizophrenia. Ind. Psychiatry J. 2012; 21(1): 49–54. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKokom: Kemenkes Beberkan Masalah Permasalahan Kesehatan Jiwa di Indonesia.2021. Reference Source\n\nKovacevic R: Mental health: Lessons Learned in 2020 for 2021 and Forward. World Bank; February 11, 2021. Reference Source\n\nLebowitz MS, Ahn WK: Effects of biological explanations for mental disorders on clinicians’ empathy. Proc. Natl. Acad. Sci. USA. 2014; 111(50): 17786–17790. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLucchetti G, Koenig HG, Lucchetti A: Spirituality, Religiousness, and Mental Health: A Review of the Current Scientific Evidence. World J. Clin. Cases. 2021; 9(26): 7620–7631. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahendra W: Pembangunan Berkelanjutan Sebagai Upaya Dalam Menjaga Keutuhan Bangsa. Jakarta: Asosiasi Profesi Widyaiswara Indonesia; 2023.\n\nMajmudar IK, Mihalopoulos C, Brijnath B, et al.: The Impact of Loneliness and Social Isolation on Health State Utility Values: A Systematic Literature Review. Qual. Life Res. 2022; 31: 1977–1997. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcKenzie SK, Oliffe JL, Black A, et al.: Men’s Experiences of Mental Illness Stigma Across the Lifespan: A Scoping Review. Am. J. Mens Health. 2022; 16: 155798832210747. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMinistry of Health of the Republic of Indonesia: Laporan Hasil Riset Kesehatan Dasar (Riskesdas).2018. Reference Source\n\nPan American Health Organization “PAHO”: Mental Health.2022. Reference Source\n\nPraharso NF, Pols H, Tiliopoulos N: Mental Health Literacy of Indonesian Health Practitioners and Implications For Mental Health System Development. Asian J. Psychiatr. 2020; 54: 102168. PubMed Abstract | Publisher Full Text\n\nPuspitasari IM, Garnisa IT, Sinuraya RK, et al.: Perceptions, Knowledge, and Attitude Toward Mental Health Disorders and Their Treatment Among Students in an Indonesian University. Psychol. Res. Behav. Manag. 2020; 13: 845–854. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoberts S: Mental Illness is a Global Problem: We Need a Global Response. Health Property Action. 10th July 2018. Reference Source\n\nRüsch N, Kösters M: Honest, Open, Proud to support disclosure decisions and to decrease stigma’s impact among people with mental illness: conceptual review and meta-analysis of program efficacy. Soc. Psychiatry Psychiatr. Epidemiol. 2021; 56: 1513–1526. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRutter M, Nikapota A: Culture, ethnicity, society and psychopathology.Rutter M, Taylor E, editors. Child and adolescent psychiatry. Oxford: Blackwell Publications; 2002; Vol. 16. : 4.\n\nSaputri WD: ODGJ dan Bayangan Praktik Pasung di Indonesia.2021. Reference Source\n\nStatista: Projected Number of People Suffering from Mental Disorder in Indonesia from 2017 to 2024.2022. Reference Source\n\nSubandi: Budaya dan Agama Pengaruhi Kesehatan Jiwa. Universitas Gadjah Mada; 2015. Reference Source\n\nSubu MA, Wati DF, Al-Yateem N, et al.: ‘Family stigma’among family members of people with mental illness in Indonesia: A grounded theory approach. Int. J. Ment. Health. 2023; 52(2): 102–123. Publisher Full Text\n\nSubu MA, Wati DF, Netrida N, et al.: Types of Stigma Experienced by Patients with Mental Illness and Mental Health Nurses In Indonesia: A Qualitative Content Analysis. Int. J. Ment. Health Syst. 2021; 15(1): 77. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTampubolon M, Silalahi F, Siagian R: Covid-19 and Mental Health Policy in Indonesia. ASEAN Journal of Psychiatry. 2021; 22(S1): 1–12. Reference Source\n\nTanaka C, Tuliao MTR, Tanaka E, et al.: A qualitative study on the stigma experienced by people with mental health problems and epilepsy in the Philippines. BMC Psychiatry. 2018; 18: 313–325. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTang S, Reily NM, Arena AF, et al.: People Who Die by Suicide Without Receiving Mental Health Services: A Systematic Review. Front. Public Health. 2022; 9: 736948. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe Jakarta Post: Menjadi Manusia’ breaks the mental health taboo.2021. Reference Source\n\nUnited Nations Office of Human Rights Office of High Commissioner: Convention on the Rights of Persons with Disabilities.2006. Reference Source\n\nUnited Nations Office of Human Rights Office of High Commissioner: Principles for the Protection of Persons with Mental Illness and the Improvement of Mental Health Care.1991. Reference Source\n\nWang J, Lloyd-Evans B, Giacco D, et al.: Social isolation in mental health: a conceptual and methodological review. Soc. Psychiatry Psychiatr. Epidemiol. 2017; 52: 1451–1461. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWidodo B: Upaya Memenuhi Hak Penyandang Disabilitas. Kementerian Hukum dan Hak Asasi Manusia Republik Indonesia [Efforts to fulfill the right of persons with disabilities. Ministry of Law and Human Rights of the Republic of Indonesia].2019. Reference Source\n\nWolf HN: Projected Number of People Suffering from Mental Disorder in Indonesia from 2017 to 2024. Statista; 2022. Reference Source\n\nWorld Health Organization Southeast Asia: UNSDG What If series: “What if … pasung were ended in Indonesia?”.2021. Reference Source\n\nWorld Health Organization SouthEast-Asia, Indonesia: UNSDG What If series: “What if … pasung were ended in Indonesia?”.2021. Reference Source\n\nWorld Health Organization: Mental Disorders.2022. Reference Source\n\nWorld Health Organization: Integrating mental health in primary health care: part 1. The context for integration of mental health services in primary health care.2023. Reference Source\n\nWorld Population Review: Depression Rates by Country 2022.2022. Reference Source\n\nYu CC, Tang B, Low JA, et al.: A qualitative study on health stigma and discrimination in the first year of the COVID-19 pandemic: Lessons learnt from a public health perspective. Front. Public Health. 2023; 11: 1143640. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYunis H, Afrita I: Legal Protection of People with Mental Disorders in Pekanbaru City Based on Laws Number 18 of 2014 Concerning Mental Health. Law and Humanities Quarterly Reviews. 2023; 2(1). Publisher Full Text Reference Source"
}
|
[
{
"id": "308769",
"date": "07 Aug 2024",
"name": "Kay Wilson",
"expertise": [
"Reviewer Expertise I am a mental health",
"disability and human rights law scholar which is the subject of my PhD from Melbourne Law School. I also have an undergraduate degree in law and psychology from Monash University."
],
"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\nDiscrimination of Persons with Mental Illness: Testing the Principles for the Protection of Persons with Mental Illness and the Improvement of Mental Health Care\nThank you for inviting me to review this paper. I think it is important for people from non-western countries to write about mental health in their jurisdictions, especially where the relevant law may not be in English or easily accessible to people in other parts of the world.\nI appreciate the efforts of the authors, but I’m afraid I have a number of concerns about this paper and do NOT think it can be indexed in its current form.\nIn summary, the authors are concerned that Mental Health Law in Indonesia does not comply with either the Principles for the Protection of Persons with Mental Illness or the Convention on the Rights of Persons with Disabilities (I’m not sure which). In particular, they are concerned about the conceptualization of mental illness arising from evil spirits, the widespread use of the shackling of people with mental illness and the general lack of mental health care in Indonesia which they claim has caused the suicide rate to be disproportionately high.\n\nGeneral Concerns\nI feel that the paper is much too general and needs to be more specific, be less descriptive. It also needs to be significantly restructured and rewritten.\nI do not understand why the authors have chosen to use what they call a “qualitative research method” based on “secondary sources,” rather than legal research methods typically used by lawyers based on primary sources like legislation, case law, law reform and other government reports, international treaties, WHO and United Nations documents, along with books and journal articles. The methodology the authors have chosen is not appropriate for this paper as it is not a scientific review based on facts. rather it is a legal analysis based on interpretation and argument. The tables are unnecessary and add little to the paper.\nThe authors need to get rid of the sections on method, results and discussion and restructure the article completely.\nI suggest the following headings:\n1. Introduction\nIn this section the authors should introduce the topic, explain the purpose of the paper and briefly set out their thesis (eg. key arguments). They should also briefly set out the structure of the paper for the reader.\n\n2.The International Human Rights Framework for Mental Health Law\n\nIn this section the authors should briefly set out for the reader what the Convention on the Rights of Persons with Disabilities (CRPD) is, how it was negotiated and why it’s relevant. (Hint: the CRPD is the leading international human rights treaty in relation to persons with mental impairments, whereas the Principles for the Protection of Persons with Mental Illness are widely regarded as being defunct. All references to them should be removed from the paper, save for any historical discussions about the evolution of the international human rights framework for mental health.) The authors should refer to any specific articles of the CRPD they’d like to discuss later in the paper. The authors should also note that many aspects of the CRPD (especially related to the abolition of mental health law) are ambiguous and controversial and subject to international debate. The authors should look at the CRPD Committee’s General Comment No 1 and CRPD literature from a range of authors such as Peter Bartlett, Anna Arstein-Kerslake, Piers Gooding, George Szmukler, Bernadette McSherry, Mary Donnelly, Brendan Kelly etc and of course me.\n3. Mental Health Law in Indonesia A. The Indonesian Legal Framework\nIn this section the authors should briefly describe in a line or two the Indonesian legal system for international readers (eg. whether it is a civil or common law system). They should also set out the key provisions of all the relevant mental health laws in more detail than they currently do, especially in relation to things like coercive treatment, access to and rights to receive treatment, use of seclusion and restraints and so on so that the reader can understand how mental health law in Indonesia works. In this section it would also be useful to include things like article 491 of the Indonesian Criminal Code which puts the responsibility on families to prevent their loved ones from roaming unattended and Article 10 of the Regulation empowering families to have their loved ones committed. This should be a substantive and meaty section of the paper. It should also refer to any relevant and significant caselaw and extra legislative sources.\nB. Mental Health Care in Indonesia\nIn this section the authors should set out what exactly typical mental health care in Indonesia looks like, how the mental health system works and problems with mental health resources. That is, this section is about the mental health system in practice. It would also be interesting to explain why there are a lack of mental health services in Indonesia. Is due to stigma, or lack of government resources, or something else?\n4. Indonesian Non-Compliance with the CRPD\nIn this section the authors should explain exactly how Mental Health Law in Indonesia and the operation of the Mental Health System do not comply with the CRPD (bearing in mind ongoing international debates about the CRPD), referring to particular articles of the CRPD. There are debates in the literature about whether low and middle income countries should try to emulate the Western medical model of psychiatric hospitals and care in high income countries, or try to create something new. The authors might want to consider this issue.\n5. Recommendations for Reform\nIn this section the authors should specify in detail what exactly the Indonesian government should do to reform Indonesian mental health law and the Indonesian mental health system (eg. trying to reduce stigma by educating the population, repealing article 491 of the criminal code, banning shackling, providing more services of a particular type etc).\n6. Conclusion\nIn this section, the authors should summarize their arguments in the paper and discuss future directions.\nReferences\n\nAll relevant sources should be referenced in accordance with the journal style.\nSpecific Concerns\nThe authors assert several times that lack of mental health treatment in Indonesia has been causing the high suicide rate. This is probably more controversial and nuanced than the authors appreciate. While there is a strong association between mental illness and suicide, there’s also some evidence that some people complete suicide for other reasons usually to do with life difficulties and relations breakdowns. See for example, (Wilson K, 2018 [Ref 1]). In paragraph 1, the assertion that ‘more than 19 and 12 million people over the age of 15’ seems to be incorrect. I do not understand the acronyms ODMK and ODGJ. What do they mean and more importantly why do they matter? I’m not sure who is putting the shackles on persons with mental illness. Where do they get them from and how do they do it? I think the reference to the EDI Conference in London should be in a footnote at the front of the paper. Also it should explain what the EDI Conference is and who runs it. I note that authors often write CDRP, rather than CRPD. On page 7 in the second last paragraph the authors state that ‘in most developed countries people voluntarily seek help from professionals’ without any citation. This is only partly true. The vast majority of people in developed countries are treated voluntarily, but there is a group of people who are involuntarily detained and treated under the relevant mental health law because they are refusing or cannot consent to hospital admission and treatment.. There are also people who consent to treatment because they know if they don’t they’ll be sectioned anyway. On page 8 in paragraph 5, the authors state that ‘After the enactment of Mental Health Law, the Indonesian government was deemed unable to protect the rights of people with mental illnesses.’ My question is deemed by whom? There are many grammatical errors within the paper.\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?\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? No",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-250
|
https://f1000research.com/articles/11-1294/v1
|
11 Nov 22
|
{
"type": "Research Article",
"title": "Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker",
"authors": [
"Darawan Rinchai",
"Damien Chaussabel",
"Darawan Rinchai"
],
"abstract": "Background Changes in blood transcript abundance levels have been associated with pathogenesis in a wide range of diseases. While next generation sequencing technology can measure transcript abundance on a genome-wide scale, downstream clinical applications often require small sets of genes to be selected for inclusion in targeted panels. Here we set out to gather information from the literature and transcriptome datasets that would help researchers determine whether to include the gene CEACAM6 in such panels. Methods We employed a workflow to systematically retrieve, structure, and aggregate information derived from both the literature and public transcriptome datasets. It consisted of profiling the CEACAM6 literature to identify major diseases associated with this candidate gene and establish its relevance as a biomarker. Accessing blood transcriptome datasets identified additional instances where CEACAM6 transcript levels differ in cases vs controls. Finally, the information retrieved throughout this process was captured in a structured format and aggregated in interactive circle packing plots. Results Although it is not routinely used clinically, the relevance of CEACAM6 as a biomarker has already been well-established in the cancer field, where it has invariably been found to be associated with poor prognosis. Focusing on the blood transcriptome literature, we found studies reporting elevated levels of CEACAM6 abundance across a wide range of pathologies, especially diseases where inflammation plays a dominant role, such as asthma, psoriasis, or Parkinson’s disease. The screening of public blood transcriptome datasets completed this picture, showing higher abundance levels in patients with infectious diseases caused by viral and bacterial pathogens. Conclusions\nTargeted assays measuring CEACAM6 transcript abundance in blood may be of potential utility for the management of patients with diseases presenting with systemic inflammation and for the management of patients with cancer, where the assay could potentially be run both on blood and tumor tissues.",
"keywords": [
"Biomarkers",
"CEACAM6",
"Transcriptional profiling",
"Literature profiling"
],
"content": "Introduction\n\nChanges in blood transcript abundance can reflect differences in relative abundance of leukocyte populations as well as transcriptional regulation secondary to immune activation (for instance inflammation, interferon, and prostaglandin responses). Quantifying these changes can thus be relevant for making clinical decisions.1,2 Robust technology platforms, such as microarrays and RNA sequencing, that enable the measurement of transcript abundance in an unbiased fashion (i.e., simultaneously measuring all RNA species that are present in a given sample) have been widely available for the past two decades. As a result, blood transcriptome studies have been conducted across a wide range of pathological or physiological states.3–7 In addition, vast amounts of blood transcriptome profiling data have been made available in public repositories such as the NCBI Gene Expression Omnibus, or EMBL-EBI’s array express.8\n\nTranscriptome profiling data can be leveraged to inform the design of targeted gene panels. These panels can serve as a basis for the development of diagnostic assays for use in clinical settings. But targeted assays can also be employed in research settings, for instance when profiling of transcript abundance needs to be performed on large scales (e.g., in thousands of samples) and with a relatively short turnaround. Notably, targeted assays could also prove valuable in resource-constrained settings, where computing infrastructure, instrument, and reagents costs are limiting. The approaches employed for targeted assay design can be data-driven (e.g., applying computational models to transcriptome profiling dataset(s) to select genes based on their predictive performance) or knowledge-driven (selecting genes based on pre-existing knowledge – e.g., for the development of an “immunology panel”). However, both data and knowledge-driven approaches can also be combined. This is illustrated in recently published work in which we describe the selection of three blood transcriptional panels designed for the monitoring of responses to SARS-CoV-2.9 Transcripts were selected first based on their membership to co-expressed gene sets, the abundance of which was found to change during COVID-19 disease (i.e., through a data-driven approach) and second based on their relevance to one of three themes, which were immunity, therapeutic development, and severe acute respiratory syndrome biology (i.e., through a knowledge-driven approach). However, the amount of information available in the literature and in public transcriptome datasets that can be leveraged for candidate gene selection can be overwhelming. Thus, we have developed an approach to identify, retrieve, structure, and aggregate such information in a manner that would support the rational selection of candidate genes for inclusion in targeted assays destined to be used in clinical or research settings.10\n\nHere we decided to focus on CEACAM6, a gene encoding a protein of the carcinoembryonic antigen (CEA) family whose members are glycosylphosphatidylinositol (GPI)-linked cell surface proteins.11,12 We employed an approach devised as part of a “collective omics data” (COD) training curriculum,13 relying in particular on the recently published COD1 training module workflow.10 Briefly, it consists of: 1) selecting a gene and retrieving background information and associated literature; 2) profiling its literature at a high level, reporting instances where it has been associated with diseases, and its relevance as a biomarker in such settings; 3) profiling the literature in more depth and reporting changes in abundance for transcripts encoded by this gene measured in whole blood; 4) profiling the abundance of the candidate gene across multiple relevant transcriptome datasets; 5) preparing a manuscript and submit it for peer-review and publication. Throughout these steps trainees parse the information being retrieved (e.g., from the title or text of articles) and record it in a structured format (i.e., a spreadsheet). They also aggregate this information in interactive circle packing plots, which are collections of circular elements used to visualize a hierarchic organization, with access to each level being achieved through zoom-in and -out functionalities.\n\nScreening the CEACAM6 literature identified a strong association with various cancers, in particular colorectal cancer where measurement of CEACAM6 blood transcript levels may be of clinical value for early detection.14,15 Associations were also found for pancreatic, lung, and breast cancer, as well as leukemia and inflammatory bowel disease. More in depth profiling of the literature (analyzing the full text) identified an array of conditions for which CEACAM6 abundance has been found to be significantly different from controls. This list was complemented by a screening of public blood transcriptome datasets. The tables employed to capture this information in a structured format are shared as extended data files. Another deliverable is the interactive circle packing plot that permits aggregation and seamless access to this and all underlying information. Altogether these resources supported manuscript preparation and interpretation/evaluation by the authors of the relevance of CEACAM6 as a biomarker. They may also support transcript selection efforts of members of the research community interested in designing blood transcriptional biomarker panels.\n\n\nMethods\n\nThe workflow implemented here to assess the potential of CEACAM6 as a blood transcriptional biomarker has been described in detail in a separate methods paper.10 The approach was devised as part of a training module focused on the development of skills for the retrieval, structuring, aggregation, and interpretation of information derived from the literature and publicly available large-scale profiling datasets. Relevant resources that have been employed and generated in the context of this work are presented in Table 1.\n\nBriefly, the process is broken down into the following steps:\n\n(1) Selecting a candidate gene: the most basic criterion is for transcripts for this gene to be detectable in blood. It could also be selected based on its membership in a pre-defined signature or gene set.\n\n(2) Retrieving background information: background information about the gene is gathered from reference datasets (e.g., OMIM [https://www.omim.org/], UniProt [https://www.uniprot.org/], Entrez Gene [https://www.ncbi.nlm.nih.gov/gene]) and the introduction section of recent publications.\n\n(3) Profiling the candidate gene’s literature at a high level: the literature associated with the candidate gene is identified (see “literature profiling section” below for details). Entities corresponding to a given theme (e.g., diseases, cell types, or molecular processes) are extracted from the title of those articles (“breast cancer” is an example of a disease entity). This permits to identify the main diseases associated with the gene of interest, and, in turn, identify instances in which the candidate gene has been found to be of actual or potential utility as a biomarker for these diseases.\n\n(4) Profiling the literature in more depth: taking advantage of Google Scholar’s full text search capabilities, this step identifies publications where the abundance level of the candidate gene’s transcripts in blood samples was found to be different in patients compared with appropriate controls.\n\n(5) Profiling the abundance of the gene across multiple relevant transcriptome datasets: to complement the previous step, public blood transcriptome datasets are screened to identify instances where the abundance level of the candidate gene’s transcripts in blood differs in patients in comparison with appropriate controls.\n\n(6) Developing resources supporting manuscript preparation and evaluation of the candidate gene: the information parsed from the literature or transcriptome datasets in earlier steps is recorded in a structured format (e.g., using a standard spreadsheet template, see details below). Using the Prezi web application (Prezi Inc., San Francisco, CA, USA), this information is aggregated in interactive circle packing plots. Spreadsheets and interactive circle plots can next be used to assess the overall relevance of the gene of interest as a candidate blood transcriptional biomarker and support the writing of the manuscript. They can also serve as a resource for investigators interested in designing blood transcriptional biomarker panels.\n\nCEACAM6 was selected based on its membership to one of the 382 modules constituting the fixed BloodGen3 module repertoire. This repertoire has been recently characterized.16 Briefly, it was constructed based on co-expression analysis through a process that was exclusively data-driven. First, the 16 reference blood transcriptome datasets that served as input were clustered separately using K-means clustering. Co-clustering events observed across the 16 reference datasets were then recorded for each gene pair. This information served as a basis for the constitution of a large co-clustering network, with nodes representing genes and edges representing co-clustering events. A weight of 1 to 16 was attributed to the graph edges depending on the number of times co-clustering events were observed. The network was then mined using graph theory to identify densely connected subnetworks that were identified as modules and added to the repertoire. This process eventually yielded 382 non-overlapping modules (at the probe level, multiple probes mapping to the same gene could be found across different modules). Next, the repertoire was thoroughly characterized functionally and an R package was developed to support BloodGen3 module repertoire analysis and visualization.17\n\nThe approach has been described in two published study guides: from a high-level perspective as part of the COD1 workflow10 and in more detail in a separate study guide dedicated to literature profiling.18 An overview of the steps implemented in the profiling of the literature associated with CEACAM6 is provided here:\n\n(1) Literature retrieval: to identify the literature associated with the candidate gene, a PubMed query is designed by combining the official gene name and symbol along with known aliases. Troubleshooting is performed as needed to minimize false positives and false negatives. For CEACAM6 the following query was generated and, as of August 16 2022, returned 642 entries:\n\nCEACAM6 [tiab] ORc “CEA Cell Adhesion Molecule 6” [tiab] OR CD66c [tiab] OR (NCA [tiab] AND (Carcinoembryonic OR CEACAM6 OR CD66c)) OR “Carcinoembryonic Antigen-Related Cell Adhesion Molecule 6” [tiab] OR “Carcinoembryonic Antigen Related Cell Adhesion Molecule 6” [tiab] OR “Carcinoembryonic Antigen-Related Cell Adhesion Molecule 6” [tiab] OR (“Normal Cross-Reacting Antigen” [tiab] AND (Carcinoembryonic OR CEACAM6 OR CD66c)) OR (“Non-Specific Cross-reacting Antigen” [tiab] AND (Carcinoembryonic OR CEACAM6 OR CD66c)) OR (CEAL [tiab] AND (Carcinoembryonic OR CEACAM6 OR CD66c)) NOT review [pt]\n\n\n\n(2) Extraction of relevant concepts: the titles of the articles associated with CEACAM6 are screened for keywords associated with diseases or physiological states and with cell types. For example, if the theme is “diseases or physiological states”, diseases entities such as “breast cancer”, “influenza infection”, “pregnancy” or “systemic lupus erythematosus” may be identified in the title of articles associated with the gene of interest.\n\n(3) Generating literature profiles: next, the prevalence of the cell types or disease entities identified in the previous step in the candidate gene’s literature is determined. Focusing on a subset of the literature, information regarding the potential relevance of the candidate gene as a biomarker can be captured in a structured format in an Excel spreadsheet.\n\n(4) Aggregating information: the underlying literature profiling information is captured and visually represented in interactive circle packing plots using the Prezi application (Prezi Inc, San Francisco, CA, USA). This serves as a basis for generating manuscript figures and the constitution of a companion resource that can be made accessible to the community.\n\nWhile screening the literature and large-scale profiling datasets trainees learn to identify and extract key information from research articles or transcriptome datasets. These include basic information, as well as elements of study design (e.g., analyte name, type, species, biological samples, measurement methods, sample size) and findings (e.g., fold change, significance). The information is captured in a standard MS Excel spreadsheet template, which can be used to record information derived from both the literature and transcriptome profiling datasets (Extended Data File 119).\n\nInformation extracted from the literature and from public transcriptome datasets was aggregated in an interactive circle packing plot generated using the Prezi web application (Prezi Inc., San Francisco, CA, USA). A free basic Prezi account can be setup for this (https://prezi.com/pricing/basic/). Starting from a blank presentation, it consisted of adding and populating circles (topics) and organizing them into a hierarchy (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/). Color-coding the circles and varying their size permitted the visualization of some of the results. Excerpts or full articles were added, as well as plots representing CEACAM6 transcriptional data profiles. Links to articles and interactive versions of the figures were also provided in order promote seamless access to information.\n\nScreening of transcriptome profiling datasets consisted of determining whether differences between levels of CEACAM6 transcript abundance in patients and their respective controls were significant. The CEACAM6 profiling data were downloaded from the “CD2K” gene expression browser (GXB) instance (http://cd2k.gxbsidra.org/dm3/geneBrowser/list) for multiple blood transcriptome datasets.20 Analyses were conducted separately for each dataset in Microsoft Excel (RRID:SCR_016137), testing for differences in variance using F-test statistics and testing for differences in expression using t-test statistics. Differences were considered significant when p was <0.05. Plots were generated using Plotly chart studio (RRID:SCR_013991, https://chart-studio.plotly.com/create/).\n\n\nResults\n\nThe first step consisted of selecting a gene that would be next evaluated for its potential relevance as a blood transcriptional biomarker. CEACAM6 was selected primarily based on its membership to a blood transcriptional signature of interest. This signature is part of a fixed blood transcriptional module repertoire (BloodGen3, see Ref. 16 and methods for details). The M10.4 module signature is functionally associated with neutrophil activation and comprises 11 other genes: BPI, LTF, CEACAM8, DEFA1, DEFA1B, DEFA2, DEFA4, OLFM4, ELANE, CTSG, and MPO (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ Step 1: candidate gene selection). In a reference collection of 16 patient cohorts,16 abundance levels of M10.4 transcripts were the highest in subjects with Staphylococcus aureus infection, respiratory syncytial virus infection and bacterial sepsis (Figure 1).\n\nA. The module fingerprint heatmap represents the proportion of transcript for a given module (rows) for which abundance levels are significantly different in case subjects compared to the respective controls for a given reference dataset (columns). Values can range from +100% (solid red: abundance for all constitutive transcripts for the module are significantly higher) to −100% (solid blue: abundance for all constitutive transcripts for the module are significantly lower). Responses are shown for four modules included in the module aggregate A38 from the BloodGen3 repertoire,16 including module M10.4 from which CEACAM6 was selected. B. The box plot represents the percentage response averaged for module M10.4, across the 16 reference datasets (we have contributed this dataset collection to GEO as part of an earlier work,16 and it is accessible under accession number GSE100150. Plots were generated using the BloodGen3 web application: https://drinchai.shinyapps.io/BloodGen3Module/.\n\nAs part of the evaluation process, it can be useful to start by retrieving and synthesizing background information about the candidate gene. For this, summaries from different reference databases, as well as introductions from recent publications on CEACAM6, were retrieved. This information was recorded in the CEACAM6 interactive circle packing plot (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ Step 2: gathering background information) and used for development of the narrative below.\n\nCEACAM6 is a glycosyl phosphatidyl inositol (GPI)-anchored cell surface glycoprotein. It is a member of the carcinoembryonic antigen (CEA) family whose members are known to play a role in cell adhesion.21 Specifically, CEACAM6 expression has been reported in granulocytes and lung and intestinal epithelial cells.22 In ileal epithelial cells of patients with Crohn’s disease, CEACAM6 has been found to act as a receptor for adherent-invasive Escherichia coli.23 It has also been found to mediate entry of Neisseria gonorrhoeae.24 CEA family members are widely used as tumor markers in serum as well as tumor immunoassays. CEACAM6 has been reported to act as an oncogene, promoting tumor progression and metastasis.25 These properties may, at least in part, be effected via the role of CEACAM6 in promoting anoikis resistance, which prevents the homeostatic elimination of anchorage-dependent cells (such as epithelial cells) that are detached from the cellular matrix.26 Since CEACAM6 membrane expression is highly specific to tumor cells, it has been suggested as a target for different cancer immunotherapies.27 It has also recently been identified as an immune checkpoint molecule, based on its role in suppressing cytotoxic T cell responses against malignant plasma cells.28\n\nTo further our understanding of the biological significance and clinical relevance of CEACAM6, we next sought to systematically screen the literature to identify associations with cell populations and diseases or physiological states.\n\nA query was designed to permit the retrieval of the literature associated with CEACAM6 (see methods for details). In total 642 PubMed entries were returned. Screening for names of diseases in the titles of literature associated with CEACAM6 identified 18 entities (Extended Data File 229). Among these, “cancer” and “colorectal cancer” were found in more than 50 CEACAM6-associated articles (202 and 65, respectively, as of March 2022). “Pancreatic cancer”, “lung cancer”, “breast cancer”, leukemia” and “inflammatory bowel disease” were found in more than 20 CEACAM6-associated articles (31, 35, 28, 35, and 30, respectively; Table 2, Figure 2A & https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/: Step 3/CEACAM6_Diseases). “Pregnancy” was found in 14 CEACAM6-associated articles. “Cholangiocarcinoma” and “myeloma” were found in more than 5 articles (7 and 9, respectively). Eight other diseases were found in only one article. Screening titles for names of cell types identified 10 entities (Extended Data File 229). The most frequently mentioned cell types among the CEACAM6 literature were granulocytes, neutrophils, T-cells and intestinal epithelial cells (Table 2, Figure 2B & https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/: Step 3/CEACAM6_Cell Types).\n\nThe prevalence of articles among the literature associated with CEACAM6 for disease entities (A) or cell type entities (B) are represented by circles of different sizes and colors, corresponding to the number of associated articles. It is possible to access underlying information by zooming into each of the circles. The Prezi presentation can be accessed at this url: https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ Step 3: background literature profiling.\n\nAltogether, this step established that CEACAM6 is associated with a large body of literature. It also permitted the identification of the main cell types and diseases associated with this gene. This information was used in subsequent literature profiling steps.\n\nThe selection of a blood transcriptional panel could take into consideration whether a given candidate gene has already been determined to be of clinical relevance as a biomarker, whether that is at the gene, transcript, or protein level. Thus, we next sought to determine if this was the case for CEACAM6 by extracting relevant information from its literature for the main disease entities identified in the previous steps.\n\nThe approach is described in detail in the methods section. In brief, starting from the CEACAM6-associated literature we searched for publications reporting the actual or potential use of CEACAM6 as a biomarker. For this we focused more specifically on the diseases that showed the highest degree of association with CEACAM6 based on the above literature profiling results (i.e., diseases mentioned in more than 20 articles, which are listed in Table 2), namely: leukemia, colorectal, pancreatic, lung, and breast cancers, as well as Inflammatory bowel disease. Next, articles associated with CEACAM6 and these diseases that also mentioned “biomarker”, “diagnostic”, “diagnosis”, “prognostic” OR “prognosis” in their title or abstract were retrieved. For articles deemed to be of interest, a standard spreadsheet template was used to capture relevant information (Extended Data File 330). Information was also aggregated in an interactive circle packing plot using the Prezi web application (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ CEACAM6/Step3: background literature profiling/CEACAM6_Diseases_Biomarker). Together, the information thus gathered served as a basis for the development of the narrative below.\n\nAs aforementioned, CEACAM6 has been noted for its oncogenic properties. Our screening of the CEACAM6 literature, which relates more specifically to its potential relevance as a biomarker in various disease settings, supports this notion. Indeed, a higher abundance of CEACAM6, whether at the transcript or protein level, in tumor tissues or serum was always associated with worse survival (in the case of colorectal,31,32 breast,33,34 pancreatic,35–39 and lung cancers40). Other studies have found CEACAM6 to be of potential value for differential diagnosis of malignant vs benign tumors for breast cancer (with CEACAM6 protein levels measured in breast tissues41) and pancreatic cancer (with CEACAM6 protein levels measured in the bile42). Notably, and of particular relevance to this report, in the case of colorectal carcinoma, measuring the abundance of CEACAM6 at the protein and transcript levels in blood alongside TSPAN8, LGALS4, and COL1A2 has been found to be of potential value for early disease detection.14,15 Furthermore, recently CEACAM6 was also included in a 10-gene signature predictive model for lung cancer prognosis.43\n\nAltogether, this review of the literature shows that measurement of CEACAM6, whether at the transcript or protein level, in tumor tissues or in blood, is considered of potential clinical value in informing the management of different types of cancers, as summarized in Table 3.\n\nMore specifically we next sought to assess the relevance of CEACAM6 as a blood transcriptional biomarker. The first pass at screening the literature (above) already identified instances where measuring blood CEACAM6 transcript is deemed of potential clinical value (i.e., for the early detection of colorectal cancer14 or the prognosis of lung cancer43). We wanted to undertake a second pass to profile the literature in more depth to identify additional studies that reported differences in the abundance of CEACAM6 transcripts in blood in patient populations.\n\nQueries were run using Google Scholar, which supports full text search. Entries were screened manually, selecting only peer-reviewed reports where CEACAM6 levels were measured in the blood of human subjects. Relevant information was recorded in a structed format in a spreadsheet using the standard template employed in the previous step. Finally, information was aggregated in the interactive CEACAM6 Prezi circle packing plot.\n\nDifferences in CEACAM6 blood transcript levels have been reported in the literature for a wide range of pathologies. Specifically, in addition to the colorectal carcinoma and lung cancer studies described above, it was found to be part of a 13-gene disease signature which was increased in patients with Parkinson’s disease as compared with asymptomatic subject.44 It was also part of a different 13-gene disease signature that was increased in patients with severe idiopathic pulmonary fibrosis compared with patients with a mild form of the disease.45 Notably, other members of this latter signature, including CTSG, DEFA3, and OLFM4, are also comprised in the M10.4 module that is part of the fixed BloodGen3 repertoire mentioned above. Other pathologies and states where blood CEACAM6 transcript levels were found to be increased are summarized in Table 4, and include asthma,46 sepsis,47 post-traumatic stress disorder,48 psoriasis,49 maternal anti-fetal rejection,50 and COVID-19.51,52 It was also found to differ based on gender (higher in male than in females)53 and notably was also increased by steroid treatment.54 These latter two findings suggest that in instances where demographics or use of steroids are not well-controlled for in the study design, differences in CEACAM6 transcript levels might be, at least in part, attributed to these factors rather than the underlying pathology. For reference, a full record of the information captured from the literature regarding those studies can be found in Extended Data File 4.55 Additional information is also found aggregated in the CEACAM6 interactive circle packing plot (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ CEACAM6/Step3: background literature profiling/CEACAM6_Diseases_Biomarker).\n\nTaken together, this in-depth review of the literature points to differences in CEACAM6 blood transcript abundance being present in patients in a wide range of diseases. Thus, suggests that assays measuring levels of CEACAM6 transcripts in blood may be employed to support biomarker development efforts across different clinical settings.\n\nLiterature reports might capture only a fraction of instances where pathophysiological changes are accompanied by changes in the abundance of CEACAM6 blood transcripts. Screening publicly available transcriptome datasets could confirm published reports and help identify other instances where levels of CEACAM6 transcript abundance differ in patients relative to control subjects.\n\nFor this, we employed a data browsing web-application, the Gene eXpression Browser (GXB),20 which provides easy access to transcriptional profiles of individual genes in curated collections of transcriptome datasets. For instance, we screened blood transcriptome data for a collection of 16 reference cohorts that were used for the construction of the BloodGen3 repertoire. These datasets are available in the CD2K instance of GXB (http://cd2k.gxbsidra.org/dm3/geneBrowser/list). CEACAM6 transcriptional profiles were retrieved for each of these cohorts and statistics run separately using MS Excel to determine the significance of changes in levels of CEACAM6 transcripts in patients vs controls (Extended Data File 556). Changes were captured in a structured format, plotted, and aggregated in the CEACAM6 circle packing plot.\n\nWe found differences in levels of CEACAM6 transcript abundance for nine of the 16 reference BloodGen3 datasets (Table 4, Extended Data File 657). The pathological or physiological states for which differences were observed did not overlap with those also listed in Table 4 that were identified in the previous step by in depth screening of the literature. Indeed, we found elevated abundance levels of CEACAM6 in patients with infections caused by Staphylococcus aureus, influenza, respiratory syncytial virus, human immunodeficiency virus, and bacterial pathogens causing sepsis, in comparison with controls (Figure 3). CEACAM6 transcript levels were not increased in patients with tuberculosis. Significant increases were also observed in non-communicable diseases such as systemic onset juvenile arthritis and Kawasaki disease but not in the context of systemic lupus erythematosus, late-stage melanoma, or chronic obstructive pulmonary disease. Finally, we also found a significant increase in abundance in the blood of liver transplant recipients under immunosuppressive therapy and in pregnant women. This transcriptome profiling dataset screen complemented our earlier literature screen, identifying nine additional diseases or physiological states in which CEACAM6 transcript is significantly changed in the blood of patients, for a total of 25 distinct diseases/states which are listed in Table 4. Plots for the nine BloodGen3 datasets are available via the GXB application and have been replotted and loaded to the CEACAM6 circle packing plot (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ CEACAM6/Step5: blood tx profiling/CEACAM6_Blood Tx).\n\nThis violin plot shows the fold change in abundance of CEACAM6 mRNA measured by RNA sequencing in the blood of human subjects across 16 reference disease cohorts, compared to their respective control subjects. In total blood transcriptome of 985 subjects was profiled. For details, see original work by Altman, Rinchai et al.16 GEO deposition: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100150; plot: https://chart-studio.plotly.com/create/?fid=dchaussabel%3A132 interactive version with values expressed as counts: http://cd2k.gxbsidra.org/dm3/miniURL/view/NH.\n\nOverall, the screening of a reference dataset collection indicated that differences in CEACAM6 levels could be observed in a wide range of conditions in which systemic inflammation is observed. The lack of overlap between the literature and transcriptome data profiling conducted in steps 4 and 5 suggests that expanding this search to a larger number of blood transcriptome datasets would likely significantly add to this list.\n\nAnother criterion for inclusion of CEACAM6 in a focused assay could be its targeting by approved drugs or drugs currently under development. The “Open Targets” database does not report any known drugs, approved or currently under development, targeting CEACAM6 (https://platform.opentargets.org/target/ENSG00000086548). However, given its recently described role as suppressor of effector CD8 T-cells,28 CEACAM6 is currently considered an immune checkpoint molecule and as such could be targeted by drugs designed to block its activity in cancer patients.27 Additionally, in preclinical mouse models antibodies targeting CEACAM6 have been shown to inhibit tumor growth and metastasis.25,58\n\nFinally, screening of reference public transcriptome datasets can also yield insights regarding the candidate gene’s regulation and restriction among circulating leukocytes. Thus, in addition to profiling 16 public blood transcriptome datasets, we examined CEACAM6 transcriptional profiles in two other reference datasets. One dataset measured transcript abundance in monocytes, neutrophils, B-cells, CD4+ T-cells, CD8+ T-cells and natural killer (NK) cells and in whole blood (GSE6042459). The second dataset measured changes in transcript abundance in whole blood exposed in vitro to a wide range of immune stimuli (toll-like receptor agonists, killed bacteria, viruses, inflammatory cytokines and interferons; GSE3010160). In addition, we screened the Broad Institute’s single cell portal61 for datasets in which CEACAM6 expression was elevated in one or more of the cell clusters.\n\nBulk leukocyte population RNAseq data showed CEACAM6 expression to be restricted to neutrophils (Figure 4) [data source: Linsley et al.59]. This observation was confirmed in a single-cell dataset in which tumor immune cell infiltrates were dissociated and profiled via RNA sequencing (Figure 5) [data source: He et al.62]. These findings were in line with the prevalence among the CEACAM6 literature of publications mentioning this cell type (https://prezi.com/view/pQ7TKEC6tgY3cuik9ckt/ CEACAM6/Step 3: background literature profiling/CEACAM6_Cell Types) (Figure 2A). However, we did not find CEACAM6 to be increased in whole blood stimulated in vitro (Figure 6) [data source: Obermoser et al.60]. This finding was to some extent surprising since blood signatures comprising CEACAM6 are often functionally associated with neutrophil activation.63–65\n\nThis box plot shows levels of abundance of CEACAM6 RNA measured by RNA sequencing in neutrophils, monocytes, B-cells, CD4+ T-cells, CD8+ T-cells and NK cells purified from the blood of human subjects, including patients with ALS, type 1 diabetes, multiple sclerosis (immediately before and 24 hours after initiation of beta interferon therapy) or sepsis and healthy controls. Values are normalized to the median calculated across all conditions. For details, see original work by Linsley et al.59\n\nGEO deposition: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60424 plot: https://plotly.com/~dchaussabel/171/.\n\nThis tSNE plot shows abundance levels of CEACAM6 measured by single-cell RNA sequencing among dissociated metastatic prostate tumor tissue cells. After quality control, this set consisted of 2,170 cells obtained from 14 patients and 15 biopsies. Clusters are labelled for dominant cell type based on marker gene expression on the plot above. Normalized transcript per million (TPM) counts for CEACAM6 are shown in blue on the plot below. For details, see original work by He et al.62 An interactive version of this plot is accessible via the Broad Institute single cell portal: https://singlecell.broadinstitute.org/single_cell/study/SCP1244/transcriptional-mediators-of-treatment-resistance-in-lethal-prostate-cancer?genes=CEACAM6#study-visualize.\n\nThe box plot represents transcript abundance levels for the CEACAM6 gene in blood samples obtained from four healthy donors, cultivated for 6 hours at 37°C in the presence of pathogens, as well as pathogen-derived and host-derived immune stimuli (HKAL=heat-killed Acholeplasma laidlawii, HKLP=heat-killed Legionella pneumophila, HKSA=heat-killed Staphylococcus aureus, Flu=live influenza A virus, RSV=live respiratory syncytial virus). For details, see original work by Obermoser et al.60 GEO deposition: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30101 plot: https://plotly.com/~dchaussabel/173/.\n\nTaken together, further profiling of reference transcriptome datasets confirmed the close association of CEACAM6 with neutrophils, which is the most abundant circulating leukocyte population in blood. It also indicates that elevated levels of CEACAM6 transcript abundance observed across a wide range of conditions may be associated with an increase in relative abundance of cells expressing this gene, rather than regulation of its expression.\n\n\nDiscussion\n\nClinical translation of biomarker signatures obtained via transcriptome profiling technologies typically involves the development of targeted transcript panels and assays. Such assays can also prove more practical for high-temporal frequency immunological monitoring applications that require profiling of thousands of samples. They could also be more readily implemented in the context of research projects conducted in low-resource settings. Targeted panel design can be informed by both data-driven and knowledge-driven approaches. However, given the large amounts of data and knowledge available for any given candidate gene, the selection process can prove daunting. Here we employed a workflow devised for screening the literature and large-scale profiling data associated with a given candidate gene, and to retrieve and aggregate relevant information in a structured format. This information and associated resources should in turn support decision-making of investigators aiming to develop targeted panels for downstream clinical or research applications.\n\nWe focused on CEA cell adhesion molecule 6 (CEACAM6). This candidate is a member of blood transcriptional signatures that are often functionally associated with neutrophil activation,63–65 which typically also includes genes encoding constituents of neutrophil granules, such as defensins (DEFA1, DEFA3, DEFA4), myeloperoxidase (MPO), bactericidal permeability increasing protein (BPI), and lactotransferrin (LTF).\n\nSeveral criteria can be used when prioritizing candidate genes for inclusion in a targeted assay, which we have applied here to CEACAM6:\n\n1) Transcripts are detectable in blood and changes can be observed across different immune states/pathologies; this criterion is met in the case of CEACAM6. An increase in levels of CEACAM6 transcripts has been reported in the literature and observed in blood transcriptome datasets for patients with infectious (e.g., bacterial sepsis), autoimmune, or inflammatory diseases (e.g., systemic lupus erythematosus, Kawasaki disease).\n\n2) Previous reports describe the candidate as being of clinical relevance as a biomarker; this criterion is also met. Indeed, CEACAM6 is part of a family that includes members which are used routinely in clinical pathology to assess tumor specimens and inform disease prognosis and treatment.66–68 CEACAM6 itself is deemed of potential value as a prognosis marker in different types of cancers.32,33,37,39,40 Notably, measuring blood CEACAM6 transcript abundance is considered of potential value for the early detection of colorectal cancer.14,15\n\n3) The functional relevance of the candidate gene in blood leukocytes is known; this criterion is partially met. CEACAM6 is associated with neutrophils in the literature. This was confirmed in our screen of reference transcriptome datasets, both at the bulk leukocyte population and single cell levels (Figures 4 & 5). However, the role played by CEACAM6 in neutrophils has not yet been fully elucidated. For instance, another reference dataset showed that CEACAM6 expression is not regulated in blood exposed in vitro to a wide range of immune stimuli (Figure 6). This finding casts some doubts on whether “neutrophil activation” should be assigned to the signature associated with CEACAM6 (by us and others). These observations may also be consistent with an earlier report that associated a “granulopoiesis signature”, which comprised CEACAM6, with low density mononuclear and polymorphonuclear populations found in peripheral blood mononuclear cell fractions.69 Furthermore, single-cell analyses recently conducted in COVID-19 patients identified a population of “developing neutrophils” that expressed neutrophil granule proteins, including module M10.4 members such as MPO, DEFA3, LTF, and ELANE, and were described as potentially being derived from plasmablasts.70 Altogether these observations suggest that measuring levels of M10.4 transcripts might permit the monitoring of changes in abundance in this population of developing neutrophils rather than reflecting overall neutrophil abundance. However, this hypothesis and the functional relevance of this subset of neutrophils remains to be validated experimentally.\n\n4) The candidate gene is a target for drugs that are approved or under development; this criterion is not met. No drugs targeting CEACAM6 have been developed to date. This may change, however since, as noted earlier, CEACAM6 has recently been found to suppress T-cell function and could thus be considered for targeting by novel immune checkpoint inhibitors in cancer patients.28\n\nAlternate candidates may be found that could be selected instead of CEACAM6 for inclusion in a targeted blood transcriptional assay. CEACAM6 was chosen for this evaluation based on its membership to module M10.4, which is part of the fixed BloodGen3 repertoire.17 Such module repertoires can be employed as a framework for the design of targeted assays, in which case only one or a few representative transcripts from a given module would usually be selected to provide coverage for the entire repertoire (those modules are formed based on co-expression and all constitutive transcripts would present with a high degree of co-linearity).9 In the case of module M10.4, other candidates to consider would be CEACAM8, BPI, MPO, LTF, DEFA1, DEFA3, DEFA4, CTSG, OLFM4, and ELANE, since all of those genes belong to the same module as CEACAM6 (Table 5). However, to date, only CEACAM6 has been investigated in depth and thus it is not yet possible to benchmark it against these other candidates. However, it can already be noted that BPI (bactericidal/permeability-increasing protein) has been found to be of potential value as a biomarker in patients with asthma,71 as well as chronic obstructive pulmonary disease.72 DEFA1 and DEFA3 have been identified as potential inflammatory biomarkers for coronary heart disease.73 CEACAM8, another member of the carcinoembryonic cell adhesion molecule family, has been found to be of potential value as a prognosis marker in patients with esophageal cancer and in patients with sepsis.74,75\n\nThis table lists targeted gene sets or gene panels comprising CEACAM6. Lists of differentially expressed genes that consists of tens or hundreds of transcripts are purposedly omitted.\n\nFinally, it is worth highlighting some of the limitations of our investigation into the relevance of CEACAM6 as a blood transcriptome biomarker. For instance, it should be noted that the screen conducted among public transcriptome data is not comprehensive. Additional blood transcriptome datasets are available in GEO and other repositories that have not yet been loaded in GXB instances. As a result, the list of conditions in which CEACAM6 blood transcript abundance changes is probably conservative and will likely grow as more datasets become available for screening.\n\nIn conclusion, the information presented here should help researchers decide whether to include CEACAM6 in the targeted assay they intend to develop. Some of our findings suggest that measuring abundance of CEACAM6 transcripts in blood could prove to be of value in the monitoring and management of patients with diseases associated with systemic inflammation. This would likely be true for other members of the BloodGen3 module M10.4/“neutrophil activation” gene sets. However, CEACAM6 presents with the distinct advantage of also being of potential value in the management of patients with cancer, whether the assay would be used to measure transcript abundance in blood or in tumor tissues.\n\n\nAuthor contributions\n\nDR and DC: Conceptualization, Data curation, Formal analysis, Visualization, Methodology Development, Writing – Review & Editing. DC: Writing – Original Draft Preparation. The contributor's roles listed above follow the Contributor Roles Taxonomy (CRediT) managed by The Consortia Advancing Standards in Research Administration Information (CASRAI) (https://casrai.org/credit/).",
"appendix": "Data availability\n\nThe project contains the following extended data:\n\n• Extended Data File 1: a spreadsheet in the MS Excel format that is used as a template to capture relevant information from the literature and from transcriptional profiling data analysis results. Figshare: Ext Data File 1 - Information Capture Form_Generic_2022 Sept14 https://doi.org/10.6084/m9.figshare.21183718.v1. 19\n\n• Extended Data File 2: a spreadsheet in the MS Excel format listing cell type and disease entities and their prevalence in the literature associated with CEACAM6. Figshare: Ext Data File 2 CEACAM6_Lit Profiles_Entities_Step3c_2022 Sept14 https://doi.org/10.6084/m9.figshare.21183748.v1. 29\n\n• Extended Data File 3: a spreadsheet in the MS Excel format used to capture information from the CEACAM6 literature regarding its actual or potential use as a biomarker. Figshare: Ext Data File 3 CEACAM6_Articles_Biomarker Relevance_Step3d_2022 Sept14. https://doi.org/10.6084/m9.figshare.21183832.v1. 30\n\n• Extended Data File 4: a spreadsheet in the MS Excel format used to capture information from the CEACAM6 literature reporting differences in blood transcript abundance in cases vs controls. Figshare: Ext Data File 4 CEACAM6_Articles_Blood transcript profiling_Step4c_2022 Sep14. https://doi.org/10.6084/m9.figshare.21184357.v1. 55\n\n• Extended Data File 5: a spreadsheet in the MS Excel format used to capture CEACAM6 transcriptional profiles from multiple datasets (one dataset per tab) and compute significance of differences in abundance observed between cases and controls. Figshare: Ext Data File 5 CEACAM6_Transcriptome data_ abundance profiles_Step5b_2022 Sept14. https://doi.org/10.6084/m9.figshare.21184363.v1. 56\n\n• Extended Data File 6: a spreadsheet in the MS Excel format used to capture relevant information regarding differences in CEACAM6 blood transcriptional abundance observed in multiple datasets. Figshare: Ext Data File 6 CEACAM6_Transcriptome data_diff expression_Step5c_2022 Sept14. https://doi.org/10.6084/m9.figshare.21184369.v1. 57\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nChaussabel D: Assessment of immune status using blood transcriptomics and potential implications for global health. Semin. Immunol. 2015 Feb; 27(1): 58–66. PubMed Abstract | Publisher Full Text\n\nLi S, Todor A, Luo R: Blood transcriptomics and metabolomics for personalized medicine. Comput. Struct. Biotechnol. J. 2016; 14: 1–7. 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}
|
[
{
"id": "155597",
"date": "09 Dec 2022",
"name": "Mattia Lauriola",
"expertise": [
"Reviewer Expertise Blood biomarkers for colon cancer",
"EGFR",
"RTK signalling"
],
"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 is quite interesting, because the authors highlight a possible role for CEACAM6 as a blood biomarker in patients with a viral or bacterial infection, thus surrogating CEAM6 as an assay for systemic inflammation. As the authors correctly pointed out, CEACAM6 transcript levels were already described for cancer diseases including colorectal cancer. In this case, it's interesting to notice that previous publications reported that CEACM6 abundance in the blood of subjects positive for FIT (faecal immunochemical test), but negative for further intestinal lesions. This probably finds support in some of the results reported here, showing an enhanced availability of CEACAM6 in circulating neutrophils. But, the authors fail to refer to this publication PMID: 322574321.\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?\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": "11238",
"date": "04 Apr 2024",
"name": "Damien Chaussabel",
"role": "Author Response",
"response": "Thank you for highlighting the importance of referencing the study associated with PMID: 32257432. We agree that this publication is relevant to our research on CEACAM6 as a potential blood biomarker. In light of your suggestion, we have added a reference to this study in our manuscript (now cited as reference #16). This inclusion helps to contextualize the role of CEACAM6 in subjects with a positive fecal immunochemical test (FIT) but no intestinal lesions, and supports our findings on its availability in circulating neutrophils. We appreciate your constructive feedback and believe that this addition enhances the clarity and relevance of our work."
}
]
},
{
"id": "192786",
"date": "03 Oct 2023",
"name": "Ritu Pandey",
"expertise": [
"Reviewer Expertise Cancer 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\nThe manuscript is a summary of CEACAM6 gene as a prognostic blood biomarker across diseases and provides a guide to capture heterogeneous information on a given gene or biomarker using publicly available processed or summarized data. The work is based on prior published work by the group on analysis of blood biomarkers.\n\nIt is not clear that the main focus of the paper is showing a method or in-depth analysis of CEACAM6 gene utilizing the method, assuming both here are few comments:\nThe authors provide for the readers a pathway to gather details on a gene and summarize the information. But it is not clear how the information is getting extracted. The data captured is voluminous at times, so are there any scripts that the authors are providing or suggesting for data retrieval? There is some amount of customized data massaging and data wrangling needed for further use, but few automated steps and scripts would be useful. Data backed with evidence keeps changing such as PubMed and needs to be updated too. The strategy is based on previous work by the authors but any automation or programmatic retrieval for any of the steps should be included here for the benefit of readers.\n\nThe statement in the Discussion #4 that no drugs have been developed for targeting CEACAM6 could be misleading since there have been efforts, at least in cancer studies to target CEACAM6 using monoclonal antibodies. The authors do mention one myeloma study. There are several experimental approaches that have been published in preclinical models and there are also clinical studies in cancer where this is being targeted as an immune checkpoint.\n\nThis study assesses changes in expression of any gene in disease cases to qualify it as a marker but equally important is what approaches have been used or what indications exist that it has been studied as a therapeutic target and if so the outcome of such study. There are several publications for studies of CEACAM6 as a therapeutic target in cancer. Examples of few of the published work from NCBI PubMed - PMID: 19334050, PMID: 35141051, PMID: 31797958, PMID: 35082925 and a clinical trial - https://clinicaltrials.gov/study/NCT03596372. These should be cited as similar approaches could be utilized for other diseases.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11239",
"date": "04 Apr 2024",
"name": "Damien Chaussabel",
"role": "Author Response",
"response": "Thank you for your constructive review and insightful comments. We understand the concerns raised regarding the clarity of our manuscript's focus and the methodologies employed for data retrieval and analysis. Allow us to address these points with additional context that we believe will clarify our intentions and the contributions of our work. Clarification of Manuscript Focus: Our current work is intended as a proof of concept paper, demonstrating the practical application of the methodological framework we detailed in a previously published paper (\"A training curriculum for retrieving, structuring, and aggregating information derived from the biomedical literature and large-scale data repositories\"). This earlier publication provides an in-depth description of the methods and serves as the foundation upon which our current study on CEACAM6 is built. We acknowledge that this may not have been made sufficiently clear in our manuscript, leading to confusion about its primary focus. We revised our introduction sections to explicitly state that this work is a demonstration of our previously published methodology applied to the CEACAM6 gene, rather than an exposition of new methodological advancements: “The methodology employed in this study is derived from our previously established “collective omics data” (COD) training curriculum, as outlined in our comprehensive methods paper, \"A training curriculum for retrieving, structuring, and aggregating information derived from the biomedical literature and large-scale data repositories.\"10. This foundational paper provides a detailed description of our systematic approach to information curation, which we have applied in the current investigation of CEACAM6. Specifically, the study utilizes the COD1 training module workflow from this curriculum, which guides the structured retrieval and aggregation of gene-specific data for biomarker assessment. The process encompasses selecting a gene of interest, in this case, CEACAM6, to comprehensively gather and synthesize relevant information from both literature and public datasets, culminating in the creation of resources like structured data tables and interactive circle packing plots. This approach not only supports the rigorous assessment of CEACAM6's potential as a blood biomarker but also serves as a demonstrative application of our validated methodological framework, providing a practical example of how such a framework can be employed to enhance biomarker discovery efforts.” Data Retrieval and Analysis: The method described in our prior paper involves a systematic but manual approach to retrieving, structuring, and aggregating information, which, as you rightly pointed out, can be labor-intensive. We recognize the importance of automation in managing the vast amount of data available in biomedical research. While our published method does not incorporate automated processes, we have, in response to the evolving needs of data curation, begun exploring the potential of Large Language Models (LLMs) to assist in manual data curation tasks. This effort is led by staff who have recently joined our group and represents an exciting direction for enhancing the efficiency and scalability of our data curation processes. Preliminary findings suggest that while LLMs are not a complete substitute for manual curation, they can significantly aid in the process by streamlining the identification and extraction of relevant information. This ongoing work acknowledges the pertinence of your feedback regarding automation and highlights our commitment to advancing our methodologies in line with technological developments. Although the results of these explorations are not included in the current manuscript, they are part of a separate study that we plan to publish in the future. This will detail our experiences and findings regarding the integration of LLMs into our data curation workflow, providing insights that could benefit the broader research community in handling similar challenges.A new paragraph has been added to the discussion, acknowledging current limitations and potential strategies for automating the information extraction workflow: “The current methodology reliance on a systematic, manual approach to data retrieval and structuring is another limitation. We recognize the potential of automation to transform this labor-intensive process. In this respect, we are actively exploring the integration of Large Language Models (LLMs) into our data curation workflow. These advanced models show promise in streamlining the identification, extraction, and structuring of relevant information, potentially mitigating the challenges associated with the sheer volume and dynamic nature of biomedical databases. Our preliminary explorations suggest that while LLMs may not fully replace the nuanced judgment of human curators, they offer significant support by enhancing efficiency and accuracy, thereby complementing our existing methodologies. Thus we are cautiously optimistic about the role of LLMs in enhancing our data analysis framework, aiming to improve efficiency while maintaining accuracy. This integration of LLMs is an ongoing effort and will be detailed further in upcoming publications.” Discussion on Therapeutic Targeting of CEACAM6: We appreciate your pointing out the need to correct and expand our discussion on therapeutic efforts targeting CEACAM6. It was not our intention to overlook significant research in this area. We have revised the relevant sections to accurately reflect ongoing and completed studies targeting CEACAM6 with therapeutic intent, citing the publications and clinical trials you mentioned. This will ensure our discussion acknowledges both the biomarker potential of CEACAM6 and its implications for therapeutic development: Recent studies and ongoing clinical trials have explored the utility of targeting CEACAM6 in various cancers, particularly through the development of monoclonal antibodies. For instance, preclinical evaluations have demonstrated the potential of CEACAM6 as a therapy target in pancreatic adenocarcinoma, utilizing antibody-drug conjugates to effectively target and diminish CEACAM6-expressing tumors (PMID: 19334050). Additionally, the blocking of CEACAM6-CEACAM1 interactions has shown promise in enhancing T cell-mediated cancer cell elimination, suggesting a role for CEACAM6 in immune modulation and its potential as an immune checkpoint target (PMID: 35141051). The breadth of research, encompassing studies on its prognostic value and therapeutic targeting in cancers, underscores CEACAM6's significance in oncology and its emerging role as a viable therapeutic target. These investigations, reflected in various studies (PMID: 31797958, PMID: 35082925) and a clinical trial registered under NCT03596372, collectively indicate a growing interest in CEACAM6 as a therapeutic target, warranting further exploration and validation in clinical settings. In summary, we are committed to improving the clarity and utility of our manuscript based on your feedback. We believe that by clarifying the relationship between our current work and our previously published methodological framework, and by addressing the points you've raised regarding data analysis and therapeutic targeting, our manuscript will provide a clearer, more comprehensive contribution to the field. Thank you again for your valuable insights, which we are confident will strengthen our paper."
}
]
}
] | 1
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https://f1000research.com/articles/11-1294
|
https://f1000research.com/articles/13-248/v1
|
04 Apr 24
|
{
"type": "Study Protocol",
"title": "Effect of diaphragmatic stretch technique on thoracic excursion and pulmonary function in COPD patients: Study protocol for randomized controlled trial.",
"authors": [
"Priyanka K. Chilhate",
"Lajwanti Lalwani (Adwani)",
"Vishnu Vardhan",
"Lajwanti Lalwani (Adwani)",
"Vishnu Vardhan"
],
"abstract": "Limited airflow is a defining feature of COPD, a respiratory disease that frequently results in reduced thoracic movement and compromised lung function. The diaphragm, which is the main breathing muscle, is essential for healthy lung expansion and ventilation. The diaphragm muscle’s flexibility and mobility are intended to be enhanced via diaphragmatic stretching. This method can enhance respiratory health and assist in returning the diaphragm to its original state. Patients with COPD may benefit from improved lung expansion and ventilation because of this. The usefulness of integrating the diaphragmatic stretch approach with traditional chest physical therapy is not well-established. Thus, research is needed to ascertain how the diaphragmatic stretch technique affects lung function and thoracic excursion in COPD patients. This study aims to ascertain how the diaphragmatic stretch technique affects thoracic excursion and pulmonary function (FEV1, FVC, FEV1/FVC, FEF25%-75%, PEFR) in individuals with COPD. There will be 58 COPD patients enrolled in total for this trial; 29 will receive traditional chest physiotherapy along with the diaphragmatic stretch technique, and 29 will receive traditional chest physiotherapy exclusively. Two weeks will pass throughout the intervention. Prior to the intervention, pre-outcome measures will be evaluated, and two weeks later, post-outcome measures will be evaluated once more. The anticipated outcome of this study is that the diaphragmatic stretch technique can enhance thoracic excursion and improve pulmonary function just as well as traditional chest physiotherapy when used in conjunction with it.",
"keywords": [
"COPD",
"diaphragmatic stretch",
"conventional chest physiotherapy",
"thoracic excursion",
"pulmonary function"
],
"content": "Introduction\n\nChronic Obstructive Pulmonary Disease (COPD) is a diverse lung illness that is typified by persistent respiratory symptoms (such as coughing, sputum production, dyspnoea, and/or exacerbations) brought on by abnormalities of the alveoli (emphysema) and/or airways (bronchitis, bronchiolitis) that result in persistent, frequently progressive airflow obstruction.1 Air entrapment and lung hyperinflation are two prominent indicators of COPD.1\n\nAs the lung volume can be considered the respiratory muscle’s length index, the diaphragm’s contraction force, lung volumes, and lung capacities can all be impacted by shortening it.2 The diaphragm’s ability to function is compromised by these two prominent COPD features. They result in a mechanical disadvantage because they shorten its operational length and alter the mechanical interaction between its numerous elements. These pathological alterations result in the diaphragm’s inability to expand and elevate the lower rib cage, which causes the lower ribs’ transverse diameter to contract during inspiration. While functional capability decreases, these changes result in an increase in breathing effort.3,4\n\nDiaphragm and rib cage movements gradually become lessened in patients with respiratory disorders due to alternate cyclical usage of the chest wall or diaphragm, which creates resistance to the chest wall and increases effort of breathing since it puts more strain on the respiratory muscles. Stretching muscle fibres encourages the growth of sarcomeres, which in turn lengthens shortened muscles. The ability of the respiratory muscles to contract would generally improve with appropriate length, leading to an increase in thoracic expansion and improved respiratory mechanics performance.2,3\n\nNumerous manual therapies have been suggested for the treatment of COPD symptoms because of the relationship between the musculoskeletal and respiratory systems. Increasing the thoracic structures’ range of motion is a common goal in respiratory mechanics. A respiratory muscle stretch aims to extend both the muscles that contract during inspiration and expiration, which are found in the chest wall. By relaxing and strengthening diaphragmatic contraction, the diaphragmatic stretch technique seeks to increase the pressure gradient between the thorax and abdomen.7\n\nThe healing process in manual therapy involves manipulating the hands for therapeutic purposes, which eventually impacts the body’s ability to heal itself. Both the individual’s general behaviour and the level of local repairs may change. Despite the benefits of manual treatment for the respiratory system, studies utilizing this approach are uncommon.4 The immediate effects of diaphragmatic stretch technique on improving thoracic excursion have been seen in a cross-over trial with washout period of three hours and can be safely recommended in clinically stable COPD patients.4 It is also discovered that diaphragmatic stretching along with conventional chest physiotherapy significantly improves pulmonary function (FEV1/FVC) and thoracic excursion in COPD patients.2 Other parameters of pulmonary function (FEF25%-75%, PEFR) are also important as they are sensitive measure of small airway obstruction and to know about the complications related to COPD.5,6 The effect of diaphragmatic stretch in addition to conventional chest physiotherapy on these parameters of pulmonary function are not known. Therefore, the goal of the current study is to determine how the diaphragmatic stretch technique along with conventional chest physiotherapy helps in improving thoracic excursion and pulmonary function in COPD patients.\n\nTrail design: A single centre, parallel-group, active controlled group, randomized control trial.\n\nMethods: Study volunteers will only be accepted by the Acharya Vinoba Bhave Rural Hospital’s Respiratory Medicine OPD in Sawangi (Meghe), Wardha, Maharashtra, with permission from the Datta Meghe Institute of Higher Education and Research’s (DMIHER) institutional ethics committee. To screen the local population, strict adherence to the study’s inclusion and exclusion criteria will be upheld.\n\nTo study the effect of diaphragmatic stretch technique on thoracic excursion and pulmonary function in COPD patients.\n\n\n\n1. To determine the effect of diaphragmatic stretch technique adjunct to conventional chest physiotherapy on thoracic excursion and pulmonary function in COPD patients.\n\n2. To determine the effect of conventional chest physiotherapy on thoracic excursion and pulmonary function in COPD patients.\n\n3. To compare the diaphragmatic stretch technique along with conventional chest physiotherapy as compared to conventional chest physiotherapy on thoracic excursion, and pulmonary function in COPD patients.\n\n\n\n1. Both men and women between 35-65 years who are diagnosed with COPD by physician.\n\n2. Patients in 2023 who meet the GOLD criteria for mild to moderate COPD. The study will include two categories: moderate 50% FEV1 80% and mild FEV1 80% expected.\n\n\n\n1. Unstable vital signs (arterial pressure < 100/60 mmHg, MAP < 80 mmHg).\n\n2. Dyspnoea score – 4-5.\n\n3. who have had abdominal or cardiothoracic surgery recently.\n\n4. A recent track record of injuries to the abdomen or chest wall.\n\n5. Any musculoskeletal disorder (scoliosis, kyphosis, severe osteoporosis).\n\n6. Any cardiovascular problems.\n\n7. History of psychiatric illness.\n\n8. Individuals who meet the GOLD criteria for COPD in 2023 and have severe to very severe disease. GOLD 4: extremely severe (FEV1 <30% expected) and severe (30% ≤ FEV1<50% projected) will not be included in the trial.\n\n\n\n1. Primary outcomes\n\nThoracic excursion: “Thoracic excursion is the difference in thoracic circumference between peak inspiration and expiration recorded while standing with arms at the sides of the trunk.” To test upper thoracic excursion, an inch of tape wrapped around the chest on both the upper and lower thoracic levels will be utilized. For upper thoracic excursion the tape will be positioned on the third intercostal gap at the midclavicular line and the fifth thoracic spinous process. The tip of the xiphoid process and the 10th thoracic spinous process will be used to quantify lower thoracic excursion. To obtain data, participants will be instructed to hold their breath during peak expiration and inspiration.2,7\n\n2. Secondary outcomes\n\nPulmonary function test: Spirometry (RMS HELIOS401) is the instrument that will be used to compute this particular measurement. Listed below are the components:\n\nFVC (Forced Vital Capacity) – “The FVC is the maximum gas volume that the patient may exhale fast and forcefully after a maximal inhale. The FVC maneuver is the name given to this procedure.”\n\nThe vital capacity (VC) and FVC should not be separated by more than 200 milliliters.\n\nFEV1 (Forced Expiratory Volume in One Second) – “The volume expired during the first second of an FVC maneuver is measured as FEV1.”\n\nValues that are typical: In people with typical respiratory function, the forced expiratory volume is as follows:\n\nFEV1 is equivalent to 75%-85% of TVC.\n\nRatio of FVC/FEV1: The ratios are calculated by dividing the predicted FVC by the predicted FEV1.2,8\n\nFEF25%-75%: “The percentage of the predicted value (%pred FEF25%-75%) is used to represent forced expiratory flow in this case. A forced expiratory flow is one that occurs on average between 25% and 75% of the required capacity.”5,9\n\nPeak expiratory flow rate – “The greatest flow that can be achieved during a forced vertical breathing exercise is known as the PEFR. Litres per second are the unit of measurement.”\n\nThe typical range for adults is 100–850 L/min.6\n\nOnce diaphragmatic stretches are administered to this group, the strain is held for 15–30 seconds. Participants will be forced to sit upright. The therapist will come up behind the patient, his hands wrapped around the thoracic cage and curled fingers pushed into the subcostal borders. The rectus abdominis muscle will be relaxed by slightly rounding the subject’s trunk. With his hands at the subcostal edge, the therapist of the individual’s lower ribs and eased them caudally when the subject exhaled. As the patient inhales, firm but gentle traction will be maintained. Two sets of ten deep breaths each will be performed for this exercise, with a one-minute break in between. In addition to diaphragmatic stretch, traditional physiotherapy will include thoracic mobility exercises (thoracic flexion on both sides, trunk rotation), purse lip breathing, diaphragmatic breathing, shoulder mobility exercises (scapular protraction–retraction, elevation–depression, flexion–extension, abduction–adduction, medial–lateral rotation, horizontal abduction–adduction, and upward–downward rotation). Once a day for two weeks, perform ten repetitions of each exercise.2,5–10\n\nControl group: All exercises related to shoulder mobility (flexion–extension, abduction–adduction, medial–lateral rotation, horizontal abduction–adduction, scapular protraction–retraction, elevation–depression, and upward–downward rotation) and thoracic mobility (lateral flexion on both sides, trunk rotation) will be provided exclusively to this group during their conventional physical therapy sessions. Once a day for two weeks, perform ten repetitions of each exercise.2,5–10\n\nSafety outcomes: Unfavorable situations are always documented.\n\nEach research subject will provide written, informed consent. The institutional ethical committee of the DMIHER will authorize the study before choosing study individuals. Participants will be selected from Acharya Vinoba Bhave Rural Hospital’s respiratory medicine outpatient department in Sawangi (Meghe), Wardha, Maharashtra. The participant will first undergo a comprehensive evaluation. The participant will be selected as per inclusion and exclusion criteria. The participant will receive comprehensive information regarding the study and intervention. Prior to the process of randomization, the demographic information of the participants will be collected in order to allocate them 1:1 Group A and Group B into two groups. The therapist will be allocating and enrolling the patients and the same therapist will be assigning the participants in both the groups. Group A will receive diaphragmatic stretching in addition to conventional chest physiotherapy exercises, while Group B will receive conventional chest physiotherapy exercises alone. Both groups will contain patients. The intervention will take place over the course of two weeks, once a day for six days a week, or six sessions a week.8 The before and after intervention measures will be examined both before and after the intervention begins.\n\nStudy design: Randomized controlled trial.\n\nStudy setting: Acharya Vinoba Bhave Rural Hospital’s OPD for respiratory medicine in Sawangi, Wardha, will be the study’s site.\n\nTargeted population: COPD patients in the age group of 35-65 years.\n\nSampling technique: Simple Random Sampling Technique\n\nAllocation: Sequentially numbered opaque sealed envelope (SNOSE) technique\n\nSample size:\n\nFormula for calculating sample size based on mean difference\n\nPrimary Variable (thoracic excursion)\n\nMean ± SD (Before) result on thoracic excursion for conventional chest therapy (Control group) = 0.9111 ± 0.1833\n\nMean ± SD (After) result on thoracic excursion for conventional chest therapy (Control group) = 1.0444 ± 0.1667\n\nDifference = 0.1333± 0.175 (As per ref. article)\n\nAccording to the reference articles.\n\nTotal number of samples required per group = 22\n\nTaking 30% dropout into account = 7\n\nThe total sample size required per group is 29.\n\nNotations:\n\nRef Article: Comparison of Intercostal Stretch Technique Versus Diaphragmatic Breathing on Dyspnea, Chest Expansion And Functional Capacity in Stable COPD.10\n\n\nDuration: 1 year\n\nEvery outcome variable result will be shown in tables and explained using descriptive statistics. Thoracic excursion and pulmonary function test mean and standard deviation (SD) will be quantitatively assessed as the first test’s outcome variables. The interquartile range (IQR) and skewed distributions will be calculated using positional average (Median) statistics. Every binary and categorical variable must be stated in terms of frequency and percentages for the purpose of the qualitative evaluation. The entire statistical evaluation of findings will be computed using the free R software version 4.3.2. At the 5% level of significance (p 0.05), the inferential statistics used for evaluating the significant difference over the outcome variables will be examined.\n\nPrimary Variable: In order to compare two groups receiving intervention at the 5% level of significance (P ≤ 0.05), we will do a baseline to endline assessment.\n\nTo ascertain the significance of the mean, the intra-difference in measurement between the before and after analysis outcome variables will be evaluated using the paired t-test. Conversely, when comparing two groups, unpaired t-tests are employed to assess intergroup differences.\n\nWe will recruit a different non-parametric test (the Chi-square, Mann Whitney, or Wilcoxon test) if the data shows signs of remaining non-normally distributed. If the quantitative evaluation findings show a non-normal distribution across the sample, the mathematical technique will be used to convert the data for the outcome variables for testing normalcy into a normal distribution.\n\n\nDiscussion\n\nChronic obstructive pulmonary disease (COPD) is defined by an abnormality of the alveoli (emphysema) and/or airways (bronchitis, bronchiolitis) that produces a continuous restriction of airflow that regularly worsens. COPD is characterized by chronic respiratory symptoms such as dyspnoea, coughing up mucus, and/or exacerbations. One of the main characteristics of COPD is restricted airflow, which frequently results in changes in lung capacity and limited thoracic movement. For those with this illness, diaphragmatic stretching therapy has shown promising results in terms of thoracic excursion and lung function. The major objective of this study is to assess the impact of diaphragmatic stretching on individuals with COPD, specifically in relation to enhanced thoracic excursion and lung function.\n\nBonnie E. Ronish et al. in their research reported that beyond FEV1, %predFEF25%-75% offers further insights into the manifestation of a disease and helps to link the anatomic pathology and deranged physiology of COPD.9\n\nDiaphragmatic stretching exercises can be incorporated into traditional physiotherapy to help patients with COPD improve their thoracic expansion and pulmonary function, as demonstrated by G. Swathi et al. (2021). The results of this study shed light on the most effective methods for managing COPD symptoms and, ultimately, improving patient outcomes.2\n\nA team of researchers looked into how senior population chest expansion and pulmonary function were affected by chest mobility exercises and respiratory muscle stretching in 2020. Fascinatingly, respiratory muscle stretching was found to be significantly more helpful than chest mobility exercises, even though FVC, FEV1, and chest expansion improved with both exercises.11\n\nIn a recent study, Anusree Sreejith and her colleagues assessed the efficacy of respiratory muscle stretches and chest mobility exercises for older adults. Group A stretched their respiratory muscles while Group B concentrated on thoracic mobility exercises over a two-week period. Stretching the respiratory muscles was more advantageous than chest mobility exercises for increasing chest expansion, FVC, and FEV1. In the elderly population, both forms of physical activity enhanced chest expansion and lung function.12\n\nA study by Do Sun Kwon et al concluded that careful monitoring should be done with COPD patients who present with low FEF25-75% values, even after having normal lung function.5\n\nA 2019 study by Aishwarya Nair and colleagues found that diaphragmatic excursion and chest expansion can be improved in COPD patients by using manual diaphragm release techniques and diaphragmatic stretch. Twenty patients took part in the trial, and they were split into two groups at random. Both methods were successful.4\n\nAccording to a study by Islam, Rofiqul et al. (2017), when combined with traditional physiotherapy, diaphragmatic and costal manipulations improve lung function, chest mobility, and total functional capacity in patients with chronic obstructive pulmonary disease (COPD).13\n\nA 2017 study by Dangi Ashwini et al. found that in people with stable COPD, diaphragmatic breathing and the intercostal stretch technique both improve chest expansion and functional capacity while reducing dyspnoea. The study concluded that there was no appreciable difference in the effectiveness of the two strategies.10\n\nStudies show that stretching the diaphragm, especially for people with COPD, can improve respiratory function. The act of ribcage extension and contraction improves thoracic excursion and mobility, enabling greater lung expansion and ventilation, and eventually improving respiratory function. Exercises that stretch the diaphragm can relieve tension, improve muscular coordination and strength, and improve breathing efficiency.\n\nDissemination: I’ve decided to present my study protocol at the last meeting.\n\nStudy status: Yet to be started.\n\nThe approval was obtained from the institutional ethics committee of Datta Meghe Institute of Higher Education and Research, Wardha with approval no. DMIHER (DU)/IEC/2023/1062, dated – 27/06/2023.\n\nAlso the trial was registered with Clinical Trial Registry of India with CTRI no – CTRI/2023/08/056408.\n\nCTRI registration date – 11/08/2023.\n\nWritten informed consent will be obtained from all study participants for participation in the study and publication of their data.",
"appendix": "Data availability statement\n\nNo data are associated with this article.\n\nSPIRIT CHECKLIST\n\nRepository name: figshare\n\nFile name: SPIRIT_Fillable-checklist-15-Aug-2013 14\n\nDOI: 10.6084/m9.figshare.24504256\n\nhttps://figshare.com/articles/journal_contribution/SPIRIT_Fillable-checklist-15-Aug-2013_doc/24504256\n\nLicence: CC by 4.0\n\n\nAcknowledgment\n\nMr. Laxmikant Umate and Mr. Manoj Patil were invaluable in developing my data analysis and determining the necessary sample size.\n\n\nReferences\n\nGlobal Initiative for Chronic Obstructive Lung Disease - GOLD: 2023 GOLD Report.[cited 2023 Mar 8]. Reference Source\n\nMpt G, Ashok C, Mpt C, et al.: Effectiveness of Diaphragmatic Stretching versus Rib Stretching on improving Pulmonary Function and Thoracic Excursion in Subjects with COPD.2021 Oct 1.\n\nPutt MT, Watson M, Seale H, et al.: Muscle stretching technique increases vital capacity and range of motion in patients with chronic obstructive pulmonary disease. Arch. Phys. Med. Rehabil. 2008 Jun; 89(6): 1103–1107. PubMed Abstract | Publisher Full Text\n\nNair A, Alaparthi GK, Krishnan S, et al.: Comparison of Diaphragmatic Stretch Technique and Manual Diaphragm Release Technique on Diaphragmatic Excursion in Chronic Obstructive Pulmonary Disease: A Randomized Crossover Trial. Pulm. Med. 2019 Jan 3; 2019: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKwon DS, Choi YJ, Kim TH, et al.: FEF25-75% Values in Patients with Normal Lung Function Can Predict the Development of Chronic Obstructive Pulmonary Disease. Int. J. Chron. Obstruct. Pulmon. Dis. 2020 Nov 12; 15: 2913–2921. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEndrian M, Noviati E, Trisnawati Y, et al.: The Effect of Pursed Lips Breathing Technique on Increasing Peak Expiratory Flow Rate (PEFR) in Medium Classification of Chronic Obstructive Pulmonary Disease Patients. J. Phys. Conf. Ser. 2019 Jul 1; 1179(1): 012148. Publisher Full Text\n\nBockenhauer SE, Chen H, Julliard KN, et al.: Measuring thoracic excursion: reliability of the cloth tape measure technique. J. Am. Osteopath. Assoc. 2007 May; 107(5): 191–196. PubMed Abstract\n\nGonzález-Álvarez FJ, Valenza MC, Cabrera-Martos I, et al.: Effects of a diaphragm stretching technique on pulmonary function in healthy participants: A randomized-controlled trial. Int. J. Osteopath. Med. 2015 Mar 1; 18(1): 5–12. Publisher Full Text\n\nRonish BE, Couper DJ, Barjaktarevic IZ, et al.: Forced Expiratory Flow at 25%-75% Links COPD Physiology to Emphysema and Disease Severity in the SPIROMICS Cohort. Chronic Obstr. Pulm. Dis. 2022; 9(2): 111–121. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAshwini D, Bhagyashri S, Medha D: Comparison of Intercostal Stretch Technique Versus Diaphragmatic Breathing on Dyspnoea, Chest Expansion And Functional Capacity in Stable Copd.2017; 7(5).\n\nRehman A, Ganai J, Aggarwal R, et al.: Effect of Passive Stretching of Respiratory Muscles on Chest Expansion and 6-Minute Walk Distance in COPD Patients. Int. J. Environ. Res. Public Health. 2020 Jan; 17(18): 6480. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSreejith A: Effectiveness of Respiratory Muscle Stretch and Chest Mobility Exercise on Pulmonary Function and Chest Expansion in Elderly Population.2020; 11: 2.\n\nIslam R: EFFECTIVENESS OF DIAPHRAGMATIC MANIPULATION ALONG WITH CONVENTIONAL PHYSIOTHERAPY FOR PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD).2017.\n\nChilhate P, Dr Lalwani L , Vardhan V: SPIRIT_Fillable-checklist-15-Aug-2013.doc. 125952 Bytes.2023. Publisher Full Text"
}
|
[
{
"id": "266535",
"date": "06 May 2024",
"name": "Eirini Grammatopoulou",
"expertise": [
"Reviewer Expertise My research area is Physiotherapy for Asthma and CORD"
],
"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\nIt is a well written manuscript. There are some minor comments mentioned below. - The abstract is complete but the last sentence is confusing. Usually, authors conclude with the aim of the study, which in this case is \"To compare the effectiveness of diaphragmatic stretch technique along with conventional chest physiotherapy to conventional chest physiotherapy on thoracic excursion, and pulmonary function in COPD patients\"\n\n- The introduction has the same problem, mentioned above. Please reword the last sentence as above. As for the objectives, in my opinion, there are two: a)To compare the effectiveness of diaphragmatic stretch technique along with conventional chest physiotherapy to conventional chest physiotherapy on thoracic excursion, and b)To compare the effectiveness of diaphragmatic stretch technique along with conventional chest physiotherapy to conventional chest physiotherapy on pulmonary function in COPD patients. - The study design is appropriate for the research question - The method has sufficient details - The datasets are clearly presented in a useable and accessible format. - The discussion section needs rewording: Last sentence, first paragraph: \"The major objective of this study is to compare the effectiveness of diaphragmatic stretch technique along with conventional chest physiotherapy to conventional chest physiotherapy on thoracic excursion, and pulmonary function in COPD patients.\"\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": []
},
{
"id": "312213",
"date": "28 Aug 2024",
"name": "Assem Khamis",
"expertise": [
"Reviewer Expertise Research methodology and biostatistics"
],
"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 investigates the potential impact of combining conventional physiotherapy with diaphragmatic stretching techniques versus using conventional chest physiotherapy alone on thoracic excursion and pulmonary function in COPD patients. The background section identified a gap in the existing literature regarding this specific comparison and outlined how this trial will contribute to the body of evidence on COPD management. Major Comments:\nRandomization: It would be beneficial if the authors could provide more detailed information on the simple randomization technique they plan to employ. Blinding: Have the authors considered blinding patients, outcome assessors, investigators, and other healthcare staff involved in the trial to minimize bias during the application of different exercises and outcome assessments? Follow-up Time Points: Additional details about the follow-up time points after the conclusion of the two-week trial would be helpful (e.g., 3, 6, 9, or 12 months).\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/13-248
|
https://f1000research.com/articles/13-247/v1
|
04 Apr 24
|
{
"type": "Software Tool Article",
"title": "Empowering Innovation in Banking Insurance: Expert System for Information Management",
"authors": [
"José Rojas Serrano",
"Raúl Mora-Aguilar",
"Alex Pacheco-Pumaleque",
"Raúl Mora-Aguilar"
],
"abstract": "Background Nowadays, financial institutions face and solve challenges to optimise Information Management (IM), so the use of new technologies such as Expert Systems (ES) is indispensable. Therefore, the objective of this research is to implement an ES to improve IM in insurance companies.\n\nMethod In terms of approach, the agile methodology SCRUM was chosen, which consists of five phases: initiation, planning and estimation, implementation, review and retrospective, launch, and thus decision making and optimisation of the IM process. In addition, the following technologies were chosen: ASP.NET as programming language, HTML as markup language, SQL Server as database management and CSS for design and visual styling.\n\nResults The results also showed a significant increase of 35% in user service, accompanied by a significant improvement of 44% in report delivery. Finally, a significant improvement of 24% was observed following the implementation of the expert system. This streamlines processes, reduces waiting times, improves the user experience in real time and optimises the management of large volumes of data in the insurance company.\n\nConclusions The system demonstrated that this tool improves decision making, reduces errors in the issuing area and provides a user-friendly interface for information management.",
"keywords": [
"expert system",
"information management",
"management",
"dashboard",
"data"
],
"content": "Introduction\n\nOver the years, financial institutions have faced and solved challenges to optimise information management and improve overall performance.1 In such organisations, precise information management is required, accompanied by communication capable of dealing with new challenges, tasks and strategies.2 In this situation, the use of new technologies such as expert systems becomes essential; they are designed to simplify processes that a human expert would find complex. An expert system is a stand-alone program that simulates the actions of an expert in a particular field. They are developed because human experts find it difficult to explain the rules they use to make judgments in the field.3\n\nThey also simulate the reasoning process that experts use to solve certain problems. On the other hand, they can be used by non-experts to improve their problem-solving skills.4\n\nThus, expert systems aim at optimising information management, which is a set of processes and technologies that can control, organise, support and access the information lifecycle, i.e. facilitate the storage, acquisition, recording and dissemination of information. This means that information becomes a resource of great strategic importance that can be used to achieve goals, improve decision making and generate knowledge, particularly in different areas.1\n\nMost research has shown that the development of expert systems (ES) for information management (IM) has the potential to have a positive impact on efficiency, accuracy and precision. Expert systems are therefore very important to organisations as an effective means of managing management plans.5–7 According to the study carried out by,5 the effectiveness of Expert Systems was determined in the Information Technology Management System of the company Sion Global in Peru. They concluded that ES have the potential to be used by companies because they can control the quality of services throughout the process.5\n\nOn the other hand,6 want to understand the principles of expert systems and in turn provide the right communication and information for system development. As a result, they found that the tests performed coincided in correcting all the errors, so they were presented well and without any problems. In conclusion, they provide an opportunity to streamline processes and obtain accurate, timely and reliable information for future work, using technological tools to optimise time and resources.6\n\nOver time, expert systems have been proven to provide effective and proven support and automation for a wide range of business decision challenges.8–11 However, most ES are very complex and require a high level of technical expertise to develop and maintain, which can be a problem for companies that do not have the capacity to develop and maintain such systems.12\n\nHowever, there is a need for further and more comprehensive research that analyses and verifies the productivity of ES in information management processes. This research paper aims to fill this gap through an analysis of the incorporation of ES for Information Management (IM), focusing on the implementation and contribution to the improvement of IM within the insurance company.\n\nFurther research is essential to analyse and confirm the impact of this tool in the area of Information Management (IM) and real-time decision making. The demand for these systems is driven by the increasing complexity of financial information, the need to simplify access to data and the urgent need for a centralised and up-to-date database for comprehensive and effective support.\n\nThis study contributes to provide practical, updated and relevant information on the implementation of ES for Information Management; streamlining processes, reducing waiting times, improving the user experience in real time and optimising the handling of large amounts of data within the insurance company.\n\nIn this sense, the objective of this research is to implement an Expert System to Improve Information Management in order to improve the quality of user service, optimising time and resources Lima, 2023.\n\n\nMethods\n\nIn this section we provide a detailed description of the methods used in the development and operation of our software, which is designed to improve business decision making.\n\nThe expert system was developed on a laptop equipped with an Intel® Core™ i9-12900K processor, 16 (8P+8E) cores up to 5.2 GHz LGA1700 chipset, accompanied by 16GB of 3200 MHz DDR4 RAM and a 1TB SSD M.2 2280 PCIe Gen4x4 NVMe solid state disc. In addition, the following technologies were chosen: ASP.NET as the programming language, HTML as the markup language, SQL Server for database management and CSS for design and visual styling.\n\nIt was worked with an agile methodology, following the 5 phases into which this methodology is divided,13,14 as shown in Figure 1.\n\nIn this phase, a thorough analysis is carried out to identify the specific requirements of the expert system, including decision rules, knowledge logic and the specific needs of the end user. In close collaboration with domain experts and end users, the elements of the product backlog are prioritised according to their relevance and contribution to the value of the expert system. In addition, an overview of the product backlog was provided and the responsibilities of each member of the development team were clearly defined. This was done to streamline decision making. In addition, the charter was drawn up, covering the project objectives and expected results (Figure 2).\n\nThe development team, together with domain experts, selects specific tasks related to implementing rules, refining the knowledge base and improving the system logic. Clear and measurable objectives are defined for the sprint, taking into account the complexity of the tasks and ensuring that the objectives are achievable in the time allotted. In addition, all user stories were described in detail and then the project’s product backlog was created. This backlog contains a complete list of all the tasks to be performed during development, including: Frame Import, Product Management, Structure Management, Channel Management, Branch Management, Risk Management, Policy Type Management, Format Management and Report Export, in order to be visible to all team members and a fundamental part of the project planning.\n\nDuring the sprint, the team focuses on the effective implementation of new rules, knowledge integration and continuous improvement of the expert system logic. Active communication and continuous collaboration between developers, domain experts and end users is essential to ensure that the system evolves according to expectations. The structure of the expert system was also defined, including the server architecture with a master database and mirror replication. In addition, minutes were taken at the start of each phase, to-do lists were drawn up and sprints were planned. Figure 3 also shows the architectural design of the expert system, with a connection and permissions via Azure Active Directory and a connection to the company database, where it provides a holistic view of the system’s operation in relation to all the components involved. The tasks of database design, dashboard creation, prototype development and implementation were carried out, culminating in the final dashboard.\n\nA detailed review of the decisions made by the expert system during the sprint is carried out to assess their accuracy and effectiveness. User feedback is essential to adjust and improve the rules and logic of the system, ensuring effective alignment with end-user expectations. In addition, a thorough verification of the system was carried out by performing unit tests to identify possible errors in the code, as shown in Figure 4, which shows the code of the frame loading procedure that will be uploaded to the Integration Services catalogue. Acceptance testing was also carried out in conjunction with the customer to ensure that the application was approved. However, Figure 5 shows the database diagram, which visualises how the data and the relationships between them are structured in the storage system.\n\nThe team reflects on the results of the sprint, identifying what worked well and areas for improvement. Corrective actions are proposed to address any challenges identified, with the aim of optimising the process and continually improving the system’s ability to learn and adapt. In addition, as the sprints progressed, testing was conducted in the presence of end users, who were empowered to request adjustments to both functionality and interface if deemed appropriate. Figure 6 provides a visual representation of the software development process. At the end of the process, we were able to establish agreements and successfully complete testing, which allowed us to improve the efficiency of delivery times and the final minutes of each phase.\n\n\nUnique features\n\nThis software has unique attributes that distinguish it from other existing solutions:\n\n• Dedicated to the banking sector: Our system is designed specifically for banking and financial organisations, adapting to their specific workflows and requirements for efficient management.\n\n• Adaptive customisation: Users can easily customise workflows, asset classification, frame upload and export functions to suit their business needs, making it a versatile solution.\n\nBy detailing these unique methods and features, we provide a clear blueprint for the development and implementation of our software tool in the banking sector, increasing its replicability and usefulness.\n\n\nUse cases\n\nIn this section we present the results obtained in the qualifications in terms of achievement of learning objectives, level of understanding and ease of use; we also specify that the system data will be downloaded automatically once it has been located using the link found in the repository.15\n\nFigure 7, shows the “Administrator” user interface, which displays the Expert System dashboard, which provides a summarised and visually appealing view of key information related to the information management of a set of products, risks and formats. The features displayed on the dashboard are the following: a) Product chart, for a given period. b) Risk list chart, for a given period. c) Format chart, for a given period. d) Last period loaded per product, information per period.\n\nInput: Access to the Dashboard view.\n\nOutput: Report of loaded graphs and periods.\n\nFigure 8, illustrates the process of registering products (a), risks (b) and loading frames (c) for a new product. The first step is to search for the product by name, which is automatically completed by industry, type of insurance, channel, risk, type of structure and format. You then select whether the product should remain active or not. Then, in order to load the frame, it is necessary to select the product, the year and the month in order to store it in the list of frames, where data such as the date of operation, the full name, the type of document, the document, the payment frequency, the start of validity, the end of validity, the product, the premium, the insured value, the credit number, the type of credit and the active status are recorded. Finally, the user can validate the information to proceed with the data export process.\n\nInput: Access the products section, access the risk section, access the plot section.\n\nOutput: Report and list of frames.\n\nFigure 9, shows three filters, Product to select, Year and Month, to export the information from the CPE Voucher list of each record, as well as the data shown in Figure 9, such as the date of operation, type of identity document, identity document number, names, paternal surname, maternal surname, place of birth, premium, policy number, start of validity, end of coverage, product name and month. Finally, the user will be able to validate the information in order to continue with the data export procedure, in this way the user will receive all the visual information personalised and adapted to the voucher.\n\nInput: Access the SUNAT file export section.\n\nOutput: Report and list of vouchers.\n\nIn Figure 10, the user with the Administrator role has the ability to generate a variety of reports related to the export of data according to the type of format, either Supervised Company Voucher (CES) or Electronic Payment Voucher (CPE), using different selection criteria such as product, year and month. These reports can be exported to the platform in different formats, such as excel, csv, txt and xlxs, and are processed by deleting duplicates and homologation, after which they are sent to the user to be managed by the Superintendency of Banking and Insurance (SBS), Sunat and Banco Pichincha. In addition, the administrator can carry out the corresponding configurations and operations so that the user can validate the information.\n\nInput: Access the SUNAT file export section.\n\nOutput: Report and list of vouchers.\n\n\nDiscussion\n\nFigure 7, shows how the use of dashboards has a positive impact on the efficiency of the interface, facilitating visualisation by providing detailed information to improve decision making and optimise time. This resource provides a global view of key data, facilitating a deep and rapid understanding of the information, allowing analysis to have a significant impact. According to Refs. 16, 17, monitoring contributes significantly to achieving results, facilitating strategic decisions, identifying risks and promoting productivity improvements. These aspects are essential to ensure the competitiveness of a company. Moreover, this tool is known to be relevant in the financial sector, highlighting its importance in process improvement and informed decision making for information management. This finding is in line with previous research conducted by Ref. 18, which emphasises that dashboards are tools that allow the sharing and visualisation of important data of an entity, simplifying the development of decisions in data management. Not only do they facilitate the understanding of important information, but they also enable the sharing of relevant data and streamline critical decision making in financial and other sectors. Dashboards are therefore a valuable tool for improving information management by presenting data in a visual way. This feature allows them to make the most of data and play an essential role in decision making.19–21 In summary, these findings highlight the importance of dashboards as critical tools that positively impact efficiency, decision making and quality of user service, making them essential resources for technology and finance professionals involved in business intelligence and data analytics.\n\nThe results shown in Figure 8, demonstrate the system’s ability to capture products, risks, data loads, etc., and to take corrective action to maximise results before the end of the month. Previously, this information was processed manually, which took longer to generate data and had a higher probability of error. This system provides technology and finance professionals with fast, centralised access to information, simplifying the management of large volumes of data within the insurance company. This feature is critical to ensuring proper user support and effective decision making; in general, according to Refs. 22, 23 they also mention process improvement in their research by demonstrating that the lack of use of information technologies limits the generation and dissemination of information, directly affecting its quality. These findings highlight the importance and benefits of having an expert system for information management, with the aim of improving both user service and effective communication between technology and financial professionals. According to Ref. 24, it is highlighted how information technologies are associated with productive processes to increase labour productivity, becoming a transformative element. Similarly,25 describes how educational management processes are improved through the implementation of an expert system that contributes to improving management by automating processes and activities related to institutional planning and evaluation, streamlining the analysis of crucial information for decision-making.\n\nFigure 9, illustrates the importance of data reports in the management of financial information, which are useful for monitoring results and achieving objectives. These reports are generated from filters applied by the administrator in relation to user support, and provide comprehensive details of the support provided on a daily basis. These findings are consistent with the research of,26,27 which indicates that the lack of summary data results in increased query times and complicates analysis. By providing a complete view of actions taken, this tool improves communication and avoids duplication of effort. The implementation of expert systems in finance can have a positive impact on efficiency, team coordination and ultimately the quality of care provided. In addition,28,29 state that data-driven reporting in information systems is now essential in the financial sector as it brings significant benefits to decision making, such as improved access to and tracking of information, integration of records from different episodes of care, ongoing coordination and support in justifying financial decisions. These results highlight the importance of reporting in data analysis, and how it contributes significantly to improving user care and coordination between technical and financial professionals.\n\nThe results shown in Figure 10, demonstrate the support provided by an evolving report; this perspective, combined with the seasonal behaviour of the financial system, enables management to make effective decisions to monitor results and achieve objectives. In addition, exporting reports on an ad hoc basis allows access to this information from any device, allowing staff to focus on core business tasks in the field, avoiding time spent on operational tasks in the office; this is evidenced in studies by Refs. 30, 31, which highlight the lack of management information systems to support decision making in companies in the financial sector due to the absence of management indicators. Similarly,32 in his research, addresses the lack of importance given by companies to data analysis and how this practice has a negative impact on the development of their activities. Finally,33 analyses how banking institutions can improve their competitiveness by improving their internal processes through the incorporation of information technologies in decision-making.\n\n\nConclusions\n\nThis study successfully developed and implemented an expert system for information management in an insurance company, specifically in the area of life insurance underwriting. Previously, this company relied on manual records. Throughout this research, the challenge of modernising the process of data collection, security, peace of mind and customer protection was met and overcome in order to provide a more efficient customer service with a higher level of service.\n\nFirstly, a dashboard in an information management system is a valuable tool that can improve data management and the quality of customer service by providing relevant information in an accessible and efficient manner. We have also seen a significant reduction in user errors and increased security in information management. In addition, an expert reporting system has significant benefits for financial staff, saving them time by providing detailed and structured information in a short period of time, making their job easier.\n\nUltimately, it can be seen that after the implementation of the expert system, information management has improved significantly, service times have been optimised and user satisfaction has increased, resulting in a significant improvement in the handling of information management.",
"appendix": "Data availability\n\nZenodo: jrojasse/SISENC: Expert System, https://doi.org/10.5281/zenodo.10674591. 34\n\nThis project contains the following underlying data:\n\n• indicadores-datos.xlsx\n\n• resultados-estadisticos.docx\n\n• SISENC.bak\n\n• SISENC.rar\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 would like to thank the issuing department of Crecer Seguros for their strong support of this study, as well as Engineer Alex Pacheco of the Faculty of Engineering and Architecture of the Universidad Cesar Vallejo, who provided valuable methodological guidance in the development of this research.\n\n\nReferences\n\nBarzaga O, Vélez H, Névarez J, et al.; Information management and decision making in educational organisations. redalyc; 2019; p. 11. Accessed: Jun. 29, 2023.\n\nDimas A: Systematic Literature Review Of Expert System, Fuzzy Logic And Artificial Neural Network Applications. Universidad Islam Indonesia; 2019. Accessed: Jun. 22, 2023.\n\nInusah F, Missah YM, Najim U, et al.: Integrating expert system in managing basic education: A survey in Ghana. International Journal of Information Management Data Insights. Apr. 2023; 3(1): 100166. Publisher Full Text\n\nRojas R, Torres S, Anchicoque A: Information management software: a proposal to counteract one of the causes of the problem of judicial congestion in Colombia. Dictamen libre. 2022; 30: 69–84. Publisher Full Text\n\nFlores D, Melgarejo V: Expert system for the SGTI in the company Sion Global Solutions. INNOVA Research Journal. 2020; 5(3.2): 235–248. Publisher Full Text\n\nLévano J, Altamirano E: Design and implementation of an expert system to optimise pest and disease control in grape cultivation. Ñawparisun - Journal of Scientific Research. 2020; 3(1).\n\nCárdenas J, Cabrera J, García J: Development Of An Expert Model Based On Fuzzy Logic For Information Technology Management. MQRInvestigar. 2022; 6(3): 496–523. Publisher Full Text\n\nStraub J: Expert system gradient descent style training: Development of a defensible artificial intelligence technique. Knowledge-Based Systems. 2021; 228: 107275. Publisher Full Text\n\nAhmadi M, Qaisari M: A review of using object-orientation properties of C++ for designing expert system in strategic planning. Computer Science Review. Aug. 2020; 37: 100282. Publisher Full Text\n\nRzepka R, Shirafuji D, Obayashi A: Limits and Challenges of Embedding-based Question Answering in Export Control Expert System. Procedia Computer Science. Jan. 2021; 192: 2709–2719. Publisher Full Text\n\nLiu B, Vu-Bac N, Zhuang X, et al.: Al-DeMat: A web-based expert system platform for computationally expensive models in materials design. Advances in Engineering Software. Feb. 2023; 176: 103398. Publisher Full Text\n\nChavez A: Implementation of an expert system with artificial intelligence for the management of computer incidences in the company Datarop Soporte Integral S.A.C., Undergraduate Thesis, Universidad Cesar Vallejo.2021. Accessed: May 16, 2023.\n\nSchwaber K, Sutherland J: The Scrum Guide.2020. Accessed: Oct. 06, 2023.\n\nBournissen M, Tumino C, Timkyw N: Scrum as a Methodological Tool for Learning to Program. Revista Iberoamericana de Tecnología en Educación y Educación en Tecnología. Oct. 2020; 26: e9–e9.\n\nRojas J, Mora R: Empowering Innovation in Banking Insurance: Expert System for Information Management.2023\n\nBecerra F, Del Río CA, Narváez C: Lessons learned from the implementation of a Management Information System designed at the University of Otavalo, Ecuador. e-Ciencias de la Información. Jan. 2021.\n\nGürkut C, Elçi A, Nat M: An enriched decision-making satisfaction model for student information management systems. International Journal of Information Management Data Insights. Nov. 2023; 3(2): 100195. Publisher Full Text\n\nGarcía A: Application of business intelligence and data analysis techniques in the Cuban business environment: challenges and prospects. Cuban Journal of Computer Science. 2020; 14(4): 191–209. Accessed: Oct. 27, 2023.\n\nCerda L, Castillo L, Barrientos N: How much progress has been made in providing analytics and business intelligence to smes? Investigación & Desarrollo. Jan. 2020; 19(2): 167–175. Reference Source\n\nPaz I, Coral M: Digital dashboard for monitoring indicators and goals of San Martín E.I.R.L. consultants’ projects. Scientific Journal of Systems and Informatics. Jan. 2021; 1(1): 24–36.\n\nBattistello L, Haug A, Suzic N, et al.: Implementation of product information management systems: Identifying the challenges of the scoping phase. Computers in Industry. Dec. 2021; 133: 103533. Publisher Full Text\n\nGonzález J, Salazar F, Raúl O, et al.: Strategic management: a tool for decision making in organisations. Journal of Interdisciplinary Studies in the Social Sciences. Jan. 2019; 21(1): 242–267. Publisher Full Text\n\nGodínez R: Disaster Risk Management through the Use of ICT: a Review. International Journal of Technology, Science and Society. Dec. 2021; 10(2): 213–237. Publisher Full Text\n\nRodríguez H: Information and communication technologies and economic growth. Economy Reports. Jul. 2017; 405: 30–45.\n\nInusah F, Missah YM, Najim U, et al.: Agile neural expert system for managing basic education. Intelligent Systems with Applications. Feb. 2023; 17: 200178. Publisher Full Text\n\nZhang H, Ren S, Li X, et al.: Developing scalable management information system with big financial data using data mart and mining architecture. Information Processing & Management. May 2023; 60(3): 103326. Publisher Full Text\n\nLuo J, Xu J, Aldosari O, et al.: Design and Implementation of an Efficient Electronic Bank Management Information System Based Data Warehouse and Data Mining Processing. Information Processing & Management. Nov. 2022; 59(6): 103086. Publisher Full Text\n\nRoeder J, Palmer M, Muntermann J: Data-driven decision-making in credit risk management: The information value of analyst reports. Decision Support Systems. Jul. 2022; 158: 113770. Publisher Full Text\n\nZhang H, Ren S, Li X, et al.: Developing scalable management information system with big financial data using data mart and mining architecture. Information Processing & Management. May 2023; 60(3): 103326. Publisher Full Text\n\nHübscher G, et al.: Graph-based managing and mining of processes and data in the domain of intellectual property. Information Systems. May 2022; 106: 101844. Publisher Full Text\n\nKouzari E, Sotiriadis L, Stamelos I: Enterprise information management systems development two cases of mining for process conformance. International Journal of Information Management Data Insights. Apr. 2023; 3(1): 100141. Publisher Full Text\n\nMa C, Sun Q, Xu M, et al.: Strategic selling agreement and information management under leakage in an e-commerce supply chain. Electronic Commerce Research and Applications. Sep. 2023; 61: 101288. Publisher Full Text\n\nZegarra L, Márquez H, León S, et al.: Use of digital channels of public-private sector banking institutions. Revista de Climatología. 2023; 23. Publisher Full Text\n\nRojas J, Mora R: Empowering Innovation in Banking Insurance: Expert System for Information Management. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "283401",
"date": "14 Aug 2024",
"name": "Gian Piero Zarri",
"expertise": [
"Reviewer Expertise Artificial Intelligence",
"Expertg Systems",
"IoT",
"Digital Twins",
"Semantic Web",
"Knowledge Representation",
"Computational Linguistics etc."
],
"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 presents an implemented software system for optimizing – by streamlining processes, reducing waiting times, improving the user experience in real time, improving the handling of large amounts of data, etc. – the Information Management procedures (the “business decision making”) proper to an insurance company, particularly in the area of life insurance underwriting. The system has been implemented on a laptop equipped with an Intel Core i9-12900K processor making use of ASP.NET as the programming language, HTML as the markup language, SQL Server for database management and CSS for design and visual styling. The development of the software has followed the usual phases (Initiation, Planning, Implementation etc.) of a standard “agile” methodology (SCRUM). In spite of the several figures introduced – see, in particular, Figure 5 that shows the database diagram, visualizing then how the data and the relationships between them are arranged in the storage system – relatively scarce significant details about the structure of the implemented system are supplied in the paper. For example, the diagram presenting the global architecture of the system (Fig. 3) is bad-structured and uninformative. Links to sites where it could be possible to find additional information about the “data and software availability” are supplied at the end of the paper. The paper includes also the description of what the Authors call “use cases” – in reality, particular features of the system like the dashboard (the Administrator’s interface) displaying information like the product chart or the risk list chart for a given period. Authors emphasize that dashboards are tools allowing the sharing and visualization of important data of an entity, simplifying the development of decisions in data management. According to them, the final evaluation of the “capacity” (usefulness, friendship etc.) of this system is positive – see, e.g., an increase of 35% in user service, of 44% in report delivery – even if no information has been supplied about the procedure employed, in case, to validate/justify these conclusions.\n\nWhat can strike an informed reader when examining this paper is that the presented system is repeatedly denoted by the Authors as an example of “Expert System”, cursorily defined as “… stand-alone programs that simulate the actions of an expert in a particular field” (page 3). This new sort of Expert System that should, moreover, represent the core of “new (?) technologies” to be used for optimising the information management techniques.\nIn reality, a simple look at the “Expert Systems (ESs)” page of Wikipedia (https://en.wikipedia.org/wiki/Expert_system) is sufficient to remind us that ESs – i.e., computer systems emulating the decision-making ability of a human expert – have made their first appearance in the 1970s and have then fully blossomed in the 1980s. Mainly implemented in the LISP language – sometimes in PROLOG – they were characterized by the use of a specific software architecture. This included a knowledge base of “facts”, represented as flat assertions about variables or by more structured “models of the world”, an inference engine, explanation and knowledge acquisition facilities, and a user interface. The inference engine was an automated reasoning system trying to match, according to “forward chaining” or “backward chaining” modalities and utilizing the so-called the RETE algorithm, the “rules” provided in a rule base with the “facts” contained in the knowledge base in order to evaluate the current state of this base and to make then decisions. Fundamental in this context was the use of “rules” and “inference engines”, totally ignored in the paper under consideration. Well-known examples of expert systems developed in the US are XCON, MYCIN and DENDRAL; in Europe, we can mention GESPI – an expert system for railway traffic planning in a large Parisian station, kept on use for a (relatively) long time, see https://www.sciencedirect.com/science/article/abs/pii/B9780080414386500096. In the early 1980s, the expert systems market had become definitely hypertrophied, with daily offers of new, more and more sophisticated, Expert Systems development “shells”. This fact, accompanied by a growing disillusionment in the business milieux caused by the discovery of all sort of Ess technical limitations – brittleness (i.e., ESs could make ugly mistakes when given unusual inputs), inability to explain their behavior, limitations to the use in very specific contexts, too expensive to maintain and update, unable to learn, etc. – led to the burst of the ES bubble, the failure of several AI company, the abandonment of a large number of ambitious programs, and the arrival of a new episode of the (periodical in fact) so-called “AI Winter”. Consequences have been really catastrophic for the whole ESs domain, with even the use of the label “Expert Systems” for books or scientific papers sometimes exposed to a rigorous taboo. In spite of all these serious (and less serious) problems, the Expert Systems discipline in its traditional form has serenely survived until now. An important AI scientific revue edited by Elsevier (impact factor 7.5) is titled “Expert Systems with Applications”; systems collected under the label of “business rules management systems” are nothing than modern version of the old ESs; “homemade” solutions developed on top of RETE-based rule engines like JESS or DROOLS which have their origin in the Expert Systems era are often used by the Semantic Web scholars to obviate the deficiencies of their hyper praised tools; etc.\n\nCould they add, then, a paragraph in their paper to show they are conscious of the long tradition of work covered by this specific label, and explain/justify in few words the differences of their approach with respect to the traditional one?\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\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? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-247
|
https://f1000research.com/articles/12-1240/v1
|
28 Sep 23
|
{
"type": "Opinion Article",
"title": "Motivation, inclusivity, and realism should drive data science education",
"authors": [
"Candace Savonen",
"Carrie Wright",
"Ava Hoffman",
"Elizabeth Humphries",
"Katherine Cox",
"Frederick Tan",
"Jeffrey Leek",
"Carrie Wright",
"Ava Hoffman",
"Elizabeth Humphries",
"Katherine Cox",
"Frederick Tan",
"Jeffrey Leek"
],
"abstract": "Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the individuals entering data science, but also increases the field's innovation and potential impact as a whole. Education is the most scalable solution to meet these needs, but many data science educators lack formal training in education. Our group has led education efforts for a variety of audiences: from professional scientists to high school students to lay audiences. These experiences have helped form our teaching philosophy which we have summarized into three main ideals: 1) motivation, 2) inclusivity, and 3) realism. To put these ideals better into practice, we also aim to iteratively update our teaching approaches and curriculum as we find ways to better reach these ideals. In this manuscript we discuss these ideals as well practical ideas for how to implement these philosophies in the classroom.",
"keywords": [
"education",
"data science",
"pedagogy",
"teaching",
"informatics"
],
"content": "Introduction\n\nData science is booming and many fields, including computational biology, have rapidly evolving data science needs.1,2 For these needs to be met, scalable education efforts need to be supported.3 Data science classes are often taught by practicing data scientists who have taken on a teaching role. This means they may have an idea of the changing landscape of data science but may lack experience in education. This phenomenon has been discussed in academia more generally, and it may be especially relevant to data science teaching.4–6 Data science experts can be very passionate about teaching the next generation, but educators also need training in education methods for writing curriculum, lecturing, creating assessments, constructing learning objectives, or the many other duties that accompany teaching roles.4,5\n\nTalent for data science careers is equally distributed, but opportunity for such careers is not.7–10 Educational barriers in STEM often begin as early as elementary school.11 However, access to education and resources as well as efforts to raise awareness have the potential to reverse this pattern.12 As a next step, helping empower educators in best practices can help make opportunities for data science careers more equitable. Data science educators must tailor their teaching methods to equip students with relevant skills, while also contextualizing the material based on the students’ interests and backgrounds.13 Furthermore, democratizing this knowledge to enhance more diverse representation in data-driven fields holds the potential to increase innovation14 while avoiding harms.15\n\nData science education programs have become increasingly popular. Organizations like The Carpentries and Dataquest, fast.ai, as well as massive open online courses (MOOCs) and formal Master’s programs and certificates in data science indicate the great demand for these materials.16–18 MOOCs, while helpful, tend to primarily benefit highly educated individuals.19 Students often need instructors who understand their needs and are willing to work with and build relationships with them. While data science instructors can access these excellent and inspiring training materials directly, educators are often in need of more guidance. For example, The Carpentries has an instructor training course that covers teaching approaches and skills that emphasize motivating, inclusive, and accessible practices.16 For implementation at the high school age level, the Introduction to Data Science curriculum from UCLA has materials for training teachers.20\n\nIn this opinion article, we combine advice from existing resources with our own education experiences for instructors who plan to take the next step in designing and implementing data science educational content. Our lab is involved in a number of data science education efforts, including training high school students, graduate students, postdocs, researchers, and university faculty, and these experiences have taught us a great deal about data science teaching that may be useful for others’ education efforts.9,21,22 We will discuss the overarching lessons we have learned as well as practical tips for how these lessons can be applied in the classroom. The deeper learning occurs when we apply or create using what we’ve learned.23 We encourage data science educators to use any advice from this discussion that best fits their classroom and audiences. We will also strive to better apply these ideals in our own teaching as we continue to learn. For summaries and lists of resources from this manuscript, see the Supplementary Materials section.\n\nThe lessons we have learned inform our teaching philosophy, summarized into these main ideals (See Figure 1).\n\n• Motivation: Aspiring data scientists face many demoralizing steep learning curves. As others have noted,16 motivation is key for learners to persist and succeed despite these challenging learning curves of data science.\n\n• Inclusivity: Diversity is lacking in data science education.24 Making data science more inclusive is not only the right thing to do, but improves innovation and understanding.14,25,26 Data science suffers when there is inequitable entry into the field.\n\n• Realism: The best learning approaches are those that attempt to prepare students for “real life” as much as possible.27 We strive to have our curriculum be hands-on and interactive in ways that reflect what our students will be doing as data scientists in their communities and outside the classroom.\n\n• Iteratively update: Students are not the only ones learning. Data science is a fast-changing field. Not only do we need to keep up with data science as a field to best prepare our students, but we also need to learn best teaching practices from education research.28\n\nA Venn diagram illustrating our teaching philosophy. Ideally, data science teaching should be motivating, inclusive and realistic. If any of these ideals are lacking, our teaching effectiveness suffers, which is why the fourth ideal includes iteratively updating our curriculum and approaches as we find better ways to meet these ideals.\n\nOur teaching philosophy depends on all these ideals together. As the diagram illustrates, when one ideal is lacking, our teaching is less effective. Without motivation, students will struggle to persevere through challenging material. Without realism, our students will not be adequately prepared for careers as data scientists. Inclusivity makes these ideals more democratic. Here, we will discuss practical implementation of motivating, realistic, and inclusive data science teaching.\n\nThe ideals and practical advice in this paper have come from our collected teaching experience in these various projects we will highlight.\n\nDataTrail is a 14-week paid educational initiative that promotes inclusivity in data science education for young adults, high school graduates, and GED recipients. We provide financial, social, and academic support, including weekly check- ins, tutoring, and internships for graduates. Our program goes beyond programming to prepare students for real-world situations. We continue to learn lessons about how our teaching has helped our students in their internships following graduation.22\n\nThe Genomic Data Science Community Network works to broaden participation in genomics research by supporting re- searchers, educators, and students from diverse institutions. These institutions include community colleges, Historically Black Colleges and Universities, Hispanic-Serving Institutions, and Tribal Colleges and Universities. Our vision is one where participation is not limited by an institution’s scientific clout, resources, geographic location, or infrastructure. These institutions play a critical role in educating underrepresented students.29 We work with and support faculty from these institutions as they address systemic bottlenecks.\n\nThe ITCR Training Network supports cancer research by equipping users and developers of cancer informatics tools with training opportunities. These audiences are professional learners with advanced degrees. They often have specific project goals that they are looking to apply data science skills to. We attempt to equip the users of cancer informatics tools with data science foundations they need. We also have other training opportunities for the developers of cancer informatics with skills and principles they can use to increase the usability of their data science tools.\n\nThe Open Case Studies project provides an archive of experiential data analysis guides that covers analyses using real- world data from start to finish.21 There are over 10 case studies that are currently focused on utilizing methods in R, statistics, data science, and public health to evaluate timely and relevant public health questions. These case studies are intended to be used by instructors to assist with teaching courses, as supplemental resources for courses, or as standalone resources for learners. They are aimed for undergraduate and graduate learners, but also have material appropriate for teaching high school students. The case studies help showcase the data science process and demonstrate the decisions involved.\n\n\nMotivation\n\nA common barrier for individuals entering data science is motivation30 to overcome the steep learning curves involved in becoming a data scientist – namely learning programming and statistics. For many students, having a computer print \"Hello world!\" isn’t enough to sustain their interest through the trial and error of background programming and statistics necessary for more inspiring data visualizations or interactive apps. Motivation is the fuel that is needed for successfully overcoming these learning curves.16 Budding potential data scientists need to be made aware that frustration, failure, and mistakes are normal and do not indicate that they are unsuited for the field!\n\nThe best motivation for data science is usually not a deep interest in programming or statistics, rather it is a data related question or problem that a budding data scientist cares about. This is why data science is such a broad and pervasive field. Data scientists may arise from a variety of different questions, problems and contexts. The best motivation for becoming a data scientist is to have a problem that has a quantitative question behind it.\n\nIt’s also worth noting that some students may never truly be interested in the programming side of data science as a career and that is also okay. It is also our goal to increase data literacy so that students who pursue other interests walk away with useful interdisciplinary skills.\n\nLearning data science is hard. This means learners tend to believe that they are “just not good at it\" and that this is a fixed intrinsic quality they possess. These beliefs can affect not only a student’s confidence but perhaps worse, a teacher’s behavior.31 We tend to attribute innate talent to one’s success instead of realizing that it is often due to dedication and practice.32 In some ways, learning to program is no different from learning a spoken or written language. Practice and mistakes build fluency. But many students become disheartened if they do not learn programming right away. Instead, we want to encourage a \"growth\" mindset.16,33 A growth mindset emphasizes that success is not about where you started, but the idea that you can continue to improve your skills if you continue practicing.\n\nThrough the DataTrail program, we have witnessed students become disheartened as data science skills become difficult to learn. To better encourage our students, we reorganized our curriculum to get to the \"fun\" things sooner. Previously, we didn’t teach data visualization until the last quarter of the course. We realized that making visuals is something students generally enjoy and can boost confidence. Students often learn best with utilizing different modalities (images and non-images for example).34 So now, we have students create visuals in the very first project (with some help of code we have pre-written for them). Not only has this helped motivate our students, but it has the added benefit of giving us more insight into what students are writing and trying with their code.\n\n\n\n• Get to the magic: Have your students see a glimpse of the \"magic\" early on. Images, plots and interactive pieces of code and apps are the most fun. You can use \"cooking show\" magic and provide your students with something 99% processed but then have them be able to customize or fill in the last bit of code.\n\n• Emphasize the \"yet\": Encourage a growth mindset by assuring the student that with practice and perseverance they will learn this even if they haven’t learned it \"yet\".16\n\n• Validate trickiness: Try to stay away from using phrases like “it’s easy”. Although you might be attempting to impart confidence, it may make students feel inadequate if they don’t also find it easy. Validating the challenges in data science can be reassuring and help renew a student’s confidence.\n\n• Assure togetherness: Sometimes frustration regarding a problem can feel lonely and impossible. Assuring the student that you are there to help can be a powerful learning tool.\n\n• Celebrate the wins: No matter how small the win, celebrate what your student has accomplished. This can mean congratulating them, but also may mean encouraging them to share their success with their peers.\n\n• Do not compare: Be careful not to compare your students’ skills with your own or with other students. Emphasize the idea that everyone has different starting points and aptitudes. What matters is not where you are today, but that everyone continues to learn.\n\n• Have madlibs code: By madlibs code, we mean code that is mostly written but has the student fill in the blanks. This allows the student to see the control they have over code without requiring them to write a whole project from scratch before they are ready to do so.\n\nFeeling a bit uncomfortable and making mistakes is an important part of learning. In fact, we remember better when we make mistakes.35 We also want everyone to feel comfortable with what they do not know. This starts with the instructor! It is incredibly valuable for a student to see how their instructor works through a problem or goes about finding a solution. It can be tempting to feel like you need to be a font of wisdom and it can feel like it undermines your authority if you let students see you struggle through a solution. However, it is just as important to model how to tackle the unknown as it is to demonstrate your knowledge and mastery. It can be very helpful to model the process it takes from not knowing something and making mistakes and iteratively figuring it out. Evidence shows that people who expect discomfort and challenge are more likely to overcome those challenges and perceive their accomplishment more positively.30\n\nIn the DataTrail program, before we begin to code, we attempt to help manage our students’ expectations about programming by discussing the role mistakes have in data science. We have a chapter about how to learn in data science with a strong emphasis that data science involves a lot of questions and failure and that is good!\n\n\n\n• Talk about mistakes you’ve made: It can be helpful if, as the educator you also tell of times you’ve made mistakes in your work. It can help students start to reverse the idea that mistakes should be hidden but instead that mistakes are normal! This is something that we’ve embraced from the Data Mishaps Night.36\n\n• Model making mistakes: Although you don’t need to purposely make mistakes in live coding, if you do see yourself starting to make a mistake, maybe don’t stop it right away. Try to let students catch your mistake instead of pointing it out to them. When they do point it out to you, be sure to be happy about the fact that as a team, you have caught the mistake.\n\n• Say \"I don’t know\": If a student asks a question that you are unsure of, say \"I don’t know\" proudly. Use this as an opportunity to demonstrate that not knowing something is expected. The class can also take the opportunity to look something up together. If the question is less relevant to the whole class, let the student know you will look into it and get back to them or you and the student can look into it together later.\n\n• Encourage iteration: Reaffirm the idea that drafts are okay. Blank pages are harder to work from than pages full of mistakes. Rather than striving for perfection on the first try, emphasize the idea that we can use version control and return to this code later to better polish it.\n\n• Normalize questions: Instead of “are there any questions?”, ask “what questions do people have?”. This small wording change can help lower the intimidation factor by implying questions are to be expected.\n\nFor people to learn, they need to feel comfortable. A great way to make people feel comfortable is by being more informal and showing it is okay to be silly. Our education group encourages using silliness as a teaching tool. Research shows that humor can increase motivation, learning, and perception of authentic teaching.37–39 Silliness defuses frustration and lowers our anxieties about a topic.30 We prioritize being silly over seeming important and solemn. Silliness is an atmosphere booster and can help educators seem more approachable. Being silly means: minimizing the use of jargon, making it okay to laugh at ourselves, and trying to connect with people. Being comfortable with yourself also makes you a good role model. Learners, particularly those who are underrepresented, benefit when they see their instructors are real people.40,41 Your own brand of in-class examples or metaphors are often the ones that stick with students the longest.\n\n\n\n• Study silly data: Data science doesn’t always have to be about life changing questions. Sometimes it can be a lot of fun to analyze datasets about movies, the best halloween candies, and bigfoot sightings.\n\n• Use GIFs and cartoons: Cartoons and GIFs can be mood boosters and can even make salient points that will stick with your students after class is over.\n\n• Use fun data examples: People like movies and pop culture. So long as the data is appropriate, it can be fun to use data examples that have material that people enjoy.\n\n• Use silly icebreakers: The more the classroom feels comfortable with each other, the more they will be ready to learn and participate. Let the class know it’s okay to be silly by asking a silly question.\n\n• Take snack breaks: Snack breaks or other kinds of breaks don’t need to be silly per se, but being silly during breaks are important to help people stay refreshed and ready to learn.\n\n\nInclusivity\n\nData science suffers from a lack of diverse perspectives. It is disproportionately white, upper class, and male; concen- trated in select geographical locations; harder to access by persons with disabilities; and challenging for first-generation students.42 Some of the largest biomedical data science institutions are located in areas with low income mobility8 and likely have contributed to lack of opportunities.43 However, income mobility can be mitigated by education.44 Inclusive and diverse research and science benefits individuals and is also more innovative.14 We therefore prioritize the promotion of Inclusion, Diversity, Anti-Racism, and Equity (IDARE) through our curriculum and in our classrooms. Everyone learns more and is more productive when we emphasize inclusive practices and continue to look for opportunities for learning and growth.45,46\n\nDespite increased awareness, large disparities in funding and support persist across primary and secondary education. These disparities have generally been at the expense of underrepresented groups such as students from Black and Indigenous communities. Primary schools with greater resources might be able to introduce data science at much earlier ages, enhancing students’ ability to pick it up and understand it.47,48 By contrast, students from under- resourced schools might have few opportunities to learn about data science. Students might also encounter barriers when gaining access to a computer and/or internet, securing childcare or time off work, and breaking into job networks (See Figure 2). These systemic disparities in education mean that learners from underrepresented groups may need more support.9\n\nThis figure represents the barriers that many members of underrepresented and underserved communities face when entering the field of data science. Some of the barriers to entering data science include knowing about data science as a career option, income security, access to an expensive computer, access to instruction, knowledge of the appropriate education programs, having connections to the industry and having the right jobs being posted, and knowing how to look for the appropriate job openings.\n\nIn user experience design, there is a saying that “you are not your user\".49 In data science education, we could just as easily say “you are not your student”. Help your students find their passion in data science realizing it might differ from yours. Students will be more motivated to persevere through the challenges of data science (such as learning programming syntax and troubleshooting confusing errors) if they are fueled by a curiosity or passion behind their data science project. Instructors should ask students about their interests and what they want to do with their career to encourage exploration that aligns with their interests9\n\nAlso realize that students from underrepresented backgrounds likely have talents that are unrecognized or unrewarded by our traditional educational systems. Students have diverse talents and likely have awareness of important problems that might be missed by instructors. Try to emphasize in the early stages of data education about how to bring these skills to the surface. Data science education needs to focus on more than just technical skillsets.\n\nIf you have been coding for some time, you have likely forgotten how frustrating it was for you when you first started. Not only should you have empathy for your students as they approach this steep learning curve, but you also should remember that your students may have very different experiences and backgrounds than yours. Be aware not everyone \"gets it\" in the same way you do. Going back through the material as if you are witnessing it for the first time with empathy for students who are completely unfamiliar and noticing what information you might take for granted as common knowledge can help. In addition, teaching a topic that you have just learned can also help.\n\n\n\n• Encourage or require office hours: Many students believe office hours are not relevant to them.50 Encourage your students to drop by and introduce themselves any time, not only when they are stuck.\n\n• Survey your students: In-class anonymous surveys can answer questions like \"why are you taking this class?\" and \"what career fields interest you?\", which can serve as a starting point for conversation.\n\n• Provide Mentorship: Young data scientists need support, particularly those from disadvantaged backgrounds. When possible, try to connect learners to supportive mentors who have time and understanding to devote to the learner. Ideally a mentor can be someone of a similar background to help encourage the learner through shared experience and understanding, but any form of mentorship is still beneficial.\n\n• Don’t require people to buy expensive things: Income insecurity can be a massive barrier to entry into the field of data science, but it doesn’t have to be. When possible, pursue cloud-based computing resources for your students to use.51 This will allow them to run more computationally costly analyses on nearly any machine, including relatively inexpensive computers like Chromebooks.8\n\nIn the DataTrail program, we attempt to mitigate many of these barriers. We provide individuals in the program with inexpensive Chromebooks that allow students to use cloud programming platforms to conduct their analyses. We pay individuals to participate in our program to help mitigate the issue of income insecurity. We also have partnered with non-profit hiring partners to place graduates of the program in internships. Even with our program’s social and financial supports, it is difficult for individuals to overcome the institutional and systemic biases that have been rooted in our society, but we hope that these supports give improved access to the individuals in our program. We encourage other data science program administrators and instructors to attempt to add financial and social support for underrepresented individuals whenever possible.\n\n\n\n• Frequently take the temperature of the room: Silence and pauses may feel awkward, but they are critical to good teaching. Allow students to have time to think. Another useful tool is using sticky notes to keep track of whether students who are actively coding need help or are doing okay. People who are doing well can put up a green post it, while people who need help with something can put up a different color post-it.16 Try to create an atmosphere that helps to decrease the intimidation factor of asking questions. Additionally, tools like Slido can help you collect interactive responses from your students from their smartphones or computers.52\n\n• Explain things in multiple different ways: Perhaps you understand things well using a particular analogy. But that analogy may not resonate with all your students. Try to think outside of the box and explain things in multiple different ways.\n\n• Do not assume everyone knows the basics: Err on the side of explaining the most fundamental piece of knowl- edge. Less experienced students will be less likely to get lost when the curriculum advances, but more experienced students may overestimate how well they know something. Everyone benefits from starting off on the same page with the basics.\n\n• Use inclusive language: Refer to guidelines for creating inclusive communities.53 Educators can unknowingly use phrases that reinforce stereotypes or perpetuate gaps in the STEM fields.16 This also means that as an educator you should always be ready to be corrected and change course should a student share with you how they could be better accommodated.\n\n• Look for ways to improve the accessibility of your classroom: This includes simple things like making sure your curriculum can be read by a screen reader and testing your curriculum for color vision compatibility with tools like ColorOracle.54 See our Supplemental information for a longer list of accessibility items to consider.\n\n• Be aware of implicit biases and stereotype threat: Though behaviors with implicit bias are unintentional, they can be very harmful all the same.55 See our Supplemental information for resources and classes to take to combat implicit bias, stereotype threat and related issues.\n\n\nRealism\n\nAs educators, a key goal is to prepare students to pursue their interests in their chosen careers. We do learners a disser- vice if we do not adequately teach them the skills they will need. Instructors must take note of the data science needs, whether within large companies or smaller community non-profits, and teach those skills. This includes collaborative \"soft\" skills, like giving/receiving feedback and code review. This also means using real data and real workflows21 as well as incorporating data ethics and domain specific contexts.56\n\nBeing realistic also means utilizing the ideas of \"just in time teaching.\".57 We want to bring the concepts we discuss into real life scenarios as quickly as possible. Anyone who has been taught a complicated board game has felt the importance of just in time teaching. It is often overwhelming to be told a long list of rules and concepts that mean nothing to you before you have even begun to apply anything. Similarly, it is highly stressful to be told to remember things and “it will make sense later.” A more effective teaching tool to tell your students something and then directly apply it in an activity. Not only does this better align with a deeper level of application on the Bloom’s taxonomy educational objectives, it also avoids oversaturation.23 Application and practice are key.\n\nPractically, this means introducing a concept and following up quickly with live coding, concluding with hands-on practice by the learners themselves. Live coding is more useful than long lectures about concepts and helps ease learners into trying the code themselves.58 Perhaps the most useful bit of live coding is when you employ strategies discussed or accidentally write errors yourself!59 If you make an error while live coding, it allows students to see that everyone’s mistakes and provides an opportunity to demonstrate how you might go about investigating an error.\n\nProviding concepts using a variety of real datasets and asking real data science questions relating to a diversity of learners can also be extremely motivating and helpful for students, especially when they try applying what they learned to other contexts.60 Not all applications of teaching in “context” are useful. We have found that this needs to be done in a careful manner that does not overwhelm the learners as well as with intention to describe the data analysis process. Focusing on simple examples with fewer datasets helps to first introduce topics, particularly for beginners. This can be followed up with more examples and discussion of when certain methods need to be used for different types of data and analyses.\n\nSoft skills like communication are critical but often overlooked in curricula. Students may need explicit training in areas such as asking questions about a project, giving effective presentations, writing professional emails, providing feedback to colleagues, or participating in meetings. In earlier iterations of DataTrail we did not emphasize these skills as we did not realize how much training our decades of professional experience had given us. We now include a unit on communication (both formal and informal) and a unit on career development as part of the DataTrail curriculum, and we continue to refine our approach.\n\nAdditionally, we realized that we need to have our students learn in a project-based manner that better reflects \"real life\" data. We restructured our curriculum to have more projects earlier so that the whole curriculum parallels the steps that are taken in a \"typical\" data science workflow. Our projects start out heavily scaffolded, with a lot of the necessary code for a project written in so students only have to fill in minor steps, but with each chapter we leave more and more of the data science process to the students to determine for themselves (See Figure 3).\n\nOur DataTrail curriculum is now structured to reflect the typical steps performed in a data analysis. Our earliest chapters cover how to form a data science question, and then the following chapters take the students through how to get data, clean data, create visualizations, collect statistics, and share those results.\n\nData science is best done as a part of a team. It involves being relatively skilled at many different fields: computer science, statistics, writing, web design, programming, etc. Likely one person will not be an expert at all these things, which is why teamwork is vital to good data science. Help your students realize that there’s no such thing as a \"lone genius\". In real life teamwork not only helps us all learn, it also creates better end products.61 Increasing the diversity of data science teams can increase the diversity of perspectives and potential solutions!\n\n\n\n• Use pair programming: Have designated time to have students practice paired programming. Or have optional or required time that students can pair programs with you or other tutors.\n\n• Cover code review: Explicitly cover techniques for how to conduct formal code review and why it is important.62,63\n\n• Highlight coding communities: Introduce your students to online or in-person coding communities such as R-Ladies, StackOverflow, etc.64\n\nData science projects can be quite varied and decisions can be stressful. Being flexibly prescriptive means giving specific instructions and making choices for them now, while preparing students for deviating from these choices later depending on what their project calls for. In practice, this means showing students one way to do something while letting them know about the existence of other relevant ways to do it that they may encounter. Data science, and code in particular, can have unlimited numbers of solutions to reach the same endpoint. Ultimately, some decisions are made based on what is comfortable to the data scientists working on the project, while other decisions may be based on what the project calls for. Instructors should give students something to start with but also acknowledge that they might use different methods in the future and that is okay.\n\n\n\n• Be aware of the stage of your audience: What concepts do your students understand well? What concepts overwhelm them? If you are at an early stage of the process where students are attempting to grapple with a lot of information at once, do not bring up alternatives.\n\n• Acknowledge the existence of alternatives If learners are likely to encounter common alternatives for particular methods in the real world, be upfront about this. This does not mean that learners necessarily need to dive into these alternatives, but simply noting the names of such methods can enable learners to recognize them in the future.\n\n• Many solutions to the same endpoint: Reinforce the idea that there may be a multitude of ways in code to reach the same endpoint. The priorities should be that the code works and is relatively readable. This can tie in well with practicing code review, which lets them see and evaluate approaches taken by others.\n\nIt is often more difficult to figure out what to skip in the curriculum as opposed to what to discuss. The best lessons are based on well-structured learning objectives with relatively narrow scope. It is often better for students to walk away understanding a few things well, rather than many things shallowly or not at all. As an enthusiastic teacher who is very knowledgeable, you may have an impulse to teach everything to your students all at once. As scientists, many of us feel an impulse to say “well actually” or “technically” and give more nuance than is needed at a particular stage. It is the educator’s job to curb these impulses and try to remain as simple and focused as possible. For example, it is incorrect to say that Docker is a virtual machine, but when explaining what Docker is, it can be helpful to explain it as \"a computer that you run on your computer to ensure the same specs as another person\". At a later point in time, when the student is ready, they might be able to replace this partially incorrect concept with a more nuanced one. Understanding nuance also means understanding what learners need or want to know and respecting that they are also busy with other things in their life.\n\nIn the DataTrail program, our original curriculum had a disproportionately deep level of coverage of statistical theory. We found that this did not match our students’ career goals or background knowledge and was overwhelming. We restructured our lessons about statistics away from high level theoretical concepts to instead be based in practical examples, focusing on how to make decisions about which tests to use and how to interpret results in plain language. Keeping it simple is also advice relative to the stage of your students. For example, in the DataTrail program, we initially keep it simple by introducing data science as a linear and step wise process. Later in the course, we expand on this to explain to our students that, the data science process is rarely linear and usually involves a lot of side investigations, dead ends, and sometimes starting from scratch entirely (See Figure 4).\n\nThis is an example image from our DataTrail course demonstrating how we sometimes use oversimplification as a tool in our curriculum. In the earlier chapters of the course, we tell students that the data science process is linear. In the latter half of the course, we add on to this concept by letting them know that actually, data science is rarely a stepwise, linear process, but instead a process that involves a number of side investigations that may or may not lead to dead ends.\n\n\n\n• Stop yourself: Interrogate why you might give a complex answer. Is it because you want people to know you are knowledgeable? Are you very enthusiastic about the material? Remember to focus on the learner. Too much nuance or focusing on exceptions to rules will likely be a disservice to their learning experience.\n\n• Chunk it out: In code outside of the classroom, you may try to reduce the number of lines and put similar steps together. However, in the classroom, it can be beneficial for you to break down each step separately. This may look like making one chunk of code into multiple separate steps that you walk through with the students. You should also explain and encourage students how to chunk out code for their own troubleshooting technique.\n\n• Keep it practical: You likely have a lot more information about a topic than you need to share. Ask yourself what practical information would your students need to know in a \"real world\" data science project? For many topics, they won’t need to know deep history or the ins and outs of each parameter of a function. We need to be selective about when history of something aids to understanding and when it does not.\n\n• Make it skimmable: You may notice we use lists and bold type in this paper to highlight main points. Respect that your students are busy and your class is not the only thing they have going on. What’s the most efficient way for you to communicate this (either in print or verbally)?\n\n• Link it out: If you have additional information for the particularly curious student, feel free to share it, but don’t make it central. Add links or a collapsible menu where students can find more information, but don’t use time in a lecture to cover it.\n\nSome of the best investigative data science starts off with a “that’s weird\". This concept applies to multiple scenarios. Science means chasing the \"why\" of an unexpected result. It may be the truth is weird, or there could be a mistake in the data handling. The only way to find out is to poke around at each step. Similarly, the best way to understand how code works is to take someone else’s code and change it. You will inevitably break the code, but as you break it, you will learn what each part of the code does. To find out how code works, investigate it piece by piece while examining the output of each part. Trying each piece of code interactively can help you build together what a longer line of code is actually doing.\n\n\n\n• Pause and think: Sometimes in an effort to complete a project quickly we can move too quickly and miss a critical clue in the data. Pauses are effective tools for thinking effectively about a project and what you are seeing.\n\nEncourage students that they do not have to answer questions right away. They can walk away, think about it for minutes or days and come back to it.\n\n• Show real examples: Real data have weirdness. Your curriculum should include an example of real data weird- ness and how someone found that weirdness. What functions were used? What aspects of the data were the first red flags that the person who did the data analysis followed? Tell the story about how we found out this weird thing about this real data.\n\n• Give them an investigative tool belt: Give your students a set of strategies they can use to investigate weirdness. What functions or tests can they use to interrogate a piece of data or weirdness in a package? Where can they go to find more information? Demonstrate Googling, StackOverflow, and package documentation as investigative tools.\n\n• Model investigative data science: In a live coding or pair programming session, encourage your students to look for abnormalities. Ask them questions about what they think about the results or what we might want to look out for. Model checking your data after each step.\n\n• Leave in the side journeys: Often, complete analyses involve several side explorations and dead ends. Although we often want to show a polished data science story, sometimes it can be beneficial to briefly demonstrate your development process and the side journeys it took to get there.\n\nThe most ground-breaking data science project is not worth anything if its results and importance cannot be communicated to others. While programming abilities are important, communication, documentation, and other professional skills are perhaps even more important – and unfortunately often harder to teach than programming. These skills have generally not been taught directly at educational institutions but historically have been passively learned through being in the workplace. But given that data science today is commonly remote work, it can be challenging for learners to build their communication and task management skills. These communication skills will be critical for learners’ success in the data science environment. Data science communication can be summarized by a few different aspects:\n\nSimple analyses with well communicated results are always better than overly complicated analyses that are poorly communicated. Data scientists translate numbers into stories that we can act on. Presenting results is just that – telling stories about the data science project journey. This also includes recognizing misleading visualizations and avoiding using them for communication. In code and results, we should be writing down our thoughts as we are developing analyses. For more about good documentation you can see our course.49 The example code that you use to teach should self-explanatory. Documentation must make sense to whoever will be using the code, whether this is the instructors, team members, or students themselves.\n\nCommunication in data science is also critical as a part of a team. Every data scientist gets stuck at some point and needs to ask someone else for help. Knowing when to keep working on something yourself, versus asking for help, is a critical soft skill for data science work.\n\n\n\n• Practice how to ask for help: Have students practice writing \"help\" posts and discuss the standard outline of what a call for help should have.64 StackOverflow and other online communities can be very helpful, but often this starts with a well-crafted post.\n\n• Be available: Always reiterate your availability (and truly be available too). When students do come to you with questions, try to be enthusiastic and supportive of them.\n\n• Automate questions: Set up systems that regularly ask your students what questions or problems they have. You can set up reminders for yourself or them.\n\n• Structured one-on-one sessions Set up structured one-on-one mentoring meetings. By structured, we mean use a document that your student fills out that asks them to answer: what are they working on? what is going well? what is not going so well? and so on.\n\n• Model good communication yourself: When live coding, add documentation and try to stick to a code style. Example code should be even more extraordinarily well documented. Emphasize stories where you have messed up code or been stuck and asked someone for help.\n\n• Low(er) stakes presentations: Have students practice presenting to their peers. Public speaking is notoriously scary, particularly if you are presenting on a new topic. The most effective way to make it less scary is to practice. Encourage your students to share their results regularly. When they do present, reaffirm that everyone is rooting for them and no one will interrogate them. Presentations by early professionals are the time to be supportive and enthusiastic, not critique the results or code.\n\n• Rubber ducking: Rubber ducking refers to the debugging code by explaining it aloud, even if no one is listening to your explanation. Encourage students to walk through their code on their own and translate it into \"normal speak\". This not only helps them troubleshoot, but also builds explanatory skills and deeper understanding of their code.\n\n\nIteratively update\n\nTo create education that is motivating, inclusive, and realistic, we need to continually update our curriculum and teaching approaches to better serve our students. To best prepare our students for practicing data science, we need to keep pace with the latest data science techniques and educational approaches. This means we should avoid viewing curriculum and teaching methods as set in stone. Instead, we should utilize systems that allow us to easily update and maintain our curriculum and teaching guides.65,66 Continuous improvement applies in a social context as well; students’ interests, career goals, and how they are feeling about the course material is an ongoing conversation.\n\n\n\n• Version control your curriculum: Not only should our data analyses be well tracked, documented and version controlled, but our curriculum should be too. Where possible, curriculum should be open source and on GitHub.65 Also consider using permissive licenses such as a Creative Commons licenses such as CC-BY which requires attribution but is otherwise open to repurpose and reuse.\n\n• Minimize maintenance pains: Create your curriculum in a way that minimizes the pain of maintenance. We use Open-source Tools for Training Resources (OTTR) to create our curriculum.65 We also utilize the exrcise package to automatically generate our exercise notebooks without solutions.67 See the Supplementary info for more resources for how to automate your curriculum maintenance.\n\n• Take notes: In each iteration of your class, take notes and debrief with your education team about strengths of your course and opportunities for improvement. You can easily track ideas and notes as issues in your GitHub repository.\n\n• Survey your students: Use short and focused surveys to take the temperature of the class. Note that some interpretation of surveys is needed. For example, if half your students feel the course speed is \"too fast\" and the other half feel that the course speed is \"too slow\", it may mean the course speed is just right.\n\nThe tips and philosophies that we have discussed here are quite general. There are many different contexts in which data science may be taught, and many different audiences. It is up to you as the educator to determine which of these ideas would be appropriate. To a certain extent, we also encourage you to experiment with tactics (you are a scientist, after all!) and see what works. Always ask your students how things are working for them. Please comment on this F1000 manuscript or leave us a GitHub issue on a related GitHub repository on one of our affiliated GitHub organizations: jhudsl and fhdsl.\n\n\nConclusion\n\nData scientists are in high demand in nearly every modern industry. There is also great potential for using data science in ways that benefit the public good.68 The insights and power of data science are exciting, so we feel that the teaching of these skills should be done with a matching level of excitement and with thoughtfulness about the implications of our work. Educational opportunities for learning these skills are not yet equitably distributed but have potential to scale to meet industry’s demands for data science. Not only will improving data science education techniques help meet the hiring demand, it will also help empower the lives of young people, researchers, and other students of data science. We have included many tools and resources to help you apply these ideals to your own teaching. We hope that this manuscript opens communication about ways to improve data science teaching approaches in ways that empower everyone in a more equitable manner. Equal opportunities for data science starts with equal opportunities for education.\n\nWe the authors will also continue to strive to apply these ideals in our teaching and expand them as we continue to learn. More useful resources for data science teaching are being made every day (see our affiliated GitHub organizations: jhudsl and fhdsl). We invite you to contact us, either through GitHub issues or email, if you know of resources that should be added to this list.\n\n\nResource guides\n\n\n\n• Summary page of practical tips This page includes all of the ideas and advice in this manuscript into one summarized page as a PDF Link.\n\n• Promoting IDARE resources This page includes links to recommended classes and resources for promoting IDARE principles in the classroom Link.\n\n• Curriculum tools This page includes tools and resources that are very useful for curriculum maintenance and creation Link.",
"appendix": "Data availability\n\nNo data is associated with this article.\n\n\nAcknowledgements\n\nWe would like to acknowledge all our colleagues that assisted us with the various projects mentioned who taught us more about teaching data science. We would also like to acknowledge the students we have taught, who continue to inspire us to be better educators and provided valuable and helpful feedback.\n\n\nReferences\n\nU.S. Bureau of Labor Statistics: Computer and information research scientists.2021. Reference Source\n\nPrzybyla M: Should You Become a Data Scientist in 2021?December 2020. Reference Source\n\nDeMasi O, Paxton A, Koy K: Ad hoc efforts for advancing data science education. PLOS Computational Biology. May 2020; 16(5): e1007695. 1553-7358. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFlaherty C: Required Pedagogy, 2023. 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Publisher Full Text\n\nWanzer MB, Frymier AB, Irwin J: An Explanation of the Relationship between Instructor Humor and Student Learning: Instructional Humor Processing Theory. Communication Education. January 2010; 59(1): 1–18. 0363-4523, 1479-5795. Publisher Full Text\n\nReupert A, Maybery D, Patrick K, et al.: The importance of being human: Instructors’ personal presence in distance programs. International Journal of Teaching and Learning in Higher Education. 21(1): 47–56, 2009. 1812-9129. Reference Source\n\nPacansky-Brock M, Smedshammer M, Vincent-Layton K: Humanizing online teaching to equitize higher education. Current Issues in Education. 2020; 21(2): 1–21. Publisher Full Text\n\nzippia: Data science demographics in the u.s.2023. Reference Source\n\nDawkins CJ: Bringing institutions into the opportunity hoarding debate. Housing Policy Debate. 2023; 33: 793–796. Publisher Full Text\n\nChetty R, Stepner M, Abraham S, et al.: The Association Between Income and Life Expectancy in the United States, 2001-2014. JAMA. April 2016; 315(16): 1750–1766. 0098-7484. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNOT-OD-20-031: Notice of NIH’s Interest in Diversity: 2023. Reference Source\n\nPuritty C, Strickland LR, Alia E, et al.: Without inclusion, diversity initiatives may not be enough. Science. September 2017; 357(6356): 1101–1102. 0036-8075, 1095-9203. Publisher Full Text\n\nMorgan PL, Farkas G, Hillemeier MM, et al.: Science Achievement Gaps Begin Very Early, Persist, and Are Largely Explained by Modifiable Factors. Educational Researcher. January 2016; 45(1): 18–35. 0013-189X, 1935-102X. Publisher Full Text\n\nLee VR, Wilkerson MH, Lanouette K: A Call for a Humanistic Stance Toward K–12 Data Sci- ence Education. Educational Researcher. 50(9): 664–672, December 2021. 0013-189X, 1935-102X. Publisher Full Text\n\nSavonen C: Documentation and Usability.2021. Reference Source\n\nAbdul-Wahab SA, Salem NM, Yetilmezsoy K, et al.: Students’ reluctance to attend office hours: Reasons and suggested solutions. Journal of Educational and Psychological Studies. 2019; 13(4): 715–732. Publisher Full Text\n\nKumar V, Sharma D: Cloud computing as a catalyst in stem education. International Journal of Information and Communication Technology Education. 2017; 13(2): 38–51. Publisher Full Text\n\nWebex: Slido2023. Reference Source\n\nLee C: What can i do today to create a more inclusive community in cs?2016. Reference Source\n\nColor oracle: 2018. Reference Source\n\nAmerican Psychological Association: Implicit bias.2023. Reference Source\n\nOliver JC, McNeil T: Undergraduate data science degrees emphasize computer science and statistics but fall short in ethics training and domain-specific context. PeerJ Computer Science. March 2021; 7: e441. 2376-5992. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNovak G: Just-in-time teaching: Blending active learning with web technology.1999. Reference Source\n\nNederbragt A, Harris RM, Hill AP, et al.: Ten quick tips for teaching with partic- ipatory live coding. PLOS Computational Biology. September 2020; 16(9): e1008090. 1553-7358. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShapiro J: Teaching with live coding in R and RStudio, 2022. Reference Source\n\nPodschuweit S, Bernholt S: Composition-Effects of Context-based Learning Opportunities on Students’ Un- derstanding of Energy. Research in Science Education. August 2018; 48(4): 717–752. 1573-1898. Publisher Full Text\n\nParker H: Opinionated analysis development. Technical Report e3210v1, PeerJ PreprintsAugust 2017. Reference Source\n\nResources for lab developers: 2022. Reference Source\n\nBacchelli A, Bird C: Expectations, outcomes, and challenges of modern code review. 2013 35th International Conference on Software Engineering (ICSE). May 2013; pages 712–721. 1558-1225. Publisher Full Text\n\nStackOverflow: How do I ask a good question?2023. Reference Source\n\nSavonen C, Wright C, Hoffman AM, et al.: Open- source Tools for Training Resources – OTTR. Journal of Statistics and Data Science Education. January 2023; 31(1): 57–65. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLau S, Eldridge J, Ellis S, et al.: The challenges of evolving technical courses at scale: Four case studies of updating large data science courses. Proceedings of the Ninth ACM Conference on Learning @ Scale, L@S’22, page 201–211, New York, NY, USA, 2022. Association for Computing Machinery. 9781450391580. Publisher Full Text\n\nShapiro J: exrcise.2019. 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}
|
[
{
"id": "214465",
"date": "27 Nov 2023",
"name": "Johanna Hardin",
"expertise": [
"Reviewer Expertise biostatistics",
"statistics and data science 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\nThe article provides direction for data science educators to teach more effectively. In particular, the authors speak to creating space so that all learners feel welcomed in and compelled to participate in the larger data science community. The authors suggest that the way to engage learners who have traditionally been kept out of data science is through motivation, inclusivity, and realism. While their work builds on scholarship that has already given very similar perspectives, the innovation is in the presentation of the direct suggestions, particularly the practical tips given within each section which are excellent.\nThe paper is well-presented and generally easy to engage with. However, I have a few suggestions that might make reading the paper slightly easier.\n1. I'm slightly confused about the background programs of the authors. What is the goal of communicating the projects? It seems like DataTrail is the main one referenced throughout the paper. Additionally, the authors say things like \"For more about good documentation you can see our course.49\" with no suggestion to the reader that you are referring to ITN. Further clarification on the links between the program and the ideas would be welcome.\n2. I might suggest adding \"Create a reproducible example\" (using reprex?) as another practical idea for imparting good communication skills.\n3. You say \"Our lab is involved in a number of data science education efforts, including training high school students, graduate students, postdocs\" ... is it really true that none of you have ever worked with undergraduates?\n4. You say \"Learning data science is hard. This means learners tend to believe that they are “just not good at it\" and that this is a fixed intrinsic quality they possess. These beliefs can affect not only a student’s confidence but perhaps worse, a teacher’s behavior.31\" But reference 31 is about gender stereotypes and whether students persist in STEM. I'm not sure it is about \"just not good at it\" or a teacher's behavior. I didn't check all of the references.\n5. There are a number of phrases with awkward wording:\nOur program goes beyond programming (pg 4) There are over 10 case studies that are currently focused on utilizing methods in R, statistics, data science, and public health to evaluate timely and relevant public health questions. (pg 4) involves a lot of questions and failure and that is good (pg6) We do learners a disser- vice (pg 9) The example code that you use to teach should self-explanatory. (pg 12) We would also like to acknowledge the students we have taught, who continue to inspire us to be better educators and provided valuable and helpful feedback. (pg 14)\n\n6. Of particular note is the 100+ times that the phrases this/these are used. I might suggest that the authors read through the manuscript and see if the language can be tightened up by removing their use. For example, \"formal Master’s programs and certificates in data science indicate the great demand for these materials...While data science instructors can access these excellent and inspiring training materials.\" What materials?\n7. The summary page of practical tips (very end, pg 14) says that the link will take the reader to a PDF, but it goes to a markdown file on GitHub.\n8. Is it important to call out computational biology in your first sentence? Why?\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": []
},
{
"id": "214470",
"date": "27 Nov 2023",
"name": "Karen Word",
"expertise": [
"Reviewer Expertise education",
"data science training",
"behavioral endocrinology",
"metabolic physiology"
],
"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-informed article, presenting opinions that are grounded in attentive experience and consistent with evidence for best practices in training. It is helpfully organized and persuasive. I have no doubt that it will be a useful resource for anyone engaged in data science training.\n\nI have several optional suggestions for improvement:\n1. The abstract cites 3 main ideals; the paper cites 4. I see no reason to omit iterative updating from the list in the abstract.\n2. The paper is nicely organized, with sections for each ideal, subheader topics relevant to each ideal, and \"Practical ideas\" for most of them. In some cases valuable examples are provided, illustrating how certain ideas have been applied in the authors' programs.\n\nThese examples are excellent and inspiring. Are there more of them? Consider featuring them more prominently e.g. in an \"applied examples\" section. \"ideas\" has an indefinite implication and isn't the word I would use. These seem to be solid, battle-tested recommendations. Maybe \"Practical suggestions\"?\n\n3. The concept of growth mindset and the power of \"yet\" are both better attributed to Carol Dweck, though possibly in different sources.\n\n4. Many items under inclusivity and realism explicitly relate to motivation. That's probably inevitable but it also stands out awkwardly - it might help to acknowledge that these ideals are often directly related.\n5. The \"model making mistakes\" bullet mentions \"live coding\" but I don't see a prior explanation of this term.\n6. In your ideas for being silly (wonderful!), you encourage using fun data examples. This is a good idea, but it is also a hazardous one, and I think that is worth a caveat that goes further than \"as long as the data is appropriate.\" Good data sets have to meet needs of simplicity, complexity, availability, and ethics. Data sets that some people find \"fun,\" in particular, may be upsetting for others (e.g. health or demographic data). Citing a resource on dataset selection may help here, or (better yet) you could expand on this issue separately under \"inclusivity\". (I'm sure there are other resources, but The Carpentries' lesson development training does have a section on this.)\n7. \"Frequently take the temperature of the room\" has a lot packed into it. Consider separating out one or two other bullets for emphasis on this vital topic? (And don't forget to account for color-blindness in post-it selection - green can be hard to find a good contrasting color for!)\n8. Under \"Realism\", the second paragraph mentions Bloom's taxonomy and \"oversaturation.\" Neither of these is discussed or defined elsewhere. I'd suggest either fleshing this out or removing the jargon.\n9. Also under \"Realism\": could some of the introductory content more usefully be a \"Practical ideas for making content relevant\" set of bullets?\n10. Under \"iteratively update\" - this seems to overlook a major obstacle to succeeding at maintenance, despite good intentions: failing to plan for it. Specifically, to reserve time, assign responsibility, and structure procedures for this important and ongoing work. Maybe worth a mention?\n\nA few notes on resources (Full disclosure: I work for The Carpentries; sharing ours only in case they are useful):\nThis paper cites an older version of The Carpentries Instructor Training Curriculum. That's fine, but if you'd like to point people at the most current version of this iteratively updated curriculum, the citation is attached (https://zenodo.org/records/5709383).\nGreg Wilson's book, Teaching Tech Together, is a separate but related resource that I would highly recommend exploring and citing.\nThe \"Curriculum Tools\" page you attach cites an outdated version of The Carpentries lesson template. We believe the newer Workbench infrastructure & documentation offers a much more robust and accessible platform for developing curriculum on GitHub.\n\nThe Carpentries' Toolkit of IDEAs publication may also be useful in your list of IDARE resources (https://zenodo.org/records/7041935).\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? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-1240
|
https://f1000research.com/articles/12-1201/v1
|
25 Sep 23
|
{
"type": "Research Article",
"title": "Towards successful aging classification using machine learning algorithms",
"authors": [
"Jesuloluwa Zaccheus",
"Victoria Atogwe",
"Ayodele Oyejide",
"Ayodeji Olalekan Salau",
"Jesuloluwa Zaccheus",
"Victoria Atogwe",
"Ayodele Oyejide"
],
"abstract": "Background: Aging is a significant risk factor for a majority of chronic diseases and impairments. Increased medical costs brought about by the increasing aging population in the world increases the strain on families and communities. A positive and qualitative perspective on aging is successful aging (SA). Successful aging refers to the state of being free from diseases or impairments that hinder normal functioning, as observed from a biological perspective. This differs from typical aging, which is associated with a gradual decrease in both physical and cognitive capacities as individuals grow older. Methods: In this study, the geriatric data acquired from the Afe Babalola University Multi-System Hospital, Ado-Ekiti was initially prepared, and three fundamental machine learning (ML) techniques such as artificial neural networks, support vector machines, and Naive Bayes—were then constructed using the data from a sample of 2000 individuals. The Rowe and Kahn Model determined that the dataset was SA based on factors such as the absence of fewer than or equivalent to two diseases, quality of life, nutrition, and capacity for everyday activities. Results: According to the experimental findings, the predictive network Artificial Neural Network (ANN) performed better than other models in predicting SA with 100% accuracy, 100% sensitivity, and 100% precision. Conclusions: The results show that ML techniques are useful in assisting social and health policymakers in their decisions on SA. The presented ANN-based method surpasses the other ML models when it comes to classifying people into SA and non-SA categories.",
"keywords": [
"Quality of Life",
"Aging",
"Machine Learning",
"ANN",
"Population"
],
"content": "Introduction\n\nThe World Health Organization (WHO) projects that by 2050, there will be nearly 1.6 billion older people in the world, or roughly 16% of the total population.1 We are currently experiencing significant sociodemographic and lifestyle changes, particularly in industrialized nations, where we are witnessing the shift from an aging to a super-aging population.2,3 Nigeria, the largest nation in Africa with a leading economy, has the 19th-highest percentage of the world’s elderly population, and it is expected that this percentage would almost treble over the next two decades.4 However, the rise of older Nigerians is taking place against a backdrop of utter poverty, unresolved development issues, socioeconomic disparity, and a loss in the traditional support and care of senior citizens.\n\nHuman life expectancy has increased globally due to advancements in medicine and social science, leading to the aging of populations becoming a problem for all nations.5,6 While the extension of life expectancy is a significant scientific achievement, it has also resulted in increased expenses for social welfare and care for the elderly.7 This demographic shift has not only influenced disease patterns and increased chronic illnesses worldwide but has also posed socioeconomic challenges for governments and families.8–10 In light of these developments, it is essential to consider the quality of life of the elderly and their preferences during this stage of life. Although everyone desires to live longer, it is more important for both individuals and society to focus on enhancing quality of life and reducing the burden of diseases in old age.11\n\nTo address the challenges associated with population aging, the concept of successful aging (SA) has emerged. SA recognizes that the aging process is unique to each individual and encompasses various aspects across disciplines.12,13 Although there is no formal definition for SA, it is widely accepted that it involves being free from chronic illnesses and having healthy physical and mental functioning.14,15 Rowe and Kahn proposed an operational hypothesis for SA, which consists of three components: active engagement in life, absence of illness or impairment, and optimal physical and cognitive functioning.16,17 This hypothesis is widely recognized in academic circles and emphasizes how elderly individuals adapt to the physical, spiritual, and social changes brought about by aging.18,19\n\nThe concept of SA has evolved from a single-dimensional focus on the presence of disease or functional decline to a multidimensional perspective aligned with the World Health Organization’s definition of health, encompassing physical, mental, social, and spiritual well-being.20 However, defining this complex and multidimensional phenomenon has proven challenging due to inherent ambiguity.21\n\nThe fact that non-genetic factors have a considerable impact on aging in addition to genetic influences is noteworthy.15 There haven’t been many long-term studies on SA, although prior research has usually concentrated on factors that affect SA.22,23 Because of the co-dependence and complexity of the factors impacting SA, traditional statistical models are inappropriate.24 Machine learning (ML) methods have been increasingly important in recent years for handling challenging, multidimensional, and nonlinear issues.25 As a result, it is possible to develop an intelligent model to forecast whether SA will exist or not.\n\nThe use of machine learning to forecast and identify social aspects of aging has been studied in some detail. For instance, the authors in Ref. 26 used a sample of 983 to train five fundamental ML models (ANN, DT, SVM, NB, and K-NN) using one ensemble technique. The outcome of the prediction was achieved by implementing a method known as majority voting, which relies on the collective decision of the developed base models. The authors attained 93% accuracy, 92% specificity, and 87% sensitivity. Authors in Ref. 27 created questionnaires and fitness tests to gather the necessary information from the elderly population. The models used were gradient boosting decision trees, random forests, deep learning, and logistic regression. In a study involving 890 samples, a deep learning model demonstrated superior performance compared to other models. The deep learning model achieved an accuracy of 89.3%, a positive predictive value of 85.8%, and a specificity of 93.1%. They came to the conclusion that the deep learning model is excellent for SA maintenance prediction. The use of machine learning approaches to successfully predict aging in the elderly was discussed in Ref. 28. For the analysis, the researchers looked at the SA and non-SA data of 975 elderly persons. The Chi-square test at P > 0.05 was used to determine the factors that had the greatest impact on the SA. In this study, several algorithms such as Adaptive Boost, Random Forest, Artificial Neural Network, Support Vector Machine, and Naive Bayes were employed to develop prediction models. The performance of these models was evaluated using various metrics. The sensitivity, which measures the ability to correctly identify positive cases, was found to be 91%. The specificity, indicating the ability to correctly identify negative cases, was determined to be 98%. The overall accuracy of the models was 95%. The F-test, which assesses the model’s overall performance, yielded a value of 90%. Additionally, the area under the curve (AUC) test, which measures the model’s ability to distinguish between positive and negative cases, resulted in a score of 88.4%. Based on these evaluations, it was concluded that the Random Forest algorithm exhibited the best performance in predicting SA in elderly individuals (presumably referring to a specific condition or event). The previous works, however, have some limitations, including: insufficient data for training the models, class imbalance in the dataset, technique used to replace missing values in the dataset, use of training ratios and hyper-parameter tuning to improve the model’s accuracy, and selection of significant aging-related features in the dataset. In order to get the optimal form of the raw data from the hospital’s electronic medical record, this study performed analysis on enough data while utilizing data preparation techniques and consultations from gerontologists. To increase the suggested system’s predictability, effective feature selection and dropout were also coupled, and classification was carried out using ANN. Therefore, in this study, three key ML models for SA prediction were created, described and evaluated. The main objective was to develop SA prediction models using geriatric data while taking into account sociodemographic, clinical, and lifestyle characteristics in the dataset, which are crucial factors for early SA prediction. In addition, the SA prediction models were used to further investigate key determinants ascertaining progression of the aging condition. The subsequent sections present and discuss the proposed SA prediction system’s development process, the results and conclusion.\n\n\nMethodology\n\nFigure 1 depicts the main steps of the proposed system architecture. Data pre-processing, feature selection, model construction, performance measurements, and successfully classifying aging are among the phases. The original dataset, which is unstructured and not beneficial for the design of the model, is created during the data pre-processing stage by sorting out variables from the electronic medical records of elderly patients. Additionally, feature selection was utilized to separate the features that are redundant from the features that support accurate prediction in the system and to extract the significant variables that are relevant to successful aging. Thirdly, Support Vector Machine, Naive Bayes, and Artificial Neural Network were among the prediction models developed for this study. During the developmental process, particular hyperparameters for the SVM and NB models were carefully selected. Thereafter, the preprocessed data, was inputted into the model, using it to train the classification model. A better learning pattern for predicting successful aging is provided by the ANN model in combination with a dropout strategy. The combined technique offers increased classification accuracy, specificity, and sensitivity when compared to the other models. ReLu and sigmoid activation functions are used in the network’s hidden and output layers during the training and testing phases, respectively. Initially, three core classification algorithms, namely artificial neural network (ANN), support vector machine (SVM), and naive Bayes (NB) models, underwent training with the purpose of identifying whether an individual possessed the status of SA or non-SA. Then, the best hyperparameters and training ratios are used to increase the models’ predictive accuracy.\n\nThe present study is retrospective and concentrates on sociodemographic, clinical, behavioral, and psychological parameters for the assessment of specific patients by accessing the medical records of older (> 60 years old) patients.29 There are multiple variables based on the preliminary data gathered. The machine learning model’s performance was validated while the most useful features from the gathered data were taken out and used as input parameters. Additionally, the factors linked to successful aging were determined through interactions with gerontology experts and analyses of relevant literature. The description of the output class variables (i.e., SA & Non-SA), are as follow: age, sex, reading proficiency, marital status, occupation, and income level are the seven parameters considered in this category of socio-demographic factors.\n\nThe clinical factors involve diseases including hypertension, heart disease, kidney, liver, bone, and muscular disorders as well as depression, eye and eyelid disorders, diabetes, and cancer.\n\nThe ability to carry out daily living activities (ADLs), life satisfaction, quality of life (QOL), a healthy lifestyle, interpersonal relationships, nutrition, physical activity, illness prevention strategies, and stress management are all included in the category of behavioral and psychosocial factors. The sociodemographic and clinical information was taken from medical records of elderly persons.\n\nThe outcome variable was split into SA-related (coded 1) and non-SA-related (coded 0) classes. Rowe and Khan’s approach,16 which consists of three fundamental elements such as maintaining good mental and physical function, ongoing involvement in life, and lack of disease and disease-related disability was used in this study to quantify SA.\n\nFor this study, 2000 older persons were included in the dataset that was taken from the Afe Babalola University Multi-System Hospital’s electronic medical record between January 2019 and April 2023 in Nigeria. The ethics research committee of the hospital granted access to conduct the study (Approval Number: AMSH/REC/AVA/133) with requirements of complying with all international guidelines and regulations. The data collected for this research was retrospective and did not involve interviews with participants. All data used in this research were anonymised and do not reveal the patient’s identity in any form. Several techniques for data pre-processing were employed to generate optimal models. The dataset employed in this study contained certain missing values. Excluding these instances from the dataset would diminish the overall quality of the data, as they could potentially possess vital information that could influence the accuracy of predictions. However, a range of methods exist to address the issue of missing values and rectify the dataset, one of which was employed to address the issue. The gaps created by the missing values were filled in using the mean value of the corresponding feature in the data set. Another problem with the data that had been acquired was data that was out of balance. An uneven data class distribution is when one class has a disproportionately smaller number of samples than the other. This decreases the effectiveness of ML algorithms.30 The dataset includes 2000 records of both successfully aged and unsuccessfully aged persons after pre-processing and balancing. Based on the absence of fewer than or equivalent to two diseases, quality of life, nutrition, and capacity for daily activities, the data was categorized as SA. Following classification of the full dataset, there were 1100 occurrences of SA and 900 instances of Non-SA.\n\nThe feature selection strategy was used to reduce the dataset dimension and enhance ML performance. Feature selection is a crucial technique in data mining that plays a significant role in eliminating redundant and irrelevant features. It holds immense importance as it helps filter out duplicate and unrelated features from the dataset. Through feature selection, statistical techniques are utilized to reduce the dataset dimension. In a summary, this method’s advantages include better comprehension, avoiding algorithm overfitting, boosting processing power, and enhancing mining performance.31,32 With the help of gerontologists and the identification of pertinent data that is relevant to the results of successful aging in the aged group, features for our model were sorted based on Rowe and Khan’s model for successful aging as well as their model for successful aging.\n\nAge, hypertension/CVD, renal illness, liver disease, neuromuscular disease, depression, eye disease, diabetes, cancer, ADLs, Nutrition Status, and quality of life (QOL) were the determinant variables that were most pertinent to SA. These characteristics were therefore thought to be the most important ones in defining SA in elderly people. The dataset has information like marital status, occupation, educational level, gender, and hospital department removed from it. This was done to increase the precision, sensitivity, and accuracy of all produced models. Figure 2 shows the correlation between selected features in the extracted dataset, and a maximum correlation is observed between renal disease and the ability to carry out daily activities.\n\nFigure 3 denotes the variables in the dataset including the feature name, feature type, and concept codes. In the dataset, NMD represents all categories of neuromuscular diseases, while QOL refers to the quality of life of each individual, and lastly ADLs represents the ability of aged people to carry out daily activities regularly.\n\nFor SA prediction, three supervised learning approaches were used. The elderly individuals were classified as either SAs or non-SAs using the ANN, Naïve Bayes, and Support Vector Machine algorithms.\n\nANN: An artificial neural network (ANN) is a technique in machine learning that emulates the natural information processing mechanisms of the human brain. Numerous processing units (neurons) make up the neural network’s structure, and they communicate with one another via weights. A nonlinear mechanism in the neural network enables parallel processing, learning, and decision-making. An ANN modifies its weighted connections by using a variety of learning cases. One of the process’s outcomes is to modify the network’s settings so that it can be retrained in a different environment.33\n\nNaïve Bayes: This algorithm’s characteristics are assumed to be unrelated to one another. It is the Bayesian theorem generalized. NB calculates the likelihood that a data sample belongs to a specific class as part of its process because it is a probabilistic model.34,35 NB is another name for independent or simple Bayes. The development of this technique is straightforward and does not necessitate difficult initial parameter estimates. As a result, it offers tremendous accuracy and speed when handling large datasets and can be applied to enormous amounts of data. However, this technique has problems with conditional class independence and access to data probabilities.36,37\n\nSupport Vector Machine: According to Zach,38 the Support Vector Machine (SVM) is a supervised learning technique utilized for classification and regression tasks. Its primary purpose is to identify the most effective classifier that can divide a given dataset into two distinct classes. When dealing with datasets that can be linearly separated, the SVM employs a linear function to determine a hyperplane that passes through the middle of the two classes. Notably, there exist multiple potential hyperplanes for separation in such cases. However, the SVM ensures the identification of an optimal function by maximizing the margin between the two classes. The margin, as described in Ref. 39, refers to the degree of separation between the classes, which is represented by the hyperplanes. In the field of machine learning, hyperparameters refer to the parameters used to regulate the learning process. They are predetermined values that are set before the model begins learning, with the aim of enhancing the learning outcomes. It is worth noting that not all hyperparameters carry equal significance. The effectiveness of the ML algorithm is more significantly impacted by some hyper-parameters than others. Table 1 lists the hyperparameters that we employed in our models.\n\nThe training and hyperparameters tuning processes are part of the classifier design process. The Support Vector Machine, Naive Bayes, and Artificial Neural Network are the classification models investigated. For all generated models, training was typically done on between 50% and 70% of the dataset. Table 1 lists the optimized hyperparameters used in various iterations of the Naive Bayes and Support Vector Machine models.\n\nInitially, epochs of 100 and 250 were utilized to train the ANN model; however, later in the experiment, a batch size of 32 and 500 epochs was used for adequate training. In order to find the best model configuration, we initially trained our models on a variety of train/test ratios (40/60, 50/50, 70/30, and 60/40). The 70/30 and 50/50 configurations produced the best accuracy with the least amount of over-fitting, and were thus presented in this study as the ideal model. The Adam optimizer was used to train the model, and network hyper-parameters like the number of hidden layers and activation function were modified as well. The ReLu activation was then used in all hidden layers, while the output layer for classification made use of a sigmoid activation function. To reduce over-fitting and improve the model’s accuracy, the dropout technique40 was applied. The proposed framework was created in Python using the Anaconda IDE and built-in modules including Scikit-Learn, Keras, Tensorflow, Numpy, and Matplotlib. All experimentation was carried out on a Dell Precision WorkStation Computer with 8GB RAM, 1TB HDD and a 3.3GHz Core i5 processor. The test dataset was used to assess the prediction performance of our model, and 20% of the test dataset was used for validation.\n\nIn this investigation, cross-validation was not employed. Since the dataset contains sufficient samples for both training and testing, the holdout validation technique was employed instead of the cross-validation method. Following the model’s training, the performance of the SVM, NB, and ANN models was assessed using the testing dataset. The most used metrics, including accuracy, precision, sensitivity, specificity, and F1 score, were utilized to assess performance. Accuracy is an indicator of the model’s classification or validation (training) accuracy. The number of true positives, true negatives, false positives, and false negatives can be estimated with the aid of a confusion matrix (Figure 4), which further assisted in evaluating the effectiveness of the suggested model. Table 2 provides the formulas needed to calculate the aforementioned measures.\n\nAccuracy: This measures the proportion of accurate predictions to all other predictions.\n\nPrecision: a metric employed to assess the accuracy of a model in predicting positive outcomes. It measures the number of cases in which the model correctly projected a positive outcome out of all the instances it predicted as positive. It simply quantifies the ratio of true positive predictions to all the positive predictions made by the model.\n\nSensitivity: It is a measurement of how accurately the model has identified the good examples. It is described as the proportion of genuine positive predictions to actual positives.\n\nSpecificity: It is used to gauge how many true negatives the model accurately detected.\n\nF1 score: It can be interpreted as the weighted harmonic mean of the precision and sensitivity.\n\nThe dataset is divided into four main groups in each of the experiments conducted in this work in order to employ the equations in Table 2: True Positive (TP), True Negative (TN), False Positive (FP), and False Negative (FN).\n\n\nResults and discussion\n\nThis section presents the findings that were drawn from the study. First, the findings from all experiments conducted on 50% of training are reported. The findings from experiments conducted on 70% of training are shown in the second section. The classification outcomes based on the actual information available are displayed in the confusion matrices. Each sample can belong to either of the two classes, 0 for unsuccessful aging or 1 for successful aging, as the dimensions of these matrices are 2*2, meaning there are two classes of data. The various performance measurements are defined in accordance with the results of the confusion matrix’s calculations. In order to comprehend how the datasets performed during the experiment utilizing the previously designed models, graphs and tables are also given and interpreted. Additionally, all three models’ performances are contrasted and critiqued.\n\nExperimental results on 50% of training\n\nIn this study, half the samples (1000 samples) were used for testing and the other half (1000 samples) for training. The confusion matrix in Figures 5, 6, and 7 were used to assess the ML algorithms (SVM, NB, and ANN). The confusion matrix was used to calculate the values of the performance measures. Figure 5 shows that the SVM model can accurately predict 550 cases of SA, whereas there were no cases of SA that were misdiagnosed. The model also properly predicted 183 non-SA cases while mispredicting 267 non-SA cases. The developed model yielded a 73.3% accuracy and a 67.3% specificity. Even though the SVM model had a sensitivity of 100%, it does not determine the total efficiency of the model when presented with unseen data in a large scale as it is evident in the F1 score (57.8%) of the said model. Figure 6 shows that the NB model can accurately predict 561 cases of SA, whereas there were no cases of SA that were misdiagnosed. Additionally, the model accurately forecasted 371 non-SA cases while mispredicting 68 non-SA cases. The generated model gave results with a precision of 84.5% and an accuracy of 93.2%. The NB model outperformed the SVM model by a large margin, and it is expected to be effective in forecasting successful aging in a fresh dataset. The confusion matrix for the ANN model on 50% of training, which correctly predicted 550 and 450 instances of SA and non-SA, respectively, is shown in Figure 7. With a 6.8% increase in accuracy, the ANN model with dropout fared better than the NB model.\n\nExperimental results on 70% of training\n\nFor this experiment, 70% of the samples (1400 samples) were assigned for training and 30% (600 samples) for testing. The confusion matrix is shown in Figures 8, 9, and 10 for the evaluation of the three machine learning methods (SVM, NB, and ANN). The confusion matrix was used to calculate the values of the performance measures. Figure 8 shows that the SVM model can accurately predict 330 SA instances, whereas there were no cases of SA that were misdiagnosed. Additionally, the model accurately forecasted 178 non-SA cases while mispredicting 92 non-SA cases. The SVM model that was designed generated accuracy and precision of 84.7% and 65.9%, respectively. Figure 9 shows that the NB model can accurately predict 332 SA instances, while there were zero cases of SA that were misdiagnosed. Additionally, the model accurately forecasted 224 non-SA cases while mispredicting 44 non-SA cases. The created model generated accuracy and precision of 92.7% and 83.6%, respectively. The NB model outperformed the SVM model by a large margin, and it is expected to be effective in forecasting successful aging in a fresh dataset. The confusion matrix of the ANN model, which was trained for 70% of the time, is shown in Figure 10, where 330 and 270 instances of SA and non-SA, respectively, were correctly predicted. With a percentage gain of 16.4%, the ANN model with dropout surpassed the NB model in terms of precision.\n\nFigure 11 shows the accuracy plot of the ANN model. Between 50 and 100 epochs, the train’s accuracy grew from 0.8 to 0.9. At 300 epochs, the validation accuracy was 0.92, and it grew from there. The reported average training accuracy was 100%. The graphic shows that the ANN model is not over-fitting, which suggests that the model can be used to successfully predict aging in the event of new data. Figure 12 shows the model’s training and validation losses. The loss function had reached its lowest after training, or 500 epochs, as seen in the graph. As supported by research, the ANN model’s low loss function has significance in providing accurate predictions on successful aging.\n\nThe performance results of all created ML models are displayed in Table 3. The number of individuals whose classifier has assigned them to a positive class (SA) and who are positive is calculated as part of the precision criterion. The proposed ANN model has the best performance by this criterion, whereas the SVM model is the least efficient technique. The NB50 model’s precision value is 93.2%, which is 0.5% higher than that of the NB70 model. The sensitivity criteria had the best value for the ANN/SVM/NB algorithms. The sensitivity criteria are crucial for locating every SA-positive person in the dataset. When it comes to identifying everyone who does not have SA, the ANN50/ANN70 model performs better than other ML models. This suggests that when these models achieve a value of 100%, they demonstrate the highest level of success in terms of specificity. When an algorithm can strike a favorable equilibrium between sensitivity and specificity, it is considered to be highly efficient. The best balance between these two requirements has been established by the optimal design suggested in this research. The F1-score, which takes into account both sensitivity and precision parameters, has a value of 100% in ANN-based models and is higher than that of the NB50/NB70 models (91.6%/91.1%).\n\nAccuracy is the most fundamental and direct indicator of a classifier’s performance, and it typically manifests itself in the accurate detection of samples. Additionally, the SVM model has the lowest classification accuracy (73.3%), and the best classifier among the other models is the ANN-based approach, which has a value of 100%. Figure 13 shows a bar chart that contrasts the machine learning algorithms designed according to their F1 score, specificity, sensitivity, accuracy, and precision.\n\n\nDiscussion\n\nThis study assessed subjective well-being by examining three key dimensions: physiological, cognitive psychological, and social functioning. This approach aligns with Rowe and Kahn’s theory.18 In order to determine if a person has SA or not, we developed prediction models that would utilize clinical and lifestyle factors as inputs. Our findings offer important new perspectives for determining SA likelihood. According to our main hypothesis, the proposed ML technique produced a potent SA status classifier. Here, we introduced a novel approach that uses three key ML techniques to forecast SA.\n\nA prediction model can be created using a variety of ML methods. The numerous fundamental model assumptions in use today’s ML approaches preclude successful application. The optimal method for dealing with a dataset that is both highly variable and noisy, such as the case with successful aging data, which is inherently diverse and inconsistent, remains uncertain. This is because it is frequently challenging to verify fundamental assumptions. Furthermore, no single ML technique yields reliable prediction outcomes. Scientists and researchers are continually seeking well-trained machine learning models that demonstrate accurate and reliable performance on a consistent basis. However, in reality, only a few biased models can occasionally be produced, therefore training model outputs are not always flawless.\n\nTable 4 presents a collection of studies that have explored the utilization of machine learning techniques to forecast and recognize instances of successful aging through diverse approaches. In this study, these studies were compared with the proposed approach. In addition, we provided an ANN-based technique to determine whether the tested individuals fall into the SA category or not. The data was preprocessed in the first phase to make it appropriate for use in data mining analysis. Thereafter, ANN was introduced, which proved more effective in predicting the SA than previously developed ML models such as SVM and NB. The results of the experiment demonstrate that by employing a holdout validation approach, the predictive system achieved outstanding performance in forecasting SA. It achieved perfect precision, specificity, accuracy, and F1-score, all reaching a flawless 100% level.\n\nBased on the findings of the current study, the examined machine learning (ML) methods demonstrate consistent accuracy in predicting successful aging (SA) in older individuals. The computed metrics indicate that the ML models, trained using specific attributes, accurately predicted SA. The use of past theoretical and empirical studies in feature selection may improve prediction accuracy by successfully reducing the number of irrelevant or superfluous variables in the model. In order to prevent overfitting, dropout regularization was also used, which improved the accuracy of the ANN model and extended the scope of its application.\n\nEven though our study performed as well as it could have for estimating the SA in older persons, there were a few potential weaknesses that need to be mentioned. First, a dataset from a single database that affects the accuracy, completeness, and generalizability of data was retrospectively examined for this study. The prediction models could have been negatively impacted by several inconsistent, insufficient, inaccurate, and irregular data items while utilizing this dataset. Therefore, the standard selection of each variable was established through conversations with the gerontology experts in order to increase data homogeneity in for the pre-processing stage. The aforementioned method made it easier for us to extract the most useful raw data from the hospital’s electronic medical record. Second, using a 2000-item sample dataset, this study only applied three significant ML algorithms. Obviously, the accuracy and generalizability of our models would be more enhanced as we assess a wider range of machine learning methods using larger, multicenter, and prospective datasets. Thirdly, the outcomes of the current investigation should be confirmed using an external validation approach. Fourthly, the link between the predictor and outcome factors was not examined in this study. There is a need for future research to explore a series of long-term factors associated with successful aging including disability, mental illness (depression, schizophrenia), substance abuse, and poor quality of life. Additionally, the suggested model can also be enhanced to provide scalable prediction models for successful aging.\n\n\nConclusion\n\nIn this study, the assessment of successful aging (SA) was carried out by considering three aspects of a persons health state, namely: physiological, cognitive psychological, and social function. The study built upon the SA model proposed by Rowe and Kahn and employed machine learning techniques to accurately predict the aging process. The study’s findings indicated that using the proposed machine learning (ML) model has the capability to improve the prediction of SA, suggesting it as a promising approach. The accuracy of all six ML models employed in this study were on average, >90%, >87%, and >86% to predict successful aging in the aging population dataset. The developed ANN models, however, reached 100% accuracy and sensitivity. The results show that machine learning offers a promising method for improving SA prediction. The results in this study have the potential to greatly benefit geriatricians and senior nurses by enhancing their ability to provide excellent assistance and care to the elderly. Additionally, the presented prediction models can serve as a reliable and adaptable tool for healthcare executives and policymakers, enabling them to enhance geriatric outcomes. For future directions, improved data instances that better point out factors important to successful aging will be acquired to developed scalable and generalizable models for predicting successful aging across different sources of data.\n\n\nDeclarations\n\nJEZ – Conceptualization, Methodology, Software, Result Analysis and Writing (Original draft preparation, final review, and editing, VAO – Software, Data Curation, and Original Draft, AJO – Investigation, Visualization, Writing (final review and editing), ASO – Software, Data Curation, Methodology, Writing(final review and editing). All authors read and approved the manuscript.",
"appendix": "Data availability\n\nZenodo: Successful Aging Dataset for Elderly Patients10.5281/zenodo.8132494\n\nThis project contains the following underlying data:\n\n• SAData.xlsx. (anonymized records of elderly individuals for the prediction of successful aging. 2000 records in total.).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nLin Y-H, Chen Y-C, Tseng Y-C, et al.: Physical activity and successful aging among middle-aged and older adults: a systematic review and meta-analysis of cohort studies. Aging (Albany NY). 2020; 12(9): 7704–7716. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChandraa CE, Abdullaha S: Forecasting mortality trend of Indonesian old aged population with bayesian method. Int. J. Adv. Sci. Eng. Inf. Technol. 2022; 12(2): 580–588. 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PubMed Abstract | Publisher Full Text\n\nCai T, Long J, Kuang J, et al.: Applying machine learning methods to develop a successful aging maintenance prediction model based on physical fitness tests. Geriatr. Gerontol. Int. 2020; 20(6): 637–642. PubMed Abstract | Publisher Full Text\n\nRaza K: Improving the prediction accuracy of heart disease with ensemble learning and majority voting rule. U-Healthcare Monitoring Systems. Elsevier; 2019; pp. 179–196. Publisher Full Text\n\nAsghari Varzaneh Z, Shanbehzadeh M, Kazemi-Arpanahi H: Prediction of successful aging using ensemble machine learning algorithms. BMC Med. Inform. Decis. Mak. 2022; 22: 258. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCai T, Long J, Kuang J, et al.: Applying machine learning methods to develop a successful aging maintenance prediction model based on physical fitness tests. Geriatr. Gerontol. Int. 2020; 20(6): 637–642. PubMed Abstract | Publisher Full Text\n\nMaryam A, Raoof N, Somayeh N: Designing a Predictive Model for Successful Aging among the Elderly Using Machine Learning Techniques.2022. Publisher Full Text\n\nNagarajan NR, Teixeira AA, Silva ST: Ageing population: identifying the determinants of ageing in the least developed countries. Popul. Res. Policy Rev. 2021; 40(2): 187–210. Publisher Full Text\n\nOlson DL: Data set balancing. In: Chinese Academy of Sciences Symposium on Data Mining and Knowledge Management. Berlin, Heidelberg: Springer; 2004 Jul 12; 71–80.\n\nChandrashekar G, Sahin F: A survey on feature selection methods. Comput. Electr. Eng. 2014; 40(1): 16–28. Publisher Full Text\n\nLi J, Cheng K, Wang S, et al.: Feature selection: a data perspective. ACM Comput. Surv. 2017; 50(6): 1–45. Publisher Full Text\n\nGuan Z-J, Li R, Jiang J-T, et al.: Data mining and design of electromagnetic properties of Co/FeSi filled coatings based on genetic algorithms optimized artificial neural networks (GA-ANN). Compos. B Eng. 2021; 226: 109383. Publisher Full Text\n\nSinaga LM, Suwilo S: Analysis of classification and Naïve Bayes algorithm k-nearest neighbor in data mining. IOP Conference Series: Materials Science and Engineering. IOP Publishing; 2020; Vol. 725(1): p. 012106.\n\nSembiring M, Tambunan R: Analysis of graduation prediction on time based on student academic performance using the Naïve Bayes Algorithm with data mining implementation (Case study: Department of Industrial Engineering USU). IOP Conference Series: Materials Science and Engineering: 2021. IOP Publishing; 2021; p. 012069.\n\nGopinath C, Manikanta J: Performance Analysis Based on Data Mining Technique in Predicting the Diabetic Disease-Decision tree and Naïve Bayes. 2019 1st International Conference on Advances in Information Technology (ICAIT): 2019. IEEE; 2019; pp. 525–528.\n\nPrasetya R, Ridwan A: Data mining application on weather prediction using classification tree, naïve bayes and K-nearest neighbor algorithm with model testing of supervised learning probabilistic brier score, confusion matrix and ROC. J. Appl. Commun. Inf. Technol. 2020; 4(2): 25–33. Publisher Full Text\n\nKhazaei S, Najafi-GhOBADI S, Ramezani-Doroh V: Construction data mining methods in the prediction of death in hemodialysis patients using support vector machine, neural network, logistic regression and decision tree. J. Prev. Med. Hyg. 2021; 62(1): E222–E230. PubMed Abstract | Publisher Full Text\n\nChidambaram S, Srinivasagan K: Performance evaluation of support vector machine classification approaches in data mining. Clust. Comput. 2019; 22(1): 189–196. Publisher Full Text\n\nSrivastava N, Hinton G, Krizhevsky A, et al.: Dropout: a simple way to prevent neural networks from overfitting. J. Mach. Learn. Res. 2014; 15(1): 1929–1958. Publisher Full Text\n\nByeon H: Exploring factors for predicting anxiety disorders of the elderly living alone in South Korea using interpretable machine learning: a population-based study. Int. J. Environ. Res. Public Health. 2021; 18(14): 7625. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "235047",
"date": "19 Feb 2024",
"name": "Brian H Chen",
"expertise": [
"Reviewer Expertise Aging biomarkers and prediction modeling using machine learning."
],
"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\nZaccheus et al. present an analysis comparing 3 machine learning approaches for the classification of \"successful aging\" (SA) from electronic medical records from 2,000 patients from a single hospital.\n\nThe paper needs further work on its premise since the authors seem to be using input variables that are part of the definition of the outcome. Furthermore, there are insufficient details on provided on the methodology.\n\nHere are my suggestions:\n\n1) The use of Rowe and Kahn definition of \"Successful Aging\" is not widely accepted. That said, it was not clear how the principles posed by Rowe and Kahn were applied to create the outcome variable.\n\n2) The authors should make clearer why they selected the input variables for SA classification. I imagine the presence of some of these input variables (e.g., diseases, ADLs, QOL) are part of the definition of \"SA.\" Are the authors merely trying to recreate Rowe & Kahn's model with the addition of other variables?\n\n3) The arbitrary selection of machine learning algorithms needs further justification. The SVM and Naive Bayes approaches, I would predict a priori, to perform worse than any neural network.\n\n4) The authors were unclear as to how the feature selection was actually conducted. We will need more detail than those variables being \"most pertinent to SA.\"\n5) The authors did not validate their models using an independent sample, which explains their overly optimistic model performance.\n\n6) The confusion matrix in Figure 4 is incorrect.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "246029",
"date": "26 Feb 2024",
"name": "Jiao Yu",
"expertise": [
"Reviewer Expertise aging",
"health disparities"
],
"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 investigates successful aging classification utilizing three machine learning algorithms, focusing on predicting successful aging through an analysis of a sample of 2000 individuals from older individuals in Nigeria. A key focus of the study was the assessment of various machine learning models for successful aging prediction. Among these models, the artificial neural network (ANN) demonstrates the best performance. While the study's main findings highlight the potential of machine learning in predicting successful aging, certain limitations require consideration.\nAbstract: Include a clear sentence in the background section stating the specific problem your research aims to address.\nAccording to the Rowe and Kahn’s (1997) framework, successful aging was frequently operationalized by the absence of major diseases, lack of activity of daily living (ADL) disabilities, high levels of physical and cognitive functioning, and active social engagement. It is unclear how the Rowe and Khan approach was applied to create the outcome variable for successful aging classification.\nIt is unclear what those limitations were in previous works. Did the previous studies fail to address the limitations mentioned in this analysis? such that they failed to select significant aging-related features?\nConcerns also arise regarding the justification of the sample size. The authors need to provide a rationale for why the chosen sample size is deemed sufficient for the study's objectives.\nIt is unclear as to how the feature selection was conducted. It is unclear whether the machine learning models utilized in this study also served as feature selection algorithms or if an alternative approach was adopted.\nI am also concerned that the high accuracy of ANN may result from overfitting, particularly in the absence of independent validation data. This may also be due to the fact that predictors are highly correlated with your outcome. You may consider a correlation analysis between predictor variables and the outcome variable. If high correlations exist, discuss their impact on model estimation.\nWhile the ANN method shows the best performance in this dataset, its generalizability remains uncertain. How these methods can be applied in practice needs further development in the discussion.\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? 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? Partly",
"responses": []
},
{
"id": "246031",
"date": "06 Mar 2024",
"name": "Peter Fedichev",
"expertise": [
"Reviewer Expertise theories of aging",
"AI/ML in biology and drug discovery",
"systems biology",
"biomarkers of aging",
"drug discovery against aging and age-related 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\nThe manuscript outlines a study conducted on a small cohort from Afe Babalola University Multi-System Hospital’s electronic records in Nigeria (January 2019 - April 2023), detailing a Machine Learning (ML) pipeline to assess SA with novel insights on feature selection and accuracy metrics.\nAlthough technically proficient, the small sample size poses limitations on model complexity and validation robustness. To enhance validation, I recommend cross-validation with external cohorts (e.g., NHANES, UK Biobank), ensuring the model's features are universally applicable.\nAdditionally, the manuscript employs a linear classifier for SA, based on continuous predictors (log odds ratio). It's crucial to evaluate how this correlates with established aging measures like the frailty index (FI) or biological age (BA). A comparison with log-linear classifiers using FI or BA, if data permits, could enrich the manuscript.\nI understand that integrating these comparisons might be demanding. I would leave to the authors if they would want to add new results or leave it for a potential future exploration.\nHowever, I believe that a fair discussion of the sample size, model limitations and the relationship between the SA and FI and BA, all supported by recent literature, is essential. Notable references include Kenneth Rockwood's work on FI (Ref [1]) and recent reviews on BA by the biomarkers of aging consortium (Ref [2]).\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/12-1201
|
https://f1000research.com/articles/12-14/v1
|
05 Jan 23
|
{
"type": "Research Article",
"title": "Artificial intelligence based glaucoma and diabetic retinopathy detection using MATLAB — retrained AlexNet convolutional neural network",
"authors": [
"Isaac Arias-Serrano",
"Paolo A. Velásquez-López",
"Laura N. Avila-Briones",
"Fanny C. Laurido-Mora",
"Fernando Villalba-Meneses",
"Andrés Tirado-Espin",
"Jonathan Cruz-Varela",
"Diego Almeida-Galárraga",
"Paolo A. Velásquez-López",
"Laura N. Avila-Briones",
"Fanny C. Laurido-Mora",
"Fernando Villalba-Meneses",
"Andrés Tirado-Espin",
"Jonathan Cruz-Varela"
],
"abstract": "Background: Glaucoma and diabetic retinopathy are the leading causes of blindness due to an irreversible damage to the retina which results in vision loss. Early detection of these diseases through regular screening is especially important to prevent progression. The image of retinal fundus is the main evaluating strategy for the glaucoma and diabetic retinopathy detection. Then, automated eye disease detection is an important application of retinal image analysis. Compared with classical diagnostic techniques, image classification by convolutional neural networks (CNN) have the potential for better cost-effective performance. Methods: In this paper, we propose the use of MATLAB – retrained AlexNet CNN for computerized eye diseases identification, particularly glaucoma and diabetic retinopathy, by employing retinal fundus images. The acquisition of the database was carried out through free access databases and access upon request. A transfer learning technique is used for retraining the AlexNet CNN. Specifically, the model divides the fundus image dataset into training and testing data. Results: As datasets were added by network training, different values were reported for validation accuracy, false positives and false negatives, precision, and recall. Thus, having NetTransfer I with a validation accuracy value of 94.3% for two classes. NetTransfer II with a validation accuracy value of 91.8% for two classes. NetTransfer III with a validation accuracy value of 89.7% for three classes. Net transfer IV with a validation accuracy value of 93.1% for three classes. Finally, NetTransfer V with a validation accuracy value of 92.1% for three classes. Conclusions: Re-training of the AlexNet network proved to be a powerful tool to create disease detection systems having high accuracy values and being able to discern between more than two diseases.",
"keywords": [
"Glaucoma",
"Classification",
"AlexNet",
"Convolutional Neural Network (CNN)",
"Diabetic Retinopathy"
],
"content": "Introduction\n\nThe leading causes of blindness and poor vision around the globe are primarily age-related eye diseases such as glaucoma and diabetic retinopathy (DR).1–4 Glaucoma is a condition caused by elevated intraocular pressure.1 The most common are open-angle glaucoma, angle-closure glaucoma, normal-tension glaucoma, and congenital glaucoma.2 On the other hand, DR is the most frequent complication of diabetes mellitus.3 It occurs because the small blood vessels in the retina swell and bleed or leak fluid, causing retinal damage and vision problems.3,4 DR has five stages or classes: normal, mild, moderate, severe and proliferative DR.4\n\nOphthalmic examination is essential for the diagnosis of glaucoma and DR. The following tests are carried out by physicians in order to perform a diagnosis for glaucoma: measuring intraocular pressure (tonometry),5 analyzing optic nerve damage with a dilated eye exam, checking areas of vision loss (visual field test),6 measuring corneal thickness (pachymetry)7 and inspecting the angle of drainage (gonioscopy).8 As most of these are imaging tests of the eye, it is essential to have accurate high quality images in order to perform a correct diagnosis of the disease. Similarly, DR is usually detected by physicians through comprehensive ophthalmologic examinations with dilation: taking cross-sectional images that show the thickness of the retina where fluid may be leaking from damaged blood vessels (optical coherence tomography)9 and injecting a special dye that place blood vessels with blockages and blood vessels leaking blood (fluorescein angiography).10 The diagnoses of these diseases require highly qualified medical personnel, therefore, expensive in terms of time and costs.\n\nThe artificial intelligence (AI) through deep learning methods provides computers with the ability to identify patterns in large image datasets and make predictions (predictive analysis).11–14 As a consequence, it is important to use AI as a tool to automatically analyze the fundus images and assist the physicians. This results in accessible, reliable, and affordable detection of glaucoma and other pathologies in general that affect vision (Table 1).\n\nRelated to AI, convolutional neuronal networks (CNNs) are a class of deep learning method, most commonly applied to analyze visual imagery. Generally, they are made of a key set of basic layers, including the convolution layer, the sub-sampling layer, dense layers, and the soft-max layer.15–22\n\nAmong the different CNNs, AlexNet by Krizhevsky et al. achieved a new state-of-the-art recognition accuracy against all the traditional machine learning and computer vision approaches that offer the opportunity to be retrained.23 AlexNet is structured with eight main layers, which consists of five convolutional layers (with max pooling after the first, second and fifth convolutional layer) and three fully connected layers; after each layer ReLu activation is performed except for the last one where instead there is a softmax layer that serves as the classification layer of the network.23,24\n\nTransfer learning is the process of taking a pre-trained network and use it as a starting point to learn a new task. Fine-tuning a network with transfer learning is usually much faster and easier than training a network with randomly initialized weights from scratch. Then, a pre-trained CNN quickly transfer learned features to a new task using a smaller number of training images. In this paper, we applied a transfer learning method to retrain the MatLab - AlexNet CNN for an effective glaucoma and diabetic retinopathy detection to make the testing and procedure accessible (Figure 1).\n\nRetinal fundus images retrieved from High-Resolution Fundus (HRF) Image Database.\n\n\nMethods\n\nTo carry out the detection of glaucoma and DR through CNN, image pre-processing and processing techniques are required. The different steps are summarized in Figure 2.\n\nFor the training of the CNN it is necessary to use retinal fundus images of the eye. Several public databases that compile different eye conditions are available on the internet. In this sense, it is possible to find free access databases and databases with access upon request. The following were used in this work:\n\n- Free access - databases\n\n○ Asia Pacific Tele-Ophthalmology Society (APTOS). Contains 3662 images of diabetic retinopathy that were used in the APTOPS 2019 blindness screening competitions. Each image has been resized and cropped to have a maximum size of 1024px. A certified clinician rated each image according to the severity of diabetic retinopathy on a scale of 0 to 4. A directory file is provided according to the previous scale: No diabetic retinopathy (0), Mild (1), Moderate (2), Severe (3), and Proliferative diabetic retinopathy (4).25\n\n○ High-Resolution Fundus (HRF) Image Database. Contains 15 images of healthy patients, 15 images of patients with diabetic retinopathy and 15 images of glaucomatous patients. They were captured by a Canon CR-1 fundus camera with a field of view of 45 degrees with a resolution of 3504×2336px.26\n\n○ Sungjoon Choi High-Resolution Fundus (sjchoi86-HRF). Created by Sungjoon Choi, assistant professor at Korea University, contains 601 fundus images of different pixel sizes divided into 4 groups: normal (300 images), glaucoma (101 images), cataract (100 images) and retina disease (100 images).27\n\n- Access upon request – databases\n\n○ Large-scale attention based glaucoma (LAG). Contains fundus images with positive (1711 images) and negative glaucoma (3143 images) samples obtained from Beijing Tongren Hospital with a resolution of 500×500px. Each fundus image is diagnosed by qualified glaucoma specialists, taking into consideration of both morphologic and functional analysis.28\n\n○ Ocular Disease Intelligent Recognition (ODIR). Contains images of 5000 patients with various eye diseases collected by Shanggong Medical Technology Co., Ltd. from different hospitals/medical centers in China. The fundus images are captured with various cameras on the market, resulting in varied image resolutions. They classify patients into eight labels based on the images of both eyes. A directory file is provided according to the following label: Normal Fundus (N), Diabetes (D), Glaucoma (G), Cataract (C), Age related Macular Degeneration (A), Hypertension (H), Pathological Myopia (M), Other diseases/abnormalities (O).29\n\nIn the case of the ODIR database, photographs labeled in their directory file as “glaucoma” (G) and “normal fundus” (N) were extracted for a total of 200 images and 2873 images, respectively. On the other hand, for the APTOS database, photographs labeled in their directory as “moderate” (2), “severe” (3) and “proliferative diabetic retinopathy” (4) were extracted for a total of 1487 images in general.\n\nThe AlexNet architecture design only supports color images (RGB), with a resolution of 227×227px. Convertidor_227_final.m code provides a small user interface that contains three functions (see the Software availability links for deeper descriptions): add a red color filter to grayscale images,30 crop black areas from images, and resize images of any dimension to a new 227×227px image.\n\nThe function of cropping black areas in the photograph by Converter_227_final.m is applied to each database. This is done to have more information on the retinal area and eliminate areas of no interest. This function binarizes the original image to obtain a black and white image of equal dimensions. Since the area where a color pixel existed now has a value of 1 and the black areas have a value of 0, the pixel location index by row and column where the value is equal to 1 is extracted as a list. Using the value of the pixel location index as image coordinates, the maximum and minimum value per row and column is determined to establish the cropping edges of the image. It should be mentioned that due to its code design, this function does not affect previously cropped images that no longer contain black areas.\n\nOnce the black borders are removed, the function to change the size of the photographs by Converter_227_final.m is applied. Then, all the database images are converted in a single dimension of 227×227px. Since, all databases satisfy the color image format (RGB). It was not necessary to add the red color filter by Converter_227_final.m code. According to their original medical classification, the obtained retinal fundus images were labeled as non-disease (Non_D), suspicious glaucoma (Sus_G) and suspicious diabetic retinopathy (Sus_R). Five storage folders were prepared for the retraining of the CNN (Table 2).\n\nIn order to develop predictive software for glaucoma disease, we are going to make use of transfer learning in order to retrain CNN AlexNet. For this, we load the pre-trained AlexNet network and also the different databases (LAG, APTOS, HFR, ODIR, and sjchoi86-HRF) containing the images of the different pathologies to be classified, thus being the glaucoma and retinopathy, besides that we use the information from Refs. 31–38 to develop our algorithm.\n\nIn order to begin training with this new dataset, the new images should be unzipped and loaded as ImageData format. AlexNet will automatically label the images based on folder names, corresponding to non-disease fundus eyes images, glaucoma fundus eyes images, and retinopathy fundus eyes images. Then, the model stores the data as an ImageData object, we must divide the data into training and validation data sets. Once the first classification is obtained, the model further divides the data into training images having an equivalent of 70% of the images and the other 30% for validation, for this we use “. splitEachLabel” which splits the images data store into two new data stores.38\n\nTraining algorithm for transfer learning\n\nInput ->Retinal fundus images (X, Y); Y = {y {Non-disease, Suspicious-Glaucoma, Suspicious-Diabetic-Retinopathy}\n\nOutput-> Re-trained model that classifies the retinal fundus images into respective Y\n\n------------------------------------------------------------------------------------------------------------------\n\nImport the pre-trained model AlexNet Network with its corresponding weights.\n\nReplace the last three layers of the Network:\n\n-Fully connected layer (Set the 'WeightLearnRateFactor' to 20 and the 'BiasLearnRateFactor' to 20; and set its output to the number of elements of Y).\n\n-Softmax layer\n\n-Classification layer\n\nTraining-progress settings\n\nMinibatchSize->It is the number of elements into the group of inputs for each iteration\n\nMaxEpoch->It is the maximum number of times that the network is going to use all the input elements\n\nInitialLearnRate ->The learning rate is a tuning parameter that determines the step size at each iteration while moving toward a minimum of a loss function.\n\nShuffle->It is the action of mixing randomly various elements from our databases\n\nValidationData ->It is a group of images from the dataset that the network is using to Validate how good the network is getting at classification\n\nValidationFrequency ->It is the number of iterations that the system does before doing a validation process to assess in real time how the training is going\n\nVerbose->Verbose mode is an option that provides additional details as to what the computer is doing and what drivers and software it is loading during startup\n\nTraining Code\n\noptions = trainingOptions('sgdm', …\n\n'MiniBatchSize',10, …\n\n'MaxEpochs',6, …\n\n'InitialLearnRate',1e-4, …\n\n'Shuffle','every-epoch', …\n\n'ValidationData',augimdsValidation, …\n\n'ValidationFrequency',3, …\n\n'Verbose',false, …\n\n'Plots','training-progress');\n\nThe aforementioned process was applied several times with the different databases acquired. Therefore, we were able to create five new networks based on the structure and weights of the original Alexnet network, the five new networks were denominated: netTransfer 1 (Storage folder 1), netTransfer 2 (Storage folder 2), netTransfer 3 (Storage folder 3), netTranfer 4 (Storage folder 4), and netTransfer 5 (Storage folder 5). The following figure resumes the architecture of all the new networks formed during the transfer learning method (Figure 3).\n\n\nResults\n\nThe results we obtained with our transfer learning code and our different databases over the course of the project was the development of five newly retrained AlexNet networks, to which we will now refer as NetTransfer networks. The confusion matrixes (CM) for the respective NetTransfer networks can be seen in Figure 4 including precision, recall, false positive (FP), false negative (FN) and accuracy values (yellow box). Additionally, the rows represent the known values and columns the predicted values.\n\nNetTransfer I network was only based on glaucoma and non-disease image cases existing in the LAG-database (Table 2), training with these datasets lead to values of validation accuracy of 94.3%. Besides that, Non_D detection also presented values of 95.5% for recall (4.5% for FN), and values of 95.6% for the precision of the system (4.4% for FP).\n\nNetTransfer II network was based on glaucoma and non-disease images cases existing in the LAG-database and the sjchoi86-HRF database (Table 2), training with these datasets lead to values of validation accuracy of 91.8%. Besides that, Non_D detection presented values of 95.9% for recall (4.1% for FN), and values of 91.8% for the precision of the system (8.2% for FP).\n\nNetTransfer III network was based on glaucoma, diabetic retinopathy and non-disease images cases existing in the LAG-database, sjchoi86-HRF database and the HRF database (Table 2), training with these datasets lead to values of validation accuracy of 89.7%. Besides that, Non_D detection presented values of 97.0% for recall (3.0% for FN), and values of 88.9% for the precision of the system (11.1% for FP).\n\nNetTarnsfer IV network was based on glaucoma, diabetic retinopathy and non-disease images cases existing in the LAG-database, sjchoi86-HRF database, HRF database and the APTOS database (Table 2), training with these datasets lead to values of validation accuracy of 93.1%. Besides that, Non_D detection presented values of 93.2% for recall (6.8% for FN), and values of 93.5% for the precision of the system (6.5% for FP).\n\nNetTransfer V network was based on glaucoma, diabetic retinopathy and non-disease images cases existing in the LAG-database, sjchoi86-HRF database, HRF database, APTOS database and ODIR database (Table 2), training with these datasets lead to values of validation accuracy of 92.1%. Besides that, Non_D detection presented values of 96.8% for recall (3.2% for FN), and values of 92.0% for the precision of the system (8.0% for FP).\n\n\nDiscussion\n\nSeveral works were presented for glaucoma detection using fundus photographs by calculating cup disk ratio (CDR). For example, Carrillo and coworkers39 developed an autonomic detection method and a novel method for cup segmentation with a percentage of success of 88.5% (Table 3). Another work from Anum Abdul and peers,40 an algorithm was provided to detect CDR and hybrid textural and intensity features. Those features were used to classify the autonomous system, and it gave improvements in the results from previous studies that only used CDR, thanks to their hybrid approach, they reached an accuracy of 92% (Table 3). Even though we did not make use of CDR characteristic, our AlexNet approach seems to reach comparable levels of accuracy (92.1%) to these previously mentioned methods without the need to calculate the CDR.\n\nIn other more rigorous studies such as Xiangyu Chen work,41 a deep CNN was developed with a total of six layers: two fully connected layers and four convolutional layers. The results drop scores of prediction from 71% to 83% from real images (Table 3). On the other hand, Hanruo Liu and peers22 made a deep learning system using a total of 241,032 images from 68,013 patients. In this work, every image was subjected to a multiple layers of grading system, in which graders were from students to senior specialists on glaucoma, from these they obtained good levels of sensitivity and specificity (82.20% and 70.40%). When compared to these other CNN systems, our AlexNet based detection system still presented comparable and even arguably better results in accuracy, sensitivity and specificity for glaucoma and DR detection (Table 3).\n\nAnother related work from Almeida and peers,42 uses image processing in MATLAB to improve the accuracy of glaucoma tests by extracting the most pertinent qualities of the images obtaining promising results with an accuracy, specificity, and sensitivity greater than 90% (Table 3), which indicates that it gives an excellent start for us to assess the glaucoma diagnosis through AI. While Almeida and co-workers seems to be better suited for glaucoma detection, our AlexNet system presented the advantage of also being able to detect more pathologies at the same time, such as DR, which was the other disease we decided to add to our detection system.\n\nAs our system is also able to detect DR, it is also pertinent to compare it to other deep learning systems that were developed for DR detection. In the study realized by Rishab Gargeya and Theodore Leng,17 they developed and evaluated a data-driven deep learning algorithm as a novel diagnostic tool for automated DR detection, which proved to reach high efficacy computer-aided model, with low-cost, which lead to correct DR diagnostics without depending on clinicians to examine and grade images manually (Table 3). A different study made by Shanthi and Sabeenian,18 used a modified AlexNet CNN system for the detection of DR in a big data training of the network (Table 3). Additionally, Amnia Salma and peers16 develop a similar system, but the use GoogleNet instead of AlexNet (Table 3). While all of these systems follow similar principles to our propose system, it is important to remark that our AlexNet pretrained network acquired higher accuracies, sensitivities and specificities than the previously mentioned systems, mostly due to using a higher number datasets. Also we decided to try to go beyond and used AlexNet to classify more diseases at the same time. The following table summarizes and compares the capabilities of detection of our AlexNet pathology detection system to all the previously mentioned works, as well as some other important studies that were not addressed (Table 3).\n\nAdditionally, for the implementation of the AlexNet architecture on open-source language, we endorse the use of TensorFlow which is a free open-source self-learning platform based on the Python language, mainly developed by Google.43 Among its many libraries we can find Keras, which is a deep learning application programming interface (API) developed for Python built on TensorFlow, from which we can build our AlexNet equivalent model. The recommended model is the sequential model of Keras which allows a user to define the model as a series of convolutional layers with max pooling.44\n\n\nConclusions\n\nIn the presented research, the training of a CNN through the use of MATLAB software and its AlexNet tool, allowed the effective recognition of two eye diseases (glaucoma and DR) through retinal fundus images. Additionally, the use of open access databases allows the replicability and reproducibility of the present study. Being the APTOS, HRF and sjchoi86-HRF databases of immediate access. Meanwhile, LAG and ODIR are databases with access upon request. The implementation of the different databases (LAG, APTOS, HRF, ODIR, sjchoi86-HRF), proved to be effective in improving the prediction percentages of the different neural network trainings.\n\nIn general, the most common eye affections are presented through a series of symptoms, such as blurred vision, spots, glare, eye fatigue, dry eyes, among others. In this way, glaucoma proves to be a condition that damages the optic nerve and generally does not present any symptoms, until the person suffering from it perceives a decrease in vision in the final stages of the disease. Based on the foregoing, it is necessary to create tools that allow an effective detection of this type of affectation, for example CNN systems as an alternative, highly reliable in the automation of processes. Additionally, this research moved its detection objective to the addition of a new disease, such as DR.\n\nFuture improvements to this algorithm could include the creation of a more user-friendly graphical interface for users who are not experts in programming language. In this way, the detection tasks will be based on the selection of options and not on the coding of algorithms. On the other hand, as previously mentioned, it is possible to replicate the AlexNet-CNN using Python, by using existing tools such as TensorFlow and Keras API. Therefore, a subsequent study will concentrate efforts on implementing the recognition system in the open-source language, to endorse the use of non-proprietary software in order to increase reproducibility.\n\n\nSoftware availability\n\nMatLab codes and scripts related to image processing, pre-processing & Training versions of the AlexNet Convolutional Neural Network (NetTransfers I-V).\n\nSource code available from: https://github.com/IscArias/EyeEvaluationSourceCode\n\nArchived source code as at time of publication: https://doi.org/10.5281/zenodo.709887945\n\nLicense: 2-Clause BSD License\n\n\nData availability\n\nFree access - databases:\n\n- Asia Pacific Tele-Ophthalmology Society (APTOS). The data download process is free and does not require authorization or registration. Follow the directions of the data host to reference the database. Link: https://www.kaggle.com/c7934597/resized-2015-2019-diabetic-retinopathy-detection/metadata/\n\n- High-Resolution Fundus (HRF) Image Database. The data download process is free and does not require authorization or registration. Follow the directions of the data host to reference the database. Link: https://www5.cs.fau.de/research/data/fundus-images/\n\n- Sungjoon Choi High-Resolution Fundus (sjchoi86-HRF). The data download process is free and does not require authorization or registration. Follow the directions of the data host to reference the database. Link: https://github.com/cvblab/retina_dataset\n\nAccess upon request – databases:\n\n- Large-scale attention based glaucoma (LAG). Database for academic purposes. An email must be written to the hosts who will provide a password to authorize the download. Once the key is obtained and entered, the download is free. It is not necessary to register on any additional platform. Follow the directions of the data host to reference the database. Link: https://github.com/smilell/AG-CNN\n\n- Ocular Disease Intelligent Recognition (ODIR). Database for academic purposes. It is required to create an account and register on the platform, providing data on the user's institution, department and country. Once registered, a request must be submitted in order to download the database. Authorized access, the user can download the database freely. Follow the directions of the data host to reference the database. Link: https://odir2019.grand-challenge.org/dataset/\n\nAdditional Codes for Image Evaluation, Image Selection from Data Bases and Confusion Matrix Plotting.\n\nSource code available from: https://github.com/IscArias/EyeEvaluationSourceCode_Extra\n\nArchived source code as at time of publication: https://doi.org/10.5281/zenodo.710261846\n\nLicense: 2-Clause BSD License",
"appendix": "References\n\nWeinreb RN, Aung T, Medeiros FA: The Pathophysiology and Treatment of Glaucoma. Journal of American Medical Association. 2014; 311: 1901–1911. PubMed Abstract | Publisher Full Text\n\nLee DA, Higginbotham EJ: Glaucoma and its treatment: A review. American Journal of Health-System Pharmacy. 2005; 62: 691–699. Oxford University Press (OUP). Publisher Full Text\n\nWang W, Lo A: Diabetic Retinopathy: Pathophysiology and Treatments. IJMS. MDPI AG. 2018; 19: 1816. PubMed Abstract | Publisher Full Text\n\nQummar S, Khan FG, Shah S, et al.: A Deep Learning Ensemble Approach for Diabetic Retinopathy Detection. IEEE Access. 2019; 7: 150530–150539. Institute of Electrical and Electronics Engineers (IEEE). Publisher Full Text\n\nGarcia-Feijoo J, Martinez-de-la-Casa JM, Morales-Fernandez L, et al.: New technologies for measuring intraocular pressure. Progress in Brain Research. 2015; 67–79. Elsevier. PubMed Abstract | Publisher Full Text\n\nPerimetry HD: Reference Module in Neuroscience and Biobehavioral Psychology. Elsevier;2017. Publisher Full Text\n\nSandhu HS: Bilateral Pigment Dispersion. Clinical Cases in Uveitis. 2021; 58–62. Elsevier. Publisher Full Text\n\nSheppard EAW, Romejko WJ: Gonioscopy. American Journal of Ophthalmology. 1947; 30: 159–164. Elsevier BV. PubMed Abstract | Publisher Full Text\n\nAumann S, Donner S, Fischer J, et al.: Optical Coherence Tomography (OCT): Principle and Technical Realization. High Resolution Imaging in Microscopy and Ophthalmology. Springer International Publishing;2019; 59–85. Publisher Full Text\n\nCouturier A, Rey P-A, Erginay A, et al.: Widefield OCT-Angiography and Fluorescein Angiography Assessments of Nonperfusion in Diabetic Retinopathy and Edema Treated with Anti–Vascular Endothelial Growth Factor. Ophthalmology. 2019; 126: 1685–1694. Elsevier BV. PubMed Abstract | Publisher Full Text\n\nYanchatuña OP, Pereira JP, Pila KO, et al.: Skin Lesion Detection and Classification Using Convolutional Neural Network for Deep Feature Extraction and Support Vector Machine. International Journal on Advanced Science, Engineering and Information Technology. 2021; 11: 1260. Insight Society. Publisher Full Text\n\nSuquilanda-Pesántez JD, Zambonino-Soria MC, López-Ramos DE, et al.: Prediction of Parkinson’s Disease Severity Based on Gait Signals Using a Neural Network and the Fast Fourier Transform. Artificial Intelligence, Computer and Software Engineering Advances. 2021; 3–18. Springer International Publishing. Publisher Full Text\n\nPereira-Carrillo J, Suntaxi-Dominguez D, Guarnizo-Cabezas O, et al.: Comparison Between Two Novel Approaches in Automatic Breast Cancer Detection and Diagnosis and Its Contribution in Military Defense. Smart Innovation, Systems and Technologies. 2021; 189–201. Springer Singapore. Publisher Full Text\n\nSuquilanda-Pesántez JD, Aguiar Salazar ED, Almeida-Galárraga D, et al.: NIFtHool: an informatics program for identification of NifH proteins using deep neural networks. F1000Research. 2022; 11: 164. F1000 Research Ltd. PubMed Abstract | Publisher Full Text\n\nAlyoubi WL, Abulkhair MF, Shalash WM: Diabetic Retinopathy Fundus Image Classification and Lesions Localization System Using Deep Learning. Sensors. 2021; 21: p. 3704. MDPI AG. PubMed Abstract | Publisher Full Text\n\nDiabetic Retinopathy Detection Using GoogleNet Architecture of Convolutional Neural Network Through Fundus Images. Nusantara Science and Technology Proceedings. 2021. Galaxy Science. Publisher Full Text\n\nGargeya R, Leng T: Automated Identification of Diabetic Retinopathy Using Deep Learning. Ophthalmology. 2017; 124: 962–969. Elsevier BV. PubMed Abstract | Publisher Full Text\n\nShanthi T, Sabeenian RS: Modified Alexnet architecture for classification of diabetic retinopathy images. Computers & Electrical Engineering. 2019; 76: 56–64. Elsevier BV. Publisher Full Text\n\nDong Y, Zhang Q, Qiao Z, et al.: Classification of cataract fundus image based on deep learning.2017 IEEE International Conference on Imaging Systems and Techniques (IST). IEEE; 2017.\n\nZhang H, Niu K, Xiong Y, et al.: Automatic cataract grading methods based on deep learning. Computer Methods and Programs in Biomedicine. 2019; 182: 104978. Elsevier BV. PubMed Abstract | Publisher Full Text\n\nShinde R: Glaucoma detection in retinal fundus images using U-Net and supervised machine learning algorithms. Intelligence-Based Medicine. 2021; 5: 100038. Elsevier BV. Publisher Full Text\n\nLiu H, Li L, Wormstone IM, et al.: Development and Validation of a Deep Learning System to Detect Glaucomatous Optic Neuropathy Using Fundus Photographs. JAMA Ophthalmology. 2019; 137: 1353–1360. American Medical Association (AMA). PubMed Abstract | Publisher Full Text\n\nKrizhevsky A, Sutskever I, Hinton GE:ImageNet Classification with Deep Convolutional Neural Networks.Pereira F, Burges CJ, Bottou L, Weinberger KQ, editors. Advances in Neural Information Processing Systems. Curran Associates, Inc.;2012.\n\nAlom MZ, Taha TM, Yakopcic C, et al.: The History Began from AlexNet: A Comprehensive Survey on Deep Learning Approaches. arXiv. 2018.Reference Source\n\nResized 2015 & 2019 Diabetic Retinopathy Detection.Reference Source\n\nHigh-Resolution Fundus (HRF) Image Database:Accessed January 15, 2022.Reference Source\n\ncvblab/retina_dataset: Retina dataset containing 1) normal 2) cataract 3) glaucoma 4) retina disease.Accessed February 12, 2022.Reference Source\n\nLi L, Xu M, Wang X, et al.: Attention Based Glaucoma Detection: A Large-Scale Database and CNN Model.2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). IEEE; 2019. Publisher Full Text\n\nDataset-数据集 - ODIR-2019 - Grand Challenge:Accessed January 27, 2022.Reference Source\n\nKorostyshevskiy V: Grayscale to RGB Converter.2022. MATLAB Central File Exchange. Retrieved September 21, 2022.Reference Source\n\nKrizhevsky A, Sutskever I, Hinton GE: ImageNet classification with deep convolutional neural networks. Communications of Association for Computing Machinery. 2017; 60: 84–90. Publisher Full Text\n\nKniestedt C, Punjabi O, Lin S, et al.: Tonometry Through the Ages. Survey of Ophthalmology. 2008; 53: 568–591. Elsevier BV. Publisher Full Text\n\nAbdulrahman A, Varol S: A Review of Image Segmentation Using MATLAB Environment.2020 8th International Symposium on Digital Forensics and Security (ISDFS). IEEE; 2020. Publisher Full Text\n\nLazcano-Gomez G, Ramos-Cadena MdlA, Torres-Tamayo M, et al.: Cost of glaucoma treatment in a developing country over a 5-year period. Medicine. Ovid Technologies (Wolters Kluwer Health). 2016; 95: e5341. PubMed Abstract | Publisher Full Text\n\nAlgren M, Fisher W, Landis AE: Machine learning in life cycle assessment. Data Science Applied to Sustainability Analysis. 2021; 167–190. Elsevier. Publisher Full Text\n\nRussakovsky O, Deng J, Su H, et al.: ImageNet Large Scale Visual Recognition Challenge. International Journal of Computer Vision. 2015; 115: 211–252. Springer Science and Business Media LLC. Publisher Full Text\n\nStewart WC, Stewart JA, Nelson LA: Ocular Surface Disease in Patients with Ocular Hypertension and Glaucoma. Current Eye Research. 2011; 36: 391–398. Informa UK Limited. Publisher Full Text\n\nLi Y, Shekhar R, Huang D: Corneal Pachymetry Mapping with High-speed Optical Coherence Tomography. Ophthalmology. 2006; 113: 792–799.e2. Elsevier BV. PubMed Abstract | Publisher Full Text\n\nCarrillo J, Bautista L, Villamizar J, et al.: Glaucoma Detection Using Fundus Images of The Eye.2019 XXII Symposium on Image, Signal Processing and Artificial Vision (STSIVA). IEEE; 2019. Publisher Full Text\n\nSalam AA, Akram MU, Wazir K, et al.: Autonomous Glaucoma detection from fundus image using cup to disc ratio and hybrid features.2015 IEEE International Symposium on Signal Processing and Information Technology (ISSPIT). IEEE; 2015. Publisher Full Text\n\nChen X, Xu Y, Kee Wong DW, et al.: Glaucoma detection based on deep convolutional neural network.2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE; 2015. Publisher Full Text\n\nAlmeida-Galarraga D, Benavides-Montenegro K, Insuasti-Cruz E, et al.: Glaucoma detection through digital processing from fundus images using MATLAB.2021 Second International Conference on Information Systems and Software Technologies (ICI2ST). IEEE; 2021. Publisher Full Text\n\nAbadi M, Barham P, Chen J, et al.: Tensorflow: A system for large-scale machine learning. 12th $$USENIX$$ Symposium on Operating Systems Design and Implementation ($$OSDI$$ 16). 2016; pp. 265–283.\n\nChollet F: Deep Learning with Python. Second ed.Manning Publications;2022; 174.\n\nArias-Serrano I, Velásquez-López P, Ávila-Briones L, et al.: Artificial intelligence based glaucoma and diabetic retinopathy detection using MATLAB — retrained AlexNet convolutional neural network. [Code] Zenodo.2022. Publisher Full Text\n\nSerrano AIA: Extended data - Artificial intelligence based glaucoma and diabetic retinopathy detection using MATLAB. [Code] Zenodo.2022. Publisher Full Text"
}
|
[
{
"id": "161036",
"date": "06 Feb 2023",
"name": "Creed Jones",
"expertise": [
"Reviewer Expertise machine learning",
"computer vision",
"eye diseases",
"biometric identification."
],
"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 presents a CNN implementation using MATLAB to determine the presence of glaucoma using labeled retinal images. The result and its conclusions are very interesting, and the open and freely verifiable nature of the work is great.\nDetailed Comments -\nThe abstract should clarify the \"two classes\" and \"three classes\" referred to.\n\nThe authors refer to a \"red color filter\" that is added to grayscale images, which is not necessary if RGB images are available. This is very confusing and needs both justification and explanation.\n\nThe use of 6 epochs needs to be justified.\n\nThe presentation of the confusion matrices is very clear and good.\n\nIt's not clear whether external knowledge of diabetes diagnoses was used (or could be used) in distinguishing DR from glaucoma.\n\nClearly calling out the available databases is very helpful for replicating/extending the results.\n\nGrammar throughout is good but needs improvement. Look at use of \"The\" at the start of sentences. Also, is there a misspelling in the title of the confusion matrices; should \"PREDICTEC\" be \"PREDICTED\"?\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": "11291",
"date": "13 Apr 2024",
"name": "Angel Arias",
"role": "Author Response",
"response": "1. The abstract should clarify the \"two classes\" and \"three classes\" referred to.The abstract should clarify the \"two classes\" and \"three classes\" referred to. Thank you for this observation, as the omission was not previously recognized. To address this oversight, the abstract has been revised for greater precision and conciseness. This revision now explicitly references the classes classified during the study and includes information detailing the new implementations of the study. 2. The authors refer to a \"red color filter\" that is added to grayscale images, which is not necessary if RGB images are available. This is very confusing and needs both justification and explanation. The mention of the red color filter has been removed from the image and text pre-processing flowchart within the manuscript. This feature was initially presented as an optional additional functionality within our code for the convenience of the reader. However, it lacks utility in the context of this study, given that the databases utilized are in RGB format. Acknowledgment of this detail is appreciated, as it was a component without relevance to the scope of the study that was not addressed throughout its duration. 3. The use of 6 epochs needs to be justified. In transfer learning, the objective is to leverage features already learned by the pre-trained model. It was posited that fewer epochs were necessary, as the focus shifts towards \"fine-tuning\" the weights in the final layers of the model for a new specific task rather than learning these features from scratch. However, following the observation made, it was recognized that this aspect required improvement given it had been inadequately covered, this version includes elements like MiniBatchSize, iterations per epoch, and validation frequency for the theoretical background. Consequently, additional training sessions with AlexNet, ResNet50, and GoogLeNet were conducted for model benchmarking, with an increased number of epochs aligning with more traditional training cycles. 4. The presentation of the confusion matrices is very clear and good. The design of the matrices, as well as all figures within the study, are original creations. Furthermore, enhancements have been implemented to ensure the images are more comprehensible and visually clear. 5. It's not clear whether external knowledge of diabetes diagnoses was used (or could be used) in distinguishing DR from glaucoma. External knowledge from medical experts on glaucoma and diabetic retinopathy is leveraged for generating extensive, accurately labelled databases. This foundation enables the data to undergo analysis, providing a basis of truth for the development of classification models by non-medical professionals. Moreover, while physicians rely on physiological criteria and specific medical evaluations for diagnosing retinal diseases using images, Convolutional Neural Networks (CNNs) identify patterns within a set of images that may or may not correlate with characteristic features of retinal diseases. Consequently, the application of Grad-CAM becomes essential to ascertain the focal points of a trained model during the discriminative process of recognition. This observation is appreciated, as it has facilitated the enhancement of previously provided information in the article and the correction of potential inaccuracies. 6. Clearly calling out the available databases is very helpful for replicating/extending the results. The rationale for providing a detailed description and citation of the databases utilized was to ensure access to information for individuals interested in conducting related studies on retinal fundus images. Appreciation is extended for acknowledging the thoroughness of the descriptions provided. 7. Grammar throughout is good but needs improvement. Look at use of \"The\" at the start of sentences. Also, is there a misspelling in the title of the confusion matrices; should \"PREDICTEC\" be \"PREDICTED\"? Consequently, a decision was made to enhance the overall clarity of the text, including the revision of sections to ensure the narrative is presented in the third person. It is anticipated that these modifications will contribute to a more assertive tone throughout the document."
}
]
},
{
"id": "213588",
"date": "27 Oct 2023",
"name": "Tae Keun Yoo",
"expertise": [
"Reviewer Expertise Ophthalmology",
"deep learning",
"machine learning",
"fundus photography"
],
"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 built a CNN model to classify glaucoma, diabetic retinopathy, and controls in the fundus photography domain using MATLAB.\nAlexnet is the first CNN model known in the world and the most primitive structure. It is one of the oldest architecture of CNNs. Why did the authors choose alexnet in defiance of many recent advances in CNN? At least use and compare resnet. It is all provided by Matlab.\n\nMatlab provides a different deep learning toolbox for each version. Write in detail which version and which toolbox the authors used.\n\nProvide Grad-CAM heatmaps.\n\nPlease describe the partitioning process for the training and test sets in detail.\n\nConsidering recent advances of deep learning in ophthalmology domains, the contribution of this study is too limited. Please review recent advances and show the strengths of this study.\n\nMany important papers in this fields are omitted in the manuscript. Please discuss several siginficant previous works and important products of fundus photography reading devices for diabetic retinopathy.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11292",
"date": "13 Apr 2024",
"name": "Angel Arias",
"role": "Author Response",
"response": "1. Alexnet is the first CNN model known in the world and the most primitive structure. It is one of the oldest architecture of CNNs. Why did the authors choose alexnet in defiance of many recent advances in CNN? At least use and compare resnet. It is all provided by Matlab. AlexNet has remained a significant neural network over time, owing to the simplicity of its architecture, which allows operation without the need for extensive computational resources. The observation provided led to the realization that benchmarking models was essential to better understand the performance of the study relative to other significant architectures. Consequently, comparisons were not only made with the ResNet50 architecture but also included GoogLeNet, thereby enriching the study with a broader variety of architectural analyses. 2. Matlab provides a different deep learning toolbox for each version. Write in detail which version and which toolbox the authors used. This observation was fully addressed by adding a new section titled \"Operational Resources.\" This section not only describes the software used, including the version of MATLAB employed for the study, but also details the hardware utilized. Appreciation is expressed for highlighting this theoretical component, which was an oversight not previously considered in the study. 3. Provide Grad-CAM heatmaps. Given the incorporation of model benchmarking in the updated version, the opportunity was taken to conduct a Grad-CAM analysis using the three trained models: netAlexNet, netResNet50, and netGoogLeNet. The Grad-CAM analysis was performed for each model across the three identification conditions considered: non-disease, suspicious glaucoma, and suspicious diabetic retinopathy. Appreciation is extended for the request of this addition, as it enhances the comprehensiveness of the work through the interpretative insight provided by the Grad-CAM heatmaps for each model and evaluated condition. 4. Please describe the partitioning process for the training and test sets in detail. The image processing section has been enhanced to address previous ambiguities and provide a more comprehensive understanding. Furthermore, a figure illustrating the data partitioning volume for segregating images into validation and training datasets has been added. A mathematical framework for model training parameters, contingent on the number of observations in the training and validation sets, has been established. This framework includes detailed descriptions of Mini Batch Size, Iterations Per Epoch, Training Set (TS), and Validation Set (VS), thereby rendering the information of the study to be more relevant and concise through the requested corrections. 5.Considering recent advances of deep learning in ophthalmology domains, the contribution of this study is too limited. Please review recent advances and show the strengths of this study. The development of predictive systems in the field of ophthalmology has been on the rise for several years with the use of Convolutional Neural Networks (CNNs) and other types of systems, many of which emulate the structures of existing networks for prediction purposes. Within this context, the presented work does not signify a paradigm shift in the state of the art, as it aligns with concepts previously implemented. Nonetheless, the study demonstrates significant utility and importance, highlighting that transfer learning via AlexNet yields highly promising results, potentially surpassing some detection methods, networks built from scratch, or studies that employed pre-established network structures. This approach advocates for the adoption of transfer learning and a streamlined methodology that does not require complex data pre-processing, thereby simplifying classification tasks and aligning with existing predictive systems. 6. Many important papers in this fields are omitted in the manuscript. Please discuss several significant previous works and important products of fundus photography reading devices for diabetic retinopathy. In response to this observation, a select number of contemporary and pertinent studies within the field, related to predictive systems for these pathologies, have been incorporated. It is noted that the aim of this work is not to compete with or replace established systems, nor is it intended to be perceived as comparable to specialized retinal fundus image technologies. Rather, it is approached as an initial step towards the development of a system capable of ensuring efficient and accessible identification tasks, with considerations for future enhancements."
}
]
}
] | 1
|
https://f1000research.com/articles/12-14
|
https://f1000research.com/articles/13-245/v1
|
02 Apr 24
|
{
"type": "Research Article",
"title": "Synthesis, characterization and preliminary antimicrobial study of some new phthalimide phenyl hydrazide derivatives",
"authors": [
"Nisreen Mahdi Alassadi",
"Mohammed Kamil Hadi"
],
"abstract": "Background: The synthesis and antibacterial efficacy of phthalimide Schiff bases derivatives (3a-f) derived from phthalic anhydride were investigated. The aim of this study was to assess the antibacterial activity of the synthesized Schiff bases against five different types of microbes in vitro. Methods: The Schiff bases were synthesized by reacting various aldehydes with the hydrazine of phthalimidobenzoic acid. The compounds were identified using FTIR and 1HNMR spectroscopy studies, and their antibacterial efficacy against four bacterial species (Staphylococcus aureus, Streptococcus pyrogens, Escherichia coli, and Pseudomonas aeruginosa) and one fungal species (Candida albicans) was assessed in vitro using a 100 µg/mL concentration of derivatives in dimethyl sulfoxide. Results: The antimicrobial activity of each compound towards the isolates was variable. Most of the compounds exhibited a slight inhibition rate towards Gram-positive and Gram-negative bacteria, particularly S. aureus, which was shown to be highly resistant to all derivatives used. However, there was moderate to high killing activity towards S. pyogenes. Conclusions: The synthesized phthalimide Schiff bases derivatives exhibited variable antibacterial activity against the tested microbes. The results suggest that further studies are required to optimize the efficacy of these compounds against harmful microorganisms.",
"keywords": [
"Schiff base",
"phthalimide",
"phthalic anhydride",
"antimicrobial"
],
"content": "Introduction\n\nThe basic goal of medicinal chemistry is to create molecules with less harmful properties that have potential efficacy as therapeutic agents. Phthalimide derivatives are one group of such agents that have a wide range of anti-inflammatory,1,2 antidiabetic,3 and antioxidant4 medical uses. There are many phthalimide derivatives as potential anticancer agents.5 Recent studies on the biological activity of phthalimide and several of its derivatives show that they possess significant biological activity that seem equivalent to or even greater than those of recognized pharmaceutical compounds.6\n\nPhthalimide derivatives are given a biological activity via the imide ring and structural core (-CO-N(R)- CO-).7 Several pharmacophore subunits, including pyrazoles and diazoles, (oxo and thioxo) triazoles, benzo- (oxazoles, imidazoles, and thiazoles), and compounds containing the azomethine group (Schiff bases), were added using the molecular hybridization method to boost the biological action of phthalimide derivatives.8 The most commonly used types of organic substances include Schiff bases - with the imine (-C=N-) -[14]; they are very helpful for creating several bioactive medicinal molecules from primary amine.7\n\nSchiff bases result from a certain series of conditions-driven chemical reactions between a primary amine and an aldehyde or ketone. Hugo Schiff described these molecules for the first time.9 Aldehydes and/or ketones undergo the substitution of nitrogen for oxygen at the carbonyl functional group (CO), resulting in the generation of imine, azomethine, anilino, or azimethine (CN) functionalities and the release of a water molecule, which is a hallmark of Schiff base components and disrupts normal cellular functions.9\n\nSchiff bases have a broad range of uses, including analytic, biological, and major areas of inorganic chemistry. They have a variety of biological effects such as anti-inflammatory,10 analgesic,11 antibacterial,12 anticonvulsant, antitubercular, anticancer, antioxidant, and anthelmintic properties. Schiff bases have grown in significance in the medical and pharmaceutical disciplines since hydrogen bonding between the azomethine’s nitrogen atom and the cell’s active centers may very well be formed.9\n\nThis research draws upon the wide scope of phthalimide derivatives’ potentiality and biological activity to produce new antibacterial and antifungal derivatives.\n\nThis study aims to boost the biological effect of the phthalimide ring and the Schiff base by creating various hybridized structures. The reason for creating various hybridized structures in this study was to enhance the biological effect of the phthalimide ring and the Schiff base. By combining these two components in different ways, the researchers aimed to explore new compounds with improved biological activity. In order to achieve this, the study employed a three-step process that involved hybridizing the phthalimide ring with functionalized aldehydes, resulting in the synthesis of nine different compounds. These compounds incorporated diverse groups such as halogens, methoxy groups, and phenolics, which are known to possess biological properties.\n\n\nMethods\n\nPhthalic anhydride was produced by Alpha Chemika India, and para-aminobenzoic acid was supplied by Thomas Baker, Mumbai, India. Glacial acetic acid, 99.98% ethanol, thionyl chloride, and hydrazine 99%, n-hexane, benzene, acetone, and ether were among the solvents and other chemicals that were purchased from commercial sources and employed in the various stages of the synthesis. Thin layer chromatography (TLC) (GF254 merk-Germany) under UV light was applied to ensure that the created substances were pure and to observe reaction progression (254 nm). S1 [(benzene: acetone) (7:3)] and S2 [(ethanol, ethylacetate, n-hexane, and toluene) (3:3:6:4)] were the solvent systems that were used. The melting points were calculated without adjustment using capillary tubes and the Stuart SMP30 apparatus, (Bibby Scientific, UK). The thin film approach acquired FT-IR spectra (υ, cm-1) using an attenuated total reflectance - Fourier transform infrared spectrometer (ATR- FTIR) (IRAffinity-1S, Shimadzu, Japan), at the University of Baghdad’s College of Pharmacy. Part of our study were conducted at the University of Tehran, Iran including Proton nuclear magnetic resonance (1H-NMR) studies, which used a Bruker Ultrashield, (Bruker Ltd, UK) 500 MHz with DMSO as the solvent.\n\n4-(1,3-dioxoisoindolin-2-yl) benzoic acid7\n\nPhthalic anhydride and 4-aminobenzoic acid were reacted in an equimolar ratio of 1 mmoL each in 15 ml of glacial acetic acid.\n\nAfter refluxing the reactants for three hours, the reaction medium was washed with 25 mL of ice-distilled water, filtered, dried, and recrystallized from absolute ethanol to get an intermediate (1).\n\nThe yield at 93% was a fluffy white powder and the melting point (m.p.) was 287–290°C. RF (0.74), FTIR: 3100–2553.75 cm-1 O-H Carboxylic acid stretching; 3067.82 cm-1. (C-H) stretching of Ar.; 1782.23 and 1766.80 cm-1 asymmetric and symmetric. Imide (C=O) str.; 1720.50 cm-1 carboxyl (C=O) str.; 1689.64–1465 cm-1 Ar.(C=C) str.; 1076 and 705 cm-1 aromatic (C-H) bend. HNMR interpretation δ = ppm (300MHz, Bruker): 10.50 (1H, s, OH), 7.62–8.12 (8H, m, 2Ar-H).\n\n4-(1,3-dioxoisoindolin-2-yl) benzoyl chloride\n\nAn addition of 10 mL of SOCl2 to the intermediate (1) (10 mmol) in 5 mL dry benzene and three hours of refluxing was done. Once cooled, the overabundance of SOCl2 and benzene were vacuum isolated and then washed with benzene to give intermediate (2).\n\nThis yield at 77% was a yellow powder, m.p. 300°C. RF 0.3. FTIR: 1782.23 cm-1 carboxyl (C=O) str; 1766.80 and 1708.93 cm-1 asym. and sym. Imide (C=O) str; 1597.06 cm-1 Ar.(C=C) str.; 1HNMR Interpretation δ= ppm (300MHz, Bruker): 7.62–8.12 (8H, m, 2Ar-H).13\n\n4-(1,3-dioxoisoindolin-2-yl) benzo hydrazide (3)14\n\nThe intermediate (2) (10 mmol - 2.67 gm) was treated with 50 mmol of hydrazine hydrate (99%) and dry benzene (15 mL).\n\nAfter refluxing the mixture for four hours, it was cooled and surplus hydrazine hydrate and solvent were separated under reduced pressure, rinsing the leftover with ether and recrystallizing it with 99% ethanol to get intermediate (3).\n\nThe yield was 65% and a white solid, m. p. 270–272°C. RF 0.6.\n\nFTIR: 3421.72 and 3340.71 cm-1 asym. and sym. primary amide (N-H) str.; 3224.98 cm-1 amide (N-H) str.; 3066 cm-1 Ar-(C-H) str.; 1681.93 and 1640.78 cm-1 asym. and sym. Of imide (C=O) str.; 1631cm-1 (C=O) amide str.; 1593 cm-1 (N-H) amide bend. 1573–1442 cm-1 Ar-(C=C) str.; 1111.86 and 771.53 cm-1 in and out of a plane (C-H) bend.\n\n1HNMR Interpretation: 5.1 ppm (2H,s, -NH2), 6.83–8.00 ppm (8H, m, Ar-H), 11.58 ppm (1H, s, -CO-NH).\n\n4-(1, 3-dioxoisoindolin-2-yl) benzohydrazide derivatives (3a-f)15,16\n\nUsing a flask with a round bottom and a magnetic stirrer, each of the aldehydes – listed in further detail in Table 1 – was dissolved in ethanol, adding three drops of glacial acetic acid.\n\nThe procedure for carrying out the synthesis of the phthalimide phenyl hydrazide derivatives and the characterization of intermediates and Schiff bases is described as follows:\n\n1. Preparation of reaction mixture\n\nEthanol (99%; 20 mL) was used as a solvent to suspend intermediate 3 (5 mmol, 1.33 g). The intermediate 3 was added to separate stirred solutions of the aldehydes.\n\n2. Refluxing\n\nThe reaction mixtures were refluxed for a further 14–16 hours. Refluxing involves heating the reaction mixture to its boiling point under controlled conditions, typically using a reflux condenser. This ensures that the reaction proceeds efficiently and allows for the completion of the desired chemical transformations.\n\n3. Monitoring the reaction\n\nThe progress of the reaction was monitored using thin-layer chromatography (TLC). TLC involves spotting a small amount of the reaction mixture onto a thin layer of adsorbent material, such as silica gel, on a glass plate. The plate is then developed in a solvent system, allowing the different components of the reaction mixture to separate based on their affinity for the adsorbent material. By comparing the TLC profile of the reaction mixture with that of the starting materials and expected products, the completion of the reaction can be determined.\n\n4. Addition of ice-cold water\n\nWhen the reaction was deemed complete based on the TLC monitoring, a total of 50 mL of ice-cold water was introduced to the reaction mixture. This addition of water is done to facilitate the precipitation of the desired product and to separate it from the reaction mixture.\n\n5. Filtration and drying\n\nAfter the addition of water, the reaction mixture was filtered to separate the precipitate from the solvent and any remaining impurities. The resulting solid was then dried to remove any traces of solvent or water. Drying can be achieved by subjecting the solid to low heat or vacuum conditions, ensuring the removal of moisture without causing decomposition of the compound.\n\n6. Recrystallization\n\nThe dried precipitate was subjected to recrystallization from ethanol. Recrystallization is a purification technique that involves dissolving the solid in a suitable solvent (in this case, ethanol) and then allowing it to slowly cool or evaporate, leading to the formation of well-defined crystals. This process helps remove impurities and obtain a higher purity of the compound.\n\n7. Characterization\n\nThe physical properties of the intermediates and Schiff bases were determined and recorded. These properties can include melting point, boiling point, color, solubility, and any other relevant characteristics. The information obtained from the characterization helps confirm the identity and purity of the synthesized compounds. Physical properties of intermediates and Schiff bases are listed in Table 2.\n\nUsing a bacterial solution with a concentration of 1.5 × 108 CFU/mL derived from the McFarland turbidity standard, an antibacterial essay using the disc-well diffusion technique was completed (number 0.50). It was used to inoculate the agar by swabbing the top of Mueller Hinton agar (MHA) plates. Under a sterile hood, the surplus liquid was left to air dry. Four wells were formed in each agar plate and were used to study the bacteria, Pseudomonas aeruginosa and Streptococcus pyogenes, and each well received (80 mL) of each synthetic drug. At 37°C, the plates were left in the incubator for 24 hours. Antibacterial activity was assessed based on measuring the diameter of the well’s surrounding inhibitory zone.17\n\nThe disc-well diffusion technique is a widely used method for assessing the antimicrobial activity of compounds against various microorganisms. This technique is particularly valuable in determining the susceptibility of bacteria and fungi to novel antimicrobial agents, such as the newly synthesized phthalimide phenyl hydrazide derivatives in this study.\n\nThe procedure involves the preparation of sterile agar plates that serve as a growth medium for the microorganisms. The agar is first inoculated with a standardized suspension of the test organism, ensuring a uniform distribution of the microorganisms across the agar surface. Once the agar solidifies, either sterile filter paper discs or wells are placed on the surface of the agar.18\n\n\nResults and discussion\n\nThe current work focused on developing new compounds incorporating the active moieties (phthalimide and Schiff base) with expected biological activity because both N-substituted phthalimides and Schiff bases are known as biologically active compounds with a wide spectrum of various applications. This target was created using the multistep synthesis shown in Figure 1.\n\nThe starting step involved phthalic anhydride used with the primary amine para-amino benzoic acid for synthesizing n-phenyl phthalimide with the assistance of glacial acetic acid as the solvent and reaction catalyst.18 Intermediate 1 (the resultant of the previous reaction) underwent an SN1 reaction with thionyl chloride to chlorinate the benzoic acid portion of intermediate 1, forming intermediate 2. This reaction occurred in the presence of benzene as a solvent. As the components started to react, hydrogen chloride (HCl) fumes were produced therefore this procedure was performed under a fume hood. After three hours of reflexing, the yellow powder was isolated, composing intermediate 2.18\n\nFor preparing hydrazide derivatives (intermediate 3), we used 50 mmol hydrazine 99% with dry benzene and 10 mmol of intermediate 2.19 The resultant white powder was recrystallized by absolute ethanol. Six aldehydes were chosen for Schiff base synthesis with intermediate 3 by condensation reaction to give intermediates 3a–f.20\n\nThe method we used to create the new Schiff bases involved converting benzoic acid to an active acyl chloride group placed in the para position of a phenyl ring attached to a phthalimide moiety, followed by the nucleophilic replacement of the chloride with hydrazine moiety. This created a position suitable for an amino group, which was then prepared for condensation with the chosen aldehydes and ketones to create the desired Schiff bases.\n\nFTIR spectrum of intermediate 1 as shown in (Table 2) compound 1 shows strong absorption bands at 1782.23 and 1766.80 cm-1 due to asymmetric. and symmetric. Imide (C=O) str. Other absorption bands appeared at 3100–2553.75cm-1 and at 1720.50 cm-1 and belong to O-H carboxylic acid str. and carboxyl (C=O) str., respectively.21\n\nFTIR spectra of intermediate of compound 2 showed O-H carboxylic acid str vanishing. The absorption bands demonstrated the success of the dehydration reaction.\n\nFinally, the FTIR spectrum of intermediate compound 3 showed two strong absorption bands at 3421.72 cm-1 and 3224.98 cm-1, respectively, corresponding to the (-NH2-NH) group, which is evidence for the attainment of hydrazine intermediate. While FTIR spectra of the prepared Schiff bases (3a–f) displayed the vanishing of these two distinctive absorption bands at 3421.72 and 3224.98 cm-1, which belong to the (-NH2-NH) group in hydrazine intermediate 3 and formation of the new distinct absorption band at 1654cm-1 due to (C=N) imine. These two facts indicate the existence of the Schiff base formation. All the underlying data for FTIR results are shown in Alassadi (2023).22\n\nAside from the FTIR spectrum of the Schiff bases [3a–f], distinct absorption bands at 1620 and 1611 cm-1 were seen, attributed to asymmetric and symmetric stretching of imide (C=O) str. Other absorptions appeared at 1716.65 cm-1 for (C=O) amide str., 1654 cm-1 for (N=C) str. of the Schiff base, and 3224.98 cm-1 for (N-H) str of amide.\n\nMoreover, the FTIR spectra of Schiff bases 3a, 3c revealed distinct absorption bands at 2916 and 2877 cm-1 asymmetric and symmetric stretching. The appearance of aliphatic (CH3) str., while 3b demonstrated two absorptions, 3267.41 cm-1 and 1519 cm-1 str for phenolic (O-H) asymm. Tables 3 and 4 include complete details of the FTIR spectrum records for compounds [1–3] [3a–3f].\n\nFurthermore, 1HNMR spectra of the produced compounds displayed distinctive unambiguous signs of intermediate 1, phthalimidobenzoic acid at σ = 7.62–8.12 ppm about aromatic protons. At σ = 10.50 ppm, a distinct signal of (OH) carboxylic proton occurred. The 1HNMR spectra of intermediate 2 revealed the elimination of the (OH) carboxyl proton peak and the emergence of multiplet peaks exclusively at σ = 7.62–8.12 ppm pertaining to protons of two aromatic rings. Intermediate 3 displayed signals at σ = 5.1 ppm and 11.58 ppm corresponding to the NH2 and NH of the hydrazine part, respectively, whereas aromatic protons emerged at σ = 6.83–8.00 ppm.\n\nThe 1HNMR spectra of Schiff base 3a revealed a signal at σ = 2.7 ppm that belonged to CH3 protons, multiplet signals at σ = 7.45–7.97 ppm that related to aromatic, and singlet signals at σ = 8.5 and 11.58 ppm that belonged to the CH of imide and NH of amide, respectively. Schiff base 1HNMR spectrum [3b] Singlet signals at σ = 11.25 ppm of phenolic OH and multiplet peaks at σ = 7.88–8.12 ppm of aromatic protons were seen.\n\nAntimicrobial activities for the resultant Schiff bases against two types of bacteria and one type of fungus were evaluated, and the results are listed in Table 4. The results indicated that Schiff bases 3d and 3f showed very high activity against Pseudomonas aeruginosa, Streptococcus pyogenes and the fungus Candida albicans.\n\nPseudomonas aeruginosa compounds and 3e and 3f showed high activity against Streptococcus pyogenes. While compounds 3a–3f were only slightly active against E. coli and there was no activity against Staphylococcus aureus and Candida albicans.\n\n\nConclusions\n\nThe collected compounds were identified using FTIR and 1HNMR studies, and their antibacterial efficacy against five different types of microbes was assessed in vitro. Four harmful microorganisms were used as test subjects for the antibacterial activity of all produced compounds. Using a 100 μg/mL concentration of derivatives in dimethyl sulfoxide (DMSO), four bacterial species – S. aureus, S. pyrogens, E. coli, and P. aeruginosa – and one fungal species – C. albicans – were tested. The antimicrobial activity of each compound towards isolates was variable. Most of them exhibited a slight inhibition rate towards G+ve and G-ve, particularly S. aureus, which was shown to be highly resistant to all derivatives used. However, there was moderate to high killing activity toward S. pyogenes.",
"appendix": "Data availability\n\nZenodo: Underlying data for synthesis, characterization, and preliminary antimicrobial study of some new phthalimide phenyl hydrazide derivatives, https://doi.org/10.5281/zenodo.7536697. 22\n\nThis project contains the following underlying data:\n\n• Data file 1: ab1021-2.pdf (RT-FT-IR (IR Affinity-1) spectrophotometer result, intermediate compound 1).\n\n• Data file 2: SOS-2.pdf (RT-FT-IR (IR Affinity-1) spectrophotometer result, intermediate compound 2).\n\n• Data file 3: H105-2.pdf (RT-FT-IR (IR Affinity-1) spectrophotometer result, intermediate compound 3).\n\n• Data file 4: SDM-2.pdf (RT-FT-IR (IR Affinity-1) spectrophotometer result, final compound 3a).\n\n• Data file 5: SNO-2.pdf (RT-FT-IR (IR Affinity-1) spectrophotometer result, final compound 3b).\n\n• Data file 6: SPY-2.pdf (RT-FT-IR (IR Affinity-1) spectrophotometer result, final compound 3c).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nBach D, Liu J, Kyung W, et al.: Bioorganic & Medicinal Chemistry Synthesis and biological activity of new phthalimides as potential anti-inflammatory agents. Bioorg. Med. Chem. 2017; 25(13): 3396–3405. Publisher Full Text\n\nLima LM, Castro P, Machado AL, et al.: Synthesis and Anti-Inflammatory Activity of Phthalimide Derivatives, Designed as New Thalidomide Analogues. Bioorg. Med. Chem. 2002; 10(9): 3067–3073. PubMed Abstract | Publisher Full Text\n\nJawed HAM, Mohammed MH, Ismeal SH, et al.: Synthesis, Characterization and Alpha Glucosidase Inhibition Activity of New Phthalimide Derivatives. Iraqi. J. Pharm Sci. 2018; 27(1): 100–108.\n\nNayab PS: New phthalimide - appended Schiff bases: Studies of DNA binding, molecular docking, and antioxidant activities. Luminescence. 2016; 32(5): 1–10.\n\nAbdulrahman HS, Hassan Mohammed M, Al-Ani LA, et al.: Synthesis of phthalimide imine derivatives as a potential anticancer agent. J. Chem. 2020 Sep 16; 2020: 1–3. Publisher Full Text\n\nFhid O, Doma AM, Zeglam TH, et al.: Synthesis, characterization and antimicrobial activity of some new phthalimide derivatives. Der. Pharma Chemica. 2015; 7(11): 240–242.\n\nSahib HA, Mohammed HM: Synthesis and Preliminary Biological Activity Evaluation of New N- Substituted Phthalimide Derivatives. Iraqi. J. Pharm Sci. 2020; 29(1): 247–252. Publisher Full Text\n\nLamie PF, Phillopes JN, El-Gendy AO, et al.: Design, synthesis and evaluation of novel phthalimide derivatives as in vitro anti-microbial, anti-oxidant and anti-inflammatory agents. Molecules. 2015 Sep 14; 20(9): 16620–16642. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhan MI, Gul S, Ali KM: Schiff Bases and Their Metallic Derivatives: Highly Versatile Molecules with Biological and Abiological Perspective, Stability and Applications of Coordination Compounds, Abhay Nanda Srivastva. IntechOpen; April 30th, 2019. Publisher Full Text\n\nBhushankumar SS, Jaychandran E, Jagtap A, et al.: Synthesis characterization and anti-inflammatory evaluation of new fluorobenzothiazole Schiff’s baseshjn. Int. J. Pharm Res. Dev. 2011; 3: 164–169.\n\nSondhi SM, Singh N, Kumar A, et al.: Synthesis, anti-inflammatory, analgesic and kinase (CDK-1, CDK-5 and GSK-3) inhibition activity evaluation of benzimidazole/benzoxazole derivatives and some Schiff’s bases. Bioorg. Med. Chem. 2006; 14(11): 3758–3765. Publisher Full Text\n\nChinnasamy RP, Sundararajan R, Govindaraj S: Synthesis, characterization, and analgesic activity of novel schiff base of isatin derivatives. J. Adv. Pharm. Technol. Res. 2010 Jul; 1(3): 342. Publisher Full Text\n\nAhamed LS: Synthesis of New Polyester-Amides from Polyvinyl Alcohol and Convert Some of Them to Polyester-Imide. Journal of Al-Nahrain University. 2011; 14(2): 29–42. Publisher Full Text\n\nBayrak H, Demirbas A, Karaoglu SA, et al.: Synthesis of some new 1, 2, 4-triazoles, their Mannich and Schiff bases and evaluation of their antimicrobial activities. Eur. J. Med. Chem. 2009 Mar 1; 44(3): 1057–1066. PubMed Abstract | Publisher Full Text\n\nYorur-goreci C, Demir Z, Altas N: Green Synthesis of New Amino Acid Schiff Bases and Their Biological Activities. Turkish Chem Soc. 2016; 3(3): 15–26. Publisher Full Text\n\nAbduljabbar TT, Hadi MK: Synthesis, Characterization and Antibacterial Evaluation of Some Coumarin Derivatives. Iraqi. J. Pharm Sci. 2021; 30(1): 249–257.\n\nBaskaran C, Velu S, Kumaran K: The efficacy of Carica paper leaf extract on some bacterial and fungal strain by well diffusion method. Asian pacific journal of Tropical Disease. 2012; 2: S658–S662. Publisher Full Text\n\nAl-hussaniy HA, Altalebi RR, Albu-Rghaif AH, et al.: The Use of PCR for Respiratory Virus Detection on the Diagnosis and Treatment Decision of Respiratory Tract Infections in Iraq. Journal of Pure and Applied Microbiology. 2022; 16(1): 201–206. Publisher Full Text\n\nAl-Azzawi AM, Ali MS: Synthesis and curing of novel phenol-formaldehyde resins containing pendant citraconimides. Al-Nahrain Journal of Science. 2008; 11(3): 15–30.\n\nOkuyama T, Howard M: Organic chemistry: a mechanistic approach. Oxford University Press; 2013.\n\nValeur E, Bradley M: Amide bond formation: beyond the myth of coupling reagents. Chem. Soc. Rev. 2009; 38(2): 606–631. PubMed Abstract | Publisher Full Text\n\nAlassadi NM: Supplementary data for Synthesis, Characterization, and Preliminary Antimicrobial Study of Some New Phthalimide Phenyl Hydrazide Derivatives.2023. Publisher Full Text"
}
|
[
{
"id": "286919",
"date": "11 Jun 2024",
"name": "Renjith Thomas",
"expertise": [
"Reviewer Expertise Organic Synthesis",
"Computational Chemistry",
"Solvation Dynamics",
"Machine Learning."
],
"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 explores the synthesis, characterization, and preliminary antimicrobial activity of new phthalimide phenyl hydrazide derivatives. It aims to expand the arsenal of antimicrobial agents by investigating the potential of these derivatives against a range of bacterial and fungal species, emphasizing their synthesis and the biological activity of the imide ring and Schiff base hybrid structures. Some Comments:\nSynthesis procedure should be given in more detail, especially the purification methods. The introduction section is poorly written, lacking clarity in setting up the study's background and significance. The literature review is inadequate and does not comprehensively cover recent advancements relevant to the compounds being studied. Objectives of the study are not clearly stated, which can confuse the reader about the study's purpose. Check the consistency of units used for molecular weights, concentrations, and spectral data, and ensure they adhere to the SI system. Some of the spectroscopy data lacks detailed explanation on how the peaks correlate to structural features of the compounds. Ensure the methods section provides enough detail for reproducibility, particularly in the synthesis and characterization processes. The manuscript needs a clearer explanation of the results and a more detailed discussion on how the findings contribute to existing knowledge. The interpretation of spectral data seems inconsistent with typical expected results, which could indicate either an error in methodology or misinterpretation of data. Some chemical structures depicted in the manuscript do not match the described synthetic pathways or the corresponding NMR and IR data provided. Ensure all figures and tables are correctly cited in the text and that their descriptions accurately reflect the data shown. The conclusion section is vague and does not effectively summarize the findings or suggest future research directions based on the study's outcomes.\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?\nNot applicable\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": []
},
{
"id": "286917",
"date": "24 Jun 2024",
"name": "Laxman V. Gavali",
"expertise": [
"Reviewer Expertise Synthesis and characterization of Schiff base and its mixed ligand metal complexes"
],
"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\n1. Authors synthesized phthalimide phenyl hydrazide derivatives and confirmed by TLC and FTIR. 2. Need to confirm by NMR, the author did not provide NMR spectra 3. The result and analysis data should reflect HNMR spectral interpretation of synthesized compounds. 4. Need antimicrobial activities pics of inhibition compared with standards. 5. The procedure for carrying out synthesis should be explained in one para.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-245
|
https://f1000research.com/articles/12-1312/v1
|
11 Oct 23
|
{
"type": "Research Article",
"title": "Combining contour-based and region-based in image segmentation",
"authors": [
"Issam Dagher",
"Elie Abboud",
"Elie Abboud"
],
"abstract": "Background: This paper presents an optimized clustering approach applied to image segmentation. Accurate image segmentation impacts many fields like medical, machine vision, object detection. Applications involve tumor detection, face detection and recognition, and video surveillance. Methods: The developed approach is based on obtaining an optimum number of clusters and regions of an image. We combined Region-based and contour-based approaches. Initial rough regions are obtained using edge detection. We have used Gabor wavelets for texture classification and spatial resolutions. Color frequencies are also used to determine the number of clusters of the Fuzzy c-means (FCM) algorithm which gave an optimum number of clusters or regions. Results: We have compared our approach with other similar wavelet and clustering techniques. Our algorithm gave better values for segmentation metrics like SNR, PSNR, and MCC. Conclusions: Optimizing the number of clusters or regions has a significant effect on the performance of the image segmentation techniques. This will result in better detection and localization of the segmentation-based application.",
"keywords": [
"Image Segmentation. Clustering. Edge detection. Colour frequencies. Texture."
],
"content": "Introduction\n\nImage segmentation is a fundamental step in computer vision for object recognition and classification. Despite many techniques and algorithms have been proposed, image segmentation remains one of the most challenging research topics because none of them can provide a coherent framework for achieving quick and efficient segmentation of images.1 Two explanations can be attributed to the complexity of image segmentation. The first is that image segmentation has many solutions for the problem i.e. for one image, there are many best results of segmentation. The second is because of noise, background, low signal-to-noise-ratio, and uninformed intensity.2 For that, it is difficult to only suggest one image segmentation method. We can distinguish between two concepts in image segmentation: region-based and contour-based techniques.\n\nRegion-based approaches partition the image into different homogenous regions based on similarities in color, location, and texture.\n\nContour-based techniques start with edge detection technique followed by linking and forming the segments.\n\nIn this paper, we tried to combine both approaches. We start with the Canny edge detector. Then we form initial regions accordingly. Those regions are optimized and merged according to similarities in color, location, and texture.\n\nOver recent years, several techniques have been developed to segment images. Wavelet-based segmentation can be found in Ref. 3. Unsupervised image segmentation4 is performed using k-means clustering. It clusters (segments) the image into different homogenous regions. In Ref. 5 Graph theory was employed using greedy decisions. Segmentation using Texture is shown in Sagiv et al.6 Shi et al.7 used smoothness and boundary continuity. Ren and Malik8 used contours and textures. In Refs. 9 and 10 the concept of superpixels was used where the redundancy of the image can be highly decreased Superpixel methods11,12 have been researched intensively using NCut, mean shift, and graph-based methods. Genetic algorithm was also employed in Ref. 13. Edge detection techniques in image segmentation is shown in Ref. 14.\n\n\nImage segmentation techniques\n\nImage segmentation is the process of dividing an image into multiple partitions. It is typically used to locate objects and change the representation of the image into something more meaningful. It is also used in multiple domains such as medical imaging, object detection, face recognition, and machine vision.\n\nImage segmentation consists of assigning a label for every pixel in an image. Moreover, different labels have different characteristics, and the same labels share the same characteristics at some point such as color, intensity, or texture. The result of image segmentation is a set of segments that collectively cover the entire image or a set of contours extracted from the image.\n\nDifferent image segmentation techniques exist like threshold-based, region growth, edge detection, and clustering methods.1\n\nThreshold segmentation15 is one of the most common segmentation techniques. It splits the picture into two or multiple regions using one or multiple thresholds. The most commonly used threshold segmentation algorithm is the Otsu method, which selects optimum threshold by optimizing deviation between groups. Its downside is that it is difficult to get correct results where there is no noticeable grayscale variation or overlap between the grayscale values in the image.2 Since Thresholding recognizes only the gray information of the image without taking into consideration the spatial information of the image, it is vulnerable to noise and grayscale unevenness, for that it is frequently combined with other methods.\n\nThe regional growth approach16 is a traditional serial segmentation algorithm, and its basic concept is to use identical pixel properties together to construct a region. An arbitrary seed pixel is chosen and compared with neighboring pixels. The region is grown from the seed pixel by adding neighboring pixels that are similar, increasing the size of the region. When the expansion of one region stops, another seed pixel that doesn’t yet belong to any region is chosen and therefore the flow is repeated.\n\nEdge detection17 is used to find the boundaries of objects in an image. It detects discontinuities in brightness. The most common edge detection technique is Canny edge detector which can be described by the 5 following steps.\n\n1. Gaussian filter is used to smooth the image.\n\n2. Get the gradient magnitude and the gradient angle of the image.\n\n3. Non-maximum suppression is applied.\n\n4. Double thresholding is applied.\n\n5. Suppress weak edges using hysteresis.\n\nFinally, the image is segmented, and edges are drowned at the boundaries of each object.\n\nClustering18 is the task of dividing the population or data points into several groups such that similar data points within the same groups are dissimilar to the data points in other groups. A common clustering algorithm is the Fuzzy C-means (FCM).\n\nFuzzy c-means (FCM) is a clustering method that permits one piece of data to be a member of two or more clusters. Based on the distance between the cluster center and the data point, this algorithm determines each data point’s membership in relation to each cluster center. The FCM algorithm can be described by the following steps:\n\n1. Randomly select ‘c’ cluster centers.\n\n2. Calculate the fuzzy membership ‘μij’ using:\n\n3. Compute the fuzzy centers ‘vj’ using:\n\n4. Repeat step 2 and 3 until ||U(k+1) - U(k)||< ԑ.\n\nThe Connected component algorithm19 scans an image and groups the pixels into components dependent on pixel connectivity, i.e. all pixels in the connected component share identical pixel intensity values and are in some way connected. Until all classes have been determined, each pixel shall be labelled with a gray level or a color (color marking) according to the portion to which it has been allocated. Connected part labeling works by scanning an image, pixel-by-pixel (from top to bottom and from left to right) to identify connected pixel regions, i.e. neighboring pixel regions that share the same collection of intensity values as V. The following is the labeling for p:\n\n• If all four neighbors are zero, give p a new label; otherwise\n\n• If only one neighbor has V= 1, give its label to p; otherwise\n\n• If more than one neighbor has V= 1, give one of the labels to p and note the equivalences.\n\nAfter screening, the identical label pairs are sorted into equivalence groups and a unique label is assigned to each class. As a final stage, a second scan is performed through the image, during which each label is replaced by the label assigned to its equivalence class.\n\nThe objective of Texture filters20 is to separate the regions in an image based on their texture content. While smooth regions are characterized with a small range of values in the neighborhood around a pixel, rough texture regions are characterized by a large range of values. Gabor Wavelets are band pass filters which extract the image local important features. A convolution is done between the image and the filters in order to get texture frequency and orientation. We have used the outputs of Gabor filters with 8 orientations and 5 wavelengths.\n\n\nMethods\n\nThe proposed approach is based on obtaining an optimum number of clusters and regions of an image obtained from the Berkeley segmentation dataset. This is done using the following three consecutive steps:\n\nI. Obtaining a good initial set of centers:\n\n• Apply edge detection. This is done using the canny edge detector.\n\n• Apply the connected component algorithm on the binary image obtained.\n\n• Using the labeled image, find the properties of each region.\n\n• Join similar regions and keep the unique ones.\n\n• Finally, find the center of each region.\n\nFigure 1 illustrates the procedures of step I.\n\nII. Reducing the number of centers\n\nThis is done using texture filters as follows:\n\n• Get the feature vectors of each center using Gabor filters.\n\n• Merge the centers according to their Euclidian distances and the results obtained from the Gabor filters using:\n\nThe Euclidian distance between 2 centers is given by:\n\nWhere Xcenter 1 and Ycenter 1 are the xy coordinates of the first center and Xcenter 2 and Ycenter 2 are the xy coordinates of the second center\n\nThe features distance between 2 centers is given by:\n\n• If the 2 centers are close to each other and approximately belong to the same texture, then merge them.\n\nThe results are shown in Figure 2.\n\nFigure 2 shows that the number of centers was reduced from 246 to 97.\n\nIII. Apply the FCM clustering algorithm:\n\nIt should be noted that the FCM clustering requires the specification of the number of clusters. Noting that in color image segmentation the similarity used by the FCM is based on Euclidian distance between RGB pixels, getting the number of clusters is done by using Color frequencies. The color frequencies21 index is computed by three steps:\n\n1. All the color frequencies of the image are computed and added to an array\n\n2. Then, the duplications in the array are removed and unique frequencies are kept\n\n3. Finally, only the main colors are kept for example if there are multiple shades of a color only the main color is kept, and the other ones are removed\n\nThe color frequencies index is equal to the size of the array and is given as an input to the FCM function. After this step is applied the number of RGB centroids is reduced from 97 centroids to only 13 (Figure 3). Then the RGB distance is computed between each pixel and the center to determine its corresponding label.\n\nOur algorithm is summarized in Figure 4.\n\nFigure 5 shows 3 images and their edge images. Figure 6 shows the edge images and their corresponding initial set of centers. The optimum number of cluster centers is shown in Figure 7. The final image segmented images are shown in Figure 8\n\n\nResults\n\nTo evaluate this work, the BSDS500 database22 is chosen. It is used for most segmentation techniques. It consists of 500 images of outdoor scenes, landscapes, buildings, animals, and humans. Figure 9 shows sample images from the database.\n\nThe following segmentation metrics23 are used to show the effectiveness of our novel approach: accuracy, F-measure, precision, MCC, dice, Jaccard, specificity. Those metrics are computed by comparing the result segmented image with the ground truth of the original image.\n\nGiven that: TP is the true positive, TN is the true negative, FN is the false negative and FP is the false positive\n\nIn this section, the results of the proposed approach are compared with different methods on the same database and using the same classification metrics. For the K-means and the SLIC we have experimented with different values of K and we have chosen the value of K which gave good segmentation results. We used K=10 for the K-means and K=100 For the SLIC.\n\nGraphical Illustration\n\nThe following figures illustrate the segmentation results of the Kmeans, SLIC, and our algorithm. Figure 10 shows the results obtained by the K-means, the SLIC, and our algorithm. The Figure shows the superior performance of our approach.\n\nResults of the K-means, the SLIC, and the proposed approach in second, third, and fourth columns respectively.\n\nComparisons based on the Segmentation metrics\n\nTable 1 shows the segmentation metrics results of our algorithm compared to the K-means, the SLIC and the CAS24 algorithms. The images of the BSD500 are used and the average segmentation metrics are shown in the table. Table 4.1 shows the accurate segmentation results of our algorithm compared to the others. It should be noted that our algorithm does not require a priori to specify the number of centers.\n\nTo show the effectiveness of the proposed method, we have followed the experiments done in Ref. 3 using 2 images: Lena and the Cameraman images (Figure 11). We have used the SNR and the PSNR as verification indices. Table 2 shows the results obtained. It clearly shows the outperformance of our approach.\n\nBigger SNR and PSNR imply better segmentation results. Our algorithm gave for the Lena image an SNR 0f 50.89 and PSNR of 7.78 which are bigger than the other 4 algorithms.\n\n\nConclusion\n\nImage segmentation has become an important topic in many fields like medical, machine vision, object detection. In this work, a new approach is proposed to improve the accuracy and performance of image segmentation. We combined Region-based and Contour-based segmentation both approaches. Edge detection, Color frequencies, and texture measures are used in developing the new algorithm. We started with Canny edge detector. Then we formed initial regions accordingly. Those regions are optimized and merged according to similarities in color, location and texture. We obtained optimum number of clusters and regions of an image. To show the effectiveness of this work, the BSDS500 database is chosen and different segmentation and clustering measures were used. The results show the improved performance of the proposed technique compared to other wavelet-based and other techniques.",
"appendix": "Data availability\n\nAll images used in this article were sourced from The Berkeley Segmentation Dataset and Benchmark (BSDS300): https://www2.eecs.berkeley.edu/Research/Projects/CS/vision/grouping/resources.html#algorithms 22\n\nZenodo. COMBINING CONTOUR-BASED AND REGION-BASED IN IMAGE SEGMENTATION. https://doi.org/10.5281/zenodo.8319898. 25\n\nThis project contains the following extended data:\n\n• Code.docx (analysis code)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nAcknowledgements go to the FOE research lab.\n\n\nReferences\n\nSaxena S, Jain S, Tripathi S, et al.: Comparative Analysis of Image Segmentation Techniques.Hura GS, Singh AK, Siong Hoe L, editors. Advances in Communication and Computational Technology. ICACCT 2019. Lecture Notes in Electrical Engineering. Vol. 668. . Singapore: Springer; 2021.\n\nFan L, Zhang F, Fan H, et al.: Brief review of image denoising techniques. Vis. Comput. Ind. Biomed. Art. 2019; 2: 7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGao J, Wang B, Wang Z, et al.: A wavelet transform-based image segmentation method. Optik. 2020; 208: 164123. Publisher Full Text\n\nYang AY, Wright J, Ma Y, et al.: Unsupervised segmentation of natural images via lossy data compression. Comput. Vis. Image Underst. 2008; 110(2): 212–225. Publisher Full Text\n\nFelzenszwalb PF, Huttenlocher DP: Efficient graph-based image segmentation. Int. J. Comput. Vis. 2004; 59(2): 167–181. [7] X. Liu, Q. Xu, J. Ma, H. J. Publisher Full Text\n\nSagiv C, Sochen NA, Zeevi YY: Integrated active contours for texture segmentation. IEEE Trans. Image Process. 2006; 15(6): 1633–1646. PubMed Abstract | Publisher Full Text\n\nShi J, Belongie S, Leung T, et al.: Image and video segmentation: the normalized cut framework. Proceedings 1998 International Conference on Image Processing. ICIP98. 1998; vol. 1: pp. 943–947.\n\nMalik J, Belongie S, Leung T, et al.: Contour and texture analysis for image segmentation. Int. J. Comput. Vis. 2001; 43(1): 7–27. Publisher Full Text\n\nWang C, Liu Z, Chan S: Superpixel-based hand gesture recognition with Kinect depth camera. IEEE Trans. Multimed. 2015; 17(1): 29–39. Publisher Full Text\n\nYang F, Lu H, Yang M: Robust superpixel tracking. IEEE Trans. Image Process. 2014; 23(4): 1639–1651. PubMed Abstract | Publisher Full Text\n\nGong Y, Zhou Y: Differential evolutionary superpixel segmentation. IEEE Trans. Image Process. 2018; 27(3): 1390–1404. PubMed Abstract | Publisher Full Text\n\nAchanta R, Shaji A, Smith K, et al.: SLIC superpixels compared to state-of-the-art superpixel methods. IEEE Trans. Pattern Anal. Mach. Intell. 2012; 34(11): 2274–2282. PubMed Abstract | Publisher Full Text\n\nAngelina S, Suresh LP, Veni SHK: Image segmentation based on genetic algorithm for region growth and region merging. 2012 International Conference on Computing, Electronics and Electrical Technologies (ICCEET), Kumaracoil, 2012. 2012; pp. 970–974. Publisher Full Text\n\nSenthilkumaran N, Rajesh R: Edge detection techniques for image segmentation - A survey of soft computing approaches. Int. J. Recent Trends Eng. 2009; 1(2): 250.\n\nWang W, Duan L, Wang Y: Fast Image Segmentation Using Two-Dimensional Otsu Based on Estimation of Distribution Algorithm. J. Electr. Comput. Eng. 2017; 2017: 1–12. Article ID 1735176. Publisher Full Text\n\nZanaty EA, El-Zoghdy SF: A novel approach for color image segmentation based on region growing. Int. J. Comput. Appl. 2017; 39(3): 123–139. 12 pages, 2017. Publisher Full Text\n\nCanny J: A Computational Approach to Edge Detection. IEEE Trans. Pattern Anal. Mach. Intell. Nov. 1986; PAMI-8(6): 679–698. Publisher Full Text\n\nHuang H, Meng F, Zhou S, et al.: Brain Image Segmentation Based on FCM Clustering Algorithm and Rough Set. IEEE Access. 2019; 7: 12386–12396. Publisher Full Text\n\nAbderaouf Z, Nadjia B, Saliha O: License plate character segmentation based on horizontal projection and connected component analysis. 2014 World Symposium on Computer Applications & Research (WSCAR), Sousse. 2014; pp. 1–5. Publisher Full Text\n\nPark B-Y, Kim H-H, Hong B-W: A Multilabel Texture Segmentation Based on Local Entropy Signature. Math. Probl. Eng. 2013; 6. 2013. ArticleID 651581.\n\nGarcia-Lamont F, Cervantes J, López A, et al.: Segmentation of images by color features: A survey. Neurocomputing. 2018; 292: 1–27. Publisher Full Text\n\nMartin D, Fowlkes C, Tal D, et al.: A database of human segmented natural images and its application to evaluating segmentation algorithms and measuring ecological statistics. Proceedings Eighth IEEE International Conference on Computer Vision. ICCV 2001, Vancouver, BC, Canada. 2001; vol. 2: pp. 416–423. Publisher Full Text\n\nBalafar MA: segmentation evaluatation, MATLAB Central File Exchange.2021. Retrieved February 5, 2021. Reference Source\n\nXiao X, Zhou Y, Gong Y: Content-Adaptive Superpixel Segmentation. IEEE Trans. Image Process. June 2018; 27(6): 2883–2896. PubMed Abstract | Publisher Full Text\n\nDagher I: COMBINING CONTOUR-BASED AND REGION-BASED IN IMAGE SEGMENTATION. [Code]. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "215122",
"date": "03 Nov 2023",
"name": "Sandra Jardim",
"expertise": [
"Reviewer Expertise Machine/Deep Learning",
"Computational Vision",
"Image Processing"
],
"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 “Combining contour-based and region-based in image segmentation” is presented an image segmentation framework that combines region and contour-based approaches. The work presented by the authors addresses an interesting and current subject, but it presents some flaws that I consider relevant and that, in my opinion, should be addressed and resolved.\nMy comments are as follows:\nThe statement \"...because none of them can provide a coherent framework for achieving quick and efficient segmentation of images\" has as reference a work published in 2019. Since then, many image segmentation approaches have been proposed. Indeed, in my opinion, some of them with very good results.\n\nThe authors should consider adding a \"Related work\" section, where they should present and discuss the most relevant and recent image segmentation approaches.\n\nThere are other and recent approaches like the one presented by the authors. Although the comparison made with the chosen methods is interesting, authors must compare the proposed method with similar approaches, to demonstrate the innovation of their proposal when compared to the most recent published works.\n\nFrom the middle of the first page to the beginning of the 5th, the authors only describe basic and well-known concepts/methods. I think that it can/should be resumed.\n\nFigure 4 - The image is not a flowchart in a standard form. The authors should consider presenting a conventional flowchart.\n\nFigure 8 - From the images presented it's difficult to evaluate the results. Indeed, it seems that the plane is not segmented.\n\nThe methods identified by acronyms in Table 2 must be identified in its full description. Additionally, a reference must be given for each one.\n\nThe conclusions are too succinct and should be rewritten in greater detail. The conclusions are too succinct and should be rewritten in greater detail. Additionally, the limitations of the proposed approach must 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? 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": "10562",
"date": "16 Nov 2023",
"name": "Issam Dagher",
"role": "Author Response",
"response": "1. As you suggested I removed the statement \"...because none of them can provide a coherent framework for achieving quick and efficient segmentation of images\" 2. I added a Related work paragraph: 3. I compared my approach with similar approaches: Content-Adaptive Superpixel Segmentation. Linear Iterative Clustering. k-means Wavelet. MVSM BSM VTSM 4. The basic and well known methods are summarized. 5. I changed the flowchart in Figure 4. 6. I changed Figure 8. 7. I explained all the methods in the Related work section. 8. I included more details in the Conclusion section. I thank the reviewer for putting his time in improving the paper."
}
]
}
] | 1
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https://f1000research.com/articles/12-1312
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https://f1000research.com/articles/11-1354/v1
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21 Nov 22
|
{
"type": "Policy Brief",
"title": "Cashew apple in Tanzania: status of utilization, challenges, and opportunities for sustainable development",
"authors": [
"Noel Dimoso",
"Neema Kassim",
"Edna Makule",
"Neema Kassim",
"Edna Makule"
],
"abstract": "Cashew apples, although widely available and rich in nutrients are still underutilized after harvest in Tanzania. Approximately 2,327,000 metric tonnes of cashew apples are lost each year. Their counterpart, the cashew nut is highly appreciated and successfully contributes to the national economy. The huge underutilization of cashew apples is a challenge that requires urgent attention in order to achieve both national and global Sustainable Development Goals (SDGs) by 2030. Improvement of the cashew apple sector could have a positive impact on global SDGs 1, 2, and 3 targets of no poverty, zero hunger, and good health and well-being respectively. At national level, this sector could contribute to the goals of the Tanzania Development Vision (TDV) 2025, namely: high quality livelihood, particularly food self-sufficiency and food security; and a strong and competitive economy, particularly a diversified and semi-industrialized economy with a substantial industrial sector comparable to typical middle-income countries. In addition, the country’s Third Five Year Development Plan III (FYDP III) 2021/22 – 2025/26 has established key strategic interventions, notably those related to competitive industrialization, energy, and food and nutrition security to ultimately achieve the goals of the TDV 2025. To be effective, however, these strategic interventions require continued strong central and local government support and active involvement of stakeholders to ensure program effectiveness yielded towards efficient utilization of widely available natural resources such as cashew apples which has cross-cutting benefits in food, agriculture, health, energy, and economic perspectives. Therefore, the work provides evidence on the utilization status, challenges, and opportunities for sustainable development in Tanzania.",
"keywords": [
"cashew apples",
"utilization status",
"sustainable development",
"Tanzania"
],
"content": "Introduction\n\nThe cashew sector is of great importance to the economy of Tanzania. As of 2015, the sector contributed around 497 billion Tanzanian Shillings, courtesy of cashew nuts (Msoka et al., 2017). However, the cashew tree bears both the cashew nut and cashew apple (Figure 1), and thus the latter is left to rot in the fields and less likely to be processed or fed to livestock. For instance, the estimated production of cashew apples in the country is about 2,327,000 metric tonnes, and yet there’s no significant commercial processing of this fruit (Dimoso et al., 2021). Unexpectedly, utilization of this fruit has been for decades hampered by several factors: high perishability and astringent nature of the fruits; inadequate public knowledge and awareness of their potential for food and nutrition security and socio-economic development; inadequate skills and technologies for value addition; and weak investment and collaboration among stakeholders (Dimoso et al., 2021). This fruit contains several important ingredients including vitamins (A and C), sugars, minerals, polyphenols and dietary fibers (Msoka et al., 2017), hence it is suitable for processing of value-added products in food, bio-energy, pharmaceutical, and biochemical processing industries.\n\nThe huge underutilization of cashew apples is a challenge that requires urgent attention in order to achieve both national and global Sustainable Development Goals (SDGs) by 2030. Considering the country’s huge production of cashew apples as raw materials in different industrial sectors, adequate utilization of these fruits could have a positive impact on global SDGs 1, 2, and 3 targets of no poverty, zero hunger, and good health and well-being respectively (United Nations, 2015). At national level, the cashew apple sector could contribute to the achievement of goals of the Tanzania Development Vision (TDV) 2025 namely: high quality livelihood, particularly food self-sufficiency and food security; and a strong and competitive economy, particularly a diversified and semi-industrialized economy with a substantial industrial sector comparable to typical middle-income countries. In addition, the country’s Third Five Year Development Plan (FYDP III) 2021/22 – 2025/26 has established key strategic interventions, notably those related to competitive industrialization, energy, and food and nutrition security to ultimately achieve goals of the TDV 2025 (United Republic of Tanzania [URT], 2021). Similarly, the National Post-Harvest Management Strategy (NPHMS) 2019-2029 addressed strategic objectives aimed at reducing postharvest losses of agricultural crops with an ultimate goal of increasing stakeholders’ income and food and nutrition security (URT, 2019). To be effective, however, these strategic interventions require continued strong central and local government support and active involvement of stakeholders to ensure program effectiveness yielded towards efficient utilization of widely available natural resources such as cashew apples which has cross-cutting benefits in food, agriculture, health, energy, and economic perspectives. Therefore, this policy brief provides local and international evidence regarding the quality of cashew apples (based on the study by Msoka et al., 2017), the utilization status and challenges (based on the study by Dimoso et al., 2021), product development interventions (based on the study by Dimoso et al., 2020) and addresses the need for strong policy and programmes in order to harness the full potential of cashew apples for sustainable development in Tanzania.\n\n\nPolicy outcomes and implications\n\nThere are several feasible usages of the cashew apple (Table 1), which if sufficiently exploited could help in part achieve the goals of the FYDP III and TDV 2025. For instance, in the arena of food and nutrition security, the FYDP III looks to reduce the prevalence of vitamin A deficiency among children aged 6-59 months to less than 20 percent, the proportion of women aged 15-49 years with anaemia from 44 to 22 percent, and reduction of acute malnutrition by year 2025, among others. The same micronutrient challenges were addressed by the Tanzania Demographic Health Survey 2010 (URT, 2011). Increasing public awareness on the health benefits of cashew apple could increase their consumption (raw or processed form) and hence reduce a prevailing health burden. With regard to industrialization, the FYDP III emphasizes on value addition in agriculture through the use of science, technology and innovation as well as research and development. Since huge postharvest losses impact nutrition (especially on micronutrient deficiencies), the NPHMS outlines strategic interventions including facilitation of awareness on postharvest management, value addition, and improving agricultural marketing infrastructure to reduce losses particularly on perishable crops such as fruits and vegetables. For these reasons, cashew apple provides a diversified quality of products for domestic and export market, and hence stimulates socio-economic development.\n\nEqually important, there is a severe unemployment burden in Tanzania, particularly among young people. A large segment (75 percent) of Tanzania’s population is under the age of 35 years. This young generation faces a great challenge to land employment immediately after finishing their qualifications. Statistically, out of one million young people, only 20 percent get employed immediately. In line with the FYDP III, an entrepreneurship approach is the feasible option to solve youths’ unemployment burden. Establishing and strengthening the Small and Medium Enterprises (SMEs) is critical due to the fact that, SMEs utilize locally available materials and have the potential to engage many people especially youth, women, and people with disabilities. There are many SMEs processing cashew nuts in cashew producing regions such as Mtwara, Lindi, Tanga, and Pwani, while not the same can be said about cashew apples. With the aforementioned benefits, cashew apple presents greater opportunities for researchers, politicians, investors and farmers to exploit its potentials, and ultimately drive forward national economy.\n\nBased on a recent study by Msoka et al. (2017), Tanzania’s cashew apple varieties are of considerable good quality. A study revealed a good quantity of valuable components such as vitamin C, carotenoid (provitamin A), sugars, polyphenols, dietary fibers, and minerals such as calcium, magnesium, sodium, potassium as well as low quantities of phosphorus, iron, and zinc. These ingredients make cashew apple a perfect raw material in food, energy, agriculture, pharmaceutical, and biochemical processing industries. From a health perspective, vitamin C, carotenoid, and polyphenols have antioxidant and anti-inflammatory activities, thus provide cashew apple an ability to reduce, prevent, or treat a number of chronic diseases such as scurvy, cancer, and neurodegenerative diseases. Since this fruit has a vitamin C content almost five times that of orange or mango, it can be used in food fortification and formulation. Furthermore, presence of sugars, dietary fibers, and minerals make cashew apple a perfect microbial substrate in different fermentation processes to produce value added products such as ethanol (as food drink or energy), organic acids, and bio-surfactant.\n\nA field survey was conducted in major cashew producing regions i.e. Mtwara and Lindi to obtain insightful information regarding the utilization aspects of cashew apple (Dimoso et al., 2021). The study revealed that the majority (98 percent) of cashew farmers consume raw cashew apples, with 62 percent consuming more than five fruits a day and about 56 percent consuming almost every day during the fruit season. However, farmers’ knowledge on the importance of eating cashew apple seemed limited. As a matter of fact, the majority of consumers (53 percent) claimed to eat cashew apple just because it is a fruit. In addition, few respondents seemed to acknowledge the contribution of fruits such as cashew apple to human health. Moreover, nearly 44 percent of farmers traditionally process cashew apple into porridge (traditionally called Mkongohu) and alcoholic drinks namely wine (traditionally called Uraka) and distilled liquor (traditionally called Nipa). With respect to challenges, lack of knowledge on postharvest handling (86 percent), and inadequate processing technologies (83 percent), among others were mostly claimed to hamper the utilization.\n\nRecently, Nelson Mandela African Institution of Science and Technology (NM-AIST) has formulated dried fruit slices and juice products from cashew apple (Dimoso et al., 2020). The formulated cashew apple products were deemed acceptable with respect to nutrient retention, shelf-life stability and sensory properties. Similarly, Tanzania Agricultural Research Institute (TARI) - Naliendele and Ndanda Mission have also been developing cashew apple juice, jam and wine (UNIDO, 2011). However, a commercialization stage of the aforementioned prototypes is yet to be attained.\n\nIt is apparent that, while few food products have been already developed, other value-added products for sectors such as bio-chemical, energy, and pharmaceutical industries remain unexplored. The current situation provides an opportunity for stakeholders to venture in cashew apple value chain. Therefore, the initiatives for product development and commercialization of cashew apple value-added products need to be formulated and implemented. This will foster the sustainable existence of cashew apple products in the market.\n\nValue addition through agro-processing of highly perishable crops such as fruits and vegetables should be emphasized. According to the Ministry of Industry and Trade survey 2013, there were only 17 fruit processing units in a country, of which none is for cashew apples (URT, 2019). Shortage of fruit processing industries account largely for the reported huge postharvest losses of such commodity. In this regard, the NPHMS has the following strategic objectives, among others that could benefit the cashew apple value chain: (1) promote availability, accessibility, affordability and adoption of tested technologies and processes to reduce post-harvest losses; (2) promote research and innovations of new and appropriate technologies and methods to reduce crop losses; (3) facilitate agricultural marketing systems to improve market access and minimize post-harvest losses. Likewise, value addition, food fortification and formulation, technology development and transfer, and commercialization of local agro-products are among the top research priorities outlined by the National Research Priorities 2021/22-2025/26 (URT, 2022) to facilitate human capital development and building of strong and competitive industrial economy.\n\nThe most successful country in cashew apple processing is Brazil. This country has about 12 different cashew apple juice processing industries alone, while others sell fresh fruits, dried fruits, jam, wine, confectionaries, and animal feeds. Equally important, the Brazilian Agricultural Promotion Agency (EMBRAPA) is the leading actor in cashew apple value chain. For instance, it developed a cashew apple variety that can remain on the ground for 1 day without being damaged or beginning to ferment. On the contrary, Tanzanian varieties are very soft and get damaged once they fall on the ground, hence they require immediate processing and/or a cold chain facility for distant transportation or long-term storage. In addition, limited access to a sustainable cold chain for perishable crops (fruits and vegetables) is a dominant challenge not only in Tanzania but the whole region of Sub-Saharan Africa (Makule et al., 2022). India has also progressed in developing cashew apple products, however, their commercialization is still a challenge.\n\nHowever, in West African countries such as Ghana, Benin and Guinea-Bissau, there is little effort regarding cashew apple usage (Monteiro et al., 2017). Benin and Ghana have started producing and marketing cashew apple juice, although the sector is still in its infancy (TechnoServe, 2017). According to Yantannou (2017), no country in Africa is processing greater than 1% of its cashew apple production. Therefore, there are greater business opportunities in the cashew apple value chain in African cashew producing countries.\n\n\nActionable recommendations\n\nShort-term recommended actions to be considered include: reinforcing access to affordable financial resources to all actors in cashew apple value chain; developing innovative and appropriate postharvest handling technologies to prolong cashew apple shelf life, and enhancing their adoption by relevant actors in the value chain; improving capacity building, extension services and access to information; designing and launching campaigns to raise awareness on the contribution of cashew apple in nutrition and income generation to farmers and all key players; and the realization of efficient utilization can be preceded by conducting market analysis, gaining understanding of consumer preference and strengthening the linkage between farmers and buyers.\n\nMedium-term recommended actions include: strengthening research and development institutions to improve research outputs that aim to improve cashew apple breeds and value additions; creating a supportive environment for partnerships and collaborations among governmental and non-governmental actors to promote cashew apple projects; encouraging and supporting youth and women to venture into the cashew apple value chain; developing cost-effective cold storage technologies to prolong the shelf-life of perishable crops; and measuring the performance and benefits of all activities in the cashew apple value chain in order to generate knowledge, support learning, track progress, and ensure accountability.\n\n\nConclusions\n\nAddressing the wastage of cashew apples in Tanzania and the underlying opportunities is necessary in order to realize the goals of the FYDP III and TDV 2025. Among other factors, astringency and high perishability characteristics, inadequate processing skills and technology, and limited access to capital have contributed to the underutilization of these fruits. Being rich in vitamins, minerals, and bioactive components, cashew apples could be processed into a number value-added products. Increasing public awareness on the importance of cashew apples as a source of food and income could accelerate their utilization. Additionally, all stakeholders including individuals, agricultural research institutions and universities, and other public and private sectors are encouraged to participate in this endeavor to facilitate research, technology transfer and development, capacity building, and improve agricultural marketing infrastructure in order to utilize cashew apples effectively and efficiently and ultimately increase food and nutrition security and socio-economic development. Furthermore, all established national policies, strategies and programmes should be supported to implement the underlying objectives in relation to the cashew apple value chain.\n\n\nData availability\n\nThe raw data for the survey conducted by Dimoso et al. (2021) is restricted. Only members of the Fruits and Vegetables for all Season (FruVaSe) project can access the data directly. However, data can be accessed upon request by non-members. Please consult Dr Edna Makule via email (edna.makule@nm-aist.ac.tz) to obtain the data file.\n\n- Data on the physio-chemical quality of cashew apples in Tanzania: https://dspace.nm-aist.ac.tz/bitstream/handle/20.500.12479/183/JA_LiSBE_2017.pdf\n\n- Data on the quality assessment of dried cashew apples: https://dspace.nm-aist.ac.tz/bitstream/handle/20.500.12479/1092/JA_LiSBE_2020.pdf\n\n- Data on the utilization status of cashew apples in Tanzania was originally presented from our published research that can be accessed at: https://doi.org/10.1177/0030727020941164\n\nThese data are under open access and can be accessed at their respective links/DOI.\n\n\nAuthor contributions\n\nDimoso N: Conceptualization, Methodology, Investigation, Writing – Original Draft Preparation, Writing – Review & Editing; Kassim N: Supervision, Conceptualization, Writing – Review & Editing; Makule E: Supervision, Conceptualization, Funding Acquisition, Project Administration, Writing – Review & Editing.",
"appendix": "References\n\nAdegunwa MO, Kayode BI, Kayode RMO, et al.: Characterization of wheat flour enriched with cashew apple (Anacardium occidentale L.) fiber for cake production. J Food Meas Charact. 2020; 14: 1998–2009. Publisher Full Text\n\nBetiku E, Emeko HA, Solomon BO: Fermentation parameter optimization of microbial oxalic acid production from cashew apple juice. Heliyon. 2016; 2: e00082. PubMed Abstract | Publisher Full Text\n\nDimoso N, Aluko A, Makule E, et al.: Challenges and opportunities toward sustainable consumption and value addition of cashew apples in Tanzania. Outlook Agric. 2021; 50(2): 169–177. Publisher Full Text\n\nDimoso N, Makule E, Kassim N: Quality assessment of formulated osmotically dehydrated cashew apple slices dried using hot air and solar driers. Int J Biosci. 2020; 17(6): 421–432. Publisher Full Text\n\nGamero A, Ren X, Lamboni Y, et al.: Development of a low-alcoholic fermented beverage employing cashew apple juice and non-conventional Yeasts. Fermentation. 2019; 5: 71. Publisher Full Text\n\nKaprasob R, Kerdchoechuen O, Laohakunjit N, et al.: B Vitamins and prebiotic fructooligosaccharides of cashew apple fermented with probiotic strains Lactobacillus spp., Leuconostoc mesenteroides and Bifidobacterium longum. Process Biochem. 2018; 70: 9–19. Publisher Full Text\n\nMakule E, Dimoso N, Tassou SA: Precooling and cold storage methods for fruits and vegetables in Sub-Saharan Africa - a review. Horticulturae. 2022; 8: 776. Publisher Full Text\n\nMathew J, Sobhana A, Mini C: Opportunities for income enhancement from cashew plantations through cashew apple processing. Proceedings of the second international cashew conference, Kampala, Uganda. CABI International. Wallingford; UK.2013; 143–149.\n\nMonteiro F, Catarino L, Batista D, et al.: Cashew as a high agricultural commodity in West Africa: insights towards sustainable production in Guinea-Bissau. Sustainability. 2017; 9: 1666. Publisher Full Text\n\nMsoka R, Kassim N, Makule E, et al.: Physio-chemical properties of five cashew apple varieties grown in different regions of Tanzania. Int J Biosci. 2017; 11: 386–395. Publisher Full Text\n\nNogueira AK, Martins JJL, Lima JG, et al.: Purification and characterization of a biosurfactant produced by Bacillus subtilis in cashew apple juice and its application in the remediation of oil-contaminated soil. Colloids Surf B Biointerfaces. 2019; 175: 256–263. PubMed Abstract | Publisher Full Text\n\nPaiva FA: Cashew by-product processing in Brazil. II International Training in Post-harvest and Industrial Processing of Cashew, African Cashew Alliance. Cotonou, Benin.2012. (accessed 4 February, 2021).Reference Source\n\nPriya AD, Setty YP: Cashew apple juice as substrate for microbial fuel cell. Fuel. 2019; 246: 75–78. Publisher Full Text\n\nRibeiro da Silva LM, Teixeira de Figueiredo EA, Silva Ricardo NM, et al.: Quantification of bioactive compounds in pulps and by-products of tropical fruits from Brazil. Food Chem. 2014; 143: 398–404. PubMed Abstract | Publisher Full Text\n\nSilva ME, Torres-Neto AB, Silva WB, et al.: Cashew wine vinegar production: alcoholic and acetic fermentation. Braz J Chem Eng. 2007; 24(02): 163–169. Publisher Full Text\n\nTalasila U, Vechalapu RR, Shaik KB: Clarification, preservation, and shelf life evaluation of cashew apple juice. Food Sci Biotechnol. 2012; 21(3): 709–714. Publisher Full Text\n\nTalasila U, Vechalapu RR: Optimization of medium constituents for the production of bioethanol from cashew apple juice using Doehlert experimental design. Int J Fruit Sci. 2015; 15: 161–172. Publisher Full Text\n\nTechnoServe: Sweet Benin - A new value chain for a better future in Benin.2017.Reference Source\n\nTeles AD, da Silva A , Meneses E, et al.: Mathematical modeling of the ethanol fermentation of cashew apple juice by a flocculent yeast: The effect of initial substrate concentration and temperature. Bioprocess Biosyst Eng. 2017; 40: 1221–1235. PubMed Abstract | Publisher Full Text\n\nUNIDO: Tanzania’s cashew value chain: A diagnostic. United Nations Industrial Development Organization;2011.\n\nUnited Nations: Transforming Our World: The 2030 Agenda for Sustainable Development. New York:UN Publishing; 2015.Reference Source\n\nURT: Micronutrients: Results of the 2010 Tanzania Demographic Health Survey. National Bureau of Statistics and ICF Macro. Dar es Salaam, United Republic of Tanzania;2011.\n\nURT: National Five Year Development Plan 2021/22-2025/26. Dodoma, United Republic of Tanzania:Ministry of Finance and Planning;2021.\n\nURT: National Post-Harvest Management Strategy 2019-2029. Dodoma, United Republic of Tanzania:Ministry of Agriculture;2019.\n\nURT: National Research Priorities 2021/22-2025/26. United Republic of Tanzania:Commission for Science and Technology;2022.\n\nYantannou S: Sweet Benin. Proceeding of the 11th African Cashew Alliance. Cotonou, Benin.2017."
}
|
[
{
"id": "203422",
"date": "26 Sep 2023",
"name": "Iheanyi William Eke",
"expertise": [
"Reviewer Expertise Biomass valorization"
],
"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 reviews the current gaps in the cashew apple value chain in Tanzania and proposes some policy-based solutions to change the status quo for sustainable development.\nMinor revision is recommended before publication:\nSome important references are missing. For example (i) Page 5 paragraph 2 \"A study revealed a good quantity of....\" (which study?) (ii) Page 4 \"A large segment (75 percent) of Tanzania’s population is under the age of 35 years. This young generation faces a great challenge to land employment immediately after finishing their qualifications. Statistically, out of one million young people, only 20 percent get employed immediately\" (reference?) etc.\n\nIn the section \"Actionable Recommendations\", it will be useful to include the relevant action party (ies) in Tanzania to see to the implementation of these recommendations. Furthermore, the authors should proffer some practical steps/activities which these action parties could take/undertake towards the implementation of these recommendations. For instance, who is the action party in \"encouraging and supporting youth and women to venture into the cashew apple value chain\", and what are some of the steps this action party could take to achieve this. This same guideline should be applied to other recommendations. This will make them more actionable.\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? Partly\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? Partly",
"responses": [
{
"c_id": "11312",
"date": "13 Apr 2024",
"name": "Noel Dimoso",
"role": "Author Response",
"response": "1. All important references were addressed in the new version as suggested 2. The section \"Actionable Recommendations\", is re-written in the new version to include the relevant action party (ies) in Tanzania to see to the implementation of these recommendations."
}
]
},
{
"id": "207201",
"date": "03 Oct 2023",
"name": "Sampson Kofi Kyei",
"expertise": [
"Reviewer Expertise Waste and Biomass valorisation",
"Industrial Chemistry",
"Environmental Chemistry"
],
"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 found manuscript entitled \"Cashew apple in Tanzania: status of utilization, challenges, and opportunities for sustainable development\" very interesting. While going through the manuscript I found that manuscript is well-recognized to an extent and could be considered as a valuable contribution, but requires a minor revision. I would like to raise some comments, and recommendations about the manuscript:\nIn-text referencing: Some sentences needs to be referenced e.g. Paragraph 2 (Page 4) has some sentences with facts that needs to be referenced accordingly.\n\nParagraph 1 (Page 5) presents a review on a study by Msoka et al. (2017). Please, change the first word in sentence 2 \"A\" to \"The\"\n\nOn the \"International Evidence of Processing of cashew apple\", it must be noted that some African countries are doing well regarding its usage/applications; e.g., Nigeria. The authors must provide a paragraph on some of these countries and their contributions.\n\nPlease add separate section dealing with various factor and challenges (technical) that can be faced during industrial scale processing/application of cashew apples/fruits.\n\nI suggest authors to write future perspectives on the cashew apple processing\n\nI should commend the authors on the \"actionable recommendations\". However, they failed to specify who/which organization or party is responsible for the implementation\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": "11313",
"date": "13 Apr 2024",
"name": "Noel Dimoso",
"role": "Author Response",
"response": "1. A suggested in-text reference is included in this version 2. A suggested correction was addressed in this version 3. On the \"International Evidence of Processing of cashew apple\" section, more cashew apple startups from different African countries were added in this version 4. A separate section dealing with various factor and challenges (technical) that can be faced during industrial scale processing/application of cashew apples/fruits is included in this version 5. A new section 'future perspectives on the cashew apple processing' is included in this version 6. A section 'Actionable recommendation' is re-written to address an organization or party that will implement those recommendations"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1354
|
https://f1000research.com/articles/11-1222/v1
|
27 Oct 22
|
{
"type": "Research Article",
"title": "Antibacterial activity of Betadine (Jatropha multifida L.) stem extract on Pseudomonas aeruginosa growth in vitro",
"authors": [
"Hendry Rusdy",
"Diah HI Damanik"
],
"abstract": "Background: Today, people use plants to treat various types of diseases and improve human health. One of the medicinal plants is the Betadine plant (Jatropha multifida L.). Betadine plants have many functions, especially the sap, leaves, fruit and seeds. The compound contents in Betadine stem sap, which is efficacious as an antimicrobial, are saponins, tannins, flavonoids and labaditin. One of the bacteria that cause infection is Pseudomonas aeruginosa. These bacteria can cause opportunistic and nosocomial infections. Methods: This study was a true experimental laboratory with a post-test only control group design. This study used Betadine stem sap extract with concentrations of 25%, 50%, 75%, 100%, gentamicin cream 10% as positive control, and dimethyl sulfoxide (DMSO) solution as negative control. This study used the Kirby-Bauer diffusion method and the bacterium Pseudomonas aeruginosa was grown on nutrient agar media, then incubated for 24 hours and calculated using calipers. Research data were analyzed using one-way ANOVA test. Results: The highest inhibition zone was group 50% (12.725 ± 0.2500 mm) while the lowest inhibition zone was group 100% (8.675 ± 0.5620 mm). Conclusions: Betadine stem extract had antibacterial activity in inhibiting the growth of Pseudomonas aeruginosa bacteria, with the 50% concentration being the most effective in inhibiting the growth of Pseudomonas aeruginosa bacteria.",
"keywords": [
"Betadine",
"sap",
"Jatropha multifida L.",
"Pseudomonas aeruginosa L.",
"Infection",
"Antibacterial",
"Nosocomial",
"Opportunistic."
],
"content": "Introduction\n\nIn Padang, West Sumatra Province, people use Betadine stem sap (Jatropha multifida L.) to heal and eliminate external wound infections by applying Betadine stem sap on the injured body part. Indonesian people call this plant a Betadine plant because it has the same potential as an external wound medicine like Betadine in duration to heal an infected external wound.1–3\n\nAccording to Ivan et al. 2019, the Betadine plant can inhibit the growth of Staphylococcus aureus and Pseudomonas aeruginosa.4 Betadine plant sap consists of multifidol, biobollein, multifidone, multifidil, flavonoid, labaditin, saponin and tannin.5 In a study conducted by Aransiola et al. 2014 about the antibacterial and antifungal activity of Betadine plant sap, they found that the minimum inhibitory concentration (MIC) of Betadine plant sap gram negative bacteria (P. aeruginosa, E. coli, and Salmonella typhi) was 66 mg/ml. These results indicate that the antibacterial activity found in the Betadine plant sap is lower in gram negative bacteria because gram negative bacteria are more resistant to antibacterials.6\n\nBased on WHO data in 2013, the mortality rate due to resistant bacterial infection is 700,000 people per year.7 P. aeruginosa is an anaerobic, nosocomial and opportunistic bacterium. P. aeruginosa bacteria live in humid environments such as surgical instruments, 74% in dental water and dental disinfecting units used for more than 24 hours. P. aeruginosa was isolated in maxillary osteomilitis and brain abscesses in patients who had dental infections. This bacteria can cause meningitis, endocarditis, pneumonia and sepsis with an average mortality of 12–25%. This bacteria is resistant to many antibacterial including amoxicillin. Antimicrobial ingredients that are effective against Pseudomonas aeruginosa are hard to find, so natural resources such as Betadine plants can be used to suppress bacterial growth.5,8,9\n\nBased on the explanation above, the authors are interested in conducting research on “Antibacterial activity of Betadine stem (Jatropha Multifida L.) extracts on Pseudomonas aeruginosa bacteria growth by in vitro”.\n\n\nMethods\n\nThis study was a true experimental study with a post-test only control group design. True experimental study measured or observed data after the treatment was given.\n\nLaboratory of Traditional Medicine and Microbiology, Faculty of Pharmacy, University of Sumatera Utara, Medan, Indonesia.\n\nStudy duration was ± 2 month, from December 2019 to January 2020.\n\nIn calculating the size of experimental research samples, we used the Federer formula:\n\nThe number of repetitions (r) are four. So, 24 samples were obtained.\n\nThe dependent variable in this study was the sensitivity test growth of Pseudomonas aeruginosa that measured by the diameter of the inhibitory zone.\n\nThe independent variable in this study was the concentration of Betadine stem sap extract used, which were 25%, 50%, 75% and 100%.\n\nThere were six controlled variable such as the growth media used for the bacterium Pseudomonas aeruginosa was nutrient broth agar, the incubation temperature of Pseudomonas aeruginosa is 37oC, the incubation time of Pseudomonas aeruginosa was 24 hours, the isolation and culture technique of Pseudomonas aeruginosa bacteria, sterilization of tools, the materials and media used, and operator skills.\n\nThere were four uncontrolled variable such as the morphology of the Betadine stem, the growth time of the Betadine stem, the state of the soil and rainfall, the environment from which the Betadine plant originated, and the storage of the Betadine stem sap extract in the laboratory.\n\nAutoclaves (Tomy ES 315, Japan), UV-VIS spectrophotometers (Orion Aquamate 8000, Germany), ovens (Memmert UN55, Germany), micropipets (Dragon Lab, China), Laminar air flow cabinet (Astec HLF I1200L), glass cuvettes, refrigerators (Thermo Scientific), incubators (Memmert, Germany), vortex mixers (Biosan, Latvia), glass tubes, glass petri dish, test tubes, inoculating loops, bunsen, measuring cups 20 ml, spatula, Vernier calipers (Electric Digital Capliper), analytical scales (Sartorious BSA323S-CW) and Erlenmeyer.\n\n\nMaterials\n\nBetadine stem sap extract 100% concentration (Jatropha multifida L.), bacterial culture of Pseudomonas aeruginosa (ATCC® 140218, pure culture stock Faculty of Pharmacy, University of Sumatera Utara, Indonesia), DMSO solution, gentamicin ointment 10% (IKAGEN®), aquadest, nutrient agar powder (Oxoid), nutrient broth agar powder (Oxoid), label paper, and 6 mm sterile paper discs.\n\nFirst, all the instruments were sterilized with the autoclave at 121°C for 15 minutes and dried with an oven 170°C for 1–2 hours. Inoculating loop and pinset were sterilized with the bunsen flame. After that, took dilution of Betadine stem sap extract 100% with DMSO using a micropipet into a glass tube and measured with sartorious analytical scales (1 ml). The nutrient agar powder (28 g) was mixed with 1000 ml aquadest in an erlenmeyer flask with a spatula. This was heated for 2 hours at 100°C and after that saved in autoclave. Then, sterilized inoculating loops were used to take the isolated P. aeruginosa colonies and these were then placed into test tubes each containing the tilt media (contained 3 ml nutrient agar). The tube was put in an incubator at 37°C for 24 hours. Took P. aeruginosa colony using sterilized inoculating loops and than put into a tube that contain 10 ml nutrient broth agar. The tube was put on vortex mixers for 1 minute. Took 3 ml bacteria and put into glass cuvets, then put into UV-VIS spectrophotometers with 560 nm wavelength. The result must be 25% transmittance. In laminar airflow cabinet took 20 ml nutrient agar using measuring cups and 1 ml bacteria suspense using micropipets into glass petri dishes. The petri dishes were shaken slowly in a figure of eight movement until homogeneous. Paper discs were soaked with 25%, 50%, 75%, 100% Betadine stem sap extract, getntamicin and DMSO for 3 minutes. Then these were placed on the surface of the nutrient agar and a little pressure was applied. The petri dishes were labelled with label paper and placed in the refrigerator for 1 hour. Then the petri dishes were put into an incubator for 24 hours at 37°C. The diameter of inhibitory zone was clear zone in the petri dish. Measured it with caliper.\n\nData was analyzed using software IBM SPSS Statistics Desktop 20.0 Windows Multilingual eAssembly (CRG2LML). The data was processed and analyzed with one way ANOVA test, and post hoc LSD (least significant difference).\n\n\nResults\n\nFrom this study, the lowest inhibition zone was produced by the Betadine stem sap extract group 100% (8.675 ± 0.5620 mm), while the highest inhibition zone was produced by the 50% (12.725 ± 0.2500 mm) Betadine stem sap extract group (Figures 1 and 2). The Saphiro-Wilk test with a significance of p > 0.05 was used for the normality test and the data were found to be normally distributed (p > 0.05) (Table 1). The data was distributed normally, so statistical analysis was continued using a one-way ANOVA analysis test and post hoc LSD to see whether there was a significant difference in the diameter of the inhibition zone between group 25%, 50%, 75%, 100%, K+, and K-. The ANOVA test showed a significant difference (p < 0.05) in the effect of the inhibition zone diameter between group 25%, 50%, 75%, 100%, K+ and K- (Table 2). The LSD post hoc test was used to determine the significance of the inhibition of the growth of Pseudomonas aeruginosa between all groups in this study. The results of the LSD post hoc test are shown in Table 3.\n\n\nDiscussion\n\nThe study used Kirby-Bauer’s method.9 This method is fast, easy, simple and produces effective results to show the antibacterial activity of a substance.9 The solvent was DMSO which is able to dissolve polar and nonpolar compounds and does not have antibacterial activity so it does not change the results.10 Factors that influence the diffusion of extracts into the media are the extent of the concentration gradient, solubility, diffused molecular mass, temperature and density of the solvent.6\n\nThe group 25%, the inhibitory zone was 12.275 mm smaller than the group 50%, which was 18.275 mm.11 This is because the group 50% had higher active ingredients than the group 25%. This is in line with previous research conducted by Brooks et al.3 and Anggita et al.12 in 2018 which states that the effectiveness of an antibacterial agent is influenced by the concentration of a given substance, the higher concentration has the higher active ingredient as an antibacterial, thus increasing the inhibition ability against microbes.\n\nThe inhibition zone group 75% the was 8.925 mm and group 100% was 8.675 mm.11 The decrease in inhibition zone diameter due to the minimum diffusion power of the dense viscous extract is because it had a high solution density. The group 75% had minimum penetration power because the minimal amount of solvent. The group 100% had minimum penetration power because there was no solvent. Molecules moved slowly because it is more difficult to pass through denser media so it takes longer and results in smaller inhibitory zones.9 This is similar to a study conducted by Komariah et al. 2013, where there was a decrease in antibacterial activity along with an increase in the concentration of the extract due to the higher concentration, the viscosity would increase so that the extract would be more difficult to diffuse into the agar media.13\n\nThe antibacterial activity of the Betadine stem sap extract is related to its antibacterial content, namely phenols, tannins, saponins and labaditin.3 Large molecule of phenol are able to activate essential enzymes in microbial cells even at low concentrations.14\n\nPhenol compounds contained in Betadine stem sap are flavonoids and tannins.10 Flavonoids work by inhibiting nucleic acid synthesis, inhibiting cytoplasmic membrane function and inhibiting energy metabolism. Flavonoids can damage the outer membrane and cytoplasm of gram-negative bacteria, disturb the exchange of nutrient and metabolite and inhibit the energy supply for bacteria.15,16\n\nTannins can cause lysis of bacterial cell membranes due to the differences in bacterial cells osmotic pressure. Tannins damage cell membranes by breaking the phosphate group H+ so the phospholipid molecule breaks down into glycerol, carboxylic acid and phosphoric acid. Saponins are also contained in Betadine stem sap. Its mechanism of action is by interfering with bacterial cell membrane stability, causing bacterial cell lysis, damaging the cell membrane and releasing various important components of microbial cells, namely proteins, nucleic acids, nucleotides and others.15,16 According to a study conducted by Barbosa et al. 2019, Betadine stem sap contains labaditin which is effective in gram-positive bacteria but less effective in gram-negative bacteria because of the more complex structure of gram-negative bacterial cell walls.17\n\nFrom the four group of Betadine stem sap extract that were tested, the strongest antibacterial activity found the group 25% and group 50%.11 However, when compared with the positive control antibiotic gentamicin, Betadine stem sap extract was not more effective than gentamicin. This is due to the fact that many gram-negative bacteria contain lipids and little peptidoglycan. The outer membrane of the Pseudomonas aeruginosa is a bilayer that serves for the selective defense of compounds entering and exiting cells. The outer membrane consists of phospholipid (inner layer) and lipopolysaccharide (outer layer). This makes it difficult for active compounds to enter the cell so antibacterial activity of Betadine stem sap extract is smaller than gentamicin.17,18\n\nThis research proves that Betadine (Jatropha multifida L.) stem sap extract has antibacterial activity on inhibiting the growth of Pseudomonas aeruginosa in vitro. This result is the first step in the possibility of utilizing papaya leaf extract as an alternative natural ingredient for antibiotics in dentistry with the need for a series of tests such as clinical trials, toxicity and side effects so that this research can be utilized by the public.\n\n\nConclusions\n\nBased on the results, Betadine stem sap extract has an antibacterial activity on Pseudomonas aeruginosa growth in vitro. The most effective concentration to inhibit the growth of Pseudomonas aeruginosa is the group 50%, with the largest inhibitory zone diameter of 12.725 ± 0.2500 mm. This study has limitations, so further research is recommended to investigate using concentrations below 50% and using dilution methods to obtain the MIC (minimum inhibitory concentration) and MKC (minimum kill concentration).\n\n\nData availability\n\nFigshare: Antibacterial Activity of Betadine (Jatropha multifida L.) Stem Extract on Pseudomonas aeruginosa Growth In-Vitro. https://doi.org/10.6084/m9.figshare.20359653.11\n\nThis project contains the following underlying data:\n\n• Data Inibition Zone of Each Repetition of Betadine Extract.csv (the file contains plain data of each concentration of Betadine stem sap extract with four repetitions)\n\n• Test of Normality.csv (The file contains normal data distribution)\n\n• Descriptives.csv (The file contains median, variance, standart deviation, minimum, maximum, range, interquartile range, skewness and kurtosis each concentration of Betadine stem sap extract).\n\n• Case Processing Summary.csv (file contains of summary valid and missing antibacterial activity each consentration).\n\n• Oneway Anova Test.csv (The file contains of data which is distinguish the antibacterial activity of each concentration of Betadine stem sap extract against Pseudomonas aeruginosa bacteria).\n\n• Post Hoc Test.csv (The file contains of data which is show the significant difference between each concentration of Betadine stem sap extract).\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\nAn earlier version of this article can be found at: https://repositori.usu.ac.id/handle/123456789/25701?show=full.\n\n\nReferences\n\nCazander G, Jukema GN, Nibbering PH: Complement activation and inhibition in wound healing. J ZORA. 2012; 2012: 1–14. Publisher Full Text\n\nIvan SS, Sudigdoadi S, Kartamihardja: Antibacterial effect of jatropha multifida l. leaf infusion towards staphylococcus aureus and pseudomonas aeruginosa. AMJ. 2019; 6(2): 95–99. Publisher Full Text\n\nSabandar CW: A review of jatropha multifida linn. Sulawesi Tenggara:Wordpress;2010; vol. 2010. : 1–3.\n\nAransiola MN, Ehikhase C, Mmegwa JC, et al.: Antibacterial and antifungal activities of jatropha multifida (ogege) sap against some pathogens. IOSR-JPBS. 2014; 9: 53–57. Publisher Full Text\n\nIrianto K: Mikrobiologi medis. Bandung:Alfabeta;2013; 239.\n\nBoundless: General biology. California:Mindtouch;2018; 521–522.\n\nDarmadi: Infeksi nosokomial problematika dan pengendaliannya. Jakarta:Salemba Medika;2008; 1–22.\n\nSadino A, Sahidin I, Wahnyuni W: Antibacterial activity of polygonum pulchrum blume ethanol extract on staphyloccocus aureus and escherichia coli. Pharmacol. Clin. Pharm. 2018; 3(2): 28.\n\nUtomo SB, Fujiyanti M, Lestari WP, et al.: Uji aktivitas antibakteri senyawa c-4-metoksifenilkaliks(4) resorsinarena termodifikasi hexadecyl trimethylammonium-bromide terhadap bakteri staphylococcus aureus dan escherichia coli. JKPK. 2018; 3(3): 201–208. Publisher Full Text\n\nOctaviani M, Fadhli H, Yuneistya E: Uji aktivitas antimikroba ekstrak etanol dari daun kulit bawang merah (allium cepa l.) dengan metodr difusi cakram. PSR. 2019; 6(1): 62–67.\n\nDamanik DHI: Antibacterial activity of betadine (jatropha multifida l.) stem extract on pseudomonas aeruginosa growth in-vitro. Thesis. Medan: University of Sumatera Utara. figshare. Dataset.2022; 1–45. Publisher Full Text\n\nAnggita D, Abdi DA, Desiani V: Ekstrak daun dan getah tanaman jarak cina (jatropha multifida l.) sebagai antibakteri terhadap pertumbuhan bakteri staphylococcus aureus secara in vitro. J. Window Health. 2018; 1(1): 29–33.\n\nKomariah, Wulansari N, Harmayanti W: Efekifitas kitosan dengan derajat deaserilisasi konsentrasi berbeda dalam menghambat pertumbuhan bakteri gram negatif (pseudomonas aeruginosa) dan gram positif (staphylococcus aureus) rongga mulut. Seminar Nasional X Pendidikan Biologi FKIP UNS. Jakarta Barat. 2013; 1–2.\n\nSeptiari BB: Infeksi nosokomial. Yogyakarta:Nuha Medika;2017; 21–25.\n\nKumoro AC: Teknologi ekstraksi senyawa bahan aktif dari tanaman obat. Yogyakarta:Plantaxia;2015; 3–9.\n\nAiyelaagbe OO, Oguntuase BJ, Arimah BD, et al.: The antimicrobial activity of jatropha multifida extracts and chromatographic fractions against sexually transmitted infection. J. Med. Sci. 2008; 8: 143–147.\n\nBarbosa SC, Cilli EM, Dias LG: Labaditin, a cyclic peptide with rich biotechnological potential: preliminary toxicological studies and structural changes in water and lipid membrane environment. J. Amino Acids. 2011; 40: 135–144. PubMed Abstract | Publisher Full Text\n\nJawetz M, Adelberg: Mikrobiologi kedokteran 25th ed. Ahli Bahasa. Nugroho A. Jakarta: ECG.2012; 239–244."
}
|
[
{
"id": "173580",
"date": "05 Jun 2023",
"name": "Khaga Raj Sharma",
"expertise": [
"Reviewer Expertise Natural products chemistry",
"extraction",
"isolation",
"characterisation of various natural products and to perform the biological activities",
"molecular docking",
"green synthesis of nanoparticles and comparison of biological activities."
],
"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 have gone through the manuscript titled Antibacterial activity of Betadine (Jatropha multifida L.) stem extract on Pseodomonas aeruginosa growth in vitro and the followings are the queries and the suggestions\nThe preparation of plant extract or the sample preparation is not well mentioned.\n\nIt will be better to justify using DMSO of high concentration as the negative control while doing the antibacterial activity.\n\nIn the photographs of the Petri plates used to perform an antibacterial activity, the positive control, negative control, and the concentrations of the sample needed to be mentioned clearly by typing the text over the plates.\n\nBetter to write materials and methods instead of procedures.\n\nMost of the activities performed in this study have been reported in the literature, it will be better to highlight the novelty of this research.\n\nIdentification of plant sample is missing. It is needed to mention the voucher specimen number of the plant. It will be clearer if the photograph of the plant is kept in the material and method section.\n\nThe paper is submitted to the Journal of Food Research, but the manuscript is related to medicinal plants and antibacterial activity. The manuscript seems not suitable for this journal. If the food values and using the plant in food properties makes relevant to this journal.\nThese are minor revisions and need to be incorporated in the revised manuscript for the acceptance of this paper.\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": "11219",
"date": "04 Apr 2024",
"name": "Diah Harezky Irene Damanik",
"role": "Author Response",
"response": "Thank you for your suggestion. I appreciate it. The new article version was clearly mention the preparation of the extract. We used DMSO 100% as negative control. We revised the petri plates figures by typing text over the plates. We revised Procedures section with Material and Method In the new article version, we added the novelty of this research. In the new article version, we added Betadine plane photograph and vocer specimen number from new references. This manuscript is related to Medical Plants Journal because it is explain about antibacterial activity."
}
]
},
{
"id": "164184",
"date": "15 Nov 2023",
"name": "Siti Nur Hazwani Oslan",
"expertise": [
"Reviewer Expertise Microalgae",
"functional food",
"Food 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\nOverall, the manuscript presents an interesting study on the antibacterial activity of Betadine stem (Jatropha Multifida L.) extracts on Pseudomonas aeruginosa bacteria growth by in vitro. The introduction provides good background information about using Betadine stem sap in West Sumatra Province to heal external wound infections and the potential of the Betadine plant as an external wound medicine. The methodology is clearly presented, with an appropriate sample size and controlled variables. However, the uncontrolled variables could be more clearly defined. The instruments and materials used are appropriate for the study. The results are presented in a clear and concise manner, with appropriate statistical analysis. However, the discussion section could be improved by providing a more in-depth interpretation of the results and how they relate to previous studies. Overall, the manuscript has potential, but some revisions are needed to strengthen the discussion and improve clarity.\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": "11317",
"date": "13 Apr 2024",
"name": "Diah Harezky Irene Damanik",
"role": "Author Response",
"response": "Thank you for your suggestion and your positive comment. I appreciate it. As your suggestion we already update the new article version. We already more clearly defined the uncontrolled variables. We added more in-depth interpretation of the results to the discussion section and the relation to the previous studies."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1222
|
https://f1000research.com/articles/11-898/v1
|
04 Aug 22
|
{
"type": "Study Protocol",
"title": "Addressing post-COVID-19 musculoskeletal symptoms through telemedicine: A study protocol",
"authors": [
"Eleuterio A. Sánchez Romero",
"Josué Fernández Carnero",
"José Luis Alonso Pérez",
"Lidia Martínez Rolando",
"Jorge Hugo Villafañe",
"Josué Fernández Carnero",
"José Luis Alonso Pérez",
"Lidia Martínez Rolando"
],
"abstract": "Objective: The purpose of the study will be to evaluate the effect of a rehabilitation program on the improvement of patients with post-COVID-19 musculoskeletal symptoms, as well as to quantify the impact of telemedicine that evaluates the evolution of pain, functionality, and quality of life. Methods: We will carry out a case-control study in post-COVID-19 musculoskeletal symptoms patients who will undergo a multicomponent rehabilitation program, together with an intervention and a follow-up using programmed telemedicine sessions. Data will be collected on the improvement of functional capacity and quality of life, in addition to assessing the evolution of musculoskeletal symptomatology, as well as pain and psychological variables. The telemedicine sessions will improve user adherence and follow-up, and the results are expected to be disseminated to the scientific community during and after the end of the study.",
"keywords": [
"COVID-19",
"Pain",
"SARS-CoV-2",
"Musculoskeletal Disease",
"Telemedicine"
],
"content": "Introduction\n\nCOVID-19 infection causes various clinical manifestations in patients, including neurological manifestations, ranging from headache, dizziness, neuralgia, and neuropathy, to musculoskeletal symptoms and myalgia.1 Musculoskeletal alterations cause pain symptoms in COVID-19 patients, appearing to be similar in all countries.2 Prolonged immobilization and mechanical ventilation (MV), as well as the restoration of respiratory and physical functions, may delay the patient’s discharge from the intensive care unit (ICU), or only achieve a partial recovery, resulting in decreased quality of life.3 ICU-acquired weakness (ICUW) impairs the peripheral skeletal and respiratory muscles of critically ill patients. This is one of the most serious consequences of long-term immobilization, resulting in delayed weaning from MV and prolonged hospital stay.4 It has been described that patients hospitalized for COVID-19 infection presented with mild to moderate generalized pain that resembled the pattern of musculoskeletal pain (myalgias or COVID-19-induced muscle pain).5 Therefore, understanding the presence and origin of possible sequelae experienced by post-COVID-19 patients should be an emerging priority for researchers and clinicians.6 Based on these underlying mechanisms of COVID-19 infection, it is very plausible that one of the possible post-COVID-19 outcomes is the development of chronic pain.7 Chronic pain represents another pandemic crisis in modern society due to its high burden and high prevalence within the general population.8 Few data are available on post-COVID-19 sequelae related to the development of pain and potential musculoskeletal repercussions, in contrast to research highlighting other dimensions of health.9 In this context, rehabilitation should be initiated immediately after the acute phase to avoid the progression of hospital-acquired weakness and to achieve rapid functional recovery.10 The pathogenesis of widespread musculoskeletal pain in COVID-19 survivors remains unclear and possibly involves the peripheral and central nervous systems.11\n\nAddressing these sequelae, early exercise and rehabilitation protocols applied during the patient’s hospitalization and after discharge from the hospital can help improve musculoskeletal pain symptoms and prevent functional deterioration.12 Physical activity with multicomponent programs has been shown to have a positive effect on function and weakness in COVID-19 infected patients, in addition to producing improvements in pain.13,14 COVID-19 has a clear functional impairment among other comorbidities.15\n\nThe use of telemedicine improves physiotherapy care by assessing musculoskeletal disorders,16 as well as allowing better dissemination of knowledge by improving access for users who cannot frequently attend their face-to-face sessions or to reinforce therapeutic adherence.17 It facilitates an active role of users, based on personalized risk assessment (biopsychosocial factors), and allows users to be tracked, obtaining data.5\n\nThe use of Big Data in health tools opens a great opportunity to move toward monitoring platforms that can offer a more complete, adapted, and updated interaction with the user, under the basis of “more users, more data, and then better feedback that allows personalized care”. Likewise, telemedicine makes it possible to improve the information available on health and self-care.18,19 The interactive environment aims to create a friendly treatment and learning environment, in addition to improving patient adherence and compliance, as this is directly related to treatment efficacy and preventive actions.\n\nTherefore, the hypothesis will be that post-COVID-19 patients with musculoskeletal symptoms undergoing a rehabilitation program plus telemedicine results in decreased pain and improves functionality and quality of life.\n\nWe will also determine the increase in adherence to treatment through the application of telemedicine in post-COVID-19 patients with musculoskeletal symptoms.\n\n\nProtocol\n\nA case-control study will be carried out between June 2022 and February 2023 with male and female patients impacted by post-COVID-19 musculoskeletal symptoms who will undergo a multicomponent rehabilitation program, together with an intervention and a follow-up using programmed telemedicine sessions. Procedures will be conducted following the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement and checklist.20 The study protocol has been approved by the Ethical Committee of the European University of Madrid (reference number CIPI/21/046). Written informed consent will be obtained from all participants and all procedures were conducted according to the Declaration of Helsinki.\n\nThe multicomponent rehabilitation program will be carried out in six weeks of intervention with two weekly face-to-face sessions that will include endurance and resistance exercises (Figure 1) for both groups (case and control). A once a week telemedicine session will be carried out with the case group only before the face-to-face sessions, consisting of education, respiratory exercise, mobility and stretching, giving them a place to provide feedback and re-evaluate patients mid-treatment (Figure 2) and will be aimed at assessing improvement and improving therapeutic adherence. This protocol will be characterized by being progressive and individualized by monitoring the load with validated tools such as the modified Borg scale and Karvonen’s formula.21,22\n\nAll participants, whether or not they were previously admitted to ICU by COVID-19, will be contacted by telephone to propose their participation in the study, after which the selected sample meeting the criteria described below that signs the informed consent will be assessed via a comprehensive clinical anamnesis and objective physical examination performed by two expert physical therapists of the rehabilitation department of the Rey Juan Carlos University Hospital of Móstoles, Madrid, Spain, between June 2022 and October 2022. To be included in the study, the patients need to be post-COVID-19 patients (ICU or non-ICU) with musculoskeletal symptoms and be of adult age (over 18 years). Exclusion criteria included: myocardial infarction, uncontrolled arrhythmia, recent pulmonary thromboembolism, terminal illness, patients undergoing lower limb unloading, lower or upper limb fractures in the last three months, severe pain (score greater than 7 on the VAS of 10 points), suffering from the previous pathology that causes neuromuscular weakness, be younger than 18 and older than 65 years old, influenced by medication that does not allow assessment of the real muscular functionality of the patient, patients with cognitive impairment that would prevent them from understanding and collaborating in the performance of the rehabilitation program plus telemedicine, patients with cardiorespiratory instability and uncontrolled arterial hypertension, systemic illness (tumor and rheumatologic diseases), recent unrelated trauma, and limiting psychiatric pathology.\n\nThe group of cases and the group of controls will have identical or similar characteristics, except that the cases will be treated with the multicomponent rehabilitation program plus telemedicine, and the control group with the multicomponent rehabilitation program only. All subjects will sign an informed consent before inclusion (flowchart, Figure 3).\n\nIn this case-control study, 120 patients (of desired homogeneous distribution of males and females) will be included and classified into the following two groups. The initial and final assessment of each potential study participant will be performed by two investigators outside each participant’s intervention group, another investigator will consider the exclusion criteria and follow the algorithm for detecting samples that are not telemedicine-prone (Figure 4) to stratify the data. Physical therapists involved in face-to-face treatment will not know which sample also has a telemedicine focus. An independent researcher with statistical expertise will conduct the analysis of the results obtained.\n\nPatients included in the study will be assessed pre - and post-intervention, using the tools and questionnaires found at https://doi.org/10.17605/OSF.IO/2T3JG in Table 1.\n\nManual grip strength\n\nGrip strength will be measured in the affected hand and in the healthy hand (measuring the maximum grip strength). For this measurement, Handgrip strength averaging the result of three attempts with the dominant hand using a Baseline© model pear dynamometer.23\n\nQuality of life\n\nQuality of life will be measured with EuroQol-5D-5L24: a test where mobility, self-care, activities of daily living, pain/discomfort and anxiety/depression are assessed.\n\nActivities of daily living\n\nActivities of daily living (ADL) will be measured with the Barthel Index, which assesses the level of independence of the subject with respect to the performance of some ADL’s.25\n\nAssessment of exercise capacity\n\nExercise capacity will be measured with a six-minute walking test (6MWT), a sub-maximal exercise test which consists of the patient walking for six minutes along a 30 - meter corridor with two cones marking the distance to be covered while being given a series of cues and monitored for oxygen saturation, heart rate and perceived exertion.26\n\nAssessment of motor impairment\n\nMotor impairment will be measured with the Berg Balance Scale (BBS). It determines the ability or inability to safely balance during a series of predetermined tasks.27\n\nAssessment of perceived pain\n\nPerceived pain will be measured with the Numerical Pain Rating Scale (NPRS), which measures pain intensity.\n\nAssessment of neuropathic pain\n\nNeuropathic pain will be measured with DN4, a questionnaire that assesses the presence of neuropathic pain.28\n\nWidespread pain\n\nThis will be classified as a continuous numerical variable measured by the Widespread Pain Index (WPI). In this index, the patient must mark with an x the areas in which he/she has presented pain during the last week.\n\nPsychological variables and self-efficacy\n\nWe will measure psychological variables related to pain sensitivity and other main signs and symptoms, such as kinesiophobia29 and self-efficacy.20,30,31 For this purpose, we will use the Chronic Pain Self-Efficacy Questionnaire, in its Spanish-validated version32 and the Tampa Scale of Kinesiophobia, also translated and validated in Spanish.33 Finally, with Beck Depression Inventory (BDI): scale that allows us to measure depressive symptoms and severity of depression in patients older than 13 years.34\n\nThese variables will be measured by being able to predict a change in the primary measurement results between the first and second measurement of the results or data collection, to facilitate this, the repository found at https://doi.org/10.17605/OSF.IO/2T3JG shows Table 2.\n\n‐ Employment status: refers to the subject’s current employment status, and will be classified as a nominal qualitative variable, with the following response modalities: “active”, “unemployed with benefits”, “unemployed without benefits”, “pensioner”.\n\n‐ Levels of physical exercise measures the average amount of physical exercise currently performed per week, and will be classified as a nominal qualitative variable, with the following response modalities: “none”, “less than three times per week”, “three times per week”, “more than three times per week”.\n\n‐ Family economic situation: this variable assesses the average annual economic income of the family unit, and is a nominal qualitative variable, with the following response modalities: “more than 40,000 euros”, between 12,000 euros and 40,000 euros”, “less than 12,000 euros”.\n\n‐ COVID-19’s (SARS-CoV-2) own condition: this variable refers to the current or past presence/absence of illness due to COVID-19 in the subject; it is a nominal qualitative variable, whose response modalities are: “no”, “yes (without symptoms)”, “yes (with symptoms/without admission)”, “yes (with symptoms/admission to ward)”, “yes (with symptoms/admission to ICU)”.\n\n‐ Loss of family members due to COVID-19 (SARS-Cov-2): refers to the loss of family members in subjects due to COVID-19 disease, being classified as a qualitative dichotomous “yes/no” variable.\n\n‐ Chronicity: refers to the number of years that the subjects in the sample have been suffering from symptoms, so it will be classified as a continuous quantitative variable.\n\n‐ Medication: refers to the number of drugs used in the treatment of pain, so it will be classified as a continuous quantitative variable.\n\nSPSS (RRID:SCR_002865) version 25.0 (IBM SPSS Statistics for Windows; Armonk, NY, USA: IBM Corp) and an α error of 0.05 (95% confidence interval) and a desired power of 80% (β error of 0.2) will be used for statistical analysis. The Shapiro-Wilk test and visual distribution will be used to assess deviations from normality. Parametric analysis will be used in case of normality, given the expected sample size. Then, a comparison of both sociodemographic data and main outcomes between case and control groups will be performed. For case and control groups and for sex, Fisher’s exact test will be used. Pearson’s Chi-square test will compare between case and control groups. In addition, Student’s t-test for independent samples will be used for age and outcomes of the measured variables, and sex and age group. Box plots will be used to illustrate the values of the measured variables of the case and control groups. Univariate correlation analysis will be performed using Pearson’s coefficient (r) to assess the relationship between the variables. Correlations will be interpreted as weak (0.00–0.40), moderate (0.41–0.69) or strong (0.70–1.00).35 In addition, a multivariate predictive analysis will use linear regression and regression trees. Linear regression will be performed using a stepwise selection method and the R2 coefficient to establish quality adjustments. The sample size will be determined by the number of patients admitted to the hospital between June 2022 and February 2023.\n\n\nDiscussion\n\nClinical symptoms associated with COVID-19 mainly affect to the respiratory tract, but they manifest heterogeneously from other organ systems including the nervous system.2,36 We hypothesize that these patients with post-COVID-19 sequelae will demonstrate a pain and potential musculoskeletal repercussions. We expect to find, that the post-COVID-19 sequelae mechanisms might be a feature of this post-COVID-19 population.\n\nThis is the first study to use the telemedicine in post-COVID-19 patients with musculoskeletal symptoms. The results of this study can be implemented in clinical practice to help clinicians deal with this challenging patient population. Furthermore, the research will allow the extraction of data on the different patient profiles, symptoms and post-COVID-19 sequelae, in addition to the different risk factors affecting post-COVID-19 patients with musculoskeletal symptoms.\n\nPatients with chronic pain (20% of the population) have many issues to deal with as there is limited access to specialised pain management centres. Post COVID-19 patients with persistent pain are at risk of not receiving the required recognition and attention by the healthcare system and therefore they will not receive the most optimal pain management for this new pain syndrome. The social repercussions of the current project are imminent since the world should be prepared for a large number (probably millions) of COVID-19 survivors with potential post COVID-19 pain sequelae.\n\n\nConclusions\n\nThis project aims to demonstrate that multicomponent approach to musculoskeletal sequelae of COVID-19 will improve pain, functionality and quality of life,37 achieving through telemedicine sessions an improvement in therapeutic adherence and follow-up. The results are expected to be disseminated to the scientific community during and after the end of the study.\n\n\nData availability\n\nNo data are associated with this article.\n\nExtended data for ‘Addressing post-COVID-19 musculoskeletal symptoms through telemedicine: A study protocol’ https://doi.org/10.17605/OSF.IO/2T3JG contains the following data:\n\n- Table 1. Baseline descriptive and clinical variables in the total sample previous intervention\n\n- Table 2. Baseline predictive variables in the total sample previous intervention\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\nAuthor contributions\n\nConceptualization, J.H.V. and E.A.S.R.; methodology, J.H.V., L.M.R. and E.A.S.R.; software, J.H.V.; validation, all authors; formal analysis, J.F.C., E.A.S.R., L.M.R., and J.H.V.; investigation, all authors; resources, J.L.A.P.; data curation, J.H.V., E.A.S.R., J.F.C., L.M.R.; writing—original draft preparation, J.H.V, J.F.C., L.M.R. and E.A.S.R.; writing—review and editing, E.A.S.R., J.F.C., L.M.R. and J.H.V.; visualization, E.A.S.R., L.M.R. and J.H.V.; supervision, all authors.; project administration, E.A.S.R. L.M.R. and J.H.V.; funding acquisition, E.A.S.R. and J.H.V. All authors have read and agreed to the published version of the manuscript.",
"appendix": "Acknowledgments\n\nThis study is supported by the Italian Ministry of Health-Ricerca Corrente 2021.\n\n\nReferences\n\nFiore E, Corbellini C, Acucella L, et al.: Musculoskeletal pain related to COVID-19 survivors after hospitalization: A short review (Dolor musculoesquelético en supervivientes del COVID-19 tras la hospitalización: Una breve revision). Retos. 2022; 44: 789–795. Publisher Full Text\n\nGlobal Burden of Disease 2020 Health Financing Collaborator Network: Tracking development assistance for health and for COVID-19: a review of development assistance, government, out-of-pocket, and other private spending on health for 204 countries and territories, 1990–2050. Lancet Lond. Engl. 2021; 398(10308): 1317–1343. PubMed Abstract | Publisher Full Text\n\nPedersini P, Corbellini C, Villafañe JH: Italian Physical Therapists’ Response to the Novel COVID-19 Emergency. Phys. Ther. 2020; 100(7): 1049–1051. PubMed Abstract | Publisher Full Text\n\nReviriego GB, Pascual BP, Ruiz AR, et al.: Spanish Experience of Pulmonary Rehabilitation Efficacy for Patients Affected by the Novel SARS-CoV-2 (COVID-19): A Case Report. Top Geriatr. Rehabil. 2020; 36(4): 212–214. Publisher Full Text\n\nSong XJ, Xiong DL, Wang ZY, et al.: Pain Management During the COVID-19 Pandemic in China: Lessons Learned. Pain Med. 2020; 21(7): 1319–1323. PubMed Abstract | Publisher Full Text\n\nSánchez Romero EA, Martínez Rolando L, Villafañe JH: Impact of Lockdown on Patients with Fibromyalgia. Electron J. Gen. Med. 2022; 19(3): em366. Publisher Full Text\n\nPedersini P, Villafañe JH, Corbellini C, et al.: COVID-19 Pandemic: A Physiotherapy Update. Electron. J. Gen. Med. 2020; 18(1): em264. Publisher Full Text\n\nSánchez Romero EA, Meléndez Oliva E, Alonso Pérez JL, et al.: Relationship between the Gut Microbiome and Osteoarthritis Pain: Review of the Literature. Nutrients. 2021; 13(3): 716. PubMed Abstract | Publisher Full Text\n\nSoares FHC, Kubota GT, Fernandes AM, et al.: Prevalence and characteristics of new-onset pain in COVID-19 survivors, a controlled study. Eur. J. Pain Lond. Engl. 2021; 25(6): 1342–1354. PubMed Abstract | Publisher Full Text\n\nCorbellini C, Villafañe J, Gugliotta E, et al.: Pulmonary Rehabilitation in post - COVID subjects with moderate lung restriction, a case series. Paper presented at: ERS 2021. The European Respiratory Society International Congress. 2021 Sept 5-7.\n\nSerrano-Ibáñez ER, Esteve R, Ramírez-Maestre C, et al.: Chronic pain in the time of COVID-19: Stress aftermath and central sensitization. Br. J. Health Psychol. 2021; 26(2): 544–552. Publisher Full Text\n\nKress JP, Hall JB: ICU-Acquired Weakness and Recovery from Critical Illness. N. Engl. J. Med. 2014; 370(17): 1626–1635. Publisher Full Text\n\nPancera S, Bianchi LNC, Porta R, et al.: Feasibility of subacute rehabilitation for mechanically ventilated patients with COVID-19 disease: a retrospective case series. Int. J. Rehabil. Res. Int. Z Rehabil. Rev. Int. Rech. Readaptation. 2021; 44(1): 77–81. PubMed Abstract | Publisher Full Text\n\nBarker-Davies RM, O’Sullivan O, Senaratne KPP, et al.: The Stanford Hall consensus statement for post-COVID-19 rehabilitation. Br. J. Sports Med. 2020; 54(16): 949–959. Publisher Full Text\n\nFernández-de-Las-Peñas C, Rodríguez-Jiménez J, Fuensalida-Novo S, et al.: Myalgia as a symptom at hospital admission by severe acute respiratory syndrome coronavirus 2 infection is associated with persistent musculoskeletal pain as long-term post-COVID sequelae: a case-control study. Pain. 2021; 162(12): 2832–2840. PubMed Abstract | Publisher Full Text\n\nMani S, Sharma S, Omar B, et al.: Validity and reliability of Internet-based physiotherapy assessment for musculoskeletal disorders: a systematic review. J. Telemed. Telecare. 2017; 23(3): 379–391. PubMed Abstract | Publisher Full Text\n\nTenforde AS, Borgstrom H, Polich G, et al.: Outpatient Physical, Occupational, and Speech Therapy Synchronous Telemedicine: A Survey Study of Patient Satisfaction with Virtual Visits During the COVID-19 Pandemic. Am. J. Phys. Med. Rehabil. 2020; 99(11): 977–981. PubMed Abstract | Publisher Full Text\n\nHawley-Hague H, Tacconi C, Mellone S, et al.: Smartphone Apps to Support Falls Rehabilitation Exercise: App Development and Usability and Acceptability Study. JMIR Mhealth Uhealth. 2020; 8(9): e15460. PubMed Abstract | Publisher Full Text\n\nMachado GC, Pinheiro MB, Lee H, et al.: Smartphone apps for the self-management of low back pain: A systematic review. Best Pract. Res. Clin. Rheumatol. 2016; 30(6): 1098–1109. PubMed Abstract | Publisher 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. J. Clin. Epidemiol. 2008; 61(4): 344–349. Publisher Full Text\n\nRosen K, Patel M, Lawrence C, et al.: Delivering Telerehabilitation to COVID-19 Inpatients:A Retrospective Chart Review Suggests It Is a Viable Option. HSS J. Musculoskelet. J. Hosp. Spec. Surg. 2020; 16: 64–70. PubMed Abstract | Publisher Full Text\n\nUdina C, Ars J, Morandi A, et al.: Rehabilitation in adult post-COVID-19 patients in post-acute care with Therapeutic Exercise. J. Frailty Aging. 2021; 10(3): 1–4. PubMed Abstract | Publisher Full Text\n\nCalvo Lobo C, Romero Morales C, Rodríguez Sanz D, et al.: Comparison of hand grip strength and upper limb pressure pain threshold between older adults with or without non-specific shoulder pain. PeerJ. 2017; 5: e2995. Publisher Full Text\n\nRamos-Goñi JM, Craig BM, Oppe M, et al.: Handling Data Quality Issues to Estimate the Spanish EQ-5D-5L Value Set Using a Hybrid Interval Regression Approach. Value Health. 2018; 21(5): 596–604. PubMed Abstract | Publisher Full Text\n\nShah S, Vanclay F, Cooper B: Improving the sensitivity of the Barthel Index for stroke rehabilitation. J. Clin. Epidemiol. 1989; 42(8): 703–709. PubMed Abstract | Publisher Full Text\n\nFerioli M, Prediletto I, Bensai S, et al.: The role of 6MWT in Covid-19 follow up. Paper presented at: ERS 2021. The European Respiratory Society International Congress. 2021 Sept 5-7.\n\nOlezene CS, Hansen E, Steere HK, et al.: Functional outcomes in the inpatient rehabilitation setting following severe COVID-19 infection. PLoS One. 2021; 16(3): e0248824. PubMed Abstract | Publisher Full Text\n\nPerez C, Galvez R, Huelbes S, et al.: Validity and reliability of the Spanish version of the DN4 (Douleur Neuropathique 4 questions) questionnaire for differential diagnosis of pain syndromes associated to a neuropathic or somatic component. Health Qual. Life Outcomes. 2007; 5(1): 66. PubMed Abstract | Publisher Full Text\n\nİnal Ö, Aras B, Salar S: Investigation of the relationship between kinesiophobia and sensory processing in fibromyalgia patients. Somatosens. Mot. Res. 2020; 37(2): 92–96. Publisher Full Text\n\nVan Liew C, Leon G, Neese M, et al.: You get used to it, or do you: symptom length predicts less fibromyalgia physical impairment, but only for those with above-average self-efficacy. Psychol. Health Med. 2019; 24(2): 207–220. PubMed Abstract | Publisher Full Text\n\nKaleth AS, Bigatti SM, Slaven JE, et al.: Predictors of Physical Activity in Patients With Fibromyalgia: A Path Analysis. J. Clin. Rheumatol. Pract. Rep. Rheum. Musculoskelet. Dis. 2022; 28(1): e203–e209. PubMed Abstract | Publisher Full Text\n\nMartín-Aragón L-R: Percepción de autoeficacia en dolor crónico. Adaptación y validación de la chronic pain selfefficacy scale. Rev Psicol SALUD. 1999; 11(1): 51–76. Publisher Full Text\n\nGómez-Pérez L, López-Martínez AE, Ruiz-Párraga GT: Psychometric Properties of the Spanish Version of the Tampa Scale for Kinesiophobia (TSK). J. Pain. 2011; 12(4): 425–435. PubMed Abstract | Publisher Full Text\n\nVega-Dienstmaier JM, Coronado-Molina O, Mazzotti G: Validez de una versión en español del Inventario de Depresión de Beck en pacientes hospitalizados de medicina general. Rev. Neuropsiquiatr. 04; 77(2): 95–103. Publisher Full Text\n\nHoch MC, Farwell KE, Gaven SL, et al.: Weight-Bearing Dorsiflexion Range of Motion and Landing Biomechanics in Individuals With Chronic Ankle Instability. J. Athl. Train. 2015; 50(8): 833–839. PubMed Abstract | Publisher Full Text\n\nSánchez Romero EA, Alonso Pérez JL, Vinuesa Suárez I, et al.: Spanish experience on the efficacy of airways clearance techniques in SARS-CoV-2 (COVID-19) at intensive care unit: An editorial and case report. SAGE Open Med. Case Rep. January 2022. Publisher Full Text\n\nCuenca-Zaldivar JN, Monroy Acevedo Á, Fernández-Carnero J, et al.: Effects of a Multicomponent Exercise Program on Improving Frailty in Post-COVID-19 Older Adults after Intensive Care Units: A Single-Group Retrospective Cohort Study. Biology. 2022; 11: 1084."
}
|
[
{
"id": "153318",
"date": "28 Nov 2022",
"name": "Wojciech Glinkowski",
"expertise": [
"Reviewer Expertise Orthopedics",
"traumatology",
"sports medicine",
"spinal surgery",
"telemedicine",
"teleorthopaedics",
"telerehabilitation"
],
"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 indicate that the experiment program will be a multicomponent rehabilitation program with an intervention and a follow-up using programmed telemedicine sessions.\nA key aspect of telemedicine is the closure of the patient-doctor loop and feedback. The authors of the summary report do not indicate if and what the feedback will be.\nThe abstract also states that \"results are expected to be disseminated to the scientific community during and after the end of the study.\" However, the key to presenting the results is to complete the research and obtain the results, hence the question of how the authors will deliver the results without getting them.\n\nThe authors indicate that \"COVID-19 infection causes various clinical manifestations in patients, including neurological manifestations, ranging from headache, dizziness, neuralgia, and neuropathy, to musculoskeletal symptoms and myalgia.\" However, the authors do not point to specific symptoms or how to distinguish them from pain syndromes unrelated to COVID-19.\nThe authors also propose that the study group should have a different study protocol which consists of \"education, respiratory exercise, mobility, and stretching, giving them a place to provide feedback and re-evaluate patients mid-treatment.” In this situation, will the group without distance assessment (I do not write telemedicine because it has not been clearly defined) also not have \"education, respiratory exercise, mobility, and stretching, giving them a place to provide feedback and re-evaluate patients mid-treatment\"? If not, the study groups cannot be compared.\nThe authors report, “Physical therapists involved in face-to-face treatment will not know which sample also has a telemedicine focus.\" This may suggest an attempt at randomization. So how is randomization going to work? How will patients be allocated to groups? If patients have different symptoms at different locations, how do the authors want to classify them as a homogeneous study group? A checklist?\nThe authors also want to compare subjects who are not informed whether they are taking painkillers or other drugs besides telling them whether they are taking medications. Taking painkillers may change the achievement of symptoms planned for collection. The introduction of additional exercises may also change the results significantly, making it impossible to compare the test group with the control group.\nIn the reviewer’s opinion, the study protocol requires explicit declarations and ensures the comparability of the test group with the control group.\nRegarding \"variables will be measured by being able to predict a change in the primary measurement results between the first and second measurement.\" What information do the authors expect to gain from the items concerning:\n\"Loss of family members due to COVID-19 (SARS-Cov-2): refers to the loss of family members in subjects due to COVID-19 disease, being classified as a qualitative dichotomous “yes/no” variable.\"\n\n\"Chronicity refers to the number of years that the subjects in the sample have been suffering from symptoms so that it will be classified as a continuous quantitative variable.\"\n\n\"Medication: refers to the number of drugs used to treat pain so that it will be classified as a continuous quantitative variable.\"\nIs the question about family members supposed to relate to the mental state and mood disorders and the more difficult participation in rehabilitation associated with it? Will the question give information about the duration of the symptoms? Will the question about the number of drugs determine which groups of medicines affecting the study’s results are used by patients?\nA final concern about the submission is how the authors explain the co-author's involvement in the data curation activity in the absence of available data from this study.\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? Not applicable",
"responses": [
{
"c_id": "9622",
"date": "01 Jun 2023",
"name": "Eleuterio A. Sánchez Romero",
"role": "Author Response",
"response": "Response: Thank you for reading our manuscript and for providing constructive comments and pointing out important details. The revision process has made the manuscript clearer and of higher quality. 1. The authors indicate that the experiment program will be a multicomponent rehabilitation program with an intervention and a follow-up using programmed telemedicine sessions. A key aspect of telemedicine is the closure of the patient-doctor loop and feedback. The authors of the summary report do not indicate if and what the feedback will be. Response: We appreciate your comments with the intention of improving the manuscript. In \"Study design\", we add \"A once a week telemedicine session will be carried out with the case group only before the face-to-face sessions, consisting of education, respiratory exercise, mobility and stretching, giving them a place to provide feedback and re-evaluate patients mid-treatment ( Figure 2) and will be aimed at assessing improvement and improving therapeutic adherence.” Thank you. 2. The abstract also states that \"results are expected to be disseminated to the scientific community during and after the end of the study.\" However, the key to presenting the results is to complete the research and obtain the results, hence the question of how the authors will deliver the results without getting them. Response: The sentence has been changed to\" the results are expected to be disseminated to the scientific community after the end of the study.” Thank you. 3. The authors indicate that \"COVID-19 infection causes various clinical manifestations in patients, including neurological manifestations, ranging from headache, dizziness, neuralgia, and neuropathy, to musculoskeletal symptoms and myalgia.\" However, the authors do not point to specific symptoms or how to distinguish them from pain syndromes unrelated to COVID-19. Response: Thank you very much for your comment. We have added the following sentence \"COVID-19 infection causes various clinical manifestations in patients, including neurological manifestations, ranging from headache, dizziness, neuralgia, and neuropathy, to musculoskeletal symptoms and myalgia. Some of the most commonly reported symptoms of COVID-19 include fatigue, cough, fever, ageusia (loss of taste), anosmia (loss of smell), and dyspnea (shortness of breath). In addition to these symptoms, some people may experience a headache, chest pain, or palpitations.” 4. The authors also propose that the study group should have a different study protocol which consists of \"education, respiratory exercise, mobility, and stretching, giving them a place to provide feedback and re-evaluate patients mid-treatment.” In this situation, will the group without distance assessment (I do not write telemedicine because it has not been clearly defined) also not have \"education, respiratory exercise, mobility, and stretching, giving them a place to provide feedback and re-evaluate patients mid-treatment\"? If not, the study groups cannot be compared. Response: Thank you very much for your comment. We have added the following sentence \"The same protocol will be performed once a week in the control group prior to the face-to-face sessions so that comparisons can be made between the two groups\". 5. The authors report, “Physical therapists involved in face-to-face treatment will not know which sample also has a telemedicine focus.\" This may suggest an attempt at randomization. So how is randomization going to work? How will patients be allocated to groups? If patients have different symptoms at different locations, how do the authors want to classify them as a homogeneous study group? A checklist?. Response: Thank you very much for your comment. We have removed that sentence/statement, since we include the same telerehabilitation protocol in face-to-face sessions, we cannot ensure the blinding of the physiotherapists who perform the intervention by the multicomponent rehabilitation program. 6. The authors also want to compare subjects who are not informed whether they are taking painkillers or other drugs besides telling them whether they are taking medications. Taking painkillers may change the achievement of symptoms planned for collection. The introduction of additional exercises may also change the results significantly, making it impossible to compare the test group with the control group. Response: Answer: Thank you very much for your comment. Since the patients belong to the referral hospital, we have the record of their medical history, which contains all their information regarding the consumption of drugs. These will be taken into account, especially those that could influence the results. If the patients meet the inclusion and exclusion criteria, the pertinent statistical analyses will be carried out, since we want to verify whether drugs consumption decreases after the intervention, taking as a reference another study in which we found results in this respect: Sánchez Romero EA, Fernández-Carnero J, Calvo-Lobo C, Ochoa Sáez V, Burgos Caballero V, Pecos-Martín D. Is a Combination of Exercise and Dry Needling Effective for Knee OA? Pain Med. 2020 Feb 1;21(2):349-363. 7. In the reviewer’s opinion, the study protocol requires explicit declarations and ensures the comparability of the test group with the control group. Response: Thank you for your comment. We have added the following sentence \"The case group and the control group will have identical or similar characteristics, except that the cases will be treated with the multicomponent rehabilitation program plus telemedicine, and the control group with the multicomponent rehabilitation program and the same protocol in face-to-face sessions\". 8. Regarding \"variables will be measured by being able to predict a change in the primary measurement results between the first and second measurement.\" What information do the authors expect to gain from the items concerning: \"Loss of family members due to COVID-19 (SARS-Cov-2): refers to the loss of family members in subjects due to COVID-19 disease, being classified as a qualitative dichotomous “yes/no” variable.\" Response: We appreciate your comment. In our study, the aforementioned variables are modulating variables. We intend to collect this information and check for a possible influence on the results. Thank you. 9. \"Chronicity refers to the number of years that the subjects in the sample have been suffering from symptoms so that it will be classified as a continuous quantitative variable.\" Response: We have modified the text to \" Chronicity refers to the number of months that the subjects in the sample have been suffering from symptoms so that it will be classified as a continuous quantitative variable.” Thank you 10. \"Medication: refers to the number of drugs used to treat pain so that it will be classified as a continuous quantitative variable.\" Is the question about family members supposed to relate to the mental state and mood disorders and the more difficult participation in rehabilitation associated with it? Will the question give information about the duration of the symptoms? Will the question about the number of drugs determine which groups of medicines affecting the study’s results are used by patients? Response: We welcome your comments. We appreciate your comment. In our study, the aforementioned variables are modulating variables. We intend to collect this information and check for a possible influence on the results. We have modified the variables section from \"Predictive variables\" to \"Modulating variables\". Thank you. 11. A final concern about the submission is how the authors explain the co-author's involvement in the data curation activity in the absence of available data from this study. Response: Thank you very much for your comment. We have removed this part from the related section."
}
]
},
{
"id": "156797",
"date": "18 Apr 2023",
"name": "Marcos Roberto Tovani-Palone",
"expertise": [
"Reviewer Expertise Public and Global Health",
"General Medicine."
],
"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 an interesting and very well written study protocol on the treatment of post-COVID-19 musculoskeletal symptoms through telemedicine.\n\nThe article is relevant and represents an important intellectual contribution to the literature. The methods used are appropriate and the description of the protocol is complete and quite clear for readers. Furthermore, the proposed objectives are relevant especially for the field of COVID-19. I really appreciate how the authors have described in detail and carefully the design of the protocol as well as all the pertinent methodology. The wisdom and accuracy in the description of data analysis is also another highlight. However, I consider that the discussion could be described in more detail, including new insights. I send below some suggestions that should be especially helpful in generating new ideas and refinement of the manuscript.\n\nReference suggestions:\n\nPMID: 34730705 PMCID: PMC8528447 - I recommend this reference given that the article provides an important discussion on the neurological findings of COVID-19.\n\nPMID: 35434056 PMCID: PMC8968610 - I recommend this reference given that the article provides an overview of the importance of ehealth, telehealth, and telemedicine for managing COVID-19 patients.\n\nHowever, these two references are only suggestions/examples and the authors should be free to search for other similar articles.\n\nOther suggestions:\n\nPlease describe the full names of all acronyms/abbreviations on their first appearance in the text of the manuscript.\n\nPlease make it clear when COVID-19 (the disease) or SARS-CoV-2 (the virus) should be used.\n\nThere are some typographical errors. Please review this.\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": [
{
"c_id": "9623",
"date": "01 Jun 2023",
"name": "Eleuterio A. Sánchez Romero",
"role": "Author Response",
"response": "This is an interesting and very well written study protocol on the treatment of post-COVID-19 musculoskeletal symptoms through telemedicine. The article is relevant and represents an important intellectual contribution to the literature. The methods used are appropriate and the description of the protocol is complete and quite clear for readers. Furthermore, the proposed objectives are relevant especially for the field of COVID-19. I really appreciate how the authors have described in detail and carefully the design of the protocol as well as all the pertinent methodology. The wisdom and accuracy in the description of data analysis is also another highlight. However, I consider that the discussion could be described in more detail, including new insights. I send below some suggestions that should be especially helpful in generating new ideas and refinement of the manuscript. Reference suggestions: PMID: 34730705 PMCID: PMC8528447 - I recommend this reference given that the article provides an important discussion on the neurological findings of COVID-19. PMID: 35434056 PMCID: PMC8968610 - I recommend this reference given that the article provides an overview of the importance of health, telehealth, and telemedicine for managing COVID-19 patients. However, these two references are only suggestions/examples and the authors should be free to search for other similar articles. Response: Thank you for reading through our manuscript. The \"Discussion\" section has been restructured in accordance to your proposal. The revision process has made the manuscript clearer and heightened the quality. Other suggestions: Please describe the full names of all acronyms/abbreviations on their first appearance in the text of the manuscript. Response: Done. Thank you. Please make it clear when COVID-19 (the disease) or SARS-CoV-2 (the virus) should be used. Response: Done. Thank you. There are some typographical errors. Please review this. Response: Done. Thank you."
}
]
}
] | 1
|
https://f1000research.com/articles/11-898
|
https://f1000research.com/articles/12-1230/v1
|
27 Sep 23
|
{
"type": "Research Article",
"title": "Correlation of age with the size of subcortical nuclei of the brain and its implication in degenerative disease: A magnetic resonance imaging study",
"authors": [
"Aditij Dhamija",
"Lydia S. Andrade",
"Prakashini K.",
"Chandni Gupta",
"Aditij Dhamija",
"Lydia S. Andrade",
"Prakashini K."
],
"abstract": "Background: Aging is a non-modifiable risk factor for neurodegenerative disease. It is well established that the brain undergoes physiological atrophy with age. So, this study was conducted to analyse the correlation between the age of the person and the size of the various subcortical nuclei of the brain and whether these measurements can serve as a useful indicator for physiological atrophy leading to degenerative disease in clinical practice. Methods: A total of 600 MRI scans from healthy individuals were examined and the measurements of subcortical nuclei were taken and subsequently analysed. Results: A statistically significant difference between the genders was observed in the sizes of the axial diameters of caudate nucleus, putamen and globus pallidus. Caudate nucleus transverse diameter showed a moderate negative correlation with age in males. Globus pallidus axial diameter with age showed weak positive correlation for males. Globus pallidus transverse diameter showed weak positive correlation with age for both males and females, but it was stronger for males compared to females. Conclusions: These results will help neurologists and neurosurgeons in analysing various early degenerative diseases and treat them accordingly.",
"keywords": [
"Aging",
"Magnetic resonance imaging",
"Neurodegenerative diseases",
"Brain",
"Neurosurgeons."
],
"content": "Introduction\n\nAging is a non-modifiable risk factor for neurodegenerative disease. It is well established that the brain undergoes physiological atrophy with age. No single study has yet been conducted on normal people comparing the sizes of all the brain structures together and comparing them with their age.\n\nDecrease in the size of the caudate nucleus is seen in Alzheimer’s disease proportionate to general atrophy of the brain.1 An increase in the size of the caudate nucleus and putamen is noted in patients suffering from Parkinson’s disease.2 It was believed to be due to compensatory changes to account for damage to basal ganglia but a decrease in the size of putamen in both early and advanced Parkinson’s disease and decrease in putamen volume in only advanced Parkinson’s disease is also noted.3 Significantly smaller subcortical nuclei and decreased sizes of caudate nucleus and putamen were seen in people suffering from depression.4 Patients suffering from mild Huntington’s disease showed atrophic changes in the caudate nucleus as well as the putamen, where putamen changes exceed caudate nucleus size changes in early disease.5 Carriers of Huntington’s disease showed smaller sizes of caudate nucleus, putamen and globus pallidus compared to non-gene carriers.6 Patients suffering with late life depression had ventricular enlargement and reduction in the size of the caudate nucleus.7 Basal ganglia sizes (in the caudate nucleus and putamen) are enlarged in patients suffering from schizophrenia.8 Caudate nucleus and putamen may be larger in people suffering from bipolar disorder while they are smaller in those suffering from major depressive disorder.9 Lesch-Nyhan disease was linked with reduction in size of the caudate nucleus and putamen.10 Motor fitness was also linked with an increase in the size of the basal ganglia, and with improved executive function.11\n\nAs there are many changes noted in the brain as the ageing process progresses, the size of these structures of the brain will help neurologists and neurosurgeons in analysing various early degenerative diseases and treat them accordingly. This study would be useful in constructing a normogram and the results would help physicians identify certain morphometric changes in size such as those seen in the basal ganglia with schizophrenia patients, which might otherwise be missed.\n\nThis study was conducted to analyse the correlation between the age of the person and the size of the various subcortical nuclei of the brain and whether these measurements can serve as a useful indicator of physiological atrophy leading to degenerative disease in clinical practice.\n\n\nMethods\n\nInstitutional ethical clearance was taken before starting the study from Kasturba Medical college and Kasturba Hospital institution ethics committee on 9.2.2021. (IEC 213 – 2021). The only relevant details required were the age and gender of the patient and no other identifying variables were used. This information was collected from the medical records of patients after due permission from the medical superintendent of the hospital and the ethics committee.\n\nWe used the STROBE reporting guidelines for our study; a completed checklist is available under Reporting Guidelines.12\n\nThis was a retrospective study conducted in the Department of Radiology, Kasturba Medical College, Manipal.\n\nMRI scans of 600 healthy people were divided into three age groups as follows:\n\nGroup 1: 1–18 years\n\nGroup 2: 19–40 years\n\nGroup 3: 41–70 years\n\nThe age of 40 was chosen as studies have indicated that brain volume and weight tends to start decreasing at a rate of 5% from this age. The shrinking of the grey matter is frequently reported after this age.13\n\nTwo months (1/3/2021–1/5/2021)\n\nThe following formula was used to get a combined standard deviation.14\n\nUsing the formula for comparison of means15:\n\nFor 85% power and 99% confidence interval,\n\nBased on this result, it was decided to keep the sample size of each group as 200 people, for a total sample size of 600 people.\n\nInclusion criteria\n\n(a) Only brain scans belonging to healthy patients were included in the study.\n\n(b) Only brain scans that showed distinct boundaries were considered for measurement.\n\n(c) All patients belonging from 1–70 years were included in the study.\n\nExclusion criteria\n\n(a) All brain scans showing pathological changes affecting the normal anatomy of the basal ganglia were excluded.\n\n(b) All scans showing alteration of the size and shape of the basal ganglia due to any pathological condition were excluded.\n\n(c) All scans with poor positioning of the patients were excluded.\n\n(d) All scans with poor image quality were excluded.\n\n(e) All patients below 1 year and after 70 years were excluded from the study.\n\n\nProtocol\n\nTools used\n\nMRI scans were used.\n\nMRI scans were preferred for the following reason:\n\n1. Clear delineation and demarcation of the various structures especially the subcortical nuclei.\n\n2. Ability to visualise structures in different axes allowing for more accurate measurement.\n\n3. Sample is less likely to be misdiagnosed as normal after an MRI scan.\n\nDetailed description of procedure/processes:\n\nThe process involved accessing the MRI scans of the patients. The only relevant details required was the age and gender of the patient and no other identifying variable was used. The information was collected from the medical records of patients after due permission from the medical superintendent of the hospital and permission from the ethics committee.\n\nThe procedure involved the following measurements: (Figure 1)\n\n1. Measurement of the size of the putamen.\n\na) Vertical/axial diameter – Greatest vertical/axial length in mm from upper margin of the putamen to its lower limit.\n\nb) Transverse diameter – Greatest transverse length in mm along the coronal plane.\n\n2. Measurement of the size of the globus pallidus.\n\na) Vertical/axial diameter – Greatest vertical/axial length in mm from upper margin of the globus pallidus to its lower limit.\n\nb) Transverse diameter – Greatest transverse length in mm along the coronal plane.\n\n3. Measurement of the size of the caudate nucleus.\n\na) Vertical/axial diameter - Greatest vertical/axial length in mm from upper margin of the caudate nucleus to its lower limit.\n\nb) Transverse diameter - Greatest transverse length in mm along the coronal plane.\n\nA) Vertical/axial diameter of the putamen; B) Transverse diameter of the putamen; C) Vertical/axial diameter of the globus pallidus; D) Transverse diameter of the globus pallidus; E) Vertical/axial diameter of the caudate nucleus; F) Transverse diameter of the caudate nucleus.\n\nFor statistical analysis, IBM SPSS Statistics for Windows Version 20.0 (USA) was used. The mean and standard deviations were calculated for the total population. Spearman’s coefficient was used to evaluate the correlation between age and the size of the parameters under consideration. Spearman’s coefficient was also calculated separately for males and females to judge whether the correlation was more significant for a particular gender with age. We used an ANOVA test to establish whether a significant mean difference exists in the sizes of the parameters for the age groups under consideration. Finally, to establish whether there was any difference in the parameters with regards to sex, we used an independent samples t-test.\n\nUnderlying data and statistical analysis is included in the Underlying Data section.16\n\n\nResults\n\nThe mean and standard deviations of all parameters of the subcortical nuclei are shown in Table 1.\n\nSpearman’s rho for correlation of all the parameters of the subcortical nuclei are shown in Table 2. Spearman’s rho analysis shows a moderate negative correlation between caudate nucleus transverse diameter and age. A weak negative correlation with age was seen with caudate nucleus axial diameter and a weak positive correlation with age was seen with globus pallidus axial diameter and globus pallidus transverse diameter. There was no statistically significant correlation between putamen axial diameters and putamen transverse diameter.\n\nBar means have been constructed to visualise the data with error bars (±2SD) to visualise the variability of data. The trends seen with age can also be visualised. (Figure 2). Agewise mean and standard deviations of all the parameters of the subcortical nuclei are shown in Table 3. Spearman’s rho for correlation of all the parameters (males and females) are shown in Table 4. In comparing the Spearman’s correlation coefficient between males and females, it was observed that caudate nucleus size showed a greater negative correlation with age in males compared to females. Caudate nucleus transverse diameter showed a moderate negative correlation with age in males and a weaker moderate negative correlation with age in females. Putamen sizes showed an increase with age in males but a decrease with age in females, but these were not found to be statistically significant. Globus pallidus axial diameter with age showed a weak positive correlation for males but it was statistically insignificant for females. Globus pallidus transverse diameter showed a weak positive correlation with age for both males and females, but it was stronger for males compared to females.\n\nThe trends seen with age can also be visualised.\n\nMean bars have been constructed to visualise the data with an error bar (±2SD) to visualise the variability of data. The trends between males and females can be observed for all parameters. (Figure 3). Analysis of variance of all parameters between groups is shown in Table 5. All parameters showed significance. This shows that a difference in size exists between the three age groups for the axial and transverse diameters of the caudate nucleus, axial and transverse diameters of the putamen, axial and transverse diameters of the globus pallidus.\n\nThe trends between males and females can be observed for all parameters.\n\nAnalysis of variance for all parameters for males is shown in Table 5. All parameters showed significance for males. This shows that a difference in size exists between the three age groups for males for the axial and transverse diameters of the caudate nucleus, axial and transverse diameters of the putamen, axial and transverse diameters of the globus pallidus.\n\nAnalysis of variance for all parameters for females is shown in Table 5. All except globus pallidus axial diameter is significant for females. This shows that a difference in size exists between the three age groups for females for the axial and transverse diameters of the caudate nucleus, axial and transverse diameters of the putamen, transverse diameter of the globus pallidus.\n\nThe final results show that caudate nucleus axial diameter showed a general decrease in size with age, but in men it showed a slight increase in size when the <18 age group was compared to the 19–40 age group which was not found to be statistically significant. This increase was offset by the greater decrease in size from the 19–40 age group and therefore the decrease in the size of caudate nucleus axial diameter was found to be greater in males compared to females. The difference of means is significant for the <18 and >41 age group and 19–40 and >41 age groups in males and for the <18 and >41 age group in females.\n\nThe decrease in size of the caudate nucleus transverse diameter seems to be greater in males compared to females. The difference of means is significant for all three age groups in both genders.\n\nPutamen axial diameter sizes seems to increase in males from <18 to 19–40 age group and then shows a slight decrease from 19–40 to >41 age group but the decrease is not significant enough to offset the initial increase. In females, it showed a minor increase from <18 to 19–40 which was not statistically significant and then decreased from 19–40 to >41 which was significant enough to offset the initial increase. This difference of means is significant in the <18 and 19–40 age group in males and for <18 and >41 age group and 19–40 and >41 age group in females.\n\nPutamen transverse diameter sizes seem to increase in males in the <18 and 19–40 age group and shows a very slight decrease from the 19–40 to >41 age group, none of which are found to be statistically significant. In females, an initial increase in size is seen from the 19–40 to >41 age group followed by a significant decline from the 19–40 to >41 age group which is enough to offset the initial increase. The difference of means is significant in the 19–40 and >41 age group in females.\n\nGlobus pallidus axial diameter seems to rise significantly in males. There is a marked increase in size from the <18 age group and the 19–40 age group, while the increase in size in the 19–40 to >41 age group is insignificant. In females, the increase in size is comparatively insignificant. The difference of means is significant only for males in the <18 and 19–40 and the <18 and >41 age groups.\n\nGlobus pallidus transverse diameter seems to rise in both males and females with the rise being slightly higher in men. The difference of means is significant for males in all three age groups and for females in the <18 and 19–40 age group and the <18 and >41 age groups.\n\nGroup statistics for all parameters (genderwise) is shown in Table 6. An independent t-test was done to compare all parameters between genders. A statistically significant difference between the genders was observed in the sizes of the caudate nucleus axial diameter (P value: 0.000), putamen axial diameter (P value: 0.000), globus pallidus axial diameter (P value: 0.001). However, no statistically significant differences in sizes of the structures with genders was found between the caudate nucleus transverse diameter, putamen transverse diameter and globus pallidus transverse diameter.\n\n\nDiscussion\n\nOur study found a general decrease in the size of the caudate nucleus. The decrease in the size of the caudate nuclei with aging supports the findings of Amal et al. and Gunning-Dixon et al.17,18 The correlation with age was strongest for caudate nucleus transverse diameter, which showed a decrease with aging. The caudate nucleus axial diameter showed weaker correlation with a general decrease in size with age, but in men, it showed a slight increase in size from the <18 age group to the 19–40 age group, which was not found to be statistically significant. This increase was offset by the greater decrease in size from the 19–40 age group and therefore the decrease in the size of caudate nucleus axial diameter was found to be greater in males compared to females. The difference of means is significant for the <18 and >41 age group and 19–40 and >41 age groups in males and for the <18 and >41 age group in females. The apparent increase in size in men may be due to similar sizes being seen in the <18 and 19–40 age group, which may result in an apparent increase in length due to inherent physiological variations in the two samples. Hence, the increase is not found to be statistically significant. The decrease in the size of caudate nucleus transverse diameter also seems to be greater in males compared to females. The difference of means is significant for all three age groups in both genders. The caudate nucleus transverse diameter showed no significant differences between the genders. This supports the findings of Rijpkema et al., who found no significant difference between the genders.19 However, a significant difference was found in the axial diameter of the caudate nucleus. Due to the transverse diameter being non-significant for gender, the volumetric relationship might become non-significant for gender and thus explain the results of Rijpkema et al.19\n\nFor both putamen axial and transverse diameter, a decrease in size is seen in both genders in the 19–40 and >41 age group. This supports the findings reported by Amal et al., Gunning-Dixon et al. and Walhovd et al. with regards to a decrease in the size of the putamen with age in the elderly.17,18,20 In our study, putamen sizes showed an initial increase in size in both genders from the <18 to 19–40 age group which was statistically significant for men. The initial increase in size in men was not compensated for by the subsequent decrease in size and hence overall the size of the putamen was found to have increased. The causes for this finding and what implications it may have can serve as grounds for future research on this topic. Our study is also able to confirm the finding of an increased size of the putamen in men as was reported by Rijpkema et al.19\n\nGlobus pallidus axial diameter seems to rise significantly in males. There is a marked increase in size from the <18 age group and the 19–40 age group, while the increase in size in 19–40 to >41 age group is insignificant. In females, the increase in size is comparatively insignificant. The difference of means is significant only for males in the <18 and 19–40 and the <18 and >41 age group. Globus pallidus transverse diameter seems to rise in both males and females with the rise being slightly higher in men. The difference of means is significant for males in all three age groups and for females in the <18 and 19–40 age group and the <18 and >41 age group. This is different from the result found by Gunning-Dixon et al. and Brabec et al.18,21 This may be due to differences in the method and site of measurements as well as the boundaries of the structure considered. Globus pallidus axial diameter was shown to have significant differences between the genders, which supports the finding of Rijpkema et al. who found a significant larger size of the globus pallidus in males.19 The transverse diameter showed no significant difference between the genders.\n\nThe data gathered from this research will be a useful tool for the clinician to assess radiological scans and detect neurodegenerative disorders early in a patient.\n\n\nConclusions\n\nIn this study, we examined the correlation between age and the sizes of the basal ganglia. A total of 600 MRI scans from healthy individuals were examined and the measurements were taken and subsequently analysed.\n\nIn males as the age advances caudate nucleus transverse diameter decreases, globus pallidus axial diameter increases. In both males and females globus pallidus transverse diameter increases with age. All dimensions of caudate nucleus, putamen and globus pallidus were found to be larger in males.\n\nAS the age advances the putamen transverse length showed an increase in size in males and a decrease in size in females, which could have clinical ramifications that should be explored in more depth in future studies.\n\nOne of the limitations of the study is that it utilised scans from a single hospital in South India, therefore, similar studies should be performed in other centres so that the findings can be generalised for the entire population.",
"appendix": "Data availability\n\nFigshare: Underlying data for ‘Correlation of age with the size of subcortical nuclei of the brain and its implication in degenerative disease: A magnetic resonance imaging study’. https://www.doi.org/10.6084/m9.figshare.23634468. 12\n\nFigshare: STROBE checklist for ‘Correlation of age with the size of subcortical nuclei of the brain and its implication in degenerative disease: A magnetic resonance imaging study’. https://www.doi.org/10.6084/m9.figshare.23641866. 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 want to acknowledge Dr. Akilesh Pandey for providing statistical support for the paper. The author also wants to acknowledge ICMR-STS for approving and funding our project.\n\n\nReferences\n\nAlmeida OP, Burton EJ, McKeith I, et al.: MRI study of caudate nucleus volume in Parkinson’s disease with and without dementia with Lewy bodies and Alzheimer’s disease. Dement. Geriatr. Cogn. Disord. 2003; 16(2): 57–63. PubMed Abstract\n\nKosta P, Argyropoulou MI, Markoula S, et al.: MRI evaluation of the basal ganglia size and iron content in patients with Parkinson’s disease. J. Neurol. 2006; 253(1): 26–32. PubMed Abstract | Publisher Full Text\n\nGeng D-Y, Li Y-X, Zee C-S: Magnetic resonance imaging-based volumetric analysis of basal ganglia nuclei and substantia nigra in patients with Parkinson’s disease. Neurosurgery. 2006; 58(2): 256–262. PubMed Abstract\n\nLisanby SH, McDonald WM, Massey EW, et al.: Diminished subcortical nuclei volumes in Parkinson’s disease by MR imaging. J. Neural. Transm. Suppl. 1993; 40: 13–21. PubMed Abstract\n\nHarris GJ, Pearlson GD, Peyser CE, et al.: Putamen volume reduction on magnetic resonance imaging exceeds caudate changes in mild Huntington’s disease. Ann. Neurol. 1992; 31(1): 69–75. PubMed Abstract | Publisher Full Text\n\nJurgens CK, Wiel L, Es ACGM, et al.: Basal ganglia volume and clinical correlates in ‘preclinical’ Huntington’s disease. J. Neurol. 2008; 255(11): 1785–1791. PubMed Abstract | Publisher Full Text\n\nSchweitzer I, Tuckwell V, Ames D, et al.: Structural Neuroimaging Studies in Late-Life Depression: A Review. World J. Biol. Psychiatry. 2001; 2(2): 83–88. Publisher Full Text\n\nMamah D, Wang L, Barch D, et al.: Structural analysis of the basal ganglia in schizophrenia. Schizophr. Res. 2007; 89(1–3): 59–71. PubMed Abstract\n\nHarris JC, Lee RR, Jinnah HA, et al.: Craniocerebral Magnetic Resonance Imaging Measurement and Findings in Lesch-Nyhan Syndrome. Arch. Neurol. 1998; 55(4): 547–553. PubMed Abstract | Publisher Full Text\n\nNiemann C, Godde B, Staudinger UM, et al.: Exercise-induced changes in basal ganglia volume and cognition in older adults. Neuroscience. 2014; 281: 147–63. PubMed Abstract | Publisher Full Text Reference Source\n\nParija B, Sahu N, Rath S, et al.: Age-related Changes in Ventricular System of Brain in Normal Individuals Assessed by Computed Tomography Scans. Siriraj Med. J. 2014; 66(6): 225–230.\n\nGupta C: Correlation of age with the size of subcortical nuclei of the brain and its implication in degenerative disease: A magnetic resonance imaging study. result.xls. [Dataset]. figshare. 2023. Publisher Full Text\n\nPeters R: Ageing and the brain. Postgrad. Med. J. 2006; 82(964): 84–88. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHiggins JPT, Li T, Deeks JJ: Chapter 6: Choosing effect measures and computing estimates of effect. Cochrane Handbook for Systematic Reviews of Interventions version. 2021; 6(2). Reference Source\n\nCharan J, Biswas T: How to calculate sample size for different study designs in medical research? Indian J. Psychol. Med. 2013; 35(2): 121–126. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGupta C: Correlation of age with the size of subcortical nuclei of the brain and its implication in degenerative disease: A magnetic resonance imaging study. Strobe checklist. [Dataset]. figshare. 2023. Publisher Full Text\n\nAmal E, Amal M, Mohamed E, et al.: A Study of volumetric variations of basal nuclei in the normal human brain by magnetic resonance imaging. Clin. Anat. 2017; 30(2): 175–182.\n\nGunning-Dixon FM, Head D, McQuain J, et al.: Differential aging of the human striatum: a prospective MR imaging study. AJNR Am. J. Neuroradiol. 1998; 19(8): 1501–1507. PubMed Abstract\n\nRijpkema M, Everaerd D, van der Pol C , et al.: Normal sexual dimorphism in the human basal ganglia. Hum. Brain Mapp. 2012; 33(5): 1246–1252. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalhovd KB, Westlye LT, Amlien I, et al.: Consistent neuroanatomical age-related volume differences across multiple samples. Neurobiol. Aging. 2011; 32(5): 916–932. PubMed Abstract\n\nBrabec J, Krásený J, Petrovický P: Volumetry of striatum and pallidum in man--anatomy, cytoarchitecture, connections, MRI and aging. Sb. Lek. 2003; 104(1): 13–65. Reference Source"
}
|
[
{
"id": "254310",
"date": "25 Mar 2024",
"name": "Vidya CS",
"expertise": [
"Reviewer Expertise Potential biomarkers in Alzheimer's 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\nStrength of the article: • Study has used 600 Scans which are a huge sample. • They have measured all parts of the basal ganglia- Caudate nucleus, putamen and globus pallidus. Weakness of the article: • This study utilised scans from a single hospital in South India, therefore, similar studies should be performed in other centres so that the findings can be generalised for the entire population.\n\nSummary • This study proves the correlation with age of the basal ganglia, and finds that gender plays a significant role, and charts the differential aging of the structures in the two sexes. • The data gathered from this research will be a useful tool for the clinician to assess radiological scans and detect neurodegenerative disorders early in a patient.\n\nMajor points • In this study, they examined the correlation between age and the sizes of the basal ganglia. A total of 600 MRI scans from healthy individuals were taken. • Globus pallidus axial diameter with age showed weak positive correlation for males. Globus pallidus transverse diameter showed weak positive correlation with age for both males and females but it was stronger for males compared to females. • A statistically significant difference between the genders was observed in the sizes of the axial diameters of caudate nucleus, putamen and globus pallidus. All of these structures were found to be larger in males.\n\nMinor points • The caudate nucleus showed a significant decrease in size, which can be a result of physiological atrophy. • The putamen transverse length showed an increase in size in males and a decrease in size in females.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11326",
"date": "13 Apr 2024",
"name": "Chandni Gupta",
"role": "Author Response",
"response": "Dear Madam, In materials and Methods: I have added the MRI machine which was used to take scans of patients. And in analysis part I have added that measurements were taken with the help of radiology experts and even the measurements were taken twice to prevent interobserver variability. Rest all remains same."
}
]
}
] | 1
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https://f1000research.com/articles/12-1230
|
https://f1000research.com/articles/12-291/v1
|
16 Mar 23
|
{
"type": "Data Note",
"title": "The identification of high-performing antibodies for Secreted frizzled-related protein 1 (sFRP-1) for use in Western Blot and immunoprecipitation",
"authors": [
"Riham Ayoubi",
"Kathleen Southern",
"Carl Laflamme",
"NeuroSGC/YCharOS collaborative group",
"Riham Ayoubi",
"Kathleen Southern"
],
"abstract": "Secreted frizzled-related protein 1 (sFRP-1) is a secreted protein, belonging to the secreted glycoprotein SFRP family. As a modulator of the Wnt/β-catenin signalling pathway, sFRP-1 has implications in human cancers and neurologic diseases. If the community had access to well-characterized anti-sFRP-1 antibodies, the reproducibility of sFRP-1 research would be enhanced. In this study, we characterized 11 sFRP-1 commercial antibodies for Western Blot and immunoprecipitation, using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many well-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 Q8N474",
"SFRP1",
"Secreted frizzled-related protein 1",
"antibody characterization",
"antibody validation",
"Western Blot",
"immunoprecipitation"
],
"content": "Introduction\n\nSFRP-1 is a secreted protein belonging to the secreted frizzled-related protein (SFRP) family.1 Having an amino acid terminal cysteine-rich domain homologous to the putative Wnt-binding domain of frizzled receptors, sFRP-1 functions as a modulator of the Wnt/β-catenin signalling pathway that is essential to multiple cellular processes.2,3\n\nDysregulated Wnt/β-catenin activity levels play a role in various disease processes.4 Epigenetic silencing of SFRP1 elevates Wnt/β-catenin activity, which has been linked to cancer.2,4 Conversely, high concentrations of sFRP-1 suppresses Wnt/β-catenin activity, which is predicted to have implications in neurological diseases, such as Alzheimer’s disease (AD).1,3–5 Targeting sFRP-1 to restore the Wnt/β-catenin signalling pathway is of current interest in AD research to discover novel therapies.3 Mechanistic studies would be greatly facilitated with the availability of high-quality antibodies.\n\nHere, we compared the performance of a range of commercially available antibodies for sFRP-1 and identified high-performing antibodies for Western Blot and immunoprecipitation, enabling biochemical and cellular assessment of sFRP-1 properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type and knockout (KO) cells.6,7 The first step is to identify a cell line(s) that expresses sufficient levels of a given protein to generate a measurable signal. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” +1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available A549 cells expressed the sFRP-1 transcript at RNA levels above the average range of cancer cells analyzed. Parental and SFRP1 knockout A549 cells were obtained from Abcam (Table 1).\n\nSFRP-1 is predicted to be a secreted protein. Accordingly, we collected concentrated culture media from both wild-type and SFRP1 KO cells and used the conditioned media to probe the performance of the antibodies (Table 2) side-by-side by Western blot and immunoprecipitation. The profiles of each of the antibodies are shown in Figures 1 and 2. The datasets can be found as Underlying data.10,11\n\n** Recombinant antibody.\n\nA549 (WT and SFRP1 KO) were treated with Brefeldin A at 3.0 μg/ml for 18 hrs. 50 μg of protein from concentrated culture media were processed for Western Blot with the indicated sFRP-1 antibodies. The Ponceau stained transfers of each blot are shown. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Antibody dilution used: MA5-32675** at 1/500; MA5-38193** at 1/500; GTX24193 at 1/1000; GTX102371 at 1/1000; A9656** at 1/1000; A2911 at 1/1000; AF1384 at 1/500; ab4193 at 1/500; ab126613** at 1/1000; ab267466** at 1/1000; ab84003 at 1/1000. Predicted band size: 35 kDa. **Recombinant antibody.\n\nImmunoprecipitation was performed on concentrate culture media using 1.0 μg of the indicated sFRP-1 antibodies pre-coupled to either protein A or protein G magnetic beads. Samples were washed and processed for Western Blot with the indicated sFRP-1 antibody. For Western Blot, MA5-38193** was used at 1/500, A9656** at 1/1000 and ab126613** at 1/1000. The Ponceau stained transfers of each blot are shown for similar reasons as in Figure 1. SM = 10% starting material; UB = 10% unbound fraction; IP = immunoprecipitated; LC = light chain. **Recombinant antibody.\n\nIn conclusion, we have screened sFRP-1 commercial antibodies by Western Blot and immunoprecipitation and identified several high-performing antibodies under our standardized experimental conditions.\n\n\nMethods\n\nAll sFRP-1 antibodies are listed in Table 2. Peroxidase-conjugated goat anti-rabbit and donkey anti-goat antibodies are from Thermo Fisher Scientific (cat. number 65-6120 and A15999).\n\nA549 WT and SFRP1 KO used are listed in Table 1. 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). Cells were starved in DMEM high-glucose containing L-glutamate and penicillin/streptomycin.\n\nA549 cells (WT and SFRP1 KO) were washed 3× with PBS and starved for ~18 hrs. Culture media were collected and centrifuged for 10 min at 500 × g to eliminate cells and larger contaminants, then for 10 min at 4500 × g to eliminate smaller contaminants. Culture media were concentrated by centrifuging at 4000 × g for 10 min using Amicon Ultra-15 Centrifugal Filter Units with a membrane NMWL of 10 kDa (MilliporeSigma cat. number UFC901024).\n\nWestern Blots were performed as described in our standard operating procedure.8 Western Blots were performed with large 8-16% gradient polyacrylamide gels and transferred on nitrocellulose membranes. Proteins on the blots were visualized with Ponceau staining which is scanned to show together with individual Western blot. Blots were blocked with 5% milk for 1 hr, and antibodies were incubated overnight at 4°C with 5% bovine serum albumin in TBS with 0,1% Tween 20 (TBST). 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 more washes with TBST. Membranes were incubated with ECL from Pierce (cat. number 32106) prior to detection with HyBlot CL autoradiography films from Denville (cat. number 1159T41).\n\nImmunoprecipitation was performed as described in our standard operating procedure.9 Antibody-bead conjugates were prepared by adding 1 μg of antibody to 500 ul of Pierce IP Buffer from Thermo Fisher Scientific (cat. number 87788) in a microcentrifuge tube, together with 30 μl of Dynabeads protein A - (for rabbit antibodies) or protein G - (for goat antibodies) from Thermo Fisher Scientific (cat. number 10002D and 10004D, respectively). Pierce IP Lysis Buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol) was supplemented with the Halt Protease Inhibitor Cocktail 100X from Thermo Fisher Scientific (cat. number 78446) at a final concentration of 1×. Tubes were rocked for ~2 hrs at 4°C followed by two washes to remove unbound antibodies.\n\nStarved A549 WT culture media were concentrated as described above. 1 ml aliquots at 0.5 mg/ml of lysate were incubated with an antibody-bead conjugate for ~2 hrs at 4°C. Following centrifugation, 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 8-16% polyacrylamide gels. Prot-A: HRP (MilliporeSigma, cat. number P8651) was used as a secondary detection system at a dilution of 0.4 μg/ml.",
"appendix": "Data availability\n\nZenodo: Antibody Characterization Report for Secreted frizzled-related protein 1, https://doi.org/10.5281/zenodo.6370454. 10\n\nZenodo: Dataset for the Secreted frizzled-related protein 1 antibody screening study, https://doi.org/10.5281/zenodo.7571170. 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’d 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 as well as the development of community-agreed protocols. Members of the group can be found below.\n\nNeuroSGC/YCharOS collaborative group: Riham Ayoubi, Aled M. Edwards, Carl Laflamme, Peter S. McPherson, Chetan Raina and Kathleen Southern.\n\nAn earlier version of this article can be found on Zenodo (doi: 10.5281/zenodo.6370454).\n\n\nReferences\n\nLiang CJ, Wang ZW, Chang YW, et al.: SFRPs Are Biphasic Modulators of Wnt-Signaling-Elicited Cancer Stem Cell Properties beyond Extracellular Control. Cell Rep. 2019; 28(6): 1511–25.e5. PubMed Abstract | Publisher Full Text\n\nBaharudin R, Tieng FYF, Lee LH, et al.: Epigenetics of SFRP1: The Dual Roles in Human Cancers. Cancers (Basel). 2020; 12(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nJia L, Piña-Crespo J, Li Y: Restoring Wnt/β-catenin signaling is a promising therapeutic strategy for Alzheimer's disease. Mol. Brain. 2019; 12(1): 104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZimmerman ZF, Moon RT, Chien AJ: Targeting Wnt pathways in disease. Cold Spring Harb. Perspect. Biol. 2012; 4(11). PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohnson ECB, Carter EK, Dammer EB, et al.: Large-scale deep multi-layer analysis of Alzheimer's disease brain reveals strong proteomic disease-related changes not observed at the RNA level. Nat. Neurosci. 2022; 25(2): 213–225. 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\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.\n\nAyoubi R, McPherson, Peter S, et al.:Antibody Characterization Report for Secreted frizzled-related protein 1. [Dataset].2022. Publisher Full Text\n\nLaflamme C:Dataset for the Secreted frizzled-related protein 1 antibody screening study. [Dataset]. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "185117",
"date": "08 Feb 2024",
"name": "Viyatprajna Acharya",
"expertise": [
"Reviewer Expertise Immunochemistry",
"metabolomics",
"cancer",
"oxidative stress."
],
"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 result can be discussed a little more elaborately. Methods are well-explained. Supporting diagram for immunoprecipitation and Western blot may be provided. The conclusion can be more explicit such as describing how many samples were actually suitable or better over others. References 8-11 are incomplete.\nThe article is well-written and maybe considered for indexing after minor corrections.\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": [
{
"c_id": "11321",
"date": "13 Apr 2024",
"name": "Kathleen Southern",
"role": "Author Response",
"response": "Dear Viyatprajna Acharya, Thank you for submitting a peer review report for this Data Note. An open-access Dataset is available under the “Data Availability” section. You can find the supporting diagrams and underlying data for Western blot and immunoprecipitation experiments within this dataset. As an organization that prioritizes open science, we ensure that all data is transparent and readily available which is why all of our publications have equivalent Datasets. The objective of this article is not to interpret the results nor score the performance of the antibodies. Given that it is formatted as a Data Note, it does not require the results to be discussed or concluded. YCharOS is a public-private organization whose mission is to characterize antibodies for every human protein and deliver the research as a collective good for the scientific community. That being said, we understand how this intention may be misinterpreted. A new version has been submitted, to include modifications to the title, introduction and results&discussion section that ensure our goals clearly are aligned and defined to all viewers. References 8-11 have been edited and will be complete in the newly submitted version. Thank you for your feedback and corrections!"
}
]
},
{
"id": "244759",
"date": "22 Feb 2024",
"name": "Oi Wah Liew",
"expertise": [
"Reviewer Expertise Biomarkers",
"antibody generation/characterization and validation",
"antigen design",
"recombinant protein expression",
"genetic engineering",
"assay development."
],
"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\nComments to the manuscript “The identification of high-performing antibodies for Secreted frizzled-related protein 1 (sFRP-1) for use in Western blot and immunoprecipitation”; Ayoubi R, Southern K, Laflamme C and NeuroSGC/YCharOS collaborative group\nGENERAL COMMENT\nThe manuscript describes the performance of 10 different commercial antibodies (rabbit or goat polyclonal and recombinant monoclonal antibodies) for detecting secreted frizzled-related protein 1 (sFRP-1) for Western blot and immunoprecipitation applications. A high expressing commercial cell line, A549, and its sFRP-1 KO counterpart was used as positive and negative controls for testing.\n\nThe work and its findings have scientific merits; however, there are several specific points that should be addressed by the authors. These are provided below:\nSPECIFIC COMMENTS\n1.\n\nThe authors selected the A549 cell line based on available data on high expression at transcript levels. However, high transcript levels do not necessarily translate to high protein expression. The A549 and A549 sFRP1 KO cell lines as well as some of the antibodies tested were from the same vendor. To have added confidence that the selected antibodies are recognizing endogenous sFRP-1 expressed in A549 cells, the authors should include a recombinant source of sFRP-1 from a different vendor in their western blots. In others words, each antibody is tested against endogenous sFRP-1 expressed in A549 cells, A549 SFRP1 KO (negative control) and recombinant sFRP-1 (eg R&D Systems cat no. 1384-SF). 2.\n\nHuman sFRP-1 is a member of the SFRP family. Since many of the antibodies selected are polyclonal in nature, the authors should assess potential cross-reactivity against other closely related family members eg human sFRP-2, sFRP-4 and sFRP-5. Sequence alignment between sFRP-1 against these family members shows stretches of 100% identical amino acids up to 22 amino acids long, portending potential cross-reactivity of anti-sFRP-1 polyclonal antibodies against these entities. Cross-reactivity of the recombinant monoclonal antibodies should also be tested since there is no epitope information for these antibodies. 3.\n\nThe results for GTX4193, GTX102371, AF1384, AB4193 and AB84003 in Figure 1 and 2 appear contradictory. In Figure 1, these antibodies could not detect sFRP-1 present in concentrated culture media collected from starved A549 cells by western blotting. However, these antibodies were able to detect sFRP-1 at ~35 kDa position in the starting material samples in Figure 2 which are essentially equivalent to the WT samples in Figure 1.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Partly\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": "11320",
"date": "13 Apr 2024",
"name": "Kathleen Southern",
"role": "Author Response",
"response": "Thank you Oi Wah Liew for your peer review report! To address your first comment, we are aware that RNA transcript and protein levels do not always correlate. That being said, we have found that an RNA expression value of 2.5 log2(TPM+1) serves as an appropriate minimal threshold level that will yield detectable protein levels in antibody screening. We understand that this method has its limitations, and in the case that we were unable to detect a strong signal of sFRP-1 in the WT, we have an alternative protocol. A further validation strategy is used to help select the optimal cell line by selecting 4-8 cancer cell lines with high RNA scores to assess and compare protein expression in cell lines in WB. Although outside the scope of our standardized protocol, we would recommend to researchers to use this study as a guide to select high-quality antibodies, then validate the antibodies using a commercial recombinant sFRP-1, as suggested. The evaluation of cross reactivity of the sFRP-1 antibodies is, once again, outside the scope of this study. We leave these subsequent studies up to the experts studying the sFRP family of proteins. This study is part of a broader collaborative initiative aimed at validating commercial antibodies for every human protein, preventing us from performing follow up studies for every protein target. To address your final comment, in Western blot, 50 μg of sample was processed onto the gel l whereas in Immunoprecipitation (IP), 100 μg of protein sample was processed. This data is found the Figure legends. This can explain the antibodies ability to detect a more concentrated amount of proteins and generate a signal in the starting material in Figure 2 as compared to Figure 1. Regardless, a successful antibody should enrich its target in the IP compared to the starting material, and deplete it from the unbound fraction, as seen for antibody MA5-32675**. For more information on how to interpret the antibody characterization data in this study, an editorial by Biddle et al., featured on our YCharOS gateway, can serve as an excellent guide. https://f1000research.com/articles/12-1344 To address comments from another reviewer’s report, a second version of this Data Note has been submitted to F1000. We encourage you to review this subsequent version as well as we believe it will help address some of your comments and provide a clearer definition of the YCharOS initiative."
}
]
}
] | 1
|
https://f1000research.com/articles/12-291
|
https://f1000research.com/articles/13-244/v1
|
02 Apr 24
|
{
"type": "Research Article",
"title": "Assessing risk perceptions that contribute to tetanus toxoid maternal vaccine hesitancy in Kilifi County, Kenya",
"authors": [
"Patience Kerubo Kiyuka",
"Rodgers Onsomu Moindi",
"Meshack Nzesei Mutua",
"Noni Mumba",
"Halimu Suleiman Shauri",
"Rodgers Onsomu Moindi",
"Meshack Nzesei Mutua",
"Noni Mumba",
"Halimu Suleiman Shauri"
],
"abstract": "Background Vaccination is one of the most effective public health interventions today. However, a growing number of people perceive vaccines as unsafe and unnecessary.\n\nMethods We used a mixed method research in which we administered a quantitative survey to men and women of reproductive age, held Focus Group Discussions (FGDs) with expectant mothers, and interviewed Key Informants (KI) to understand maternal vaccine hesitancy within a rural setting of Kilifi County, Kenya.\n\nResults Of the 104 people surveyed, 70% of the participants were aware of the vaccine that expectant women receive, with 26% stating that they know people in their community who have refused or were hesitant to take maternal vaccination. Reasons for refusals include religion and rumours that have spread in the community that the tetanus toxoid vaccine was a family planning method. Stockout of the vaccine was identified as one of the healthcare factors affecting vaccine uptake. Healthcare workers were the most trusted source for information about maternal vaccines.\n\nConclusion Dissemination of accurate information and continuous engagement with community members can build trust and confidence in maternal vaccines.",
"keywords": [
"vaccine hesitancy",
"maternal vaccines",
"tetanus toxoid",
"expectant mothers"
],
"content": "Introduction\n\nGlobally, the World Health Organization (WHO) estimates that in 2019 alone, 2.4 million children died in their first month of life (WHO 2020). Among the causes of these deaths are infectious diseases. Although substantial progress has been made in child survival since 1990, neonatal deaths remain relatively high in sub-Saharan Africa compared to other regions. Children born in sub-Saharan Africa are ten times more likely to die in their first month than their counterparts in high-income countries (WHO 2020). Maternal immunisation can contribute to a significant reduction in neonatal morbidity and mortality. For instance, it is estimated that maternal tetanus vaccine reduces mortality from neonatal tetanus by 94% (Blencowe et al. 2010). Immunization of pregnant women offers a chance to transplacentally transfer protective antibodies to the fetus, conferring protection to the vulnerable infants in the first six months of life when they are exposed but have not developed adequate functional antibody response (Marshall et al. 2016).\n\nDespite the compelling benefits achieved through vaccination, there is a growing concern about vaccine hesitancy. The WHO Strategic Advisory Group of Expert on Immunization defines vaccine hesitancy as a ‘delay in acceptance or refusal of vaccination despite the availability of vaccination services’, which varies across time, place and the vaccine. Vaccine-hesitant individuals may accept all vaccines but remain concerned about vaccines; some may refuse or delay some vaccines but accept others; others may refuse all vaccines (Larson et al. 2014, 2015). In 2019, WHO listed vaccine hesitancy among the top ten public health threats that need attention, a rallying call to governments, public health officials, and advocacy groups to pay attention to this issue. Left unchecked, vaccine hesitancy and misinformation that can spread rapidly through the internet (Cornwall 2020; Enserink 2020) can significantly contribute to a decrease in immunisation rates and hamper the uptake of newly introduced vaccines (Schaetti et al. 2009; Larson, Brocard, and Garnett 2010). For example, in North East Nigeria, vaccine myths, hesitancy, and misinformation that spread within the communities provided significant setbacks to the campaign to eradicate polio (Usman, Bologna, and Stamidis 2019).\n\nCurrently recommended vaccines for pregnant women include tetanus toxoid, influenza vaccine and Tdap vaccine (Williams et al. 2019), although countries have different guidelines and can choose which vaccines to administer. The Kenya Expanded Programme on Immunization recommends that expectant women receive tetanus toxoid vaccine. However, the Ministry of Health is exploring evidence-based strategies ahead of the anticipation of rolling out the influenza vaccine (McMorrow et al. 2017; Dawa et al. 2019). The success of these vaccines depends on whether mothers decide to use them.\n\nSeveral factors that contribute to vaccine hesitancy have been reported. These include expectant women’s levels of knowledge and attitude towards the safety and efficacy of the vaccine (Bushar et al. 2017; Eppes et al. 2013), how the healthcare worker interacts with mothers (Bukenya and Freeman 1991) and health systems factors such as healthcare practices and vaccine logistical issues (Sridhar et al. 2014). Literature specifically looking at maternal vaccination in Kenya is sparse. Most studies have focused on coverage and implementation of Antenatal Care (ANC), and on whether ANC services contribute to better neonatal care and assessment of ANC services as a package (Afulani et al. 2019; Arunda, Emmelin, and Asamoah 2017). In this study, we aimed to assess factors contributing to maternal tetanus toxoid vaccine hesitancy within a rural setting of Kilifi County in Kenya.\n\n\nMethods\n\nWe obtained scientific and ethical approval from the Pwani University Ethics Review Committee; ERC/PU-STAFF/002/2020. The study got approval from the National Commission for Science Technology and Innovation (NACOSTI) under license number NACOSTI/P/20/6193. The county government Department of Health Services authorised the study to be carried out in Kilifi County.\n\nThe study design was cross-sectional, using a mixed methods approach for data collection where both quantitative and qualitative data were collected. We used the qualitative data for cross-validation and corroboration of the findings within the study. Since study activities were conducted during the COVID-19 pandemic, the study team followed the infection control guidelines put in place by the County Department of Health Services to reduce SARS-CoV-2 infections such as social distancing; regular hand washing; use of personal protective equipment to protect oneself and participants; and measuring temperatures of study team before each field visits. Eligible participants gave written consent before participation in the study.\n\nThe study was conducted in Kilifi County, located along the Kenyan Coast. In Kenya, the health delivery system is currently a devolved function of the 47 counties. It is organised into six levels but anticipated to transition to four levels: level four, National referral hospitals; level three, county hospitals; level two, primary care facilities (formerly the dispensaries and health centres); and level 1, community hospital (Muinga et al. 2020).\n\nOur study randomly sampled expectant women attending ANC at Kilifi County Hospital (KCH), a level three hospital, and two dispensaries serving KCH, Mnarani and Ngerenya dispensaries, which are in level two selected based on the volume of expectant women they receive. We aimed to balance the study population selection to allow us to have a mix of both town settings (Mnarani) and rural settings (Ngerenya). We also randomly selected men and women of reproductive age at the community level in four different locations/wards (Tezo, Chasimba, Kibarani and Sokoni) and used Community Health Extension Officers to access our study population. The selection of study wards was based on immunisation coverage from Kilifi County’s Kenya Health Information System (KHIS). According to the 2019 KHIS data, the percentage of women who received their first tetanus toxoid vaccine ranged from 6% to 61.2% (lowest to highest) across the 35 administrative wards. We split the percentage of tetanus toxoid vaccine coverage into four quartiles (0-25, 25-50, 50-75 and 75-100) and then selected wards from each quartile as a representative.\n\nTo guide the assessment of the factors contributing to the maternal vaccine hesitancy, we adapted WHO’s behavioral and social drivers (BeSD) of vaccination framework (Figure 1). The BeSD model comprises four key domains of behavioural and social drivers of vaccination which, put together, influence vaccine uptake:\n\n1. Thinking and feeling, which includes the cognitive and emotional responses of people to vaccine-preventable diseases and vaccines;\n\n2. Social processes, which include social norms about vaccination and receiving recommendations to be vaccinated.\n\n3. Motivation, which includes the intention, willingness, and hesitancy of people to get vaccinated; and\n\n4. Practical issues, which include the experiences people have when trying to get vaccinated, including barriers faced, e.g. accessing the clinic or costs of transport to the clinic.\n\nData collection question guides and questionnaire design were based on quantitative surveys, interview guides and priority indicators corresponding to the BeSD framework’s four domains (Brewer et al. 2017). The questionnaire had a mix of open-ended questions and closed questions on a five-point Likert scale. Senior members of the research team reviewed the questionnaire and question guides and modified them appropriately to fit the local context while retaining the intended meaning. The questions were translated into Kiswahili, a local language for ease of administration. Interview guides were used flexibly to support rich and broader discussion around maternal vaccine hesitancy issues.\n\nBefore data collection the study team underwent training on the overall aims and objectives of the study, the consenting process and the data quality and management processes. Following the training, we conducted Focus Group Discussions (FGDs) comprising of 10-12 expectant women, and administered survey questionnaires to randomly selected men and women of reproductive age (n=104). For the FGDs, we targeted high volume facilities that could allow us to capture a diverse population of expectant women and balance town and rural areas. We used convenient sampling to identify expectant women for the FGDs. They (FGDs) were conducted at participating hospitals during maternal child health clinic days. FGDs lasted between 60-90 minutes. We also conducted interviews with six key informants lasting between 30-60 minutes. Key informants included healthcare workers involved in administering maternal vaccines and County healthcare vaccine managers. Interviews with KI were conducted at their workstations, either in the clinic or at their hospital office workstations. Both the FGDs and KIs were audio-recorded using an encrypted audio recorder. The interviews were also captured by a note-taker in handwritten notes. Two researchers (PKK and ROM) conducted all the interviews face-to-face. All study participants provided written informed consent. Data collection was done between September and October 2020.\n\nQuantitative survey data was analysed using STATA version 16. Baseline characteristics of participants including gender, marital status, level of education, and religion are presented as frequencies and percentages. Audio transcripts were transcribed verbatim in MS Word. For analysis, a predetermined coding structure consisting of the four domains of the BeSD conceptual framework was used. Code reports were generated and analysed by PKK and ROM\n\n\nResults\n\nThe survey respondents were a random sample of 104 adults. Their characteristics and summary are shown in Table 1. Women made up 63 (61%) of the study population, and 80 (77%) of the participants were married. Most participants had primary-level education. The median age was 33 years.\n\nTo assess the level of awareness, we asked respondents whether they had ever heard of a vaccine, whether they knew which vaccines expectant women receive and whether they had ever heard of the tetanus toxoid vaccine. Almost all respondents, 98% (102/104), were aware of vaccines, but only 70% (73/104) knew which vaccine women receive when they are expectant. Interestingly, 93% (97/104) reported knowing the existence of tetanus vaccine.\n\nExpectant mothers reported that the healthcare worker informs them about the vaccine they received, although they don’t interrogate what the vaccine does.\n\nWhen you are told you are being given the tetanus injection, you know it protects both you and the child concerning tetanus, so we don’t ask questions with regard to its purpose … We are not usually told why we are getting the injection. Expectant Mother FGD4\n\nHealthcare workers agree with the mothers, that they are aware that they should receive a vaccine. Sometimes, the mothers themselves can inquire why their counterparts were receiving the vaccine and not them. As per the Kenya Expended Programme for Immunization schedule, mothers are supposed to get the vaccine according to their number of pregnancies. What the mothers aren’t aware of is the importance of receiving the vaccine.\n\nI could say that most mothers know they are supposed to get immunisation when expectant … Knowledge is low in terms of knowing like what the vaccine does, why they are being immunised and what it entails. There is a gap there, but they know they are supposed to come to the clinic. They know that when they come, they’re supposed to get a vaccination for tetanus and several jabs. Key informant 01\n\nOf all the participants interviewed, 26% (27/104) reported that they knew people in their community who had ever refused a vaccine when expectant and 8% (8/104) had ever heard of negative information about vaccines in the recent past.\n\nSome of the reasons for vaccine refusal include rumours in the community that the tetanus vaccine is for family planning.\n\nYou hear people say that they are for family planning; people say that they reduce your fertility. Expectant Mother FGD4\n\nThere are also instances where expectant mothers fail to receive the vaccine due to home deliveries.\n\nThere is a neighbour who was expectant from home … For all the nine months she has been home … She even delivered at home recently. Expectant Mother FGD2\n\nThere were also concerns about women receiving an HIV test during their ANC visits.\n\nGetting tested (for HIV) is why they fear coming to clinic … Because when you come, you cannot get services until your HIV status is known. Expectant Mother FGD1\n\nThe respondents also adduced religious reasons. Indeed, several studies have examined whether religion influences childhood immunisation uptake (Costa et al. 2020; Fournet et al. 2018), including the adolescent human papillomavirus (Best et al. 2019). Within our setting, participants reported that people from particular religious groups do not subscribe to vaccine uptake when expectant or even for their children.\n\nThere are those who don’t come to the clinic at all and they have other reasons like religion … There is a church that doesn’t believe in hospital and its services … They say God will help … They conceive and get to delivering without any vaccinations … God keeps them safe … They exist, but there are not so many; others are in that sect but still come for clinic … But those who hold on to that faith don’t come totally. Key informant 002\n\nThe decision on whether a young mother will seek vaccination is partly informed by the advice she will receive from decision-makers in the homestead. At least within our settings, a mother-in-law or older woman has a role in influencing health care services including vaccination.\n\nThere are those old women, our grandmothers, who in their time did not go to the hospital or anywhere when they became expectant; even in delivery, they got assistance from village Traditional Birth Attendants (TBAs) so as a daughter-in-law when you marry into that home, it is not easy to convince this woman to go to the hospital because they say I gave birth to your husband and I did not go to the hospital and I gave birth without any issues and right now he has grown without any problems, he is okay till now he has married you, so don’t stress yourself, just stay here I will look after you or a friend of mine will look after you. Expectant Mother FGD1\n\nThe Wellcome Global Monitor Report 2018 the world’s largest study into how people around the world think and feel about science and major health challenges, estimates that globally, 73% of people highly trust healthcare workers for their sources of information. We asked participants to rank from a list of healthcare workers, family or other relatives, radio/TV and friends, which are their most trusted sources of information about vaccines for expectant mothers. We found that 77% (80/104) of participants used healthcare workers as their source of information about vaccines for expectant mothers. Most participants, 84% (87/104) ranked healthcare workers as their most trusted source of information, with 34% (35/104) ranking their friends as the least they could consult on information about maternal vaccines.\n\nAs the healthcare workers are the frontline government service providers, we tested the level of trust in the government and whether participants thought vaccines should be compulsory. Approximately 77% (80/104) and 20% (21/104) of the participants strongly agree or agree, respectively, that they trust that the government is deciding in their best interest with regard to vaccines for expectant mothers. In contrast, 53% (55/104) and 23% (24/104) of the participants strongly agree or agree, respectively, that vaccines for expectant mothers should be made compulsory.\n\nAmong the key informants, one reason maternal vaccine uptake is low is vaccine stockout, which affects vaccine delivery.\n\nAt times we get stock outs … yes as much as they (expectant mothers) would wish to get the vaccine by the time they come the vaccine is not there. Key informant 4\n\nThe attitude of the healthcare worker also plays a role on whether a mother will come back to take the vaccine or even visit the antenatal clinic.\n\nAnother thing which will make these mothers not to come is the attitude of the health provider at the facility. If a mother comes every day and am like you are shouting at me you are not giving me attention, it is like I tell you are not listening to me you are so arrogant I will not come back, I would rather stay at home. Key informant 6\n\nHealthcare workload was noted as affecting vaccine delivery, especially in the lower-level health facilities whose main responsibility is to administer vaccines and offer other ANC services.\n\nOnly one nurse runs majority of our dispensaries and only one staff … running a facility you are the one giving immunizations, you are the one taking care of the pregnancy, you are the one taking care of the sick ones who are coming in, so it is actually hectic and by the end of the day they also need to rest … come at night, they cannot work day and night, at night they are home … and over the weekends again they are taking their offs. Key informant 5\n\nSince 2013, the Kenyan government has introduced two policies to reduce maternal and neonatal deaths: the abolition of client user fees and the provision of free maternity services in public health facilities (Pyone, Smith, and Van Den Broek 2017). We, therefore, tested to what extent other factors such as cost in terms of fare to the clinic, waiting time at the clinic, the time needed to get to the clinic, the timing of the clinic and distance to the clinic prevented expectant mothers from going to get the vaccine. In all instances, these factors affected vaccine uptake only to some extent (Figure 2).\n\n\nDiscussion\n\nIt is well-accepted that maternal vaccination significantly reduces neonatal morbidity and mortality (Blencowe et al. 2010). However, a growing number of people perceive vaccines as unsafe and unnecessary (Omer et al. 2009). In this study, we sought to understand factors that influence maternal vaccine uptake. We report results from the contextual influences and individual/social group influences.\n\nAlmost everyone reported general knowledge of the existence of vaccines. However, few knew how the tetanus toxoid maternal vaccine works and why it is administered to mothers. The lack of knowledge can be partly explained by the low education levels of our study participants; most of them had primary-level education. It is important to note that participants generally agreed that the tetanus vaccine was good for the mothers. Several factors limited maternal vaccine uptake. Rumours and misinformation around the tetanus vaccine within the community caused fears among expectant mothers. It was perceived that the tetanus vaccine was a family planning method, a message reinformed when the Kenyan government rolled out a tetanus vaccination campaign among school-going girls. The fact that boys were excluded from the campaign made the community suspicious that the vaccine was to control fertility among young women. The majority of Kenyans identify themselves with a particular religion. Indeed, in this study, almost all of the participants were Christians. We found that particular religious groups or sects were against modern medicine and particularly advised their congregants against using family planning methods. Additionally, they made those who heard the rumours about tetanus vaccine as a form of birth control to avoid going for the vaccine. It is worth noting that the government, through the Public Health Department, has put in place mechanisms to trace those missing out on vaccination and sometimes using the law to encourage vaccine uptake.\n\nAlthough there has been concerted efforts by the Kenyan government to increase hospital access by rural mothers, a study conducted by Moindi et al., exploring risk perceptions associated with home deliveries estimated that approximately 26% of mothers in Kilifi County delivered at home (Moindi et al. 2016). We found that Traditional Birth Attendants (TBAs) remained important because mothers could access them easily and faster, especially if the dispensaries were far. Some mothers only sought the services of these TBAs throughout their pregnancy and, as a result, miss out on vaccinations. Within our setting, healthcare-seeking behaviours are partly influenced by older women within the homestead. We found that if these older women did not go to ANC clinics, they tended to discourage young mothers married to their sons from attending the clinic for vaccines when expectant.\n\nGlobal trends indicate that healthcare workers remain the most trusted sources of information on health matters. In this study, the majority of the participants said they could consult healthcare workers on information related to vaccines. Very few people searched the internet if they had issues with vaccines. Considering this is a predominantly rural population, the cost of internet and smartphones could be a limiting factor.\n\nHealth system factors such as vaccine stockout were also identified by the key informants as a challenge to vaccine delivery. As much as the healthcare workers would like to maintain a high vaccine coverage, issues such as delays in vaccine delivery to the health facilities meant that even when mothers showed up and demanded vaccination, the vaccines were out of stock, causing a missed opportunity. Similar to what has been found in Ethiopia (Gebremichael et al. 2018), Tanzania (Maluka et al. 2020) and Uganda (Kajungu et al. 2020), we observed that if a healthcare worker was harsh, abusive or rude, it could discourage women from attending ANC clinics, which has a ripple effect on the uptake of vaccines by the mothers.\n\nMost of our study populations were drawn from rural areas, including rural towns. It has been shown that rural areas tend to have lower education and health literacy (Das et al. 2017), factors important for vaccine uptake (Lorini et al. 2018). Therefore, our findings need to be interpreted within the context in which the study was done. Future studies are required to explore in-depth maternal vaccine hesitancy issues in urban areas in which the population have varying education levels and socioeconomic status.\n\n\nConclusion\n\nOur study highlights factors that contribute to low maternal vaccine uptake. Continuous community engagement is required to address the fears, misconceptions, and rumours around tetanus vaccine uptake, which is important for laying the ground for future vaccine rollout for expectant mothers.",
"appendix": "Data availability\n\nHarvard Dataverse - https://doi.org/10.7910/DVN/2T6T5G (Kiyuka 2024).\n\nThis project contains the following underlying data:\n\n• Delinked _risk perception maternal vaccine study data.xlsx (delinked raw data)\n\n• KI and FGD interview guides.docx\n\n• Survey questionnaire.docx.\n\nData available at the Harvard Dataverse https://doi.org/10.7910/DVN/2T6T5G, (Kiyuka 2024) under the CC0 1.0 license\n\n\nAcknowledgement\n\nThis research would not have been possible without the immense support of the Kilifi County Department of Health, Community Health Volunteers, local chiefs and community members who participated in the study. We thank Pwani University for the scientific and ethical review. This manuscript was submitted for publication with the permission of the Director KEMRI.\n\n\nReferences\n\nAfulani PA, Buback L, Essandoh F, et al.: Quality of Antenatal Care and Associated Factors in a Rural County in Kenya: An Assessment of Service Provision and Experience Dimensions. BMC Health Serv. Res. 2019; 19(1): 684. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArunda M, Emmelin A, Asamoah BO: Effectiveness of Antenatal Care Services in Reducing Neonatal Mortality in Kenya: Analysis of National Survey Data. Glob. Health Action. 2017; 10(1): 1328796. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBest AL, Thompson EL, Adamu AM, et al.: Examining the Influence of Religious and Spiritual Beliefs on HPV Vaccine Uptake Among College Women. J. Relig. Health. 2019; 58(6): 2196–2207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlencowe H, Lawn J, Vandelaer J, et al.: Tetanus Toxoid Immunization to Reduce Mortality from Neonatal Tetanus. Int. J. Epidemiol. 2010; 39(SUPPL. 1): i102–i109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrewer NT, Chapman GB, Rothman AJ, et al.: Increasing Vaccination: Putting Psychological Science Into Action. Psychol. Sci. Public Interest. 2017; 18(3): 149–207. PubMed Abstract | Publisher Full Text\n\nBukenya GB, Freeman PA: Possible Reasons for Non-Completion of Immunization in an Urban Settlement of Papua New Guinea. P. N. G. Med. J. 1991; 34(1): 22–25. PubMed Abstract\n\nBushar JA, Kendrick JS, Ding H, et al.: Text4baby Influenza Messaging and Influenza Vaccination Among Pregnant Women. Am. J. Prev. Med. 2017; 53(6): 845–853. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCornwall W: Officials Gird for a War on Vaccine Misinformation Fears of a Rushed COVID-19 Vaccine and Rise of Social Media Demand New Messaging Strategy. Science. 2020; 369: 14–15. American Association for the Advancement of Science. PubMed Abstract | Publisher Full Text\n\nCosta JC, Weber AM, Darmstadt GL, et al.: Religious Affiliation and Immunization Coverage in 15 Countries in Sub-Saharan Africa. Vaccine. 2020; 38(5): 1160–1169. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDas S, Mia MN, Hanifi SMA, et al.: Health Literacy in a Community with Low Levels of Education: Findings from Chakaria, a Rural Area of Bangladesh. BMC Public Health. 2017; 17(1): 203. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDawa J, Chaves SS, Nguz AB, et al.: Developing a Seasonal Influenza Vaccine Recommendation in Kenya: Process and Challenges Faced by the National Immunization Technical Advisory Group (NITAG). Vaccine. 2019; 37(3): 464–472. PubMed Abstract | Publisher Full Text\n\nEnserink M: Fact-Checking Judy Mikovits, the Controversial Virologist Attacking Anthony Fauci in a Viral Conspiracy Video. Science. 2020 May. Publisher Full Text\n\nEppes C, Alison W, Whitney You KA, et al.: Barriers to Influenza Vaccination among Pregnant Women. Vaccine. 2013; 31(27): 2874–2878. Publisher Full Text\n\nFournet N, Mollema L, Ruijs WL, et al.: Under Vaccinated Groups in Europe and Their Beliefs, Attitudes and Reasons for Non Vaccination Two Systematic Reviews. BMC Public Health. 2018; 18(1): 196. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGebremichael MW, Worku A, Medhanyie AA, et al.: Women Suffer More from Disrespectful and Abusive Care than from the Labour Pain Itself: A Qualitative Study from Women’s Perspective. BMC Pregnancy Childbirth. 2018; 18: 392. BioMed Central Ltd. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKajungu D, Muhoozi M, Stark J, et al.: Vaccines Safety and Maternal Knowledge for Enhanced Maternal Immunization Acceptability in Rural Uganda: A Qualitative Study Approach. PLoS One. 2020; 15(12 December): e0243834. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKiyuka P: Replication Data for: Assessing Risk Perceptions That Contribute to Tetanus Toxoid Maternal Vaccine Hesitancy in Kilifi County, Kenya. Harvard Dataverse. 2024. Publisher Full Text\n\nLarson HJ, Brocard P, Garnett G: The India HPV-Vaccine Suspension. Lancet. 2010; 376: 572–573. Elsevier. PubMed Abstract | Publisher Full Text\n\nLarson HJ, Jarrett C, Eckersberger E, et al.: Understanding Vaccine Hesitancy around Vaccines and Vaccination from a Global Perspective: A Systematic Review of Published Literature, 2007-2012. Vaccine. 2014; 32: 2150–2159. Elsevier BV. PubMed Abstract | Publisher Full Text\n\nLarson HJ, Jarrett C, Schulz WS, et al.: Measuring Vaccine Hesitancy: The Development of a Survey Tool. Vaccine. 2015; 33(34): 4165–4175. Publisher Full Text\n\nWilliams L, Anna RM, Mwananyanda L, et al.: Maternal Vaccine Knowledge in Low- and Middle-Income Countries—and Why It Matters. Hum. Vaccin. Immunother. 2019; 15: 283–286. Taylor and Francis Inc. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLorini C, Santomauro F, Donzellini M, et al.: Health Literacy and Vaccination: A Systematic Review. Hum. Vaccin. Immunother. 2018; 14(2): 478–488. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaluka SO, Joseph C, Fitzgerald S, et al.: Why Do Pregnant Women in Iringa Region in Tanzania Start Antenatal Care Late? A Qualitative Analysis. BMC Pregnancy Childbirth. 2020; 20(1): 126. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarshall H, McMillan M, Andrews RM, et al.: Vaccines in Pregnancy: The Dual Benefit for Pregnant Women and Infants. Hum. Vaccin. Immunother. 2016; 12: 848–856. Taylor and Francis Inc. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcMorrow ML, Emukule GO, Obor D, et al.: ‘Maternal Influenza Vaccine Strategies in Kenya: Which Approach Would Have the Greatest Impact on Disease Burden in Pregnant Women and Young Infants?’ Edited by David L. Swerdlow. PLoS One. 2017; 12(12): e0189623. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoindi RO, Ngari MM, Nyambati VCS, et al.: Why Mothers Still Deliver at Home: Understanding Factors Associated with Home Deliveries and Cultural Practices in Rural Coastal Kenya, a Cross-Section Study Global Health. BMC Public Health. 2016; 16(1): 114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMuinga N, Magare S, Monda J, et al.: Digital Health Systems in Kenyan Public Hospitals: A Mixed-Methods Survey. BMC Med. Inform. Decis. Mak. 2020; 20: 2. BioMed Central Ltd. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOmer SB, Salmon DA, Orenstein WA, et al.: Vaccine Refusal, Mandatory Immunization, and the Risks of Vaccine-Preventable Diseases. N. Engl. J. Med. 2009; 360(19): 1981–1988. PubMed Abstract | Publisher Full Text\n\nPyone T, Smith H, Van Den Broek N: Implementation of the Free Maternity Services Policy and Its Implications for Health System Governance in Kenya. BMJ Glob. Health. 2017; 2(4): e000249. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchaetti C, Hutubessy R, Ali SM, et al.: Oral Cholera Vaccine Use in Zanzibar: Socioeconomic and Behavioural Features Affecting Demand and Acceptance. BMC Public Health. 2009; 9(1): 99. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSridhar S, Maleq N, Guillermet E, et al.: A Systematic Literature Review of Missed Opportunities for Immunization in Low- and Middle-Income Countries. Vaccine. 2014; 32: 6870–6879. Elsevier Ltd. PubMed Abstract | Publisher Full Text\n\nUsman S, Bologna L, Stamidis KV: The Core Group Partners Project in North East Nigeria: Community Engagement Strategies to Combat Skepticism and Build Trust for Vaccine Acceptance. Am. J. Trop. Med. Hyg. 2019; 101(4): 68–73. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Newborns: Improving Survival and Well-Being’. 2020.2020. Reference Source"
}
|
[
{
"id": "291099",
"date": "23 Jul 2024",
"name": "Nasir Yusuf",
"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\nYour Report\nPlease provide a full report, expanding on your answers to the questions above. In particular, if you answered “no” or “partly” to any of the questions, please give constructive and specific details as to how the authors can address any criticisms. Please indicate clearly which points must be addressed to make the article scientifically sound. (50 words min.)\nGeneral comments:\nThe paper is quite timely and will add significantly to the wealth of knowledge on maternal and to some extent, adult immunization especially in the context of ongoing global efforts to immunize all along life-course.\nComments on specific sections\nIntroduction\n“The Kenya Expanded Programme on Immunization recommends that expectant women receive tetanus toxoid vaccine” – As of 2019, nearly all countries, especially those that procure their vaccines through the UNICEF Supply Division had replaced tetanus toxoid vaccine (TT) with tetanus and diphtheria toxoid (Td) vaccines based on the recommendation of the WHO Strategic Advisory Group of Experts (SAGE). This latter vaccine provides protection both against tetanus and diphtheria. You may wish to mention this in the appropriate section of the paper\n\n“Several factors that contribute to vaccine hesitancy have been reported. These include expectant women’s levels of knowledge and attitude towards the safety and efficacy of the vaccine (Bushar et al. 2017; Eppes et al. 2013), how the healthcare worker interacts with mothers (Bukenya and Freeman 1991)” – You may wish to revisit the paper cited here as it refers to missed opportunities for immunization (MOI) which is influenced by factors beyond hesitancy. For example, it is unclear how vaccine logistical issues, which contributes to MOI will affect hesitancy.\n\nIn the introduction section of the paper, it will be useful to provide and/or cite literatures on the importance and influence on immunization uptake by males, especially the heads of the households. This will allow for a better understanding of why males were also interviewed\n\nMethods – Study populations\nIt will be useful to give a bit of an insight into the random sampling method of the expectant women attending ANC and men and women of reproductive age at the community level in four different locations/wards\n\nAny reason why the coverage of the first dose of TT was used rather than at least two doses (TT2+)? One dose TT is not known to confer any level of immunity against tetanus, while a child born to a mother who receives at least two well-spaced doses is considered to be protected at birth (PAB) against tetanus.\n\nMethods – data collection\nHow many FGDs were conducted?\nResults\n\nGeneral vaccination knowledge and awareness\nIt will be useful to disaggregate this data by sex, to assess the knowledge about maternal immunization between males and females.\nDiscussion “Rumors and misinformation around the tetanus vaccine within the community caused fears among expectant mothers. It was perceived that the tetanus vaccine was a family planning method, a message reinformed when the Kenyan government rolled out a tetanus vaccination campaign among school-going girls. The fact that boys were excluded from the campaign made the community suspicious that the vaccine was to control fertility among young women” - It will be useful to know if the same perception holds for tetanus vaccines given through the routine immunization system, during ANC visits. The delivery of tetanus and diphtheria toxoid-containing vaccines along life-course: 3 primary series of DTP during infancy, 1st booster dose at 2nd year of life, 2nd booster dose during school entry (4 - 7 years) and 3rd booster during early adolescence (9 - 15 years) does not have gender discrimination and may help to dispel the existing rumor\nOverall comments\nThe paper may require some minor changes to address the queries raised While I am not familiar with the journal’s policies, I strongly suggest that a sub-heading be included on the limitations to the research as there appears to be a handful Final recommendation The paper should be indexed after the minor changes in line with the queries/comments/suggestions made above and those that might be made by the other reviewers\nI have also attached a copy of the paper with my comments and queries highlighted for the different sections. https://f1000research.s3.amazonaws.com/linked/665275.Assessing_risk_perceptions_that_contribute_to_tetanus_toxoid_maternal_vaccine_hesitancy_in_Kilifi_County%2C_Kenya--_Nasir_Yusuf..pdf\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-244
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https://f1000research.com/articles/13-242/v1
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02 Apr 24
|
{
"type": "Research Article",
"title": "pH-Induced structural changes in xylanase GH11 from Thermoanaerobacterium saccharolyticum",
"authors": [
"Ki Hyun Nam"
],
"abstract": "Background Glycosyl hydrolase 11 (GH11) xylanase is utilized in various in industrial applications such as baking, fruit juice production, pulp processing, and animal feed. Thermophilic GH11 from Thermoanaerobacterium saccharolyticum (TsaGH11) exhibits maximum activity at acid pH with high catalytic efficiency toward beechwood xylan. TsaGH11 activity is pH dependent, exhibiting relative low hydrolase activity at basic pH. However, the effect of a basic pH environment on the structure of TsaGH11 correlated with enzyme activity remains unknown. To understand pH-dependent activity changes, the crystal structure of TsaGH11 at basic pH was determined and compared with that of TsaGH11 at acid pH.\n\nMethods TsaGH11 was crystallized at basic pH of 8.5, and the crystal structure was determined at 1.95 Å resolution. The structure, flexibility, and water molecules of TsaGH11 at pH 8.5 and pH 4.3 were compared.\n\nResults The open and closed conformations of TsaGH11 at pH 8.5 are reported. Subtle movements of the side chains of amino acids involved in the substrate-binding cleft and catalytic residues were observed. The overall temperature factor of TsaGH11 at pH 8.5 was higher than that at pH 4.6. The position of water molecules near the catalytic residues in TsaGH11 exhibited variations in different pH environments.\n\nConclusions The structural comparison of TsaGH11 at basic and acidic pH offers valuable insights into the pH-dependent functionality of TsaGH11, enhancing our understanding of these structural alterations.",
"keywords": [
"xylanase",
"glycosyl hydrolase 11",
"GH11",
"pH",
"conformational change",
"structure",
"flexibility"
],
"content": "Introduction\n\nEndo-xylanases (EC 3.2.1.8) cleaves the β-1,4 glycosidic bonds in the xylan backbone, converting the polymeric xylan into xylose or xylooligosaccharides.1 In the carbohydrate-active enzyme database (CAZy), various glycoside hydrolase (GH) families (GH 5, 7, 8, 9, 10, 11, 12, 16, 26, 30, 43, 44, 51, and 62) are classified into xylanase.2,3 Each of these xylanase families exhibits distinct amino acid sequence, amino acid length, functional domains or enzymatic activity.4 Among them, GH11 has been considered a “true xylanase” because it exhibits high specificity and selectivity toward xylan substrates compared with other endo-xylanase GH families.1,5,6 GH11 xylanases is utilized as valuable biocatalysts in various industrial fields such as pulp, food, feed, textile, pharmaceutical, and biorefinery industries.7,8 The optimal activity conditions for xylanases vary based on environmental factors such as pH, temperature, salt, and metal ions.9,10 The industrial application field or scope of xylanase changes depending on its unique optimal pH activity.11 For example, in baking and fruit juice clarification, which require high activity at acidic pH, acidophilic xylanases are preferred,7,12 whereas in the pulp industry, where basic pH is desired, alkaliphilic xylanases are preferred.9\n\nHemicellulose-degrading thermophilic anaerobe Thermoanaerobacterium saccharolyticum prefers growing in high temperatures (30°C–66°C) and acidic conditions (pH 3.85–6.35).13 This strain acts as a biological catalyst for producing ethanol from cellulosic biomass.13–15 T. saccharolyticum ferments various carbohydrates, including glucose, cellobiose, xylan, xylose, starch, arabinose, mannose, and galactose.16 The enzymatic and structural characterization of GH11 from T. saccharolyticum (TsaGH11) has been previously reported.6 TsaGH11 exhibits maximum xylanase activity at pH 5.0 and 70°C, with specific activities of 5,622.0 and 3,959.3 U/mg for beechwood and oat spelt xylans, respectively. TsaGH11 exhibits superior catalytic performance, with kcat values of 34015.3 s−1, for beechwood xylan. Optimal enzyme activity of TsaGH11 was observed at pH 5.0, with relatively high activity at pH 4–6. However, hydrolase activity of TsaGH11 decreased to 60% at pH > 7.0. Activity variations are also observed depending on the buffering environment.6 For example, at pH 8, the Tris solution exhibits approximately 50% activity, whereas sodium phosphate solution shows <20% activity, and beyond pH 9, the relative enzyme activity drops to <20%.6 Consequently, TsaGH11 displays high activity in an acidic pH range but exhibits decreased activity in a basic pH environment, but the structural analysis of how pH can affect the activity of TsaGH11 still remains unknown.\n\nTo investigate the structural changes in TsaGH11 in response to pH, an extended crystallographic experiment of TsaGH11 was performed, and the crystal structure of TsaGH11 at pH 8.5 (TsaGH11pH8.5) was subsequently determined at 1.95 Å resolution. The crystal structure features of TsaGH11pH8.5 were described and compared with those of TsaGH11 at pH 4.6 (TsaGH11pH4.6). These structural analyses contribute to our understanding of the pH-dependent activity of TsaGH11.\n\n\nMethods\n\nFollowing chemicals were used in this study: Luria-Berani broth medium (LPS solution, Catalog No. LB-05, Daejeon, Republic of Korea,), ampicillin (LPS solution, Catalog No. AMP25), Isopropyl β-D-1-thiogalactopyranoside (LPS solution, Cat No. IPTG025), Tris (Sigma-Aldrich, St. Louis, MI, USA, Catalog No. T15760), NaCl (Sigma-Aldrich, Catalog No. S9888), Ammonium acetate (Sigma-Aldrich, Catalog No. A7262), Glycerol (Sigma-Aldrich, Catalog No. G5516).\n\nThe preparation of purified protein was similar to that in a previous report.6 In brief, vector DNA containing the TsaGH11 gene with an N-terminal hexahistidine tag was transformed into Escherichia coli BL21(DE3). Cells were grown in LB broth medium supplemented with ampicillin (50 μg/mL) at 37°C. When the culture optical density at 600 nm reached 0.6–0.8, protein expression were induced by addition of 0.5 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) and then incubated at 18°C while shacking for overnight. After harvesting the cells and disrupting them via sonication, the supernatant was loaded onto a Ni-NTA affinity resin (Qiagen, Hilden, Germany) in a column. The resin was washed with 50 mM Tris-HCl (pH 8.0), 200 mM NaCl, and 20 mM imidazole, and then proteins were eluted with 50 mM Tris-HCl (pH 8.0), 200 mM NaCl, and 300 mM imidazole. To cleave the N-terminal hexahistidine tag, elution fractions were pooled and incubated with thrombin at 22°C overnight. Samples were concentrated using Centricon (Sartorius, 10-kDa cutoff) and loaded onto a Sephacryl S-100 10/300 column (GE Healthcare, Chicago, IL, USA) in 10 mM Tris-HCl (pH 8.0) and 200 mM NaCl. The purified protein was concentrated to ~20 mg/mL using a Centricon for crystallization. Protein concentrations were determined using a NanoDrop 1000 spectrophotometer (ThermoFisher).\n\nCrystallization screen of TsaGH11 was initially performed using the sitting-drop vapor diffusion method at 22°C. Purified TsaGH11 solutions (500 nL) were mixed with equal volume of crystallization solution from commercially available crystallization kits (Hampton Research, Aliso Viejo, CA, USA) on 96 × 2-well MRC nanoplates (Innovadyne). Microcrystals were obtained under four conditions with the following crystallization solutions: (i) Salt RX H10: 0.1 M Tris-HCl, pH 8.5, and 4.0 M ammonium acetate; (ii) Crystal screen B9: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, and 30% (v/v) 2-methyl-2,4-pentanediol; (iii) Index A11: 0.1 M HEPES, pH 7.5, and 3.0 M sodium chloride; and (iv) Index A12: 0.1 M Tris-HCl, pH 8.5, and 3.0 M sodium chloride. To obtain large crystals, crystal optimization experiments were performed using the hanging-drop vapor diffusion method at 22°C. Suitable TsaGH11 crystals for X-ray diffraction experiment were obtained under condition (i) by scaling up to mix 2 μL of the protein solution with 2 μL of the reservoir solution in 24-well VDX crystallization plates (Hampton Research).\n\nThe X-ray diffraction data were collected on beamline 11C at Pohang Light Source II (PLS-II, Pohang, Republic of Korea).17 The TsaGH11 crystal was immersed in a cryoprotectant solution consisting of a reservoir solution supplemented with 20% (v/v) glycerol for 10 s. The TsaGH11 crystal was mounted on the goniometer under a liquid nitrogen stream at 100 K. Diffraction data were recorded using a Pilatus 6M detector. Diffraction images were indexed, integrated, and scaled using the HKL2000 program.18\n\nThe electron density map of TsaGH11 structure was obtained via molecular replacement method using MOLREP (version 11.2.08).19 Crystal structure of TsaGH11 at pH 4.6 (PDB code: 8IH0)6 was used as search model. Manual model building was performed using COOT (version 0.9.6).20 Structure refinement was performed using phenix.refine in PHENIX.21 Water molecules were automatically added during the refinement using the default parameters in PHENIX.21 The final coordinates of TsaGH11pH8.5 was validated using MolProbity.22 Structural figures were generated using PyMOL (version 2.4.1.; http://pymol.org/2). The structure factor and coordinates were deposited at the Protein Data Bank under access code 8X1D (https://www.rcsb.org/structure/8X1D).\n\nDifferences in the secondary structures of TsaGH11pH8.6 and TsaGH11pH4.6 were analyzed using 2StrucCompare23 with the Dictionary of Secondary Structure of Proteins (DSSP)24 and the STRuctural IDEntification (STRIDE)25 method. The B-factor and normalized B-factor were analyzed using PHENIX.21\n\n\nResults\n\nProtein conformation depends on environmental factors such as pH, temperature, and interactions.26,27 Although TsaGH11 exhibits high activity at acidic pH, this activity diminishes at basic pH,6 and the crystal structure of TsaGH11 at an acidic pH (pH 4.6, which is close to that at optimal activity) has been determined.6,28 To comprehend the change in TsaGH11 activity influenced by pH from a structural perspective, an extended crystallization assessment was conducted to obtain the crystal structure of TsaGH11 at basic pH. Microcrystals of TsaGH11 were obtained from four new crystallization solutions: (i) 0.1 M Tris-HCl, pH 8.5, and 4.0 M ammonium acetate; (ii) 0.1 M Tris-HCl, pH 8.5, and 3.0 M sodium chloride; (iii) 0.1 M HEPES, pH 7.5, 3.0 M sodium chloride; and (iv) 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate, pH 6.5, and 30% (v/v) 2-methyl-2,4-pentanediol. These crystallization conditions at three different pH values (6.5, 7.5, and 8.5) were distinct from those previously reported (pH 4.6) (Figure 1a). Among them, the crystallization conditions (i) of TsaGH11 grown at pH 8.5 differ only in pH from those previously reported for TsaGH11pH4.6 (0.1 M sodium acetate, pH 4.6, and 4.0 M ammonium acetate), which showed the same crystal morphology as TsaGH11 (Figure 1a). Therefore, crystallization condition (i) was considered to be the optimal condition with the least influence from the crystallization solution constituents. The growth rate of TsaGH11 crystals under condition (i) was 2–4-fold longer than the crystal growth time at pH 4.6. The TsaGH11pH8.5 crystal diffracted up to 1.95 Å (Figure 1b), and although crystals were obtained under conditions (ii), (iii), and (iv) (Figure 1a), they did not exhibit sufficient diffraction intensity to determine the crystal structure.\n\n(a) Crystallization screen results for TsaGH11. TsaGH11 crystals were grown under (i) 0.1 M sodium acetate, pH 8.5, and 4.0 M ammonium acetate, (ii) 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, and 30% (v/v) 2-methyl-2,4-pentanediol, (iii) 0.1 M HEPES, pH 7.5, and 3.0 M sodium chloride, and (iv) 0.1 M Tris-HCl, pH 8.5, and 3.0 M sodium chloride. (b) Diffraction pattern of TsaGH11 crystals grown with 0.1 M sodium acetate, pH 8.5, and 4.0 M ammonium acetate.\n\nThe TsaGH11pH8.5 crystal belongs to the tetragonal space group P43212 with unit cell parameters (a = b = 72.79 Å and c = 165.63 Å) and contains two molecules in an asymmetric unit (Table 1). The space group and unit cell parameters of the TsaGH11pH8.5 crystal are nearly identical to those of the TsaGH11pH4.6 crystal (P43212, a = b = 73.11 Å, and c = 165.42 Å). The crystal structure of TsaGH11pH8.5 was solved up to 1.95 Å, with Rwork and Rfree values of 0.171 and 0.209, respectively. The electron density map of the TsaGH11 structure was clearly observed for all amino acids (Thr29–Trp211). TsaGH11pH8.5 exhibits a β-jelly roll fold, resembling that of the right hand. The catalytic residues and substrate-binding cleft are located between the finger and thumb domains (Figure 2a). In the asymmetric unit of TsaGH11pH8.5, molecule A has a rigid conformation due to crystal packing, whereas molecule B has relatively high flexibility of the thumb domain, exposed to the solvent region in crystal packing (Figure 2b). The average temperature factors of the A and B molecules of TsaGH11pH8.5 were 28.17 and 37.16 Å2, respectively. The superimposition of the A and B molecules of TsaGH11pH8.5 showed similarity with a root-mean-square (r.m.s.) deviation of 0.222 Å. The palm and finger domains of molecules A and B display high similarity, but the positions of their thumb domains differ significantly (Figure 2c and 2d). At the thumb domain, Cα atoms from Arg139, Pro143, Asp146, and Thr148 between molecules A and B exhibited subtle movements of 1.09, 1.86, 1.26, and 1.60 Å, respectively (Figure 2d). The surface structure of molecule A of TsaGH11pH8.5 displays an open conformation for the substrate-binding cleft located between the thumb and finger domains (Figure 2e). At subsites +1 and +2, the distance between Pro40 (atom: CB) and Trp40 (CH2) was 5.84 Å (Figure 2e). At subsites –1 and –2, the distances between Asn62 (OD1) and Arg139 (NH2) and between Arg139 (NH1) and Tyr200 (OH1) were 7.02 and 7.93 Å, respectively. The distance between the catalytic Glu105 (OE2) and Glu198 (OE1) residues was 5.17 Å. Conversely, the surface structure of molecule B of TsaGH11pH8.5 displayed a closed conformation between the thumb and finger domains (Figure 2f). At subsites +1 and +2, the distance between Pro40 (CB) and Trp40 (CZ2) was 3.71 Å (Figure 2f). At subsites −1 and −2, the distances between Asn62 (OD1) and Arg139 (NH2) and between Arg139 (NH1) and Tyr200 (OH1) were 5.71 and 8.38 Å, respectively. The distance between the catalytic Glu105 (OE2) and Glu198 (OE1) residues was 5.13 Å (Figure 2f). Consequently, molecules A and B in the asymmetric units of TsaGH11 represent the open and closed conformations of the substrate-binding cleft, respectively, due to the crystal packing effect. These differing conformations of TsaGH11pH8.5, influenced by crystal packing, are similar to those observed in the previously reported TsaGH11pH4.6 crystal because of identical protein crystal packing within the same space group.6\n\n(a) Cartoon representation of TsaGH11, resembling the right-hand structure with palm, finger, and thumb domains. (b) B-factor putty representation of TsaGH11pH8.5 for molecules in the asymmetric unit. (c) Superimposition of two TsaGH11pH8.5 molecules in the asymmetric unit. (d) Close-up view of the superimposition of the thumb domain of the open (green) and closed (cyan) conformations of TsaGH11pH8.5. Surface structure of the (e) open and (f) closed conformations of the substrate-binding cleft in TsaGH11pH8.5.\n\nThe xylanase activity of TsaGH11 at pH 4.6 and pH 8.5 was approximately 97% and 35%, respectively,6 and the crystal structures of TsaGH11pH4.6 and TsaGH11pH8.5 therefore represent structural conformations at relatively high and low activity ranges, respectively. Among the crystal structures of TsaGH11pH4.6 and TsaGH11pH8.5, molecules A and B have the same conformation and were consequently compared. pH induces alterations in the ionization state of amino acid side chains and can affect the secondary structure of proteins.29,30 Consequently, the secondary structures of TsaGH11pH8.5 and TsaGH11pH4.6 were analyzed using DSSP and ESSS method. In the TsaGH11 open conformation, secondary structural differences were observed in Val40, Gly89, Asn90, and Asn167 (Figure 3a). Val40, Gly89, and Asn90 were located above the substrate-binding cleft in the finger domain, and Asn167 was positioned on the surface opposite the substrate-binding site and did not directly influence substrate-binding or activity (Figure 3b). In the TsaGH11 closed conformation, secondary structural differences were present in Asn59, Cys60, Gly61, Gly89, Asn90, Ser144, Gly147, Thr166, Asn167, Qln201, and Ser202 (Figure 3a). Asn59, Cys60, Gly61, Gly89, Asn90, Qln201, and Ser202 are located in the finger domain and lie above the substrate-binding cleft, and Ser144 and Gly147 are positioned in the thumb domain and are presumed to be involved in substrate recognition. Thr166 and Asn167 are located opposite the substrate-binding cleft and do not directly affect substrate-binding (Figure 3c). Accordingly, changes in the secondary structure were commonly observed in the main chain of Gly89 and Asn90 of the finger domain, as well as of Asn167, positioned on the opposite surface of the substrate-binding cleft in both the open and closed conformations of TsaGH11. Although differences in secondary structure were noted in the main chain, no significant structural changes were observed in the conformation of the side chains.\n\n(a) Secondary structure analysis of the TsaGH11 structures using DSSP and STRIDE. Different secondary structure regions are indicated by red bars. (b) Cartoon representation of the different secondary structure regions between TsaGH11pH8.5 and TsaGH11pH4.6. (c) Superimposition of the catalytic and substrate-binding clefts of the open and closed conformations of TsaGH11pH8.5 and TsaGH11pH4.6.\n\nThe superimposition of the TsaGH11pH8.5 and TsaGH11pH4.6 open conformations had an r.m.s. deviation of 0.075 Å (Figure 3c). In the open conformation, the distances between the side chains of the two catalytic residues Glu105 and Glu198 from TsaGH11pH8.5 and TsaGH11pH4.6 were 5.17 and 5.17 Å, respectively. At subsites +1 and +2, the distance between Trp36 (CZ) and Pro143 (CB), which determines the size of the opening between the thumb and finger domains, in TsaGH11pH8.5 and TsaGH11pH4.6 were 5.84 and 5.60 Å, respectively. At subsite −1, the distances between Asn62 (OD1) and Arg139 (NH2) from TsaGH11pH8.5 and TsaGH11pH4.6 were 7.02 and 6.84 Å, respectively. At subsite −2, the distances between Arg139 (NH1) and Tyr200 (OH) from TsaGH11pH8.5 and TsaGH11pH4.6 were 7.93 and 8.30 Å, respectively. Overall, the active site regions of the TsaGH11pH8.5 and TsaGH11pH4.6 open conformations are almost identical, whereas the distance between the finger and thumb domains involved in the substrate recognition site of TsaGH11pH8.5 is slightly wider than that in TsaGH11pH4.6.\n\nThe superimposition of the closed conformations of TsaGH11pH8.5 and TsaGH11pH4.6 had an r.m.s. deviation of 0.094 Å (Figure 3c). In the closed conformation, the distances between the side chains of the two catalytic residues Glu105 and Glu198 in TsaGH11pH8.5 and TsaGH11pH4.6 were 5.13 and 5.21 Å. At subsites +1 and +2, the distances between Trp36 (CZ) and Pro143 (CB) and between TsaGH11pH8.5 and TsaGH11pH4.6 were 3.71 and 3.82 Å, respectively. Notably, different side chain conformations of Arg139 involved in substrate recognition were observed between TsaGH11pH8.5 and TsaGH11pH4.6. At subsite −1, the distances between Asn62 (OD1) and Arg139 (NH2) from TsaGH11pH8.5 and TsaGH11pH4.6 were 5.71 and 4.99 Å, respectively. At subsite −2, the distances between Arg139 (NH1) and Tyr200 (OH) from TsaGH11pH8.5 and TsaGH11pH4.6 were 8.02 and 8.41 Å, respectively.\n\nThe flexibility of protein conformation can be affected by pH.31 To understand whether pH affects the flexibility of TsaGH11, the temperature factor of TsaGH11pH8.5 and TsaGH11pH4.6 was investigated. The overall B-factor values of the open/closed conformations of TsaGH11pH8.5 and TsaGH11pH4.6 were 28.17/37.16 and 18.14/21.80 Å2, respectively (Figure 4a). At both pH 8.5 and 4.6 for TsaGH11, the flexibility tendencies of the closed and open conformations differed, with the closed conformation exhibiting higher flexibility than the open conformation, which can be attributed to protein packing. In the B-factor plot, the tendencies of each open and closed conformation for TsaGH11pH8.5 and TsaGH11pH4.6 were similar. However, the B-factor values for these conformations of TsaGH11pH8.5 were 1.55 and 1.70-fold higher than those of TsaGH11pH4.6. This result indicates that the molecular flexibility of TsaGH11 is relatively high at basic pH. The crystal structures of TsaGH11pH8.5 and TsaGH11pH4.6 were obtained from different crystals, and B-factor effects may occur because of variations in the crystal conditions. Accordingly, the normalized B-factor of TsaGH11pH8.5 and TsaGH11pH4.6 was analyzed and compared (Figure 4b). In the open conformation, Asn88 in the finger domain and Arg139–Gln149 in the thumb domain in TsaGH11pH4.6 showed relatively higher flexibility than TsaGH11pH8.5. In the closed conformation, the area around Lys180 of the palm domain in TsaGH11pH4.6 has a relatively higher flexibility than that in TsaGH11pH8.5.\n\nProfile of (a) B-factor and (b) normalized B-factor for the open and closed conformations of TsaGH11pH8.5 and TsaGH11pH4.6. (c) Superimposition of water molecules in the substrate-binding cleft from TsaGH11pH8.5 (blue) and TsaGH11pH4.6 (red). (d) Superimposition of water molecules in the substrate-binding cleft for the open (green) and closed (cyan) conformations of TsaGH11pH8.5 and TsaGH11pH4.6. Water molecules are indicated by spheres.\n\nChanges in pH can affect the charge state of amino acids and subsequently influence the coordination or position of water molecules around protein amino acids.32,33 Water molecules share characteristics with the hydroxyl group in the xylan substrate, and their positions around the active substrate can subsequently offer insights into the substrate-binding moiety. Therefore, water molecules in the substrate-binding cleft and the active site of TsaGH11 were investigated. In the open conformation of TsaGH11, the subtle movement of water molecules in TsaGH11pH8.5 and TsaGH11pH4.6 at subsites −2, –1, +1, and +2 were approximately 0.22–0.77, 0.26, 0.48, and 0.34 Å, respectively, and between the catalytic residues in TsaGH11pH8.5 and TsaGH11pH4.6 was approximately 0.19 Å (Figure 4c). In the closed conformation of TsaGH11, the subtle movement of water molecules from TsaGH11pH8.5 and TsaGH11pH4.6 at subsites –2, −1, +1, and +2 were approximately 0.16–0.48, 0.09–0.22, 0.42, and 0.26 Å, respectively, and between the catalytic residues from TsaGH11pH8.5 and TsaGH11pH4.6 was approximately 0.17 Å (Figure 4c). Consequently, the average change in the position of these water molecules at different pH levels was <0.5 Å, and no specific directionality was observed in these positions.\n\nUnlike the difference in the position of the water molecules caused by pH, the overall change in the position of water molecules in the open and closed structures in TsaGH11pH8.5 and TsaGH11pH4.6 was substantial. In the superimposition of the open and closed conformations of TsaGH11pH8.5, the subtle movements of water molecules at subsites −2, –1, +1, and +2 were approximately 0.23–0.38, 0.22, 0.26, and 0.71 Å, respectively, and between the catalytic residues in TsaGH11pH8.5 was approximately 0.61 Å (Figure 4d). In the superimposition of the open and closed conformations of TsaGH11pH4.6, the subtle movements of water molecules at subsites −2, −1, +1, and +2 were approximately 0.12–0.41, 0.37, 0.72, and 0.92 Å, respectively, and between the catalytic residues in TsaGH11pH4.6 was approximately 0.64 Å (Figure 4d). Overall, a minor structural change occurred in the position of water molecules in the substrate-binding cleft of TsaGH11 because of the pH. However, the change in the position of water molecules resulting from the open and closed conformational changes in the substrate-binding cleft of TsaGH11 was more significant than the pH effect.\n\n\nDiscussion\n\nXylanase GH11 is of significant industrial importance. The high enzyme activity of TsaGH11 exhibits pH-dependent hydrolase activity, with increased activity at acidic pH and reduced activity at basic pH. To understand the correlation between pH-dependent function and structure, a crystallography study on TsaGH11 was conducted, producing four new crystallization conditions. The crystal structure of TsaGH11 under condition (i) was determined at 1.95 Å. However, diffraction data for TsaGH11 crystals under conditions (ii), (iii), and (iv) could not be collected. Although crystal optimization and diffraction data collection for conditions (ii–iv) were not obtained in this study, this crystallization information can be used for future crystallographic studies for elucidation at basic or other pH values (see below).\n\nTo understand the changes in TsaGH11 activity caused by different pH values from a structural perspective, the crystal structure of TsaGH11pH8.5 determined in this study was compared with that of the previously reported TsaGH11pH4.6. Upon comparing the open and closed conformations of TsaGH11 at the two pH conditions, subtle structural differences in the side chain shift, flexibility, and water molecule position were observed. Comparing the TsaGH11pH8.5 and TsaGH11pH4.6 structures, alterations in the secondary structure were commonly noted at the Gly89, Asn90, and Asn167 regions in both open and closed conformations. Amino acids in the Gly89 and Asn90 regions, which are located near the substrate access region in the substrate-binding cleft, may be implicated in substrate recognition. However, Asn167, situated opposite the substrate-binding site, may not be involved in direct substrate recognition or activation. Conversely, changes in the secondary structure of more amino acids in the finger domain were observed between the closed and open conformations. Given the crucial role of the finger domain, alongside the thumb domain, in substrate recognition, alterations in the main chain of related amino acids might directly or indirectly affect enzyme activity. The variations in the secondary structure between the open and closed conformations indicate that the structural effect of pH on the main chain varies depending on the TsaGH11 conformation.\n\nIn the superimposition of the crystal structures of TsaGH11pH8.5 and TsaGH11pH4.6, a slight positional shift of approximately <0.5 Å is observed for the side chains of amino acids involved in the substrate-binding cleft and the active site of TsaGH11. However, these small changes in the positions of these amino acids are limited in explaining the structure and activity variations observed because of the influence of pH. Conversely, a substantial conformational change was noted in the side chain of Arg139 in the closed conformation of TsaGH11 in response to pH alterations. This residue is involved in substrate recognition on the thumb domain, and this pH-induced conformational change in Arg139 may therefore be noteworthy. Nevertheless, considering that the pKa of Arg is 12.48, its charge remains constant at pH 4.6–8.5. Therefore, the preferred conformation of the Arg139 side chain results from complex factors such as the arrangement and mobility of water molecules around Arg139 that are influenced by changes in pH.\n\nB-factor analysis revealed that the flexibility of amino acids in TsaGH11pH8.5 was similar to that in TsaGH11pH4.6 in both open and closed conformations. However, the B-factor value of the TsaGH11pH8.5 structure was >1.5-fold that of the B-factor value of TsaGH11pH4.6. The higher flexibility of TsaGH11 at this basic pH may provide insight into future understanding of the function of GH11 depending on pH. However, even if the crystallization conditions are similar and the data collection conditions are the same, an absolute comparison cannot be made because the two crystals are not identical.\n\nCharge state of amino acids can be influenced by pH, potentially affecting the arrangement of water molecules around the substrate-binding site. Our analysis of water molecules in the TsaGH11 structures revealed a difference in the number of water molecules in TsaGH11 between basic and acidic pH. This disparity may result from crystal structure resolution rather than a direct effect of pH, making direct comparison challenging. In addition, a small movement in the position of water molecules in the substrate-binding cleft was observed depending on pH, but no specific trends or significant changes were notable. To quantitatively analyze water molecules according to pH, they need to be investigated according to changes at various pHs, which requires crystal structures formed at these different pHs. The change in the position of the water molecules in the open and closed conformation structures at TsaGH11pH8.5 and TsaGH11pH4.6 was greater than the change in the position of the water molecules caused by changes in pH. Consequently, the location of the water molecules indicates the influence of pH on protein conformation. Accordingly, to accurately compare water molecules in the active site depending on pH, proteins of the same conformation must be compared.\n\nIn summary, to understand the relationship between the structure and function of TsaGH11 at different pH values, the crystal structure of TsaGH11pH8.5 was determined and compared with that of TsaGH11pH4.6 to explain the structural differences between the different pH values. Structural comparison of TsaGH11pH8.5 and TsaGH11pH4.6 identified differences in secondary structure, conformational changes of amino acids in the substrate-binding cleft, and flexibility depending on pH. Although these results could provide useful insight into understanding the pH-dependent function of GH11, no significant changes in the crystal structure were observed to be the cause of the decreased activity of TsaGH11 at basic pH. Accordingly, in future research, crystal structures at basic pH (>pH 9.0) must be determined or at various other pHs and trends in molecular movement investigated to observe structural changes induced by changes in pH. Nevertheless, this result offers valuable information, suggesting that structural changes in TsaGH11 may occur due to pH variations. When combined with crystal structures obtained at other pH values in the future, these findings will contribute useful insights for explaining the pH-dependent structure and function in future studies.",
"appendix": "Data availability\n\nThe atomic coordinates and structure factor for the TsaGH11 at pH 8.5 has been deposited in the Protein Data Bank (https://www.rcsb.org/), accession code 8X1D: https://www.rcsb.org/structure/8X1D.\n\n\nAcknowledgements\n\nI thank the staff at the 11C beamline at Pohang Accelerator Laboratory for their assistance with data collection. The editing and publication were supported by Kookmin University.\n\n\nReferences\n\nPaës G, Berrin J-G, Beaugrand J: GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol. Adv. 2012; 30: 564–592. PubMed Abstract | Publisher Full Text\n\nCantarel BL, Coutinho PM, Rancurel C, et al.: The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009; 37: D233–D238. 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}
|
[
{
"id": "263879",
"date": "21 May 2024",
"name": "Rohit Rai",
"expertise": [
"Reviewer Expertise Biomass conversion",
"fungal strain improvement",
"cellulases",
"hemicellulases",
"and auxiliary enzymes",
"genomics and proteomics"
],
"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 authors for the work done and the writeup. The work is significant and enriches the literature. In my opinion, this manuscript can be accepted, however, there are some minor issues that I would like the authors to fix first: 1. I believe that the Title of the manuscript can be improved. 2. The keywords of the manuscript are weak. I suggest picking up more catchy keywords that go well with the work done. 3. I would suggest the authors to add the rationale for naming the enzyme TsaGH11 for the clarity of readers. 4. I could detect some minor mistakes like: -> In the introduction section, Line 1, Endoxylanases \"cleaves\" should be replaced with \"cleave\". -> In the introduction section, Line 6-7, \"GH11 xylanases is utilized\" should be corrected to \"GH11 xylanases are utilized\". -> In the section \"Protein preparation\" under methodology, Line 5, correct the word \"shacking\" to \"shaking\". -> In the section \"Structure determination\" under methodology, Line 5, correct \"was validated\" to \"were validated\". -> Authors are suggested to go through the manuscript one more time and try to rectify any other mistakes like these. 5. A separate \"conclusion\" section will be better.\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? Partly",
"responses": []
},
{
"id": "273964",
"date": "31 May 2024",
"name": "Satya Narayan Patel",
"expertise": [
"Reviewer Expertise Molecular biology",
"Enzymology",
"Bioprocess",
"enzyme kinetics",
"protein characterization"
],
"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 entitled \" pH-Induced structural changes in xylanase GH11 from Thermoanaerobacterium saccharolyticum ” written and discussed very well. We can accept the manuscript with following minor correction.\n\nWhat is the reason to select pH 8.5 for the crystal structure study. Why not pH 7 or 9. Protein preparation: what is the shaking RPM at when the cells was incubated at 18C. Protein preparation: How long the cells breakdown performed using the sonication and temperature. Protein preparation: what is the purity of protein for performing the crystallography.\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? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-242
|
https://f1000research.com/articles/13-240/v1
|
02 Apr 24
|
{
"type": "Brief Report",
"title": "Environmental exposure to multiple chemical elements in Peruvian populations: a review of selected studies",
"authors": [
"Carlos A. Sanchez",
"Michelle Lozada-Urbano",
"Estela E. Ospina",
"Michelle Lozada-Urbano",
"Estela E. Ospina"
],
"abstract": "Background Population-based exposure assessments for heavy metals and metalloids (by governmental and private institutions) are common in Peru, but most studies generally focus on the analysis of a single chemical element, like lead or mercury, and lack an appropriate reference regarding the health impact on the exposed population. The complex/mixed chemical interactions within the human body have not yet been studied for all long-term health effects.\n\nMethods We reviewed laboratory results from five studies, between 2005-2013, that analysed multiple elements (between 13 and 17 chemical elements in each study) in spot urine samples from Peruvian communities considered exposed and not exposed. All laboratory analysis were performed using inductively coupled plasma mass spectrometry (ICP-MS) at the Environmental Health Laboratory Division of the Centers for Disease Control and Prevention (CDC) of the United States.\n\nResults Six chemical elements (total arsenic, caesium, cobalt, lead, molybdenum, and thallium) were present in almost all spot urine samples (>98% of participants), evidencing exposure (qualitative assessment). Exposure to other chemical elements like barium, cadmium, tungsten, antimony and uranium, varied among localities, while chemical elements like beryllium and platinum were rarely detected (<3% and <10% of participants, respectively) in spot urine samples. Most geometric means of urine concentration for total arsenic, lead, cadmium and mercury are higher for the Peruvian locations than for national estimates in Canada and the United States, but not in all locations.\n\nConclusion Comparing averages across different populations can be misleading but comparing periodic values from the same population in the future could evidence an exposure trend. Future studies are needed to develop reference levels for exposed Peruvian populations. This study highlights potential health risks from exposure to environmental chemical elements and can be the first step towards understanding and mitigating human exposure to heavy metals and metalloids for known exposed populations in Peru.",
"keywords": [
"heavy metals",
"inductively coupled plasma mass spectrometry",
"arsenic",
"cadmium",
"lead",
"mercury",
"Peru"
],
"content": "Introduction\n\nMost human diseases rely on laboratory confirmation to establish the presence of disease, but this may be an unmet expectation in environmental exposure assessments because there is currently a knowledge gap between data generated by scientific research and the practical applications of that knowledge to Public Health interventions.1 Human exposure assessment to chemical elements is complex, and “the ability to measure chemicals in humans is far outpacing the ability to reliably interpret these data for Public Health purposes”.2 Biomonitoring (measuring chemicals in human biological samples) can fail to provide information to support Public Health decisions, mostly because results can be difficult to interpret in proper context and the absence of relevant environmental legislation produces a dangerous oversight that is common to many developing countries.3 Regardless, data from human exposure to environmental contaminants is constantly produced, creating a need to assess relationships with potential adverse health impacts and identify potential sources and pathways.2\n\nHuman exposure to environmental chemical elements by air, dust, or water, is inherent to local mining or oil extractive activities, and is a major public health issue in Peru. Environmental and biological evaluations are constantly being carried out by both governmental and private institutions to assess human exposure to different chemical elements. There are plenty of isolated reports regarding exposure to certain heavy metals/metalloids (i.e., lead and mercury) in populations considered not to be occupationally exposed (i.e., children), at levels that would be considered a clinical emergency in other countries.4–6 Suggested explanations for these apparent discrepancies in Peruvian children include genetic adaptation,7 physiological changes from living at high altitudes,8 and the interaction between chemicals inside the human body.9 These “grey literature” observational studies report high levels of heavy metals when compared to other countries, but are seldom included in the scientific literature. We summarize results from official reports of five evaluations performed in Peru by the Division of Laboratory Sciences (DLS) at the National Center for Environmental Health (NCEH) of the Centers for Disease Control and Prevention (CDC) of the United States and compare the results with national reports from other countries. The objective of the study is to identify valuable conclusions that can be drawn from CDC’s DLS analysis in Peru between 2005 and 2013.\n\n\nMethods\n\nResearchers at CDC’s DLS have been pioneers in developing laboratory techniques to measure a broad spectrum of chemical elements in human biological samples (biomonitoring),10 and their laboratories have international prestige and are considered “reference laboratories” by the World Health Organization.\n\nAll exposure assessments responded to community concerns about industrial contamination of natural resources (Figure 1). The city of La Oroya (3745 meters above sea level) includes one of the largest smelting facilities in the world. Three communities are within the area of influence of open pit mines: the province of Espinar (3929 m.a.s.l.), the town of Ayash (3503 m.a.s.l.) is downstream from a top-five world copper production mine, and the Andean capital of Cerro de Pasco (4330 m.a.s.l.) was built over an ancient Pre-Columbian silver mine. Huepethue (414 m.a.s.l.) is a modern day “boom town” in the rainforest where prospectors from all over the world arrive looking for gold in the Amazon riverbeds.\n\nAll studies focused on a subgroup of the total population. Three assessments (Ayash, Huepethue, and Espinar) relied on convenience sampling to recruit participants, and two studies in La Oroya and Cerro de Pasco included random sampling.\n\nAt the request of Peruvian health authorities, five multi-element evaluations in five populations in Peru (Table 1) were conducted at CDC’s DLS to determine the “spot” (collected at a single time point) urine concentrations of up to 17 chemical elements by laboratory analytical methods using inductively coupled plasma with mass spectrometry (ICP-MS). The elements analysed include alkali metals (caesium), alkaline earth metals (barium, beryllium, strontium, uranium), metalloids or semi-metals (antimony, arsenic), transition elements (cadmium, cobalt, manganese, mercury, molybdenum, platinum, tungsten), and base metals (tin, lead, thallium). All the studies were approved by Ethics Committees both in Peru and in the United States, and all culminated in reports for the Regional Health Directorates (DIRESAS for its acronym in Spanish), which are local branches of the Peruvian Ministry of Health (MoH). Most of these assessments include a questionnaire, but here we will only detail tabulated laboratory results.\n\nThe percentage of urine samples with a detectable concentration for each chemical element is presented in Figure 2 and geometric means for four elements are plotted in Figure 3. The National Health and Nutrition Examination Survey (NHANES) in the United States is designed to assess the health and nutritional well-being of children and adults using a representative sample (noninstitutionalized, civilian) of the entire population.16 Findings from the NHANES survey are used to determine the prevalence and risk factors of major diseases and are also the basis for national standards.17 Data from national surveys help develop public health policy, health programs and services, and expand the scientific knowledge on a population’s health,18,19 but biomarker measures from NHANES are not useful for demonstrating temporality, nor are they useful for evaluating causation or reverse causation.20\n\nNote: Strontium, manganese, mercury, and tin were only reported in 2 of the exposure assessments.\n\nThere are some very specific considerations needed before appropriately interpreting these results from spot urine samples regarding the presence or absence of exposure: 1) representativeness, 2) limit of detection, 3) chronic exposure, 4) the variability of spot blood or urine levels, and 5) no universal “safe” level.\n\nBias is inherent to convenient sampling. Also, minimum sample size was not achieved, so the results from any of these assessments cannot be extrapolated outside the study participants.\n\nICP-MS has a level of detection (LOD) below which it cannot determine the presence of a particular chemical element. The LOD has decreased significantly over the years, while the number of chemical elements analysed has increased (Table 1).\n\nExposures to high doses in a short period of time (acute) to chemical elements are well documented, mostly in occupational or accidental settings. In most acute cases, there is usually no previous exposure levels, and blood monitoring shows a “peak” in the levels of the chemical element that progressively declines as the body eliminates the toxic threat in the urine (sometimes with concomitant treatment with chelating agents), and life-threatening blood levels have been well correlated with clinical symptoms, so constant blood monitoring in a hospital setting (or using a 24-hour urine with creatinine correction) is suggested. In a different way, cases of low doses over a long period of time (chronic) exposures may not be aware of signs and symptoms of disease and may not even be aware they have been exposed, making it difficult to identify when the exposure began. The incubation or latency period can take years and the cause for disease is generally multifactorial. Consequently, unaware patients are more likely not to seek medical attention, allowing the toxic effect to go unconstrained so a spot blood or urine sample will not differentiate between past or current exposure.\n\nUrine is the product of blood filtration, so the decision between spot blood or urine sample is usually more of a “practical” concern (invasive vs. non-invasive procedure), considering potential cases have no apparent disease and cannot yet be considered a patient. Still, spot measurements of chemical biomarkers may not be a reliable surrogate for average or peak exposure levels.21 Blood or urine levels vary constantly during the day because the chemical element present at any time in body fluids represents not only that which has been recently ingested, breathed, or eaten, but also that which has been metabolized previously in the body tissue “reserves” (for example, bones and fat), with individual variations between metabolic rates, urinary flow or creatinine excretion rates.21 In this way, environmental chemicals acquire a role in the body’s physiological processes, entering and leaving the tissues, changing their concentration in blood and eventually, urine. Measurement errors associated with spot measures reflect variable exposures and rapid biological clearance that contribute to exposure misclassification and increase the likelihood for biased statistical associations.22\n\nFor some metals like lead and mercury, reference levels exist based on empirical biomarker–response relationships from epidemiological studies, but for most other chemical elements reference levels are not available.23 When any level of a certain metal/metalloid in body fluids is considered potentially dangerous in the long term (i.e., lead poisoning), primary prevention (avoiding exposure altogether) can be the only viable public health alternative.24 This attitude is relatively new. Until relatively recently, blood lead levels were believed to have a correlation with the clinical manifestations presented by chronically exposed people (especially children). The lead poisoning pandemic progressively showed that exposures to very low doses of lead in the environment over long periods of time can be toxic, even without clinical symptoms.2 The existence of a “safe level” (a concentration below which the risk is considered negligible) was initially desired and assumed, but studies continued to show harmful subclinical effects in young children brain development, each time at lower blood lead level.25,26 Thus, the CDC’s “level of concern” for blood lead in children progressively decreased from 40 μg/dL in the 1970s to 10 μg/dL in the 1990s (later adopted by the WHO). These “levels of concern” for blood lead were not based on any correlation with clinical symptoms, but rather with the 95th percentile in a sample population of the United States, were designed to trigger Public Health interventions and were never intended to guide individual treatment or prognosis. Instead of adopting the next “level of concern” at 5 μg/dL, in 2012 the CDC concluded that “there is no safe level for blood lead free of risk to the health of children”.27\n\n\nResults\n\nFive environmental exposure assessments analysed spot urine samples from the following study populations: 343 participants from La Oroya in 2005;11 253 participants from Ayash in 2006;12 354 participants from Cerro de Pasco in 2007;13 98 participants from Huepethue in 2010;14 and 180 participants from Espinar in 201315 (Figure 1 & Table 1).\n\nEvidence of exposure – Qualitative analysis For this analysis, any “detectable” level (above the LOD) is considered evidence of “exposure”, regardless of the amount detected. The percentage of spot urine samples with evidence of exposure varied between locations (Figure 2, data not available for La Oroya). Six chemical elements (total arsenic, caesium, cobalt, molybdenum, lead and thallium) were detected in almost all samples tested (average over 98%), while two other elements (beryllium and platinum) were very seldom detected, <3% and <10% respectively. Other chemical elements like barium, cadmium and tungsten were reported (on average) to be present in over 90% of all samples, while antimony (range 51-96%) and uranium (range 41-83%) were variably prevalent in different locations. Exposure to antimony was more frequent (96%) in samples from participants in Cerro de Pasco, and less frequent (<65%) in other locations. Similarly, uranium was detected more frequently (between 68% and 83%) in 3 Andean locations (Ayash, Cerro de Pasco, and Espinar), but less frequently (41%) in urine samples from the rainforest town at Huepethue. Data for strontium, mercury, manganese, and tin was available for 2 of the 5 locations (Figure 2).\n\nComparison among populations – Quantitative analysis For this analysis, urine concentration geometric means were retrieved from official reports for selected chemical elements and compared to geometric means from nationally representative studies in the United States28 and Canada,29 that are also available in France.30 The (not statistically valid) comparison was made for 3 of the 5 sites using geometric means and estimated 95th percentile in the United States. Chemical elements like total arsenic and lead appear to have a higher geometric mean in Peru when compared to national averages from the United States and Canada, but cadmium and mercury have a lower geometric mean in some locations in Peru (Figure 3).\n\n\nDiscussion\n\nThe health implications for environmental exposure vary among chemical elements and the sources of environmental contaminants vary by location. In Peru, total arsenic, caesium, cobalt, lead, molybdenum, and thallium are almost universally present in urine samples from all five locations. However, there are some key issues that must be considered before attempting to assess human impact from exposure to chemical elements: 1) these are complex/mixed exposures, 2) there is individual variability, and 3) the potential confounding factor from natural exposure.\n\nComplex exposures People can be exposed to more than one chemical at the same time, and studies analysing only one chemical element at a time ignore the potential interactions between chemicals inside the human body. These interactions can range from synergy (a cooperation of two or more substances to produce a combined effect greater than the sum of their separate effects) to antagonism (a substance acts against or blocks the action of another substance). Much remains unknown about the health effects of these mixed interactions where several environmental toxics (including heavy metals, pesticides, and hydrocarbons), from different environmental sources (natural and/or artificial), and through different environmental exposure pathways (air, soil, water and food) can increase the risk of developing diseases. Few human exposure studies analyse multiple elements from a single biological sample, and even when they do, reference information regarding health effects may not be available for all detectable elements.\n\nDisease can be expressed in a different way and at a different time by different people, which complicates the interpretation of spot biomonitoring for Public Health action. Every person’s age, nutritional, socioeconomic and developmental status affects the human body’s ability to absorb, metabolize and excrete the toxic agent, and when and how these exposures manifest clinically. Children, for example, are considered at higher risk due to their increased metabolism and may be currently exposed to hundreds of known chemicals that have not been tested for their toxicity and their effect on human development.31,32\n\nWhen trying to identify health effects for an exposed population, it is common practice to compare exposure levels to similar non-exposed populations (i.e., case-control studies), but finding an appropriate comparison group can be complicated, especially when the extension of the exposure has not been well defined and the control group (considered to be not exposed) actually has some exposure level that the researchers were not aware of.33 For example, arsenic is a known contaminant of natural water sources in Latin America, regardless of the presence or absence of industry.34 These “exposures of unknown origin” are not exclusive to developing countries, and some heavy metals are detected regularly in not-occupationally exposed populations in the Unites States (although sometimes in minimal concentrations) including blood and urine of children31 and pregnant women.35,36\n\n\nConclusions\n\nSome Peruvians are exposed to several chemicals. Biomonitoring alone does not explain at what time, dose, and for how long the exposure occurred, which is essential to estimate the health impact of the inadvertent exposure. Relevant reference levels should be developed for each exposed population. Meanwhile, biomonitoring studies can help prioritize Public Health strategies for different populations in Peru.",
"appendix": "Data availability\n\nThe data for this article consists of bibliographic references, which are included in the References section.\n\n\nAcknowledgements\n\nWe would like to thank Ellen E. Yard, Laura Conklin, Fuyuen Y. Yip, the lead investigators of the studies, for their support on making available data required for this study. A la Dirección de Investigación de la Universidad Peruana de Ciencias Aplicadas por el apoyo bridado para realización de este trabajo de investigación a través del incentivo UPC-EXPOST-2024-1.\n\n\nReferences\n\nBrownson RC, Kreuter MW, Arrington BA, et al.: Translating Scientific Discoveries Into Public Health Action: How Can Schools Of Public Health Move Us Forward? Public Health Rep. 2006 Jan-Feb; 121(1): 97–103. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBahadori T, Phillips RD, Money CD, et al.: Making sense of human biomonitoring data: Findings and recommendations of a workshop. J. Expo. Sci. Environ. Epidemiol. 2007; 17: 308–313. PubMed Abstract | Publisher Full Text\n\nJoyce S: Focus-Growing Pains in South America. Environ. Health Perspect. 1997 August; 105(8): 794–799. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarsh DO, Turner MD, Smith JC, et al.: Fetal methylmercury study in a Peruvian fish-eating population. Neurotoxicology. 1995 Winter; 16(4): 717–726. PubMed Abstract\n\nEspinoza R, Hernández-Avila M, Narciso J, et al.: Determinants of blood-lead levels in children in Callao and Lima metropolitan area. Salud Publica Mex. 2003; 45(Suppl 2): 209–219. Publisher Full Text\n\nGuillén-Mendoza D, Escate-Lazo F, Rivera-Abbiati F, et al.: Lead in umbilical cord blood of neonates born in northern Lima. Rev. Peru. Med. Exp. Salud Publica. 2013 Apr; 30(2): 224–228. PubMed Abstract | Publisher Full Text\n\nLombardi G, Lanzirotti A, Qualls C, et al.: Five hundred years of mercury exposure and adaptation. J. Biomed. Biotechnol. 2012; 2012: 472858. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaylor L, Ashley K, Jones RL, et al.: Field evaluation of a portable blood lead analyzer in workers living at a high altitude: a follow-up investigation. Am. J. Ind. Med. 2004 Dec; 46(6): 656–662. PubMed Abstract | Publisher Full Text\n\nJefferson JA, Escudero E, Hurtado ME, et al.: Excessive erythrocytosis, chronic mountain sickness, and serum cobalt levels. Lancet. 2002 Feb 2; 359(9304): 407–408. Publisher Full Text\n\nLanphear B: Still Treating Lead Poisoning After All These Years. Pediatrics. 2017 Aug; 140(2): e20171400. PubMed Abstract | Publisher Full Text\n\nSerrano F: Estudio sobre la contaminación ambiental en los hogares de La Oroya y Concepción y sus efectos en la saldu de sus residentes. Study Report. Saint Louis, Missouri: Saint Louis University, School of Public Health; 2005.\n\nYip F, Azziz-Baumgartner E, Luber G, et al.: Heavy metal levels among people living in Communities on the Ayash River Basin: Huari, April 4-14, 2006. Study Report. Atlanta, GA: Centers for Disease Control and Prevention (CDC), National Center for Environmental Health (NCEH); 2007.\n\nConklin L, Sánchez CA, Neri A, et al.: Reporte Final: Exposiciones a metales pesados en niños y mujeres en edad fértil en tres comunidades mineras Cerro de Pasco, Perú 21 de Mayo – 4 de Julio de 2007. Study Report. Atlanta, GA: Centers for Disease Control and Prevention (CDC), National Center for Environmental Health (NCEH); 2008.\n\nYard EE, Horton J, Schier JG, et al.: Mercury exposure among artisanal gold miners in Madre de Dios, Peru: a cross-sectional study. J. Med. Toxicol. 2012 Dec; 8(4): 441–448. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMesa de Diálogo Espinar-Sub Grupo de Medio Ambiente: Informe Final Integrado de Monitoreo Sanitario Ambiental Participativo de a Provincia de Espinar. Study Report. Lima, Peru: Ministerio de Salud, Centro Nacional de Salud Ambiental y Protección del Ambiente para la Salud (CENSOPAS); 2013. Reference Source\n\nCDC (Centers for Disease Control and Prevention): National Health and Nutrition Examination Survey. About the National Health and Nutrition Examination Survey; 2014. [accessed 28 September 2022]. Reference Source\n\nCDC (Centers for Disease Control and Prevention): Fourth National Report on Human Exposure to Environmental Chemicals (Updated Tables). Atlanta, GA: CDC; 2015. [accessed 28 September 2022]. Reference Source\n\nCDC (Centers for Disease Control and Prevention): Introduction to NHANES - Overview. [accessed 28 September 2022]. Reference Source\n\nSecond Report on Human Biomonitoring of Environmental Chemicals in Canada: Results of the Canadian Health Measures Survey Cycle 2 (2009–2011).2013. [accessed 28 September 2022]. Reference Source\n\nHill AB: The environment and disease: association or causation? Proc. R. Soc. Med. 1965; 58: 295–300. Publisher Full Text\n\nAylward LL, Hays SM, Smolders R, et al.: Sources of variability in biomarker concentrations. J. Toxicol. Environ. Health B Crit. Rev. 2014; 17: 45–61. Publisher Full Text\n\nArmstrong BG: Effect of measurement error on epidemiological studies of environmental and occupational exposures. Occup. Environ. Med. 1998; 55: 651–656. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSobus JR, DeWoskin RS, Tan YM, et al.: Uses of NHANES biomarker data for chemical risk assessment: trends, challenges, and opportunities. Environ. Health Perspect. 2015; 123: 919–927. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRosen JF, Mushak P: Primary prevention of childhood lead poisoning--the only solution. N. Engl. J. Med. 2001 May 10; 344(19): 1470–1471. PubMed Abstract | Publisher Full Text\n\nRogan WJ, Ware JH: Exposure to lead in children–how low is low enough? N. Engl. J. Med. 2003; 348(16): 1515–1516. Publisher Full Text\n\nLanphear BP, Hornung R, Khoury J, et al.: Low-level environmental lead exposure and children’s intellectual function: an international pooled analysis. Environ. Health Perspect. 2005; 113(7): 894–899. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCenters for Disease Control and Prevention, Advisory Committee on Childhood Lead Poisoning Prevention: Low Level Lead Exposure Harms Children: A Renewed Call for Primary Prevention. Atlanta, GA: Centers for Disease Control and Prevention; 2012. Reference Source\n\nCaldwell KL, Hartel J, Jarrett J, et al.: Inductively Coupled Plasma Mass Spectrometry to Measure Multiple Toxic Elements in Urine in NHANES 1999-2000. At. Spectrosc. 2005 January/February; 26(1).\n\nHaines DA, Saravanabhavan G, Werry K, et al.: An overview of human biomonitoring of environmental chemicals in the Canadian Health Measures Survey: 2007-2019. Int. J. Hyg. Environ. Health. 2017 Mar; 220(2 Pt A): 13–28. Publisher Full Text\n\nFréry N, Vandentorren S, Etchevers A, et al.: Highlights of recent studies and future plans for the French human biomonitoring (HBM) programme. Int. J. Hyg. Environ. Health. 2012 Feb; 215(2): 127–132. PubMed Abstract | Publisher Full Text\n\nCouncil on Environmental Health: Chemical-management policy: prioritizing children’s health. Pediatrics. 2011; 127(5): 983–990. PubMed Abstract | Publisher Full Text\n\nGrandjean P, Landrigan PJ: Neurobehavioural effects of developmental toxicity. Lancet Neurol. 2014; 13(3): 330–338. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnticona C, Bergdahl IA, Lundh T, et al.: Lead exposure in indigenous communities of the Amazon basin, Peru. Int. J. Hyg. Environ. Health. 2011; 215(1): 59–63. Publisher Full Text\n\nArsenic in drinking water in Latin America and its effect on public health: Pan American Center for Sanitary Engineering and Environmental Sciences (CEPIS-BS/SDE/PAHO). Lima, Peru: December 2004. Reference Source\n\nWoodruff TJ, Zota AR, Schwartz JM: Environmental chemicals in pregnant women in the United States: NHANES 2003-2004. Environ. Health Perspect. 2011; 119(6): 878–885. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBraun JM, Kalkbrenner AE, Just AC, et al.: Gestational exposure to endocrine disrupting chemicals and reciprocal social, repetitive, and stereotypic behaviors in 4- and 5-year-old children: the HOME study. Environ. Health Perspect. 2014; 122(5): 513–520. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "275606",
"date": "10 Jun 2024",
"name": "Marina Piscopo",
"expertise": [
"Reviewer Expertise effects of heavy metals and others pollutants on the reproductive health of human and marina orgsnisms"
],
"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 article titled “Environmental exposure to multiple chemical elements in Peruvian populations: a review of selected studies” the authors reviewed laboratory results from five studies, between 2005-2013, that analysed multiple elements (between 13 and 17 chemical elements in each study) using inductively coupled plasma mass spectrometry (ICP-MS) in spot urine samples from Peruvian communities exposed and not exposed. This also because the complex/mixed chemical interactions within the human body have not yet been studied for all long-term health effects. The authors found that Six chemical elements (arsenic in total, caesium, cobalt, lead, molybdenum molybdenum, and thallium) were found in almost all spot urine samples (more than samples (>98% of participants), indicating exposure (qualitative assessment). Exposure to other chemical elements such as barium, cadmium, tungsten, antimony and uranium differed between sites, while beryllium and platinum were rarely detected in spot urine samples.\n\nMost urinary geometric mean concentrations of total arsenic, lead, cadmium and mercury were greater for the Peruvian sites than for the than national estimates in Canada and the United States, but not in all sites.\nI find an interesting work but I suggest a major revision.\n\nThe suggestions I would make are as follows:\nThe authors should define the criteria for subject selection because there may be confounding factors. E.g. were the subjects smokers? were they drinkers? were they drug addicts? how long have they lived in the areas under consideration? do they have illnesses? are they exposed to toxic substances in the workplace?\nActually, urine is not the best matrix for the accumulation of pollutants but semen. There are many recent works that prove this. The authors should consider reading these works and updating their work citing them. I suggested citing these papers because the paper is not up to date with the current literature where semen has been considered the most responsive matrix for pollutant accumulation for several years. Among other things, semen accumulates area-specific pollutants that make it possible to understand in which area a subject resides. I believe that such considerations must be made. All this in order to enrich a work on the determination of pollutants on urine that is in some ways obsolete.\n(Ref 1-5)\nsemen is so receptive that microplastics have been found: (Ref-6)\nfor cadmium, seasonal variations in accumulation and effects have been observed. the measurements were taken over what period? all at once? Read and quote : (Ref-7)\nThe work does not add much to the fact that there may or may not be interactions between pollutants and thus synergistic effects\nI believe that to make the article more appealing you should include a nice color image that summarizes the results, the molecular mechanism and the message the authors want to give\n\nBetter define the limitations of this study\n\nEnglish revision required\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? I 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": "287341",
"date": "18 Jun 2024",
"name": "Lufeng Chen",
"expertise": [
"Reviewer Expertise environmental behavior and risk assessment of heavy metals"
],
"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 seeks to analyze multiple elements in urine samples from Peruvian communities for investigating complex/mixed chemical interactions within the human body and long-term health effects. The outcomes of this study are expected to provide basic evidence of health risks posed by chemical elements, and can be the first step towards understanding and mitigating human exposure to heavy metals and metalloids for known exposed populations in Peru. In general, the topic of this manuscript is of interest to the readership of F1000Research, the methods used are common, the data presented are reliable, and the results observed are credible. However, there are several concerns that need to be addressed and listed below.\n1) Introduction, you should clearly state the objectives of this study, or present your hypothesis according to the knowledge gaps.\n2) Suggest to provide details of analytical methods, ICP-MS, and QA/QC of each study, to assess the differences among labs.\n3) You should provide more details of statistical methods.\n4) As mentioned in conclusion, this study is the first step towards understanding and mitigating human exposure to heavy metals and metalloids for known exposed populations in Peru, what about the future research perspectives are?\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? 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",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-240
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https://f1000research.com/articles/12-282/v1
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14 Mar 23
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{
"type": "Research Article",
"title": "Validation of Quality-of-Life assessment tool for Ethiopian old age people",
"authors": [
"Ahmed Muhye",
"Netsanet Fentahun",
"Netsanet Fentahun"
],
"abstract": "Background: A valid and reliable quality of life (QOL) assessment tool is critical for identifying health issues, evaluating health interventions, and establishing the best health policies and care plans. One of the tools for this goal is the World Health Organization's Quality of Life Old module (WHOQOL-OLD). It is validated and available in more than 20 languages globally, except Amharic (the widely spoken language in Ethiopia). As a result, the purpose of this study was to translate it into Amharic language and validate it among the elderly people in Bahir Dar City, Northwestern Ethiopia.\n\nMethods: This was a cross-sectional study conducted among 180 community-dwelling old age people in Bahir Dar City, Ethiopia, from January 16 to March 13, 2021. Psychometric validation was achieved through Cronbach’s alpha of the internal consistency reliability test and construct validity from confirmatory factor analysis.\n\nResults: The study participants were aged between 60 and 90 years, with a mean age of 69.44. Females made up 61.7% of the study population, and 40% of them could not read or write. The results showed a relatively low level of quality of life, with a total transformed score of 58.58±23.15. The Amharic version of the WHOQOL-OLD showed a Cronbach’s Alpha value of 0.96 and corrected item-total correlations of more than 0.74. The confirmatory factor analysis confirmed the six-domain model with a chi-square (X2) of 341.98 and a p-value less than 0.001. The comparative fit index (CFI) was 0.98, Tucker-Lewis’s index (TCL) was 0.97, and the root mean square error of approximation (RMSEA) was 0.046.\n\nConclusion: The Amharic version of the WHOQOL-OLD indicated good internal consistency reliability and construct validity. The tool can be utilized to provide care to Ethiopian community-dwelling old age people.",
"keywords": [
"Quality of life",
"WHOQOL-OLD",
"Validity",
"Reliability",
"Old age people",
"Ethiopia"
],
"content": "Introduction\n\nAdvancement in public health sector along with changes in clinical interventions have resulted in a rise in life expectancy in almost every area of the world.1 People are living longer around the world, but they are not necessarily healthier.2,3 At the same time, the number of years spent living with impairments and chronic illnesses is increasing. The health of old age people is changing more frequently and faster as they live longer lives, which affects their quality of life.4,5\n\nThe World Health Organization (WHO) described QOL as “individuals’ perception of their position in life in the context of the culture and value systems in which they live and in relation to their goals, expectations, standards, and concerns”.6 However, assessing and improving QOL in old age are a difficult undertaking. This is related to the complicated concept of QOL, the identification of many instruments, and the subjectivity of how older people and healthcare practitioners judge their patients' health.7–9 Despite this, if old age people have their independence, autonomy, and good physical health, as well as remain active, find purpose in their lives, and fulfill their social obligations, their QOL may be good or at least maintained.10–12\n\nFurthermore, WHOQOL-OLD has been developed specifically for measuring QOL in old age people13 and its novel form contains a total of 24 items assembled into six domains, each with four items: autonomy (AUT), past, present, and future activities (PPF), sensory abilities (SAB), social participation (SOP), death and dying (DAD), and intimacy (INT).14\n\nThere is a vast disparity in the proportion of old age people aged 60 years and above who report their QOL across countries.9 Sensory abilities and intimacy scored the highest QOL sub-scale in high-income countries,15–17 while social participation (SOP) scored the highest QOL sub-scale in low-income countries.18,19\n\nAvailable studies in Ethiopia did not use the WHOQOL-OLD. They instead used other tools, such as the medication-related quality of life (MRQoL),20 Control, Autonomy, and Self-realization (CASP),21 and the World Health Organization Quality of Life-brief version (WHOQOL-BREF).22,23 To the best of our knowledge, these tools were neither developed for nor have yet been rigorously validated for Ethiopian old age people. Still, the accessible tools for evaluating QOL are usually designed and validated in developed nations, which have distinct cultural, socio-economic, and life standards contrary to those of African nations. Furthermore, the majority of old age Africans are illiterate, making it difficult to use QOL questionnaires that demand users to read and write.24\n\nThe lack of validated instruments troubles the accuracy of the data generated and its extrapolation to a larger population, as well as the ability to compare findings through studies. Subsequently, low-quality data can have a detrimental impact on policies and services, as well as efficient use of resources.25 Therefore, this study aimed to translate and validate the WHOQOL-OLD tool for Ethiopian old age people.\n\n\nMethods and Materials\n\nThis study was conducted in Bahir Dar City, the capital of the Amhara Regional State. Bahir Dar is located in Amhara Regional State, Northwest Ethiopia, which is 565 kilometers away from Addis Ababa, the capital city of Ethiopia.\n\nA cross-sectional study design was conducted from January 16 to March 13, 2021.\n\nThis study utilized two groups of the population. The first group were health care experts used for content validation, and the second group were community-dwelling old age people for psychometric validation. For the expert judgment, 10 healthcare experts were purposefully selected based on the guideline recommendation for the Delphi technique.26 For the psychometric validation, a participant-to-variables ratio of 10:1 was followed as a rule of thumb.27 Since the mini nutritional assessment tool has 18 items, a minimum of 180 study participants were selected, and the study population was used for this WHOQOL-OLD tool validity study too. Community-dwelling old age people selected in multistage cluster sampling from Belay Zeleke, one of the sub-cities of Bahir Dar City, Northwest Ethiopia were used for this study. Community-dwelling people age 60 years and above, living in the city administration at least for six months, being capable of describing their lived experience, and being able to understand and speak the local Amharic language were included. While those who had significant spine curvature (scoliosis or kyphosis) and had both extremities amputated were excluded. The detailed study methods for study population, sample size, and sampling procedures were described in the previous study.28\n\nThis tool validation study was conducted in three stepwise phases. The first phase was to review existing QOL assessment tools for old age people. In the second phase, selection, translation, and review of the tool by experts were conducted. In the last phase, psychometric validation among community-dwelling old age people was performed.\n\nQuality of life (QOL) has been conceived and assessed in a variety of ways based on the paradigm, discipline, target community, and time frame of the study investigating it.29 Around the world, numerous tools have been established for measuring QOL in adults and validated for the elderly.9,30 Only in Africa, 14 unique tools were identified from 22 studies to measure QOL in old age people.24 Furthermore, instruments have been developed specifically for measuring QOL in old age people, including the WHOQOL-OLD,13 the Elderly Quality of Life Index (EQLI),31 the Older People’s Quality of Life (OPQOL) questionnaire,32 and the World Health Organization Quality of Life-AGE questionnaire (WHOQOL-AGE).33\n\nThe WHOQOL-OLD novel form contains a total of 24 items assembled into six domains, each with four items: autonomy (AUT), past, present, and future activities (PPF), sensory abilities (SAB), social participation (SOP), death and dying (DAD), and intimacy (INT). The module evaluates mostly the two-week duration of testing in self-report or interviewer-administered form. Although each object is rated on a Likert scale of 1 to 5, they differ in their anchors. Each domain provides an individual score ranging from 4 to 20. The component values can also be converted to a scale of 0 to 100. Furthermore, summing the individual item values yields total scores from 24 to 120, with higher scores indicating better QOL.14\n\nThe WHOQOL-OLD instrument was chosen from the available QOL measurement tools to translate and culturally adapt for the context of our community because it: (1) is designed specifically for elderly people;13 (2) is the most comprehensive multidimensional instrument that covers multiple components of QoL;13,14,34 (3) contains items that are particularly relevant for old age people and are absent from the other instruments, such as autonomy, intimacy, and death and dying;13 (4) is subjective and culturally sensitive;35,36 (5) showed good reliability and validity in the assessment of QOL for older participants with multi-language versions;37,38 and (6) is freely available for research use.14\n\nThe English version of the WHOQOL-OLD questionnaire was initially translated into the Amharic local mother tongue version independently by bilingual internists and human nutritionists trained at master’s degree level. These two translators were selected respectively as they are experienced in care providing for old age people and nutrition research and might be familiar with the intent of each item and/or the tool as a whole. The two Amharic versions were then combined, and any inconsistencies were settled by consensus. The translated Amharic version was next translated back into the original English language to ensure the accuracy of the translation. This was done again by two independent bilingual, native Amharic-speaking language translators trained at masters’ degree level. Finally, the experts’ group reviewed both versions of the translations and reached a conclusion on all items to get a final version of the translated questionnaires (Figure 1).\n\nData were collected from two groups: healthcare experts and community-dwelling old age people, in exploratory mixed qualitative and quantitative methods. Each expert evaluated the content validity of the tool through face-to-face contact. The experts and old age people’s comments were used for words, grammar, clarity, appropriate scoring and applicability of items. After incorporating the experts’ comments, psychometric validation was conducted among community-dwelling old age people.\n\nSix urban health extension workers and six bachelor of science nurses collected the data after two days of training. The principal investigator and a master’s degree trained nutritionist supervised the data collection process. The data were collected through face-to-face interviews using the standardized Amharic version of the questionnaires. Assistance from family members or caregivers was also used.\n\nThe international business machines corporation statistical package for the social science (IBM SPSS) version 2339 (RRID:SCR_002865, URL: http://www-01.ibm.com/software/uk/analytics/spss/) and the extension of Analysis of Moment Structures (AMOS) via the maximum likelihood estimation method40 were used to analyzed the data. Socio-demographic characteristics of the study participants were expressed in descriptive statistics. Whereas, the statistical analysis of the WHOQOL-OLD tool in this study was done in stages. The values for all negatively phrased items coded with a number of 1, 2, 6, 7, 8, 9, and 10 on the tool were first reverse-scaled to match the values for positively phrased questions. Second, the statistic assumptions of normality and outliers were verified. Using the squared Mahalanobis distance (d2) greater than 0.05 for each item,40 no more severe multivariate outliers were discovered, and none were deleted. Furthermore, normalized kurtosis values and critical ratios of less than 5.00 indicated that the data were normally distributed.40 Thirdly, total and mean scores were computed for each domain. Finally, the overall total score was translated into a score with a range of 0 to 100.\n\nContent validity and acceptability\n\nTo assess the acceptability of the Amharic version of the WHOQOL-OLD, the response rate and floor and ceiling effects of summary scores were examined. If more than 15% of respondents received the lowest bad health score or the highest good health score possible score, there were floor and ceiling effects.41\n\nConstruct Validity\n\nExploratory and confirmatory factor analyses were performed, respectively, to check construct validity. The principal component analysis (PCA) with Promax rotation was performed to evaluate the sample adequacy and check whether the items in the translated questionnaires were organized comparably to the novel questionnaires. Oblique rotation was used rather than orthogonal since we expected that the factors of the tool would be intercorrelated, as previously verified by other studies.17,42 The Kaiser-Meyer-Olkin (KMO) test at a minimum level of 0.60 was used to determine whether the items were sufficiently correlated to allow for factor analysis.43 Whereas, Bartlett's test of sphericity with a p-value less than 0.05 was used to examine the inter-correlations between items. In addition, the eigenvalues of more than one rule and a graphic review of the scree plot were employed to decide the number of factors to maintain. Items had to be related to a single component, and each rotated component had to have at least four items to assess component affiliation. The proportion of explained variance of more than 60% was used to measure the factors' ability to describe the data.43\n\nThe data were then exported to AMOS version 23 for confirmatory factor analysis (CFA).40 A predefined six-factor model in first and second-order CFA was used to test the construct validity of the Amharic version of the WHOQOL-OLD tool. The first model is a congeneric measuring model that depicts the six-factor structure in which each item on the questionnaire was linked to the underlying latent construct of its predicted aspect. The second-order factor was introduced to see if the construct “QOL” could be represented by a single dimension.43\n\nAt least one test from each of the four typical model fit indexes was used for the acceptability of CFA suggested variables. These included the chi-squared test (X2) from the overall model fit, the goodness-of-fit index (GFI), the root mean square error of approximation (RMSEA), or the standardized root mean square residual (SRMR) from the absolute fit indexes; and the comparative fit index (CFI), the normed fit index (NFI), non-normed fit index (NNFI), or Tucker-Lewis index (TLI) from the relative or incremental fit index; and the Akaike Information Criteria (AIC) or Bayesian Information Criteria (BIC) from the predictive fit indicators.44–46 The recommended model is usually the one with the least AIC and BIC statistic value46 and an RMSEA of less than 0.08.44,45 While the GFI, CFI, NFI, and NNFI scores more than 0.90, especially those near one, indicated good fitness.44,45\n\nThe CFA also took into account for both convergent and divergent validity. Convergent validity was evaluated using the factor loading, AVE, and composite reliability (CR) tests. Good convergent validity was considered if the total correlations and factor loading or inter-item correction values exceeded 0.50 and 0.30, respectively.43\n\nThe AVE and composite reliability (CR) values were calculated as:\n\nWhere, Li is the factor loading for ith construct n is the number of item indicators for a construct and ei is the error variance term for a construct.\n\nThe values of AVE of 0.5 or more and composite reliability (CR) of 0.7 or higher were used to see if the items logged under each facet/domain were estimating the same concept.43\n\nThe divergent or discriminant validity of the Amharic version of the WHOQOL-OLD construct was achieved when the coefficient of cross-loading (correlation among the components) did not exceed 0.85.43 Additionally, the value of maximum shared variance (MSV) being less than the value of AVE was used as an indication of divergent validity.43\n\nReliability\n\nCronbach's alpha (α) was used to measure internal consistency, and a value greater than 0.7 was taken as a benchmark.47 In addition, construct reliability (CR) based on the factor loading after CFA and a coefficient of more than 0.70 was considered satisfactory.43 Furthermore, the Pearson correlation coefficient was used to correct the reliability coefficient for the 24 items of the Amharic version of the WHOQOL-OLD scale.\n\nData quality control\n\nData collection questionnaires were adapted from previously validated standards. The data collectors and supervisors took two days of training on the study’s purpose and the utilization of data collection tools. Statistical data assumptions were checked following the prescribed processes.\n\n\nResults\n\nA total of 180 community-dwelling old age people aged from 60 to 90 years participated in this study. The mean age was 69.44, with a standard deviation of 6.8. The majority of the study participants were females (61.7%) and orthodox religious followers (73.9%). More than half (53.3%) of the respondents were married and lived with their spouses, and 40% of them could not read and write (Table 1).\n\nContent validity and acceptability\n\nAs experts reviewed, every item in the tool was socially acceptable and had no sensitive words. Minor changes, such as word and phrase expansion and substitution of more relevant Amharic terminology and phrases were made to make the items clear and more accurate. Moreover, there were no major difficulties encountered throughout the data collection period, and the scale was completed on each participant in 25 to 35 minutes. The result showed a 100% response rate without missing any item. No significant concern was raised in their remarks about the understandability of the questions and response items. The ceiling and floor effects of each domain in the Amharic version of WHOQOL-OLD varied from 1.8 to 7.7% and 0 to 2.9 %, respectively.\n\nConstruct validity\n\nAll variables of the tool were correlated with more than 0.306 in the matrix correlation, satisfying the requirement of the presence of two or more correlated variables with more than a 0.30 coefficient. In addition, the measure of sampling adequacy, located on the diagonal of the anti-image correlation matrix of SPSS, was greater than 0.80 for each variable in the first iteration. This is commendable and does not necessitate the removal of any items. Furthermore, the Kaiser-Meyer-Olkin (KMO) measure of sampling adequacy was 0.943, and Bartlett’s test of sphericity was statistically significant (X2 = 3,915.790; n = 180; df = 276; P<0.0001). These indicate that all the 24 variables that remained in the analysis satisfied the criteria for appropriateness of factor analysis.\n\nIn the same way, the 24 variables appeared to measure five underlying components using the latent root criterion, commonly known as the Kaiser criterion (eigenvalues greater than 1.0). These variables are responsible for 78.2% of the total variance explained. The results were identical when a fixed six component based on prior knowledge was used. While the scree plot suggested that six factors would be appropriate when considering the changes in eigenvalues. Moreover, the communality value was satisfactory for all variables, with a minimum value of 0.687. Since each variable has more than 0.50, there is no need for communality variable removal.\n\nWith four items on each component, all of the 24-items are heavily factor loaded with more than 0.5. Explicitly, Factor 1 was loaded with the four items of PPF activities. The four autonomy (AUT) components, on the other hand, were loaded onto Factor 2. The loadings of the factors ranged from 0.649 to 0.846. Furthermore, there were no instances of cross-loading between the components.\n\nThe extended analysis of EFA; CFA) was used to see if the results fit a postulated measurement model. The results of the first-and second-order CFA showed that all WHOQOL-OLD facets are adequately represented on the linked items by substantial standardized loadings above 0.5 (Figure 2). When the goodness of fit index parameters of both models was compared using standard structural equation modelling (SEM) procedures, it was clear that adding the second-order common component did no influence on the model fit. All four indices displayed an acceptable fit, except the value of the goodness-of-fit index (GFI) and adjusted goodness-of-fit index (AGFI), which are slightly below 0.90 (Table 2).\n\nThe CFA also took into account both convergent and divergent validity. The scaling analysis revealed that almost all of the items had good correlations with their respective sub-scales (r≥0.65), indicating that the instrument has strong convergent validity. Additionally, the findings confirmed that all item loadings on their own factor were greater than 0.800, which is required for convergent validity.\n\nFurthermore, AVE and composite reliability (CR) values for each construct of the Amharic version of WHOQOL-OLD were more than 0.5 and 0.7, respectively. The values for the total score of the tool were respectively 0.68 and 0.92, which are more than the acceptable range. The AVE estimations ranged from 69.8% for SAB to 77.6% for PPF activities, respectively. Thus, all constructs exceed the 50% rule of thumb, which states that items measuring similar restrictions are loaded into one domain. The AVE values are also larger than the MSV values, which is important for divergent or discriminant validity. Additionally, the calculated correlation coefficient between all six components of the model in IBM-SPSS-AMOS does not exceed 0.85. As a result, we conclude that the measuring tool for the construction of the Amharic version of WHOQOL-OLD has attained divergent or discriminant validity (Table 3).\n\nReliability\n\nThe Cronbach’s Alpha (α) values of the Amharic version of WHOQOL-OLD were above 0.90, varying from 0.902 for SAB to 0.932 for PPF activities. The total scale has a Cronbach’s alpha (α) value of 0.963. Meanwhile, Cronbach’s alpha coefficient of each domain as well as the total scale did not increase when each item was deleted, indicating that all had constructive contributions to their facets as well as the total scale (Table 4).\n\n\n\n1. Sensory abilities (SAB)\n\n\n\n2. Autonomy (AUT)\n\n\n\n3. Past, present and future activities (PPF)\n\n\n\n4. Social participation (SOP)\n\n\n\n5. Death and dying (DAD)\n\n\n\n6. Intimacy (INT)\n\nIn addition, the Pearson correlation revealed high correlation coefficients between items and their theorized domains (inter-item relations) and the six domains themselves as well (Table 5).\n\nIn comparison to the other domains, the correlation coefficients between items and their postulated domains were substantially higher. Furthermore, the domains themselves were moderately correlated with each other. The lowest correlation was observed between SAB and PPF activities with a correlation coefficient value of 0.489. The highest correlation was observed between the correlation of SOP and INT with DAD, both with a correlation coefficient value of 0.744. Additionally, all of the domains were highly connected with the total QOL score, with the SAB and INT having the lowest (0.726) and highest (0.867) correlation coefficients with the overall QOL score, respectively (Table 6).\n\n** Values are statistical significance (p<0.001) between facet- facet and total score relation.\n\n\nDiscussion\n\nThis is the first study examination of the psychometric properties of the WHOQOL-OLD for a representative sample of the Ethiopian population aged 60 years and older. The results revealed that all items in the Amharic version of the WHOQOL-OLD were simple to understand and respond to, indicating that the scale is practicable. Similar findings were reported from psychometric studies of Korea42 and Iran.48 In addition, all of the domain scores and the overall score revealed less than 15.0% ceiling and floor effects, which is acceptable for all subscales.41 This classification indicated that the Amharic version of WHOQOL-OLD had no significant floor and ceiling effects, indicating its discriminant ability. This is consistent with the other cultural studies conducted in Korea42 and Iran.48\n\nIn terms of content validity, this study yields statistically significant item-facet correlation coefficients that are identical to those found in China.37 Moreover, the results of CFA for a six-factor model indicated acceptable construct validity that best fit the study data and was congruent with the reported priori factor structure of the original scale13,14 and in the validation studies of Vietnam,17 Korea,42 Iran,48 and the Netherlands.15\n\nOur analysis also revealed the psychometric qualities of the Amharic version of the WHOQOL-OLD, such as RMSEA of 0.047, CFI of 0.975, GFI of 0.867, and NFI of 0.917. These are comparable to, if not better than, those reported in the worldwide WHOQOL-OLD field research14 and those of other country versions in the Netherlands,15 Vietnam,17 Korea,42 and Iran.48\n\nThe CFA-based fit indices in this study are also acceptable as measures of divergent validity, which is a subtype of construct validity.43 There was no evidence of scaling error, as the tool’s items discriminate significantly between their own and other domains, demonstrating divergent validity.\n\nFurthermore, all corrected item-total correlations and factor loadings based on the six-factor CFA model appear higher than 0.30, which is consistent with a study from Vietnam.17\n\nInternal consistency Cronbach's alpha value in the current study demonstrated high-reliability coefficients and item-scale respective inter-item correlations for the total and subdomains of the Amharic version of WHOQOL-OLD. The findings are higher than compared to those of prior research conducted in Vietnam,17 Korea,42 and Iran.48 This could be because of socio-cultural differences, with older people residing in different countries. There could also be a chance of reporting bias based on respondents' willingness and ability to provide accurate responses, especially when it comes to the length of time in the interview.\n\nTo our knowledge, this is the first study that adapt and validate the WHOQOL-OLD tool in Ethiopia. This study has strengths, as the data collection and the validation were conducted both from experts and community-dwelling old age people, which could have decreased some bias. Data collection was conducted by experienced health extension workers and nurses.\n\nDespite these strengths, this research has few limitations. The primary weakness is the self-reported nature of the tool, which can lead to the under-or overrepresentation of results. Second, it was conducted among community-dwelling old age people in urban locations; as a result, the findings may not apply to those living in rural or institutional settings. Third, test-retest reliability and sensitivity to change of the instruments could not be tested due to the study's cross-sectional design.\n\n\nConclusion\n\nThe current study found that the translated Amharic versions of the WHOQOL-OLD tool indicated robust internal consistency and construct validity. The instrument can be utilized in routine care provision activities among the community-dwelling old age people in Bahir Dar, Northwestern Ethiopia. Other social care-providing organizations can also use the Amharic version of WHOQOL-OLD to estimate the impacts of their policies, services, or targeted interventions might have on elder people. However, since Ethiopia is a country of socio-cultural diversity, more research on multiethnic and multi-cultural issues is required.\n\n\nEthical approval\n\nThis research was conducted as part of a Ph.D. dissertation that received ethical approval from Bahir Dar University (R.N./IRB/003/2021). In addition, participantion was entirely voluntary, and every participant gave informed consent.\n\n\nAuthors’ contribution\n\nMuhye Ahmed planned the research, analyzed the data, and wrote the paper. Fentahun Netsanet was involved in the design, data analysis, manuscript preparation, and critical evaluation of the study. Both authors read and approved the final manuscript.",
"appendix": "Data availability\n\nDryad: Data from: Validation of Quality-of-Life assessment tool for Ethiopian old age people. https://doi.org/10.5061/dryad.zkh1893dq. 49\n\nThis project contains the following underlying data:\n\n- Quality of life SPSS data (spss.sav)\n\n- README data (MD document)\n\nThe study questionnaire. 49 This project contains the following extended data:\n\n- The study questionnaire 49\n\n\n\n- STROBE checklist- for quality of life as cross-sectional study. 49\n\nData are available under the terms of licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.\n\n\nAcknowledgements\n\nWe would like to thank Bahir Dar University for allowing us to perform this research. 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Resarch Sq. 2019; 1–26.\n\nTaherdoost H: Validity and Reliability of the Research Instrument; How to Test the Validation of a Questionnaire/Survey in a Research. IJARM. 2016; 5(3): 28–36. Publisher Full Text\n\nShariff NJ: Utilizing the Delphi Survey Approach: A Review. J. Nurs. Care. 2015; 04(03): 246–251. Publisher Full Text\n\nKyriazos TA: Applied Psychometrics: Sample Size and Sample Power Considerations in Factor Analysis (EFA, CFA) and SEM in General. Psychology. 2018; 09(08): 2207–2230. Publisher Full Text\n\nSeid AM, Babbel NF: Validation of Nutritional Assessment Tool for Ethiopian Old Age People. Int. J. Med. Public Heal. 2022; 12(4): 1–9.\n\nHambleton P, Keeling S, McKenzie M: The jungle of quality of life: Mapping measures and meanings for elders. Australas. J. Ageing. 2009; 28(1): 3–6. Publisher Full Text\n\nTheofilou P: Quality of Life: Definition and Measurement. Eur. J. Psychol. 2013; 9(1): 150–162. Publisher Full Text\n\nPaschoal SMP, Jacob Filho W, Litvoc J: Development of elderly quality of life index- EQOLI: Theoretical-conceptual framework, chosen methodology, and relevant items generation. Clinics. 2007; 62(3): 279–288. PubMed Abstract | Publisher Full Text\n\nBowling A: The Psychometric Properties of the Older People’s Quality of Life Questionnaire, Compared with the CASP-19 and the WHOQOL-OLD. Curr. Gerontol. Geriatr. Res. 2009; 2009(3): 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCaballero FF, Miret M, Power M, et al.: Validation of an instrument to evaluate quality of life in the aging population: WHOQOL-AGE. Health Qual. Life Outcomes. 2013; 11(1):1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFang J, Power M, Lin Y, et al.: Development of short versions for the WHOQOL-OLD module. Gerontologist. 2012; 52(1): 66–78. PubMed Abstract | Publisher Full Text\n\nWHO Quality of Life Assessment Group: What quality of life? The WHOQOL Group. World Health Forum. 1996; 17(4): 354–356.\n\nBowling A, Gabriel Z: Lay theories of quality of life in older age. Ageing Soc. 2007; 27(6): 827–848. Publisher Full Text\n\nLiu R, Wu S, Hao Y, et al.: The Chinese version of the world health organization quality of life instrument-older adults module (WHOQOL-OLD): Psychometric evaluation. Health Qual. Life Outcomes. 2013; 11(1): 156. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGonzález-celis AL, Gómez-benito J: Quality of life in the elderly: Psychometric properties of the WHOQOL-OLD module in Mexico. Health (Irvine Calif). 2013; 05(12A): 110–116. Publisher Full Text\n\nIBM Corp: IBM SPSS Statistics for Windows, Version 23.0. Armonk, NY: IBM Corp; 2015.\n\nArbuckle JL: IBM SPSS AmosTM 25 User’s Guide. Chicago: IBM SPSS; 2017.\n\nTerwee CB, Bot SDM, de Boer MR , et al.: Quality criteria were proposed for measurement properties of health status questionnaires. J. Clin. Epidemiol. 2007; 60: 34–42. Publisher Full Text\n\nKim HY, Nho JH, Kim JY, et al.: Validity and reliability of the Korean version of the world health organization quality of life instrument-older adults module. Geriatr Nurs (Minneap). 2021; 42(2): 548–554. PubMed Abstract | Publisher Full Text\n\nHair JF, Black WC, Babin BJ, et al.: Multivariate Data Analysis. 8th ed. United Kingdom: Annabel Ainscow; 2019.\n\nMorrison TG, Morrison MA, McCutcheon JM: Best Practice Recommendations for Using Structural Equation Modelling in Psychological Research. Psychology. 2017; 08(9): 1326–1341. Publisher Full Text\n\nShi D, Lee T, Maydeu-Olivares A: Understanding the Model Size Effect on SEM Fit Indices. Educ. Psychol. Meas. 2019; 79(2): 310–334. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVrieze SI: Model selection and psychological theory: A discussion of the differences between the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). Psychol. Methods. 2012; 17(2): 228–243. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaber KS: The Use of Cronbach’s Alpha When Developing and Reporting Research Instruments in Science Education. Res. Sci. Educ. 2018; 48: 1273–1296. Publisher Full Text\n\nRezaeipandari H, Morowatisharifabad MA, Mohammadpoorasl A, et al.: Cross-cultural adaptation and psychometric Validation of the World Health Organization quality of life-old module (WHOQOL-OLD) for Persian-speaking populations. Health Qual. Life Outcomes. 2020; 18(67): 1–7.\n\nMuhye A: Data from: Validation of Quality-of-Life assessment tool for Ethiopian old age people. Dataset. Dryad. 2023 [cited 2023 Jan 27]. Publisher Full Text"
}
|
[
{
"id": "208814",
"date": "22 Nov 2023",
"name": "Rozeta Drãghici",
"expertise": [
"Reviewer Expertise Gerontopsychology",
"Social Gerontology",
"Clinical Psychology"
],
"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 “Validation of Quality of Life assessment tool Ethiopian old age people” by Muhye and Fentahun (2023) was aimed at validating and adapting the World Health Organization Quality of Life for Older Adults questionnaire (WHOQOL-OLD) to the Ethiopian population. The results showed a successful validation of the translated instrument, which was easy to understand and respond to by the participants. The authors were very rigorous with their methodology and statistical analysis by taking into consideration all the necessary aspects. They also provided access to their data, thus making the results reproducible, which is an applauding effort as it promotes the principles of open science.\nThe clarity of writing and the structure of the paper represent the aspects that need some tweaking. For example, the introduction is quite short, and it could be improved by presenting and reviewing some papers that have tried to validate and adapt other questionnaires to the Ethiopian population, while explaining why WHOQOL-OLD is a better choice. Moreover, parallels between the prior-used methodology and the one chosen by the authors can be drawn to explain what this paper adds to it. It was noted that there is a section named “Review of existing quality of life assessment tools”, however this section was also incomplete as it did not explain why the other questionnaires do not work as well and how the WHOQOL-OLD overcomes this shortcomings.\nThroughout the paper, there were a couple of mentions regarding nutritionists and their help in this study, but the link between this paper aimed at validating a psychometric tool and the study involving a “mini nutritional assessment” is not clear. It could be of great interest to also focus on nutrition when assessing quality of life, especially when speaking of older adults that have many afflictions that require carefully-designed diets, but this needs to be expanded in writing. Lastly, the results should only be reported once, either in text or in a table, so it is not necessary to have both.\nThe paper shows good scientific efforts and validating questionnaires is not an easy endeavour. With some minor improvements, we believe your efforts will be even more obvious to the reader and thus, more appreciated. We wish you the best of luck with your research.\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": []
},
{
"id": "219042",
"date": "22 Nov 2023",
"name": "Clelia Oliveira Lyra",
"expertise": [
"Reviewer Expertise 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 manuscript analyses a valid and reliable quality of life (QOL) assessment tool based on the World Health Organization's Quality of Life Old module (WHOQOL-OLD) because there isn’t translation to Amharic (the widely spoken language in Ethiopia).\nThe manuscript is very important for science, especially in Ethiopia and countries that speak Amharic. It is well-written; however, 37/49 references aren't from the last five years. Because of this, it should be to increase the proportion of current literature (2019-2023). The methodology is appropriate, the results are well-described, and the conclusion meets the objectives.\nI suggest you remove the ± symbol, as described in the summary: The results showed a relatively low level of quality of life, with a total transformed score of 58.58±23.15” as they demonstrate the standard deviation. When representing the mean and its respective standard deviation, represent it this way: 58.58 (SD 23.15).\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": "10648",
"date": "28 Mar 2024",
"name": "Ahmed Muhye",
"role": "Author Response",
"response": "We appreciate the time and effort that the reviewer has dedicated to providing valuable feedback on our manuscript, \"Validation of Quality-of-Life Assessment Tool for Ethiopian Old Age People.\" My co-author and I have revised the manuscript accordingly and would like it to be reconsidered for indexing. Concerning the references, we have tried our best to use the current and in the last five years. However, the problems are: 1) there is a scarcity of research on the validity of tools for quality of life among old age people, and 2) we have done this research from January 16 to March 13, 2021. Hence, the references we used may seem old as we compare them to these years (2023). Finally, we are grateful to the reviewers for their insightful comments on our paper. Please let us know if anything further is required at this time, and we thank you very much for considering our revised manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/12-282
|
https://f1000research.com/articles/12-747/v1
|
26 Jun 23
|
{
"type": "Research Article",
"title": "Adsorption of Pb (II) ions on variable charge oxidic calcined substrates with chemically modified surface",
"authors": [
"José G. Prato",
"Fernando Millán",
"Marialy Rangel",
"Andrés Márquez",
"Luisa Carolina González",
"Iván Ríos",
"César García",
"Carlos Rondón",
"Enju Wang",
"Marialy Rangel",
"Andrés Márquez",
"Luisa Carolina González",
"Iván Ríos",
"César García",
"Carlos Rondón",
"Enju Wang"
],
"abstract": "Background: The adsorption process is an alternative method for treating natural and waste waters, with heavy metals. Oxidic lithological materials, rich in iron and aluminum amphoteric oxides, with pH-dependent surface charges, are a reliable medium for ionic adsorption. Being thermally resistant, these materials can be used to prepare a calcined substrate which is chemically treated in an acid or alkaline solution to enlarge surface positive or negative charge density, making it possible anion as well as cation adsorption reactions from aqueous solutions. Oxidic lithological materials use is a low-cost alternative for filtering system because of its availability and ease of preparation and application.\nMethods: Present paper shows results of the adsorption reaction of Pb+2 ions on calcined substrates prepared with oxidic lithologic material. The study was performed on the substrate with chemically modified surface in alkaline medium as well as on non-treated surface.\nResults: Results show L-type isotherms for the adsorption on the activated substrate, indicative affinity between adsorbate and adsorbent. Average value of adsorption capacity (k) for activated substrate is around 3.7 times greater (1791.73±13.06) compared to the respective average k value for the non-activated substrate (491.54±31.97), during the adsorption reaction, 0.35 and 0.26 mmolH+ of proton are produced on the activated and non-activated substrate respectively using a 1 mM Pb+2 solution and 72.2 and 15.6 mmolH+ using a 10 mM Pb+2 solution. This acidification agrees with the theoretic model of transitional metals chemisorption on amphoteric oxides of Fe, Al, Ti and Mn present in lithological material used for the preparation of adsorbent substrates confirming the information given by the L-type isotherms.\nConclusions: Results suggest that these oxidic lithologic materials show great potential as an alternative technique for water treatment and heavy metal retention from contaminated waters using a low-cost and reliable adsorption system.",
"keywords": [
"ionic adsorption",
"calcined substrate",
"Pb(II) ions",
"isotherms"
],
"content": "Introduction\n\nLead (Pb) is a toxic element with the greatest global distribution among heavy metals,1–3 it reaches water sources through various anthropogenic activities such as pipe corrosion, mining, oil refining, metal processing, glass production, battery manufacturing, among other industrial activities. Lead pipes were used regularly for water supply network until the seventies however, old constructions still remain and new residential buildings contain plumbing devices for water services.4–6 Recently lead-contaminated water in some High Schools in Brooklyn, New York has been detected at high concentrations, exceeding the Environmental Protection Agency’s (EPA’s) action level of 0.015 mg/L.4,5 Depending on the local water characteristics, such as pH, hardness and temperature, the lead in the pipes and faucets can dissolve, becoming a health risk for the consumers.6 However, lead contamination is also the consequence of non-treated industrial wastes from paintings, batteries, ceramics factories, and mining activities.2,3 Leaded fuels are still used in many South America countries with great impact to the environment.7\n\nThe conventional methods for removing heavy metals from water and sewage have been well described in literature.1,2,8–10 However, most of these industrial procedures are expensive and few supply companies can offer these systems. Some of them, such as precipitation, coagulation and sedimentation have disadvantages of generating sludge that requires further treatment, which increases operational costs. Non-conventional procedures have been investigated including the use of different types of biomass and organic adsorbents as agricultural by-products and its conversion to activated carbon,9,11,12 biopolymers.9,13 Some fungal biomasses have been used with 80 to 100 % percentage retention.14 Natural and synthetic zeolites have been also used for lead removal from water showing great affinity and selectivity.15,16 Amorphous nanoaluminophosphates have also been proved for lead removing from aqueous solution with efficiency between 40 and 70%,17,18 used rice straw derived biochar as amendment in variable charge soils for Pb immobilization, avoiding its run off through the soil and protect the rivers. Although most of these methods may be efficient, they are expensive and/or difficult application at medium and large scale.\n\nIn a previous study19–21 some oxidic lithological materials were described and characterized in order to use them for preparing a calcined substrate and apply it for ionic adsorption from aqueous solution. The high content of amphoteric iron and aluminium, as well as titanium and manganese oxides, with pH dependent variable charges surfaces. As a consequence of this particular property, these lithological materials are versatile for preparing calcined adsorbing substrates which have been applied in water softening,22–24 water treatment and organic matter removing.25,26 The study of copper and zinc adsorption on this kind of substrate revealed that these transitional metals participate in a specific chemisorption reaction which is pH dependent, especially copper ions.19,27 The last study suggests that other transitional metals may participate in similar kind of specific adsorption reaction. By means of acid treatment of calcined substrate, adsorption of oxyanions as sulphate and phosphate adsorption have also been reported in the literature.21,28,29 The main objective of the present work is to study the relative affinity between the oxidic calcined surface and Pb (II) ions, and its potentiality as water treatment system for lead ions removing.\n\n\nMethods\n\nThe raw oxidic lithological material (OLM) was collected from a natural deposit, a mine, 5 kg were extracted manually with the help of pickaxes and shovels in the coodinates 8o 28´47´´ N and 71o 23´47´´ W. This zone is an arid type, where the temperature varies between 17 and 30 oC along the year, and maximum rainfall of 200 mm per year. The OLM has already been chemically characterized,19–21 consisting mainly of Fe, Al as well as Ti and Mn which can form refratory amphoteric oxides. Due to its thermal resistence this lithologic material is used by potters for preparing bricks by thermal treatment.\n\nThe lithologic material was crushing using a rubber hammer so as not to destroy the mineral structures, and sieved for 5 minutes, using Octagon 200CL Digital Sieve Shaker (Endecotts Ltd, England) to obtain particle-size fractions of 800 μm, then mixed up with distillated water in order to obtain a homogeneous saturated paste with an easily moldable consistency. With the use of a 60 mL syringe, 3 mm diameter “spaghettis” are extruded and cut out into 5 mm long pieces, are dried in ambient air for 24 hours, then in a furnace at 150 oC another 24 hours (FELISA FE-293, Jalisco, Mexico). Finally, the dried solid adsorber is calcined up to 750 oC at the rate of 6.25 oC min-1, across four hours (Thermolyne FB141OM muffle, Thermo Scientific, Waltham, USA) and then cooled down for 12 hours, until 20 oC. The calcination process favors the oxides formation and cementation of the pellets to avoid dispersion in the aqueous solution. Also, during the calcination process, organic matter fraction, which is very small, is complete burned out, so only the oxidic phase participates in the adsorption reaction.\n\nThe calcined substrate is chemically treated in alkaline media with 0.1 N NaOH solution for 12 hours in a flask at room temperature, in order to enlarge the negative charge density on the surface because of the oxide deprotonation reaction. The product is then called activated substrate. (The non-treated substrate is labeled with the name of non-activated substrate). After this time the substrate is washed out with distilled water until neutral pH is achieved, then dried in the furnace at 120 oC for 12 hours.\n\nAdsorption studies\n\nThe adsorption study was performed in triplicate in isothermal conditions (20 ± 2 oC) using batch equilibration procedure, treating 2 g of activated and non-activated calcined substrate, with increasing volume of 5, 10, 15, 20, 25, 30 and 40 mL of 0.001 M Pb+2 solution, prepared from CH3COOPb analytical grade Merck reagent, during 24 hours. in 100 mL glass beakers. Suspensions were periodically shaken every hour. Differences between Ci and Ceq were assumed to be due to adsorption. Adsorption isotherms were obtained by plotting the amount of lead adsorbed (qe), against the Pb+2 equilibrium concentration (Ceq) and fitted to the linear forms of the Freundlich and Langmuir equations.21,30–33\n\nFreundlich Isotherm is an empirical model which assumes an adsorption process characterized by multy layer adsorption on heterogeneous surfaces. The model is described by the equation 1 and the linear form by equation 2.21,30,31 A graph representation of log (qe) vs log (Ceq) is a straight line, with slope equal to n and intercept equal to log (KF):\n\nIn equations (1) and (2), qe is the amount adsorbed per adsorbent weight unit, Ceq is the equilibrium concentration of adsorbate in solution after adsorption, KF is the Freundlich constant related to adsorption capacity, and n is a constant related to adsorption intensity or energetic homogeneity of active sites of adsorption. n may take values near unity or greater. The lower the value of n is, the lower the energy heterogeneity in the active adsorption sites.\n\nThe Langmuir model describes a reversible process with the formation of adsorbate monolayers on the adsorbent surface. The nonlinear and linear forms of the Langmuir isotherm are described in Equations (3) and (4)21,22,33:\n\nIn equations (3) and (4), qm is the adsorption capacity, which represents the maximum amount of adsorbate in a monolayer, and KL is the Langmuir constant related to the affinity between adsorbate and adsorbent. The parameters of the isotherm are obtained by plotting 1/qe versus 1/Ceq, resulting in a straight line with slope equal to 1/KL*qm and the intersection equal to 1/qm.\n\nThe best fit between the isotherm function and the experimental data was verified by carrying out linear regressions of the isotherm linear equation. In addition, the adjustment of each isotherm was verified by comparing the experimental value obtained from the amount adsorbed (qe exp) with the value obtained by calculating it by means of the isotherm equation (qe calc) and determined the linear correlation between the two values given by the linear regression coefficient (r).\n\nLead analysis\n\nPb+2 analyses were performed with a Varian Graphite Furnace Atomic Absorption Spectrophotometer, Spectra AA Zeeman 220, with a pyrolytic coated graphite tube (Palo Alto, California, USA). The spectrophotometer is dotted with a Varian auto sampler model EL-97113008. A Varian Uranium hollow cathode lamp was used.\n\npH and electric conductivity studies\n\nSolution pH and electric conductivity (EC) variations were studied, in triplicate, using the same isothermal batch equilibration procedure, as in adsorption study. pH was measured with a HI 211 pHmeter (HANNA instruments, Smithfield, Rhode Island, USA), calibrated with commercial buffer solutions of pH 4 and 7. EC was measured with a Trans Instrument HC3010 Conductimeter (Petro Centre, Bukit Merah, Singapure), calibrated with standard reference. All experimental data34 were worked out with the Excel software (Microsoft, Los Angeles, USA)\n\n\nResults\n\nFigure 1a shows the adsorption isotherms of Pb+2 ions on the activated and non-activated substrates. There are two relevant aspects to consider. First of all, the isotherm profiles show but don´t confirm information which kind of interaction between Pb+2 ions and substrate surface may take place. In addition, the system under study coincides with a L-type isotherm, that is, at low equilibrium concentrations the amount adsorbed increases rapidly, while at high concentrations it decreases, due to the fewer adsorption sites available on the adsorbent].\n\nFigure 1b shows linear fitting of adsorption data to the Freundlich model for the activated and non-activated substrates, while the Table 1 shows the fitted equations according to the Freundlich model, r, KF, and n values for activated and non-activated substrates, by triplicated trials. In both cases data present relatively good linearity, r being more favorable for the activated substrate, the negative charge density on the surface is likely to be more homogeny than in non-activate substrate.\n\nFreundlich parameters are different for the activated substrate compared with the adsorption on the non-activated substrate. Average value of KF, for activated substrate is around 3.7 times greater (1791.73 ± 13.06) with a relative standard deviation (RSD) of 0.72 %, compared to the respective average KF value for the non-activated substrate (491.54 ± 31.97 with an RSD of 6.5 %). Similarly, the n values suggest greater adsorption intensity on the activated substrate in relation to the non-activated substrate. The smallest negative charge density on the non-activated substrate surface is a limiting factor for the adsorption of Pb+2 ion.\n\nHowever, to prove adjustment to the model it is also necessary to show how good experimental data fit to the theoretic model. Figure 2 shows the graphical correlation between calculated and experimental qe data for the activated and non-activated substrates. Table 2 shows fitted equations for the linear functions. There is good linear correlation showing acceptable adjustment with the Freundlich model. However, calculated values of qe are biased from the experimental data. The average difference is about 15.16 ± 6.63 % in the case of the activated substrate and 17.41 ± 18.15 % for the non-activated substrate.\n\nFigure 3 shows adsorption data fitting according to the Langmuir model and Table 3 shows fitted equations and values of r, k1 and k2 values for the activated and non-activated substrates, by triplicated. The experimental data shows great reproducibility, correlation coefficients are more satisfactory for the activated substrate in relation with the non-activated substrate. The K1 value for the activated substrate is about 20 times greater than for the non-activated substrate.\n\nFigure 4 show the graphical correlations between calculated and experimental values of qe for the activated and non-activated substrates and Table 4 shows fitted equations for the linear functions. There is also good linear correlation between calculated and experimental data however, calculated values of qe are even more biased from the experimental data compared with the Freundlich model. The average difference is 25.29 ± 23.67 % in the case of the activated substrate and 27.22 ± 16.02 % for the non-activated substrate.\n\nFigure 5 shows pH variation during adsorption reaction of Pb+2 ions on raw material, non-activated and activates substrates, by triplicate, from a 1 mM Pb+2 ions solution. In all cases adsorption reaction take place with production of protons and solution acidification. Experiments are highly reproducible, so reaction takes place through the same mechanism in all the replicates.\n\nFigure 6 shows pH variation, by triplicate, as a function of mmol of Pb+2 added to 2 g of substrate from a 1 mM Pb+2 solution, for raw material, activated and non-activated substrate. On the calcined substrates, the reaction takes place at lower pH values, so there are more active sites for the adsorption reaction to occur, with a higher production of protons.\n\nTable 5 shows initial and final concentrations of H+ ions during the adsorption reaction of Pb+2 ions and the net amount of mmol of H+ ions produced in the whole reaction, when a 1 mM Pb+2 solution is used. Adsorption reaction on raw material produces 0.29 μmol of H+ and 0.26 μmol on non-activated substrate. However, adsorption reaction on activated substrate produces 0.35 μmol of H+ ion, which is 1.4 times greater than in the case of non-activated substrate.\n\nFigure 7 shows EC, variation, by triplicate, during adsorption reaction of Pb+2 ions on raw material and non-activated and activates substrates, when a 1 mM Pb+2 solution is used for the reaction of adsorption. EC in the solution is basically produced by ions in the solution, i.e., CH3COO- and Pb+2 ions, as well as H+ ions produced in the adsorption reaction. As EC decreases, it suggests that Pb+2 ions are adsorbed on the substrates surfaces, as well as on the raw material. The adsorption reaction produces ion immobilization being unable to make a net contribution to the EC of the solution.\n\nFigure 8 shows a comparative view of the EC of the solutions for all three cases when a 1 mM Pb+2 solution is used. Although conductivity decrease due to adsorption of Pb+2 ions, solution in contact with activated substrate present greater conductivity due to the highest production of H+ ions during the adsorption reaction. These H+ ions have a net contribution to the EC of the solution producing an increasing of the conductivity in the solution which is in contact with the substrates.\n\nFigure 9 shows pH variation, by triplicate, during adsorption reaction of Pb+2 ions on raw material, non-activated and activates substrates, from a 10 mM of Pb+2 ions solution. As in the former cases, the reaction also produces acidification of the solution in contact with the substrates due to the production of H+ ions, which also increases as the concentration of Pb+2 ions increases.\n\nFigure 10 shows comparative pH variations during adsorption reaction on the raw material as well an on the activated ad non-activated substrates when a 10 mM of Pb+2 solution is used. As it can be observed, the acidification process is more accentuated in the case of the adsorption reaction on the activated substrate, as is expected. The similarity of the curves is indicative that the experiments are highly reproducible as in the previous case (Figure 9), so reaction takes place through the same mechanism in all the replicates.\n\nTable 6 shows initial and final concentrations of H+ ions during the adsorption reaction of Pb+2 ions and the net amount of mmol of H+ ions produced in the whole reaction, when a 10 mM Pb+2 solution is used. Adsorption reaction on raw material produces 23.3 μmol of H+ ion and 15.6 μmol of H+ on non-activated substrate. However, adsorption reaction on activated substrate produces 72.2 μmol of H+ ion which is 4.6 times greater than in the case of non-activates substrate and 3 times greater than in the case of adsorption reaction on crude material. Moreover, this amount of H+ ions is almost 200 times greater than in the former case when a 1 mM Pb+2 solution is used for adsorption reaction.\n\nFigures 11 and 12 shows EC, variation by triplicate, during adsorption reaction of Pb+2 ions on raw material and non-activated and activates substrates, when a 10 mM Pb+2 is used. As it was pointed out in the former case, EC in the solutions decreases, because Pb+2 ions are adsorbed on the substrate’s surfaces, as well as on the crude material. Nevertheless, the decreasing of the EC in the solutions in contact with the crude material and non-activated substrate is greater due to the minor production of H+ ion during the adsorption reaction, while the EC is greater in the solution in contact with the activated substrate.\n\n\nDiscussion\n\nThe amphoteric oxides of Fe, Al, Mn and Ti presents on the substrate surface, might modify surface charges according to pH value, that is to say, in alkaline media, a deprotonation reaction of the oxides take place, increasing surface negative charge density, contrary, in acid media, surface oxide protonation occur, increasing positive charge density according to equation (5)35–37:\n\nLiterature22,28,36,38 also suggests a mechanism for the adsorption of transitional metals on these kind of surfaces, through the formation of an inner sphere complex between metal ion and the oxidic surface, according to the equation (6)\n\nSuch a kind of reaction modifies surface charge increasing the positive charge density with the formation of H3O+ ion, which could let to anion adsorption producing acidification. This kind of adsorption is defined as specific adsorption or chemisorption, presenting great tendency to irreversibility.36\n\nThe isotherm profiles, as it was pointed out before, suggest but don’t confirm information about the interaction between Pb+2 ions and calcined substrate surface, however L-type isotherm is indicative of great affinity between Pb+2 ions and calcined substrate surfaces,31,32,38,39 and suggests chemisorption between de Pb+2 ions and the oxidic surface. Literature report similar type of isotherms for other transitional metals as copper in similar kind of substrates27,40 and variable charge substrate.41–43 In general, the adsorption phenomenon is most intensive on activates surfaces just because the alkaline solution produces the deprotonation of the oxides, generating negative charges on adsorbent substrate surface according to reaction (5). Therefore, the probability for the Pb+2 ion adsorption is greater on the activated substrate than on the non-activated substrate.\n\nThe flat part of the curve (Figure 1a) suggests formation of a saturated monolayer of Pb+2 ions on the surface as is predicted by the Freundlich and Langmuir models and chemisorption should occur on a single monolayer. This type of isotherm, points to the formation of a covalent bond between Pb+2 ions and the substrate surface that is formed by amphoteric metallic oxides as iron, aluminum, titanium and manganese oxides with variable surface charges.19,26,37,43\n\nHowever, the Langmuir model has its own limitations when used to explain the adsorption process on non-homogeneous surfaces. This model was developed for gas adsorption on homogeneous surfaces; therefore, the model might fail when adsorption take place on irregular surfaces. One of the disadvantages of this model is to assume the formation of a monolayer on a homogeneous surface where all the available sites for the adsorption are equivalent and the ΔHad is independent of the degree of surface coverage. However, on a non-homogeneous or irregular surface the adsorption sites are non-equivalent and the ΔHad varies from one place to another. Consequently, those places which led to a more stable bonding are first occupied. The interaction between adsorbed molecules might affect the affinity between the adsorbate and adsorbent, and as surface coverage increases ΔHad decreases and also increases the repulsion between the adsorbed molecules. Which at the same time might causes the mobility of the molecules through the surface and different places can be occupied. As a result, a physisorbed layers can be formed over the chemisorbed layer.31,33,38,39\n\nOn the contrary Freundlich model adapts better to non-homogeneous surfaces, consequently, the adsorption from aqueous phase on non-homogeneous or irregular surfaces like the calcined substrate surface, the Freundlich model fits better.21,31–33,38\n\nThe pH measurements during the adsorption reaction showed a significant acidification along the reaction, which agree with the literature35–37,42 about transitional metals chemisorption on amphoteric surface with variable charge. This acidification process became more intense as the concentration of Pb+2 ions in the solution increases. These facts, the type of adsorption suggested by the isotherm and the acidification process, could be interpreted in terms of a covalence formation between Pb+2 ions and the calcined substrate in a specific adsorption reaction or chemisorption, according to the model presented in the equation 7 suggest by the literature.19,27,35\n\nAccording to the results in this investigation, the adsorption reaction is more favorable on the activated substrate where more adsorption active sites are available. The small negative charge density on the non-activated substrate is a limiting factor for the adsorption to occur. Similar results have been reported in the literature for the adsorption of Cu+2 ions.27,40,43 Therefore, it is expected that other transitional metals can suffer such a kind of reaction on the surface of these kinds of substrates, being possible their separation from contaminated waters during a filtration process in a granular media.\n\nIn general, adjustment data by Freundlich and Langmuir models fits well with experimental data, especially for activated adsorbent substrates. However, in both cases calculated values are biased from the experimental data, especially for the Langmuir model, probably because on the irregular and roughness surface. This represent less homogeneity of the negative charge density on the surface, so not all adsorbent positions are equivalent. Therefore, the condition that surfaces must have positions for adsorption, which are all equivalents and only one molecule or ion can occupy one single place is no longer fulfilled. In fact, both models pursue to explain the same type of isotherm but Freundlich is an empirical model with less straightening conditions compared to the Langmuir which was developed on valuable ideal theoretical considerations difficult to respect in the case of the calcined substrate.\n\nNot applicable.",
"appendix": "Data availability\n\nFigshare: Adsorption of Pb (II) ions on Variable Charge Oxidic Calcined Substrates with Chemically Modified Surface https://doi.org/10.6084/m9.figshare.22266772.v2. 34\n\nThis project contains the following underlying data:\n\n- Study Adsorption Pb Freundlich model.xlsx\n\n- Study Adsorption Pb Langmuir model.xlsx\n\n- Study Adsorption Pb H+ produced.xlsx\n\n- Study pH Adsorption Pb.xlsx\n\n- Study CE Adsorption Pb.xlsx\n\n\nAcknowledgements\n\nThe authors give thanks to the Universidad Nacional de Chimborazo for supporting this work through the research projects program\n\n\nReferences\n\nXie Y, Yuan X, Wu Z, et al.: Adsorption behavior and mechanism of Mg/Fe layered double hydroxide with Fe3O4-carbon spheres on the removal of Pb (II) and Cu (II). J. Colloid Interface Sci. 2019; 536: 440–455. Publisher Full Text\n\nNiu Y, Qu R, Sun C, et al.: Adsorption of Pb (II) from aqueous solution by silica-gel supported hyperbranched polyamidoamine dendrimers. J. Hazard. Mater. 2013; 244-245: 276–286. Publisher Full Text\n\nKaur M, Kumari S, Sharma P: Removal of Pb (II) from aqueous solution using nanoadsorbent of Oryza sativa husk: Isotherm, kinetic and thermodynamic studies. Biotechnol. Rep. 2020; 25: e00410. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLatham S, Jennings JL: Reducing lead exposure in school water: Evidence from remediation efforts in New York city public schools. Environ. Res. 2022; 203: 111735. PubMed Abstract | Publisher Full Text\n\nRabin R: The lead industry and lead water pipes “A modest campaign”. Am. J. Public Health. 2008; 98: 1584–1592. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSantucci RJ Jr, Scully JR: The pervasive threat of lead (Pb) in drinking water: Unmasking and pursuing scientific factors that govern lead release. Proc. Natl. Acad. Sci. U. S. A. 2020; 117(38): 23211–23218. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNdungu K, Zurbrick CK, Stammerjohn S, et al.: Lead sources to the Amundsen Sea, West Antarctica. Envirom. Sci. Technol. 2016; 50(12): 6233–6239. Publisher Full Text\n\nCaviedes Rubio DI, Muñoz Calderón RA, Perdomo Gualtero A, et al.: Tratamientos para la remoción de metales pesados comúnmente presente en aguas residuales Industriales: Una revisión. Revista Ingeniería y Región. 2015; 13(1): 73–79. Publisher Full Text\n\nAlghamdi AA, Al-Odayni AB, Saeed WS, et al.: Efficient adsorption of lead (II) from aqueous phase solutions using polypyrrole-based activated carbon. Materials. 2019; 12(12): 2020. Publisher Full Text\n\nRenu, Agarwal M, Singh K: Heavy metal removal from wastewater using various adsorbents: A review. J. Water Reuse Desal. 2017; 7(4): 387–419. Publisher Full Text\n\nSherugar P, Padaki M, Naik NS, et al.: Biomass-derived versatile activated carbon removes both heavy metals and dye molecules from wastewater with near-unity efficiency: Mechanism and kinetics. Chemosphere. 2022; 287: 132085. PubMed Abstract | Publisher Full Text\n\nShi Q, Sterbinsky GE, Prigiobbe V, et al.: Mechanistic study of lead adsorption on activated carbon. Langmuir. 2018; 34: 13565–13573. PubMed Abstract | Publisher Full Text\n\nLv QV, Hu X, Zhang X, et al.: Highly efficient removal of trace metal ions by using poly (acrylic acid) hydrogel adsorbent. Mater. Des. 2019; 181: 107934. Publisher Full Text\n\nEnamorado Horrutiner Y, Villanueva Tagle M, Hernández Díaz I, et al.: Caracterización de biomasa inactiva de Aspergillus Niger 0-5 como sorbente de Pb (II). Quím. Nova. 2011; 34(7): 1141–1146. Publisher Full Text\n\nCashin VB, Eldridge DS, Yu A, et al.: Surface functionalization and manipulation of mesoporous silica adsorbents for improved removal of pollutants: A review. Environ. Sci. Water Res. Technol. 2018; 4: 110–128. Publisher Full Text\n\nYuna Z: Review of the natural, modified, and synthetic zeolites for heavy metals removal from wastewater. Environ. Eng. Sci. 2016; 33: 443–454. Publisher Full Text\n\nRondón W, Sifontes AB, Freire D, et al.: Remoción de plomo en soluciones acuosas empleando nanoaluminofosfatos amorfos. Rev. Ambient. Água. 2015; 10(1): 59–70. Publisher Full Text\n\nJiang TY, Jiang J, Xu RK, et al.: Adsorption of Pb (II) on variable charge soils amended with rice-straw derived biochar. Chemosphere. 2012; 89(3): 249–256. PubMed Abstract | Publisher Full Text\n\nMillán F, Prato JG, García M, et al.: Adsorción de iones Cu+2 y Zn+2 por materiales litológicos de carga variable, provenientes de suelos del estado Mérida, Venezuela. Rev. Téc. Ing. Univ. Zulia. 2013; 36(3): 195–201.\n\nMillán F, Zerpa D, Prato JG, et al.: Caracterización química de tres fracciones granulométricas de materiales litológicos oxídicos. In extensu Publication. Proceedings of XXI Congreso de la Sociedad Venezolana de la Ciencia del Suelo. UNET, San Cristóbal. 2015. 978-980-6300-94-1. Reference Source\n\nPrato JG, Millán FC, González LC, et al.: Adsorption of phosphate and nitrate ions on oxidic substrates prepared with a variable-charge lithological material. Water. 2022; 14: 2454. Publisher Full Text\n\nPrato JG, Millán F, Ríos A, et al.: Uso de materiales litológicos oxídicos para la dureza en aguas naturales. Inf. Tecnol. 2022; 33(2): 145–156. Publisher Full Text\n\nMillán F, Prato JG, López MA, et al.: Estudio de la retención de iones calcio por materiales térmicamente modificados provenientes de suelos de la región de San Juan de Lagunillas, estado Mérida, Venezuela. Rev. Téc. Ing. Univ. Zulia. 2009; 32(1): 48–54.\n\nPrato JG, González-Ramírez LC, Pérez MC, et al.: Adsorción de la dureza del agua sobre lechos de rocas volcánicas de Ecuador. Inf. Tecnol. 2021; 32(2): 51–60. Publisher Full Text\n\nMillán F, Prato JG, Montilla T, et al.: Using of variable charge adsorption beds for filtration of residual waters. Rev. Téc. Ing. Univ. Zulia. 2018; 41(1): 98–110.\n\nPrato J, Millán F, González L, et al.: Evaluación de materiales litológicos oxídicos como adsorbentes para el tratamiento de efluentes y aguas residuales. Novasinergia. 2021; 4(2): 93–110. Publisher Full Text\n\nMillán F, Prato JG, González L, et al.: Cu+2 chemisorption on calcined substrates made with an oxidic refractory variable charges lithological material. Rev. Téc. Ing. Univ. Zulia. 2019; 42(1): 10–18.\n\nPrato JG, Ruiz LB, Djabayan P, et al.: Adsorción de iones fosfatos de aguas naturales a partir de lechos calcinados de suelos lateríticos. Arboleda JR, editor. Investigación y Academia: la Visión desde la Universidad Ecuatoriana. Red Iberoamericana de Pedagogía (REDIPE); 2019; (pp. 133–151). Cap. 8.\n\nPrato JG, Navas SA, Ríos AC: Adsorción de iones SO42- en aguas naturales empleando lechos de arcilla amarilla.García VJ, Márquez CO, Giménez E, et al., editors. Avances en Ingeniería 2021. Ediciones Universidad Nacional de Chimborazo (Unach); 2022; (pp. 205–222). Cap. 9. Publisher Full Text\n\nDahliyanti A, Yunitama DA, Rofiqoh IM, et al.: Synthesis and characterization of silica xerogel from corn husk waste as cationic dyes adsorbent. F1000Res. 2022; 11(305): 305. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFoo KY, Hameed BH: Insights into the modeling of adsorption isotherm systems. Chem. Eng. J. 2010; 156: 2–10. Publisher Full Text\n\nAl-Ghouti MA, Da’ana DA: Guidelines for the use and interpretation of adsorption isotherm models: A review. J. Hazard. Mater. 2020; 393: 122383. PubMed Abstract | Publisher Full Text\n\nKalam S, Abu-Khamsin SA, Kamal MS, et al.: Surfactant adsorption isotherms: A review. ACS Omega. 2021; 6: 32342–32348. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPrato J, Millán F, González Ramírez LC, et al.: Adsorption of Pb (II) ions on Variable Charge Oxidic Calcined Substrates with Chemically Modified Surface. [Data]. Figshare. 2023. Publisher Full Text\n\nMcBride MB: Environmental chemistry of soils. Oxford: Ed. Oxford Univ; 1994.\n\nQafoku NP, Van Ranst E, Noble A, et al.: Variable charge soils: Their mineralogy, chemistry and management. Adv. Agron. 2004; 84: 159–215. Publisher Full Text\n\nXu RK, Qafoku NP, Van Ranst E, et al.: Adsorption properties of subtropical and tropical variable soils: Implication from climate change and biochard amendment. Adv. Agron. 2016; 135: 1–58. Publisher Full Text\n\nAdamson A: Physical chemistry of surfaces. 5th ed; England: Wiley Interscience Publications; 1990; 421–426.\n\nMasel R: Principles of adsorption and reaction on solid surfaces. England: Wiley Interscience publications; 1996; 235–248.\n\nMillán F, Prato JG, Zerpa D, et al.: Copper adsorption on calcined substrates from three granulometric fractions coming from two refractory variable charges lithological materials. International Journal of Recent Development in Engineering and Technology. 2017; 6(8): 7–17.\n\nJiang J, Xu RK, Li SZ: Effect of ionic strength and mechanism of Cu (II) adsorption by Goethite and γ – Al2O3. J. Chem. Eng. Data. 2010; 55: 5547–5552. Publisher Full Text\n\nYang JK, Lee SM, Davis AP: Effect of background electrolytes and pH on the adsorption of Cu (II) /EDTA onto TiO2. J. Colloid Interface Sci. 2006; 295: 14–20. PubMed Abstract | Publisher Full Text\n\nGu S, Kang X, Wang L, et al.: Clay mineral adsorbents for heavy metal removal from wastewater: A review. Environ. Chem. Lett. 2019; 17(2): 629–654. Publisher Full Text"
}
|
[
{
"id": "183567",
"date": "05 Sep 2023",
"name": "Nicolae Dinca",
"expertise": [
"Reviewer Expertise chemistry"
],
"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 work is topical because it scientifically substantiates the possibility of valorizing some indigenous raw materials in the process of purifying residual waters containing Pb+2 resulting from human activity.\nThe experimental design described on page 4 above, considers the sample volume as a variable factor and the constant Pb+2 concentration (0.001 M), while the results suggest that the sample volume is constant and the concentration is variable. I believe that the confusing text from Methods Adsorption studies (page 4, lines 6-8) should be corrected.\nCi is not defined in the text (page 4, line 8).\nIf the values of column n in Table 1 are well calculated, then they do not correspond to equations (1) and (2) in the form of the work dated 26 Jun 2023, 12:74. I believe that these equations should be corrected by replacing n with 1/n.\nFig.1 indicates that at low and medium initial (Ci) Pb+2 concentrations, the adsorption speeds (at 24h) are higher for the activated material.\nOn page 6, line 5, k1 and k2 appear which are not defined in the text and do not appear in eqs. (3-4). K1 (page 6 line 7) is identical to k1 from line 5?\nTechnological perspectives that could complement the conclusions (optional):\nThe isotherms in Fig. 1 show that an optimal option in practical applications would be the use of two ion exchange columns linked in series: the first one containing non-activated substrate (cheaper) and the second one containing activated substrate.\n\npH and conductivity measurements can be accessible technical options for monitoring the purification process.\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": "10255",
"date": "03 Apr 2024",
"name": "JOSE PRATO MORENO",
"role": "Author Response",
"response": "We thank the reviewer for the importance has given to our research, the time spent correcting the manuscript, their knowledge, experience, and willingness to improve the article. Comment 1: The experimental design described on page 4 above, considers the sample volume as a variable factor and the constant Pb+2 concentration (0.001 M), while the results suggest that the sample volume is constant and the concentration is variable. I believe that the confusing text from Methods Adsorption studies (page 4, lines 6-8) should be corrected. Response 1: Seven samples of 2 g of substrate, activated and non-activates, were treated with increasing aliquots of 5, 10, 15, 20, 25, 30 and 40 mL of a 1 mM Pb+2 solution. Samples are let to stand, in isothermal conditions, during 24 hours, and periodically shacked. So, the number of millimoles in each one of the samples is known. Comment 2: Ci is not defined in the text (page 4, line 8). Response 2: It is corrected, defining Ci in the text, section on adsorption studies. Comment 3: If the values of column n in Table 1 are well calculated, then they do not correspond to equations (1) and (2) in the form of the work dated 26 Jun 2023, 12:74. I believe that these equations should be corrected by replacing n with 1/n. Response 3: “n” values are god, what is wrong is equation 2, where exponential term is not n but 1/n. therefore, equations 1 and 2 become: Comment 4: Fig.1 indicates that at low and medium initial (Ci) Pb+2 concentrations, the adsorption speeds (at 24h) are higher for the activated material. Response 4: Taking into account the observation made, the wording has been modified regarding Fig 1, in the results and discussion sections: Results: Isotherm graph Figure 1a shows the adsorption isotherms of Pb+2 ions on the activated and non-activated substrates. Although the isotherm profile shows but doesn't confirm information about of the interaction between Pb+2 ions and substrate surface, L-type isotherm is associated with great affinity between sorbent and sorbate. At low equilibrium concentrations, the amount adsorbed increases rapidly, while at high concentrations it decreases, getting to a saturation zone. At low concentration non-activated substrate shows less affinity for Pb+2 ions compared to activated substrate, however, at higher concentration the adsorption isotherm become linear increasing Pb+2 adsorption. It might suggest collateral mechanism for the lead ions adsorption. Discussion: Figure 1a, shows the isotherm for non-activated substrate. At low concentrations, a similar kind of adsorption but much less intense, showing less affinity for Pb+2 adsorption. However, at higher concentrations, adsorption increases according to a linear model. Most likely acetate ions, being strong base, deprotonates oxides in favor of Pb+2 adsorption, according to the reaction (7) FeOH + CH3COO¯ → FeO¯+ CH3COOH Therefore, adsorption of Pb+2 ions take place after oxide deprotonation via acetate ion, according to a multilayer physic adsorption model. After all, acetate ions, being a strong base, might compete in the oxide deprotonation to form molecular acetic acid. Comment 5: On page 6, line 5, k1 and k2 appear which are not defined in the text and do not appear in eqs. (3-4). K1 (page 6 line 7) is identical to k1 from line 5?. Response 5: k1 and k2 have been defined in the text and equations 3 and 4 have been adjusted, as detailed below: In equations 3 and 4, qe is the amount adsorbed per adsorbent weight unit, Ceq is the equilibrium concentration of adsorbate in solution after adsorption, k1 is the Langmuir constant related to the affinity between adsorbate and adsorbent, and k2 is the adsorption capacity, which represents the maximum amount of adsorbate in a monolayer. The parameters of the isotherm are obtained by plotting Ceq/qe versus Ceq, resulting in a straight line with slope equal to 1/(k1*k2) and the intersection equal to 1/k2. Thank you again for your review. Sincerely, José G. Prato, Fernando Millán, Marialy Rangel, Andrés Márquez, Luisa Carolina González, Iván Ríos, César García, Carlos Rondón, Enju Wang"
}
]
},
{
"id": "196304",
"date": "03 Nov 2023",
"name": "Wei Wang",
"expertise": [
"Reviewer Expertise Mineral material",
"adsorption",
"catalyst"
],
"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 presents the adsorption of Pb (II) ions on variable charge oxidic calcined substrates with chemically modified surface. Authors should consider the following observations:\n\n1. Include some novel findings as in numerical results in abstract.\n\n2. The quality of the data analysis is not solid enough.\n\n3. The adsorption mechanism was important and needed to discuss in-depth with characterization support.\n\n4. Compare the present research with the previous literatures.\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? Yes",
"responses": [
{
"c_id": "11160",
"date": "13 Apr 2024",
"name": "JOSE PRATO MORENO",
"role": "Author Response",
"response": "We thank to the reviewer for their comments Comment 1: Include some novel findings as in numerical results in abstract. Response 1: The abstract has undergone revision, corrected and structured in accordance with the journal's guidelines. The reported values in the results paragraph, correspond to the main quantitative data obtained in the research. Comment 2: The quality of the data analysis is not solid enough. Response 2: The manuscript underwent a comprehensive review, leading to enhancements in the presentation of results through the implementation of valuable recommendations provided by the reviewers. Comment 3: The adsorption mechanism was important and needed to discuss in-depth with characterization support. Response 3: The OLM has undergone both physical and chemical characterization, with the results referenced in the published and cited literature. However, the authors have chosen to incorporate some of these findings into the methodology section. Furthermore, in response to the reviewer's valuable suggestions, the enhancement of adsorption results analysis has been achieved. Notably, particular attention has been given to incorporating material characterization in the analysis. Comment 4: Compare the present research with the previous literatures. Response 4: The results have been compared with other reported investigations and have been added to the paper. Thank you again for your review. Sincerely, José G. Prato, Fernando Millán, Marialy Rangel, Andrés Márquez, Luisa Carolina González, Iván Ríos, César García, Carlos Rondón, Enju Wang"
}
]
},
{
"id": "196306",
"date": "03 Nov 2023",
"name": "Titus Chinedu Egbosiuba",
"expertise": [
"Reviewer Expertise Materials synthesis for wastewater treatment",
"Adsorption studies",
"Kinetic and Isotherm models",
"Reusability study and the Mechanism of adsorption studies."
],
"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\nF1000 Research Review The study reported “Adsorption of Pb (II) ions on variable charge oxidic calcined substrates with chemically modified surface”. The authors prepared oxidic calcined and chemically modified substrates for the removal of Pb (II) ions from wastewater. I recommend the reconsideration of the manuscript for approval after the following comments are addressed:\nComments\nThe language of the manuscript must be improved by a native English editor. There are a number of grammatical errors.\n\nI suggest the addition of continuous line numbering to enhance review effectiveness.\n\nThe abstract must be summarized and rewritten to briefly capture the background, aim of the study, methodology, key results, and the main conclusion. Additional quantification of the results in the abstract is recommended.\n\nIn the introduction, describe the hazardous effects of the Pb(II) ions heavy metals. The suggested literatures can guide the authors.\n\nI suggest the addition of more treatment techniques such as photocatalysis, adsorption, advanced oxidation process, membrane filtration. Also, each of the mentioned techniques must be referenced. The recommended literature can guide the authors.\n\n2nd paragraph: “Amorphous nanoaluminophosphates have also been proved for lead removing from…” I suggest removing be changed to removal. The entire statement must also be rephrased accordingly.\n\nHow was the OLM chemically characterized and where are the results?\n\nUnder the preparation of adsorbent, “The lithologic material was crushing…” Crushing or crushed?\n\nWhy use furnace to dry at 150 oC. Is drying done with furnace or oven?\n\nHow is oxides formation favored by calcination? Reference please.\n\nKindly remove this statement from the bracket. “(The non-treated...substrate).\n\nThe suggested literatures can be used to reference the model equations.\n\nBe consistent in the use of either Pb(II) ions or Pb+2.\n\nI suggest the removal of grid lines from the graphs.\n\nTable 1 and 3 shows the Freundlich and Langmuir isotherm parameters, not fitted equations.\n\nMerge Table 1 and 2. Evaluate the qe parameter and present in Table 1.\n\nAlso merge Table 3 and 4.\n\nUnder pH and electric conductivity study, “….and activates substrates” Is it activates or activated?\n\nThere is no conclusion at the end of the manuscript, is that the journal format?\n\nI recommend the following references must be added to enrich the manuscript1-18.\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? No",
"responses": [
{
"c_id": "11161",
"date": "13 Apr 2024",
"name": "JOSE PRATO MORENO",
"role": "Author Response",
"response": "We thank to the reviewer for their comments Comment 1: The language of the manuscript must be improved by a native English editor. There are a number of grammatical errors. Response 1: The linguistic aspects of the manuscript in English have undergone a review and necessary corrections. Comment 2: I suggest the addition of continuous line numbering to enhance review effectiveness. Response 2: The magazine format template does not include continuous numbering in the lines of the manuscript. Comment 3: The abstract must be summarized and rewritten to briefly capture the background, aim of the study, methodology, key results, and the main conclusion. Additional quantification of the results in the abstract is recommended. Response 3: The abstract has been meticulously crafted to align with the stipulated guidelines of the journal (300 words). The information has been expanded following the suggestions given. Notably, the results paragraph incorporates main quantitative data obtained in the research. Comment 4: In the introduction, describe the hazardous effects of the Pb(II) ions heavy metals. The suggested literatures can guide the authors. Response 4: The introduction has been improved in accordance with the suggestions provided by the reviewer. Comment 5: I suggest the addition of more treatment techniques such as photocatalysis, adsorption, advanced oxidation process, membrane filtration. Also, each of the mentioned techniques must be referenced. The recommended literature can guide the authors. Response 5: The authors do not intend to provide a comprehensive \"state of the art\" on lead removal. Nevertheless, we have enhanced the introduction based on the literature recommended by the reviewer. Comment 6: 2nd paragraph: “Amorphous nanoaluminophosphates have also been proved for lead removing from…” I suggest removing be changed to removal. The entire statement must also be rephrased accordingly. Response 6: The suggested change has been made. Comment 7: How was the OLM chemically characterized and where are the results?. Response 7: The OLM has undergone both physical and chemical characterization, with the results referenced in the cited literature. However, the authors have chosen to incorporate some of these findings into the methodology section. Comment 8: Under the preparation of adsorbent, “The lithologic material was crushing…” Crushing or crushed?. Response 4: Correction, the word is “crushed”. Comment 9: Why use furnace to dry at 150 ºC. Is drying done with furnace or oven?. Response 9: The drying process occurs in two steps: first, air drying for 24 hours, followed by oven drying for an additional 24 hours. These sequential drying steps ensure the complete removal of water from the substrate. Any residual occluded water in the pellet maybe a risk of explosion during the calcination process, leading to the destruction of the pellet. Comment 10: How is oxides formation favored by calcination?. Response 10: Throughout thermal treatment, oxygen exhibits high reactivity, making surface oxidation the most likely reaction in the substrate. This process is a routine procedure for oxide formation in laboratory settings. “Brett NH. (1991). Magnesium and Alkaline-Earth Oxides. Concise Encyclopedia of Advanced Ceramic Materials. https://doi.org/10.1016/B978-0-08-034720-2.50080-0”. Comment 11: Kindly remove this statement from the bracket. “(The non-treated...substrate). Response 11: The correction has been made. Comment 12: The suggested literatures can be used to reference the model equations. Response 12: The literature recommended by the reviewer has been utilized to enhance the references pertaining to adsorption models. Comment 13: Be consistent in the use of either Pb(II) ions or Pb+2. Response 9: The use of Pb(II) or Pb+2 ions has been revised, following the reviewer's suggestions. Comment 14: I suggest the removal of grid lines from the graphs. Response 14: Thanks for the suggestion, the authors prefer to use the grid lines because they allow a better visualization of the data in the graphs. Comment 15: Table 1 and 3 shows the Freundlich and Langmuir isotherm parameters, not fitted equations. Response 15: The table headers have been modified in accordance with the provided suggestions. Comment 16: Merge Table 1 and 2. Evaluate the qe parameter and present in Table 1. Response 16: Thanks for the suggestion, the authors prefer that the Tables remain separated. Comment 17: Also merge Table 3 and 4. Response 17: Thanks for the suggestion, the authors prefer that the Tables remain separated. Comment 18: Under pH and electric conductivity study, “….and activates substrates” Is it activates or activated?. Response 18: Correction: The accurate term is \"activated\". Comment 19: There is no conclusion at the end of the manuscript, is that the journal format?. Response 19: The conclusion has been incorporated into the manuscript. Comment 20: I recommend the following references must be added to enrich the manuscript. Response 20: The references have been downloaded and reviewed. The most pertinent ones have been incorporated into the discussion. Sincerely, José G. Prato, Fernando Millán, Marialy Rangel, Andrés Márquez, Luisa Carolina González, Iván Ríos, César García, Carlos Rondón, Enju Wang"
}
]
}
] | 1
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https://f1000research.com/articles/12-747
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https://f1000research.com/articles/12-991/v1
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16 Aug 23
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{
"type": "Research Article",
"title": "Graph neural network-based anomaly detection for river network systems",
"authors": [
"Katie Buchhorn",
"Edgar Santos-Fernandez",
"Kerrie Mengersen",
"Robert Salomone",
"Edgar Santos-Fernandez",
"Kerrie Mengersen",
"Robert Salomone"
],
"abstract": "Background: Water is the lifeblood of river networks, and its quality plays a crucial role in sustaining both aquatic ecosystems and human societies. Real-time monitoring of water quality is increasingly reliant on in-situ sensor technology. Anomaly detection is crucial for identifying erroneous patterns in sensor data, but can be a challenging task due to the complexity and variability of the data, even under typical conditions. This paper presents a solution to the challenging task of anomaly detection for river network sensor data, which is essential for accurate and continuous monitoring. Methods: We use a graph neural network model, the recently proposed Graph Deviation Network (GDN), which employs graph attention-based forecasting to capture the complex spatio-temporal relationships between sensors. We propose an alternate anomaly threshold criteria for the model, GDN+, based on the learned graph. To evaluate the model's efficacy, we introduce new benchmarking simulation experiments with highly-sophisticated dependency structures and subsequence anomalies of various types. We also introduce software called gnnad. Results: We further examine the strengths and weaknesses of this baseline approach, GDN, in comparison to other benchmarking methods on complex real-world river network data. Conclusions: Findings suggest that GDN+ outperforms the baseline approach in high-dimensional data, while also providing improved interpretability.",
"keywords": [
"Anomaly Detection",
"Graph Deviation Network",
"Graph Neural Network",
"Multivariate Time Series",
"Graph Attention Forecasting",
"Spatio-temporal Data",
"Complex Systems"
],
"content": "Introduction\n\nRiver network systems play a vital role as freshwater habitats for aquatic life, and as support for terrestrial ecosystems in riparian zones, but are particularly sensitive to the anthropogenic impacts of climate change, water pollution and over-exploitation, among other factors. As a United Nations Sustainable Development Goal,1 water quality is a major environmental concern worldwide. The use of in-situ [1] sensors for data collection on river networks is increasingly prevalent,2,3 generating large amounts of data that allow for the identification of fine-scale spatial and temporal patterns, trends, and extremes, as well as potential sources of pollutants and their downstream impacts. However, such sensors are susceptible to technical errors relating to the equipment, herein defined as anomalies, for example due to miscalibration, biofouling, electrical interference and battery failure. In contrast, extreme events in rivers occur as result of heavy rain and floods. Technical anomalies must be identified before the data are considered for further analysis, as they can introduce bias in model parameters and affect the validity of statistical inferences, confounding the identification of true changes in water variables. Trustworthy data is needed to produce reliable and accurate assessments of water quality, for enhanced environmental monitoring, and for guiding management decisions in the prioritisation of ecosystem health.\n\nAnomaly detection in river networks is challenging due to the highly dynamic nature of river water even under typical conditions,4 as well as the complex spatial relationships between sensors. The unique spatial relationships between neighbouring sensors on a river network are characterised by a branching network topology with flow direction and connectivity, embedded within the 3-D terrestrial landscape. Common anomalies from data obtained from in-situ sensors are generally characterised by multiple consecutive observations (subsequence or persistent5), including sensor drift and periods of unusually high or low variability, which may indicate the necessity for sensor maintenance or calibration.6 Such anomalies are difficult to detect and often associated with high false negative rates.7\n\nEarlier statistical studies have focused on developing autocovariance models based on within-river relationships to capture the unique spatial characteristics of rivers.8 Although these methods are adaptable to different climate zones, and have recently been extended to take temporal dependencies into account,9 data sets generated by in-situ sensors still pose significant computational challenges with such prediction methods due to the sheer volume of data.10 Autocovariance matrices must be inverted when fitting spatio-temporal models and making predictions, and the distances between sites must be known. Previous work,11 aimed to detect drift and high-variability anomalies in water quality variables, by studying a range of neural networks calibrated using a Bayesian multi-objective optimisation procedure. However, the study was limited to analyzing univariate time series data, and the supervised methods required a significant amount of labeled data for training, which are not always available.\n\nThere are limited unsupervised anomaly detection methods for subsequence anomalies (of variable length), and even less so for multivariate time series anomaly detection.5 One such method uses dynamic clustering on learned segmented windows to identify global and local anomalies.12 However, this algorithm requires the time series to be well-aligned, and is not suitable for the lagged temporal relationships observed with river flow. Another method to detect variable-length subsequence anomalies in multivariate time series data uses dimensionality reduction to construct a one-dimensional feature, to represent the density of a local region in the recurrence representation, indicating the recurrence of patterns obtained by a sliding window.13 A similarity measure is used to classify subsequences as either non-anomalous or anomalous. Only two summary statistics were used in this similarity measure and the results were limited to a low-dimensional simulation study. In contrast, the technique introduced by Ref. 14, DeepAnT, uses a deep convolutional neural network (CNN) to predict one step ahead. This approach uses Euclidean distance of the forecast errors as the anomaly score. However, an anomaly threshold must be provided.\n\nDespite the above initial advances, challenges still remain in detecting persistent variable-length anomalies within high-dimensional data exhibiting noisy and complex spatial and temporal dependencies. With the aim of addressing such challenges, we explore the application of the recently-proposed Graph Deviation Network (GDN),15 and explore refinements with respect to anomaly scoring that address the needs of environmental monitoring. The GDN approach15 is a state-of-the-art model that uses sensor embeddings to capture inter-sensor relationships as a learned graph, and employs graph attention-based forecasting to predict future sensor behaviour. Anomalies are flagged when the error scores are above a calculated threshold value. By learning the interdependencies among variables and predicting based on the typical patterns of the system in a semi-supervised manner, this approach is able to detect deviations when the expected spatial dependencies are disrupted. As such, GDN offers the ability to detect even the small-deviation anomalies generally overlooked by other distance based and density based anomaly detection methods for time series,16,17 while offering robustness to lagged variable relationships. Unlike the commonly-used statistical methods that explicitly model covariance as a function of distance, GDN is flexible in capturing complex variable relationships independent of distance. GDN is also a semi-supervised approach, eliminating the need to label large amounts of data, and offers a computationally efficient solution to handle the ever increasing supply of sensor data. Despite the existing suite of methods developed for anomaly detection, only a limited number of corresponding software packages are available to practitioners. In summary, we have identified the following gaps in the current literature and research on this topic:\n\n1. An urgent need exists for a flexible approach that can effectively capture complex spatial relationships in river networks without the specification of an autocovariance model, and the ability to learn from limited labeled data, in a computationally efficient manner.\n\n2. Lack of data and anomaly generation schemes on which to benchmark methods, that exhibit complex spatial and temporal dependencies, as observed across river networks.\n\n3. Lack of open-source software for anomaly detection, which hinders the accessibility and reproducibility of research in this field, and limits the ability for individuals and organisations to implement effective anomaly detection strategies.\n\nOur work makes four primary contributions to the field:\n\n1. An improvement of the GDN approach via the threshold calculation based on the learned graph is presented, and shown to detect anomalies more accurately than GDN while improving the ability to locate anomalies across a network.\n\n2. Methods for simulating new benchmark data with highly-sophisticated spatio-temporal structures are provided, contaminated with various types of persistent anomalies.\n\n3. Numerical studies are conducted, featuring a suite of benchmarking data sets, as well as real-world river network data, to explore the strengths and limitations of GDN (and its variants) in increasingly challenging settings.\n\n4. User-friendly, free open-source software for the GDN/GDN+ approach is made available on the pip repository as gnnad, with data and anomaly generation modules, as well as the publication of a novel real-world data set.\n\nThe structure of the remainder of the paper is as follows: The next section details the methods of GDN and the model extension GDN+, and describes the methodology of the simulated data and anomaly generation. In the Results section we present an extensive simulation study on the benchmarking data, as well as a real-world case study. The performance of GDN/GDN+ is assessed against other state-of-the-art anomaly detection models. Further details and example code for the newly-released software are also provided. The paper concludes with a discussion of the findings, and the strengths and weaknesses of the considered models.\n\n\nMethods\n\nConsider multivariate time series data Y=y1…yT, obtained from n sensors over T time ticks. The (univariate) data collected from sensor i=1,…,n at time t=1,…,T are denoted as yit. Following the standard semi-supervised anomaly detection approach,18,19 non-anomalous data are used for training, while the test set may contain anomalous data. That is, we aim to learn the sensor behaviour using data obtained under standard operational conditions throughout the training phase and identify anomalous sensor readings during testing, as those which deviate substantially from the learned behaviour. As the algorithm output, each test point yt is assigned a binary label, at∈01, where at=1 indicates an anomaly at time t, anywhere across the full sensor network.\n\nThe GDN approach15 for anomaly detection is composed of two aspects:\n\n1. Forecasting-based time series model: a non-linear autoregressive multivariate time series model that involves graph neural networks is trained, and\n\n2. Threshold-based anomaly detection: transformations of the individual forecasting errors are used to determine if an anomaly has occurred, if such errors exceed a calculated threshold.\n\nThe above components are described in more detail below.\n\nForecasting-based Time Series Model. To predict yt, the model takes as input w∈ℕ lags of the multivariate series,\n\nThe i-th row (containing sensor i’s measurements for the previous w lags) of the above input matrix is represented by the column vector, xit=yit−1…yit−w. Prior to training, the practitioner specifies acceptable candidate relationships via the sets C1,…,Cn, where each Ci⊆12…n and does not contain i. These sets specify which nodes are allowed to be considered to be connected from node i (noting that the adjacency graph connections are not necessarily symmetric).\n\nThe model implicitly learns a graph structure via training sensor embedding parameters vi∈ℝd for i=1,…,n which are used to construct a graph. The intuition is that the embedding vectors capture the inherent characteristics of each sensor, and that sensors which are “similar” in terms of the angle between their vector embeddings are considered connected. Formally, the quantity eji is defined as the cosine similarity between the vector embeddings of sensors i and j:\n\nThe above describes how the trainable parameters vkk=1n yield a graph. Next, the lagged series are fed individually through a shallow Graph Attention Network20 that uses the previously constructed graph. Here, each node corresponds to a sensor, and the node features for node i are the lagged (univariate) time-series values, xit∈ℝw. Allow a parameter weight matrix W∈ℝd×w to apply a shared linear transform to each node. Then, the output of the network is given by\n\nThreshold-based Anomaly Detection. Given the learned inter-sensor and temporal relationships, we are able to detect anomalies as those which deviate from these interdependencies. An anomalousness score is computed for each time point in the test data. For each sensor i, we denote the prediction error at time t as,\n\nThe behavior of water quality variables may differ across space, for example, water level at high-altitude river network branches are generally characterised by rainfall patterns, whereas water level downstream near a river outlet can also be influenced by tidal patterns. A fixed threshold across the network does not allow for any local adaptations in error sensitivity. For this reason, this work also considers the novel sensor-specific threshold calculation,\n\nThe following is a method for simulating synthetic datasets with persistent anomalies inspired by the statistical models recently used to model river network data.9 Let S denote an arbitrary set of individual spatial locations, with locations s1,s2,…,sn∈S chosen by experimental design21 or otherwise. Consider a linear mixed model with n×1 response Y, and n×m design matrix X of explanatory variables spatially indexed at locations s1,s2,…,sn,\n\nNote that other distributions may be used. Above,\n\nExamples of the field are shown for t=1,2,3. Sensor locations are shown as white dots.\n\nWe consider two scenarios in generating simulated data: 1) spatial relationships characterised by Euclidean distance only, where the covariance matrix, ΣZ, is constructed via the kernel function given in Equation 4, and 2) data simulated on a river network, where ΣZ is constructed via the kernel function given in Equation 5. Together, this approach provides a variety of simulated data with highly-sophisticated dependency structure, see Figure 2.\n\nBoth simulations use the same (x, y) coordinates for sensor locations. The direction of flow is from top to bottom for SimRiver. Red dots indicate sites for which time series have been shown in Figure 3 and Figure 4.\n\nTwo points si, sj on a river network are said to be flow-connected if they share water flow, and flow-unconnected otherwise. We define stream distance, hRivsisj, as the shortest distance separating si and sj when travelling along a given river network. Tail-up covariance models for river networks, introduced in,8 effectively represent spatial relationships when variables are dominated by flow (e.g. pollutants enter a stream and only impact downstream locations). By construction, the tail-up covariance function only allows for correlation between flow-connected sites:\n\nOnce the base multivariate time series is constructed as above, it is modified to include persistent anomalies as follows. Hyperparameters are, nanomaly≥0, the number of subsequence anomalies and, λanomaly>0, the average length of an anomalous subsequence, for each anomaly type. In this example, we consider two types of anomalies, high-variability and drift, see Algorithm 1.\n\ninput : Time series data Y=y1…yT, number of locations n, expected length of each anomaly type λdrift and λvar, number of anomalies, ndrift and nvar, variability anomaly scale ζ, and drift anomaly parameter δ.\n\nfor anomaly∈driftvar do\n\nfor i=1,…,nanomaly do\n\nDraw location S∼Uniform12…n\n\nDraw time t∼Uniform1…T\n\nDraw length L∼Poissonλanomaly\n\nif anomaly=drift then\n\nv←δ2δ…Lδ // drift\n\nelse\n\nv∼N0ζ2IL×L // variability\n\nyS,t:t+L←yS,t:t+L+v\n\nThe Python package gnnad introduced in this paper extends and generalises the research code originally implemented by Ref. 15, which is incompatible with newer package dependencies and offers only a command line interface. The code is refactored to be modular and user-friendly, with a scikit-inspired interface, and extended to include visualisation, data and anomaly generation modules, as well as the GDN+ model extension. A continuous integration/continuous deployment (CI/CP) pipeline is established with unit testing to ensure that changes to the code are tested and deployed efficiently. Comprehensive documentation now accompanying the codebase enhances readability for future developers, facilitating maintenance, reuse, and modification. Furthermore, rigorous error handling is implemented to improve the software experience. The software developments have resulted in a more robust, user-friendly and easily distributable package that is available via https://github.com/KatieBuc/gnnad and the pip repository, gnnad. See below for example code that shows the process of fitting the GDN+ model.\n\nfrom sklearn.model_selection import train_test_split\n\nfrom gnnad.graphanomaly import GNNAD\n\nfrom gnnad.generate import GenerateAnomaly\n\n# split train test for input data frame, X\n\nX_train, X_test = train_test_split(X, shuffle=False)\n\n# generate anomalies on test set\n\nanoms = GenerateAnomaly(X_test)\n\nX_test = anoms.generate(anoms.variability, lam=3, prop_anom=0.07, seed=45)\n\nX_test = anoms.generate(anoms.drift, lam=11, prop_anom=0.07, seed=234)\n\ny_test = anoms.get_labels()\n\n# instantiate and fit GDN model object\n\nmodel = GNNAD(threshold_type=\"max_validation\", topk=6, slide_win=200)\n\nfitted_model = model.fit(X_train, X_test, y_test)\n\n# sensor based threshold based on GDN+\n\npred_label = fitted_model.sensor_threshold_preds(tau=99)\n\n# print evaluation metrics\n\nfitted_model.print_eval_metrics(pred_label)\n\n\nResults\n\nThis section presents a summary of the main findings for anomaly detection using GDN/GDN+ on both simulated and real-world data. To ensure quality of data, the aim for practitioners is to maximise the ability to identify anomalies of different types, while minimising false detection rates. We define the following metrics in terms of true positive (TP), true negative (TN), false positive (FP) and false negative (FN) classifications. In other words, the main priority is to minimise FN, while maintaining a reasonable number of FP, such that it is not an operational burden to check the total number of positive flags. Accordingly, we use recall, defined by TPTP+FN, to evaluate the performance on the test set and to select hyperparameters. That is, the proportion of actual positive cases that were correctly identified by the model(s). We also report the performance using precision TPTP+FP, accuracy TP+TNTP+TN+FP+FN and specificity TNTN+FP.\n\nTo evaluate model performance, three existing anomaly detection models are used as benchmarks: 1. The naive (random walk) Autoregressive Integrated Moving Average Model (ARIMA) prediction model from Refs. 7, 26; 2. HDoutliers,17 an unsupervised algorithm designed to identify anomalies in high-dimensional data, based on a distributional model that allows for probability assignment to an anomaly; and 3. DeepAnT,14 an unsupervised, deep learning-based approach to detecting anomalies in time series data.\n\nData are generated using the linear-mixed model described in Equation 2, with differing spatial dynamics: SimEuc where the random effect, Z, is characterised by Euclidean distance only, and SimRiver where Z simulates complex river network dynamics,27 using the same site locations and covariate values, X. Detecting anomalies that involve multiple consecutive observations is a difficult task that often requires user intervention, and is the focus of this study. We consider scenarios with drift and high-variability anomaly types, which together contaminate 13.2% of the test data, given ndrift=5,λdrift=11,nvar=24,λvar=3, see Table 1.\n\nFigure 3 visualises aspects of the SimEuc dataset, where sensor 37 and sensor 8 are in close (Euclidean) proximity, resulting in a high correlation between the locations (0.65), as anticipated. Note that sensor 23 exhibits anomalous behavior, high-variability and drift, consecutively, over time. Compared to the SimRiver dataset, shown in Figure 4, we note how the time series from sensor 37 and sensor 8 are no longer strongly correlated (0.07), despite their close proximity, as they are not flow-connected in the simulated river network.\n\nA Savitzky-Golay filter smoothens the time series (purple line). On the bottom, sensor 23 illustrates high-variability and drift anomalies, consecutively (red dots).\n\nDrift anomalies (red dots) are shown in data from sensor 4. A Savitzky-Golay filter is used to smoothen the time series for visual representation (purple line).\n\nTable 2 shows the performance of the different anomaly detection methods. The best performance in terms of recall is highlighted in bold, while the second-best performance is underlined. We observe that GDN/GDN+ outperforms most other models in terms of recall, which is the fraction of true positives among all actual positive instances. Specifically, GDN has a recall score of 83.3% on SimEuc and 72.7% on SimRiv, while GDN+ has the second highest recall score of 85.6% on SimEuc and 78.0% on SimRiv. Although ARIMA performed best in terms of recall, the high percentage of detected anomalies, 81.6% and 85.6%, is impractical to use (discussed below) and results in low accuracy scores of 28.6% and 25.3%, respectively. HDoutliers did not flag any time point as anomalous in any test case. DeepAnT tends to classify most samples as negative, resulting in a low recall score. These results suggest that GDN/GDN+ are best able to detect a high proportion of actual anomalies in the datasets.\n\nFigure 5 shows the classifications of anomalies in the simulation study. For reasons mentioned, recall is the performance metric of interest, but we also consider the trade-off between recall and precision. Lower precision means that the model may also identify some normal instances as anomalies, leading to false positives. In the context of river network anomaly detection, FP may be manually filtered, but it is critical to minimise FN. Note that GDN+ outperforms GDN in minimising the FN count, but at the cost of increasing FP, in both data sets. Such a trade-off is acceptable and considered an improvement in this context. Conversely, while ARIMA has the highest recall score, the number of FP classifications is impractical for practitioners to deal with (>70% of the test data). We also note that drift anomalies are harder to detect than high-variability anomalies, with drift as the majority of FN counts, in all cases.\n\nThe authors of the GDN model demonstrated its efficacy in detecting anywhere-within-system failures at time t by applying a threshold to all sensors within a system. However, the use of sensor-based thresholds in GDN+ has the advantage of indicating anomalies at the individual sensor level. In the context of monitoring river networks, it is crucial to identify the anomalous sensor, i, at a given time t. The percentage of true positives detected at the correct sensor, i, using the sensor-based anomaly threshold, Ait, in GDN+, was 92% and 89% for SimEuc and SimRiver, respectively. Similarly, the rate of true positives detected in the neighbourhood of the correct sensor i were 96% and 91%, respectively. This granularity of information is essential for large networks consisting of independent sensors that are separated by significant spatial distances, where the cost of time and travel for sensor replacement or maintenance is substantial.\n\nThis section explores the anomaly detection performance of GDN/GDN+ across multiple simulated data sets. The approach is as follows. First, ten new sets of spatial sampling locations are created, and for each set a Gaussian random field evolving over time is simulated, as per Equation 3. For each set of locations, we again consider both the Euclidean spatial characterisation (SimEuc), and the river network spatial characterisation (SimRiver), yielding a total of 20 benchmark data sets. In the first case, we use the Euclidean covariance model in Equation 4, parameterised by, σ2∈15, and, α∈515, with independent noise parameter, σ02∈01, and regression parameters β0∈110, and, β1∈110, for the linear model in Equation 2. The values of the parameters are chosen uniformly at random. The Tail-up covariance model in Equation 5 is used in the second case, parameterised as above.\n\nThen, anomalies are generated with the following parameters: drift δ∈36, variability ζ∈1215, length of anomalies λdrift∈510, λvar∈210, and the number of anomalies, ndrift∈50,100, nvar∈50,100 (see Algorithm 1). Across all simulations, the size of the data set is fixed to have length, T=4000, and number of sensors, n=40.\n\nFigure 6 illustrates the anomaly detection performance for GDN and GDN+, run on each data set with sliding window length w=3, and Top-K hyperparameter K=5. Note that the total number of anomalies can be seen at the bar height of TP+FN. In every scenario, GDN+ improves the FN count (red line), but at the cost of an increased TP count (orange line). Whether such a tradeoff is tolerable depends on how critical it is in practical scenarios that true anomalies are successfully detected. Note, that performance varies from one scenario to the next. Nevertheless, despite the simulated datasets being extremely noisy and complex, GDN and GDN+ appear to succeed in successful anomaly detection when other methods cannot.\n\nNote that GDN+ consistently decreases false negatives (red line) in every case, but also increases false positives (orange line).\n\nThis case study examines water-level data collected from eight sites located across the Herbert river, a major river system located in the tropical region of Australia, as shown in Figure 7. The time series data is highly non-stationary, characterised by river events caused by abnormal rainfall patterns, with some coastal sites exhibiting shorter periodicity trends which can be attributed to tidal patterns, see Figure 8. The spatial relationships are complex, and depend on the surrounding water catchment areas, spatial rainfall patterns, dams, and other impediments. In-situ sensors are prone to various anomalies such as battery failure, biofouling (accumulation of microorganisms, plants, algae, or small animals), and damage. In some cases, anomalies can manifest as the absence of a water event (i.e., flatlining) rather than the presence of abnormal time series patterns (i.e., spikes, variability, drift). In real-world scenarios, anomalies can persist for extended periods, and resolving them may require traveling to remote locations to inspect and repair sensors. As seen in Figure 8, anomalies at time t are largely attributed to Sensor 4, which was out of water for long periods of time.\n\nActual anomalies (red dots) are shown, along with the predicted anomalies (orange line) on the bottom.\n\nThe Herbert river is a challenging data set for all of the anomaly detection models, due to the sparse placement of sensors across the network, i.e., fewer sensors at greater distances apart resulting in weaker spatial relationships, and the test set contains a high proportion of anomalies (58%; see Table 1). GDN applied to the real-world dataset yields a recall of 29.2%, with GDN+ improving recall to 34.8%, see Table 3. Model performance suffers primarily due to the failure to detect the large anomaly spanning across 2022-01-10 in Figure 8. This may be attributed to the learned graph relationships being characterised by river events in the training data, and without such events, it is difficult to identify when a sensor is flat-lining. However, the model successfully identified anomalies spanning across 2021-12-27 and 2022-01-03, which coincided with river events.\n\nFigure 9 shows the learned graph adjacency matrix, A. Sensor 1, separated geographically by a large distance from the other sensors, has weaker relationships with the other nodes. Interestingly, the attention weights indicate that sensor 3 is strongly influenced by sensor 6, with tidal patterns from sensor 6 being evident in the predictions of sensor 3. Large error scores indicating an anomaly spanning across 2021-12-27 are primarily observed in sensor 2, impacted by anomalous sensors 3 and 4, where the predicted values are low. However, due to the small network of sensors in this case study, it is difficult to determine which sensor had the anomaly.\n\nThe edge weightings are determined by αij, which indicates attention and depend on model input, Xt.\n\nAdjusting the threshold in the GDN+ model can only enhance performance to a limited extent, since some anomalies may have insignificant error scores due to the underlying time series model. For instance, the anomaly spanning across 2022-01-10 has negligible error scores because the prediction model was performing well and no river events had occurred, making it challenging to detect the flat-lining type of anomaly in this particular scenario. Therefore, relying solely on the model may not be sufficient in practice, and we recommend implementing some basic expert rules. We introduce another model variant GDN++, by applying a simple filter to the time series ensuring that all values are positive, used in conjunction with adjusting the threshold calculation (GDN+). That is, an anomaly at time, t, on sensor, i, is flagged if, maxIyit<0Ait=1. GDN++ successfully detects all anomalies.\n\n\nDiscussion\n\nMultivariate anomaly detection and prediction models for spatio-temporal sensor data have the potential to transform water quality observation, modelling, and management.7,8 The provision of trustworthy sensor data has four major benefits: 1. It enables the production of finer-scale, reliable and more accurate estimates of sediment and nutrient loads, 2. It provides real-time feedback to landholders and managers, 3. It guides compliance with water quality guidelines, and 4. It allows for the assessment of ecosystem health and the prioritisation of management actions for sustaining aquatic ecosystems. However, technical anomalies in the data provided by the sensors can occur due to factors such as low battery power, biofouling of the probes, and sensor miscalibration. As noted by Ref. 7, there are a wide variety of anomaly types present within in-situ sensor data (e.g., high-variability, drift, spikes, shifts). Most anomaly detection methods used for water quality applications tend to target specific anomalies, such as sudden spikes or shifts.28–30 Detecting persistent anomalies, such as sensor drift and periods of abnormally high variability, remains very challenging for statistical and machine learning research. Such anomalies are often overlooked by distance and kernel based methods, yet must be detected before the data can be used, because they confound the assessment of status and trends in water quality. Understanding the relationships among, and typical behaviours of, water quality variables and how these differ among climate zones is thus an essential step in distinguishing anomalies from real water quality events.\n\nWe investigated the graph-based neural network model, GDN,15 for its ability to capture complex interdependencies between different variables in a semi-supervised manner. As such, GDN offered the ability to capture deviations from expected behaviour within a high-dimensional setting. We developed novel bench-marking data sets for subsequence anomaly detection (of variable length and type), with a range of spatio-temporal complexities, inspired by the statistical models recently used for river network data.9 Results showed that GDN tended to outperform the benchmarks in anomaly detection. We developed a model extension, GDN+, by adjusting the threshold calculation. GDN+ was shown to further improve performance. A replication study with multiple benchmarking data sets demonstrated consistency in these results. Sensor-based thresholds also proved useful in terms of identifying which neighbourhood the anomaly originated from in the simulation study.\n\nWe used a real-world case study of water level in the Herbert river, with non-stationary time series characterised by multiple river events caused by abnormal rainfall patterns. In this case, most of the anomalies appeared as flat-lining, due to the river drying out. Considering an individual time series, such anomalies may not appear obvious, as it is the failure to detect river events (in a multivariate setting) that is indicative of an anomalous sensor. Despite the challenges in the data, GDN+ was shown to successfully detect technical anomalies when river events occurred, and combined with a simple expert-based rule, GDN++, all anomalies were successfully detected.\n\nThere are two recent methodological extensions to the GDN approach. First, the Fused Sparse Autoencoder and Graph Net31 which extends the GDN approach by augmenting the prediction-based loss with a reconstruction-based term arising from the output of a sparse autoencoder, and a further extension that allows the individual sensors to have multivariate data. Second, a probabilistic (latent variable) extension is trained using variational inference.32 Since these were published contemporaneously to the present research, and only the latter provided accompanying research code, these approaches were not considered in the paper. Future extensions of this work could consider incorporating the above methodological extensions, as well as developing on the existing software package.\n\nOther applications could consider the separation of river events from technical anomalies. In terms of interpretability, since the prediction model aggregates feature data from neighbouring sensors, anomalous data can affect the prediction of any other sensor within the neighbourhood. Therefore, large error scores originating from one sensor anomaly can infiltrate through to the entire neighbourhood, and impairs the ability to attribute an anomaly to a sensor. The extensive body of literature on signal processing for source identification has the potential to inspire future solutions in addressing this issue.33,34\n\nIn summary, this work extends and examines the practicality of the GDN approach when applied to an environmental monitoring application of major international concern, with complex spatial and temporal interdependencies. Successfully addressing the challenge of anomaly detection in such settings can facilitate the wider adoption of in-situ sensors and could revolutionise the monitoring and management of air, soil, and water.\n\n\nConclusions\n\nThis work studied the application of Graph Deviation Network (GDN) based approaches for anomaly detection on the challenging setting on river network data, which often feature sensors that generate high-dimensional data with complex spatio-temporal relationships. We introduced alternative defection criteria for the model (GDN+/GDN++), and their practicality was explored on both real and simulated benchmark data. The findings indicated that GDN and its variants were effective in correctly (and conservatively) identifying anomalies. Benchmark data were generated via an approach that was also introduced in this paper, along with open-source software, and may serve useful in the development and testing of other anomaly-detection methods. In short, we found that graph neural network based approaches to anomaly detection offer a flexible framework, able to capture and model non-standard, highly dynamic, complex relationships over space and time, with the ability to flag a variety of anomaly types. However, the task of anomaly detection on river network sensor data remains a considerable challenge.\n\n\nAuthor contributions\n\nKB; Investigation, Formal Analysis, Methodology, Software, Validation, Visualisation, Writing – Original Draft Preparation. RS; Methodology, Supervision, Writing – Review & Editing. KM; Funding Acquisition, Conceptualisation, Supervision, Writing – Review & Editing. ES; Data Curation, Visualisation, Writing – Review & Editing.",
"appendix": "Data availability\n\nZenodo. Water level across the Herbert river. DOI: 10.5281/zenodo.8053358.\n\nThis project contains the following underlying data:\n\n• herbert_train.csv (sensor data).\n\n• herbert_test.csv (sensor data with sensor anomalies flags).\n\nData are available under the terms of the Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nŁukasz Mentel; Software. Cameron Roberts; Data Curation. James McGree; Writing – Review & Editing. A version of this manuscript has been uploaded onto the pre-print server, arxivs.org as https://arxiv.org/abs/2304.09367.\n\n\nReferences\n\nUN General Assembly Transforming our World: The 2030 Agenda for Sustainable Development. United Nations. 2015. (A/RES/70/1).\n\nMarinho e Silva G, Campos DF, Brasil JAT, et al.: Advances in technological research for online and in situ water quality monitoring—A review. Sustainability. 2022; 14(9): 5059. Publisher Full Text\n\nRitchie JC, Zimba PV, Everitt JH: Remote sensing techniques to assess water quality. Photogramm. Eng. Remote Sens. 2003; 69(6): 695–704. Publisher Full Text\n\nKang JM, Shekhar S, Henjum M, et al.: Discovering teleconnected flow anomalies: A relationship analysis of dynamic neighborhoods (RAD) approach. International Symposium on Advances in Spatial and Temporal Databases. Springer; 2009; pp. 44–61.\n\nBlázquez-Garca A, Conde A, Mori U, et al.: A review on outlier/anomaly detection in time series data. ACM Computing Surveys (CSUR). 2021; 54(3): 1–33. Publisher Full Text\n\nBourgeois W, Romain A-C, Nicolas J, et al.: The use of sensor arrays for environmental monitoring: interests and limitations. J. Environ. Monit. 2003; 5(6): 852–860. Publisher Full Text\n\nLeigh C, Alsibai O, Hyndman RJ, et al.: A framework for automated anomaly detection in high frequency water-quality data from in situ sensors. Sci. Total Environ. 2019; 664: 885–898. PubMed Abstract | Publisher Full Text\n\nVer Hoef JM, Peterson EE: A moving average approach for spatial statistical models of stream networks. J. Am. Stat. Assoc. 2010; 105(489): 6–18. Publisher Full Text\n\nSantos-Fernandez E, Ver JM, Hoef EE, et al.: Bayesian spatio-temporal models for stream networks. Comput. Stat. Data Anal. 2022; 170: 107446. Publisher Full Text\n\nPorter JH, Hanson PC, Lin C-C: Staying afloat in the sensor data deluge. Trends Ecol. Evol. 2012; 27(2): 121–129. PubMed Abstract | Publisher Full Text\n\nRodriguez-Perez J, Leigh C, Liquet B, et al.: Detecting technical anomalies in high-frequency water-quality data using artificial neural networks. Environ. Sci. Technol. 2020; 54(21): 13719–13730. PubMed Abstract | Publisher Full Text\n\nWang X, Lin J, Patel N, et al.: Exact variable-length anomaly detection algorithm for univariate and multivariate time series. Data Min. Knowl. Disc. 2018; 32: 1806–1844. Publisher Full Text\n\nMin H, Feng X, Ji Z, et al.: A novel computational approach for discord search with local recurrence rates in multivariate time series. Inf. Sci. 2019; 477: 220–233. Publisher Full Text\n\nMunir M, Siddiqui SA, Dengel A, et al.: DeepAnT: A deep learning approach for unsupervised anomaly detection in time series. IEEE Access. 2018; 7: 1991–2005.\n\nDeng A, Hooi B: Graph neural network-based anomaly detection in multivariate time series. Proceedings of the AAAI Conference on Artificial Intelligence. 2021; vol. 35: pp. 4027–4035.\n\nSchmidl S, Wenig P, Papenbrock T: Anomaly detection in time series: A comprehensive evaluation. Proc. VLDB Endow. 2022; 15(9): 1779–1797. Publisher Full Text\n\nWilkinson L: Visualizing Big Data outliers through distributed aggregation. IEEE Trans. Vis. Comput. Graph. 2017; 24(1): 256–266. PubMed Abstract | Publisher Full Text\n\nGoldstein M, Uchida S: A comparative evaluation of unsupervised anomaly detection algorithms for multivariate data. PLoS One. 2016; 11(4): e0152173. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNassif AB, Talib MA, Nasir Q, et al.: Machine learning for anomaly detection: A systematic review. IEEE Access. 2021; 9: 78658–78700. Publisher Full Text\n\nVelivcković P, Cucurull G, Casanova A, et al.: Graph attention networks. International Conference on Learning Representations (ICLR). 2018.\n\nBuchhorn K, Mengersen K, Santos-Fernandez E, et al.: Bayesian design with sampling windows for complex spatial processes. arXiv preprint arXiv:2206.05369. 2022.\n\nCressie N, Frey J, Harch B, et al.: Spatial prediction on a river network. J. Agric. Biol. Environ. Stat. 2006; 11(2): 127–150. Publisher Full Text\n\nVer JM, Hoef EP, Theobald D: Spatial statistical models that use flow and stream distance. Environ. Ecol. Stat. 2006; 13(4): 449–464. Publisher Full Text\n\nShreve RL: Statistical law of stream numbers. J. Geol. 1966; 74(1): 17–37. Publisher Full Text\n\nPeterson DP, Fausch KD: Upstream movement by nonnative brook trout (salvelinus fontinalis) promotes invasion of native cutthroat trout (oncorhynchus clarki) habitat. Can. J. Fish. Aquat. Sci. 2003; 60(12): 1502–1516. Publisher Full Text\n\nRob J: Hyndman and George Athanasopoulos. Forecasting: principles and practice. 3rd ed.OTexts; 2021.\n\nVer Hoef J, Peterson E, Clifford D, et al.: SSN: An R package for spatial statistical modeling on stream networks. J. Stat. Softw. 2014; 56: 1–45.\n\nTalagala PD, Hyndman RJ, Leigh C, et al.: A feature-based procedure for detecting technical outliers in water-quality data from in situ sensors. Water Resour. Res. 2019; 55(11): 8547–8568. Publisher Full Text\n\nHill DJ, Minsker BS: Anomaly detection in streaming environmental sensor data: A data-driven modeling approach. Environ. Model Softw. 2010; 25(9): 1014–1022. Publisher Full Text\n\nBa A, McKenna SA: Water quality monitoring with online change-point detection methods. J. Hydroinf. 2015; 17(1): 7–19. Publisher Full Text\n\nHan S, Woo SS: Learning sparse latent graph representations for anomaly detection in multivariate time series. Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. 2022; pp. 2977–2986.\n\nChen W, Tian L, Chen B, et al.: Deep Variational Graph Convolutional Recurrent Network for Multivariate Time Series Anomaly Detection. International Conference on Machine Learning. PMLR; 2022; pp. 3621–3633.\n\nScharf LL, Demeure C: Statistical signal processing: detection, estimation, and time series analysis. Prentice Hall; 1991.\n\nTelford WM, Telford WM, Geldart LP, et al.: Applied geophysics. Cambridge University Press; 1990.\n\n\nFootnotes\n\n1 In-situ refers to an instrument in direct contact with the medium of observation.\n\n2 It seems that the authors of Ref. 15 mistakenly denote this addition as concatenation in the paper, however, their corresponding reference code computes addition."
}
|
[
{
"id": "199872",
"date": "28 Sep 2023",
"name": "Ailin Deng",
"expertise": [
"Reviewer Expertise Anomaly detection"
],
"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 provide detailed analysis on a previous anomaly detection method, GDN and improve it by proposing a new threshold selection methodology based on the learned local graph structure, denoted as GDN+. The work mainly focuses on the river network systems and further provides benchmarking data generation which is specifically designed for the river network or similar systems' analysis. They show the GNN-based method’s effectiveness in the river network systems in their study.\nPros:\nThe threshold selection based on the neighborhood sensors is interesting and reasonable. It enables a more flexible threshold for sensors based on the learned graph structure.\n\nThe authors provide detailed code implementation and python package for the method.\n\nThey also provide methods for generating data based on spatio-temporal structures.\n\nThe case study is interesting and effective to show the interpretability in this river system scenario.\n\nCons:\nIt would be interesting to have an ablation study on the effect of the \\tau selection, it seems the default setting is 99 (or should it be 99%?), it would be good to see how different \\tau will affect the recall or other performance metrics.\n\nMinor:\nIn table 2, some of the methods are bold, but it seems they are not achieving the best recall performance, such as ARIMA.\n\nIn GDN+ threshold part, should the denotation exclude i for A_{ji}? As the A_{ij} includes {i=j} and the description is “across the neighborhood of i” which might not include sensor i itself.\n\nSome of the claims could be rephrased more gently or targeted at a more specific domain of problem, such as anomaly detection in river network systems. Page 4 of 18: “Lack of open-source software for anomaly detection…”. For anomaly detection, there are some existing open-source packages, such as PyOD (Zhao et al., 20191).\n\nIn overall, I think this paper has a clear writing and detailed study in anomaly detection in the specific river system and provides open-source code for method and data generation for this kind of problem. Some ablation study and minor or typos can be further addressed.\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": [
{
"c_id": "10958",
"date": "28 Mar 2024",
"name": "Katie Buchhorn",
"role": "Author Response",
"response": "The authors thank the reviewer for their thoughtful feedback. Please see the responses below: Cons: - Tau is introduced as a percentile (as opposed to percentage), and ranges between 0-100. As per the suggestion, a complete ablation study has been added to the Appendix. Minor: - We utilised bold to highlight points of discussion (particularly poor or particularly good performance). However, to avoid confusion the choice of formatting has been updated so that bold denotes the highest recall value, and underline denotes the second highest. - Yes, the GDN+ threshold notation should exclude i for A_{ji}, this has been amended. - Wording has been changed to “Limited open-source software for anomaly detection…”."
}
]
},
{
"id": "208772",
"date": "20 Oct 2023",
"name": "Maurício Araújo Dias",
"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\nIn recent years, there has been an increasing interest in distinguishing anomaly detection from outlier detection (Chandola et al., 20091; Chandola et al., 20122; Kittler et al., 20143; Dias et al., 20194; Dias et al., 20225). According to the scientific literature, the former differs from the latter by categorizing outliers based on some taxonomy, in addition to just detecting them. In 2009 and 2010, a small taxonomy was used in Chandola et al. (20091) and Chandola et al. (20122). In 2014, Kittler’s Taxonomy, a more complete taxonomy, was introduced in Kittler et al. (20143). In 2020, Kittler’s Taxonomy was used as a basis to detect anomalies (high variability) mainly in rivers and in a spatial context, as described in Dias et al. (20194). In 2022, a detection of anomalies (drift) based on Kittler’s Taxonomy, in a river and mainly in a temporal context, was described in Dias et al. (20225).\nThe reviewed article, which presents a graph neural network-based anomaly detection for river network systems, is in agreement with the aforementioned papers. In the reviewed article, the anomaly detection process deals with the complexity and variability of the data from spatio-temporal relationships between sensors for accurate and continuous monitoring of river water quality. Another positive aspect of the reviewed article is that it actually describes anomaly detection, in contrast to many articles present in the scientific literature that describe outlier detection despite using the term anomaly detection. Moreover, the work is clearly and accurately presented. A negative aspect of the reviewed article is that it could have had more references on this distinguishing and on anomaly taxonomies. It would also be interesting to highlight in the beginning of the article which taxonomy the authors based on to categorize anomalies as being of the following types: high-variability, drift, spikes, and shifts (ref. 7 cited by the article maybe?).\n\nIn general, the study design is appropriate. My only suggestions are, please: (1) To add north arrow and scale bar to Figures 1, 2, and 7. (2) To consider presenting the algorithm in page 9 (Algorithm 2, maybe?) in the same style that Algorithm 1 was presented in page 8. The work is technically sound.\n\nThere are sufficient details of methods and analysis provided to allow replication by others. The reviewed article provides researchers with many mathematical definitions regarding the steps of the methodology used in the work. Those mathematical definitions allow researchers to replicate the work more accurately. The analysis process is supported by a number of real and simulated benchmark data.\n\nThe statistical analysis and its interpretation is appropriate since the work validated its results based on well-established metrics, as follows: (1) The quantity of truly relevant results was measured using Recall. (2) The efficiency of results was measured using Accuracy. (3) The relevancy of results was measured using Precision. (4) The ratio of true negatives to all negative outcomes was measured using Specificity.\n\nThe source data and software underlying the results of this work are all available on the Internet to ensure full reproducibility. The authors add “Data Availability” and “Software Availability” subsections to the end of the paper. My only suggestion is to distinguish and highlight “real” and “simulated” benchmark data in the subsection “Data Availability”.\n\nThe conclusions drawn are adequately supported by the results. However, I would like to highlight a certain feature present in the reviewed article, although I do not particularly consider it a flaw. The contents of the “Discussion” and “Conclusions” sections of the reviewed article are most commonly found in the scientific literature merged to form a broader “Conclusions” section than that presented in the reviewed article. For example, suggestions for future work are normally part of the “Conclusions”, but in the reviewed article they appear in the “Discussion” (in a scientific article, it seems a bit strange to “discuss” something that has not yet been done). The scientific literature usually discusses the results found. This is done in the reviewed article, but merged with the “Results” section, rather than in the “Discussion”.\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": "10959",
"date": "28 Mar 2024",
"name": "Katie Buchhorn",
"role": "Author Response",
"response": "The authors thank the reviewer for their thoughtful feedback. Please see the enumerated responses below: 1. Clarification of the anomaly taxonomy has been added in the introduction, including reference 7. Thank you for highlighting these papers. We considered the inclusion of the above references, however since as their definition of “drift” differs, they were not included to avoid confusion. 2. North arrow and scale have been added to Figure 7 (Figure 1 & 2 are simulated data with arbitrary values for the scale and direction). Algorithm 1 is pseudo-code, whereas on the following page, an excerpt of python code is provided. Thus, we feel it is necessary to have a distinction in presentation. 5. The “Data availability” section has been updated with this clarification."
}
]
}
] | 1
|
https://f1000research.com/articles/12-991
|
https://f1000research.com/articles/13-239/v1
|
28 Mar 24
|
{
"type": "Study Protocol",
"title": "Assessment of Immunization Coverage and its Determinants Amongst Children in an Urban Area. Study Protocol of a Cross Sectional Study",
"authors": [
"Janhvi Thakur",
"Dr. Sonali Choudhari",
"Dr. Sonali Choudhari"
],
"abstract": "Abstract*\nIntroduction The country’s immunization rate is frequently below the international and national goals, and it is not distributed evenly. Children should be immunized for several reasons, chief among them being that it is the main defense against a variety of serious and frequently life-threatening illnesses. Every year, it prevents debilitating illness and disability and saves millions of lives throughout the world. The urban population in India is experiencing exponential growth. However, the public sector’s urban healthcare delivery system has encountered difficulties in keeping up with the rapid pace, exhibiting limitations in its reach and falling short of meeting the increasing demands. There is a need for government to pay attention at immunization rates and related variables in children (12–23 months) in the urban area.\n\nObjectives\n• To assess the overall immunization coverage rate for children in the urban area. • To assess the determinants associated with immunisation coverage in an urban area. • To explore healthcare access and infrastructure: Examine the availability and accessibility of healthcare facilities and vaccination services within the urban area.\n\nMethod Information will be collected using semi- structured questionnaire in kobo collect tool. The parents of the child will be asked whether they have their immunization cards with complete immunization of their children.\n\nStudy implications This study seeks to appraise the participant’s current immunization status with association to various determinants related to immunisation coverage. The study will also explore the availability of health infrastructure in association with immunization coverage. Furthermore, the gathered data may be utilized in further studies.",
"keywords": [
"Child health",
"immunization coverage",
"urban health",
"vaccination."
],
"content": "Introduction\n\nThe first line of defence against disease has been described as immunization, which is also one of the best health benefits available to children.1 Vaccines have the biggest success stories in the field of public health. Globally, childhood immunization against vaccine-preventable diseases (VPD) is acknowledged as one of the most affordable initiatives to reduce childhood fatalities and morbidities.2 Each year, it saves millions of lives worldwide and averts crippling disease and disability.3 The challenge of low immunization coverage is pervasive, affecting urban slum populations to a similar extent as remote rural areas. According to an initial scenario based on projected proportions of unimmunized children in both rural and urban areas, indicates that nearly half (44%) of the unimmunized and under-immunized children in the top 10 nations, which collectively housed over half of such children in 2017, resided in urban areas. Notably, nearly every fifth unimmunized child (18%) was found to live in a slum, highlighting the specific vulnerability of these urban environments in terms of immunization coverage.4\n\nSince 1974, the World Health Organization (WHO) - supported Expanded Programme on Immunization (EPI) has played a pivotal role in significantly increasing global access to vaccines. A noteworthy decline in the number of childhood illnesses that can be prevented and fatalities has been achieved for the six vaccine-preventable diseases (VPDs) initially targeted. These diseases include tuberculosis, diphtheria, pertussis, tetanus, measles, and poliomyelitis. The success in the early years of the program demonstrates the effectiveness of vaccination efforts in curbing the impact of these serious diseases on child health and mortality. The Universal Immunization Programme (UIP) was introduced in 1985 by the Government of India (GOI), which expedited its own EPI (started in 1978) with the goal of reaching a target coverage of 90% by 1990. Every year, the UIP provides care for nearly 26 million infants and 125 million children under the age of five.5\n\nDespite the ongoing awareness campaigns and concerted efforts in India’s immunization program, the coverage of immunization for children continues to fall short of the targets set by the Universal Immunization Program (UIP).1 Over the past few decades, India’s urban population has grown dramatically, making up approximately one-third of the nation’s total population. The population projections suggest that by the year 2045, approximately 800 million individuals in India will be residing in urban areas.6 According to a recent NFHS-5 survey based on information from vaccination cards or mother memory, in India 62.0% the percentage of children aged 12-23 months are fully vaccinated, and in urban areas, it is only 75.5%. Furthermore, based solely on information from vaccination cards, the percentage of children in India between the ages of 12 and 23 months who are fully vaccinated is 77.9% nationwide, and 83.3% in urban areas.7 The reach of the public sector urban health delivery system has been constrained, and its adequacy remains significantly lacking.6 Reaching Children Full Immunization (CFI) would achieve Sustainable Development Goal 3 (SDG 3) goal 3.2 and ensure a decrease in childhood mortality.8\n\nBy effectively using vaccinations, the majority of affluent countries have decreased the occurrence of diseases that can be prevented by vaccines.9 The current health delivery system is still unable to meet the demands of the urban poor population. Less than 4% of India’s government primary healthcare facilities are located in metropolitan regions. Our study will highlight a need for government to pay attention to poor health services.10\n\nIn the scope of this study, our primary focus will be on evaluating immunization coverage. This assessment is crucial for strategic planning of immunization programs, pinpointing vulnerable groups that necessitate targeted resource allocation, and forecasting potential epidemics of vaccine-preventable diseases. By conducting this evaluation, we aim to contribute valuable insights that can inform and enhance public health initiatives related to immunization.6\n\nUrban slums may have poor coverage rates because, unlike rural regions where immunization services are given at the village level, urban communities still primarily receive them in clinical or hospital settings.11 In Low and Middle Income Countries (LMICs), household income and social standing, parental awareness, and religious and cultural attitudes are significant demand-side drivers of child vaccination coverage. In terms of supply-side variables, distance to the immunization session site, poor service quality, and a lack of facility resources are known causes of children not receiving vaccinations.12 In order to accommodate the expanding urban population, it is necessary to improve the urban infrastructure for health at all scales, including large cities and small villages.11\n\nBy reducing the number of cases, reducing the clustering of cases within households, and lengthening the period between outbreaks, immunization programs in urban settings can have a major impact on the mortality associated with vaccine preventable disease.13 In the low-income states with the largest birth cohorts, the government might also train and reward a greater range of private-sector health workers to assist in administering the immunizations.5 When immunization is a priority for urban health, EPI administrators must identify special initiatives for disease prevention in cities.14 In order to ensure that vaccinations and their administration are suitable, sustainable, and acceptable, it is imperative that communities and civil society be included. In order to break down social and cultural barriers, restore lost trust in vaccination programs, and promote the locally appropriate use of vaccines, community-based organizations have increased their involvement in immunization efforts.4\n\nAssessing the overall immunization coverage rate for children in the urban area is crucial for understanding the level of protection against vaccine-preventable diseases. This information helps identify gaps in vaccination coverage and formulate targeted interventions to improve immunization rates and public health outcomes. While previous research has exhaustively documented the elements that affect immunization demand in India, the association between children immunization outcomes in low-income countries and the accessibility of health facilities has not yet been thoroughly examined. In this study, we will also be assessing the immunisation coverage and its determinants amongst children in an urban area.\n\nAssessment of immunisation coverage and its determinants, amongst children (0-23 months) in the urban area of the Wardha district.\n\n\n\n1. To assess the overall immunization coverage rate for children in the urban area.\n\n2. To assess the determinants associated with immunisation coverage in an urban area.\n\n3. To explore healthcare access and infrastructure: Examine the availability and accessibility of healthcare facilities and vaccination services within the urban area.\n\n\nMethod\n\nData collection for this study will be facilitated through the use of a semi-structured questionnaire implemented in the Kobo Collect Tool https://www.kobotoolbox.org/. The questionnaire will encompass inquiries about sociodemographic parameters, the immunization status of participants’ children, and reasons underlying noncompliance with immunization. The parents will be asked whether they have their immunization cards with complete immunization of their children. If a birth certificate, vaccination record, or delivery summary of discharge is unavailable, the mother will be asked to confirm the child’s age.\n\nThis study will be cross-sectional in nature.\n\nThe study will be carried in School of Epidemiology and Public Health urban field practice area, DMIHER, Wardha.\n\nThe study will be carried out between November 2023 and May 2024.\n\nThe interpersonal questions about vaccination will be asked to the parents of 0-23 month children. The parents will be asked whether they have their immunization cards with complete immunization of their children. This study will include the children ages 0-23 months living in urban areas. Children ages more than 23 months and living in rural areas will be excluded from the study.\n\n\n\n• The present study will include children of age group 0-23 months.\n\n• The parents who will give written consent for the study.\n\n\n\n• Children above the age of 23 months.\n\n• The parents who will not give written consent for the study.\n\nTo calculate the required sample size we used\n\nEstimate a proportion with absolute precision\n\nAlpha (a) 0.05\n\nEstimated proportion (p) 0.62\n\nEstimated error (d) 0.05\n\nCALCULATE\n\nMinimum sample size needed: 363\n\nThe present study will be conducted using convenient sampling method.\n\nIn this study, we will scrutinize variables related to demographic information and the accessibility and proximity of participants to health centres offering comprehensive immunization services. This examination aims to understand and analyze the potential impact of demographic factors and the availability of nearby health facilities on the immunization patterns observed in the study population. Table 1 elaborates the variables related to immunization coverage.10\n\n* Abbreviations used Universal Health Coverage (UHC).\n\n* Anganwadi Centre (AWC).\n\n* Non Governmental Organization (NGO).\n\nA semi-structured questionnaire with the following two sections will be used to gather information:\n\nSection A: Sociodemographic information of the participants. Sex, Birth order, Age of child, Mothers education, Mother’s occupation, Mother’s age, Religion of household, Social category.\n\nSection B: Other determinants associated with immunization coverage.\n\nGovernment UHC, Government hospital, Private clinic/hospital, Private provider, AWC, NGOs.\n\nThe questionnaire will be translated to the local vernacular language Marathi.\n\nThe absence of a comprehensive sampling frame and reliance on convenience sampling may compromise the representativeness of the obtained sample, thereby hindering the ability to draw meaningful generalizations to the broader population under investigation. Additionally, the survey may be susceptible to biases, as respondents might selectively provide answers, introducing potential distortions in the data. Furthermore, the lack of detailed information regarding immunization status could introduce recall bias, further complicating the accuracy and reliability of the study findings.\n\nThe data collected will be entered into a Microsoft Excel sheet and subsequently analyzed using the Statistical Package for the Social Sciences (SPSS), version 27 https://www.ibm.com/support/pages/node/1101369 as an alternative we will use R software R: The R Project for Statistical Computing (r-project.org). Then analysed data will be tabulated in the form of tables. The classification of children’s immunization status in this study will be based on specific criteria. A child will be considered to have a “complete” immunization status if they have acquired 1 dose of the BCG vaccine, 3 doses each of diphtheria, pertussis, and tetanus (DPT3) vaccines, along with oral polio vaccines, and 1 dose of the measles vaccine. Conversely, if any one or more of these vaccines will be missing, the child’s immunization status will be labelled as “partial.” Conversely, if the child has not received any vaccines, their status will be classified as “not” immunized. This classification system provides a comprehensive framework for assessing the extent of immunization coverage among the study participants.\n\nThe study protocol will be publish in indexed journal and will be presented in seminars and conference.\n\nThe study has been started after getting approval from the IEC department of DMIHER (DU) and is under process.\n\n\nDiscussion\n\nWHO/UNICEF vaccination coverage estimates rely on data derived from vaccination coverage surveys that systematically break down coverage information by various demographic and contextual factors. Analyses of Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS) conducted between 2005 and 2013 have consistently revealed that DTP3 coverage tends to be lower among children from economically disadvantaged households. Conversely, DTP3 coverage demonstrates an upward trend with increasing economic status in the majority of low- and middle-income countries. These findings underscore the socio-economic disparities that can influence vaccination coverage outcomes.9\n\nIn India, the percentage of government primary health care services in urban areas is less than 4%. The AWC to total population ratio is lower (1:1260) in rural areas and nearly five times (1:6114) in urban areas, according to an analysis of ICDS coverage in both rural and urban areas.10\n\nIn order to enhance vaccination programs in regions with poor coverage, the World Health Organization (WHO), the United Nations Children’s Fund (UNICEF), and other GAVI Alliance partners created and implemented the Reaching Every District (RED) strategy in 2002. An assessment of five African countries that had adopted the (RED) in 2005 discovered that vaccination rates had risen in four of the five countries and that the percentage of districts with DTP3 (three doses of the diphtheria, tetanus, and pertussis vaccine) coverage above 80% had more than doubled. In these five countries, the number of children without vaccinations dropped from 3 million in 2002 to 1.9 million in 2004.15\n\nThe research conducted by Anu Rammohan and Niyi Awofeso demonstrated that the district’s income per capita serves as a robust predictor of improved immunization outcomes for children. Additionally, the study found that the mother’s education level at the district level exerts a statistically significant and positive influence on immunization outcomes, as evident across all the models employed in the analysis. These findings highlight the interconnected role of economic factors and maternal education in shaping positive immunization outcomes at the district level.16\n\nIn a cross-sectional survey carried out in Delhi, India, the findings revealed a significant association between maternal education and the utilization of healthcare services, as well as the complete immunization of children. Similarly, in another cross-sectional survey conducted in Pakistan, both maternal education and the parents’ comprehensive awareness about vaccinations were identified as factors linked to the full immunization of their children.17\n\nThe study “Perplexing condition of child full immunisation in economically better off Gujarat in India: An assessment of the factors associated with it” examines, 50% of children in Gujarat between the ages of 12 and 23 months in 2015–2016 failed to get all recommended vaccinations. Compared to their contemporaries, Children whose mothers possessed a Maternal and Child Protection (MCP) card and those who received “high” levels of maternal health services were found to have an elevated likelihood of receiving Children Full Immunization (CFI). Compared to the people living in the poorest homes, the richest households had around three times higher probability of acquiring CFI. Macro-level analysis indicate that higher-order births, maternal health care, and poverty are the three primary elements of Gujarat’s CFI coverage.8\n\nThis study aims to assess the current immunization status of participants. Additionally, the gathered data holds the potential for application in future studies. By conducting this research, valuable insights into the barriers to child immunization in urban areas can be gained, allowing for the identification of measures to overcome these challenges.\n\nIt is important to acknowledge that this study is limited to its scope, as it does not encompass the assessment of the healthcare worker’s or healthcare facility’s service quality. The quality of services is a crucial aspect that can influence both cost and coverage. Additionally, it plays a significant role in determining the cost-effectiveness of expanding Universal Health Coverage (UHC) and the functions of Integrated Child Development Services (ICDS). Finally, since the study will be limited to one Indian region, it will be necessary to see whether it can be generalized to other Indian towns and other nations.\n\nWith reference number DMIHER (DU)/IEC/2023/32 on 19/12/2023, the Institutional Ethics Committee in its meeting held on Dt. 19/12/2023 has approved the following research study proposal to be carried out under the School of Epidemiology and Public Health Dept. of Community Medicine, Jawaharlal Nehru Medical College and Acharya Vinoba Bhave Rural Hospital, Datta Meghe Institute of Higher Education and Research (DU).\n\nWritten consent form from all the study participants will be obtained while gathering the information.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: STROBE checklist for Assessment of Immunisation Coverage and its Determinants, Amongst Children (0-23 months) in the Urban Area of the Wardha District. A Cross Sectional Study, https://doi.org/10.6084/m9.figshare.25340656.v1. 18\n\nData are available under the terms of the CC BY 4.0 Attribution license (CC BY 4.0).\n\n\nReferences\n\nPhukan RK, Barman MP, Mahanta J: Factors Associated with Immunization Coverage of Children in Assam, India: Over the First Year of Life. J. Trop. Pediatr. 2009 Aug 1; 55(4): 249–252. PubMed Abstract | Publisher Full Text\n\nSarker AR, Akram R, Ali N, et al.: Coverage and Determinants of Full Immunization: Vaccination Coverage among Senegalese Children. Medicina (Mex). 2019 Aug 14; 55(8): 480. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsfaw AG, Koye DN, Demssie AF, et al.: Determinants of default to fully completion of immunization among children aged 12 to 23 months in south Ethiopia: unmatched case-control study. Pan Afr. Med. J. 2016 Mar 16 [cited 2023 Dec 12]; 23(100): 100. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nMantel C, Cherian T: New immunization strategies: adapting to global challenges. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz. 2020; 63(1): 25–31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSharma A, Kaplan WA, Chokshi M, et al.: Role of the private sector in vaccination service delivery in India: evidence from private-sector vaccine sales data, 2009–12. Health Policy Plan. 2016 Sep 1; 31(7): 884–896. PubMed Abstract | Publisher Full Text\n\nJoy TM, George S, Paul N, et al.: Assessment of vaccine coverage and associated factors among children in urban agglomerations of Kochi, Kerala, India. J. Family Med. Prim. Care. 2019 Jan; 8(1): 91–96. PubMed Abstract | Publisher Full Text\n\nNFHS-5_Phase-II_0.pdf: [cited 2023 Nov 5]. Reference Source\n\nGoli S, James KS, Pallikadavath S, et al.: Perplexing condition of child full immunisation in economically better off Gujarat in India: An assessment of associated factors. Vaccine. 2020 Aug 10; 38(36): 5831–5841. PubMed Abstract | Publisher Full Text\n\nShukla VV, Shah RC: Vaccinations in Primary Care. Indian J. Pediatr. 2018 Dec 1; 85(12): 1118–1127. Publisher Full Text\n\nAssociation Between Child Immunization and Availability of Health Infrastructure in Slums in India|Global Health| JAMA Pediatrics|JAMA Network.[cited 2023 Sep 4]. Reference Source\n\nKapadia-Kundu N, Kanitkar T: Primary Healthcare in Urban Slums. Econ. Polit. Wkly. 2002 Jan 1; 37: 5086–5089.\n\nSumman A, Nandi A, Schueller E, et al.: Public health facility quality and child immunization outcomes in rural India: A decomposition analysis. Vaccine. 2022 Apr 6 [cited 2023 Aug 22]; 40(16). 2388–2398. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAgarwal S, Bhanot A, Goindi G: Understanding and Addressing Childhood Immunization Coverage in Urban Slums. Indian Pediatr. 2005; 42: 653–663. PubMed Abstract\n\nAtkinson SJ, Cheyne J: Immunization in urban areas: issues and strategies. Bull. World Health Organ. 1994; 72(2): 183–194. PubMed Abstract\n\nVandelaer J, Bilous J, Nshimirimana D: Reaching Every District (RED) approach: a way to improve immunization performance. Bull. World Health Organ. 2008 Mar; 86(3): A-B. PubMed Abstract | Publisher Full Text\n\nRammohan A, Awofeso N: District-level variations in childhood immunizations in India: The role of socio-economic factors and health infrastructure. Soc. Sci. Med. 2015 Nov 1; 145: 163–172. PubMed Abstract | Publisher Full Text\n\nGlatman-Freedman A, Nichols K: The effect of social determinants on immunization programs. Hum. Vaccin. Immunother. 2012 Mar 13; 8(3): 293–301. Publisher Full Text\n\nThakur J: STROBE checklist for Assessment of Immunisation Coverage and its Determinants, Amongst Children (0-23 months) in the Urban Area of the Wardha District. A Cross Sectional Study. figshare. Online resource. 2024. Publisher Full Text"
}
|
[
{
"id": "284252",
"date": "08 Jul 2024",
"name": "Siddharth Agarwal",
"expertise": [
"Reviewer Expertise Maternal and child healthcare",
"urban slum healthcare",
"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\nWe recommend adding a few details and factual statements which will enrich the manuscript:\n\nRecommendations for strengthening the Abstract:\na) This abstract can be made more concise and engaging for F1000 readers by eliminating repetition and redundant information. This approach ensures clarity and maintains the readers' interest throughout the text.\nb) Introduction: The authors would do well to specify clearly the urban slum setting of the study. It will also be good for the readers of F1000 to mention one sentence about the intra-urban disparities in child immunization status, emphasizing that the urban poor particularly contribute to the low immunization status in urban areas (please see details under Recommendations for strengthening the Introduction).\nc) Objectives: Only the primary study objective could be mentioned in the abstract. Consistency in using the urban area versus an urban area will improve the abstract.\nd) Method: Briefly explaining what complete immunization means for a child in the age group 0-23 month will strengthen the abstract (please also see details under Recommendations for strengthening Methods).\ne) Study Implications: Authors are urged to state clearly what impact the data/study will have and minimize describing the study objectives.\nRecommendations for strengthening the Introduction:\na) Citing recent research related to Intra-urban differences in Immunization Status among Urban Poor in Developing countries and in India: The authors have highlighted lower immunization status among the urban poor in top 10 nations. It would benefit the manuscript to mention the parameters on which these nations have been rated as top 10 and also list the countries in a footnote or endnote. The authors are urged to consider mentioning Low-and Middle-Income countries or alternative category and provide a reference.\nAdditionally, citing related research from India will further enrich the document by providing context for the country in which the study is based. The authors could provide examples of disaggregated data examining intra-urban differences in immunization status. An example which can support this argument is the analysis of urban constituent of India National Family Health Survey (NFHS) by wealth-index that unmasks the disparities in Indian cities with respect to child and maternal health, provision for health care and housing conditions. (Agarwal S, 2011 [Ref 1]). Intra-urban differences in health conditions have been studied in Bangladesh in the form of Bangladesh Urban Health Survey 2013 (https://www.measureevaluation.org/publications/tr-15-117. (UHS, 2013). The authors could also examine the availability of disaggregated urban data from NHFS-4 or NFHS-5. We have cited this study in our own work for the authors to refer to it for complete and accurate referencing (mentioned under bullet-points related to citations under recommendations for strengthening introduction). Authors can refer to this citation for the following reasons-\n\ni.\n\nCitation is incomplete in the manuscript. Citation 10 in the manuscript is missing the author's names.\n\nii.\n\nCite reference in the manuscript where necessary. The authors have referred to the above paper at more than a few places in their manuscript. Variables and outcome measures have been highly informed from the cited study. Almost all variables used in Table 1 are informed from the cited study. Presence of an urban health center (UHC) within 2 km of the slum and AWC within 2 km of slum have been used as exposures of interest. The study also uses 'complete', 'partial', 'not' immunized as outcome measures similar to the cited study and other similar studies..\n\nb) Please acknowledge authors and year where the sentences have been nearly placed verbatim from the references. It will also benefit the manuscript to write a summary of findings from the studies referenced wherever the authors would prefer to write summary and to avoid verbatim quotations. Please see examples below:\nFor example, According to an initial scenario based on projected proportions of unimmunized children in both rural and urban areas, indicates that nearly half (44%) of the unimmunized and under-immunized children in the top 10 nations, which collectively housed over half of such children in 2017, resided in urban areas. Notably, nearly every fifth unimmunized child (18%) was found to live in a slum, highlighting the specific vulnerability of these urban environments in terms of immunization coverage has been nearly lifted from Mantel and Cherian, 2020 (reference 4). If used verbatim, it will be important to acknowledge the authors in the text itself and mention the sentence in quotes.\nThe sentence \"Our study will highlight a need for government to pay attention to poor health services. Here again, it will be important to acknowledge the authors (reference 10) in the text itself and mention the sentence in quotes. Also, it is inappropriate to use an objective of another research as such in the present paper. The other improvement that is required is that our primary focus\" refers to the primary focus of the research of authors cited on reference 10.\nThe sentences: \"In the scope of this study, our primary focus will be on evaluating immunization coverage. This assessment is crucial for strategic planning of immunization programs, pinpointing vulnerable groups that necessitate targeted resource allocation, and forecasting potential epidemics of vaccine-preventable diseases. By conducting this evaluation, we aim to contribute valuable insights that can inform and enhance public health initiatives related to immunization have been picked from Joy et al, 2019.\" It will be important to acknowledge the authors and study. Also, it is inappropriate to use focus or objectives of another research as such in the present paper.\nc) Complete and accurate referencing: The authors have provided references. They are urged to provide complete references where necessary. For example, in citing Reference 10, it would be helpful to include the missing authors, names, year of publication, and page numbers.\nd) Review of protocols: Since this paper described only a study protocol, it will benefit the manuscript to include a paragraph discussing reviews of different protocols that have been used for similar studies exploring similar objectives. A few studies that can be helpful resources have been cited under citations at the end of this review, namely the studies by Ghei et. al, 2010 [Ref 3] (We have provided this as an example while urging the authors how they wish to analyze immunization data that they are collecting for children 0 to 23 months. The reviewers have urged them to consider analyzing data for age-appropriate immunization, since data for children of different ages will give immunization coverage findings at different ages and not of complete immunization. ), Murhekar et. al, 2015 [Ref 4] and Singh et. al, 2019 (Ref 5). The authors are urged to look up other studies as well.\nRecommendations for strengthening the Methods:\na) The methods section mentions that parents will be asked if they have the immunization card with the complete immunization status of their child. Please provide details for following:\n1. What does complete immunization mean for a child in the age group 0-23 month? Is it age appropriate? E.g. What if the child is 1-month-old old or 6-month-or 8-month-old? It will be vital for the authors to make this clear in the manuscript and explain how the analysis of complete immunization will be done for those say 9-months-old. (Please see Bhanot et al, 2005 ([Ref 2], cited below). We have cited this to provide an example of intra-urban health disparities which the authors could use similar studies to strengthen the introduction of the manuscript under review. The introduction needs strengthening to provide the readers of F1000 cogent data about the current state of knowledge on immunisation in urban India with use of data that reflects intr-urban disparities so that the point the authors wish to emphasise that urban slum immunisation is poor, can come to the fore more clearly.\n\n2. Is there a protocol to explain to the parent what complete immunization status means? It will be good to briefly describe how the parent will be explained complete immunization.\n3. Is there a protocol for a circumstance when the parent does not have or has lost the immunization card? It will be important to briefly describe how the probes will be administered to the parent where the card is not available or will such children be included in the study based on recall. Please add these above to the inclusion and exclusion criteria mentioned in the manuscript.\n4. Considering the Govt of India protocol now has two doses of measles vaccine before 18 months (Verma et al, 2011 [Ref 6]), the authors should explain the rationale for considering 1 dose of measles as complete immunization.\nb) Sampling Design: The authors have mentioned that the study will be cross- sectional. It will enhance the protocol to provide details about how the sample will be collected and how the data collectors will be trained.\nc) Sample Size: The authors have mentioned the minimum sample size needed. It will benefit the protocol to explain the expected drop-out rate and how the sample size will accommodate dropouts.\nd) Survey Tool: A brief description of the survey tool will also help the readers of F1000 better understand the protocol.\ne) In the revision of the manuscript, the authors should consider revising the tense of the sentences. For example, several sentences should be revised from \"study will be\" to \"study was\" carried out, considering the fact the time frame of the study would have elapsed in the revised manuscript.\nRecommendations for strengthening the discussion:\n\nIn light of the fact that this manuscript describes a study protocol, the discussion should focus on the protocol of the presented study in relation with study protocols used by other researchers to study child immunization. The authors should discuss how and why the present protocol is built on previous protocols and how this is more robust or similarly robust.\nIn terms of variables of child immunization, how the authors have utilized existing protocols to strengthen the study of variables will be valuable to mention.\nIn its present state, most sections of the discussion part are a presentation of different studies and could belong to the introduction.\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": []
},
{
"id": "284251",
"date": "16 Jul 2024",
"name": "Andrea Wendt",
"expertise": [
"Reviewer Expertise Epidemiology",
"Data analysis",
"Study designs"
],
"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 OF THE ARTICLE The article presents the rationale and the design of a cross-sectional study on immunization coverage and on important determinants of immunization of children up to the age of 23 months in urban areas of the Wardha district in India. Against the background of the rapidly increasing urban population in India, the presented study will generate valuable information with respect to immunization coverage and its determinants.\nThis peer-review report contains several suggestions on how the description of the study might be optimized. The authors should include more detailed information on various aspects to facilitate the insight of the audience.\n\nGENERAL ISSUES Please write out abbreviations at their first occurrence. Please check the syntax in your article. There are some sentences with mistakes.\n\nNOTES ON INTRODUCTION\nBackground General: Please include information on which facilities provide immunization services for children in urban areas in India. Please explain which facilities you focus upon in particular and why (Why are UHC and AWC so important?). This might help the foreign reader to contextualize your research. You mention certain determinants of immunization only in the Discussion. You should consider to include this information already in the Introduction. Can you give a percentage that particularly describes immunization coverage of the urban poor population? Paragraph 3, line 6: According to the NFHS-5 report, the percentage of 62% is not correct. The correct percentage for the NFHS-5 (years 2019-2021) is 76.4%. Paragraph 3, line 8: This, again, is the percentage for the years 2015-16 (NFHS-4). The value for the years 2019-21 (NFHS-5) is 83.8% for India overall. Paragraph 4, last sentence: This is an anticipation of the conclusion of the planned research and should be avoided in the study protocol.\nRationale Sentence 3, first half: Could you please give references for this statement and explain what you mean with it? Sentence 3, second half: You refer to reference 10 in your manuscript. This study examined the association between immunization rate and accessibility of health care facilities. As I understand, you do not want to examine associations. Is this correct? Please specify more clearly what you intend to do.\n\nAims Please explain why you study 0- to 23-months-old children and not 12- to 23-months-old children. Please describe the Wardha district (e.g., structure of rural and urban areas including population sizes; definition of the particular urban area that is the focus of the study, including social structure; etc.).\n\nNOTES ON METHODS\nFirst paragraph With the term “semi-structured questionnaire”, do you mean a questionnaire with open questions only, i.e., with no predefined response options? Could you please specific this? Who is being asked the questions in the questionnaire? Mother, father, both, or probably also someone else? What do you mean with “reasons underlying noncompliance with immunization”? (How) does the study team get access to the documents mentioned (i.e., birth certificate, vaccination record, or delivery summary of discharge)? You might consider to publish the questionnaire together with the publication of the results of your study or even with a revised version of the study protocol.\nStudy place/setting Do the participants answer the questionnaire using the Kobo Collect tool in the School of Epidemiology and Public Health or at home? If at home, what about parents without computers or internet access? Do the parents get help in using the Kobo Collect tool or shall they use it completely on their own? What about illiterate parents? Do you recruit participants from the School of Epidemiology and Public Health urban field practice area? Please specify the region from which subjects are recruited.\nInclusion criteria You might want to add the bullet point “Place of residence in urban area”\nExclusion criteria You might want to add the bullet point “Place of residence in rural area”\nSample size You might want to specify the statement “To calculate the required sample size” with the amendment “for the estimation of the immunization coverage rate”. Please give a reference for the formula. Please define the part of the formula \"Z1-α/22\" as well. Please state which underlying population size you took as the basis for the calculation. You wrote “Estimate a proportion with absolute precision”. Please describe this differently. There is certainly no absolute precision. You used an immunization coverage rate of 62% for the calculation of the required sample size. Please indicate that this is the nationwide proportion of immunized 12- to 23-months-old children in the years 2015-2016 (NFHS-4).\nSampling method Please indicate throughly how participants are recruited. Even though you apply convenience sampling, do you focus on particular subjects of the urban population (in your background section, you specifically mention urban slum populations)?\nData collection procedure As I understand, the questionnaire has three and not two sections:\nquestions on immunization questions on socio-demographic factors questions on availability and accessibility of facilities\nYou might want to update this. Overall, the table is confusing as you repeat most of the information on different lines. Which questions are asked for the information on Government UHC, Government hospital, Private clinic/hospital, Private provider, AWC, NGOs? Do these questions relate to which facilities are nearby or do they relate to where the children have been/are usually immunized? How do you assess if a UHC or AWC is less or more than 2 km away? Do you use residential addresses to calculate this or do parents define this by themselves? Please indicate why you chose 2 km as the cut-off point? Please indicate which questions are asked to assess which vaccinations have been received. The entry in the table “Sample calculation for urban children within or beyond 2 km of UHC and with or without AWC” might be moved to the section Analysis plan as this refers to data analysis. You defined the abbreviation UHC as “universal health coverage” but I guess you rather mean “urban health centre”.\nAnalysis plan and expected results Please indicate all planned analyses. You have already mentioned the computation of percentages of children with immunization coverage and within/outside 2 km of certain healthcare facilities. Do you also plan to analyze the responses on the socio-demographic questions? As I understand, you do not plan to conduct association analyses or stratified analyses (e.g., by socio-demographic factors). Is this correct? If so, I particularly suggest that you check whether it is possible to compare your study population with the base population in the study area for which you want to make statements (possibly using the sociodemographic information assessed with your questionnaire). This might help to discuss and appraise your study results. In general, as the analyses you are going to conduct are not clear, it is difficult to imagine the conclusions that you might draw from your research as well as the implication of your research. Do you plan to describe immunization coverage stratified by the age of the children? If you study 0- to 23-months-old children, younger children do certainly lack several vaccinations just because they are younger.\nDissemination Do you also plan to publish the study protocol in an indexed journal? Do you generally plan to publish the results of your work?\nNOTES ON DISCUSSION\nStudy implications What do you mean with \"The gathered data holds the potential for application in future studies\"?\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? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-239
|
https://f1000research.com/articles/12-976/v1
|
14 Aug 23
|
{
"type": "Research Article",
"title": "Radiographical assessment of post and core placement errors encountered by Saudi dental students at different educational levels",
"authors": [
"Turki Alshehri",
"Nourhan M. Aly",
"Raand Altayyar",
"Deena Alghamdi",
"Shahad Alotaibi",
"Passent Ellakany",
"Nourhan M. Aly",
"Raand Altayyar",
"Deena Alghamdi",
"Shahad Alotaibi",
"Passent Ellakany"
],
"abstract": "Background: Dental post and core is one of the common procedures performed after endodontic treatment. The aim of this study was to radiographically assess the quality of post and core procedures performed by dental students at different education levels in addition to determining the most critical errors encountered during their clinical practice. Methods: A retrospective cross-sectional study design was conducted in the College of Dentistry, Imam Abdulrahman Bin Faisal University. A total of 550 periapical radiographs (PAs) of cemented posts were retrieved from the records of patients treated by dental students. Parameters and guidelines for assessing the quality of post treatment have been determined and statistically analyzed. A P value <0.05 was considered statistically significant. Results: The study included 502 students and most of them were females (66.5%). Data were obtained from 502 patients (62% females) with fiber posts used in 98.2% of the cases. About 50% of the posts were inserted in premolars, 62.9% in the upper arch, and 66.7% were restored with crowns as a final restoration. Regarding the quality of posts, 98.4% showed good preparation quality and 98% showed good radiographic quality. The post diameter was equal to 1/3 of the root diameter in 31.9% of the cases; post length was equal to 2/3 of root length in 5% of the cases and equal to or more than crown height in all cases (100%). Length of the remaining gutta percha (GP) was between 3–5 mm in 38.8%, and there was no gap between the post and remaining GP in 95.6% of the cases. There were no statistically significant differences between dental students at different clinical educational levels regarding the quality of post placement. Conclusions: The quality of post and core procedures performed by students showed acceptable radiographic quality and were within the recommended standards.",
"keywords": [
"Dental students",
"Post and Core",
"Radiograph",
"Gutta Percha",
"Endodontically treated."
],
"content": "Introduction\n\nRestoration of endodontically treated teeth (ETT) with extensive coronal tooth loss requires the placement of dental posts and core that adds retentive features to the coronal restoration.1 Several post systems were developed either in the form of custom-made posts using gold or non-precious metals, or prefabricated stainless steel or titanium posts.2 Aesthetic posts were recently introduced as alternative options including ceramic and glass fiber posts with variable shapes and sizes.3\n\nSuccess of post and core procedures depends on following the proper sequence of the treatment plan in addition to the accuracy of each step performed prior to post placement.4 One of the reliable methods used for evaluating the post placement procedure is taking periapical radiographs (PAs) prior to, during and after post cementation.5 Several factors affect the longevity of dental posts such as proper filling and obturation, acceptable apical seal, and absence of clinical and radiographic signs and symptoms.6\n\nDental students are required to perform several clinical procedures as a prerequisite for graduation. One of these procedures is post and core placement in ETT followed by a final prosthetic restoration.4,7 Students perform post and core procedures in their clinical years following well-designed rubrics for each procedure under the supervision of their faculty supervisors to achieve the optimum outcome in each step of the treatment plan.4,5 Accordingly, these rubrics provide proper assessment of the students’ practice and skills level, and also helps in improving their ability to perform self-assessment for each specific dental procedure.\n\nThe evaluation criteria of the post and core quality include coronal tooth preparation, radicular canal preparation and post-operative cementation of the fiber post. Several studies illustrated the capability of undergraduate dental students in post placement in ETT among Saudi Universities.4,7,8 However, no studies were conducted to assess the students’ abilities and skills in post and core placement in the Eastern Province region. Hence, the aim of this study was to radiographically assess the quality of post and core performed by dental students at different educational levels in addition to determining the most critical errors encountered during their clinical practice. The null hypothesis states that there would be no statistically significant differences in the performance of dental students at different educational levels.\n\n\nMethods\n\nA retrospective cross-sectional study was conducted in the College of Dentistry, Imam Abdulrahman Bin Faisal University. A total of 550 periapical radiographs (PAs) of cemented fiber posts were collected and retrieved from the records of patients treated by dental students at Imam Abdulrahman bin Faisal University Dental Hospital. The sample size was estimated assuming 80% study power and 5% alpha error.9 The study was approved by the institution research board (IRB-2022-02-285) of Imam bin Abdulrahman bin Faisal university, dammam, Saudi Arabia.\n\nAll PAs of prefabricated posts cemented on ETT performed by undergraduate dental students in the fourth, fifth, sixth and internship years from 2018 till 2022 were included. These PAs were assessed according to the following criteria by four trained investigators (Figure 1).4,8,10\n\nPre-operative and post-operative PAs were assessed to confirm the tooth status before post placement and to determine if any errors resulted from the post placement. Poor-quality PAs, those with missing treatment details, or missing postoperative PAs were excluded. Medicor Imaging Picture Archiving and Communication System (Weasis is a free medical DICOM viewer) Dental Enterprise Viewer was used to visualize the PAs using patients’ IDs. Dental arch, tooth number, and the type of post (metal or fiber) were recorded in an excel sheet. Moreover, the assessment of the quality of canal preparation (acceptable: outline of the preparation was following the canal contour and unacceptable: canal preparation did not follow the canal outline or ledge resulted during preparation) and the quality of PAs were added to the excel sheet where the followed evaluation criteria of PAs were extracted from a previous study criteria.11 The length of the placed post was measured starting from the beginning of the restoration to the apical tip of the post as well as the crown height and root length which were measured from the cementoenamel junction to the root apex. Additionally, the length of the remaining gutta-percha in the canal, the root width and post width at the middle half of the root, and the gap between the post and gutta-percha if available, were it was measured using a digital ruler of the viewer software. Any abnormalities noticed in the PAs were also recorded in the sheet.\n\nDescriptive data were calculated as frequencies, percentages, means and standard deviations (SD). Comparisons between the three study groups were done using chi-square test for qualitative variables, and one-way ANOVA for quantitative variables. Data were analyzed using IBM SPSS for Windows (Version 23.0). P value <0.05 was considered statistically significant. An alternative proprietary free suggested software is ocscsistatistics.\n\n\nResults\n\nThe study included 502 students (348 fifth and sixth year students, 101 fourth year students and 53 interns) and most of them were females (66.5%). Data were obtained from 502 patients (62% females) with fiber posts used in 98.2% of the cases (Table 1). Table 2 shows the different parameters of included posts. About 50% of the posts were inserted in premolars, 62.9% in the upper arch, and 66.7% restored with crowns as a final restoration. Regarding the quality of posts, about 98% showed good preparation and radiographic quality. As for post assessment according to the ideal prosthetic criteria (Table 3); the post diameter was equal to 1/3 of the root diameter in 31.9% of the cases, post length was equal to 2/3 of root length in 5% of the cases, post length was equal to or more than crown height in all cases (100%), the length of the remaining GP was between 3–5 mm in 38.8%, and there was no gap between the post and remaining GP in 95.6%. There were no statistically significant differences between dental students at different clinical educational years regarding the quality of post placement according to the criteria mentioned in the methods.\n\n* Statistically significant at p value <0.05.\n\n\nDiscussion\n\nSuccess and longevity of post and core restorations depend on several criteria such as post preparation dimensions in relation to tooth dimensions, post length relative to tooth length in addition to material of the used post. All these criteria can be radiographically evaluated, thus, the current study aimed to radiographically assess the quality of post and core procedures performed by dental students at different education levels in addition to determining the most critical errors encountered during their clinical practice.\n\nThe study findings showed that 98.4% of the students did post preparations of acceptable quality. According to the criteria mentioned in the methodology, about 31.9% of students placed posts of diameter equivalent to 1/3 of the root diameter, while only 5% of the students used posts of length equal to 2/3 of root length in their cases. The acceptable length of the remaining GP (3–5 mm) was reported in 38.8% of the cases. Nonetheless, no gap was noticed between the posts and remaining GP in 95.6% of the cases which ensures optimum adaptation of the posts cemented by the students. The quality of students’ performance in post placement was acceptable and comparable among different clinical educational years. Thus, the null hypothesis was accepted.\n\nResults of the current study showed that 63.3% of the posts were cemented in maxillary teeth which comes in line with previous studies.4,8,12–15 Ease of isolation, absence of saliva and absence of tongue movements that can obscure vision and affect the quality of post restoration in the maxillary arch might be a valid explanation for this percentage.16 In case of type of the teeth restored, students commonly treated premolars followed by anterior teeth, while molars were less frequently treated. Similarly, a previous study reported that premolars were the most restored teeth with post and cores by undergraduate dental students.8 Another study showed that incisors were the most frequently restored teeth with posts followed by premolars.4 Selection of teeth by students might be related to the ease of post preparation and placement, so most students prefer treating single rooted teeth as several complications can be encountered while treating multi-rooted teeth including perforations and root fractures.17\n\nMetal posts were placed in nine cases only, while fiber posts were cemented in 493 cases. The high esthetic demand of patients was the cause of this difference where metal post can affect the shade of the definitive restoration. Also, placement of fiber posts provides better adhesion to the tooth through resin cements and reduces the percentage of vertical root fractures that might result from torquing the serrated metal posts.18–20\n\nMost of the restored teeth (95.6%) showed no gap between the cemented post and GP. This comes in agreement with Almaghrabi et al. 14 who stated that about 93% of cases did not show any gaps. Also, Mathar et al.8 reported that 82.9% of cases showed no gaps between the cemented post and GP. In evaluating the post length in relation to root length, 92.6% of the cases were following the optimum guidelines of exceeding 2/3 of the root length. Similarly, Almaghrabi et al.15 showed that post length was less than 2/3 of the root length in 61% of cases. However, Meshni et al.4 found that the post to root length ratio in almost half of the patients was 2:1.\n\nThe study findings showed that almost 31% of the cases were treated with post diameter equivalent to 1/3 of the root diameter. In line with these findings, previous studies reported that the diameter of the cemented posts was equivalent to 1/3 of the root.21,22 Additionally, another study conducted at Qassim University dental clinics showed that 81% of the post cases were of length equal to 1/3 of the root.8 This optimum post diameter dimensions agrees with Trabert et al.23 who recommended a post diameter not exceeding 1/3 of the root width to increase fracture resistance of the restoration22 in addition to reducing the possibility of root fracture.24\n\nThe ideal amount of the remaining GP in the root after post preparation ranges between 3-5 mm, and this was found in 38.8% of the cases. This comes in agreement with Al Maghrabi et al.15 who used the same criteria in their cases. They reported 3-5 mm remaining GP in 68% of cases done in King Abdulaziz university.15 Also, a different study performed in Jazan University found that 55.7% of the assessed cases were within the same range of remaining GP.4\n\nThe high percentages of cases following the standard guidelines of post and core placement and cementation among variable teeth (incisors, premolars and molars) might be justified by the presence of Faculty supervision with each student in the educational clinics to limit the complications or errors that can happen in the patient’s mouth. Additionally, following explicit calibrated rubrics by students and Faculty members in placing post and core restorations and assessing their quality might have positively affected the treatment outcome. Inclusion of different students of various dental educational levels presents generalized findings on the performance of students in the dental college of Imam Abdurrahman University. This can improve the dental curriculum of undergraduate students in order to enhance their knowledge and psychomotor skills.\n\nHowever, the current study had some limitations such as being restricted to Eastern province so the findings cannot be generalized to the broader dental population in Saudi Arabia. Also, it included undergraduate students with the exclusion of postgraduate students since the postgraduate endodontic and prosthodontics boards were recently introduced in the dental college and the total number of enrolled students do not exceed ten students. Further studies are needed to compare the performance of undergraduate and postgraduate students. Moreover, assessment of post and core quality needs to be extended in other Saudi dental colleges to detect the weaknesses in students’ performance.\n\n\nConclusions\n\nDental students showed acceptable performance in placing post and cores in ETT following the guidelines of post placement. No significant differences were reported between the performances of students of various educational years. Most of the students used narrow posts relative to the tooth diameter. Dental students’ fear of perforations of narrow canals or furcation perforations pushed them to treat mainly premolars and incisors and to use narrower posts than the proper diameter. Therefore, students need to have more confidence in their qualities to improve their clinical skills.",
"appendix": "Data availability\n\nZenodo. Radiographical Assessment of Post and Core Placement Errors Encountered by Saudi Dental Students at Different Educational Levels, 10.5281/zenodo.8126789v.\n\nThis project contains the following underlying data:\n\n• Post data.xlsx (post and core data done by students).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nSorrentino R, Di Mauro MI, Ferrari M, et al.: Complications of endodontically treated teeth restored with fiber posts and single crowns or fixed dental prostheses-a systematic review. Clin. Oral Investig. 2016; 20(7): 1449–1457. Publisher Full Text\n\nAkkayan B, Gülmez T: Resistance to fracture of endodontically treated teeth restored with different post systems. J. Prosthet. Dent. 2002; 87(4): 431–437. Publisher Full Text\n\nGoracci C, Ferrari M: Current perspectives on post systems: a literature review. Aust. Dent. J. 2011; 56: 77–83. Publisher Full Text\n\nMeshni AA, Al Moaleem MM, Mattoo KA, et al.: Radiographic Evaluation of Post-core Restorations fabricated by Dental Students at Jazan University. J. Contemp. Dent. Pract. 2018; 19(1): 66–72. PubMed Abstract | Publisher Full Text\n\nMudaysh Bajawi A, Al-Sagoor SA, Abdullah Alhadi A, et al.: Radiographic assessment of the quality of root canal treatments performed by practitioners with different levels of experience. Biomed. Pharmacol. J. 2018; 11(3): 1609–1616. Publisher Full Text\n\nChandra A: Discuss the factors that affect the outcome of endodontic treatment. Aust. Endod. J. 2009; 35(2): 98–107. PubMed Abstract | Publisher Full Text\n\nSingh AK: Dentists’ knowledge, practices, and mishaps in relation to post placement for endodontically treated teeth. Int. J. Med. Oral Res. 2022; 7(2): 39. Publisher Full Text\n\nMendonca CG, Almedia JR, Takeshita WM, et al.: Radiographic analysis of 1000 cast posts in Sergipe State, Brazil. Rev. Odontol. UNESP. 2017; 46(5): 255–260. Publisher Full Text\n\nJohnston KM, Lakzadeh P, Donato BMK, et al.: Methods of sample size calculation in descriptive retrospective burden of illness studies. BMC Med. Res. Methodol. 2019; 19(1): 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMathar MI, Almutairi AR: Radiographic assessment of the quality of post & core restorations performed by dental students at Qassim University dental clinics. Int. J. Med. Sci. 2020; 7. Publisher Full Text\n\nAbdullah A, et al.: QUALITY OF PERIAPICAL RADIOGRAPHS TAKEN BY UNDERGRADUATE DENTAL STUDENTS AT QASSIM UNIVERSITY.2015.\n\nJamani KD, Aqrabawi J, Fayyad MA: A radiographic study of the relationship between technical quality of coronoradicular posts and periapical status in a Jordanian population. J. Oral Sci. 2005; 47(3): 123–128. PubMed Abstract | Publisher Full Text\n\nAl-Hamad KQ, Al-Omari M, Al-Wahadni A, et al.: Radiographic assessment of post-retained crowns in an adult Jordanian population. J. Contemp. Dent. Pract. 2006; 7(4): 29–36. PubMed Abstract | Publisher Full Text\n\nMeshni AA, Al Moaleem MM, Mattoo KA, et al.: Radiographic Evaluation of Post-core Restorations fabricated by Dental Students at Jazan University. J. Contemp. Dent. Pract. 2018; 19(1): 66–72. PubMed Abstract | Publisher Full Text\n\nAlmaghrabi J, Alesawi A, Attar E, et al.: Radiographic Analysis of Posts Performed by Undergraduate Dental Students: A Cross-Sectional Study. Clin. Cosmet. Investig. Dent. 2022; 14: 37–43. Published 2022 Jan 23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCamcı H, Salmanpour F: Effect of saliva isolation and intraoral light levels on performance of intraoral scanners. Am. J. Orthod. Dentofac. Orthop. 2020; 158(5): 759–766. PubMed Abstract | Publisher Full Text\n\nAlfahadi HR, Al-Nazhan S, Alkazman FH, et al.: Clinical and radiographic outcomes of regenerative endodontic treatment performed by Endodontic Postgraduate Students: A Retrospective Study. Restor Dent Endod. 2022; 47(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nUthappa R, Mod D, Kharod P, et al.: Comparative evaluation of the metal post and fiber post in the restoration of the endodontically treated teeth. J Dent Res Rev. 2015; 2(2): 73. Publisher Full Text\n\nSharma S, Sharma S, Jayan B, et al.: A clinical and radiographic comparative evaluation of treatment outcome of different fiber post systems with conventional cast metal post and core system. J. Dent. Def. Sect. 2022; 16(2): 130. Publisher Full Text\n\nWang X, Shu X, Zhang Y, et al.: Evaluation of fiber posts vs metal posts for restoring severely damaged endodontically treated teeth: a systematic review and meta-analysis. Quintessence Int. 2019; 50(1): 8–20. PubMed Abstract | Publisher Full Text\n\nNimigean VR, Buţincu L, Nimigean V: A radiographic study regarding post retained restorations. Romanian J. Morphol. Embryol. 2012; 53(3 Suppl): 775–779. PubMed Abstract\n\nAdanir N, Belli S: Evaluation of different post lengths’ effect on fracture resistance of a glass fiber post system. Eur. J. Dent. 2008; 2(1): 23–28. PubMed Abstract | Publisher Full Text\n\nTrabert KC, Caput AA, Abou-Rass M: Tooth fracture--a comparison of endodontic and restorative treatments. J. Endod. 1978; 4(11): 341–345. PubMed Abstract | Publisher Full Text\n\nDeutsch AS, Musikant BL, Cavallari J, et al.: Root fracture during insertion of prefabricated posts related to root size. J. Prosthet. Dent. 1985; 53(6): 786–789. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "214866",
"date": "24 Oct 2023",
"name": "Manal Matoug-Elwerfelli",
"expertise": [
"Reviewer Expertise Restorative dentistry and Endodontics"
],
"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\nComments:\nI thank the authors for submitting this manuscript and appreciates the resources, time and effort invested by the authors in producing this manuscript. However, I highlight several issues that needs to be addressed. Additionally, the English language and grammar needs to be improved throughout the manuscript. I elaborate on the main issues below:\nTitle\nSuggested change in title; Radiographic assessment of dental post and core placement at different educational levels in an undergraduate student clinic: a 4?-year retrospective study\nKeywords\nPlease ensure keywords are suitable Mesh terms\nAbstract\nTo be edited taken the below comments into consideration\nIntroduction\nThe introduction needs to be improved, with a better structure including clinical/educational relevance of study and gap of knowledge, hence why the study was conducted.\nThe authors are advised to read classical references of dental posts such as;\nFernandes A. S., Dessai G. S. Factors affecting the fracture resistance of post-core reconstructed teeth: a review. Int. J. Prosthodont. 14, (2001).\n\nTrope M., Maltz D. O., Tronstad L. Resistance to fracture of restored endodontically treated teeth. Dent. Traumatol. 1, 108-111 (1985).\n\nThe authors mention “Accordingly, these rubrics provide proper assessment of the students’ practice and skills level, and also helps in improving their ability to perform self-assessment for each specific dental procedure.” Please elaborate on the rubrics? Consider adding as a supplementary file.\nMethods\nAs a general comment, The experimental design needs to be explained in more detail.\nPlease read for further guidance;\nhttps://doi.org/10.1111/j.1365-2591.2009.01679.x\n\nhttps://doi.org/10.7717/peerj.13858\n\nhttps://doi.org/10.1016/j.jdent.2004.01.002\nI have mentioned a few of the most important points that must be included;\nAny sample size calculation to determine power of the study? Please explain\n\nPlease add a statement about patient consent was waived due to nature of study. Also please add statement about anonymous patient information status.\n\nPlease correct; dammam To Dammam\n\nCan the authors mention was the post placement placed on primary (non-surgical) root canal treatment or re-treatment cases?\nHow were cases selected for undergraduate students? Please discuss the necessity for preoperative use of the AAE case difficulty assessment form and similar tools, especially in selecting appropriate teeth for inexperienced operators. Which cases were deemed as too difficult for students, and should this strategy be revised, or recommendations made considering the results?\nPlease add; average staff to student ratio during clinical supervision\nPlease provide further details about how the radiographs were taken? Parallel technique? Digital or manually developed?\nPlease provide further details about; post placement and to determine if any errors.\nPlease provide further details about the investigators (These PAs were assessed according to the following criteria by four trained investigators). Are they students, specialists, consultants? How many years of training?\nWere the investigators calibrated? This should be added..How was calibration performed?\nPlease clearly state inclusion and exclusion criteria.\nPlease clearly mention how root canal treatment and canal obturation was performed?\nThe authors mention (the assessment of the quality of canal preparation (acceptable: outline of the preparation was following the canal contour and unacceptable: canal preparation did not follow the canal outline or ledge resulted during preparation) and the quality of PAs were added to the excel sheet where the followed evaluation criteria of PAs were extracted from a previous study criteria (REF 11). Based on what criteria was the post/core assessed? on what criteria was the quality of canal preparation assessed? Please provide a suitable reference. Also the reference for the criteria of PAs is unsuitable, please use international guideline criteria\nResults\nThe authors state, “There were no statistically significant differences between dental students at different clinical educational years regarding the quality of post placement according to the criteria mentioned in the method.” These results are generally non-logical, is the quality of dental post/core placement for a 4th year dental student comparable to dental interns.\nFindings of the study need to be explained in more detail.\nIs the statistical analysis the most appropriate? Please consult a statistician and report the results in details\nAll table to be edited, as per above comment. Please consult a statistician for improvements\nDiscussion\nPlease add suitable reference to the first paragraph.\nThe authors must mention the endodontic pre-clinical and clinical teaching and training that the students have been taught? Additionally, what year do they start endodontic treatment? Post placement?\nThe discussion should consist of comments on the methodologies chosen and comparison with previous studies.\nThe authors keep referring to standard guidelines, please further elaborate. Which international guidelines are the authors referring too?\nLack of clinical data to further support radiographic assessment to determine success/survival should be added\nPlease add strengths of study?\nAdditionally limitations can be added, please add\nConclusion\nHow was the below statement extracted from the results; “Dental students’ fear of perforations of narrow canals or furcation perforations pushed them to treat mainly premolars and incisors and to use narrower posts than the proper diameter. Therefore, students need to have more confidence in their qualities to improve their clinical skills.” ?? Please remove if not directly extracted from the study results….\nPlease re-write the conclusion based on the results of the study\nReferences\nErrors in references are noted, To be carefully edited\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? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "11194",
"date": "13 Apr 2024",
"name": "Turki Alshehri",
"role": "Author Response",
"response": "Dear Editor and Reviewers, We would like to thank you for inviting us to resubmit our revised manuscript. We wanted to express our sincere appreciation for the time and effort you dedicated to reviewing our manuscript. Your thoughtful feedback and insights have been instrumental in refining the quality and impact of our work. We have carefully incorporated your suggestions into the revised manuscript, and we are confident that these revisions have significantly strengthened the overall content and presentation. Your thorough review has contributed to elevating the manuscript's potential to make a meaningful contribution to the prosthodontics community. In response to your invaluable comments, we have diligently revised the manuscript to address your concerns. Below, we have summarized the main points you raised and provided our responses, highlighted in yellow. Thank you for your time, consideration, and ongoing support. Sincerely Authors Comments: 1. I thank the authors for submitting this manuscript and appreciate the resources, time, and effort invested by the authors in producing this manuscript. However, I highlight several issues that need to be addressed. Additionally, the English language and grammar need to be improved throughout the manuscript. I elaborate on the main issues below: • Title: Suggested change in title; Radiographic assessment of dental post and core placement at different educational levels in an undergraduate student clinic: a 4-year retrospective study • Response: Thank you for your valuable comment. The title was adjusted in the manuscript page number 1 according to the reviewer’s suggestion. 2. Keywords: Please ensure keywords are suitable Mesh terms. • Response: Thank you for your raising this comment. Key words were adjusted in the manuscript page number 15. 3. Abstract To be edited take the below comments into consideration 4. Introduction 1. The introduction needs to be improved, with a better structure including the clinical/educational relevance of the study and the gap of knowledge, hence why the study was conducted. The authors are advised to read classical references of dental posts such as; Fernandes A. S., Dessai G. S. Factors affecting the fracture resistance of post-core reconstructed teeth: a review. Int. J. Prosthodont. 14, (2001). Trope M., Maltz D. O., Tronstad L. Resistance to fracture of restored endodontically treated teeth. Dent. Traumatol. 1, 108-111 (1985). • Response: Thank you for your valuable comment. The introduction section was modified as requested on page numbers 1,2. 2. The authors mention “Accordingly, these rubrics provide a proper assessment of the student’s practice and skills level and also helps in improving their ability to perform self-assessment for each specific dental procedure.” Please elaborate on the rubrics. Consider adding it as a supplementary file. • Response: Thank you for your comment. The rubrics were added in the methods section. They were extracted from previously published articles (5, 9, 11, 15) and verified by the prosthodontics faculty department in the dental college. The rubrics were formulated to be comprehensive including assessment of the quality of radiogragraphs, quality of obturation as well as quality of post and core preparation and placement. These criteria are explained in the methods section on pages 4-7 as well as in Table 1 and Figure 1 • Methods 5. As a general comment, the experimental design needs to be explained in more detail. Please read for further guidance; https://doi.org/10.1111/j.1365-2591.2009.01679.x https://doi.org/10.7717/peerj.13858 https://doi.org/10.1016/j.jdent.2004.01.002 • Response: Thank you for your valuable comment. Methods are explained in detail in page numbers 4-7. I have mentioned a few of the most important points that must be included. 6. Any sample size calculation to determine the power of the study? Please explain. • Response: Thank you for your important comment. The sample size was clarified in the methods section page number 3. 7. Please add a statement about patient consent being waived due to the nature of the study. Also please add a statement about anonymous patient information status. • Response: Thank you for your valuable comment. The statements were added in the methods section on page 4. 8. Please correct; dammam To Dammam • Response: The city name was corrected in the methods section of the manuscript on page 3. 9. Can the authors mention was the post placement placed on primary (non-surgical) root canal treatment or re-treatment cases? • Response: Thank you for your valuable comment. The inclusion and exclusion criteria were clarified in the methods section on page 4. 10. How were cases selected for undergraduate students? Please discuss the necessity for preoperative use of the AAE case difficulty assessment form and similar tools, especially in selecting appropriate teeth for inexperienced operators. Which cases were deemed as too difficult for students, and should this strategy be revised, or recommendations made considering the results? • Response: Thank you for your important comment. Guidelines reference was added in the methods section on page 4. 11. Please add, the average staff-to-student ratio during clinical supervision • Response: Thank you for your valuable comment. The ratio was added in the methods section in the manuscript page number 5. 12. Please provide further details about how the radiographs were taken. Parallel technique? Digital or manually developed? • Response: Thank you for your comment. The technique was added in the methods section of the manuscript on page 3. 13. Please provide further details about; post placement and to determine if any errors. • Response: Thank you for your comment. The errors are explained in detail in the methods section page number 4-7. 14. Please provide further details about the investigators (These PAs were assessed according to the following criteria by four trained investigators). Are they students, specialists, consultants? How many years of training? • Response: Thank you for your valuable comment. Criteria were mentioned in the methods section on page 4. 15. Were the investigators calibrated? This should be added. How was calibration performed? • Response: Thank you for your valuable comment. The calibration method was added in the methods section on page 4. 16. Please clearly state inclusion and exclusion criteria. • Response: Thank you for your valuable comment. The criteria were clarified in the methods section on page number 4. 17. Please clearly mention how root canal treatment and canal obturation were performed. • Response: Thank you for your valuable comment. The procedure was added in the methods section on page number 4. 18. The authors mention (the assessment of the quality of canal preparation (acceptable: outline of the preparation was following the canal contour and unacceptable: canal preparation did not follow the canal outline or ledge resulted during preparation) and the quality of PAs were added to the excel sheet where the followed evaluation criteria of PAs were extracted from a previous study criteria (REF 11). Based on what criteria was the post/core assessed? on what criteria was the quality of canal preparation assessed? Please provide a suitable reference. Also, the reference for the criteria of PAs is unsuitable, please use international guideline criteria • Response: Thank you for your comment. References to the guidelines used to assess post and core treatment quality were added in the methods section pages 4-5. • Results 19. The authors state, “There were no statistically significant differences between dental students at different clinical educational years regarding the quality of post-placement according to the criteria mentioned in the method.” These results are generally non-logical, is the quality of dental post/core placement for a 4th year dental student comparable to dental interns? • Response: Thank you for your valuable comment. The quality of treatment was comparable because the treatment procedures were done under faculty supervision from both departments’ endodontics and prosthodontics. This might explain the lack of significant difference in the treatment quality of all dental years included in the study. This justification was mentioned in pages 12 and 13. 20. The findings of the study need to be explained in more detail. • Response: Thank you for your valuable comment. The findings were thoroughly explained in the discussion section on pages 11 and 12. 21. Is the statistical analysis the most appropriate? Please consult a statistician and report the results in detail. • Response: Thank you for your comment. All comments were adjusted in the result section pages 8-10. 22. All tables to be edited, as per the above comment. Please consult a statistician for improvements • Response: Thank you for your valuable comment. The result section was adjusted as recommended on pages 8-10. • Discussion 23. Please add a suitable reference to the first paragraph. • Response: Thank you for your important comment. References were added to the introduction on page 3. 24. The authors must mention the endodontic pre-clinical and clinical teaching and training that the students have been taught. Additionally, what year do they start endodontic treatment? Post placement? • Response: Thank you for your valuable comment. All details were added in the methods section page number 11. 25. The discussion should consist of comments on the methodologies chosen and a comparison with previous studies. • Response: Thank you for your comment. The discussion was adjusted according to the suggestion. 26. The authors keep referring to standard guidelines, please further elaborate. Which international guidelines are the authors referring to? • Response: Thank you for your valuable comment. The guidelines of post and core placement and endodontic case selection were added to the methods (Table 1 and Figure 1) on pages 4-7. 27. Lack of clinical data to further support radiographic assessment to determine success/survival should be added. • Response: Thank you for your comment. The data were added in the methods section and compared with previous similar studies. 28. Please add the strengths of the study. • Response: Thank you for your valuable comment. Strengths are available in the discussion section on page 13. 29. Additionally, limitations can be added, please add • Response: Thank you for your valuable comment. Limitations are mentioned in the discussion section on page 13. • Conclusion 30. How was the below statement extracted from the results; “Dental students’ fear of perforations of narrow canals or furcation perforations pushed them to treat mainly premolars and incisors and to use narrower posts than the proper diameter. Therefore, students need to have more confidence in their qualities to improve their clinical skills.”?? Please remove if not directly extracted from the study results…. Please re-write the conclusion based on the results of the study. • Response: Thank you for your comment. The conclusion was adjusted on page 13. • References 31. Errors in references are noted, and to be carefully edited. • Response: Thank you for your valuable comment. All references were adjusted according to journal guidelines in the reference section."
}
]
},
{
"id": "224915",
"date": "21 Dec 2023",
"name": "Yuanita Lely Rachmawati",
"expertise": [
"Reviewer Expertise 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\nComments:\nI appreciate the hard work that all authors have put into this research. However, some details need to be added\n\nKeywords Please check the selected words in the MeSH\nMethods Please explain in more detail about sample size calculation.\nWhat Intraoral X-ray imaging unit was used and how the PA technique was taken\n“These PAs were assessed according to the following criteria by four trained investigators”. Please add information related to the investigator: who are they, how they got the training, and how to measure the agreement between them.\nFigure 1 looks blurry, the writing needs to be clarified.\nResults At Methods section mentions “A total of 550 periapical radiographs” but in the Result section “The study included 502 students”. Please explain whether the analysis unit was PA or student, and the reasons why there are differences in numbers.\nOne-way ANOVA was used in this study. One-way ANOVA is a statistical test that is used to measure differences in average data on numerical scale variables. The authors can add a table that informs the mean and SD values of the variables.\nDiscussion\nIt is necessary to add references in the first paragraph.\nPlease add the reference of the standard guidelines of post and core placement and cementation among variable teeth\nConclusion The content of the conclusion is focused on the research objectives and results\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? No",
"responses": [
{
"c_id": "11193",
"date": "13 Apr 2024",
"name": "Turki Alshehri",
"role": "Author Response",
"response": "Dear Editor and Reviewers, We would like to thank you for inviting us to resubmit our revised manuscript. We wanted to express our sincere appreciation for the time and effort you dedicated to reviewing our manuscript. Your thoughtful feedback and insights have been instrumental in refining the quality and impact of our work. We have carefully incorporated your suggestions into the revised manuscript, and we are confident that these revisions have significantly strengthened the overall content and presentation. Your thorough review has contributed to elevating the manuscript's potential to make a meaningful contribution to the prosthodontics community. In response to your invaluable comments, we have diligently revised the manuscript to address your concerns. Below, we have summarized the main points you raised and provided our responses, highlighted in yellow. Thank you for your time, consideration, and ongoing support. Sincerely Authors Comments: I appreciate the hard work that all authors have put into this research. However, some details need to be added. • Keywords 1. Please check the selected words in the MeSH • Response: Thank you for your valuable comment. Keywords were adjusted in the manuscript on page 15. • Methods 1. Please explain in more detail about sample size calculation. • Response: Thank you for your comment. The modifications were done in the methods section of the manuscript on page 3. 2. What Intraoral X-ray imaging unit was used and how the PA technique was taken? • Response: Thank you for your raising this important point. The modification was done in the methods section of the manuscript on pages 4-5. 3. “These PAs were assessed according to the following criteria by four trained investigators”. Please add information related to the investigator: who are they, how they got the training, and how to measure the agreement between them. • Response: Thank you for your important comment. The assessment method was clarified in the methods section of the manuscript on page 4. 4. Figure 1 looks blurry; the writing needs to be clarified. • Response: Thank you for your valuable comment. Figure resolution was adjusted in the methods section on page 6. • Results 1. At Methods section mentions “A total of 550 periapical radiographs” but in the Result section “The study included 502 students”. Please explain whether the analysis unit was PA or student, and the reasons why there are differences in numbers. • Response: Thank you for your raising this important point. This difference in the total number mentioned in the results was due to the missing data of 48 cases, and this statement was added in the results section on page 8. 2. One-way ANOVA was used in this study. One-way ANOVA is a statistical test that is used to measure differences in average data on numerical scale variables. The authors can add a table that informs the mean and SD values of the variables. • Response: Thank you for your valuable comment. Table 1 includes the requested information on page 8. • Discussion 1. It is necessary to add references in the first paragraph. • Response: Thank you for your valuable comment. References were added to the introduction and rearranged in the reference section page number 14 and 15. 2. Please add the reference of the standard guidelines of post and core placement and cementation among variable teeth • Response: Thank you for your valuable comment. The guidelines used were added in Table 1 and the reference of previous studies (5, 9, 11, 15) where the guidelines were extracted and added in the methods section pages 5-7. • Conclusion 1. The content of the conclusion is focused on the research objectives and results. • Response: Thank you for your valuable comment. The conclusion was adjusted on page 13."
}
]
}
] | 1
|
https://f1000research.com/articles/12-976
|
https://f1000research.com/articles/13-235/v1
|
28 Mar 24
|
{
"type": "Research Article",
"title": "Using X, Facebook QR codes to optimise recruitment to a feasibility trial Enhancing Men’s Awareness of Testicular Diseases (E-MAT) in a cluster randomised Study Within A Trial (SWAT): Lessons learned.",
"authors": [
"Frances Shiely",
"Eoghan Cooke",
"Megan McCarthy",
"Darren Dahly",
"Janas Harrington",
"Gillian W. Shorter",
"Martin P. Davoren",
"Josephine Hegarty",
"Aileen Murphy",
"Ann Kirby",
"David Murphy",
"Steve Robertson",
"Michael J. Rovito",
"Serena Fitzgerald",
"Alan O'Connor",
"Mícheál O'Riordan",
"Mohamad M Saab",
"Eoghan Cooke",
"Megan McCarthy",
"Darren Dahly",
"Janas Harrington",
"Gillian W. Shorter",
"Martin P. Davoren",
"Josephine Hegarty",
"Aileen Murphy",
"Ann Kirby",
"David Murphy",
"Steve Robertson",
"Michael J. Rovito",
"Serena Fitzgerald",
"Alan O'Connor",
"Mícheál O'Riordan",
"Mohamad M Saab"
],
"abstract": "Background Eight out of ten adults use social media, yet its efficacy in recruitment in clinical trials remains under-explored. The purpose of this SWAT was to determine which recruitment method, X, Facebook or QR code via posters, was more efficient and cost effective for recruiting participants to the host trial.\n\nMethods A cluster randomised cross-over design evaluated three recruitment strategies, X, Facebook and QR code. Seven Gaelic Athletic Association (GAA) clubs were randomised to receive either X, Facebook, or QR code. The seven clubs were re-randomised twice more, two weeks apart. There were two primary outcomes: 1. proportion of participants who consent to participate, relative to the number of players contacted; and 2. proportion of participants who consent to participate, relative to the number of players who clicked the link to register their interest.\n\nResults Fifty participants were randomised to three recruitment methods, and 47 were retained in the host trial. Participants mainly heard about the study through friends, with some engagement via social media platforms Facebook and X, and little to no engagement with the QR code. Primary outcomes were hindered by the inability to disaggregate data by GAA club. Economic outcomes revealed QR code as the costliest strategy, and while X was cheaper than Facebook in terms of the number of clicks, Facebook demonstrated better recruitment and retention and thus reduced the costs per participant.\n\nConclusions While the inability to disaggregate data by club was a limitation, the study revealed that Facebook outperformed X and QR codes in terms of recruitment and participant retention and was thus considered to be more cost effective. The findings emphasise the importance of considering engagement patterns and cost-effectiveness in designing recruitment strategies for clinical trials, especially within the dynamic landscape of social media use.",
"keywords": [
"Cluster randomised controlled trial",
"feasibility study",
"recruitment",
"SWAT",
"social media",
"testicular neoplasms",
"men’s health."
],
"content": "Introduction\n\nSuccessful trial recruitment is challenging, with fewer than 50% of trials meeting their targets.1 The evidence available to trialists to support decisions on design, conduct and reporting of randomised trials is sparse, suggesting further trial methodological work is needed.2 PRioRiTy I3 & II4 studies identified the most important unanswered research questions in recruitment and retention, respectively, and one of the top ten recruitment priorities was the use of technology in the recruitment process. Eight out of ten adults use social media, yet its efficacy in recruitment in clinical trials remains under-explored.5 The purpose of this study within a trial (SWAT) was to determine which recruitment method (X, formerly Twitter), Facebook, or quick response [QR] codes via posters) was more efficient and cost effective for recruiting participants to the primary host trial. We also aimed to determine if the recruitment method influenced retention in the host trial. The SWAT protocol is registered in the Northern Ireland SWAT repository as SWAT 162.\n\n\nMethods\n\nWe used a cluster randomised cross-over design to evaluate the three recruitment strategies (X, Facebook and QR code). Seven Gaelic Athletic Association [1] (GAA – Irish football and hurling) clubs agreed to participate in the SWAT and were randomised using Research Randomizer (https://www.randomizer.org/) to either Facebook (n = 2), X (n = 3) or QR code (n = 2) for a period of two weeks. After two weeks, the seven clubs were re-randomised to either one of the other recruitment methods, i.e., the two Facebook clubs were then randomised to get either X or QR. After a further two weeks, the GAA clubs changed to the final remaining recruitment method for one further two-week period. Clubs were asked to post the Facebook and X posts twice per week between 12pm and 1pm. We were dependent on the clubs to do the posting when we directed them to but had no control over this occurrence. In relation to the QR code, 10 posters were displayed in each club for the two-week period of their randomisation.\n\nParticipants were eligible to participate in the SWAT if they were assigned male at birth, members (i.e., players and coaches) of the target GAA clubs, residing in the Republic of Ireland, and aged 18 to 50 years (age group at risk for testicular diseases).\n\nTwo PPI collaborators on the host trial are members of the participating GAA clubs and were involved in the development of the grant application which included the SWAT. They provided background information on player demographics, determining the potential recruitment strategies for the SWAT, and identified the appropriate time in the GAA season to start the recruitment. Both collaborators were compensated for their time and are included as co-authors (AOC and MOR).\n\n\n\n1. Proportion of participants who consent to participate in the host trial, relative to the number of players contacted via each recruitment method.\n\n2. Proportion of participants who registered their interest to participate, relative to those consented to the host trial via each social recruitment method.\n\n\n\n1. Proportion of participants randomised who remain to the conclusion of the study.\n\n2. Unit cost per person who registered their interest by clicking the link/scanning QR code.\n\n3. Unit cost per person consented to the host trial.\n\n4. Unit cost per person retained at end point of the host trial.\n\nTitle\n\nEnhancing Men’s Awareness of Testicular Diseases (E-MAT): A Feasibility Study (ClinicalTrials.gov Identifier: NCT05146466).\n\nAim of host trial\n\nTo examine the feasibility of conducting a definitive trial to test the effect of E-MATVR (Virtual Reality) (intervention) compared to E-MATE (Electronic information only) (control) on testicular knowledge and testicular self-examination behaviours among male GAA players over three months. We developed a three-level Virtual Reality (VR) educational game called “Enhancing Men’s Awareness of Testicular diseases” or E-MATVR, delivered using a VR headset, handheld controllers, and voiceover.6,7 E-MATVR uses light humour to educate men about testicular diseases and encourages them to examine their testicles and seek medical help for symptoms of concern. The feasibility study compares E-MATVR to a traditional electronic intervention that uses plain text and images via a Tablet or E-MATE. The primary outcomes measured in the feasibility trial were testicular knowledge and testicular self-examination behaviours. The feasibility trial took place in nine geographically distributed GAA sports clubs in County Cork, a southern region in Ireland, over a three-month period. For each of the nine participating GAA clubs, individual participants were randomised to either the intervention or control arm. Risk of contamination was low due to the geographical dispersion of the GAA clubs.\n\nOutcomes were measured at baseline (T0, pre-engagement with E-MATVR or E-MATE), immediately post-test (T1, post engagement with E-MATVR or E-MATE), and three months post-test (T2) using electronic surveys. We expected that players would pass the study link to other players. To capture this, at T0 we asked the participants if they learned about either of the three recruitment methods directly, link through WhatsApp, or if they were referred by a friend.\n\nFacebook\n\nThe GAA club has a record of self-identified males on the club Facebook page, which gives us the total number targeted (denominator). We were dependent on the clubs to make the Facebook posts.\n\nX\n\nOn X there is an Engagement Application Programming Interface (API) which measures engagements - a count of the number of time a user has interacted with the X post, how often it has been favourited, liked, reposted, replied, and shared. We were dependent on the clubs to make the X posts.\n\nQR code\n\nThe QR code was displayed by means of a professionally designed poster at each club. Ten posters were displayed in each club for the 2-week period of their randomisation. We were able to monitor the number of people who used the QR code.\n\nMicro-costing techniques were used to estimate cost-per-strategy. Costs include direct design and distribution for each strategy; print (received from the company who created the posters and Facebook and X posts), collection costs (travel as per the University’s travel allowance) and personnel costs (valued using national salary scales for staff grade level as per national guidelines8). Trial data were used to identify and measure the quantity of each resource and market values were employed to value them in Euros, for the year 2022.\n\nExploratory data analysis was conducted, and outliers reconciled. Analysis was conducted on an intention-to-treat basis using the cluster randomisation scheme. Analysis was conducted using R (version 4.0.3; R Project for Statistical Computing, Vienna, Austria) and, in all cases, a 2-sided type I error rate of 0.05 was taken as statistically significant.\n\n\nResults\n\nNine GAA clubs were recruited to the host trial. Seven agreed to participate in the SWAT. Fifty participants, from seven GAA clubs, were randomised to the three recruitment methods. Table 1 shows the number of male members in each club, i.e., target population. In total, 47 out of 50 SWAT participants were retained in the host trial.\n\n* NA = Not available.\n\n^ Unable to ascertain which of the clubs the clicks came from.\n\nAt T0 we asked participants where they heard about the feasibility trial (Table 2). The majority heard about it exclusively from a friend (n = 20). Facebook and X were the next most common. Only one participant heard about the trial through the QR code.\n\nWe had two primary outcomes: 1) the proportion of participants who consent to participate, relative to the number of players contacted via each recruitment method; and 2) the proportion of participants who consent to participate, relative to the number of players who clicked the link to register their interest via each recruitment method. We were unable to disaggregate our data by GAA club thus we were unable to present data for the primary outcomes. We worked with a design company and used one Facebook link, one X link and one QR code link for ALL of the GAA clubs.\n\nHowever, we are able to present some useful data, to assist others who use these recruitment methods in the future. The data presented in Table 3 are for the 16 people who entered the host trial, but not coming exclusively from the SWAT. Though X had the most clicks, it had fewer people who consented to the trial when compared to Facebook. Engagement via the QR code was poor.\n\nWe were able to identify the peak hours of use for X and Facebook, using the Engagement API which provides access to post impression and engagement metrics. X peaks in use at 12pm, 6pm and 9pm. Facebook peaks in use at 8am and 8pm. In terms of the days of the week that showed most usage, X peaked on Tuesday and Thursday while Facebook peaked on Friday. This may have been the days the X and Facebook posts were made but we do not have that information from each club to clarify this.\n\nWe had four secondary outcomes. Of the 50 participants randomised to the SWAT, 47 were retained. As so few were lost to follow-up (n = 3), we could not assess primary retention across the three recruitment methods. The remaining three secondary outcomes were economic outcomes related to cost-per-strategy. 1) unit cost per person who registered their interest by clicking the link/scanning QR code; 2) unit cost per person consented to the host trial; 3) unit cost per person retained at end point of the host trial. We were unable to disaggregate the SWAT information (n = 50) from the host feasibility trial (n = 74). Thus, the information presented below, and in Tables 4 and 5, is for the host trial. We first determined the total costs per recruitment strategy. As can be seen in Table 4, the QR code was the most expensive, while X and Facebook had equivalent total costs. As per Tables 4 and 5, in all cases, the QR code was the most expensive. While X was cheaper than Facebook in terms of the number of clicks, the engagement was better with Facebook resulting in more being consented and retained through Facebook, thereby reducing costs per participant.\n\n1 Design company cost €151 equally split between 3 strategies (Source: Trial documentation).\n\n2 Poster design (€160), printing (€113.65) and delivery (€106.91) (Source: Trial documentation).\n\n3 Research Assistant salary €31,617 pa (Source: Trial documentation).\n\n\nDiscussion\n\nThe results of our study provide insights into the effectiveness and cost-effectiveness of different recruitment methods in the context of a community sports club setting. Our study involved nine GAA clubs (n = 74), with seven participating in the SWAT (n = 50) who were randomised to three recruitment methods. Most participants heard about the study exclusively from a friend, highlighting the importance of interpersonal networks in disseminating information within the GAA community; replicated in other studies showing the centrality of social networks on and offline in transmitting health care information.9 This is likely a feature of communication in all sports clubs in the community. Facebook and X were also prominent sources of information, with only one participant discovering the study through the poster with QR code. This indicates the limited effectiveness of QR codes as a standalone recruitment method in this context. When compared to other social media recruitment methods Facebook and X, the QR code was also relatively expensive. We do not recommend using it in a trial in the community. X and Facebook set-up costs were equal, but initial engagement, i.e., numbers of clicks, was greater in X, thereby reducing the cost per participant. However, the proportion who consented from the engagement was greater with Facebook, thus Facebook can be considered cost effective compared to X when considering those consented and retained.\n\n\n\n1. The inability to disaggregate data by GAA club due to the use of a single Facebook link, one X link and one QR code link for ALL of the GAA clubs is a limitation. Understanding the aggregate is useful, but there may be diversity in recruitment that is under-explored, such as impact on recruitment by individual or group characteristic (e.g., ethnicity10). Creating separate links (Facebook, X, QR code) for each of the GAA clubs would have allowed for a more granular analysis of the recruitment process. This would have provided valuable insights into the effectiveness of each method within individual clubs and could have informed targeted recruitment strategies.\n\n2. Monitoring X and Facebook interactions in a sport club setting is challenging, as it was not possible to disentangle the SWAT participant data from general GAA club data. The reason for this was because we did not have direct administrative access to the club accounts. To conduct recruitment in the way we did, and to be able to evaluate it, researchers would need to be given user/administrator rights to each club’s Facebook and X accounts.\n\n3. In addition to members of the GAA club, there were other individuals that follow the GAA Club’s X and Facebook pages, so relying on club membership to determine the denominator was not meaningful.\n\n4. Many of the participants heard about the study from friends, therefore, we were unable to determine which recruitment method they were recruited through.\n\n5. While we were focused on three recruitment methods, as we can see in Table 1, some people accessed the Facebook and X links via Text Message or WhatsApp, making it difficult to track the reach of the recruitment method.\n\n6. We were overambitious when defining our outcomes and for a small SWAT, there were too many. The ‘keep it simple’ approach – fewer outcomes – would have been better.\n\n7. It is evident that the hours of use for X and Facebook which would help identify suitable times to post information on the study in future trials. For this community of users, X spikes in use at 12pm, 6pm, and 9pm. Facebook peaks in use at 8am and 8pm. In terms of the days of the week that showed most usage, X peaked on Tuesday and Thursday while Facebook peaked on Friday. This may have been the days the X and Facebook posts were made but we do not have the required information from each GAA club to determine that.\n\n\nConclusion\n\nIn conclusion, we have tentative evidence on the ability to recruit males to healthcare trials which demonstrated better value for money through Facebook, followed by X, with little to no-engagement with QR codes. Engaging with social networks is essential to support recruitment. The limitations of data tracking and customisation to evaluate recruitment methods in research studies are highlighted, especially when dealing with multiple groups or recruitment methods in a pragmatic community setting. We encourage others to evaluate their recruitment methods in SWATs to support or refute our conclusions and support trial engagement. These insights can inform future research, particularly future definitive trials, allowing for more robust recruitment of participants, data collection and analysis, ultimately enhancing the validity and reliability of research findings.\n\nEthical approval for this SWAT was obtained from the Clinical Research Ethics Committee (CREC), University College Cork in December 2021 (CREC Review Reference Number: ECM 06/2023 PUB). We confirm that we obtained written, informed consent from all participants enrolled in this study.",
"appendix": "Data availability statement\n\nThe data underlying the results are available as part of the article and no additional source data are required, except for social media data and the data from the QR code posters. The social media data came from the Facebook page and X pages of the GAA clubs. This data is in the form of posts, likes, followers and clicks. The QR code posters contained data on clicks only. The social media data cannot be shared due to the ethical and copyright restrictions surrounding social media data. The Methods section contains detailed information to allow replication of the study. Also, the study is small due to its nature and it could potentially identify the GAA clubs if we release it publicly. Any queries about the methodology should be directed to the corresponding author. If someone requests the data or have questions about the methodology, we are happy to discuss this with them.\n\nWe await reporting guidelines for SWATs which are being led by the University of York and are expected to be published in 2024.\n\n\nAcknowledgements\n\nWe wish to express our appreciation to the GAA clubs who facilitated the data collection for this SWAT, and to their members for partaking.\n\n\nReferences\n\nGardner HR, Fraser C, MacLennan G, et al.: A protocol for a systematic review of non-randomised evaluations of strategies to improve participant recruitment to randomised controlled trials. Syst. Rev. 2016; 5(1): 131. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTreweek S, Bevan S, Bower P, et al.: Trial forge guidance 1: what is a study within a trial (SWAT)? Trials. 2018; 19(1): 139. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHealy P, Galvin S, Williamson PR, et al.: Identifying trial recruitment uncertainties using a James Lind Alliance priority setting partnership–the PRioRiTy (Prioritising recruitment in randomised trials) study. Trials. 2018; 19(1): 147. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrunsdon D, Biesty L, Brocklehurst P, et al.: What are the most important unanswered research questions in trial retention? A James Lind Alliance Priority Setting Partnership: the PRioRiTy II (Prioritising Retention in Randomised Trials) study. Trials. 2019; 20(1): 593. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFox S: The social life of health information, 2011: Pew Internet & American Life Project Washington, DC.2011.\n\nSaab MM, Landers M, Cooke E, et al.: Feasibility and usability of a virtual reality intervention to enhance men’s awareness of testicular disorders (E-MAT). Virtual Real. 2019; 23: 169–178. Publisher Full Text\n\nSaab MM, Landers M, Cooke E, et al.: Enhancing men’s awareness of testicular disorders using a virtual reality intervention: A pre–post pilot study. Nurs. Res. 2018; 67(5): 349–358. PubMed Abstract | Publisher Full Text\n\n(HIQA) HIaQA: Guidelines for the Economic Evaluation of Health Technologies in Ireland. Dublin.2020.\n\nWright K: Social networks, interpersonal social support, and health outcomes: A health communication perspective. Front. Commun. 2016; 1: 10. Publisher Full Text\n\nDawson S, Banister K, Biggs K, et al.: Trial Forge Guidance 3: randomised trials and how to recruit and retain individuals from ethnic minority groups—practical guidance to support better practice. Trials. 2022; 23(1): 672. PubMed Abstract | Publisher Full Text | Free Full Text\n\n\nFootnotes\n\n1 https://www.gaa.ie/"
}
|
[
{
"id": "289144",
"date": "19 Jun 2024",
"name": "Nikolaos Boumparis",
"expertise": [
"Reviewer Expertise Digital health",
"addiction",
"randomised controlled trials",
"systematic reviews and meta-analyses."
],
"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 investigates the effectiveness and cost-effectiveness of three recruitment methods (X, Facebook and QR codes) for a feasibility trial aimed at increasing male awareness of testicular disease.\n\n- The manuscript is well written and generally easy to follow. The inclusion of a patient and public involvement component is appreciated as it ensures that the design and conduct of the study is informed by the target population.\n- However, the inability to disaggregate data by GAA club due to the use of a single link for each recruitment method severely limits the findings.\n- The inability to present primary outcomes due to data aggregation issues is a major drawback.\n\n-The aim of the study was to evaluate different social media-based recruitment methods. However, the high incidence of participants being referred by friends dilutes the ability to accurately assess which recruitment method was most effective.\n- The study appropriately highlights the limitations and provides some good lessons for future studies.\n\n- Although the manuscript states that \"exploratory data analysis was performed\" and \"outliers were reconciled\", these statements lack sufficient detail to ensure reproducibility. The manuscript should explicitly state the criteria used to identify outliers, and any impact of outlier handling on the results and conclusions should be discussed to provide transparency on how these decisions may have influenced the results.\nOverall, a lot of things went wrong in this study, but it is still a useful paper because it describes several lessons learned that could prevent future studies from making the same mistakes. It also provides some valuable insights of different recruitment methods for clinical trials in similar contexts.\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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-235
|
https://f1000research.com/articles/12-1098/v1
|
01 Sep 23
|
{
"type": "Study Protocol",
"title": "Lower limb rehabilitation using modified constraint-induced movement therapy and motor relearning program on balance and gait in sub-acute hemiplegic stroke: a comparative study",
"authors": [
"Nitika S. Chavan",
"Raghumahanti Raghuveer",
"Raghumahanti Raghuveer"
],
"abstract": "Background: A stroke is described by the World Health Organization as “a clinical syndrome with rapidly developing symptoms that consist of a focal (or global, in a situation of coma) disruption of cerebral function that lasts more than 24 hours or leads to mortality without a known cause other than a vascular origin”. Stroke is the most prevalent cause of impairment and mortality on a global scale. Modified constraint-induced movement therapy (mCIMT) is an approach to therapy for motor disabilities that involves constraining the movements of the nonparetic limb, diligent practice and behaviour modification to extend the time the paretic limb is utilized for daily tasks. The motor relearning program (MRP) method involves many aspects of motor learning theory and is helpful in providing instructions for retraining practical skills (including walking, standing and sitting in balance and transferring abilities). So, the objective of this study is to assess the impact of the MRP and mCIMT on balance and gait in sub-acute hemiplegic stroke patients. Methods: In this study, each group will consist of 17 people in total. The randomization procedure will be conducted using a computer-generated random number system. For sample distribution, we will use the sequentially numbered opaque sealed envelope technique. Outcome measures will be as follows: Berg balance scale, Dynamic gait index, Trunk impairment scale, Functional reach test, 10 Meter walk test and Fall efficacy test. Each patient will be evaluated prior to and during treatment at baseline and six weeks later. Conclusions: There is sufficient evidence to derive the conclusion that the functional mobility and balance of stroke victims can be improved with physiotherapy. Therefore, this study will try to seek the comparison of mCIMT and MRP in sub-acute stroke subjects and compare the two regimes to determine which one will be superior. Registration: CTRI (CTRI/2023/05/052674; 16/05/2023).",
"keywords": [
"Hemiplegic Stroke",
"Modified constraint-induced movement therapy",
"Motor relearning program",
"Berg balance scale",
"Dynamic gait index"
],
"content": "Introduction\n\nStroke, which is deemed by the World Health Organization (WHO) to be the “quickly growing clinical evidence of a permanent (or worldwide) brain function impairment with sign and symptoms lasting 24 hours or more or causing mortality with no apparent cause other than the vascular origin”.1 Stroke incidence ranges from 105 to 152/100,000 per year, making it the third most prevalent cause of impairment and the second-leading cause of mortality worldwide.2,3 In India, the prevalence of stroke considerably rises with age; compared to younger persons, the risk is higher for those over 55 years old and lower for those between 45 and 54 years old (0.80% vs. 1.97%, respectively). Stroke risk is higher in men than in women. African Americans, Hispanics, and Americans have a higher risk of stroke compared to other races. Americans are more likely to have a stroke.4 Stroke is divided into two distinct subtypes based on its aetiology: ischemic and haemorrhagic. The ischemic type of stroke, which affects 85% of patients, arises whenever the vascularity of the brain tissue is damaged as the blood clot blocks or plugs a blood vessel in the brain. However, 15% of acute strokes are haemorrhagic strokes, which are brought on by a burst blood vessel or an abrupt haemorrhage. Subarachnoid and intracerebral haemorrhage are the two main forms of haemorrhagic attacks.5\n\nThere are numerous causes of stroke. Common risk factors include smoking (12%), heredity, hypertension, diabetes mellitus, high cholesterolemia (15%) and lack of physical activity.4 Alcohol consumption that is mild to moderate carries a slightly lower risk of ischemic stroke, however higher drinking significantly boosts the risk.6 Common stroke problems include gait impairment that makes it difficult to maintain postural alignment as well as stiffness, fatigue, and loss of balance on the affected side. One of the most frequent problems following a stroke is paralysis. Usually, opposing the brain side of the body that has been harmed by a stroke undergoes the paralysis. It can affect the overall side of the body, the face, upper limb, lower limb or even one of the legs. Hemiplegia refers to this type of unilateral paralysis. There are several anatomical and functional abnormalities that are followed by hemiplegia. These people frequently have functional mobility and balance issues as a result of their movement paralysis.7 Without using more resources, a planned program can considerably raise documented patient activity levels during inpatient stroke therapy.\n\nThe main goal of stroke treatment is to promote activity in daily life (ADL) independence while restoring function.8 There are numerous physiotherapy approach treatments for stroke, including body weight supported treadmill training, electromechanical-assisted training, virtual reality therapy, constraint-induced movement therapy, motor relearning program, robot-assisted training, mirror therapy and proprioceptive neuromuscular facilitation. All methods for restoring voluntary control and mobility after a stroke operates according to its own principles.9 Major studies have revealed that muscle weakness is the main thing preventing physical function from recovering.9 Conventional exercises are ones that are performed all around the world. These include exercises such as passive motion, exercise at the gym, gait training, electrical stimulation, and functional re-education.10 Modified constraint-induced movement therapy (mCIMT) is a type of therapeutic intervention for those with motor disabilities. The established method for treating the paretic upper limb enhances the functional usage by preventing “learned disuse” that occurs after a stroke.11,12\n\nThree main elements of mCIMT include the use of repetitive, structured, practice-intensive therapy in the more paretic limb, constraint of the non-paretic limb and a variety of behavioural strategies that translate improvements made in a clinical setting to everyday life. Recently, mCIMT has also been used to the paretic lower limb with the goal of improving neurological function and prevent “learned misuse”. One of the rehabilitation techniques utilised predominantly with the post-stroke population is the motor relearning program (MRP). This technique incorporates several elements of motor learning theory and includes practical advice for retraining practical abilities (such as a balanced sitting position, sitting and standing, skill transfer, and walking).13 With good feedback and practise, this approach focuses on the growth of active movement control and task-specific learning. It is less frequently encountered to use facilitation tactics in preference for verbal direction, demonstrations and manual recommendation.14\n\nThree main elements of mCIMT include the use of repetitive, structured, practice-intensive therapy in the more paretic limb, constraint of the non-paretic limb and a variety of behavioural strategies that translate improvements made in a clinical setting to everyday life. Recently, mCIMT has also been used to the paretic lower limb with the goal of improving neurological function and prevent “learned misuse”. One of the rehabilitation techniques utilised predominantly with the post-stroke population is the motor relearning program (MRP). This technique incorporates several elements of motor learning theory and includes practical advice for retraining practical abilities (such as a balanced sitting position, sitting and standing, skill transfer, and walking).13 With good feedback and practise, this approach focuses on the growth of active movement control and task-specific learning. It is less frequently encountered to use facilitation tactics in preference for verbal direction, demonstrations and manual recommendation.14\n\n\n\n1. To study the effect of mCIMT in addition to conventional therapy on balance (using the Berg Balance Scale (BBS)) and gait (using the Dynamic Gait Index (DGI)) in sub-acute hemiplegic stroke.\n\n2. To study the effectiveness of MRP along with conventional therapy on balance (BBS) and gait (DGI) in sub-acute hemiplegic stroke.\n\n3. To compare mCIMT and the MRP in improving balance and gait in sub-acute hemiplegic stroke patients along with conventional therapy.\n\nA single-centre, two arm, parallel group, comparative open labelled superiority trial will be conducted.\n\n\nMethods\n\nThe model consent form, data collection form and schedule of enrolment, interventions and assessments can be found as Extended data.24 This protocol adheres to the SPIRIT guidelines.25\n\nAfter gaining clearance from the Institutional Ethics Committee (IEC) of Datta Meghe Institute of Higher Education and Research (Deemed to be University), participants will be enrolled from the Physiotherapy Outpatient Department of Acharya Vinoba Bhave Rural Hospital Sawangi, Meghe, Wardha, Maharashtra. A total of 34 participants will be made aware of the study’s objectives and procedures and will be asked to sign written patient consent forms. All hemiplegic stroke patients who meet the inclusion and exclusion parameter will be included in the study. They will be further separated into Group A and Group B by means of simple random selection. Each group will consist of 17 people in total. The randomization procedure will be conducted using a computer-generated random number system. For sample distribution, we will use the sequentially numbered opaque sealed envelope technique. There will be no blinding procedure in this study. The principal investigator will generate allocation, enrol participants and assign participants to interventions. A departmental committee made up of the Post Graduate (PG), Guide, the Head of Department (HOD), the Principal of the Ravi Nair Physiotherapy College (RNPC) and a member of the Research Guidance Cell will oversee the project. Through routine treatment sessions, we will make sure that the patients follow the suggested treatment plan closely. If necessary, individuals will receive counselling or telephone reminders about their therapy appointments. Prior to and following the analysis, the outcome measures will be assessed. The study’s outcome indicators are as follows: The BBS, DGI, Trunk Impairment Scale (TIS), Functional Reach Test (FRT), 10 Meter Walk Test (10MWT) and Fall Efficacy Scale (FES) along with conventional treatment for balance and gait. mCIMT will be given in Group A in addition to conventional therapy, whereas Group B will receive the MRP in addition to conventional therapy. Figure 1 and Figure 2 depict the study design.\n\nPatients will be included if they fulfil the following inclusion criteria: i) Sub-acute stroke in both men and women between the ages of 45 and 65 years; ii) Mini-Mental State Examination score ≥24; iii) Modified Rankin Scale ≤3; iv) patients with Brunnstrom stage for hand and leg ≥4; v) Modified Ashworth Scale ≤2; and vi) be able to comprehend and adhere to instructions.\n\nThe exclusion criteria will be as follows: i) Individuals who are experiencing balance problems as a result of neurological conditions other than stroke (for instance cerebellar impairment, inner ear dysfunction, or Parkinson’s disease); ii) individuals suffering from unstable angina, symptomatic heart failure, or uncontrolled hypertension; iii) acute stroke (flaccid stage); iv) physician determined unstable cardiovascular conditions; v) the patient has been diagnosed as having organ failure, including the heart, kidneys, and lungs; and iv) patients with any traumatic musculoskeletal injury to lower limbs.\n\nCriteria for discontinuing allocated interventions for a given trial participant\n\nIf any patients in any of the allocated groups develop any complication (e.g., deep venous thrombosis), their participation will be discontinued in the study. The patients will then receive appropriate care and offered outpatient rehabilitation as needed. Study participants will be retained in the trial (unless they withdraw their consent) to enable follow-up data collection and to prevent missing data.\n\nAdherence and concomitant care\n\nDuring the first consultation, the importance of following the study guidelines and adhering to the allocated group will be highlighted. Exercise adherence will be recorded as a percentage of completed exercises during the first follow up (after the six-week intervention) for both groups. Exercise adherence will be taken into consideration when performing the pre-protocol analysis.\n\nAll enrolled patients will be encouraged to contact the principal investigator directly if experiencing problems related to their allocated group intervention. The principal investigator will then fill out a standardized form at these calls. Patients can use medicines and nutritional products as needed, prescribed by their physician. To avoid study-contamination, patients will be asked to adhere to the allocated rehabilitation intervention and not to seek alternative health-care services during the course of the study. Patients will be advised to contact their general practitioner or the principal investigator as needed.\n\nThe physiotherapy intervention will be given to Groups A and B for six weeks. The intervention will be provided for 60 minutes, five days each week. Both Group A and Group B will receive conventional treatment. Group A will receive mCIMT along with the conventional therapy, while Group B will receive the motor relearning program along with the conventional therapy. Treatment will be provided to both groups for six weeks.\n\nModified constraint-induced movement therapy (mCIMT)\n\nExercises will be given to participants that have a functional focus and will be under supervision. The affected lower extremity will be the focus of these exercises. Based on the desired movements, the therapist (principal investigator) recommended these exercises.\n\nThe 30-minute mCIMT approach will consist of the following movements: Transfer package (10 minutes per session), side stepping, ball kicking, stair climbing, and knee control on a step.\n\nMotor Relearning program (MRP)\n\nParticipants receive task-specific guidance based on the MRP. This method will be applied for 30 minutes. The actions will be practiced in both sitting and standing and should target an individual’s particular deficits: supine to side-lying to sitting, looking up at ceiling (ensure that centre of body mass does not move back when head is tilted back), without moving one’s feet, turning to gaze over each other’s shoulders and scanning the surroundings for specific items, reaching motions in multiple directions while moving the head and trunk, scooting in bed, altering the base of support (standing with your feet together, in tandem, with one foot on a step, or on one leg), squatting to pick up an object and cross over stepping.\n\nConventional therapy\n\nConventional therapy includes: i) Passive and active assisted range of motion exercises for upper and lower extremities; ii) stretching exercises for flexor synergy component shown in Table 1; iii) strengthening exercises with the help of THERABAND shown in Table 2; iv) balance training including practicing reaching beyond arm’s length while sitting and standing; and v) walking training that includes challenge to dynamic balance (e.g., obstacle courses).\n\n\n\n• Scapular retraction or hyperextension, shoulder abduction, elbow flexion, forearm supination, wrist and finger flexion\n\n• Pelvic retraction\n\n• Hip flexion, abduction, external rotation, knee flexion, ankle dorsiflexion, inversion\n\n\n\n• Pectoralis major, Pectoralis minor, Latissimus dorsi, Biceps brachii, brachioradialis, Supinator muscle, Flexor digitorum profundas, Flexor digitorum superficialis and Palmaris longus\n\n• Piriformis and Thoracolumbar fascia\n\n• Gluteus minimus, Gluteus medius, Psoas major, Iliacus sartarius, Rectus femoris, Hamstring, Tibialis anterior\n\n\n\n• Scapular retraction or hyperextension, shoulder abduction, elbow flexion, forearm supination, wrist and finger flexion\n\n• Pelvic retraction\n\n• Hip flexion, abduction, external rotation, knee flexion, ankle dorsiflexion, inversion.\n\n\n\n• Rhomboid, Latissimus dorsi muscle, Deltoid, Triceps, Pronator teres, Extensor digitorium, Extensor digiti minimi.\n\n• Quadratus lumborum\n\n• Adductor mangus, Adductor longus, Adductor brevis, Gracillis, Gluteus maximus, Quadriceps, Gastrocnemius\n\nTime frames at baseline and six weeks later.\n\nPrimary outcomes\n\n1. Change in Berg Balance Scale (BBS)\n\nThe BBS is a scale with 14 items that is frequently used and is a standardized balance assessment that uses observation to quantitatively assess a patient’s capacity for balance, either statically or while engaging in a variety of planned routine daily tasks. For evaluating static and dynamic balance following a stroke, The inter-rater and intra-rater reliability of BBS for the patients with stroke is 0.97 and 0.98, respectively.15 Each item on the scale will be given a score between 0 and 4, giving the patient an overall ranking of 56. A score of 0 means you didn’t complete the project, and a score of 4 means you did it independently.16\n\n2. Change in Dynamic Gait Index (DGI)\n\nThe goal of the DGI is to examine dynamic balance while in motion. Eight of the tasks ask participants to keep their balance when walking normally and while doing so in various conditions (such as adjusting their speed, turning their heads to go around obstacles, pivoting around and climbing steps). Each item is given a score between 0 and 3 points, with a maximum score of 24. A higher DGI score indicates greater independent functional mobility. The DGI has been shown to yield ratios of subject variability to total variability with excellent interrater reliability 0.96 and test-retest reliability 0.98.17\n\nSecondary outcomes\n\n1. Change in Trunk Impairment Scale (TIS)\n\nThe TIS assesses post-stroke trunk movement, static and dynamic sitting balance, and trunk movement coordination. The TIS is used to analyse motor dysfunction of the trunk after a stroke, static and dynamic seated balance and coordination of trunk movement. Overall reliability for clinical care and research in the TIS, 0.96.18\n\n2. Change in Functional Reach Test (FRT)\n\nUtilising a yardstick fastened to the wall at the acromion’s height, functional reach is determined. Functional reach has been shown to exhibit test-retest reliability, interobserver consistency, criterion validity, and concurrent concept validity in earlier investigations. Additionally, it has been demonstrated that in patients undergoing rehabilitation, functional reach is sensitive to clinically significant changes in balance.19\n\n3. Change in 10 Meter Walk Test (10MWT)\n\nAmbulation speed is a crucial component of gait and is frequently utilised in clinical and research settings as an objective indicator of functional mobility. In healthy older adults, gait speed can also be determined using the 10MWT. Therefore, to obtain the most accurate clinical evaluation of walking speed, we advise performing the 10MWT.20\n\n4. Change in Fall Efficacy Scale (FES)\n\nThe FES International, a tool designed to measure patient’s fears about falling, has strong psychometric qualities. The 16 items on the Persian FES were factor analysed. The Persian FES showed outstanding test-retest reliability, according to the results. In stroke patients, FES showed that the assessment of fear of fall was appropriate and acceptable. Concerns of falling during physical and social activities could be addressed using the FES. Additionally, it can be applied in a clinical context to identify individuals who have a fear of falling.21\n\nWe estimated the sample size using a power analysis with 80% power and 5% Type 1 error for the main variables. The BBS score, in comparison to the difference in mean score pre and post treatment for mCIMT group from baseline to end visits. For the study, we used the previously determined effect size difference in percentage from the RCT.22 Formula using mean difference:\n\nMean ± SD (Pre) result on BBS for mCIMT = 48.8 ± 4.7\n\nMean ± SD (Post) result on BBS for mCIMT = 52.5 ± 3.5\n\nDifference = 3.7\n\nPooled std. dev. = (4.7 + 3.5)/2 = 4.1\n\nConsidering 10% dropout = 2\n\nTotal samples required = 15 + 2 = 17 per group.\n\nTotal sample size required = 15\n\nNotations:\n\nα=Type I error at 5%\n\nZβ=0.841−β=Power at80%\n\nσ=std.dev=0.5pooledstd.dev\n\nBefore group allocation, screening of the participants as per the inclusion and exclusion criteria will be carried out. This will be followed by baseline assessment of the outcome measures as mentioned. All participants will undergo the randomization process and are allocated into either group A or Group B. The intervention will be administered for an hour daily, five days per week for six weeks. The post intervention data for the outcomes will be recorded after the last intervention session day. The data will be compiled and analysed for studying the results. The study interventions will be administered by the principal investigator under the supervision of the guide throughout the duration of the study. The patients will be instructed and reminded of the sessions in advance through messages sent to their mobile phones so that adherence to the study is ensured. Furthermore, if the patient misses their sessions due to any reason, the standby days from the week will be utilized such that the patient receives a total of 30 sessions of intervention in the six week duration.\n\nAs per in the sample size calculation we have given a 10% dropout rate so that it does not interfere with the results of our study.\n\nThe data collection forms can be found as Extended data.24\n\nThe evaluation data will be derived from a pre-set spreadsheet with varied baseline attributes. The research data will be stored in a safe database. Hard copies of evaluation forms, signed informed consent forms, and other non-electronic documents will be safely preserved in the study setting. Every month until the trial is over, a complete backup of the data entries will be performed. The lead investigators will supervise the data gathering and reporting processes. The accuracy of the research papers must be properly reviewed. At the end of the study, the Excel spreadsheet will be published and delivered to the statistician for the necessary analysis. A checklist can be used to avoid data loss due to ineffective staff processes. Due to the thorough follow-up assessment of this trial, participant retention and completion of follow-up assessments are anticipated to be quite high. The patients in this trial will be invited to follow-up exams after six weeks.\n\nSamples taken in accordance with the protocol and recorded on a basis that includes all relevant characteristics. Dataset of outcome variables including demographic, physical, laboratory and vitals information will be collected and tabulated in Excel, and will be analysed using R-Software version 4.3. Demographic variables such as age and gender and physical examination (height, weight, BMI), laboratory parameters (haemoglobin, Erythrocyte Sedimentation Rate (ESR), Liver Function Test (LFT), Kidney Function Test (KFT)), and vitals (respiratory rate, pulse rate, systolic blood pressure, diastolic blood pressure and SpO2 levels) will be collected. Outcome variables such as BBS, DGI, TIS, 10MWT, FRT and FES will be presented over descriptive statistics with categorical tabulation for frequency and percentage, while quantitative measurements with minimum, maximum, mean and standard deviation.\n\nThe primary outcome variables will include the BBS for measuring balance and the DGI for measuring gait outcome variables, the secondary outcome variables include the TIS, FRT, 10MWT and FES. Variables as primary and secondary parameters for their measuring assessment at different time visits will be assessed to find the significance in mean at 5% level of significance at P-value < 0.05. Statistical analysis will be performed for hypothesis testing for paired pre and post analysis using a paired t-test for normal data or non-parametric test such as Wilcoxon signed-rank test for non-normal data. Similarly, an unpaired t-test will be used for two independent groups for the change in parameters readings of primary and secondary variables at two different visits.\n\nData over the outcome variables will be analysed for normality (normal distribution) using Kolmogorov–Smirnov test. If data results over non normal distribution then alternate non parametric test will be used.\n\nConfounding variables will be analysed with generalised linear model to find the random and fixed effects over the outcome variables. Association analysis for finding significance of cofounding parameters will be examined by using Chi-squared test or Fisher’s exact test or by using multi-variant analysis.\n\nFull analysis set for the values of outcome variables will be analysed for the results missing data will be covered with imputation method by calculating the mean and median over the existing data.\n\nData monitoring\n\nWe will have a data monitoring committee lead by the PI for maintaining and integrating of the data.\n\nHarms\n\nThe whole procedure is going to held under the supervision of clinicians and departmental committee During the trial, harms and adverse event will be immediately reported to the committee. The final dataset will be uploaded to the institutional research website and will be accessible to concerned authorities.\n\nAuditing\n\nEvery month, auditing of the trial is going to be conducted. Any deviation from the protocol will be documented and will be addressed.\n\n\nEthics and dissemination\n\nDatta Meghe Institute of Higher Education and Research, Sawangi Wardha granted ethical approval (date, 21/03/2023) (reference number, DMIHER (DU)/IEC/2023/813). This protocol has been registered on CTRI (trial registration number, CTRI/2023/05/052674; registration date, 16/05/2023).\n\nThe study has been approved by the Scrutiny Committee at the college level on 01/03/2023 and by the IEC at the university level on 21/03/2023 following which, CTRI registration was also done. As per the suggestions through these committees the study has already been modified and approved. So further changes could not be carried out.\n\nMembers of the trial committee will provide the consent form to the participants in the trial and will inform and explain all the potential benefits and risks to the participants.\n\nThe study program will be elaborated to the participant and one of their relatives, and the principal investigator will take personal information as a part of procedure. The consent form will include the confidentiality statement and signatures of the principal investigator, patient and two witnesses. Whenever it’s necessary to divulge details for the study, consent will be obtained from the patient with complete assurance of their confidentiality.\n\nThe Principal Investigator will have access to the final trial datasheet.\n\nThe whole procedure is going to held under the supervision of clinicians and the departmental committee i.e., Guide, Head of department, Principal and member of Research Guidance Cell.\n\nAfter the trial session, the participations are going to be under supervision for about four weeks so that if there will be any harm, the Principal Investigator will take care of the participants.\n\nWe will present the work in International Conference Proceedings and publish in an indexed journal.\n\nStudy status\n\nThe study is yet to begin.\n\n\nDiscussion\n\nThe study’s primary objective is to determine how well mCIMT and MRP work to treat balance and gait issues. These cause a rise in the risk of falling, which further reduces the functional independence of those who had sub-acute stroke. In a previous study, the experimental group received mCIMT for two weeks, while the control group received neurodevelopmental therapy (NDT). The findings showed that mCIMT for lower limb had a superior impact on improving motor function compared with NDT.22 Using a randomized controlled trial, the study was done to determine how well the MRP worked to improve balance and upright mobility in sub-acute stroke patients. The results suggested that MRP showed a good impact on post-stroke survivors with the experimental group receiving MRP in addition to conventional physical therapy (RPT) for a duration of five days per week for eight weeks.23 Both interventions were found to be beneficial in hemiplegic stroke when compared with a negative control group. But there is dearth of literature reflecting the superiority of either of these interventions when compared with each other. Therefore, our study will compare the two regimes to evaluate which is more successful while looking at the effectiveness of these therapies in sub-acute stroke patients.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Extended data - Nitika.docx, https://doi.org/10.5281/zenodo.8172474. 24\n\nThis project contains the following extended data:\n\n- Model consent form\n\n- Data collection form\n\n- Schedule of enrolment, interventions and assessments.\n\nZenodo: SPIRIT- Nitika.docx, https://doi.org/10.5281/zenodo.8172339. 25\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nI’d like to express my gratitude to Mr. Lakshmikant Umate, biostatistician, for data analysis planning and sample size.\n\n\nReferences\n\nHarjpal P, Qureshi MI, Kovela RK, et al.: Efficacy of Bilateral Lower-Limb Training Over Unilateral Lower-Limb Training To Reeducate Balance and Walking in Post-Stroke Survivors: A Randomized Clinical Trial. Cureus. 2022 Oct 27 [cited 2023 Aug 1]; 14: e30748. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nKovela RK: EFFECTIVENESS OF PROPRIOCEPTIVE NEUROMUSCULAR FACILITATION TECHNIQUES IN IMPROVING MUSCLE STRENGTH IN A PATIENT WITH HEMIPLEGIA. JMPAS. 2022 Jun 30; 11(3): 4951–4952. Publisher Full Text\n\nPuri S, Kovela RK, Qureshi MI, et al.: Effect of Brunnstrom Movement Therapy Combined with Neurodevelopmental Therapy on Balance and Mobility in a Patient with Acute Stroke: An Interesting Case Report. JPRI. 2022 Jan 12; 6–9. Publisher Full Text\n\nTrimble B, Morgenstern LB: Stroke in Minorities. Neurol. Clin. 2008 Nov; 26(4): 1177–1190. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTadi P, Lui F: Acute Stroke. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023 [cited 2023 Jul 4]. Reference Source\n\nLee SJ, Cho YJ, Kim JG, et al.: Moderate alcohol intake reduces risk of ischemic stroke in Korea. Neurology. 2015 Dec 1; 85(22): 1950–1956. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTyson S, Burton L, McGovern A: The effect of a structured programme to increase patient activity during inpatient stroke rehabilitation: a Phase I cohort study. Clin. Rehabil. 2016 Feb; 30(2): 191–198. Publisher Full Text\n\nJaiswal PR, Dadgal R, Qureshi MI, et al.: Rehabilitating a patient with ischemic stroke & epileptic disorder: A case report. Med. Sci. 2022 May 17; 27(123): 1. Publisher Full Text\n\nA review of stroke rehabilitation and physiotherapy. Stroke. [cited 2023 Jul 4]. Publisher Full Text\n\nTaub E, Miller NE, Novack TA, et al.: I Technique to Improve Chronic Motor Deficit After Stroke.1993. Reference Source\n\nMorris DM, Taub E: Constraint-Induced Therapy Approach to Restoring Function After Neurological Injury. Top. Stroke Rehabil. 2001 Oct 1; 8(3): 16–30. PubMed Abstract | Publisher Full Text\n\nTaub E, Uswatte G, Mark VW, et al.: The learned nonuse phenomenon: A implications for rehabilitation. Eura. Medicophys. 2006; 42(3): 241–256. PubMed Abstract\n\nCarr JH, Shepherd RB: A Motor Learning Model for Stroke Rehabilitation. Physiotherapy. 1989 Jul 10; 75(7): 372–380. Publisher Full Text\n\nSingha R: MOTOR RELEARNING PROGRAM VERSUS PROPRIOCEPTIVE NEUROMUSCULAR FACILITATION TECHNIQUE FOR IMPROVING BASIC MOBILITY IN CHRONIC STROKE PATIENTS-A COMPARATIVE STUDY. IJPR. 2017 Nov 11; 5(6): 2490–2500. Publisher Full Text\n\nBerg K, Wood-Dauphinee S, Wiliams J, et al.: Measuring balance in the elderly: validation of an instrument. McGill University; 1993. Reference Source\n\nAlghadir AH, Al-Eisa ES, Anwer S, et al.: Reliability, validity, and responsiveness of three scales for measuring balance in patients with chronic stroke. BMC Neurol. 2018 Sep 13; 18(1): 141. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShumway-Cook A, Gruber W, Baldwin M, et al.: The Effect of Multidimensional Exercises on Balance, Mobility, and Fall Risk in Community-Dwelling Older Adults. Phys. Ther. 1997 Jan 1; 77(1): 46–57. PubMed Abstract | Publisher Full Text\n\nVerheyden G, Nieuwboer A, Mertin J, et al.: The Trunk Impairment Scale: a new tool to measure motor impairment of the trunk after stroke. Clin. Rehabil. 2004 May 1; 18(3): 326–334. PubMed Abstract | Publisher Full Text\n\nDuncan PW, Studenski S, Chandler J, et al.: Functional Reach: Predictive Validity in a Sample of Elderly Male Veterans. J. Gerontol. 1992 May 1; 47(3): M93–M98. PubMed Abstract | Publisher Full Text\n\nPeters DM, Fritz SL, Krotish DE: Assessing the Reliability and Validity of a Shorter Walk Test Compared With the 10-Meter Walk Test for Measurements of Gait Speed in Healthy, Older Adults. J. Geriatr. Phys. Ther. 2013 Mar; 36(1): 24–30. Publisher Full Text\n\nAzad A, Hassani Mehraban A, Mehrpour M, et al.: Clinical assessment of fear of falling after stroke: validity, reliability and responsiveness of the Persian version of the Fall Efficacy Scale-International. Med. J. Islam Repub. Iran. 2014 Nov 18; 28: 131. PubMed Abstract\n\nCandan SA, Livanelioğlu A: EFFECTS OF MODIFIED CONSTRAINT-INDUCED MOVEMENT THERAPY FOR LOWER LIMB ON MOTOR FUNCTION IN STROKE PATIENTS: A RANDOMIZED CONTROLLED STUDY. Int. J. Physiother. 2017 Oct 9; 4: 269–277. Publisher Full Text\n\nNaz A, Batool S, Ahmad A, et al.: Effectiveness of motor relearning program on balance and upright mobility in sub-acute stroke patients: A randomized control trial: Motor Relearning Program in Sub-Acute Stroke Patients. Pakistan BioMedical Journal. 2022 Jan 31; 5: 313–317. Publisher Full Text\n\nChavan NS: Extended data - Nitika.docx (Version v1). [Dataset]. Zenodo. 2023 Jul 21 [cited 2023 Jul 21]. Publisher Full Text\n\nChavan NS: SPIRIT- Nitika.docx. [Dataset]. Zenodo. 2023 Jun 7 [cited 2023 Jul 21]. Publisher Full Text"
}
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[
{
"id": "235564",
"date": "08 Feb 2024",
"name": "Ingela Marklund",
"expertise": [
"Reviewer Expertise Rehabilitation Medicine and 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\nThank you for the opportunity to review this study “Lower limb rehabilitation using modified constraint-induced movement therapy and motor relearning program on balance and gait in sub-acute hemiplegic stroke: a comparative study”. The authors aimed to evaluate the effect of mCIMT in addition to conventional therapy on balance and gait, the effectiveness of MRP along with conventional therapy on balance and gait and compare mCIMT and the MRP in improving balance and gait in sub-acute stroke patients. The topic is interesting and there is a lack of studies regarding mCIMT.\nIntroduction When crosschecking the references, I have doubts about whether the cited articles can really be used to make these statements (ref. 1-3, 6, 8, and 9). Please check the references and make sure that the reference really refers to a statement that can be seen as a result of the referenced work. The reference 7 and 10 are placed before the sentence instead of after and I lack a reference for conventional therapy in section three and for mCIMT and MRP in section four. Conventional therapy needs further explanation and a reference, what is it in your context, I doubt it is the same over the world. The sentence, “there are several anatomical and functional abnormalities that are followed by hemiplegia”, please explain what you mean with several anatomical abnormalities?. CIMT comprises four components: i) intensive training of the more-affected arm; ii) training with a behavioral technique called shaping; iii) the ‘transfer package’, where problem-solving is used to overcome perceived barriers to more-affected arm uses in ADL; and iv) restraint of the less-affected arm for 90% of waking hours during the treatment period (Ref 1). Shaping is also used in Lower-extremity CIMT and I miss this part in the present study. The phenomenon “learned nonuse” is more commonly used according to CIMT for the upper extremity and also used in your reference 11 and 12. Section five is a duplication of section four.\nThe study aims are clearly described.\nMethods The section Protocol is clearly described but the references for extended data are not in numerical order and I can not clearly understand if it is two or three assessments for outcome measures. Two in the text but three marks (x) in figure 2 (outcomes variables). Inclusion and Exclusion criteria are well written and does not need to be adjusted. Section Interventions, please describe the size of the intervention’s groups, are all 17 receiving the intervention at the same time or in smaller groups or individual? Did the principal investigator conduct both intervention and assessment? This is not clearly described and if so how can it affect the results? The interventions mCIMT, MRP and conventional therapy needs to be explained in more details to provide the opportunity for other researchers to replicate the study. Not only which exercise but also dose and intensity. Please describe what 10 minutes of transfer package includes. I also miss in the introduction how you came to the conclusion that 30 minutes a day for six weeks is enough? CIMT is often conducted six hours a day for two weeks and in your reference mCIMT was conducted 120 minutes a day for two weeks. Section Outcome measures, please use references with validity and reliability tests for the stroke population when possible. For example, BBS (Ref 2), 10MWT (Ref 3 or Ref 4), and DGI (Ref 5). Section Sample size calculation, I don’t understand. You wrote “we used the previously determined effect size in percentage from the RCT” but in the reference you referred to has not used BBS? Please explain where the data for the BBS you use in the calculation comes from. Is 17 in each group enough to show, as you write in the discussion part \"to evaluate which is more successful while looking at the effectiveness of these therapies in sub-acute stroke patients\" In the EXCITE trial (Ref 6), there were 106 and 116 in each arm. Section Data collection methods and Data management are well written and I have no more questions except of the need of clarification if it is two or three assessments as I mention earlier. Section Statistical analysis, These variables has not been explained before, please move from statistical section to another, for example Protocol and describe the characteristics you will collect and from where, medical journals or examination? Demographic variables such as age and gender and physical examination (height, weight, BMI), laboratory parameters (haemoglobin, Erythrocyte Sedimentation Rate(ESR), Liver Function Test (LFT), Kidney Function Test (KFT)), and vitals (respiratory rate, pulse rate, systolic blood pressure, diastolic blood pressure and SpO2 levels) will be collected.\nI have no further questions or comments and look forward to following the results and discussion in the present study.\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? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": []
},
{
"id": "235555",
"date": "20 Mar 2024",
"name": "Givago Silva Souza",
"expertise": [
"Reviewer Expertise Digital Health",
"Balance",
"Mobility"
],
"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\nAbstract:\nPlease indicate the names of the groups in the abstract.\nIntroduction:\nIt would be important to write a paragraph about balance and mobility in hemiplegic patients and the consequences that their losses could bring to the patients.\nMethods:\nI suggest including the use of accelerometry to evaluate the static balance and instrumented Timed Up and Go test.\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": []
},
{
"id": "235562",
"date": "16 Sep 2024",
"name": "Qurba Kiran",
"expertise": [
"Reviewer Expertise Neuromuscular Physical therapy"
],
"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 focuses on two key rehabilitation techniques: Modified Constraint-Induced Movement Therapy (mCIMT) and the Motor Relearning Program (MRP) applied to improve balance and gait in patients with sub-acute hemiplegic stroke. Hemiplegic stroke causes significant impairments in motor functions, especially affecting one side of the body, resulting in reduced mobility and balance. The study compares the effectiveness of these two interventions in enhancing motor recovery in the lower limbs. The findings of this comparative study may have direct implications on physical therapy practices. Clinics and rehabilitation centers can adopt more targeted approaches to improve outcomes for stroke survivors based on the results. The article highlights a comparative approach to two evidence-based rehabilitation techniques, contributing to the body of knowledge on effective stroke rehabilitation strategies, particularly in improving gait and balance in sub-acute hemiplegic stroke patients. The results may guide clinicians in selecting the most appropriate intervention for patient-specific needs. •\n\nBaseline comparability need to be addressed\n•\n\nRevise the potential benefits and potential risks\n•\n\nAdd some operational definitions of terminologies which are used in title\n\n•\n\nReferences should be revised as more than five years old references are not encouraged\n\n•\n\nAdd some literature regarding your topic at national level\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? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/12-1098
|
https://f1000research.com/articles/13-233/v1
|
27 Mar 24
|
{
"type": "Research Article",
"title": "Normalized Pulse Volume as a Superior Predictor of Respiration Recovery and Quantification of Nociception Anti-nociception Balance Compared to Opioid Effect Site Concentration: A Prospective, Observational Study",
"authors": [
"Onishi Tatsuki",
"Yoshika Onishi",
"Yoshika Onishi"
],
"abstract": "Background Quantifying pain and the balance between nociception and anti-nociception (NANB) in sedated patients is challenging. Traditional opioid titration methods overlook individual differences, while existing indices like the Noxious Stimulation Response Index (NSRI) lack correlation with effect-site concentration (Ce). The Normalized Pulse Volume (NPV), used in polygraphs, has potential for pain quantification but is underexplored. This study aimed to assess NPV’s efficacy as a pain monitoring tool compared to Ce and to explore its potential in various clinical settings.\n\nMethods The study included 39 patients undergoing surgery under total intravenous anesthesia from July 2013 to May 2014. Selection criteria were an American Society of Anesthesiologists physical status classification system (ASA score) of 1 or 2 and surgeries with minimal fluid resuscitation or blood loss. Exclusion criteria were significant posture changes, massive hemorrhage, and high perfusion index variation. NPV and Ce were measured using the Masimo SET adult SpO2 sensor.\n\nResults Out of 39 patients, 9 were excluded. NPV at recovery of spontaneous respiration (RoR) was 2.62 (95% CI: 2.26–2.98) with a coefficient of variation (CoV) of 36.3%, while total Ce was 1.48 ng/ml (95% CI: 1.14–1.84) with a CoV of 62.4%. NPV showed a narrower CoV than Ce (p < 0.05, 1.93*10−5), indicating less variability. NPV outperformed Ce in predicting RoR, suggesting a more accurate reflection of NANB balance. Its superiority in stable measurement underlines its potential as a reliable pain indicator. The study’s limitations include temporal differences in NPV and Ce calculations, affecting comparative analysis.\n\nConclusion NPV demonstrates promise as an objective, reliable indicator of pain or NANB, showing a strong correlation with Ce. Its application could improve pain assessments in clinical settings, optimizing patient care and analgesic administration. Future research should integrate NPV with other vital signs for a comprehensive pain monitoring system.",
"keywords": [
"Nociception",
"anti-nociception",
"normalized pulse volume",
"objective pain monitoring"
],
"content": "Introduction\n\nObjective quantification of pain, or more specifically the balance between nociception and anti-nociception (NANB), has long been a challenging task, especially in sedated or anesthetized patients.1 The absence of a universally accepted, objective pain monitoring system renders titration of analgesics, particularly opioid analgesics, highly challenging in diverse clinical settings—ranging from the operating room under general anesthesia to intensive care units, and extending to special populations like pediatrics, geriatrics, unconscious patients, non-native speakers, and those undergoing various forms of local anesthesia such as epidural, spinal, and nerve block procedures.2–5\n\nTraditionally, the titration of opioid analgesics was empirical; however, several contemporary medical facilities now rely on drug pharmacokinetic simulations to estimate the effect-site concentration (Ce).6–9 While these simulations provide a standardized approach, they often overlook individual variations in drug sensitivity, body composition, and distribution volume. Furthermore, intraoperative fluid resuscitation or blood loss can introduce additional variables that the simulations may not account for. This can inadvertently compromise patient experience, leading to either inadequate analgesia or excessive drug effects, such as respiratory depression with opioids or local anesthetic systemic toxicity.\n\nWhile attempts have been made to numerically quantify pain or NANB, such as the Noxious Stimulation Response Index (NSRI) and the Surgical Pleth Index (SPI), their adoption in clinical practice remains limited.10–13 Notably, despite the potential advantages of these indices, previous studies have not compared them against the established standard of Ce. This may partly explain their limited widespread acceptance. Moreover, the accuracy and relevance of these indices in the face of hemodynamic events have been debated, further impeding their universal adoption.14–21\n\nOne notable parameter is the normalized pulse volume (NPV), which represents the ratio of the pulsatile to non-pulsatile component in pulse oximetry. Historically used in polygraphs,22,23 recent research has shown its potential to reflect mental stress. This parameter has also been explored in contexts like peripheral nerve block success and fluid volume assessment.24–26 However, its utility as an indicator for pain or NANB quantification remains largely unexplored.\n\nTherefore, our study aimed to delve deeper into the realm of objective pain monitoring, exploring the efficacy, limitations, and potential of existing and emerging technologies.\n\nWhile the challenges and limitations of current pain monitoring systems have been recognized, the potential use of NPV as a marker for the NANB during sedation or anesthesia remains largely unexplored. NPV represents the ratio of the pulsatile (AC) component to the non-pulsatile (DC) component in pulse plethysmography. Historically, this ratio has been used in fields such as physiological psychology, where it is known to decrease with psychological stress, and is thus applied in tools such as polygraphs. In anesthesiology, companies such as Masimo have utilized this measure as the Perfusion Index (PI) to assess circulatory plasma volume. This suggests that under conditions where changes in circulatory plasma volume are minimal, NPV could potentially serve as a reliable indicator of physical stress.\n\nSeveral studies have observed changes in blood flow in areas targeted by local anesthetics such as epidural, spinal, and nerve blocks, with some research tracking these effects using NPV or PI. However, the application of NPV as a measure of analgesic efficacy under general anesthesia has not been explored. Although some evidence suggests that NPV might better reflect vascular resistance and sympathetic nerve α action than other parameters, its exclusion from initial parameters in tools such as the Surgical Stress Index (SSI) indicates that its potential in this realm is yet to be fully realized.\n\nGiven this background, our study hypothesized that NPV accurately reflects the NANB. We aimed to validate the utility of NPV as a novel indicator for the balance of nociceptive stimulation and analgesic efficacy. Additionally, our research explored the relationship between NPV and Ce, which is the standard titrating protocol. Furthermore, by utilizing multiple wavelengths, spanning both infrared and visible light, we strived to refine NPV measurements, ensuring its applicability even under challenging clinical scenarios such as severe anemia, hypovolemia, extreme peripheral vasoconstriction, varying skin pigmentation, and external light interference.\n\nIn essence, our goal was to ascertain the validity of NPV in quantifying pain or NANB and to elucidate the relationship between NPV and Ce in a clinical setting.\n\n\nMethods\n\nThe design and protocols were reviewed and approved by Tokyo Metropolitan Bokutoh Hospital Ethics Committee the local ethics committee in March 2017, under reference number 29-11.\n\nFor the analysis of the relationship between NPV and the Ce, we recruited 39 patients scheduled to undergo surgery under total intravenous anesthesia between July 2013 and May 2014 [Table 1-3].\n\nThe inclusion criteria were as follows: patients with an ASA score of 1 or 2, indicating healthy individuals or those with only mild systemic diseases. Only patients undergoing surgeries where there would be no changes in the position of the surgical field relative to the sensor, minimal fluid resuscitation or blood loss, and no concomitant use of epidural, spinal, or nerve block anesthesia were included.27–33 At our institution, this primarily pertained to otolaryngology and dental and oral surgeries.\n\nThe exclusion criteria were as follows: patients undergoing surgeries that might involve significant posture changes or that have the potential for massive hemorrhage. Cases with high perfusion index variation (PVI > 25) or low perfusion index (PI < 1) during induction were excluded.34–44 Cases with insufficient data sets or outliers were also excluded. Of the 38 initially recruited patients, 29 patients are included as 9 were excluded based on the above criteria: 3 due to an insufficient data set, 3 with a high PVI at extubation, and 3 with a low PI at induction.\n\nPatients recruited for this segment of the study were equipped with the Masimo SET® Pulse Oximetry adult SpO2 adhesive sensor (Masimo Corporation, Irvine, CA, United States of America) to measure NPV, in addition to routine monitoring. Anesthesia was induced using a bolus of fentanyl and a continuous infusion of remifentanil and propofol, ensuring that the Bispectral Index™ (BIS™, Medtronic, Minneapolis, MN United States of America) remained between 40 and 60. Fentanyl was titrated to approximately 1 ng/ml towards the end of the operation, with remifentanil adjusted accordingly.45\n\nA respiratory rate of eight breaths per minute was maintained until the recovery of spontaneous respiration (RoR). Both NPV and Ce for fentanyl and remifentanil were recorded upon RoR. The estimated Ce was derived using the built-in pharmacokinetic simulations—Shafer model for fentanyl and Minto/Schnider model for remifentanil—provided by the Fortec ORSYS perioperative patient information system (Philips, Netherlands). The total Ce was adjusted considering remifentanil’s greater potency, in alignment with the previous study. The coefficient of variation (CoV) for both NPV and total Ce was evaluated.\n\nPatients were instrumented with the Masimo RainbowSET® Technology adhesive sensor on their fingertips. Continuous recordings were conducted in conjunction with other vital signs from the time of entry to the operating room. The Ce of the drugs was calculated using the built-in functions of the Philips Orsys anesthesia chart, employing the Shafer method for fentanyl and the Minto/Schnider method for remifentanil. Fentanyl was titrated to achieve an estimated Ce of 1 ng/ml at the end of surgery. We ensured the absence of respiratory depression from sedatives or muscle relaxants. The recovery of spontaneous respiration was defined at 8 breaths/minute, and at this juncture, we compared the NPV with the estimated Ce. For this comparison, the respiratory depressive potency ratio between fentanyl and remifentanil was set at 1:2, based on previous research findings,45 and the sum of the effective site concentration of remifentanil and 0.5 times the effective site concentration of fentanyl was recorded (henceforth referred to as CE).\n\nPython 3.10 was used to calculate the demographics of cases, the multivariate outlier detection by Mahalanobis distance, the difference in CoV with Z-test, and to bootstrap the distribution of the CoV and the significance level.\n\n\nResults\n\nMultivariate outlier detection by Mahalanobis distance revealed no case corresponding to outliers as the critical value for the Chi-square distribution with 95% confidence was 5.99. Demographics of the included cases are shown in Tables 1, 2, and 3. NPV on RoR was 2.62 [dimensionless number] with a 95% confidence interval of 2.26–2.98, and a CoV of 36.3%. Conversely, CE on RoR was 1.48 [1.14–1.84] [ng/ml], with a CoV of 62.4% [Figure 1]. The Z test and the test for CoV showed that NPV on RoR was narrower than CE with a significance level of < 0.05 (1.93*10−5) [Figures 2–4]. In the bootstrapped distribution, the mean and median coefficients of variation for CE were higher than those for NPV, indicating greater relative variability. The confidence interval for NPV was relatively narrow, indicating that the estimation of the coefficient of variation is stable. Alternatively, the confidence interval for CE was wide, indicating a significant uncertainty in the estimation of the coefficient of variation. Although there were areas where the confidence intervals overlapped, differences in the central values were evident. These findings suggest that CE is more variable than NPV [Figure 5].\n\nCE: Weighted Sum of Estimated Effect Site Concentration of Fentanyl and Remifentanil; NPV: Normalized Pulse Volume.\n\nCE: Weighted Sum of Estimated Effect Site Concentration of Fentanyl and Remifentanil; NPV: Normalized Pulse Volume.\n\nCE: Weighted Sum of Estimated Effect Site Concentration of Fentanyl and Remifentanil; NPV: Normalized Pulse Volume.\n\nCE: Weighted Sum of Estimated Effect Site Concentration of Fentanyl and Remifentanil.\n\nCE: Weighted Sum of Estimated Effect Site Concentration of Fentanyl and Remifentanil.\n\n\nDiscussion\n\nThe presence of pain is harmful and associated with both all-cause and cancer-related mortality.46–50 Conversely, narcotic analgesics used for pain relief have a negative impact on cancer progression and survival.51,52 Moreover, drug abuse is a social issue.53–55 Therefore, there is a great social demand for the proper use of analgesics and the quantification of pain, or NANB, as the basis for the use of analgesics, as well as the quantification of NANB and other sensory information.56,57\n\nA range of potential bioindicators for quantifying and othering pain include autonomic parameters such as electromyography, heart rate variability, and skin conductance,58 as well as biomarkers in psychiatric disorders, including neuroimaging, metabolite levels, and gene expression changes.59 Other potential bioindicators include functional near-infrared spectroscopy (fNIRS) machine learning,60 and mechanistic, translational, and quantitative pain assessment tools.61 Brain-based biomarkers for pain, particularly those identified through neuroimaging and machine learning, have also been proposed.62 However, the lack of validated objective markers for nociception and pain remains a challenge.63\n\nThe NPV demonstrated a superior predictive capability for the RoR, compared with the CE. In the context of assessing NANB, the NPV provided a more accurate reflection than drug simulation techniques. This suggests a stronger correlation between NPV and the balance of noxious stimuli and analgesia.\n\nBuilding on these findings, there is potential to develop a multimodal approach that integrates the strengths of NPV with other measurements. Such a holistic approach could further enhance the accuracy and reliability of pain assessments in diverse clinical settings.\n\nIt is important to note that while NPV is calculated on a beat-to-beat basis, CE is computed only every minute. This temporal discrepancy might influence the comparative analysis between NPV and CE.\n\nOur team is keen on advancing this research by testing the efficacy of a pain monitoring system that employs NPV as its primary parameter, combined with other vital signs. Such a comprehensive instrument could offer a more nuanced and accurate pain assessment in clinical settings, further optimizing patient care and ensuring optimal analgesic administration. As this study was conducted with only one focus, RoR, it is necessary to study the predictive effect of stimuli that change over time.64\n\nThis design and protocols were reviewed and approved by Tokyo Metropolitan Bokutoh Hospital Ethics Committee the local ethics committee in March 2017, under reference number.29–11 Written consent to participate in the study was obtained from the participants at the anaesthesiology pre-operative consultation, not on the day of surgery, and it was explained that there would be no disadvantage in withdrawing. The entire study was conducted in adherence with the Declaration of Helsinki.65\n\n\nAuthor contribution\n\nOT: Conceptualization, Data curation, Formal Analysis, Methodology, Writing – original draft, Writing – review & editing\n\nYO: Writing – original draft, Writing – review & editing",
"appendix": "Data availability\n\nNormalized pulse volume as a superior predictor of respiration recovery and quantification of nociception anti-nociception balance compared to opioid effect site concentration: A prospective, observational study GitHub-https://github.com/bougtoir/npv_nanb\n\nThis project contains the following underlying data: main data file with age, gender (NPV ad Ce npv_2023_.csv), original consent form in Japanese (npv_nanb_consent_form.doc), translated consent form in English (npv_nanb_consent_form_en.doc), participant information sheets (npv_profile_.csv), STROBE Statement—Checklist of items that should be included in reports of cohort studies (strobe_checklist_npv.doc), and Jupyter notebook which includes codes to reproduce results (npv_2023.ipynb).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication) (http://creativecommons.org/publicdomain/zero/1.0/).\n\nSTROBE guideline for cohort study.\n\n\nAcknowledgments\n\nWe thank Iwamuratea and Chiron for their assistance with environment management.\n\nWe also thank Onishi Kotoha and Onishi Ione for their assistance. This study would not have been possible without their assistance.\n\nWe would like to thank Editage (www.editage.jp) for English language editing.\n\n\nReferences\n\nLedowski T: Objective monitoring of nociception: a review of current commercial solutions. Br. J. Anaesth. 2019; 123(2): e312–e321. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKotfis K, Zegan-Barańska M, Szydłowski Ł, et al.: Methods of pain assessment in adult intensive care unit patients – Polish version of the CPOT (Critical Care Pain Observation Tool) and BPS (Behavioral Pain Scale). Anaesthesiol Intensive Ther. Polish version. 2017; 49(1): 66–72. PubMed Abstract | Publisher Full Text\n\nRodríguez I, Herskovic V, Gerea C, et al.: Understanding monitoring technologies for adults with pain: systematic literature review. J. Med. Internet Res. 2017; 19(10): e364. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChang VT, Sorger B, Rosenfeld KE, et al.: Pain and palliative medicine. J. Rehabil. Res. 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Transplant. Proc. 2016; 48(4): 1055–1058. PubMed Abstract | Publisher Full Text\n\nLoupec T, Nanadoumgar H, Frasca D, et al.: Pleth variability index predicts fluid responsiveness in critically ill patients. Crit. Care Med. 2011; 39(2): 294–299. PubMed Abstract | Publisher Full Text\n\nKeller G, Cassar E, Desebbe O, et al.: Ability of pleth variability index to detect hemodynamic changes induced by passive leg raising in spontaneously breathing volunteers. Crit. Care. 2008; 12(2): R37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPişkin Ö, Öz İİ: Accuracy of pleth variability index compared with inferior vena cava diameter to predict fluid responsiveness in mechanically ventilated patients. Medicine. 2017; 96(47): e8889. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLu W, Dong J, Xu Z, et al.: The pleth variability index as an indicator of the central extracellular fluid volume in mechanically ventilated patients after anesthesia induction: comparison with initial distribution volume of glucose. Med. Sci. Monit. 2014; 20(386–92): 386–392. Publisher Full Text\n\nHaas S, Trepte C, Hinteregger M, et al.: Prediction of volume responsiveness using pleth variability index in patients undergoing cardiac surgery after cardiopulmonary bypass. J. Anesth. 2012; 26(5): 696–701. PubMed Abstract | Publisher Full Text\n\nDesebbe O, Boucau C, Farhat F, et al.: The ability of pleth variability index to predict the hemodynamic effects of positive end-expiratory pressure in mechanically ventilated patients under general anesthesia. Anesth. Analg. 2010; 110(3): 792–798. PubMed Abstract | Publisher Full Text\n\nFu Q, Mi WD, Zhang H: Stroke volume variation and pleth variability index to predict fluid responsiveness during resection of primary retroperitoneal tumors in Hans Chinese. Biosci. Trends. 2012; 6(1): 38–43. PubMed Abstract | Publisher Full Text\n\nCai QF, Mi WD, Yuan WX: The ability of pleth variability index to predict fluid responsiveness in mechanically ventilated patients under general anaesthesia. Zhonghua Wai Ke Za Zhi Chin J. Surg. 2010; 48(21): 1628–1632. PubMed Abstract\n\nMonnet X, Guérin L, Jozwiak M, et al.: Pleth variability index is a weak predictor of fluid responsiveness in patients receiving norepinephrine. Br. J. Anaesth. 2013; 110(2): 207–213. PubMed Abstract | Publisher Full Text\n\nGarcía-Soler P, Camacho Alonso JM, González-Gómez JM, et al.: Noninvasive hemoglobin monitoring in critically ill pediatric patients at risk of bleeding. Monitorización no invasiva transcutánea de la concentración de hemoglobina en pacientes críticos pediátricos con riesgo de sangrado. Med. Intensiva. 2017; 41(4): 209–215. PubMed Abstract | Publisher Full Text\n\nGelberg J, Jonmarker C, Stenqvist O, et al.: Intravenous boluses of fentanyl, 1 μg kg−1, and remifentanil, 0.5 μg kg−1, give similar maximum ventilatory depression in awake volunteer. Br. J. Anaesth. 2012; 108(6): 1028–1034. PubMed Abstract | Publisher Full Text\n\nSmith BH, Elliott AM, Hannaford PC: Pain and subsequent mortality and cancer among women in the Royal College of General Practitioners Oral Contraception Study. Br. J. Gen. Pract. 2003; 53(486): 45–46. PubMed Abstract\n\nMacfarlane GJ, McBeth J, Silman AJ: Widespread body pain and mortality: prospective population based study. BMJ (Clin Res Ed). 2001; 323(7314): 662–665. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVelik-Salchner C: Computed advisory systems in daily practice for predicting concentrations and effects of combined anesthetics: a new field in anesthesia? Minerva Anestesiol. 2015; 81(11): 1151–1152. PubMed Abstract\n\nRasmussen LS, Larsen K, Houx P, et al.: The International Study of Postoperative Cognitive Dysfunction. The assessment of postoperative cognitive function. Acta Anaesthesiol. Scand. 2001; 45(3): 275–289. Publisher Full Text\n\nShu AH, Wang Q, Chen XB: Effect of different depths of anesthesia on postoperative cognitive function in laparoscopic patients: a randomized clinical trial. Curr. Med. Res. Opin. 2015; 31(10): 1883–1887. PubMed Abstract | Publisher Full Text\n\nAmaram-Davila J, Davis M, Reddy A: Opioids and cancer mortality. Curr. Treat. Options Oncol. 2020; 21(3): 22. Publisher Full Text\n\nOswald N, Halle-Smith J, Kerr A, et al.: Perioperative immune function and pain control may underlie early hospital readmission and 90 day mortality following lung cancer resection: A prospective cohort study of 932 patients. Eur. J. Surg. Oncol. 2019; 45(5): 863–869. PubMed Abstract | Publisher Full Text\n\nKata V, Novitch MB, Jones MR, et al.: Opioid addiction, diversion, and abuse in chronic and cancer pain. Curr. Opin. Support. Palliat. Care. 2018; 12(2): 124–130. PubMed Abstract | Publisher Full Text\n\nFlorence C, Luo F, Rice K: The economic burden of opioid use disorder and fatal opioid overdose in the United States, 2017. Drug Alcohol Depend. 2021; 218: 108350. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrausz RM, Westenberg JN, Ziafat K: The opioid overdose crisis as a global health challenge. Curr. Opin. Psychiatry. 2021; 34(4): 405–412. PubMed Abstract | Publisher Full Text\n\nChen X, Thee C, Gruenewald M, et al.: Comparison of surgical stress index-guided analgesia with standard clinical practice during routine general anesthesia: a pilot study. Anesthesiology. 2010; 112(5): 1175–1183. PubMed Abstract | Publisher Full Text\n\nFarhang B, Mathews DM: Pain monitor: reality or fantasy in ambulatory patients. Curr. Opin. Anaesthesiol. 2019; 32(6): 727–734. Publisher Full Text\n\nWalter S, Gruss S, Limbrecht-Ecklundt K, et al.: Automatic pain quantification using autonomic parameters. Psychol. Neurosci. 2014; 7(3): 363–380. Publisher Full Text\n\nJakubów P, Kosciuczuk U, Garkowski A, et al.: Possibility of assessing pain with biomarkers in psychiatric disorders.2021. Publisher Full Text\n\nFernandez Rojas R, Huang X, Ou KL: A machine learning approach for the identification of a biomarker of human pain using fNIRS. Sci. Rep. 2019; 9(1): 5645. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArendt-Nielsen L, Curatolo M: Mechanistic, translational, quantitative pain assessment tools in profiling of pain patients and for development of new analgesic compounds. Scand J. Pain. 2013; 4(4): 226–230. PubMed Abstract | Publisher Full Text\n\nvan der Miesen MM , Lindquist MA, Wager TD: Neuroimaging-based biomarkers for pain: state of the field and current directions. Pain Rep. 2019; 4(4): e751. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCowen R, Stasiowska M, Laycock H, et al.: Assessing pain objectively: the use of physiological markers. Anaesthesia. 2015; 70(7): 828–847. Publisher Full Text\n\nMelia U, Vallverdú M, Borrat X, et al.: Prediction of nociceptive responses during sedation by linear and non-linear measures of EEG signals in high frequencies. PLoS One. 2015; 10(4): e0123464. Publisher Full Text\n\nDeclaration of Helsinki: BMJ. 1996; 313. Publisher Full Text"
}
|
[
{
"id": "260349",
"date": "10 May 2024",
"name": "Tatsuhiko Arafune",
"expertise": [
"Reviewer Expertise No new data collection was required",
"and this paper describes the main idea of this study to the minimum necessary. On the other hand",
"as noted in the comments above",
"additional information would have enhanced the quality of this paper."
],
"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\nSUMMARY: This study evaluated the validity of normalized pulse volume (NPV) as a novel measure for quantifying pain and the balance between nociception and antinociception in sedated patients. 39 total venous anesthesia surgical patients were compared to NPV and effect site concentration (Ce), showing that NPV has a narrower coefficient of variation than Ce and is more NPV is a promising objective and reliable indicator of pain or NANB and may contribute to pain assessment and analgesic optimization in clinical practice.\nStrengths of the Study: The strength of this study is that NPV offers less variability and higher reliability than conventional pain assessment methods; NPV correlated strongly with Ce and showed excellent predictive performance, especially during recovery of spontaneous breathing. This allows more precise pain management for individual patients, facilitates postoperative recovery, and reduces the risk of over- or undermedication with analgesics. Thus, NPV is an important tool for improving pain assessment in clinical practice.\nComments to authors: A wide range of wavelengths from near-infrared to green are used for pulse wave measurement. Each wavelength has its own advantages and disadvantages, and it is difficult to say which wavelength is optimal. Normalized Pulse Volume,” the wavelength of the light source used for pulse wave measurement was 810 nm. What is the wavelength of Masimo's sensor used for measurement in this study? If it is clear, it is desirable to specify it. We would also like to confirm if there are any differences compared to previous studies that used NPV for stress measurement.\nSince NPV is an index of vascular tone, it is possible that NPV can be obtained as a clearer index for symptoms such as cancer, which requires stronger pain relief. On the other hand, a situation in which a patient feels strong pain is likely to be accompanied by body movement, which can be assumed to have a negative impact on NPV measurement. If NPV is to be compared with CE, it is necessary to consider whether NPV is superior in detecting not only weak pain that the patient can voluntarily suppress, but also strong pain that is accompanied by body movement.\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": []
},
{
"id": "273068",
"date": "26 Jun 2024",
"name": "Mika Särkelä",
"expertise": [
"Reviewer Expertise Patient monitoring"
],
"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\nTatsuki and Onishi have compared normalized pulse volume and estimated analgesic effect site concentration in 39 surgical patients. I regret my delayed report, but that is partly caused by inaccuracies in the manuscript.\n\n1. Term \"normalized pulse volume\" (NPV) is not commonly used in the field of anesthesia monitoring. After checking the original article (Sawada Y, et al., 2001 [Ref 1]) it turned out to be just plethysmographic waveform amplitude, also known as perfusion index (PI). I think it is misleading to introduce new name to already established parameter, it only causes confusion among readers. Later in the text authors admit that NPV is also known as PI. Authors have used Masimo device in data recording, it remains unclear if the authors have recorded plethysmogram waveform and derived NPV by themselves, or just recorded the PI calculated by Masimo device and renamed that as \"NPV\". The unit of PI and NPV is \"%\", it is not dimensionless parameter as stated in Figure 1. Further, contrary to what authors claim, NPV/PI is used in the commercial nociception parameters like SPI (originally known as SSI). In the article of (Huiku M, et al., 2007 [Ref 2]) it is called as PPGA. Therefore, the criticism for existing methods presented in the introduction apply also to NPV/PI.\n2. Even though NPV varies less at RoR phase than Ce it does not mean it would be \"superior predictive\" over Ce. For assessing this, the authors should take NPV and Ce value before and after the RoR, and evaluate if those values overlap. For example, prediction probability (Pk) analysis is commonly used for the purpose (Smith WD, et al., 1996 [Ref 3])\n3. Manuscript contains negligence errors, for example Age is mentioned to be \"dimensionless\" variable in Table 1, but I assume it is presented in years.\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": []
}
] | 1
|
https://f1000research.com/articles/13-233
|
https://f1000research.com/articles/13-232/v1
|
27 Mar 24
|
{
"type": "Research Article",
"title": "Improving vocational guidance through an expert system: Temporary decreasing and enhancing student self-awareness",
"authors": [
"Julia Huayta-Gómez",
"Alex Pacheco",
"Julia Huayta-Gómez"
],
"abstract": "Background The vocational guidance process in educational institutions faces important challenges in managing trials and errors in diagnoses. Technological tools are identified as an effective solution to address these problems. This research seeks to improve career guidance in educational institutions through the implementation of an expert system. The main objective is to reduce test processing time and achieve greater efficiency in students’ self-knowledge regarding their interests, based on the personalities of the Holland Test.\n\nMethods The development of the expert system followed a six-model approach. First, an organisational model was created to assess the scope and feasibility of the project. Next, a task and agent model was developed to investigate the impact and look for improvements. A knowledge model was then developed to analyse the relevant knowledge bases. A communication model was also developed to evaluate the communication interface of the system. Next, a design model was created to provide guidelines for the implementation of the system. Finally, the implementation of the knowledge system was carried out to ensure its correct functioning.\n\nResults The implementation of the expert system has shown significant improvements in the vocational guidance process. It was possible to reduce the time needed to apply the test, thus optimising the psychologist’s time and allowing a greater capacity for analysis. In addition, an improvement in the effectiveness of the students’ self-knowledge in relation to their vocational interests based on the personalities of the Holland Test was observed.\n\nConclusions This study contributes to career guidance in educational institutions by introducing an innovative expert system. This technological solution optimizes the career guidance process, benefiting psychologists administering tests and students seeking self-knowledge about their career interests.",
"keywords": [
"expert system",
"vocational guidance",
"Holland test",
"vocation"
],
"content": "Introduction\n\nExpert systems were developed during the early 1960s and 1970s. An important quality they possess is that they provide fast and accurate problem solving and are able to solve a given problem and determine whether the problem is within their ability to solve. Their use is aimed at any field that requires human expertise; problems, in fact, become a potential scenario for a successful use of expert systems (Laperrière & Reinhart, 2014; Kumar et al., 2023; Castilla et al., 2023). On the other hand, the structure of an expert system is organised around three main elements: Knowledge base, which consists of a large amount of information about a particular topic in a data structure on which the application is developed. Fact base, which is a working memory with data that remains unchanged about the situation in which the application is to be performed and the results that are obtained throughout the deduction process. Inference engine, is the core of the Expert System and implements the elements of the knowledge base, thus building reasoning and detecting the knowledge of interest, using and chaining them, building a solution plan without depending on the domain and specificity of the case treated (Berrío & Ospina, 2014; Cabello, 2018). This helps solve problems that normally require human experts by mimicking the reasoning process that experts use to solve specific problems. In terms of vocational guidance, the expert system allows the student to identify his or her true interests and skills, as well as to have the necessary information about existing vocational options, while also being a support tool for the vocational counsellor (Chatti et al., 2019; Castilla et al., 2020).\n\nVocational guidance is part of a very important process in the life of young people and adolescents because it favours the development of the future as a professional (Vera et al., 2021; Quiroga et al., 2020). The process of career guidance is important because it is a form of psychological assistance aimed at helping counselees to elaborate their vocational identity and to be better able to make independent decisions to meet their own needs (Miller, 2021; Admass, 2022). Career choice is an extension of the personality and an attempt to implement a particular style of behaviour in professional life. Therefore, vocational interest is basically just another aspect of personality and interest inventories (tests) (Skarpaas & Hellekjær, 2021). People are divided into 6 different types, each corresponding to a work environment, which are: conventional, entrepreneurial, investigative, artistic, social and realistic (Alfaro-Barquero & Chinchilla-Brenes, 2017; Van Thang et al., 2021). Each person projects their views about occupations, about themselves and about the work environment they prefer. This is done by using stereotypes, which are important in the psychological and sociological field.\n\nIt should be noted that in Ecuador (Yungán et al., 2017), a research on an expert system to improve the assignment of teachers to different chairs achieved an efficiency of 93.33% compared to the manual, which had an efficiency of 33.33%.This indicates that an automated process outperforms the manual process by 60%, which is significantly improved by using the expert system. In Turkey (Dahil et al., 2015) observed that in the current economic and market conditions, people need to continuously improve and renew their skills, so institutions should have implemented programmes that not only provide vocational and technical training, but also provide programmes to acquire broad and transferable skills, as well as occupation-specific skills, in order to meet the expectations for solving the problems of vocational and technical education in their country. In Spain (Martínez-Vicente & Rocabert, 2016), it has been shown that vocational development is associated with career readiness. It can be concluded that, after career readiness, the students in the sample have sufficient career readiness and that career development plays an important role in achieving this. In Bolivia (Alvarado-Gisbert, 2020), it was shown that it is crucial for students to be guided with vocational training, taking into account their professional profile, as well as having the necessary information about the academic offer, the work scenario, the demands and requirements of each career, which allows the student to plan their professional future. In Peru (Flores & Gardi, 2020) it has been shown that the implementation of an expert system for the SGTI in a company manages to optimise the average time for the evaluation of the maturity levels, optimising the levels of reliability and efficiency. In Peru (Barzola & Flores, 2017), the implementation of an Expert System for Vocational Guidance Support applied in an educational institution achieved great support in reducing the total time of the vocational guidance process, the total time of the analysis of the vocational test and increasing the total time of the interview with the student, fulfilling the purpose of supporting the work of the counsellor and the student.\n\nAt a global level, career guidance is very important because it allows for a better self-knowledge according to the needs of the environment and the changes experienced by society, specifically, it is a guidance process that is closely linked to the search for identity (Bravo-Cobeña et al., 2021). It has the necessary tools to discover tastes, attitudes and skills in an objective and proactive way in the process of choosing a professional career. In Peru, the number of secondary school students applying to higher education institutions is really worrying; local statistics show that 4 out of 10 secondary school graduates apply to university (INEI, 2015). In 2017, only 35.3% of secondary school graduates from the provinces of Lima enrolled in a higher education institution (INEI, 2018). This indicates that there is a lack of career guidance and little use of technological tools for its application (Casillas-González, 2021; Hasan et al., 2022).\n\nThe career guidance process faces a number of challenges that need to be better addressed in order to maximise its effectiveness and usefulness. Such as limited human resources and expertise, as the lack of trained psychologists or guidance counsellors in schools makes it difficult to provide personalised and specialised guidance. Diversity of interests and abilities, as students have a wide range of interests and abilities which can make it difficult to identify appropriate career options for each individual. Limited knowledge of options, as students may have limited knowledge of the different career options available in the country and schools often lack the capacity to provide up-to-date career information. Lack of tools and technology, the absence of technological tools and expert systems can hinder the efficient delivery of career guidance, lack of access to up-to-date information and interactive resources can limit the effectiveness of the process.\n\nVocational guidance is a process involving different actors and it is essential to establish fluid and collaborative communication in order to provide comprehensive support to students. The active participation of parents in this process is also essential, as they play a key role in supporting and guiding their children’s choices.\n\nAt present, many educational institutions carry out their career guidance processes manually, which leads to delays and errors due to the number of tests to be analysed, and in some cases career guidance is non-existent. This is particularly the case in the fifth year of secondary education in educational institutions such as I.E. P San Pedro - Quinocay, in the province of Yauyos, which carries out a simple process of vocational guidance that does not allow it to correctly orient its students and consequently less than 50% of the students are sure of the professional career they are going to follow (Gutierrez-Valenzuela, 2021), This is due to various factors such as doubts and conflicts when choosing a career, difficulty in finding organised information about careers and higher education institutions, they do not manage to discover for themselves a professional field that is really attractive to them (Martínez-Vicente & Rocabert, 2016). An expert system for career guidance facilitates the process of career guidance, which is done manually. Therefore, the objective of this research is to implement an expert system to reduce the time foreseen to carry out vocational guidance activities and the effectiveness of the student’s self-knowledge, guaranteeing a correct vocational guidance. This research describes the importance of an expert system for the improvement of the vocational guidance process, using as a reference a methodology applied exclusively in expert systems.\n\nThe innovation of this study lies in the use of technological tools and the development of an expert system to improve the process of career guidance in educational institutions. This approach addresses the problems of time constraints of the psychologist in charge, possible errors in diagnosis and delayed testing of students. Furthermore, the division of the expert system development into 6 models allows for a rigorous planning and design of the system, optimising the process of vocational guidance in a more effective and efficient way. The implementation of the knowledge system also improves students’ self-awareness, which is beneficial for both students and test administrators. In short, this innovation uses technology to improve and optimise the career guidance process in educational institutions.\n\n\nMethods\n\nIn this section, we provide a detailed description of the methods used in the development and operation of our expert system (Huayta-Gómez & Pacheco, 2024).\n\nDevelopment technologies: Our expert system was meticulously crafted using a combination of cutting-edge technologies. The development of the Test rules and calculations is based on Python, a high-level, cross-platform, open-source programming language. The Front-end is based on Angular 11.0, an open source Javascript framework that guarantees a responsive and dynamic user interface, while the Back-end is based on C#, a modern object-oriented programming language. For the ApiRest services, use was made of Netcore 3.1, an open source cross-platform framework that aims to compile internet-connected and cloud-enabled applications. The database engine used was SQL Server 2019 for functional table maintenance data integrated with Netcore. The data model for solving Test Integrated with Python is based on MongoDB (MongoDB Atlas, 2024).\n\nCustomisation for educational institutions: The basic framework of our software was customised to suit the specific requirements of educational institutions. For this purpose, the categorisation functions, user roles and results were adapted to the specific needs of the educational sector. The user roles are: Administrator, Tutor and Student.\n\nMinimum requirements of the expert system: Our expert system for the improvement of the vocational guidance process can operate on any web hosting platform that meets the following characteristics:\n\nSQL Server 2019/MySQL\n\nWindows 7 onwards\n\nServer:\n\nIntel Core™ i5 processor. RAM memory 8GB\n\nClients:\n\nIntel Core™ i3 and above\n\nThis software tool has distinctive features that set it apart from existing solutions:\n\nPersonalised adaptation: The expert system is uniquely tailored to each student’s preferences, providing specific recommendations tailored to their profile.\n\nInformation: The expert system has information on higher education institutions, careers and professions of interest to the student.\n\nInteractive: The expert system has an interactive environment that includes images and music, so that the student does not get bored in the process of answering the questions.\n\n\nCase studies\n\nStudent profile/vocational test\n\nTo demonstrate the functionality of the software, we present a specific use case involving the student taking the vocational test. In this case, the learner enters the Vocational Test section Figure 1, selects the background image he/she wishes to display during the test, such as music, in order to make it an interactive environment. Once the test has started, the student proceeds to answer the questions based on the Holland Test Figure 2, culminating with the completion of the test, the student can visualise his or her results and the recommendations of careers and vocations based on his or her profile Figure 3.\n\nSource: self made.\n\nSource: self made.\n\nSource: self made.\n\nInput: Test answer input\n\nResult: Holland personality test results and recommendations for vocations and careers according to your profile.\n\nIn this scenario, it becomes clear how the expert system makes it easier for the tutor or counsellor to visualise the results of the students in their care Figure 4, resulting in significant time savings by eliminating the need to assess each form test. This freed-up time can be effectively used to provide highly personalised guidance to each student, taking into account their particular interests and addressing any additional concerns related to the information provided by the expert system Figure 5.\n\nSource: self made.\n\nSource: self made.\n\nInput:\n\nAccess the “Review Test” module.\n\nOutput:\n\nVisualisation of the tests taken by the students in your charge.\n\nDetail of results per student.\n\nIn this scenario, the collection, processing and dissemination of relevant information about academic disciplines Figure 6, vocations Figure 8 and educational establishments Figure 7 takes place, enabling the student to acquire a more comprehensive knowledge about the opportunities available and the institutions where he/she could acquire his/her future training, as well as the responsibilities inherent to the practice of the vocation of his/her choice.\n\nSource: self made.\n\nSource: self made.\n\nSource: self made.\n\nInput: Access the module “Careers and Institutions”.\n\nOutput: Information on careers, vocations and institutions.\n\nThese use cases demonstrate how the software enhances the vocational guidance process for students in an educational institution by providing valuable tools and necessary information.\n\n\nDiscussion\n\nThe study highlights the ability of the expert system to adapt to the individual preferences and characteristics of the user, adding an important dimension of interaction and engagement. The immediate feedback provided in the form of results and recommendations can be critical to the student’s career decision-making process, clearly demonstrating how the software adds value to the career guidance process by combining technology, personalisation and accurate feedback. As a result, the software presents itself as a promising tool for improving the effectiveness and experience of careers guidance. These results show a significant difference before and after the implementation of the expert system in the improvement of the participants’ self-awareness, as well as an increased reliability of the results. This is in line with (Farahani et al., 2023) who conclude that an expert system provides a systematic and structured framework for analysing data, allowing for more reliable and accurate diagnosis. These findings support the reliability of the results.\n\nThe study shows how the expert system becomes a valuable tool for the tutor as it facilitates access to student performance information without the need to spend time analysing test answers to obtain results, allowing the tutor to focus more on the individual needs of each student. These results support the previous claims of (Barzola & Flores, 2017), who showed that the implementation of an expert system can reduce the expected time to complete activities, reducing the time of the tutoring process by approximately 7.65 hours. In addition, the findings are also consistent with those of (Orbezo, 2017) who obtained an average reduction in analysis time of 20.3%. It is also in line with the results of (Castillo, 2013) who concluded that career guidance can be simplified and improved through an expert system, which has a positive impact on the efficiency of the process, especially for young people.\n\nThe study demonstrates the ability of the expert system to facilitate easier and faster access to key information. By collecting and processing data on academic disciplines, professions and higher education institutions based on the student’s profile, the system creates a space where students can explore a wider range of career options in a more informed way. The dissemination of this information is crucial to enable students to make informed decisions about their academic and professional future. These findings support the conclusions of (Chacon, 2015), who postulates that the implementation of an expert system broadens the scope of career guidance by enabling more students to access appropriate guidance for their future careers. This is achieved by providing essential information about the different career options available, as well as a test that allows students to accurately identify their true interests and abilities.\n\n\nConclusions\n\nThe use of expert systems in the professional process has proved to be an effective solution to meet the challenges and improve the quality of this process in schools. The following conclusions can be drawn from the research carried out\n\n1. Reduction of the time needed: Expert systems make it possible to streamline the careers guidance process by reducing the time needed to administer tests and carry out assessments. This optimises the time of guidance psychologists, allowing them to serve a larger number of students and to analyse the results more thoroughly.\n\n2. Improving the effectiveness of self-awareness: By using expert systems such as the Holland Test, students can learn more about their interests and vocations. These systems analyse students’ answers and provide information on career options that match their characteristics. This provides more accurate and personalised guidance.\n\n3. Increasing the efficiency of the decision-making process: Expert systems provide students with objective and proactive information for career choice. By providing appropriate tools and resources, they help students make informed choices and develop independent decision-making skills.\n\n4. Optimisation of the career guidance process: The implementation of expert systems in educational institutions benefits both psychologists and students. These systems enable more efficient administration of vocational tests, improve the quality of diagnoses and provide additional support to guidance counsellors.\n\nThe study was carried out following the ethical principles approved by the Ethics Committee of the National University of Cañete on August 1, 2022, reference number: std003-010822. Furthermore, the guidelines of the Declaration of Helsinki were also followed throughout the study. Respondents gave written consent to conduct the investigation and process data. Written consent was provided prior to the survey. Respondents could not continue with the survey if they were unwilling to consent or otherwise withdraw.",
"appendix": "Data availability\n\nZenodo: Data from the expert system for the vocational guidance process, https://doi.org/10.5281/zenodo.10794555 (Pacheco & Huayta-Gómez, 2024).\n\nThis project contains the following underlying data:\n\n- Pretest and Posttest.xlsx\n\nThe data are available under the terms of the Creative Commons Attribution 4.0 International (CC-BY 4.0) licence.\n\n\nAcknowledgement\n\nSpecial thanks to the Universidad Nacional de Cañete, to the professors and collaborators for the realization of this scientific article.\n\n\nReferences\n\nAdmass WS: Developing knowledge-based system for the diagnosis and treatment of mango pests using data mining techniques. International Journal of Information Technology (Singapore). 2022; 14(3): 1495–1504. Publisher Full Text\n\nAlfaro-Barquero A, Chinchilla-Brenes S: Construcción y validación de un instrumento de evaluación de preferencias y habilidades vocacionales para carreras científico-tecnológicas. Revista Tecnología En Marcha. 2017; 30(4): 138. Publisher Full Text\n\nAlvarado-Gisbert JR: Orientación vocacional y definición de proyectos de vida en los estudiantes de 6to de secundaria de la Unidad Educativa “Franz Tamayo” de la provincia de Trinidad Pampa Nor Yungas. Universidad Mayor San Andrés; 2020. Reference Source\n\nBarzola R, Flores J: Sistema experto para el apoyo en la orientación vocacional aplicado al colegio “San Andrés” en el distrito de Los Olivos. Universidad de San Martín de Porres - USMP. Lima, Perú: Universidad de San Martín de Porres; 2017.\n\nBerrío JGR, Ospina HAT: Prototipo de sistema experto en diagnóstico médico basado en síntomas de los pacientes. Caso de estudio: esclerosis múltiple. Tecnura. 2014; 18: 205–216. Publisher Full Text\n\nBravo-Cobeña G, Pin-García L, Solís-Pin S, et al.: La psicopedagogía y su relación con la Orientación Vocacional y Profesional de los estudiantes de bachillerato. Domino de Las Ciencias. 2021; 7(1): 658–676. Publisher Full Text\n\nCabello M: Arquitectura de pizarrón de un sistema experto ilustrada con el diagnóstico médico. Vega A, editor. Alberto Vega Aguayo; 2018.\n\nCasillas-González N: Orientación vocacional: significados, causas, consecuencias y tratamiento. Un abordaje desde la psicoterapia. 2021. Reference Source\n\nCastilla R, Pacheco A, Franco J: Digital government: Mobile applications and their impact on access to public information. SoftwareX. 2023; 22: 101382. Publisher Full Text\n\nCastilla R, Pacheco A, Robles I, et al.: Digital channel for interaction with citizens in public sector entities. World Journal of Engineering. 2020; 18(4): 547–552. Publisher Full Text\n\nCastillo P: Sistema experto basado en redes neuronales para la orientación vocacional profesional universitaria aplicado al colegio de ciencias “Arquimedes.2013; 1–72.\n\nChacon P: Sistema experto aplicado al proceso de orientación vocacional en las escuelas profesionales de ingeniería de la Universidad Nacional de Ucayali. Universidad Nacional de Ucayali; 2015. Reference Source\n\nChatti S, Laperrière L, Reinhart G, et al.: Expert Systems. CIRP Encyclopedia of Production Engineering. 2019; 642–642. Publisher Full Text\n\nDahil L, Karabulut A, Mutlu İ: Problems and Solution Offers Related to the Vocational and Technical Orientation in Turkey. Procedia. Soc. Behav. Sci. 2015; 174: 3572–3576. Publisher Full Text\n\nFarahani A, Naderpour H, Konstantakatos G, et al.: Developing a Fuzzy Expert System for Diagnosing Chemical Deterioration in Reinforced Concrete Structures. Appl. Sci. 2023; 13(18): 10372. Publisher Full Text\n\nFlores D, Gardi V: Sistema experto para la SGTI en la empresa Sion Global Solutions. INNOVA Research Journal. 2020; 5(3.2): 235–248. Publisher Full Text\n\nGutierrez-Valenzuela H: Orientación Vocacional en la I.E.P San Pedro.2021.\n\nHasan MZ, Uddin MS, Islam MS: An expert system for selecting optimal cloud-service provider. International Journal of Information Technology (Singapore). 2022; 14(3): 1555–1563. Publisher Full Text\n\nHuayta-Gómez J, Pacheco A: Expert system in the vocational guidance process.2024. Publisher Full Text\n\nINEI: Encuesta nacional a egresados universitarios y universidades, 2014. INEI; 2015. Reference Source\n\nINEI: Perú: Indicadores de Educación por departamento, 2007-2017.2018. Reference Source\n\nKumar P, Motia S, Reddy SRN: Integrating wireless sensing and decision support technologies for real-time farmland monitoring and support for effective decision making: Designing and deployment of WSN and DSS for sustainable growth of Indian agriculture. International Journal of Information Technology (Singapore). 2023; 15(2): 1081–1099. Publisher Full Text\n\nLaperrière L, Reinhart G: Expert Systems. CIRP Encyclopedia of Production Engineering. 2014; 492–492. Publisher Full Text\n\nMartínez-Vicente J, Rocabert E: Desarrollo vocacional y preparación para la carrera profesional en estudiantes universitarios. INFAD de Psicología. 2016; 5(1): 405. Publisher Full Text\n\nMiller IS: One Life Heals Another: Beginnings, Maturity, Outcomes of a Vocation, by Franco Borgogno, (A. Elgar, trans.), International Psychoanalytic Books, New York, 2021, 169 pp. American Journal of Psychoanalysis. 2021; 81(4): 539–543. Publisher Full Text\n\nMongoDB Atlas: MongoDB Atlas. MongoDB totalmente gestionada en la nube.2024. Retrieved March 6, 2024. Reference Source\n\nOrbezo D: Sistema experto para la orientación vocacional de la institución educativa Fe y Alegría 11 [Universidad César Vallejo]. Universidad César Vallejo; 2017. Reference Source\n\nPacheco A, Huayta-Gómez J: Data from the expert system for the vocational guidance process. [Data set]. Zenodo. 2024. Publisher Full Text\n\nQuiroga-Garza ME, Flores-Marín DL, Cantú-Hernández RR, et al.: Effects of a vocational program on professional orientation. Heliyon. 2020; 6(4): e03860. Publisher Full Text\n\nSkarpaas KG, Hellekjær GO: Vocational orientation – A supportive approach to teaching L2 English in upper secondary school vocational programmes. International Journal of Educational Research Open. 2021; 2: 100064. Publisher Full Text\n\nVan Thang D, Mangla M, Satpathy S, et al.: A fuzzy-based expert system to analyse purchase behaviour under uncertain environment. International Journal of Information Technology (Singapore). 2021; 13(3): 997–1004. Publisher Full Text\n\nVera KLT, Cevallos FAM, Sardi GAS, et al.: Sistema de orientación vocacional profesional en la construcción de proyectos de vida. South Florida Journal of Development. 2021; 2(2): 3405–3415. Publisher Full Text\n\nYungán J, Vaca-Barahona B, Santillán C, et al.: Desarrollo De Un Sistema Experto Para Mejorar La Asignacion Del Docente A Las Diferentes Catedras En La Facultad De Informática Y Electrónica Utilizando El Modelo De Mycin. European Scientific Journal, ESJ. 2017; 13(25): 236. Publisher Full Text"
}
|
[
{
"id": "274749",
"date": "07 Jun 2024",
"name": "Sri Tutur Martaningsih",
"expertise": [
"Reviewer Expertise Educational research and evaluation"
],
"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\nHaving novelty and good benefits, it is a starting point that can be developed to be used more widely. Moreover, by integrating it with technological developments, it enables easy access and use.\n\nIn my opinion, career directions are developing increasingly diverse and more specific. On the other hand, disruption occurs in various fields of work. This makes demands for individual competence and readiness to be relevant to new areas of work. Therefore, the expert system used needs to be developed with increasingly specific substance. Vocational schools have many departments, each with relevant competency and character prerequisites. For this reason, detecting suitability of competencies and talents. As well as: Interests and characters needs to be made more clear. It is hoped that the expert system can fulfill the need for individual career planning to be more effective.\n\nTest products on a wider range of subjects, if necessary across countries with different cultures and individual characteristics. A wider range of test subjects will enrich the feedback obtained, in order to continuously improve the expert system being developed.\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? Yes",
"responses": []
},
{
"id": "283550",
"date": "19 Jun 2024",
"name": "Eko Pramudya Laksana",
"expertise": [
"Reviewer Expertise School counseling",
"guidance and counseling",
"education"
],
"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 introduction, it would be advantageous to incorporate research concerning the counseling and guidance process that involves the utilization of established instruments.\nThis article significantly advances our understanding of expert systems, presenting findings that are highly relevant and carry important implications. However, the data analysis requires further depth, necessitating the incorporation of more robust arguments.\nThe author effectively integrates the research findings with pertinent theoretical frameworks, thereby establishing a robust foundation for the results obtained. This article offers a comprehensive and insightful examination of the topic, demonstrating significant potential as a basis for future scholarly investigation.\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/13-232
|
https://f1000research.com/articles/13-229/v1
|
27 Mar 24
|
{
"type": "Review",
"title": "Effect of Black Cumin (Nigella sativa) on Prostate Health: Narrative Review",
"authors": [
"Meshari A. Alzahrani",
"Ibrahim Abunohaiah",
"Yousuf Altuwaijry",
"Muath Alahmadi",
"Osama Qasim",
"Abdulaziz Alzahrani",
"Shamshad Begum Loni",
"Mohammed Shareef",
"Raed Almannie",
"Saleh Binsaleh",
"Ibrahim Abunohaiah",
"Yousuf Altuwaijry",
"Muath Alahmadi",
"Osama Qasim",
"Abdulaziz Alzahrani",
"Shamshad Begum Loni",
"Mohammed Shareef",
"Raed Almannie",
"Saleh Binsaleh"
],
"abstract": "A growing amount of research is shedding light on functional foods and nutritional supplements’ potential health and disease-preventative advantages. Black cumin (Nigella sativa L.), an esteemed nutraceutical herb, is well-known for its multiple health advantages among health-conscious individuals, researchers, and pharmaceutical businesses. Black cumin and its principal bioactive ingredient, thymoquinone (TQ), have been found to lower oxidative stress and inflammation, while also enhancing immunological function, cellular viability, and energy metabolism. They protect against metabolic, cardiovascular, digestive, hepatic, renal, pulmonary, reproductive, and neurological diseases, as well as cancer. Black cumin works as a countermeasure to minimize the toxicity and side effects of pharmaceuticals. Furthermore, the possible effects of black cumin on prostate health and disorders like benign prostatic hyperplasia and prostate cancer are not well understood. This narrative review seeks to reveal knowledge gaps. This study intends to guide future research into the possible uses of black cumin and TQ in prostate health and illness.",
"keywords": [
"Black cumin",
"Nigella sativa",
"Black seed",
"Thymoquinone",
"Prostate."
],
"content": "Introduction\n\nThe prostate, a small gland in the male reproductive system, plays a vital role in the production of seminal fluid, which nourishes and transports sperm. However, prostate-related issues, including benign prostatic hyperplasia (BPH) and prostate cancer (PCa), are common concerns in older men.1–3 As conventional treatments evolve, complementary and alternative approaches are being explored to improve prostate health. One such approach involves the use of Black Cumin, scientifically known as Nigella sativa, which has gained attention because of its potential effects on prostate health.4–7\n\nBlack cumin is a plant belonging to the family Ranunculaceae. It is native to certain regions of Asia and the Middle East and has a long history of use in traditional medicine and culinary practices. Black cumin is also referred to by various other names, including black seed, black caraway, kalonji, and the Habitat of Al-Baraka or Al-Habba Al-Saouda.6,8–11 This plant produces small, black seeds that have been used for medicinal purposes for centuries (Figure 1).12 These seeds have a distinct flavor, aroma and are often used as spices for cooking. The oil extracted from black cumin seeds is used in various culinary and herbal preparations.8,9\n\nThis figure has been reproduced with permission from Ref. 12.\n\nBlack Cumin is historically revered for its medicinal properties and has been used in traditional medicine for centuries. The seeds are a rich source of bioactive compounds with various health benefits.9 Recent studies have highlighted Black cumin’s potential effect on the prostate, raising interest in its role in mitigating prostate-related issues.6,9,13 Thymoquinone (TQ) (2-isopropyl-5-methyl-benzoquinone)14 is the primary bioactive component found in the volatile oil extracted from black seeds (Figure 2).15\n\nThis figure has been reproduced with permission from Ref. 15.\n\nBlack cumin seeds contain a variety of bioactive compounds other than TQ, including thymoquinones and flavonoids. These compounds are believed to contribute to the health benefits of Black cumin. It has been traditionally used to address a range of health concerns, including digestive, respiratory, cardioprotective, antidiabetic, anti-inflammatory, antiviral effects, immune system function, nephroprotective, and hepatoprotective properties; antioxidant activity; skin problems; renal and prostate conditions.4–9,15–21 It is important to note that while black cumin has a long history of traditional use and promising preliminary research, more extensive studies are needed to fully understand its potential effects on health and establish its safety and efficacy. Among the various options, Black cumin has emerged as a promising candidate for health enhancement owing to its minimal toxicity and multifaceted modes of action.21\n\nThis review explores the emerging evidence regarding the effects of Black cumin on prostate health. While conventional medical treatments remain the cornerstone of managing prostate conditions such as BPH and PCa, investigating the potential benefits of natural compounds, such as Black cumin, could pave the way for novel therapeutic approaches. This article delves into the current state of knowledge regarding the effects of Black cumin on prostate health, highlighting both its traditional use and the scientific research that underpins its potential benefits. As our understanding deepens, a more comprehensive picture of the role of Black cumin in prostate health will emerge, shedding light on its potential as a complementary strategy alongside established medical interventions.\n\n\n2. Methods\n\nThe literature search was conducted in scientific databases MEDLINE/PUBMED, by using keywords such as “black cumin” and “black seed,” “N. sativa” and “active compounds,” “N. sativa” and “Thymoquinone” and “prostate cancer,” “benign prostatic hyperplasia, “prostate cancer.” All the included articles published in English till 2023 were selected. Two senior authors (M.A.A. and R.M.) were individually tasked with gathering the relevant information. These details included author identities, year of publication, subjects involved, type of intervention, and the main outcomes of studies reporting the potential effect of black cumin on prostate health. If disagreements arose, a third reviewer reached a consensus. Our approach did not impose any constraints on the publication dates of the articles. We eliminated non-English literature, articles lacking relevance, duplicates, abstract-only publications, articles without full-text availability, reviews, and books. After identifying pertinent articles, we scrutinized the reference lists of these articles and recent reviews to ensure comprehensive coverage, avoiding omissions. We identified 2 articles related to our search. Following the predetermined inclusion and exclusion criteria, 13 articles were excluded because they did not meet our requirements. Ultimately, 11 articles fulfilled our criteria, reporting on Black cumin and its effects on the prostate, which formed the basis for our review. A flowchart of the article selection process is shown in Figure 3.\n\n\n3. Results\n\nEleven relevant articles were published between 2007 and 2021. Ten articles reported the effect of Black cumin on PCa, while one article was on BPH. Most of the studies were experimental in vivo and in vitro. The extracted data on the potential benefits of Black cumin on the prostate based on human and animal models are summarized in Table 1 and Table 2.\n\n\n\n- TQ effectively inhibits DNA synthesis, proliferation, and viability in cancerous prostate epithelial cells (LNCaP, C4-2B, DU-15, and PC-3), while not impacting non-cancerous BPH-1 cells.\n\n- This effect was attributed to the down-regulation of AR and E2F-1 (a transcription factor).\n\nIn Table 1, most studies were conducted in Turkey and the USA, but the majority of continental representations were from Asia. A xenograft human prostate cancer cell line model has been used in most studies. All studies used the active component of Nigella sativa (thymoquinone, TQ), as it is the major ingredient of black seed oil and extract. The treatment dose and duration were variants among studies. Combining TQ with standard PCa chemotherapeutic agents can enhance the efficacy of bone-preventive adverse events in metastatic PCa while reducing toxicity. In BPH, significant reductions in PI, prostate volume (PV) Dihydrotestosterone (DHT) levels, prostate-specific antigen (PSA), and serum malondialdehyde (MDA) were observed along with noticeable increases in serum antioxidant capacity.\n\n\n4. Discussion\n\nNigella sativa, also known as black seed or black cumin in English, Habat Al-Baraka in Arabic, and Tikur azmud in Amharic, has a long history of widespread culinary use. It has been employed as a spice and flavoring agent in a variety of dishes, including bread, yogurt, pickles, sauces, and salads.32 This versatile seed has also held a prominent place in traditional remedies across Arabian countries, Far East Asia, Europe, and Africa, earning it the nickname “The herb from heaven” by early herbal specialists.33 The Prophet Mohammed (PBUH) himself praised its healing properties, stating, “Hold on to the use of this black seed, as it has a remedy for every illness except death.”34 Additionally, Avicenna, a renowned physician from the 10th century famous for his work “The Canon of Medicine,” recommended Nigella seeds for boosting the body’s energy and aiding recovery from fatigue and dispiritedness. Notably, Nigella sativa is referenced for its therapeutic qualities in the Holy Bible and is referred to as Melanthion by Hippocrates and Dioscorides.35,36 The medicinal applications of Black cumin seeds in various traditional herbal systems are vast and encompass a wide range of ailments. These include respiratory disorders, pain management (such as chronic headaches and back pain), diabetes, paralysis, infections, inflammation, hypertension, and digestive tract issues, with various preparations used for administration. Furthermore, it has been applied topically for conditions such as blisters, nasal abscesses, orchitis, eczema, and swollen joints.9 Considering the extensive history of traditional medicinal uses of Black cumin and their active components such as TQ, there is a compelling opportunity to explore this valuable herb as an effective herbal medicine with multiple pharmacological actions. Based on the published experimental studies, our review highlights the potential benefits of Black cumin for treating prostate diseases such as BPH and PCa (Figure 4).\n\nIn 2019, there were an estimated 9.0 million cases (95% CI 73.2 to 118 million) of BPH cases worldwide. This number marks a significant increase compared to the 51.1 million cases (95% CI 3.1 to 69.3 million) recorded in the year 2000.37 BPH is a prevalent age-related condition of the prostate gland in men and is characterized by symptoms such as urinary tract obstruction, increased urination frequency, urinary retention, diminished urinary tube diameter, altered urine flow pressure, and post-urination dribbling.38 This condition entails enlargement of the prostate gland due to excessive proliferation of cellular components, notably mesenchymal cells. Common therapeutic approaches encompass α-adrenergic antagonists, 5-α-reductase inhibitors, and alternative remedies with natural products.39 Recent research has highlighted the relationship between oxidative stress (OS) and BPH. Notably, patients with BPH exhibit elevated levels of the lipid peroxidation biomarker MDA, coupled with suppressed plasma antioxidant levels.39,40 This underscores the potential utility of antioxidant interventions in the management of BPH. Nonetheless, conventional treatments such as alpha-adrenergic receptor blockers and 5-alpha reductase inhibitors present side effects and economic constraints, prompting the exploration of natural compounds as lead candidates for drug development or adjunctive therapies. Investigative studies have highlighted promising alternatives and complementary options for managing mild BPH, including Serona repens, Pygeum africanum, and Secale cereals. This approach has gained traction owing to factors such as accessibility, cost-effectiveness, and comparatively superior safety profiles compared to prevailing pharmaceutical interventions. Additionally, the global trend towards harnessing natural sources for the treatment of otherwise challenging diseases has bolstered interest in botanicals and other natural reservoirs, with Nigella sativa emerging as a highly endorsed contender within this paradigm.39\n\nA study using the BPH rate model reported that the administration of Black cumin seed oil at doses of 00 and 800 mg/kg resulted in a discernible reduction in DHT levels.6 Intriguingly, these findings indicated that the Black cumin oil, to a certain extent, displayed a more pronounced decrease in DHT levels within the BPH model compared to finasteride.6 Similarly, Hiipakka et al. reported that treatment with polyphenols derived from green tea diminished DHT production and hindered prostate cell proliferation. Given Black cumin’s composition of polyphenolic compounds,41 it stands to reason that the suppression of 5α-reductase activity potentially contributes to the beneficial impacts of this botanical.\n\nAmong the fatty acids, Black cumin oil contains a substantial amount of essential unsaturated fatty acids, including approximately 1% omega-3, 25% omega-9, and 58% omega-6.8,42 Prior work by Abdel-Rahman et al. posited that fatty acid-enriched compounds might impede the proliferation of prostate cells by reducing testosterone and DHT concentrations43 This aligns with the findings of Liang et al., who demonstrated the inhibitory role of fatty acids on 5α-reductase.42 Increased prostate weight serves as an indicative marker for diagnosing BPH, and the Prostate Index (PI) is frequently used to gauge BPH progression.44 A study on the rate of the model reported that both 00 and 800 mg/kg doses of Black cumin seed oil significantly decreased both PI and PV in the context of BPH.6 Recent insights have revealed the potential of PV and PSA concentrations in predicting the growth of prostate cells. Notably, PSA can serve as a surrogate index for PV and as a diagnostic marker for assessing the risk of prostate carcinoma.44 Hence, an elevated PSA level corresponds to heightened proliferation of prostate cells. A study on the rate of the BPH model reported that treatment with N. sativa seed oil at doses of 00 and 800 mg/kg prominently reduced PSA concentrations compared to the BPH model control group.6 Ren et al. highlighted the ability of polyphenols to repress PSA gene expression,45 suggesting that the ability of N. sativa to reduce PSA levels may be attributed to the presence of polyphenols.6\n\nConsequently, the observed effect of N. sativa oil in hindering lipid peroxidation, and by extension, its potential anti-BPH effects, is likely attributable to its reservoir of antioxidant and free-radical-quenching compounds. A study concerning serum MDA levels, further underscored this assertion, as these parameters were notably elevated in the BPH group compared to the control group.6 Remarkably, in this animal study, within the N. sativa oil-treated groups, a significant reduction in serum MDA levels was evident compared to the BPH group. This reduction strongly signifies the shielding effects of the constituents present in N. sativa oil, thereby potentially enhancing serum antioxidant capacity and concurrently lowering MDA levels. The observed decline in MDA levels appeared to align with the inherent antioxidant potency of plants.6\n\nThe increasing global incidence of cancer poses significant medical challenges. In response, there has been a growing endeavor to explore potent natural anticancer treatments as alternatives to existing chemotherapeutic approaches, which often have limited applicability.\n\nPCa is one of the most prevalent malignancies affecting men,46 and recent research has unveiled the noteworthy role of TQ, a prominent bioactive compound in Nigella sativa, in influencing PCa markers (Table 2). TQ, a pivotal constituent of black seed oil, has a wide spectrum of pharmacological effects including potent anti-inflammatory properties47 and notable antioxidant activity.48 Furthermore, TQ was the predominant bioactive compound extracted from Black cumin. Its abundance has been linked to its antineoplastic properties against a diverse array of tumors.49,50 TQ has garnered attention for its antineoplastic properties in various cancers, including pancreatic cancer,48 lung cancer, colon cancer,51 and leukemia.52 Research has shown that TQ not only curbs growth and triggers cell apoptosis and cell cycle arrest, but also deters metastasis and angiogenesis. These multifaceted effects are attributed to its modulation of key signaling pathways such as Akt,53 NF-κB,54 mitogen-activated protein kinase (MAPK), and Signal transducer and activator of transcription 3 (STAT3).55 In this compilation, we have summarized the present scientific knowledge concerning the anticancer properties of Nigella sativa, along with elucidating its mechanism of action, with a specific focus on PCa.\n\nFindings from the study on the effect of TQ on human PCa cell lines DU15 and human prostate cancer cell line (PC3) revealed that TQ effectively curbed the metastatic attributes and restrained the process of epithelial-mesenchymal transition (EMT) within PCa cells through its active downregulation of the TGF-β/Smad2/3 signaling pathway. Furthermore, these outcomes lend support to the proposition that thymoquinone holds promising potential as a therapeutic agent against PCa, functioning by precisely targeting the TGF-β pathway.22 However, the relationship between the TQ and EMT in PCa remains unclear. Furthermore, the precise mechanism underlying TQs inhibition of the metastatic phenotype remains to be fully elucidated.\n\nA study explored the combination of docetaxel and TQ in hormone-refractory prostate cancer cells (DU-15) and its impact on PI3K and ERK signaling pathways.23 The combination of docetaxel and TQ showed a significant increase in cytotoxic and apoptotic effects compared to using each agent separately, with the effect becoming stronger at higher doses. Interestingly, the presence of LY29002 did not substantially alter cell viability when combined with docetaxel and TQ, unlike cells treated with LY29002 alone. - However, introducing FR18020 reduced cell viability significantly when combined with docetaxel and TQ, compared to cells treated solely with the inhibitor. The study suggests that the cytotoxic effect of docetaxel and TQ is connected to the inhibition of the PI3K/Akt signaling pathway in DU-15 cells.23 This combined approach has the potential to offer an alternative to contemporary oncological practices. Additionally, the synergistic use of docetaxel and TQ holds promise for potentially reducing the dosage of docetaxel and mitigating its associated adverse effects while maintaining therapeutic effectiveness for patients with castration-resistant prostate cancer (CRPC).23\n\nIn an in vitro study on human prostate carcinoma LnCaP cells, TQ decreased cell viability and enhanced apoptosis by activating caspase-9.24 Furthermore, a study on the mechanism of action of TQ in androgen receptor (AR)-independent (C-2B) and AR naïve (PC-3) PCa cells showed that TQ suppressed the proliferation of human prostate C-2B cancer cells by triggering the activation of JNK and growth arrest and DNA-damage-inducible 45 alpha (GADD45a), concurrently upregulating apoptosis-inducing factor-1 while downregulating Bcl-2-related proteins, including BAG-1, Bcl-2, Bcl2A1, Bcl2L1, and BID25 Furthermore, C-2B and PC3 cells revealed the potential of TQ to suppress proliferation by inducing the accumulation of reactive oxygen species (ROS) and reducing glutathione (GST) levels in both cells.25 In addition, TQ exhibited a pro-oxidant cytotoxic mechanism involving oxidative DNA damage facilitated through a copper-dependent pathway by mobilizing and reducing endogenous cellular copper across various PCa cell lines, including DU15, LNCaP, PC3, and C2B.26 This pro-oxidant cytotoxic mechanism provides a more comprehensive understanding of the anticancer efficacy of plant-derived antioxidants.26 One study reported that TQ, a naturally derived herbal product, holds promise as a potential treatment for both hormone-sensitive and hormone-refractory PCa. Additionally, given its targeted effect on cancer cells, we posit that thymoquinone could be safely employed as a preventive measure against the onset of PCa.27 A study on a human prostate tumor xenograft mouse model27 showed that TQ exerts inhibitory effects on the expression of AR and E2F-1, which are crucial for the proliferation and viability of androgen-sensitive and androgen-independent prostate cancer cells, both in vivo and in vitro. The efficacy of TQ is evident in its ability to diminish the levels of AR and E2F-1 while promoting the activation of pro-apoptotic proteins, including p53, p21Cip1, p27Kip1, and Bax, in androgen-sensitive prostate cancer cells.27 TQ inhibited tumor growth in xenografts originating from androgen-independent C-2B prostate cancer cells in nude mice. Consistent with its effect on cultured cells, this outcome correlated with a substantial reduction in AR and E2F-1 expression and the initiation of apoptosis. Consequently, our perspective is that thymoquinone holds promise as a potential therapy for PCa, particularly in hormone-refractory cases.27 Additionally, TQ dose-dependency increased the inhibitory effect of thymoquinone on DNA synthesis, proliferation, and viability of cancerous cells (LNCaP, C-2B, PC-3, and DU15), but not in non-cancerous prostate (BPH-1) epithelial cells.27 Another study reported that TQ effectively blocked angiogenesis both in vitro and in vivo,28 exhibited preventive effects on tumor angiogenesis in the PC3 mouse model, and curbed human prostate tumor growth at a low dose with minimal chemo-toxic side effects. Notably, this study observed a heightened sensitivity of endothelial cells to TQ-induced phenomena, including apoptosis, suppression of proliferation, and hindered migration, in contrast to PC3 cancer cells. Furthermore, TQ effectively restrained the activation of extracellular signal-regulated kinase induced by vascular endothelial growth factor but did not affect the activation of vascular endothelial growth factor receptor 2.28 These findings led to the conclusion that thymoquinone can efficiently inhibit prostate tumor growth at an early tumor stage (50 mm3) at a dose of 6 mg/kg/day.28 A study on the nanoparticle optimization of Nigella sativa reported the successful development and characterization of a nano-based carrier for Nigella sativa essential oil using optimization techniques, and a methyl thiazolyl-diphenyl-tetrazolium bromide (MTT) assay was performed to compare the in vitro cytotoxicity using two different cell lines (i.e., HCT 116 for colorectal carcinoma and PC3 for prostatic cancer). This study demonstrated the enhanced properties of nanoparticulated oil, including improved efficiency in suppressing cancer cell viability compared to free oil.29 Another study reported that TQ can block metastatic processes induced by IL-7 in prostate cancer cells, thereby controlling tumor progression, migration, and invasion.30 An in vitro study found that the combination of TQ and zoledronic acid (ZA) led to increased cytotoxic effects and apoptosis in prostate cancer cell lines resistant to both hormones and drugs. This novel combination approach could serve as an alternative strategy for patients with limited treatment options due to poor performance status and those who are not viable candidates for traditional therapies. In addition, compared with cytotoxic agents, it exhibits a minimal profile of hematological and non-hematological toxicity.31\n\nThese studies suggest that Black cumin may play a role in slowing the progression of prostate cancer; however, clinical trials in humans are necessary to determine its efficacy and safety. It is important to approach these findings with caution and consult medical professionals before considering complementary or alternative treatments, particularly for serious conditions such as cancer.\n\nThis review has some limitations, including factors that may affect its quality, validity, and reliability. However, this is the first article that summarized in a comprehensive review the growing evidence and insights from in vitro and vivo studies that explored the potential efficacy of Black cumin (Nigella sativa L.) on prostate health and conditions such as BPH and PCa.\n\nSuggestions and prospective pathways for harnessing the advantages of Black cumin (Nigella sativa L.) in promoting prostate health may encourage researchers to conduct further rigorous clinical trials to substantiate the specific benefits of Black cumin on prostate health. These studies should encompass diverse populations, incorporate long-term assessments, and explore in-depth research to unravel the precise mechanisms by which Black cumin compounds interact with prostate cells and influence hormonal balance. This information will aid in a better understanding of their potential therapeutic effects. Furthermore, we determined the optimal dosage and duration of Black Cumin supplementation to maximize the prostate health benefits. This involves investigating both short- and long-term effects at various dosage levels. Additionally, we explored the synergistic effects of incorporating Black cumin into combination therapies with existing treatments for prostate cancer. This could potentially enhance therapeutic outcomes and minimize adverse effects. In addition, we identified and isolated the key bioactive compounds in Black cumin that are responsible for its positive effects on prostate health. This knowledge could lead to the development of targeted supplements and medications. Continued evaluation of the safety profile of Black cumin supplementation, particularly in the context of long-term use, and potential interactions with medications is needed. Future endeavors should focus on optimizing its application through research-backed dosages and combination therapies, and effectively communicating its potential benefits to the public and healthcare practitioners.\n\n\n5. Conclusions\n\nThymoquinone (TQ), a bioactive molecule found in Nigella sativa, is known for its antioxidant, anti-inflammatory, and anticancer effects on prostate tissues. Over the past decade, these effects have been examined both in vivo and in vitro. We anticipate that the findings of this review will be used to advance the possible therapeutic options derived from Black cumin for human prostate health. According to the findings of our review, the TQ component of Nigella sativa revealed interesting prospective advantages for prostate health. TQ is most likely to promote pro-oxidant-induced cell death, reduce tumor angiogenesis, induce apoptosis, and prevent metastasis in PCa experimental models. Combining TQ with standard PCa chemotherapeutic agents can enhance the efficacy of bone-preventive adverse events in metastatic PCa while reducing toxicity. Significant reductions in PI, PV, DHT, PSA, and serum MDA levels as well as significant improvements in serum antioxidant capacity have been reported in BPH experimental models. This natural product can then be utilized to treat various diseases and has become a popular functional food. Future clinical trials are required to explore the safety and efficacy of Black cumin and TQ in terms of their pharmacological advantages.",
"appendix": "Data and software availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nThe authors would like to thank the Deanship of Scientific Research at Majmaah University for supporting this work under Project Number No. [R-2024-1015].\n\n\nReferences\n\nLee CH, Akin-Olugbade O, Kirschenbaum A: Overview of prostate anatomy, histology, and pathology. Endocrinol Metab Clin North Am. 2011; 40(3): 565–575. Publisher Full Text\n\nVerze P, Cai T, Lorenzetti S: The role of the prostate in male fertility, health and disease. Nat Rev Urol. 2016; 13(7): 379–386. PubMed Abstract | Publisher Full Text\n\nCannarella R, Condorelli RA, Barbagallo F, et al.: Endocrinology of the Aging Prostate: Current Concepts. Front Endocrinol (Lausanne). 2021; 12: 554078. Published 2021 Feb 22. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhazdair MR, Ghafari S, Sadeghi M: Possible therapeutic effects of Nigella sativa and its thymoquinone on COVID-19. Pharm Biol. 2021; 59(1): 696–703. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEsharkawy ER, Almalki F, Hadda TB: In vitro potential antiviral SARS-CoV-19- activity of natural product thymohydroquinone and dithymoquinone from Nigella sativa. Bioorg Chem. 2022; 120: 105587. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHannan MA, Rahman MA, Sohag AAM, et al.: Black Cumin (Nigella sativa L.): A Comprehensive Review on Phytochemistry, Health Benefits, Molecular Pharmacology, and Safety. Nutrients. 2021; 13(6): 1784. Published 2021 May 24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMajdalawieh AF, Fayyad MW, Nasrallah GK: Anti-cancer properties and mechanisms of action of thymoquinone, the major active ingredient of Nigella sativa. Crit Rev Food Sci Nutr. 2017; 57(18): 3911–3928. PubMed Abstract | Publisher Full Text\n\nKou B, Liu W, Zhao W, et al.: Thymoquinone inhibits epithelial-mesenchymal transition in prostate cancer cells by negatively regulating the TGF-β/Smad2/3 signaling pathway [published correction appears in Oncol Rep. 2023 Mar;49(3)]. Oncol Rep. 2017; 38(6): 3592–3598. PubMed Abstract | Publisher Full Text\n\nDirican A, Atmaca H, Bozkurt E, et al.: Novel combination of docetaxel and thymoquinone induces synergistic cytotoxicity and apoptosis in DU-145 human prostate cancer cells by modulating PI3K-AKT pathway. Clin Transl Oncol. 2015; 17(2): 145–151. PubMed Abstract | Publisher Full Text\n\nKus G, Ozkurt M, Kabadere S, et al.: Antiproliferative and antiapoptotic effect of thymoquinone on cancer cells in vitro. Bratisl Lek Listy. 2018; 119(5): 312–316. PubMed Abstract | Publisher Full Text\n\nKoka PS, Mondal D, Schultz M, et al.: Studies on molecular mechanisms of growth inhibitory effects of thymoquinone against prostate cancer cells: role of reactive oxygen species. Exp Biol Med (Maywood). 2010; 235(6): 751–760. PubMed Abstract | Publisher Full Text\n\nZubair H, Khan HY, Sohail A, et al.: Redox cycling of endogenous copper by thymoquinone leads to ROS-mediated DNA breakage and consequent cell death: putative anticancer mechanism of antioxidants. Cell Death Dis. 2013; 4(6): e660. Published 2013 Jun 6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKaseb AO, Chinnakannu K, Chen D, et al.: Androgen receptor and E2F-1 targeted thymoquinone therapy for hormone-refractory prostate cancer. Cancer Res. 2007; 67(16): 7782–7788. PubMed Abstract | Publisher Full Text\n\nYi T, Cho SG, Yi Z, et al.: Thymoquinone inhibits tumor angiogenesis and tumor growth through suppressing AKT and extracellular signal-regulated kinase signaling pathways. Mol Cancer Ther. 2008; 7(7): 1789–1796. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDawaba AM, Dawaba HM: Application of Optimization Technique to Develop Nano-Based Carrier of Nigella Sativa Essential Oil: Characterization and Assessment. Recent Pat Drug Deliv Formul. 2019; 13(3): 228–240. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlshyarba M, Otifi H, Al Fayi M, et al.: Thymoquinone inhibits IL-7-induced tumor progression and metastatic invasion in prostate cancer cells by attenuating matrix metalloproteinase activity and Akt/NF-κB signaling. Biotechnol Appl Biochem. 2021; 68(6): 1403–1411. PubMed Abstract | Publisher Full Text\n\nDirican A, Erten C, Atmaca H, et al.: Enhanced cytotoxicity and apoptosis by thymoquinone in combination with zoledronic acid in hormone- and drug-resistant prostate cancer cell lines. J BUON. 2014; 19(4): 1055–1061. PubMed Abstract\n\nJaved S, Shahid AA, Haider MS, et al.: Nutritional, phytochemical potential and pharmacological evaluation of Nigella Sativa (Kalonji) and Trachyspermum Ammi (Ajwain). J Med Plant Res. 2012 Feb 9; 6(5): 768–775. Publisher Full Text\n\nAhmad I, Tripathi J, Manik S, et al.: Preliminary phytochemical studies of the miracle herb of the century, Nigella sativa L. (Black Seed). Indo Am J Pharm Res. 2013; 3(4): 3000–3007.\n\nBukhari AA, Sahih-ul-Bukhari: Access date September 9, 2023. Reference Source\n\nTariq M: Nigella sativa seeds: folklore treatment in modern day medicine. Saudi J Gastroenterol. 2008; 14(3): 105–106. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNadkarni KM, Nadkarni AK: Indian materia medica. Bombay: Popular Prakashan; 1982; vol. 1. : 278–279.\n\nGBD 2019 Benign Prostatic Hyperplasia Collaborators: The global, regional, and national burden of benign prostatic hyperplasia in 204 countries and territories from 2000 to 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet Healthy Longev. 2022; 3(11): e754–e776. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNg M, Baradhi KM: Benign Prostatic Hyperplasia. StatPearls. Treasure Island (FL): StatPearls Publishing; August 8, 2022.\n\nHansen BJ, Hald T: Review of current medical treatment of benign prostatic hyperplasia. Eur Urol. 1993; 24: 41–49. Publisher Full Text\n\nMerendino RA, Salvo F, Saija A, et al.: Malondialdehyde in benign prostate hypertrophy: a useful marker? Mediators Inflamm. 2003; 12(2): 127–128. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHiipakka RA, Zhang HZ, Dai W, et al.: Structure-activity relationships for inhibition of human 5alpha-reductases by polyphenols. Biochem Pharmacol. 2002; 63(6): 1165–1176. PubMed Abstract | Publisher Full Text\n\nLiang T, Liao S: Inhibition of steroid 5 alpha-reductase by specific aliphatic unsaturated fatty acids. Biochem J. 1992; 285 ( Pt 2)(Pt 2): 557–562. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbdel-Rahman MK: Effect of pumpkin seed (Cucurbita pepo L.) diets on benign prostatic hyperplasia (BPH): chemical and morphometric evaluation in rats. World J Chem. 2006; 1(1): 33–40.\n\nRoehrborn CG, Boyle P, Gould AL, et al.: Serum prostate-specific antigen as a predictor of prostate volume in men with benign prostatic hyperplasia. Urology. 1999; 53(3): 581–589. Publisher Full Text\n\nRen F, Zhang S, Mitchell SH, et al.: Tea polyphenols down-regulate the expression of the androgen receptor in LNCaP prostate cancer cells. Oncogene. 2000; 19(15): 1924–1932. PubMed Abstract | Publisher Full Text\n\nWang L, Lu B, He M, et al.: Prostate Cancer Incidence and Mortality: Global Status and Temporal Trends in 89 Countries From 2000 to 2019. Front Public Health. 2022; 10: 811044. Published 2022 Feb 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHossen MJ, Yang WS, Kim D, et al.: Thymoquinone: An IRAK1 inhibitor with in vivo and in vitro anti-inflammatory activities. Sci Rep. 2017; 7: 42995. Published 2017 Feb 20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDur A, Kose H, Kocyigit A, et al.: The anti-inflammatory and antioxidant effects of thymoquinone on ceruleine induced acute pancreatitis in rats. Bratisl Lek Listy. 2016; 117(10): 614–618. PubMed Abstract | Publisher Full Text\n\nAttoub S, Sperandio O, Raza H, et al.: Thymoquinone as an anticancer agent: evidence from inhibition of cancer cells viability and invasion in vitro and tumor growth in vivo. Fundam Clin Pharmacol. 2013; 27(5): 557–569. PubMed Abstract | Publisher Full Text\n\nKhan MA, Chen HC, Tania M, et al.: Anticancer activities of Nigella sativa (black cumin). Afr J Tradit Complement Altern Med. 2011; 8(5 Suppl): 226–232. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAcharya BR, Chatterjee A, Ganguli A, et al.: Thymoquinone inhibits microtubule polymerization by tubulin binding and causes mitotic arrest following apoptosis in A549 cells. Biochimie. 2014; 97: 78–91. PubMed Abstract | Publisher Full Text\n\nSalim LZ, Othman R, Abdulla MA, et al.: Thymoquinone inhibits murine leukemia WEHI-3 cells in vivo and in vitro [published correction appears in PLoS One. 2015;10(3):e0120034]. PLoS One. 2014; 9(12): e115340. Published 2014 Dec 22. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXu D, Ma Y, Zhao B, et al.: Thymoquinone induces G2/M arrest, inactivates PI3K/Akt and nuclear factor-κB pathways in human cholangiocarcinomas both in vitro and in vivo. Oncol Rep. 2014; 31(5): 2063–2070. PubMed Abstract | Publisher Full Text\n\nZhang L, Bai Y, Yang Y: Thymoquinone chemosensitizes colon cancer cells through inhibition of NF-κB. Oncol Lett. 2016; 12(4): 2840–2845. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWoo CC, Hsu A, Kumar AP, et al.: Thymoquinone inhibits tumor growth and induces apoptosis in a breast cancer xenograft mouse model: the role of p38 MAPK and ROS. PLoS One. 2013; 8(10): e75356. Published 2013 Oct 2. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "297489",
"date": "08 Aug 2024",
"name": "Rodney Hull",
"expertise": [
"Reviewer Expertise Cancer cell biology",
"multi-omic profiles of cancers specific to different populations. The effect of various compounds on transcriptome ad spliceosome profiles"
],
"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 review covers the use of black cumin (Nigella sativa) to treat prostate ailments such as prostate cancer and Benign prostate hyperplasia. The review is generally well done and overs a topic whose review is worthwhile and would act as an important resource for future studies regarding the use of this plant and its extract as a future potential therapy. However, there are a few issues with the review which need to be addressed,\n1) In the abstract what s meant by the phrase functional foods- I do not hink this is the right term to use 2) In the abstract the use of the wors esteemed to describe the herb - this is not the appropriate word to use here 3) Many of the keywords used appear in the title and as such are redundant. Different keywords should be used 4) In the Methods section the authors state that they tried to avoid omission and include all pertinent information, but they also state that they removed all articles without free full text availability. while this is a practical omission it does mean that important information has been omitted based purely on the information ot being accessible. How pertinent are the omitted articles to the topic. 5) The number of total articles is incorrectly given as 2 in the text and should be 24 6) The title of table 1 is confusing and not correctly written 7) In table 1 should vitro not be in vitro 8)In results the sentence ending experimental in vivo and in vitro, sounds incomplete. 9) The authors state that most studies were from Turkey and Asia. Why are they classing Turkey as solely Asia and not Europe 10) When describing the different studies and methods the phrase \"were variants\" is incorrect and should be described as being variable. 11) The phrase bone-preventive adverse when referring to bone metastasus should be preventing adverse effects in bine or something similar 12) In table 2 the major findings for the Kaseb study are written wih dash type bullets which is dfferent to the other entries 13) In the discussion the use of the phrase compelling opportunity is not correct. The word oppurtunity should be replaced with words such as reason or motivation 14) Under the potential efficacy section is the 9,0 million figure give initially correct? It appears to be too low or the second figure of 51.1 million is too high 15)Should BPH rate model be rat model 16)Many treatments and compounds such as LY29002 did are used without any introduction or explaination 17) In the paragraph beginning in an in vitro study of human prostate cancer TQ is introduced again \"that TQ, a naturally derived herbal product\" which is redundant. This also gives the feeling that the different studies are merely being summarized independently and the results of these studies are not being integrated and discussed as a whole.\nIf these issues are addressed I fully recommend that the paper be accepted and indexed.\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? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-229
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https://f1000research.com/articles/13-228/v1
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27 Mar 24
|
{
"type": "Systematic Review",
"title": "Wine Consumer Studies: Current Status and Future Agendas",
"authors": [
"Vageesh Neelavar Kelkar",
"Jyothi Mallya",
"Valsaraj Payini",
"Vasanth Kamath",
"Vageesh Neelavar Kelkar",
"Jyothi Mallya",
"Vasanth Kamath"
],
"abstract": "Background As wine has become more than just a drink, exploring wine consumer studies provides a better understanding of various factors that shape the wine industry. Therefore, this paper aims to review and map the landscape of wine consumer literature using bibliometric analysis and systematic review. It identifies the key areas, clusters, antecedents, mediators, moderators, and outcomes to propose the framework for future research directions.\n\nMethods This study adopts an integrative review approach: a bibliometric and systematic review. The data for this study were retrieved from the Scopus database. While the bibliometric analyses are conducted using VoSviewer software, a systematic review is conducted using a content analysis approach.\n\nResults Four main topics in the extant wine consumer literature are identified: sustainability and wine, wine preferences and choice, wine consumer behavior, and wine consumer insights. The five critical areas of wine consumers’ literature recognized are decision-making, consumer preferences, consumer behavior, segmentation, and consumer involvement. This study also recognizes theoretical and methodological advancements in the wine consumer literature.\n\nConclusions The findings contribute to advancing knowledge development, identifying research gaps and shedding light on future research in the wine consumer domain. The results offer practical insight for wine industry stakeholders, researchers, and influencers.",
"keywords": [
"bibliometrics",
"systematic review",
"integrative review",
"environmental",
"economic",
"sociocultural",
"sustainability"
],
"content": "1. Introduction\n\nSince ancient times, wine has been admired as a cultural icon, a symbol of sophistication, and a source of enjoyment. Beyond its gastronomic appeal, the world of wine is a fascinating domain where science, culture, and consumer behaviour intertwine (Mitchell et al., 2009; Mouret et al., 2013). Consequently, over the past two decades, wine consumers’ preferences and decision-making processes have attracted much interest from researchers and industry professionals alike (Aqueveque, 2023; Moscovici et al., 2022; Payini, 2021; Payini et al., 2022; Vecchio et al., 2023). Accordingly, much research has been done on how consumer choose wines (Wright et al., 2023). Therefore, it is essential to understand the factors that influence wine preferences, consumption patterns, and selections. Though traditional research methodologies, such as bibliometric analysis (Martinho, 2021; Weatherbee et al., 2019) and systematic reviews (Campo et al., 2022; Carollo et al., 2022; Schäufele and Hamm, 2017), have long been employed to analyze and synthesize knowledge within wine business domains, an integrating these approaches offers a unique opportunity to gain comprehensive insights into wine consumers’ behavior. It is found that most of the reviews pertain to particular theme, such as wine tourism experience (Gómez et al., 2019; Kotur, 2023), wine consumption (Wright et al., 2023), sustainability in wine industry (Nave et al., 2021), sustainable wine (Maesano et al., 2019), and willingness to pay (Schäufele and Hamm, 2017). Additionally, none of these reviews attempts to encompass the entirety of wine consumption. Further, there are no studies that examined the conceptual and intellectual configuration latent in this emergent research field. Such omissions motivated the researchers to combine quantitative and qualitative methods in order to consolidate the existing literature and provide a road map for future research. Therefore, this integrative review aims to provide the current state of knowledge of wine consumers’ behavior. The findings of this study are helpful for researchers, practitioners, and policymakers.\n\nBibliometrics, as a quantitative analysis of scientific publications, provides a valuable means to map and assess the existing body of research in a particular field (Mukherjee et al., 2022a). By systematically identifying and analyzing relevant publications, bibliometrics enables researchers to uncover key trends, knowledge gaps, and emerging research areas. In the context of wine consumers’ behavior, bibliometric analyses can shed light on the evolution of wine consumer research, influential authors, and predominant themes or theories. It serves as a foundational step in understanding the overall landscape of research on wine consumers (Donthu et al., 2021).\n\nOn the other hand, systematic reviews offer a rigorous and structured approach to identifying patterns, discrepancies, and evidence-based findings (Mulrow, 1994). By employing predefined inclusion and exclusion criteria, systematic reviews ensure objectivity and reproducibility in selecting relevant studies (Moher et al., 2009). In the context of wine consumers’ behavior, systematic reviews can help identify the factors influencing consumer choices, preferences, and decision-making processes. By combining the quantitative analysis of bibliometrics with the qualitative synthesis of systematic reviews, this study offers a holistic view of the existing body of wine consumer literature. It allows the identification of theoretical and methodological research gaps.\n\nThis integrative review addresses several critical questions, such as the following: What are the publication trends of wine consumer literature? What is the performance of research constituents, such as authors, journals, and articles? What are the critical areas and clusters of wine consumer literature? What are the antecedents, mediators, and outcomes of wine consumption? Which theoretical frameworks have been most frequently employed to understand wine consumers? How can future research directions be shaped to enhance our understanding of wine consumers’ behavior? By combining bibliometric analysis and systematic review methodology, this study seeks to contribute to the wine consumer knowledge base by identifying research gaps and proposing potential areas for future investigation. The proposed framework helps to identify the underlying gaps in a research domain across theory development and methods.\n\n\n2. Methods\n\nTo achieve the objectives set in this research, a bibliometric analysis was conducted using VOSViewer. In addition, a systematic literature review was conducted as the bibliometric analysis alone is considered insufficient to explore and further the research practices in the field (Ali et al., 2022).\n\nThe Scopus database was the data source for this study. Scopus indexes content from over 25,000 active titles and 7,000 publishers—all rigorously vetted and selected by an independent review board. It is the largest database of peer-reviewed literature and is widely used for similar studies (Donthu et al., 2021).\n\nThe keywords “wine” and “consum*” were searched in the article title head of the Scopus database. After restricting to the “Business, Management, and Accounting” subject area, 317 articles were obtained. After excluding editorials, book chapters, and non-English articles, the final dataset extracted was 262 articles (Mallya, Jyothi, et al., 2024). The final query string is as follows: ((TITLE (consum*) AND TITLE (wine)) AND (LIMIT-TO (SUBJAREA, “BUSI”)) AND (LIMIT-TO (DOCTYPE, “ar”)) AND (LIMIT-TO (LANGUAGE, “English”)) AND (LIMIT-TO (SRCTYPE, “j”)).\n\nVoSviewer, a free software available is used to conduct various analyses. It is a popular and frequently used software by researchers for constructing and visualizing bibliometric networks. These networks may include journals, contributors, or individual publications, and they can be built based on citation, bibliographic coupling, cocitation, or coauthorship relations. This software also offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from a body of scientific literature (van Eck and Waltman, 2010).\n\nBibliometrics analyses, a branch of library science, have been used in various disciplines, including consumer behavior research (Baber et al., 2023; Haba et al., 2023). Utilizing quantitative methods, it analyses bibliographic information to derive insightful conclusions (Mukherjee et al., 2022b). This approach is more advantageous (Mukherjee et al., 2022a), making it more appropriate for the current study. It supports a huge corpus of data and involves a variety of bibliographic metrics. Its quantitative character of analyses yields impartial results. Additionally, the networks and graphs produced by this program allow users higher visibility of the data points (Donthu et al., 2021).\n\nHowever, bibliometric approaches have certain limitations, such as making qualitative claims about research based on quantitative data (Wallin, 2005). Quantitative metrics such as citation counts, h-indexes, and journal impact factors are typically utilized in bibliometric analyses. Although these metrics provide a quantitative evaluation of research output, they may not capture the complexity and quality of scientific work. Advancing theory and methodology frequently requires a deeper understanding of research content, context, and impact, which bibliometric indicators may not adequately reflect. This dependency may hinder the study’s findings. Therefore, to fill this gap, the current study also systematically reviews selected articles to support a few qualitative assumptions.\n\n2.4.1 Bibliometric analyses\n\n2.4.1.1 Descriptive analysis\n\nThe descriptive analysis includes the number of publications in a given dataset over a specific period. It provides an overview of the volume of research output in a particular field or topic. The annual and last four decades of publication growth were analyzed.\n\n2.4.1.2 Performance analyses\n\nIn bibliometric studies, performance analysis refers to assessing the research output of people (for example, authors), organizations (institutions and funding agencies), nations, sources, and documents using bibliometric data. It includes information about the quantity and quality of research constituents, such as the number of publications, citations, impact factor of journals, and H-index. Thus, the pattern in the research constituents (journals, articles, and authors) was also explored as recommended (Donthu et al., 2021). The performance of the various research constituents, such as journals, authors, articles, and countries, was assessed regarding productivity, influence, and authorship structure. The multiple matrices used are total publications (TP), total citations (TC), number of cited publications (NCP), total citations per publication (TC/TP), number of active years (NAY), productivity per active year (PAY), number of contributing authors (NCA) and h and g indexes (Ali et al., 2022). These analyses were conducted using MS Excel software.\n\n2.4.1.3 Science mapping\n\nScience mapping is a bibliometric technique that uses patterns of citation, cocitation, and coauthorship in the scientific literature to visually demonstrate subjects’ structure and evolution. It provides a thorough overview of the research landscape within a specific field by enabling researchers to spot clusters of linked research, notable authors, and important research subjects. This analysis includes cocitation mapping, bibliographic coupling analysis, and keyword co-occurrence. The current study uses keyword-cooccurrence and bibliographic coupling analysis to uncover the domains and themes of the wine consumption literature landscape. While keyword co-occurrence analysis examines the frequency of keywords or terms within a set of documents and identifies co-occurrence patterns, bibliographic coupling analysis identifies relationships between documents based on shared references. Both of these methods help identify clusters of related documents, identify central or influential documents, and analyze the relationships between studies in a given field.\n\n2.4.2 Systematic review\n\nDespite the clear advantages of bibliometric analyses, it is important to remember that bibliometric techniques alone are insufficient for advancing theory and practice (Ali et al., 2022). Each review method contributes to the overall body of knowledge and comprehension, provided that they form knowledge theoretically (Donthu et al., 2021; Fan et al., 2022). Content analysis has been successfully used in wine research as a research method (Bonn et al., 2018; Carollo et al., 2022; Nave et al., 2021; Weatherbee et al., 2019). The primary purpose of the content analysis was to synthesize the extant wine consumer literature to gain a comprehensive understanding of it. Furthermore, the content analysis aims to understand the wine consumption literature’s theoretical and methodological advancement and propose research frameworks for future studies.\n\n\n3. Results and discussion\n\nThe first research question was to understand the research publication trends. To this effect, descriptive analysis was conducted (Figures 1 and 2). While Figure 1 presents the direction of wine consumption literature for the last four decades, Figure 2 reveals the annual growth of publications and citations. According to Moed et al. (2004), the count of publications’ productivity and the citation counts represent academic influence and impacts (Meyer et al., 2018).\n\nSource: Authors own.\n\nSource: Authors own.\n\nThe data presented in Figure 1 highlight a significant increase in research activity over approximately four decades within this subject area. Specifically, the number of documents produced has notably increased, from only six in the earliest period (1985-1994) to 149 in the most recent period (2015-2023). These data suggest a growing interest and investment in this field, potentially due to the wine consumer study’s increasing importance and relevance for the hospitality industry. However, there have been fluctuations between different periods regarding citation trends. For example, the average number of citations in the third period was significantly more (51 citations per document) than in the fourth period (13 citations per document). It is also worth noting that the most recent period (2015-2023) shows a high volume of document production (149) but a relatively low citation count (1986), which may be attributed to the recency of the research and its ongoing evaluation by the wine consumers’ research community.\n\nFigure 2, the year wise distribution of the publications, shows somewhat inconsistent growth regarding the number of articles. For example, 2020 witnessed the highest number of publications (31 articles), followed by 2019 and 2012, with 21 articles each. However, the articles published in 2009 received the highest number of citations, nearly 15% of the total citations across 15 documents. Thus, it can be inferred that 2020 and 2009 are the most productive and impactful years in wine consumers’ literature.\n\nThe second research objective was to analyze the performance of various research constituents, such as authors, journals, articles, and countries. For this, citation analysis was used.\n\n3.2.1 Most productive authors\n\nThe top ten most productive authors were identified based on the number of publications (at least five articles) and citations (a minimum of 75 citations). Table 1 demonstrates that Johan Bruwer, with 27 papers and 1417 citations, is the most prolific author, followed by Nelson Barber and Tim H. Dodd, who have eight articles. Tim H. Dodd and Nelson Barber received 492 and 314 citations, respectively. Bruwer Johan has been active in the wine consumer subject domain for 12 years (NAY=12) and has the highest h-index of 19. At the same time, Anthony Saliba J. emerged as one of the most prolific authors, receiving 320 citations across five documents. Steve Goodman has the highest TC/CP ratio, indicating that the four cited publications contributed by the author carry an average of 73.50 citations.\n\n3.2.2 Most influential articles\n\nAn analysis of the top 15 most cited articles in wine consumer studies based on the number of citations was conducted. Table 2 provides the total number of citations and average citations per year of the top 15 articles in the domain of wine consumption literature. As evident, the article “The Hedonic Nature Of Wine Tourism Consumption: An Experiential View” (Bruwer and Alant, 2009) was an influential publication with 252 citations. Bruwer and Alant used the experiential view of consumption to better understand wine tourists’ motivation. The other most cited works include articles titled “Consumer Attitudes Regarding Environmentally Sustainable Wine: An Exploratory Study of The New Zealand Marketplace” (Forbes et al., 2009). and “Differential Effects of Experience, Subjective Knowledge, And Objective Knowledge on Sources of Information Used in Consumer Wine Purchasing” (Dodd et al., 2005). However, the articles titled “Millennial Generation Attitudes toward Sustainable Wine: An Exploratory Study on Italian Consumers” (Pomarici and Vecchio, 2014) and “Exploring Environmental Consciousness and Consumer Preferences for Organic Wines Without Sulfites” (D’Amico et al., 2016) are the fastest growing articles in terms of influence, with an average of 21 and 19 citations per year, respectively.\n\n3.2.3 Journal impact\n\nThe most influential journal was identified based on a number of publications and citations. The journals published at least five articles, and 100 citations were included in the analysis. The source impact (productivity and influence) analysis helps understand the distribution of core journals in the research area. Table 4 shows the top seven journals in the research area sorted by the number of publications and citations. The h-index 26 for the International Journal of Wine Business Research (IJWBR) indicates that IJWBR has at least 26 documents, each receiving at least 26 citations. IJWBR is the only journal that comprehensively covers business disciplines, continents, and countries on all topics connected to wine consumer literature, such as perspectives on alcoholic beverages such as beer, craft beer, and spirits. Thus, it can be concluded that wine consumption is widely acknowledged in wine business research literature. Following IJWBR, the British Food Journal (BFJ), the Journal of Food Products Marketing (JFPM), and the Journal of Cleaner Production (JCP) are positioned as the second and the third most impactful journals in this domain (Tables 3 and 4). These results also indicate that wine consumption is well documented in food science, food product marketing, and environmental/sustainability research literature.\n\n3.2.4 Top contributing countries\n\nThe following is a list of the top ten countries according to the nationality of the corresponding author. Table 5 presents the total publications, total cited publications, total citations (TC), average citations per publication, average citations per cited publication, number of active years, productivity per active year, and H-index for the ten leading countries in the wine consumption literature. According to this table, the most influential country is the United States of America, with 21 active years, 67 publications, and 2376 citations. However, in terms of the H-index, Australia topped the list with an H-index of 27. Additionally, the highest number of publications are also from the United States of America. Interestingly, despite having eight active years and an H-index, Canada topped the list regarding average citations per publication and cited publications, followed by New Zealand.\n\nThe third objective of this study was to identify the critical areas and distinct clusters of wine consumption literature. The study uses keyword co-occurrence analysis and bibliometric coupling analysis to achieve this.\n\n3.3.1 Keyword co-occurrence analysis\n\nKeyword co-occurrence analysis refers to examining the co-occurrence of keywords in scientific publications and constructing a network of keywords based on their relationships. Identifying the frequency of keywords could uncover potential future research opportunities. Therefore, the current study conducts keyword co-occurrence analysis using VoSviewer software. The minimum number of occurrences was set to five. VOSviewer provides various visualization techniques to represent coword networks, such as network and overlay visualization (Figure 3). The keyword co-occurrence analysis resulted in six clusters. The keyword co-occurrence analysis resulted in five critical areas of wine consumer literature: decision making, consumer preferences, consumer behavior, segmentation, and consumer involvement. The clusters and items are presented in Table 6.\n\nSource: Generated by the authors using VOS-viewer software.\n\nThe size of the nodes in Figure 3 reflects the occurrence of using the terms. Overlay visualization, a feature in VOSviewer that allows the classification of keywords based on a time scale, is conducted. It is evident that the word “wine/wines” is the most used keyword (145 occurrences), followed by consumer behavior/behavior (96 occurrences). The other keywords are market segmentation (23 occurrences), human (21 occurrences), wine consumption (21 occurrences), and marketing (16 occurrences). Keywords that appeared more than 10 times are consumers, segmentation, United States of America, China, consumer attitude, consumption, gender, and Italy. The items are colored differently according to publishing year (average for the cluster). This study highlights phrases that debuted recently (the average publication year was 2020) in a brighter yellow. A color bar displayed at the corner has the same explanation; the scores of the items are decided by the publishing date (Figure 3). According to Figure 3, the most recent topics studied were sustainable development, sustainability, willingness to pay, organic wine, and price.\n\n3.3.2 Bibliographic coupling analysis\n\nBibliographic coupling is a measure of similarity that employs citation analysis to build a relationship of similarity between documents. It occurs when two works’ bibliographies reference the same third work. This indicates that there is a possibility that the two works address a similar topic (Weinberg, 1974). It is helpful in various fields since it helps researchers find related past research. Bibliographic coupling uniquely contributes to the measurement of centeredness, with increasing coupling between the precenter and postcenter periods (Youtie et al., 2013). Bibliographic coupling analysis is also helpful in identifying clusters of related articles. Therefore, this study embraces bibliographic coupling analysis to identify the different clusters of wine consumption literature based on a minimum of 50 citations per document. This analysis resulted in four clusters of 41 documents, represented in four colors (Figure 4). The total number of citations across these 41 articles is 4422 (approximately 56%).\n\nSource: Generated by the authors using VOS-viewer software.\n\nCluster one, represented in red, has 13 articles named Sustainability and Wine, published between 2009 and 2016. The most cited article in this cluster was “Consumer attitudes regarding environmentally sustainable wine: an exploratory study of the New Zealand market place.” (Forbes et al., 2009), followed by “Millennial generation attitudes to sustainable wine: an exploratory study on Italian consumers” (Pomarici and Vecchio, 2014). The other articles in this cluster discuss environmental impacts (Amienyo et al., 2015; Point et al., 2012), the carbon intensity of wine distribution (Cholette and Venkat, 2009), wine labeling and packaging (Barber, 2010; Galati et al., 2019) and environmental consciousness (D’Amico et al., 2016). Interestingly, a majority of studies have explored consumers’ attitudes toward sustainable/green/organic wines (Forbes et al., 2009; Mann et al., 2012; Pomarici and Vecchio, 2014; Sogari et al., 2015; Tait et al., 2019; Wiedmann et al., 2014).\n\nCluster two, represented in green has 11 “Wine Preferences and Choice” articles. The articles in this cluster were published between 2007 and 2012. The most cited article in this cluster is “A regional brand image and perceived wine quality: the consumer perspective (Johnson and Bruwer, 2007). This cluster’s second most cited article compares international wine consumer choice (Goodman, 2009). Few studies have investigated the reasons (Charters and Pettigrew, 2008; Ritchie, 2007), perception (Liu and Murphy, 2007), motivation (Somogyi et al., 2011), preferences (Casini et al., 2009), and determinants (Camillo, 2012; Hussain et al., 2007; Yu et al., 2009) of wine consumption. Studies have also investigated the role of brand image (Johnson and Bruwer, 2007) and country of origin (McCutcheon et al., 2009) in wine choice.\n\nThe third cluster, represented in blue, is named “Wine Consumer Behavior” and has nine articles. The articles in this cluster were published between 1997 and 2012. The most cited in this cluster is “The use of quality and reputation indicators by consumers: the case of Bordeaux wine” (Landon and Smith, 1997). Studies in this cluster have investigated wine consumer behavior using different factors, such as country of origin (Balestrini and Gamble, 2006; Bruwer and Buller, 2012; Dimara and Skuras, 2005; Orth et al., 2005), information search (Atkin et al., 2007), wine involvement (Barber et al., 2007), grape vintage year (Gil and Sánchez, 1997), and functional and production aspects (Vrontis et al., 2011).\n\nThe fourth cluster, represented in yellow is “Wine Consumer Insights: Tourism, Generations, and Preferences.” This cluster has eight articles on diverse aspects, such as wine tourists’ consumption behavior (Bruwer et al., 2013; Bruwer and Alant, 2009; Carlsen and Boksberger, 2015), sensory preferences (Bruwer et al., 2011), general differences (Agnoli et al., 2011; Mueller et al., 2011), the role of demographics (Bruwer et al., 2012) and product involvement (Bruwer and Huang, 2012). The most cited article in this cluster is “the hedonic nature of wine tourism consumption: an experiential view” (Bruwer and Alant, 2009), followed by the article “consumer behavior and sensory preference differences: implications for wine product marketing” (Bruwer et al., 2011). The articles published in this cluster were published between 2009 and 2015.\n\nThe fourth objective of the study was to develop a conceptual framework based on the antecedents, mediators, and outcomes reported in the wine consumer literature. As mentioned in the methodology section, the documents forming bibliographical coupling were systematically reviewed to gain comprehensive insight into wine consumers’ literature. Three articles were excluded from this review because they did not pertain to wine consumer behavior. Figure 5 illustrates the framework developed by integrating the antecedents, mediators, and outcomes reported in the wine consumer literature.\n\nSource: Author’s own.\n\n3.4.1 Antecedents of wine consumer research\n\nAll the antecedents that predominantly influence wine consumer behavior are further categorized into five subcategories: Personal, Social, Extrinsic, Intrinsic, and Environmental.\n\nPersonal factors comprised variables related to the individual, such as wine knowledge, environmental orientation, experience, enjoyment, cognitive dimensions, involvement, habits, preferences, brand familiarity, consumption frequency, and purchase frequency. These factors can vary from person to person and can influence their preferences, choices, and decision-making processes when purchasing and consuming wine. For example, consumers with higher levels of objective wine knowledge are likelier to use intrinsic cues during wine purchase than extrinsic cues, such as country of origin (Bruwer and Buller, 2012). Similarly, it is found that wine-tasting experience significantly correlated with attitude toward brand loyalty. Consumers having an enjoyable and memorable experience are more likely to repurchase and promote the wine brand to others (Bruwer et al., 2013).\n\nAdditionally, enjoyment, situational and lifestyle-related factors are found to be crucial (Charters and Pettigrew, 2008). Specifically, enjoyment was critical across groups, irrespective of age and gender (Charters and Pettigrew, 2008). Other personal factors that impact consumers’ consumption or purchase behaviors are consumption frequency, curiosity, purchase frequency, habits, and brand familiarity (Balestrini and Gamble, 2006; D’Amico et al., 2016; McCutcheon et al., 2009).\n\nA systematic review revealed that social factors, such as consumers’ living environment, situational factors, social image, social acceptance, and social context, were also found to be antecedents to wine consumption and purchase (Agnoli et al., 2011; Charters and Pettigrew, 2008; Iazzi et al., 2019; Liu and Murphy, 2007; Orth et al., 2005). For example, a study conducted among millennials revealed that consumers living in urban areas, being female and older, are likely to buy sustainable wine (Iazzi et al., 2019). The literature shows that wine consumption’s second most important factor is the situational factor (Charters and Pettigrew, 2008). While social image impacted wine consumption (Liu and Murphy, 2007), social context and acceptance were found to have an impact on wine preference (Agnoli et al., 2011; Orth et al., 2005).\n\nThe third antecedent identified through the systematic review was extrinsic factors comprising variables such as country of origin, price, labeling, brand, vintage year, certification, food pairing, bottle design, wine types, medal won, advertising, purchasing channels, and packaging. Price is the most studied extrinsic variable by researchers (Agnoli et al., 2011; Atkin and Sutanonpaiboon, 2007; Balestrini and Gamble, 2006; Bonn et al., 2016; Bruwer and Buller, 2012; Forbes et al., 2009; Galati et al., 2019; Gil and Sánchez, 1997; Johnson and Bruwer, 2007; Liu and Murphy, 2007; McCutcheon et al., 2009; Orth et al., 2005; Somogyi et al., 2011; Tait et al., 2019), followed by labeling (Barber et al., 2007; Bruwer et al., 2011; Bruwer & Buller, 2012; Casini et al., 2009; D’Amico et al., 2016; Forbes et al., 2009, p. 200; McCutcheon et al., 2009; Sogari et al., 2015; Somogyi et al., 2011; Yu et al., 2009) and country of origin (Atkin and Sutanonpaiboon, 2007; Bruwer and Buller, 2012; Gil and Sánchez, 1997; Johnson and Bruwer, 2007; Liu and Murphy, 2007; McCutcheon et al., 2009, 2009). The other popular extrinsic variables studied were wine brands (Casini et al., 2009; D’Amico et al., 2016; Johnson and Bruwer, 2007; Liu and Murphy, 2007; McCutcheon et al., 2009; Yu et al., 2009), bottle design, including packaging and wine stopper design (Atkin and Sutanonpaiboon, 2007; Barber et al., 2007; Bruwer and Buller, 2012; D’Amico et al., 2016), wine types (Atkin and Sutanonpaiboon, 2007; Bruwer and Li, 2007; Johnson and Bruwer, 2007; Somogyi et al., 2011), and recommendation by peers and sales assistance (Bruwer et al., 2011; Bruwer and Buller, 2012; Casini et al., 2009; McCutcheon et al., 2009; Somogyi et al., 2011; Yu et al., 2009). Researchers have also explored the role of food pairing (Casini et al., 2009; Somogyi et al., 2011; Yu et al., 2009) and wine consumption in a few instances. The impact of medals won (Casini et al., 2009; Yu et al., 2009), certification (Sogari et al., 2015), aesthetics (Charters and Pettigrew, 2008), and purchasing channels (Johnson and Bruwer, 2007) were also studied by researchers.\n\nThe fourth antecedent is identified as an intrinsic factor. It included characteristics that are inherent to the wine itself. Examples include quality (McCutcheon et al., 2009; Sogari et al., 2015, p. 201; Tait et al., 2019), taste (Bruwer and Buller, 2012; D’Amico et al., 2016), naturalness (D’Amico et al., 2016; Galati et al., 2019), sensory attributes (Bonn et al., 2016; Galati et al., 2019), color (Bruwer and Buller, 2012; Mann et al., 2012), vintage year (Bruwer and Buller, 2012; Gil and Sánchez, 1997; McCutcheon et al., 2009), alcohol level (McCutcheon et al., 2009; yu et al., 2009), and grape variety (Casini et al., 2009; Goodman, 2009; McCutcheon et al., 2009; yu et al., 2009). Additionally, studies have also investigated the impact of environmental factors as the fifth antecedent comprising sustainability (Tait et al., 2019), organic supply (Bonn et al., 2016; D’Amico et al., 2016; Galati et al., 2019; Mann et al., 2012; Wiedmann et al., 2014), environmental protection, benefits, and values.\n\n3.4.2 Mediators\n\nThe systematic review suggests that wine consumer researchers have rarely used any mediators. For example, the only study that used an exploratory approach to investigate wine consumers’ attitudes toward sustainable-labeled wine adopts an attitude that mediates the relationship between consumers’ beliefs about the wine and their wine consumption (Sogari et al., 2015). Furthermore, the findings of this study revealed that attitude toward sustainable-labeled wine is shaped by both environmental and quality beliefs about sustainable wine.\n\n3.4.3 Moderators\n\nSimilar to mediators, wine consumer research studies have rarely adopted any moderators. Trust was the only moderator used in the study (Bonn et al., 2016). It is suggested that consumer perceptions of suppliers are the basis for deciding whether to believe a winemaker’s claim that their products and operations are sustainable (Bonn et al., 2016).\n\n3.4.4.Demographic moderating variables\n\nIn addition to the moderating variable mentioned above, studies have examined the moderating role of demographic variables, such as age (Sogari et al., 2015), income, education (Barber, 2010), and gender (Atkin and Sutanonpaiboon, 2007; Barber, 2010).\n\n3.4.5 Outcomes\n\nThe systematic review identifies several outcome variables discussed in the extant literature, namely, willingness to pay (Barber, 2010; D’Amico et al., 2016; Forbes et al., 2009; Galati et al., 2019; Pomarici and Vecchio, 2014; Skuras and Vakrou, 2002; Tait et al., 2019), purchase intention, behavioral intention, wine selection (Agnoli et al., 2011; Bonn et al., 2016; Bruwer et al., 2011; Bruwer and Buller, 2012; Camillo, 2012; Casini et al., 2009; Gil and Sánchez, 1997; Goodman, 2009; Liu et al., 2017; McCutcheon et al., 2009; Ritchie, 2007; Sogari et al., 2015), wine consumption (Balestrini and Gamble, 2006; Bruwer et al., 2012; Charters and Pettigrew, 2008; Hussain et al., 2007; Mann et al., 2012; Mueller et al., 2011; Somogyi et al., 2011; Yu et al., 2009), consumer wine quality perception (Johnson and Bruwer, 2007), tasting experience (Bruwer et al., 2013), and wine tourists’ motivation (Bruwer and Alant, 2009a).\n\n3.4.6 Theoretical and methodological advancement\n\nThe fifth objective of the study was to explore the theoretical and methodological advancement in a wine consumer study. All 39 articles were subjected to systematic review, and the findings are discussed in the following section. Wine consumer scholars have used many theories, such as McFaden’s random utility theory (Tait et al., 2019), Lancasters’ characteristics theory (Mann et al., 2012; Tait et al., 2019), and the theory of consumer behavior (Camillo, 2012). Ego-involvement and Persuasion theory (Bruwer and Huang, 2012), Age-Generational Cohort theory (Bruwer et al., 2011; Bruwer and Alant, 2009), VBA theory (Sogari et al., 2015), Brand loyalty (Bruwer et al., 2013), and Reputation model (Landon and Smith, 1997). However, a majority of studies remain atheoretical.\n\nThe systematic review suggests that the majority of the researchers contributed to the wine consumer literature through quantitative studies (N=30), followed by mixed methods (N=5) and qualitative methods (N=4). Only one case study was found.\n\nThis study’s sixth and final objective is to recommend future research directions in wine consumer research. Although the previous wine literature sheds light on some of the critical areas related to consumers, it is found that there is a scope for future research related to environmental, economic, and sociocultural issues. Some crucial areas within these issues are identified (Figure 6), and future directions are discussed in the following section.\n\nSource: Author’s own.\n\n3.5.1 Antecedents\n\nEnvironmental aspects\n\nBy addressing environmental issues related to wine consumption, producers can contribute to the industry’s overall sustainability, minimize ecological impacts, and meet the growing demand for environmentally friendly products. Additionally, taking proactive measures to address these issues helps ensure wine-producing regions’ long-term viability and resilience in the face of climate change and environmental challenges. Therefore, future studies should focus on some environmental aspects, such as wine consumers’ environmental knowledge, education, consciousness, and impact on their purchase intention, preference, and willingness to pay for sustainable wine. Researchers can also focus on the role of sustainability attributes on wine consumption preferences, choices, and consumption. Another potential area of research is the role of certification and its impact on wine-purchasing behavior. Future studies can also measure the role of environmental attributes on actual wine consumption.\n\nEconomic aspects\n\nThe economic attributes of wine consumer behavior refer to the factors and considerations influencing consumers’ choices and behaviors about purchasing and consuming wine. Future researchers can consider key economic attributes: price, brand image, brand communication, advertising, brand promotion, and sales channels. For example, a recent study conducted to understand the impact of brand communication and brand image on brand preference revealed that both variables positively affected brand preferences (Gómez-Rico et al., 2023). Wine sales channels are another critical variable to consider in future studies. There is a correlation between the usage of sales channels and per capita consumption and wine preferences (Szolnoki and Hoffmann, 2014).\n\nSociocultural aspects\n\nSociocultural aspects play a significant role in wine consumption. For example, wine is often deeply rooted in cultural traditions and heritage (Black and Ulin, 2013). It is associated with specific regions, countries, and communities, reflecting their history, customs, and social identity (Trivellato et al., 2014). Wine consumption is also linked to social and emotional well-being (Bauer and Mills, 2021). It is also associated with special occasions, rituals, and ceremonies, adding to its sociocultural significance. Therefore, future research can focus on the sociocultural aspects of wine, such as cultural diversity, rituals, consumption practice, cultural value, consumption traditions, social norms, social gathering, celebrations, status, lifestyle choices, ceremonial practice and cultural symbolism, and its impact on consumer preference and choices. Future research can also focus on the impact of sociocultural aspects on the emotional and social well-being of wine consumers.\n\n3.5.2 Mediators\n\nFuture studies can also focus on mediating variables such as attitude, motivation, trust, and satisfaction. For example, attitudes can mediate the relationship between wine-related stimuli (e.g., marketing messages, product attributes) and consumer behavior (e.g., purchase intentions, consumption, willingness to pay, wine preferences, and brand loyalty). Similarly, wine consumers’ motivation can also be important in determining wine consumption behavior. It can influence wine consumption occasions, preferences for certain types of lifestyles, and engagement in wine activities, such as wine tourism. Trust is another important factor in consumer behavior. behavior Trust in wine brands, producers, or retailers can mediate the relationship between wine-related stimuli and consumers. Trustworthy wine-related information and certifications can enhance purchase intentions. Future studies can also examine the mediating role of consumer satisfaction. Consumer satisfaction can mediate the relationship between brand image and brand loyalty. Satisfied consumers are likelier to exhibit repeat purchases, positive word-of-mouth, and brand loyalty.\n\n3.5.3 Moderators\n\nModerator variables play a crucial role in understanding the nuances of wine consumption and how it varies across different individuals and contexts. Some moderators that can be considered in future studies are age, income, gender, generation, culture, personality traits, and country.\n\nAge can moderate wine consumption patterns, preferences, and behaviors. For example, younger consumers may be more experimental and open to trying different wine styles, while older consumers might have more established choices and seek specific wine characteristics. Furthermore, age can also influence the context in which wine is consumed, such as social occasions or personal relaxation. Another significant moderator is income. Higher-income individuals may be more likely to purchase premium/luxury/sustainable wines. Income can also impact the frequency and occasions of wine consumption. Gender is another critical moderator that can be considered in future studies. Research suggests that gender differences exist in wine choice, with variations in the preference for specific wine styles, labeling aesthetics, or marketing messages (Alpeza et al., 2023).\n\nAdditionally, gender can influence the social context of wine consumption and the roles individuals play in wine-related activities. Future research can also focus on the generational differences in values, wine knowledge, consumption preferences, habits, and frequency by their respective social and historical contexts. The moderating role of personality traits can also be investigated in future studies. For example, individuals with higher innovativeness may be more inclined to try different wine varieties. The cultural context of the country can moderate wine consumption practices. For example, a comparative study between new and old wine countries can be considered. Each country has its unique wine culture and consumption norms. Factors such as wine availability, legal regulations, and historical wine traditions can shape consumer behavior within a country.\n\n3.5.4 Outcomes\n\nDespite the extensive focus of researchers on various outcomes, including willingness to pay, behavioral intention, wine consumption, quality perception, and tourists’ experience, this research suggests that there remains ample opportunity for further investigation. Examples include wine choice, preferences, sustainable wine consumption, brand loyalty, and emotional/social well-being. Furthermore, future studies can also focus on actual wine consumption. For example, research on well-being can include the role of wine consumption across different social occasions/gatherings. Understanding wine consumption’s emotional and social dimensions can provide insights into its broader impact on individuals’ well-being.\n\n3.5.5 Theoretical directions\n\nIt is recommended that future studies use the consumer decision-making process (CDMP) model, which provides an understanding of wine consumers’ various decision-making stages, such as problem recognition, information search, evaluation of alternatives, purchase, and postpurchase evaluation. These models can also be applied to investigate consumers’ choice of wine products, considering price, brand, taste, labeling, and recommendations. In addition, this research explores several theories that can be adopted in the future and are discussed below.\n\nExperiential consumption theory (Holbrook and Hirschman, 1982) emphasizes the significance of experiential aspects, such as sensory pleasure, emotions, and fantasies, in consumer behavior and can also be considered by wine consumer scholars. This theory argues that experiential or hedonic dimensions shape consumer preferences and satisfaction. Since its inception, experiential consumption theory has been widely adopted and expanded upon by scholars in consumer behavior. However, this theory is sparingly adopted in wine consumer studies (Bruwer and Alant, 2009).\n\nAnother theory that can be considered in wine consumer studies is the diffusion of innovation theory (Rogers, 2010). This theory describes how new products, ideas, and behaviors gradually spread among the population. It contends that adoption starts with innovators and early adopters and then spreads through the people to the early and late majority. In wine consumer studies, this theory can be adopted to examine the adoption of new wine products, profiling wine consumers based on the adoption of new wine products and the acceptance of new wine products, practices, or technologies among consumers. This theory can also be adopted to investigate the role of opinion leaders in adopting new wine products.\n\nThis review identifies the theory of planned behavior (TPB) as a valuable framework for assessing the behavioral antecedents of wine consumption. It is found that TPB better predicts wine consumption in restaurants than Theory of Reasoned Action (TRA) (Agnoli et al., 2016; Agnoli and Outreville, 2023). The TPB (Ajzen, 1987) is a psychological theory that explains and predicts human behavior in various social contexts. This theory suggests that attitudes, subjective norms, and perceived behavioral control influence people’s actions.\n\nCognitive dissonance theory (Festinger, 1957) is a social psychology theory that seeks to explain the psychological discomfort (cognitive dissonance) that arises when individuals hold conflicting beliefs, attitudes, or values. This theory has been used in the consumer behavior literature to measure the cognitive dissonance of medical tourists (Majeed et al., 2022) and travel behavior (Kah and Lee, 2016). In a wine consumer study, this theory is used to understand how tensions may arise for individuals approaching each experience and where to avert perceived risks (d’Ament et al., 2022). However, this theory can be used in other areas of wine consumption, such as dissonance between price and quality, brand loyalty and consumer preference, wine recommendations and consumption experience.\n\nAccording to Maslow’s hierarchy of needs (Maslow, 1943), individuals are motivated to fulfill their needs sequentially, from the most basic to higher-order psychological needs. This theory was used to segment wine consumers (Divine and Lepisto, 2005) and understand wine tourists’ motivation (Park et al., 2008). Future studies can use this theory to understand the relationship between psychological needs, safety, emotional experience, social status, and wine consumption behavior.\n\nSelf-determination theory (SDT) (Deci and Ryan, 1985) is one of the psychological theories of motivation that can be considered in future wine consumption studies. The theory focuses on the innate psychological needs that drive human behavior and the conditions that foster personal growth and well-being. This theory is used to understand the relationship between motivation and wine club attributes (White and Thompson, 2009) and attitude toward domestic wine (Ye et al., 2017). However, future wine consumer studies can further explore this theory to understand the role of intrinsic/extrinsic factors on consumer behavior. For example, how can social interactions, such as wine festivals or wine-tasting events, enhance wine consumers’ experience? How can wine education contribute to wine consumers’ competence and overall experience?\n\nExpectancy-value theory (EVT) (Atkinson, 1957) is another motivational theory that wine researchers can use to understand how expectancies and values about different antecedents, such as environmental, economic, and sociocultural attributes. For example, how consumers’ expectations and values regarding the health benefits of wine shape their purchase and consumption frequency. Wine consumer scholars have adopted this theory to explore the relationship between experience and current consumption behavior (Melo et al., 2010, p. 202) and to predict wine consumption (Cox, 2009).\n\n3.5.6 Methodological directions\n\nLongitudinal studies play a crucial role in enhancing the wine consumer literature by providing valuable insights into consumer behavior and its evolution. It helps in pursuing consumers’ preferences and consumption trends and changes in the decision-making process. Therefore, future studies can adopt a longitudinal study approach to investigate how consumers’ preferences for different types of wines evolve. Studies can also explore the long-term impact of wine education on consumers’ knowledge and competence in wine selection. Other research approaches recommended are experimental (for example, wine label information and purchase intention), cross-cultural (between new world wine and old wine countries), mixed method, case studies, such as the impact of wine tourism on local wineries’ business, and ethnographical studies.\n\n\n4. Implications\n\nThis integrative review yields several noteworthy implications for future research and practical applications. First, the publication trends reveal the growth trajectory of wine consumer literature from 1985 to 2023. Second, the performance analyses reveal the most influential authors regarding the number of publications, citations, active years, and H-index. Third, this study also identifies the most influential works in the wine consumer literature. This finding serves as a reading list for future researchers to understand the studies’ theories, methods, research context, findings, and implications. Fourth, this study contributes to the literature by identifying the most influential journals and productive countries. Fifth, the science mapping techniques (keyword co-occurrence and bibliographic coupling analysis) used in this study provide a holistic knowledge map of wine consumer literature. This visualization helps future researchers identify the topics and areas of wine consumer literature that have already received much attention.\n\nSimilarly, the systematic review also has several implications. First, it summarizes the literature on wine consumers regarding antecedents, mediators, moderators, and outcomes integrated in the extant literature. Based on the systematic review, this study classifies antecedents of previous studies into five subcategories and provides an integrative framework. Second, it also summarizes the extant literature in terms of theoretical and methodological advancement. Second, this study also highlights the theoretical and methodological advancements in the wine consumer literature. This helps future researchers identify the knowledge gaps in terms of theory and research methods adopted by wine consumer scholars. Third, based on the identification of antecedents, mediators, moderators, and outcomes, this study proposes a framework for future directions. The framework also provides theoretical and methodological recommendations for future study.\n\n\n5. Conclusions and limitations\n\nIntegrating bibliometric analysis and systematic review in the wine consumer literature has provided insights into the present state of research and highlighted critical trends, knowledge gaps, and significant clusters. The bibliometric analysis demonstrated the expansion of research on wine consumer behavior, demonstrating a growing scholarly interest in the preferences, behavioral intention, willingness to pay, wine quality perception, and decision-making processes of wine consumers. It highlighted the areas of emphasis and the intellectual network within the subject by identifying important authors, influential publications, the most contributing countries, and the most impactful journals. It also identifies critical areas of wine consumer research. Thus, these analyses not only give a picture of the current state of the literature but also lay the groundwork for future research endeavors.\n\nIn contrast, the systematic review provided a comprehensive analysis of the content and findings of the selected papers. It identified the antecedents, mediators, moderators, and outcomes of the wine consumer literature by synthesizing current research. In addition, the article discusses the methodology and theoretical frameworks utilized in the wine consumer literature. This combination helped to uncover knowledge gaps and inconsistencies, paving the way for future research endeavors. Furthermore, it provided insights into the personal, social, extrinsic, intrinsic, and environmental factors that influence wine consumption behavior. Combining quantitative analysis of publication trends and citation metrics with qualitative synthesis of study findings, this multidisciplinary strategy has comprehensively examined the current literature. By expanding upon the results of this study, researchers can continue to contribute to the growth of wine consumer behavior knowledge, which will ultimately help the wine business and wine consumers.\n\nThis study is based on referred English articles from the Scopus data collection. Therefore, the findings may not reflect papers in other databases, such as the Web of Science of Google Scholars. Thus, future research may consider data from multiple sources to provide comprehensive insight into the wine consumer literature. Since the inclusion of articles in the systematic review is based on the bibliographic coupling analysis, it is challenging to claim absolute inclusion of all articles related to wine consumption.",
"appendix": "Data availability\n\nFigshare: Wine consumer behavior New, https://doi.org/10.6084/m9.figshare.25157096.v3 (Mallya et al., 2024a).\n\nThis project contains the following underlying data:\n\n• scopus (3).csv\n\nFigshare: PRISMA checklist and flowchart for: ‘Wine Consumer Studies: Current Status and Future Agendas’. https://doi.org/10.6084/m9.figshare.25200755.v1 (Mallya et al., 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\nThe VOSviewer software is available freely.\n\n\nReferences\n\nAgnoli L, Begalli D, Capitello R: Generation Y’s perception of wine and consumption situations in a traditional wine-producing region. Int. J. Wine Bus. Res. 2011; 23(2): 176–192. Emerald Group Publishing Ltd. Publisher Full Text\n\nAgnoli L, Capitello R, Begalli D: Behind intention and behaviour: factors influencing wine consumption in a novice market. Br. Food J. 2016; 118(3): 660–678. 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Publisher Full Text\n\nQuester PG, Smart J: The influence of consumption situation and product involvement over consumers’ use of product attribute. J. Consum. Mark. 1998; 15(3):220–238. Publisher Full Text\n\nRitchie C: Beyond drinking: The role of wine in the life of the UK consumer. Int. J. Consum. Stud. 2007; 31(5): 534–540. Publisher Full Text\n\nRogers EM: Diffusion of Innovations. 4th ed.Simon and Schuster; 2010.\n\nSchäufele I, Hamm U: Consumers’ perceptions, preferences and willingness-to-pay for wine with sustainability characteristics: A review. J. Clean. Prod. 2017; 147: 379–394. Elsevier Ltd. Publisher Full Text\n\nSkuras D, Vakrou A: Consumers’ willingness to pay for origin labelled wine: A Greek case study. Br. Food J. 2002; 104(11): 898–912. Publisher Full Text\n\nSogari G, Corbo C, Macconi M, et al.: Consumer attitude towards sustainable-labelled wine: an exploratory approach. Int. J. Wine Bus. Res. 2015; 27(4): 312–328. Emerald Group Holdings Ltd. Publisher Full Text\n\nSomogyi S, Li E, Johnson T, et al.: The underlying motivations of Chinese wine consumer behaviour. Asia Pac. J. Mark. Logist. 2011; 23(4): 473–485. Publisher Full Text\n\nSzolnoki G, Hoffmann D: Consumer segmentation based on usage of sales channels in the German wine market. Int. J. Wine Bus. Res. 2014; 26(1): 27–44. Emerald Group Publishing Ltd. Publisher Full Text\n\nTait P, Saunders C, Dalziel P, et al.: Estimating wine consumer preferences for sustainability attributes: A discrete choice experiment of Californian Sauvignon blanc purchasers. J. Clean. Prod. 2019; 233: 412–420. Elsevier Ltd. Publisher Full Text\n\nTrivellato F, Halevi L, Antunes C: Religion and Trade: Cross-Cultural Exchanges in World History, 1000-1900. Oxford University Press; 2014. Publisher Full Text\n\nVecchio R, Toccaceli D, Pacciani A, et al.: Shrinking the market space: consumer (overlapping) preferences for organic wines and three alternative competitors. Int. J. Wine Bus. Res. 2023; 35(3): 467–486. Publisher Full Text\n\nVrontis D, Thrassou A, Czinkota MR: Wine marketing: A framework for consumer-centred planning. J. Brand Manag. 2011; 18(4–5): 245–263. Publisher Full Text\n\nWallin JA: Bibliometric methods: pitfalls and possibilities. Basic Clin. Pharmacol. Toxicol. 2005; 97(5):261–275. PubMed Abstract | Publisher Full Text\n\nWeatherbee TG, Sears D, MacNeil R: Mapping wine business research in the International Journal of Wine Business Research: 2007-2017. Int. J. Wine Bus. Res. 2019; 31(4): 591–601. Publisher Full Text\n\nWeinberg BH: Bibliographic coupling: A review. Information Storage and Retrieva. 1974; 10: 189–196. Publisher Full Text\n\nWhite CJ, Thompson M: SELF DETERMINATION THEORY AND THE WINE CLUB ATTRIBUTE FORMATION PROCESS. Ann. Tour. Res. 2009; 36(4): 561–586. Publisher Full Text\n\nWiedmann KP, Hennigs N, Behrens SH, et al.: Tasting green: An experimental design for investigating consumer perception of organic wine. Br. Food J. 2014; 116(2): 197–211. Publisher Full Text\n\nWright DK, Yoon H, Morrison AM, et al.: Drinking in style? Literature review of luxury wine consumption. Br. Food J. 2023; 125(2): 679–695. Emerald Publishing Limited. Publisher Full Text\n\nYoutie J, Kay L, Melkers J: Bibliographic coupling and network analysis to assess knowledge coalescence in a research center environment. Res. Eval. 2013; 22(3):145–156. Publisher Full Text\n\nYuan J, Jang S: The effects of quality and satisfaction on awareness and behavioral intentions: Exploring the role of a wine festival. J. Travel Res. 2008; 46(3):279–288. Publisher Full Text\n\nYe BH, Zhang HQ, Yuan J, et al.: Intentions to Participate in Wine Tourism in an Emerging Market: Theorization and Implications. J. Hosp. Tour. Res. 2017; 41(8): 1007–1031. Publisher Full Text\n\nYu Y, Sun H, Goodman S, et al.: Chinese choices: A survey of wine consumers in Beijing. Int. J. Wine Bus. Res. 2009; 21(2): 155–168. Publisher Full Text"
}
|
[
{
"id": "354256",
"date": "09 Jan 2025",
"name": "Amol Dhaigude",
"expertise": [
"Reviewer Expertise Bibliometric analysis",
"SLRs",
"Case Method",
"SCM",
"PLS-SEM"
],
"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 presents an integrative review of the literature on wine consumers' behavior, employing bibliometric analysis and systematic review methodologies. The manuscript is structured into sections covering the introduction, methods, results and discussion, and conclusions, which aim to map the existing body of research, identify gaps, and propose future research directions. While the effort to provide a comprehensive overview is evident, there are several areas where improvements could significantly enhance clarity, coherence, logical progression, flow, and organization.\nFirst, the flow of information. The transition from introducing wine as a cultural icon to the specifics of consumer behavior research feels abrupt. There is a leap from general admiration of wine to detailed methodologies without a smooth transition that guides the reader through the rationale behind the chosen methods. For example, \"Since ancient times, wine has been admired as a cultural icon... Therefore, this integrative review aims to provide the current state of knowledge of wine consumers' behavior.\"\nSecond, Coherence between paragraphs. The coherence between sections is weakened by the jump from discussing the motivation behind the review to detailed methodological descriptions. A brief overview of the study's structure could enhance coherence. Examples: \"Such omissions motivated the researchers... ….. Methods.\"\nThird, the logical progression: The logical progression from identifying research gaps to proposing a methodological approach is somewhat obscured by dense paragraphs and a lack of clear signposting. Examples: \"Such omissions motivated the researchers... an integrating these approaches offers a unique opportunity...\"\nFourth, regarding the clarity of information, some sections are overloaded with details that could be streamlined for clarity, especially the methods and results sections.\nFifth, some inconsistencies are found. For example, different forms of this word have been used in the text. For example, 'co-occurrence' and 'cooccurrence', 're-visit' and 'revisit'. Please pick one style and use it consistently throughout the text.\nThe above feedback could significantly improve its readability and impact. All the best.\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.) Partly",
"responses": []
},
{
"id": "354257",
"date": "11 Jan 2025",
"name": "Jighyasu Gaur",
"expertise": [
"Reviewer Expertise Supply chain",
"consumer research"
],
"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 research conducted by the authors is timely and relevant. The authors have done a decent job and identified critical areas.\n\nPlease find below my detailed review report.\n- The research conducted by the authors is both timely and relevant, addressing an important topic that holds significance in the current academic or professional landscape. - The authors have identified critical areas that contribute meaningfully to the ongoing discourse in their field of study. - Their efforts demonstrate a good understanding of the subject matter and a commendable ability to pinpoint issues that require attention or further exploration. - However, I would like to draw attention to a few grammatical errors present in the manuscript, which should be corrected to enhance the overall readability and professionalism of the work. - These minor issues, once addressed, will ensure that the research is presented in the best possible manner. I recommend the authors carefully proofread the document or use professional editing tools or services to rectify these errors.\nOverall, the paper is well-structured and presents valuable insights. I wish the authors all the best in revising their work and look forward to seeing the final version published.\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.) Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-228
|
https://f1000research.com/articles/13-226/v1
|
27 Mar 24
|
{
"type": "Study Protocol",
"title": "Contextual factors related to vector-control interventions for malaria: a scoping review and evidence and gap map protocol",
"authors": [
"Timothy Hugh Barker",
"Grace McKenzie McBride",
"Mafalda Dias",
"Raju Kanukula",
"Sabira Hasanoff",
"Danielle Pollock",
"Carrie Price",
"Alinune Nathanael Kabaghe",
"Ellie A. Akl",
"Jan Kolaczinki",
"Zachary Munn",
"Timothy Hugh Barker",
"Mafalda Dias",
"Raju Kanukula",
"Sabira Hasanoff",
"Danielle Pollock",
"Carrie Price",
"Alinune Nathanael Kabaghe",
"Ellie A. Akl",
"Jan Kolaczinki",
"Zachary Munn"
],
"abstract": "Objective This scoping review will identify existing literature regarding contextual factors relevant to vector-control interventions to prevent malaria. We will use the findings of the scoping review to produce an interactive evidence and gap map. The map will assist in the priority setting, development, and conduct of targeted systematic reviews. These systematic reviews seek to assist the Vector Control and Insecticide Resistance Unit of the World Health Organization’s Global Malaria Programme by informing recommendation development by their Guidelines Development Group.\n\nIntroduction Malaria contributes substantially to the global burden of disease, with an estimated 247 million cases and 619,000 deaths in 2021. Vector-control is key in reducing malaria transmission. Vector-control interventions directly target the mosquito, reducing the potential for parasite infections. These interventions commonly include insecticides used in indoor residual spraying or insecticide-treated nets and larval source management. Several new vector-control interventions are under evaluation to complement these. In addition to estimating the effects of interventions on health outcomes, it is critical to understand how populations at risk of malaria consider them in terms of their feasibility, acceptability, and values.\n\nInclusion Criteria Eligible studies will have assessed the contextual factors of feasibility or acceptability of the interventions of interest, or the valuation of the outcomes of interests. These assessments will be from the perspective of people who receive (residents) or deliver (workers or technicians) the vector-control intervention for the purpose of preventing malaria.\n\nMethods We will conduct this scoping review in accordance with the JBI methodology for scoping reviews and report in line with the Preferred Reporting Items for Systematic Reviews and Meta-analyses extension for Scoping Reviews (PRISMA-ScR). We will construct the evidence and gap map following guidance from the Campbell Collaboration.",
"keywords": [
"Malaria",
"vector-control",
"acceptability",
"feasibility",
"valuation of outcomes",
"contextual factors"
],
"content": "Introduction\n\nMalaria is a life-threatening infectious disease spread by Anopheles mosquitoes infected with the Plasmodium parasite.1 In 2021 there were an estimated 247 million cases of malaria and an estimated 619,000 deaths in 84 endemic countries.2 Currently, malaria case incidence sits at approximately 59 cases per 1000 people in populations at risk, with an even greater prevalence reported among pregnant women.2 However, between 2000 and 2021 there was sustained and measurable progress made to combat this disease, with the number of malaria endemic countries decreasing from 108 to 84.2 One of the major contributors to this decrease was the development of prevention strategies. Of these prevention strategies, ‘vector-control’ plays a critical role in the fight against the global burden of malaria. Vector-control includes interventions that are specifically designed to either target (and kill) the Anopheles mosquitoes, or to reduce the likelihood that populations at risk are exposed to these infected vectors.3 Currently, the World Health Organization (WHO) provides explicit, evidence-based recommendations for several vector-control interventions, including insecticide-treated nets (ITNs), indoor-residual spraying (IRS), larviciding, and house modifications/screening. However, the effectiveness of these interventions varies.2–4\n\nThe WHO’s Global Malaria Programme (GMP) is responsible for coordinating global efforts to control, prevent and eliminate malaria. A key component of this service involves the development of guidelines using the best-available evidence of the effects of these specific vector-control interventions on health outcomes. As stipulated in the WHO handbook for guideline development,5 the WHO guideline development process requires Guideline Development Groups (GDGs) to consider two sets of factors that determine the direction and strength of a recommendation.5 The first set of factors relates to the ‘health effects’ and include the evidence on the benefits (epidemiological impact) and harms of interventions, and the certainty of that evidence.6 These are determined through the systematic review for appropriately selected, patient-important outcomes.6 The second set of factors are ‘contextual’ and include: resource implications (is the intervention resource intensive?), equity (will the intervention reduce or increase health inequities?), feasibility of the intervention (is the intervention feasible to implement?), and acceptability of the intervention (is the intervention acceptable to key stakeholders?), as well as the valuation of the outcomes (are the health outcomes considered important by key stakeholders?).5–7 These factors should all be judiciously considered by a GDG in the development of each recommendation on an intervention that appears in a WHO guideline.\n\nAs the GDG must make judgments on each of these factors, they should be well-informed regarding each of them. Synthesized evidence from relevant and rigorous systematic reviews can be a valuable source of information.7 However, for some factors, other evidence sources are often considered. Evidence related to ‘equity’ is often reported in studies of the benefits and harms of interventions in terms of particular groups who may (or may not) benefit from the intervention or who may be overlooked in the rollout of interventions.8 This type of data can sometimes be sourced from quantitative studies if they report PROGRESS-Plus criteria.8,9 The remaining factors, ‘resource implications’, ‘feasibility’, ‘acceptability’, and ‘valuation of outcomes’, may also be informed by a rigorous systematic review of the appropriate and relevant primary studies.6\n\nThere has been a concerted effort by the WHO GMP to update its guidelines on vector-control interventions using systematically collected evidence. However, there has been no previous scoping review on the contextual factors associated with vector-control initiatives. In this protocol, we outline the protocol of a scoping review and an evidence and gap map to provide the WHO with an overview of the quantity and type of studies available addressing the contextual factors of ‘feasibility’ and ‘acceptability’ of specific vector-control interventions, and of ‘valuation of the outcomes of interest’. Given that considerations associated with the factor of ‘resource implications’ (e.g., costs, resources, cost-effectiveness etc.) are specific to the site/study/time-point under investigation, this factor can be assessed in many, and often inconsistent, ways. Therefore, the production of a map of this evidence was determined to not be useful, and as such it will not be considered as part of this scoping review.\n\nThis scoping review, and the production of the proposed evidence and gap map will enable the WHO to consider whether to commission future, targeted systematic reviews or primary studies in these areas.\n\n\nReview question\n\nWhat evidence exists regarding the ‘feasibility,’ and ‘acceptability of specific vector-control interventions for the prevention of malaria’ and the ‘valuation of the outcomes of interest’?\n\n\nMethods\n\nEvidence and gap maps are described as “a systematic presentation of all relevant evidence of a specified kind for a particular sector, sub-sector, or geography”.10 The proposed scoping review will be conducted in accordance with the JBI methodology for scoping reviews.11,12 It will be reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) extension for Scoping Reviews (PRISMA-ScR).13 The search will be peer reviewed by another information specialist using the PRESS Guidelines criteria and appropriate revisions included.14 The evidence and gap map will be constructed following the guidance from the Campbell Collaboration.15 This review is appropriate to be conducted as a scoping review, as it aims to identify the type of evidence available in the field of malaria vector-control and to examine how research is conducted on that topic.16\n\n\nEligibility criteria\n\nStudies will be eligible for inclusion where they have investigated the concepts of this scoping review (below) in adults and children who are residents, or part of nomadic communities, of a region with ongoing malaria transmission. Studies will also be eligible for inclusion where they have investigated the concepts of this scoping review in deliverers (workers or technicians) of a vector-control intervention. Studies regarding experimental hut trials for vector-control interventions that use human sleepers will also be included, where the study relates to the participants’ acceptability of the intervention.\n\nStudies will be eligible for inclusion in this scoping review where they addressed the contextual factors of feasibility, acceptability, and valuation of outcomes of participants (defined in the introduction) in response to a vector-control intervention as listed below.\n\nThis review will explicitly not consider studies that investigate the contextual factors of ‘resource implications’ or ‘equity’ of a vector-control intervention. ‘Resource implications’ can be site/study/time-point specific and assessed in many, and often inconsistent, ways. This information may also be contained in the studies evaluating the benefits and harms of an intervention. However, studies that mention equity implications relating to ‘acceptability,’ ‘feasibility,’ or ‘valuation of the outcomes of interest’ will be identified with our search. Studies with information on factors related to vector-control interventions, such as factors adjunct to the intervention that may influence the implementation strategy, will be included. These factors may include the durability of the vector-control intervention, and education programs run alongside deployment of the intervention, which may impact the acceptability or feasibility of the intervention.\n\nStudies will be eligible for this scoping review where they have investigated the above contextual factors in response to the implementation of one of the following vector-control interventions:\n\n• Insecticide-treated nets\n\n• Indoor-residual spraying\n\n• Outdoor-residual spraying\n\n• House screening and other housing modifications for malaria prevention\n\n• Eave tubes\n\n• Spatial repellents\n\n• Endectocides\n\n• Mosquito traps\n\n• Topical repellents\n\n• Larval source management practices (i.e., larviciding, habitat modification, habitat manipulation or biological control by means of natural predators of mosquito larvae)\n\n• Attractive targeted sugar baits\n\n• Vector-control interventions not specified above (i.e., insecticide-treated clothing or hammocks, insecticide treated wall linings and genetically modified mosquitoes amongst others yet to be identified)\n\nThis scoping review will only consider the above concept if it was investigated as part of, or alongside the deployment of, one or more vector-control interventions for malaria prevention. Where the intervention has been used to prevent other vector-borne diseases, these studies will not be considered eligible. Finally, contextual factors related to other interventions utilized for malaria prevention or treatment (e.g., vaccination, mass drug administration and education programs etc.) will also not be considered. Only studies that have provided data regarding vector-control interventions will be eligible for this review. The presence of other background interventions will not impact on study eligibility as long as they are ubiquitous within the study population (e.g., ITN installation with ubiquitous education programs). There will be no exclusions based on publication date, language or publication status (i.e., published, in press, in progress, pre-print). For studies published in languages other than English, we will use DeepL Translator17 to determine whether the study meets the inclusion criteria. Where studies are published in a language other than English and meet the inclusion criteria, DeepL translations will be reviewed by a person fluent in the language.\n\nThis scoping review will only consider peer-reviewed research articles of any methodology. Due to the nature of contextual factors research, studies may utilize diverse methods in their data collection and no restriction will be placed on the types of studies considered eligible.\n\nThe search strategy aims to locate both published and unpublished studies and was developed with the input of a medical librarian.\n\nAn initial limited search of PubMed via NCBI was undertaken to identify relevant articles on this topic. The terminology contained in the titles and abstracts of relevant articles, as well as related subject headings, will inform a full search strategy. The search strategy, including all identified keywords and subject headings, will be adapted for each included database or information source, by using Polyglot18 and with the aid of a medical librarian. The databases to be searched include PubMed (NCBI [contains MEDLINE]), Embase (Elsevier), Cochrane Database of Systematic Reviews (CDSR; Wiley), the Cochrane Central Register of Controlled Trials (CENTRAL; Wiley), Scopus (Elsevier) and WHO Global Index Medicus. The full search strategy for PubMed (NCBI), and the results of this search are available online.\n\nFollowing the search, all identified records will be collated and uploaded into EndNoteTM. Duplicates will be removed using the Deduplicator in the Systematic Review Accelerator.19 Records will then be imported into Covidence where any remaining duplicates will be identified and removed. All records will then be screened on their titles and abstracts by two or more independent reviewers against the eligibility criteria for the review. A record without an abstract will be included for full-text retrieval. Piloting of this screening process will take place on 5% (or minimum five records) of the records imported into Covidence. Piloting of screening will take place between all reviewers. Results of the piloting will then be compared; more piloting will occur if agreement reached is less than 70% between all reviewers. Following piloting, the remaining records will be screened at the title and abstract level independently, so that each record will be screened by at least two people.\n\nPotentially relevant records will be exported from Covidence, and the full text of each record will be retrieved. The records will then be imported to EppiReviewer.20 The full text of each relevant record will be assessed against the eligibility criteria by two or more independent reviewers. Another pilot test will occur on 5% (or minimum five reports) of the reports included for screening at the full-text level. Additional piloting will occur if agreement reached is less than 70% between all reviewers. Following piloting, the remaining reports will be screened in detail against the inclusion criteria by two or more independent reviewers, so that each report is screened by at least two people. For reports that do not meet the eligibility criteria after being screened at the full-text level, the reasons for their exclusion will be documented and reported in the appendices of the final scoping review. Any disagreements that arise between the reviewers at any stage of the selection process will be resolved through discussion, or with additional reviewers. The results of the search and screening process will be reported in full in the final review and presented in a PRISMA 2020 flow diagram.21\n\nReasons for exclusion at the full-text level may be due to:\n\n• Conference abstract (no associated full text)\n\n• Study protocol\n\n• Expert opinion/editorial/letter\n\n• Not malaria\n\n• Not contextual factor of interest\n\n• Not vector-control intervention\n\n• Not appropriate population/setting (e.g., modelling study).\n\nAll studies that meet the eligibility criteria following screening at the full-text level will undergo data extraction within EppiReviewer. Data will be extracted from all eligible studies by two or more independent reviewers. Piloting and training of the reviewers on the extraction form as it exists within EppiReviewer will occur, and a data dictionary of terms will be produced and iteratively updated to guide extractors (described below). Any disagreements between reviewers during extraction will be resolved through discussion or consultation with a third reviewer who was not involved in the original extraction. If appropriate, authors of papers will be contacted to request missing or additional data where required. The data will firstly be extracted according to the demographic characteristics of the study and include the following items:\n\n• First author name\n\n• Year of publication\n\n• Country/city/region in which the study took place\n\n• Year/month the study took place.\n\nFollowing this, the studies will be coded within EppiReviewer. Coding will be based on the following three categories, and structured to generate the evidence and gap map (described below):\n\n1. Vector-control intervention\n\na. Insecticide-treated net\n\nb. Indoor-residual spraying\n\nc. Outdoor-residual spraying\n\nd. House improvements/screening\n\ne. Eave tubes\n\nf. Spatial repellents\n\ng. Mosquito traps\n\nh. Endectocides\n\ni. Topical repellents\n\nj. Larval source management practices\n\nk. Attractive targeted sugar baits\n\nl. Vector-control intervention not specified by the WHO.\n\n2. Contextual factors\n\na. Acceptability (of the intervention(s) of interest) from the perspective of:\n\ni. The public\n\nii. The deliverer\n\nb. Feasibility (of the intervention(s) of interest) from the perspective of:\n\ni. The public\n\nii. The deliverer\n\nc. Valuation of the outcomes of interest (i.e., potentially affected by the interventions of interest).\n\nd. Factors related to the intervention.\n\n3. Study methods\n\n• Experimental studies\n\n• Observational studies\n\n• Utility/health status studies\n\n• Close-ended questionnaires/surveys\n\n• Open-ended questionnaires/surveys\n\n• Focus groups\n\n• Interviews\n\n• Literature review\n\n• Systematic review\n\n• Scoping review.\n\nTo facilitate a common and shared language between extractors before and during data extraction and coding, a data dictionary of terms will be developed and updated iteratively as new concepts are identified, explored and agreed upon by the review team (Table 1). This practice will ensure that concepts of similar meaning and definitions are extracted and coded consistency between multiple extractors. Due to the iterative nature of developing a data dictionary, new terms are likely to be added to this repository using the inductive coding functions available in EppiReviewer. As such, the below should only serve as an example of the current terms considered as part of the data dictionary.\n\nThis is an example of the development of a data dictionary that will take place during the extraction and coding of the studies considered eligible for this review.\n\n\n\n• Not accepting the distribution of the benefits, harms, and costs\n\n• Not accepting costs or undesirable effects in the short term for desirable effects (benefits) in the future\n\n• Attaching more value (relative importance) to the undesirable consequences than to the desirable consequences or costs of an option (because of how they might be affected personally or because of their perceptions of the relative importance of consequences for others)\n\n• Morally disapproving (i.e. in relationship to ethical principles such as autonomy, nonmaleficence, beneficence or justice)\n\nAll extracted data, regardless of presentation in the evidence and gap map as described below, will be narratively synthesized and presented in tables, with further visual formats to be considered at the time of analysis, to provide frequency counts and descriptive statistics of the following items.\n\n• When and where the studies were conducted\n\n• The types and formats of the bodies of evidence identified\n\n• The vector-control interventions investigated\n\n• The contextual factors investigated.\n\nThe results of the data extraction and coding will be presented in an evidence and gap map that will be developed using the EppiMapper software v4.0.40 The evidence and gap map will be organized according to the data coding hierarchy as presented above. An example of what the final evidence and gap map will appear as is presented in Figure 1.\n\nThe data has been organized based on the contextual factors of interest (columns) against the vector-control interventions of interest (rows). Each colored circle represents the study methods used, with the size of the circle indicating how many studies exist for each category. Green = quantitative studies, Aqua = Qualitative studies, Blue = mixed-methods studies, Purple = evidence reviews. This figure was produced by the authors of this study as an example only.\n\nThis scoping review is a review of primary and secondary studies and as such, does not require ethics approval. In addition, there will be no collection or analysis of individual participant data. All study files (data extraction forms and EppiReviewer.json files) will be made publicly available via a project space using open science platforms. A full review report will be submitted to the Vector Control & Insecticide Resistance Unit, Global Malaria Program, and the Vector Control Guidelines Development Group, WHO, to inform potential targeted systematic reviews to be undertaken on these factors in the future. A version of this report will be submitted for publication in an open access peer-reviewed journal.\n\nThis scoping review is being conducted for the purposes of informing future WHO systematic reviews and guideline development. Guideline development panel members, which include various diverse stakeholders including the public, patients, end users, experts and decision-makers may guide the interpretation and implementation of the results of this scoping review.\n\nThis study has been completed.\n\n\nContributorship statement\n\nConceptualization: THB, ZM, EAA, JK and colleagues from the Global Malaria Program, WHO\n\nWriting – Original draft preparation: THB, GMM, MD, RK, SH, DP, ANK, ZM\n\nData curation: CP led the development of the search strategy.\n\nWriting – Review and editing: THB, GMM, MD, RK, SH, DP, CP, ANK, EAA, JK, ZM",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors would like to acknowledge and thank staff from the Global Malaria Programme, WHO, for their input and support.\n\n\nReferences\n\nGlobal Malaria Programme: WHO Guidelines for Malaria.2022. Reference Source\n\nWHO: World malaria report 2022. Geneva: World Health Organization; 2022. Licence: CC BY-NC-SA 3.0 IGO.\n\nWHO: World malaria report 2023. Geneva: World Health Organization; 2023. Licence: CC BY-NC-SA 3.0 IGO;\n\nWHO: A framework for malaria elimination. World Health Organization; 2017.\n\nWHO: WHO handbook for guideline development. World Health Organization; 2014.\n\nAlonso-Coello P, Schünemann HJ, Moberg J, et al.: GRADE Evidence to Decision (EtD) frameworks: a systematic and transparent approach to making well informed healthcare choices. 1: Introduction. BMJ. 2016; 353: i2016. Publisher Full Text\n\nSchunemann H: GRADE handbook for grading quality of evidence and strength of recommendation. Version 3.2. GRADE Working Group; 2008 [updated October 2013; cited 2023 11th July]. Reference Source\n\nOliver S, Kavanagh J, Caird J, et al.: Health promotion, inequalities and young people’s health: a systematic review of research.2008.\n\nO’Neill J, Tabish H, Welch V, et al.: Applying an equity lens to interventions: using PROGRESS ensures consideration of socially stratifying factors to illuminate inequities in health. J. Clin. Epidemiol. 2014; 67(1): 56–64. PubMed Abstract | Publisher Full Text\n\nCampbell F, Tricco AC, Munn Z, et al.: Mapping reviews, scoping reviews, and evidence and gap maps (EGMs): the same but different- the “Big Picture” review family. Syst. Rev. 2023; 12(1): 45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeters M, Godfrey C, McInereney P, et al.: Scoping Reviews.Aromataris E, Munn Z, editors. JBI Manual for Evidence Synthesis. JBI; 2020.\n\nPeters MDJ, Marnie C, Tricco AC, et al.: Updated methodological guidance for the conduct of scoping reviews. JBI Evid. Synth. 2020; 18(10): 2119–2126. Publisher Full Text\n\nTricco AC, Lillie E, Zarin W, et al.: PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann. Intern. Med. 2018; 169(7): 467–473. PubMed Abstract | Publisher Full Text\n\nMcGowan J, Sampson M, Salzwedel DM, et al.: PRESS peer review of electronic search strategies: 2015 guideline statement. J. Clin. Epidemiol. 2016; 75: 40–46. PubMed Abstract | Publisher Full Text\n\nWhite H, Albers B, Gaarder M, et al.: Guidance for producing a Campbell evidence and gap map. Campbell Syst. Rev. 2020; 16(4): e1125. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMunn Z, Peters MDJ, Stern C, et al.: Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach. BMC Med. Res. Methodol. 2018; 18(1): 143. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeepL SE: DeepL Translator. Cologne, Germany: 2017. Reference Source\n\nClark JM, Sanders S, Carter M, et al.: Improving the translation of search strategies using the Polyglot Search Translator: a randomized controlled trial. J. Med. Libr. Assoc. 2020; 108(2): 195–207. PubMed Abstract | Publisher Full Text\n\nClark J, Glasziou P, Del Mar C, et al.: A full systematic review was completed in 2 weeks using automation tools: a case study. J. Clin. Epidemiol. 2020; 121: 81–90. PubMed Abstract | Publisher Full Text\n\nThomas J, Brunton J, Graziosi S: EPPI-Reviewer 4.0: software for research synthesis. London: Social Science Research Unit, Institute of Education; 2010.\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. Int. J. Surg. 2021; 88: 105906. PubMed Abstract | Publisher Full Text\n\nWHO: Malaria terminology, 2021 update. Geneva: World Health Organization; 2021. Licence: CC BY-NC-SA 3.0 IGO.\n\nElnaiem DA, Dakein O, Alawad AM, et al.: Outdoor Residual Insecticide Spraying (ODRS), a New Approach for the Control of the Exophilic Vectors of Human Visceral Leishmaniasis: Phlebotomus orientalis in East Africa. PLoS Negl. Trop. Dis. 2020; 14(10): e0008774. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJones C, Matta A, Pinder M, et al.: House screening for malaria control: views and experiences of participants in the RooPfs trial. Malar. J. 2022; 21(1): 294. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKnols BGJ, Farenhorst M, Andriessen R, et al.: Eave tubes for malaria control in Africa: an introduction. Malar. J. 2016; 15(1): 404. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Endectocide and ectocide products for malaria transmission control. Geneva: World Health Organization; 2022 [cited 2023 11th July]. Licence: CC BY-NC-SA 3.0 IGO. Reference Source\n\nGlobal Malaria Programme, WHO: Vector control products targeting outdoor malaria transmission.[cited 2023 11th October]. Accessed 11th October 2023. Reference Source\n\nQualls WA, Müller GC, Traore SF, et al.: Indoor use of attractive toxic sugar bait (ATSB) to effectively control malaria vectors in Mali, West Africa. Malar. J. 2015; 14(1): 1–8.\n\nWorld Health Organization: Guidance framework for testing genetically modified mosquitoes. Second ed.2021.\n\nDistiller SR: Values and Preferences (Glossary Index).2023 [cited 2023 11th July]. Reference Source\n\nTufanaru CMZ, Aromataris E, Campbell J, et al.: Chapter 3: Systematic reviews of effectiveness.Aromataris EMZ, editor. JBI Manual for Evidence Synthesis. JBI; 2020. Reference Source\n\nMoola SMZ, Tufanaru C, Aromataris E, et al.: Chapter 7: Systematic reviews of etiology and risk.Aromataris EMZ, editor. JBI Manual for Evidence Synthesis. JBI; 2022. Reference Source\n\nZhang Y, Coello PA, Brożek J, et al.: Using patient values and preferences to inform the importance of health outcomes in practice guideline development following the GRADE approach. Health Qual. Life Outcomes. 2017; 15(1): 52. PubMed Abstract | Publisher Full Text | Free Full Text\n\nReja U, Manfreda KL, Hlebec V, et al.: Open-ended vs. close-ended questions in web questionnaires. Developments in Applied Statistics. 2003; 19(1): 159–177.\n\nKitzinger J: Qualitative Research: Introducing focus groups. BMJ. 1995; 311(7000): 299–302. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJamshed S: Qualitative research method-interviewing and observation. J. Basic Clin. Pharm. 2014; 5(4): 87–88. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAromataris E, Pearson A: The Systematic Review: An Overview. Am. J. Nurs. 2014; 114(3): 53–58. Publisher Full Text\n\nHiggins JP, Thomas J, Chandler J, et al.: Cochrane handbook for systematic reviews of interventions. John Wiley & Sons; 2019.\n\nMunn Z, Peters MDJ, Stern C, et al.: Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach. BMC Med. Res. Methodol. 2018; 18(1): 143. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDigital Solution Foundry and EPPI Centre: EPPI-Mapper. EPPI Centre, editor. University College London; 2022."
}
|
[
{
"id": "278283",
"date": "31 May 2024",
"name": "Salum Azizi",
"expertise": [
"Reviewer Expertise Evaluation of mosquito control interventions"
],
"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 protocol is well prepared to provide information on quantity and type of studies available that addresses contextual factors of ‘feasibility’, ‘acceptability’ and ‘valuation of the outcomes of interest’ to facilitate evidence-based recommendation on vector control interventions by the WHO. However, the author should consider addressing the following minor issues:\nRephrase the statement “These interventions commonly include insecticides used in indoor residual spraying or insecticide-treated nets and larval source management” as it sounds as if insecticides on iself is an intervention. The interventions here are indoor residual spraying, insecticide treated nets and larvae source management which uses insecticide or might not eg larvae source management might includes other strategies such as habitat modification or manipulation without necessarily involving insecticides. By excluding resource implications which is very much contributing to intervention feasibility, a clear definition and limitation for term “feasibility” is needed. The current definition in the introduction does not clearly provide information what it entails. Add ethical violations among the reasons for exclusion at the full-text level articles Figure 1. Correct the term “feasability” to “feasibility”\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": []
},
{
"id": "289708",
"date": "28 Jun 2024",
"name": "Justin Pulford",
"expertise": [
"Reviewer Expertise Malaria control/vector control"
],
"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 outlines the protocol for a planned scoping review and evidence and gap map intended to provide the WHO with an overview of the quantity and type of studies available addressing the contextual factors of ‘feasibility’ and ‘acceptability’ of specific vector-control interventions, and of ‘valuation of the outcomes of interest’. The study objectives are clearly described, the study design is appropriate and sufficiently detailed. Overall, this is a very well written protocol. I only have a few questions and or suggested edits to make, all of which I would consider minor:\nIntroduction The authors define five sets of ‘contextual’ factors: resource implications, equity, feasibility, acceptability and valuation. The authors then state that their planned scoping review will only focus on the last three of these factors, excluding resource implications and equity. Clear and reasonable justification is given for excluding ‘resource implications’, but the justification for excluding ‘equity’ remains somewhat unclear. Are the authors contending that equity cannot be appropriately assessed via systematic review or that it is unnecessary to do so because equity considerations can be derived from other sources? If the latter, the argument put forth appears somewhat weak (as could be true of all factors) and is also perhaps better placed in the paragraph below alongside the justification for excluding ‘resource implications’.\nMethods Data extraction: There might also be value in recording the institutional affiliation of the first authors. This would provide some insight into which countries are leading the research effort.\nMight there also be value in coding whether the ‘valuation of the outcomes of interest’ comes from ‘the public’ or ‘the deliverer’? This would be consistent with the coding approach for the other two factors and seems like an important element to capture.\nWhat is meant by ‘d. factors related to the intervention’? This is not clear without an accompanying explanation.\nWhy have codes for ‘systematic review’ and ‘scoping review’ been included? Wouldn’t papers of this type have been excluded from review?\nWill multiple responses to ‘3.study methods’ codes be allowed? E.g. a study questionnaire could include both open and closed questions or a study could include both surveys and interviews\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/13-226
|
https://f1000research.com/articles/13-225/v1
|
27 Mar 24
|
{
"type": "Review",
"title": "Animal Venoms as Potential Source of Anticonvulsants",
"authors": [
"Syafiq Asnawi Zainal Abidin",
"Anthony Kin Yip Liew",
"Iekhsan Othman",
"Farooq Shaikh",
"Anthony Kin Yip Liew",
"Iekhsan Othman",
"Farooq Shaikh"
],
"abstract": "Abstract* Epilepsy affects millions of people worldwide, and there is an urgent need to develop safe and effective therapeutic agents. Animal venoms contain diverse bioactive compounds like proteins, peptides, and small molecules, which may possess medicinal properties against epilepsy. In recent years, research has shown that venoms from various organisms such as spiders, ants, bees, wasps, and conus snails have anticonvulsant and antiepileptic effects by targeting specific receptors and ion channels. This review underscores the significance of purified proteins and toxins from these sources as potential therapeutic agents for epilepsy. In conclusion, this review emphasizes the valuable role of animal venoms as a natural resource for further exploration in epilepsy treatment research.",
"keywords": [
"Epilepsy",
"Anticonvulsant",
"Animal Venom",
"Bioactive Compounds",
"GABA",
"NMDA"
],
"content": "1. Introduction\n\nEpilepsy is a global epidemic that affects more than 50 million people worldwide, making it one of the most common neurological diseases.1 Almost 80% of epileptic patients come from low- and middle-income countries.1 The Task Force of the International League Against Epilepsy (ILAE) defined epileptic seizure as a transient occurrence of symptoms caused by abnormally excessive brain neuronal activity. Epilepsy is a brain disorder prone to epileptic seizures and consequences from cognitive, neurobiological, psychological, and social aspects.2 There are several types of epileptic seizures, depending on the symptoms. One-third of the epileptic seizures occurred as generalized seizures, whereas two-thirds began as focal seizures. Generalized seizures can be classified into six groups: tonic-clonic, myoclonic, atonic, tonic, clonic, and absence seizures.3 All these symptoms happen without warning and involve loss of consciousness on the patient. Tonic seizures are characterized by constant muscle contraction, while tremors in the limbs indicate clonic seizures. Tonic-clonic seizures have symptoms that combined both tonic and clonic seizures symptoms. The contraction of limb muscles is followed by limb extension and tremors with back arching for around ten to thirty seconds.\n\nEpileptogenesis is the gradual development of epilepsy in a normal brain.4 The causes of epilepsy can be identified as structural or genetics. Structural causes of epilepsy include brain tumors, brain trauma, and other neurodegenerative diseases. Brain areas prone to trauma causing epileptogenesis include structures of the temporal lobe such as the amygdala, hippocampus, and piriform cortex.5 Brain electrical activity is usually non-synchronous in normal humans, while patients suffering from epileptic seizures will have excessive synchronized firing of neuronal firing, which causes a paroxysmal depolarizing shift. Neuronal biochemical receptors play an essential role in epileptogenesis, primarily glutamate receptors (ionotropic and metabotropic). When the receptors are activated, Ca2+ ions will increase within the area of the cells. Therefore, glutamate is seen as one of the most critical molecules in epileptogenesis as it causes excitotoxicity, i.e., neurons are severely depolarised.4\n\nEpilepsy treatment may include drugs, surgery, and even diet changes. The standard first-line therapy for patients newly diagnosed with epilepsy is usually by antiepileptic drugs (AEDs) such as phenobarbital, phenytoin, carbamazepine, or valproic acid. Second line medications such as oxcarbazepine, gabapentin, topiramate, felbamate, and lamotrigine are also applied in the treatment.6 No single AED is proved to be more effective than another, with all drugs producing some side effects depending on the individual treated. These drugs used have a 70% to 80% success rate in treating epilepsy, while the remaining 20% to 30% still suffer from seizures or more significant adverse effects.7\n\nSince epilepsy is caused by the malfunction of ion channels, Gamma-aminobutyric acid (GABA)-ergic neuron inhibition, and excess glutamate release, most AED will target these specific pathways.8 Drugs that target ion channels include carbamazepine, oxcarbazepine, phenytoin, and lamotrigine, which block sodium channels.9 Gabapentin binds on volt-age-dependent calcium channel proteins in rat models and is believed to have GABAergic effects. GABA-mediated inhibition is vital as the binding of GABA to their receptors leads to an influx of negatively charged chloride ions (Cl-) which in turn causes cell hyperpolarisation. Barbiturates and benzodiazepines treat epilepsy by targeting the GABAergic transmission and increasing chloride ion influx.10 Glutamate, which is a primary excitatory neurotransmitter were also believed to play a part in epilepto-genesis. Application of antagonists to the glutamate receptor such as N-methyl-D-aspartate (NMDA) demonstrated anticonvulsant effects in animal models. Valproate, felbamate, and topiramate are NMDA receptor antagonists which are currently used. However, these drugs are known to present several undesirable side effects.8\n\n\n2. Animal venom as a potential source of anticonvulsants\n\nThe earth’s flora and fauna are an important reservoir of naturally derived therapeutic agents. Since ancient times, humans have utilized these resources to treat diseases and improving wellbeing. One significant source is the venom and toxins from venomous and poisonous animals. The venom consists of proteins, enzymes, inorganic ions, and nucleotides, which can induce a plethora of effects, including necrosis, coagulation, haemorrhagic, and neurotoxicity depending on the type of venom.11 Targeted sites of venom are specific and diverse due to the different constitutions and may target receptors and channels such as neuro-junctions and ion channels.12 Animal venom has been regarded as an essential source of potential therapeutic agents in human diseases such as neurodegenerative diseases, cardiovascular diseases, autoimmune diseases, and cancer.13–16 In this literature review, the different types of venom used in treating epilepsy is discussed.\n\nNeuroprotective potential of various venom fractions and components from venomous spider species has been identified (Table 1). Arylamine-enriched fraction isolated from the venom of funnel-web grass spider Agelenopsis aperta demonstrated significant anticonvulsant properties by antagonizing and blocking NMDA receptor and dihydropyridine (DHP) calcium channels.17 Overexcitation of NMDA receptors and DHP calcium channels were found to be responsible for the pathophysiology of epilepsy.18,19 In the study by Jackson and Parks,17 arylamine-enriched venom fraction was administered both intravenously (i.v.) on male Sprague-Dawley rats induced with epilepsy using kainic acid (KA), picrotoxin (PIC), and bicuculline (BIC). Subjects administered with KA when paired with the venom fractions demonstrated less to nonconvulsive behavior until 70 minutes. Symptoms of seizures subsided after 4 hours with no deaths observed in the 10 subjects. Subjects administered with BIC and PIC paired with the venom fraction (i.v.) also shows closely similar observations and seem mildly sedated at the same time responsive to external stimuli.\n\nActive fraction (PbTx1.2.3) from Brazillian orb-weaver spiders Parawixia bistrata demonstrated potential anticonvulsive activity in synaptosomes model from rat cerebral cortex.20 Glutamate and gamma-Amnobutyric acid (GABA) uptake balance is crucial in maintaining normal brain function. Functioning as the primary excitatory neurotransmitter in the brain, the increase of glutamate activity is critical in epileptogenesis.21 In contrast, GABA counterbalances neuronal excitation by acting as the primary inhibitory neurotransmitter. Hence, changes to GABA balance in the brain may trigger seizures.22 PbTx1.2.3 was demonstrated to increase glutamate uptake while inhibiting GABA uptake in cortical synaptosomes in a dose-dependent manner. Drugs that stimulate GABA concentration are potent anticonvulsants such as vigabatrin and tiagabine.22 Moreover, PbTx1.2.3 successfully protected neurons in the rat retinal glaucoma model from excitotoxic death.20 Therefore, PbTx1.2.3 may serve as a template for potential anticonvulsant and neuroprotection drug development.\n\nFrPbAII is another compound found in P. bistrata venom, which was studied for anticonvulsive and anxiolytic properties. Bicuculline was injected into Area-tempestas of male Wistar rats to induce seizures and treated with FrPbAII. The toxin component significantly inhibited seizures elicited by bicuculline. In addition, FrPbAII was demonstrated to block GABAergic transporters that caused epilepsy.23 Animal behavior study using male Wistar rats also showed anticonvulsive properties of FrPbAII. Rats were induced with seizures using pentylenetetrazol and were treated with diazepam, nipecotic acid, and FrPbAII. All subjects treated with diazepam, nipecotic acid, and FrPbAII showed anticonvulsive properties with reduced immobility, increased exploratory walking, rearing, and head-dips than saline control pentylenetetrazole (PTZ)-induced seizure subjects.24\n\nParawixin-10 is another polyamine found in P. bistrata venom which elicits anticonvulsive properties. Parawixin-10 was administered via i.c.v. injection using a cannula and kainic acid (KA), NMDA, and PTZ to induce seizures. Parawixin-10 demonstrated anticonvulsive properties with the lowest dose required for KA compared to NMDA and PTZ indicating that the mode of action for Parawixin-10 is through the inhibition of excitatory transmission of non-NMDA receptors. Neurochemistry data from the study also showed an increase in L-glutamate and glycine uptake, wherein elevated levels of both compounds are responsible for epilepsy. However, the important mode of action for Parawixin-10 has yet to be pinpointed and thus requires further investigation and studies.25 Additional study on P. bistrata venom fraction, RT10, which comprised of Parawixins 1 and 2, demonstrated neuroprotective effects on neuron-glia primary culture against high L-glutamate concentrations.26\n\nSeveral subtypes of α and β neurotoxins have been described from the venom of Asian scorpion Buthus martensi Karsch (BmK) (Table 2). These neurotoxins were found to modulate voltage-gated sodium channels (VGSCs).28,29 Antinociceptive effects from BmK venom were demonstrated by the activity of BmK I (α-like neurotoxin) and BmK IT2 (β-like neurotoxins).30,31 A study by Zhao, et al.32 in PTZ and pilocarpine-induced epilepsy rats showed significant anticonvulsant activity from the administration of BmK IT2. The effects of BmK IT2 were attributed to its ability to modulate sodium channels in the hippocampus. A further study with a different toxin from BmK, Bmk-AS, demonstrated similar antiepileptic activities in PTZ and pilocarpine-induced epilepsy in the rat model.33 In another study, a novel peptide synthesised and derived from the Malaysian forest scorpion venom, Hetermetrus spinifer, was shown to reduce inflammation in PTZ-induced epilepsy in-vivo.34 The 25 amino acid peptide named HsTx2 alleviate epilepsy progression by targeting the circ_0001293/miR-8114/TGF- β2 axis, which is responsible for inflammation response in astrocytes.34\n\nBee and wasp venom is rich in compounds that act on various biological systems, especially in the nervous system. These compounds include peptides, amines, enzymes, and amino acids (Table 3).35 Both peptides and acyl polyamines have been studied to treat many neurology-related diseases. A single study on mellitin, a major component of the venom from Apis mellifera (honey bee), demonstrated anticonvulsant effects in bicuculine-induced seizures in rats.36 Mellitin could potentially induced its neuroprotective activities via activation of phospholipase A2 and consequently modulating the GABAergic and glutamergic systems.36 Denatured crude venom from Polybia occidentalis (Yellow-banded Polybia wasp) identified dose-dependent effectiveness in treating KA-induced seizures rat model. This finding suggests that venom-induced anticonvulsive activities by antagonizing NMDA-glu receptors. Additional results include in-vivo anticonvulsive effects in rats with PIC- and BIC-induced seizures.37 Recent study on a venom peptide isolated from Polybia occidentalis, occidentalin-1202, pinpointed anti-seizure effects by blocking glutamate and kainic acid interaction with the kainite receptor.38 A different study on the venom of Polybia ignobilis (Brazilian social wasp) demonstrated a similar outcome by preventing seizures induced by KA, PIC, and BIC.39\n\nLow molecular weight fractions of the venom from Polybia paulista (Neotropical social wasp) exhibited anticonvulsant activities in 60% of animals (Wistar rats) induced with PTZ.40 Compared with diazepam treatment, both offer protection from seizures, but the venom demonstrated fewer sedation effects.40 Additionally, peptides isolated from Polybia paulista, Ppnp7 and neuropolybin, demonstrated tonic-clonic seizure protection in 80% of PTZ-induced rats.41 Agelaia vicina venom showed inhibition of GABA and glutamate uptake responsible during epileptogenesis. The venom targeted enzymes accountable for the regulation of ion flow, thus disrupting ion concentration gradient. Additionally, free amino acids were found to inhibit GABA and glutamate uptake.42 Philanthus triangulum F. wasp venom contains components such as β-PTX and δ-PTX, which show effects on animal glutamatergic neuro-junctions. These components were found to inhibit the uptake of glutamate in the neuromuscular synapse on locusts. A study showed a significant decrease in glutamate uptake on hippocampal slices of rats incubated with δ-PTX (74% decrease) and a less significant reduction with incubation in β-PTX (18%). Based on the findings, the venom from Philanthus triangulum F. wasps demonstrated potentials as a source of anticonvulsant agents due to its interference with glutamate uptake, a critical factor in epileptogenesis.43 Besides PTZ-induced seizures, a treatment using wasp venom peptide from Chartegellus communis (Social wasp), Chartergellus-CP1, showed neuroprotective effects in pilocarpine-induced epilepsy.44 In the study, electroencephalographic abnormalities that are associated with pilocarpine-induced seizures were significantly reduced upon administration of Charthergellus-CP1.44\n\nAnt venom contains an arsenal of molecules that ranges from proteins, peptides, free amino acids, alkaloids, formic acid, and several other organic molecules.46 Like other venomous organisms, the venom has been a subject of interest to uncover its properties and therapeutic potential, including as an anticonvulsive agent (Table 4). The venom of Dinoponera quadriceps (South American giant ant) has been studied for anticonvulsant effects. An initial study by Noga, et al.47 demonstrated the pro-and anticonvulsant effects of the crude venom in-vivo. Injection of crude venom (DqTX) in the lateral ventricle region of mice brain showed procursive behavior and tonic-clonic seizures.\n\nInterestingly, the effects were negated via pre-administration of the same but denatured venom (AbDq), hence, protected the animals against seizures and death.47 Similar results were noted in another study by Lopes, et al.48 Different administration routes of D. quadriceps venom in mice seizure models were responsible for neuroprotective or neurotoxic effects. Intraperitoneal administration of the venom demonstrated increased latency to seizure with an increased survival rate in the PTZ-induced seizure model. In contrast, endovascular treatment-induced neurotoxic effects by reducing the seizure latency time. In another study utilising PTZ-induced seizure model, three different peptides from Dinoponera quadriceps (M-PONTX-Dq3a, M-PONTX-Dq3b, and M-PONTX, Dq3c) also showed anticonvulsant properties by reducing neuroinflammation caused by reactive oxygen species.38\n\nIn a subsequent study by Noga, et al.,49 the anticonvulsant effects from the fractions of D. quadriceps crude venom were investigated. The crude venom was fractionated using high-performance liquid chromatography (HPLC) and yielded six fractions labelled DqTX1 – DqTX6. The fractions were administered intracerebroventricularly in BIC-induced seizure rats, and the anticonvulsant effects were determined. DqTX-6 showed significant neuroprotection with 62.5% protection from seizures and 100% protection from death. Since BIC induces seizures by interfering with GABA receptors, the mode of action for the DqTX-6 fraction is most likely to be GABAergic.49\n\nConopeptides from the venom of marine cone snails belonging to the genus Conus have been identified with potentials as antinociceptive, antiepileptic, neuroprotective, and cardioprotective agents.50 There are at least four peptide families with neuroprotective and cardioprotective activities from Conus snail venom, namely, conantokins, omega-conotoxin (ω-Conotoxin), mu-conotoxin (μ-Conotoxin), and kappa-conotoxin (κ-Conotoxin) (Table 5).51 Conantokins are of particular interest due to their potential in treating epilepsy. Seven types of conantokin peptides were identified, and all were described as NMDA receptor antagonists.52\n\nConantokin-G (Con-G) is a well-studied conantokin from the venom of Geography cone snail Conus geographus. It was advanced into clinical trial phase 1 to treat intractable epilepsy and potential neuro-protectant in ischemic stroke.53 The peptide demonstrated significant antiepileptic activities in animal models of epilepsy, such as maximal electroshock, PTZ induced, and Frings audiogenic seizures.54–56 Anticonvulsive mode of Con-G was via the dose-dependent inhibition of NMDA responses.57 Besides Con-G, Conantokin-R (Con-R) from Conus radiatus Conantokin-L (Con-L) from Conus lynceus showed significant anticonvulsant effects when administered intracerebroventricularly to subjects induced with Frings audiogenic seizures.58,59 Ziconotide, a synthetic derivative of ω-Conotoxin from Conus magus, demonstrated anticonvulsant and anxiolytic effects by potentially reducing extracellular concentrations of glutamate via N-type calcium channel inhibition.60\n\n\n3. Future directions\n\nThe potential of venom as a source of anticonvulsants warrants further exploration and investigation, extending beyond its current focus to encompass other venomous animals which could potentially include snakes. Snake venom is a complex mixture of proteins, peptides, and small molecules that serve as a defence mechanism and aid digestion for snakes towards their prey. Despite its toxicity, snake venom can be an essential source of therapeutic compounds, as demonstrated by its potential in treating cardiovascular disease and as an anti-microbial, anti-viral, anti-fungal, and anti-cancer agent.61 To date, there is only a few studies the anticonvulsant potential of snake venom via Ophiophagus hannah (king cobra) and Micrurus mipartus (Costa Rican coral snake). Saha, et al.62 isolated a non-protein toxin called KC-MMTx from O. hannah crude venom and demonstrated its neuroprotective activity in animal models of epilepsy. KC-MMTx presented significant protection against seizures induced by strychnine, PTZ, and yohimbine, and its potential in interfering with the GABAergic and glycine receptors was touted. Remarkably, toxins from Costa Rican coral snake (MmTX1 and MmTX2) were found to specifically target GABA receptors and significantly improve its sensitivity via allosteric binding.63 Moreover, the ability of snake venom toxins, particularly three-finger toxins (3FTXs), to bind with nicotinic acetylcholine receptors (nAChR) presents another promising avenue in this field. This is noteworthy because the overactivation of nAChR is frequently associated with tonic-clonic convulsions and epilepsy in mammals.64–67 In addition to snake venoms, venoms from sea anemone could also be another important source of therapeutic proteins and peptides as anticonvulsants.68 Several sea anemone toxins extracted from Stichodactyla heliantus, Actinia equina, Anemonia eryhtrae, Anemonia sulcata, Bunodosoma caissarum, Bunodosoma granulifera and Heteractis magnifica were found to selectively target Kv1 channels.69 These findings hold particular importance as Kv1 ion channels play a clinically relevant role in the pathogenesis of neurological diseases, including epilepsy.70\n\n\n4. Conclusions\n\nEpilepsy remains one of the most critical health burdens in the world. However, the disease currently presents a significant challenge in discovering and developing therapeutic agents that are safe and effective. Venom-based therapeutics has been a subject of focus due to their potential to combat various disorders such as cardiovascular diseases and cancer. This present review demonstrates that animal venom could exert anticonvulsant effects by targeting and regulating specific receptors, modulating uptakes of molecules such as glutamate and glycine, and antagonizing ion channels. In addition, the advancement of proteomic and genomic technology has presented us with the ability to characterize and purify proteins with therapeutic potentials accurately. More proteins/compounds can be isolated and tested in-vivo for anticonvulsant activities. Animal venom represents a promising avenue for researchers to further explore and investigate its compounds as a source of potential antiepileptic/anticonvulsive agents.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors would like to acknowledge the Monash University Malaysia, Proteomics and Metabolomics Platform and the Jeffrey Cheah School of Medicine and Health Sciences (JCSMHS), Monash University Malaysia for research facilities and publication support.\n\n\nReferences\n\nDisease, G.B.DInjury, IPrevalence, C: Global, regional, and national incidence, prevalence, and years lived with disability for 310 diseases and injuries, 1990-2015: a systematic analysis for the Global Burden of Disease Study 2015. Lancet. 2016; 388: 1545–1602. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFisher RS, Acevedo C, Arzimanoglou A, et al.: ILAE official report: a practical clinical definition of epilepsy. Epilepsia. 2014; 55: 475–482. PubMed Abstract | Publisher Full Text\n\nManford M: Recent advances in epilepsy. J. Neurol. 2017; 264: 1811–1824. 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Drug Discov. Devel. 2009; 12: 231–239. PubMed Abstract\n\nOlivera BM, Cruz LJ, De Santos V, et al.: Neuronal calcium channel antagonists. Discrimination between calcium channel subtypes using omega-conotoxin from Conus magus venom. Biochemistry. 1987; 26: 2086–2090. PubMed Abstract | Publisher Full Text\n\nMalmberg AB, Gilbert H, McCabe RT, et al.: Powerful antinociceptive effects of the cone snail venom-derived subtype-selective NMDA receptor antagonists conantokins G and T. Pain. 2003; 101: 109–116. Publisher Full Text\n\nWilliams AJ, Dave JR, Phillips JB, et al.: Neuroprotective efficacy and therapeutic window of the high-affinity N-methyl-D-aspartate antagonist conantokin-G: in vitro (primary cerebellar neurons) and in vivo (rat model of transient focal brain ischemia) studies. J. Pharmacol. Exp. Ther. 2000; 294: 378–386. PubMed Abstract\n\nLu XC, Williams AJ, Wagstaff JD, et al.: Effects of delayed intrathecal infusion of an NMDA receptor antagonist on ischemic injury and peri-infarct depolarizations. Brain Res. 2005; 1056: 200–208. PubMed Abstract | Publisher Full Text\n\nWilliams AJ, Ling G, Berti R, et al.: Treatment with the snail peptide CGX-1007 reduces DNA damage and alters gene expression of c-fos and bcl-2 following focal ischemic brain injury in rats. Exp. Brain Res. 2003; 153: 16–26. PubMed Abstract | Publisher Full Text\n\nDonevan SD, McCabe RT: Conantokin G Is an NR2B-Selective Competitive Antagonist of N-Methyl-d-aspartate Receptors. Mol. Pharmacol. 2000; 58: 614–623. PubMed Abstract | Publisher Full Text\n\nWhite HS, McCabe RT, Armstrong H, et al.: In vitro and in vivo characterization of conantokin-R, a selective NMDA receptor antagonist isolated from the venom of the fish-hunting snail Conus radiatus. J. Pharmacol. Exp. Ther. 2000; 292: 425–432. PubMed Abstract\n\nJimenez EC, Donevan S, Walker C, et al.: Conantokin-L, a new NMDA receptor antagonist: determinants for anticonvulsant potency. Epilepsy Res. 2002; 51: 73–80. PubMed Abstract | Publisher Full Text\n\nZamani M, Budde T, Bozorgi H: Intracerebroventricular administration of N-type calcium channel blocker ziconotide displays anticonvulsant, anxiolytic, and sedative effects in rats: A preclinical and pilot study. Epilepsy Behav. 2020; 111: 107251. PubMed Abstract | Publisher Full Text\n\nZainal Abidin SA, Lee YQ, Othman I, et al.: Malaysian Cobra Venom: A Potential Source of Anti-Cancer Therapeutic Agents. Toxins. 2019; 11: 75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaha A, Gomes A, Chakravarty AK, et al.: CNS and anticonvulsant activity of a non-protein toxin (KC-MMTx) isolated from King Cobra (Ophiophagus hannah) venom. Toxicon. 2006; 47: 296–303. 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}
|
[
{
"id": "276839",
"date": "17 May 2024",
"name": "Benedict C Offor",
"expertise": [
"Reviewer Expertise Venomics"
],
"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\nA review entitled Animal venoms as a potential source of anticonvulsants by Zainal Abidin and colleagues is very exciting and informative. Considering the challenges and stereotypes associated with the sufferers of epilepsy, there is a need to explore natural sources including venom from organisms for potential therapeutic solutions. The authors demonstrated that venom components from selected venomous organisms interact with receptors, channels, and transporters and induce anticonvulsant activities. Furthermore, venom components could stimulate GABA concentration, and modulation of L-glutamate and glycine uptake by interfering with NMDA and GABAergic transporter making them possible anticonvulsant agents. It would have been more interesting if the authors had presented a Figure summarising possible mechanisms of action of these venom toxins in inducing anticonvulsant activities. Thus, proposing the interactions of these venom toxins with receptors, channels, transporters and downstream responses to the perturbation.\nThe review will be beneficial to both researchers in the field of venomics, pharmacology, physicians, and ordinary people. However, there are some changes I would suggest to improve the manuscript.\nAbstract Add scorpion venom in the abstract since there is a sub-heading (2.2) about it and highlights about the roles in voltage-gated sodium ion channels, as a potent anticonvulsant agent.\nIntroduction Page 3, Paragraph 1: Reference to back up the definition of epilepsy by the Task Force of the International League Against Epilepsy (ILAE). Page 3, Paragraph 2: Ca2+, 2+ should be in superscript Page 3, Paragraph 3: The first sentence could be supported with reference especially “diet changes as methods to treat epilepsy” Page 3, Paragraph 3: Cl-, - should be in superscript Page 3, Paragraph 5: I would suggest venom and venom toxins with potential effects against epilepsy since there were no approved venom-based drugs available to treat epilepsy. Section 2.1 sub-heading: I suggest removing (Table 1) Page 4, Paragraph 1: If “Subjects” was used to refer to “rats”, I suggest using the latter throughout Page 4, Paragraph 2: “A’ of Aminobutyric should be written with lowercase font Table 2: Voltage-gated? Table 3: Could be moved to sub-section 2.3. Page 5, Paragraph 1: in vivo? Page 5, Paragraph last: Apis mellifera should be in italics\nThe authors’ “Future directions” to explore the venoms of snakes and sea anemones is interesting, considering the role of neurotoxins (three-finger toxins) in snakebite envenoming victims. The interaction of this toxin at the neuromuscular junction inhibits presynaptic voltage-gated calcium channels by so doing causes paralysis of the snakebite victims.\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": []
},
{
"id": "293539",
"date": "24 Jun 2024",
"name": "Cletus Anes Ukwubile",
"expertise": [
"Reviewer Expertise Ethnopharmacology",
"Pharmacognosy and Natural Products Research."
],
"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 has rightly included in the review most essential parameters. This review draws the attention of the audience on the potentials of venom as anticonvulsant agent. The language use was concise and interesting. However, there is the need to provide scientific names to some of the organisms that serve as venom sources. The use of only common names are scientifically incomplete. The author should also be specific in the conclusion. For instance more proteins/compounds can be..... Proteins are compounds. It should be More compounds be...\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": []
},
{
"id": "293545",
"date": "08 Jul 2024",
"name": "Zhijian Cao",
"expertise": [
"Reviewer Expertise Animal venom peptides"
],
"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 short review about Animal Venoms as Potential Source of Anticonvulsants written by Syafiq Asnawi Zainal Abidin, Anthony Kin Yip Liew, Iekhsan Othman, and Farooq Shaikh. Epilepsy is a global epidemic that affects more than 50 million people worldwide, making it one of the most common neurological diseases. Epilepsy remains one of the most critical health burdens in the world. The discovery of anti-epilepsy agents with high effect and low toxicity is still the most urgent need today and future. Animal venom is confirmed to be one significant and potential source of natural drugs including anticonvulsants. Overall, the theme of this review is very meaningful and interesting. Moreover, the structure and organization of this review is logically clear. From a scientific perspective, the article reviews and summarizes all anti-epileptic peptides and components derived from animal venom sources. Moreover, the direction and focus of future attention and research have also been proposed. All in all, I recommend that this review could be considered to be accepted after a revision. However, some minor questions still need to be modified. Minor points\nThe authors should summarize and provide the molecular characteristics of the animal venom-derived anti-epileptic peptides (such as PbTx1.2.3, FrPbAII, BmK I, BmK IT2, Ppnp7, neuropolybin, Chartergellus-CP1, M-PONTX-Dq3a, M-PONTX-Dq3b, and M-PONTX, Dq3c, and so on), for example the primary amino acid sequences, cysteine pairs, molecular weights, and so on. The language of this review is good. However, there are still some errors in the following. “synthesised” should be adjusted to “synthesized”; “in-vivo” should be adjusted to the italicized “in-vivo”; “mice brain” should be adjusted to “mouse brain”; “mice seizure models” should be adjusted to “mouse seizure models”.\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": []
}
] | 1
|
https://f1000research.com/articles/13-225
|
https://f1000research.com/articles/13-223/v1
|
27 Mar 24
|
{
"type": "Research Article",
"title": "Tumor-driven stromal reprogramming in the pre-metastatic lymph node",
"authors": [
"Michelle Piquet",
"David A Ruddy",
"Viviana Cremasco",
"Jonathan Chang",
"Michelle Piquet",
"David A Ruddy",
"Viviana Cremasco"
],
"abstract": "Background Metastatic dissemination is critically reliant on the formation of a receptive niche, a process which is thought to rely on signals derived from the primary tumor. Lymph nodes are continuously exposed to such signals through the flow of afferent lymph, allowing the potential reprograming of lymphoid tissue stroma in support of metastases or immunosuppression. The objective of this study was therefore to better characterize tumor-driven transcriptomic changes occurring to specific stromal populations within the tumor-draining lymph node.\n\nMethods We utilize single cell RNA sequencing of dissociated LN tissue extracted from tumor-bearing and naïve mice to profile the reprograming of tissue stroma within the pre-metastatic lymph node.\n\nResults Resulting data provides transcriptomic evidence of tumor-induced imprinting on marginal reticular cells (MRCs) and floor lymphatic endothelial cells (fLECs) populating the subcapsular sinus. These alterations appear to be unique to the tumor-draining LN and are not observed during inflammatory antigenic challenge. Notably, MRCs exhibit characteristics reminiscent of early desmoplastic CAF differentiation, fLECs engage distinct chemoattractant pathways thought to facilitate recruitment of circulating cancer cells, and both stromal populations exhibit signs of metabolic reprograming and immune-modulating potential.\n\nConclusions Cumulatively, these findings build upon existing literature describing pre-metastatic niche formation and offer several promising avenues for future exploration.",
"keywords": [
"Tumor Draining Lymph Node",
"scRNAseq",
"metastasis",
"Stromal Cell",
"Fibroblast",
"Endothelial Cell",
"pre-metastatic Niche"
],
"content": "Introduction\n\nAccumulation of genetic changes underpinning malignant transformation is the trigger point of cancer initiation.1,2 However, these cell intrinsic alterations alone are insufficient for successful growth and progression of solid tumors. Rather, survival of the nascent tumor requires a co-evolved and permissive microenvironmental niche, wherein tissue stroma must be coopted to provide the structural, metabolic, and immune evasive support network necessary for tumor growth and eventual metastatic dissemination.1–3 The therapeutic potential of exploiting this interdependence has spurred significant effort to unravel the complexities of the tumor microenvironment, though the processes by which normal tissues are rendered tumor-permissive remain incompletely understood.\n\nSpecific microenvironmental requirements likewise exist for the formation of secondary tumor growth, as the engraftment and survival of circulating cancer cells is equally reliant on the existence of a receptive niche. Reflective of these exigencies, fewer than 0.01% of circulating tumor cells are thought to successfully establish tumor metastases.4 Moreover, the site of eventual metastatic engraftment is non-random, with specific organotropic patterns varying by cancer indication – an observation which serves as the basis of Stephen Paget’s longstanding “seed and soil” hypothesis.5–7 Mounting evidence now suggests that successful metastasis additionally follows a reprograming of stromal elements at these distant sites, mediated by secretion of factors and extracellular vesicles originating from the primary tumor.8–13 The resulting modifications form a more favorable microenvironment, termed the premetastatic niche (PMN).9 Decoding these microenvironmental alterations and identifying the affected cell types may open a window to the requisite conditions for early tumor cell engraftment, growth, and immune evasion, and potentially reveal new points of therapeutic intervention. However, in-depth study of these processes may be experimentally challenging given variability in exact timing and location of metastases.\n\nMore predictable is the spread of cancer cells to the regional lymphatic lymph node (LN), which are frequently the first site of tumor metastasis in most forms of carcinoma.14 This prevalence of metastatic spread to the draining LN is almost certainly a factor of direct exposure to tumor-derived signals, as such signals pool within the afferent lymphatics before invariably draining to the sentinel node.15–19 Moreover, lymphangiogenesis and increased lymph flow is believed to be an essential step that precedes LN metastasis.15,20,21 While exposure to afferent lymphatic flow facilitates the requisite acquisition of antigens and tissue signals for functional adaptive immunity, drainage of tumor-derived factors has the potential to modulate these responses, thereby conditioning the pre-metastatic LN in favor of tumor support and immune suppression.22 Indeed, recent reports have demonstrated tumor-induced alterations to LN fibroblastic reticular cells (FRCs) – a stromal population which comprises the essential infrastructure supporting lymphocyte homeostasis and coordinating immune interactions.23–25 Changes to FRCs of the tumor draining LN (tdLN) included increased activation and proliferation, disrupted homeostatic chemokine production driving aberrant immune cell localization, and altered matrix production. However, while the observed reprograming of LN stroma has a putative role in metastasis support and immune suppression, many of the described alterations overlap with the stromal response program associated with general inflammation and infection.26 In this regard, the degree to which these previously reported findings are in fact unique or specific to tumor-derived factors requires further examination.\n\nHere we expand on previous exploration of tumor-induced reprogramming through single cell transcriptomic analysis of stroma-enriched samples, enabling a more robust exploration of subset-specific transcriptional shifts. We demonstrated exquisite specificity in stromal reprograming associated with the premetastatic tdLN, wherein select subsets of FRCs and lymphatic endothelial cells (LECs) populating the LN subcapsular sinus (SCS) are differentially affected by tumor-derived signals. Amongst these findings, we confirm functional alterations reflective of matrix remodeling, identify engagement of distinct axes of chemotaxis, and identify transcriptional signs of altered metabolism and immunomodulatory potential. Importantly, these alterations were additionally compared to LN stromal responses following antigenic challenge in the absence of live tumor cells, allowing confirmation of the tumor-specificity of these response programs. Ultimately, we believe these findings help to broaden our understanding of pre-metastatic communication and tissue imprinting, and may direct future experimental exploration of metastatic niche dependencies with potential for therapeutic intervention.\n\n\nMethods\n\nAll animal work was approved and performed in accordance with the guidelines from the Institutional Care and Use Committee (IACUC) at Novartis Institutes for BioMedical Research (Protocol 20 IMO 035) and in compliance with the Guide for the Care and Use of Laboratory Animals. All efforts were made to ameliorate any potential suffering of animals.\n\nExperiments were performed in eight-week-old, sex-matched C57Bl/6 mice purchased from Charles River Laboratories. Mice were maintained under specific pathogen-free conditions in accordance with institutional and National Institute of Health guidelines.\n\nMC38 cells were received from NCI under MTA# 38699-15, expanded, frozen and collected in the NIBR cell line repository. Cell lines were maintained in Dulbecco’s Modified Eagle Medium (Gibco, 11965-092) containing 10% heat-inactivated FBS (VWR, 1500-500), 1% Penicillin-Streptomycin (Gibco, 15140-122), and 1% L-glutamine (Gibco, 25030-81) for one week prior to implant. Prior to inoculation into recipient animals, cell lines were tested and found to be free of mycoplasma and viral contamination in the IMPACT VIII PCR assay panel (IDEXX BioResearch, Missouri).\n\nThe present study used tissues collected from naïve mice (n=4), mice bearing live MC38 tumors (n=3), or fixed MC38 tumor cells (n=3). Mice were randomly assigned to treatment groups. In preparation for inoculation, MC38 cells were detached using 0.25% trypsin, washed, and resuspended in sterile PBS prior to implantation. For the “fixed cell” control treatment condition, MC38 cells were additionally incubated in 4% paraformaldehyde in sterile PBS for 20 minutes at a concentration of 106 cells/mL before washing and resuspension in sterile PBS. For both conditions, 5 × 105 cells were implanted subcutaneously on the animal’s lower-right flank. Animals are anesthetized by isoflurane inhalation prior to treatment. Mice were monitored for tumor growth, changes in body weight and condition 3 times per week. Mice were euthanized by CO2 inhalation on day 12 after treatment, and both the tumor-draining and contralateral non-draining inguinal lymph nodes were collected. No animals were excluded from analysis.\n\nSingle-cell suspensions of LNs were prepared for analysis by flow cytometry or single cell RNAseq. LNs were dissected and incubated at 37 °C in RPMI containing 0.1 mg ml−1 DNase I (Invitrogen), 0.2 mg ml−1 collagenase P (Roche) and 0.8 mg ml−1 dispase (Roche) for 50–60 min, as previously described. Liberated cells in suspension were collected into cold medium containing 2% fetal bovine serum and 5 mM EDTA every 15–20 min and replaced with fresh digestion medium. Following complete digestion of the LN, cells were passed through a 70-μm cell strainer, washed and resuspended in cold PBS.\n\nSingle-cell suspensions were resuspended in flow cytometry buffer (PBS, 2% FBS, and 2 mmol/L EDTA). Cells were blocked with Fc block and then stained with different fluorochrome-conjugated antibodies for 20 min on ice. The following antibodies were used (clone, fluorophore, concentration): anti-CD45 (30-F11, BUV396, 1:500), anti-CD31 (390, Pacific Blue, 1:300), and anti-PDPN (8.1.1, APC, 1:300). CountBright Absolute Counting Beads (Invitrogen, C36950) were included for quantification of cell counts. Samples were analyzed on a BD flow cytometry Fortessa instrument and analyzed with FlowJo. Raw data available.27\n\nSingle cells obtained form LN digestion were resuspended in mouse FC block (Miltenyi #130-092-575). Biotinylated PDPN (8.1.1, 1:100) antibody was used for positive selection, using the EasySep Selection Kit (Stemcell Technologies #18559). Cells were then washed in cold PBS, counted, and resuspended at 106 cells/mL for sequencing.\n\nThe 10x Genomics Chromium Single Cell 3’ Reagents v3 kit (10× Genomics, Pleasanton, CA) was used under standard conditions and volumes to process cell suspensions for 3’ transcriptional profiling. The volumes of cell suspensions were calculated to achieve a target cell recovery of 6000 cells for all dissociated samples, following the manufacturer’s guidelines. The resultant purified cDNAs were quantified on an Agilent Tapestation (Agilent, Santa Clara, CA) using High Sensitivity D5000 ScreenTapes and Reagents. The final single cell 3’ libraries were quantified using an Agilent Tapestation using High Sensitivity D1000 ScreenTapes and Reagents. Following this, the libraries were diluted to a concentration of 10 nM in Qiagen Elution Buffer, subjected to denaturation, and loaded onto an Illumina MiSeq at 6 μM, utilizing the MiSeq Reagent Kit v3 (Illumina, San Diego, CA) to assess sample quality and achieve loading normalization for the HiSeq4000. The normalized libraries were loaded onto an Illumina cBOT at a concentration of 160 picomolar and sequenced on a HiSeq4000. The sequencing process included a 28-base-pair first read, followed by two 8-base-pair index reads, and concluded with a 91-base-pair second read, all by using 2 HiSeq4000 SBS kits at 50 cycles each. All sequence intensity files were generated using the Illumina Real Time Analysis software. The resulting intensity files were then subjected to demultiplexing and aligned to the mouse genome, version mm10, using the 10x Genomics CellRanger v3.0.1 software package.\n\nAll computational analyses and visualizations were conducted within the R programming environment, using version 3.6.3. The Seurat package (v3.2.3) was employed for quality control and downstream analysis of single-cell RNA-seq data.28 The count matrices were then subjected to comprehensive analysis using the Seurat workflow. Cells that exhibited low quality characteristics, defined as those with fewer than 200 expressed genes, more than 6000 expressed genes, or exceeding 30% mitochondrial content, were excluded from the dataset. Following this, the count matrices were merged and normalized using SCTransform. Principal component analysis was executed, focusing on 2000 highly variable genes. To select the appropriate number of principal components (PCs), the Elbow plot heuristic was used. A shared nearest neighbor (SNN) graph was constructed using the first 20 PCs through Seurat’s FindNeighbors function, and cell clustering was performed using a Louvain algorithm with FindClusters. A resolution parameter of 0.8 was chosen to generate an extensive collection of cell clusters, effectively capturing diverse cell types. Cluster markers were identified using Seurat’s FindAllMarkers function. Dimensionality reduction was visualized using the uniform manifold approximation and projection (UMAP) method.\n\nThe dataset was methodically divided into subsets, specifically isolating floor lymphatic endothelial cells (fLEC), marginal reticular cells (MRC), and b-zone reticular cells (BRC). These subsets underwent a re-clustering process using 15 principal components (PCs) at a resolution parameter of 0.3, with the optimal number of PCs determined using the Elbow heuristic.\n\nDifferential gene expression analyses were conducted on each subset of cells with an average log-fold change above 0.25, as part of the Seurat workflow. This analysis compared Live Draining vs. Live Non-Draining cells. Pathway enrichment analyses were executed using the ClusterProfiler package (v3.14) and its enrichGO function, using Biological Process, Cellular Component, and Molecular Function ontologies.29 Pathway enrichment was computed for all cluster marker genes within fLEC, MRC, and BRC subsets, specifically focusing on those with an avg_logFC > 0.25 and an adjusted p-value < 0.001. Significantly enriched pathways (adjusted p-value < 0.05) were selected and visually represented using ggplot2. Finally, to effectively illustrate the significance of the top hits derived from the list of differentially expressed genes, violin plots were employed as a visual tool.\n\n\nResults and discussion\n\nHealthy tissue stroma is not thought to be inherently permissive to the growth of malignant cells, and the reprogramming of these tissues is believed to represent a requisite step to successful growth and progression of the tumor. Normal tissue fibroblasts, for instance, have long been known to exhibit cancer-restrictive characteristics, and it is therefore likely that the functional attributes of fibroblasts must first be modulated – coopted by the cancer to support rather than restrict growth and invasiveness.30–32 The necessity of such microenvironmental reprogramming likely extends not only to the establishment of the primary tumor, but metastatic lesions as well. Successful engraftment of circulating cancer cells requires a supportive niche, and thus metastatic cancers must orchestrate a second iteration of this reprogramming process within distant tissues.8–13\n\nBy design, lymph nodes are strategically positioned to intercept tissue-derived signals and antigen. Established tumors, however, appear to coopt the lymphatic infrastructure to facilitate metastatic dissemination. In this context, lymphatic drainage offers an efficient means of pre-conditioning tissue stroma for metastatic niche formation, and functions as a direct channel for the distribution of signals which may in fact subvert anti-tumor immunity. Indeed, efficiency of lymphatic drainage is positively correlated with metastatic potential, and lymphangiogenesis is a hallmark of metastatic niche formation.33 In the pre-metastatic lymph node, expansion of both endothelium and FRCs has been documented.\n\nHowever, stromal expansion in LNs is not a tumor-specific response program. Indeed, subcutaneous delivery of fixed tumor cells is sufficient to elicit LN swelling and expansion of FRCs, LECs, and BECs at a level comparable to that observed with live tumor growth (Figure 1A). To explore more deeply the functional alterations occurring within the stromal compartment that specifically correlated with live tumor growth, we performed single cell RNA sequencing of cells isolated from draining and non-draining LNs in mice inoculated with either live or fixed MC38 cancer cells. We additionally enriched for PDPN-expressing LECs and FRCs to enable robust subset-level analyses. Within the resultant dataset, we identified 7 distinct clusters of fibroblastic cells and 4 clusters of lymphatic endothelial cells, each of which was annotated based on well-established identity markers (Figure 1B, E).34–37\n\nTumor draining and contralateral non-draining inguinal lymph nodes were excised and enzymatically digested for analysis. A) Quantification of cell numbers assessed by flow cytometry (n=5 mice per condition). B) UMAP visualization of total lymph node fibroblasts, colored by cluster identify. C, D) Quantification of the change in population proportion (amongst fibroblast subsets), along with total number of differentially expressed genes. C. dLN vs ndLN of mice growing live tumors. D. dLN vs ndLN of mice receiving fixed tumor cells. E) UMAP visualization of total lymph node lymphatic endothelial cells, colored by cluster identify. F, G) Quantification of the change in population proportion (amongst endothelial subsets), along with total number of differentially expressed genes. F. dLN vs ndLN of mice growing live tumors. G. dLN vs ndLN of mice receiving fixed tumor cells. H) Schematic representation of lymph node architecture and anticipated location of metastases engraftment. Inset depicts a micrometastasis surrounded by the following stromal subsets of interest: fLECs, MRCs, and BRCs.\n\nThe seeding of micrometastases within tumor-draining lymph nodes predictably occurs within the subcapsular sinus (SCS), where tissues are most readily exposed to lymph borne materials and migrating cancer cells (Figure 1H).38,39 Interestingly, we demonstrate here that unique cellular constituents of this specific microanatomical compartment were selectively impacted by the upstream tumor (Figure 1C, F). Marginal reticular cells (MRCs) and floor lymphatic endothelial cells (fLECs) exhibited the greatest degree of transcriptional alteration in the tumor-draining LN relative to those of contralateral non-draining LNs. Perivascular cells (PRCs), though not localized to the SCS, likewise exhibited significant transcriptomic changes, which may reflect support of vascular expansion.\n\nUnexpectedly, we also found that the overall cellular representation of these populations, along with B-zone reticular cells (BRCs), were disproportionately increased in the tumor-draining LN (Figure 1C, F). This appears to differ from the pattern of stromal expansion that occurs in response to normal antigenic challenge. While exposure to fixed tumor cells elicited stromal activation and expansion – as previously demonstrated - this proliferative response seemed to occur proportionately amongst fibroblast and endothelial subsets and involved comparatively fewer transcriptomic alterations (Figure 1D, G). Ultimately, we predict that selective induction of transcriptional changes and disproportionate expansion of stromal subsets comprising the SCS in the tdLN reflects the establishment of a niche supportive of metastatic engraftment and survival.\n\nWhile the exact microenvironmental preferences of primary and secondary lesions may differ, and the means by which these alterations are driven may be distinct, there are almost certainly commonalities in tumor-induced stromal reprogramming. For instance, the aberrant production of extracellular matrix, characteristic of the desmoplastic response, is broadly observed across cancer indications. These responses are largely driven by conversion of resident fibroblast populations to tumor-supportive cancer associated fibroblasts (CAFs). Within the LN SCS, resident fibroblast populations include primarily MRCs that underly the sinus endothelium, and a proportion of BRCs that populate the interfollicular space. As both populations exhibited shifts specific to the tdLN, we re-clustered each population and performed differential transcriptomic analyses to identify tumor-specific changes (Figure 2A-D). Amongst these changes, MRCs most notably exhibited increases in a broad spectrum of ECM components and matrix remodeling enzymes reminiscent of desmoplastic CAFs of the primary tumor, including upregulation of fibronectin, a critical ECM protein involved in development, wound healing, and cancer metastasis (Figure 2A,B).40 Interestingly, PDAC-derived exosomes were recently reported to induce elevated fibronectin expression in the pre-metastatic liver - a process which was found to be essential for niche formation.41\n\nA) (top) UMAP visualization of MRCs, colored by treatment condition. (bottom) Pathways significantly enriched in MRCs of live-tumor-draining LNs relative to non-draining LNs. B) (top) Volcano plots of differentially expressed genes between MRCs of draining vs non-draining LNs. Select genes of interest are highlighted. (bottom) Violin plots of select genes differentially expressed in MRCs of the live-tumor draining LN. Expression is shown across all four experimental conditions; live draining, live non-draining, fixed draining, and fixed non-draining. C) UMAP visualization of BRCs, colored by treatment condition. D) Volcano plots of differentially expressed genes between BRCs of draining vs non-draining LNs. Select genes of interest are highlighted. E) (top) UMAP visualization of fLECs, colored by treatment condition. (bottom) Pathways significantly enriched in fLECs of live-tumor-draining LNs relative to non-draining LNs. F) (top) Volcano plots of differentially expressed genes between fLECs of draining vs non-draining LNs. Select genes of interest are highlighted. (bottom) Violin plots of select genes differentially expressed in fLECs of the live-tumor draining LN. Expression is shown across all four experimental conditions; live draining, live non-draining, fixed draining, and fixed non-draining. G) Dotplot displaying expression of transcripts upregulated across both MRCs and fLECs in the live tdLN. The size of the dot represents percentage of cells expressing transcript, while the color indicates average level of expression within the population.\n\nIn addition to ECM proteins, matrix metalloproteases (MMPs) likewise play a pivotal role in cancer progression and metastatic dissemination through matrix remodeling.42,43 Along these lines, we observed increases in both MMP2 and MMP9 specifically in MRCs of the tdLN (Figure 2B). While it is unclear from transcriptomic signature alone how the structure of the ECM is specifically remodeled in the SCS, or the extent to which this may impact the nascent metastasis, expression of both has previously been linked to niche formation and vascular remodeling in pre-metastatic tissues and are thus of particular interest.9,44,45\n\nInterestingly, previous reports have noted significant tumor-induced enlargement of the collagen-rich LN conduits – a branched network of fibers which normally functions as a transport system for small soluble materials through the LN cortex and paracortex.25 In this context, Increased conduit thickness correlated with greater transport of larger, normally size-excluded molecules, and the authors speculated that these alterations may result in abnormal distribution of tumor-derived materials to deeper areas of the LN parenchyma. This is notably counter to the effects observed during acute inflammation-associated LN expansion. Under such conditions, LN conduits are also structurally disrupted, but size exclusivity of molecular transport through the network is nevertheless maintained.46,47 This distinction is particularly intriguing, as size exclusivity of LN conduits is believed to be a function of plvap-lined gating channels that traverse the sinus-lining floor LECs (fLECs), rather than an intrinsic feature of conduit size itself.48 Lymph-borne molecules small enough to pass through these trans-endothelial channels subsequently gain access to the conduit network. We thus speculate that matrisomal dysregulation surrounding fLECs and the underlying MRCs, such as those we find describe within this dataset, may in fact account for, or contribute to, this distinct loss of regulated conduit access in tdLNs.\n\nBRCs likewise exhibited upregulation of some ECM-related transcripts in the tdLN, however the overall extent of differentially expressed genes in this subset was markedly less expansive (Figure 2C, D). Nevertheless, we note that BRC representation within the dataset was significantly greater in the tdLN, possibly reflecting a greater proliferative response without significant functional divergence from baseline properties of BRCs in a resting LN. As BRCs are essential to the homeostatic maintenance of naïve B cells within the LN, proliferative expansion of the BRC subset may functionally mirror the known preferential accumulation of B cells in tumor draining nodes.49,50 In turn, accumulation of B cells within the tdLN has been shown to drive pro-metastatic lymphangiogenesis, and thus expansion of the B cell support network may be an indirect, but requisite factor in support of this process.21\n\nCell recruitment, migration and positioning into and within the LN is a highly regulated process, guided by an array of precisely coordinated chemotactic gradients. Principal among these chemotactic cues are the homeostatic chemokines Ccl19, Ccl21, and Cxcl13, each of which is primarily produced by subsets of LN FRCs.51–54 Previous studies characterizing changes in the tdLN have highlighted a transcriptional downregulation of these cues within 3 days of tumor implantation, and subsequent loss of normal immune cell compartmentalization. Such perturbations would seemingly be detrimental to the initiation of adaptive immune responses, which depends on precise cellular positioning. Indeed, genetic mouse models of homeostatic chemokine disruption exhibit impaired immunity. However, it is notable that all forms of inflammation and antigenic challenge, not just exposure to tumor-derived factors, can trigger transient downregulation of these factors.55–61 As such, the immunological consequences of chemokine downregulation following tumor inoculation remain unclear. Within our dataset, however, we did not observe significant transcriptional alterations to Ccl19, Ccl21, or Cxcl13 amongst any stromal subset (data not shown). This may be reflective of the later timepoint at which we collected our data, and the transient nature of these fluctuations.\n\nWhile we do not observe dysregulation of these FRC-associated chemokines, re-clustering and differential analysis of the fLEC population did in fact reveal engagement of pathways related to leukocyte migration (Figure 2E, F). In particular, we observed dramatic increases in the inflammation-associated chemokines Cxcl9, Cxcl10 and Ccl20 (Figure 2F). These changes were exclusively depicted within the fLEC population, suggesting specific chemoattraction of cell types expressing the corresponding cognate receptors to the SCS. Interestingly, the Ccl20/Ccr6 axis has been well explored in the context of metastatic colorectal cancer, wherein CCr6-expressing cancer cells are recruited to the liver by Ccl20-expressing periportal stromal cells.62 Expression of Ccl20 by floor LECs in the tdLN may be similarly utilized by migrating cancer cells in lymphatics. Critically, Ccl20 is absent on neighboring ceiling LECs, allowing the formation of a differential gradient of chemokine across the LN SCS. Analogous chemotactic gradients of Ccl19 and Ccl21 across the SCS have been experimentally demonstrated as critical for the recruitment of migrating dendritic cells into the LN.63\n\nBy contrast, Cxcl9 and Cxcl10 are interferon induced chemokines that are most well described in the recruitment and activation of antigen experienced, Cxcr3-expressing T and NK cells.64,65 Expression of these chemokines is therefore consistent with the broader interferon response signature of exhibited by fLECs of the tdLN (Figure 2E). In the context of cancer, these chemokines are notable for their role in recruitment of tumor-infiltrating lymphocytes and are thought to be important for driving immunologically “hot” tumor phenotypes.66 Expression of Cxcl9 and Cxcl10 within the LN is additionally known to support positioning of memory T cells to the interfollicular region and is critically important for antiviral immune responses.67,68 Cumulatively, these observations may implicate expression of Cxcl9/Cxcl10 by fLECs as a beneficial means to direct antigen responsive immune cells to site of future metastatic engraftment. On the other hand, Cxcr3 may also be expressed by migrating cancer cells, and the Cxcl9/Cxcl10/Cxcr3 signaling axis has in fact been implicated in the growth and metastasis of tumors to various organs, including the LN.69–72 Thus, it remains unclear whether increased expression of these chemokines in the premetastatic LN favor metastasis engraftment or anti-tumor immunity.\n\nWhile MRCs and fLECs exhibited unique subset-specific responses in the tdLN, we also noted a handful of upregulated transcriptional elements common across both populations (Figure 2G). Importantly, upregulation of each was observed only in the draining LN of mice bearing live tumors but did not occur in the LNs of mice inoculated with fixed tumor cells (Figure 2G). As such, we believe these genes to be uniquely induced in response to tumor-derived signals.\n\nExposure to factors produced by an upstream tumor may elicit responses that skew immune education, and thus in this context, the striking increase in IL33 – a cytokine with numerous immunological effects that are both context and cell-type specific - was particularly intriguing.73 Notably, IL33 is a known driver of ST2+ T-reg expansion and may have an important role in the induction of Treg-mediated tolerance.74–77 In the context of cancer metastasis, ST2-expressing Tregs have been shown to support tumor development, and in vivo inhibition of IL-33 signaling has been shown to disrupt formation of metastases in mouse models.74 Additionally, elevated IL33 expression has been described in fibroblasts of lung metastases, wherein signaling is thought to contribute to a supportive niche through skewing immunity towards a Th2 response.78 Tumor-induced IL33 expression across stromal subsets in the LN SCS may therefore have important implications for suppression of anti-tumor responses. Along these lines, recent reports have indeed suggested that metastatic spread to the LN can elicit immunological tolerance through the preferential induction of antigen-specific Tregs.79 The functional consequence of this redirected immune response is thus believed to be favorable for subsequent metastatic outgrowth in distant organs.\n\nBy contrast, it is also notable that, under infectious conditions, IL33 secretion by LN fibroblasts has been shown to be a stress response program critical for CD8 T cell immunity.80 It is thus possible that IL33 upregulation in tdLNs may alternatively engage both anti-tumor immunity or immune suppressive elements, the balance of which may be a critical determinant of tumor progression and metastatic spread.\n\nInterestingly, a recent report has also implicated IL-33 signaling as a driver of fibroblast-to-CAF differentiation in oral squamous cell carcinoma.81 In this context, IL-33 was found to be upregulated and stabilized by signaling from a novel lncRNA (termed Lnc-CAF), which resulted in acquisition of an activated CAF phenotype and subsequently supported tumor growth. Critically, Lnc-CAF was found to be distributed via tumor cell-derived exosomes, offering a plausible means by which this pathway might mediate preconditioning of LN stroma. Cumulatively, these studies suggest that IL-33 may function not only as a modulator of immunity in the metastatic microenvironment, but as a driving factor in the stromal acquisition of CAF-like features and niche formation.\n\nThe upregulation of LDHA and PKM transcript was likewise common across both MRCs and fLECs (Figure 2G). This is particularly noteworthy within the context of niche formation and metastasis, as both these genes encode metabolic enzymes associated with the switch to aerobic glycolysis and have long been associated with metabolic adaptation in cancer cells.82,83 Preferential utilization of aerobic glycolysis, even in the presence of sufficient oxygen, is termed the Warburg Effect, and is characteristic of cancer cell metabolism.84 Despite several decades of research, a full functional account of this metabolic preference remains incompletely understood. However, disruption of this process by targeting of LDHA drives beneficial anti-tumor effects.85–88\n\nNotably, Riedel et al. recently demonstrated that inhibition of LDHA could reverse tumor-directed FRC activation phenotypes, suggesting a putative metabolic switch in stroma that may be similar to that of cancer cells.24 The authors proposed a model wherein elevated levels of lactate produced in the primary tumor drains to the sentinel lymph node, modulating FRC function and conditioning the pre-metastatic niche. Supportive of this hypothesis, they observed higher expression of LDHA near lymphatic vessels of the primary tumor, and elevated levels of lactate in the draining LN. By contrast, our data suggest that LDHA is in fact intrinsically upregulated in both MRCs and fLECs as well, potentially further contributing to the regional build-up of lactate.\n\nWhether this response is secondary to the drainage of lactate from the primary tumor, or rather a response to other yet unidentified signals, remains unknown. However, a recent demonstration that CAFs from the primary tumor can in fact impart Warburg-like metabolism via exosomal transfer of metabolites offers an intriguing alternative whereby CAF-derived exosomes passing through lymphatic drainage may likewise contribute to induction of metabolic preconditioning at the site of future LN metastasis.89 Nevertheless, both the means by which LDHA/PKM are upregulated and the metabolic and functional consequences of these alterations bear further exploration.\n\n\nConcluding remarks\n\nMetastatic progression is the greatest cause of mortality across most cancer indications, and thus developing new means of clinical intervention in this process is clearly of paramount importance. We believe the findings discussed herein provide an important resource for understanding the early impact of cancer-associated signals on metastatic niche formation. Additionally, we provide comparative analysis against LN stroma following antigenic challenge with fixed cancer cells, allowing us to discern changes that relate to factors actively produced by tumors from generalized inflammatory response programs. Transcriptomic changes discussed herein thus represent tumor-specific responses that may prove to be attractive targets for preventative or therapeutic intervention. However, further experimental exploration will be required to establish causal relationships between these transcriptional changes and metastatic success rate. Additionally, the specific identity of secreted factors driving LN preconditioning are not explored in this study - though paired analyses of primary tumors and tdLN might prove informative in this regard. Ultimately, we suggest that continued exploration along these lines may critically enable the identification of novel pressure points against which transformative therapeutic or preventative intervention may be directed.\n\n\nAccession numbers\n\nGene Expression Omnibus at NCBI: Tumor-driven stromal reprogramming in the pre-metastatic lymph node [Mus musculus (house mouse)]. Accession number GSE248905; http://identifiers.org/geo: GSE248905",
"appendix": "Data availability\n\nOpen Science Framework: Underlying data for ‘Tumor-driven stromal reprogramming in the pre-metastatic lymph node’, https://www.doi.org/10.17605/OSF.IO/WDV3H. 27\n\nThis project contains the following underlying data:\n\n• Data File: Tumor dLN_A1_A01.fcs\n\n• Data File: Tumor dLN_A2_A02.fcs\n\n• Data File: Tumor dLN_A3_A03.fcs\n\n• Data File: Tumor dLN_A4_A04.fcs\n\n• Data File: Tumor dLN_A5_A05.fcs\n\n• Data File: Tumor NdLN_B1_B01.fcs\n\n• Data File: Tumor NdLN_B2_B02.fcs\n\n• Data File: Tumor NdLN_B3_B03.fcs\n\n• Data File: Tumor NdLN_B4_B04.fcs\n\n• Data File: Tumor NdLN_B5_B05.fcs\n\n• Data File: Killed dLN_C1_C01.fcs\n\n• Data File: Killed dLN_C2_C02.fcs\n\n• Data File: Killed dLN_C3_C03.fcs\n\n• Data File: Killed dLN_C4_C04.fcs\n\n• Data File: Killed dLN_C5_C05.fcs\n\n• Data File: Killed NdLN_D1_D01.fcs\n\n• Data File: Killed NdLN_D2_D02.fcs\n\n• Data File: Killed NdLN_D3_D03.fcs\n\n• Data File: Killed NdLN_D4_D04.fcs\n\n• Data File: Killed NdLN_D5_D05.fcs\n\n• Mouse FCS data key.xlsArrive Author Checklist.pdf\n\nOpen Science Framework: ARRIVE checklist for ‘Tumor-driven stromal reprogramming in the pre-metastatic lymph node’, https://www.doi.org/10.17605/OSF.IO/WDV3H. 27\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\nHanahan D, Weinberg RA: Hallmarks of cancer: the next generation. 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}
|
[
{
"id": "309554",
"date": "24 Aug 2024",
"name": "Sanjiv Luther",
"expertise": [
"Reviewer Expertise lymph nodes",
"stromal cells",
"immunity",
"scRNAseq"
],
"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\nPiquet and coauthors address in this study the interesting question of how the lymph node (LN) stroma changes or is reprorammed upon draining a tumor site with alterations presumably contributing to tumor metastasis to this site along with immune suppression. They present insightful scRNAseq datasets describing how different murine LN stromal cell types react to either a live or a fixed inoculation with the MC38 colorectal cancer cell line, when compared to a nondraining LN. While both types of inoculation lead to a comparable LN swelling, including a strong amplification of the LN fibroblasts, lymphatic endothelium (LEC) and blood endothelium (BEC), consistent with a strong inflammatory response in both settings, the impact of live tumor cell inoculation shifted much more the proportions and transcriptional profile of distinct subsets of stromal cells compared to injection with fixed tumor cells, pointing to tumor-specific factors driving these changes. The transcriptional shifts were most pronounced among two fibroblast subsets, termed MRC and BRC, as well as among two LEC subsets that are also those thought to be most exposed to the incoming lymph and its factors. The resource provided by the authors should be of great interest to all scientists interested in tumor metastasis or anti-tumor immunity. The manuscript is well written, the data are of high quality and appropriately displayed; and the findings are discussed in an insightful way.\nMajor points: 1) The clustering of the different subsets of fibroblasts, or lymphatic or blood endothelial cells is presented without any tables or heatmaps showing the top differentially expressed genes for each subset, so that one can judge the cells clustered for example as MRC or BRC. Currently one would be forced to redo all the bioinformatic work again, based on the individual data files provided. Such additional data would help considerably the expert reader to assess and interpret the data and the labeling of the clusters, especially as the frequencies of the FDC and MRC populations look higher compared to other scRNAseq data sets (eg. Rodda/Cyster Immunity 2018) or relative to the analysis by flow cytometry (eg. Huang/Luther, PNAS 2018), also relative to TRC and MedRC. Any histological stainings (with antibodies or by ISH) validating the key scRNAseq data, including the subset identification/clustering would greatly enhance the value of the data; eg. are the MRC-like cells really still restricted to the SCS-lining area, as are the fLEC-phenotype cells 2) Similarly, no tables are provided as supplement to list the DE genes in the various settings as only part of them are mentioned in the figure 2, and they are limited to the ones showing an increase with none labeled showing a decrease in a live tumor cell draining LN (vs the nondraining LN). This reviewer can imagine that labeling also part of the downregulated genes may render the data and its discussion more complex but then at least tables containing these data should be provided to allow an interested reader to look into them without need to reanalyze all the data. They may contain data relevant for the main question of the paper; eg. how does the LN suppress anti-tumor immunity or get prepared for tumor metastasis. Please improve also the description in the legend so that one understands why the log2 fold changes is negative for transcripts enriched in drLN.\n\n3) The draining LN response is investigated on day 12 after tumor cell inoculation, comparing live tumor cell vs fixed tumor cell injection which is an elegant approach. As the same number of cells is injected in the setting of live cells as of fixed cells, but the final number of live tumor cells is not stated for d12 (but is presumably much higher, by a factor of several fold), the authors should probably acknowledge in the discussion the large difference in final tumor cell material in the two settings that is likely to contribute to the transcriptional differences observed, besides larger differences in the tissue cells of the primary injection site during the time period upto d12. Thus, the difference in factors infusing the LN is not only due to the live tumor cells but also due to the difference in final tumor cell numbers and their differential effects on the peripheral tissue in the two settings.\n4) It is unclear whether the authors verified if any of the live tumor injected mice showed tumor cell metastasis to the draining LNs which got analyzed. That could have been analyzed by flow cytometry (CD45- cells with specific FSC/SSC characteristics; or a non-stated epithelial marker) or by other means. This information would be valuable to know given the likely difference between premetastatic vs metastatic LNs stroma.\nMinor points:\nThe results start with a rather lengthy intro and part of it could be incorporated into the introduction where some of these points are already raised. BRC are claimed to populate the interfollicular space; please explain the rational or the publication stating this. Enzymatic digestion (‘as previously described’): please add reference with a more detailed protocol as this aspect is key for appropriate reproduction Mention at beginning that MC38 are a colorectal carcinoma cell line In the conduit section: conduits are not simply fibers (although they appear that way histologically and contain fibers) but have also basement membranes thereby forming true tubes/channels; thus the term fiber is not ideal. Similar, the term ‘transendothelial channels’ is not appropriate even when talking of the SCS where occasionally such channels traversing the SCS can be observed but the majority of conduits do not seem to traverse the endothelium. ‘Exhibited of’ (please drop ‘of’) IL33 discussion: may add another reference showing role of IL33 for memory T cell response (Marx et al.,2024 [Ref 1]) Please spell out LDHA and PKM at first mentioning and possibly the reaction they catalyze to inform the non-specialist reader. Fig.1B and D: I assume these Umaps show data compiled from all 4 groups of mice (please state clearly in legend); it would be of interest to display the Umaps of each group separately (in a supplementary figure) for readers to understand the stromal cell clustering in a 2D space for the 4 groups.\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? Partly",
"responses": []
},
{
"id": "296538",
"date": "14 Sep 2024",
"name": "Christopher McGinnis",
"expertise": [
"Reviewer Expertise Cancer immunology",
"metastasis biology",
"single-cell genomics"
],
"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 by Piquet et al, the Authors use single-cell RNA-sequencing (scRNA-seq) to compare lymph node (LN) stromal cell transcriptional profiles in mice bearing live and fixed tumors to disentangle changes in LN stromal cells related to pro-metastatic remodeling mechanisms from changes linked to antigenic challenge. The authors make the following claims:\n\nDevelopment of the LN pre-metastatic niche involves changes in the proportions and gene expression profiles of specific subtypes of fibroblasts and endothelial cells comprising the subcapsular sinus, in addition to other LN cell populations (e.g., b-zone reticular cells and perivascular cells). MRCs in the live tdLN are induced into a desmoplastic CAF-like state associated with upregulation of ECM components and remodeling genes such as fibronectin and Mmp2/9. Authors speculate that tumor-reprogrammed MRCs contribute to altered regulation of LN conduit access. fLECs increase expression of pro-inflammatory cytokines (e.g., Ccl20 and Cxcl9/10) in tdLNs, raising the question of whether TILs/NK cells or Cxcr3+ metastatic tumor cells (or both) are preferentially recruited to the subcapsular sinus. MRCs and fLECs enact a coordinate gene expression program in the live tdLN associated with increased Il33 and aerobic glycolysis genes, providing new insights into stromal cell signaling and metabolism mechanisms in the LN metastatic niche.\n\nMajor Comments\n\nDo the authors have evidence showing that mice harboring MC38 tumors actually form LN metastases? Or at least what proportion of the mice form mets? The MC38 tumor model is not thought to robustly metastasize (e.g., only ~50% of orthotopically-transplanted tumors form LN metastases; Greenlee & King, 2022), especially after subcutaneous injection. Thus, it is unclear whether the signatures described in the paper truly represent the pre-metastatic niche LN. Without adequately addressing this concern, the authors need to recontextualize their observations to focus on the effects of primary tumor-mediated reprogramming on the tdLN rather than the pre-metastatic niche.\n\n“Within the resultant dataset, we identified 7 distinct clusters of fibroblastic cells and 4 clusters of lymphatic endothelial cells, each of which was annotated based on well-established identity markers” – Authors should include either reference to which markers were used or, better yet, a heatmap or dotplot showing expression levels for marker genes in each annotated cell type.\n\n“Perivascular cells (PRCs), though not localized to the SCS, likewise exhibited significant transcriptomic changes, which may reflect support of vascular expansion” – While entirely possible, it is unclear how the observed increase in the numbers of DEGs suggests support of vascular expansion. Authors should analyze more deeply the genes that are differentially expressed (e.g., GSEA, targeted analysis of known proangiogenic factors expressed by PRCs, etc.) before making this claim.\n\nThe Authors make many claims throughout the manuscript about proliferative expansion of certain fibroblast and endothelial cell subsets in tumor-draining lymph nodes, but do not show any direct evidence of this increased proliferation. Since annotating proliferative cells via Mki67 and Hells expression in scRNA-seq data is possible, I recommend the Authors compare the proportions of proliferative subsets in all experimental groups to test/strengthen these claims.\n\nThe Authors do not describe how they handled the removal of doublets during scRNA-seq analysis. The presence of doublets could significantly confound data interpretation – particularly in instances where the underlying cell type distributions between samples are known to differ, as in this case – and, thus, needs to be addressed to ensure the observations are not artefactual in nature.\n\nIn the Methods section, the Authors state that “The present study used tissues collected from naïve mice (n=4), mice bearing live MC38 tumors (n=3), or fixed MC38 tumor cells (n=3)” and then “No animals were excluded from analysis.” However, the described scRNA-seq analyses do not incorporate insights gained from the naïve mouse samples. Comparing naïve and fixed tumor samples could provide key insight for distinguishing the effects of live tumors on the tdLN. Moreover, including comparisons between naïve and fixed tumor samples would be critical for pinpointing the observed effects that are specifically due to antigenic challenge. Alternatively, if naïve samples were not used, the Methods section should be edited to clarify this point.\n\nIn Fig. 2G, the authors show genes that are specifically enriched in tdLN MRCs and fLECs. How were these genes identified? Is Il33 expression between tdLNs isolated from mice harboring live and fixed tumors statistically-significantly different? The up-regulation between tdLN and ndLN is clear in both live and fixed tumor settings, but tdLNs in fixed tumor samples also increase expression of Il33 compared to ndLNs, suggesting that this observation may not be live tumor-specific.\n\nMinor Comments\n\nAuthors state “In the pre-metastatic lymph node, expansion of both endothelium and FRCs has been documented” – true, but authors should cite appropriate literature references.\n\nHow did authors verify that MC38 tumor cells were successfully fixed after 4% PFA exposure?\n\nFig. 1A: Authors should clarify in the legend the reference point they used to calculate relative cell count. Imagining it was the average of the non-draining LN, but should be explicit to avoid confusion. Authors should also clarify how each cell type was identified using their flow cytometry panel.\n\nFig. 1B and E: Authors do not ever define some of the acronyms used here (e.g., TRC, FDC)\n\nPage 7: “In this context, Increased conduit thickness…” – ‘Increased’ should not be capitalized.\n\nFig. 2B/E/F – authors should be explicit about what the volcano plot colors scheme to ensure clarity of interpretation. Also, are the p-values presented raw or adjusted?\n\nAs far as I can tell, the Authors use increased expression of fibronectin by MRCs in the tdLN to support the claim that they are induced into a desmoplastic CAF-like state. This may indeed be the case, but more thorough analyses/discussions are needed to sufficiently support this claim. I would suggest leveraging publicly-available scRNA-seq data of desmoplastic CAFs (if such data exists) to assess similarly in transcriptional signatures. Alternatively, the language can be edited to lessen the claimed connection.\n\n“Indeed, genetic mouse models of homeostatic chemokine disruption exhibit impaired immunity.” Need reference.\n\nShould correctly note gene/protein identifiers (e.g., italics for gene names, proteins capitalized, etc.).\n\nThe 30% mitochondrial gene expression threshold is quite high. Authors should interrogate whether any high pMito clusters were retained in analyses that could confound interpretation.\n\nOn balance, I believe that the presented work represents a useful advance for the field, and I recommend its indexing, assuming that the concerns addressed above are satisfactorily addressed. Moreover, I would also like to specifically note that the manuscript is extremely well-written.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-223
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https://f1000research.com/articles/13-221/v1
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27 Mar 24
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{
"type": "Research Article",
"title": "Derivation and validation of a mortality risk prediction model in older adults needing home care: Updating the RESPECT (Risk Evaluation for Support: Predictions for Elder-Life in their Communities Tool) algorithm for use with data from the interRAI Home Care Assessment System",
"authors": [
"Maya Murmann",
"Douglas G. Manuel",
"Peter Tanuseputro",
"Carol Bennett",
"Michael Pugliese",
"Wenshan Li",
"Rhiannon Roberts",
"Amy Hsu",
"Douglas G. Manuel",
"Peter Tanuseputro",
"Carol Bennett",
"Michael Pugliese",
"Wenshan Li",
"Rhiannon Roberts"
],
"abstract": "Background Despite an increasing number of risk prediction models being developed within the healthcare space, few have been widely adopted and evaluated in clinical practice. RESPECT, a mortality risk communication tool powered by a prediction algorithm, has been implemented in the home care setting in Ontario, Canada, to support the identification of palliative care needs among older adults. We sought to re-estimate and validate the RESPECT algorithm in contemporary data.\n\nMethods The study and derivation cohort comprised adults living in Ontario aged 50 years and older with at least 1 interRAI Home Care (interRAI HC) record between April 1, 2018 and September 30, 2019. Algorithm validation used 500 bootstrapped samples, each containing a 5% random selection from the total cohort. The primary outcome was mortality within 6 months following an interRAI HC assessment. We used proportional hazards regression with robust standard errors to account for clustering by the individual. Kaplan–Meier survival curves were estimated to derive the observed risk of death at 6 months for assessment of calibration and median survival. Finally, 61 risk groups were constructed based on incremental increases in the observed median survival.\n\nResults The study cohort included 247,377 adults and 35,497 deaths (14.3%). The mean predicted 6-month mortality risk was 18.0% and ranged from 1.5% (95% CI 1.0%–1.542%) in the lowest to 96.0 % (95% CI 95.8%–96.2%) in the highest risk group. Estimated median survival spanned from 36 days in the highest risk group to over 3.5 years in the lowest risk group. The algorithm had a c-statistic of 0.76 (95% CI 0.75-0.77) in our validation cohort.\n\nConclusions RESPECT demonstrates good discrimination and calibration. The algorithm, which leverages routinely-collected information, may be useful in home care settings for earlier identification of individuals who might be nearing the end of life.",
"keywords": [
"activities of daily living",
"geriatric assessment",
"mortality",
"prognosis",
"forecasting",
"Kaplan-meier estimate",
"proportional hazards models"
],
"content": "Introduction\n\nRisk prediction models are increasing being developed within the healthcare space1,2 for a variety of purposes including, for example, to predict an individual’s life expectancy, support the diagnosis of disease, or estimate the risk of experiencing adverse outcomes. This is largely due to the growth in the availability of routinely collected healthcare data as well as innovations in machine learning,3 which have led to increasingly complex models with potentially improved predictive accuracy.2 In clinical care settings, prediction models can be used to support clinical decision-making and ensure care is aligned with patients’ needs, preferences and goals.4 For policy makers, prediction models can also be used to forecast population-level needs and inform health system planning.5\n\nDespite the number of available prognostic indices, few have been widely adopted into clinical practice6 and only a minority have been evaluated for their impact on clinical outcomes, including patient benefit.2,7,8 A variety of barriers continue to hinder adoption and evaluation, including the lack of model validation studies as well as failure to revise and update previously developed models.9 Model validation is a process that seeks to assesses a model’s performance and generalizability.10 Validation is necessary prior to considering model implementation into clinical practice. Likewise, regular re-assessments of model performance are needed to account for changes in, for example, patients’ characteristics, outcome prevalence, and health policies. Despite this, once a model has been developed, revisions are rare as are subsequent validation exercises.11\n\nThe Risk Evaluation for Support: Predictions for Elder-life in their Communities Tool (RESPECT) is a risk communication tool powered by a prediction algorithm that estimates an older adults’ risk of death within 6 months.12 RESPECT is presently used in home and community settings in Ontario, Canada, to support earlier identification of palliative care needs among older community-dwelling individuals, goals of care conversations, and health system planning. It is also available as a web calculator on ProjectBigLife.ca. RESPECT was initially developed and validated using routinely collected Resident Assessment Instrument for Home Care (RAI-HC) data in Ontario between 2007 and 2013. However, with the introduction of a new comprehensive assessment instrument within home and community care across the province in 2018—the interRAI Home Care (interRAI HC) Assessment System—an updated algorithm is required to support continued use of RESPECT. The objective of this study was to re-estimate and validate RESPECT in contemporary interRAI HC data.\n\n\nMethods\n\nSince 2004, the care needs of home care clients expected to require at least 60 days of service (i.e. long-stay clients) have been determined using the RAI-HC, a standardized, multi-dimensional assessment instrument that contains information across a variety of elements including sociodemographic information, cognitive and functional capacities, chronic diseases and comorbidities, and signs of health instability, as well as recent use of health care.13–15 In April 2018, the RAI-HC was replaced by interRAI HC, an updated version of the assessment instrument that contains similar data elements.16 RESPECT was initially developed and validated using RAI-HC data between 2007 and 2013. To estimate the 6-month mortality risk in a contemporary cohort, we validated and assessed RESPECT in the interRAI HC data collected between April 1, 2018 and September 30, 2019.\n\nRecord-level interRAI HC data was linked to other provincial health administrative databases housed and analyzed at ICES. ICES is an independent, non-profit research institute whose legal status under Ontario’s health information privacy law allows it to collect and analyze health care and demographic data, without consent, for health system evaluation and improvement.\n\nThe model derivation cohort consisted of adults aged 50 years or older who were eligible for publicly funded home care in Ontario and received at least interRAI HC assessment between April 1, 2018 and September 30, 2019. Assessments with missing information on sex and dependence across activities of daily living (ADLs) were excluded. The exclusion criteria applied to create our study cohort are presented in Figure 1. The internal validation cohort comprised 500 bootstrapped samples, each containing a random selection, with replacement, of 5% of the total cohort.\n\nThe primary outcome was death within 6 months of an interRAI HC assessment. The Registered Persons Database, a registry of health card numbers that have been issued under the Ontario Health Insurance Plan to all eligible residents of Ontario, was used to ascertain death date.\n\nAll predictors in the original RESPECT model12 were included unless the variable was not available in the interRAI HC instrument. Predictors include measures of physical function (dependence in ADLs or instrumental ADLs [IADLs], and worsening ADLs); cognitive impairment (worsening decision-making capacity); sociodemographic factors (age, sex at birth); diseases (stroke, congestive heart failure [CHF], coronary heart disease [CHD], Alzheimer’s disease and other dementias, multiple sclerosis, Parkinson’s disease, cancer, chronic obstructive pulmonary disease [COPD]); healthcare use (number of hospital admissions or emergency department visits in the last 90-days); symptoms of reduced health (vomiting, edema, dyspnea, low fluid intake, weight loss, decrease in food or fluid consumption); prescription and receipt of life-sustaining therapies/treatments (chemotherapy, dialysis, oxygen therapy, ventilator or respirator); and clinician diagnosis of an end-stage disease. Missing data on a predictor was considered as not present with the exception of worsening ADLs and worsening decision-making capacity. Other cohort characteristics (i.e., the year that the interRAI HC assessment was performed and the reason for assessment) were also included to account for remaining heterogeneity and temporal trends. Predictors in the original RESPECT model that were not available in the interRAI HC data and, therefore, not included in the re-estimated model are as follows: education, hypertension, asthma, emphysema, renal failure, and any interactions with at least one of the aforementioned variables. In total, there were 27 predictors with 51 degrees of freedom in the final model. All predictors were specified as categorical variables except for age, which was modelled using a restricted cubic spline with five knots, placed at the 5th, 27.5th, 50th, 72.5th and 95th percentiles of the age distribution.\n\nWe estimated a Cox proportional hazards regression predicting death within 6 months of an interRAI HC assessment. All assessments performed between April 1, 2018 and September 30, 2019, were included and follow-up was censored by death or end of follow-up (i.e., 6 months after the assessment date). A robust sandwich variance estimator was used to account for within-subject correlations given the possibility of multiple assessment records for individual home care users within the study period.\n\nFor model validation, bootstrap sampling with replacement was performed. We generated 500 bootstrapped samples, each containing a random selection of 5% of the total cohort. Then, coefficients from the derivation model were applied to the validation cohort to estimate the 6-month predicted mortality risk. Predictive performance was assessed in the validation cohort using two predictive accuracy measures, discrimination and calibration. Discrimination was assessed using the c statistic. Calibration was assessed for the overall model as well as across all predictors by comparing predicted risk of death at 6 months and observed risks that were derived from Kaplan-Meier estimates of the survival function.\n\nTo create risk bins, we first examined the median survival across percentiles. To estimate the median survival of individuals who survived past 6 months, we extended the follow-up period for each assessment to the most recent data available at the time of this study (i.e., June 29, 2022). Then, bins were constructed based on recommendations of clinical experts who identified meaningful differences in life expectancies that would be helpful in decision-making. This resulted in the creation of 61 risk bins. As the bin number increases, the 6-month mortality risk decreases and median survival increases (Table 1). Between bins, the incremental increase in median survival varies. For example, the incremental increase in median survival for bins 1-5 (i.e., individuals with high mortality risks) is approximately 3 weeks, while increases in median survival for bins 56-61 (i.e. individuals with a lower mortality risk) is greater than 2 months. Sample sizes for each risk group, their predicted 6-month mortality risk and median survival are presented in Table 1. See Table 2 for derivation of RESPECT Risk Score and Bin.\n\n\n\n• CHF = Congestive Heart Failure\n\n• CHD = Coronary Heart Disease\n\n• MS = Multiple Sclerosis\n\n• ADL = Activities of Daily Living\n\n• IADL = Instrumental Activities of Daily Living\n\n• Chemo = Chemotherapy\n\n• ED = Emergency Department\n\n• Typ = Type\n\n• ASS = Assessment\n\n• Yr = Year\n\nThe data used in this project is authorized under section 45 of Ontario’s Personal Health Information Protection Act and does not require approval by a Research Ethics Board.\n\n\nResults\n\nThe derivation cohort comprised of 247,377 community-dwelling older adults who used home care during our study period (Table 3). They contributed to a total of 405,689 interRAI HC assessments, covering 822,051.47 person-years (PYs) of follow-up. The median number of interRAI HC assessments performed per adult was 1 (interquartile range [IQR] 1-2), with a maximum of 10 assessments. Within 6 months of assessment, 35,497 (14.35%) of home care users died and 42,515 (10.48%) of assessments were associated with a death within 6 months. The validation cohort consisted of 5% of the derivation cohort, resulting in 500 boostrapped samples with an average of 19,255.02 interRAI HC assessments and 41,105.61 PYs of follow-up per sample. The median number of assessments per adult in each sample was 1 (IQR 1-1) with a maximum of 3.91 visits per person. Within 6 months of an interRAI HC assessment, an average of 20,058 (10.69%) of home care users died and 2,128.77 (10.49%) of assessments were associated with a death within 6 months. No assessments were excluded due to missing data on predictors included in the model (see Figure 1 for cohort creation).\n\n* Maximum follow up was June 29, 2022.\n\nA summary of characteristics of home care clients included in this study is provided in Table 4. In the derivation cohort, the mean (SD) age was 80.5 (10.8) years at the time of assessment and the majority of patients were female (61.9%). Alzheimer disease or other dementias was the most prevalent of the included comorbidities (33.4%) followed by coronary heart disease (30.4%) and stroke (17.0%). Other comorbidities included in the model (coronary heart failure, multiple sclerosis, Parkinson’s, cancer and chronic obstructive pulmonary disease [COPD]) had a prevalence of less than 15%. The most common symptoms of health instability reported were dyspnea (43.0%) and edema (34.7%). Other symptoms had a prevalence of less than 11%. Only 1.7% and 1.6% of patients received chemotherapy or dialysis, respectively, while 5.1% received oxygen, ventilator or respirator. A small proportion (2.3%) of home care patients had a prognosis of having fewer than 6 months to live and most did not have an inpatient admission (68.8%) or emergency department visit (75.8%) over the past 90 days. A significant proportion of the home care users (77.9%) required extensive assistance (score of at least 4) in performing IADLs (i.e., preforming ordinary housework, meal preparation or using the phone). A smaller proportion (18.0%) required extensive assistance (score of at least 4) in performing ADLs (i.e., maintaining personal hygiene, using the toilet, locomotion and eating). However, nearly half (49.3%) had reported worsening capacity to perform ADLs and more than a quarter (27.7%) reported worsening decision-making capacity. The majority of interRAI HC assessments were first assessments (58.9%) and were in 2019 (53.8%). The derivation and validation cohorts are comparable across all baseline characteristic (Table 4).\n\n1 Averaged over 500 bootstrap samples.\n\n2 Ordered (implemented or not implemented).\n\nTable 5 presents the hazard ratios (HR) for the derivation cohort derived from the Cox proportional hazard regression. Total dependence in ADLs (self-performance score of 6) (HR 3.2, 95% confidence interval [CI] 3.0-3.5) and diagnosis of an end-stage disease (HR 2.8, 95% CI 2.7-3.0) were most predictive of 6-month mortality. These were followed by ADL self-performance score of 5 (HR 2.0, 95% CI 1.9-2.1), a reported history of needing oxygen therapy without COPD (HR 1.8, 95% CI 1.7-1.9), total dependence in IADLs (HR 1.8, 95% CI 1.6-2.0), chemotherapy without cancer (HR 1.6, 95% CI 1.2-2.1), chemotherapy with cancer (HR 1.6, 95% CI 1.5-1.7) and ADL self-performance score of 4 (HR 1.6, 95% CI 1.5-1.6). The remaining predictors had a HR less than 1.5. Of the signs and symptoms of health instability, weight loss was most predictive of 6-month mortality (HR 1.5, 95% CI 1.4-1.5) followed by a noticeable decrease in food or fluid consumption (HR 1.4, 95% CI 1.4-1.5). Edema was least predictive of 6-month mortality (HR 1.0, 95% CI 1.0-1.1). Worsening decision-making capacity and worsening ADL status had hazard ratios of 1.0 (95% CI 1.0-1.1) and 1.4 (95% CI 1.2-1.5), respectively.\n\nThe calibration plot displays the mean predicted 6-month mortality risk against the Kaplan-Meier survival estimates across all 61 risk bins in the validation cohort (Figure 2). The model is well-calibrated across most risk bins; the calibration-in-the-large was 1.19 percentage points, on average, and the calibration slope was 0.88 (95% CI: 0.86-0.91). The model over-predicts risk (by 5.2% to 15.5%) in the highest mortality risk bins (bins 1 to 6), where the median survival was less than 6 months. To a smaller extent, the model underpredicts risk (by a magnitude of 0.5% to 2.6%) among individuals with moderate mortality risk (i.e., a mortality risk between 10% to 30% or bins 12-26). Overall, model c-statistic was 0.76 (95% CI 0.75-0.77) at 6 months, suggesting good discriminative ability in the validation cohort. Calibration was also evaluated in several subgroups of predictors, including functional status (i.e., ADL and IADL scale scores), select diseases, and the receipt of select life-sustaining therapies/treatments (Figure 3). The model is well-calibrated across all subgroups, with less than a 1.6 percentage point deviation from the observed 6-month mortality risk.\n\nThe mean predicted 6-month probability of death in our full study cohort was 18.0% and ranged from 1.51% in the lowest risk bin (95% CI 1.0%–1.542%) to 95.95% in the highest bin (95% CI 95.75%–96.15%) (Table 1, Figure 2). Median Kaplan–Meier survival (Figure 4) varied from 36 days (12–130d at the 25th and 75th percentiles) in the highest risk group to over 3.5 years (>1,413d at the 11th percentile) in the lowest risk group.\n\n\nConclusions and Discussion\n\nRESPECT is a prediction model of 6-month mortality among older, community-dwelling home care recipients aged 50 years and above. The re-estimated model using interRAI HC data has good predictive performance, with an overall model c-statistic of 0.76. As was observed in our previous model,12 functional limitations remained most predictive of 6-month mortality. Lastly, nearly 15% of clients died within 6-months, which is significantly greater than the proportion of assessments that had an identified prognosis of less than 6 months to live (2.3%). This highlights the potential role of tools like RESPECT in supplementing the clinical gestalt question (e.g., “Would I be surprised if this patient died in the next 6 or 12 months?”) for identifying patients who can benefit from a palliative approach to care.\n\nRESPECT offers several benefits compared to other available prediction models. First, existing mortality prognostic indices have been largely focused on particular segments of the population5,17; for instance, a limited setting (e.g., hospitalized patients,18–22 veterans23 and long-term care residents24) or specific diseases and conditions (e.g., dementia,24 cardiovascular disease,25 or functional status26,27). RESPECT, however, can be used more broadly among community-dwelling frail older adults. Secondly, existing indices for community-dwelling adults often utilize longer prognostic timeframes (e.g., 2-years,26,27 4-years17 or 5-years5) whereas RESPECT predicts mortality within 6-months, which can support care planning and goals of care conversations for those nearing the end of life. Third, RESPECT was developed using routinely collected data that is readily available in many regions, as interRAI instruments are used internationally in more than 35 countries including New Zealand, Hong Kong and Singapore.28 In this regard, RESPECT has the potential to be widely adopted across multiple populations and regions. In settings where interRAI data is unavailable, there may be other routinely used frailty assessments that capture many of the predictors included in the RESPECT algorithm, such as limitations in ADLS and IADLs, comorbidities, symptoms, healthcare use and changes in health status. These include, for instance, the Comprehensive Assessment and Referral Evaluation (CARE),29 the Functional Autonomy Measurement System (SMAF),30 the OARS Multidimensional Functional Assessment Questionnaire (OMFAQ),31 and the Katz Index of ADLs32 among others. Such data sources offer potential opportunities for external validation of RESPECT as well as the development of similar prediction models for use in clinical settings. Lastly, the use of RESPECT is not limited by, or reliant on, initiation by healthcare professionals or other health providers. It can also be used independently by patients and families through the web-based tool available at ProjectBigLife.ca, as a mechanism for advocating for their care needs.\n\nRESPECT is presently being used in home and community care settings in Ontario (including retirement homes) to help clinicians recognize patients with reduced life expectancies to inform care planning or trigger a referral to palliative care. While the willingness to use prognostic indices among clinicians has been previously documented,33 a variety of implementation factors must be addressed to support its adoption.34 RESPECT has, therefore, been designed so it can be used with minimal training and can be integrated into existing work processes, easily, reliably and at a low cost by leveraging readily available and routinely collected information. From a system perspective, RESPECT can be used by healthcare providers and organizations to inform capacity planning. For example, results from this analysis are being used by home and community care providers to highlight existing service gaps and support the design of clinical care pathways within home and community care programs that matches appropriate services to individuals with varying levels of need.\n\nWhile the RESPECT algorithm demonstrates a good prognostic ability, the findings show current limitations of prognostication, particularly with regards to misclassification. REPSECT moderately overpredicts mortality among the highest risk bins. However, from a clinical application standpoint, these bins capture users with extremely poor prognosis who would likely benefit from the earlier provision of palliative care. The ability to prognosticate those near the end of life can be improved by including additional predictors, such as biomarker data, which will likely become an important area of future work to improve the predictive performance of algorithms like RESPECT.\n\n\nConclusion\n\nRESPECT is a prognostic tool that estimates 6-month mortality risk in community-dwelling home care recipients aged 50 and above in Ontario, Canada. The model relies on variables readily available in routinely collected data, including age, sex, comorbidities, symptoms of health instability, healthcare service and treatment use as well as functional measures to accurately predict a home care client’s risk of death within 6 months. RESPECT demonstrates good discrimination and calibration, and our findings here suggest it could be useful in home care settings for earlier identification of individuals who might be nearing the end of life.",
"appendix": "Data availability\n\nThe data set for this study is held securely in coded form at ICES. Although data sharing agreements prohibit ICES from making the data set publicly available, access may be granted to those who meet prespecified criteria for confidential access, available here. The full data set creation plan and underlying analytic code are available from the corresponding authors on request, with the understanding that the computer programs may rely on coding templates or macros that are unique to ICES and are therefore inaccessible or may require modification.\n\nOSF: TRIPOD Checklist for ‘Derivation and validation of a mortality risk prediction model in older adults needing home care: Updating the RESPECT (Risk Evaluation for Support: Predictions for Elder-Life in their Communities Tool) algorithm for use with data from the interRAI Home Care Assessment System’. https://osf.io/hzpcf/.\n\n\nReferences\n\nChen L: Overview of clinical prediction models. Ann. Transl. 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PubMed Abstract | Publisher Full Text\n\nWalter LC, Brand RJ, Counsell SR, et al.: Development and validation of a prognostic index for 1-year mortality in older adults after hospitalization. JAMA. 2001; 285(23): 2987–2994. Publisher Full Text\n\nInouye SK, Peduzzi PN, Robison JT, et al.: Importance of functional measures in predicting mortality among older hospitalized patients. JAMA. 1998; 279(15): 1187–1193. Publisher Full Text\n\nBihorac A, Ozrazgat-Baslanti T, Ebadi A, et al.: MySurgeryRisk: Development and Validation of a Machine-Learning Risk Algorithm for Major Complications and Death after Surgery. Ann. Surg. 2019; 269(4): 652–662. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDelahanty RJ, Kaufman D, Jones SS: Development and Evaluation of an Automated Machine Learning Algorithm for In-Hospital Mortality Risk Adjustment Among Critical Care Patients. Crit. Care Med. 2018; 46(6): e481–e488. Publisher Full Text\n\nWeissman GE, Hubbard RA, Ungar LH, et al.: Inclusion of Unstructured Clinical Text Improves Early Prediction of Death or Prolonged ICU Stay. Crit. Care Med. 2018; 46(7): 1125–1132. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFan VS, Au D, Heagerty P, et al.: Validation of case-mix measures derived from self-reports of diagnoses and health. J. Clin. Epidemiol. 2002; 55(4): 371–380. PubMed Abstract | Publisher Full Text\n\nMitchell SL, Kiely DK, Hamel MB, et al.: Estimating prognosis for nursing home residents with advanced dementia. JAMA. 2004; 291(22): 2734–2740. PubMed Abstract | Publisher Full Text\n\nCappola AR, Fried LP, Arnold AM, et al.: Thyroid Status, Cardiovascular Risk, and Mortality in Older Adults: The Cardiovascular Health Study. JAMA J. Am. Med. Assoc. 2006; 295(9): 1033–1041. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCarey EC, Walter LC, Lindquist K, et al.: Development and validation of a functional morbidity index to predict mortality in community-dwelling elders. J. Gen. Intern. Med. 2004; 19(10): 1027–1033. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaliba D, Elliott M, Rubenstein LZ, et al.: The Vulnerable Elders Survey: A Tool for Identifying Vulnerable Older People in the Community. J. Am. Geriatr. Soc. 2001; 49(12): 1691–1699. PubMed Abstract | Publisher Full Text\n\ninterRAI: Improving Health Care Across The Globe. interRAI; Accessed February 8, 2022. Reference Source\n\nCARE LTC Assessor’s Manual: June 29, 2018. Reference Source\n\nFunctional Autonomy Measuring System (SMAF): 2002. Reference Source\n\nLu S, Feng Q: OARS Multidimensional Functional Assessment Questionnaire (OMFAQ).Gu D, Dupre ME, editors. Encyclopedia of Gerontology and Population Aging. Springer International Publishing; 2020; 1–5. Publisher Full Text\n\nWallace M: Katz Index of Independence in Activities of Daily Living.2007. Reference Source\n\nParikh RB, Manz CR, Nelson MN, et al.: Clinician perspectives on machine learning prognostic algorithms in the routine care of patients with cancer: a qualitative study. Support Care Cancer. 2022; 30(5): 4363–4372. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBruun A, White N, Oostendorp L, et al.: An online randomised controlled trial of prognosticating imminent death in advanced cancer patients: Clinicians give greater weight to advice from a prognostic algorithm than from another clinician with a different profession. Cancer Med. 12: 7519–7528. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "297110",
"date": "15 Jul 2024",
"name": "Sophie Pilleron",
"expertise": [
"Reviewer Expertise epidemiology",
"cancer"
],
"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 aimed to re-estimate and validate the RESPECT score, which predicts the 6-month mortality risk in adults aged 50 years or older who are eligible for publicly funded home care in Ontario and who received at least one assessment between April 1, 2018, and September 30, 2019. The paper is well-written and follows the TRIPOD recommended structure, making the assessment easier. Overall, the method is robust. This review follows the TRIPOD checklist for prediction model validation. Title: The title mentions the study's objective (i.e., validate), the target population (i.e., older adults needing home care), and the outcome to be predicted (i.e., mortality risk). It could be more specific by mentioning that the study is conducted in Canada and the outcome is 6-month mortality risk. Abstract: The abstract provides a fair summary of the study. However, \"interRAI home\" should be explained for those unfamiliar with this system. The first sentence of the results section could be rephrased, as the cohort does not include deaths. Introduction: The first two paragraphs of the introduction discuss prediction/prognostic models in general and are not specific to the study. Only the third paragraph is specific to the study. It is recommended to keep this third paragraph, which provides the necessary context for this specific study. There is a typo in the first sentence: “increasingly” should replace “increasing”. Objective: The objective is specific and clearly states the study is about re-estimating and validating an existing score. Method:\nAuthors should clarify the reasons for excluding “assessments with missing information on sex and dependence across activities of daily living,” as it is not recommended to exclude records due to missing data. They also need to justify the exclusion of people who responded \"Other\" for sex and those with no follow-up time or who died on the day of assessment (understanding they were not dead at the time of assessment). Authors should expand IKN and OHIP in the flowchart. Predictors: Authors should detail the coding for each predictor, as some coding is unclear, such as the number of hospital admissions or emergency department visits in the last 90 days. They wrote, “Missing data on a predictor was considered as not present with the exception of worsening ADLs and worsening decision-making capacity.” They should explain the reason for considering missing data as not present and clarify how they handled missing data on worsening ADLs and worsening decision-making capacity. Statistical analysis: Did the authors test for non-proportional hazards? Could the authors explain why they assessed calibration for all predictors? How was calibration assessed?\nResults:\nAuthors wrote that “No assessments were excluded due to missing data on predictors included in the model,” while they explained they excluded some records with missing data in the method. Could they clarify either the method or this sentence? Could the authors explain how prognosis was assessed in “A small proportion (2.3%) of home care patients had a prognosis of having fewer than 6 months to live”? Could the authors clarify whether Table 5 presents a univariable or multivariable Cox model? TRIPOD recommends showing univariate associations. Model specification: TRIPOD guidelines recommend presenting the “full prediction model to allow predictions for individuals (i.e., all regression coefficients and model intercept or baseline survival at a given time point).” This is presented in Table 2. The current paragraph under model specification describes predictors. Because individual predictors included in a model cannot be interpreted, it is recommended that the authors consider rewriting this paragraph.\nDiscussion: - The statement “As was observed in our previous model, functional limitations remained most predictive of 6-month mortality” is not supported by the results, as individual predictors cannot be interpreted. - The sentence “Lastly, nearly 15% of clients died within 6 months, which is significantly greater than the proportion of assessments that had an identified prognosis of less than 6 months to live (2.3%)” is not a result of this study and has not been presented. - The statement “RESPECT, however, can be used more broadly among community-dwelling frail older adults” is unclear. Why only frail adults? How do the results support that statement? - The authors wrote that “RESPECT predicts mortality within 6 months, which can support care planning and goals of care conversations for those nearing the end of life.” It is recommended to rephrase this sentence because goals of care should be discussed much earlier, not only near the end of life.\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": []
}
] | 1
|
https://f1000research.com/articles/13-221
|
https://f1000research.com/articles/12-1008/v1
|
21 Aug 23
|
{
"type": "Case Report",
"title": "Case Report: Basaloid squamous cell carcinoma",
"authors": [
"Samiha Jameel Ahmed Khan",
"Madhuri Gawande",
"Alka Hande",
"Swati Patil",
"Archana Sonone",
"Aayushi Pakhale",
"Madhuri Gawande",
"Alka Hande",
"Swati Patil",
"Archana Sonone",
"Aayushi Pakhale"
],
"abstract": "The upper aerodigestive tract is where basaloid squamous cell carcinoma (BSCC), a rare variation of conventional SCC, is most frequently found. The hypopharynx, tonsil, supraglottic larynx, tongue (base), and head-neck regions are particularly susceptible to BSCC. Clinically, the presentation of BSCC is similar to that of conventional SCC, but it has a poorer prognosis than traditional SCC. BSCC is distinguished histopathologically by a dimorphic pattern, a distinctive basal cell component paired with a squamous component, and a squamous component. However, its similar features to conventional SCC make it difficult to diagnose. Therefore, histopathology and immunohistochemistry play a crucial role in diagnosing such tumors. Here we present the case of a 70-year-old male diagnosed with BSCC involving the tongue.",
"keywords": [
"Basaloid squamous cell carcinoma",
"dimorphic pattern",
"basaloid cells",
"comedo necrosis "
],
"content": "Introduction\n\nThe aggressive squamous cell carcinoma of oral cavity (OSCC) form known as basaloid squamous cell carcinoma (BSCC) is rare. Wain et al.1 were the first to report the existence of BSCC, which was later proved to be a high-grade variety of SCC that is most common in the head and neck.2 Males over the age of 50 are more likely to develop BSCC. It is regarded as a high-grade tumor with a higher risk of nodal metastasis (64%) and distant metastasis (44%), compared to typical SCC.3 The larynx and hypopharynx, which are parts of the upper-aerodigestive-tract, are often impacted. The tongue (base) is most frequently affected (61%), and BSCC is more common in the oral cavity to the rest of the body. The palate, the retromolar trigone, the gingival-mucosa, and the floor-of-the-mouth (30%) are other affected locations.4,5 In terms of histopathology, the presence of solid epithelial cells with malignant characteristics and a basaloid appearance distinguishes BSCC the most.6 The invading tumor exhibits a variation of development forms including cords and nests, trabeculae, cysts and glands.7 Based on histopathologic and immunohistochemical findings, BSCC is distinct from conventional SCC. In addition, BSCC exhibits a different clinical behavior and prognosis than traditional SCC.8 Compared to traditional SCC, the prognosis for BSCC is worse. Despite having different histological characteristics, BSCC is frequently misdiagnosed as neuroendocrine tumors, small cell carcinoma, adenosquamous carcinoma, and adenoid cystic carcinoma.9,10 Here, we describe a case of BSCC in a 70-year-old man that affected the right lateral border of the tongue.\n\n\nCase report\n\nA male patient aged 70 was referred to our Institute with a painful ulcer over the right lateral border of the tongue for two years. He also had pain that was dull type, continuous in nature, and non-radiating. He also complained of a burning sensation when eating spicy food. He was experiencing difficulty in mastication and deglutition, and the tongue movements were restricted. He experienced weight loss, loss of appetite, decreased salivation, and hoarseness of voice. The patient had a habit of kharra (smokeless tobacco) chewing two-three times a day for two years. He was also a chronic bidi smoker, from 20-25 years (two-three times per day). He claimed to have quit the habit ten years before.\n\nExtra-oral findings revealed bilateral submandibular LN (lymph nodes), which were tender and palpable, measuring approximately 3 × 4 cm along its maximum dimension [Figure 1].\n\nIntraoral examination revealed an ulceroproliferative lesion of approximately 2 × 3 cm on the lateral border of the tongue (right side) [Figure 2], which was extending supero-inferiorly from the dorsal surface to the ventral surface of the tongue, anteroposteriorly from 46 region to the RMT and involving soft palate. The lesion showed typical malignant features. The margins were everted and induration was present on palpation. A provisional diagnosis was made of malignancy of the tongue.\n\nFurther, a tongue MRI with contrast was performed, which showed a heterogeneously enhancing mass lesion on the tongue (right side) with areas of necrosis within, abutting the lingual septum medially and extending into the infratemporal fossa laterally measuring approximately 7.6 × 4.5 × 4.3 cm. There was evidence of multiple subcentimetric to centimetric heterogeneously enhancing lymph nodes in the submental, bilateral submandibular, and jugulodigastric region, the largest being 4.3 × 3.2 cm in size in the right submandibular region with necrotic areas within. Impression of the tongue MRI revealed the abovementioned characteristics, suggesting tongue carcinoma with lymphadenopathy [Figure 3].\n\nAn incisional biopsy was done at our institute. The details of the biopsy report are mentioned below.\n\nHaematoxylin and eosin-stained tissue section revealed an overlying dysplastic parakeratinising stratified squamous epithelium and underlying fibro cellular connective tissue (CT) stroma [Figure 4].\n\nAt low-power view [Figure 5], it was evident that the epithelial cells invaded the CT in the form of islands. Some of these islands consisted of basaloid and squamous cells. These islands showed cystic spaces with a central area of comedo-necrosis. There was presence of malignant epithelial cells arranged in an organoid pattern displaying lobules of neoplastic epithelial cells. Fibrous CT septa separated these cells. The tumor cells were compactly arranged and showed cellular pleomorphism. The CT were comprised of collagen fibers and a few fibroblasts. Numerous endothelial cells-lined blood vessels with intravasated and extravasated red blood cells (RBCs) were seen. Moderate to chronic inflammatory cell infiltrates were also seen.\n\nUnder the high-power view [Figures 6, 7], all findings of the low power view were confirmed. The periphery of neoplastic islands showed cuboidal to low-columnar basaloid cells with palisading nuclei. The nuclei were ovoid-shaped, showing nuclear hyperchromatism and scant cytoplasm. The neoplastic cells showed characteristics like cellular pleomorphism, nuclear pleomorphism and hyperchromatism; there was increase in the nuclear-cytoplasmic ratio, and abnormal mitosis was also evident. There was presence of chronic inflammatory cell infiltrate chiefly comprising of lymphocytes.\n\n\nDiscussion\n\nBSCC, a distinct variation of conventional SCC, more commonly affects males in the age group of 60 to 70.11 Wain et al.1 originally identified BSCC as an uncommon, histologically different, and extremely aggressive subtype of SCC in 1986. These four main histologic characteristics were used to make the diagnosis of BSCC: (a) cells present in solid groups in a lobular arrangement, close to the surface mucosa; (b) small, densely packed cells with scant cytoplasm; (c) dark/hyperchromatic nuclei without nucleoli; and (d) small, cystic spaces consisting of mucin-like material.12\n\nSimilar to our situation, BSCC is said to be more common in older age groups.13 However, compared to conventional SCC, several investigations have indicated an equal frequency in both sexes.14 In terms of etiology and pathology, basaloid SCC is comparable to conventional SCC. The majority of BSCC patients are seen to have a long history of alcohol and tobacco consumption.\n\nSimilar to conventional SCC, BSCC has a painless irregular mass that is hard, verrucous or smooth,15 and may or may not be ulcerative.13,15–17 Because of this, it is quite challenging to distinguish it from traditional SCC. Therefore, the histopathologic and immunohistochemical characteristics play a major role in the diagnosis.8 It can be difficult for a pathologist to diagnose BSCC using an incisional biopsy since BSCC shares many histological characteristics with other neoplasms that have a similar microscopic appearance.\n\nBasal-cell-carcinoma, adenoid-cystic carcinoma (solid variety), adeno-squamous carcinoma, basal-cell adenocarcinoma, salivary-duct carcinoma, and neuro-endocrine carcinoma are all included in the differential diagnosis for BSCC. When compared to the others, adenoid cystic carcinoma (ACC) most closely resembles BSCC. According to Klijanienko et al., it can be challenging or impossible to distinguish between BSCC and ACC, particularly in incisional biopsies. Clinically, BSCC is thought to be more destructive than traditional SCC.10 In comparison with traditional SCC, BSCC has a worse prognosis and survival rate. Less than half as many BSCC patients survive compared to those with traditional SCC.18\n\nPositive staining of cyto-keratin 13 (CK-13) in the well-differentiated-squamous cells distinguishes SCC from BSCC, however the majority of basaloid cells in BSCC does not exhibit immunoreactivity.8 In a study by Ricardo et al.,16 it was discovered that BSCC has higher levels of the PCNA (proliferating-cell nuclear-antigen), AgNOR (argyrophilic-nucleolar-organizing region), and p53 protein than SCC did. Additionally, matrix megalloproteins (MMP-1, 2 and 9) expression levels were observed to be higher in BSCC than in SCC, stating that BSCC exhibits a more destructive/aggressive behavior than SCC.6\n\nWhile distant metastasis is around six times higher in BSCC than in traditional SCC, local recurrences are less common.5 In contrast to just 13% of conventional SCC, Winzenburg et al. reported 52% distant metastasis of BSCC.18\n\nThere isn’t a definite treatment consensus. The majority of the literature has recommended radiotherapy combined with surgery to remove the tumour and lymph nodes as the initial course of treatment.19 Concurrent chemoradiotherapy (CCRT) was used as the main form of treatment in our situation.\n\nAlthough there is still a lot of disagreement on how to compare the clinical trajectory and prognosis of BSCC and traditional SCC. It has been established that BSCC is a worse version of traditional SCC. Compared to SCC, it has a worse prognosis and a higher recurrence rate. In order to better understand and distinguish unusual lesions like BSCC from conventional SCC and improve therapy and prognosis, it is necessary to report them.\n\n\nConsent\n\nPrior written informed consent was obtained from the patient and other individuals involved 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\nZenodo: Figure 4, https://doi.org/10.5281/zenodo.7944356. 20\n\nZenodo: Figure 5, https://doi.org/10.5281/zenodo.7944418. 21\n\nZenodo: Figure 6, https://doi.org/10.5281/zenodo.7944429. 22\n\nZenodo: Figure 7, https://doi.org/10.5281/zenodo.7944441. 23\n\nZenodo: CARE checklist for Case Report: Basaloid Squamous Cell Carcinoma, https://doi.org/10.5281/zenodo.7902239. 24\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nI am thankful to all the participants for their contribution and support in this study.\n\n\nReferences\n\nWain SL, Kier R, Vollmer RT, et al.: Basaloid-squamous carcinoma of the tongue, hypopharynx, and larynx: report of 10 cases. Hum. Pathol. 1986; 17: 1158–1166. PubMed Abstract | Publisher Full Text\n\nBarnes L, Ferlito A, Altavilla G, et al.: Basaloid squamous cell carcinoma of the head and neck: clinicopathological features and differential diagnosis. Ann. Otol. Rhinol. Laryngol. 1996; 105: 75–82. PubMed Abstract | Publisher Full Text\n\nGupta B, Bhattacharyya A, Singh A, et al.: Basaloid squamous cell carcinoma - A rare and aggressive variant of squamous cell carcinoma: A case report and review of literature. Natl. J. Maxillofac. Surg. 2018; 9: 64–68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPaulino AF, Singh B, Shah JP, et al.: Basaloid squamous cell carcinoma of the head and neck. Laryngoscope. 2000; 110: 1479–1482. Publisher Full Text\n\nSoriano E, Faure C, Lantuejoul S: Course and prognosis of basaloid squamous cell carcinoma of the head and neck: A case-control study of 62 patients. Eur. J. Cancer. 2008; 44: 244–250. PubMed Abstract | Publisher Full Text\n\nSah K, Kale A, Hallikerimath S: Basaloid squamous cell carcinoma involving floor of the mouth. J. Oral Maxillofac. Pathol. 2008; 12: 61–63. Publisher Full Text\n\nSatish BN, Prashant K: Basaloid squamous cell carcinoma-a case report. Int. J. Dent. Clin. 2010; 18: 291–294. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYu GY, Gao Y, Peng X, et al.: A clinicopathologic study on basaloid squamous cell carcinoma in the oral and maxillofacial region. Int. J. Oral Maxillofac. Surg. 2008; 37: 1003–1008. PubMed Abstract | Publisher Full Text\n\nMorice WG, Ferreiro JA: Distinction of basaloid squamous cell carcinoma from adenoid cystic and small-cell undifferentiated carcinoma by immunohistochemistry. Hum. Pathol. 1998; 29: 609–612. PubMed Abstract | Publisher Full Text\n\nTsubochi H, Suzuki T, Suzuki S: Immunohistochemical study of basaloid squamous cell carcinoma, adenoid cystic carcinoma and mucoepidermoid carcinoma in the upper aerodigestive tract. Anticancer Res. 2000; 20: 1205–1211. PubMed Abstract\n\nVasudev P, Boutross-Tadross O, Radhi J: Basaloid squamous cell carcinoma: two case reports. Cases J. 2009; 2: 9351. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShinno Y, Nagatsuka H, Siar CH: Basaloid squamous cell carcinoma of the tongue in a Japanese male patient: A case report. Oral Oncol. 2005; 41: 65–69. Publisher Full Text\n\nEreño C, Gaafar A, Garmendia M: Basaloid squamous cell carcinoma of the head and neck: A clinicopathological and follow-up study of 40 cases and review of the literature. Head Neck Pathol. 2008; 2: 83–91. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIde F, Shimoyama T, Horie N, et al.: Basaloid squamous cell carcinoma of the oral mucosa: A new case and review of 45 cases in the literature. Oral Oncol. 2002; 38: 120–124. Publisher Full Text\n\nHeera R, Ayswarya T, Padmakumar SK, et al.: Basaloid squamous cell carcinoma of oral cavity: Report of two cases. J. Oral Maxillofac. Pathol. 2016; 20: 545. PubMed Abstract | Publisher Full Text | Free Full Text\n\nColetta RD, Cotrim P, Vargas PA: Basaloid squamous carcinoma of the oral cavity: Report of 2 cases and study of AgNOR, PCNA, p53, and MMP expression. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2001; 91: 563–569. PubMed Abstract | Publisher Full Text\n\nRadhi J: Basaloid squamous cell carcinoma.Li X, editor. Squamous Cell Carcinoma. Coratia: Intech Publications; 2012.\n\nWinzenburg SM, Niehans GA, George E, et al.: Basaloid squamous carcinoma: A clinical comparison of two histologic types with poorly differentiated squamous cell carcinoma. Otolaryngol. Head Neck Surg. 1998; 119: 471–475. PubMed Abstract | Publisher Full Text\n\nMorales-Puebla JM, Toro-Rojas M, Segura-Saint-Gerons R, et al.: Squamous cell carcinoma: Report of five cases. Med. Oral Patol. Oral Cir. Bucal. 2010; 15: e451–e455. Publisher Full Text\n\nKhan SJA: Figure 4 (Version v1). Zenodo. 2023. Publisher Full Text\n\nKhan SJA: Figure 5 (Version v1). Zenodo. 2023. Publisher Full Text\n\nKhan SJA: Figure 6 (Version v1). Zenodo. 2023. Publisher Full Text\n\nKhan SJA: Figure 7 (Version v1). Zenodo. 2023. Publisher Full Text\n\nKhan SJA, Gawande M, Hande A, et al.: Basaloid Squamous Cell Carcinoma: A Case Report. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "207241",
"date": "12 Oct 2023",
"name": "Muhammad Kashif",
"expertise": [
"Reviewer Expertise HNSCC",
"Oral Pathology",
"Oral Immunology",
"Tumour 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\nThe title seems too much generic in its current form.\n\nThe author used three terms for OSCC \"conventional\", \"traditional\", \"typical\". Please be consistent with a single term and the suitable one is \"conventional\".\n\nWhat is \"RMT\"? Define abbreviations in its first use.\n\nHow have the authors declared tongue carcinoma just on MRI findings? Clarify it.\n\nIn figure 4, I am unable to identify any type dysplasia in overlying squamous epithelium. It is just a hyperplastic epithelium.\n\nDid authors performed immunohistochemistry? If no, then why did they discussed it in discussion section?\n\nDiscussion needs to rephrased on logical grounds with comparison of findings of this case with already published data. Currently, it seems merely an introduction section.\n\nAdd conclusion section.\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": [
{
"c_id": "10596",
"date": "29 Nov 2023",
"name": "Samiha Khan",
"role": "Author Response",
"response": "1. The title has been changed to Basaloid Squamous Cell Carcinoma of the Tongue: A Case Report 2. The term conventional SCC has been implied in place of typical and traditional SCC. 3. RMT: Retromolar trigone. Full form is mentioned in the revised manuscript. 4. The MRI reports showed a heterogenously enhancing mass lesion on the tongue with areas of necrosis within. Lymphadenopathy was also seen. Based on clinical and radiological correlation, the diagnosis was made of tongue carcinoma. 5. The epithelium is hyperplastic and changes have been made. 6. Immunohistochemistry (IHC) was not performed in our case. However, IHC plays a crucial role in differentiating BSCC from conventional SCC. Hence, we have mentioned IHC results and reports from different authors in the literature. 7. Few changes have been made in the discussion. New data is added according to case reports from different authors. 8. Conclusion is added."
}
]
},
{
"id": "219403",
"date": "22 May 2024",
"name": "Abikshyeet Panda",
"expertise": [
"Reviewer Expertise Salivary Biochemistry and Salivomics Cancer Biology Histopathology and Cytology Immunohistochemistry Genomics",
"RNAomics",
"and Proteomics Diagnostic Appliances"
],
"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\nTo The editorial Team Dear Sir /Mam Kindly accept my gratitude for considering my name as a reviewer.\nIn my opinion, the article is well scripted with pertinent details.\nYet in my opinion few revisions are required. I am outlining the areas which needs clear revisions, after which it can be accepted. 1. There is a clear distinctive extra oral swelling apparent on the right side. Yet a proper description for the same is not available in the case report. Please mention whether it is a jaw swelling or soft tissue swelling. For clarity a description of the extra oral swelling must be provided. 2. The colour pattern of Figure 7 is not matching with other histopathological images. A better image matching with other images need to be provided. 3. Under the heading – “Histopathological and immunohistochemical report” – there is no Immunohistochemical findings provided. IHC findings need to be provided with supporting images. As there is a segment in discussion justifying IHC, the Case report should contain IHC findings with supporting images. The authors are requested to Kindly address these issues\nThank You\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\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/12-1008
|
https://f1000research.com/articles/12-182/v1
|
16 Feb 23
|
{
"type": "Software Tool Article",
"title": "Application of computer vision techniques for 3D matching and retrieval of archaeological objects",
"authors": [
"Diego Jiménez-Badillo",
"Omar Mendoza-Montoya",
"Salvador Ruiz-Correa"
],
"abstract": "Background: As cultural institutions embark in projects oriented to digitise art and archaeological collections in three dimensions, the need for developing means to access the resulting 3D models has become imperative. Shape recognition techniques developed in the field of computer vision can help in this task.\nMethods: This paper describes the implementation of three shape descriptors, specifically shape distributions, reflective symmetry and spherical harmonics as part of the development of a search engine that retrieves 3D models from an archaeological database without the need of using keywords as query criteria.\nUse case: The usefulness of this system is obvious in the context of cultural heritage museums, where it is essential to provide automatic access to archaeological and art collections. The prototype described in this paper uses, as study case, 3D models of archaeological objects belonging to Museo del Templo Mayor, a Mexican institution that preserves one of the largest collections of Aztec cultural heritage.\nConclusions: This work is part of an ongoing project focused on creating generic methodologies and user-friendly computational tools for shape analysis for the benefit of scholars and students interested in describing, interpreting and disseminating new knowledge about the morphology of cultural objects.",
"keywords": [
"3D shape matching and retrieval",
"content-based shape engine",
"archaeological shape recognition"
],
"content": "Introduction\n\nAround the world, many professionals face the challenge of disseminating information of cultural heritage collections in such a way that objects can be known and studied, anywhere in the world, and preferably without the need of physical contact to guarantee their long-term preservation (Ekengren et al., 2021). To achieve that goal, cultural institutions have embarked on ambitious 3D digitisation projects and researchers have been looking for better means to improve access to the resulting 3D models (Clark et al., 2002; Ekengren et al., 2021).\n\nDigitisation indeed have been very successful thanks to the surprising evolution of photogrammetry and laser scanning, which makes possible to model the surface of objects with very little effort and in a relatively short period of time (Pieraccini et al., 2001). In fact, the continued adoption of these techniques has generated thousands, if not millions, of 3D digital models valuable for research and conservation. The geometric and morphological analysis of such models, for example, is now common in the cultural heritage field, as the bibliographic survey by Pintus et al. (2016) demonstrates.\n\nUnfortunately, the search for better means to access collections has not achieved the same level of success. Many times, digital models are produced and then stored in a repository without implementing appropriate means to retrieve the 3D information (Ekengren et al., 2021; Koller et al., 2009). Currently, the conventional way to locate models in a database consists of formulating a query by using keywords that describe the objects’ features; for example, the system is instructed to retrieve all 3D models corresponding to “tripod vessels” or “anthropomorphic figures”. However, this strategy works only if the categories used in the query are registered in the ontology and metadata built for that particular repository. For instance, if the term bowl does not exist in the database thesaurus, the search engine won’t find vessels that are similar but have been registered with another name. Another limiting factor is the language in which the objects are described, because the system might recognize “bowl”, but not terrine (French), cuenco or cajete (Spanish). Of course, these problems could be fixed using multilingual thesaurus and customized text-parsers, but such solution can hardly encompass all possible languages and semantic meanings of object’s descriptions. Additional problems may arise if the most relevant keywords to describe an object are unknown at the time of cataloguing the objects, or if important keywords to identify the objects are unknown to the users of the system.\n\nIn order to overcome these limitations and unlock the potential of 3D models for dissemination and research of cultural heritage objects, it would be better to have a system entirely focused on intrinsic visual characteristics of the objects, specifically a system that process queries analysing the shape of the objects without relying exclusively on keywords as search criteria. The development of such a system requires the computation of a numerical representations of shape for each object (i.e. its shape descriptor), and the implementation of algorithms that compare all the shape descriptors stored in a database (i.e. a matching operation) to facilitate the retrieval of 3D models (Funkhouser et al., 2003; Tangelder & Veltkamp, 2008).\n\nThis paper describes the first stage of an ongoing project oriented to such goal. It describes the implementation of a search-engine module, based on three types of shape descriptors and five dissimilarity measures that facilitate the matching and retrieval operations. The system, called ArcheoShape, will function as a kind of search engine that instead of using keywords will recognize objects automatically by comparing their computational (i.e. numerical) shape descriptions. The benefits of this system are most clear in the context of museums, where it is necessary to find and retrieve 3D models from large collections.\n\n\nBasic requirements\n\nA system of shape recognition must be able to discover shape similarities between partially isometric objects, that is, between objects that share shape characteristics even if they are not identical. For example, a researcher might need 3D models of all the anthropomorphic figurines in a museum. In this case, the query should not be affected by the fact that one object lacks a head, while another is missing a leg. Also, it must retrieve several complete models of the same class, regardless of whether they differ in certain details (Gal & Cohen-Or, 2006). The three objects shown in Figure 1 illustrate this situation; they belong to the same class of anthropomorphic figures, but their heads and arms show some morphological differences.\n\nThey are similar in their overall geometry, but differ in some details, such as the design of the head and the position of the arms. A recognition system must be able to find the 3D models of these objects, despite their partial differences in shape.\n\nThe second requirement is that the system be able to detect similarities without being affected by the variations of rotation, translation, reflection and scale of the 3D models. Ideally, different combinations of translation, rotation, and scale applied to equal objects during the digitisation process should not affect the system’s capacity to recognise their similarity.\n\nTo fulfil those requirements, it is necessary to apply a specialized set of methods of computer vision specifically designed to identify objects’ similarities efficiently, within the processing limits of today’s computers and that are sufficiently discriminatory to resolve the requirements of cultural heritage institutions.\n\n\nDevelopment of a search-engine module\n\nThe development of shape recognition systems has been the subject of research since the 1980s, especially in the fields of computer vision, geometric modelling, and machine learning (Besl & Jain, 1985; Bustos et al., 2004, 2005; Campbell & Flynn 2001; Jain & Mishra 2014; Lara López et al., 2017; Loncaric 1998; Tangelder & Veltkamp 2008; Theologou et al., 2014; Veltkamp & Hagedoorn, 1999). In the early 2000’s. Funkhouser et al. (2003) developed a system for retrieving 3D models applying the shape descriptor of spherical harmonics, implementing an interface that allowed queries by example and also sketch-based searches. Another early system was developed by Paquet and Rioux (2000) with shape descriptors based on tensors of inertia, distribution of normal vectors, distribution of cords and multiresolution analysis. Its interface allows entering a combination of parameters such as scale, shape or colour to search the database. Other innovations were due to Suzuki (2001) who included the processing of material data (colour and texture) as search criteria; although its descriptors require normalization of 3D models via PCA.\n\nIn the field of cultural heritage, Rowe et al. (2001) and Rowe and Razdan (2002) implemented a shape-based search engine for analysis and retrieval of native American ceramic vessels. Objects were modelled as parametric surfaces and the interface allows query by example and sketch-based query, and links to descriptive data. Another interesting system was designed by Schurmans et al. (2002) according to specific archaeological research objectives. For example, indicators of craft specialization can be gathered from the morphology of ceramic vessels. This involves matching shapes, as well as text, numeric, and vessel data calculated with the system tools.\n\nThose projects demonstrate that the effectiveness of a recognition system depends above all on implementing efficiently two basic procedures. The first one consists in calculating a “shape descriptor”, that is a numerical representation of the form of each 3D model. Such descriptor can represent the global geometry of the object or a sample of its local features. The computation of shape descriptors involves a combination of mathematical, statistical, and more recently Machine Learning methods to represent shape in a numerical array or feature vector (Tangelder & Veltkamp, 2008). Some examples of characteristics encoded by shape descriptors are the curvature or orientation of a certain quantity of patches drawn around points chosen in a random manner (Jiménez-Badillo et al., 2013), or alternately, signals calculated with spherical functions (Kazhdan & Funkhouser, 2002; Kazhdan et al. 2003), reflective symmetry (Kazhdan & Funkhouser 2002; Kazhdan et al., 2004a), spin-images (Johnson and Hebert, 1999), shape-contexts (Mori et al., 2001), histograms of spherical orientations (Roman-Rangel et al., 2016), and many others as described in bibliographic surveys by Bustos et al. (2004, 2005), Lara López et al. (2017), and Rostami et al. (2019).\n\nThe final objective is that the shape of the object is characterized in the best possible manner, as to constitute a “signature” (numerical representation) of the object readable by a computer. As mentioned above, the numerical descriptor must represent the shape regardless the object’s position, orientation and scale.\n\nThe second procedure consists in creating an index of the numerical representations of all the objects (i.e. their shape descriptors), to facilitate the matching operation. The comparison between 3D models is done by measuring their degree of similarity with a mathematical function, such as Euclidean distance, that indicates the degree of their resemblance, so that when a query is implemented the system can rank objects from the more to the less similar (Bustos et al., 2004; Tangelder & Veltkamp, 2008).\n\nThe search-engine module developed over the course of this project is based on the implementation of three different global descriptors, namely shape distributions (Osada et al., 2002), reflective symmetry (Kazhdan et al., 2002, 2004a, 2004b) and spherical harmonic functions (Kazhdan and Funkhouser, 2002; Kazhdan et al., 2003).\n\nAs for determining the degree of dissimilarity between objects, five measures have been implemented: Euclidean distance, City block (Manhattan) distance, Chebychev distance1, Minimum Coordinate distance, and Bhattacharyya distance. Each dissimilarity measure has been implemented in two norms: the probability density function (pdf), and the cumulative distribution function. Therefore, considering the quantity of descriptors and distance measures, the system offers in total thirty manners to calculate dissimilarity among pairs of 3D models (Table 1).\n\nThe following sections describe, in layman’s terms, the methods to compute the three shape descriptors selected for the implementation of the search-engine module.\n\nThe simplest shape descriptors included in the search-engine module are five probability distributions proposed by Osada et al. (2002). The names given to the descriptors depend on the type of calculation, “A” stands for angle and “D” for distance:\n\n• A3: The angle between three random points on the surface of the 3D model.\n\n• D1: The distance between the centroid of the model and one random point on its surface.\n\n• D2: The distance between two random points on the surface.\n\n• D3: The square root of the area of the triangle formed by three random points sampled on the surface.\n\n• D4: The cube root of the volume of the tetrahedron formed by four random points sampled on the surface.\n\nAs Osada et al. (2002) recommend, we compute those variables for a very large sample of points selected from the surface-mesh of each 3D model, specifically 1,048,576 points (i.e. 1024 × 1024 points). The measurements were then transformed into a frequency histogram (probability distribution), which could then be used as the global signature of the object’s shape. Once the shape histograms for all the objects had been computed, a normalization step was necessary to standardize the scales of all the histograms in order to avoid matching errors due to variations in the size of the objects. The objective is finding the scale that produces the minimal dissimilarity measure during the comparison of two object’s histograms. To achieve this, one of the methods proposed by Osada et al. (2002) involves the following steps: align both shape distributions (i.e. histograms) so that the mean sample in each distribution equals 1; then find the minimum value D(f (x), sg (sx)) for values of log s from -10, 10, in 100 equally spaced intervals (where f and g represent the shape distributions of two models). Finally, select the minimum value among the results and use it as the dissimilarity measure for the two normalised shape distributions. This guarantees that two objects of the same shape but different sizes are recognized as similar, and vice versa, two objects of the same size but different shape are recognised as different.\n\nThe resemblance between any pair of objects can be determined by applying a function that measures dissimilarity between distributions (i.e. histograms), for example Euclidean distance or any of the other measures mentioned in Table 1.\n\nFigure 2 shows histograms resulting from the descriptor A3 (angle between three random points), representing the shape of four archaeological objects. Notice the probability distributions of the two models on the left, reflecting the differences between the long, wavy form of the serpentiform sceptre and the flat, wide anthropomorphic figurine. For an elongated figure, the angles between vectors tend to concentrate around the mode, while for flat objects the histogram would have a flat distribution because there would not be a predominant value of angle between vectors. In contrast, the images on the right correspond to two vessels whose histograms are quite similar because their shapes are also alike. Through this kind of comparison, the recognition system manages to identify similarities or differences between archaeological objects.\n\nNotice the great difference between the histogram of the serpentiform scepter (first object on the left), which shows the mode close to zero, and the histogram of the flat anthropomorphic figure (second from left to right). On the other hand, the great similarity of the histograms corresponding to the Tlaloc vessels located on the right side can be appreciated. Comparing these histograms allows the recognition system to determine whether or not two objects belong to the same class.\n\nThe second representation of shape, more complex but at the same time more effective, is the reflective symmetry descriptor proposed by Kazhdan et al. (2002, 2004a, 2004b). As these authors point out, symmetry —or the lack of it — is one of the most distinctive characteristics of any object.\n\nGiven a 3D model, denoted by function g, the concept of reflective symmetry implies that there is a reflection function γ, such that g=γg. This means that the pointwise distance between the points of surface g and the points of surface γg is zero.\n\nKazhdan et al. (2002) propose quantifying reflective symmetry with respect to several cutting planes, oriented on perpendicular axes that pass through the centroid of the model. For any given plane P cutting the shape f, the method consists in finding the function g such that g=γ with f−g as small as possible. Mathematically this is expressed as:\n\nwhere SD stands for Symmetry Descriptor. The more symmetric the shape f with respect to plane P, the smaller the value of f−g. Large values of f−g indicate that the surface is less symmetric.\n\nThe calculation of reflective symmetry can be performed quicker and more efficiently by transforming the description of the surface mesh (3D model) into a discrete volumetric representation (i.e. voxel grid). The process starts by immersing the triangular surface mesh inside a regular 3D grid. When a triangle of the mesh intersects a voxel of the 3D grid, such voxel is assigned a value of 1. Such rasterization process allows determining where the points and triangles of the mesh are located on the 3D grid. Notice that there are voxels in the grid that do not intersect the 3D mesh and therefore lack any information. For calculating the reflective symmetry descriptor, it is convenient to add to these voxels information related to how far they are from the surface of the model, for which the distance transform is used. This transform consists of assigning each voxel the distance to the nearest voxel belonging to the model. Then, the distance is transformed to a measure of similarity with the Gaussian function. Additional voxelization methods available can be found in Aleksandrov et al. (2021) and Huang et al. (1998). The resulting discrete representation consists of a 3D set of voxels, which appears like the archaeological model shown in Figure 3.2\n\nOnce the voxel grid has been labeled in this way, the descriptor can be calculated. Broadly speaking, what it is done is to assume that when passing a cutting plane through the voxel grid there is perfect reflective symmetry between the two halves, so that one of the two halves can be replaced with the other if that property were fulfilled. Then, the reflective symmetry distance is calculated in the real model and compare it with the assumed model to measure any difference. If both representations are equal (zero distance), then there is perfect symmetry and a radius of 1 is assigned to the corresponding plane. If not, a value less than 1 is assigned according to how different these figures are.\n\nFinally, the measures of symmetry obtained from a number of cutting planes (i.e. axes of symmetry) are concatenated to generate a 3D graph, describing the model’s global symmetries. Values near 1 indicate perfect symmetry, while those near zero indicate that the two halves of a model are too asymmetrical. This graph is used to compare an object with any other for the matching and retrieval application. Visual representations of the descriptors obtained from three archaeological models are shown in Figure 4.\n\nAs with the histograms shown in Figure 2, reflexive symmetry descriptors offer another method for calculating dissimilarity between 3D models.\n\nA third way of describing shapes on a computer is to consider them as outcomes of mathematical functions. Each stroke of a drawing, for example, can be regarded as a mix of 2D functions. The numerical representation of the whole drawing would be the sum of many functions. In practice, the functions are unknown, but they can be calculated by applying standard mathematical procedures such as the Fourier Transform, which would find the specific mix of simple functions that represent the complete drawing.\n\nSomething similar happens with 3D objects, but in that case the function describing the shape is defined on the surface of the sphere. One way of describing the shape of a surface is calculating the so-called spherical harmonic functions (Figure 5). Intuitively, we can think of the spherical harmonic functions as “Lego” pieces that, together, help built the shape of complex 3D objects. This is possible, because mathematically speaking, spherical harmonics constitute a complete set of orthogonal functions and therefore form an orthonormal basis, upon which any function defined on the sphere (like the shape of a 3D model) can be expressed as the sum of these spherical harmonics.\n\nThe simplest function is the sphere and from there higher order functions are derived. To obtain the mathematical description of a 3D model it is necessary to decompose the general form into constituent elements. The more complex the shape of an object, the more harmonic functions will be needed to describe it. The results of the decomposition are used to compare the shape of 3D models. Image by Inigo.quilez - Own work, CC BY-SA 3.0, (available here).\n\nThe exact combination of spherical harmonic functions needed to describe a particular object can be found though a harmonic analysis. This method divides the complex surface of a 3D model into sums of relatively simple components.\n\nHarmonic analysis is the branch of mathematics that deals with the problem of representing functions as the combination of basic elements called waves or harmonics. Typically, the term harmonic refers to functions with sinusoidal variations, but more strictly, it indicates any solution of Laplace’s Equation. The Fourier series is an example of a complete set of harmonics, which consists of sine and cosine waves of different frequencies.\n\nIn this work, we adopted the Spherical Harmonic Transform (SHT) to obtain a reduced representation of a 3D mesh. This method is a powerful tool for describing data on a sphere using spherical harmonics as basic functions. Given a function fθφ in the spherical coordinates θ and φ, the decomposition of fθφ in spherical harmonics Ylmθφ is written as:\n\nHere, l≥0 and m are integers such that m≤l, clm is the coefficient of the harmonic Ylmθφ, and the general form of Ylmθφ is:\n\nwhere Plmx is a Legendre polynomial:\n\nThe problem in the Spherical Harmonic Transform is to calculate the coefficients clm.\n\nIn practice, it is not possible to calculate the coefficients of all the spherical harmonic functions. For this reason, we limit the order of the harmonics to a fixed value b (for instance 16 or 32) so that:\n\nFinally, the coefficients clm are estimated by finding the least-squares solution to equation 5. That is to say, for a set of n points θ1φ1θ2φ2…θnφn where fθφ is evaluated, we calculate the values of the coefficients clm that minimize:\n\nTo describe a 3D mesh using the Spherical Harmonic Transform, we define the function frθφ as the intersection between the voxelized version of the 3D mesh and the sphere of radix r, both centered at the origin. The function frθφ takes the value 1 only if the sphere intersects a voxel of the mesh at the point (θ,φ), otherwise, this function is 0. The Spherical Harmonic Transform is applied to different radii so that the functions frθφ are characterized by their corresponding harmonic coefficients.\n\nThe simplest harmonic function is the sphere, so if the object resembles a balloon, only one harmonic component of degree zero is enough for describing it. However, if the model has a more complex shape, then it is essential to calculate several higher order harmonic functions.\n\nThere are several methods to compute shape descriptors based on spherical harmonics. Some require a priori registration of the model along principal axes (Saupe and Vranic 2001; Vranic & Saupe, 2001; Vranic et al., 2001), but these are not good to process 3D models of the same class digitised with different orientations (Funkhouser et al., 2003). A method that solves that limitation is the one proposed by Kazhdan and Funkhouser (2002), and Kazhdan et al. (2003) and it is the one implemented during this project. In practice, the descriptor is computed as follows:\n\n1. The 3D model is subjected to a voxelization process, like the one applied in the case of reflective symmetry (c.f. Huang et al. 1998). The size of the voxel grid is 64 × 64 × 64.\n\n2. The 3D model is aligned with its voxel representation in such a way that is centre of mass coincides with the centre of the voxel grid.\n\n3. A voxel is assigned a value of 1 if it contains any point on the surface of the 3D model, and 0 otherwise.\n\n4. The voxel grid is decomposed into 32 spheres of radii 1 to 32, which produces 32 spherical functions.\n\n5. Each sphere is decomposed as a sum of its first 16 spherical harmonics.\n\n6. Finally, these different signatures are combined to obtain a 32 × 16 signature for the 3D model. The result is a 2D image that represents the decomposition coefficients for each harmonic function and each radii (Figure 6).\n\nTo compare two objects using their harmonic representations, it is simply necessary to compute the Euclidean distance between them: “Thus, finding the K closest models to a query is equivalent to solving the nearest-neighbour problem” (Kazhdan & Funkhouser, 2002). Figure 6 shows the spherical harmonics descriptor for three objects.\n\n\nUser interface\n\nSome early systems were tested with collections of 3D models produced with computer-aided design (parametric models) software and acquired on the internet. In contrast, we have developed a first module (mesh analyser) of a search engine called ArcheoShape that uses real archaeological objects. At this stage, the objective is to assess how good are the shape descriptors described in the previous sections to match and retrieve real archaeological objects, before deploying the entire system within a museum environment. The module developed over the course of this project is freely available in the following GitHub repository (Mendoza-Montoya, 2023b), which contains the source code, written in C++, ready to be compiled in Windows and Linux, as well as an executable file. Instructions to compile are included in the GitHub repository. A sample of ten 3D models of archaeological artefacts are also provided under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International. These resources will allow any user to test the mesh-analyzer module in a local computer.\n\nTo test the implementation of the shape descritors, we used a sample of nearly 500 archaeological artefacts from the Museo del Templo Mayor. The collection is available for research purposes through specific agreements with Instituto Nacional de Antropología e Historia.3\n\nThe Museo del Templo Mayor preserves objects discovered between 1978 and 1982 within the area occupied by the Sacred Precinct of Tenochtitlan, the most important religious centre of the Aztecs and nowadays a famous archaeological site adjacent to Zócalo square in Mexico City (Matos Moctezuma, 1988). The core collection includes more than 8000 objects from ritual offerings found in the main pyramid temple (i.e. Templo Mayor) of the site and its surroundings, and include ritual artefacts, flora, fauna, and human remains (López Luján, 1994; Nagao, 1985). The collection has increased considerably in recent years thanks to the excavations conducted in the same site by different research teams led by archaeologists Barrera Rivera and Islas Domínguez (2018), Barrera Rodríguez, and López Luján (2012, 2019). Indeed, between 2012 and 2019, 43 new offerings, containing 13,925 artefacts and 35,648 samples of organic material have been reported. Digitization of this collection is still at a very early stage, but we have been able to acquire a sample of 495 objects, including stone-masks, anthropomorphic and zoomorphic figures, clay vessels (bowls, pots, jars, braziers), religious paraphernalia like sceptres, earplugs, ritual pendants, as well as flint sacrificial knifes, flutes, and models of drums made of clay or stone. The implementation of the prototype was divided into two independent offline and online jobs. The main offline task consists in computing the shape distributions, reflective symmetry and spherical harmonics descriptors of all the archaeological 3D models available.\n\nThe actual matching and retrieval operations are done online through the following steps:\n\n• First step. Through an open-file window, the user enters a query model consisting of a point cloud or surface mesh (i.e. query model) as an example of the class of objects he wants to retrieve from the database. For example, an anthropomorphic figure like the one shown in Figure 7. This step avoids the input of keywords as search criteria.\n\n• Second step. The user selects the shape descriptor (shape histograms; reflective symmetry; or spherical harmonics) to apply it to the query model. There are no rules to select an algorithm, it is expected that the user tries different options to see which one works best for a specific set of archaeological objects.\n\n• Third step. The system compares the shape descriptor of the query object with the shape descriptors of all 3D models stored in the repository. The search engine calculates the distance between the shape descriptor of the query model and the descriptors of all the other models stored in the database.\n\n• Fourth step. The models that match the shape of the query model are ranked from the more to the least similar.\n\n• Fifth step. Finally, the system presents the results on the screen sorted from the most to the least similar. There is no limit on the number of results displayed by the system.\n\nAbove, on the left, the consultation model (i.e. anthropomorphic sculpture) is shown; below left illustrates obtaining the reflexive symmetry descriptor for that query model; on the right are the search results obtained when the user requests to compare the query model with the models stored in the repository. It can be seen that the system retrieves all objects similar to the query model.\n\nFigures 7, 8 and 9 illustrate the user interface during three query examples. The first window (top-left) shows the query model. The icons on the left side allow the user to select one of the three shape descriptors that have been implemented, while several options on the right allow the user to change the appearance of the model (e.g. visualise the query models as point cloud, triangular mesh or solid volume, or alter the colour). In the next window (bottom-left), the user can set the parameters necessary for calculating the shape descriptor of the query model, particularly the distance measure applicable for the matching operation. It is worth noticing that the system offers predefined parameters that work in all cases, but the user can set them to follow his/her own preferences. In choosing the predefined parameters, the main criteria were to ensure that the system had good shape recognition power in a short computation time. Once the user presses enter, the search engine proceeds to compare the query model with the descriptors of the models stored in the database and retrieve the results, which are shown in the window illustrated on the right-hand side of the figures.\n\nIn this case, all copies of anthropomorphic figures were requested from the system applying the descriptor of harmonic functions.\n\nIn this case stone masks were recovered. It should be noted that, despite the fact that the query model lacks a fragment, the system was able to produce the expected results, even recovering a mask fragment that clearly belongs to the class of the objects that the user expected.\n\n\nConclusions\n\nComputer tools for shape matching and retrieval designed specifically for archaeological research could improve access to collections in museum institutions. The development of ArqueoShape is a step forward in this direction.\n\nThe search-engine module developed over this project is generic, so we expect they would prove helpful in other contexts. The capacity of our system to perform matching and retrieval of real archaeological objects through the application of shape distributions, reflective symmetry, and spherical harmonics descriptors is significant. However, an extra module to provide full database capabilities to store, update and edit the 3D models are still under construction. Also, we expect to perform a benchmark analysis, whose results will be published shortly. Particularly important for further development is the implementation of additional shape descriptors that target local features, since these would help to refine the queries to specific details on the objects geometry.\n\nWe plan to embed the search-engine module described here into a web platform which will be organized around three main application channels:\n\nThe first channel would be a service platform for the automatic recognition, analysis, and classification of cultural heritage objects based on morphology. Any user can upload a collection of 3D models to have it analysed with the software tools developed throughout the project. For this operation, the user will not need any knowledge of Computer Vision or Machine Learning because all necessary software will be accessible through a very easy-to-use interface.\n\nThe second channel called research will be designed to encourage specialized collaboration between experts in Computer Vision, Machine Learning, and shape analysis interested in developing new algorithms, applications, and tools for morphological analysis of cultural heritage. Including our current deep learning applications for shape analysis and retrieval. This collaboration will facilitate access to papers, project proposals, discussion forums, and source code. New solutions to technical problems will be expected to evolve from this site. For example, one pervasive challenge when applying machine learning to archaeology is the lack of enough data to train automatic learning models. This channel could provide a forum for discussing new solutions, such as conditions for applying transfer-learning techniques to train models with external knowledge.\n\nThe third channel will be named People Interaction. Through this channel, scholars, students, and anyone interested in the project can establish collaboration for future projects and share data and resources from all over the world. The main objective is to create synergy to facilitate access to new 3D digital collections and to define new initiatives of morphological analysis with applications to archaeology and the Humanities.",
"appendix": "Data availability\n\nZenodo: omendoza83/ArcheoShape-Data: ArcheoShape 0.2. https://doi.org/10.5281/zenodo.7591490 (Mendoza-Montoya, 2023a).\n\nThis project contains the following underlying data:\n\n- Models. (10 triangular meshes of Aztec objects).\n\n- Resources. (6983 numerical shape descriptors, computed from 495 archaeological objects).\n\n- Icons. (Images for the user interface).\n\n- Screenshots. (Images of 495 archaeological objects, used to present results at the end of a search and matching operation).\n\nData are available under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC-BY-NC-ND 4.0).\n\n\nReferences\n\nAleksandrov M, Zlatanova S, Heslop DJ: Voxelisation algorithms and data structures: A review. Sensors. 2021; 21: 8241. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarrera Rivera A, Islas Domínguez A: Arqueología urbana en la reconstrucción arquitectónica del recinto sagrado de Tenochtitlan. 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Proceedings of the 2002 ACM Symposium on Applied Computing, SAC ’02. March 2002; pp. 483–487. Publisher Full Text\n\nEkengren F, Vallieri M, Dininno D, et al.: Dynamic collections: A 3D web infrastructure for artifact engagement. Open Archaeology. 2021; 7: 337–352. Publisher Full Text\n\nFunkhouser T, Min P, Kazhdan M, et al.: A search engine for 3D models. ACM Transactions on Graphics. 2003; 22(1): 83–105. Publisher Full Text\n\nGal R, Cohen-Or D: Salient geometric features for partial shape matching and similarity. ACM Transactions on Graphics. 2006; 25(1): 130–150. Publisher Full Text\n\nHuang J, Yagel R, Filippov V, et al.: An accurate method for voxelizing polygon meshes. VVS ’98 Proceedings of the 1998 IEEE symposium on Volume visualization. North Carolina: ACM; 1998; pp. 119–126.\n\nJain S, Mishra S: Survey paper on various 3D view based retrieval methods. International Journal of Engineering Research & Technology. 2014; 3(2): 470–473.\n\nJiménez-Badillo D, Ruiz-Correa S, García Alfaro W: Developing a recognition system for the retrieval of archaeological 3D models. Contreras F, Farjas M, Melero FJ, editors. CAA-2010. Fusion of Cultures. Proceedings of the 38th Annual Conference on Computer Applications and Quantitative Methods in Archaeology, Granada, Spain. Oxford: Archaeopress, BAR International Series 2494. 2013; pp. 325–332. Publisher Full Text\n\nJohnson AE, Hebert M: Using spin-images for efficient multiple model recognition in cluttered 3-D scenes. IEEE Transactions on Pattern Analysis and Machine Intelligence. 1999; 21(5): 433–449. Publisher Full Text\n\nKazhdan M, Funkhouser T: Harmonic 3D shape matching. SIGGRAPH ’02: ACM SIGGRAPH 2002 Conference Abstracts and Applications. 2002; p. 191. Publisher Full Text\n\nKazhdan M, Chazelle B, Dobkin D, et al.: A reflective symmetry descriptor. Proceedings of the 7th European Conference on Computer Vision, ECCV02, Copenhagen, May, 2002. Lecture Notes on Computer Sciences, 2352 (Part II). 2002; pp. 642–656.\n\nKazhdan M, Funkhouser T, Rusinkiewicz S: Rotation invariant spherical harmonic representation of 3D shape descriptors.Kobbelt L, Schröder P, Hoppe H, editors. Proceedings of the 2003 Eurographics/ACM SIGGRAPH Symposium on Geometry Processing (SGP ’03). 2003; pp. 156–164. Publisher Full Text\n\nKazhdan M, Chazelle B, Dobkin D, et al.: A Reflective Symmetry Descriptor for 3D Models. Algorithmica. 2004a; 38: 201–225. Publisher Full Text\n\nKazhdan M, Funkhouser T, Rusinkiewicz S: Symmetry descriptors and 3D shape matching. Proceedings of the 2004 Eurographics/ACM SIGGRAPH Symposium on Geometry Processing (SGP ’04). 2004b; pp. 115–123. Publisher Full Text\n\nKoller D, Frischer B, Humphreys G: Research challenges for digital archives of 3D cultural heritage models. Journal on Computing and Cultural Heritage. 2009; 2(3): pp. 1–17. article 7. Publisher Full Text\n\nLara López G, Peña Pérez Negrón A, de Antonio Jiménez A, et al.: Comparative analysis of shape descriptors for 3D objects. Multimedia Tools and Applications. 2017; 76(5): 6993–7040. Publisher Full Text\n\nLoncaric S: A survey of shape analysis techniques. Pattern Recognition. 1998; 31(8): 983–1001. Publisher Full Text\n\nLópez Luján L: The offerings of the Templo Mayor of Tenochtitlan. Colorado: University Press of Colorado; 1994.\n\nLópez Luján L: Proyecto Templo Mayor: Séptima temporada (2007-2012).García NMR, editor. Memoria 2007-2012 de la Coordinación Nacional de Arqueología. México: INAH; 2012; pp. 1939–1942. Reference Source\n\nLópez Luján L: Proyecto Templo Mayor: Séptima y octava temporadas. Nava PFS, editor. La arqueología oficial mexicana a principios del siglo XXI: Estudios de caso. México: INAH; 2019; pp. 341–345. Reference Source\n\nMatos Moctezuma E: The Great Temple of the Aztecs: Treasures of Tenochtitlan. London: Thames and Hudson; 1988.\n\nMontoya OM: omendoza83/ArcheoShape-Data: ArcheoShape 0.2 (v0.2.1-alpha). [Data]. Zenodo. 2023a. Publisher Full Text\n\nMontoya OM: omendoza83/ArcheoShape: ArcheoShape 0.3 (v0.3.0-alpha). Zenodo. [Code]. 2023b. Publisher Full Text\n\nMori G, Belongie S, Malik H: Shape contexts enable efficient retrieval of similar shapes. Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001. 2001; pp. 723–730.\n\nNagao D: Mexica buried offerings: A historical and contextual analysis. Oxford: Archaeopress, BAR International Series; 1985; 235.\n\nOsada R, Funkhouser T, Chazelle B, et al.: Shape distributions. ACM Transactions on Graphics. 2002; 21: 807–832. Publisher Full Text\n\nPaquet E, Rioux: Nefertiti: A tool for 3-D shape databases management. SAE Transactions: Journal of Aerospace. 2000; 108(1): 387–393.\n\nPieraccini M, Guidi G, Atzeni C: 3D digitizing of cultural heritage. Journal of Cultural Heritage. 2001; 2: 63–70. Publisher Full Text\n\nPintus R, Pal K, Yang Y, et al.: A survey of geometric analysis in cultural heritage. Computer Graphics Forum. 2016; 35(1): 4–31. Publisher Full Text\n\nRoman-Rangel EF, Jimenez-Badillo D, Marchand-Maillet S: Classification and retrieval of archaeological potsherds using histograms of spherical orientations. ACM Journal on Computing and Cultural Heritage. 2016; 9(3): 1–23. Publisher Full Text\n\nRostami R, Bashiri FS, Rostami B, et al.: A survey on data-driven 3D shape descriptors. Computer Graphics Forum. 2019; 38(1): 356–393. Publisher Full Text\n\nRowe J, Razdan A, Collins D, et al.: A 3D digital library system: Capture, analysis, query, and display. Proceedings of the Fourth International Conference on Digital Libraries (ICADL). 2001.\n\nRowe J, Razdan A: Digital library system. Proceedings of the Second ACM/IEEE-CS Joint Conference on Digital Libraries – JCDL’02. 2002. Publisher Full Text\n\nSaupe D, Vranic DV: 3D model retrieval with spherical harmonics and moments.Radig B, Florczyk S, editors. Proceedings of the DAGM 2001. 2001; pp. 392–397.\n\nSchurmans U, Razdan A, Simon A, et al.: Advances in geometric modeling and feature extraction on pots, rocks and bones for representation and query via the Internet.Burenhult G, Arvidsson J, editors. Archaeological Informatics: Pushing the Envelope. CAA2001. Computer Applications and Quantitative Methods in Archaeology. Proceedings of the 29th Conference, Gotland, April 2001, Oxford: Archaeopress, BAR International Series 1016. 2002; pp. 191–202.\n\nSuzuki MT: A Web-based retrieval system for 3D polygonal models. Proceedings of the Joint 9th IFSA World Congress and 20th NAFIPS International Conference (Cat. No. 01TH8569). 2001; pp. 2271–2276. Publisher Full Text\n\nTangelder JWH, Veltkamp RC: A survey of content based 3D shape retrieval methods. Multimedia Tools and Applications. 2008; 39: 441–471. Publisher Full Text\n\nTheologou P, Pratikakis I, Theoharis T: A review on 3D object retrieval methodologies using a part-based representation. Computer-Aided Design and Applications. 2014; 11(6): 670–684. Publisher Full Text\n\nVeltkamp RC, Hagedoorn M: State-of-the-art in shape matching. Technical Report. UU-CS-1999-27, Utrecht University, the Netherlands.1999. [12 December 2022]. Reference Source\n\nVranic DV, Saupe D: 3D shape descriptor based on 3D Fourier Transform.Fazekas K, editor. Proceedings of the EURASIP Conference on Digital Signal Processing for Multimedia Communications and Services (ECMCS 2001). 2001; pp. 271–274. [12 December 2022]. Reference Source\n\nVranic DV, Saupe D, Richter J: Tools for 3D-object retrieval: Karhunen-Loeve transform and spherical harmonics.Dugelay J-L, Rose K, editors. Proceedings of the IEEE 2001 Workshop Multimedia Signal Processing. 2001; pp. 293–298.\n\n\nFootnotes\n\n1 Also known as the L∞ metric, Chevychev distance determines which distance between two vectors is the greatest of their differences along any coordinate dimension.\n\n2 The voxel grid preserves the topological characteristics of the original 3D model. These include connectivity, separation, coverage, and tunnelling. Connectivity registers the way voxels must be linked to each in order to preserve the specific shape of the object. Separation registers empty spaces and how these interact in the voxelised object. Coverage, register how “thin” or thick” the voxelised object is. Tunnelling registers the penetration of two voxelised elements of the object, that is how two or more parts of the object overlap and/or penetrate into each other (Aleksandrov et al., 2021).\n\n3 The authors can provide details of the legal and administrative procedures involved in sharing the collection."
}
|
[
{
"id": "163745",
"date": "24 Feb 2023",
"name": "Edgar Roman-Rangel",
"expertise": [
"Reviewer Expertise Machine learning",
"Computer vision",
"Representation learning",
"Computational archaeology."
],
"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 software tool that implements a retrieval engine for 3D models of archaeological nature. The retrieval machine combines several shape descriptors and distance functions to obtain different ways of indexing the 3D models.\nThe need for this tool is well motivated, and the results shown in the document seem both correct and relevant. Moreover, without a doubt the tool is an interesting application and will constitute an asset for improving the work of archaeologists.\nHowever, there is one details that need to be addressed. Concretely, the document focusses more on the mathematical details of the 3D shape descriptors, rather than focussing on the implementation details of the tool itself. Improving this aspect of the presentation will help fit the paper into the scope of the journal.\nAdditionally, there a few minor observations:\nThe fourth paragraph of the introduction states \"...analysing the shape of the objects without relying exclusively on keywords...\". The term for that concept is Content-based Information Retrieval (CBIR).\n\n\"... without being affected by the variations of ...\". The term \"affine variations\" will be more specific.\n\nThe section named \"Development of a search-engine module\" reads more like related work, and not like the description of the search engine.\n\nThe third paragraph of page 5, says that there are thirty combinations of descriptors-distances, and makes reference to Table 1. However, Table 1 only shows the different distances.\n\nThe functions D(f (x), sg (sx)), in page 6 are not defined.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\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? No\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": "11263",
"date": "04 Apr 2024",
"name": "Diego Jiménez-Badillo",
"role": "Author Response",
"response": "Reviewer comment: \"The fourth paragraph of the introduction states \"...analysing the shape of the objects without relying exclusively on keywords...\". The term for that concept is Content-based Information Retrieval (CBIR).\" Response: We added the term Content-based Information Retrieval (CBIR) in the corresponding paragraph of the Introduction. Reviewer comment: The section named \"Development of a search-engine module\" reads more like related work, and not like the description of the search engine. Response: We added more details of the MeshAnalizer module, including a new figure illustrating its architecture. Reviewer comment: \"The third paragraph of page 5, says that there are thirty combinations of descriptors-distances, and makes reference to Table 1. However, Table 1 only shows the different distances.\" Response: We moved the Table 1 reference immediately after the mention of the four distance measures implemented. This would avoid confusion on the kind of information that reader may expect in Table 1. Reviewer comment: \"The functions D(f (x), sg (sx)), in page 6 are not defined.\" Response: We defined the functions. Also, the reviewer considers that the paper only describes the software tool partly and that there are no enough details of the code, method and analysis. Response: Regarding the methods and analysis, we consider that these are sufficiently covered in the explanation of the three descriptors implemented, where the principles, methods and analysis of each algorithm are explained. As for the tool itself, we included more details of MeshAnlizer architecture, as well as a lengthy explanation of how it functions. We believe that this improves the section “Development of a Search Engine Module”."
}
]
},
{
"id": "200597",
"date": "22 Sep 2023",
"name": "Federica Maietti",
"expertise": [
"Reviewer Expertise Digital Heritage",
"3D Survey",
"Digital Representation",
"3D Modeling",
"Diagnostic procedures",
"Heritage 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\nThe article is focused on 3D digitization of heritage artefacts and archaeological collections, and on the increasing need for developing means to access the resulting 3D models. In particular, the paper explores shape recognition techniques, deepening three shape descriptors (distributions, reflective symmetry and spherical harmonics) as part of the development of a search engine that retrieves 3D models from an archaeological database. Aztec archaeological objects belonging to the Templo Mayor Museum, in Mexico City, are the use case proposed to support the tool description, explanation and applicability.\nThe topic is very relevant nowadays, since main challenges and research directions are oriented toward an improvement in robustness and efficiency of the 3D digitization process, also for collections of objects, increasing the accuracy and completeness of surface appearance, and increasing data sharing, dissemination and usability. Retrieve 3D models from large collections is a curatorial and research need to be addressed. Possible uses in other contexts and for other collections are given due consideration, and the search-engine module is expected to be tested other contexts.\nFuture developments are correctly specified: an extra module to provide full database capabilities to store, update and edit the 3D models is foreseen; a benchmark analysis will be delivered; the implementation of additional shape descriptors helping to refine queries is mentioned as well.\nSome minor comments:\nThe State of the Art concerning heritage digitization via photogrammetry (photomodelling / Structure from Motion) and laser scanning can be improved, as well as data segmentation and classification. The statement: “Currently, the conventional way to locate models in a database consists of formulating a query by using keywords that describe the objects’ features” does not consider latest innovations in semantic web.\nIn general, references on Machine Learning and new avenues in shape recognition can be improved. Just some suggestions:\nhttps://doi.org/10.5194/isprs-archives-XLVIII-M-2-2023-1359-2023\nhttps://doi.org/10.3390/rs11070847\n\nThe workflow for the implementation of the ArcheoShape search-engine module is clearly described, focusing on comparing computational shape descriptions. Anyway, tool “architecture” should be described in more detail, in order to provide means for replication of the software development by other users.\n\nExpanded query criteria should be listed and explained.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\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? Partly\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": "11264",
"date": "04 Apr 2024",
"name": "Diego Jiménez-Badillo",
"role": "Author Response",
"response": "Thanks for your comments and suggestions, which have allowed us to improve this manuscript by doing the following changes: Reviewer comment: The State of the Art concerning heritage digitization via photogrammetry (photomodelling / Structure from Motion) and laser scanning can be improved, as well as data segmentation and classification. The statement: “Currently, the conventional way to locate models in a database consists of formulating a query by using keywords that describe the objects’ features” does not consider latest innovations in semantic web. In general, references on Machine Learning and new avenues in shape recognition can be improved. Response: We extended the Introduction with descriptions and references on photomodelling / Structure from Motion, as well as advances in Semantic Web and deep-learning for accessing cultural heritage information, particularly the use of ontologies, as well as segmentation and annotation techniques. We also added comments on the papers that you recommended. The second reviewer also considers that the paper only describes the software tool partly and that there are no enough details of the code, method and analysis. Response: We offer the same response given to Reviewer 1: Regarding the methods and analysis, we consider that these are sufficiently covered in the explanation of the three descriptors implemented, where the principles, methods and analysis of each algorithm are explained. As for the tool itself, we included more details of MeshAnlizer architecture, as well as a lengthy explanation of how it functions. As for a technical description of the source code, we consider that as the implementation of the whole system is still a work in progress and likely to change over time, readers that want more details -or want to replicate the software- are better served by documenting the source code with commentaries on functionality directly on the source code. This is available in the GitHub repository, from which anyone can download the source code to compile it as such, adapt it or replicate it freely for his own purposes. Documenting the software in this manner, would guarantee that as the module changes the users can always get an explanation of the latest progress."
}
]
}
] | 1
|
https://f1000research.com/articles/12-182
|
https://f1000research.com/articles/12-92/v1
|
24 Jan 23
|
{
"type": "Review",
"title": "Bacterial pneumonia associated with multidrug-resistant Gram-negative pathogens: Understanding epidemiology, resistance patterns, and implications with COVID-19",
"authors": [
"Dalal Hammoudi Halat",
"Carole Ayoub Moubareck",
"Carole Ayoub Moubareck"
],
"abstract": "The ongoing spread of antimicrobial resistance has complicated the treatment of bacterial hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP). Gram-negative pathogens, especially those with multidrug-resistant profiles, including Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Pseudomonas aeruginosa, and Acinetobacter spp., are an important culprit in this type of infections. Understanding the determinants of resistance in pathogens causing pneumonia is ultimately stressing, especially in the shadows of the COVID-19 pandemic, when bacterial lung infections are considered a top priority that has become urgent to revise. Globally, the increasing prevalence of these pathogens in respiratory samples represents a significant infection challenge, with major limitations of treatment options and poor clinical outcomes. This review will focus on the epidemiology of HAP and VAP and will present the roles and the antimicrobial resistance patterns of implicated multidrug-resistant (MDR) Gram-negative pathogens like carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Pseudomonas aeruginosa (CRPA), carbapenem-resistant Enterobacterales (CRE), as well as colistin-resistant Gram-negative pathogens and extended-spectrum β-lactamase (ESBL)-producing Enterobacterales. While emerging from the COVID-19 pandemic, perspectives and conclusions are drawn from findings of HAP and VAP caused by MDR Gram-negative bacteria in patients with COVID-19.",
"keywords": [
"hospital-acquired pneumonia",
"ventilator-associated pneumonia",
"antimicrobial resistance",
"Gram-negative multi-drug resistant pathogens."
],
"content": "Introduction\n\nOriginating from the ancient Greek “pneumon”, or lung, pneumonia is defined as inflammation of the parenchyma of either one or both lungs, which is usually, but not always, caused by infection, and remains a foremost cause of hospitalization among both adults and children,1 with a hospitalization rate close to 400 per 100 000 population in the United states2 and over seven million hospitalizations per year worldwide.3 Pneumonia has to be considered in patients with acute onset of fever, chills, cough, dyspnea, fatigue, purulent sputum, anorexia, and pleuritic chest pain.4 Pneumonia represents the eighth most expensive condition for hospitalization, with an estimated total cost exceeding USD 9.5 billion per year in US hospitals.5\n\nAlthough a causative pathogen may stay unrecognized, bacteria, viruses, fungi, and parasites may be implicated in pneumonia.6 While viruses like influenza A and B, coronaviruses, rhinoviruses, respiratory syncytial viruses, parainfluenza viruses, and others, are vey frequent pathogens in pneumonia,6–8 bacterial pneumonia continues to be one of the most serious public health problems due to its medical and economic burden.9\n\nAccording to the American Thoracic Society,10 pneumonia can be classified into community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator associated pneumonia (VAP). While any pneumonia acquired outside the hospital or in community settings may be considered as CAP, HAP is defined as a pneumonia occurring 48 hours or more after hospital admission, and which was not incubating at the time of admission. On the other hand, VAP refers to pneumonia occurring more than 48–72 hours after endotracheal intubation.10,11 As of 2016, the term “healthcare-associated pneumonia” (HCAP) is no longer recognized in medical literature. This category of pneumonia was referred to cases acquired in healthcare facilities including nursing homes, hemodialysis centers, and outpatient clinics, or during hospitalization within the past 90 days.11 HCAP was a condition used to identify patients at risk of pneumonia caused by multidrug-resistant (MDR) pathogens depending upon specific risk factors and illness severity. However, this categorization appeared to be excessively sensitive and may have led to increased, inappropriate, broad-spectrum antibiotic use. Although patients having recent contact with healthcare facilities were at a higher risk for infection with such MDR pathogens, this risk remained small for most patients and the overall incidence of these pathogens was low, since it did not exceed 7% in high quality studies, and did not directly relate to patient mortality.12–14 Accordingly, purposeful removal of the category of HCAP was done in 2016, and it was not classified as a discrete type of pneumonia in the 2017 guidelines on the management of HAP and VAP from Europe and Latin America.15\n\nDespite the availability of guidelines for management of HAP and VAP,16 and the growing trend in understanding these infections, successful treatment remains complex to achieve,17 and the incidence does not seem to be decreasing.18 In this review, both the epidemiological and microbiological properties of HAP and VAP shall be highlighted, with focus on implicated Gram-negative MDR pathogens and their resistance patterns. Finally, and in the light of COVID-19, the importance of these pathogens in HAP and VAP shall be discussed according to relevant literature reporting them in the wake of the global pandemic.\n\n\nRisk factors and epidemiology of HAP and VAP\n\nHAP and VAP represent some of the most common and serious infections occurring in hospitalized patients,19 and remain important causes of morbidity and mortality despite advances in antimicrobial therapy, numerous supportive care modalities, and the use of a wide-range of preventive measures.11,18 Although the Centers for Disease Control and Prevention (CDC) estimate that over two-thirds of HAP in the United States occur in non-ventilated patients, there is a major gap in research on HAP, as most hospitals routinely track VAP, and most of the knowledge we have about nosocomial pneumonia including incidence, risk factors, mortality and prevention come from ventilated patients.20 The most significant risk factors for HAP are old age21 and comorbidities including coronary heart disease, diabetes, chronic lung disease, chronic renal failure, and thyroid disorders.22,23 Mechanical ventilation,24 especially if prolonged for more than two weeks,21 reintubation or tracheostomy,25 major chest or abdominal surgery,26 as well previous antibiotic exposure, especially to broad-spectrum antibiotics,27 are possible risk factors for VAP. Of note, some studies have reported an increased incidence of HAP when the gastric pH is increased with the use of medications including H2 receptor blockers, antacids, or proton pump inhibitors.28,29\n\nHAP remains a highly prevalent and morbid hospital-acquired infection, second only to nosocomial bloodstream infections,30 and its incidence ranges from 5-20 cases per 1000 hospital admissions, with highest rates observed among immunocompromised, surgical and elderly patients.31 It is reported to affect nearly 0.5 to 1.7% of all hospitalized patients, and to be the leading cause of mortality among all hospital-acquired infections.9 HAP frequently causes prolonged hospital stay, increased antimicrobial usage, and additional cost of treatment.32\n\nVAP is the most prevalent nosocomial infection in the intensive care unit (ICU), where it constitutes about 25% of ICU infections.33 About 10% of patients on mechanical ventilation may develop VAP.34 Moreover, according to results of meta-analysis, the attributable mortality rate in VAP was higher for surgical patients and those with severe illness at the time of admission.35 Patients with VAP usually have a longer hospital course and excess mortality, and invite higher healthcare costs than similarly ill patients but without VAP.16\n\nAmong ICU patients, both HAP and VAP are associated with high morbidity and mortality rates, since these patients are already weak and critically ill. The estimated all-cause mortality in such patients is between 25-50%. Globally, HAP and VAP are considered the leading causes of death due to hospital-acquired infection, with an estimated global mortality of 20–30% due to HAP, and 20–50% due to VAP.36 In a comparative analysis of longitudinal prospective studies, and in the ICU setting, HAP and VAP were responsible for 82% and a 38% rise in the risk of 30-day mortality respectively.37 With the current standards of therapy, the clinical success rates for patients admitted to the ICU with HAP or VAP are often below 60%, and this may be explained by challenges of antibiotic therapy in critically ill patients, complexity of identifying microbial etiologies, relatively low penetration of most antibiotics into the lungs, as well as frequency of difficult-to-treat or highly resistant pathogens in that setting.38\n\n\nMicrobiology of HAP and VAP: The role of MDR Gram-negative pathogens\n\nConcise knowledge of the microbial etiologies of HAP and VAP allows better identification of patients at high risk of infection caused by problematic pathogens, such as MDR Gram-negative and extended spectrum beta-lactamase (ESBL)-producing Enterobacterales, in addition to carbapenemase-producing Gram-negative bacteria. This should guide better selection of antibiotics and assessment of treatment protocols.39 A persistent clinical dilemma regarding the causes of HAP and VAP resides in that detection of a microorganism from a respiratory tract sample does not necessarily indicate it as the causative agent of pneumonia.40 HAP and VAP may be caused by a wide variety of pathogens and can be polymicrobial.\n\nEvidence indicates that Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Haemophilus infuenzae, Pseudomonas aeruginosa, Moraxella catarrhalis, and Escherichia coli were the most identified causes of typical pneumonia, while atypical pneumonia is mostly attributed to pathogens like Legionella pneumophila, Chlamydia pneumoniae, and Mycoplasma pneumoniae. Despite the fact that S. pneumoniae is the most important cause of CAP globally, Gram-negative bacteria are commonly related to HAP and VAP.9 In general, the implicated in HAP and VAP are Staphylococcus aureus (especially methicillin-resistant S. aureus (MRSA) strains), Pseudomonas species (especially P. aeruginosa), Acinetobacter species, E. coli, in addition to Klebsiella species (including extended-spectrum β-lactamase (ESBL)-producing and the extensively drug-resistant (XDR) Enterobacterales). These pathogens account for nearly 80% of all episodes.41,42 Pneumonia etiology is thought to have shifted towards Gram-negative pathogens,9 and this may be perpetuated by overuse of existing antimicrobial agents, which has led to the development of adaptive resistance mechanisms by bacteria; lack of good antimicrobial stewardship resulting in increased resistance; and lack of adequate infection control practices.43\n\nThe involvement of Gram-negative bacteria in HAP and VAP differs across studies in different world regions. In a systematic review and meta-analysis conducted on Asian countries, and among a sum of 14295 organisms identified in VAP, the most predominant culprit was Acinetobacter baumannii (26%), followed by P. aeruginosa (22%), K. pneumoniae (14%), and S. aureus (14%).44 Similarly, in the Southeast Asian region, a part of the world with limited health resources and underestimation of infectious diseases, a comparison of causative agents of VAP among 24 different studies showed that Acinetobacter spp., followed by P. aeruginosa, and then K. pneumoniae were the commonest Gram-negative organisms implicated in the disease.45\n\nIn European ICUs, and according to a prospective, multicenter, observational study on HAP and VAP, the most common isolates identified were S. aureus, with a prevalence of 16% for methicillin-sensitive and 16% for methicillin-resistant, P. aeruginosa (23%), and A. baumannii (19%).46 In a large study enrolling patients with VAP from 27 ICUs in nine European countries, the dominant isolates were S. aureus in Spain, France, Belgium and Ireland, P. aeruginosa in Italy and Portugal, Acinetobacter in Greece and Turkey, and E. coli in Germany.47 Other reports document the high prevalence of Enterobacterales in nosocomial pneumonia, like a report from Poland48 citing 42.0 % of Enterobacterales, 37% of A. baumannii, 16% of P. aeruginosa, and 5% of S. maltophila. In 2017, and in an investigation from Serbia on HAP and VAP causes, Gram-negative agents were mostly isolated; the most common pathogens were Acinetobacter spp. and P. aeruginosa, accounting for over 60% of isolates.49 Similarly, in a 10-year surveillance study in a tertiary medical center in Lebanon on VAP causes, Gram-negative organisms were predominant among isolated pathogens (95%), with A. baumannii being the leading culprit (33%), followed by P. aeruginosa (17%) and E. coli (12.%).50 Parallel results were reported in Saudi Arabia in a 6-year analysis by El-Saed and Colleagues.51 In a study from the United Arab Emirates involving a 20-bedded, mixed, medical and surgical ICU, K. pneumoniae was the most prevalent organism (21%) in VAP, followed by S. aureus (16%), and P. aeruginosa (16%).52\n\nIn the United States, and in an antimicrobial surveillance program in 2010 intended to establish the pathogens most likely to cause HAP or VAP, a consistent group of 6 organisms (S. aureus [28.0%], P. aeruginosa [21.8%], Klebsiella species [9.8%], E. coli [6.9%], Acinetobacter spp. [6.8%], and Enterobacter spp. [6.3%]) caused approximately 80% of HAP or VAP. Lower prevalence of Serratia species, Stenotrophomonas maltophilia, and community-acquired pathogens, such as pneumococci and Haemophilus influenza were reported.53 In 2016, a report by the Centers of Disease Control and Prevention (CDC)41 indicated a similar ranking in VAP for S. aureus, P. aeruginosa, and Klebsiella spp., followed by Enterobacter spp. and E. coli. The incidence was different in an investigation carried in the ICU on patients with HAP or VAP, with S. maltophilia being most prevalent (34%), followed by P. aeurginosa (40%), A. baumannii (32%), and S. aureus (28%).54 As such, the etiological diagnosis of bacterial causes of HAP and VAP shows variable distribution of frequent pathogens, underlining the necessity for incessant, vigilant monitoring of these data across the continuum of HAP and VAP in different areas worldwide.\n\n\nResistance patterns of the important MDR Gram-negative bacteria implicated in HAP and VAP\n\nThe common MDR Gram-negative pathogens recognized for their role in HAP and VAP are A. baumannii, P. aeruginosa, and K. pneumoniae. Below, the roles and the antimicrobial resistance patterns of carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant P. aeruginosa (CRPA), carbapenem-resistant Enterobacterales (CRE), colistin-resistant Gram-negative pathogens, and extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, in HAP and VAP are summarized, and presented in Figure 1. This is especially important in light of the World Health Organization (WHO) classification of some of these pathogens as critical priority bacteria and urgent threats that should be addressed appropriately.55\n\n\nCarbapenem-resistant A. baumannii (CRAB)\n\nA. baumannii is an organism with extensive resistance to antimicrobial agents and with a profile perfectly compliant to healthcare settings, where it grows as cause of HAP and VAP.56 Carbapenem resistance in A. baumannii is convened by several mechanisms acting in concert, including decrease in its outer membrane permeability, overactivity of efflux pumps, and increased production of cephalosporinases belonging to the AmpC group. However, the most predominant mechanism of carbapenem resistance in A. baumannii remains the production of carbapenemases of Ambler classes B and D.57 Moreover, there are also reports of specific Ambler class A carbapenemases among A. baumannii strains.58\n\nThe earliest case report of CRAB in nosocomial pneumonia was described in a mechanically ventilated patient in the ICU of a Spanish hospital in 1998.59 Since then, an escalating trend of resistance among A. baumannii isolates has grown to become a concerning issue in clinical settings,42 and this organism appears endemic in countries of North Africa and the Middle East, and has caused several outbreaks in European countries as well.60 The documentation of CRAB was not necessarily correlated with in-hospital mortality,61 but previous exposure to antibiotics and the severity of VAP were identified as risk factors for infection, and could be minimized by judicious use of carbapenems and colistin.62\n\nThe rates of carbapenem resistance among A. baumannii in VAP and HAP is variable with some reports of 60%63 and other studies with numbers as high as 86%.60,64 Drug-resistant A. baumannii in VAP is reported to confer longer hospital stays and increased mortality, which can exceed 60%.65,66 The length of hospital stay, previous antibiotic treatment, duration of mechanical ventilation, disease severity, and predominance of drug-resistant A. baumannii strains in hospital environments have been recognized as risk factors for VAP due to MDR A. baumannii.62 Plasmids of CRAB isolates that harbor genetic determinants coding for different carbapenem-hydrolysing class D β-lactamases (blaOXA-23, blaOXA-58, blaOXA-58-like, and blaOXA-72, result in high-level resistance to all carbapenems.42 For example, in Brazilian university hospitals, CRAB isolates with plasmids carrying OXA-23-encoding gene were identified in a range of about 70%67 to 100%68 of VAP cases. Likewise, 100% of A. baumannii strains identified in a study on VAP from Pakistan were CRAB, of which 95% positively amplified blaOXA-23 gene.69 In China, a recent 7-year analysis of the molecular epidemiology of VAP showed that CRAB caused 65% of A. baumannii VAP cases, and carbapenem resistance was related to expression of OXA-23 and OXA-24, as well as efflux pump-encoding genes (AdeABC and AdeFGH). Infection with CRAB was significantly associated with longer mechanical ventilation time and longer antibiotic administration after VAP diagnosis.70 Also in China, according to a retrospective analysis, CRAB-induced HAP occurred mostly in patients with underlying diseases, and those who received antimicrobial therapies including broad-spectrum β-lactams, invasive mechanical ventilation, and catheterization. The genes encoding OXA-23 were detectable in 97% of the strains.71 In Iran, as reported in an investigation of CRAB in VAP, resistance rates to both imipenem and meropenem were above 90%, and the frequencies of OXA-23 and OXA-24 were 58 and 31% respectively, with 42% of the strains harboring the insertion sequence ISAba1 upstream of OXA carbapenemases capable of modulating their expression and transfer.72 In Vietnam, over 80% of A. baumannii strains from HAP were carbapenem-resistant with the carbapenemase genes blaOXA-23-like, blaOXA-58-like, and blaNDM-1, with rates of 78, 10, and 6%, respectively.73 The rates of carbapenem resistance in A. baumannii were as high as 97% in a VAP study involving three European countries, Greece, Spain, and Italy. Resistance was associated with an acquired carbapenemase, OXA-23 (80%), OXA-40 (5%), OXA-58 (2%) or OXA-23/58 (2%). Almost 65% of CRAB isolates were XDR or pandrug resistant, and belonged to a predominant clonal lineage, suggesting the presence of an epidemic clone and highlighting the difficulty in empirical treatment of CRAB.74 The expansion of resistance in CRAB isolates and their increasing detection in nosocomial infections like HAP and VAP necessitate precise and regular programs of surveillance and control.\n\n\nCarbapenem-resistant P. aeruginosa (CRPA)\n\nAlthough a wide spectrum of bacteria can cause HAP and VAP, P. aeruginosa remains one of the most frequent causative pathogens.41 Multifaceted, opportunistic, and drug-resistant, P. aeruginosa continues to be a major source of infections in HAP and VAP with high morbidity and mortality. Its enormous potential for variation and the large number of virulence factors the pathogen has at its disposal allow it to be adaptable and flexible, giving it the opportunity to customize its response to healthcare settings where it lingers as a major concern.75 In 2019, the CDC reported that P. aeruginosa has a carbapenem resistance rate of up to 12% in the US.76 An epidemiological analysis in 2015 involving 50 countries showed that the international resistance rates of P. aeruginosa to carbapenems vary from 10% wide range to 60%.77 Numerous resistance mechanisms drive the emergence of CRPA, most often including porin deficiency (especially OprD), efflux pump overactivity (mainly MexAB-OprM and MexCD-OprJ), and, less frequently, carbapenem-inactivating enzymes.78\n\nIn a pediatric ICU, the rate of CRPA among VAP samples was 52%, and risk factors for the infection included length of stay until the diagnosis of VAP, presence of central venous catheters, prior use of cefepime, ciprofloxacin, colistin, and teicoplanin.79 Furthermore, in a study of VAP in the ICU of three hospital centers in 2020, CRPA isolates showed high resistance for both imipenem and meropenem, with respectively 74% and 68%, and were most likely to exhibit upregulation of efflux pumps or porin loss.80\n\n\nCarbapenem-resistant Enterobacterales (CRE)\n\nThe Enterobacterales are frequently isolated in clinical cultures and are typical inhabitants of the digestive system in both humans and animals. Globally, the threat posed by CRE to human health is on the rise, imposing an urgent antimicrobial resistance threat. When opposed to strains that are carbapenem-susceptible, CRE frequently have numerous resistance genes that restrict treatment options, entail longer treatment durations, impose higher costs, and require therapies with higher toxicities.81 In fact, Enterobacterales can become resistant to carbapenems by three possible mechanisms: efflux pump overactivity, outer membrane porin loss or mutation, and carbapenemase production, which remains the major resistance mechanism.82 Efflux pumps belonging to the resistance-nodulation-division (RND) are reported to contribute to carbapenem resistance, such as the common AcrAB-TolC RND system.83 Furthermore, reduced carbapenem susceptibility in Enterobacterales may result from reduced expression of outer membrane porins such as OmpF and OmpC, which mediate drug permeability.84 However, carbapenemases remain the key determinants of resistance in CRE and they belong to different Ambler classes: Class A like KPC, Class B like NDM, IMP and VIM, and class D like OXA enzymes.57 Noteworthy, CRE with high efflux activity or permeability defects may express any of these mechanisms paired to production of other β-lactamases such as AmpC cephalosporinases or extended-spectrum β-lactamases (ESBLs), indicating the heterogeneity of mechanisms driving the development of carbapenem resistance.85\n\nIn pneumonia, antibiotic resistance profiles of Enterobacterales have gradually changed, indicating that close monitoring of those pathogens is fundamental for preventing further rise of resistance, development of treatment guidelines, and improving clinical therapy. For example, in China, an analysis of CRE in HAP over one decade showed an increase in the prevalence of these organisms from 0.8% to 11.6%.86 In 2021, a prospective cohort study involving 5 tertiary referral centers in Korea detected 4% prevalence of CRE in HAP and 1% in VAP.87 In another investigation, both carbapenem-resistant K. pneumoniae encoding OXA-48, and carbapenem-resistant Enterobacter cloacae encoding VIM-1, were identified in VAP, among a diverse group of β-lactamases.80\n\n\nColistin-resistant Gram-negative bacteria\n\nA cationic, polypeptide antibiotic, bactericidal against Gram-negative bacteria, colistin (polymyxin E)88 has re-emerged as a possible antibiotic treatment option for MDR Gram-negative bacteria in HAP and VAP.89 Its revival was prompted by its high effectiveness against MDR A. baumannii, K. pneumoniae and P. aeruginosa.90 Polymyxins target on the outer membrane of Gram-negative bacteria using electrostatic interactions that develop between the positively charged polymyxin molecule and the negatively charged phosphate group that forms part of the lipid A residue of the bacterial cell wall lipopolysaccharide (LPS). Upon binding to the LPS and phospholipids in the outer cell membrane, polymyxins competitively displace divalent cations from the phosphate groups of membrane lipids, destabilizing the outer cell membrane, and causing leakage of intracellular contents and cell death.91 Undesirably, the use of polymyxins among the few enduring useable options for the therapy of MDR Gram-negative pathogens has prompted bacterial resistance. Such resistance may be chromosomal and associated with the modifications of lipid A, or may be encoded on transposable elements, namely mobile colistin resistance (mcr) genes. A review of the mechanisms of Gram-negative bacterial resistance to polymyxin has been meticulously presented elsewhere.88\n\nWith the increase in the magnitude of resistance towards colistin among Gram-negative bacteria,92 reports of such resistance being an important drive of increased mortality are emerging.93 In one survey, about 48% of A. baumannii isolated from patients with VAP in Greece, Italy, and Spain were colistin-resistant, with several amino acid substitutions in the PmrCAB two-component system.94 With this system being responsible for addition of phosphoethanolamine to lipid A, its modifications reduce the net negative charge of the outer membrane, thereby affecting colistin binding and preventing loss of integrity and disruption of the cell membrane.95 Likewise, in 2015, colistin-resistant A. baumannii isolates were identified at a hospital system in Pennsylvania from patients with VAP, with lipid A modification by the addition of phosphoethanolamine accounting for colistin resistance.96\n\nA prospective cohort research done in 2022 on MDR Gram-negative pathogens recovered from intubated patients with VAP showed colistin resistance rates of 3-20% among MDR A. baumannii, K. pneumoniae, as well as P. aeruginosa.97 Also, in a 5-year retrospective study following over 5,500 patients in four general ICUs in Barcelona, Spain, the rate of colistin resistance among P. aeruginosa isolated from HAP or VAP specimens was 15%.98 These numbers warrant careful attention to colistin use, and thorough re-evaluation of its introduction to antimicrobial therapy. According to an expert opinion published in 2021, the use of colistin in VAP has limited efficacy and significant nephrotoxicity.99 The addition of the drug to the medication regimen did not show significant differences in patient mortality,97 indicating that its use should rather be reassessed as newer agents become available, to prevent further buildup of colistin resistance among MDR Gram-negative pathogens.\n\n\nExtended-spectrum β-lactamase (ESBL)-producing Enterobacterales\n\nHAP and VAP due to ESBL-producing Enterobacterales represent also a growing problem. Indeed, ESBL producers are endemic in many countries, and 5 to 25% of ICU patients are carriers of these pathogens on admission. HAP and VAP caused by ESBL-producers are associated with a higher mortality than HAP and VAP due to susceptible Enterobacterales because the resistance profile decreases the adequacy rate of empiric therapy.100 The spread of pathogens harboring ESBLs with concomitant resistance to carbapenems further complicates treatment outcomes.101 On molecular level, genes encoding carbapenem resistance, colistin resistance, and ESBLs are carried on highly mobile genetic elements, making them capable of easy transfer horizontally among bacteria with resulting additional dissemination and increase in resistance rates.102\n\nESBL-producing Enterobacterales have been repeatedly described in HAP and VAP. In one study from Croatia, 4% of K. pneumoniae isolates and 2% of E. cloacae isolates were producers of ESBL, with group 1 CTX-M β-lactamases detected in patients with VAP.80 In another report from France, ESBL-producing Enterobacterales accounted for 27% of VAP cases in a monocenter retrospective study among mechanically ventilated patients in the ICU.103 Similar findings were reported in another study from Italy, were both carbapenemase-producing and ESBL-producing K. pneumonia were identified in patients with VAP in the ICU.104\n\n\nMDR Gram-negative pathogens causing pneumonia in COVID-19 patients\n\nThe coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made a serious public health threat worldwide with different populations at risk.105 The pandemic has resulted in millions of infections globally and has stressed both the healthcare and the economic systems to the extreme,106 with over 650 million cases confirmed and a death toll reaching almost 7 million bereavements worldwide, as of November 2022.107 Severe COVID-19 has sculpted critical challenges for research and medical communities, with older age, male sex, and comorbidities (hypertension, diabetes, cardiovascular disease, chronic pulmonary disease, chronic kidney disease, chronic liver disease, and cancer) being the common risks for severe disease. Given that SARS-CoV-2 viral entry is primarily through the respiratory tract, upper and lower respiratory tract involvement is the most common manifestation.108 Observational studies report that COVID-19 patients suffer from secondary bacterial infections, worsening the disease and increasing mortality, particularly in those who require invasive mechanical ventilation. However, the rates of these bacterial co-infections and secondary infections remained low (5-7%),109,110 although critically sick ICU patients had higher rates.111 Numerous studies of COVID-19 patients admitted to the ICU show that most patients were empirically administered antibiotics, increasing the prevalence of MDR pathogens.111,112 In general, the rates of VAP in patients with COVID-19 who were critically ill was reported to rise above 50%,113–117 with an estimated mortality exceeding 40%, and an increase in the number of patients requiring intensive care.118 In a multicenter study, VAP accounted for 50% of all hospital-acquired infections in patients with COVID-19, with 28% prevalence of Gram-negative pathogens as agents in VAP.119 In another case series, 2% of HAP and 33% of VAP were documented among COVID-19 patients admitted to the ICU, with VAP resulting in more acute respiratory distress syndrome (ARDS), and being associated with more acute kidney injury, long mechanical ventilation longer, and longer ICU stay.120\n\nAcross studies of COVID-19 patients diagnosed with VAP, frequent growth of Gram-negative bacteria has been revealed in multiple studies, with predominantly high rates of P. aeruginosa.118 In 2022, Velásquez-Garcia and Colleagues121 conducted a systematic review on causative agents of VAP and their antibiotic resistance patterns in COVID-19 patients and most collected studies were from France (32%), Italy (20%), Spain (12%), as well as the United States (8%). The prevalence of Gram-negative bacteria was highest in VAP, with ranges of 7.5-72.5% for P. aeruginosa, 6.9-43.7% for K. pneumonia, 1.6-20% for E. cloacae, and 1.2-20% for A. baumannii. Likewise, a late systematic literature review summarizing available evidence regarding VAP in patients undergoing mechanical ventilation because of ARDS secondary to SARS-CoV-2 infection, reported Gram-negative bacteria to be the predominant microorganisms (>70% in most series) followed by Gram-positive bacteria (mostly S. aureus). Also, since most cases of COVID-19-related VAP are diagnosed more than 7 days from initiation of invasive mechanical ventilation, patients are at increased risk for MDR strains.122\n\nOnly few studies investigated the susceptibility patterns among Gram-negative pathogens, and the main resistance mechanisms reported by these studies include the production by Gram-negative pathogens of ESBL, AmpC, and carbapenemases. Table 1 summarizes some findings of Gram-negative pathogens described in this review in patients with COVID-19-related VAP and remarkable data about their resistance. The published research revealed only limited information on the patterns of antibiotic resistance, as well as scarce data from low- and middle-income countries. As such, every effort should be implemented for monitoring and preventing these infections in the light of COVID-19 and bacterial resistance, and for provoking health systems preparedness for future pandemics.\n\n\nConclusions\n\nWith the above data, it is evident that the advent of Gram-negative pathogens with important antimicrobial resistance profiles has mounted with time in HAP and VAP, hindering treatment and adversely affecting clinical outcomes. Moreover, the increased recognition of these pathogens in patients with COVID-19 backs up recent distresses regarding the emergence of MDR bacterial co-infections during the global pandemic. As such, the development of approaches for alleviating the effect of these infections in this patient population should be a compulsory element of management tactics for COVID-19 patients, and part of the alertness for future outbreaks. It is evident that the dwindling antibiotic pipeline, and the major decline in the approval of new antibiotics or new classes, are exerting precarious pressure on demanding infections like HAP and VAP. As such, more research, more funding, and more focus into advanced surveillance methods like whole genome sequencing, and innovative methods of antibiotic discovery like deep learning and artificial intelligence to address MDR Gram-negative pathogens, will ultimately influence the presentation of HAP and VAP, as well as other threatening infections.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors would like to acknowledge Laveena Ramesh, for her technical assistance in preparation of Figure 1.\n\n\nReferences\n\nGrief SN, Loza JK: Guidelines for the Evaluation and Treatment of Pneumonia. Prim. Care. 2018 Sep; 45(3): 485–503. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGu CH, Lucero DE, Huang CC, et al.: Pneumonia-Associated Hospitalizations, New York City, 2001-2014. Public Health Rep. 2018; 133(5): 584–592. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShi T, Denouel A, Tietjen AK, et al.: Global and Regional Burden of Hospital Admissions for Pneumonia in Older Adults: A Systematic Review and Meta-Analysis. J. Infect. Dis. 2020 Oct 7; 222(Supplement_7): S570–S576. PubMed Abstract | Publisher Full Text\n\nKaysin A, Viera AJ: Community-Acquired Pneumonia in Adults: Diagnosis and Management. Am. Fam. Physician. 2016 Nov 1; 94(9): 698–706. 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J. Infect. Public Health. 2017 Nov 1; 10(6): 740–744. PubMed Abstract | Publisher Full Text\n\nKanafani ZA, El Zakhem A, Zahreddine N, et al.: Ten-year surveillance study of ventilator-associated pneumonia at a tertiary care center in Lebanon. J. Infect. Public Health. 2019 Aug; 12(4): 492–495. PubMed Abstract | Publisher Full Text\n\nEl-Saed A, Balkhy HH, Al-Dorzi HM, et al.: Acinetobacter is the most common pathogen associated with late-onset and recurrent ventilator-associated pneumonia in an adult intensive care unit in Saudi Arabia. Int. J. Infect. Dis. 2013 Sep; 17(9): e696–e701. PubMed Abstract | Publisher Full Text\n\nRahman M, Hashmey R, Abuhasna S: Ventilator Associated Pneumonia: A 22-Month Prospective Observational Study from a Tertiary Care Centre in United Arab Emirates. Int. J. Infect. Dis. 2008 Dec 1; 12: e370–e371. Publisher Full Text\n\nJones RN: Microbial etiologies of hospital-acquired bacterial pneumonia and ventilator-associated bacterial pneumonia. Clin. Infect. Dis. 2010 Aug 1; 51 Suppl 1: S81–S87. PubMed Abstract | Publisher Full Text\n\nBehnia M, Logan SC, Fallen L, et al.: Nosocomial and ventilator-associated pneumonia in a community hospital intensive care unit: a retrospective review and analysis. BMC. Res. Notes. 2014 Apr 11; 7: 232. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTacconelli E, Carrara E, Savoldi A, et al.: Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 2018 Mar; 18(3): 318–327. PubMed Abstract | Publisher Full Text\n\nAyoub Moubareck C, Hammoudi HD: Insights into Acinetobacter baumannii: A Review of Microbiological, Virulence, and Resistance Traits in a Threatening Nosocomial Pathogen. Antibiotics (Basel). 2020 Mar 12; 9(3). Publisher Full Text\n\nHammoudi Halat D, Ayoub MC: The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel). 2020 Apr 16; 9(4): E186. Publisher Full Text\n\nMoubareck C, Brémont S, Conroy MC, et al.: GES-11, a novel integron-associated GES variant in Acinetobacter baumannii. Antimicrob. Agents Chemother. 2009 Aug; 53(8): 3579–3581. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLópez-Hernández S, Alarcón T, López-Brea M: Carbapenem resistance mediated by beta-lactamases in clinical isolates of Acinetobacter baumannii in Spain. Eur. J. Clin. Microbiol. Infect. Dis. 1998 Apr; 17(4): 282–285. PubMed Abstract | Publisher Full Text\n\nChaari A, Mnif B, Bahloul M, et al.: Acinetobacter baumannii ventilator-associated pneumonia: epidemiology, clinical characteristics, and prognosis factors. Int. J. Infect. Dis. 2013 Dec 1; 17(12): e1225–e1228. PubMed Abstract | Publisher Full Text\n\nÖzgür ES, Horasan ES, Karaca K, et al.: Ventilator-associated pneumonia due to extensive drug-resistant Acinetobacter baumannii: risk factors, clinical features, and outcomes. Am. J. Infect. Control. 2014 Feb; 42(2): 206–208. PubMed Abstract | Publisher Full Text\n\nInchai J, Liwsrisakun C, Theerakittikul T, et al.: Risk factors of multidrug-resistant, extensively drug-resistant and pandrug-resistant Acinetobacter baumannii ventilator-associated pneumonia in a Medical Intensive Care Unit of University Hospital in Thailand. J. Infect. Chemother. 2015 Aug; 21(8): 570–574. PubMed Abstract | Publisher Full Text\n\nChittawatanarat K, Jaipakdee W, Chotirosniramit N, et al.: Microbiology, resistance patterns, and risk factors of mortality in ventilator-associated bacterial pneumonia in a Northern Thai tertiary-care university based general surgical intensive care unit. Infect. Drug Resist. 2014 Aug 16; 7: 203–210. 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}
|
[
{
"id": "163960",
"date": "24 Apr 2023",
"name": "Ghassan Dbaibo",
"expertise": [
"Reviewer Expertise Infectious diseases and sphingolipid biochemistry"
],
"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 excellent current review of the topic of hospital-acquired pneumonia and ventilator-associated pneumonia in the setting of increasing resistance among the responsible Gram-negative organisms.\nThere are some missing references.\n\nThere are some problems with grammar, spelling, and syntax that could be improved\n\nTitle maybe a bit misleading “Bacterial Pneumonia” since the focus is on HAP and VAP.\n\nMethodology is absent. Perhaps a statement indicating how the authors decided to perform this review would be appropriate. How did they choose the references in this review, including some but not others? What questions were they looking to answer? If this is a descriptive review, what is the scope (geography, age, setting, time-frame, etc.)?\n\nIt may have made more sense to start with ESBL Enterobacterales since they emerged first, among the categories highlighted, followed by the others (instead of starting with carbapenem-resistant organisms).\n\nPage 4, third paragraph (of the pdf version of the article): “Evidence indicates….”, this statement requires at least one, preferably more references.\n\nPage 4, third paragraph: “Pneumonia etiology is thought…”, this should be HAP etiology, as overall pneumonia is still dominated by S. pneumoniae.\n\nPage 4, last paragraph: “Parallel results were reported…”, do the authors mean “Similar results were….”?\n\nThroughout: full bacterial name only needed with first mention, subsequently abbreviation can be used, e.g. S. maltophilia (misspelled on at least one occasion)\n\n1Page 6, first paragraph: parentheses not closed (bla…)\n\nThroughout: The resistance enzymes should be presented consistently, e.g. bla-OXA versus OXA\n\nPage 6, second paragraph, line 7: “wide range” seems to be misplaced between the lower and upper limit\n\nPage 6, third paragraph, line 3: “opposed” should be replaced by “compared”, it reads better\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? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "11279",
"date": "04 Apr 2024",
"name": "Dalal Hammoudi Halat",
"role": "Author Response",
"response": "This is an excellent current review of the topic of hospital-acquired pneumonia and ventilator-associated pneumonia in the setting of increasing resistance among the responsible Gram-negative organisms. We thank the reviewer for their opinion on the article, and we will address below their comments to improve the contents. Our point-by-point itemized responses are shown below each comment in bold face. There are some missing references. Upon recommendation of the reviewer, we have added a total of five new references, in pages 4, 8 and 11 of the article. They are as follows: Gadsby NJ, Musher DM. The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures. Clin Microbiol Rev. 2022;35(4):e0001522. doi:10.1128/cmr.00015-22 Miyashita N. Atypical pneumonia: Pathophysiology, diagnosis, and treatment. Respir Investig. 2022;60(1):56-67. doi:10.1016/j.resinv.2021.09.009 Rodríguez-Martínez JM, Poirel L, Nordmann P. Extended-spectrum cephalosporinases in Pseudomonas aeruginosa. Antimicrob Agents Chemother. 2009;53(5):1766-1771. doi:10.1128/AAC.01410-08 Mills JP, Marchaim D. Multidrug-Resistant Gram-Negative Bacteria: Infection Prevention and Control Update. Infect Dis Clin North Am. 2021;35(4):969-994. doi:10.1016/j.idc.2021.08.001 Klompas M, Branson R, Cawcutt K, et al. Strategies to prevent ventilator-associated pneumonia, ventilator-associated events, and nonventilator hospital-acquired pneumonia in acute-care hospitals: 2022 Update. Infect Control Hosp Epidemiol. 2022;43(6):687-713. doi:10.1017/ice.2022.88 The editorial team will kindly adjust the numbering of references in the manuscript. There are some problems with grammar, spelling, and syntax that could be improved As advised by the reviewer, we have improved the above aspects of the article. Title maybe a bit misleading “Bacterial Pneumonia” since the focus is on HAP and VAP. Upon recommendation of the reviewer, the title was modified to indicate focus on HAP and VAP. Methodology is absent. Perhaps a statement indicating how the authors decided to perform this review would be appropriate. How did they choose the references in this review, including some but not others? What questions were they looking to answer? If this is a descriptive review, what is the scope (geography, age, setting, time-frame, etc.)? We thank the reviewer for this question. Since this was a narrative review, a statement indicating how the search was done was added at the end of the introduction section. It may have made more sense to start with ESBL Enterobacterales since they emerged first, among the categories highlighted, followed by the others (instead of starting with carbapenem-resistant organisms). We agree with the reviewer, and we have reorganized the paragraphs according to the request. We presented the organisms with the following order in the manuscript: extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, carbapenem-resistant Enterobacterales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant P. aeruginosa (CRPA), and colistin-resistant Gram-negative pathogens. Kindly adjust the numbering of references in the manuscript. Page 4, third paragraph (of the pdf version of the article): “Evidence indicates….”, this statement requires at least one, preferably more references. We agree with the reviewer, and we have added the following two references, in page 4, at the end of the mentioned paragraph: Gadsby NJ, Musher DM. The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures. Clin Microbiol Rev. 2022;35(4):e0001522. doi:10.1128/cmr.00015-22 Miyashita N. Atypical pneumonia: Pathophysiology, diagnosis, and treatment. Respir Investig. 2022;60(1):56-67. doi:10.1016/j.resinv.2021.09.009 The editorial team will kindly adjust the numbering of references in the manuscript. Page 4, third paragraph: “Pneumonia etiology is thought…”, this should be HAP etiology, as overall pneumonia is still dominated by S. pneumoniae. Indeed, we agree on this comment from the reviewer, and this was stated at the beginning of this section. The sentence mentioned has been adjusted accordingly. Page 4, last paragraph: “Parallel results were reported…”, do the authors mean “Similar results were….”? The sentence was adjusted accordingly. Throughout: full bacterial name only needed with first mention, subsequently abbreviation can be used, e.g. S. maltophilia (misspelled on at least one occasion) We have adjusted the bacterial names, as advised, and corrected the spelling errors. Page 6, first paragraph: parentheses not closed (bla…) As advised by the reviewer, we have closed the parentheses in above mentioned line. Throughout: The resistance enzymes should be presented consistently, e.g. bla-OXA versus OXA. We thank the reviewer for thorough review of the writing. The manuscript was checked to ensure all enzymes are represented by name (example: OXA), while reference to genes included bla (example: bla-OXA ). Page 6, second paragraph, line 7: “wide range” seems to be misplaced between the lower and upper limit We have removed, as advised, the terms “wide range” from the mentioned line. Page 6, third paragraph, line 3: “opposed” should be replaced by “compared”, it reads better We have replaced, as advised, the mentioned term with “compared”."
}
]
},
{
"id": "195137",
"date": "09 Oct 2023",
"name": "Arjana Tambić Andrašević",
"expertise": [
"Reviewer Expertise Antibiotic resistance surveilalnce"
],
"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 describes the epidemiology, risk factors and aetiology of hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) indicating that multidrug resistant (MDR) gram-negative bacteria are on the rise. Incidence of MDR bacteria differs from country to country and authors are citing many studies on incidence of these pathogens in VAP and in intensive care units from different parts of the world. Authors are giving a nice review of resistance mechanisms to critically important antibiotics, colistin and beta-lactams, carbapenems in particular. Special attention is given to the high incidence of MDR pathogens causing VAP in COVID patients. Importance of close monitoring of VAP and HAP aetiology is stressed as well as the importance of investing in development of new antibiotics. However, more should be discussed on the role of infection prevention and control in reducing VAP and HAP and in particular infections caused by MDR bacteria.\nSpecific comments:\nNumerous resistance mechanisms drive the emergence of CRPA, most often including porin deficiency (especially OprD), efflux pump overactivity (mainly MexAB-OprM and MexCD-OprJ), and, less frequently, carbapenem-inactivating enzymes. – add important mechanism: hyperproduction of AmpC cephalosporinases\n\nNumerous studies of COVID-19 patients admitted to the ICU show that most patients were empirically administered antibiotics, increasing the prevalence of MDR pathogens.111,112\n\nThe review should also reflect on the following: Incidence of VAP caused by MDRO was increased in COVID patients also due to the poor implementation of hand hygiene and standard precautions and improper use of gloves in cohorted COVID patients. In general, the role of infection prevention and control in reducing VAP and HAP and MDR spread should be more discussed.\n\nConclusions: the importance of improving hand hygiene, standard precautions and contact isolation in prevention of MDRO spread and specific measures to prevent VAP should be mentioned in conclusions\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? 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": "11280",
"date": "04 Apr 2024",
"name": "Dalal Hammoudi Halat",
"role": "Author Response",
"response": "The article describes the epidemiology, risk factors and aetiology of hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) indicating that multidrug resistant (MDR) gram-negative bacteria are on the rise. Incidence of MDR bacteria differs from country to country and authors are citing many studies on incidence of these pathogens in VAP and in intensive care units from different parts of the world. Authors are giving a nice review of resistance mechanisms to critically important antibiotics, colistin and beta-lactams, carbapenems in particular. Special attention is given to the high incidence of MDR pathogens causing VAP in COVID patients. Importance of close monitoring of VAP and HAP aetiology is stressed as well as the importance of investing in development of new antibiotics. However, more should be discussed on the role of infection prevention and control in reducing VAP and HAP and in particular infections caused by MDR bacteria. We thank the reviewer for their opinion on the article, and we will address below the comments suggested to improve the contents. Our point-by-point itemized responses are shown below each comment in bold face. Specific comments: Numerous resistance mechanisms drive the emergence of CRPA, most often including porin deficiency (especially OprD), efflux pump overactivity (mainly MexAB-OprM and MexCD-OprJ), and, less frequently, carbapenem-inactivating enzymes. – add important mechanism: hyperproduction of AmpC cephalosporinases We agree with the reviewer and the above mechanism has now been added in the manuscript in page 8, in 2nd paragraph, with the below reference: Rodríguez-Martínez JM, Poirel L, Nordmann P. Extended-spectrum cephalosporinases in Pseudomonas aeruginosa. Antimicrob Agents Chemother. 2009;53(5):1766-1771. doi:10.1128/AAC.01410-08 The editorial team will kindly adjust the numbering of references in the manuscript. Numerous studies of COVID-19 patients admitted to the ICU show that most patients were empirically administered antibiotics, increasing the prevalence of MDR pathogens.111,112 The review should also reflect on the following: Incidence of VAP caused by MDRO was increased in COVID patients also due to the poor implementation of hand hygiene and standard precautions and improper use of gloves in cohorted COVID patients. In general, the role of infection prevention and control in reducing VAP and HAP and MDR spread should be more discussed. We have added the following lines and listed two references in page 11, 1st paragraph, line 8: “Prevalence of MDR Gram-negative bacteria is also attributed to improper compliance of hand hygiene and contact isolation, such as glove and gown usage, by hospital staff. (Mills & Marchaim, 2021). Moreover, given that such errors also increase HAP and VAP occurrence among COVID-19 patients, specific infection prevention strategies (such as preventing reintubation, minimizing sedation, providing early enteral nutrition, among others) have become increasingly pivotal to implement. (Klompas , et al. 2022)” Mills JP, Marchaim D. Multidrug-Resistant Gram-Negative Bacteria: Infection Prevention and Control Update. Infect Dis Clin North Am. 2021;35(4):969-994. doi:10.1016/j.idc.2021.08.001 Klompas M, Branson R, Cawcutt K, et al. Strategies to prevent ventilator-associated pneumonia, ventilator-associated events, and nonventilator hospital-acquired pneumonia in acute-care hospitals: 2022 Update. Infect Control Hosp Epidemiol. 2022;43(6):687-713. doi:10.1017/ice.2022.88 The editorial team will kindly adjust the numbering of references in the manuscript. Conclusions: the importance of improving hand hygiene, standard precautions and contact isolation in prevention of MDRO spread and specific measures to prevent VAP should be mentioned in conclusions We agree with the reviewer, and have added the following lines to page 13, in the Conclusion section: “Such public health issues necessitate more stringent implementation of hand hygiene, contact isolation and other VAP prevention strategies such as preventing reintubation and minimizing sedation for patients.”"
}
]
}
] | 1
|
https://f1000research.com/articles/12-92
|
https://f1000research.com/articles/12-316/v1
|
22 Mar 23
|
{
"type": "Study Protocol",
"title": "Vegetables as a vehicle for antimicrobial resistance (vAMR): An agroecosystem exploration from the One Health perspective in India",
"authors": [
"Pachillu Kalpana",
"Timo Falkenberg",
"Sandul Yasobant",
"Deepak Saxena",
"Christiane Schreiber",
"Timo Falkenberg",
"Sandul Yasobant",
"Deepak Saxena",
"Christiane Schreiber"
],
"abstract": "Introduction: Antimicrobial resistance (AMR) has emerged as one of the leading threats to public health. AMR possesses a multidimensional challenge that has social, economic, and environmental dimensions that encompass the food production system, influencing human and animal health. The One Health approach highlights the inextricable linkage and interdependence between the health of people, animals, agriculture, and the environment. Antibiotic use in any of these One Health areas can potentially impact the health of other areas. There is a dearth of evidence on AMR from the natural environment, such as the plant-based agriculture sector. Antibiotics, antibiotic-resistant bacteria (ARB), and related AMR genes (ARGs) are assumed to present in the natural environment and disseminate resistance to fresh produce/vegetables and thus to human health upon consumption. Therefore, this study aims to investigate the role of vegetables in the spread of AMR through an agroecosystem exploration from a One Health perspective in Ahmedabad, India. Protocol: The present study will be executed in Ahmedabad, located in Gujarat state in the Western part of India, by adopting a mixed-method approach. First, a systematic review will be conducted to document the prevalence of ARB and ARGs on fresh produce in South Asia. Second, agriculture farmland surveys will be used to collect the general farming practices and the data on common vegetables consumed raw by the households in Ahmedabad. Third, vegetable and soil samples will be collected from the selected agriculture farms and analyzed for the presence or absence of ARB and ARGs using standard microbiological and molecular methods. Discussion: The analysis will help to understand the spread of ARB/ARGs through the agroecosystem. This is anticipated to provide an insight into the current state of ARB/ARGs contamination of fresh produce/vegetables and will assist in identifying the relevant strategies for effectively controlling and preventing the spread of AMR.",
"keywords": [
"Antimicrobial resistance",
"antibiotic-resistant bacteria",
"antibiotic-resistant genes",
"vegetables",
"fresh produce",
"agroecosystem",
"One Health"
],
"content": "Introduction\n\nThe worldwide emergence of antimicrobial resistance (AMR), altering lifesaving antibiotics, is a significant public health challenge.1 The estimation exhibited that AMR is accountable for 700,000 mortalities annually worldwide and as per the current rate of resistance-related deaths, it is projected to rise to about 10 million mortalities annually by 2050.2 The impact of AMR is not confined to human mortalities but is also extended to related economic losses, estimated at around $100-210 trillion in healthcare-related expenses.3 A dearth of reliable data and evidence from low-middle income countries such as India contributes to underestimating the rate of AMR and related threats. Conversely, the recent Global Antimicrobial Resistance and Use Surveillance System (GLASS)-AMR 2021 report consisting of data from the national surveillance has reported the average increased burden of AMR with a significant focus on human clinical settings in India.4\n\nThe major contributing factors to the AMR issue are not limited to the overuse and increased misuse of antibiotics (prescription and consumption) in human settings.5 The prophylactic use and practice of sub-lethal doses of antibiotics in livestock as growth promoters to maintain health and productivity contribute to a significant part.6 Most antibiotics used in human and animal sectors are not entirely metabolized in the bodies; a high percentage of administered drugs are discharged into water and soil through municipal wastewater, animal manure, sewage sludge, and biosolids.7 The relationship between the consumption of antibiotics is directly associated with the emergence and promotion of antibiotic resistance in the microbial population of multiple sectors, including humans, animals, and the environment.8\n\nThe environmental dimension of AMR has received comparatively less focus than AMR in human or animal health. Directly connecting antibiotics, animal production, and the environment is the practice of recycling animal waste as manure for reintroducing organic materials and nutrients to the soil to improve crop productivity.9 At the same time, it presents a major pathway for the dissemination of antibiotic residues, antibiotic-resistant bacteria (ARB), and AMR genes (ARGs).10 Thus, agricultural sources are considered a critical source and dissemination route for AMR.11 The spread of antibiotic resistance in the agricultural ecosystem is a major concern because agriculture is closely related to food safety and human health. The exposure of humans to foodborne bacterial pathogens, including ARB, through the food chain, has been reported in recent decades in foodborne outbreaks.12\n\nThe enrichment of ARB and ARGs in agricultural soil, even without the apparent application of antibiotics via human agriculture practices, has raised concerns because soil ARB and ARGs can be disseminated to plants, leading to the potential spread from farms to consumers.13 There are many potential pathways by which soil-associated ARB and ARGs can transfer to plant microbiomes contributing to the emergence and spread of plant resistome to the human food chain.14,15 Food consumption represents a major route for human exposure to ARGs in environmental microbiomes.16 Some studies indicate that the consumption of raw fruit and vegetable is a potential pathway for disseminating ARGs to human microbiomes.17 It has been suggested that the long-term use of organic fertilizers causes ARGs enrichment not only of soils but also of plant phyllosphere microbiomes.14 There are many potential pathways by which soil-associated ARB and ARGs can be transferred to plant microbiomes contributing to the emergence and spread of plant resistome to the human food chain. Fresh produce can be contaminated with bacterial pathogens at multiple points throughout its production by direct contact with fecal waste during farming, wastewater irrigation, use of biosolids or animal manure as fertilizer.11,18 While these potential contamination pathways have been studied well for traditional pathogens, their relative contributions to the contamination of fresh produce with ARB and ARGs have not been quantified. This is essential to capture the unexplored factors contributing towards the issue of AMR to hinder the spread. Therefore, this study findings will contribute towards the data from the foods of plant origin which connects with a link of dietary exposure to humans.\n\nThe study aim is to investigate the presence of antibiotic-resistant bacteria and the distribution of antibiotic-resistant genes across the vegetable and soil at the farm level in alignment with a one health approach in Ahmedabad city, India to provide an evidence about resistance spread for future intervention strategies.\n\n\nProtocol\n\nEthics approval has been obtained from the Research Ethics Committee, Center for Development Research (ZEF), University of Bonn, Germany (17c_22), and the Institutional Ethics Committee of the Indian Institute of Public Health Gandhinagar, India (TRC/2022-23/10). All details collected in the study will be kept confidential and complies with the Declaration of Helsinki. Written informed consent will be taken from each participant. All methods will be carried out in accordance with relevant guidelines and regulations.33\n\nThis study aims to provide insights into the knowledge gap and investigate the role of vegetables in spread of antimicrobial resistance through an agroecosystem exploration from a One Health perspective in one of the western communities of India. More specifically, it aims to investigate the presence of antibiotic resistant bacteria and the distribution of antibiotic resistant genes across the soil-vegetable continuum at the farm level with a One Health approach in Ahmedabad city, India.\n\nThe specific research questions are:\n\n1. Which antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) are already published or known to (or can be supposed to) be widespread in soil-plant-fruit continuum of the South Asia region?\n\n2. What is the risk of AMR spread across soil-plant-fruit continuum in agriculture farms of Ahmedabad, India?\n\n2.1. How can the general agriculture practices of farmers in the region of Ahmedabad, India be characterized and which potential risk factors can be identified?\n\n2.2. Can ARB and/or ARGs be detected in the fresh produce/vegetables that are consumed raw or/and in the soil where these plants grow in the region of Ahmedabad, India?\n\nThis present study is an interdisciplinary social-ecological study with the prime aim to investigate and characterize the antimicrobial resistance in vegetables and soil on harvest, which network in an intimate proximity and their possible transmission pathway along the environment-human direction using a One Health approach. A mixed-method approach is adopted: secondary data analysis (review) and primary data collection including a survey of the general agricultural practices and laboratory analysis (microbiological and molecular), which will be merged in a triangulation concept to converge the findings and generate outcomes related to the possibility of vegetables as vehicles for AMR.\n\nThe proposed study will be conducted in one of the largest and most populous cities of the Western state, Gujarat, India, known as Ahmedabad (Figure 1). Ahmedabad is located in the central part of Gujarat on the banks of the Sabarmati river, with a population of 5,633,927.19 Ahmedabad's population has a combination of both vegetarian (60%) and non-vegetarian (40%) consumption patterns.20 Gujarat state has an outstanding contribution to the country’s horticulture sector.21\n\nAhmedabad city is located in the north-central part of the Ahmedabad district in Gujarat. Ahmedabad municipality was established in 1873 and later upgraded to Ahmedabad Municipality Corporation (AMC), divided into six municipal zones (north, south, east, central, west and new west) consisting of a total of 64 wards. Ahmedabad Urban Development Authority (AUDA) was established on 1st February 1978 with the prime objective to carry out the sustained, planned development of the area falling outside the periphery of Ahmedabad Municipal Corporation. The AUDA encompasses an area of 186,600 hectares, including Ahmedabad City (Municipal Corporation of 44,950 Hectares). The AUDA developed a comprehensive development plan for Ahmedabad city and the district, including the current general agriculture zone and the prime agriculture zone. The general agricultural zone is intended to provide areas with large parcels that are conducive to growing crops and the keeping of farm animals and poultry for the production of milk, wool, eggs, and other farm products. This zone is also intended to permit limited commercial and light industrial activities that support agriculture or are connected to the agricultural industry. The prime agriculture zones represent large, generally contiguous blocks of land that enable current and future opportunities for agriculture.\n\nThe increasing urbanization of Ahmedabad city observably led to developing more residential areas in the central part, shifting the agriculture practitioners involved in both livestock and plant production to the outskirts of the urban and peri-urban areas of the city. A large part of the general agriculture zones of the city is located adjacent to the city's sewage treatment plant. The general agriculture zone in the east of the city is known as a hotspot for livestock farmers. This area produces a significant amount of animal waste, the primary fertilizer source of the farms in this agriculture zone. The agriculture zone on the city's west side is located far from the sewage treatment plant and only small-scale livestock farming is being practiced.\n\nThis study is planned to be implemented in the general agriculture zones of Ahmedabad city because of the established and in-process use of land for agriculture purposes.\n\nThe study starts with a large-scale literature-based analysis of the information on the qualitative resistance data, abundances, and patterns on ARB and ARGs on fresh produce and food production environment in context of South Asia (Research question 1). The field exploration starts with recruitment of farms, followed by a survey of the general agricultural practices in the study area and for the identification of vegetables that are produced by the farmers and also consumed raw, to identify potential risk factors for the spread of resistances (objective 2.1). The sampling of the raw consumed vegetables and the agricultural soil will be performed at the farm-level. The sampled vegetables and soil will then be microbiologically analyzed for the presence and quantity of ARB and ARGs. The gained information on the current state of ARB and ARGs on fresh produce and the agricultural soil will be reported from Ahmedabad, India (objective 2.2). Further, the findings of all the three objectives will result in the identification of possible factors that may play a role in the spread of AMR through plant-based food to human due to consumption of ARB/ARGs contaminated vegetables. Recommendations of intervention strategies will be developed to support involved actors and decision-makers of Ahmedabad, India.\n\nMethods for research question 1\n\nTo understand the AMR background in the South Asia region in general, a systematic review methodology will be used. This systematic review aims to screen, assemble, summarize and evaluate the peer-reviewed and published evidence on the transmission of antibiotic resistances from differently fertilized soil to plants in the South Asia context, and to assess the evidence for possible human health related risks associated with consumption of antibiotic resistance contaminated vegetables produced on such fertilized soils.\n\nThe search strategy (Table 1) is designed to identify published studies on ARB, ARGs in the soil, plants, and plants parts produced on manure amended soil and associated human health related issues. The interest is in identifying studies which looked upon the ARB and ARGs contamination of plants and plant produce (i.e., vegetables) through any pathway of spread from soil to plants. The identification includes both lab-based and field-based studies. The systematic literature review will be conducted using two scientific online databases: PubMed and Web of Science. The time limitation will be set to the last 10 years so that the studies selected are up-to-date and to represent knowledge that is scientifically state-of-the-art, or allow identification of recent trends in resistance spread, respectively. The key search terms are generated to encapsulate the four main concepts and therefore the review pertains to: Antibiotic resistance; bacteria and genes; fresh produce/vegetables/plants/fruits; health effects; South Asia. The table below shows the terms and how they are combined.\n\nThe published peer-reviewed literature that documents information regarding the ARB and/or ARGs presence in plants, plant produce, vegetables, and the plant-fruit-soil continuum will be included in the review. Studies documenting the impact of plants and plant produce containing ARB and/or ARGs on human health will also be included. The review will be restricted to studies that explicitly explored the South Asia region's ARB and ARGs plant and soil environment context. The geographical restriction will involve the field site of the study conducted in South Asia, irrespective of the authors' affiliations. There will be no restriction on the design of the study. Studies published in languages other than English will be excluded. The outcomes targeted by this review will include the incidence of ARB and ARGs on plants and plant produce, from the soil environment, and the possible related human health risks due to consumption of such plant produce to define/plan next research steps more precisely.\n\nData will be extracted from the eligible studies to summarize and tabulate important findings. Data will be extracted and tabulated about the type and prevalence of ARB/ARGs, type of food source, study design, location of the study, methodological approach, key findings. The results form an important evidence base for the selection of ARB and ARGs for the next objective of the study.\n\nMethod for research question 2\n\nThe AMR field investigation is intended to capture a baseline for the further exploration of trends in vegetables and the soil used for the production of vegetables. It includes selective bacteria cultivation and identification, antibiotic resistance (pattern), and resistance genes. According to Masterton (2008), the basic protocol includes microbiological culturing and a validated antimicrobial susceptibility testing method for the first step.22 The basic protocol includes methods to gain better insights into the collection of ARGs that may circulate in the environment, leading to new bacterial serotype-resistance gene combinations and can be transmitted to humans through food consumption.23 The molecular methodology thus will be followed with the basic protocol to quantify the selected ARGs.\n\nSampling procedure for agriculture farms\n\nThe agriculture farm areas for this study will be selected from the general agriculture zones of Ahmedabad city. A preliminary screening will be performed in Ahmedabad city to identify the main areas involved in agricultural practices located in the urban part of the general agriculture zones, i.e., within the city’s six municipal zones to be included in this study. This screening is important given the unavailability of a database of agricultural farms in Ahmedabad city. Snowball sampling will be used to recruit the farms engaged with agriculture production. The researchers will visit the farmers physically for recruitment process in the study. Farmers will be informed about the purpose of the study and written informed consent will be obtained from the farmers. The farmers will also be informed about their right to withdraw consent at any point of time during the study period. Consent will be confirmed again before initiating the interviews and surveys. Two copies of the consent form will be prepared along with the signatures or thumb impression of farmer. One copy will remain with the farmer and one with the researcher. The farmer and farm households will be asked to list six nearby farms engaged in agriculture production activity. This process will be repeated until the desired sample size is reached. About 300 odd farms based on the type of agricultural product is aimed to be recruited from different zones of the city. The second screening of farms will be done with the principal inclusion criteria for the recruitment as vegetable production. Thus, depending on the number of farms engaged in agricultural production in a given locality, the equal number of representative farms from the different zones of the city will be surveyed and enrolled in the study. The enrolled 300 farms which will be surveyed for the general agricultural practices will then be assessed for the vegetable producing farms. 150 vegetable producing farms from the total vegetable producing farms will be selected from the different zones of the city based on their vegetable production for the next investigation step.\n\nSource of data and data collection methods\n\nA set of questions will be asked to each 300 farms engaged in agriculture production. The structured questionnaire for interviewing the farmers will be divided into five main sections: demographic characteristics, general farming practices, agriculture inputs, irrigation water and post-harvest practice. The questionnaire will also have aspects on information on the different types of crops as well as vegetables that are cultivated and those that are consumed raw by the household. This cross-sectional survey aims to identify the vegetable producing farms and the five major vegetables produced by the farms and also consumed raw by the households. The field observation will be used to validate the general farming system, fertilizer and pesticide use along with the questionnaire during the farm visits. This survey will be focused in collecting and documenting data on the general agriculture practices of farmers to explore factors, such as the use of fertilizers, pesticides, and irrigation water in farming system.\n\nSelection of bacteria for microbiological analysis\n\nThe selection of bacteria is based on the recommendation of the World Health Organization (WHO).23 The guidance mentions that the food of plant origin commonly intended to be consumed by humans, either fresh, minimally processed, or consumed after cooking, in that the consideration should be given to the pathogens of importance to human health and where AMR may be a hazard. The list of bacteria consists as below:\n\na. Escherichia coli (E. coli) as a measure of hygienic production and faecal indicator in general\n\nb. Salmonella species as a pathogenic representative of human- and animal-derived contamination\n\nc. Pseudomonas species as a common environmental bacterial contaminant serving as a sentinel for AMR\n\nIn addition to these bacteria recommended for screening by the WHO, selected species of other important bacteria can further be included in the study according to the initial systematic review of this study.\n\nSelection of AMR genes (ARGs) for molecular analysis\n\nThe choice of ARGs to be included in this study will be based on the systematic review conducted for research question 1. At least two ARGs will be selected based on the most found ARGs in the context of vegetables through the systematic review. This process is important as it will provide an overview of the major ARGs which are circulating in the selected geographical area and thus comparing the presence of these genes also in Ahmedabad, India.\n\nSampling procedure for microbiological analysis\n\nThe samples for resistance investigations will be biological samples for microbiological and molecular analysis. Sampling will include soil and vegetable samples grown on the selected agricultural farms as they are considered significant vehicles for the spread of AMR. Samples will be collected when vegetables reach the marketing stage. The farm households' top five vegetables produced and consumed raw will be identified through the first survey. Five vegetable samples and the consecutive soil sample in duplicate will be collected from each selected farm. A simple random sampling method will be used for collecting vegetable samples from each farm.\n\n\n\na) Vegetable sampling: The vegetable samples will be collected when they reach their commercial size through simple random sampling from each selected farm. A total of one vegetable sample in duplicates will be collected from each selected farm, thus it will be two vegetable samples from each farm. All the vegetable samples will be collected aseptically by utilizing a sterile zipper bag. After collecting samples, they will be transported to the laboratory within two hours in an icebox.24\n\nb) Soil sampling: There will be only one soil sample collection from each selected farm. The one soil sample in duplicates will be collected for the corresponding above selected vegetable sampling. The soil samples will be collected near the roots of the plants at a depth of 10 cm. The sampling will be taken out by utilizing a sterile shovel, and the collection of the sample will be in a sterile falcon tube.25\n\nSample processing:\n\na) Vegetable sample: Vegetable samples collected from each farm will be analysed for selected bacterial contamination. The farms' samples will be first freed from any adhering soil particles. The samples will then be processed following safe handling procedures recommended for human consumption purposes (e.g., handled after hand washing, trimmed of spoiled parts, and washed thoroughly under sterile water). Vegetable samples will be chopped into small pieces with a sterile knife. 25 g of each sample will be added to 225 ml of 0.1% peptone water and will then be shaken using a horizontal shaker for 30 min at 200 rpm to get a homogenous suspension, equal to an initial dilution of 100. Finally, a dilution series ranging from 10-1-10-10 will be prepared from this initial dilution for further processing.26\n\nb) Soil sample: The soil samples collected in the falcon tubes will be processed for further investigation. 10 g of soil will be taken from the collected soil and mixed with 90 ml of 0.1% peptone water in a beaker.26 The mixture will be mixed well using a horizontal shaker for 30 min at 200 rpm to have the initial dilution for processing. The 10-fold serial dilution will be prepared from the initial dilution to have the dilution ranging from 10-1-10-10 for identification and enumeration of selected bacteria.\n\nE. coli: A selective HiCromeTM E. coli Agar (Himedia, India)27 will be used for cultivation of E. coli. The dilution range of 10-1 – 10-10 will be prepared and five consecutive dilutions of 100 μl will be spread on the agar plates. The plates will be incubated at 44°C for 24 hours. After incubation, E. coli will grow as blue-green colonies, and the results of the total bacterial count will be expressed as a colony-forming unit (CFU)/g of sample. The colonies will be subjected to biochemical confirmation, including an Indole production test to confirm the positive or negative isolates. The positive results for indole production isolates will be confirmed as E. coli.28\n\nSalmonella species: A similar procedure as for E. coli will be carried out to identify and enumerate Salmonella species. Briefly, each 100 μl from the dilution range of 10-1 – 10-10will be spread on the selective media Xylose Lysine Deoxycholate (XLD) Agar. The plates will be incubated at 37°C for 24 h. After incubation, the bacterial colonies will appear pink to red-colored with or without centers. The typical colonies will be further subjected to an array of biochemical tests such as oxidase, indole production, and catalase for further confirmation26\n\nPseudomonas species: A selective and differential medium, Cetrimide Agar (Himedia, India), will be prepared to identify and enumerate Pseudomonas spp. Each 100 μl from the dilution range 10-1 – 10-10 will be spread on the selective media Cetrimide agar.29 The plates will be incubated at 42°C for 48h. After incubation, the presumptive colonies will be identified further by a classical biochemical method, including triple sugar iron and oxidase tests.29\n\nThe antimicrobial resistance pattern of the bacteria isolated from the vegetable and soil samples will be performed by antimicrobial susceptibility testing (AST). The determination of antimicrobial susceptibility will be performed by Kirby-Bauer disk diffusion technique using Muller Hinton Agar.30 To check the sensitivity of the drugs, different panel of antibiotic-impregnated discs recommended for the bacterial isolates will be used as per the Clinical and Laboratory Standards Institute (CLSI) guidelines.31\n\nFor pure subculture isolation, two bacterial colonies will be taken from each the vegetable and soil sample plates. The isolated colonies will be separately mixed well under aseptic conditions in physiological saline and dissolved to get a homogenous mixture comparable to 0.5 McFarland standard. The diluted bacterial suspension will then be transferred to Muller-Hinton agar plate using sterile cotton swab and the plates will be seeded uniformly rubbing the swab against the entire agar surface. After the inoculums get dried, antibiotic impregnated disks will be applied aseptically to the surface of the inoculated plates at an appropriate distance using sterile forceps. The plates will then be incubated at 37°C for 24h.32 The same procedure will be followed for all the bacterial isolates included in this study: E. coli, Salmonella species and Pseudomonas species.\n\nThe analysis of the antibiotic susceptibility tests will be determined by the zone of inhibition. The inhibition zone will be measured for the different antibiotics used as per the bacterial isolates. The interpretation of susceptible, intermediate and resistant categories will be assigned on the basis of the critical points recommended by the CLSI guidelines.31\n\n\n\nI. DNA extraction:\n\na) Soil sample: The soil sample collected will be processed for DNA extraction. The HiPurATM Soil DNA purification kit will be used for the isolation of DNA from soil samples. The protocol provided with the kit will be followed for isolation of complete DNA from the soil samples. The extracted DNA will be stored in elution buffer. The eluate containing the pure soil DNA will be stored at 2-8°C if processed within short-term (24-48 hours), otherwise for long-term duration -20°C or lower temperature (-80°C) is recommended by the manufacturer.\n\nb) Plant sample: The plant parts sample collected will be processed for DNA extraction. The isolation of plant genomic DNA will be processed using HiPer® Plant Genomic DNA Extraction kit. The whole plant genomic DNA will be extracted following the protocol provided with the kit. The eluate containing pure extracted genomic DNA will be stored for short term storage (24-48 h) at 2-8°C as recommended. For long-term storage, -20°C or lower temperature (-80°C) is recommended. The Elution Buffer will help to stabilize the DNA at these temperatures.\n\nII. Detection and quantification of ARGs\n\nThe extracted DNA of both, soil and plant samples, will be analyzed for the presence and the quantification of ARGs. The standardized protocol for the detection and quantification after standardization will be performed by Quantitative Polymerase Chain Reaction (qPCR). Melting curves will obtained to confirm the amplification specificity. The qPCR reactions will be performed by triplicates, using a fixed dilution of raw DNA extract.\n\nThe quantification standards will be obtained using TaqManTM Comprehensive Microbiota control. Standard curves (Ct per log copy number) for quantification of all genes will be obtained for each run. Gene copy number of standards will be determined via the genomic DNA concentration, applying the DNA copy number and the Dilution calculator algorithms. Three technical replicates will be run for the standard curves; complete reaction mixes plus nuclease free water, but without DNA sample were used as a negative control for qPCR reactions. ARGs concentration in samples will be calculated using the standard curve equation and the measure Ct value. The quality control of raw Ct values for standard curve and unknown samples will be performed before the analysis. The limit of quantification (LOQ) will be defined as the lowest point on the linear part of the standard curve: 100 gene copies per reaction for ARGs for 16S rDNA. Copy numbers of all ARGs will be normalized to gram of sample (gene copies g−1).\n\nData from this study will be available at the Center for Development Research (ZEF), Bonn, Germany, after the completion of this study. Researchers who meet the criteria for access to confidential data are encouraged to approach Ms. Ana Maria, Coordinator Fortschrittskolleg ‘One Health’, Center for Development Research (ZEF), Bonn, Genscherallee 3, 53113 Bonn, Germany. Email: health@uni-bonn.de\n\n\nConclusion\n\nThe benefit and expected outcome of this study will be the collection of baseline data for the AMR in the fresh produce and soil in the Ahmedabad, India. This will be the first of its kind study bringing exploration of the agroecosystem and One Health approach together in India AMR loads in vegetables and corresponding soil will be linked to the agricultural practices followed by the farmers. With the objectives of this study, it will not only develop evidence on the possible routes of AMR spread and risk factors, but also will facilitate recommended WHO AMR surveillance in the plant-based agriculture through One Health approach. This vAMR study targets two broad level of dissemination. First the results will be published in the scientific journals as part of the evidence contribution from India. Second the key findings will be disseminated through the regional workshops with the policy makers, program managers, and other relevant stakeholders engaged in the concerned sectors. Recommendations from this study could be a potential source for the future surveillance of AMR for benchmarking its status, developing intervention strategies and prioritizing effective evidence-based actions. This will also provide the evidence for including the different reservoirs of environment as one of the major AMR surveillance point in the Indian National Action Plan for AMR surveillance.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nRepository: PRISMA-P checklist for ‘Vegetables as vehicle for antimicrobial resistance (vAMR): An agroecosystem exploration from the One Health perspective in India’. https://doi.org/10.6084/m9.figshare.22188334. 33\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 wish to thank the team of experts from the Ahmedabad Municipal Corporation, Department of Health & Family Welfare, Department of Animal Husbandry, Government of Gujarat, India, and selected agricultural farmers from Ahmedabad city, India for their valuable inputs and suggestions in the development phase of the study. We would also like to thank our colleagues at the Centre for One Health Education, Research & Development, Indian Institute of Public Health Gandhinagar, India, for facilitating the study permission and providing all the administrative support for the same.\n\n\nReferences\n\nRobinson TP, Bu DP, Carrique-Mas J, et al.: Antibiotic resistance is the quintessential One Health issue. Trans. R. Soc. Trop. Med. Hyg. 2016; 110: 377–380. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPokharel S, Raut S, Adhikari B: Tackling antimicrobial resistance in low-income and middle-income countries. BMJ Glob. Health. 2019; 4: e002104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAntimicrobial Resistance: Tackling a crisis for the health and wealth of nations.\n\nGLASS-AMR: Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report: 2021.2021. Accessed 11 Nov 2021. Reference Source\n\nAyukekbong JA, Ntemgwa M, Atabe AN: The threat of antimicrobial resistance in developing countries: causes and control strategies. Antimicrob Resist. Infect. Control. 2017; 6: 6. Publisher Full Text\n\nGraham DW, Bergeron G, Bourassa MW, et al.: Complexities in understanding antimicrobial resistance across domesticated animal, human, and environmental systems. Ann. N. Y. Acad. Sci. 2019; 1441: 17–30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSkandalis N, Maeusli M, Papafotis D, et al.: Environmental Spread of Antibiotic Resistance. Antibiotics. 2021; 10: 640. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCristino JM: Correlation between consumption of antimicrobials in humans and development of resistance in bacteria. Int. J. Antimicrob. Agents. 1999; 12: 199–202. Publisher Full Text\n\nHoover NL, Law JY, Long LAM, et al.: Long-term impact of poultry manure on crop yield, soil and water quality, and crop revenue. J. Environ. Manag. 2019; 252: 109582. PubMed Abstract | Publisher Full Text\n\nTien YC, Li B, Zhang T, et al.: Impact of dairy manure pre-application treatment on manure composition, soil dynamics of antibiotic resistance genes, and abundance of antibiotic-resistance genes on vegetables at harvest. Sci. Total Environ. 2017; 581-582: 32–39. Publisher Full Text\n\nHe Y, Yuan Q, Mathieu J, et al.: Antibiotic resistance genes from livestock waste: occurrence, dissemination, and treatment. npj Clean Water. 2020; 3: 1–11. Publisher Full Text\n\nZhang L, Kinkelaar D, Huang Y, et al.: Acquired antibiotic resistance: Are we born with it? Appl. Environ. Microbiol. 2011; 77: 7134–7141. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOndon BS, Li S, Zhou Q, et al.: Sources of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistance Genes (ARGs) in the Soil: A Review of the Spreading Mechanism and Human Health Risks. Rev. Environ. Contam. Toxicol. 2021; 256: 121–153. PubMed Abstract | Publisher Full Text\n\nChen QL, Cui HL, Su JQ, et al.: Antibiotic Resistomes in Plant Microbiomes. Trends Plant Sci. 2019; 24: 530–541. Publisher Full Text\n\nZhang YJ, Hu HW, Chen QL, et al.: Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes. Environ. Int. 2019; 130: 104912. PubMed Abstract | Publisher Full Text\n\nBhunia AK, Liu Y, Kniel K, et al.: Characteristics and Global Occurrence of Human Pathogens Harboring Antimicrobial Resistance in Food Crops: A Scoping Review.2022; 6: 824714.\n\nRahman M, Alam M-U, Luies SK, et al.: Contamination of Fresh Produce with Antibiotic-Resistant Bacteria and Associated Risks to Human Health: A Scoping Review. Int. J. Environ. Res. Public Health. 2021; 19: 360. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlegbeleye OO, Singleton I, Sant’Ana AS: Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review. Food Microbiol. 2018; 73: 177–208. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMinistry of Home Affairs: Census of India Website: Office of the Registrar General & Census Commissioner, India.2011. Accessed 25 Nov 2021. Reference Source\n\nTimes of India: “Veg” Gujarat has 40% non-vegetarians|Ahmedabad News - Times of India.2016. Accessed 25 Nov 2021. Reference Source\n\nGujarat Livelihood Promotion: Horticulture - Sector Overview|Sector wise Development|Activities|Gujarat Livelihood Promotion Company.2011. Accessed 25 Nov 2021. Reference Source\n\nMasterton R: The importance and future of antimicrobial surveillance studies. Clin. Infect. Dis. 2008; 47: S21–S31. Publisher Full Text\n\nWHO: Joint FAO/WHO expert meeting in collaboration with OIE on foodborne antimicrobial resistance: role of the environment, crops and biocides: meeting report.2018. Accessed 17 Nov 2021. Reference Source\n\nSchwaiger K, Helmke K, Hölzel CS, et al.: Antibiotic resistance in bacteria isolated from vegetables with regards to the marketing stage (farm vs. supermarket). Int. J. Food Microbiol. 2011; 148: 191–196. PubMed Abstract | Publisher Full Text\n\nCerqueira F, Matamoros V, Bayona JM, et al.: Antibiotic resistance gene distribution in agricultural fields and crops. A soil-to-food analysis. Environ. Res. 2019; 177: 108608. Publisher Full Text\n\nAbdus Sobur M, al Momen Sabuj A , Sarker R, et al.: Antibiotic-resistant Escherichia coli and Salmonella spp. associated with dairy cattle and farm environment having public health significance. Vet World. 2019; 12: 984–993. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAntony AC, Paul MK, Silvester R, et al.: Comparative evaluation of EMB agar and hicrome E. coli agar for differentiation of green metallic sheen producing non E. Coli and typical E. Coli colonies from food and environmental samples. J. Pure Appl. Microbiol. 2016; 10: 2863–2870. Publisher Full Text\n\nKannan MN, Badoni A, Chamoli V, et al.: Advances in Agriculture and Natural Sciences for Sustainable Agriculture (October 12 &13, 2018) Isolation and characterization of bacterial isolates from agriculture field soil of Roorkee region. ~ 108 ~. J. pharmacogn. phytochem. 2018; 5: 108–10.\n\nRuiz-Roldán L, Rojo-Bezares B, Lozano C, et al.: Occurrence of pseudomonas spp. In raw vegetables: Molecular and phenotypical analysis of their antimicrobial resistance and virulence-related traits. Int. J. Mol. Sci. 2021; 22: 12626. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEUCAST: Disk Diffusion Method for Antimicrobial Susceptibility Testing-Antimicrobial susceptibility testing EUCAST disk diffusion method.2021.\n\nWeinstein MP, Patel JB, Bobenchik AM, et al.: M100 Performance Standards for Antimicrobial Susceptibility Testing A CLSI supplement for global application. Performance Standards for Antimicrobial Susceptibility Testing Performance Standards for Antimicrobial Susceptibility Testing. 2020.\n\nGaredew L, Hagos Z, Addis Z, et al.: Prevalence and antimicrobial susceptibility patterns of Salmonella isolates in association with hygienic status from butcher shops in Gondar town, Ethiopia. Antimicrob. Resist. Infect. Control. 2015; 4: 1–7.\n\nKalpana P, Falkenberg T, Yasobant S, et al.: PRISMA-P-checklist_vAMR_Kalpana P et al, 2023.doc. figshare. Online resource. 2023. Publisher Full Text"
}
|
[
{
"id": "187877",
"date": "11 Aug 2023",
"name": "Karin Schwaiger",
"expertise": [
"Reviewer Expertise Microbiology",
"antibiotic resistance",
"bacteriology",
"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 describe a study design to determine the extent to which vegetables are a vehicle for antimicrobial resistance in Ahmedabad, India. For this purpose, they first intend to conduct a systematic review on the occurrence of antibiotic resistant bacteria (ARB) and AR genes (ARGs) on vegetables (and in soil) in South Asia. This is followed by agriculture farmland surveys to find out, among other things. about general agricultural practices and prevailing household consumption patterns. Based on the results of the upstream research, vegetable and soil samples will be collected from selected farms and analyzed for the presence of ARB and ARGs using bacteriological and molecular biological techniques.\nOverall, the study is logically and consecutively structured and explained in an understandable way. It should be emphasized that the authors apparently already have practical experience, as they are aware of some difficulties (e.g., lack of databases of agricultural farms), but found solutions for these (e.g., snowball system). It is also very good that an ethical statement is already available. The rationale for, and objectives of, the study are clearly described – although I think the term “One Health” is somewhat overused or lofty. It is true that antibiotic-resistant bacteria may play an important role for humans along the food chain. This study aims to determine prevalences, which of course can lead to a better understanding and consequently (indirectly by implementing appropriate measures/intervention strategies) also to a risk reduction. Humans themselves or samples of them, however, are not taken into account in the investigations. In this respect, I would recommend using the term \"One Health\" in a somewhat less inflationary way.\nI have a few more comments regarding the wording of the methodology:\nIntroduction: The authors state that “The prophylactic use and practice of sub-lethal doses of antibiotics in livestock as growth promoters to maintain health and productivity contribute to a significant part.” to the AMR issue. I would be careful with this wording: In many countries, growth promoters have long been banned. Of course, this does not mean that antibiotics can no longer be used at all in animals, but only for therapeutic purposes (not prophylactic).\nCorrectly, the authors recognize that organic fertilizers (e.g., manure) may play an important role in ARB transmission. They also seem to take this important point into account in their own research (important data would be e.g. animal species, storage time, temperature, hygienization measures). When later comparing the results of the present study with those of other countries, it should be recognized that in vegetable cultivation often no organic fertilizers (only mineral fertilizers) are used for hygienic reasons (e.g. in Germany). This might then explain (besides irrigation water) differences in the prevalences of certain (AR) bacteria (especially faecal indicators such as E. coli or Salmonella).\nMethods for research question 1: The authors will conduct a systematic review. They state that data will be extracted and the results will form an evidence base for the selection of ARB and ARGs for the next objective of the study. This is basically a valid approach. However, since the review focuses on Southeast Asia and not much data is available here yet, this may miss some important ARB and ARGs. Therefore, I would suggest expanding the search in this regard by including studies from other countries as well. In any case, antibiotics important in human medicine should be considered (e.g. according to WHO/Ranking of medically important antimicrobials).\nMethods for research question 2: The AMR field investigation seems to be very well thought out. A personal visit to the farms is also very important in my experience to inform the farmers about the basic idea and to arouse interest in participating. The selection of bacteria is also sensible in principle (faecal indicators, pathogens, environmental bacteria), but I am not sure if a sufficient number of E. coli and Salmonella will be isolated to do a statistical analysis afterwards (the prevalence in other studies is quite low). However, since the authors state that they will include the results of their systematic review anyway, I assume this will not be a problem (but then, not only the occurrence of ARBs should be searched but also that of bacteria on vegetables in general).\nSelection of AMR genes: See comment in “Methods for research question 1”.\nSampling procedure: It is not clear to me how many samples are actually to be taken: first it says \"Five vegetable samples....will be collected\", but then at \"Vegetable sampling\" it says “A total of one vegetable sample…will be collected”. How does that come about? Is it related to the 5 different vegetable types (top five)? Please clarify/correct/rephrase.\nIdentification and enumeration of bacteria: Possibly, one could consider investigating the aerobic mesophilic bacterial count as well, if bacteriology is performed anyway. This is only a small additional effort (even if the soil samples probably have to be diluted more than to 10^-10) and provides information about the general hygiene status of vegetables from this region (after following safe handling procedures). E. coli: the authors state that E. coli will be confirmed by a positive indole test. Since other Enterobacteriaceae are indole positive as well, I assume that the mentioned “biochemical confirmation” is able to differentiate these species from E. coli? Salmonella: I think that for Salmonella detection in this highly heterogeneous microbiota in the sample material, pre-enrichment is mandatory. It is also important to use not only peptone water but buffered peptone water to neutralize the acid produced by other competing bacteria. Please follow established protocols.\nAntimicrobial susceptibility testing: The authors will use the disk diffusion technique. This is basically a valid method – but why not using microdilution? In my opinion, this method would be better suited for the intended high throughput. Anyhow, it should follow an established protocol. In the description of the procedure it is not quite clear if it is intended to take the two bacterial colonies directly from the selective agar plates (it is important to take the colonies from neutral agar plates incubated in consistent times and temperatures). Since a biochemical confirmation of the colonies was conducted beforehand, I think my concern is unfounded, but please clarify. It is also not clear if a total of two bacterial colonies are taken or two bacterial colonies from each duplicate.\nMolecular analysis: Plant sample: Why using a plant genomic DNA extraction kit if it is intended to investigate bacterial DNA? Of course, there might be some bacterial endophytes in the plant cells, but that is certainly not the overwhelming majority – most of the bacteria will be contaminants on the surface of the vegetables. Detection and quantification of ARGs: This part of the investigation seems a bit separated from the rest of the study. Does that mean that the isolated bacteria will not be tested for ARGs, only the sample material (soil, vegetables) itself? This can be done, but it should be kept in mind that this will limit the informative value: Since many resistance genes are found in different bacterial species and, additionally, the microbiota differ greatly among different vegetable species, the results should be interpreted very carefully (e.g., only a very small fraction of the tetracyline resistance genes will origin from E. coli, but no definite statement is possible). It is also not possible to determine multidrug resistances, and it cannot be differentiated between opportunists and pathogens (e.g. for risk estimation). Standard curve: If only the sample material itself will be investigated for the presence of ARGs: I assume that the standard curve is created in the respective DNA-free (e.g. irradiated) sample material (vegetables, soil suspensions) in order to take any matrix effects into account?\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": "11270",
"date": "04 Apr 2024",
"name": "Pachillu Kalpana",
"role": "Author Response",
"response": "Comment 1: The authors describe a study design to determine the extent to which vegetables are a vehicle for antimicrobial resistance in Ahmedabad, India. For this purpose, they first intend to conduct a systematic review on the occurrence of antibiotic resistant bacteria (ARB) and AR genes (ARGs) on vegetables (and in soil) in South Asia. This is followed by agriculture farmland surveys to find out, among other things. about general agricultural practices and prevailing household consumption patterns. Based on the results of the upstream research, vegetable and soil samples will be collected from selected farms and analyzed for the presence of ARB and ARGs using bacteriological and molecular biological techniques. Response: Thanks for your time and reviewing the draft in detail. Changes: NA Comment 2: Overall, the study is logically and consecutively structured and explained in an understandable way. It should be emphasized that the authors apparently already have practical experience, as they are aware of some difficulties (e.g., lack of databases of agricultural farms), but found solutions for these (e.g., snowball system). It is also very good that an ethical statement is already available. Overall, the study is logically and consecutively structured and explained in an understandable way. It should be emphasized that the authors apparently already have practical experience, as they are aware of some difficulties (e.g., lack of databases of agricultural farms), but found solutions for these (e.g., snowball system). It is also very good that an ethical statement is already available. The rationale for, and objectives of, the study are clearly described – although I think the term “One Health” is somewhat overused or lofty. It is true that antibiotic-resistant bacteria may play an important role for humans along the food chain. This study aims to determine prevalence, which of course can lead to a better understanding and consequently (indirectly by implementing appropriate measures/intervention strategies) also to a risk reduction. Humans themselves or samples of them, however, are not taken into account in the investigations. In this respect, I would recommend using the term \"One Health\" in a somewhat less inflationary way. Response: Thank you very much for your kind review. Yes, as a part of the study, the base information was gathered before planning for the study and to be aware of the difficulties during the process. The ethical clearance was obtained from both institutions for conducting the study. Thank you. You also very well mentioned the importance of ARB and its role in humans through the food chain, which describes it well as a One Health concept. But we agree completely that if we are not able to approach all the sectors of One Health, it is better to use the term, however, keeping it less inflammatory. Taking that into account, the manuscript has been updated. Changes: The whole manuscript is updated. Comment 3: I have a few more comments regarding the wording of the methodology: Introduction: The authors state that “The prophylactic use and practice of sub-lethal doses of antibiotics in livestock as growth promoters to maintain health and productivity contribute to a significant part.” to the AMR issue. I would be careful with this wording: In many countries, growth promoters have long been banned. Of course, this does not mean that antibiotics can no longer be used at all in animals, but only for therapeutic purposes (not prophylactic). Response: Thank you. I agree that many developed countries banned the use of antibiotics as growth promoters and, therefore, reframed the sentence to make it much more globally sound. There are countries such as India where, due to a lack of policies for antibiotic use in animals, prophylactic use still plays a very prominent role. Changes: The manuscript is updated from lines 15-23 in track changes mode. Comment 4: Correctly, the authors recognize that organic fertilizers (e.g., manure) may play an important role in ARB transmission. They also seem to take this important point into account in their own research (important data would be e.g. animal species, storage time, temperature, hygienization measures). When later comparing the results of the present study with those of other countries, it should be recognized that in vegetable cultivation often no organic fertilizers (only mineral fertilizers) are used for hygienic reasons (e.g. in Germany). This might then explain (besides irrigation water) differences in the prevalences of certain (AR) bacteria (especially faecal indicators such as E. coli or Salmonella). Response: Thank you for taking this point into account. This will be a good point of view to see during analysis. During the comparison of results, this might be a good explanation point for the results. Changes: No changes Comment 5: Methods for research question 1: The authors will conduct a systematic review. They state that data will be extracted and the results will form an evidence base for the selection of ARB and ARGs for the next objective of the study. This is basically a valid approach. However, since the review focuses on Southeast Asia and not much data is available here yet, this may miss some important ARB and ARGs. Therefore, I would suggest expanding the search in this regard by including studies from other countries as well. In any case, antibiotics important in human medicine should be considered (e.g. according to WHO/Ranking of medically important antimicrobials). Response: Yes, we agree that the scope of review in only including the published literature from Southeast Asia might lead to skip other important ARB and ARGs reported from other countries. However, one of the major reasons for only selecting these areas is to have a focus on scarcity of data from this region and concentrate attention on the need for more studies in this area. This is also decided as per the mandate of the funded project. Regarding the WHO suggestion, the selection of bacteria is according to the WHO guidance for the importance of their role in plant-based food and their role in spread of AMR. Changes: No changes Comment 6: Methods for research question 2: The AMR field investigation seems to be very well thought out. A personal visit to the farms is also very important in my experience to inform the farmers about the basic idea and to arouse interest in participating. The selection of bacteria is also sensible in principle (faecal indicators, pathogens, environmental bacteria), but I am not sure if a sufficient number of E. coli and Salmonella will be isolated to do a statistical analysis afterwards (the prevalence in other studies is quite low). However, since the authors state that they will include the results of their systematic review anyway, I assume this will not be a problem (but then, not only the occurrence of ARBs should be searched but also that of bacteria on vegetables in general). Response: Thank you for appreciating the investigation plans. The review will provide us with the idea of prevalence, as you have also quite clearly mentioned, which will help us in the process. I agree with you about the importance of including the total occurrence of bacteria on vegetables, which can have added value. However, the limited time and resources available to complete the project led to the compromise of this idea, focusing on some specific bacteria with much more in focus according to the WHO guidelines. Indeed, our final analysis method does not only include ARB because identification is done in two steps: first, cultivation of bacteria species of interest, and second, resistance tests of these isolates. That was a result of the review and practical possibilities in the labs, therefore not clear when writing this study concept. Changes: No changes Comment 7: Selection of AMR genes: See comment in “Methods for research question 1”. Sampling procedure: It is not clear to me how many samples are actually to be taken: first it says \"Five vegetable samples....will be collected\", but then at \"Vegetable sampling\" it says “A total of one vegetable sample…will be collected”. How does that come about? Is it related to the 5 different vegetable types (top five)? Please clarify/correct/rephrase. Response: I hope the reply to the comment for research question 1 clarifies this one here. The top five vegetables will be selected after the survey. During the sample collection, one vegetable sample and its soil sample will be collected in duplicate from every selected vegetable-producing farm. The collected samples from all investigated farms together will represent the top five vegetables. The sentence has been rephrased for clarification. Changes: The manuscript is updated from lines 275-286 in track changes mode. Comment 8:Identification and enumeration of bacteria: Possibly, one could consider investigating the aerobic mesophilic bacterial count as well, if bacteriology is performed anyway. This is only a small additional effort (even if the soil samples probably have to be diluted more than to 10^-10) and provides information about the general hygiene status of vegetables from this region (after following safe handling procedures). E. coli: the authors state that E. coli will be confirmed by a positive indole test. Since other Enterobacteriaceae are indole positive as well, I assume that the mentioned “biochemical confirmation” is able to differentiate these species from E. coli? Salmonella: I think that for Salmonella detection in this highly heterogeneous microbiota in the sample material, pre-enrichment is mandatory. It is also important to use not only peptone water but buffered peptone water to neutralize the acid produced by other competing bacteria. Please follow established protocols. Response: I hope the reply to the comment for research question 1 clarifies this one here. The top five vegetables will be selected after the survey. During the sample collection, one vegetable sample and its soil sample will be collected in duplicate from every selected vegetable-producing farm. The collected samples from all investigated farms together will represent the top five vegetables. The sentence has been rephrased for clarification. We agree that investigating the aerobic mesophilic bacterial count will be a small additional effort, but as you mentioned, soil samples will need to be diluted more. Additionally, we use selective agar for coliforms. Therefore, we have considered not only reporting E. coli but also accounting for the total coliform count for the samples, which is often an indicator of cleanliness and hygiene. Regarding the biochemical confirmation of E. coli with indole due to the very selective media that will be used for the isolation of E. coli. Although the manufacturer says there could be growth of Salmonella in very rare cases. The bacterial isolates can be differentiated with their color on the agar plates but indole positive E. coli and Salmonella which is an indole negative bacterium can be a confirmatory test that while proceeding further there is no contamination. However, with the consultation with labs, we considered going with IMViC tests to differentiate the Enterobacteriaceae family members further. The pre-enrichment process for Salmonella detection is well understood. The suggestion provided is well taken and the buffered peptone water will be used for the process. The BPA will be used for the non- selective enrichment process which will be followed by the very selective media for isolation of Salmonella. The authors thought of following the published articles protocol due to the non-sample specific protocol for Salmonella detection in established protocols such as BAM during the manuscript preparation. But doing pre-enrichment, we are not able to count real Salmonella concentrations. The researchers of the articles which has been referenced in the manuscript have used the same media and method for the isolation of Salmonella from vegetable samples as we choose, and they were able to find relevant numbers of Salmonella. Changes: The manuscript is updated from lines 321-331 in track changes mode. Comment 9: Antimicrobial susceptibility testing: The authors will use the disk diffusion technique. This is basically a valid method – but why not using microdilution? In my opinion, this method would be better suited for the intended high throughput. Anyhow, it should follow an established protocol. In the description of the procedure it is not quite clear if it is intended to take the two bacterial colonies directly from the selective agar plates (it is important to take the colonies from neutral agar plates incubated in consistent times and temperatures). Since a biochemical confirmation of the colonies was conducted beforehand, I think my concern is unfounded, but please clarify. It is also not clear if a total of two bacterial colonies are taken or two bacterial colonies from each duplicate. Response: The disk diffusion method is been chosen due to its much use and less expense in manual work regarding less technical equipment as compared to the microdilution method. You can test more than one antibiotic in parallel on the same plate, whereas microdilution needs a single dilution series for every antibiotic. In the beginning of the study, during the conceptual phase, it was not clear how many bacterial colonies will be found during the process. The idea is to test several, but eventually not all bacterial colonies (depending on their numbers found and the workload we can afford) from both, the vegetable and the respective soil, to compare their resistance patterns. The text is revised. Changes: The manuscript is updated from lines 360-363 in track changes mode. Comment 10: Molecular analysis: Plant sample: Why using a plant genomic DNA extraction kit if it is intended to investigate bacterial DNA? Of course, there might be some bacterial endophytes in the plant cells, but that is certainly not the overwhelming majority – most of the bacteria will be contaminants on the surface of the vegetables. Detection and quantification of ARGs: This part of the investigation seems a bit separated from the rest of the study. Does that mean that the isolated bacteria will not be tested for ARGs, only the sample material (soil, vegetables) itself? This can be done, but it should be kept in mind that this will limit the informative value: Since many resistance genes are found in different bacterial species and, additionally, the microbiota differ greatly among different vegetable species, the results should be interpreted very carefully (e.g., only a very small fraction of the tetracyline resistance genes will origin from E. coli, but no definite statement is possible). It is also not possible to determine multidrug resistances, and it cannot be differentiated between opportunists and pathogens (e.g. for risk estimation). Standard curve: If only the sample material itself will be investigated for the presence of ARGs: I assume that the standard curve is created in the respective DNA-free (e.g. irradiated) sample material (vegetables, soil suspensions) in order to take any matrix effects into account? Response: The protocol has been updated concerning the extraction kit that will ultimately be used for DNA extraction in the study. This results from a methodical harmonization with the other researchers who are working in this field, and it was previously shown that the kit worked on both types of samples selected in this study. The disk diffusion method will be used to test the isolated bacteria for AMR susceptibility. Gene detection of ARG within individual isolates will not be done. We know that, thus, we underestimate phenotypically expressed resistances and do not detect non-expressed multi-resistances, but we thought that ARG occurrence in the environment (soil and samples) does tell us more about the resistance spread of human-relevant antibiotics. ARG analysis in both the isolates and samples is out of our monetary budget and available time frame. Thus, we had to restrict and select the better analysis for our research objectives and keep in mind that this will limit the informative value, as you stated. However, the sample will be investigated by isolating the DNA from the complete sample using the whole metagenomic sequencing method. The AST patterns will provide us with information regarding the specific bacteria selected as per WHO suggestions, and the Whole metagenomic sequencing will provide us with more in-depth information of ARGs. This can also help the researchers compare the much better methodology to be followed in the near future and according to the budget. Whole metagenomic sequencing will help identify and cluster many gene fragments into groups. The resistant genes will be identified using the AMR databases and the potential connections of metagenomic results to phenotypically observed data. With the changed investigation plan, I hope the standard curve will no longer be required. Changes: The manuscript is updated from lines 399-411 and 416-527 in track changes mode. Thank you very much for your comments and suggestions and for reviewing the manuscript. I hope we clarified them and updated the manuscript for better understanding and adaptability."
}
]
},
{
"id": "195948",
"date": "25 Sep 2023",
"name": "William Calero-Cáceres",
"expertise": [
"Reviewer Expertise Antibiotic resistance",
"bacteriophages",
"molecular analysis",
"eDNA",
"Salmonella",
"Whole-genome sequencing"
],
"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 Kalpana et al. offers a compilation of methodologies intended to address two research questions: \"1. Which antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) are prevalent, or presumed to be widespread, within the soil-plant-fruit continuum in the South Asia region?\" and \"2. What is the risk of AMR spreading across the soil-plant-fruit continuum in agricultural farms of Ahmedabad, India?\" The article is classified as a \"Study Protocol\"-type and is supported by F1000Research.\nHowever, the title \"Vegetables as a vehicle for antimicrobial resistance (vAMR): An agroecosystem exploration from the One Health perspective in India\" implies that conclusive research has been conducted, leading readers to expect evidence within the article supporting the notion that vegetables act as vectors of AMR determinants. I recommend modifying the title to more accurately reflect the content, emphasizing that this manuscript primarily proposes protocols for similar studies.\nThe criteria for the \"Selection of AMR genes (ARGs) for molecular analysis\" are vague. Why only two ARGs? Most studies often include common ARGs like sul1, tetA, ermB. The rationale should be modified to emphasize clinically relevant or emerging ARGs.\nConcerning the source of data and data collection methods, the reasoning behind choosing 300 samples needs a thorough explanation.\nIn the section on the identification and enumeration of bacteria, standardized methodologies like ISO or BAM should be detailed. The mentioned methodologies lack validation. For instance, direct plating is suggested for Salmonella enumeration, but ISO 6579 recommends pre-enrichment and enrichment steps. The methodological limitation for Salmonella does not allow direct quantification from the sample.\nIn procedures for antimicrobial susceptibility testing, the rationale for selecting specific antibiotics should be included. As it stands, the description does not significantly contribute to current knowledge or provide guidance for conducting studies as suggested.\nRegarding molecular analysis, it is mentioned that qPCR will be applied for the quantification of specific ARGs. However, the selection rationales for these genes are missing. Please include references detailing the initial validation of the techniques you intend to develop.\nBased on my experience, this article is currently incomplete and requires more in-depth analysis to serve as a foundational resource for studies about AMR following the One Health approach. I earnestly recommend publishing your article once the protocols are described in greater detail and, ideally, results are included.\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? Not applicable",
"responses": [
{
"c_id": "11271",
"date": "04 Apr 2024",
"name": "Pachillu Kalpana",
"role": "Author Response",
"response": "Comment 1: The manuscript by Kalpana et al. offers a compilation of methodologies intended to address two research questions: \"1. Which antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) are prevalent, or presumed to be widespread, within the soil-plant-fruit continuum in the South Asia region?\" and \"2. What is the risk of AMR spreading across the soil-plant-fruit continuum in agricultural farms of Ahmedabad, India?\" The article is classified as a \"Study Protocol\"-type and is supported by F1000Research. Response: Thanks for your time reviewing the work and your kind reflections. Changes: No change Comment 2: However, the title \"Vegetables as a vehicle for antimicrobial resistance (vAMR): An agroecosystem exploration from the One Health perspective in India\" implies that conclusive research has been conducted, leading readers to expect evidence within the article supporting the notion that vegetables act as vectors of AMR determinants. I recommend modifying the title to more accurately reflect the content, emphasizing that this manuscript primarily proposes protocols for similar studies. Response: You are totally right; thanks for the advice. The title has been changed to: ''Agroecosystem exploration for Antimicrobial Resistance in Ahmedabad, India: A Study Protocol.'' Changes: The title of the manuscript has been revised. Comment 3: The criteria for the \"Selection of AMR genes (ARGs) for molecular analysis\" are vague. Why only two ARGs? Most studies often include common ARGs like sul1, tetA, ermB. The rationale should be modified to emphasize clinically relevant or emerging ARGs. Response: Thank you for pointing this out. The sentence reflected the need to select at least two; however, if the review finds more, they will also be included in the molecular analysis process. To clear up any misunderstanding, the sentence has been rephrased. Also, with the updated investigation plan, a greater number of ARGs can also be analysed. Changes: The manuscript is updated from lines 268-270 in track changes mode. Comment 4: Concerning the source of data and data collection methods, the reasoning behind choosing 300 samples needs a thorough explanation. Response: Thanks for your kind reflections. The manuscript has been updated to clarify the idea of the samples. In the first step, 300 farms will be selected for the survey, and in the second step, 300 samples, including 150 vegetable samples and 150 soil samples, will be collected. Choosing 300 samples for the survey depends heavily on funding availability and the time frame. We have added the same limitation. “The limitation is because of funding and time frame available.” Changes: The manuscript is updated from lines 221-222 and 226-231 in track changes mode. Comment 5: In the section on the identification and enumeration of bacteria, standardized methodologies like ISO or BAM should be detailed. The mentioned methodologies lack validation. For instance, direct plating is suggested for Salmonella enumeration, but ISO 6579 recommends pre-enrichment and enrichment steps. The methodological limitation for Salmonella does not allow direct quantification from the sample. Response: Thank you for your suggestion. The reason for the identification and enumeration of bacteria not according to standardized methods like ISO and BAM is that those are developed and optimized for human samples or other samples containing low background flora, such as drinking water or food. Environmental samples, e.g., soil and plants, as investigated here, or even wastewater or manure, contain much more background flora, which interferes with the culture assays up to non-analyzability, especially if target bacteria concentrations are low. For medical/hygienic surveillance purposes, pre-enrichment is okay, but that leads to non-quantifiable results concerning the original concentrations in a sample. Choosing a methodology that is known to work with environmental samples and, moreover, is adapted to them seems to be more useful for our research objective, and the intended results are more likely to be yielded. Therefore, the published articles that have reported the data on the same have been used as reference for the methodology. Changes: The manuscript has been updated, and a note has been added from lines 346-357 in track changes mode. Comment 6: In procedures for antimicrobial susceptibility testing, the rationale for selecting specific antibiotics should be included. As it stands, the description does not significantly contribute to current knowledge or provide guidance for conducting studies as suggested. Response: You are right; we missed that information in part. The antibiotic panel selection is mainly based on the pre-selected bacteria. We added information about the selection of antibiotics for susceptibility testing into the chapter “Method for research question 2.” Concerning the testing method, we are not sure if the sentence was not clearly describing the rationale. We revised the text of the three sub-chapters dealing with antimicrobial susceptibility testing. Changes: The manuscript is updated from lines 260-265 in track changes mode. Comment 7: Regarding molecular analysis, it is mentioned that qPCR will be applied for the quantification of specific ARGs. However, the selection rationales for these genes are missing. Please include references detailing the initial validation of the techniques you intend to develop. Response: The manuscript has been updated concerning molecular analysis to improve the data and answer the objectives. We switched to whole metagenomic analysis instead of qPCR because of a discussion with the labs working in the field of AMR. It has been argued that the qPCR method is more sensitive and suitable for absolute quantification of target genes, while whole metagenomics has the potential to provide an overview of the genes as well as of the respective relative abundance of the antibiotic resistance genes. This switch will help focus on the selected genes through review and also find the presence of new resistant genes. The rationale behind the selection of ARGs depends on the first objective, which will provide evidence-based and reported data on the presence of ARGs in Southeast Asia for better geographical comparisons. Changes: The manuscript is updated from lines 416-527 in track changes mode. Comment 8: Based on my experience, this article is currently incomplete and requires more in-depth analysis to serve as a foundational resource for studies about AMR following the One Health approach. I earnestly recommend publishing your article once the protocols are described in greater detail and, ideally, results are included. Response: Thanks for your reflection. The idea of having a protocol paper prior to the real field data collection is to provide insight into the suggested study methods. We value your suggestion and will prepare a separate manuscript once the data collection and evaluation are completed. We hope that the recent changes made to the manuscript will now be sufficient to provide a resource for conducting studies in this field of AMR. Changes: The whole manuscript has been updated."
}
]
}
] | 1
|
https://f1000research.com/articles/12-316
|
https://f1000research.com/articles/11-1174/v1
|
17 Oct 22
|
{
"type": "Research Article",
"title": "Smoking behavior intervention based on implicit approach: a cross-sectional pilot study",
"authors": [
"Stephani Raihana Hamdan",
"Marisa F. Moeliono",
"Wilis Srisayekti",
"Marisa F. Moeliono"
],
"abstract": "Introduction: Indonesia is the country with the highest smoking rate in Southeast Asia and the third-highest globally. Smoking has become one of Indonesia's biggest addiction problems. The goal of this research is to develop smoking behavior intervention based on an implicit approach. Methods: This article contains a two-step study that was part of a comprehensive study on smoking behavior in Indonesia. The first study, applying measurement of Stroop task to 117 male-university-students with results revealed that smoking behavior was associated with attention bias. This result is the basis for developing an implicit approach-based intervention. In the second study, the research aims to develop an intervention by investigating the effects of the experimental retraining by manipulating the automatic-avoidance-action tendencies using an approach-avoidance task (AAT) on 40 male university student smokers that proved to have an attentional bias in the first study. Results: The outcomes of the studies showed that the retraining (six weeks, twice a week) proved to shape the AAT effect and reduce the cigarettes consumption of the smokers. This pilot research becomes initial step to develop smoking cessation interventions in Indonesia using an implicit cognition approach.",
"keywords": [
"Smoking",
"attentional bias",
"Stroop Task",
"approach-avoidance task",
"implicit cognition",
"retraining"
],
"content": "Introduction\n\nSmoking has become one of the major addiction problems in Indonesia. As the highest country with the smoking rate in Southeast Asia and the third highest in the world.1 Indonesia is still facing unsolved smoking problems. Smoking is an addictive behavior. Today, smoking cigarette is one of the biggest addictive behavior problems, especially in Indonesia. In Indonesia, smoking behavior among youth has increased by almost 144%, which can be a problem for the Indonesian youth.2–4 As addictive behavior, smoking is really dangerous for health,41–44 psychological,42,45 educational,42,46,47 and financial life.42,48 Smoking intervention applied today is only given as explicit information due to gaining health awareness.5–9 The most common intervention in Indonesia was the cigarette smoking hazard campaign.10,11 But still, 86% of smokers smoke even if they know about the smoking hazard.12 This suggests that the intervention in Indonesia was not successful in reducing smoking behavior.\n\nThe implicit approach appears as an alternative that is in need. One of the new approaches to shaping cognitive behavior is the implicit approach. This approach gives attention to associative and unconscious factors. The implicit approach succeeded in Europe and the United States.13–15 The main concept is to build intervention to train implicit behavior as an automatic behavior form.13,16 Smoking as an addictive behavior has been proved caused by implicit association factor and could be trained to reduce by implicit approach.17–22 This research tried to develop an alternative smoking intervention based on an implicit approach that has never been applied in Indonesia.\n\nFirst, the study aimed to measure attentional bias among smokers using the Stroop task to prove that smoking addiction is because of strong implicit association that we got from the comparison between smokers and nonsmokers.23–25 Second, the study aimed to apply implicit intervention using retraining approach-avoidance task (AAT) as an intervention to shape smoking-avoidance behavior.21,26,27 A two-step study can be illustrated in the following flow chart (Figure 1).\n\n\nMethods\n\nThe present pilot research aimed to measure and develop an intervention for smoking behavior in the Indonesian population. This study is broken down into two distinct phases. The first phase was conducted over a week which succeeded in recruiting a number of participants both smokers and nonsmokers. The measurement of Study 1 was carried out within two weeks of early February 2020 in a laboratory setting. From the results of study 1, it was found that participants were able to participate in the intervention in study 2. The implementation of study 2 for 6 weeks after the implementation of study 1.\n\nThe first phase is measuring attentional bias using a smoking Stroop task in the Indonesian language to prove that smoking addiction is because of a strong implicit association from the comparison between smokers and nonsmokers in Indonesia. The main concept of developing an intervention to implicit behavior is to prove that implicit factors shape smoking behavior. One of the factors that sustains addictive behaviors is attention bias. Various research results have shown that attention bias affects smoking behavior among smokers.23,28–31\n\nThe second step of this pilot study was to develop and apply implicit intervention using retraining AAT as an intervention to shape smoking-avoidance behavior in an experimental laboratory setting. The main concept of the second phase of the study was to develop an implicit intervention for smokers based on the results of the first phase. Implicit approach intervention was based on the approach-avoidance concept. The effort to adopt an implicit intervention is by investigating the effects of the experimentally-retraining using AAT. AAT is designed both for measurement and also as a form of intervention. AAT’s form of intervention is to manipulate and form automatic-avoidance-action tendencies.21,22,34 These studies were performed in conformity with the guideline of the Declaration of Helsinki. These studies involving human participants were reviewed and approved by the Universitas Islam Bandung Academic Ethics Committee (Ethical Approval Letter Number: 710/B.04/Bak-k/XII/2020). All participants provided their written informed consent for conducting and publication of this research.\n\nStudy 1 was conducted with 117 participants with 65 smokers and 52 nonsmokers (Mean Age=21,74 years, SD=0,82). For each group of participants, the researcher limits the minimum number of participants to 50 people, which is the number of participants considered sufficient.49 Inclusion criteria for all participants are male college students aged in late adolescents (age 18-22),50 with criteria for grouping participants as smokers was if they routinely smoke at least ten cigarettes/day. Inclusion criteria for nonsmoker participants was not smoking for at least two years in a row before this study. The exclusion criteria used for participants required that participants were not color blind nor have a brain injury, not using addictive substances. None of the participants included suffered from any disease, disability, or condition that might make the experimental tasks objectively difficult.\n\nParticipant Recruitment Process\n\nAll participants were recruited to the study through open recruitment which was announced on the campus social media. Researchers found that male smokers were the easier demographic to obtain. For nonsmoker participants, we also conduct direct recruitment of class leaders who giving text messages announcement to participants candidate according to the nonsmoker criteria. No coercion to take part in the study was used and participants will be involved only if they are interested. All participants who were willing to be part of the experiment registered themselves with the contact person (head researcher) in the announcement. Confidentiality of participant data is maintained and only known by the main contact. All scheduled participants are ensured according to the criteria.\n\nAll participants who registered were directed to come to the psychology laboratory the study was performed every four weeks. From the initial recruitment the study registered 153 participants but there were 36 people who failed to participate in the study due to various obstacles such as schedule conflicts, usually the condition of the conflict between the class schedule and the measurement, the condition of the participant who suddenly gets sick or has a sudden business that cancels participation in this study. All of the participants provided written informed consent and completed the smoking habit survey to categorize the smoking level of participants (light: 10 cigarettes/day; moderate: 11-20 cigarettes/day; heavy: more than 20 cigarettes/day).6 For smoker participants, they also fill out a letter of willingness to take part in the intervention study if needed (Study 2). All Stroop task are conducted in a laboratory setting with control environment such as room’s lighting and temperature with comfortable room settings. After conducting the Stroop task and debriefing, they get compensation for snacks and drinks after completing all measurement procedures.\n\nSmoking Stroop Task Development\n\nIn this first study, the instruments used was the smoking Stroop task that was developed by the authors in Indonesian language to measure the smoking-behavior attention bias among participants. Stroop task was chosen for this study as it is one of the most commonly used measures of attentional bias.23,32,33 The Stroop task procedure is a test in which words appear one by one in the middle of the screen. Research participants were asked to press certain buttons according to the colors that appeared without thinking about the words listed on the screen. The Stroop task was completed by the participants using a laptop computer with 15 inches and conducting by software of Inquisit LAB 4.0.2.0 software (Millisecond Software, US, RRID:SCR_022151), software from the website that installed to the laptop. To run stroop task, are also free alternative software to run stroop task script such as DMDX.51,52 The researchers also determine each color that appears and the two buttons that must be pressed, namely the A or L button for a certain color using the index finger of the right hand on the L button and the index finger of the left hand on the A button. Only one index finger is used because the index finger is the easiest finger to use to press keyboard keys. The A and L keys are selected also considering the location of the two letters in the middle row and each at the left-right end of the laptop keyboard. This procedure was tested and has gone through expert validation conducted by researchers before being carried out.\n\nThe Stroop task running with five fixed colors (red, blue, green, yellow and purple) for participants to learn. Research participants were given four color options for each task. The first session is used as an example with color words. The word combinations of words and colors can match or differ. For example, the test may say the word yellow, even though it's written in red color. The task for the participant is to pay attention to the color, not the word.\n\nThe following smoking questions of the Stroop task were color answer choices divided into five sessions with fixed different color combinations. The participants performed the Stroop task immediately after the exercise session with the same principle as the practice. During the Stroop task, the researcher only supplied four color choices in each session so that the participant did not experience difficulties in answering and so that the participant's attention was not disturbed by the many color choices because the more color choices, the more buttons would be needed to answer.\n\nThe order of the combination of answers has been pre-determined and given in a non-sequential manner so that it seems that it has undergone randomization (pseudorandomized).23 This procedure aims to avoid the learning process of the participant. When the participants worked on the next section, they returned to their original condition without memorizing the color answer choices in the previous section. In the smoking Stroop task, we measured differences in the reaction of two groups of words that appear on the screen, namely words related to smoking word stimuli (e.g smoking, ashtray, cigarette butt, etc) and neutral word stimuli (e.g house, umbrella, mountains, etc). There are 12 words in each group with similar lengths and sounds. All of the words had been surveyed, analyzed and approved by an Indonesian language expert. Figure 2 is an illustration of the Stroop task screen which has been translated into English. Participants in the study actually looked at the screen in Indonesian language.\n\nStroop Task Measurement\n\nThe Stroop Task measured reaction time of the participants milliseconds (ms). The reaction time data was obtained from time between the word appearing in the Stroop task until the participant presses the answer button. The milliseconds data was collected automatically in the Inquisit Lab software in which Stroop task is performed. The maximum duration of the Stroop task was 10 minutes.\n\nIn this study, the research aims to measure attentional bias using Smoking Stroop task data. Data Stroop task can provide results that prove that smoking addiction based on presumption that strong implicit association can be obtained from the comparison between smokers and nonsmokers. If the smoker's reaction time is longer than a nonsmoker, we can conclude smokers have attentional bias. Analysis of variance (ANOVA) is applied to the results to investigate which participant may have an attentional bias to smoking-related stimuli only and not neutral word stimuli. The data saved from the installed software was stored in ratio scales (milliseconds).\n\nData is considered valid if three criteria were met.23 First, if reaction time is between 200 ms-5000 ms, this is normal range for participants to answer. If reaction time is less than <200ms, it considered invalid answers because it means too quick to answer without paying attention to the task. Data was also considered invalid if the reaction time was more than >5000 ms because this suggests the participant was thinking too much and is no longer automatic response. Second, data with more than 2 SD (standard deviation) was also discarded because it is considered abnormal data. Third, the error answer must less than 20% to be considered normal and the data does not contain any major errors. The reaction data from the Stroop task was analyzed using ANOVA. All data results were processed and analyzed using Official SPSS 23.0 belongs to laboratory when conducting this study (IBM corporation, 2015, RRID:SCR_002865).\n\nIn Study 2, all participants were obtained from the recruitment results of study 1. There were 52 participants that proved to have an attentional bias get contacted for further study. They were briefed on the longer duration of second study (6 weeks) and they were included in the study if they committed to all procedures needed. We obtained 40 smoker participants (Mean Age=21.74; SD=.82) who are willing to participate in the intervention activities of study 2. They were divided randomly into 2 groups, the experimental and control groups. The experimental group consisted of 24 smoker participants and control group consisted of 16 smoker participants. All experimental AAT intervention was conducted in a laboratory setting for 12 session (twice per week). During the retraining weeks, all participants completely filling smoking survey that monitors the number of cigarettes consumed each day that collected by researcher team. For the control group, they were informed that the daily smoking survey is the form of intervention that is given in the study. This detail was added so that participant in control group feel they are being treated. In experimental group, the participants divided into 2 types of intervention based on the form of AAT given, direct or indirect AAT. Explanation of the procedure for each form of AAT will be discussed later. In Table 1, the division of the participants can be seen for Study 2:\n\nApproach-avoidance task (AAT) development\n\nIn study 2, all of the content of the AAT was developed by authors for Indonesian background and was then tested, analyzed and get approval valid by the researchers. The procedure of AAT in this study was using a 15-inch laptop computer and Joystick. The laptop (ACER Aspire with 4GB Memory and intel core i3) was used to show pictures for the AAT. The pictures contained stimuli with two types of content, that is smoking-related pictures and Neutral-related pictures. Instruction for AAT is to control a flight simulator joystick from Logitech with model of Logitech Extreme 3D Pro Joystick Flight Simulator (see Figure 3 below) with two alternative actions, push or pull every time participant saw a picture appeared in laptop screen. In Figure 3, we can see photo illustration of individuals working on an AAT. The individual in the image is a research assistant and has given consent for his photo to be published.\n\nThe AAT program is developed for measurement and a form of intervention. The AAT is used as a measurement of the accuracy and time duration of the participant in responding according to the task. The task of the subject is to respond to the stimuli that appear, as quickly as possible by pushing or pulling the joystick. The joystick is connected to the computer and arises from a zooming effect where the subject pulls the joystick and the effect decreases when the subject pushes the joystick. The image will be lost when the joystick is 30° closer to or away from the subject. The joystick is returned to the neutral position when the image disappears as a signal for the next image to appear (See Figure 4). The screen background is white and the instructions are black.\n\nZooming effect with pull (left) and Decrease effect with push (right).\n\nBefore being given the smoking AAT, each participant was given an exercise consisting of two different colored blank pictures for the practice session. Participants were instructed to pull the Joystick when a blue image appears and push the Joystick to a red image. The instructions given to the participants to complete the task was to push the joystick when smoking related picture appeared and to pull the joystick when a neutral (non-smoking related) picture appeared. The overall score was obtained by comparing differences between pull-push reaction time in smoking-related stimuli and neutral-related stimuli.\n\nThe main purpose of the retraining AAT is to create avoidance action tendencies toward smoking-related objects by manipulating the task. For intervention purpose, AAT is used as retraining task which can predict the effect of shaping avoidance behavior toward cigarette stimuli. The implementation of AAT intervention was given in two forms, direct and indirect AAT retraining.27 In the retraining AAT, pictures can be showed in two position; landscape or portrait. The procedure for giving AAT in one administration is 100 trials, consisting of 20 exercise trials and 80 trials of AAT. The practice trial consisted of 10 appearance of a blue image and 10 appearances of a red image. The method of retraining AAT is by experiment with pretest-posttest control group design (See Table 2).\n\nThe ATT direct trial consisted of 20 cigarette-related images and 20 neutral images that appeared twice in landscape format only. The data obtained from each trial is from pushing or pulling reaction times.21,22,27,35 The indirect AAT trial consisted of 20 smoking related images showed in landscape format and 20 neutral images in portrait format. When pictures appeared in laptop screen, participants were instructed to push the joystick when landscape picture appeared (contain smoking-related), this means push task given to implicitly train the participants avoid smoking-related pictures. The opposite way, participants instructed to pull the joystick when portrait form appeared (neutral related picture), this means pull task given to implicitly train the participants to approach the neutral related pictures.21,22,27,35 The differences of direct and indirect AAT can be seen in Table 3 below.\n\nApproach-avoidance task (AAT) measurement\n\nAll data in the AAT was collected by the laptop automatically. The setting of the research is a laboratory setting with same controlled environment used for Study 1. The AAT program used was Inquisit Lab 4.0.2.0 software (Millisecond Software, US, RRID:SCR_022151). The latency score obtained from the AAT is said to be the AAT effect. The score is obtained from the difference between each type of image's pushing or pulling reaction times in each combination. In the training and intervention sections, a 'False' mark is given as a form of task reminder and feedback. Each image is presented in a pseudorandomized order (pre-determined random order) where combination of pictures showed has been pre-determined and given in a non-sequential manner so that it seems that it has undergone randomization.\n\nThe effects of retraining the AAT was analyzed by t-paired sample to compare which retraining form more effective, and experiment-control posttest data result was analyzed using the t-independent test to investigate if AAT retraining could shape smoking-avoidance behavior tendencies. All ATT data results were analyzed using Official SPSS 23.0 (IBM corporation, 2015, RRID:SCR_ 016479).\n\n\nResults\n\nThe following is a presentation of the results of the two studies carried out,53 followed by a discussion of the analysis of the results and limitations of this research.\n\nThe first study was conducted on 117 participants using a Stroop task to measure attentional bias by comparing reaction time data between smokers and nonsmokers. The result shown in Table 4 suggest that smokers have a longer reaction time than nonsmoker participants. The mean reaction time of smoker participants was 868,62 ms with a standard deviation (SD) of 173, 43 ms, and the mean reaction time of nonsmoker participants was 715.45 ms with SD of 131.28 ms.\n\nFurther results were analyzed between smoker and nonsmoker data in smoking-related stimuli using ANOVA (See Table 5). This analysis tests a null hypothesis (H0) which states that there is no difference in data between smokers and nonsmokers. To test the hypothesis, it is necessary to look at the probability test value of the F test in ANOVA. If the F probability value (Sig) is smaller than the F table value, which is 3.85 at a 95% confidence level (α value =0.05), then H0 is rejected and H1 is accepted. From result in Table 5 below it can be concluded that the difference in smoking related stimuli show significant F (3,85)=20.665, p value stimuli 0.000<0.05. F-value showed variation between sample means (in this case stimuli and neutral) within the smokers and nonsmokers. It shows a significant difference between smokers and nonsmoker participants in reaction time to smoking-related stimuli. In contrast, analysis also showed that no significant differences in neutral related stimuli (F (3,85)=0.567, p value neutral 0.453>0.05). The test result can be seen in Table 5 below.\n\nThis result can be the foundation for selecting a smoker with attention bias. From 65 smoker participants that pass the criteria for having attention bias, there were 52 participant that had a longer reaction time in smoking-related stimuli than neutral related stimuli. The result also shows that the majority of smokers (80%) in the study have attention bias. Unconscious factors shape this generalized smoking behavior. Thereby the intervention of smoking behavior should adopt from the implicit approach.\n\nThe second study was conducted on 40 of the smoker participants who showed an attentional bias in the first study and were willing to take part in the experiment. Data from a daily survey of participants that monitors the number of cigarettes consumed each day are not explicitly describe in the results because the numbers did not show a significant change. Except in the light smoker group in direct AAT after the fourth week with resulting reducing about 10% of cigarette consumption.\n\nThe AAT score obtained is the subject's tendency data where a positive score indicates a tendency to approach the object being measured, while a negative score indicates a tendency to avoid (avoidance) the object being measured. The results used to analyze the effect of retraining AAT came from the t-paired sample that compares the data between indirect and direct AAT that can see in Table 6 below.\n\nFrom Table 6 it can be seen that the average pretest of the direct AAT group was 10,4 ms, and the indirect AAT group was 85,66 ms. In posttest data, the average of the direct AAT group was -153,3 ms, and the indirect AAT group was 79,22 ms. The negative data in direct ATT that this group had a tendency to avoid (avoidance) smoking-related stimuli. This contrasts the results of the indirect AAT group which showed positive score that indicates a tendency to approach the smoking picture stimuli. The differences in data in the pre posttest indirect AAT group was -163,7 ms, but in indirect AAT, the number is -6,444 ms. This means a huge difference in data between direct and indirect AAT. The larger negative or minus (-) difference between pre-test and posttest in direct AAT showed that direct ATT more effectiveness of forming greater avoidance behavior tendencies than direct AAT form. This earlier result leads to the conclusion that direct AAT is more effective in shaping avoidance tendencies to smoking-related stimuli. The further result of experiment groups that showed difference of direct and indirect groups can be seen in Table 7.\n\nFurther analysis was conducted to know which form of retraining ATT had more effective avoidance tendencies toward smoking-related stimuli by comparing data between direct and indirect AAT that were analyzed by t-paired sample (See Table 7). To test the hypothesis, it is necessary to look at the probability test value of the t test. If the value of t probability value (Sig) is less than the alpha value of 0.05, then H0 is rejected and H1 is accepted. This analysis tests a null hypothesis (H0) which states that there is no difference in data between pre-test and post-test. The result showed, in the direct ATT group, there was significant differences (t(10)=3.412, p<.05). The indirect ATT group gave another result that showed no significant differences between pre-test and posttest data (t(12)=0,098, p>.05). These results show that the direct AAT form was a more effective intervention than the indirect AAT form to shape avoidance tendencies to smoking-related stimuli. The further result showed in Table 8.\n\nThe last analysis was conducted to prove that retraining AAT has an effect that could shape smoking-avoidance behavior tendencies by comparing the experimental and control groups. The null hypothesis (H0) proposed is there no difference scores between of the experimental group and the control group. The results are described in Table 8 above. This was analyzed by a t-independent test that compared experiment-control posttest data. The results showed that direct AAT had significantly different results when compared to the control group (t(10)=2,685, p<.05). Showing that direct ATT shows an influence on the formation of avoidance behavior tendencies on smoking picture stimuli. By contrast, the comparison between the indirect AAT and control group show no significant differences (t(12)=0,189, p>.05). These results show that only direct AAT form intervention that has impact to shaping smoking-avoidance behavior tendencies.\n\n\nDiscussion\n\nThe main findings of the first study were as follows: The study with Stroop task measurements revealed that smoking behavior was associated with attention bias. The background of the majority of smoking participants who experience attentional bias and included in this study were moderate smokers.\n\nSmoking as addictive behavior is sustained by an implicit condition which was an attention bias toward smoking-related stimuli among smokers.17–19 In the first study, using a Stroop task proved that smoking addiction is, at least in part, because of the strong implicit association that smokers have compared to nonsmokers. The result showed that the reaction time of smokers was longer than nonsmokers. This result can be used as the basis to develop an intervention with the implicit approach conducted in the second study. This result also confirms that smoking behavior is caused by conscious behavior and is heavily influenced by implicit associations. Data on Indonesian smokers who are participants in this study showed similarities with various previous implicit studies on addiction, especially smoking cigarettes addiction.17,24,25,28,29,32,36,37\n\nThe main findings of the second study were as follows: automatic action tendencies to approach cigarette smoking was changed successfully using new adaptation training that was developed from a direct AAT retraining form which shows a significant difference between before and after intervention (See Table 7) and significantly different than the control group (Table 8). From the measurement results of the pretest and posttest, AAT found a decrease in score from the beginning of the experiment until the end of the experiment that showed indications that retraining could affect the behavior of participants causing them to avoid smoking stimuli. This result can strengthen the data finding that retraining is an effective intervention in shaping behavior, in this case, avoidance behavior.13–16,20,34,21,22\n\nThe comparative data results between the direct AAT and the indirect groups in showed no significant difference between pretest and posttest (Table 7) and no significant difference with control group (See Table 8). These result concluded retraining in the form of indirect AAT is not effective to shape avoidance behavior tendencies to smoking related stimuli. The result of indirect AAT group showed that intervention using inexplicit instruction in the task has no significant effect. This contradiction between direct and indirect forms of AAT needs further research and analysis to understand factors that cause direct intervention to be more effective in Indonesian smokers than indirect. Previous western background studies have succeeded in making interventions for alcohol addiction using an implicit approach that are indirect and subtle.14–16 Researchers initially assumed that developing smoking-related intervention could have the same basic assumption. In this case, alcohol is an addictive object that is accepted as part of social consumption in western culture, just as cigarettes are part of a social ritual among males in Indonesian culture.1 But as the result of Study 2 differ from previous studies, it suggests that the different object stimuli can be one of the reasons for determine effectiveness of form intervention.\n\nResult on the effectiveness of direct AAT also can be considered in providing form of interventions for shaping healthy behavior in Indonesian culture. The straight forward instruction for participant in direct ATT to push (avoidance) the smoking related picture easier to perceive consciously and form stronger behavioral tendencies, in this case avoidance behavior. This could mean that concrete and direct instructions are easier to understand and apply in the Indonesian population. The direct AAT instructions make it easier for participants to know the behavior they want to change or intervene in, in this case avoiding smoking stimuli. This could form the basis for the development of smoking reduction interventions by using directly stated instructions to avoid smoking-related stimuli. Experimentally this form of instruction is more effective showing significant results compared to indirect instructions. In direct AAT, the participants more quickly realized cigarettes or smoking related stimuli that should be avoided. Whereas in indirect AAT, participants did not immediately realize that they were asked to avoid smoking stimuli. Indirect instructions showed insignificant results in Indonesian smokers. This is still an assumption from the results of this study and needs more further analysis.\n\nThis pilot study has categorized the level of smoking addiction among smoker participants. However, this data is only done so that there is a balance between the types of smokers in each group. There is some suggestion to include considerations of reducing cigarette smoking consumption based on the level of nicotine addiction.38 From the result in study 2, regarding changes in cigarette consumption a decrease in cigarette consumption, around 10%, among light smokers in the direct AAT group that emerged in the 4th week. However, this is a very small number of participants and weak as evidence. This result needs further research and analysis.\n\nAs a pilot study, this research still has many limitations. The number of participants is still very limited amid the large smoking population in Indonesia. For future research, it is recommended to develop retraining with more participants. Participants who only come from the student population with upper-middle socioeconomic levels should also be expanded to include various types of smokers from various demographics. Social and cultural factors also need to be addressed in smoking behavior research. Indonesia is a country with a large range of social diversity and large socio-cultural influences in developing interventions. The condition of cigarettes having free access to an extraordinary rush of advertisements in Indonesia is certainly a cognitive obstacle to quitting smoking.39\n\nThe experiments in this study carried out was the laboratory using strict procedures during retraining. However, the conditions between the time of the experiment were a factor that could not be controlled. So, there are still many possibilities that influence participants' smoking behavior.40 Control conditions over longer periods of time need to be carried out if better retraining is needed. AAT intervention in these experimental retraining conditions is given through a laboratory computer (laptop) which, as a media, are only accessed through certain software and are not connected to the internet. As a developed country, Indonesia still has limited resources, especially in online research. In another country, currently, interventions are being developed online and even implemented on smartphone devices.17,18 This pilot study is conducted in experimental research in a laboratory setting that would be improved if it was developed in the context of the reality of smokers in everyday life.\n\n\nConclusions\n\nFrom these two studies conducted, the main conclusion is that the Stroop task measurement revealed that smoking behavior was associated with attention bias. The results showed that the reaction time of smokers was longer than nonsmoker participants. This result can be used as evidence of smoking intervention techniques based on an implicit approach, specifically for Indonesian target population. Automatic action tendencies to approach cigarette smoking were changed successfully using a new adaptation training developed from the retraining Approach Avoidance Task (AAT). The form of AAT that proved to effect and more effective in shaping smoking-avoidance behavior tendencies is direct AAT. The development of interventions in efforts to stop smoking must continue to be carried out, with the results of this study being an alternative intervention through an implicit approach.\n\n\nData availability\n\nOSF: Smoking behavior intervention based on implicit approach: a pilot study in Indonesia, https://doi.org/10.17605/OSF.IO/3PFSR.53\n\nThis project contains the following underlying data:\n\n- Smoking Stroop Task in Indonesian\n\n○ Rekap Smoking ST.xlsx (Raw data of Smoking Stroop Task from Study 1 in excel file)\n\n○ Indonesian Smoking Stroop Task Script.txt (Script file from Stroop Task in Indonesian in simple text form)\n\n○ Smoking Stroop Task Fix.iqx (Script file from Stroop Task in Indonesian in inquisit form)\n\n○ Tata Laksana Stroop Task.docx (Smoking Stroop Task protocol in Indonesian language)\n\n- Approach Avoidance Task (AAT) Smoking in Indonesia\n\n○ Form Isian AAT.docx (Daily form for smoking survey during AAT retraining in Study 2)\n\n○ Raw Data Reaction Time AAT.xlsx (Raw data of experiment and control groups in Study 2)\n\n○ Tata Laksana AAT.docx (Smoking AAT protocol in Indonesian language)\n\n○ AAT Pictures Folder (a folder containing 20 images used in smoking AAT consists of 10 images in portrait -P initials and 10 landscape- L initials images in jpg form)\n\n○ ALAT UKUR AAT.iqx (AAT measurement script for pretest and posttest in inquisit form)\n\n○ ALAT UKUR AAT SCRIPT.txt (AAT measurement script for pretest and posttest in simple text form)\n\n○ DIRECT AAT.iqx (AAT Direct retraining script in inquisit form)\n\n○ DIRECT AAT SCRIPT.txt (AAT Direct retraining script in simple text form)\n\n○ INDIRECT AAT.iqx (AAT Indirect retraining script in inquisit form)\n\n○ INDIRECT AAT SCRIPT.txt (AAT Indirect retraining script in simple text form)\n\nOSF: Smoking behavior intervention based on implicit approach: a pilot study in Indonesia, https://doi.org/10.17605/OSF.IO/3PFSR.53\n\nThis project contains the following extended data:\n\n- Smoking Survey in Indonesian\n\n○ Buku Soal.docx (File document from the question book related to smoking survey in Indonesian)\n\n○ Lembar Jawaban.docx (the answer sheet for filling out the question book related to smoking survey in Indonesian)\n\n○ Smoking Survey Data (Raw data of Smoking Survey in excel file)\n\n○ Surat Kesediaan.docx (Inform Consent form of Participants)\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\nSoftware availability\n\nAll software instruments used in this research can be accessed in millisecond.com website. SPSS software can be purchased in IBM website. DMDX is an alternative software for measurement reaction time and visualization of experimental scripts (both stroop task and AAT) which can be obtained free of charge on the website http://www.u.arizona.edu/~kforster/dmdx/download.htm",
"appendix": "Acknowledgements\n\nAll experimental activities in this research get facilities and had been carried out in the psychology laboratory of Universitas Islam Bandung (Unisba). The Universitas Islam Bandung also provided support in paying the article processing charge.\n\n\nReferences\n\nReitsma MB, Kendrick PJ, Ababneh E, et al.: Spatial, temporal, and demographic patterns in prevalence of smoking tobacco use and attributable disease burden in 204 countries and territories, 1990–2019: a systematic analysis from the Global Burden of Disease Study 2019. Lancet. 2021; 397(10292): 2337–2360. PubMed Abstract | Publisher Full Text\n\nJanah MR: Pengaruh Pelatihan Kontrol Diri Dengan Menggunakan Metode Tehnik Gerakan Mengontrol Perilaku Merokok (TGMPM) Untuk Mengurangi Perilaku Merokok Pada Siswa SMK Harapan Kartasura (Doctoral dissertation, Universitas Muhammadiyah Surakarta).2011.\n\nFalikhah N: Bonus Demografi Peluang dan Tantangan Bagi Indonesia. 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Publisher Full Text\n\nHamdan SR: “Smoking Behavior Intervention Based on Implicit Approach: A Pilot Study in Indonesia.” OSF. June 30. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "237729",
"date": "14 Feb 2024",
"name": "Muna Barakat",
"expertise": [
"Reviewer Expertise Clinical Pharmacy and 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\nThank you for the invitation to review this work entitled “Smoking behavior intervention based on implicit approach: a cross-sectional pilot study,” which aims to develop a smoking behavior intervention based on an implicit approach. This study is considered relatively new for South Asian countries, and I believe it will have an important impact in the future.\nSome comments were raised and must be addressed: Abstract: The authors need to write the conclusion separately from the results. Add the findings of the abstract in detail (I mean numbers, percentages..etc) Introduction: It’s too short! The authors need to elaborate in the problem of smoking globally, it’s consequences, prevalence…then highlight the context of Indonesia to end up with a rationale and research question.\nMethods: Please add the details of a smoking Stroop task to pave the path for the reader to understand the methods more.\nIt’s preferable to keep the limitations to the end of the discussion 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? 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": "11227",
"date": "04 Apr 2024",
"name": "Stephani Raihana Hamdan",
"role": "Author Response",
"response": "Dear reviewer, Thank you for your comments and suggestion regarding our article. In the latest revised article, we have improved our writing based on your input points: 1. We add the conclusion separately from the results in abstract. We also add results numbers in both study in research. 2. We are trying to add to the description of the smoking problem globally and we elaborate it to Indonesia as the context in which this cigarette research was carried out. 3. We are adding some details of a smoking Stroop task in methods to give more clear picture to the reader. 4. We change the limitations to the end of the discussion section according to your input. Best regard, Author"
}
]
},
{
"id": "248952",
"date": "01 Mar 2024",
"name": "Mohd Nazir Mohd Nazori",
"expertise": [
"Reviewer Expertise Health promotion and mental 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 article contains all necessary information that allow reader to understand what has been done and the outcome of the study.\nThe sentences used were appropriate to the context. However, I do suggest the authors to revise the content to be more concise. There were many sentences that were redundant and unnecessary for the reader.\nReaders of this journal at least possess the basic knowledge of statistics. Therefore, sentences that elaborated the decision making process for hypothesis testing eg: \"To test the hypothesis, it is necessary to look at the probability test value of the t test. If the value of t probability value (Sig) is less than the alpha value of 0.05, then H0 is rejected and H1 is accepted. This analysis tests a null hypothesis (H0) which states that there is no difference in data between pre-test and post-test.\" is in my opinion unnecessary and makes the article messy.\nThere were multiple tables that could be combined and simplified into a single table as it use similar test.\nThe introductory content for Method was redundant with the details presented below. I suggest to simplify it further to provided an overview of the whole research. The overview of each phase can be provided at the start of \"Study 1\" and \"Study 2\".\nIn Study 2, participants were divided randomly into 2 groups but end up with unequal group sizes. I suggest the author to justify/explain why this happened.\nIncidentally, the group participants were almost equal proportion in terms of their type of smoker. Where this intentional during the randomization procedure? if yes, please elaborate the steps of randomization.\nFor AAT development, I suggest the author to briefly explain the validation process done to provide validity evidence of the intervention.\nThere were descriptive statistics mentioned in the Method section, I suggest these statistics to be moved into the Result section for consistency of content.\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": "11228",
"date": "04 Apr 2024",
"name": "Stephani Raihana Hamdan",
"role": "Author Response",
"response": "Dear reviewer, Thank you for your comments and suggestion regarding our article. In the latest revised article, we have improved our writing based on your input points: 1. We tried to delete and revise sentences that were redundant and unnecessary according to your comments 2. We tried combined and simplified into a single table that has similar data 3. We revised and tried to simplify it further, especially in the methods section into \"Study 1\" and \"Study 2\" according to your suggestions 4. We add an explanation regarding random matching in participants who appear to have unequal group sizes but are actually equal in terms of the number of smoking levels. 5. We added a brief explanation of the validation process done by experts in AAT development according to your comment. 6. We have moved the statistics in the methods into the Result section according to your input. Best regard, Authors"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1174
|
https://f1000research.com/articles/13-217/v1
|
22 Mar 24
|
{
"type": "Systematic Review",
"title": "Safety of remimazolam in comparison with midazolam for colonoscopy: A systematic review and meta-analysis",
"authors": [
"Nimra Hasnain",
"Muhammad Abdullah Khalid",
"Mahnoor Sadiq",
"Malaika Jawaid Siddiqui",
"Aiman Anjum",
"Uzair Munaf",
"Laila A.Budhwani",
"Ibtehaj Ul Haque",
"Gauhar Afshan",
"Nimra Hasnain",
"Muhammad Abdullah Khalid",
"Mahnoor Sadiq",
"Malaika Jawaid Siddiqui",
"Aiman Anjum",
"Uzair Munaf",
"Laila A.Budhwani",
"Gauhar Afshan"
],
"abstract": "Background Remimazolam is an ester-based ultra-short-acting benzodiazepine that efficiently achieves sedation within a short period and is now being assessed as a suitable alternative to midazolam. This meta-analysis aims to pool the available data assessing and focusing on the safety aspect of remimazolam compared with midazolam.\n\nMethods A multi-center randomized control trial for patients undergoing endoscopic procedures like colonoscopy was conducted, comparing remimazolam to placebo for the midazolam group as the intervention group. The safety of remimazolam was the primary endpoint of this meta-analysis.\n\nResults A total of 3 studies were included. The total study population was 697, including the placebo, remimazolam, and midazolam groups. The types of studies included are i. randomized, double-blind, parallel-group, active-controlled clinical trial ii. prospective, randomized, parallel-group study comparing remimazolam to placebo (blindly), RCT, and iii. prospective, double-blind, randomized, parallel-group study RCT.; Treatment-emergent adverse effects included vascular disorders (P=0.42), cardiac disorders (p=0.06), respiratory, thoracic, and mediastinal disorders (p=0.26), infections and infestations (0.88), hematologic abnormalities such as anemia (p=0.63), and derangements in Blood pressure (systolic p=0.47 and diastolic p=0.68 and respiratory parameters (p=0.34). Analysis of the reported data suggests that the remimazolam group had a significantly higher incidence of treatment-emergent adverse effects compared to the midazolam group (RR: 0.84; 95% CI [0.78, 0.91]; P <0.00001; I2 = 5%).\n\nConclusions In conclusion, this meta-analysis of three randomized controlled trials showed outcomes favoring both remimazolam and midazolam as successful sedatives, yet the higher requirement of top-up dosage and rescue sedatives in the midazolam group indicates that remimazolam can be used as its replacement, especially in colonoscopy procedures.",
"keywords": [
"Colonoscopy",
"remimazolam",
"midazolam",
"sedation",
"anesthesia."
],
"content": "Introduction\n\nColonoscopy is one of the most widely performed diagnostic procedures. It has advanced surgical oncology due to its role in earlier cancer detection. Although relatively less time-intensive and invasive, patients often require the administration of opiates, sedatives, and hypnotics to help ameliorate post-procedural pain.1 Benzodiazepines (a class of sedatives approved by the FDA) have resulted in their ubiquitous use due to their multiple therapeutic benefits as anti-anxiolytic and antiseizure and their established sedating and analgesic properties.2 Moreover, various drugs can be employed for different populations and procedures due to their diverse potency and efficacy. Midazolam is currently employed for colonoscopy due to its high safety profile and ultra-short-acting properties. It is classically preferred over agents with a narrow therapeutic index, such as diazepam.3,4 However, midazolam, with a relatively longer mean half-life (three hrs; 1.8–6.4 hr), is associated with a slow return of cognition and carries a risk of systemic accumulation; therefore, limiting its use in patients with chronic kidney disease.2,5 Hence, alternative agents such as remimazolam with a similar biochemical structure and efficacy have been recently explored for their safety profile owing to their shorter recovery time.6,7 Unlike midazolam, this has been attributed to its earlier inactivation, hence decreasing the systemic effects.5 As an ultra-short-acting, ester-based drug, remimazolam can be administered intravenously to achieve sedation within 3–3.5 minutes.8 Rendering its quicker induction and recovery, as seen across trials, including bronchoscopy and colonoscopy, remimazolam was approved for use in the US as an anesthetic.7,9\n\nThis systematic review aims to evaluate the adequacy of remimazolam in replacing midazolam in colonoscopic procedures. Our review specifically looks at the randomized control trials comparing the safety of remimazolam and midazolam in patients undergoing colonoscopies to determine if the clinical effectiveness of remimazolam can be safely determined and whether this emerging drug could successfully replace midazolam in the future or not.\n\n\nMethods\n\nThe Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA 2020) standards and PRISMA checklist were used to conduct this meta-analysis.10,11 The literature search, quality assessment, data extraction, and statistical analysis were all accomplished by two independent reviewers (MA Khalid, M Sadiq). A third reviewer (MJ Siddiqui) was consulted in case of conflict for screening procedures. The report did not need ethics committee approval because raw data of human beings were not involved. The ultimate selection of studies for inclusion was determined through unanimous agreement among all authors. Additionally, we examined the reference lists of original papers, published reviews, systematic reviews, and meta-analyses to identify any trials that were not initially part of the database. Our search strategy was designed to encompass every randomized controlled trial (RCT) examining the efficacy of remimazolam in procedural sedation during colonoscopy.\n\nStudies that fulfilled our PICO criteria were included. Studies that were meta-analyses or not released as published reports or case reports and studies in which the PICO criteria were not matched were all excluded.12,13 We also excluded clinical trials in which remimazolam was compared to any drugs other than midazolam. Non-human studies and publications in languages other than English were also excluded. We lastly excluded the latest meta-analysis, which focused on efficacy as it was outside the scope of our topic.12\n\nPubMed/MEDLINE and the Cochrane Library databases were searched for this meta-analysis up to July 17th, 2023. MedRxiv and BioRxiv were also searched for preprints and other related articles. All significant studies were included using the relevant medical subject headings (Mesh terms). The used search strategy was: ((Remimazolam) OR (ONO 2745)) OR (ONO-2745)) OR ((CNS7056)) OR ((methyl 3-(8-bromo-1-methyl-6-(2-pyridinyl)-4H-imidazo(1,2-a)(1,4)benzodiazepin-4-yl)propanoate)) AND ((Midazolam) OR (Midazolam Maleate)) OR ((Maleate, Midazolam)) OR (Dormicum)) OR (Versed)) OR (Midazolam Hydrochloride)) OR (Hydrochloride, Midazolam)) OR (Ro 21-3981)) AND ((Colonoscopy) OR (Colonoscopic Surgical Procedures)) (Extended data: File 112).\n\nStudies were included based on the following PICO selection criteria: (a) the population of interest was colonoscopy patients; (b) the outcome was safety/side effects with an intervention group of remimazolam with midazolam being the control group.\n\nTo enhance our search, we investigated the titles and abstracts for all the articles. Subsequently, all the selected articles were imported into EndNote Reference Library version X4 (Clarivate Analytics, Thomson Reuters Corporation, Philadelphia, Pennsylvania). One duplicate study was identified, which was eliminated. The articles were then screened on three levels: title, abstract, and full text. A quality assessment test was performed using Cochrane Collaboration’s tool for assessing the risk of bias; for reference, see the Extended data: File 2.12,13\n\nThe Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) standards were used to conduct this meta-analysis.10,11 The literature search, quality assessment, data extraction, and statistical analysis were all accomplished by two independent reviewers. A third reviewer was consulted in case of conflict for screening procedures.\n\nAll statistical analyses were performed using Review Manager (version 5.4; Copenhagen: Nordic Cochrane Centre, The Cochrane Collaboration, 2014).14 The first two outcomes, completion of colonoscopy and need for rescue sedation, were subjected to sensitivity analysis to assess the specific impact of each study. However, the rest of the outcomes were reported only in two of the included studies, so sensitivity analysis could not be applied. To visually check the pooled data, forest plots were established. The outcomes of the reports were merged using a random-effects model and calculated as risk ratios (RR) with 95 % confidence intervals (CIs). In all cases, a p-value of less than 0.05 was considered significant. Higgins’s I2 statistic was used to quantify heterogeneity across studies, with I2 values between 25 and 50% representing mild heterogeneity, 50 to 75% representing moderate heterogeneity, and greater than 75% signifying severe heterogeneity.15\n\n\nResults\n\nA preliminary search of the three electronic databases yielded thirteen potential studies. Four articles were selected based on the comparison of remimazolam and midazolam. After exclusions were done based on the similarity of the intervention and control group with no combination agents, three studies were left for analysis. The PRISMA flowchart (Figure 1, Extended data: File 2) summarizes the results of our literature search.12\n\nFrom: Moher D, Liberati A, Tetzlaff J, Altman DG, The PRISMA Group (2009). Preferred Reporting Items for Systematic Reviews and Meta Analyses: The PRISMA Statement. PLoS Med 6(6): e1000097. doi: 10.1371/journal.pmed1000097.\n\nThe PRISMA flowchart was used in our systematic review and meta-analysis to shortlist articles. The articles were included based on similar PICO and underwent specific exclusion and inclusion criteria to form the final list.\n\nThree randomized controlled trials (RCTs) were used to compare remimazolam and midazolam.16–18 The Pambianco et al. study was a randomized, double-blind clinical trial. Patients received either remimazolam or midazolam for sedation during colonoscopy, with supplemental oxygen and fentanyl. Sedation adequacy was assessed by the Modified Observer’s Assessment of Alertness/Sedation score (≤3), and additional doses were given as needed. Success meant achieving sufficient sedation without rescue medication or ventilation.16\n\nThe Rex et al. phase III study was a randomized, double-blind study comparing remimazolam to placebo for outpatient colonoscopy, with an additional group receiving open-label midazolam. Study medications were administered by the endoscopist, and fentanyl was given before the drugs. The primary endpoint required successful colonoscopy completion, no rescue medication, and limited medication doses within specific time intervals.17\n\nAnother Rex et al. study was a randomized, double-blind trial comparing remimazolam to placebo, with an open-label arm for midazolam, in sedating 79 ASA III/IV patients during colonoscopy. It was the third Phase III trial for remimazolam in procedural sedation, focusing on evaluating remimazolam’s safety as the primary endpoint.18\n\nAll three studies included patients aged 18 to 70, scheduled to undergo a routine diagnostic or therapeutic colonoscopy. The patients had an ASA Score of I, II, or III, were within a weight range of 55–130 kg, and their BMI was 18 to 33 kg/m2 or less.12\n\nAccording to the quality assessment table, all studies carried a rigorous methodological approach and were linked with a low risk of bias; Table 1.12\n\nResults of the meta-analysis\n\nOf the three included studies, the total study population was found to be 697, including the placebo, remimazolam, and midazolam groups.16–18 The analyzed outcome was the safety of the two drugs as assessed by the incidence of treatment-emergent adverse effects (TEAEs) such as vascular disorders, cardiac disorders, respiratory, thoracic, and mediastinal disorders, infections and infestations, hematologic abnormalities such as anemia, and derangement in hemodynamic and respiratory parameters. The characteristics of the three studies are presented in the Extended data: File 3 and Extended data: File 4. The results are represented as forest plots in the Extended data: File 5.12\n\nTreatment-emergent adverse effects\n\nA multitude of possible adverse effects were observed and reported for the placebo, remimazolam, and midazolam groups, including vascular disorders, cardiac disorders, respiratory, thoracic, and mediastinal disorders, decreased respiratory rate, infections, and infestations, increased diastolic blood pressure, increased systolic blood pressure, and anemia. Analysis of the reported data suggests that the TEAEs have a significantly higher incidence in remimazolam (RR: 0.84; 95%CI [0.78, 0.91]; P <0.00001; I2 = 5%) compared to the midazolam group.\n\n\nDiscussion\n\nOur meta-analysis comprising three RCTs with a total study population of 697 aims to evaluate the safety profile of remimazolam as an alternative sedative in patients undergoing colonoscopy. In accordance with the results, it is indicated that remimazolam is an overall safe sedative that can be considered for use as a replacement for midazolam in patients undergoing colonoscopy. Unlike the previous meta-analysis “Efficacy of Remimazolam for Procedural Sedation in American Society of Anesthesiologists (ASA) I to IV Patients Undergoing Colonoscopy”, this systematic review and meta-analysis maintain a strict focus on the safety aspect of remimazolam. The primary outcome highlights all the treatment-emergent adverse effects, not the procedural success predictors such as completion of endoscopy, need for rescue sedative, and additional need for top-up dosages.19\n\nIn the three RCTs to draw a comparison between remimazolam and midazolam, remimazolam was found to have a similar safety profile when compared to midazolam. However, pooled effects revealed remimazolam to be associated with increased treatment-emergent adverse effects. The mean terminal elimination half-life of remimazolam was estimated at 0.75 hours, and that of midazolam was 4.3 hours. Remimazolam was found to have a shorter half-life, early bioavailability, and early return of the patient to conscious levels.18 The early recovery is also explained by the ultra-short-acting nature of the drug, as discussed earlier.20 Another possible explanation for this early recovery with remimazolam compared with midazolam is the difference in nature of the metabolites of the two drugs. Midazolam has an active metabolite, a-hydroxy-midazolam, which has the potential risk of repeat sedation when the active metabolite becomes bioavailable, whereas no metabolites of remimazolam have been reported to cause repeat sedation.21 Additionally, remimazolam has a lesser degree of drug interaction in comparison to midazolam and uneventful use in a patient with myotonic dystrophy endorses its safety profile.22,23\n\nThese findings are in contrast to a previous meta-analysis evaluating the safety and efficacy of remimazolam in various endoscopic procedures.24 Remimazolam was linked with fewer cases of hypotension in comparison to midazolam. Additionally, both groups carried an equal risk of undergoing postoperative hemodynamic and respiratory derangements. The discrepancy could be attributed to the absence of subgroup analysis on patients undergoing colonoscopy, a larger sample size (1996 vs. 697), and a more diverse patient population than ours. Moreover, in order to achieve a similar anesthesia effect, often larger doses of remimazolam need to be administered, which could explain the increased incidence of TEAEs.25 Isolated incidences of anaphylaxis and failure of flumazenil to fully reverse the sedative effects of the drug have raised suspicions regarding the reported exceedingly safe nature of the drug.26–28 Meanwhile, bradycardia, hypotension, and injection site pain occurred less often in the remimazolam group.29,30 Furthermore, the drug may become less popular with patients due to its inability to decrease postoperative nausea and vomiting.31\n\nAlthough many important characteristics highlighting the effectiveness and potential of remimazolam as an alternative sedative are available, the high failure rate of the drug in inducing sedation in 11/44 patients in one clinical trial cannot be ignored. This is coupled with the fact that one patient was seen to have an adverse event (hypotension and oxygen desaturation).32 Thus, it is evident that the use of remimazolam is subject to a higher risk of TEAEs.\n\nThe review had some limitations, including statistical heterogeneity in some meta-analyses, reliance on observational data, and potential bias in included studies. Fentanyl dose may have contributed to inconsistent results in the Pambianco and Rex Phase III study. Future reviews may consider pooling results from studies with the same dose for the same procedure. This review focused on randomized controlled trials. This meta-analysis incorporated only three trials, which implies that the conclusion may lack decisiveness. However, the results indicated that several outcomes had a sufficient sample size and statistical significance.\n\n\nConclusions\n\nThe studies included in the meta-analysis showed that both the drugs under observation had multiple TEAEs, with remimazolam having a higher frequency of adverse effects compared to midazolam. Nonetheless, patients administered with midazolam were at a higher risk of repeat sedation.\n\nIn conclusion, despite a significant difference in the safety profile, the data indicates that more research and, specifically, more RCTs must be performed to find the most effective sedative agent with the least possible treatment-emergent side effects. Furthermore, other aspects of safety, such as depth of sedation and further intra-procedural and post-procedural outcomes, need to be assessed in future studies.",
"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: Extended data for ‘Safety of remimazolam in comparison with midazolam for colonoscopy: A systematic review and meta-analysis’, https://doi.org/10.6084/m9.figshare.24105291.v2. 12\n\nThis project contains the following extended data:\n\n• Supplementary file 1: This includes the relevant search string(s) and the databases used.\n\n• Supplementary file 2: This includes the PRISMA flowchart.\n\n• Supplementary file 3: This includes the quality assessment tool and articles included.\n\n• Supplementary file 4: This includes the 3 Randomized Control Trials and a table showing their characteristics and findings.\n\n• Supplementary file 5: This includes the relevant forest plot comparing Remimazolam and Midazolam with specific p-values. Treatment emergent adverse effects are focused in this study, with further subcategories of adverse effects being discussed.\n\nFigshare: PRISMA checklist for ‘Safety of remimazolam in comparison with midazolam for colonoscopy: A systematic review and meta-analysis’, https://doi.org/10.6084/m9.figshare.24105321.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\nReferences\n\nBrown SR, Hicks TC, Whitlow CB: Diagnostic and Therapeutic Colonoscopy. Shackelford’s Surgery of the Alimentary Tract, 2 Volume Set. 2019 Jan 1; pp. 1689–1699. Publisher Full Text\n\nDeVane CL: Clinical pharmacokinetics and pharmacodynamics of anxiolytics and sedative/hypnotics. Applied Clinical pharmacokinetics and pharmacodynamics of psychopharmacological agents. 2016; pp. 247–266. Publisher Full Text\n\nBackman ES, Triant VA, Ehrenfeld JM, et al.: Safety of midazolam for sedation of HIV-positive patients undergoing colonoscopy. HIV Med. 2013 Jul; 14(6): 379–384. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTowne AR, DeLorenzo RJ: Use of intramuscular midazolam for status epilepticus. J. Emerg. Med. 1999 Mar 1; 17(2): 323–328. Publisher Full Text\n\nBauer TM, Ritz R, Haberthür C, et al.: Prolonged sedation due to accumulation of conjugated metabolites of midazolam. Lancet. 1995 Jul 15; 346(8968): 145–147. PubMed Abstract | Publisher Full Text\n\nNoor N, Legendre R, Cloutet A, et al.: A comprehensive review of remimazolam for sedation. Health Psychol. Res. 2021; 9(1). PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang M, Zhao X, Yin P, et al.: Profile of Remimazolam in anesthesiology: A narrative review of clinical research Progress. Drug Des. Devel. Ther. 2022 Jan 1; 16: 3431–3444. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPastis NJ, Yarmus LB, Schippers F, et al.: Safety and efficacy of remimazolam compared with placebo and midazolam for moderate sedation during bronchoscopy. Chest. 2019 Jan 1; 155(1): 137–146. PubMed Abstract | Publisher Full Text\n\nGarrett A, Flowers J, Ng V, et al.: Remimazolam for sedation during upper gastrointestinal endoscopy in an adolescent. J. Med. Cases. 2022 Oct; 13(10): 495–498. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHutton B, Salanti G, Caldwell DM, et al.: The PRISMA extension statement for reporting of systematic reviews incorporating network meta-analyses of health care interventions: checklist and explanations. Ann. Intern. Med. 2015 Jun; 162(11): 777–784. PubMed Abstract | Publisher Full Text\n\nHasnain N, Khalid MA, Sadiq M, et al.: PRISMA checklist for ‘Safety of remimazolam in comparison with midazolam for colonoscopy: A systematic review and meta-analysis. [Dataset]. Figshare. 2023. 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Publisher Full Text\n\nSchüttler J, Eisenried A, Lerch M, et al.: Pharmacokinetics and pharmacodynamics of remimazolam (CNS 7056) after continuous infusion in healthy male volunteers: part I. Pharmacokinetics and clinical pharmacodynamics. Anesthesiology. 2020 Apr 1; 132(4): 636–651. PubMed Abstract | Publisher Full Text\n\nNordt SP, Clark RF: Midazolam: A review of therapeutic uses and toxicity. J. Emerg. Med. 1997 May 1; 15(3): 357–365. Publisher Full Text\n\nYuan R, Flockhart DA, Balian JD: Pharmacokinetic and Pharmacodynamic Consequences of Metabolism-Based Drug Interactions with Alprazolam, Midazolam, and Triazolam. J. Clin. Pharmacol. Engl. 1999; 39(11): 1109–1125. PubMed Abstract | Publisher Full Text\n\nFukuda M, Tachibana S, Nishihara N, et al.: Remimazolam for a Patient with Myotonic Dystrophy Type 1 Who Underwent Endoscopic Retrograde Cholangiopancreatography under General Anesthesia: a Case Report. JA Clin. Rep. 2021; 7(1): 17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu X, Wang H, Yuan S, et al.: Efficacy and Safety of Remimazolam in Endoscopic Sedation—A Systematic Review and Meta-Analysis. Front. Med. 2021; 8: 655042. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHirata N, Hayamizu K, Yamakage M: How to Administer Remimazolam for Anesthesia Induction. J. Anesth. 2020; 34: 962. Publisher Full Text\n\nTsurumi K, Takahashi S, Hiramoto Y, et al.: Remimazolam Anaphylaxis during Anesthesia Induction. J. Anesth. 2021; 35: 571–575. PubMed Abstract | Publisher Full Text\n\nYamamoto T, Kurabe M, Kamiya Y: A Mechanism of Re-sedation Caused by Remimazolam. J. Anesth. 2021; 35: 467–468. PubMed Abstract | Publisher Full Text\n\nYamamoto T, Kurabe M, Kamiya Y: Re-sleeping after Reversal of Remimazolam by Flumazenil. J. Anesth. 2021; 35: 322. PubMed Abstract | Publisher Full Text\n\nDoi M, Morita K, Takeda J, et al.: Efficacy and Safety of Remimazolam versus Propofol for General Anesthesia: a Multicenter, Single-Blind, Randomized, Parallel-Group, Phase IIb/III Trial. J. Anesth. 2020; 34(4): 543–553. PubMed Abstract | Publisher Full Text\n\nDoi M, Hirata N, Suzuki T, et al.: Safety and Efficacy of Remimazolam in Induction and Maintenance of General Anesthesia in High-Risk Surgical Patients (ASA Class III): Results of a Multicenter, Randomized, Double-Blind, Parallel-Group Comparative Trial. J. Anesth. 2020; 34(4): 491–501. PubMed Abstract | Publisher Full Text\n\nWorthington MT, Antonik LJ, Goldwater DR, et al.: A phase Ib, dose-finding study of multiple doses of remimazolam (CNS 7056) in volunteers undergoing colonoscopy. Anesth. Analg. 2013 Nov 1; 117(5): 1093–1100. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "272753",
"date": "07 May 2024",
"name": "Wissam Ghusn",
"expertise": [
"Reviewer Expertise Gastroenterology"
],
"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 presents a detailed and comprehensive examination of the safety profiles of remimazolam compared to midazolam, focusing on their use in colonoscopy procedures, which is highly relevant to clinical practice. The use of PRISMA guidelines and the involvement of multiple independent reviewers strengthen the reliability of the findings. However, the study is limited by the inclusion of only three studies, which may not provide a robust enough evidence base to conclusively determine safety profiles. The exclusion of broader comparative studies may overlook additional data that could influence safety outcomes. Additionally, the statistical section could be enhanced by clarifying the handling of potential confounders and providing a rationale for the choice of a random-effects model, particularly given the low heterogeneity indicated by the I2 statistic. These aspects, if addressed, could significantly enhance the manuscript's contribution to understanding the safety implications of these sedatives in clinical settings.\nSpecific comments:\nAbstract: The abstract succinctly summarizes the study but could benefit from a clearer statement of the primary outcome, which seems to focus on the safety profile of remimazolam. Introduction: The introduction thoroughly sets the stage by outlining the clinical importance of sedatives in colonoscopy and the pharmacological profiles of remimazolam and midazolam. However, it could be enhanced by directly linking these sedatives' pharmacokinetics to their clinical effects and potential safety implications. Methods: The criteria are well-defined, but the rationale for excluding studies that compare remimazolam with drugs other than midazolam should be clarified, as it might limit understanding of its safety in a broader pharmacological context.\nData Sources and Search Strategy: Clearly outlined, yet the manuscript would benefit from a brief rationale for the chosen databases and terms, enhancing transparency regarding potential publication bias. Results: Data Presentation: The results are clearly presented with an appropriate use of forest plots for visual representation. However, including a table summarizing the study characteristics (sample size, population demographics, study design) would provide a clearer, at-a-glance understanding of the data foundation. Analysis of Adverse Effects: While the relative risk calculation is appropriate, discussion about the absolute risk and the clinical significance of these differences would provide a more nuanced understanding of the safety profiles. Discussion: This section robustly discusses the implications of the findings and contrasts them with existing literature. It would be strengthened by discussing potential mechanisms behind the observed higher incidence of treatment-emergent adverse effects with remimazolam. Limitations: Well-addressed, but could further discuss the implications of the homogeneity of study designs included and the potential impact of different healthcare settings on safety outcomes. Conclusions: The conclusions are appropriate and cautious given the limited number of studies. However, proposing specific directions for future research, particularly in different patient demographics or longer follow-up periods, would be beneficial.\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? Partly\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": "272757",
"date": "09 May 2024",
"name": "Peter Vilmann",
"expertise": [
"Reviewer Expertise my expertice is endoscopy including sedation for endoscopy"
],
"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 is a systematic review and meta-analysis on the safety of Remimazolam (RM) in comparison with Maidazolam (M) for colonoscopy. The focus of the article was safety and side effects of RM with M as control. The methodology used is up to standards of a meta-analysis and the article is well written. The conclusion of the study is that both drugs are safe to use although the authors found more treatment-emergent adverse event in the RM group. The results and conclusions are based only on 3 randomized trails with a limited number of patients (697) and the 3 articles did not have the same endpoint, one with a composite endpoint of 3 criteria. In addition to this 2-3 of the included studies used fentanyl in addition making it difficult to interpret the safety results. Several of the present authors have published another meta-analysis using the same 3 randomized articles comparing these 2 drugs regarding the efficacy of Remimazolam. The new sedativum looks promising but there are at present more meta-analyses than good quality studies on Remimazolam. The authors also conclude that more reseach is warranted.\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\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/13-217
|
https://f1000research.com/articles/13-215/v1
|
22 Mar 24
|
{
"type": "Software Tool Article",
"title": "Digital transformation in public health: a software tool for efficient health record management and improved healthcare delivery",
"authors": [
"Yuceli Barturen-Diaz",
"Dilmer Olivera-Burga",
"Alex Pacheco",
"Yuceli Barturen-Diaz",
"Dilmer Olivera-Burga"
],
"abstract": "Background In today’s world, the abundance of data in many areas of society has increased the need to use efficient technological tools to analyse, accurately and clearly present information. The objective was to develop a virtual platform to increase efficiency in the control of medical records (MR) and reduce errors in the recording of clinical data. To improve the quality of medical care in public health centres.\n\nMethod The research used a methodology that follows a four-stage process for the development of the medical records management software. It started with planning where the user stories and their priority were defined. In the design phase, the system architecture and code structure were developed. Subsequently, in the coding phase, pair programming with incremental implementation was emphasised. Finally, in the testing phase, automatic and manual integration tests were carried out, documented by means of acceptance tests to ensure the quality of the developed software.\n\nResults The web-based platform has led to a significant increase in the number of patients seen, resulting in significant improvements in resource management at the health centres. In addition, the reduction in the incidence of errors highlights the superior accuracy in recording and tracking medical information, promoting a safer and more efficient care environment for patients.\n\nConclusions The main focus of this study is the management of medical records, with the aim of reducing the time spent on registration, ensuring secure access to information, reducing documentation errors and facilitating instant data retrieval through a web-based platform. The results show the effectiveness of this methodology and its positive impact on the management of medical records.",
"keywords": [
"Virtual platform",
"medical records",
"management",
"error rate",
"patient attendance rate",
"electronic reporting."
],
"content": "Introduction\n\nIn today’s fast-paced world, the drastic increase in the production of data in various areas of society has created a growing demand for efficient technological tools that facilitate the analysis and presentation of this data in an accurate and understandable manner.1 Web-based technology has changed the way we access information and accomplish tasks. It allows us to do things faster and with greater security on any device.2 These systems, which you can access through web browsers, provide a wide variety of applications and services. These range from managing data to automating processes.3 En este sentido, el desarrollo de sistemas web ha creado nuevas oportunidades para la colaboración y el trabajo en equipo, permitiendo una mayor conectividad y productividad en diversos contextos, tanto a nivel local como global.4 Furthermore, storing and processing vast amounts of data has facilitated knowledgeable, evidence-centered decision-making across various fields, including scientific investigation and data analysis.5 Key advantages of online systems consist of ensuring safety, confidentiality, and equal access to data.6\n\nIn this context, technology has greatly affected all areas of our society, including medical practice. To improve health services and provide more efficient and safe medical care, healthcare professionals rely on web-based health record (HHR) systems as an essential tool.7,8 According to Ministerial Resolution No. 214-2018-MINSA, electronic health records (EHRs) are digital records of a patient’s medical history and treatment that include organised and detailed information about the patient’s health.9 These records are electronic and stored on computer systems only accessible to authorized healthcare professionals. This ensures fast and secure management, access, and exchange of medical information.10\n\nMost research has shown that the development of web-based health record (H.R.) management systems has the potential to have a positive impact on the efficiency, accuracy, coordination and safety of health care, which in turn improves the overall quality of health services.11–13 A report by Ref. 14, has highlighted a current issue in the Peruvian healthcare industry due to the insufficient use of Electronic Health Records (EHR). In order to tackle this problem, the “Dr. Phuyu” project proposes to be implemented. “Phuyu” is the Quechua word for “cloud”. This project aims to bring together the medical records of the public and private sectors on a modern and compatible software platform that is completely integrated with the Ministry of Health (MINSA). This will make it easy to manage medical records transparently. Alternatively: On the other hand,15 describes a system for healthcare workers to obtain medical records online via handheld gadgets, removing dependence on desktop or laptop computers. Attaining this goal necessitates the integration of blockchain technology to oversee medical data archival. A sample produced with Hyperledger Composer and security measures regulates medical information’s secrecy and protection. Their article16 shows that Health Information Technology (HIT) has a major role in today’s medicine, giving astonishing advantages in healthcare, like improved access to information and tracking, combining records from different episodes of care, ongoing coordination, clinical decision support and efficient prescriptions. It also17 introduces an Electronic Health Record (EHR) that utilizes a standardized model. This has helped reduce process discrepancies, enhance end results, and pave the way for potential digitization advancements in medical facilities.\n\nHowever, there is still not enough trustworthy and current proof in the scientific community about using online systems to manage medical records (MR). This shortage includes concerns like interoperability, privacy and security issues, reluctance to change among medical staff, and limitations in technology infrastructure. Further research is required to assess and verify the impact of this tool on health records and real-time decision making. The demand for such systems is because of the growing complexity of medical information, the significance of easing access to clinical data, and the crucial requirement for a centralised and current database that enables comprehensive and effective care.\n\nThis research helps to fill the information gap by exploring the advantages and struggles of using a web-based system in a public health centre. It gives important data to enhance medical attention and administrative procedures related to medical records. The goal is to examine how this system can enhance medical record management, improve medical care efficiency, aid decision making based on data, and enhance coordination among health professionals at the health centre.\n\nThe aim of this study is to introduce an online system to boost productivity in overseeing patients’ files, thereby enhancing medical assistance quality and optimizing clinical data management at San Juan de la Libertad Health Centre in Bagua Grande, Amazonas, Peru.\n\n\nMethods\n\nIn this segment, we provide an in-depth and comprehensive analysis of the strategies used in the development and implementation of our IT tool specifically designed for public health records management.\n\nMaterials\n\nThe characterisation of our software tool is for public health centres, which led to a correct collection of information and identification of the client’s needs. For the entire development we used a laptop equipped with an Intel(R) Core (TM) i9-12900K processor, 16 (8P+8E) cores up to 5.2 GHz LGA1700 chipset, accompanied by 16GB of 3200 MHz DDR5 RAM and a 1TB SSD M.2 2280 PCIe Gen4x4 NVMe solid state disc.\n\nWe opted to use the agile extreme programming (XP) approach, which consists of four structural activities implemented in sequential phases.18 Refer to Figure 1 for a visual representation.\n\nNOTE: Figure 1 illustrates the phases of software development using four central figures with solid fill. In addition, all the rectangular figures with rounded corners provide details of the activities to be carried out in each phase.\n\nPlanning phase\n\nAll customer requirements were considered during this planning phase, resulting in essential system features. The first feature allows users to access the system and register. Users can choose from three roles: administrator, support user, or client user. The second feature enables user registration in triage, as well as recording diagnoses and care details. The third need allowed making reports, producing medical records and notifying via email or text message (SMS).\n\nDesign stage\n\nThe best user stories were chosen using a straightforward approach. Also, we made CRC (Class-Responsibility-Collaboration) tasks or cards, which helped us understand the system better. See Table 1 for more details.\n\nCodification phase\n\nThe system code is hosted in the following repository.19 The website design was created using HTML and CSS for appearance, and JQuery was used for movement and interaction. Other components like Vanilla JS, Axios, Datatable, Sweet Alert, Ladda, and APIs were included in Json format to deliver the patient history via text message. To ensure the web system operates correctly, we used PHP programming language version 7.2 supported by Codeigniter 8.002 framework. MySQL v.10.0 was used to administer the database.\n\nTest phase\n\nA thorough verification of the system was carried out by running unit tests to identify any bugs in the code and enhance its quality. Acceptance testing was also carried out in conjunction wikth the customer to ensure the application was approved. Figure 2 shows the architectural design of the web system, which provides a comprehensive view of how the system works in relation to all the components involved.\n\n\nResults\n\nIn order to facilitate the use and replication of the project, all resources, including system files and test data, are hosted in the Zenodo.org repository. These resources are available for immediate download without any restrictions.19–21\n\nFigure 3 shows the user interface of the “super administrator”, which displays the web system dashboard, which provides a summarised and visually appealing view of key information related to the medical care of a set of patients. the features displayed on the dashboard are the following: a) Number of medical staff, patients, care, diagnoses and medical records. b) Statistical graph of information on the type of services provided. c) Statistical graph of care information for the last 3 days. d) Number of users with their photos.\n\n• Entry:\n\n○ Login with password and user previously assigned.\n\n○ Access to the main control panel (dashboard).\n\n• Output:\n\n○ Static view of users\n\n○ Statistical view of types of healthcare services.\n\n○ Statistical view of patients seen in the last three days.\n\nFigure 4 illustrates the care process, Figure 5 the triage process and Figure 6 the recording of a new patient’s history. The first step in the care process is to search for the patient by name or surname, which automatically fills in the patient’s first and last name fields on the form. Information is then entered into the relevant fields, such as the type of service, the healthcare professional who will be attending the patient, the amount to be paid and a description of the care to be provided. The patient is then directed to the triage area, where data such as blood pressure, temperature, heart rate, respiratory rate, oxygen saturation, weight and height are recorded. Finally, the assigned medical staff will complete the patient’s medical history according to the symptoms and conditions presented.\n\nImput\n\n\n\n○ Login with a previously assigned user name and password.\n\n○ Access the Surgical module and select the different options according to the procedure: Nursing - Triage - Clinical History.\n\n○ Nursing: Select ‘New’.\n\n○ Triage: Select ‘Pending Triage’ and then ‘Triage’.\n\n○ Clinical History: Select ‘No attention’ and then ‘Attention’.\n\nOutput\n\nCare process\n\n○ “Care” Register the patient for care (name, doctor, type of service, etc.).\n\nTriage process\n\n○ “Triage” and record the patient’s vital signs (temperature, weight, height, blood pressure, etc.).\n\nClinical history process\n\n○ “Clinical history” and record your diagnosis, clinical pathology, pathological anatomy, prescription and other necessary data.\n\nFigure 7 shows two alternatives for providing the patient with their medical records. The first alternative is to send it by email, as shown in Figure 8. The second option is to send a text message to the patient’s mobile phone number, as shown in Figure 9. This ensures that the patient receives all information relevant to their medical care in a personalised manner.\n\nInput\n\n\n\n• Access the main control panel (dashboard).\n\n• Select the “Surgery” module, then “Medical History”.\n\n• Scroll to the top and select the “With Attention” type.\n\n• Then select the “View” option and click on the tab to the side.\n\nOutput\n\nSend email\n\n• A window will appear where we will check the email and file to send.\n\nSend SMS\n\n• A window will appear where we verify the phone number and press “Send”.\n\nDaily reports\n\nIn Figure 10, the Super Administrator user has the ability to generate a variety of reports related to daily care, daily medical records, diagnoses and service types using various selection criteria such as start and end date and patient name. These reports can be exported in PDF and Excel formats. In addition, the super administrator can carry out the corresponding configurations and operations, and also has access to the exchange rate of the dollar to the Peruvian sol, as well as the general sales tax (IGV), which is 18%.\n\nInput\n\n\n\n• Enter the “Reports” module and select the different types of reports: Daily History, Daily Attendance, Diagnoses and Type of Service.\n\n• Select the export format: Excel or pdf “Print”.\n\nOutput\n\n\n\n• View the file with the information organised according to the previously selected format.\n\n\nDiscussion\n\nFigure 4 shows how dashboards can improve the efficiency, clinical decision-making and quality of care. This tool presents essential information comprehensively, allowing for quick, detailed comprehension and analysis with meaningful implications. The dashboard monitors progress, supports strategic decision-making, identifies and manages risks and enhances productivity. These factors are essential for ensuring an institution’s competitiveness.22 The medical industry clearly illustrates the usefulness of this tool, emphasising its significance in improving processes and making informed decisions. This observation is consistent with the earlier study by Ref. 23, which outlines that dashboards allow for the sharing of important data in a consolidated and visual format, streamlining decision-making. Dashboards are a useful tool for improving clinical interactions as they simplify information, enable the sharing of data, and streamline decision-making processes. This is achieved by visually displaying the transfer of information. Dashboards make the most of data, allowing them to play a significant role in decision-making across several sectors.24 Overall, these findings emphasise the importance of dashboards as vital tools that increase efficiency, aid clinical decision-making and enhance the quality of care, making them valuable resources for healthcare professionals.\n\nThe results shown in Figure 5, 6 and 7 stress the significance and advantages of adopting a web-based system for health care registration, triage, and medical records (MR). This system enables healthcare experts to swiftly and centrally retrieve patient information, hence facilitating the production of precise and comprehensive medical documents. This is crucial for ensuring proper medical treatment and enabling efficient clinical decision-making. MR systems can get patient info faster and more precise.25 Digital medical records are a significant upgrade, giving quick access to records and enhancing readability, safety and organisation in medical data management. It shows how different specialities and hospitals can communicate better, acting as a necessary tool to aid primary and hospital care to communicate, solving a major issue with paper records.26,27 The main benefits include effective care, good medical records and smoother, coordinated communication between various medical fields. Moreover28 stresses the need to keep and share patient data with relevant professionals to enhance patient care. These findings demonstrate the benefits of using an online system to store medical records, improving communication between healthcare professionals and ultimately leading to better medical care.\n\nIn Figure 8, 9 and 10, it is emphasised that sending patients medical history updates through emails and text (SMS) is an efficient way of communication. These methods aid in conveying medical care information and even allow for tailored prescription sharing, thereby improving patient interaction. Connecting these communication means to the web system is also considered crucial for providing patients with high-quality care. This connection is clear and emphasises the significance of employing these avenues to improve medical attention. It is crucial to stress the trustworthiness of SMS messages, which are direct, accurate, brief, affordable, and permit instant data viewing.29 SMS is known for being fast and reliable, making it useful even in areas with limited coverage. This benefits a wide range of users. Research30 has shown that SMS delivery of information has a significant impact, as it allows for accurate and personalised data transmission. It is an effective strategy for improving communication with patients. These methods offer a cheap, clear, and efficient way of spreading healthcare knowledge. Email has become an essential tool in work and communication procedures, making it easier to exchange information.31 Providing precise digital information can be particularly valuable in teaching patients how to manage their health conditions. Furthermore, email is a cost-efficient and productive method of preserving continuous contact with patients, which is vital in the care of chronic diseases.\n\nFigure 11 demonstrates how the reports produced by the web system, using filters applied by the super administrator, contribute to better daily care. The system offers comprehensive information on the daily care provided, showing how closely the web system performance relates to health professionals’ output. It is clear that more effective reporting leads to improved health worker results. This research agrees with study,32 which found that reports about daily care filtered through a web-based system play a vital part in coordinating medical teams. This tool improves communication and avoids doing the same work twice by showing the actions taken. Using web-based systems in healthcare can boost efficiency, encourage team coordination and, in turn, enhance the quality of care. In addition, it is vital to report medical records on the web nowadays, as stated by Ref. 16. This approach provides valuable advantages to healthcare, including better access to and follow-up of information, integration of records from varying care sessions, continuous coordination, and clinical decision support. This study highlights the significance of reporting in electronic health records, which leads to enhanced medical care and better collaboration among health professionals.\n\n\nConclusion and future work\n\nThis study has created a web system for managing medical records in a health centre that before relied on paper records. The challenge of modernising patient medical data collection, storage and accessibility in the traditional healthcare environment has been addressed and overcome.\n\nAt first, we found issues with the paper-based record system such as inefficiency, trouble accessing and organising information, and the potential for critical data loss. We tackled these challenges by implementing a web-based system which made it easier to manage medical records. This switch to digital also enabled faster access, better readability, and more secure medical information. Ultimately, this transition significantly improved the quality of medical records.\n\nMoreover, the introduction of the internet-enabled programme has eased information exchange and organisation among different healthcare sectors. The capacity to access patient data centrally has streamlined the production of precise and elaborate files, ultimately boosting the effectiveness of medical practitioners. The capacity to access patient data centrally has streamlined the production of precise and elaborate files, ultimately boosting the effectiveness of medical practitioners. What’s more, the seamless cooperation between medical specialities and hospitals has emerged as a primary benefit, surmounting a major weakness of the printed layout.\n\nFinally, experts suggest utilizing state-of-the-art information technologies to enhance research results, for instance by implementing systems that employ artificial intelligence and exploit device connectivity via the Internet of Things (IoT). In addition to this, developing evaluation tools to measure the advantage and disadvantage of applying this new module on the patient practice is crucial.",
"appendix": "Data availability\n\nZenodo: OliveraBurga/GitHubCentroSaludSJL: Software tool for efficient health record management and improved healthcare delivery, https://doi.org/10.5281/zenodo.10055291. 19\n\nThis project contains the following underlying data:\n\n• OliveraBurga/GitHubCentroSaludSJL-v.1.0.zip\n\nZenodo: OliveraBurga/BasededatosMySQL: My sql DataBase for Electronic Health Record Management Software Tool, https://doi.org/10.5281/zenodo.10059169. 21\n\nThis project contains the following underlying data:\n\n• OliveraBurga/BasededatosMySQL-V1.0.0.zip\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 are grateful to the health centre in San Juan de la Libertad for their valuable support and assistance during this research. The authors also wish to express their appreciation to Alex Pacheco from the Faculty of Engineering and Architecture at Universidad Cesar Vallejo for his guidance on the methodology for this study.\n\n\nReferences\n\nAkbulut S, et al.: Designing a Private and Secure Personal Health Records Access Management System: A Solution Based on IOTA Distributed Ledger Technology. Sensors. May 2023; vol. 23(11): p. 5174. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCastilla R, Pacheco A, Franco J: Digital government: Mobile applications and their impact on access to public information. SoftwareX. May 2023; 22: 101382. Publisher Full Text\n\nAucancela L, Rojas M: Web applications, a source of solutions and exclusion for education in times of COVID-19. Revista Scientific. Nov. 2021; 6(22): 397–417. Publisher Full Text\n\nVidal C, Sánchez A, Serrano J, et al.: Academic experience in rapid web information systems development with Python and Django. Formación universitaria. Oct. 2021; 14(5): 85–94. Publisher Full Text\n\nGupta S, Suman S, Kumar S, et al.: Development of web GIS based accident information system for safe and sustainable transport. Mater Today Proc. Aug. 2023. Publisher Full Text\n\nGil J, Viega M: Electronic medical records: confidentiality and privacy of clinical data. REVISTA MEDICA DEL URUGUAY. Nov. 2018; 34(4). Publisher Full Text\n\nCan O: The security and privacy aspects in semantic web enabled IoT-based healthcare information systems. Semantic Models in IoT and eHealth Applications. Jan. 2022; 89–116. Publisher Full Text\n\nRaghunathan K, McKenna L, Peddle M: Factors in integrating academic electronic medical records in nursing curricula: A qualitative multiple case studies approach. Nurse Educ. Today. Jan. 2023; 120: 105626. Publisher Full Text\n\nMinsa: Resolución Ministerial N.° 214-2018-MINSA - Norms and legal documents - Ministry of Health - Peruvian State Platform.2018. 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Revista peruana de computación y sistemas. Nov. 2022; 4(1): 51–67. Publisher Full Text\n\nVillanti A, et al.: Tailored text message and web intervention for smoking cessation in U.S. socioeconomically-disadvantaged young adults: A randomized controlled trial. Prev. Med (Baltim). Dec. 2022; 165: 107209. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElleuch M, Ismaili O, Laga N, et al.: Process fragments discovery from emails: Functional, data and behavioral perspectives discovery. Inf. Syst. Sep. 2023; 118: 102229. Publisher Full Text\n\nKademane A, Kumar P, Chaudhary B: Influence of the electronic health record on nursing practice in the hospital setting. Salud, Ciencia y Tecnología. Aug. 2023; 3(S1): 453. Publisher Full Text"
}
|
[
{
"id": "260296",
"date": "14 Sep 2024",
"name": "John Batani",
"expertise": [],
"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\nAbstract (methodology) ; mention the tools used in developing the software\nIntroduction:\nI am not sure if this sentence is appropriately placed \" En este sentido, el desarrollo de sistemas web ha creado nuevas oportunidades para la colaboración y el trabajo en equipo, permitiendo una mayor conectividad y productividad en diversos contextos, tanto a nivel local como global\". Please verify this.\n\"A report by Ref. 14, has highlighted a current issue in the Peruvian healthcare industry due to the insufficient use of Electronic Health Records (EHR)\" - is the issue you are addressing insufficient use? If yes, do you solve this by developing additional systems that will still be insufficiently used?\nIt is unclear how using the \"cloud\" would address the insufficient use of EHRs. Are the reasons for the \"insufficient use\" to do with such systems not being hosted on the cloud? I think you should write the point in a way that makes your readers easily understand your argument.\n\n\"removing dependence on desktop or laptop computers\". State a reason(s) why dependence on desktop or laptop computers is worse than dependence on handheld gadgets.\nState the objectives of this study\nMethodology - lacks justifications for the choices made and such justifications should ideally be backed by the literature.\n\n\"This research helps to fill the information gap by exploring the advantages and struggles of using a web-based system in a public health centre.\" I dont see how this was done . Wasn't the aim to develop an EHR? Proofread and check the spellings, e.g. \"wikth\" Who was the \"customer\" involved in acceptance testing? Are they patients or healthcare professionals? Was ethical clearance sought to involve the \"customer\" in this study? Were there any medical professionals involved in this study to guide the researchers?\n\nShare the complete URL to your Zenodo.org repository link.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-215
|
https://f1000research.com/articles/11-163/v1
|
09 Feb 22
|
{
"type": "Research Article",
"title": "Genre analysis of introduction section in electrical engineering undergraduate laboratory reports",
"authors": [
"Veeramuthu Veerappan",
"Mokhtarrudin Ahmad",
"Mohd Afizal Aris",
"Wei Hui Suan",
"Mokhtarrudin Ahmad",
"Mohd Afizal Aris",
"Wei Hui Suan"
],
"abstract": "Background This study examines the genre of Engineering Laboratory Reports (ELR) introduction section written by Electrical Engineering Undergraduates in a higher learning institution. The aims of this study are to identify the rhetorical moves and combinations of move patterns used by engineering students to write introduction section of ELR. Methods A genre analysis was conducted to identify writing patterns and convention practices of engineering undergraduate students thus a corpus of N= 35 was selected from electrical engineering students in their final year of study. This study adopted Genre Theory as its theoretical framework, [1] analytical framework and [2] BCU approach for analysis procedure. A pilot test was conducted to determine the model that fits the best to describe moves and steps of ELR. The study benchmarks a move or step to be present in at least 60% of the reports. Results The finding shows the introduction consists of one main move which is providing background information of the experiment and followed by four subsequent steps which are reference to research purposes, reference to theoretical knowledge in the field, providing an overview of the study and identification of main research apparatus. The move 1 and all four steps identified above are viewed as conventional move and steps of introduction section only among undergraduates in academic context. The exemplification of finding pave ways to address grey areas of improvement in scientific written genre among laboratory instructors and academics. The method employed in this study may be replicated to analyse other sections of scientific and technical reports such as method, result, discussion and conclusion (MRDC). Conclusions This study posits the importance of collaboration between English for Academic (EAP) practitioners such as English-writing instructors and discipline specific specialist from engineering field to further improve on genre-based writing instruction, and to identify student learning needs.",
"keywords": [
"Introduction section",
"laboratory reports",
"move analysis",
"engineering discourse"
],
"content": "Introduction\n\nAmong the many academic genres, writing an investigative article has grown a lot of curiosity and thoughtfulness among the academicians and researchers.3 has introduced his “move analysis” to examine the structure of introduction section in the engineering research articles. In his 1990 research, Swales suggested a “3-move schema” in writing introductions for any articles which is known as the “Create A Research Space” (CARS) model. This study contributes to a better understanding among practitioners in this discourse community on how to write effective research articles but not much study has been conducted to analyze undergraduate engineering laboratory reports.4 in his paper, “Writing a Laboratory Report for Senior Electrical Engineering Courses: Guidelines and Recommendations,” mentioned that in engineering pedagogics, specifically in the electrical engineering courses, laboratory report can be use as the measurement to evaluate the understanding of the theory taught in the classes.\n\nThe primary job of any scientific Introduction is to establish the purpose for doing the experiment that is to be reported. Thus, the introduction and the theoretical background were usually combined into one introductory section depending on the length and complexity of the report.4 stated that the introduction creates the reader’s overall understanding of the rest of the report. He mentioned that students should only write a maximum of two A4 papers to avoid any irrelevant information being mentioned and stated in the introductory paragraph. Moreover, the introductory paragraph should also make a reference to the appropriate theory and the importance of the previous studies whenever necessary. Not all undergraduate students have experienced writing ELRs in high schools or before varsity admission.5\n\nThe ability to write an effective introductory paragraph and abstract or summary will assist the writing process, as these sections, especially the introduction contains a synopsis of the whole report. According to6 the inquiry based ELRs foster questioning, designing experiments and interpreting results are essential processes to become experimental scientist.10 The introduction or the introductory paragraph is one of the central sections of a laboratory report. To have the readers have a better understanding and a clear guideline of the report, the introduction should also provide relevant background information and puts the study into context of the depth and challenges of an experiment.11 Additionally, the introduction should include a brief overview of relevant and latest publications in the respective field.\n\nAccording to the university’s guideline, an introduction of an Engineering Laboratory Report (ELR) should consist of an overview of the topic under experiment, a clear statement of purpose, the reasons to initiate the experiment, as well as general content to assist reader’s understanding into subject matter. The engineering faculty also requires students to discuss underpinning theory that leads to experiment, a short literature review on the theory, questions and even ambiguities which arose from the chosen theory. The current study attempts to fill the existing gap by investigating the specific discourse features in the Introduction section used among engineering students in writing ELR at tertiary level. The purpose of this study is to investigate what are the moves and steps as well as the combination of move and step patterns used by engineering undergraduates in writing the introduction section of ELR. These aims are to be realized with the use of Genre Theory.3,7 mentioned that Genre Theory has evolved from the study of discourse and linguistic analysis to further describe and explain why the members which belongs to a certain discourse community use the language the way they do. The interpretative characteristic of genre theory made it widely accepted and used in genre-based studies among academics and linguists.8\n\n\nMethods\n\nA genre analysis was conducted to determine the moves and steps that occur in the introduction section by adapting the categories outlined by Ref. 1 framework. Prior to using Ngowu’s model, a pilot test was conducted to examine the suitability of this model to the current study on introduction section of ELR. 15 ELRs were selected and examined to determine the match in description. There were more than 60% match in the categories outlined by the model and ELRs under examination, making it the most suitable analytical framework that can be modified and replicated. The total sample size collected was N=74. These samples were further minimized and scrutinized to select the ELRs that contain most complete and comprehensive information. Quality of data, amount of information, nature of topic, scope of study, design and method used in a qualitative study are the few factors used in determining sample size.9 In this study, the sample was based on selected ELR’s that achieved a score of 4 marks out of 5 marks. The sample size of this study is maintained at N=35 as these samples best represented the electrical engineering laboratory genre and reached a saturation level with similar recurring moves and steps. To further validate the data, semi-structured interview was conducted with an engineering content specialist. The total intake of electrical engineering students in this tertiary institution is not more than 100 students a year and, in each trimester, these students are engaged in writing at least 4 ELRs. The data consist of ELRs that have obtained a higher rating of at least 4 out of 5 marks. The procedures for conducting move analysis in this study adapted a corpus-based model outlined by Ref. 2 BCU approach.\n\nAs to address the trustworthiness of this study, a coding protocol was developed with definitions and examples for mandatory, conventional and optional moves and an inter-rater reliability check was conducted among three coders, consisting firstly the researcher, secondly an engineering content specialist and thirdly a language expert to determine disagreement or discrepancies and the coding protocol was revised. This coding scheme assists in identification of introduction section and also controls the variability in the analysis, which guides other coders apart from the researcher himself to identify the moves and steps. Some textbooks and research articles were also used as a guide such as the textbooks written by Refs. 8, 9 on engineering and technical writing and research articles reporting engineering writing,12–14 and genre-based studies of written discourse in other engineering disciplines.15–17 There were three coders involved in the development and modification of the coding scheme who is the researcher himself, secondly an engineering content specialist and thirdly a language instructor. The reason of including two other coders apart from the researcher is to ensure inter-coder reliability. The second and third coders were trained to read two similar samples of ELR’s and identify the moves and steps in the Introduction section.\n\nEthical Approval Number: EA1582021 approved by Technology Transfer Office, Multimedia University.\n\n\nResults and discussion\n\nIn order to depict how the texts are analysed, the extracts of text from ELR corpus which show moves and steps are exemplified. The move and steps are identified such as (M1S1 means Move 1 Step 1). The extracted text used for exemplification is bolded and italicised to show the differences in analysis. The analysis shows that the introduction consists of one main move which is providing background information of the experiment and followed by three subsequent steps which are reference to research purposes, reference to theoretical knowledge in the field, providing an overview of the study and identification of main research apparatus. This finding has more than 80% consistency to the findings of a previous studies by Refs. 17, 18 on biochemistry articles.\n\nMove 1 of the ELR is written to present background information of the experiments consists of 4 steps. Firstly, Move 1 Step 1 the reference to research purposes. This statement is written prior to all other information as to guide the writer throughout the reporting process of laboratory experiment. All the reports have stated at least two objectives that it aimed to achieve in the experiment. Move 1 Step 2 provides an overview of the topic under study. This step is important to give readers general information about the experiment. Move 1 Step 3 provides the theoretical knowledge of the field under study. Move 1 Step 4 is identification of main research apparatus. This step mainly outlines the apparatus used in the current experiment. It was observed that in Move 1 Step 4, most of the ELRs did not provide detailed description of the apparatus used.\n\nThe Move 1 Step 1, reference to research purposes is written to state the objectives of the initial experiment. This move can be considered the most important move in the introduction section to inform readers the main aims of conducting the experiment. The completed report can be understood by readers if the objectives are clearly stated before moving on to other steps in the introduction section. Based on the analysis of 35 ELR’s compiled, this step occurred as Move 1 Step 1 in 24 ELR’s or 69% from the total percentage. This is a significant finding as it is representative to the overall moves in introduction section.\n\nMove 1 Step 2 provides an overview of the topic under study. It gives general information about what the experiment is all about, states the characteristics of the variables under study, the main terms used in this experiment, short definition of the functions of each variables and features used in the experiment that gives an overall view of the experiment which has been conducted. The analysis reveal that this move has occurred in 24 reports or 69% of the total report. This has made this move conventional in the introduction section based on occurrence rate. Although this step frequently occurs in the reports, yet its sequence is not in accordance. It was observed that this step has occurred only in 9 reports as step 2. This shows that the move pattern in introduction section is not always in sequence of M1S1-M1S2-M1S3-M1S4.\n\nMove 1 Step 3 provides reference to the theoretical knowledge in the field. This move provides students or readers with sufficient mathematical or theoretical background to understand how the experiment works, what has the earlier assumptions indicated and how the experiment is related to the theoretical knowledge. This section may be written in short, if it can be well understood and connection can be made with the measurement of an experiment. Based on the analysis on 35 ELR’s, this step occurred in 21 reports, which totals up to 60% of occurrence from the overall reports. This finding is significant, making this step as a conventional step in writing introduction section. However, the analysis also shows that this step occurred as step 3 in Move 1 in 17 instances or 49% only.\n\nThe Move 1 Step 4 is written to state the main apparatus used to conduct the experiment. In this step, all the equipment used are usually outlined and very small number of ELR’s provide detailed description of each apparatus used for the experiment. Based on the analysis of 35 ELR’s compiled, this step occurred in the introduction section of 33 ELR’s or 94% of the total reports. This is a significant finding as it is representative to the overall moves in introduction section. However, another finding shows that this step has occurred as Move 1 Step 4 in only 17 ELR’s or 49% only. Hence, this indicates that the identification of main apparatus has occurred as other steps in move 1. This shows that not all steps in ELR’s occur in a pre-determined sequential step. The analysis also indicates that Move 1 Step 1 was not written in 3 ELR’s.\n\nIn this section, the analysis of ELR’s focuses to determine the sequence of move and steps with which steps to begin and end the introduction section. As noted in previous analysis, the length of each steps varies with Move 1 Step 1 that states the objectives of the study to be the shortest of all 4 steps in move 1. In this step, students use action verbs to state the objectives without detailed elaboration. This step clearly states the aims to be achieved by the end of an experiment. It is clear that 24 ELR’s or 69% of the reports began with the statement of objectives. Although most of the reports starts with M1S1, this finding cannot be generalized to overall ELR’s as some start from M1S1. 7 ELR’s or 20 % of the overall reports starts with M1S2, 2 ELR’s or less than 6% of the reports start with M1S3 and only 1 report or 3% starts from M1S4 and 17 ELR’s or 49% of the total reports end with M1S1. This is the last step in presenting background information of the experiment. This step is frequently adopted to end the introduction section and before moving to method section. Next, 9 ELR’s or 26% of the reports end with M1 S3, while 6 ELR’s or 17% of the reports end with M1S2 and only 3 report ends with M1S1. Based on the occurrence of each steps in Move 1 of introduction section, move 1 and all three steps identified and discussed above are viewed as mandatory and conventional steps of introduction section. The model proposed in Table 1 below encapsulates the Move and Steps made by undergraduate students of Electrical Engineering in writing their laboratory reports.\n\n\nConclusion\n\nThere are several conclusions that can be drawn from this study. Mismatches between the guidelines set by the university and the final output of students are identified, firstly, the omission of background theories or pertinent literature review. The historical background of previous studies is important as it can be replicated and used for the current experiment. It is also to convince the readers the theory is viable to be used in the experiment. Secondly, it is lacking in the content to orientate the readers with enough general ideas into the subject of experiment. Thirdly, although it is the most applicable approach to enforce students experiential learning, this may not contribute or add on to the body of knowledge in engineering field. This study propose collaboration between English for Academic (EAP) practitioners such as English writing instructors and discipline specific specialist from engineering field to further improve on genre-based writing instruction to identify students’ learning needs. The limitation of this study is it focuses only on ELR written in electrical engineering domain and findings cannot generalized to other sub-disciplines and the omission of data triangulation from various sources such as interviewing and expert validation which could contribute to better understanding of why a particular discourse community writes the text the way they do.\n\n\nData availability\n\nFigshare. Genre Analysis of introduction section in electrical engineering undergraduate laboratory reports. DOI: https://doi.org/10.6084/m9.figshare.14881911 19\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nWe acknowledge Dr. Shamala Paramasivam from UPM has given permission to include her name and affiliation in this publication for her advice in conducting this research.\n\n\nReferences\n\nNwogu KN: The medical research paper: Structure and function. Engl. Specif. Purp. 1997; 16(2): 119–138. Publisher Full Text\n\nBiber D, Connor U, Upton TA: Discourse on the move: Using corpus analysis to describe discourse structure. John Benjamins Publishing; 2007; (Vol. 28. ).\n\nSwales J: Genre Analysis. Cambridge: Cambridge University Press; 1990\n\nMasoud MI: Writing a laboratory report for senior electrical engineering courses: Guidelines and recommendations. Proceedings of 2017 IEEE Global Engineering Education Conference, EDUCON 2017. [7942870] IEEE Computer Society. 2017; (pp. 340–346). Publisher Full Text\n\nParkinson J: The student laboratory report genre: A genre analysis. Engl. Specif. Purp. 2017; 45: 1–13. Publisher Full Text\n\nKalaskas AB: Science lab report writing in postsecondary education: Mediating teaching and learning strategies between students and instructors (Doctoral dissertation, George Mason University).2013.\n\nBhatia VK: Integrating products, processes and participants in professional writing. Candlin CN, Hyland K, editors. Writing: Texts, Process and Practices. New York: Addison Wesley Longman Ltd.; 1999a.\n\nBhatia VK: Applied Genre Analysis: A MultiPerspective Model. Ibérica. 2002; 4: 3–19.\n\nMorse JM: Determining sample size. Qual. Health Res. 2000; 10: 3–5. Publisher Full Text\n\nBeer D, McMurrey D: A guide to writing as an engineer. New York: John Wiley & Sons; 1997.\n\nLannon JM: Technical Writing. 6th ed.New York: HarperCollins College Publishers; 1993.\n\nFlowerdew L: The problem-solution pattern in apprentice vs. professional technical writing: An application of appraisal theory. Aston G, Bernardini S, Stewart D, editors. Corpora and language learners. Amsterdam: John Benjamins; 2004; (pp. 125–135).\n\nFlowerdew L: Corpus-based analyses of the problem–solution pattern: A phraseological approach. Amsterdam: John Benjamins; 2008.\n\nMcKenna B: How engineers write: An empirical study of engineering report writing. Appl. Linguis. 1997; 18(2): 189–211. Publisher Full Text\n\nHopkins A, Dudley-Evans T: A genre-based investigation of the discussion sections in articles and dissertations. Engl. Specif. Purp. 1988; 7: 113–121. Publisher Full Text\n\nKanoksilapatham B: A corpus-based investigation of scientific research articles: Linking move analysis with multidimensional analysis. (Unpublished doctoral dissertation). Georgetown University, Washington, DC.2003.\n\nKanoksilapatham B: Rhetorical structure of biochemistry research articles. Engl. Specif. Purp. 2005; 24: 269–292.\n\nKanoksilapatham B: Rhetorical moves in biochemistry research articles. Discourse on the move: Using corpus analysis to describe discourse structure. 2007; 73–119.\n\nVeerappan V, Ahmad M, Aris M, et al.: Genre Analysis of Introduction Section in Electrical Engineering Undergraduate Laboratory Reports. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "126416",
"date": "04 Apr 2022",
"name": "Ilyana Jalaluddin",
"expertise": [
"Reviewer Expertise Literacy studies",
"ESL writing skills",
"Technology and literacy"
],
"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 discussed the background of the study and methodology in great detail.\nThe findings manage to give an overall overview of how moves have actually been used in the engineering report. However, the findings lack discussion such as the indication of what it means if the certain steps occur less in the report. The authors only state percentage and perhaps it will be more clear if the authors provide discussion and interpretation of the findings so that readers will have better view of what it means when occurrence is low or high in the report.\nConclusion summarises the whole thing by pointing out the strengths and weaknesses of the study. But it is not connected properly to the findings. How or in what way does it mismatch with the university guidelines? What content is lacking here? Perhaps, the authors can explain further on these two matters as it helps to elaborate more about the 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? 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": "9522",
"date": "27 Apr 2023",
"name": "Veeramuthu Veerappan",
"role": "Author Response",
"response": "Dear Dr Ilyana, Thank you for the feedback provided. Below are our revision based on each comments. List of Amendments : Details of amendment made in the manuscript: Only a paraphrased and simplified version of the revision was added in the manuscript. The full text was not reported in the manuscript due to word limitation allowed by publisher. Reviewer 1 The findings lack discussion such as the indication of what it means if the certain steps occur less in the report. Provide discussion and interpretation of the findings. The following is added and paraphrased: The introduction section of the ELR corpus consists of one main move, which is presenting background information, and four subsequent steps: referencing research purposes, providing an overview of the subject under study, referencing theoretical knowledge in the field, and identifying the primary apparatus used to conduct the experiment. The majority of the ELRs examined featured all four processes, but the study also discovered that the sequence and frequency of these steps varied among the ELRs examined. Overall, the study's findings are highly consistent with research on biochemistry articles from earlier studies, showing that this structure is typical in the industry. Therefore, authors in the field of ELR typically start their introductions by giving a general overview of the subject and establishing the background information for their experiment. This indicates ELR writers assume their readers are already familiar with the subject and do not need to provide a thorough introduction.This would imply that ELR writers are especially interested in identifying and resolving distinct issues within their field. This study suggest that ELR writers are more concerned with presenting their own research than they are with summarising earlier work in the same topic.This may also indicate that ELR writers have a keen interest in finding and solving specific research gaps in their area of study. The specific research problem or hypothesis that they provide holds mores significance to ELR writers.When analysing these results, it's critical to keep in mind that the percentages provided only reflect the frequency of each move over the whole ELR corpus and may not necessarily be representative of all introductions in the field. Furthermore, it's likely that the frequency of each motion may differ based on several factors. Yet, these results offer helpful information about the general structure and relevance of introductions in the field of ELR. Reviewer 1 Conclusion summarises the whole thing by pointing out the strengths and weaknesses of the study. But it is not connected properly to the findings. How or in what way does it mismatch with the university guidelines? What content is lacking here? Revision made: The study's conclusion is based on several findings made during the investigation of the ELR corpus. First, the study identified discrepancies between university guidelines and students' final outputs, particularly the exclusion of underpinning theories or important literature reviews. The students require more guidance in comprehending the expectations of the genre and the significance of incorporating background information is corroborated by this study. Additionally, the study revealed that there wasn't enough content in the introduction section of the ELR corpus to give readers a clear understanding of the experiment's topic. This finding is similar to the findings of other studies that students require assistance in honing their writing skills so they can incorporate the relevant details they need to engage with their readers. Reviewer 1 The findings of the study also confirmed that while experiential learning is a good strategy, it might not always add to the body of knowledge in the engineering area. Collaboration between English for Academic (EAP) practitioners and subject matter experts from the engineering profession is necessary to advance genre-based writing instruction and to determine students' learning needs. Overall, the study's results call for a need for collaborative effort to enhance writing skills as well as the need to support students in comprehending the requirements of the ELR genre. The study's conclusion highlights various discrepancies between the recommended format for lab reports following the university’s guidelines and the actual report the students' produce. Firstly, the absence of underpinning theories or relevant literature review, which is important to convince readers that the theory guides the current study. Next, there is a lack of sufficient general information to guide and engage readers to the study's purpose and need. These results are consistent with the Faculty’s report guidelines that the introduction section should give a general overview of the subject and the report's purpose and that its content should be sufficiently general to allow readers to easily engage and comprehend the contents of the report. Hence, the findings specifically found these two discrepancies: The findings claim that that students frequently neglected to mention the background theories or relevant literature in the introduction section which is crucial because it can be replicated, reproduced, and reapplied to the current study. It is also important to convince the readers that the theory is still valid to be used for their investigation. Study findings also revealed that the introductions lacked the necessary general information to guide readers through the project's subject matter and provided readers with little information to comprehend the relevance and context of the study."
}
]
},
{
"id": "139566",
"date": "20 Jun 2022",
"name": "Donnie Tulud",
"expertise": [
"Reviewer Expertise Genre analysis and discourse analysis"
],
"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 aims to examine the genre of Engineering Laboratory Reports (ELR) introduction section written by Electrical Engineering Undergraduates in a higher learning institution. The aims of this study are to identify the rhetorical moves and combinations of move patterns used by engineering students to write the introduction section of ELR. However, there are several issues that I want to clarify specifically with the following parts:\nIntroduction\nThough the writer has presented the problems well, still; this part lacks related concepts and studies that could substantiate the current study so as to establish the research gap. In here, the writer can provide pieces of information to make the study more problematic. Thus, it is necessary for the writer to use other studies as reference that have explored other research introduction as corpora.\nMethods\nWhy did you not consider the framework of JOHN SWALES which is the CARS model in analyzing the introduction, since you made mention of CARS model in your introduction? I believe the CARS model in describing introduction is much more comprehensive than Ngowu. Swale's model should also be considered because his framework might also generate a more comprehensive result. It can also be a confluence of these two models to see if the two have similar or different move or steps in presenting the research introduction.\n\nResults\nThe meat of determining move structure is through identifying linguistic markers that realize the move or steps. Therefore, in presenting the results, the writer should include salient linguistic markers that realize each step and move. Also, the writer, should also get the frequency of each move and step to determine what move is obligatory, optional, non-evident and conventional. By doing such, the reader will know the most common moves being used and neglected in writing research introduction. Moreover, it is recommended to provide samples from the corpora on how these moves and steps are realized and presented in Engineering Laboratory Reports (ELR) introduction section written by Electrical Engineering Undergraduates\nOverall, the research paper is excellent in terms of presentation and overall findings. However, there is just a need to add more literature and related studies to give substance to the problem and establish the gap. As mentioned, there is a need to add linguistic features to the analyses so that it would be easier for the readers to identify characteristics of each move and step.\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? Yes",
"responses": [
{
"c_id": "9523",
"date": "27 Apr 2023",
"name": "Veeramuthu Veerappan",
"role": "Author Response",
"response": "Dear Dr Donnie, Thank you for the feedback provided. Below are our revision based on each comments given. List of Amendments : Details of amendment made in the manuscript. Only a paraphrased and simplified version of the revision was added in the manuscript. The full text was not reported in the manuscript due to word limitation. Introduction Reviewer 2 The writer can provide pieces of information to make the study more problematic. Thus, it is necessary for the writer to use other studies as reference that have explored other research introduction as corpora. Revision with justification: There are several related concepts and studies that could substantiate the current study and establish the research gap. Analysis of genre in academic writing has received a lot of attention (Swales, 1990; Bhatia, 1993; Hyland, 2000). Finding the norms, expectations, and communication goals of certain discourse groups is the task of genre analysis (Swales, 1990), and offers a theoretical framework to analyze the genre of ELR introductions. Writing skills in engineering education has been the focus of studies, and it has been determined that engineering students have difficulty writing clearly (Larson & Murray, 2008; Lunsford, 2012). Notable studies (Swales, 1990; Hyland, 2000; Samraj, 2002) have been conducted on the moves and writing styles employed in academic writing. The concept and framework bridge the research gap for all the reason stated above, making this study significant and relevant. There may be a few causes for the recent lack of attention paid to this subject. Research in the field of engineering education has switched its attention to other areas, namely the use of technology in teaching and learning, assessment procedures, or diversity and inclusion in engineering classrooms. Moreover, the material already available on ELR introduction sections may be deemed sufficient and complete. In addition, the scant attention paid to this field in recent years may also have been a result of a lack of funding or other resources for research in this field. Methods Reviewer 2 Why did you not consider the framework of JOHN SWALES which is the CARS model in analyzing the introduction, since you made mention of CARS model in your introduction? Justification This study adopted Ngowu's framework because it is better suited to meet the study's objectives and unique research problems. The Ngowu's framework has been adopted or accepted in the field of engineering education research. The intention was also to apply and test this framework for assessing the introduction section of ELRs. It's also possible that the study compared the findings after using both frameworks for their analysis, but this may be beyond the scope of this study and could be recommended for future study. Generally, the choice of framework depends on various criteria, including the research topic, aims, and the researcher's experience and skill with the framework. Since the research was conducted on all IMRDC sections of ELR, Ngowu (1997) framework was found to be more suitable. Results Reviewer 2 Therefore, in presenting the results, the writer should include salient linguistic markers that realize each step and move. Also, the writer, should also get the frequency of each move and step to determine what move is obligatory, optional, non-evident and conventional. Response Thank you for your comments on our study. We appreciate your feedback and have carefully considered your suggestions. Regarding the lack of linguistic markers in our study, we acknowledge that these are important in analyzing the introduction section of Engineering Laboratory Reports (ELRs). However, we focused on identifying the rhetorical moves and move patterns used by engineering students in writing the introduction section of ELRs. The linguistic markers are not included as they have been published in a previous study (DOI: 10.2991/978-2-494069-61-9_24 and https://www.atlantis-press.com/proceedings/cless-22/125980201 We agree that combining the framework used in our study with the linguistic markers identified in previous research could provide a more comprehensive analysis of ELRs. Therefore, we plan to consider incorporating these markers in future research to enhance the analysis of ELRs. We appreciate your suggestions and feedback, and we will make sure to incorporate them into future research. Thank you for your feedback. We agree that providing samples from the corpora on how the moves and steps are realized in the introduction section of ELR would have been useful for the readers. We have categorised the type of moves to obligatory, conventional and optional in the revision. However, due to the limited word count of the journal, we had to prioritize providing more significant information on the study's aims, methodology, and findings. Therefore, we hope that the description of the methodology used, and the findings of the study provided in this manuscript will be sufficient for readers to understand the study's contribution to the field."
}
]
}
] | 1
|
https://f1000research.com/articles/11-163
|
https://f1000research.com/articles/13-214/v1
|
22 Mar 24
|
{
"type": "Study Protocol",
"title": "Comparative study of arterial doppler with digital subtraction angiography in lower limb peripheral arterial disease: a protocol",
"authors": [
"Priyal Shrivastava",
"Shivali Kashikar",
"Shivali Kashikar"
],
"abstract": "Background One of the serious cardiovascular conditions is peripheral arterial disease; in which distinctive feature is diminished blood supply towards the lower extremities, frequently because of atherosclerotic occlusive disease.\n\nMethods We will compare arterial Doppler with digital subtraction angiography in peripheral lower limb occlusive arterial sickness; to determine Peripheral Arterial Disease along with its location and stenosis severity on Duplex Ultra-Sonography and Digital Subtraction Angiography; and to determine the segment-to-segment agreement of the arterial tree within Duplex Ultra-Sonography and Digital Subtraction Angiography.\n\nImplications This will encourage the participants for periodic investigation and proper use of medications which will improve hospital/facility outcome. It will be helpful for older individuals how are more susceptible to peripheral artery disease. A fair accurate treatment options will be given to patients.\n\nLimitations Findings will only be applicable to our organization because the study will be done at one tertiary care hospital, limiting their external validity and generalizability.",
"keywords": [
"peripheral arterial disease",
"smoking",
"on Duplex Ultra-Sonography",
"Digital Subtraction Angiography."
],
"content": "Introduction\n\nPeripheral arterial disease (PAD) is a major cardiovascular condition, presenting with deficient blood supply affecting the lower extremities, frequently as a result of atherosclerotic occlusive disease.1\n\nApproximately 10% to 25% of people over the age of 55 have PAD in their lower limbs, and the frequency rises with age. The most prominent risk factors for peripheral arterial disease include being over the age of 50 years, experiencing diabetic complications, engaging in nicotine consumption, and having dyslipidemia.2 PAD itself poses a risk factor for coronary disease regardless of severity as well as for brain-vascular incidents. Individuals with PAD have a possibility of death within 10 years as compared to those without the disease.2\n\nPatients with PAD might show symptoms or might not. The size and location of the affected artery, the extent of collateral circulation as well as the metabolic demands placed on the ischemic tissue during exercise, all of this influence the presence of symptoms.3 The majority of symptomatic individuals present with claudication, rest pain, colour changes of the limb, local tissue loss, and gangrene. An amputation may be necessary in severe cases.3\n\nDigital subtraction angiography represents a minimally invasive technique that serves as the standard approach for percutaneous revascularization therapy in non-responsive patients with medical therapy. But while working with people who have destructive lower limb ischemia, for appropriate therapy, re-planning, and evaluation of subsequent treatment outcomes and consequences, proper interpretation of diagnostic DSA findings is essential.4 Several other alternative imaging procedures including Duplex Ultrasound, CT and MR angiographies, and Intra-arterial Contrast Angiography are also available.\n\nDUS is usually the first investigation of choice, owing to its easy availability, low cost, and the non-invasive nature of the procedure. However, it does not come without its limitations. DUS is largely operator dependent; hence the user’s level of expertise can affect its quality. Moreover, deep-seated arteries, such as the infragenicular arteries in the lower limbs may prove difficult to assess, particularly if edema is present.2 In addition to giving insight into the vessel’s morphology and activity, color Doppler imaging also provides detail about the vessel’s wall.5\n\nEven though digital subtraction arteriography has been around for a while, duplex ultrasonography is still a common imaging method utilized in most vascular centers.6 On the other hand digital subtraction arteriography can be used for therapeutic as well as diagnostic purposes. With this technique, deep-seated arteries can be better visualized and smaller vessels and collaterals with the slow flow can be detected. Nonetheless, its shortcomings lie in its high radiological risk, kidney failure, and the invasive nature of the treatment all must be considered. DSA is frequently associated with post-procedure complications such as hematoma, aneurysms, and thromboembolism.2\n\nThere are other causes of PAD; The main factor causing PAD is atherosclerosis. Stroke and myocardial infarction risk are decreased by medical treatment that targets atherosclerotic risk factors which are the main factors that lead to mortality in people with PAD.7\n\nMaximum systolic velocity at the location of a blockage can be used to measure variations in a cross-sectional area of the arterial lumen.8\n\nManagement strategies differ for patients with lower extremities arterial illnesses. While Angioplasty is frequently used to treat individuals with ischemia that poses a risk to their limbs, Amputation or revascularization via surgery, Conservative management is usually used for temporary claudication.\n\nThe appropriate line of action is determined by the disease’s intensity, this may call for pairing therapies. Hence, individuals with limb-threatening ischemia need to be thoroughly evaluated. A proper treatment plan for each patient can be created with the help of knowledge about agreement between two different treatment modes, invasive and non-invasive.\n\nAim: To compare arterial Doppler with digital subtraction angiography in distal occlusive arterial disorders of the lower limbs.\n\n\n\n1. To evaluate risk factors for Peripheral Occlusive Arterial Disorder.\n\n2. To assess the presence, location, and severity of stenosis in Peripheral Arterial Disease using Duplex Ultrasonography.\n\n3. To assess the presence, location, and severity of stenosis in Peripheral Arterial Disease using Digital Subtraction Angiography.\n\n4. To determine the segment-to-segment agreement of the arterial tree between Digital Subtraction Angiography and Duplex Ultrasonography.\n\n\nMethods\n\nStudy design: The research shall be Prospective cross-sectional which will be executed in hospital.\n\nStudy setting: Sawangi, Wardha, Maharashtra’s Acharya Vinoba Bhave Rural Hospital’s radiology department will carry out this research. Hospital offering tertiary care that is fully equipped.\n\nStudy population: Patients with complaint of peripheral vascular disease who would be due for duplex ultra-Sonography or digital subtraction angiography and patients with clinical suspicion of PAD reporting to OPD. Meeting the criteria for inclusion and exclusion in the study.\n\nStudy period: 2 years\n\nType of sampling: purposive sampling will be used in this study.\n\nFormula:\n\nSample size: The investigations will take place among patients seeking treatment for peripheral vascular disease; a total number of 78 patients will be enrolled. The list of patients undergoing treatment or opd patients will be obtained from respective sister incharge.\n\n\n\n1. Individuals who have a clinical suspicion of having peripheral artery disease.\n\n2. Patients of age over the age of 18.\n\n3. Patients ready to take part in the investigation.\n\n4. Giving the history of chronic peripheral vascular disease.\n\n\n\n1. Pregnant woman\n\n2. Patients with blood disorders\n\n3. Those who are vulnerable to contrast agents\n\n4. Patients with prior angioplasty or vascular procedures\n\n5. Patient less than 18 years of age.\n\nThe examination will be stated and reports including causes, signs and symptoms, and consequences will be acquired from patients via interview (themes shown in Table 1). It will be noted whether there are any peripheral pulses or bruits.\n\nDuplex ultrasonography - Aloka Hitachi USG machine Arietta S70 with linear frequency probe 12-18 mega Hz with colour Doppler.\n\nThe procedure will be explained to the patient before and after taking consent with colour-coded duplex Sonography, Doppler measurements, and wave-form analysis, throughout the aortic branching to the area of the leg, the entire arterial tree of the target limb will be examined.\n\nDigital substraction angiography - performed using a Philips Azurion 7 M12 angiography unit.\n\nThe procedure will be explained to the patient and consent will be taken. Patients planned for DSA will be investigated for all routine scan including HIV & HBsAg.\n\nUnder strict sterile management and observation of an anaesthesiologist femoral artery punctured in a patient lying on your back after getting at the associated vessel via the Transfemoral path, dye will be infused with the catheter into the targeted vessel.\n\n\n\n1. Social and demographic details\n\n2. Hypertension, smoking, alcohol, diabetes mellites, hyperlipidaemia.\n\nProtocol among Duplex-Ultrasonography and Digital Subtraction Angiography will be assessed using kappa (k) statistics and Sensitivity, Specificity, Positive Predictive Value; Negative Predictive Value will be assessed using appropriate statistical tests. SPSS software will be used.\n\nInformation will be displayed as graphical representations, statistics, and illustrations. The results will be examined and compared with those of other studies that will be comparable.\n\n\n\n• This will encourage the participants for periodic investigation and proper use of medications which will improve hospital/facility outcome.\n\n• It will be helpful for the condition of peripheral arteries is more common in older adults.\n\n• Further accurate treatment options will be given to patients.\n\nPost IEC approval, data of 24 patients has been collected so far.\n\nResults will be made available to the institutional scientific committee. The research will be presented at national and international diagnostic/intervention radiology conferences, it will also be submitted as an original article to peer-reviewed journals.\n\nInstitutional ethics committee permission from the ethics committee has been received on 21.03.2023 from the DMIHER University.\n\nRef.No. DMIMS (DU)/IEC/2023/765\n\nAll the participants selected for the study will be explained in detail regarding the research proposal; signed consent and information will be kept enclosed.\n\n\nDisscusion\n\nOutcome would be measured in terms of agreement between degree of stenosis detected for different segments with Duplex-Ultrasonography and Digital Subtraction Angiography and to evaluate threat components for Peripheral Occlusive Arterial Disease along with its location and stenosis.\n\n\nConclusion\n\n\n\n• The condition of peripheral arteries is more likely to affect elderly individuals.\n\n• Tobacco use is one of the most prevalent contributory factors that affect men.\n\nFindings will only be applicable to our organization because the study will be done at one tertiary care hospital, limiting their external validity and generalizability.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAronow WS: Peripheral arterial disease of the lower extremities. Arch. Med. Sci. 2012 May 9; 8(2): 375–388. PubMed Abstract | Publisher Full Text\n\nSarangi S, Srikant B, Rao DV, et al.: Correlation between peripheral arterial disease and coronary artery disease using ankle brachial index-a study in Indian population. Indian Heart J. 2012; 64(1): 2–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBiswas S: Comparison of CD and DSA in Diagnosing PVD. Int. J. Surg. Surg. Tech. 2017 [cited 2023 Aug 9]; 1(2). Publisher Full Text Reference Source\n\nRadiation|Free Full-Text|Digital Subtraction Angiography (DSA) Technical and Diagnostic Aspects in the Study of Lower Limb Arteries.[cited 2023 Aug 9]. Reference Source\n\nJandaghi AB, Mardanshahi Z, Alizadeh A, et al.: The Role of Color Doppler Ultrasound Arterial Mapping for Decision Making in the Treatment of Patients with Lower Extremity Peripheral Arterial Disease. Surg. Sci. 2013 Sep 27; 04(10): 415–420. Publisher Full Text\n\nEiberg JP, Grønvall Rasmussen JB, Hansen MA, et al.: Duplex Ultrasound Scanning of Peripheral Arterial Disease of the Lower Limb. Eur. J. Vasc. Endovasc. Surg. 2010 Oct; 40(4): 507–512. Publisher Full Text\n\nOutcomes for Clinical Studies Assessing Drug and Revascularization Therapies for Claudication and Critical Limb Ischemia in Peripheral Artery Disease - PMC.[cited 2023 Aug 9]. Reference Source\n\nDiagnosis of arterial disease of the lower extremities with duplex ultrasonography - PubMed.[cited 2023 Aug 9]. Reference Source"
}
|
[
{
"id": "262528",
"date": "29 May 2024",
"name": "Sanjum Sethi",
"expertise": [
"Reviewer Expertise Peripheral arterial disease",
"pulmonary embolism"
],
"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 current study aims to compare use of Doppler ultrasound to traditional digital subtraction angiography in patients with lower extremity peripheral arterial disease. The paper is extremely unclear as to the main objective of the analysis and what question it will answer. If the idea is a comparison between doppler ultrasound and digital subtraction angiography, DSA is known to be superior, but usually reserved for more severe patients given that it is an invasive procedure.\nThe paper needs to be rewritten to project a clear hypothesis.\nIntroduction: Under introduction, several paragraphs need to be reworded to make them concise and more readable. The last two paragraphs in the introduction section are disjointed and are not related to the paragraphs above and are stand alone lines. I am assuming the authors want to describe the premise of using Doppler ultrasound however it is unclear from the last line in the introduction which does not seem to be connected to the rest of the introduction.\nRationale: The authors mention “the appropriate line of action is determined by diseases intensity, this may call for pairing therapies”. This line is unclear.\nAim: Under the aim of the study, the authors mention that they aim to compare Doppler and angiogram in distal occlusive arterial disease. The authors need to specify what distal means.\nMethodology/ Patient population Furthermore, under patient population the authors mentioned that they will include patients with complaints of peripheral vascular disease that come to the clinic/ OPD\nWhat are these complaints? They state that they will obtain records of patients with PAD from nursing supervisor- how are they documenting this and keeping a log? DO they keep a log of complaints? Do they keep a log of the diagnosis? Who makes the diagnosis? Furthermore, importantly, the authors make no mention of which patients will undergo Doppler ultrasound, how will they determine that which patient should undergo digital substation angiography? Who will be performing these ultrasounds, and making decisions regarding need for angiography, who will be performing the angiography and making comparison with the ultrasound?\nImplications\nUnder implications the authros mention that this will help participants to adhere to medications- how will conducting a test help participants with medication adherence? You cannot draw such implications from this paper It states that it will help with the 'condition of peripheral arterial vessels in older adults\" - how? why older? You are including everyone over 18 - so why older?\nConclusion\nThe authors conclude that PAD is prevalent in olders adults and smokers- and has no bearing on the paper. They need to concentrate on available data on doppler ultrasound and DSA and shortcomings that the study is looking at.\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? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-214
|
https://f1000research.com/articles/13-213/v1
|
21 Mar 24
|
{
"type": "Software Tool Article",
"title": "Web/Mobile system innovation: An efficient revolution in warehouse management.",
"authors": [
"CAROLINA LUCIA ZAVALETA SAENZ",
"Alexis Romero Ruiz",
"Alex Pacheco"
],
"abstract": "In today’s society, the amount of data available in many area has made it more important than ever to use effective technological tools for accurate and clear analysis and presentation of information. Therefore, the main objective of the research is to implement a Web/mobile system to improve inventory management in a private company. It has been developed under an agile extreme programming XP methodology, taking into account the following phases, which are carried out four structural activities planning, design, coding and testing. In addition, the following technologies were chosen: such as with programming languages PHP, with markup language PHP, MySql v. 10.0 as database system MySql v. 10.0, and cascading style sheets CSS for visual customisation. Therefore, the results showl a 13% improvement in the efficiency of the percentage of spools to be located (PSL, a 28% a better control of the index of percentage of inventoried coils (IC) and an 1,1% difference in efficiency of the Productivity per user (PU) index. With the implementation of a web-based web/mobile inventory management system to improve inventory control and mobile to better control of a company inventory management, using as a reference the most agile methodology to diversify the cases and functionalities contained in the system.",
"keywords": [
"Information Technology",
"Web/Mobile System",
"Inventory Management",
"Extreme Programming (XP)."
],
"content": "Introduction\n\nIn recent years, society has experienced continuous exponential growth, which has led to the need for effective tools for the analysis and visualization of information systems technologies suitable for business growth, continuous development, and the use of information systems with large increases in resources. Compliance with requirements and provision of information.1 In this environment, it’s a way of simplifying certain tasks on the internet, and a static website is primarily a means of communication. Web-based information systems are examples of web applications that have evolved from dynamic web pages to database-based information systems. There are systems with additional functions such as system tracking.2 Traditional software systems have been extensively studied, quantum software maintenance is still a new area of research, but it is a critical element in ensuring the quality of the entire quantum computing system.3 In this sense, we are in a globally connected society that is always updated with instant information.4 In addition, there is a personalised digital system accessible to all, which, thanks to the improvement of technology, makes it possible to sell products or services via the internet and also includes media of great importance.5\n\nIn this context, technology has exploded in all areas of our society, and technology is no exception, in the constant search for optimising production and service delivery: more efficient and safer management; The inventory control system for the mobile/web production floor has become one of the most important and crucial factors for companies to maintain their stability and success.6 Improve performance, efficiency, and understand the different levels of companies that manage their manufacturing inventory levels in different waysBy evaluating internal controls, we can determine the level of reliability and risk in inventory management.7–9 A process-based inventory management system has been implemented for the inventory management of incoming and outgoing goods.10\n\nThe development of a proper stock policy is essential to maintain a certain level of operation of the inventory system operation and relatively low maintenance costs. In this way, inventory management contributes to the consolidation of warehouses and provides greater efficiency in accounting entries thanks to the records made in the various inventory sheets that describe the actions carried out both in the warehouse outflows and in the purchase, sale, production, maintenance and service of an organisation. To ensure fast and efficient production, we use an inventory management system that helps reduce the cost costs and time spent on shipping raw materials and products.11–13 It requires change management processes and the use of mobile applications. It can increase the productivity of employees in the workplace. It is a reuse-based approach to defining, implementing, and assembling independent, loosely coupled components into a system.14 A good inventory management system will always have a positive impact on customer satisfaction in dealing with the uncertainty of demand.15\n\nNumerous studies have shown that the development of web/mobile inventory management systems has the potential to positively impact inventory efficiency, accuracy, coordination, and security. Reduce inventory carrying costs and increase operational efficiency with a manageable and easy-to-use system with a web interface that provides convenient and efficient inventory management and integrates barcodes and cloud computing, Arduino-based wireless station nodes,16 IoT, and secure form channels to access data through a dedicated web portal. On the other hand, develop an intelligent system implemented in a web-based environment to integrate multiple stores and ensure effective coordination of all stores and optimise inventory management performance by integrating multiple systems and ensuring effective coordination and monitoring. It has been compared to analyse the combined impact of interest rates and inflation on inventory systems in different countries in the context of rising inflation and linear demand over time affecting inventory costs. In his article, he developed a web application for the efficient development of a slippage inventory in an economical way.17–19 Based on Ref. 20 their multi-item inventory model thakes into account warehouse capacity constraints, demand uncertainty, and lead times.\n\nHowever, the technical community still lacks reliable, accurate, and up-to-date data on the implementation of a web/mobile inventory management system, including the process that begins with the distribution of raw materials, most likely, unprinted rolls. Positioning, return and switching of flows between actions, manual calculations and security issues, incidents that result in duplication of information or duplication of information or abandonment of parts of the technological infrastructure. Under these conditions, web and mobile systems have been designed and implemented for the production area, facilitating the use of mobile/web systems for better control of the distribution and location of rolls during processing, as well as more efficient inventory management.\n\nThis study contributes to filling the knowledge gap by examining in detail the specific benefits and challenges associated with the implementation of web/mobile system to improve inventory management for a private company. The development of this system allows collaborative work between the company, the worker and the customer, being a diversified, modern help that will effectively improve inventory management effectively, in this way there will be economic productivity.\n\nTherefore, the objective of this research is to implement a mobile/web system to improve inventory management, improve processes in the production area and inventory management in the company Emusa Peru S.A.C., Chorrillos.\n\n\nMethods\n\nTwo laptops equipped with Quick Emulator (QEMU) Virtual Central Processing Unit (CPU) processors version 2.5 + 2.60 GHz were used, accompanied by 32 GB of Random access memory (RAM) with C# from Microsoft Visual Studio.Net 2019 with ASP.NET Core Runtime 3.1.25 with Angular frame interface and Ionic 6 with a standard Windows Server 2016 operating system or higher with internet information services version 10 with base Oracle Data Platform, Visual Studio 19 were used for the development of the web/mobile system to improve inventory management.\n\n• Implementation\n\nWe chose to use the agile extreme programming XP methodology, taking into account the following phases that are executed in the four structural activities as shown in Figure 1.21\n\n\n\n• Operation\n\nPlanning phase\n\nThe description of the users based on the indicators (Pending Dispatch, Pending Inventory, Pending Location). The first requirement is to access the system, registration of the users (Administrator, support user, client user). The second requirement allowed the creation of task, the third requirement allowed the creation of a task, the third requirement allowed the creation of task is in progress with its respective location and the fourth one generated report about that in process this or in what process it stayed or if it finished the task.\n\nDesign phase\n\nUsers with a simple design were selected. In addition, tasks (CRC Cards) were created to allow even better system analysis and compression, as shown in Figure 2.\n\nCoding phase\n\nThe structure of the web registry has been programmed using the HTML tag language, CSS for the customisation layer, JavaScrip to make it more dynamic, among other technologies such as Axios, JQuery, Sweet alert and Ladda. For the operation of the web system, the programming language PHP8, and the database administrator MySql v. 10.0. Figure 3 shows the lines that pointing to a production development environment. As shown in Figure 3.\n\nTesting phase\n\nA verification was carried out The system was verified by performing unit tests to find some kind of role in the codes and improve their quality, the acceptance test was carried out, which was supervised together with the client to approve the application. Figure 4 shows the software development flow visually. As shown in Figure 4. Also, Figure 5 also shows the database diagram, which shows ta is structured and the relationships between them.\n\n\nResults\n\nFigure 6 and Figure 9 show the process of accessing the Web/Mobile system, as shown in the two web/mobile access interfaces.\n\nIn the case of the access web access, you will need to enter your username and password.\n\nIn Figure 7, the user has the option to generate queries, select the indicators option, and select the chart to monitor.\n\nIn Figure 8, the user has the ability to create queries and select chart to monitor.\n\nIn Figure 9, in the case of the Mobile interface, you will need to enter your username and password. Then select the type of product you wish to trade. Select the warehouse where they will perform the operation.\n\nFigure 10, select an option from the indicators (Pending to Locate, Pending to Inventory, or Pending by Dispatch). Place the data you want to enter and a code will be generated that will be located in the rack, this way it will be done by making a count and it will also decrease according to how the days go on in the following indicators for a better control. In this way, it will be easier for the workers in the production area to have a better management and control of it.\n\n\nDiscussion\n\nIn Figures 6 and 9, the asset management system in the web/mobile system access interface allows the browser (user) to interact with the machine ensuring fault tolerance, visual appeal, control and, most importantly, meeting the user’s expectations. The relationship between the asset management system and web/mobile system access is undeniable. This is in line with the assertion that the critical processes applied within the company to develop new web systems help to increase sales within the company and even without this, you still need to reopen your main POS system. Thanks to the web system developed, most of the company’s products can be found in an organised way in Internet search engines. Web applications are widely used todays of the convenience of the web browser as a thin machine client and the independence of the operating system.22,23 Saving money and improving management are two benefits of using web/mobile applications. Mobile configuration has been shown to improve overall system performance by introducing clustering capabilities.24\n\nIn Figure 7 and Figure 10, registering a new code (inventory) allows users to create and facilitate better service delivery, on both web and mobile platforms, to improve inventory automation. The link between registration and web/mobile platforms cannot be denied. This is in line with what he says are some of the advantages offered by information systems that are integrated with current technological tools that allow fast and flexible communication. The system will allow the company to optimise inventory management, which will be reflected in lower costs for inventory management ordering, storage, among other variables.25,26 It is presented as a very effective strategy to improve the mobile/web system and optimise inventory management on different platforms. Mobile: Addresses data privacy, mutual authentication, session key agreements, and prevention of potential attacks.27\n\nIn Figure 8, the user has the option to generate queries and select the graph to monitor. This shows the close relationship between query generation, web performance, and the selection of images to view, and this relationship is undeniable. This is in line with what he says is an important feature of a performance tracking system, allowing users to identify critical performance issues and take action quickly. It collects and analyses the data and provides with detailed information to the system administrators. Custom control provides with additional functionality for a more modern and up-to-date control system.28,29 The ability to provide detailed information in an easy-to-manage digital format can be useful for good governance. In addition, it is effective and cost-efficient to maintain constant communication with production staff for good inventory management. Regular updates are required to monitor production and support this utility.30\n\n\nConclusion and future work\n\nThis study has successfully completed the development and implementation of a web/mobile inventory management system in a company that relied on existing manual management. During the course of the study, modernisation issues of production data collection, storage, and availability in terms of inventory management were addressed and overcome.\n\nInitially, the inherent limitations of manual recording systems were identified, including lack of efficiency, difficulties in accessing and organising information, and the risk of data loss in any process. The implementation of web/mobile systems has emerged as a viable solution to address these shortcomings. By moving of various processes to a digital environment has made production information has become more available, readable, and secure. These changes have significantly improved the quality of management and efficiency in the manufacturing industry by providing relevant information in an accessible and efficient manner.\n\nIn addition, the creation of a web/mobile system facilitated communication and coordination between departments. Centralised access to data from each process optimises the creation of detailed and accurate records, increasing the word efficiency of production specialists. Interaction between different regions and different locations proved to be one of the main advantages, overcoming one of the limitations.\n\nIn short, new researchers are encouraged to use the latest information technologies to achieve optimal results in assessments, such as expert systems and/or artificial intelligence systems. Exploiting the connectivity of devices through the Internet of Things (IoT). In addition, it is important to develop evaluation tools to measure the positive and negative impact of the implementation of this new module on the patient experience.",
"appendix": "Data availability\n\nZenodo: Base da datos y indicadores Emusa 2023\n\nhttps://doi.org/10.5281/zenodo.10695480. 31\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZavaleta C., Romero A. y Pacheco, A. An efficient revolution in warehouse management, based on a web/mobile platform.\n\nSource code available from: https://github.com/1979ARR/GitHubProyectoEMUSA_App. 32\n\nSources: https://github.com/1979ARR/GitHubProyectoEMUSA_FuentesyBD. 33\n\nArchived source code at time of publication:\n\nhttps://zenodo.org/uploads/10695480. 31\n\nLicense: MIT License\n\n\nAcknowledgements\n\nWe would like to thank the company EMUSA Perú S.A.C. located in the production area of the headquarters in Chorrillos, which participated in the entire research development process. Also, to Alex Pacheco, an engineer from the Faculty of Engineering and Architecture of the Universidad Cesar Vallejo, for his methodological advice on this study.\n\n\nReferences\n\nQuezada-Sarmiento R, et al.: Servicio y Gestión de las Tecnologías de Información en las empresas//Service and Management of Information Technologies in companies. UNEMI SCIENCE. Jun. 2018; 11(26): 170–175. Publisher Full Text\n\nRojas AM, Amaya SP, Calderon JM: PBR Compiler: Automatic system description generator software. IFAC-PapersOnLine. Jan. 2022; 55(4): 219–224. Publisher Full Text\n\nOpenja M, Morovati MM, An L, et al.: Technical debts and faults in open-source quantum software systems: An empirical study. Journal of Systems and Software. Nov. 2022; 193: 111458. Publisher Full Text\n\nMontero Caro MD: New Opportunities for Participation in the Framework of the Open Government Model. Deusto Studios. Jan. 2020; 68(1): 425–447. Publisher Full Text\n\nAcosta Rivera CE, Tintín Caiza ARR: The Internet and Electronic Commerce as SME Development. Digital Visionary. Apr. 2017; 1(2): 19–38. Publisher Full Text\n\nJadán-Maza VK, López-González CP: Good Practices of Control and Inventory Management for the Association of Agricultural Producers of Llanitos Verdes. SCIENCEMATRIA. Sep. 2021; 7(2): 248–278. Publisher Full Text\n\nRivadinayra OC, Cueva JAP, Cardenas GAM: Review of the Literature on Inventory Management in the Textile Industry. Qantu Yachay. Apr. 2022; 2(1): 26–40. Publisher Full Text\n\nZambrano XG, Enríquez JS: Evaluation of the Internal Control of the Inventory Management of IMPORELLANA S.A. in Santo Domingo, 2017 period. Social and Economic Sciences. Jun. 2019; 3(1): 38–57. Publisher Full Text\n\nGuzmán KJT, Zurita CIN, Álvarez JCE: Inventory Management Model for Agricultural Commodity Trading Enterprises. SCIENCEMATRIA. Oct. 2019; 5(1): 683–702. Publisher Full Text\n\nGarcía-Pacheco MC, Andrés-Laz EMS: DESIGN OF A PROCESS MANAGEMENT SYSTEM FOR INVENTORY MANAGEMENT. CASE: IRONMONGERY QUIROZ. PEER-REVIEWED MULTIDISCIPLINARY SCIENTIFIC JOURNAL “YACHASUN,”. Oct. 2021; 5(9 Special Issue October): 180–204. Publisher Full Text\n\nQiu R, Sun Y, Sun M: A robust optimization approach for multi-product inventory management in a dual-channel warehouse under demand uncertainties. Omega (Westport). Jun. 2022; 109: 102591. Publisher Full Text\n\nVélez SMV, Linares SAP: Importance of Inventory Systems in Organizations through a Literature Review. AlphaPublications. Feb. 2022; 4(1.1): 342–357. Publisher Full Text\n\nBose R, Mondal H, Sarkar I, et al.: Design of smart inventory management system for construction sector based on IoT and cloud computing. e-Prime - Advances in Electrical Engineering, Electronics and Energy. Jan. 2022; 2: 100051. Publisher Full Text\n\nGelogo YE, Kim H-K: Development of Mobile Enterprise Inventory Management System Application with CBD. International Journal of Software Engineering and Its Applications. 2014; 8(1): 385–396. Publisher Full Text\n\nAmirul Islam M, Islam ME, Rashid A: Stochastic optimization of level-dependent perishable inventory system by Jackson network. Ain Shams Engineering Journal. Apr. 2023; 14(4): 101935. Publisher Full Text\n\nBose R, Mondal H, Sarkar I, et al.: Design of smart inventory management system for construction sector based on IoT and cloud computing. e-Prime - Advances in Electrical Engineering, Electronics and Energy. Jan. 2022; 2: 100051. Publisher Full Text\n\nMadamidola OA, Daramola OA, Akintola KG: WEB BASED INTELLIGENT INVENTORY MANAGEMENT SYSTEM. International Journal of Trend in Scientific Research and Development. Jun. 2017; Volume-1(4). Publisher Full Text\n\nKhakbaz T, Mensi W, Tirkolaee EB, et al.: The combined effects of interest and inflation rates on inventory systems: A comparative analysis across countries. International Journal of Production Economics. Dec. 2023; 266: 109035. Publisher Full Text\n\nPerera ENC, Gunaratne AMCT, Samarasinghe SBD: Participatory Landslide Inventory (PLI): An Online Tool for the Development of a Landslide Inventory. Complexity. 2022; 2022: 1–10. Publisher Full Text\n\nAlawneh F, Zhang G: Dual-channel warehouse and inventory management with stochastic demand. Transportation Research Part E: Logistics and Transportation Review. Apr. 2018; 112: 84–106. Publisher Full Text\n\nBuiles JAJ, Bedoya DLR, Bedoya JWB: Software Development Methodology for Robotic Educational Platforms Using ROS-XP. Polytechnic Magazine. Dec. 2019; 15(30): 55–69. Publisher Full Text\n\nPijuchkun Chumpi B, José Rosvel Carrera Sánchez M: Implementation of a web system to improve sales management at Botica La Receta – Jaén, Cajamarca, 2022. Amazon Polytechnic University. Jul. 2023. Accessed: Nov. 03, 2023. Reference Source\n\nHernández-Rueda K, Vargas MPM, Casillas MD: Evaluating the Performance of a Web Application. South Florida Journal of Development. Jan. 2022; 3(1): 445–457. Publisher Full Text\n\nPishchulov G, Richter K: Inventory rationing and sharing in pre-sell distribution with mobile communication technologies. International Journal of Production Economics. Oct. 2009; 121(2): 584–600. Publisher Full Text\n\nCalderón-Bedoya VM, Jiménez-Gómez M, de mesa Torres OL, et al.: Implementation of the Globally Harmonized System (GHS) for the labelling of chemical substances, using quickly reaction codes. Polytechnic Magazine. Mar. 2023; 19(37): 29–42. Publisher Full Text\n\nHernandez HA, Cruz-Gil YL, Saavedra MDP, et al.: DESIGN OF AN INVENTORY MANAGEMENT SYSTEM FOR THE WAREHOUSE TÉCNITALLER S.A.S DE LA CIUDAD NEIVA-HUILA, COLOMBIA. Revista de Investigaciones Universidad del Quindío. Nov. 2021; 33(2): 143–152. Publisher Full Text\n\nDeebak BD: Lightweight authentication and key management in mobile-sink for smart IoT-assisted systems. Sustainable Cities and Society. Dec. 2020; 63: 102416. Publisher Full Text\n\nLiu H, Ren X, Zhang X, et al.: Investigating the Effects of Ionospheric Scintillation on Multi-Frequency BDS-2/BDS-3 Signals at Low Latitudes. Space Weather. Jun. 2023; 21(6). Publisher Full Text\n\nHashmani RK, Konyushikhin M, Shan B, et al.: New monitoring interface for the AMS experiment. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. Jan. 2023; 1046: 167704. Publisher Full Text\n\nBlauth DA, Ducati JR: A Web-based system for vineyards management, relating inventory data, vectors and images. Computers and Electronics in Agriculture. May 2010; 71(2): 182–188. Publisher Full Text\n\nZavaleta, Romero: Base de datos y indicadores Emusa. [en línea]. [consulta: 22 febrero 2024].2023 [2023]. Reference Source\n\nZavaleta, Romero: FuentesyBD: Sistema Móvil/Web para la gestión de inventario de EMUSA. [en línea], [sin fecha].[consulta: 22 febrero 2024]. Reference Source\n\nZavaleta, Romero: FuentesyBD: Sistema Móvil/Web para la gestión de inventario de EMUSA. [en línea], [sin fecha].[consulta: 22 febrero 2024]. Reference Source"
}
|
[
{
"id": "260276",
"date": "21 May 2024",
"name": "Aamir Rashid",
"expertise": [
"Reviewer Expertise Supply Chain Management"
],
"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 very much for this research presentation. The research has researched that is very relevant and required in this era. However, the research lacks in providing the rationale of the study. The literature is not sufficiently provided that questions the motivation behind this research. The methodology and results sections need significant improvement and currently are not in a position to be approved. The discussion should make it clear how and what the study is exactly contributing such as what new insights were gained. Basically, what this means is that the study should provide insight that better explains real-life phenomena. The discussion should include in-depth analysis such as not only looking at results but also at the contexts of previous studies, the methodologies applied, definitions used etc. When done in a good way, this should help make it clear what the paper contributes.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? No\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? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
},
{
"id": "318135",
"date": "17 Sep 2024",
"name": "Sadia Samar Ali",
"expertise": [
"Reviewer Expertise Smart warehousing"
],
"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\nAfter a comprehensive review of the paper, several critical issues emerged.\nThe discrepancy in the paper title, too, as it does not suggest or address the main focus, may not be adequately represented as per the scope of the work. When dealing with interactions between multiple areas, the literature review should be considered separately to ensure clarity and coherence. Moreover, the literature review related to context along with proposed work presented in the paper need to meet the rigorous standards expected for indexing. Research gap to bridge the knowledge gaps in terms of area selected and analysis chosen are not included. The codes needs to be extended , and the discussions regarding the code based cases, some useful insights, expertise, the way the information is collected are not discussed. The lack of clarity in the various codes selection and validation, no data validation and judgement are considered and the absence of clear identification of parameters are not significant.\nImplications for researchers, managers, and policymakers and future research directions must be included in terms of the proposed areas. Furthermore, due to no proper integration of the methodology process needs to be clearly elucidated, and hence raising questions about the validity and reliability of the code findings. The discussion and conclusions of the obtained results must be well improved, highlighting the insights of the research findings, and with support from earlier literature, the article has the potential to provide a comprehensive review. However, the identified issues need to be justified for publication in terms of new knowledge contributed by carrying out the research.\nIt is important to note that while the rejection is based on these identified issues and shortcomings highlighted. Best Regards…\n\nIs the rationale for developing the new software tool clearly explained? No\n\nIs the description of the software tool technically sound? No\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? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-213
|
https://f1000research.com/articles/12-1173/v1
|
20 Sep 23
|
{
"type": "Research Article",
"title": "Editorial practices, perceived quality, and expedient scholarly publishing in a developing nation: a mixed methods study",
"authors": [
"Amin Bredan",
"Osama Tashani",
"Omran Bakoush",
"Amin Bredan",
"Osama Tashani"
],
"abstract": "Background: Scholarly literature from the developing world is low and the scientific impact in some countries, including Libya, is much lower compared with their peers. This study explores the editorial practices and editors’ perspectives to gain insight into the standard of scholarly publishing in Libya. Methods: Between 21st January and 12th February, 2022, the editors-in-chief (EC) of Libyan academic journals were invited to complete a questionnaire on editorial practices, degree of satisfaction with submitted and published manuscripts, review processes, and journal performance, as well as challenges facing the journals. Journal websites were examined for quality, and indexation coverage and citations were assessed. We examined the number of citations in Google Scholar for all 2019 articles published in each journal. Descriptive statistics were used to quantitatively summarize the data and thematic analysis was used for the narrative text. Results: 48 ECs completed the questionnaire. The EC was affiliated with the institution that owns the journal in 92% of cases. Most EC (83%) were satisfied with the peer-review quality, 69% believed that most of their published papers add new ideas or findings, and 96% were satisfied with their journal performance. However, despite the high degree of satisfaction, only one journal was indexed in Web of Science or Scopus and only 17% of the journals were indexed in Google Scholar. A qualitative assessment of journal websites revealed shortcomings in publishing practices in a large proportion of the journals. Conclusions: The discordance between the satisfaction of the journal editors and the journal quality indicators points to a break in the quality system of Libyan academic publishing. Similar expedient publishing practices might exist in other countries as well. A comprehensive action plan led by academic institutions to enforce high standards for scholarly publishing is needed to advance research and high-quality scholarly publications in developing countries.",
"keywords": [
"Citation counts",
"Journal affiliation",
"scholarly publishing",
"Science editors",
"Libya"
],
"content": "Introduction\n\nQuality scholarly publications are known as the most effective means of disseminating locally produced scientific research findings to the global scientific community. However, there is increasing concern about the quality, integrity, and accessibility to research published locally.1 Journals may become poor venues for knowledge dissemination if they fail to provide adequate peer review, quality control, and content preservation. Researchers from developing countries face the challenges of generating sufficient high-quality research and sharing their research findings due to academic, technological, socio-political, and economic factors.2\n\nMany developing countries have increased their rates of contribution to the world’s scientific output, measured as the number of publications and the number of citations.3 However, Libya maintained low scholarly publishing rates when compared to other countries in the region, including those with considerably lower economic indices.4 Over many years, the Libyan government and later private ventures established numerous new universities, expanded the scope of MSc degree programs, and recently initiated PhD programs in various fields, including sciences, as well as built research centers. Moreover, there has been a notable increase in the number of scholarly journals. However, the overall research performance indicators remain modest. Researchers are recognized and rewarded by their academic peers, and this is a strong drive for publishing high quality research. Implicit in this is that high quality research is published in high quality journals.\n\nThe quality of journals is intimately linked to the quality of editorial practices. Guidelines have been published by the Committee on Publication Ethics (COPE)5 and the Council of Science Editors (CSE).6 Guidelines have also been published for medical journals by the World Association of Medical Editors (WAME)7 and the International Committee of Medical Journal Editors (ICMJE).8 The regional association Forum for African Medical Editors (FAME)9 also provides support and resources for best editorial practices. The major abstract-indexing databases of Web of Science10 and Elsevier's Scopus11 specify criteria required for indexation. Publishing research papers in journals that do not adhere to editorial best practices is a waste of research funds and findings. Moreover, poor-quality journals could lead to a decrease in the quality of science at both the institutional and national levels, with university staff and research scientists getting recognized without gaining the required research expertise, including in publishing ethics and research integrity. Such a situation could have a negative impact on the academic environment and on researchers' aspirations and practices when conducting research. The effects of all that could filter down to university and graduate students, and beyond.\n\nGaining an understanding of the status and functioning of local, national, academic journals would shed light not only on their editorial quality, but could also indicate the areas that need improvement in order to raise the country's research quality and performance. This study aimed to explore the editorial practices of editors related to scholarly publishing in Libya and quality indicators of the academic journals. We also sought the editors’ perspectives on the standards of academic publishing in Libya and their satisfaction with journal performance.\n\n\nMethods\n\nEthical approval for the main research project \"Publishing practices in scholarly journals in Middle East and North Africa\" was obtained from UAEU Social Sciences Research Ethics Committee (ERS_2021_8420). The questionnaire was prefaced with a description of the study aim, declaration of ethics approval, statement of the voluntary nature of participation, and the ability to withdraw. Consent was signaled by the answer to the first question.\n\nThis study was carried out between January 21st and February 12th, 2022. Our target consisted of the editors-in-chief (EC) of academic journals affiliated with Libyan academic institutions and professional societies. Online survey links were sent by the primary investigator (AB) via editors contact emails identified in the journal website. Participants received a standard follow-up email reminder two weeks after they received their original invitation to participate.\n\nWe designed a questionnaire consisting of 10 parts. The questionnaire administered in English and Arabic and distributed using SurveyMonkey.19 The themes of the questions were guided by the editorial policies published by the CSE6 and the basic journal selection criteria for indexation of the Web of Science.10 The questionnaire was reviewed independently by three editors of an international journal who were not affiliated with a local or regional institution. They were asked to assess the face validity of the survey items and to provide feedback on the clarity and conciseness of the questions. No ambiguous questions or other issues were identified in the questionnaire and therefore no changes were made.\n\nWe then posted the questionnaire using an online survey program SurveyMonkey (https://www.surveymonkey.com/) that allows respondents to answer the questions but does not allow duplicate responses. The link to the online survey and the cover letter were then sent by electronic mail to the EC. A reminder was sent after two weeks to those who had not responded. In total, 51 questionnaires were returned. The responses were downloaded as a Microsoft Excel file (2007). Descriptive and inferential statistical analysis was done in SPSS statistical software (version 26.0, IBM). PSPP (https://www.gnu.org/software/pspp/) is a freely accessible software application that can run the same analysis used in this study.\n\nThe 10 parts of the questionnaire were as follows:\n\n1. The journal’s current status;\n\n2. Background questions about the editors' affiliations;\n\n3. Editor satisfaction;\n\n4. The editorial process;\n\n5. The peer review process;\n\n6. Satisfaction with peer review reports;\n\n7. Journal indexing;\n\n8. Journal funding and support;\n\n9. Editorial independence;\n\n10. Challenges and opportunities.\n\nTo enhance the trustworthiness of the interpretations from the survey quantitative data, a word cloud was generated of all the words in all the respondents’ answers to the question about challenges faced by the journals, after translating Arabic text to English. The entire text was analyzed in an online word cloud generator (https://monkeylearn.com/word-cloud).\n\nIn addition, the websites of the journals were visited by one investigator (AB) and information was collected on various aspects, such as the presence of an International Standard Serial Number (ISSN), the editorial board's geographic diversity, the organization of the archives, and general website functionality. Moreover, we examined the listing of the journals in Google Scholar and the number of citations in Google Scholar for all articles published in 2019 in each journal. The findings were entered in Microsoft Excel (2007).\n\nThe coded data were transferred to SPSS and analyzed by another investigator (OT). The results were analyzed by the percentage of participants selecting the different answers to each question. The 95% confidence intervals are given as ranges inside brackets. The responses to the two open-ended questions about challenges and opportunities were analyzed by thematic analysis. The journal quality assessment and Google citations are reported as frequency and percentage statistics.\n\n\nResults\n\nIn total, 51 questionnaires were returned. However, three responses were excluded because they did not have the basic content of a published academic journal such as an official website. Therefore, the study included 48 academic journals published by national institutions. Some EIC skipped answering some questions, but their available answers were included in the analysis. The results are reported for the available answers.\n\nJournal ownership\n\n40 of the 48 journals are owned by academic institutions (83%, 95% CI: 70–93%). The others are owned by a professional society, a professional syndicate, or a research center.\n\nEditorial boards\n\nThe EC was affiliated with the institution that owns the journal in 44 out of 48 journals (92%, 95%CI 80–98%). In 29 journals (60%, 45–74%), all the editors other than the editor-in-chief were associated with the owning institution. In nine journals (19%, 9–33%), the editors were associated with various national institutions, and 10 journals (21%, 10–35%) have a mix of nationally and internationally affiliated editors.\n\nJournal funding\n\nThree journals did not respond to the question about journal funding. 32 of the 45 responding journals 32 of 45 journals (71%, 95%CI 56–84%) are supported by the institution that owns the journal, and 22% (10–37%) by author processing charges (APCs). Professional societies played a minor role (3/45, 7%). In the 35 journals supported by the journal owner, the support covered the website cost of 27 journals (77%, 60–90%), software for journal management or similarity check of six journals (17%, 7–34%) and financial rewards for editors and/or reviewers of 14 journals (40%, 24–58%).\n\nPeer review process\n\nA total of 46 of the 48 journals reported their peer review process. Reviewers are recruited within two weeks in 31 of 46 journals (67%, 52–80%). Many or all peer reviews are done by individuals who are not members of the editorial board in 85% of the journals (95% CI: 71–94%). However, there was heavy reliance on the journals' reviewer committees. These committees were the main source of reviewers in 38 of the 46 journals that responded to this question (83%, 69– 92%) (Figure 1). The EC performs peer review and writes reports with various frequencies in 22 journals (48%, 33– 63%) (Figure 2). On the other hand, editors other than the EC never undertake peer review or do so rarely in 26 of the 46 journals (57%, 41–71%). On the other hand, editors other than the EC never undertake peer review or do so rarely in 26 of the 46 journals (57%, 41–71%).\n\nTwo EC abstained from answering the question about editorial board members performing peer review. In the other 46 journals, the EC performs peer review and writes reports with various frequencies in 22 journals (48%, 33–63%) (Figure 2). On the other hand, editors other than the EC never undertake peer review or do so rarely in 26 of the 46 journals that responded to this question (57%, 41–71%).\n\nWith two EC abstaining, 11 of the 46 responding EC (24%, 13–39%) said that they implement a similarity check against the Crossref database using iThenticate plagiarism checker, four (9%, 2.4–21%) use online programs (not specified), and 22 (48%, 33–63%) use Google. Nine (20%, 9–34%) do not perform any check for similarity against the published literature.\n\nOnly 10 journals (22%, 11–36%) use an electronic journal management system to communicate with authors and reviewers. The most prevalent communication medium is email (n = 35, 76%, 61–87%). Interestingly, in one case, communication was by ‘personal contact’.\n\nThe minimum number of reviewer reports required to make a decision was two or three in 41 of the 46 responding journals (89%, 76–96%). Four journals required only one, and one journal reported no reviewers.\n\nAcceptance and rejection rates\n\nOver half of the 46 journals that answered this question (26/46, 57%, 95%CI: 18–48%) reject ‘some’ manuscripts at the initial stage of editorial evaluation, whereas 14 of the 46 journals (30%, 18–46%) reject only ‘a few’ or none of them without peer review. Only six journals (13%, 5–26%) reject ‘many’ (Figures 3 and 4).\n\nThe overall acceptance rate of all received manuscripts was >40% in 36 of the 46 journals that responded to this question (78%, 64–89%). On the other hand, the acceptance rate was <20% in only two journals (4.3%, 0.5–15%) (Figure 3B). No journal had an acceptance rate <10%.\n\nProof-reading of published manuscripts\n\nMost journals proof-read Arabic and/or English manuscripts. However, one-quarter of them (24%, 13–39%) do not proof-read the articles before publication.\n\nIndexing in abstract and citation databases\n\nIn asking about inclusion of the journals in abstract and citation databases, we gave Web of Science and/or Scopus as one choice, and as another, Arabic Citation Index (ARCI), a new index established by collaboration between Clarivate Analytics and the Egyptian Knowledge Bank and funded by the Egyptian government. Four journals did not provide information on indexing in databases. Of the 44 responding journals, 20 (45%, 30–61%) stated that they were not in any such database. One journal was verified to be indexed in Scopus and Web of Science. 10 journals described as indexed in ARCI could not be verified due to the unavailability of a publicly available ARCI journal list.\n\nOf the 32 editors who responded to the question about submission of their journals to an index, 30 (94%) answered that they had submitted. Three journals (13%, 4–29%) had been submitted to Web of Science or Scopus and one (3%) to Arabic Citation Index, but the entities to which the other 24 journals had been submitted were not disclosed. Notably, 21 of 23 EC (91.3%, 72–99%) cited lack of funding as an impediment to submission to abstract-indexing databases.\n\nAssessment of satisfaction with the journals\n\nSatisfaction with the journal's performance\n\nWe asked the EC about their satisfaction with their journals' ‘performance’, and 46 of them (96%, 86–99%) were either satisfied (n = 29) or reasonably satisfied (n = 17) (Figure 5). Only two EC were not satisfied.\n\nOf 48 editors, 33 (69%, 54–81%) believed that all or most of the papers they publish add new ideas or new research findings (Figure 5). The other 29% (17–44%) felt that only some papers had novelty, and one EC did not know.\n\nSatisfaction with the manuscripts submitted to peer review\n\nMost of the EC (n = 33, 69%, 54–81%) were satisfied with the quality, clarity and organization of most or all of the manuscripts submitted to peer review, and 28 of them (58%, 43–72%) were satisfied with the accuracy of the language of all or most peer reviewed manuscripts (Figure-6).\n\nSatisfaction with the quality of peer review reports\n\nA total of 46 EC answered the question about satisfaction with reviewer reports. A large majority (38, 83%, 69–92%) were satisfied most of the time or always. 42 of them provided the reasons for their satisfaction. Roughly half of them were satisfied with comprehensiveness and thoroughness of the reports, the questions they raise, and/or the suggestions and helpful comments they provide (Table 1). The lowest frequencies of satisfaction were with the punctuality of the reports (24%) and inclusion of comments on the novelty and significance of the research (26%). Four editors gave the reasons for their dissatisfaction with the reviewer reports, two of whom mentioned the absence of all five reasons for satisfaction listed in Table 1.\n\nAttempts to influence editorial decisions\n\nAttempts by superiors or the institutions to influence editorial decisions were described as rare by 96% of the EC and as ‘sometimes’ by the others.\n\nChallenges and opportunities\n\nAt the end of the questionnaire, the participants were asked to express their views on the challenges they face in the quality of journal publishing. 36 EC provided responses. Thematic analysis of the answers revealed two themes. One is the lack of financial and institutional support, exemplified by what one participant wrote:\n\n“The most prominent limitation is the lack of support, even from the university, which the Journal is supposed to represent, not to mention the difficulties of the publishing process.” (OB#28)\n\nAnother participant was more specific about the financial impact on the publishing process:\n\n“[the challenges we face include] unavailability of financial support from the parent institution. … .. Failure to provide basic programs such as the scientific theft detection program. Failure to release members of the editorial board to perform their duties to the fullest. The prevailing custom now is [this is] a voluntary work and they give you 300 Libyan Dinars every six months, which is not even enough to cover internet expenses. Non-disbursement or awards to reviewers.” (OB#36)\n\nThe second theme identified concerns the reviewing process and a clear dissatisfaction of the editors with the quality and quantity of manuscripts submitted. One participant wrote the following:\n\n“[the main challenge in my opinion is] the reviewing process, [lack of] scientific quality and language quality of the submitted manuscripts.” (OB#24)\n\nThese two themes were again identified when the participants were asked to express their opinions on the opportunities available to overcome the challenges facing the journal publishing quality. They overwhelmingly suggested that financial and institutional (governmental or otherwise) is needed to overcome several challenges. In addition, there was a trend in the participant responses pointing to the technical and academic training and know-how of the publishing process of the editorial staff and the institution. One participant discussed in his response the need for education within the institutions to raise awareness of the importance of scientific publishing:\n\n“the state institutions, researchers, universities and research centers are required to understand the importance of scientific publishing to upgrade these institutions and to develop a national strategy that focuses on a specific number of the field, providing them with the necessary technical and financial support, and finding a clear mechanism for communication with international institutions interested in publishing and finding a clear mechanism to facilitate the payment of the required subscriptions.” (OB#2)\n\nA word cloud (Figure 7) of the answers to the question about the challenges faced by the journals shows that the EC view inadequate support and particularly financial support as the main challenge to raising the quality of the journals.\n\nAssessment of journals was made difficult by the inaccessibility of some journals’ websites or their content. Seemingly, this was caused by technical problems or updates or changes to the websites. One journal website was not accessible for review and the content of three other journals was not available for review. Thus, only 44 out of the 48 journals was accessible for this assessment.\n\nScope, publication types, and language\n\nOverall, the journals cover a wide range of basic and applied sciences, social sciences and liberal arts, and some of them publish in a combination of different fields of science simultaneously, such as chemistry, medicine, botany, and information technology. Some journals publish articles in a wider variety of disciplines, including a combination of applied sciences and humanities.\n\nAccording to the website information, in addition to publishing research articles and reviews, some journals publish conference proceedings and summaries of books, theses, dissertations, and reports on seminars.\n\nInternational Standard Serial Number (ISSN) and editorial board\n\nExamination of the journals’ websites showed only 30 journals displaying ISSN clearly on the website (75%, 59–87%) and in six journals (15%, 6–30%) it was embedded inside pdf files of entire issues consisting of up to hundreds of pages.\n\nWe examined whether the names of the editorial board members and their affiliations are mentioned. A total of 41 journals mentioned their editorial board members whether on the website as such or inside combined files containing entire issue or volumes. However only 17 journals mentioned details of their editors’ affiliations.\n\nWebsite organization and navigation\n\nA general qualitative assessment was made of the structure and functionality of the journal websites. The findings were extremely varied. Whereas some journal websites were professionally structured and organized and fully functional, including but not limited to the very few journals with professional publishers, the websites of a large number of journals had various types of defects, including broken links, disordered archives, missing essential information, and/or language mistakes. We also noticed that the secure socket layer certificate (SSL) was recently expired on a journal website, generating a security warning from the browser.\n\nSome journals were difficult to navigate or required several clicks to reach the desired information. In one journal, three clicks are needed to arrive at the table of content of a selected issue, and then two more to download the article file. Random cases of a journal website going offline for a while were encountered. Some of these seem to have been during website update or maintenance, but no ‘maintenance’ page was used to temporarily substitute for the home page. We were unable to access the several journals of the second largest university over several months, and we received no response from the webmaster to our inquiry. Consequently, these journals are not included in this study.\n\nNotably, a few journals advertised on their websites impact factors that are known as or suspected of being fake.\n\nJournal archives\n\nAlmost all the journals provide the articles only as pdf files. In some journals, some issues are missing or are not in proper chronological order, or the issues/volumes are numbered but do not mention the year.\n\n13 journals (30%) publish their articles only as pdf files of entire issues containing many articles and reaching several hundred pages, most of which include journal information in the first several pages of the pdf files. Journal information of varied quality is in the first several pages of each pdf file in nine journals and on the website in two. The other two journals provide no information about the journal. Notably, four journals have repositories of separate pdf files for the articles, two of which do not provide any journal information anywhere, one gives it in a separate pdf file dedicated to journal information, and one has it on a website page.\n\nPolicies\n\nPeer review policy\n\nWe considered that a clear statement about the peer review policy is adequate even if it is brief, providing that it mentions whether peer review is blinded and mentions the type of blinding. Of the reviewed journals, 15% specify double blind review, 17% describe the review only as being confidential, 48% simply state that the manuscripts are reviewed by experts, and 20% provide no information on peer review. One journal publishes the names of the members of the reviewer committee; there were only nine reviewers to cover multiple fields.\n\nOpen access policy\n\nAll the journals are full open access, of which only nine journals (20%) have a clear policy of either requiring no APC or stating the amount. Notably, some journals that have APC do not specify the amount but refer to it in vague ways that do not inspire confidence.\n\nHuman and animal study ethics\n\nBased on the Helsinki Agreement,12 the protocol for any study on animals or humans should be reviewed by an independent ethics committee (institutional review board), and in the case of humans, informed consent should be obtained from the participants in advance. An ethics statement was frequently absent in many journals. In some journals, none of the articles surveyed contained such a statement, while in other journals, it was included only in some articles. When ethics approval was obtained, it was not always from an ethics committee but from an administrative official. Moreover, when an ethics declaration was present, it did not always include both approval and consent. When consent was obtained, it was not stated whether it was oral or written.\n\nAs the results of the questionnaire showed that only one journal was indexed in Web of Science or Scopus, we searched for the journals in Google Scholar by using their names as ‘source’. Only eight journals (17%, 8–31%) were listed and the remaining 40 journals were not listed in Google Scholar. In the eight Google-indexed journals, half of the journals had international editorial boards, but in the unindexed journals only six (15%, 6–31%) had international editorial boards (RR 3.7, CI:1.12–12.25, p = 0.03). The difference is significant at p < 0.03.\n\nAs seven of the eight Google-indexed journals publish in fields of science, we compared their editorial board compositions with unindexed journals also publishing in sciences. Four of the seven indexed science journals (57%, 18–90%) had international editorial boards, whereas only three out of 13 unindexed journals (23%, 5–53%) had international boards (RR 2.5, CI: 0.76–8.07, p = 0.14).\n\nWe looked up the number of citations in Google Scholar for all articles published in 2019 in the eight journals indexed by Google Scholar. Three journals had no citations, and in all of them, all the editors were from the institution that owns the journal. In contrast, the editorial boards of four of the five cited journals (80%) were affiliated with a mixture of international and national institutions.\n\nAmong the cited journals, one had an article-citation rate of 90%, with an average of 5.8 citations per cited article, one had a rate of 40% with 1.2 citations per cited article, and three had rates in the range of 18–22%, with an average of 0.2–0.3 citations per article. One of the five journals is with a professional publisher, three use OJS, and the fifth uses a free open-source content management system.\n\n\nDiscussion\n\nThe gatekeeping role of high standard editorial practices is believed to be necessary to maintain the integrity of the scientific literature and minimize the risks of bad or low-quality science entering the scholarly record. Evidence-based publishing practices does benefit from scholarly communication while subpar standard journals may unprofessionally publish quantity rather than quality. Understanding what influences the quality of scholarly publications should be of the highest priority to academic institutions and policy-makers, especially given the consequences on the nation’s science advancement.\n\nMany researchers who lack an appropriate funding system are unable to pay the large author publication fees charged by publishers, and the number of journals with good standing but without publication fees has been diminishing rapidly.13 This pushes these researchers to publish in local journals, which dictates the need for establishing robust criteria for publishing practices and policies of local journals, particularly state-sponsored journals. This study provides an overview of the publishing practices in Libya and identifies several shortcomings. This study's findings would be useful for establishing robust criteria to enhance trust in publishing practices and policies of journals affiliated with institutions, particularly those that are not included in the major abstract-indexing databases.\n\nThe ISSN is an essential, unique identifier assigned by multiple centers around the world for a fee of only 25–50 euros (https://portal.issn.org/sites/default/files/guidelinespublishers_merged-eng-final.pdf). Yet 15% of the journals did not have an ISSN and 18% of them did not display it on the website. Website display of a valid ISSN is a basic requirement of inclusion in Directory of Open Access Journals (DOJA)14 and other indexes.\n\nThe affiliations of the editorial boards are also not shown on many journal websites. This omission could have been due to lack of awareness, a suggestion that is supported by the other side of the coin, where two journals provided multi-page curricula vitae of the editors.\n\nProper functionality is important for any type of website. Awkward navigation, broken links, repeated downtime and language mistakes reflect negatively on the journal. Many of the journal websites we surveyed had such issues.\n\nOne notable though not surprising finding is the association between international composition of the editorial board and indexing in Google Scholar, and possibly with citation of journal articles in Google Scholar as well. The importance of an international editorial board is highlighted by Elsevier's basic criteria for acceptance in Scopus, which includes geographic diversity of the editors.11 However, geographic diversity should not be interpreted in a narrow sense, particularly in countries with small populations and tight social relations. More commonly, geographic diversity is understood to mean international diversity. An international editorial board can provide wider and more varied expertise, as well as greater editorial independence. Unfortunately, the criteria set by the committee appointed by the Libyan government for accreditation of Libyan scientific journals run counter to these precepts by dictating that the members of the editorial boards should be affiliated with the institution that owns the journal. A more effective approach for promoting the quality of the journals is to require or at least encourage international diversity of editorial boards.\n\nA limited number of journals post the logos of indexes and impact factors that ore bogus or at least have a bad reputation, and even display an ‘impact factor’ when they are not even indexed in Google Scholar. This is detrimental to the prospect of receiving submissions from serious scientists. In this study, the Google Scholar-cited journals do not do this. When an official body exists to oversee the quality of journals, this should be banned. The official committee mentioned in this report does not address this issue in its criteria.\n\nIn a study of acceptance rates, the overall acceptance rate in ‘ordinary’ open access publishers, including universities and societies, was about 50%.15 According to the estimates of the EC in our study, the acceptance rate of all submitted manuscripts was more than 50% in half of the journals. We speculate that some of the latter have rather high acceptance rates. Notably, of the 14 journals that rejected none or a few manuscripts without peer review, seven of them had an overall acceptance rate of > 50% and four had a rate of 40–50%.\n\nThe EC expressed a high degree of satisfaction with the performance of their journals, but this is not reflected in the indexation and citation records of the journals. There is growing concern in the scientific community over the quality of research and with its visibility and citation metrics in international indexation databases. However, the editors-in-chief of Libyan journals do not seem to take journal metrics into account in their perception of their journals’ performance.\n\nMost of the journals do not receive financial support to improve the environment and tools for managing scholarly journals, such as a journal management system and similarity check software. Indeed, lack of sufficient support was the most frequently cited challenge to journal quality improvement. More important is that paying reviewers, combined with the widespread and relatively heavy reliance on specific reviewer committees, could affect the quality of peer review. Moreover, as the reviewer committees are associated with the journals, they are members of the journal, and it can be argued that they are internal and not external reviewers. Internal reviewers initially screen the manuscripts to check their suitability for peer review by external reviewers who are experts in the relevant fields.\n\nBesides the inadequacy of financial resources, there is apparent inadequacy of knowledge and technical knowhow, which was alluded to by one of the responses to the question about challenges and opportunities. Browsing many journals makes this deficiency evident. A special case in point is that html versions of the articles are absent in almost all the journals. However, we stress that recruiting competent technical expertise requires adequate support from the journal owner.\n\nThe indexing in platforms such as Web of Science and Scopus for assessment of the quality of locally and regionally focused journals is not without obvious bias. While there is agreement that Clarivate Analytics’ Web of Science and Elsevier’s Scopus databases generally contain rigorously assessed, high quality journals, journals from developing countries may get rejected because their research is said to be ‘not internationally significant’ or only of ‘local interest' to developing countries. Only one journal in our study is included in these indexes. But we should mention that we have not included two international Libyan journals because they are not published by a Libyan institution. Both are indexed in Web of Science and one has an impact factor and a CiteScore. In general, institutional academic journals are more likely to be affected by academic in-group bias and to be motivated to lower their standards for articles sharing the journal’s institutional affiliation.16\n\nMany Libyan journals are published in Arabic or both Arabic and English. Therefore, we felt it important to assess the indexation and citation of the journals in this index. However, there is no publicly available journal list for ARCI and information on the selection criteria is sparse. The ARCI selection criteria have been described as a “subset of the Web of Science Core Collection selection process” and are based on “traditional scientific publishing standards and the scholarly research norms of the Arab region”.17\n\nIndexation of Libyan journals in Google Scholar was inconsistent and incomplete, whether one is searching for individual articles or for journals as ‘source’. Technical defects are suspected. Moreover, some Libyan journals do not publish individual files of the articles but only complete issues, which prevents their indexation\n\nIn summary, we discovered defects and deficiencies that affect the performance of the journals in substantial portions of the journals, including affiliations of editors, sources of reviewers, journal management system, medium of communication with authors and reviewers, similarity check of submitted manuscripts, proof-reading of accepted manuscripts, and website organization and functionality. Moreover, the performance of the journals in terms of indexation and citation metrics was at a very low level.\n\nNotably, there was a clear discrepancy between the high level of the editors-in-chief’s satisfaction with journal performance and the journals’ quality indicators. We do understand that lack of funding can cause deficiencies such as unavailability of similarity check software. However, it has not escaped our notice that reasons related to the desire to maintain the status quo can be hypothesized. A viewpoint article in Nature18 lamented that the purpose of research publication has shifted from disseminating knowledge to “getting a publication” for the sake of promotion. Most of the journals in Libya are published by the universities, and a large portion of their academic publications are used for local faculty promotion. Thus, these journals are more likely to be motivated to lower their standards for articles written by authors who share the journal’s institutional affiliation.\n\nLow quality publishing practices will continue to thrive as long as criteria for career advancement of university faculty members are not aligned with robust internationally accepted research performance metrics such as journal rank, citation frequencies, and H-index. We believe that raising the standard of the editorial practices and implementing more versatility and transparency in the peer review and publication process will enhance trust in the scholarly contributions of the developing world. Putting less emphasis on publications in the home journals and assigning more weight to publications in international journals may minimize the impact of academic in-group bias on the quality of the country’s scholarly publications.\n\nOne limitation is that we missed several journals from a major academic institution because all the journal websites were down for an extended period of time and the university did not respond to our inquiries. It turned out that the websites were being updated, and the information was still missing after several months during which the data were being analyzed and the manuscript was being written.\n\n\nConclusions\n\nThe discordance between journal quality indicators and the journal editors’ satisfaction with the performance of their journals points to a broken quality system in scholarly publishing of home academic institutions. A comprehensive plan for immediate attention and subsequent action to raise the standard of academic publications, coupled with technical and training support, are needed to enhance the scientific impact in developing nations.",
"appendix": "Data availability\n\nZenodo: Scholarly publishing in a developing nation. https://doi.org/10.5281/zenodo.8048249. 19\n\nThe project contains the following underlying data:\n\n• Underlying_data_230615.xlsx. (Anonymised survey responses).\n\nZenodo: Scholarly publishing in a developing nation. https://doi.org/10.5281/zenodo.8048249. 19\n\nThis project contains the following extended data:\n\n• SurveyMonkey_316823458.pdf. (Blank English and Arabic questionnaire used in this study).\n\nZenodo: SRQR checklist for ‘Scholarly publishing in a developing nation’. https://doi.org/10.5281/zenodo.8048249. 19\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 thank the editors-in-chief who participated in the survey and the editors who assessed the face validity of the questionnaire.\n\n\nReferences\n\nGomez CJ, Herman AC, Parigi P: Leading countries in global science increasingly receive more citations than other countries doing. Nat. Hum. Behav. 2022; 6: 919–929. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoya-Anegón F, Herrero-Solana V: Worldwide topology of the scientific subject profile: a macro approach in the country level. PLoS One. 2013; 8(12): e83222. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGonzalez-Brambila CN, Reyes-Gonzalez L, Veloso F, et al.: The Scientific Impact of Developing Nations. PLoS One. 2016; 11(3): e0151328. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBredan A, Benamer HTS, Bakoush O: Visibility of Arab countries in the world biomedical literature. Libyan J. Med. 2011; 6: 6325. Publisher Full Text\n\nCommittee on Publication Ethics: Principles of Transparency and Best Practice in Scholarly Publishing 2018.Reference Source\n\nEditorial Policy Committee - Council of Science Editors: White paper on promoting integrity in scientific journal publications Wheat Ridge, CO, USA 2018.Reference Source\n\nWorld Association of Medical Journal Editors: Policies.2022. Reference Source\n\nInternational Committee of Medical Journal Editors: Recommendations 2022.Reference Source\n\nForum for African Medical Editors: FAME editorial guidelines 2022.Reference Source\n\nClarivate: Web of Science Journal Evaluation Process and Selection Criteria 2022.Reference Source\n\nElsevier Scopus: Content policy and selection.2022. Reference Source\n\nWorld Medical Association: WMA declaration of Helsinki - Ethical principles for medical research involving human subjects 2022.Reference Source\n\nMoksness L, Olsen SO: Perceived quality and self-identity in scholarly publishing. J. Assoc. Inf. Sci. Technol. 2020; 71(3): 338–348. Publisher Full Text\n\nDirectory of Open Access Journals: Guide to applying.2022. Reference Source\n\nBjörk B-C: Acceptance rates of scholarly peer reviewed journals: A literature survey. El profesional de la información. 2019; 28(4): 1699–2407.\n\nReingewertz Y, Lutmar C: Academic in-group bias: An empirical examination of the link between author and journal affiliation. J. Informet. 2018; 12(1): 74–86. Publisher Full Text\n\nEl-Ouahi J: The Arabic Citation Index-Toward a better understanding of Arab scientific literature.2022.\n\nMartinson BC: Give researchers a lifetime word limit. Nature. 2017; 550(7676): 303. PubMed Abstract | Publisher Full Text\n\nBakoush O, Bredan A, Tashani O: Scholarly publishing in a developing nation. Dataset. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "207959",
"date": "03 Nov 2023",
"name": "Hamid Jamali",
"expertise": [
"Reviewer Expertise Scholarly communication"
],
"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 illustrates a picture of scholarly journal publishing in Libya by presenting the results of a survey of journal editors and some analysis of data collected through desk research from journals' websites. The results are mainly related to 48 journals and their editors who responded to the questionnaire.\n\nIt is helpful to know about the status quo of journal publishing in a developing country and the challenges faced by those journals and in this regard, the paper is useful. However, I found the analysis a bit too descriptive and there is some room for improvement.\nTo start with, I think the paper needs to provide some background about journal publishing in Libya as the context. When did journal publishing start, how many journals exist, in what language are they published and so on? Some information about the country would also be useful as context (population, number of universities, number of papers published by Libyan researchers in Scopus in one year as an example etc). This information should be available somewhere or at least collectable via some desk research. The authors have relied on the questionnaire to find some facts about journals while I believe that type of information could be more accurately collected via desk research (e.g. indexation, language and so on). The initial analysis should not be limited only to those journals that completed the questionnaire, it should cover all Libyan journals if possible.\n\nThe survey results are presented appropriately (simple frequency and percentage) but I expected a bit more at least from free-text questions. The word cloud doesn't reveal much really as it only includes a few general terms such as journal, institution etc. So the authors might see if they can improve the analysis to add more depth and insight.\n\nThe paper can benefit from better coverage of the relevant literature. I have provided a few references here1-[ref-6. Some are examples of papers that discuss journal publishing in individual developing countries (Pakistan and Nigeria), and some are discussions particularly about journal publishing in the Arab world (which Libya is part of). One is generally about journal publishing in the world (Khanna et al) which has good points and information about local journals and non-English journals. And finally, Jamali et al (disclaimer: my own paper on local journals in Australia) has information about challenges faced by local journals that occasionally result in their discontinuation.\nThe discussion has good points, but you can also consider the value of local/national journals in your discussion. Local/national journals have functions that can be distinct from international journals.\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? Yes",
"responses": [
{
"c_id": "10600",
"date": "29 Nov 2023",
"name": "Omran Bakoush",
"role": "Author Response",
"response": "Response to Reviewer Reports Reviewer-1: Hamid Jamali, Charles Sturt University, Wagga Wagga, NSW, Australia We would like to thank Reviewers for taking the necessary time and effort to review the manuscript. We sincerely appreciate all your valuable comments and suggestions, which helped us in improving the quality of the manuscript. Point by point responses Review comment: It is helpful to know about the status quo of journal publishing in a developing country and the challenges faced by those journals and in this regard, the paper is useful. However, I found the analysis a bit too descriptive and there is some room for improvement. Authors' Reply: Although the analysis design of the study was primarily descriptive, we elaborated on the findings using qualitative analysis of respondents' responses to open questions on challenges facing their journals. Further, we used the data generated from desk research on journal quality to elaborate on the survey responses. The mixed methods approach was used to integrate insights gained from the survey, desk research data, and open responses, which was helpful in enhancing the validity of the interpretations. Review comment: To start with, I think the paper needs to provide some background about journal publishing in Libya as the context. When did journal publishing start, how many journals exist, in what language are they published and so on? Some information about the country would also be useful as context (population, number of universities, number of papers published by Libyan researchers in Scopus in one year as an example etc). This information should be available somewhere or at least collectable via some desk research. Authors' Reply: To comply with the reviewer's request, we have added the following in the introduction: Libya is an Arab country with an estimated surface area of 1,775,500 km2 and a population of about 6.7 million. Most of the population live in the main coastal cities, namely Tripoli (the capital) and Benghazi (second largest city). Since the start of oil exportation from Libya in the 1960s, living standards have risen. Undergraduate and postgraduate institutions have been expanded and improved over the years. The first Libyan university was established in 1957 (https://mhesr.gov.ly/?page_id=126). The number of universities has expanded over time, and according to the ministry of education, there are now 26 public universities in Libya with 350,000 university students. 20 The first initiative to formally promote research in Libya began in the mid-seventies with the establishment of the National Commission of Scientific Research, formally charged with planning and supporting scientific research. Over many years, the Libyan government, expanded the scope of MSc degree programs, and recently initiated PhD programs in various fields, including sciences, as well as built research centers. However, overall research performance indicators remain modest. The Libyan Journal of Science, the first scholarly journal published in Libya, was launched in 1971. It is improbable that it is the currently active journal by the same name because the numbering of the annual volumes goes back only to the late nineties. Jamahiriya Medical Journal was launched in 1976 and continues to be listed in Scopus (without metrics) though it ceased its activity in 2011. A recent bibliometric study (Jaradat) 21 based on the Scopus database for Libya's scientific output from 1948 to 2022 revealed a total number of 10,475 articles in the Scopus database, 10361 of them in English (99%). On the other hand, another study (Mahmood) 22, based on the Directory and Book of Abstracts of Libya’s National Centre for Scientific Research for 2001-2004, revealed that 45% of the research output was reported in English, and the rest was in Arabic. Review comment: The authors have relied on the questionnaire to find some facts about journals while I believe that type of information could be more accurately collected via desk research (e.g. indexation, language and so on). The initial analysis should not be limited only to those journals that completed the questionnaire, it should cover all Libyan journals if possible. Authors' Reply: We collected data about editorial journal qualities from the websites only of the journals the editors of which participated in the study. The aim was to integrate the data from the questionnaire with those from desk searches for the journal editorial qualities. This yielded perhaps the most notable finding of the discrepancy between the editors-in-chiefs' perception of journal performance and objective criteria of journal editorial performance. Furthermore, most of the other journals either did not have publishing websites or were not active at the time of the search. The relevant section of the methods has been modified slightly and augmented as follows: To integrate results of desk research with the results from the questionnaire, the websites of the journals the editors of which returned questionnaire responses were visited by one investigator (AB) and information was collected on various journal qualities. These included but were not limited to the presence of an International Standard Serial Number (ISSN), the editorial board's geographic diversity, the organization of the archives, and general website functionality. Moreover, data were collected on the listing of the journals in Google Scholar and the number of citations of all articles published in 2019, as well as indexation in the database of the Arab Citation & Impact Factor (Arcif). Review comment: The survey results are presented appropriately (simple frequency and percentage) but I expected a bit more at least from free-text questions. The word cloud doesn't reveal much really as it only includes a few general terms such as journal, institution etc. So the authors might see if they can improve the analysis to add more depth and insight. Authors Reply: \"Financial support\" is one the three most prominent terms in the word cloud. Nevertheless, we replaced the figure with a new figure that includes more words and thus gives a clearer picture. Review comment: The paper can benefit from better coverage of the relevant literature. I have provided a few references here1-[ref-6. Some are examples of papers that discuss journal publishing in individual developing countries (Pakistan and Nigeria), and some are discussions particularly about journal publishing in the Arab world (which Libya is part of). One is generally about journal publishing in the world (Khanna et al) which has good points and information about local journals and non-English journals. And finally, Jamali et al (disclaimer: my own paper on local journals in Australia) has information about challenges faced by local journals that occasionally result in their discontinuation. Authors Reply: We thank the reviewer for suggesting the references. We have added the following in the discussion: \"A recent study on over 25,000 journals that use PKP's Open Journal Systems platform found only 1.2% indexed in the Web of Science and 7.2% in Scopus. A recent review of Pakistani journals revealed that 97% of the journals are in the lowest category and 97% do not have an impact factor. 26 In many developing countries, the majority of the journals are university-based.\" We also added the following at an appropriate place in the discussion: But its impact can go deeper. A study on Australian journals reported that funding issues represented a major cause of journal discontinuation. 28 Review comment: The discussion has good points, but you can also consider the value of local/national journals in your discussion. Local/national journals have functions that can be distinct from international journals. Authors Reply: We have added the following text in the discussion: However, local journals should not be undervalued. Researchers might prefer to publish in international journals, but local journals have distinct, useful functions. Whereas international journals provide a platform for researchers to share their research globally, local journals provide a platform for issues and developments relevant to the local community that might not be considered relevant to international journals. Local journals also foster cooperation between local researchers and provide a platform for publishing in their native language. Nevertheless, there is a need for establishing robust criteria for publishing practices and policies of local journals, particularly state-sponsored journals."
}
]
},
{
"id": "216185",
"date": "03 Nov 2023",
"name": "Andreas Nishikawa-Pacher",
"expertise": [
"Reviewer Expertise Meta-scientific infrastructures"
],
"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\nThanks for inviting me to review the paper on Libyan journals performances and the perceptions of their editors regarding the journals' quality. It offers an interesting read, with some fascinating insights that complement the conventional knowledge about the scientific publication system. Conventionally, meta-scientific analyses tend to focus on journals that are indexed in Web of Science or Scopus, and that are published in English language and that conform to the so-called 'Global North' standards; this manuscript, in contrast, investigated an aspect of the scholarly publication system within a rather local setting in Libya.\nA key insight is that there is a discrepancy between the editors' own assessment of their journals' performances on the one hand, and more or less 'objective' indicators on the other hand. What is also of interest are some of the \"anomalies\" (when compared to the usual convention), such as the fact that one journal pursues the editorial processing only via personal contact (rather than an online submission system or via e-mail), or that some of the journals lack a professional online presentation (e.g., websites with bogus \"Impact Factors\", or journal websites that only offer PDF versions rather than HTML versions of the texts, with too-many clicks necessary to access the scientific content). It is also remarkable that 80% of the journals seem to be open access and operate free of charge (i.e., Diamond Open Access, albeit not necessarily part of DOAJ).\nThe introduction is well written, and the manuscript structure conforms to the usual IMRaD-structure. However, I believe the paper would gain in strength with some additional information.\nFirst, given that readers (like me) may not be an expert in the methodical approach used here, it would be great if the authors at least partly referenced the general standards of such expert surveys and quantitative interviews, and to show how their own approach conforms to these standards.\nSecond, is it possible to offer at least the list of journals that are covered by this study? The authors do not have to identify the responses (available at Zenodo) with the journals, but just having a catalogue of the journal sample would be interesting.\nThird, I think the focus on Web of Science, Scopus and Google Scholar merits a complementary view with similar (but 'emerging') databases, such as Dimensions, or, more importantly, the \"open data\"-based CrossRef, LENS, and OpenAlex. The journal coverages differ from each other, and from my knowledge, the latter three or four databases are likewise widely used. And if readers had knowledge about the journals being members of, say, CrossRef, then more data could be fetched via CrossRef metadata.\nFourth, did the authors further delve into some of the concerning matters, such as the fact that bogus impact factors were displayed? Is there anything to say with regards to \"predatory\" publication structures that may be at play behind some journals? Why does a website present such questionable metrics -- is it an innocent lack of knowledge, or is there a deceiving intent behind it? Would an expert survey even be able to unearth a \"predatory\" practice, given that respondents may not be honest in their responses? Another issue worthwhile to be addressed would be whether the journals use PIDs (especially DOIs), and if so, what kind of metadata are deposited behind the DOIs.\nFifth, the whole manuscript revolves around analyzing Libyan journals against a global standard -- in the Discussion section, could anything be stated, at least briefly, about this \"imposition\" of common norms upon the Libyan system? Is there some kind of incompatibility between the global norms and the local practice? The wording of \"colonialism\" may be an overstretch here, but at least I got the impression that some readers may be interested in hearing more about this concept in this context.\nFinally, there are some minor inconsistencies or errors, such as \"DOAJ\" being abbreviated as \"DOJA\", or that the abbreviation of \"EC\" was introduced for editors-in-chief, but then \"EIC\" is used later, etc. These are just minor matters.\nAs a further, very general remark, it seemed to me that the paper could better integrate current research on similar topics, at least briefly, so as to embed their own investigation into the relevant literature. Having just 10 references to peer-reviewed works does not really do justice to the fact that a lot is being researched on similar meta-scientific issues regarding the scientific journal landscape (e.g., on AJOL [\"African Journals Online]1, on journals that publish in LOTE [languages other than English]2, on possibly \"predatory\" practices3, or, to cite merely one of our own examples4, whether a journal really attains the status of \"open access\" if the website poses even minor technical barriers in accessing the content (e.g., no HTML but only PDF versions).\nDespite these few remarks on how the manuscript could possibly enhance its quality, the paper already offers a novel study with interesting insights for science at large.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "10601",
"date": "29 Nov 2023",
"name": "Omran Bakoush",
"role": "Author Response",
"response": "Response to Reviewer Report Reviewer-2: Andreas Nishikawa-Pacher, Diplomatic Academy Vienna, Vienna, Vienna, Austria; We thank reviewer for reviewing our manuscript and describing our study as novel and insightful. We also appreciate his comments, which enabled us to add value to our manuscript. Point by point responses Review comment: First, given that readers (like me) may not be an expert in the methodical approach used here, it would be great if the authors at least partly referenced the general standards of such expert surveys and quantitative interviews, and to show how their own approach conforms to these standards. Authors Reply: We based the questionnaire on the editorial policies published by the Council of Science Editors and on the Web of Science basic journal selection criteria for indexation. We augmented the description of questionnaire design as follows \"We designed a questionnaire consisting of 10 parts following the best practices in designing questionnaire items and organizing the questionnaire.\" The questionnaire was pre-tested by the researchers and then piloted online by three editors of an international journal who were not affiliated with a local or regional institution. It was ensured that the logic of the online questionnaire functioned correctly, and any ambiguous or misunderstood questions were re-worded. 23. Gehlbach, H., & Brinkworth, M. E. (2011). Measure twice, cut down error: A process for enhancing the validity of survey scales. Review of General Psychology, 15(4), 380–387 (PMID: 29210756). 24. Gehlbach H, Artino AR Jr. The Survey Checklist (Manifesto). Acad Med. 2018 Mar;93(3):360-366. doi: 10.1097/ACM.0000000000002083. PMID: 29210756. Review comment: Second, is it possible to offer at least the list of journals that are covered by this study? The authors do not have to identify the responses (available at Zenodo) with the journals, but just having a catalogue of the journal sample would be interesting. Authors Reply: We uploaded a list of the journals included in the study to a repository: Therefore, the study included 48 academic journals published by national institutions (list available at https:// 10.5281/zenodo.10155318). Review comment: Third, I think the focus on Web of Science, Scopus and Google Scholar merits a complementary view with similar (but 'emerging') databases, such as Dimensions, or, more importantly, the \"open data\"-based CrossRef, LENS, and OpenAlex. The journal coverages differ from each other, and from my knowledge, the latter three or four databases are likewise widely used. And if readers had knowledge about the journals being members of, say, CrossRef, then more data could be fetched via CrossRef metadata. Authors Reply: We have now checked for indexation of the journals in the Arab abstract-indexing database, eMarefa, and added the following: \"On the other hand, Marefa (e-Marefa.net) is an abstract-indexing database established in 2008 for peer-reviewed literature from Arab countries published in Arabic, English or French. It indexes over 4000 journals and is the basis of the Arab Citation & Impact Factor (ARCIF, https://emarefa.net/ARCIF/). Of the 48 journals included in this study, 13 (27%) are listed in e-Marefa.com, with ARCIF factors ranging from zero to 1.3.\" \"We did not search for the journals in the Arab Impact Factor (AIF) (https://www.arabimpactfactor.com/), produced by the Association of Arab Universities, because the content is not accessible, there are no links to the journals, and there is no description of where or how citations are counted.\" Review comment: Fourth, did the authors further delve into some of the concerning matters, such as the fact that bogus impact factors were displayed? Is there anything to say with regards to \"predatory\" publication structures that may be at play behind some journals? Why does a website present such questionable metrics -- is it an innocent lack of knowledge, or is there a deceiving intent behind it? Would an expert survey even be able to unearth a \"predatory\" practice, given that respondents may not be honest in their responses? Another issue worthwhile to be addressed would be whether the journals use PIDs (especially DOIs), and if so, what kind of metadata are deposited behind the DOIs. Authors Reply: The relevant text now reads as follows: Notably, a few journals advertised on their websites impact factors that are known as or suspected of being fake. Advertising a questionable impact factor can be detrimental to a journal, and any claim to having an impact factor should specify its source. When the source of a published impact factor is not specified, a deceiving intent to provide false impression about journal status is suspected. Review comment: Fifth, the whole manuscript revolves around analyzing Libyan journals against a global standard -- in the Discussion section, could anything be stated, at least briefly, about this \"imposition\" of common norms upon the Libyan system? Is there some kind of incompatibility between the global norms and the local practice? The wording of \"colonialism\" may be an overstretch here, but at least I got the impression that some readers may be interested in hearing more about this concept in this context. Authors Reply: We added the following in the discussion: Yet, it is important to note that the lack of research skills, experience, and research funding is an important factor in the low-quality research in developing countries. Furthermore, in Libya as well as other developing nations, quantitative bibliometric criteria are used to assess research production for promotion decisions, regardless of the quality of publications. This could be strengthening the expedient editorial practices in many university-based journals Review comment: Finally, there are some minor inconsistencies or errors, such as \"DOAJ\" being abbreviated as \"DOJA\", or that the abbreviation of \"EC\" was introduced for editors-in-chief, but then \"EIC\" is used later, etc. These are just minor matters. Authors Reply: Done. Thank you. Review comment: As a further, very general remark, it seemed to me that the paper could better integrate current research on similar topics, at least briefly, so as to embed their own investigation into the relevant literature. Having just 10 references to peer-reviewed works does not really do justice to the fact that a lot is being researched on similar meta-scientific issues regarding the scientific journal landscape (e.g., on AJOL [\"African Journals Online]1, on journals that publish in LOTE [languages other than English]2, on possibly \"predatory\" practices3, or, to cite merely one of our own examples4, whether a journal really attains the status of \"open access\" if the website poses even minor technical barriers in accessing the content (e.g., no HTML but only PDF versions). Authors response We have provided more information from nine more references."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1173
|
https://f1000research.com/articles/13-208/v1
|
21 Mar 24
|
{
"type": "Research Article",
"title": "Efficacy of green tea (Camellia sinensis Linn) 3% extract cream on improvement of striae distensae",
"authors": [
"Sartika Ayuningsih",
"Nelva Karmila Jusuf",
"Imam Budi Putra",
"Nelva Karmila Jusuf",
"Imam Budi Putra"
],
"abstract": "Background Striae distensae (SD) is a skin condition that frequently causes dermatological consultations and although asymptomatic, it may can cause itch and burning sensation. Green tea extract contains polyphenol, including flavanol, flavandiol, flavonoid, phenolic acid, amino acids and minerals which play a role in the repair of stretch marks through anti-inflammatory mechanism, increase collagen production, fibroblast proliferation, and skin hydration.\n\nObjective To determine the efficacy of green tea extract cream on striae distensae.\n\nMethods This is a pre-experimental clinical trial with a pretest-posttest design on 36 subjects with striae distensae. Diagnosis establishes through history taking and clinical evaluation. Imam Nelva Alviera (INA) score was used as SD severity before and after the application of the 3% green tea extract cream carried out at weeks 0, 2, 4, 6, and 8. Side effects and subjects’ satisfaction were also recorded. Cochran test was carried out to see the difference before and after treatment, with a p-value <0.05 considered significant.\n\nResults Majority of study subjects were 18–25 years (77.8%), had history of pregnancy (75%), had a history of menarche at the age of 12 years (27.8%) and all subjects had striae alba. There was significant decrement in INA score for striae distensae (p<0.001) after eight weeks administration of 3% green tea extract cream. Clinical improvement and no side effects were also noted. All subjects were satisfied.\n\nConclusions The use of 3% green tea extract cream can improve the appearance of SD.",
"keywords": [
"striae distensae",
"stretch mark",
"INA score",
"green tea extract",
"Camellia sinensis linn"
],
"content": "Introduction\n\nStriae distensae or known also as stretch marks are skin condition that causes frequent dermatological consultations. Striae distensae (SD) appear as fusiform or linear lesions with certain length and witdh.1 The main etiology of SD remains unclear and are common in different conditions, for example pregnancy, weight changes and adrenocortical excess. The prevalence of SD is estimated at 40-70% in adolescents.1,2\n\nTreatment of striae distensae become great challenges because often the current available treatments did not provide satisfactory result. The aim of SD is to induce dermal collagen production, fibroblastic activity, such as to improve tissue strength, increasing skin elasticity, and skin hydration. Several treatments that have been known for the treatment of SD include topical tretnoin, laser, radiofrequency, microdermabrasion, and platelet rich plasma.3,4\n\nOver decades, natural products to improve skin condition have been developed. In Indonesia, plant extracts are used as medicine. Green tea gains its popularity amongst scientists because of variety health benefits.5,6 Green tea (Camellia sinensis Linn) contains catechins that have significant effects for health because of their anti-inflammatory and antioxidant activities. There are various types of catechin such as epicatechin (EC), epicatechin gallate (ECG), epigallocatechin (EGC), dan epigallocatechin gallate (EGCG) that may also help in skin regeneration. Catechin may induce fibroblast proliferation, epithelialization, and collagen synthesis. Study by Hajiaghaalipour et al. found the use of Camellia sinensis Linn extract may increase cell proliferation, angiogenesis and collagen development.7–9 Essential fatty acids in green tea extract, such as linoleic acid, oleic acid and tocopherol have the potential to help increasing skin hydration, skin elasticity, and antioxidant.10 This study aimed to find the efficacy of green tea extract in striae distensae.\n\n\nMethods\n\nThis study is a pre-experimental study with a pretest–posttest design carried out from December 2022 to March 2023 at the Department of Dermatology and Venereology, Prof. dr. Chairuddin Panusunan Lubis, Universitas Sumatera Utara Hospital. All subjects participated in this study had signed informed consent and this study was conducted in accordance with the Declaration of Helsinki. This research was conducted after obtaining approval from the health research ethics committee No:1254/KEPK/USU/2022 obtained from the University of North Sumatra Research Ethics Committee.\n\nThe minimum sample size in this study was 36 people.\n\nGreen tea was obtained from the Sidamanik green tea plantation, North Sumatra, then the process of making 3% green tea extract cream is carried out at the Medicinal Plant Research and Development Laboratory of the Indonesian Herbal Traditional Medicine Association, Medan.\n\nThe participants of this study were 36 women with striae distensae, aged 18–35 years, who came to the outpatient clinic of the Department of Dermatology and Venereology, Prof. dr. Chairuddin Panusunan Lubis, Universitas Sumatera Utara Hospital, Indonesia. All participants were evaluated through history taking and clinical examination. Participants were excluded from the study if they are pregnant, with history of pregnancy, and were on oral, topical, or intervention treatment for striae distensae within last month. Subjects were also excluded from the study if they did not use the cream for three consecutive days and the total use of the cream was less than seven weeks.\n\nSubjects were asked to apply one fingertip unit of cream on striae distensae lesion in each femur every morning and night, and being evaluated every two weeks (weeks 2, 4, 6 and 8), research subjects were asked to come back to have the Imam Nelva Alviera (INA) score calculated, and document SD lesions as well as assessing side effects that occurred during research period. Striae distensae severity was measured using INA (Imam, Nelva, Alviera) score,20 assessment of striae distensae includes the number of lines, the size of the longest striae distensae line, color, and the presence or absence of itching. The INA score were assessed before and after using the green tea extract cream. The questionnaire can be found as Extended data.27\n\nData collected from weeks 0, 2, 4, 6, and 8 were analyzed using SPSS version 22.0 software. They were analyzed using the Shapiro-Wilk normality test. The Cochran test was used to compare the INA score before and after the application of green tea extract cream, with p-value <0.05 was considered significant.\n\n\nResults\n\nIn this study, all research subjects completed all follow-up until the 8th week.26 The majority of subjects with age range of 18–25 years (77.8%) (Table 1), with the youngest age was 18 years and the eldest at 32 years. Most of the subjects menarch age was 12 years (27.8%) (Table 2), with family history of SD (75%) (Table 3), and all of the subjects were presented with striae alba.\n\nAfter the data were collected, the Shapiro-Wilk test was conducted to show the normality of the data and Cochran test was carried out to assess the comparison of stiriae distensae severity with INA score before and after the application of green tea extract cream. At the beginning of the study, there were 31 subjects (86.1%) with severe striae distensae. After using green tea extract cream for eight weeks, a significant decrease in subjects with severe striae distensae became 15 subjects. The p-value obtained through the test is <0.001 (Table 4). The McNemar test also showed that from the beginning of the study towards the end of study, there was a significant improvement in striae distensae severity from the beginning of study towards week 4, week 6, and week 8. (Table 5). In this study, the 3% of green tea extract cream did not cause any side effects and all of the participants were satisfied.\n\n* Cochran test.\n\n* Posthoc Test.\n\n\nDiscussion\n\nStriae distensae may happen in several age range, but the prevalence show an increasing trend starting from adolescents.11 The majority subjects in this study were in the age group of 18-25 years old. This study is in accordance with Putra et al. study in 155 subjects with striae distenesae, the mean age was 19 years old.12 In a study by Amal et al. with 72 health workers with striae distensae, most of the subjects were with the age range of 18-25 years (93.1%).13\n\nMenarche age in majority of subjects were 12 years. A study by Marques, Madeira and Gama showed that the mean age for menarche was 12.4 years.14 Menarche show hormonal maturation from hypothalamic pituitary ovarian (HPO). One of the hypotheses of striae formation was the estrogen influence as the result of HPO axis maturation. Estrogen may decrease adhesion between collagen fibers and cause the striae lesion. Aryunisari et al. concluded that early age of menarche increases the risk of striae formation.15,16\n\nMajority of the participants in this study do have family history of striae distensae. This study is in accordance with Sipahutar et al. study in 202 women with striae distensae, 83.7% had family history of striae distensae.17 Gosh et al. also showed than 73.3% subjects with SD have family history of striae distensae.18 It was assumed that there were gene expression involvement in fibroblast metabolism that code elastin, collagen, and fibronectin was lower compared to normal skin.19\n\nThere is no single therapy that is truly effective in treating striae distensae. This research is a preliminary study on the use of green tea extract to treat striae distensae. The result of this study showed that 3% green tea extract cream decrease striae distensae severity that was scored with INA score from the beginning of the treatment towards the eight weeks of the treatment. INA score was the newest score that can assess striae distensae severity more specific. The INA score was differentiated into 3 categories, such as mild (<3), moderate (3–6), and severe (>6).20\n\nStriae distensae treatment aim to decrease redness, edema, irritation from striae rubrae, increasing collagen production and elastin fibers, to help in collagen arrangement, increase hydration and decreasing inflammation in striae alba. Epigallocatechin gallate (EGCG) in green tea was proven to increase the expression of transforming growth factor β1 (TGF-β1) in fibroblast proliferation stimulation and regeneration of collagen tissue by inducing collagen and elastin.9 It was suggested that green tea had about twenty times more powerful antioxidant than vitamin E. Study by Yaghmayei et al. showed than Camellia sinensis Linn extract can accelerate inflammation phase because of the antioxidant effect in the formation of collagen synthesis and increasing fibroblast proliferation.21,22 The EGCG in green tea can increase the regulation of klotho gene expression in normal epidermal keratinocytes by protein kinase A (PKA)-cAMP responsive element-binding protein (CREM) signalling, that cause differentiation of keratinocytes. Epigallocatechin gallate mediate TGF-β1 to induce collagen contraction in fibroblasts by suppressing myofibroblast differentiation and decreasing the gene expression from connective tissue growth factor and collagen type I gene.23\n\nReactive oxygen species (ROS) can cause damaging effect on cell, tissue, and interfere with wound healing process. Antioxidant or free radical scavengers play roles in wound healing by accelerating the healing time, improving the appearance of healed tissue, and at the same time protecting the tissue from oxidative damages. Green tea may aid in wound healing because of its phytoconstituents which is rich in flavonoid and phenolic and high free radical scavenging activity.9\n\nSafety profile of green tea extract has been mentioned in several studies, including a study by Meethama et al. in 20 participants who were given green tea extract in different concentration as 2%, 4.5%, and 7% didn’t show any skin irritation. Kim et al. also reported that green tea extract may be used as anti-inflammation without toxicity effect.24,25\n\nIn this study there are still limitations where not all confounding factors could be excluded in the research subjects. Therefore, further research with a randomized controlled trial design is needed to further evaluate the efficacy of green tea extract against striae distensae.\n\n\nConclusion\n\nThe use of 3% green tea extract cream can improve the appearance of striae distensae and the use of this extract showed there are no side effects and all of the subjects were satisfied. This study shows that green tea extract cream was effective and can be considered as striae distensae treatment.",
"appendix": "Data availability\n\nZenodo: Data collected. https://doi.org/10.5281/zenodo.8427287. 26\n\nZenodo: Data set side effect and satisfaction subject. https://doi.org/10.5281/zenodo.8418988. 27\n\nThis project contains the following extended data:\n\n- Questionnaire\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 express our gratitude to the Head of Cosmetic Division, Department of Dermatology and Venereology, Faculty of Medicine Universitas Sumatera Utara and to Prof. dr. CPL Universitas Sumatera Utara Hospital.\n\n\nReferences\n\nEl Nagdy HAA, Atwa EMA, Morsi HM, et al.: Brief Overview About Striae Distensae. Journal of Pharmaceutical Nevative Results. 2023; 14(2): 1270–1275.\n\nMaari C, Powell J: Anetoderma and Other Atrophic Disorders of the Skin.Kang S, Amagai M, Bruckner AL, et al.: Fitzpatrick’s Dermatology. 9th Edition. United States: McGraw-Hill Education; 2019; p.1197.\n\nLokhande AJ, Mysore V: Striae Distensae Treatment Review and Update. Indian Dermatol Online J. 2019; 10: 380–395. PubMed Abstract | Publisher Full Text\n\nHuang Q, Su L, Wu T, et al.: New Progress in Therapeutic Modalities of Striae Distensae. Clinical, Cosmetic and Investigational Dermatology. 2022; 15: 2101–2115. Publisher Full Text\n\nNarayanaswamy R: Cosmetic potential of Southeast Asian Herb: an overview. Phytochemistry Reviews. 2015; 14(3): 419–428. Publisher Full Text\n\nFajar R, Wrasiati, Suhendra: The Content of The Flavonoid Compound and Antioxidant Activity of Green Tea Extract in the Treatment Temperature and Time Brewing.2018; 6(3): 196–202.\n\nSandeep K, Nisha S, Shweta A: Green Tea Polyphenols: Versatile Cosmetic Ingredient. IJARPB. 2012; 3: 348–362.\n\nKapoor M, Howard R, Hall I, et al.: Effects of Epicatechin Gallate on Wound Healing and Scar Formation in a Full Thickness Incisional Wound Healing Model in Rats. The American Journal of Pathology. 2004; 165: 299–307. Publisher Full Text\n\nHajiaghaalipour F, Kanthimathi MS, Abdulla MA, et al.: The effect of Camellia Sinensis on Wound Healing Potential in an Animal Model. Evidence-based Complementary and Alternative Medicine. 2013; 2013: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGianeti MD, Mercurio DG, Campos P: The Use of Green Tea Extract in Cosmetic Formulations: Not only an Antioxidant Active Ingredient. Dermatologic Therapy. 2013; 26: 267–271. Publisher Full Text\n\nKeen MA: Striae Distensae: What's New at the Horizon? BJMP. 2016; 9(3): 919.\n\nPutra IB, Jusuf NK, Aryunisari CG: Correlation between Body Mass Index with Striae in Female Adolescent. Bali Med J. 2020; 9(3): 773–775. Publisher Full Text\n\nAmal AY, Putra IB, Jusuf NK, et al.: Evaluation of the Severity of Striae Distensae using the New Scoring System. Bali Med J. 2023; 12(2): 1287–1290.\n\nMarques P, Madeira T, Gama A: Menstrual Cycle among Adolescents: Girl's Awareness and Influene of Age at Menarche and Overweight. Rev. Paul. Pediatr. 2022; 40: e2020494. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPriya BN, Mallikarjun HB, Srinivas R, et al.: The Relation between Ages at Onset of Menarche with Skin Changes among 10-16 years School Going Girls. IAR J. Med. Sci. 2023; 4(3): 26–30.\n\nAryunisari CG, Putra IB, Jusuf NK: The Relationship between Age of Menarche with Striae among Female Students. Bali. Med. J. 2020; 9: 400–403. Publisher Full Text\n\nSipahutar SA, Jusuf NK, Putra IB: The Association Between Waist-Hip Ratio Index and Striae Distensae. Bali. Med. J. 2021; 10(3): 1111–1114.\n\nGhosh A, Swaroop MR, Ravindranath M, et al.: Comparative Study of Efficacy and Safety of Fractional CO2 Laser and Microneedling Fractional Radiofrequency (MnRF) in the Treatment of Striae Distensae. IP Indian Journal of Clinical and Experimental Dermatology. 2020; 6(3): 277–286. Publisher Full Text\n\nShen Y, Pang Q, Xu J: Comprehensive Pathogenesis and Clinical Therapy in Striae Distensae: An Overview and Current Perspective. CJPRS. 2022; 4(4): 203–207. Publisher Full Text\n\nPutra IB, Jusuf NK, Amal AY: Pilot Study of New Scoring System Severity of Striae Distensae. Bali. Med. J. 2022; 11(3): 1915–1918. Publisher Full Text\n\nVyavhare SB, Ravsaheb MS: A Review on Herbal Cosmetics. Research Journal of Modernization in Engineering Technology and Science. 2023; 5(4): 2385–2396.\n\nYaghmayei P, Moshrefjavadi F, Nilforooshzade MA, et al.: Effects of Watery and Alcoholic Extract of Green Tea on The Process of Open Skin Wounds Healing in Male Rat (NMRI). Medical Sciences Journal. 2010; 20: 69–75.\n\nXu FW, Lv YL, Zhong YF, et al.: Beneficial Effects of Green Tea EGCG on Skin Wound Healing: A Comprehensive Review. Molecules. 2021; 26(20): 6123. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMeethama P, Kanalayavattanakula M, Louritha N: Development and Clinical Efficacy Evaluation of Anti-greasy Green Tea Toner on Facial Skin. Rev. Bras. Farmacogn. 2018; 28: 214–217. Publisher Full Text\n\nHk K, Sy C, Chang HK, et al.: Human Skin Safety Test of Green Tea Cell Extracts in Condition of Allergic Contact Dermatitis. Toxicol Res. 2012; 28(2): 113–116. Publisher Full Text\n\nAyuningsih S: Data collected. [Dataset]. Zenodo. 2023. Publisher Full Text\n\nAyuningsih S: Data set side effect and satisfaction subject. [Data set]. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "262328",
"date": "26 Apr 2024",
"name": "Yuli Kurniawati",
"expertise": [
"Reviewer Expertise Dermatology cosmetic and aesthetic"
],
"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 research of Phytopharmaca about striae distansae is one of a novel study. Green tea extract cream have rich flavonoid, phenolic and High free radical scavenging activity induced colagen production and elastin fibers in striae distensae. The INA score is the new criteria for Severity scoring of striae distensae and will be applicable in daily practice. The strengths of the research are the first novel research using a phytopharmaca green tea extract which play a role in the repair of stretch marks. The second, criteria striae distensae severity was measured using INA ( Imam, Nelva, Alviera) score as a new scoring of SD. The third, the result had improve the appearance of SD. The weaknesses of this research are the study was single arm study without comparation with another treatment. The second, the research didn’t mention how to make the extract cream. And the third, the validation of INA score not yet established. The further research still need with multi-centre study and more sample.\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": "262329",
"date": "06 Jun 2024",
"name": "PRASETYADI MAWARDI",
"expertise": [
"Reviewer Expertise Dermatology",
"Cosmetology",
"Venereology",
"Skin cancer",
"dermatopathology"
],
"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 use of green tea cream (Camellia sinensis Linn) 3% extract cream) could be an alternative treatment for Striae distensae (SD) in the future. What is interesting is that researchers used the INA score parameters developed by researchers to assess the effectiveness of SD treatment. It's just that the INA score parameter assessment methodology is not explained adequately in the manuscript, how to minimize the subjectivity of the INA score measurement. If carried out by two or more different assessors, it is not explained in the statistical analysis what the Cohen's kappa value of the assessment is. Presentation of research results should be added in the form of graphs or pictures, so that it does not give a monotonous impression, compared to presenting data in tables. So it can make it easier for readers to understand the research results and can also increase the quality of the research. Although research has mentioned several limitations of this study, it is recommended to conduct a randomized control study and the use of more objective parameters in assessing clinical and histologic improvement in the treatment of SD.\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/13-208
|
https://f1000research.com/articles/13-206/v1
|
21 Mar 24
|
{
"type": "Software Tool Article",
"title": "Management information system, a strategic tool to enhance decision making in micro and small businesses",
"authors": [
"SILVIA JACQUELINE CRUZ MARTINEZ",
"EDDIE DAMIAN ASTO CASTRO",
"Alex Pacheco",
"SILVIA JACQUELINE CRUZ MARTINEZ"
],
"abstract": "Background Nowadays, companies face continuous changes, which force them to be more versatile by managing large volumes of data, which do not always become relevant information for decision making. Therefore, the objective of this research is to implement a management information system to improve administrative management in micro and small businesses.\n\nMethod it was developed under the approach of the agile methodology “SCRUM” following its 5 phases; In addition, the visual basic programming language in ASP.NET was used for the development of the source code and Microsoft SQL Server 2019 and its extensions: Ma-nagement Studio for data processing, “Integration Services” for the migration to the new dimensional model, Reporting Services for reports and Looker Studio for dashboards.\n\nResults The implementation of a management information system based on a dashboard allowed managers to obtain relevant information quickly and easily, optimizing decision-making times. In addition, the system allowed for homogeneous comparisons by level, which made it easier to identify deviations in commercial goals and the implementation of corrective actions such as adjustments in goals, changes in productivity, among others. Another result was the visualization of the monthly behavior of the financial system, which helped management structure short, medium and long-term strategies; in addition to the export of reports for “offline” analysis, which facilitates the work of employees in the field.\n\nConclusions This allows reducing the time invested in generating reports, improving the efficiency and precision of the analysis. In addition, it has facilitated the identification of opportunities for improvement in administrative and commercial management, specifically in average productivity and the weighted average rate per advisor.",
"keywords": [
"Web system",
"dashboard",
"SIG",
"Datamart",
"Looker Studio."
],
"content": "1. Introduction\n\nCurrently, companies face continuous changes, which force them to be versatile, to reinvent themselves and to manage large volumes of data that are not always relevant information for decision making; This is when micro and small companies in the financial sector find themselves at a point where the interpretation, analysis and application of information is essential to keep up with the competitive and globalized world.1 In this context, the technological tools that emerge every day help in everyday processes, allowing the integration, optimization and automation of processes to meet the objectives of organizations, generating significant changes and benefits.2 One of these tools is Management Information Systems, which in recent years have been the subject of much research to apply them in various fields, being considered a powerful option to create competitive advantages, increase organizational capacity in the face of change, reduce time in making decisions and obtaining accurate information.3\n\nIn previous times, micro and small companies in the microfinance sector managed their data on paper, an overwhelming situation for the documentary staff who had to generate reports, which is why companies found themselves in the need to systematize the processes.4 Management information systems provide advantages to obtain valuable, reliable, updated information, and can be applied in different functional areas of the organization.5 In addition, it allows improving information control, provides support for operational processes, and makes correct decisions in any area in which they operate.6\n\nIn this sense, this management information system is an interesting proposal to improve administrative management, since it consists of recording data more efficiently, minimizing errors, saving time on manual work, reducing costs, and resolving customer queries faster.3 In addition, GIS allows the generation of reports automatically with relevant information, informing in a summarized and graphical way the current situation of the organization, obtaining a decision source that allows implementing strategies to lead the market.7\n\nThe implementation of a management information system is an important tool in the business world, and it has a positive impact on information analysis and decision making.8 However, there is a sector that still does not use this tool due to lack of knowledge about how to develop them and how to take advantage of their benefits, either at the enterprise level or in the cloud.9 It is likely that research is needed to explore the impact of this tool on administrative management and decision-making at the level of micro and small businesses, focusing on rural and municipal savings banks.10\n\nThis research aims to explore and publicize the impact of implementing a management information system as a strategic tool to improve administrative management and enhance decision making in MYPES11; quickly and efficiently managing the large volume of information generated by companies, reducing time when providing relevant and reliable information to make decisions, leading to multiple analyzes and reports with the information obtained, even reducing costs in labor or paperwork.12 Therefore, the objective of this research is to implement a management information system to improve administrative management in a rural bank, such is the case of the savings and credit company “Los Andes SAC” based in Lima.\n\nThe contribution of this research when implementing a management information system is to improve administrative management, minimizing errors due to manual work, automating the registration of information, reducing time when generating reports and analyzing accurate information for decision making.13 In addition, it contributes to innovation since it plays a key role when introducing and promoting new technologies, allowing resources to be used efficiently.14\n\nIf we relate other research with the same topic that we are presenting, with the purpose of analyzing and comparing; We find the following study15 where it determines that the Jardín Azuayo Savings and Credit Cooperative lacks relevant information for making business decisions, which is why it proposes the development of a management information system based on the definition of key performance indicators, with the It makes up for the absence of information and helps generate knowledge. On the other hand, we have another investigation16 that seeks to solve the lack of truthful and quality information in the Portoviejo savings and credit cooperative, specifying that this is the indispensable basis in decision-making when granting loans, for This proposes the development of a web data management system that guarantees the integrity, accuracy and relevance of the information. Finally, in this research17 they seek to solve the lack of control in administrative management in the Savings and Credit Cooperative “Por el Pan y el Agua” through the implementation of a web application for the internal management of the cooperative, this application manages to control the administration, organization and availability of information efficiently and effectively.\n\n\n2. Methods\n\nIn this section, we detail the methods used in the development and operation of our software; which has been designed to enhance decision-making in micro and small businesses.\n\nBasic programming language in ASP was used .NET for source code development and Microsoft SQL Server 2019 and its extensions: Management Studio for data processing, Integration Services for migration to the new dimensional model, Reporting Services for reports and Looker Studio for dashboards.\n\nWe worked with the agile SCRUM methodology, following the 5 phases into which this methodology is divided.18\n\n2.2.1 Home\n\nIn this phase, the vision statement of the system was made, explaining the need of the company and the objective of the project. Also, the charter was drawn up, which contains a statement of the objectives and expected results. Additionally, the collaboration plan and roles were drafted, detailing the people participating in the research; The epics, the description of the users involved, the risks and completion criteria were written (Figure 1).\n\n2.2.2 Planning and estimation\n\nIn this phase, the user stories, lists of requirements (Product Backlog), the stacks of the 4 sprints were created where the requirements that the team will develop and the project planning were recorded (Figure 2).\n\nThis is the stage in which we translate the core of the business and transfer it to the system so that they respond according to the needs of the organization. If something is not well defined, we could be developing something that is not needed and that will not be used, which is why it is important going through several reviews, prototyping and requesting all conformities from the areas involved.\n\n2.2.3 Sprint implementation\n\nIn this phase, the initiation minutes for each phase, pending list and sprint planning, database design, dashboard design, prototype implementation and obtaining the final dashboard were developed.\n\nIn the case of the database, a star-type dimensional model has been chosen where gt_saldos represents the fact or Fact table (A) and the tables with initials “ge_” (B) represent the dimensions (Figure 3A).\n\nWe identify which is the main table “A” and highlight 3 of the main dimensions as an example “B”.\n\n2.2.4 Review and retrospective\n\nburndown chart was made for each sprint (Figure 4).\n\n2.2.5 Launch\n\nIn this phase, the deliverables and closing minutes of each phase were sent (Figure 5).\n\nThis computer tool has characteristics that differentiate it from existing solutions:\n\n• Focused on the microfinance system: our software is designed specifically for micro and small companies in the financial sector, adapting to specific requirements to improve decision making in administrative management, adapting to their workflows.\n\n• Tailored customization: users can easily customize the reports they really need to access, allowing queries, filters at the row and column level, showing detailed information to obtain reports adapted to the needs of companies, which makes it in a versatile solution.\n\nBy explaining the method and unique features, we provide a clear model for the development and implementation of our IT tool in microfinance institutions, promoting its replicability and usefulness.\n\n\n3. Use cases\n\nIn this section, we present the results of the learning outcome scores, the understanding aspect, and the user experience aspect.\n\nFigure 6 shows the main menu interface that was built in Looker Studio, which is a tool that turns your data into clear reports and dashboards.19 In this interface you can view the portfolio stock on the day of consultation and the variations in placements (credits) and deposits (savings). Additionally, a line graph is included that represents the trend of these indicators in the last twelve months. The general menu always remains visible showing the divisions that make up the company and in each division the relevant reports for each of them have been grouped; It is worth mentioning that this dashboard may vary in content and design according to the requirements of each division.\n\nThe important thing was not only to define the key indicators, but also to show their movement over time to help predict behavior patterns. The prototype shows the Dashboard embedded within the main GIS form, specifically in the “General Management” section.\n\n3.1.1 Input\n\n\n\n• Access to the “Dashboard” view\n\n3.1.2 Output\n\n\n\n• Static report “Management Summary”\n\nFigure 7 shows one of the most consulted reports of the daily portfolio, located within the Business Management division, in which we can see the details of the placements by region, and with the drill down, by office and by advisor; The drill down also works for the columns, in a first view we see the stock and if we activate the option (+) we can see the variations. The report allows queries of previous dates and filters by placement channel or sales force, maintaining the structure of the report after applying the filters. Additionally, the company’s Business Management division has other reporting options such as zero disbursements, amortizations, monthly evolution, productivity and harvests.\n\nThe image represents what the report should look like already integrated into the system.\n\n3.2.1 Input\n\n\n\n• Access the “Business Management” section\n\n• Select “Daily Portfolio”\n\n3.2.2 Output\n\n\n\n• Daily portfolio report with the main commercial indicators at the end of the day\n\nFigure 8 shows the structure of the monthly evolutionary report, which is within the Business Management division. In this report we are going to visualize the same commercial variables of the Daily Portfolio report, with the difference that is shown graphically and in an initial period of 6 months; The report allows you to change the start and end date to compare more months, in addition to filtering by region, office, advisor, channel, establishment or product.\n\n3.3.1 Input\n\n\n\n• Access the “Business Management” section\n\n• Select “Monthly Evolutionary”\n\n3.3.2 Output\n\n\n\n• Evolutionary report with the main commercial indicators according to the filters applied\n\nFigure 9 shows the options available to export information from both a graph and a report. Options are XML, CSV (comma delimited), PDF, MHTML (web file), Excel, TIFF File, and Word; The described options are enabled for all main menu options, plus this functionality keeps the grouping components in the target format.\n\n3.4.1 Input\n\n\n\n• Access the export section in any of the reports\n\n• Select “Excel”\n\n3.4.2 Output\n\n\n\n• Excel file with the information structured according to the last view of the report\n\n\n4. Discussion\n\nFigure 6 determines how we can optimize times by obtaining relevant information for the company without the need to perform specific searches, this is because the dashboards built in looker studio have the particular characteristic of obtaining information from the data and centralizing the indicators to know the situation at the beginning of the day. This agrees with what he indicates20 in his research, where he explains the importance of implementing a dashboard in companies to identify key indicators, risk factors and make strategic decisions in order to obtain optimal results that guarantee the competitiveness of the company. Which is reflected in the 78.1% reduction in time in analysis and generation of reports. It also agrees with7 where it is mentioned that dashboards are tools that allow you to view relevant information, have a clear perspective of the current situation of an organization, facilitating decision making. Finally, this also agrees with21 where it indicates that dashboards are a powerful tool for managing information, allowing you to know the current situation of companies and allowing reports to be more efficient, placing the institution in a better position compared to its competitors. generating competitive advantages.22\n\nIn Figure 7, through reporting services, the ability of the system to be able to make homogeneous comparisons by level is demonstrated, which makes it possible to determine deviations in regions, offices and/or advisors at the date of consultation and carry out corrective actions that help maximize results before the end of the month, information which was previously processed manually, taking longer to generate data and with a greater probability of error; This agrees with23 those who analyze how information technologies can be associated with production processes to improve labor productivity, becoming a transformative element. In the same way24 specify how administrative management processes are improved through the implementation of a web system, which contributed to the increase in sales and the reduction of time in the rental and reservation processes, streamlining the analysis of useful information for the decision making. Finally,25 they also make reference to the improvement of processes in their research by demonstrating that the non-use of information technologies limits the process of generating and disseminating information in SMEs and directly affects its quality.\n\nIn Figure 8, we determine how short, medium and long-term strategies can be structured with the help of an evolutionary report. This vision, accompanied by the seasonal behavior of the financial system, provides management with the ability to make effective decisions and to know in What time to launch aggressive or conservative campaigns to control results and achievement of objectives.26 This is supported by the study of Ref. 27 those who demonstrated the lack of management information systems that support decision-making in companies in the sector due to the lack of management indicators. Likewise, Ref. 25 in their research they analyze how SMEs can improve their competitiveness through improvements in decision-making by including information technologies in their internal processes. Finally, Ref. 28 their study shows how to define information quality criteria and the appropriate use of data in SMEs to clarify information management in decision-making to support business activities.\n\nIn Figure 9, the versatility of the system is determined to avoid dependence on connectivity to analyze the indicators, exporting any of the reports according to the need of the moment, we can access this information offline from any device and have the staff Dedicate yourself to the core of the business in the field without having to invest time in operational tasks in the office. As demonstrated in the study Ref. 27 where they show the need to carry out their research to develop a comprehensive proposal for linking GIS and management of indicators that supports decision making in a rural area of Ecuador. This also agrees with the statement made23 when specifying that emerging companies suffer from problems of access and generation of information since, due to their structure, they treat information in a basic way. Finally, Ref. 28 they analyze how small and medium-sized companies often do not give due importance to data analysis and the negative impact that this practice has on the development of their activities.\n\n\n5. Conclusions\n\nIt is concluded that the implementation of a management information system to improve administrative management turned out to be a beneficial contribution in the treatment and analysis of information globally, which allowed the time dedicated to generating reports to be reduced by 21.2% in addition to reducing the error rate in manual records by 100%. This time savings provided the opportunity to improve business indicators through reports for decision making.\n\nThe first improvement is associated with the reduction of time invested in generating reports, which allowed more space for adequate analysis of the information, in addition to reducing the high probability of error due to manual data recording; it also allowed the self-generation of reports and visualization on a dashboard that allows identifying opportunities for improvement in administrative and commercial management in a more efficient and orderly way, making each member of the organization focus on their area.\n\nFinally, the system has an additional advantage and that is that it handles the information securely, only controlling access to members of the organization and in accordance with the permissions that have been assigned to each user, ensuring that sensitive information is not filter through other channels.\n\nThe preparation and continuous training of the organization’s personnel is recommended for the correct use of the Management Information system. It is suggested to prepare an improvement plan to strengthen the system, or a maintenance plan in case an update to the reports is necessary. In addition, it is suggested to prepare a contingency plan for possible errors during the execution of the system.",
"appendix": "Data availability\n\nZenodo: DataDashboard, https://doi.org/10.5281/zenodo.10614354. 29\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 Caja Los Andes for its strong support with this study and engineer Alex Pacheco from the Faculty of Engineering and Architecture of the Cesar Vallejo University for his methodological advice in this research.\n\n\nReferences\n\nSutherland J: More Praise for Scrum: The Art of Doing Twice the Work in Half the Time.2014; vol. 3.\n\nFernández Torres A, Gonzáles Valero M, Esparza Cruz N, et al.: Estructura de los procesos de software en los sistemas de información gerencial que se aplica en la parte agrícola. J. Sci. Res. Dec. 2020; 5(CININGEC): 800–807. Publisher Full Text\n\nAlvarado R, Acosta K, Mata de Buonaffina YV, et al.: Necesidad de los sistemas de información gerencial para la toma de decisiones en las organizaciones. InterSedes. Jul. 2018; 19(39): 17–31. Publisher Full Text\n\nSociedad UY, Katiuska G, Guzmán V: Sistema de información gerencial para el control de costos de empresas agroindustriales del Cantón Daule. Revista Universidad y Sociedad. 2021; 13(5): 605–614. Accessed: Oct. 05, 2023.\n\nVargas Encalada EE, Rengifo Lozano RA, Guizado Oscco F, et al.: Sistemas de información como herramienta para reorganizar procesos de manufactura. Revista Venezolana de Gerencia. 2019. Accessed: Oct. 11, 2023.\n\nBravo Cobeña CM, Valdivieso Guerra P, Arregui Pozo R: Los sistemas de información en la toma de decisiones gerenciales en las empresas comerciales de Portoviejo. ECA Sinergia. 2018; vol. 9(2): pp. 45–54. ISSN 1390-6623, ISSN-e 2528-7869, Vol. 9, No. 2 (Julio - Diciembre), 2018, págs. 45-54. Accessed: Oct. 11, 2023.\n\nAngel F, Lois B, Del Río CA, et al.: Lecciones aprendidas de la implementación de un Sistema de Información Gerencial diseñado en la Universidad de Otavalo, Ecuador. E-Ciencias de la Información. Jan. 2021; 11(1): 90–92. Publisher Full Text\n\nLitvaj I, Stancekova D: Knowledge Management Embedment in Company, Knowledge Repositories, Knowledge Management Significance and Usage in Company. Procedia Economics and Finance. 2015; 23: 833–838. Publisher Full Text\n\nMacías Arteaga MF, Mero Velez JM: Importancia de Planeación Estratégica en Empresas en el Siglo XXI.2022. Publisher Full Text\n\nBegazo Villanueva JD: La toma de decisiones y la gestión por objetivos en la empresa peruana. Gestión en el Tercer Milenio. Dec. 2014; 17(34): 21–27. Publisher Full Text\n\nHuacchillo LA, Ramos Farroñan EV, Pulache Lozada JL: La gestión financiera y su incidencia en la toma de decisiones financieras. Revista Universidad y Sociedad. 2020; 12(2): 356–362. Accessed: Sep. 08, 2023.\n\nPuello P, Cabarcas A, Martelo RJ: SISTEMA DE INFORMACIÓN GERENCIAL PARA LA ADMINISTRACIÓN DE RECURSOS EDUCATIVOS. Formación Universitaria. 2013; 6(5): 13–20. Publisher Full Text\n\nReason J: Human error: models and management. BMJ. Mar. 2000; 320(7237): 768–770. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArregocés I, De La Costa U, Díaz Hernández J, et al.: Integración de Scrum y RUP para el desarrollo de software de planes turísticos basado en preferencias de usuario. Ingeniería e Innovación. Jul. 2022; 10(1). Publisher Full Text\n\nGómez Espinoza HO: Metodología para la implementación de un sistema de información gerencial para el gestor transaccional inclusivo de la Cooperativa de Ahorro y Crédito Jardín Azuayo. Polo del Conocimiento: Revista científico - profesional. 2022; 7(4): 56. ISSN-e 2550-682X, Vol. 7, No. 4 (ABRIL 2022), 2022. Publisher Full Text\n\nDelvalle Morán FJ: Análisis del Sistema de Información en la toma de decisiones del sector crediticio de cooperativas de ahorro y crédito de la ciudad de Portoviejo. DSpace Repository. 2020. Accessed: Oct. 11, 2023.\n\nBaque García YM: Implementación de un aplicativo web para la gestión interna de la cooperativa de ahorro y crédito ‘por el pan y el agua,’.Jan. 2023. Accessed: Oct. 11, 2023.\n\nTimkyw N, Bournissen JM, Tumino MC: Scrum como Herramienta Metodológica para el Aprendizaje de la Programación. Revista Iberoamericana de Tecnología en Educación y Educación en Tecnología. Oct. 2020; (26): e9. Publisher Full Text\n\nMoraes GG: Google looker studio: a experiência de implementação em uma empresa de compliance.2023. Accessed: Oct. 13, 2023.\n\nCalle Paz II, Valles Coral MA: Dashboard digital para el monitoreo de indicadores y metas de los proyectos de consultores San Martín E.I.R.L. Revista Científica de Sistemas e Informática. Jan. 2021; 1(1): 24–36. Publisher Full Text\n\nGonzález J, Salazar F, Ortiz R, et al.: Gerencia estratégica: herramienta para la toma de decisiones en las organizaciones. Telos: Revista de Estudios Interdisciplinarios en Ciencias Sociales. Jan. 2019; 21(1): 242–267. Publisher Full Text\n\nSizwe N: Integration of the Management Information System for Competitive Positioning. Procedia Manuf. Jan. 2020; 43: 375–382. Publisher Full Text\n\nDíaz Rodríguez HE: Tecnologías de la información y comunicación y crecimiento económico. Eco. Inform. Jul. 2017; 405: 30–45. Publisher Full Text\n\nFrancia K, Lopez R: Desarrollo de un sistema web para la mejora en la gestión administrativa del hospedaje Mis Recuerdos de la ciudad de Chiclayo en el año 2019.2022. Accessed: May 25, 2023.\n\nRendón Fernández RJ, Cañizares Galarza PF, Romero Fernández A: Los sistemas de información gerencial en pequeñas y medianas empresas del sector turístico de la provincia los Ríos, Ecuador. Revista UNIANDES Episteme. 2019; 6(3): 369–382. ISSN-e 1390-9150, Vol. 6, No. 3, 2019 (Ejemplar dedicado a: julio - septiembre (01/07/2019)), págs. 369-382. Accessed: Oct. 05, 2023.\n\nAguilar C: Calidad de gestión administrativa financiera en las municipalidades, 2020. Ciencia Latina Revista Científica Multidisciplinar. Nov. 2020; 4(2): 613–634. Publisher Full Text\n\nQuispe Otacomal AL, Padilla Martínez MP, Telot González JA, et al.: Sistema de información gerencial para las cajas solidarias de Ecuador.2018. Accessed: Oct. 05, 2023.\n\nVillacís Yank JA, Moreno Mejía MA: Caracterización de la gestión de la información contable en las Pymes comerciales de Ambato – Ecuador. Cuadernos de Contabilidad. Aug. 2021; 22: 1–13. Publisher Full Text\n\nAsto, Cruz: DataDashboard. [Data set]. Zenodo. 2024. Publisher Full Text\n\nAsto, Cruz: Código Fuente. Zenodo. [Software]. 2024. Publisher Full Text"
}
|
[
{
"id": "290837",
"date": "15 Jul 2024",
"name": "Asefeh Asemi",
"expertise": [
"Reviewer Expertise Business informatics"
],
"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 authored by Martinez, Castro and Pacheco discusses a Management Information System (MIS) designed specifically for micro enterprises, in the industry. It addresses the issue of handling datasets to assist in decision making processes. Constructed using the SCRUM approach this system integrates Visual Basic in ASP.NET, Microsoft SQL Server 2019 and Looker Studio to offer dashboards. Its main objective is to streamline tasks by automating report generation reducing errors and providing real time information that is pertinent. The systems tailored. Offline accessibility benefit field personnel by cutting down time spent on generating reports and enhancing data analysis accuracy. The authors describe the development journey from planning to implementation and evaluation to ensure that the tool can be replicated successfully. They also showcase the systems impact through case studies which reveal a 78.1% decrease in time taken for analysis and report generation. While the article presents a rationale along with technical details and methodology making it scientifically valid the conclusions drawn are supported by the study results. Including information on long term performance outcomes and its applicability, across sectors could further enrich this research.\n\nSuggestions, for Improvement Strengthen the Explanation; Provide a comparison with existing solutions emphasizing gaps that the proposed Management Information System (MIS) addresses. Detailed Technical Specifications; Incorporate information, rationale for technology selections and potential challenges encountered during development. Replication Guidelines; Integrate code snippets, pseudocode or a repository link to assist researchers in replicating the work. Interpretation of Results; Elaborate on the Key Performance Indicators (KPIs) utilized in the dashboards and reports explaining their significance, in decision making processes. Quantitative Analysis; Present findings and user feedback to validate the tools efficacy and influence.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\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? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
},
{
"id": "334736",
"date": "06 Nov 2024",
"name": "Marian Stoica",
"expertise": [
"Reviewer Expertise Management information systems",
"computer programming",
"emerging technologies of the information society"
],
"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\nAt the first reading of the article, it proposes a decision-making process automation solution for small and medium-sized businesses. However, during the course of the material, no novel aspects are highlighted in relation to products and software tools of the same type, already existing on the IT market (see ERP type applications). A hybrid methodological approach is emphasized, which calls on the agile SCRUM methodology in connection with established software tools for the development of software applications (.NET, SQL Server). Not enough detail is provided on the methodological approach and the business analysis component so that the solution can be extended or replicated by other entities. The generally valid aspects of the SCRUM methodology are highlighted, and these in a minimalist manner. Regarding the results provided by the proposed software product, aspects regarding internal software features such as assistability, maintainability, testability or portability are not mentioned. Conclusions on the proposed software tool do not cover basic aspects such as reliability and capability. The justification and development of all the aspects mentioned above can give the proposed article a much higher practical level. I also recommend that authors include at least one tester in the development team to validate viable and credible testing strategies. At the same time, I recommend the approach and inclusion in the development of the proposed product of the scalability feature.\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? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-206
|
https://f1000research.com/articles/13-205/v1
|
21 Mar 24
|
{
"type": "Research Article",
"title": "Do hospitalizations push households into poverty in India: evidence from national data",
"authors": [
"Shyamkumar Sriram",
"Muayad Albadrani",
"Muayad Albadrani"
],
"abstract": "Introduction High percentage of OOP (Out-of-Pocket) costs can lead to poverty and exacerbate existing poverty, with 21.9% of India’s 1.324 billion people living below the poverty line. Factors such as increased patient cost-sharing, high-deductible health plans, and expensive medications contribute to high OOP costs. Understanding the poverty-inducing impact of healthcare payments is essential for formulating effective measures to alleviate it.\n\nMethods The study used data from the 75th round of the National Sample Survey Organization (Household Social Consumption in India: Health) from July 2017-June 2018, focusing on demographic-socio-economic characteristics, morbidity status, healthcare utilization, and expenditure. The analysis included 66,237 hospitalized individuals in the last 365 days. Logistic regression model was used to examine the impact of OOP expenditures on impoverishment.\n\nResults Logistic regression analysis shows that there is 0.2868 lower odds of experiencing poverty due to OOP expenditures in households where there is the presence of at least one child aged 5 years and less present in the household compared to households who do not have any children. There is 0.601 higher odds of experiencing poverty due to OOP expenditures in urban areas compared to households in rural areas. With an increasing duration of stay in the hospital, there is a higher odds of experiencing poverty due to OOP health expenditures. There is 1.9013 higher odds of experiencing poverty due to OOP expenditures if at least one member in the household used private healthcare facility compared to households who never used private healthcare facilities.\n\nConclusion In order to transfer demand from private to public hospitals and reduce OOPHE, policymakers should restructure the current inefficient public hospitals. More crucially, there needs to be significant investment in rural areas, where more than 70% of the poorest people reside and who are more vulnerable to OOP expenditures because they lack coping skills.",
"keywords": [
"Poverty",
"Out-of-Pocket Health Expenditures",
"India",
"Healthcare"
],
"content": "Introduction\n\nThe protection of households from financial risks that are associated with medical expenses is one of the key objectives of health systems.1 India is actively taking steps to offer its population universal health coverage (UHC). As the core of UHC, financial protection is regarded as essential. India is ranked third in the Southeast Asian region in terms of “countries with highest OOP expenditure on health,” according to the World Health Organization. OOP costs are people’s direct payments to healthcare providers at the time-of-service usage, according to the World Health Organization (WHO).2 OOPs are defined as completely private transactions (payments made by patients to private physicians and pharmacies), official patient cost-sharing (user fees/copayments) within predetermined public or private benefit packages, and informal payments (payments made in excess of the prescriptions covered by benefits, both in cash and in kind). OOPs can therefore occur through market transactions, as an explicit part of a policy, or both. OOP health spending may rise whenever families choose to utilize and receive healthcare services, but they are not shielded from high expenses since healthcare is expensive.3\n\nOOP costs make up around 62.6% of all health spending in India, which is one of the highest percentages in the world.4 In India, OOP health costs account for a sizeable amount of total household spending, which inadvertently drives down spending on other essential items and lowers household wellbeing overall. In contrast to the “health for all” idea that was more prevalent in the previous decade, the present policy discussion is about “health for all with financial protection”.5 The National Health Policy 2017 of India places a high priority on affordability and the reduction of financial risk.6 In order to improve fair financing, it is not thought that OOP healthcare payments are a good way to pay for medical services. OOP payments are not a cost-effective way to pay for healthcare, and they may have a negative impact on equity and push vulnerable people into poverty.7 High OOP medical costs can deplete savings and ruin credits, negatively affect medication adherence, quality of life, and other health outcomes.8 OOP payments that are relatively significant have the potential to put vulnerable households into poverty and exacerbate the poverty of households who are already poor.\n\nAccording to the 2011 World Bank Poverty Line of USD 1.90, around 21.9% of India’s 1.324 billion people live below the poverty line.9 High OOP health costs have an impact on household finances and cause many to fall into poverty, according to the evidence.10 According to a research conducted in India, OOP healthcare payments caused 2.2% of the population to live below the poverty level.11 OOP health costs in India cause the impoverishment of up to 39 million people each year.12,13 The incidence and depth of poverty can indeed be increased by OOP health expenses, according to the data. Furthermore, poverty has a detrimental effect on one’s health.14 The most significant methods used by households to cover costs include selling assets and borrowing money. OOP healthcare payments worsen both the occurrence and degree of poverty.15 In India, majority of health insurance plans solely cover only hospitalization costs.16\n\nAn expected situation in a country with a good health financial protection system is that no one should be forced into poverty as a result of incurring medical costs because of healthcare utilization.17,18 While some households may spend a higher percentage of their income on healthcare, others may spend a much smaller percentage of their income on healthcare and still be considered to be pushed below the poverty line. According to a recent World Bank Group analysis, OOP payments made up a sizeable portion of all healthcare costs in Central and Eastern European nations. Additionally, patients in poor nations pay out-of-pocket for healthcare treatments at a rate of half a trillion dollars annually (about $80 per person).19 Unfortunately, the poor suffered greatly as a result of these costs.\n\nIt becomes more challenging for the Poor People’s Health Insurance Program to offer coverage to households that enter poverty if more people are made poorer by OOP expenses. Even those households who are not particularly near to the poverty threshold may become impoverished as a result of OOP expenses. It becomes challenging for the insurance programs for the poor to remain adaptable enough to permit frequent entry and exit without involving significant administrative expenditures due to the dynamic character of poverty. Additionally, understanding how OOP health spending affects poverty is essential for formulating effective measures to alleviate it. The impact of OOP health expenditures on poverty and the numerous factors that influence the occurrence of poverty are the primary research questions this study would focus on. These are the specific inquiries: (i) What steps may be taken to prevent poverty from spreading? And (ii) what are the variables influencing the incidence of household poverty brought on by OOP medical expenses in India? Using the most recent Social Consumption and Health Survey from the National Sample Survey Organization (NSSO), this study makes an effort to determine how OOP payments affect poverty in India.20 Implementing strong policies can shield households from the frequent and high costs of the healthcare system due to a lack of resources. This analysis is valuable for formulating policies and programs to fight poverty in India, specifically to develop methods for reducing financial risk.\n\n\nMethods\n\nThe study employed national representative unit-level cross-sectional data from the 75th round of the National Sample Survey Organization (Household Social Consumption in India: Health). The survey was conducted under the stewardship of the Ministry of Statistics and Programme Implementation, Government of India during the time period of July 2017-June 2018. The survey schedule collects the information pertaining to the demographic-socio-economic characteristics, morbidity status, utilization of healthcare services and healthcare expenditure across ambulatory, inpatient, delivery and immunization care for households and individuals. A two-stage stratified random sampling design was adopted in the survey with census villages and urban blocks as the First Stage Units for rural and urban areas respectively and households as the Second Stage Units. Overall sample size consisted of the 1,13,823 households and 5,57,887 individuals (including the death cases). The analysis however, circumscribed 66,237 individuals who were hospitalized in the last 365 days of the survey (without childbirth episodes). The detailed information on the survey design can be found in the official report released by the National Sample Survey Organization.\n\nTo study the effects of various factors on the occurrence of impoverishment due to OOP health expenditures, the logistic regression model will be used. The logistic regression model is preferred since the dependent variable is dichotomous. “Whether a household falls below poverty line after making OOP healthcare payments?” will be used as the dependent variable. A dichotomous variable for impoverishment will be created with 0 for not falling below poverty line after making OOP healthcare payments and 1 for falling below poverty line after making OOP healthcare payments. Thus, the dichotomous variable created for incidence of impoverishment in the household will serve as the dependent variable for the logistic regression model. The independent variables include the various characteristics of the households.\n\n\nResults\n\nDescriptive statistics of the sample are shown in Table 1 which shows that 47.34% of households reported presence of at least one child (aged 5 years and less) in the household. 30.54% of households reported presence of at least one elderly person (aged 60 years and above) in the household. 41.85% of households reported presence of at least one secondary educated member in the households. 55.54% of households were located in the rural areas and 44.46% of households were located in in urban areas. Majority, 20.54% of households reported socioeconomic status of household as lowest income quartile and 19.64% of households reported socioeconomic status of household as highest income quartile. 44.09% of households were small (1-4 members). 47.01% of households were medium (5-8 members) and 8.90% of households were large (9 and more). 37.02% of households reported that at least one member in the household used a private healthcare facility for hospitalization.\n\nTable 2 shows the incidence of poverty. 15.95% of total households reported poverty which increased to 18.89% after making OOP payments. In rural areas, the incidence of poverty was 18.90% which increased to 21.90 after making OOP payments. In urban areas, the incidence of poverty was 9.30% which increased to 11.30 after making OOP payments. The incidence of poverty in lowest income quartile was 66.98% which increased to 71.03% after making OOP payments. The incidence of poverty was 17.34% for less than 5 days duration of stay in hospital which increased to 18.89% after making OOP payments, while the incidence of poverty was 13.23% for more than 20 days duration of stay in hospital which increased to 32.73% after making OOP payments. The incidence of poverty was 11.23% for at least one member in the household used private healthcare facility which increased to 26.23% after making OOP payments while the incidence of poverty was 18.02% when no member in the household used private healthcare facility which increased to 19.02% after making OOP payments. The incidence of poverty was 24.23% when at least one child aged 5 years and less in the household which increased to 28.01% after making OOP payments. The incidence of poverty was 17.65% where at least one elderly person aged 60 years and above in the household which increased to 20.93% after making OOP payments.\n\nTable 3 shows the intensity of poverty due to OOP health expenditures. The poverty gap increased from 19.45% to 23.01% after making OOP payments. In rural areas, the intensity of poverty before making OOP payments was 19.01% which increased to 21.01% after making OOP payments while in the urban areas, the intensity of poverty before making OOP payments was 20.01% which increased to 21.01% after making OOP payments. The intensity of poverty before making OOP payments in lowest income quartile was 21.01% which increased to 23.01% after making OOP payments while in the highest fifth income quartile it increased from 0% to 41.01% after making OOP payments. The intensity of poverty before making OOP payments was 19.34% for less than 5 days duration of stay in hospital which increased to 22.34% after making OOP payments and the intensity of poverty before making OOP payments was 22.13% for more than 20 days duration of stay in hospital which increased to 42.01% after making OOP payments. The intensity of poverty before making OOP payments was 19.43% if at least one member in the household used private healthcare facility which increased to 33.67% after making OOP payments.\n\nTable 4 shows the logistic regression analysis results for the incidence of poverty due to OOP health expenditures. Logistic regression analysis shows that there is 0.2868 lower odds of experiencing poverty due to OOP expenditures in households where there is the presence of at least one child aged 5 years and less present in the household compared to households who do not have any children. There is 0.601 higher odds of experiencing poverty due to OOP expenditures in households in urban areas compared to households in rural areas. There is a decrease in the odds of experiencing poverty due to OOP expenditures in households with an increase in household income. Both medium and larger households have lower odds of incurring poverty due to OOP health expenditures compared to smaller households. With an increasing duration of stay in the hospital, there is a higher odds of experiencing poverty due to OOP health expenditures with an odds of 1.4013 of experiencing poverty due to OOP expenditures for a 5-10 duration of stay in hospital compared to other stay durations compared to 13.9702 higher odds of experiencing poverty due to OOP expenditures for more than 20 days duration of stay in hospital. There is 1.9013 higher odds of experiencing poverty due to OOP expenditures if at least one member in the household used private healthcare facility compared to households who never used private healthcare facilities for treatment. There is 4.6781 higher odds of experiencing poverty due to OOP expenditures if the household has members who suffer from chronic illnesses.\n\nAlso, most importantly, there is a 0.2765 lower odds of experiencing poverty due to OOP expenditures if at least one member is covered by health insurance, highlighting the importance of health insurance coverage in protecting households from impoverishment due to OOP health expenditures.\n\n\nDiscussion\n\nOur studies indicate that the population’s overall poverty rate was 18.89% after OOP payments, and that the normalized poverty difference among households that were already poor due to OOP medical expenses widened by 3.06%. Our findings fall short of World Bank estimates, according to which 21.9% of the population lived below the poverty line, calculated using the updated World Bank Poverty Line.21 Another research that used NSS data for the years 1995–1996 indicated that 2.2% of the population was living in poverty as a result of OOP health expenses.22 The results we have obtained indicate that after making OOP payments, the prevalence of poverty has increased among households belonging to various SES levels. According to the results of the logistic model, all households in all other quintiles of expenditure have lower probability of being poor than the poorest families. The likelihood of being financially poor as a result of OOP health expenses decreased steadily as the socioeconomic status of the households rose, with the richest households having the lowest probabilities. This result is in line with other research that has been published in the literature.23,24\n\nOur study showed that the presence of at least one child aged 5 years and less present in the household increases the incidence of poverty after making OOP payments. Studies carried out in Ethiopia also demonstrated that presence of at least one child aged 5 years and less present in the household increases the incidence of poverty after making OOP payments.25 Our study showed that households in urban areas experienced increased incidence of poverty after making OOP payments compared to rural areas. Research carried out in low-income countries like Uganda, Malawi and Nigeria showed that households in urban areas experienced increased the incidence of poverty after making OOP payments compared to rural areas.26 Similar studies in Ethiopia found that households in urban areas experienced increased the incidence of poverty after making OOP payments compared to rural areas.27 Our studies show that households in lowest income quartiles experienced increased incidence of poverty after making OOP payments compared to higher income quartiles. Research on this issue demonstrated that households in lowest income quartiles experienced increased incidence of poverty after making OOP payments compared to higher income quartiles.28 Another study in Kenya found that households in lowest income quartiles experienced increased incidence of poverty after making OOP payments compared to higher income quartiles.29 Similar study carried out in Uganda showed that low-income households experienced increased incidence of poverty after making OOP payments compared to their higher income counterparts.30\n\nOur study showed that medium and large sized households experienced increased the incidence of poverty after making OOP payments compared to small sized households. Findings from a study done in Turkey found that household size played an important role in increased incidence of poverty after making OOP payments.31 A study in India found that medium and large sized households experienced increased the incidence of poverty after making OOP payments compared to small sized households.32 Similar study in India found that medium and large sized households experienced increased the incidence of poverty after making OOP payments.33 Our study shows that with increased duration of stay in hospital increases the incidence of poverty after making OOP payments. Other research carried out in India showed that with increased duration of stay in hospital increases the incidence of poverty after making OOP payments.34 Another study in India found that with increased duration of stay in hospital increases the incidence of poverty after making OOP payments.35 Similar study in Bangladesh found that duration of hospital stay has profound impact on increasing the incidence of poverty after making OOP payments.36 Our study showed that the presence of at least one member in the household who used private healthcare facilities increases the incidence of poverty after making OOP payments. A study carried out in Kenya showed that using private healthcare facility increases the incidence of poverty after making OOP payments.29 Another study carried out in Tajikistan found that using private healthcare facility increases the incidence of poverty after making OOP payments.37 Similar study in Turkey found that using private healthcare facility increases the incidence of poverty after making OOP payments.38\n\nOur studies show that the proportion of members with chronic illness in each household increases the incidence of poverty after making OOP payments. A study carried out in India demonstrated that number of members with chronic illness in each household increases the incidence of poverty after making OOP payments.39 Another study in Nepal found that a greater number of members with chronic illness in each household increases the incidence of poverty after making OOP payments.40 Further research on this issue in low middle income countries found that family members with chronic illness increases the incidence of poverty after making OOP payments.41 Our study showed that presence of at least one member is covered by insurance increases the incidence of poverty after making OOP payments compared to members not covered by insurance.\n\nIt comes to light that long-term illness plays a significant role in predicting poverty brought on by OOP payments. According to studies, hospitalizations are also significantly influenced by chronic conditions.42 In our analysis, the odds of poverty were more than twice as high for households with at least one member suffering from a chronic illness than they were for homes without such a member. Further studies conducted on this issue came to the same conclusion that chronic diseases are key factors driving households into poverty; the location of hospitalization, whether in a public or private institution, has an impact on health expenses.43,44 Around 49% of all available beds are in the private sector, which is home to a sizable network of unregulated private hospitals in India.45 Our research demonstrated that a person’s hospitalization location also affects whether or not OOP payments will cause them to become impoverished.\n\nA study in Turkey found that presence of at least one member is covered by insurance increases the incidence of poverty after making OOP payments compared to members not covered by insurance.38 Another study in Ghana found that members with insurance experienced increased the incidence of poverty after making OOP payments compared to members not covered by insurance.46 Similar study in Nigeria found that hat members with insurance experienced increased the incidence of poverty after making OOP payments compared to members not covered by insurance.47\n\nOur research demonstrates that, both in urban and rural areas, the prevalence of poverty has increased as a result of OOP payments. The proportion of persons who become poor after completing OOP payments has grown in urban regions relative to rural ones, although only slightly. This is because only poor people are taken into account. This demonstrates how OOP health expenses are higher for urban residents, which forces them into poverty. The results of the logistic regression also indicate that households in urban regions are more likely than those in rural areas to become impoverished as a result of OOP health expenses. According to evidence from the literature, the number of urban poor people is constantly growing as a result of poor people moving from rural areas to cities in pursuit of economic possibilities. The majority of these migrants settle in crowded city slums with subpar living circumstances.48 According to the most recent census, 33% of Indians reside in urban settings, and 250 million more will do so by the year 2030. In this group, 27% of urban residents are below the poverty line.49\n\nOur estimations may have been skewed by the increased migration from rural to urban regions in quest of employment. Although there is a benefit to living in an urban area in terms of access to health care, most urban poor people do not have access to this benefit.50 The National Rural Health Mission was established by the GOI in 2005 to address the health needs of the rural population. The National Urban Health Mission was not established by the government until 2014 to assist the urban poor, strengthen the health infrastructure in urban areas, and lower OOP health expenditures.51 The absence of political will to address the health needs of the urban poor is demonstrated by the delay in developing the urban health program for the underprivileged. The National Urban Health Mission and other programs meant to mitigate the OOP burden of the urban population are not performing successfully, as seen by the higher likelihood of poverty among the urban population. Additionally, the majority of urban poor people who depend on daily income are unable to be admitted to hospitals, which may hinder their ability to go to work. However, none of the current health insurance plans available give coverage for outpatient care; the present health insurance programs for the poor only cover hospitalization. Due to the present health insurance programs for the poor’s lack of coverage for outpatient care and their desire to avoid losing their jobs, they may be forced to pay OOP, which will raise their costs. Additionally, compared to households with fewer individuals, larger households are less likely to become impoverished as a result of OOP health expenses. Larger families may be able to arrange for a member of the family to serve as a caretaker in the event of illness or incapacity, which is one of the most likely causes. Furthermore, many common ailments may not require hospitalization because of this family caregiving. Evidence from the United States demonstrates that home health care services have cut down on hospital visits and length of stays.52\n\nIn India, 400 million people live on less than $1.25 per person per day, and according to our data, these poor people spend 11–15% of their total income on OOPHE on average.53 OOPHE accounts for a substantial percentage of total spending, hence governments should offer health insurance to the poor to lessen their susceptibility to both health and economic shocks. The use of private clinics for medical treatment is the second factor contributing to the high OOPHE.54 In India, private facilities account for more than 75 percent of health expenditures. Because of their superior health infrastructure and higher level of service, private institutions are preferred over public ones. In order to transfer demand from private to public hospitals and reduce OOPHE, policymakers should restructure the current inefficient public hospitals. More crucially, there needs to be significant investment in rural areas, where more than 70% of the poorest people reside and who are more vulnerable to CHE because they lack coping skills.",
"appendix": "Data availability\n\nThe data from the National Sample Survey Organization (NSSO) of the Government of India was used for the study. Social Consumption (Health), NSS 75th Round for 2017-2018 was used for this analysis. The survey covered whole of the Indian Union. Data can be obtained from the Government of India or from the corresponding author by reasonable request.\n\n\nReferences\n\nRahman T, Gasbarro D, Alam K: Financial risk protection from out-of-pocket health spending in low- and middle-income countries: a scoping review of the literature. Health Res. Policy Syst. 2022; 20(1): 83. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGlossary|DataBank: 2024. Reference Source\n\nJalali FS, Bikineh P, Delavari S: Strategies for reducing out of pocket payments in the health system: a scoping review. Cost. Eff. Resour. Alloc. 2021; 19(1): 47. 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Res. 2016; 16(1): 77. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKumar K, Singh A, Kumar S, et al.: Socio-Economic Differentials in Impoverishment Effects of Out-of-Pocket Health Expenditure in China and India: Evidence from WHO SAGE. PLoS One. 2015; 10(8): e0135051. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJayathilaka R, Joachim S, Mallikarachchi V, et al.: Do chronic illnesses and poverty go hand in hand? PLoS One. 2020; 15(10): e0241232. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIndia: International Health Care System Profiles|Commonwealth Fund.2024. Reference Source\n\nAkazili J, Ataguba JE, Kanmiki EW, et al.: Assessing the impoverishment effects of out-of-pocket healthcare payments prior to the uptake of the national health insurance scheme in Ghana. BMC Int. Health Hum. Rights 2017; 17(1): 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAregbeshola BS, Khan SM: Out-of-Pocket payments, catastrophic health expenditure and poverty among households in Nigeria 2010. Int. J. Health Policy Manag. 2018; 7(9): 798–806. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKuddus A, Tynan E, McBryde ES: Urbanization: a problem for the rich and the poor? Public Health Rev. 2020; 41(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPathak D, Vasishtha G, Mohanty SK: Association of multidimensional poverty and tuberculosis in India. BMC Public Health. 2021; 21(1): 2065. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSclar ED, Volavka-Close N: Urban Health: An Overview. Elsevier eBooks; 2011; 556–564. Publisher Full Text\n\nRaichowdhury S, Khetrapal S, Chin B: Core interventions contributing to the effectiveness of the National Urban Health Mission in India. J. Glob. Health 2023; 13. Publisher Full Text\n\nArsenault-Lapierre G, Henein M, Gaid D, et al.: Hospital-at-Home Interventions vs In-Hospital Stay for Patients With Chronic Disease Who Present to the Emergency Department. JAMA Netw. Open. 2021; 4(6): e2111568. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Bank Group: Report finds 400 million children living in extreme poverty. World Bank; 2013. Reference Source\n\nFactors that affect Health-Care utilization: National Library of Medicine.2018. Reference Source"
}
|
[
{
"id": "261054",
"date": "05 Apr 2024",
"name": "Seetharaman Narayanan",
"expertise": [
"Reviewer Expertise Public Health",
"Health Economics"
],
"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\nAssessment: 1. Presentation and Literature Review: The article is well-structured and clearly presented. It provides a comprehensive review of relevant literature, highlighting the importance of the research problem and situating the study within the existing body of knowledge.\n2. Study Design and Academic Merit: The study design is appropriate for addressing the research questions. The use of nationally representative survey data from the NSSO enhances the generalizability and academic merit of the findings.\n3. Methods and Repeatability: The methods section provides sufficient details on the data source, variables, and analytical techniques (logistic regression) to allow for replication by others. A short discussion on the suitability of the World bank definition of poverty line (over any other definition of poverty line) would be helpful.\n4. Statistical Analysis: The statistical analysis appears appropriate, with logistic regression models employed to examine the factors influencing the incidence of poverty due to OOPHE. The interpretation of the results is generally sound.\n5. Data Availability: The authors mention that the data can be obtained from the Government of India or by reasonable request. It would be preferable to provide more specific information on data accessibility to enhance transparency and reproducibility.\n6. Conclusions and Support: The conclusions drawn are generally supported by the results presented. The authors highlight the crucial role of health insurance coverage in protecting households from impoverishment due to OOPHE and the need for policy interventions to improve access to public healthcare facilities, particularly in rural areas.\nStrengths: - Nationally representative data enhances generalizability. - Comprehensive literature review and sound methodology. - Highlights the role of health insurance and public healthcare access in alleviating poverty due to OOPHE.\nSuggestions: - Clarify the applicability of the World Bank defined poverty line (vis-a-vis any other methodology to define the poverty line currently in use, in India) in the analysis. - Provide more specific information on accessing the source data data from NNSO, to enhance reproducibility. - Discuss potential limitations and directions for future research. - Expand on the policy implications and recommendations for addressing the identified issues.\nOverall, the article makes a valuable contribution to understanding the impoverishing effects of OOPHE in India and identifying factors that influence household poverty.\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": "261053",
"date": "10 Apr 2024",
"name": "Sumedh Bele",
"expertise": [
"Reviewer Expertise public health and health services research"
],
"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 research article – Do hospitalizations push households into poverty in India: evidence from national data.\nThis study makes valuable addition to the literature around the impact of out of pocket (OOP) medical expenditures on poverty. Authors have appropriately analysed large dataset to demonstrate the impact of OOP on poverty. I just have few minor comments to further strengthen this article:\n- I would recommend authors to add citations for few key statements in the introduction section such as, :India is actively taking steps to offer its population universal health coverage (UHC)\", \"India is ranked third in the Southeast Asian region in terms of “countries with highest OOP expenditure on health,” according to the World Health Organization\".\n- In its current format it is a little hard to understand key take home message from this study. So, I would suggest authors to carve out a \"conclusion\" section which provides succinct conclusion of this 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?\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": []
},
{
"id": "261034",
"date": "15 May 2024",
"name": "Olaide Sekinat Opeloyeru",
"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 introduction is attractive to read but the authors need to pass the message of the write up through existing literature. There is no trace of past research related to this work in India. I am aware that a lot of work has been done in India which people have referenced. The authors need to insert a section separately on the literature review as well to show the gap filled in the existing literature. As it is, it is difficult to see the new contribution to existing literature.\n\nThe sub-heading under the methodology “Factors affecting incidence of impoverishment due to OOP health expenditures” should be removed and the authors should avoid the use of future words like “will” since the work has been done and is not a proposal (an example of this is under methodology second paragraph, line 2.) The authors should explain how each variable was partitioned or designed for their study.\n\nAppropriate statistics were used but the interpretation and how data were reported should be fine-tuned. For example some statistics were reported in 3 decimal places and others in 4 decimal places, there should be consistency. Also, the interpretation of logistic regression should be improved on for readers to appreciate your work (for example, health services received through OOP in the urban area increases the chance or odds of living below the poverty by 60% compared to rural area which is in contrast to what you put in your paper as “There is 0.601 higher odds of experiencing poverty due to OOP expenditures in households in urban areas compared to households in rural areas”).\n\nThe authors joined discussion of results with the conclusion. A separate heading should be created for conclusions and appropriate language should be used. For example, where the author used “coping skills”, I want to suggest the author use “coping strategies”\nOn a general note, appropriate language and good editorial work is needed for this study e.g. “Similar study in Nigeria found that hat members with insurance experienced increased the incidence of poverty after making OOP payments compared to members not covered by insurance”.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-205
|
https://f1000research.com/articles/13-203/v1
|
21 Mar 24
|
{
"type": "Software Tool Article",
"title": "The Flux Operator",
"authors": [
"Vanessa Sochat",
"Aldo Culquicondor",
"Antonio Ojea",
"Daniel Milroy",
"Aldo Culquicondor",
"Antonio Ojea",
"Daniel Milroy"
],
"abstract": "Converged computing is an emerging area of computing that brings together the best of both worlds for high performance computing (HPC) and cloud-native communities. The economic influence of cloud computing and the need for workflow portability, flexibility, and manageability are driving this emergence. Navigating the uncharted territory and building an effective space for both HPC and cloud require collaborative technological development and research. In this work, we focus on developing components for the converged workload manager, the central component of batch workflows running in any environment. From the cloud we base our work on Kubernetes, the de facto standard batch workload orchestrator. From HPC the orchestrator counterpart is Flux Framework, a fully hierarchical resource management and graph-based scheduler with a modular architecture that supports sophisticated scheduling and job management. Bringing these managers together consists of implementing Flux inside of Kubernetes, enabling hierarchical resource management and scheduling that scales without burdening the Kubernetes scheduler. This paper introduces the Flux Operator – an on-demand HPC workload manager deployed in Kubernetes. Our work describes design decisions, mapping components between environments, and experimental features. We perform experiments that compare application performance when deployed by the Flux Operator and the MPI Operator and present the results. Finally, we review remaining challenges and describe our vision of the future for improved technological innovation and collaboration through converged computing.",
"keywords": [
"high performance computing",
"converged computing",
"cloud computing",
"Kubernetes",
"batch workloads",
"workload manager"
],
"content": "1. Introduction\n\nPortability, manageability, and modularity of complex, heterogeneous workflows is becoming increasingly important for high performance computing (HPC). In particular, the need for workflows to be extended to cloud environments is a key component of collaboration across an increasingly diverse set of computational resources, and a likely solution for “green computing” to ensure energy efficiency and optimal usage of shared resources.1 Other demands for flexibility of compute include the increasing use of internet of things “IoT” remote devices to conduct research,2,3 an explosion of hardware available on cloud platforms,4,5 and the dynamic addition of external resources.6 A powerful demonstration of need also comes from a series of events organized by the European Commission to assemble experts for discussion on innovation in the “computing continuum,” citing a strong need for flexibility for distributed systems, green and dynamic technologies, and an emphasis on open source software. The discussion continues with workshops emphasizing the importance of shaping Europe’s digital future. Given this landscape, any entity involved in the business of scaled computing will fall behind if these technological needs are not prioritized.4\n\nIn cloud computing communities, machine learning workloads are also becoming increasingly important,7–10 and the cloud container orchestration technology Kubernetes is becoming the de facto standard for orchestration of these workflows following its success orchestrating microservices. As of June of 2023, the Kubernetes project had over 74,000 contributors, making it the second largest open source project ever after Linux, and the “most widely used container orchestration platform in existence” (the CNCF project report). It is the chosen platform for orchestration at over 70% of Fortune 500 companies. In recent years, the growing need for supporting batch workflows has led to the creation of the Kubernetes batch working group. The group designs and implements application programming interfaces (APIs) to enable cloud-native batch workflows and jobs, and works to transition Kubernetes from primarily a stateless, service-oriented architecture to one that can support states and jobs. The first stable release of highly parallel Indexed Jobs marked an unofficial declaration of Kubernetes supporting what, at face value, looked like more traditional workflows from HPC. With this development, the needs of the cloud computing communities overlapped better with the needs of HPC than ever before.\n\nBatch processing has a long history in HPC, and consequently the community has deep expertise. The need to embrace more cloud-like features results from changing workload demands. While a traditional HPC job is, e.g., a parallel simulation with tightly-coupled problem subdomains, modern workflows include the gamut from ensembles of simulations to artificial intelligence (AI) and services. A standard workflow is no longer a single job that writes to a shared filesystem, but rather an assortment of tasks that vary in their needs for hardware, storage, and running times. Modern workflows are typically specified via directed acyclic graphs (DAGs) that not only indicate direction or order of dependencies, but also utilization of different architectures, services, and virtualization technologies. To support these workflows the high performance computing community needs the portability, flexibility, and automation enabled by cloud, and the ability to span both applications and services.\n\nIt would be in the best interest of cloud communities to learn from and adopt the best technological innovations from HPC and vice versa. These common interests are a motivation for collaboration, and the time is right for the convergence of not just these communities but the technologies themselves. This collaboration, or the convincing of one community to engage with the other, is arguably more challenging than development work. When approaching those on the HPC side, discussions of cloud adoption focus on performance, costs11,12 and security.13 Approaching from the cloud side, there can be a lack of understanding of high performance computing technologies, and how they differ from or might potentially improve microservices. The concerns about performance, cost, and security of cloud can be addressed by the fact that cloud environments can be public, private, or both. A technology such as Kubernetes could be deployed on-premises. In the case of the second, the cloud computing community needs convincing that they too can benefit from the adoption of HPC technologies. Increasing performance and efficiency by using techniques from HPC, and providing better transparency of underlying resources by way of low-level performance analysis, can lower costs and time to completion. A solution that falls in the middle would likely bring together the best of both worlds, but could come with compromises such as paying a performance penalty for flexibility. Ideally, a converged approach would improve performance of cloud-native technologies through effective hardware use, with increased flexibility offsetting any potential performance compromises for running with a higher level of abstraction.\n\nTo facilitate collaboration between cloud and high performance computing communities and create effective converged environments, each communities’ needs must be determined and addressed. First, a solid demonstration is needed that there are benefits for both cloud and HPC to take on attributes of the other side. For HPC, this means more modularity, portability, and automation. For cloud, this means more performant workflows, efficient use of hardware, schedulers, and communication protocols that span networking, applications, and storage. Secondly, examples of technologies that can bring together the performance of HPC with the flexibility of clouds in a best-of-both-worlds environment must be prototyped. This vision, or the space of technologies that exists between cloud and HPC can be described with the term “converged computing”.14,15 In a converged computing landscape of the future not only will technologies from traditionally disparate communities be brought together, but traditionally disparate communities will be united culturally to identify shared goals and foster deeper, more fruitful collaborations.\n\nWhile many areas of work can be tackled, it was logical to start with a workflow manager analogous to Kubernetes in the high performance computing community, with the common use case of running simulations or machine learning tasks. The Flux Framework, a novel hierarchical framework for resource management and scheduling, provides abstractions that parallel those in Kubernetes, including modularity, well-defined developer and user interfaces, and an ability to integrate and manage different types of resources.16 It stands out from other resource managers because of its ability to manage the exploding complexity of modern workflows described previously. To start with modularity, in the same way that several components are combined to create Kubernetes, components from Flux Framework are assembled together to manifest in a workload manager that is referred to simply as “Flux.” This modularity can mean, for example, that a component of Flux could be used in Kubernetes, or vice versa. For developer interfaces, arguably a core ingredient of convergence is having common programming languages or bindings. Kubernetes, as it was developed at Google, chose to use the Go programming language, also designed at Google.17 Flux also provides a rich landscape of language bindings, one of which is Go. These shared interfaces and modularity make convergence possible.\n\nGiven the overlapping need to schedule jobs, the first work in this space was to integrate the Flux scheduler “Fluxion” as a scheduler plugin for Kubernetes called “Fluence”.15 The rationale for this early work was that Flux could benefit Kubernetes in several ways. Firstly, Flux represents and schedules resources via directed graphs, which is notably different from the default Kubernetes scheduler that selects work for nodes based on a feasibility score. In fact, Flux was created to address significant limitations of traditional HPC resource managers and schedulers by facilitating workload portability, handling high throughput job requests, and employing sophisticated techniques for flexible and fine-grained task placement and binding.16 Enabling the Flux scheduler in Kubernetes would bring this same graph-based and hierarchical resource-aware approach to Kubernetes, and this early work demonstrated exactly that – improved performance against the default Kubernetes scheduler.18 More efficient scheduling was demonstrating by enabling MPI-based CORAL2 workloads to run and scale in Kubernetes that, by way of Fluence, avoided pathological resource mappings and resource starvation.14 This work also demonstrated a valuable point – that the scheduling provided by a workload manager must be able to concretely meet the resource demands of a workflow, but to do so efficiently and effectively to maximally utilize a set of computational resources.\n\nAside from the technological benefits that might come from convergence of these two specific technologies for end users and developers, enabling Flux to run in the cloud would also provide benefits for cloud vendors attempting to attract a larger HPC customer base. Current products that target HPC researchers (e.g., AWS Batch, ParallelCluster, Google Batch, Azure CycleCloud) present a more familiar experience and may help transition users to the cloud. Other products that do not deliver a familiar command line interface would require an on-boarding process. The realization that workflows could be seamlessly portable by way of Flux, and Flux could serve as a vehicle for the workflow to move between cloud and HPC, inspired the next round of work discussed in this paper. By making the full Flux workflow manager, with all components assembled, available in Kubernetes, workflow specifications that work on HPC with Flux would also work in a cloud environment. For cloud vendors, the HPC user base could more easily make a smooth transition to using cloud too.\n\nThis paper introduces the Flux Operator,19 the next step in work to explore integration of a traditional HPC scheduler within Kubernetes. The Flux Operator is a Kubernetes operator20 that handles all the setup and configuration of a fully fledged Flux cluster inside of Kubernetes itself, allowing the user to efficiently bring up and down an entire HPC cluster for a scoped set of work that optimizes for important aspects of HPC. This paper first reviews the design and architecture of the Flux Operator (Section 2), discussing Kubernetes abstractions for efficient networking and node setup. We then discuss how these design decisions impact essential needs such as workflows that use message passing interfaces (MPI), and experimental features like scaling and elasticity (Section 4). Finally, experimental work demonstrates the Flux Operator enable superior performance for a well-known HPC application over the MPI Operator, the primary available option at the time for running MPI workflows (Section 3). The paper concludes with discussion for anticipated future work, considerations for workflow design, and vision for the future (Section 5).\n\n\n2. Methods\n\nThis section details the architecture of the Flux Operator, first describing the design and needs of Flux, and how those are satisfied in Kubernetes. From the standpoint of a software architect, the task of designing the Flux Operator could be approached as a problem of matching software design patterns. Knowing that Kubernetes provides a set of components and application programming interfaces, a key challenge was to assemble the components in a way that would deploy the full Flux Framework stack running inside of Kubernetes. An ideal design might aim to achieve the keystone properties of Kubernetes applications, including but not limited to fault tolerance, load balancing, and elasticity. Abstractions for storage, networking, and workloads could be selected for this design, and with a mindset of portability, meaning that the software components would be in containers themselves. The following sections refer to two roles – an operator developer, or someone that designs and implements the Flux Operator itself, and an operator user, an individual that installs the operator and uses it. These architecture sections start with an overview of Kubernetes Operators, and then describe each component of Flux, and a mapping from traditional bare metal solutions to abstractions in Kubernetes.\n\n2.1.1 Kubernetes operators\n\nWhile individual components such as pods or services could be individually implemented and created in the Kubernetes cluster, the advent of programmatic operators in 2016 has hugely simplified this process for the developer user. A Kubernetes operator serves as a controller for one or more Kubernetes objects, meaning that a developer can express all of the custom logic needed for an application of interest in code that is compiled and run in Kubernetes. The operator implements a custom resource whose behavior is dictated by a custom resource definition (CRD), a YAML file with a specification of variables for the controller to use. For the Flux Operator, this custom resource is called a “MiniCluster”. The basic design of a controller is a loop, running a reconciliation process until a cluster reaches a desired state requested by a user via this custom resource definition YAML specification. This is a declarative model in that the operator user can specify high level constructs such as the cluster size and application to run, and they don’t need to know the details of setting up a Flux cluster, nor do they need to consider orchestration or update of components. This approach is advantageous in that it exposes only the amount of detail that is needed for some number of jobs, and the complexity that would require niche expertise is hidden.\n\n2.1.2 Flux Framework\n\nThe Flux Framework is a novel, graph-based resource manager that is typically deployed on-premises at HPC centers.16 It won an R&D 100 award in 2021,21 and is slated to be the primary scheduler for the upcoming exascale-class system “El Capitan” at Lawrence Livermore National Laboratory. It is called a framework because several projects combine together to form the resource manager known as Flux. A summary of these projects is described in Table 1, and the interested reader is directed to the learning guide for an in-depth overview.\n\nWhile Flux can be described in terms of its modules or components, for the work here it will described as it is seen in the space of Kubernetes abstractions.\n\n2.1.3 A Flux MiniCluster\n\nThe node Flux is typically deployed across nodes on an HPC cluster, where each node can be thought of as an addressable compute or storage unit, and as having a unique network address. Moving into the space of cloud, the physicality of the server goes away, and instead the basis of a node is a virtual machine. However, while Kubernetes itself is deployed on nodes, a fundamental object is the pod – an abstract slice of a node that is tasked with some unit of work to run one or more containers, and allocated a particular set of resources. Since the Kubernetes scheduler is designed to assign more than one pod to a single node, the first task in defining this cluster was to ensure that there was a mapping of one pod per actual physical node. The reason for this mapping is due to Flux not being able to detect running on a partial node, which is a result of its use of the portable hardware locality (hwloc) library to discover resources. Pod isolation in Kubernetes is based on a kernel technology, cgroups, which allows for resource management on the level of the kernel. However, this abstraction does not take hardware into account, and so regardless of a resource specification, hwloc will detect the resources of the entire node. In the context of two pods running on one node, despite any resource management done via cgroups, the library would erroneously discover the resources of the entire node twice. This means that Flux would detect double the resources that are actually available, and could schedule too much work on a single physical node that, to the resource manager, is seen as two separate nodes with identical resources. The 1:1 mapping of pods to nodes was originally achieved by way of a resource specification, a strategy that required the user to ask for just under the upper limit of CPU and memory offered by their cloud instance of choice. This strategy was later improved to not require knowledge of the instances by way of rules for pod affinity and anti-affinity. These are essentially constraints that tells the scheduler to ensure one pod per node, each with a hostname for Flux.\n\nThe cluster While it would be possible to deploy individual pods onto nodes, early Kubernetes offered further abstractions for sets of pods such as deployments and Stateful or Replica sets, and in 2015, an abstraction called a Job that was the first of its kind to approximate a traditional HPC job with the intention to run and complete. As of 2021, the batch working group introduced the indexed mode addition to Job where the same work could be done in parallel, expecting 1 to N completions. In that each node of a simple Flux cluster would be identical aside from subtle differences in startup, although other abstractions were considered, an indexed Job was ultimately chosen. The indexed Job is ideal in that it inherits needed features from the base Job such as having states, and adds an ability to create duplicates of the pods. To create pods it uses a batched approach, which is also advantageous to introduce an indexed ordering that ensures the bigger numbers are downscaled first. This allowed us to easily design the operator to use the index 0 pod as the lead broker, and any scaling up or down of the cluster (Section 4.1) would never risk deleting the lead broker. Within this cluster context, given the assignment of one pod to one node, for the remainder of this paper the terms “node\" and “pod\" are used interchangeably as they are mapped to the same resources, memory and CPU.\n\nNetworking One of the foundational components of Flux Framework is the scalable tree-based overlay network, or “TBON” that connects the core modules for scheduling and resource management. The Flux TBON is a rooted tree that features leader and follower processes (brokers), each of which is typically mapped to one node. The leader expects follower brokers to connect to it. Mapping this design to the indexed Job, the role of lead broker can be assigned to index 0, and the follower brokers to indices 1 through N-1. Along with being easy to remember, this design decision allows pods to be created in order of their index with the lowest first, which is ideal to have the lead broker up earlier for the follower brokers to find. ZeroMQ22 is used for the discovery of the node and to bootstrap the cluster. In this process, the follower brokers identify their place in the cluster by way of their rank in a shared system configuration file, and then connect to the lead broker on a specific port via transmission control protocol (tcp). If the lead broker is not up first the worker will wait to try connecting again, and by default the ZeroMQ library falls back to a tcp default retry timeout that increases exponentially. In practice this means delayed cluster startup times waiting for the follower brokers to retry. The scheduler and resource manager combined with this set of brokers that can communicate to run jobs is called a Flux instance. A Flux instance can be on the system level, meaning shared by many users, or owned by a single user. In both cases, the Flux instances handle user requests for submitting or otherwise interacting with jobs. The instance itself is hierarchical because it can spawn sub-instances whose resources are a subgraph of their parent.\n\nThe networking setup can give each pod a unique address that can be written into the Flux system configuration, and used to identify lead and follower brokers. For the first naive implementation, the Flux Operator created the pods, retrieved the IP addresses after creation from the Kubernetes API, and then added corresponding entries to the /etc/hosts file for domain name system (DNS) resolution. Automated management of the hosts file proved to be a bad design because it required restarting all the pods to recreate a configuration file with known hostnames. Instead, a later design created a Headless Service for the MiniCluster, meaning that each pod could be given a label, a key value pair, that was known to the Headless Service, and discovering the labeled pod would add it to the network provided by the service. The Job controller then assigns a predictible hostname, and the Headless Service makes the name discoverable to DNS. This series of steps is essential for Flux to identify each broker, and is supported by way of unique pod names that are published as A records. This simplified the creation of the cluster, and allowed for networking readiness as soon as the service object was ready. Once this is done and the brokers have connected over TCP, further communication for the overlay network is done via ZeroMQ sockets.16 However, for the cases of workflows that use a message passing interface (MPI), Flux has built-in modules for MPI and communication, meaning that Flux simply uses standard MPI libraries that can rely on sophisticated networking fabrics or other high speed interconnects. This reliance on cloud hardware has proven to be a challenge when deploying the Flux Operator to different cloud providers, and is a focus of collaborative work.\n\nVolume mounts In terms of configuration, Flux requires a system configuration file, a ZeroMQ CURVE certificate used to encrypt communication, and a means to start the brokers. In a traditional HPC setup, this means could be using a systemd service, however in a Kubernetes environment with containers, it means a start command for the container with conditional logic for the lead vs. follower brokers. In Kubernetes, all of the above configuration can be achieved via volume mounts provided via ConfigMap objects. By way of mounting configuration files and other needed files to each pod container as read-only volumes, all nodes in the cluster have access to them. These are mounted at /etc/flux and /flux_operator for configurations and the starting script, respectively, and the choice of a root path affords discoverability.\n\nThe curve certificate presented a bootstrapping design problem, as the standard way to generate it is via Flux itself (ZeroMQ is compiled within and exposed via the flux keygen command). However, this content was also required to exist for the read-only volume before starting the pod container. For the earliest design of the Flux Operator, a one-off certificate generator container was brought up that ran this key generation command, and the key was printed to the log to be retrieved by the operator. It could then be straightforward to write into the ConfigMap to be shared by the MiniCluster pods. In a later design, by way of collaboration with authors of this paper following Kubecon Amsterdam’2323 this bootstrapping problem was further improved by compiling ZeroMQ directly into the Flux Operator, and using cgo to interact with it directly to generate the certificate content for the ConfigMap inside the operator. This removed an entire step to generate the one-off pod and reduced startup latency, and is a beautiful example of how sharing ideas and collaboration can lead to improvements in design and functionality. The open source nature of these projects is key for enabling collaboration that can result in faster innovation.24,25\n\nA Flux container image The libraries and software needed for Flux must be built into a common Flux container that is replicated by the indexed Job. This container would need to support running configuration steps for Flux upon start, and additionally include any application of interest to be run by the user. This is a design flaw in that most containerized applications for HPC have not been built with Flux, and would need to be built again to install not only Flux, but required shared libraries. While the HPC community is attuned to building and optimizing components for different architectures, ideally a more modular, cloud-native solution would not require such a substantial time investment. Approaches need to be investigated that can achieve separation of application logic from Flux while not impacting performance, and further work is needed to investigate this. Once required software and configuration files are present, setup continues to create either a single-user or site-wide installation of Flux. The Flux Operator opts for a single-user design, and enables customization via variables exposed on the CRD. This customization includes (but is not limited to) archiving of data, creating multiple users, starting in an interactive mode, starting a RESTful application programming interface, or creating a custom batch job. The final component of the container is the “entrypoint” or the command that is run when the container is started. This varies between the lead and follower brokers, where the lead broker typically starts with a command to run a job, and the follower broker starts expecting to connect and receive work.\n\nThe first requirement for using the Flux Operator is access to a Kubernetes cluster with sufficient permission to deploy each of the abstractions discussed in Section 2, including Deployment, Service, Job, and ConfigMap. The Flux Operator pre-built container images are provided for nodes with amd64 or arm64 architectures. Operation comes down to deploying these objects with the kubectl command line tool and then using the same tool to deploy the MiniCluster CRD. Upon creation, the operator reconciles in a loop until the state of objects in Kubernetes matches the desired state specified in the CRD. This desired state encompasses the creation of the MiniCluster, which includes an indexed Job with a group of pods for the cluster, each containing a flux broker and volumes for configuration. A Headless Service networks the pods together to complete the MiniCluster. The specific attributes of the cluster (e.g., size, application image, command) can be customized in this YAML file, resulting in a Flux MiniCluster that exists to run a command and clean up (akin to a batch job), or an interactive cluster that can address several use cases and interactions discussed in Section 4. The final Flux MiniCluster is illustrated in Figure 1.\n\nThe custom resource definition “CRD” that describes the specification for the cluster is provided by the user as a YAML file. Upon creation, the operator reconciles in a loop until the state of objects in Kubernetes matches the desired state specified in the CRD. This desired state encompasses the creation of the MiniCluster, which includes an indexed Job with a group of pods for the cluster, each containing a Flux broker and volumes for configuration. A Headless Service (purple) networks the pods together to complete the MiniCluster.\n\n\n3. Results\n\nThe Flux Operator is compared to another state-of-the-art Kubernetes Operator, the MPI Operator, which at the time of the experiments was considered the main option in the field for running MPI workloads.26 The MPI Operator started as part of the Kubeflow project and defines an “MPIJob” custom resource. Unlike the Flux Operator that coordinates between brokers with ZeroMQ, the MPI operator coordinates workers via secure shell (SSH). It requires an extra launcher node that serves the sole purpose of coordinating the workers, and akin to the Flux Operator, uses dedicated hostnames with an equivalent Headless Service. This launcher node conceptually could be thought of as analogous to the lead broker of the Flux instance in that it serves as an entrypoint for submitting jobs, however the main difference is that the Flux lead broker is considered part of the cluster to perform work. The MPI launcher node is not, and in practice this means the user will need to always incur the costs of an extra node just for the launcher. In practice, choosing a cheaper node for the launcher is a logical choice.\n\nExperiments were conducted on Amazon Web Services Elastic Kubernetes Engine (EKS), using the hpc6a.48xlarge instance type hpc6a with the elastic fiber adapter (EFA) intending to test the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)27 in a strong-scaling configuration across cluster sizes and ranks of 64/6016, 32/3008, 16/1504, and 8/752, respectively (Figure 2). This design was chosen to mirror previous work.18 LAMMPS is used by the Collaboration of Oak Ridge, Argonne, and Livermore (CORAL) as a representative scalable science benchmark as part of CORAL-2. In testing, LAMMPS runs in parallel on MPI ranks (processes) across nodes, a molecular simulation28 and the problem size 64×16×16 was chosen that would adequately test strong scalability across the chosen rank and node counts. LAMMPS scalability depends on network latency, and the experiment results report the total wall time recorded by the LAMMPS run as a metric for performance. A cluster setup that enables lower latency will run faster, and ideally the simulation should get faster as the number of nodes is increased with strong scaling. A second metric time of interest is the time for the launcher to submit and complete a job. For Flux this means timing the flux submit command that is given the command to run LAMMPS, and for the MPI Operator it means timing the mpirun command that does the same. The final metric time of interest was the total cluster creation and deletion times, which can be calculated based on the total runtime of the MiniCluster minus the LAMMPS total wall time. This time would include each pod preparing the broker, starting Flux, and networking with the lead broker. The runtime would ideally decrease across these chosen rank and node sizes.\n\nA single Kubernetes cluster of size 65 was created (blue outline) to test subsequently smaller cluster sizes, including 64 pods (6016 ranks), 32 pods (3008 ranks), 16 pods (1504 ranks), and 8 pods (752 ranks). An extra node (blue) is needed for the MPI Operator launcher to supplement the nodes doing work (green).\n\nTo ensure the nodes of the cluster are consistent and do not influence results, experiments were run on the same Kubernetes cluster, and simply used smaller portions of it. As the MPI Operator requires an extra launcher node, the maximum cluster size needed (64) was increased by 1, resulting in a size 65 node cluster for these experiments. Finally, a modified version of the MPI Operator was used14 to allow it to scale to over 100 MPI ranks.\n\nThe experiments proceeded as follows. The main Kubernetes cluster of size 65 is first created. Then, for each of the Flux Operator and MPI Operator:\n\n1. Launch Job/create MiniCluster for size 64, 32, 16, 8\n\n2. Run LAMMPS x 20\n\n3. Record timings and save configuration files and logs\n\nFor each experiment run, a single “throwaway” run is first performed to pull the container with Flux and LAMMPS to the node, where it is cached for further runs. This ensures that time recorded in creating the MiniCluster does not include pulling the container image, which would have variability depending on the image size. The experiments are then run in an automated fashion using Flux Cloud, a simple experiment orchestration tool for running experiments with Flux MiniClusters on Kubernetes. All experiment code, configuration files, and tagged containers are available.29,30\n\nCluster creation and deletion We created and deleted clusters of 8, 16, 32, and 64 nodes in 20 repetitions, observing a small increase in median times (Figure 3) indicating that the indexed job can efficiently create pods. All sizes were created and ready in under a minute with an interquartile range for any given size between approximately 1 and 5 seconds, and a maximum difference of approximately 10 seconds between the fastest time of the smallest cluster and the slowest time of the largest cluster. Likely this variability reflects the slowest or last node to come up, as the cluster is not considered to be completely up until all nodes are ready. Due to the design of the MPI Operator, there was not a corresponding measure of creation time appropriate for comparison, so the two are not comparable side by side.\n\nTimes are calculated as the total time from creation to deletion, and subtraction of the time it took to run and job within. One outlier for size 6016 ranks stands out – one instance of the largest cluster completing creation, run, and deletion in a time closer to 50 seconds. These experiments were run on Amazon Web Services with the hpc6a.48xlarge instance type and the elastic fiber adapter for networking.\n\nLAMMPS total wall time A primary time of interest for running LAMMPS is the total wall time, which is reported by the LAMMPS software itself. Consistently better performance of the Flux Operator over the MPI Operator was observed, with median times that are approximately 5% faster, meaning that the Flux Operator software completed the same workload more efficiently (Figure 4). While the differences in means for this experiment are small, this improvement would likely be more prominent for longer experiments, and could lead to reduction in total costs. Identifying the underlying reasons for the improved performance is another task suitable for investigation with performance tools in future work.\n\nThe Flux Operator is consistently faster, a result that could be more impactful for longer running experiments.\n\nLauncher times Comparing launchers (flux submit for the Flux Operator, and mpirun for the MPI Operator) there is a slightly larger time difference (Figure 5), where both generally perform well under strong scaling (the time goes down). What is unknown is whether there is an inflection point at larger scales where the MPI Operator might plateau or otherwise show a different pattern. The resources were not available to run these larger experiments at the time, but these patterns and scaling can be explored in future work.\n\nThe Flux Operator is consistently faster, a result that could be more impactful for longer running experiments.\n\nDesign considerations Anticipating interest in running experiments of this type, where there is generally some operator in Kubernetes that is going to pull one or more containers to Kubernetes and perform scoped work, we provide a visualization of the steps that have salient times. In Figure 6, there is a distinction between an operator setup that is using autoscaling (right) vs. not (left), and costs that are incurred once (blue) vs. repeated (green). Cluster creation generally means the start and setup of instances, along with any networking and devices that are needed. The primary difference between the two scenarios is that an autoscaling cluster is going to be adding new nodes, meaning that the cluster will need to provision those nodes, and the user will be required to wait. Thus, this update process for the cluster that requires the user to wait (and pay for the time) becomes a repeated cost. This also means that a typically one-time cost of pulling a container may occur several times, primarily when new nodes are added. Note that this diagram assumes experiments running on one cluster. An autoscaling setup that employs bursting to new clusters would need to consider the additional time of creating and deleting the new clusters.\n\nFor a single cluster without autoscaling (left) many of the operations are one-time costs (blue), while for an autoscaling cluster that needs to provision new nodes and pull containers to them, the costs become repeated (green). An efficient approach might maximally use provisioned resources while waiting.\n\nIt is suggested to the reader to consider these times, along with the differences between a setup with autoscaling versus one without or potentially bursting, for future experiments when anticipating costs. Notably, the setup time for any particular operator could be generally consistent, and variance has been seen (but is not reported here) in the other steps between cloud providers. A more critical study and understanding of these times is warranted for future work.\n\n\n4. Use cases\n\nOnce it was possible to run and complete a basic workflow (discussed in Section 3), development thinking moved toward adding desired use cases for such a workload manager in Kubernetes. This section will describe early work to enable scalability and saving state, elasticity and autoscaling along with workflow integration. These features for workflows, along with the core design of the Flux Operator, are considered experimental in the sense that they are implemented with the goal of testing and improvement in mind. The below represents a sample of this work, and more experiments can be found in the examples directory of the repository.\n\nThe goal of experiments to save state would involve starting a Flux MiniCluster, running some number of jobs, pausing them, saving the state of the job queue, and then bringing it down to bring up a different sized cluster to load the jobs into, where they would continue running. This concept of saving state is similar to forensic container checkpointing in Kubernetes and checkpoint/restart (e.g., Ref. 31) in HPC, and would be useful for pausing workflows for cost savings or waiting on resource availability. These experiments varied based on when the queue was paused. In the earliest tests, job completion was required before saving state, while for later tests, jobs were stopped mid-run.\n\nIn practice saving state meant waiting for the queue, pausing, and then saving to an archive in a volume shared between two MiniClusters. Initially, the Operator waited for the first MiniCluster pods to terminate and the new MiniCluster to come up before restoring the jobs. We observed that jobs would successfully save and load into the new cluster, maintaining job identifiers and size, however when stopping a running queue, 1-2 jobs could be lost between the transfer. While the reason for this loss would be interesting to understand, as it is an experimental prototype for a feature, the work is beyond the scope of this paper, and akin to other features discussed here, should be pursued with a compelling research use case. When this time comes, more analysis would be needed to understand exactly what is going on. The majority of jobs (e.g., roughly of 9 out of 10) transition successfully, meaning that a job on the previous queue can get scheduled to a new larger or smaller cluster. As would be expected, if a job is moved onto a cluster lacking enough resources, it would logically not be scheduleable. A write-up and tutorial to reproduce this work is available.\n\nWhile this early use case of saving state was simple, it was a glimpse into the idea that scheduled workflows could in fact be moved. In changing the size of the resources available by way of creating a new MiniCluster, it was the earliest prototype for what might be called scaling or elasticity, discussed next.\n\nElasticity can be thought of as automated dynamic scaling.32 Instead of making a cluster larger or smaller by way of saving state and loading into a different size, true elasticity means changing the size of a single cluster, which in the context of the Flux Operator means that Flux must adapt dynamically. To enable MiniCluster elasticity we added limited support for resource dynamism within Flux. Our method is analogous to resource dynamism in Slurm in that it relies on configuring predefined resources. Support for resource dynamism by integrating arbitrary resources on demand is future work. The following steps enable an elastic Flux MiniCluster:\n\n• A max size variable is added, meaning more nodes are defined in the system configuration file than actually exist.\n\n• Flux is told to create a cluster at a size that is between 1 and this max size.\n\n• Any change request to the CRD (from a user or API) validates the request, and updates the indexed Job.\n\n• An update to increase in size creates new pods, and an update to decrease in size terminates pods.\n\nThe above also carries the constraints that the cluster cannot be smaller than one node (only a lead broker) or larger than the initial maxSize. The larger indices are terminated first and the operator does not allow reduction to size zero, so the lead broker is never at risk of deletion – such a request would delete the entire MiniCluster that relies on it. The reason this works is that Flux sees the initial set of pods that do not exist as simply being down, which happens frequently in a high performance computing environment. When the nodes are created their corresponding follower brokers start, ping the lead broker on the port to connect (typically port 8050) and then they seamlessly join the cluster. From the standpoint of the user, they change the “size” value in their MiniCluster CRD, apply it, and then see their cluster grow or shrink. The Flux instance run by the lead broker simply sees a node come online. On the Kubernetes side, this ability for the indexed Job to have elasticity requires a minimum Kubernetes version of 1.27.\n\nAt this point, it needed to be decided what might trigger this change in size. Elasticity was implemented in two ways, first with an application-driven approach that required extra permissions to be given to the in-cluster service account, allowing the application inside the cluster to ask for more or fewer pods directly. It was then discovered that Kubernetes has autoscaling APIs intended for this use case. This autoscaling approach is discussed in the next section.\n\nIn Kubernetes there are two types of scaling – horizontal and vertical. Horizontal typically refers to adding pods, while vertical refers to adding resources to existing pods. Both are based on the idea that resources should change in response to changing workload needs – if cluster or resources are too big, they are made smaller, and vice versa. In the case of the Flux Operator the primary interest was horizontal autoscaling, or changing the number of pods to dynamically increase or decrease the size of the MiniCluster to respond to the demands of a workload. This led to an initial implementation based on horizontal pod autoscaling (HPA) using the HorizontalPodAutoscaler API resource, a cluster API to watch a selected set of pods for resource consumption and increase or decrease the number depending on utilization. For the simplest cases, a default autoscaler was first deployed that considers a metric such as percent CPU usage and uses an algorithm to calculate a target scale value for the number of pods. This could be tested by running a CPU intensive simulation to observe the autoscaler adding and removing pods. However, the approach was not fine-tuned enough to the potential needs of an application being run by Flux. Instead of an arbitrary decision to add or remove pods based on CPU, a design more specific to Flux is warranted. As an example, one design might be that the Flux lead broker makes decisions about when and how to scale depending on the content of the queue. Another valid design would be to allow for changing the size of a single running job. Both of these ideas, and more generally designs for autoscaling, are valid and prime for future work.\n\nWith this in mind, we implemented a custom metrics API, meaning implementing an equivalent API endpoint controller that would be called by an autoscaler with instructions for how to scale the cluster. This resulted in the Flux metrics API, a standalone API that runs directly from the lead broker pod and provides decisions about scaling up or down based on the size or other metrics about the queue. With this API, it was possible to demonstrate an autoscaling operation running based on a trigger coming directly from Flux. More work will be needed to test this setup with real workflows. In the meantime, more details about this setup and basic elasticity are available in an external post.\n\nOne notable feature about the implementation of the autoscaling approaches described above is that regardless of whether the request comes directly from a user changing a value in a file or an application or a programmatic autoscaler, the same internal logic (functions) is used to validate and then perform the patch.\n\nMulti-tenancy refers to the ability to support multiple users on the same resources. In Kubernetes, ownership of resources is typically designated by namespaces, service accounts, custom permissions on connected resources like storage, and role based access controls (RBAC). Recognizing these challenges, as an early approach there are several modes of interaction:\n\n• Single user: the user owns an entire MiniCluster, and uses the default Flux user in the container\n\n• Multiple users: controlled via PAM authentication\n\n• Multiple users: controlled via RESTFul API access\n\nIn anticipation of the last two cases that implement multi-tenancy, a RESTful application programming interface (API) was designed that runs from the lead Flux broker pod, and thus exposes interactions with Flux to submit, get info, cancel, and otherwise interact with jobs via Flux Python bindings exposed by the API. This is made possible by exposing the internal port that the API is running on via an external NodePort and forwarding a port to an external client for interaction.\n\nIn all cases of requiring authentication, the Flux RESTful API uses an OAuth2 based approach, storing a database of user identifiers and encoded passwords, and first authenticates by using a base64 encoded username and password (typical of a basic authentication scheme), and then provides the user with an expiring token that can be used for further interaction. In the case of a single Flux user behind a multi-tenant API, the authentication and authorization occurs, allowing all users to submit jobs to a shared queue. In the case of true multi-tenancy with PAM, the custom resource definition asks for usernames (and optionally, passwords) in advance, and then creates the accounts on the system that are checked after authentication. The installation of flux-accounting can then be enabled for the lead broker’s queue, and use a traditional fair-share algorithm to determine job priority. This work can be extended with more cloud-native approaches that take advantage of namespaces and roles, such as is described later (Section 4.6).\n\nTo complete the early work in autoscaling, we considered the concept of bursting,33 which means not just extending the size of a local cluster, but actually extending work to external resources. The bursting work for Flux would extend this approach to not just deploy external resources, but allow the lead broker to connect to brokers that are deployed in the other clusters. As an example, a Kubernetes cluster running on Google Cloud might burst to a cluster running on Compute Engine (CE), or to a cluster on Amazon Elastic Kubernetes Service (EKS).\n\nTo implement a prototype for bursting, we chose a simple design first. A plugin service would be running from the lead broker of a primary cluster, and the running user would load one or more bursting plugins into it. Each bursting plugin is targeted to a particular provider (e.g., EC2 or CE). While there are many ways to trigger a burst, a simple approach of looking for an attribute “burstable” on a job set to true was chosen first. This request could be done on the command line. Upon discovery of this attribute, the bursting service attempts to schedule the job with the plugin. Each plugin is free to decide if the request is satisfiable by its own custom terms. If the burst is satisfiable, the job is assigned to the bursting plugin, and the plugin creates a new cluster or assign the job to an existing cluster. In the case of creation, the technique of telling the primary cluster that there are more nodes that are expected (and start down) than there actually are is used, and assign them namespaced hostnames that will correspond to the bursted cluster. The calls that are necessary to bring up the second cluster are run, which might mean deploying Terraform configuration files or creating a second Kubernetes cluster via API calls, and then the cluster starts just as a local MiniCluster would. The key difference, however, is that the lead broker of the primary cluster is exposed as a NodePort service that can be discovered by the external cluster. The secondary brokers, all followers, then come up, find their hostnames in the ranked system configuration, and connect to the lead broker IP address from another cluster. To the user, they simply see that the nodes are down, and then they come up when the cluster is ready. Jobs that are scheduled on the primary broker queue that possibly could not run due to insufficient resources can then run. At the time of this writing, the main bursting service is implemented along with four bursting plugins for each of GKE, EKS, CE, and a local burst.\n\nFinally, the bursting service is designed to be modular and flexible. Aside from being able to load different plugins, it allows for customization of the function provided to select a burstable plugin, to interact with the queue, and to select jobs. A mock version of a Flux job is also available for development. The work in bursting is still early, and akin to elasticity, work on these prototypes should continue to eventually develop more hardened Flux modules and algorithms for bursting.\n\nRunning a single MiniCluster to create an isolated Flux cluster in Kubernetes is an initial step, but it is insufficient for real-world use cases of complex workflows. While it would be possible to shell into or otherwise interact with the cluster and run a workflow tool that implements Flux as an executor,34–36 this also does not enable features needed for complex, heterogeneous workflows that might require different sizes or configurations of MiniClusters. We are considering integration of the MiniCluster custom resource definition as a first-class citizen into workflow tools in future work.\n\nAfter the Kubecon Amsterdam’23 presentation, collaborators (including author AC) were quickly motivated to add the Flux Operator as a job type to the workflow tool Kueue, a Kubernetes-native job submission operator that handles managing multi-tenancy of Kubernetes batch jobs that can be produced by a number of operators. We are developing a similar approach to control the creation and management of a MiniCluster through workflow tools, an idea being implemented into the Snakemake34 workflow tool as a Kueue executor plugin. Defining even an example workflow for high performance computing is a non-trivial problem, as many codes are either private or challenging to port. This initial work with the Flux Operator sets the stage for studies of integrations of this type. Tackling this early problem is a two-fold challenge to design technologies and inspire more collaborative opportunities for the HPC community.\n\n\n5. Discussion\n\nThis work demonstrates improved performance using the Flux Operator for running an HPC workflow in a cloud-native environment. This early innovation comes with strengths, limitations, and identification of important future work that includes workloads and scheduling, storage, tenancy, and cost-estimation, among others.\n\nA discussion of limitations and further hopes for innovation is needed for transparency of this work. First, it is a design flaw that the main execution container is required to have Flux and the application of interest. This means that any user of the Flux Operator is required to rebuild their container in full to include Flux, which requires knowledge of Flux, and in the case of using the message passing interface (MPI) knowledge of MPI. While container requirements are provided alongside the documentation, a better approach would not place such requirements on the application container. While the dependencies and complexity exist to enable advanced capabilities, the authors believe there are approaches that can improve upon this strict requirement.\n\nA next limitation is the creation of the entire MiniCluster using a single indexed Job. While this is the ideal for the time being, as the indexed Job is released with core Kubernetes, an eventual refactor to use a JobSet would be desired, which can create multiple Indexed Jobs underneath, however allowing for different configurations for the lead and follower brokers, and an ability to define different groups of nodes each as a Replicated Job under the same network namespace. Allowing for different sets of nodes would not only make it possible to separate logic between the lead and follower brokers, but also allow for creation of a MiniCluster with different pod specifications mapped to different resource needs. JobSet would also allow for better definition of a success policy, or explicitly reporting job completion when the lead broker exits. Author VS created a prototype using JobSet, anticipating its integration in Kubernetes core.\n\nFor next steps of work for experimental features, the Flux software itself needs innovation for the set of the hacks that were implemented. The ability to scale up and down dynamically without “registering” the non-existent nodes in the Flux system configuration is a good example, along with a more hardened approach for bursting that likely comes down to plugins written directly in C or C++ alongside Flux. Especially the work in bursting is early and exciting, and will be continued in future work. Notably, the experiment application did not require use of storage, and while there are several tutorials and examples for different cloud solutions, this is an entire area of the design that requires further work and thinking.\n\nAnother challenge is that of poor workflow consistency and reproducibility. While there are scattered workflow tools that are used by HPC centers (e.g., national labs), these authors consider much of the HPC community behind with respect to the reproducible workflow movement. Part of this work moving forward is to not only identify proxy applications and workflows, but also to containerize them, and make it quick for an interested party to run them easily in a cloud environment. Part of this work will not only be understanding how they work in containers and across a Kubernetes cluster, but also developing means to assess performance.\n\nAn understated challenge in the converged computing space is also culture and communication. As stated in the introduction, convincing one side to be open to ideas from the other is a non-trivial task. For basic communication, if there is discussion between HPC and cloud community members, a simple term like “node” or “scheduler” can mean something different. This might be tackled through discussion, and creation of a shared lexicon that allows for talking about comparable distractions. This introduces a further challenge when looking at the means for communication. Academic groups tend to write papers (and industry groups less so), and developing software in research is made more complex by the publication incentive structure that wants to highlight new research results.37 Practically speaking, both the HPC and cloud communities will need to meet one another half way. This might mean researchers presenting work at (traditionally) more cloud-oriented conferences and venues, or cloud developers participating in more traditionally research-oriented venues. For both, it means distributing knowledge through blogs and other common mediums. This work calls out to cloud vendors an immense desire to work together. While it is understandable that there is a primary concern about direct comparison, there is a path for respectful collaboration, developing technologies that can work across clouds, and learning from one another.\n\nThese experiments were run on one cloud with a particular networking fabric and instance type, and at a maximum scale of 64 nodes, which is very small for traditional HPC. However, the recent work to train large language models38 provides a common use case for needing scaled resources, and might allow for shifting incentives toward that. One of the most challenging decision points for running experiments of this nature is the sheer size of the space of potential experiments that could be run. As the goal of this work was to compare the two operators with an HPC application, the choices made reflect that goal, and a desire to optimize performance (choosing a configuration to support low network latency) as much as possible. These same experiments run on other instance types, interconnects, or even regions could have different results. Further experiments should be pursued that continue to test scale, elasticity, and performance in the space of networking, I/O, and application metrics.\n\nThe Flux Operator brings several features that could be helpful to more general Kubernetes workflows. The first is that using a Flux cluster inside of Kubernetes gets around some of the infamous etcd limits or bottlenecks.39 Submitting to Flux does not stress Kubernetes application programming interfaces or etcd, and could scale to hundreds of thousands to potentially millions of jobs.16 The second is the hierarchical way of looking at heterogeneous tasks. Kubernetes would benefit from having more flexibility about telling tasks where they can go, and then binding them to exactly the resources needed. This brings up tension between a more manual vs. automated decision made by the Kubernetes kubelet. The Flux Operator does something that is not native to Kubernetes to help this issue. By way of allocating a pod to a node and giving control to Flux, possibly ineffective bindings decisions that are made by the kubelet can be avoided. The Flux Operator allows Flux, a workload manager accustomed to making intelligent resource bindings, to take control. Ideally there should (or could) be a mechanism in Kubernetes to enable more performance oriented decisions that the kubelet makes. Having a consistent view of resources that the Kubelet is exporting as the final truth via cgroups is not necessarily desirable, and there are several reasons why. The first is that there are many ways to slice up a node, and a “best” way depends on the application in question. For example, some applications may perform well given an equal split, while others might be optimally be broken across sockets. This suggests that granularity on the level of the socket and below is needed, which is not currently exposed in Kubernetes, but being worked on. A concrete example comes from the MuMMI workflow40,41 that requires a task to be bound to CPU cores closest to a PCI express bus to minimize communication latency with a GPU. This level of granularity is not currently exposed in Kubernetes, and arguably there need to be more consolidated efforts to understand applications on this level. This is a key area for innovation and collaboration, and understanding basic design patterns for networking, I/O, and application performance is likely a good start. Ideally applications that are running in Kubernetes today could be better understood via performance analysis, and a decision made about if the time required to optimize is worth to be invested for the potential benefit.\n\n\n6. Conclusions\n\nThe popularity and economic clout behind cloud computing presents a challenge for the high performance computing community – to resist new paradigms of cloud-native technologies and fall behind, losing talent and customers, or to embrace it, pursuing technological innovation, and viewing the shift as an opportunity for collaboration and growth. The latter approach, a movement identified as “converged computing” is a good path to take, and this work represents an early start towards that desired future. The work here starts with one of the highest levels for running workflows – the orchestration tool – and has thought about the convergence of the HPC workload manager Flux Framework with the cloud orchestration framework Kubernetes. The Flux Operator is an example of convergence of technologies in this workload management space, and has demonstrated superior performance to the current equivalent in the space. In sharing this process of thinking about design to implementation, the authors of this paper hope to start discussion with the larger community that spans cloud and HPC for how to think about working on convergence for other types of software and technology. This work is a shining example of the collaboration and fun possible. The sharing of these results at Kubecon Amsterdam’23,23 inspired collaboration, discussion, and excitement about the converged computing movement. Projects and work are underway to address gaps that have been identified, and each a collaboration between computer scientists and cloud developers. The authors of this paper hope that this early work inspires, and allows for continued discussion for innovation in this space for not just workloads and scheduling, but also the challenges around it – storage, tenancy, and cost-estimation, among others. Through collaboration and creativity of design, pathways can be discovered for moving seamlessly between the spaces of cloud and HPC. Converged computing is a paradigm shift, and it’s up to the HPC and cloud communtities to decide to embrace change and grow from it, or fight it off. This work chooses the first approach, and embraces it with hopes for a better future, and stronger more reproducible science.",
"appendix": "Data availability\n\nZenodo: Underlying data for’The Flux Operator’, converged-computing/operator-experiments: F1000Research submission release, https://doi.org/10.5281/zenodo.10248093. 29\n\nThis archive contains the following underlying data:\n\n• *.yaml: configuration files\n\n• results: experimental data\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 would like to thank the entire Flux Framework team for regular discussion on design points, their immense expertise and experience in this space, and a safe, fun environment to learn and grow. We give our gracious thank you to both Amazon Web Services and Google Cloud for their support.\n\n\nReferences\n\nBharany S, Sharma S, Khalaf OI, et al.: A systematic survey on energy-efficient techniques in sustainable cloud computing. Sustainability. 2022; 14(10): 6256. Publisher Full Text\n\nSadeeq MM, Abdulkareem NM, Zeebaree SRM, et al.: Iot and cloud computing issues, challenges and opportunities: A review. Qubahan Academic Journal. 2021; 1(2): 1–7. Publisher Full Text\n\nZhu W, Hou AB, Yang R, et al.: Quakeflow: a scalable machine-learning-based earthquake monitoring workflow with cloud computing. Geophys. J. Int. 2023; 232(1): 684–693.\n\nThompson NC, Spanuth S: The decline of computers as a general purpose technology.March 2021. Accessed: 2023-8-31. Reference Source\n\nReuther A, Michaleas P, Jones M, et al.: Ai and ml accelerator survey and trends. 2022 IEEE High Performance Extreme Computing Conference (HPEC). IEEE; 2022; pp. 1–10.\n\nJena B, Nayak GK, Saxena S: High-performance computing and its requirements in deep learning. High-Performance Medical Image Processing. 2022; pp. 255–288. Publisher Full Text\n\nSpjuth O, Frid J, Hellander A: The machine learning life cycle and the cloud: implications for drug discovery. Expert Opin. Drug Discov. 2021; 16(9): 1071–1079. PubMed Abstract | Publisher Full Text\n\nGeorge J, Saha A: End-to-end machine learning using kubeflow. 5th Joint International Conference on Data Science & Management of Data (9th ACM IKDD CODS and 27th COMAD). 2022; pp. 336–338.\n\nKreuzberger D, Kühl N, Hirschl S: Machine learning operations (mlops): Overview, definition, and architecture. IEEE Access. 2023.\n\nLiu P, Bravo-Rocca G, Guitart J, et al.: Scanflow-k8s: Agent-based framework for autonomic management and supervision of ml workflows in kubernetes clusters. 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid). IEEE; 2022; pp. 376–385.\n\nMunhoz V, Castro M, Mendizabal O: Strategies for fault-tolerant tightly-coupled hpc workloads running on low-budget spot cloud infrastructures. 2022 IEEE 34th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD). IEEE; 2022; pp. 263–272.\n\nMunhoz V, Castro M: Hpc@ cloud: A provider-agnostic software framework for enabling hpc in public cloud platforms. Anais do XXIII Simpósio em Sistemas Computacionais de Alto Desempenho. SBC; 2022; pp. 157–168.\n\nJangjou M, Sohrabi MK: A comprehensive survey on security challenges in different network layers in cloud computing. Arch. Comput. Methods Eng. 2022; 29(6): 3587–3608. Publisher Full Text\n\nMilroy DJ, Misale C, Georgakoudis G, et al.: One Step Closer to Converged Computing: Achieving Scalability with Cloud-Native HPC. 2022 IEEE/ACM 4th International Workshop on Containers and New Orchestration Paradigms for Isolated Environments in HPC (CANOPIE-HPC). IEEE; 2022; pp. 57–70.\n\nMisale C, Milroy DJ, Gutierrez CEA, et al.: Towards standard Kubernetes scheduling interfaces for converged computing. Smoky Mountains Computational Sciences and Engineering Conference. Springer; 2021; pp. 310–326.\n\nAhn DH, Bass N, Chu A, et al.: Flux: Overcoming scheduling challenges for exascale workflows. Futur. Gener. Comput. Syst. 2020; 110: 202–213. 0167-739X. Publisher Full Text Reference Source\n\nPike R; Go at google. Proceedings of the 3rd annual conference on Systems, programming, and applications: software for humanity. 2012; pp. 5–6.\n\nMisale C, Drocco M, Milroy DJ, et al.: It’s a Scheduling Affair: GROMACS in the Cloud with the KubeFlux Scheduler. 2021 3rd International Workshop on Containers and New Orchestration Paradigms for Isolated Environments in HPC (CANOPIE-HPC). 2021; pp. 10–16. Publisher Full Text\n\nSochat V, Ojea A: flux-framework/flux-operator.September 2023. Publisher Full Text\n\nDobies J, Wood J: Kubernetes operators: Automating the container orchestration platform. O’Reilly Media; 2020.\n\nHeney P: R&D 100 award winners announced in Process/Prototyping and Software/Services categories.2021. Accessed: 2023-9-1. Reference Source\n\nHintjens P: ZeroMQ: Messaging for Many Applications. Oreilly and Associate Series. O’Reilly Media, Incorporated; 2013. 9781449334062. Reference Source\n\n(2023)]CNCF_Cloud_Native_Computing_Foundation2023-pi CNCF [Cloud Native Computing Foundation]. Enabling HPC & ML workloads with the latest kubernetes job features- michał woźniak & vanessa sochat.May 2023.\n\nDong JQ, Weifang W, Zhang Y (s): The faster the better? innovation speed and user interest in open source software. Inf. Manag. July 2019; 56(5): 669–680. Publisher Full Text\n\nTuomi I: Internet, innovation, and open source.January 2001.\n\nBiliaiev M: Enabling openmpi workloads on bare-metal infrastructure using kubernetes.2021. Reference Source\n\nThompson AP, Aktulga HM, Berger R, et al.: LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput. Phys. Commun. 2022; 271: 108171. Publisher Full Text\n\nvan Duin ACT , Dasgupta S, Lorant F, et al.: ReaxFF: A reactive force field for hydrocarbons. J. Phys. Chem. A. October 2001; 105(41): 9396–9409.\n\nSochat V: converged-computing/operator-experiments: F1000Research Submission Release.December 2023. Publisher Full Text\n\nSochat V, Ojea A: flux-framework/flux-operator.September 2023. Publisher Full Text\n\nMoody A, Bronevetsky G, Mohror K, et al.: Design, Modeling, and Evaluation of a Scalable Multi-Level Checkpointing System. Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC’10, USA, IEEE Computer Society. 2010; pp. 1–11. 9781424475599. Publisher Full Text\n\nThurgood B, Lennon RG: Cloud computing with kubernetes cluster elastic scaling. Proceedings of the 3rd International Conference on Future Networks and Distributed Systems, ICFNDS’19, New York, NY, USA. Association for Computing Machinery; 2019. 9781450371636. Publisher Full Text\n\nDrako D: The need for speed: From electric supercars to cloud bursting for design. Proceedings of the 2022 International Symposium on Physical Design. 2022; pp. 1–1.\n\nMölder F, Jablonski KP, Letcher B, et al.: Sustainable data analysis with snakemake. F1000Res. January 2021; 10: 33. PubMed Abstract | Publisher Full Text | Free Full Text\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\nColonnelli I, Cantalupo B, Merelli I, et al.: StreamFlow: Cross-Breeding cloud with HPC. IEEE Trans. Emerg. Top. Comput. October 2021; 9(4): 1723–1737. Publisher Full Text\n\nMerow C, Boyle B, Enquist BJ, et al.: Better incentives are needed to reward academic software development. Nat. Ecol. Evol. May 2023; 7(5): 626–627. PubMed Abstract | Publisher Full Text\n\nShen Y, Heacock L, Elias J, et al.: ChatGPT and other large language models are double-edged swords. Radiology. April 2023; 307(2): e230163. PubMed Abstract | Publisher Full Text\n\nLarsson L, Tärneberg W, Klein C, et al.: Impact of etcd deployment on kubernetes, istio, and application performance. Softw. Pract. Experience. October 2020; 50(10): 1986–2007. Publisher Full Text\n\nDi Natale F, Bhatia H, Carpenter TS: A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, number Article 57 in SC’19, New York, NY, USA. Association for Computing Machinery. November 2019; pp. 1–16.\n\nBhatia H, Di Natale F, Moon JY, et al.: Generalizable Coordination of Large Multiscale Workflows: Challenges and Learnings at Scale. SC21: International Conference for High Performance Computing, Networking, Storage and Analysis. 2021; pp. 1–16. Publisher Full Text"
}
|
[
{
"id": "267225",
"date": "07 Jun 2024",
"name": "Rafael Ferreira da Silva",
"expertise": [
"Reviewer Expertise Distributed computing",
"scientific workflows",
"high performance computing"
],
"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 introduces an approach to converged computing by integrating the Flux Framework within Kubernetes. This integration aims to leverage the benefits of both HPC and cloud-native environments to improve workflow portability, flexibility, and manageability. The Flux Operator enables hierarchical resource management and scheduling within Kubernetes, addressing the growing need for efficient and scalable batch workload orchestration. This paper details the design decisions, component mappings, and experimental features of the Flux Operator, highlighting its ability to enhance performance compared to existing solutions like the MPI Operator. Experiments conducted using AWS Elastic Kubernetes Service (EKS) demonstrates improved performance of the Flux Operator in running HPC applications such as LAMMPS.\nMinor comments for improvements:\n- The definition of modern workflows in the introduction should be broadened to include AI-HPC workflows. These workflows are characterized by their dynamic behaviors, human-in-the-loop processes, conditionals, and loops. Incorporating this definition will provide a more comprehensive overview of the current landscape of HPC workflows and highlight the increasing complexity and versatility of these tasks.\n- In Section 2.1.3, it would be beneficial to provide insights on potential approaches for achieving separation of application logic from Flux without impacting performance. This could include exploring containerization strategies that decouple the application and Flux components, using lightweight virtualization techniques, or employing modular software design principles that isolate application-specific logic from the underlying workload management framework.\n- The experimental evaluation in Section 3.1 would benefit from including an experiment that compares the overall time-to-solution for running an experiment using the Flux Operator versus the MPI Operator. Specifically, it would be useful to analyze the overhead or cost associated with preparing the environment for the operator (e.g., pulling the container) and the subsequent performance gains over time compared to the MPI Operator.\n- It would be helpful to briefly discuss the cause of the outlier observed for 6016 ranks in Figure 3.\n- In Section 3.2, the variability shown in Figure 3 would be better expressed if a distribution of nodes-ready times (per node) were included. Presenting this data would offer a more granular view of the time it takes for individual nodes to become ready, highlighting any significant deviations and providing insights into the factors influencing node startup times.\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": []
},
{
"id": "284364",
"date": "11 Jun 2024",
"name": "David Hancock",
"expertise": [
"Reviewer Expertise return on investment of research computing",
"high performance computing and cloud systems architecture and deployment."
],
"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 presents a comparison of two operators to execute HPC workflows within Kubernetes. It provides detailed background and motivations for using Flux as well as motivations for \"converged computing\" in general. Ultimately it aims to show better efficiency at modest scale of the Flux Operator over the MPI Operators for LAMMPS\nSome minor tweaks would improve readability as well as ideas for future work.\n\nLanguage in the Abstract: Referring to Kubernetes as a \"batch workload orchestrator\" seems odd, certainly a de facto standard but most approaching Kubernetes would not be approaching it from a batch mindset. It is certainly tied together later on when speaking about Kueue but I think the audience from either HPC or Cloud might balk at that descriptor.\n\nLanguage in the in Introduction: \"While a traditional HPC job is, e.g...\" This sentence with an abbreviated example given embedded makes it very difficult to read/parse, consider... As an example a traditional HPC job is/may be/can be...\nThe data in Table 1 are concise enough that a table seems unnecessary at all and either a text-based description or just pointer to the guide would suffice. It does not seem to contribute to the overall article much.\n\nThe conclusion is quite philosophical and well-beyond the original stated goal. Perhaps a better way to start it is to wrap up the technical conclusion based on the original premise and then use the remainder to move into that area or add another section on motivations in/after the discussion. I don't disagree with many of those thoughts they just seem a bit out of sync with the specific goal.\n\nAnother curiosity or area of exploration in other work would be to look at this challenge from a user/operator perspective, what is the uptake among the current user base from an HPC center and certainly there are LLNL plans to use Flux at scale what interest is being seen elsewhere? Conversely understanding uptake of the MPI Operator from a Cloud perspective would be interesting if such data are available. These are perhaps out of scope for this article but questions many readers may have with respect to Flux.\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/13-203
|
https://f1000research.com/articles/13-202/v1
|
21 Mar 24
|
{
"type": "Research Article",
"title": "Predictors of hypertension among diabetic patients in the Ejisu municipality of Ghana",
"authors": [
"Florence Brenyah",
"Charles Apprey",
"Jacob K. Agbenorhevi",
"Felix C. Mills-Robertson",
"Charles Apprey",
"Jacob K. Agbenorhevi",
"Felix C. Mills-Robertson"
],
"abstract": "Introduction The co-existence of hypertension with diabetes mellitus among diabetic patients is a setback to public health. About 40-75% of diabetic patients present with hypertension. The co-existence of hypertension and diabetes can accelerate complications such as stroke, myocardial infarction, nephropathy, and mortality. Available data indicate the devastating effects of hypertension and diabetes on individuals, families, and the economy as catastrophic. Therefore, knowing the predictors of hypertension among diabetic patients would inform the lifestyle and management of the two conditions.\n\nObjective The study focused on predictors of hypertension among diabetic patients in the Ejisu Municipality of Ghana.\n\nMethods The study employed a quantitative approach with a sample size of 120. Data were collected on sociodemographic characteristics, family history, 24-hour dietary recall, blood pressure, fasting blood glucose, glycated haemoglobin, total lipid profile, and anthropometrics. Data were analyzed using SPSS version 27.\n\nResults Out of 120 respondents, 85% were females with 77.5% above 50 years of age. A majority (66.7%) had a family history of diabetes with 76.7% having hypertension as a comorbidity. Fasting blood glucose was found to be 8.519 times more likely to present with hypertension. Systolic blood pressure, carbohydrate, and sodium intakes were 6.1%, 2.9%, and 0.1% respectively. However, diabetic patients with high HbA1c were 97% less likely not to present with hypertension.\n\nConclusion Hypertension was found to be the most common comorbidity among diabetic patients in Ghana. Glycaemic control, systolic blood pressure, and dietary factors specifically carbohydrate and sodium intake were significant predictors of hypertension among the study participants.",
"keywords": [
"Predictors",
"Hypertension",
"Diabetic Patients",
"Ejisu Municipality",
"Ghana"
],
"content": "Introduction\n\nDiabetes is acknowledged as one of the major causes of morbidity, disability and death.1–3 Globally, an estimated 1.13 billion and 463 million people are affected with hypertension and diabetes respectively. The implication is that 1 in every 11 adults aged between 20-79 years is affected by one or both health conditions.4 The more serious development is the emergence of hypertension among diabetic patients. Most discussions on diabetes and hypertension have centered on their common risk factors (physical inactivity, unhealthy dietary behaviour, excessive smoking, and alcohol consumption), the magnitude of people involved, and the management of both conditions.4,5 The combined effects of the occurrence of these two health conditions have serious implications for individuals’ well-being and state welfare.6 Studies have shown that not only is the high incidence and complications associated with the co-existence of hypertension and diabetes in patients is significantly straining the healthcare system and providing a challenge to treatment but also largely associated with increased healthcare costs and plunging families into poverty.6–8 For instance in low-resourced countries, the co-existence of hypertension and diabetes exacerbates the already fragile healthcare system, aggravates the plight of people with low socioeconomic status, and has a double burden on the government healthcare budget and gross domestic product.9–13 This may have serious repercussions for quality of life, worsen life expectancy, and distort government budget allocations for development. Moreover, the devastating effects of hypertension and diabetes may thwart the World Health Organization’s (WHO) goal of decreasing 1/3 of morbidity and mortality rates from non-communicable diseases (NCDs) by 2030. 5,14 The achievement of the content of the Global NCD Compact 2020-2030 which aims at preventing and controlling NCDs dwells on member states adopting policies and programmes that improve NCDs outcomes and save the lives of people living with NCDs. The 2020-2030 Global NCDs Agenda’s success may centre on human resources implicated in the surging NCDs occurrence.\n\nIn sub-Saharan Africa, some studies have been done separately on hypertension and diabetes among patients and community members in urban settings.15–21 Studies of hypertension among diabetic patients in peri-urban communities are scanty. This study seeks to identify predictors of hypertension among diabetic patients in the Ejisu Municipality of Ghana.\n\nIn Ghana, hypertension and diabetes have continuously been among the top 10 causes of morbidity, hospital admissions, and mortality22–24 in both urban and rural areas yearly. 25–31 These rankings are based on hospital-based data though it is known that most hypertension and diabetes cases are cared for at faith-based and herbal medicine centres and these are largely unreported cases. Again, a section of the population may not be aware of the existence of hypertension or diabetes as their health condition. Also, other people ignore they have the disease as reported by WHO and the International Diabetes Federation.4\n\nGeographically, the occurrence of hypertension and diabetes just like any other health condition may be in segments based on the contents of the social gradient of health. The implication is that the degree of occurrence of hypertension and diabetes is affected by geographical variability due to differences in dietary behaviour, occupational status, socio-cultural factors, environmental influences, health seeking behaviour among others. The Ejisu Municipality is characterized as a diabetes-endemic zone with a high incidence of diabetes.32–35 Studies have mentioned that 40-75% of diabetic patients present with hypertension and this significantly increases the development of diabetes-related complications and mortality.36,37 Also, studies have reported that knowledge of conditions surrounding the occurrence of health conditions such as diabetes and hypertension may facilitate individual’s efforts in self-management of their health.38 This is especially essential due to the possible differences in the prevalence, knowledge, treatment, and management of hypertension and diabetes globally and regionally. Therefore identifying the predictors of hypertension among diabetic patients in the municipality would provide evidence-based information for health stakeholders to develop appropriate mitigation mechanisms. Again, the outcome of this study may also serve as baseline data to guide the conduct of many research works on hypertension and diabetes.\n\n\nMethods\n\nThe study was conducted in the Ejisu and the Onwe Government Hospitals from March 2022 to July 2022.\n\nThe current study adhered to STROBE checklist for study reporting. We therefor adopted a baseline cross-sectional study design with quantitative approach.\n\nThe study population covered all type II diabetic patients attending the diabetic clinic in the two hospitals in Ejisu Municipality.\n\nThe study adopted simple probability technology to recruit respondents (YES or NO) based on the folded paper. Participants who selected YES were considered for the study and were further taking through informed consent processes.\n\nInclusion and exclusion criteria were developed. The inclusion was participants above 18 years of age, diagnosed with diabetes <10 years, and void of any diabetes-related complications. All other patients aside from the above were excluded from the study.\n\nTo achieve an 80% power to detect a 1% difference in HbAlc, the sample size was σ determined using the expression adopted by Noordij et al.39 The equation is presented as:\n\nWhere n is the sample size, μ1refers to the population mean in the interval group (HbAlc = 9.9) μ2 is the population means in the control group (HbAlc = 8.9,) and represents the difference the investigator seeks to detect. The power of the test was set at 99% and at 5% significance where a = 1.96 for alpha (0.05) and b = 0.842 for power 0.80 and beta (0.20).\n\nThe sample size (n = 59.82) was approximated to be 60 participants for each hospital making 120.\n\nQuestionnaires made up of socio-demographic characteristics, 24-hour dietary recall, and anthropometric and blood pressure measurements were administered to patients. Again, the study also took the biochemical parameters of the participants.\n\nAnthropometric parameters\n\nHeight and body weight were measured using a stadiometer and a standard digital scale (Hewer brand, manufactured by G.S.T Corporation, New Delhi, India). The impedance of the body of each patient was calculated using Bioelectrical Impedance Analysis (BIA) by imputing the age, gender, and height. The patient was asked to stretch the arms parallel to the floor at shoulder level. The BIA consequently generates visceral fat (VF), muscle mass, body fat, and body mass index which were used as the standard references for the study\n\nDietary assessment procedure using 24-hour dietary recall\n\nThe triple-pass method was adapted for the 24-hour dietary recall.40 The respondents had to mention the time at which the food or drink was consumed, a full description of the food or drink, including brand names where available, quantity consumed, based on household measures and food modules, foods eaten in combination, and any leftovers.\n\nBlood pressure measurement\n\nEach participant’s blood pressure was measured three times and the average was recorded using an automated sphygmomanometer (Intelli Sensetm boots blood pressure monitor) at the upper arm; recording the systolic and diastolic measurements. This was done after the participant had been allowed to rest for 15 minutes on arrival.\n\nBiochemical parameters\n\nA venous blood (5 mL) was drawn from the patients between 7 am and 9 am each day after an overnight fast according to the protocol declaration of Helsinki. Between these hours, 2 mL and 3 mL of the drawn blood were transferred carefully into separate tubes containing sodium fluoride and a gel-clot activator. Plasma was obtained from each participant’s blood sample for further analysis of plasma glucose concentration after allowing the samples in the sodium fluoride tubes to stand for about 2 hours. The blood samples in the gel-clot activator tubes were centrifuged at 3000 rpm for 10 minutes to obtain serum for each sample for further biochemical analysis.\n\nData were cleaned and entered into an IBM statistical package for social science (IBM SPSS) version 20. Data were stored electronically and secured with a password. Data would be discarded 3 years after the publication of this paper.41\n\nData from the anthropometric measurement was analysed into body mass index (BMI). The BMI was calculated as weight divided by square height (kg/m2) and categorised into (underweight <18.5, normal weight >18.5 <25, overweight < 25 >29.9 and Obese (≥ 30). The blood pressure was also categorized as normal (systolic 90-120 mmHg, diastolic 60-80 mmHg), pre-hypertension (systolic 120-140 mmHg, diastolic 80-90 mmHg) and hypertension (systolic 140-190 mmHg, diastolic 90-100 mmHg). The 24-hour dietary recall data were entered into the Nutritional Analysis Template. Appropriate commands were employed on the Nutritional Analysis Template to generate the results.\n\nIn analysing the blood samples, the concentration of each participant’s plasma glucose, total cholesterol, and HDL-cholesterol was measured via the use of the glucose oxidase-peroxidase method (GOD-POD method) whereas blood triglyceride and glycated haemoglobin (HbAlc) were measured using the Fortress Diagnostic Reagents and the CLOVER Alc® Self Analyzer, respectively. Also, LDL-cholesterol level was calculated using the Friedwald Equation.42 The analysed data were presented as Tables in frequencies and percentages with statistical interpretations.\n\n\nResults\n\nA majority (85%) of the participants were females. Over 77.5% of the participants were more than 50 years of age. It was found that 44.2% of participants were married, and 55.8% had Junior High/Middle School leaving certificates as their highest level of education as shown in Table 1.\n\nThe study examined the family and participants’ medical history. In total, 66.7% of the participants had a family history of diabetes. Again, 40% of the participants had lived with diabetes for more than 5 years. The study found that 76.7% of the participants had hypertension as a comorbidity. All the participants were on combined medication for diabetes and hypertension or diabetes alone as shown in Table 2.\n\nThe study found that 36.7% and 25.8% were overweight and obese respectively. Also, 42.5% of participants recorded elevated visceral fat while 90.1% recorded high body fat. Again, with systolic blood pressure, 35.8% and 49.5% recorded prehypertension and hypertension levels respectively while 33.3% and 45.5% recorded pre-hypertension and elevated blood pressure levels in the diastolic as presented in Table 3.\n\nAbout 55.8% of the respondents have high fasting blood glucose levels. Also, 47.5% had elevated glycated levels. In measuring lipid profile, 62.5% and 37.5% of the respondents were within the normal range of high-density lipoprotein (HDL) and low HDL respectively. The majority of the respondents 82.5% were within the normal range of low-density lipoprotein. Again, 40.8% of participants were within the elevated range of total cholesterol while 40.8% of them recorded elevated triglyceride levels as shown in Table 4.\n\nThe study found that 50.8% of participants met the RDA of caloric intake and 84.2% met the protein requirement. Almost all the participants (99.2%) met the RDA for carbohydrate intakes with 62.5% meeting the recommended intakes of dietary fiber. With the micro-nutrients, the overwhelming majority did not meet the RDA of calcium (99.2%) and potassium (88.3%). About (60.8%) and (36.7%) met the RDA of dietary sodium and zinc intakes respectively while the majority of the respondents (91.7%) met the recommended intakes of dietary copper as shown in Table 5.\n\nThe model correctly predicted that 88 out of the 102 patients who reported hypertension had hypertension with an accuracy rate of about 96%. The accuracy level for a correct prediction of patients who did not report hypertension was 64%, predicting that 18 out of the 28 patients who reported without hypertension did not have hypertension. Overall, the model accurately predicted 88.3% of the observed results as shown in Table 6.\n\nFrom Table 7, DM patients who had high HbA1c were less likely to report to the hospital with hypertension the odds of 0.028. The results also showed that, as the fasting blood glucose (FBG) of the diabetic patients increased, they were 8.519 times or 751.9% more likely to present with hypertension. The diabetic patients with high systolic blood pressure also had 6.1% odds of presenting with hypertension with every one unit increase in systolic blood pressure. As the intake of carbohydrates increases, there is a decreasing odd (2.9%) of diabetic patients presenting with hypertension. The results also indicated that increasing the intake of sodium by diabetic patients increases (0.1%) the odds of presenting with hypertension.\n\n\nDiscussion\n\nIn this section, we discussed the results of this study in comparison with other studies conducted and published by various authors on the subject matter. Our discussion is also patterned along sociodemographic characteristics, medical history, biochemical, anthropometric, and blood pressure parameters, dietary intakes, and predictors of hypertension among diabetic patients.\n\nThe study found that female participants formed the majority group probably because studies have found more women than men visit clinics to seek health care.43,44 The majority of the study participants were above 50 years and this is consistent with research outcomes reporting both diabetes and hypertension as associated with increasing age.45–47 Emphasizing this, a study by Atibila et al.,46 in the Dormaa Ahenkro Municipality in Ghana, reported that increasing age (≥ 45 years) was associated with a 2.75 increased odds of developing hypertension. Again, Bai et al.,47 reported an increasing prevalence of diabetes as age increased. The current study found that the majority of the participants were married. This is consistent with other studies that reported on gender sensitivity in males and females regarding hypertension and diabetes occurrence.48,49 For instance, the study of being married was an important risk factor for hypertension and tended to be a significant risk factor for mortality in men as reported by Ramezankhani, Azizi, & Hadaegh.48 The implication is that the current study outcome of the association of marriage with hypertension and diabetes is in consonance based on females and contrary when men are considered as reported by Ramezankhani, Azizi, & Hadaegh.48 Another study by Tuoyire & Ayetey49 reported on the contrary that, married men had significantly higher odds of hypertension than females. Further study findings revealed by Ford & Robitaille50 mentioned that married people had better HBA1C values than their single counterparts. In terms of educational status, the majority of the participants had a middle/secondary school certificate as their highest level of education. This is consistent with other studies’ results which have reported a higher percentage of type 2 diabetic patients had little education.51,52 The implication is the likelihood of poor glycaemic control and poor blood pressure management which may be due to poor knowledge on hypertension and diabetes.\n\nIn the assessment of medical history, the majority of the study participants had a family history of diabetes and hypertension, and this finding is consistent with other research outcomes which report that a family history of diabetes and hypertension increases an individual’s risk of developing the condition.53–56 Again, the current study found a high occurrence of the co-existence of hypertension and diabetes and this is consistent with the study by Haile et al.,31 and Berbari et al.57\n\nThe anthropometric assessment revealed that more than half of our study participants were overweight and obese which has implications for the occurrence of hypertension and diabetes. This is in consonance with the study outcome of Patel, et al.,58 which revealed that among their study participants, every standard deviation higher in BMI was associated with a 1.65 and 1.60 times higher probability of developing diabetes and 1.42 and 1.28 times higher probability of developing hypertension, for men and women respectively. This is similar to a study by Ofori-Asenso et al.,59 which reported a greater prevalence of overweight and obesity in Ghana. Clearly, not only is obesity associated with hypertension and diabetes but also has strong links to the increase of visceral fat.58 A little below half of the participants recorded high visceral fat and an overwhelming number of the participants recorded high body fat. This ties well with the assertion by Agyemang-Yeboah et al.60 that excess amounts and distribution of body adiposity have been implicated in the development of cardio-metabolic diseases such as heart attack, stroke, insulin resistance, and non-alcoholic fatty diseases. For instance, evidence-based research by Strong, et al.,61 reports that a 10% increase in overweight and obesity causes an increment of 4% in diabetes and 4.9% in hypertension in India. Again, Strong et al.61 put forward that, 35.8% and 33.3% of participants recorded high systolic and diastolic blood pressure signifying pre-hypertension. Tan & Thakur,62 assert that studies have shown a J-curve association between blood pressure among diabetic patients and with risk of myocardial infarction and death. In corroborating the assertion of Tan & Thakur,62 the review of Gaffney, et al.63 equally mentioned that a “J” or “U-shaped curve” in the association between diastolic BP and cardiovascular events has been observed in epidemiological studies, suggesting that both high diastolic BPs and low diastolic BPs below are associated with a higher risk of cardiovascular disease (CVD) events and these have the tendency of exacerbating the condition of diabetic patients. Petrie, Guzik, & Touyz,64 gave confirmatory reports that several studies have linked poorly controlled high blood pressure among diabetic patients to higher increase in heart diseases, renal diseases, and stroke. Equally, a study outcome by John Hopkins University in 202365 revealed that high blood pressure is twice more likely to strike a person with diabetes than a person without diabetes. The study also emphasised that a person with diabetes and high blood pressure is four (4) times more likely to develop heart disease than someone who does not have either of the conditions.65\n\nThe outcome of the biochemical analysis in our study revealed that more than half of the participants had their fasting blood glucose poorly controlled and 33.3% of the respondents had their haemoglobin A1C (HbA1c) poorly controlled. A study by Li, Xu, Liu, et al.66 confirmed that Poor glycemic control (HbA1c ≥8%) has been associated with decreased survival in the general population of diabetic patients on maintenance hemodialysis among patients in China. Similarly, the study outcome of Cheneke, et al.67 found that even though the study participants were on diabetes treatment, the majority of them were found to have poor glycemic control. Similar studies in the sub-Saharan Africa context by Govender, et al.,68 and Legese, et al.,69 have shown that poor fasting blood glucose and haemoglobin A1C status have been found among diabetic patients. Again, we found that 40.8% of the study participants in our research recorded high total cholesterol levels with a little below half recording high triglyceride levels above 1.71mmol/L. Also, a little below half of our study participants had low HDL levels and just (17.5%) recorded elevated LDL levels. Studies have found that healthy subjects without metabolic syndrome increasing triglyceride levels within the normal range can trigger a continuous increase in type 2 diabetes incidence.70 Therefore proper management of dyslipidemia could help reduce the development of hypertension among diabetic patients and reduce hypertension-associated complications such as nephropathy.67,69\n\nDietary behaviour is associated with the onset of hypertension and diabetes. Our study found that the majority of the respondents met the recommended dietary allowance (RDA) of protein and carbohydrates while about half of the respondents met the RDA of caloric intake. A Research outcome from the Chinese Centre for Disease Control and Prevention stated that the ratio of macronutrients to total dietary energy for diabetics is recommended to be: 15 to 20 % protein, 45% to 60% carbohydrate, and 20% to 35% fat. Our study participants are therefore commended for meeting that requirement. However, we found 37.5% of respondents did not meet the RDA of fibre which aids in the prevention and management of diabetes, reduction of cholesterol, protection of the heart as well as management of weight. Again, we found a majority of the respondents recorded inadequate intake of calcium, potassium, and zinc (micro-nutrients). These minerals are considered important in maintaining the homeostasis of glucose metabolism. Similarly, the study by Baqar, et al.71 revealed that only 7% and 5% of participants met dietary sodium and potassium requirements respectively.\n\nIn assessing the predictors of hypertension and diabetes, factors such as the level of HbA1c, FBS, systolic blood pressure, intakes of carbohydrates, and sodium were the main determinants in our study. For instance, our study results seem to suggest that, relating to glycemic control parameters, individuals with higher HbA1c were less likely to have hypertension, while increasing fasting blood glucose (FBG) values increased the likelihood of an individual having hypertension. Our finding is contrary to the results of Bower et al.,72 who reported that higher HbA1c was associated with an increased risk of hypertension. Differences in outcomes relating to HbA1c in our study and that of Bower et al.72 may be due to certain confounders of which we are not privy. Based on our study results, we share a similar opinion with operational research studies outcomes that have reported that poor glycaemic control increases one’s risk of developing diabetes-related complications, including hypertension in diabetic patients.18,73,74 Again, our study outcome revealed that, high systolic blood pressure was associated with an increase in the likelihood of hypertension. Studies have reported that systolic hypertension is more highly associated with cardiovascular events than diastolic hypertension.75,76 In relating this finding to our study outcomes, we realized that barring all other confounders, our study participants may be at a higher risk of experiencing adverse cardiovascular events. Also, our study found that increased intake of carbohydrates was predictively associated with reduced odds of participants’ hypertension occurrence. This finding in our study is a bit complicated especially when we are aware that, a study by Wheatley et al.77 has reported that carbohydrate restriction positively impacts glycaemic control in diabetic patients. Our study could not readily ascertain the reasons for the differences in outcomes. However, the study outcome of Bonsembiante et al.78 and Li et al.79 seem to offer an explanation that; a high carbohydrate diet relying on carbohydrates with a low glycaemic index and higher fibre content can be beneficial for diabetic patients, whereas rapidly digestible, high glycaemic index carbohydrates negatively impact glycaemic control in such patients and predispose them to complications like hypertension.\n\nFinally, we found that increased intake of sodium by study participants increased their odds of presenting with hypertension. This is evidenced in published literature highlighting high sodium intakes and associated risks such as the development of hypertension.80–82 This is consistent with study outcomes which report high salt and processed food intake in sub-Saharan Africa.63,83,84\n\n\nConclusion\n\nThe study found the prevalence of systolic and diastolic hypertension among diabetic patients to be 49.2% and 45.0% respectively. The study concludes that sociodemographic characteristics, family history, anthropometric variables, blood pressure and unhealthy dietary behaviour are key in the occurrence of hypertension among diabetic patients\n\nThe study is limited in scope mainly due to the fact that, participants were recruited from only two hospitals in the municipality. It would have been more appropriate to sample participants across minimum of two regions in Ghana thus making the results valid for generalization. Despite this limitation, the outcome of this study may give a baseline data for health researchers for further studies.\n\nThe study calls for preventive measures such as health promotion and education on the risk factors of hypertension and the repercussions on diabetes within the population in order to control the tide of the co-existence of hypertension and diabetes among patients.\n\nIt is suggested that future research should cover the health-seeking behaviour and management of the co-existence of hypertension and diabetes in rural areas in Ghana.\n\nInformed consent was conducted with the patients. The study participants were approached face to face and the purpose of the study were explained to them. Those who consented to participate in the study were given written consent forms to sign and date in duplicates.\n\n• Approval of the research protocol:\n\nThe KNUST Committee for Human Research, Publication, and Ethics approved the study by vetting thoroughly the content of the study proposal with approval number CHRPE/AP/168/22.",
"appendix": "Data availability\n\nDryad: Predictors of hypertension among diabetic patients in the Ejisu Municipality of Ghana, https://doi.org/10.5281/zenodo.10431520. 85\n\nThis study contains the following files:\n\n• Data on hypertension among diabetic patients. This data consist of all the parameters on hypertensive and diabetic patients who participated in this study from two hospitals name Hospital A and B.\n\n• Questionnaire. This questionnaire covers the family and medical history, knowledge on diabetes, lifestyle practices, 24hour dietary recall, anthropometric measurements, and biochemical parameters.\n\n• Raw Data on hypertension among diabetic patients (Baseline data). This dataset is in SPSS. To access this data, one needs to have SPSS installed on the computer.\n\n• Coding Scheme: The data used the coding scheme below in the SPSS:\n\nFBG - Fasting Blood Glucose\n\nHDL - High-Density Lipoprotein\n\nLDL - Low-Density Lipoprotein\n\nTG - Triglyceride\n\nVF - Visceral Fat\n\n\n\n• Analysed Dataset: This is the results of the analysed that uploaded as ‘supporting tables out of the study data’\n\n• Participant information sheet: This document provided information about the nature and processes of the study for the participants to make informed decisions and confirm participation by signing consent form or otherwise.\n\n• Consent forms: This sheet signed by participants meant they have willingly given their consent to participate in the study.\n\nData is available under the terms of the CC BY 4.0 Attribution 4.0 International. https://creativecommons.org/licenses/by/4.0/.\n\n\nReferences\n\nMagliano DJ, Boyko EJ: IDF Diabetes Atlas 10th edition scientific committee. 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Publisher Full Text\n\nBrenyah F, Apprey C, Agbenorhevi JK, et al.: Predictors of hypertension among diabetic patients in the Ejisu Municipality of Ghana. [Dataset]. Dryad. 2024. Publisher Full Text"
}
|
[
{
"id": "263927",
"date": "06 May 2024",
"name": "Irene A Kretchy",
"expertise": [
"Reviewer Expertise Social and behavioral 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\nPredictors of hypertension among diabetic patients in the Ejisu municipality of Ghana General comments Hypertension in patients with diabetes is a major problem and this study focused on the predictors of hypertension among this population in the Ejisu Municipality of Ghana. Generally, the paper is well written with some issues listed below to be addressed.\nTitle: Avoid the label diabetic patients. Replace with patients with diabetes. Correct this throughout the write-up\nAbstract: The background should reflect the study title which is to look at the predictors of hypertension in diabetes. Issues of co-existence and comorbidity could be emphasized in the main background. Objective: this should be rephrased as an objective with an active verb. Methods: This should also provide information on the study design and inclusion of participants. Which factors were targeted as predictors of hypertension? These have to be specified and how they were measured also indicated Results: provide information on the extent of hypertension and the predictors that can follow.\nIntroduction The background of the study and the arguments about the extent of the problem are well-presented. It will be helpful to expand on the social gradient of health geographically concerning the occurrence of hypertension and diabetes in Ejisu. How do geographical variability due to differences in dietary behaviour, occupational status, socio-cultural factors, environmental influences, health seeking behaviour affect diabetes and hypertension in the community.\nMethods The study setting is not well described especially to help readers who may not be familiar with the setting to appreciate the context.\nWhat are the population sizes for the two facilities and would a proportionate distribution of the samples be better preferred?\nStudy variables: the background section and problem did not adequately focus on the study variables and it would be helpful to show how these variables determine hypertension in diabetes as indicated in the study title and objectives.\nWhat language was used for data collection and how were translation and quality assured? Results The results section is fine. Only 18 of the participants were male. How could that be explained in terms of sampling? Were there any biases?\nDiscussion Please explain why males are in the minority. The strengths of the study should be highlighted.\nConclusion It will be good to add the implications of the study findings.\nLimitations Other limitations related to selection and recall bias should be mentioned.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-202
|
https://f1000research.com/articles/13-200/v1
|
21 Mar 24
|
{
"type": "Study Protocol",
"title": "Assessment of Morbidity Profile and Perceptions in regards to Physical Activity amongst Display Screen Equipment Users working in a University Located in Central Rural India: A Mixed method study",
"authors": [
"Dipali Khode",
"Abhay Mudey",
"Abhay Mudey"
],
"abstract": "Introduction Sedentary nature of desk job workers makes them prone to various diseases, and using display screen equipment increases the risk. This study focused on the intricate associates linked with sedentary behavior, physical activity patterns, and morbidity profiles among display screen equipment users employed at a university in central rural India. Sedentary lifestyles, particularly those prevalent in desk-based occupations, contribute significantly to non-communicable diseases, including hypertension, diabetes, and cardiovascular diseases. Display screen users face additional risks such as vision-related issues, strain on eyesight, and musculoskeletal disorders.\n\nObjective The study aimed to comprehensively understand the morbidity profile and perceptions of physical activity among display screen equipment users.\n\nMethod This shall be a cross-sectional study with a mixed method component conducted at a medical university located in central India from January 24 to June 2024. A sample size of 97 participants was determined based on a previous study, and data collection shall be done utilizing systematic random sampling. Data will be gathered using the International Physical Activity Questionnaire (IPAQ) and Standardized Nordic Scale for musculoskeletal disorders through an online survey.\n\nStudy implication This study aims to elicit morbidity patterns among Display screen users and their perceptions and practices regarding physical activity. This will also increase awareness regarding physical activity and associated morbidities regarding display screen use.",
"keywords": [
"Physical activity",
"Desk job workers",
"Display screen users",
"Sedentary behavior",
"Morbidity",
"perception",
"Mixed method research."
],
"content": "Introduction\n\nThe World Health Organization (WHO) defines physical activity as any movement initiated by the skeletal muscles that requires energy expenditure. This includes all types of movement, whether during leisure, transportation, or occupational activity. Participation in both moderate- and vigorous-intensity physical activities has been demonstrated to improve overall health.1 Devices or equipment with alphanumeric or graphic display screens such as laptops, touch screens, and similar devices are collectively referred to as display screens.2 In the modern context, the majority of working adults are prone to accumulate a significant portion of their sedentary time in the workplace, surpassing the duration of sitting during leisure activities. Recognized as a distinct risk factor for adverse health outcomes, sedentary behavior is now acknowledged independently of insufficient physical activity.3 Sedentary behavior is described as activities performed while sitting or reclining, with energy expenditure not exceeding 1.5 times the basal metabolic rate. Individuals in desk-based occupations experience extended periods of high sitting times during their work hours.4 Lack of physical activity increases the likelihood of developing cardiovascular diseases and chronic conditions, such as diabetes, hypertension, and obesity.5 Nevertheless, occupational sitting stands out as the primary mover of sedentary behavior in numerous industrialized nations, leading the World Health Organization (WHO) to identify the workspace as a high priority for health promotion.3 Work-related energy expenditure has declined significantly over the last five decades, marking a shift towards increased sedentary behavior and reduced physical activity among workers. This trend is expected to persist through 2030.6\n\nHealthcare professionals constitute a group facing both physical and mental burdens. The challenges of rotating work shifts, demanding tasks, and family-related responsibilities create difficulties in planning and engaging in physical exercise. Numerous studies emphasize that healthcare professionals not only lack sufficient physical activity but also engage in unhealthy dietary habits and alcohol misuse, placing them at an elevated risk of professional burnout.7 Individuals who extensively use computers often face a significant issue with work-related musculoskeletal disorders specifically affecting the neck among others.8 Extended duration of sitting in adults are commonly correlated with a heightened risk of diabetes, obesity, cardiovascular diseases, lower back pain, and increased overall mortality.9 Based on the report from the National Institute of Family and Health Welfare, India represents 17% of the 11 million occupational disease cases, amounting to 1.9 million cases, and 17% of the global occupational disease deaths, which total 0.12 million.10\n\nInsufficient physical activity is responsible for 6% of global deaths, contrast to a previous study that proposed a higher estimate of 9%.7 There is evidence indicating that the use of digital screens is associated with dry eye disease. Additionally, the use of digital devices has been shown to alter blinking dynamics. Furthermore, it has been established that dry eye can impact the mental health and work productivity of individuals who use digital screens.11 Examining physical performance differences between males and females, particularly in scenarios where time and environmental constraints impose limitations on ergonomic choices for task completion.12 Affecting individuals from various backgrounds who use computers, computer vision syndrome has emerged as a significant public health concern, potentially evolving into an occupational epidemic in the twenty-first century.13 Research conducted in Loni Maharashtra, findings revealed that 93.3% of the study participants experienced more than one health issue related to computer usage. The predominant complaint was musculoskeletal problems (73.3%), followed by ocular issues (65.3%) and psychosocial concerns (46.0%). Another study conducted in India reported that 75.5% and 59.4% of respondents reported discomfort related to musculoskeletal issues and computer vision syndrome, respectively.14\n\n\nRationale\n\nA sedentary lifestyle is a high-risk factor for the development of non-communicable diseases, such as hypertension, diabetes mellitus, dyslipidemia, stroke, and cardiovascular disease.\n\nDisplay screen equipment users have an additional risk of screen time, leading to morbidities such as ophthalmic complaints, headache, vertigo, and other vision deformities.\n\nThis study assesses the pattern of physical activity level and morbidity profile simultaneously and aims to provide a holistic understanding of the health status of display screen equipment users.\n\nThis comprehensive approach allows for the identification of potential associations between sedentary behavior and health conditions among desk job workers, while qualitative inquiry with the study participants will enable a better understanding of their subjective perceptions.\n\n\nAim\n\nAssessment of Morbidity profile and perceptions regarding Physical Activity among display screen equipment users working in a university located in central rural India.\n\n\n\n1. To study the socio demography profile of display screen equipment users.\n\n2. To determine the Morbidity profile amongst study participants.\n\n3. To study the display screen use duration and association with morbidity amongst study participants.\n\n4. To assess the perceptions in regards to physical activity amongst study participants.\n\n\nMethods\n\nThe current study will utilize a cross-sectional design incorporating a mixed-method approach.\n\nThe current study will be conducted at a university located in rural central India.\n\nThe male and female employees (>18 years) using Display screen equipment.\n\nStudy participants working at the university using display screen equipment and were willing to participate in the study.\n\nThe study participants not using Display screen equipment shall be excluded from study.\n\nThe study will be carried out between January 2024 to June 2024.\n\nConsidering the prevalence reported in previous studies to be 0.933.14 The sample size was calculated using the following formula:\n\nAlpha (α) 0.05\n\nEstimated proportion (p) 0.933\n\nEstimated error (d) 0.05\n\nEstimated sample size = 97\n\nA systematic random sampling procedure will be used, where a list of all eligible employees will be extracted from the head office, and the sampling fraction will be obtained by dividing the total population by sample size, which will be used as interval(n). The 1st number will be chosen randomly, and then every nth number after the 1st will be included as a study participant. An interview technique using the online tool Kobo Collect (https://www.kobotoolbox.org/) will be used. This will be done until the desired sample size is achieved.\n\n\nVariable\n\nThe study variables that shall be studied are as follows:\n\n1. Demographic data\n\n2. Job desk workers\n\n3. Display screen users\n\nThis study will be using the International Physical Activity Questionnaire (IPAQ)13 and the Standardized Nordic Scale for musculoskeletal disorders.14 Participants will engage in face-to-face interviews utilizing a pre-tested questionnaire after obtaining their informed consent. This tool will be referred to as the Kobo collection tool. The pre-structured questionnaire will be used to collect information about the physical activity among job desk workers with the help of the kobo collection tool. The questionnaire will contain sociodemographic data, display screen use, and morbidity patterns.\n\nAn in-depth interview guide will be used to conduct qualitative inquiries among randomly selected participants until data saturation is reached. All important information about variables, data sources, and methods is shown in Table 1.\n\nThe list of all eligible employees shall be obtained from head office.\n\nThe study participants shall be selected using a systematic random sampling method. To ensure that participants fully understood the research goals, the purpose of the study will be explained to them in their local language. Those willing to participate asked to provide written informed consent. Similarly, in-depth interviews with randomly selected study participants will be conducted until the point of data saturation.\n\nThere may be some bias include in the study,\n\n1. Recall bias: Bias arises when the participants inaccurately remember the report information about past exposure and health problems. To minimize recall bias, the standardized well-structured questionnaire is used, and training the interviewer and establishing a rapport with participants can enhance the accuracy of the information provided.\n\n2. Social desirability bias: In qualitative inquiry related to perceptions and practices in regards to physical activity bias may occur as participants tend to give information to be aligned with existing social norms.\n\nThe Datta Meghe Institute of Higher Education and Research (DU), Ethical approval (DMIHER (DU)/IEC/2023/36) was granted by the Institutional Ethical Committee on Human Research for this study on dated 20/12/2023. Additionally, written informed consent will be obtained from all the participant before their inclusion in the study. Privacy and confidentially will be maintained throughout the study. Measures will be taken to minimize any potential harm or risks to the participants such as referrals for the medical consultation if needed.\n\nThe data will be analysis by the ‘R’ statistical software 4.3.2 version, available at https://www.-project.org/ and the data entered in Microsoft excel spreadsheet. Graphs, proportions, and frequency charts will be ustilized to present the descriptive data. The chi-squared test will be used for comparative analysis.\n\nThe qualitative data analysis will be done using Thematic content analysis.\n\nThis study shall generate evidence regarding the existing patterns of physical activity and the use of display screens. Morbidity among the study participants, which should also lead to sensitization of study participants and intervention strategies to be planned accordingly.\n\n\nDiscussion\n\nA cross-sectional descriptive study conducted in Mumbai by Shrivastav et al. India (2011). This study aimed to assess the prevalence of health issues among professionals in the software industry. In total, 178 participants were included in this study. The prevalence of visual is 67%, musculoskeletal is 63%, and stress is 44% are found. This study focused on ocular discomfort, musculoskeletal disorders, and psychosocial problems among computer screen users.14\n\nThe qualitative study was conducted in a United Kingdom city of a small software engineering company, on “they should stay at their desk until the work is done”: a qualitative study examining perceptions of sedentary behavior in a desk-based occupational setting to explore the desk-based office workers’ perception of factors that influence their behavior. It is essential to consider this discovery when implementing modifications that diminish sedentary behavior in the workplace.3\n\nGurhan Kayhan conducted a survey involving young female desk job workers to investigate the relationship between daily physical activity (PA) level and low back pain (LBP) in young women, to take an appointment for physical examination at the personal nutrition training center in Ankara, Turkey. To explore the correlation between daily physical activity levels and the occurrence of lower back pain. A total of 240 job desk women were included in the study, and the main finding was a U-shaped relationship between physical activity and lower back pain disability score in young women.9\n\nShah and colleagues conducted a cross-sectional descriptive study in Kathmandu Metropolitan City, Nepal. This study aimed to evaluate the occurrence rates of cardiovascular disease, musculoskeletal disorders, and job-related stress among individuals who use visual display screens in office settings. Among the study population, 36.7% experienced work-related stress, which was moderately challenging to manage. Additionally, this research aims to comprehend the awareness and utilization of preventive measures in this population. This study had 95% CI factors associated, and prevalence is (<0.01) was considered statistically significant.13\n\nA cross-sectional study was conducted at a tertiary care hospital in New Delhi, India to evaluate work-related neck pain among individuals with desk-based occupations. The study included a total of 441 participants, revealing a higher prevalence of this burden among females than males in the desk job workforce. The primary factor identified was prolonged computer usage of 4-6 hours, which emerged as the most significant predictor for WRNP. Subsequently, work-related aspects, such as screen height and posture, were also found to be associated with WRNP.8\n\nA systematic review conducted by Garlich et al. at the Cullen Eye Institute, Baylor College of Medicine, indicated that the connection between screen use and dry eye was particularly noteworthy. This is because patients experiencing dry eye may have a detrimental impact on their quality of life, potentially attributable to ocular pain and visual disturbances arising from tear film instability. The interconnection between dry eye and quality of life was observed in both health- and vision-related aspects. Furthermore, there is a correlation between dry eye and mental health, especially among individuals with an extensive use of digital screens.11\n\nYu et al. conducted a survey on Musculoskeletal problems among visual display unit workers in an international bank in Hong Kong. A self-administered questionnaire was used to gather information pertaining to work that involved the use of a visual display unit. All 121 employees were included in the study, of whom 70 were male and 51 were female age–18-41 years. Musculoskeletal issues, particularly neck, back, shoulder, and wrist pain, were most frequently observed. Employees predominantly experienced 30% of the back pain and neck pain cases.15\n\nKristel Oha et al. conducted a cross-sectional investigation of individual and work-related risk factors for musculoskeletal pain in computer users at two universities in Estonia. This study aimed to assess the prevalence of musculoskeletal pain (MSP) across different body parts in the preceding year and explore its correlation with individual attributes and work-related risk factors. The study included 412 participants. High prevalence rates were observed, with neck pain being the most common at 51%, followed by low back pain at 42%, wrist/hand pain at 35%, and shoulder pain at 30%.16\n\n\n\n1. To increase employees’ awareness of the importance of physical activity and strategies to mitigate health challenges associated with prolonged display screen equipment use by desk workers.\n\n2. The insights obtained can help healthcare professionals understand the problem and interventions planned to promote physical activity in display screen users.\n\n3. Recommendations on employee well-being programs that address both physical activity and morbidity identified in this study contribute to a healthier workforce and work environment.\n\nThe cross-sectional nature of the study restricts the generalization of the findings to other settings, so the findings could have limited external validity.\n\nThis study was approved by the institutional ethics committee. The supervisor created and approved the study’s data collection tool, which will now be evaluated for piloting in the study area.",
"appendix": "Data availability\n\nNo data associated with this article.\n\nRepository Name: Figshare\n\nFile name: STROBE checklist for “Assessment of morbidity profile and perceptions in regards to physical activity amongst display screen equipment users working in a university located in central rural India: A mixed method study.”, DOI: 10.6084/m9.figshare.25341730.v1.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPhysical activity: [cited 2023 Dec 8]. Reference Source\n\nWorking with display screen equipment (DSE).\n\nCole JA, Tully MA, Cupples ME: “They should stay at their desk until the work’s done”: a qualitative study examining perceptions of sedentary behaviour in a desk-based occupational setting. BMC. Res. Notes. 2015 [cited 2023 Nov 8]; 8: 683. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChau JY, Sukala W, Fedel K, et al.: More standing and just as productive: Effects of a sit-stand desk intervention on call center workers’ sitting, standing, and productivity at work in the Opt to Stand pilot study. Prev. Med. Rep. 2015 Dec 12; 3: 68–74. Publisher Full Text\n\nBoateng G, Batsis JA, Halter R, et al.: Activity Aware: An app for real-time daily activity level monitoring on the amulet wrist-worn device. Proc. IEEE Int. Conf. Pervasive Comput. Commun. Workshops. 2017 Mar; 2017. Publisher Full Text\n\nChau JY, Daley M, Srinivasan A, et al.: Desk-based workers’ perspectives on using sit-stand workstations: a qualitative analysis of the Stand@Work study. BMC Public Health. 2014 Jul 25; 14: 752. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaridi M, Filippopoulou T, Tzitzikos G, et al.: Correlating physical activity and quality of life of healthcare workers. BMC. Res. Notes. 2019 Apr 4; 12: 208. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWork-related neck pain among desk job workers of tertiary care hospital in New Delhi, India: Burden and Determinants - PMC.[cited 2023 Nov 8]. Reference Source\n\nKayihan G: Relationship between daily physical activity level and low back pain in young, female desk-job workers. IJOMEH. 2014 Oct; 27(5): 863–870. PubMed Abstract | Publisher Full Text\n\nRaj IS, Sundaram SP: Morbidity profile of workers and workplace assessment in selected soap industries in Puducherry. Int. J. Commun. Med. Public Health. 2021 Nov 24; 8(12): 6040–6046. Publisher Full Text\n\nAl-Mohtaseb Z, Schachter S, Shen Lee B, et al.: The relationship between dry eye disease and digital screen use. Clin. Ophthalmol. 2021 Sep 10; 15: 3811–3820. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoberts D, Gebhardt DL, Gaskill SE, et al.: Current considerations related to physiological differences between the sexes and physical employment standards. Appl. Physiol. Nutr. Metab. 2016 Jun; 41(6 Suppl. 2): S108–S120. PubMed Abstract | Publisher Full Text\n\nDas A, Shah S, Adhikari TB, et al.: Computer vision syndrome, musculoskeletal, and stress-related problems among visual display terminal users in Nepal. PLoS One. 2022 Jul 19; 17(7): e0268356. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShrivastava SR, Bobhate PS: Computer related health problems among software professionals in Mumbai: A cross-sectional study. Int. J. Health Allied Sci. 2012 Apr 1; 1(2): 74. Publisher Full Text\n\nYu ITS, Wong TW: Musculoskeletal problems among VDU workers in a Hong Kong Bank. Occup. Med. 1996 Aug 1; 46(4): 275–280. PubMed Abstract | Publisher Full Text\n\nOha K, Animägi L, Pääsuke M, et al.: Individual and work-related risk factors for musculoskeletal pain: a cross-sectional study among Estonian computer users. BMC Musculoskelet. Disord. 2014 May 28; 15: 181. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "309356",
"date": "12 Sep 2024",
"name": "Emily Rogers",
"expertise": [
"Reviewer Expertise Physical activity",
"human health",
"exercise",
"sedentary behaviour",
"vascular physiology."
],
"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\nOverview of Study Proposal The current study proposes to understand the morbidity profile and perceptions of physical activity among display screen equipment users. The authors plan to recruit 97 participants to complete the IPAQ to determine physical activity levels and the Standardized Nordic Scale for Musculoskeletal Disorders to determine musculoskeletal problems. They intend to then run cross-sectional analyses between sedentary time/physical activity and morbidity/pain/eye problems using Chi-squared tests. This study holds promise; however, it would be necessary for the authors to expand upon their statistics. I think that the authors should also examine the relationship between their variables using Pearson’s correlation. The authors seem to be using questionnaires that they have created themselves on Kobo to ask questions about sedentary time and morbidity. This is okay, however I would suggest that the authors include these questionnaires in their proposal so that the reviewers can. Vet them.\nAbstract Please also mention that you will be collecting sociodemographic data, display screen use data, and morbidity data in the methods section of the abstract. The abstract currently makes the reader think that your study will only be looking at the association between physical activity and musculoskeletal disorders.\nIntroduction Please provide a citation for the following sentence “Sedentary behavior is described as activities performed while sitting or reclining, with energy expenditure not exceeding 1.5 times the basal metabolic rate.”\nData Analysis Please also use Pearson’s correlation analyses to examine the relationship between your variables.\nDiscussion This discussion immediately dives into prior studies, and it is initially difficult for the reader to determine whether or not you actually already conducted the study you are proposing herein and are stating the results in the discussion. Please restate the purpose of the study you are currently proposing in the first paragraph of your discussion to alleviate any confusion.\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? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
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https://f1000research.com/articles/13-200
|
https://f1000research.com/articles/13-198/v1
|
20 Mar 24
|
{
"type": "Study Protocol",
"title": "Study of thyroid disorders in pregnancy and their effects on feto-maternal outcomes",
"authors": [
"Jalormy Joshi",
"Amardeep Tembhare",
"Amardeep Tembhare"
],
"abstract": "The second most common endocrine disease that occurs during pregnancy is thyroid disease. Overt and subclinical thyroid dysfunction can lead to adverse effects on both the fetus and the mother. Thyroid diseases during pregnancy affect maternal outcomes and neuropsychological development of the fetus. The objectives of this study were to investigate the effects of thyroid disorders on maternal health and its maternal and perinatal outcomes and to formulate a plan for the management of thyroid disorders in pregnancy. This prospective observational study involved 165 pregnant women. They will be assessed using thyroid function tests, and patients with deranged thyroid function will be treated and followed up. Pregnancy and outcomes were recorded. The findings of this research will offer important new information regarding possible side effects linked to thyroid issues in mothers as well as the clear advantages of therapy. Maternal thyroid diseases have several risk factors in addition to clear advantages of treatment.",
"keywords": [
"Thyroid disorders",
"Pregnancy",
"Maternal outcomes",
"Fetal outcomes"
],
"content": "Introduction\n\nThe second most prevalent endocrine problem during pregnancy is thyroid abnormalities, which include hypothyroidism, subclinical hypothyroidism, hyperthyroidism, and subclinical hyperthyroidism.1 During pregnancy, the mother’s thyroid gland undergoes several changes. If a patient is unable to adjust to these changes, her thyroid function becomes erratic.2 It is well recognized that both overt and subclinical thyroid disorders have negative effects on the growing fetus and expectant mothers.\n\nBefore or during pregnancy, thyroid disorders can have a variety of effects, including reduced fertility, damage to the trophoblast or embryo, increased risk of miscarriage and stillbirth, higher rates of congenital abnormalities, cretinism, infant mortality, and disruption in psychomotor development.3\n\nProfound deficiency gives rise to both maternal and fetal hypothyroidism, contributing to adverse obstetric consequences, such as stillbirths, spontaneous abortion, and preterm birth.4 Maternal thyroid hormones play a vital role in fetal brain development, particularly during the first 20 weeks of gestation.5 Pregnancy outcomes and cognitive development of the fetus are both greatly affected by thyroid problems.6,7 Prenatal neurodevelopmental problems are caused by anomalies in the thyroid stimulating hormone (TSH) production or elevated serum T4 levels.7,8 During the initial stages of pregnancy, deficiencies in thyroid synthesis (hypothyroidism, subclinical hypothyroidism, and hypothyroxinemia) and the presence of thyroid antibodies are linked to compromised intelligence and motor skills in offspring.\n\nWe aim to study effects of thyroid disorders on pregnancy and its outcomes.\n\n\n\n1. To study effects of thyroid disorders on maternal health and it’s outcomes.\n\n2. Effect of thyroid in perinatal outcome.\n\n3. To formulate plan of management on thyroid disorders in pregnancy.\n\n\nProtocol\n\nAn observational study will be conducted in which all pregnant women of less than 20 weeks of gestational age will be presented to the outpatient department, and serum TSH levels will be measured. Pregnant women with deranged TSH levels will be followed-up for delivery, and their maternal and fetal outcomes will be observed.\n\nOver the course of two years, the study will be conducted at the Department of Obstetrics and Gynecology at J.N.M.C., AVBRH, D.M.I.H.E.R. (Deemed University), Wardha.\n\n\n\n1. Pregnant women willing to participate in the study.\n\n2. Pregnant women with abnormal thyroid function test.\n\n3. 3 women willing for follow up till delivery.\n\n4. Singleton pregnancy without any medical or surgical complications.\n\n\n\n1. Multifetal gestation.\n\n2. Pregnant women with chronic disorders like diabetes, hypertension, liver and renal disorders.\n\n3. Pregnant women not willing for follow up till delivery.\n\nA total of 165 patients were recruited in this study. The following formula was used to determine sample size:\n\nFormula used for sample size calculation is, Daniel formula,\n\nHere, n is the sample size required,\n\nZα/2 is the level of significance at 5%, that is, 95% confidence interval = 1.96.\n\nP = Prevalence of thyroid disorders in pregnancy = 12% = 0.12\n\nD = Desired error of margin = 5% = 0.05\n\nStatistical Method: Chi-square Test\n\nSoftware used: R Studio version 4.3.1\n\nFormula Reference: Daniel et al.\n\n\nMethods\n\nEthical clearance was obtained from the institutional ethics committee. After informed, valid, and written agreement was acquired, each woman was informed about the study’s design and goals, as well as the importance of assessing thyroid function tests in pregnant women and their effects on fetal and maternal outcomes. We submitted applications for intramural grants, synopsis concessions, and ICMR money. A total of 165 pregnant women with deranged TSH levels who met the inclusion and exclusion criteria were observed. Thyroid function tests will be performed before 13 weeks of pregnancy. Pregnant women with a deranged thyroid profile will be followed through birth, and the postpartum period and neonates will be followed until 21 days of life. There will be a thorough review of your menstrual, obstetric, personal, and family histories. A thyroid function test of the neonate was performed on day 4 of life.\n\nVenous blood samples will be obtained from the patient to assess the serum TSH, free T3, and free T4 levels. Samples will be taken and allowed to clot in a test tube devoid of anticoagulants.\n\nVital Immuno-Diagnostic Assay System tests were performed on the subjects (VIDAS). If abnormal serum TSH levels were discovered, VIDAS was used to examine the FT3 and FT4 readings. All panel tests were based on the enzyme-linked fluorescent assay (ELFA) method.\n\nWe anticipate that there may be negative effects of thyroid abnormalities in mothers in this trial, as well as clear advantages of receiving therapy on time.\n\nWe will aim to publish the study’s output in an indexed journal.\n\nThe study is not yet started.\n\n\nDiscussion\n\nThe purpose of this study was to assess pregnancy outcomes in women with abnormal thyroid function test results. All women who had been diagnosed with abnormal thyroid function test results started on treatment and were followed up until delivery.3\n\nTreatment is recommended for pregnant women with overt or subclinical hypothyroidism regardless of the presence of TPO antibodies. Levothyroxine is recommended for both overt and subclinical hypothyroidism, regardless of the presence of TPO antibodies.\n\nEarly recognition and proper management of thyroid dysfunction in pregnant women are crucial, as poorly controlled thyrotoxicosis substantially amplifies the chances of adverse fetomaternal outcomes. Additionally, maternal thyroid-stimulating antibodies or antithyroid agents pass through the placenta, both of which could potentially disturb fetal thyroid activity, which might affect the fetal outlook.9\n\nPrevious research has indicated a higher prevalence of thyroid issues in younger age groups. These differences could be attributed to demographic shifts such as delayed marriages, delayed pregnancies, and longer gaps between childbirths. Moreover, disparities between urban and rural areas are more pronounced in patients with hypothyroidism. Additionally, a significant number of pregnant women with thyroid disorders have lower levels of education. This factor may contribute to a lack of awareness and disregard for early symptoms, leading to inappropriate healthcare-seeking behaviors and potential complications during pregnancy.10\n\nIt has been observed that many hyperthyroid women tend to have multiple pregnancies. Multiple pregnancies can deplete micronutrients and other essential elements, potentially leading to thyroid dysfunction in multi-gravida women. Furthermore, there are fewer chances of hypothyroid women with spontaneous labor, and they are at a higher risk of undergoing caesarean section.\n\nThe increasing costs of thyroid profile testing in the private healthcare sector and, in contrast, limited access to laboratories offering these tests in the government sector result in the underdiagnosis of subclinical thyroid dysfunction during its early stages.11\n\nThis underscores the importance of routine screening for thyroid disorders during antenatal checkups in all pregnant individuals.\n\nAmong individuals with hyperthyroidism, abortion is most common. Hypothyroidism, on the other hand, is associated with low birth weight (LBW) because of its association with conditions such as preeclampsia. Insufficient fetal thyroxine levels can disrupt the development of the newborn’s pituitary-thyroid axis, growth hormone secretion in the fetal pituitary gland, vascular responsiveness and maturation, and cardiovascular balance during fetal development.11\n\nIn addition, a number of problems such as preterm birth, jaundice, respiratory distress syndrome, neonatal sepsis, meconium aspiration syndrome, and birth asphyxia can occur in newborns born to women with thyroid abnormalities.11\n\nInformed, valid and written consent will be taken from all our participants who are included in the study.\n\nApproval from the Institutional Ethics Committee has been issued, dated 21/07/2022. The Reference number was DMIMS (DU)/IEC/2022/112.",
"appendix": "Data availability statement\n\nCurrently no data is associated with this article as this is a study protocol.\n\nZenodo: SPRIT checklist for ‘Study of thyroid disorders in pregnancy and their effects on feto-maternal outcomes’, DOI: 10.5281/zenodo.10685225.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nKhan I, Okosieme OE, Lazarus JH: Current challenges in the pharmacological management of thyroid dysfunction in pregnancy. Expert. Rev. Clin. Pharmacol. 2017 Jan; 10(1): 97–109. Epub 2016 Nov 8. PubMed Abstract | Publisher Full Text\n\nAllan WC, Haddow JE, Palomaki GE, et al.: Maternal thyroid deficiency and pregnancy complications: implications for population screening. J. Med. Screen. 2000; 7(3): 127–130. PubMed Abstract | Publisher Full Text\n\nGhirri P, Lunardi S, Boldrini A: Iodine supplementation in the newborn. Nutrients. 2014 Jan 20; 6(1): 382–390. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Assessment of iodine deficiency disorders and monitoring their elimination: a guide for programme managers. Geneva: WHO; 2007.\n\nPu-Yu S, Huang K, Hao J-H, et al.: Maternal Thyroid Function in the First Twenty Weeks of Pregnancy and Subsequent Fetal and Infant Development: A Prospective Population-Based Cohort Study in China. J. Clin. Endocrinol. Metabol. 1 October 2011; 96(10): 3234–3241. PubMed Abstract | Publisher Full Text\n\nZhou M, Wang M, Li J, et al.: Effects of thyroid diseases on pregnancy outcomes. Exp. Ther. Med. July 5, 2019; 18: 1807–1815. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNoten AME, Loomans EM, Vrijkotte TGM, et al.: Maternal hypothyroxinaemia in early pregnancy and school performance in 5-year-old offspring. Eur. J. Endocrinol. Nov 2015; 173(5): 563–571. PubMed Abstract | Publisher Full Text\n\nWilliams FLR, Watson J, Ogston SA, et al.: Maternal and Umbilical Cord Levels of T4, FT4, TSH, TPOAb, and TgAb in Term Infants and Neurodevelopmental Outcome at 5.5 Years. J. Clin. Endocrinol. Metabol. 1 February 2013; 98(2): 829–838. PubMed Abstract | Publisher Full Text\n\nMoleti M, DiMauro M, Sturniolo G, et al.: Hyperthyroidism in the pregnant woman: Maternal and fetal aspects. J. Clin. Transl. Endocrinol. 2019 June; 16: 100190. PubMed Abstract | Publisher Full Text | ,Free Full Text\n\nVaidya B, Anthony S, Bilous M, et al.: Detection of Thyroid Dysfunction in Early Pregnancy: Universal Screening or Targeted High-Risk Case Finding? J. Clin. Endocrinol. Metabol. January 2007; 92(1): 203–207. Publisher Full Text\n\nKumar R, Bansal R, Shergill HK, et al.: Prevalence of thyroid dysfunction in pregnancy and its association with feto-maternal outcomes: A prospective observational study from a tertiary care institute in Northern India. Clin. Epidemiol. Glob. Health. December 11, 2022; 19: 101201. Publisher Full Text"
}
|
[
{
"id": "280112",
"date": "16 Sep 2024",
"name": "Claudia A Riedel",
"expertise": [
"Reviewer Expertise gestational hypothyroxinemia"
],
"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 objective of this work is to analyze thyroid diseases in 165 pregnant women who have altered TSH. Follow them during pregnancy and then see the outcome of the neonate until day 21st. My main concern is with the strategy because the authors will include pregnant women if TSH is altered outside the normal range. However, they do not consider those women who have normal TSH and low T4. It is very well known that this condition, named hypothyroxinemia, is harmful to fetus development. My other concern is regarding the description in the methodology of which parameters they will look in the offspring.\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? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-198
|
https://f1000research.com/articles/13-196/v1
|
20 Mar 24
|
{
"type": "Study Protocol",
"title": "Exploring the status of mother and adolescent daughter communication on reproductive health: a cross-sectional study",
"authors": [
"Vijiya Kashyap",
"Dr. Sonali Choudhari",
"Dr. Sonali Choudhari"
],
"abstract": "Introduction Adolescents between the ages of 10 and 19 are especially susceptible to problems with sexual and reproductive health (SRH), including unwanted pregnancy, sexually transmitted infections (STIs), and unsafe abortion. Approximately 18% of individuals within this age group reside in India. During this stage, puberty represents a major transition, especially concerning reproductive changes. Sexual and reproductive health conversations with adolescents help to establish their perceptions, attitudes, and values. Mother-daughter conversations serve as an important source of information for adolescent girls, yet many lack access to this knowledge. This study aimed to assess the present status of communication about reproductive health between mothers and their adolescent daughters.\n\nObjectives This study aims to evaluate the knowledge, attitude and information sources regarding reproductive health among adolescent daughters, also assessing how frequently they engage in communication on these topics.\n\nMethods A community-based cross-sectional study involving both urban and rural areas will be conducted in the Wardha district. The pre-tested questionnaire survey will be used for this study to gather data using a simple random sampling method. A descriptive approach will outline the frequency, communication type, and number of topics for discussions regarding reproductive health between mothers and adolescent daughters. To investigate the communication status between mother and adolescent daughter the chi-square test will be applied.\n\nStudy implications The findings from this study could contribute significantly to implementing policies, interventions, and educational initiatives that promote better mother-daughter communication about reproductive health issues, ultimately leading to better adolescent health outcomes.",
"keywords": [
"adolescent girl",
"India",
"knowledge and attitude",
"mother and daughter communication",
"reproductive health"
],
"content": "Introduction\n\nAdolescents between the ages of 10 and 19 are considered to be one of the most susceptible populations to a variety of sexual and reproductive health (SRH) problems.1 Reproductive health comprises all aspects of one’s physical, mental, and social well-being, not just the lack of illness or disability, about the reproductive system and its processes and functions.2 Every individual has the right to achieve optimal physical and mental well-being, with sexual and reproductive health being essential components. The worldwide Strategy includes a monitoring framework consisting of sixty indicators. This framework aims to help countries and their allies maintain accountability, avoid unnecessary deaths, maintain general health and well-being, and create supportive environments. The goal that no one is “Left Behind” ensures that all women, children, and adolescents can reach their full potential without facing discrimination.3 The Sustainable Development Goals (SDGs) of the United Nations have acknowledged and emphasised the significance of sexual and reproductive health (SRH) as well as rights in promoting gender equality, overall health, and comprehensive social and economic development.4 India holds the largest number of adolescents globally, totalling 1,428.6 million individuals, representing 18% of its population between the ages of 10 and 19.5,6\n\nAdolescent sexual and reproductive health problems are a major concern in low-income countries. 95% of pregnancies worldwide emerge in nations with lower and middle economic standings, and adolescents between the ages of 15 and 19 account for 11% of all pregnancies worldwide. Offspring born to mothers in their adolescence face a higher risk of early childhood stunting, which impact their cognitive and physical development and reduces their future productivity. Adolescents face many challenges such as early marriage, the higher chance of maternal mortality, unsafe abortions, violence, and STIs like HIV/AIDS. Moreover, improved communication between mothers and their adolescent daughters could lessen the negative effects on society, such as expulsion from school for lack of knowledge.5,7,8 Communication is an essential process that parents use to convey information, knowledge, expectations, values, and beliefs to their children.9\n\nNowadays, there is a growing concern for the health of adolescents due to civilization, urbanisation, and lifestyle changes.10 Adolescents face many unfulfilled healthcare needs as well as obstacles, such as insufficient experience and education regarding healthcare access. Adolescent births per 1,000 girls in the 15–19 age range are 11 in 2023 and decision-making on reproductive rights and sexual and reproductive health is 66 percent in the year between 2007-2022.6 Around 2.1 million children and young people were estimated to have passed away in just 2021; adolescents between the ages of 10 and 19, accounted for 43% of these deaths.11 Laws have a substantial influence on the health and well-being of adolescents. Some prevent adolescents from harm (e.g., by prohibiting child marriage); others may be harmful by restricting their access to necessary products and services, like contraception.12\n\nSocio-cultural hindrance between mothers and adolescents regarding sexual and reproductive health include shame, generational divides, gender differences, mothers’ education, mothers’ perceptions of their children’s understanding, mothers’ occupations, traditional and religious misconceptions, and a lack of time dedicated to these conversations.13 Adolescents need adults who can relate to them, talk to them, spend time with them, and genuinely care about them.14 One of the most important health-promoting variables for adolescents is their mothers. Their daughters’ general attitudes and behaviours regarding health, including SRH, are greatly influenced by them. They might serve as a valuable resource for their daughters when it comes to learning about SRH.15\n\nIndividuals between the ages of 10–19 face various challenges while transitioning from childhood to adulthood and one of the reasons for this problem is the lack of sufficient and precise knowledge about sexual and reproductive matters.16 One of the known obstacles to successfully implementing the programmes is the social taboo and stigma associated with educating adolescents about reproductive health. Numerous unintended pregnancies result in abortions, and unsafe and occasionally self-induced abortions can result in death or serious health issues. On the other hand, a lot of these issues can be resolved with strong proof and open discussion.10 Global research has demonstrated that parents can be an effective source of information for adolescents regarding sexual health. Research suggests that healthy reproductive practices among adolescents can be prevented and their health can be improved through effective mother-adolescent-daughter communication.17\n\nMany developed nations have carried out studies on parent-adolescent communication about reproductive health. However, there are few studies examining the communication about reproductive health between mothers and adolescent daughters in low- and middle-income countries.9 The United Nations’ goal of providing all people with access to sexual and reproductive health care cannot be achieved unless we reach adolescents through various interventions, such as interacting with parents in low and middle-income nations. To help policymakers, programme planners, and implementers create effective interventions to address adolescent reproductive health issues. This study aims to assess the reproductive health communication between mothers and adolescent daughters.\n\nThis study aims to analyse the mother and adolescent daughter communication status on reproductive health in urban and rural areas of Wardha district.\n\n\n\n1. To assess the knowledge and attitude of reproductive health in adolescent daughters.\n\n2. To find out the source of knowledge on reproductive health.\n\n3. To assess the communication frequency.\n\n\nMethods\n\nEthical approval was obtained from the Datta Meghe Institute of Higher Education and Research (DU) Institutional Ethics Committee (approval number: DMIHER (DU)/IEC/2023/31), on 20th December 2023. Additionally, written informed consent will be obtained from all the participants before their inclusion in the study. Privacy and confidentiality will be strictly maintained throughout the study. Measures will be taken to minimize any potential harm or risks to the participants such as referrals for medical consultation if needed. We will ensure that the interviewee has privacy and feels comfortable throughout the interview.\n\nCommunity-based cross-sectional study will be conducted.\n\nWardha district’s rural and urban areas will be selected for the present study.\n\nSchool-going adolescent girls in the Wardha district’s rural and urban areas, between the age group 13 to 19 will be included in the study.\n\nGirls between the ages of 13 and 19 must be enrolled in school, living with their biological mother and who are willing to participate in the study.\n\nThe study excluded girls who lived in hostels, had mothers who passed away, lived with their stepmother, or refused to grant consent to be part of the study.\n\nAccording to the previous study titled “reproductive health communication between mother and adolescent daughter”,18 the P value was found to be 50% and the sample size was calculated using the following formula.\n\nAlpha (α) = 0.05\n\nEstimated proportion (p) = 0.5\n\nEstimated error (d) = 0.05\n\nMinimum sample size required 385\n\nHence, the current status of mother and daughter communication on reproductive health will be assessed by analyzing data collected from a sample of 385 adolescent girls.\n\nSimple random sampling will be employed for selecting the girls who will participate in the interview.\n\nThe primary outcome variables for this study will be related to knowledge and attitude, the amount of topics covered on reproductive health, the frequency and types of interactions that occur between mother and daughter when it comes to sexual and reproductive health, as well as socio-demographic data, knowledge sources, and barriers related to sexual and reproductive health (Table 1: lists the main study parameters, their variables, data sources, and data collection method).\n\nInformation on the mother-adolescent daughter’s communication status on reproductive health will be collected using pre-tested and pre-validated, close-ended questionnaires in both English and Hindi language. The objective to assess the knowledge and attitude of reproductive health in adolescent daughters will be covered using a knowledge and attitude questionnaire under the variable topics discussed on reproductive health in mother-daughter interactions. Knowledge score will be assessed through dichotomized techniques that is ‘Yes’ (1) and ‘No’ (0) and attitude will be scored using a Likert scale that is Strongly agree (1), Agree (2), Nor agree/Nor disagree (3), Disagree (4), Strongly disagree (5).\n\nThe data collection process will be carried out electronically using the Kobo toolbox after informed consent has been obtained, and it should take about ten minutes. The online survey will be completed by the participants.\n\nSelection bias: If the sample is not representative of the entire population, the study’s findings regarding the communication patterns between mothers and daughters regarding reproductive health might not be accurate. This can be overcome by using a random sampling technique.\n\nResponse bias: Instead of telling the truth participants might answer that they believe is socially acceptable or desirable. This can be reduced by rapport building with the participants to create a comfortable and non-judgemental environment.\n\n\nData analysis plan and expected outcomes\n\nThe information gathered from the Kobo toolbox will be imported into a Microsoft Excel spreadsheet and subjected to statistical analysis utilising the R Statistical Software https://www.r-project.org. The data will be tallied and visualised using tables and graphs. The mother’s and the adolescent daughter’s communication status will be investigated through bivariate analysis. To determine whether socio-demographic information and communication status are related, the Chi Square test will be applied.\n\nInvestigating how the quality and extent of communication between mothers and daughters influence adolescent health behaviours. It helps in understanding the frequency, depth, and comfort level of discussions between mothers and daughters regarding reproductive health topics. It also identifies barriers that hinder open communication, such as being culturally unacceptable, feelings of shame, ignorance, and lack of communication skills. Communication on these topics is less likely to suffer from adverse issues related to reproductive health than those who have less knowledge, believe that communicating on this topic has no importance or feel embarrassed to talk on such topics.\n\nThe study protocol will be publish in indexed journal and will be presented in seminars and conference.\n\nThis study is not yet started. The proposal of the study clited for ethical approval to the IEC department of DMIHER (DU) and is under process.\n\n\nDiscussion\n\nA cross-sectional study on the discussion of reproductive health issues between a mother and her adolescent daughter in Bangladesh was carried out by Zakaria et al. (2019). This study found that 78% of students said they had their first conversation with their mothers after the onset of their period, and 62% of students said that their mothers were the main source of information about reproductive health. These findings aligned with past research conducted in developing nations. the principal information source about reproductive health was found to be positively correlated with a high communication level in this study. This suggests that if students learned about reproductive health primarily from friends, classmates, or the internet, they were less likely to have positive interactions with their mothers.18\n\nOnly 23.1% of parents reported having at least two conversations about SRH issues in the previous year, according to the Bekele et al. (2022) study. This level of communication is also in line with results from other research conducted in Ethiopia, which showed that even though it is acknowledged to be important, the discussion is infrequent. it is, however, higher than the outcomes of a study conducted in Dera Town and lower than other findings from Southern Ethiopia and overseas in the USA. These discrepancies could be caused by social-economic, cultural, and variations in how each group experiences and learns about SRH from their mothers.8\n\nShiferaw et al. (2014) reported that 36.9% of participants said they had discussed sexual and reproductive health (SRH)-related matters with their parents in the preceding year. A related investigation done in Hawasa and Ethiopia, uncovered that students who had literate mothers were more likely to discuss these issues than students who had illiterate mothers. Differences in communication abilities, the significance of SRH conversations, and the accessibility of information regarding sexual and reproductive health could all contribute to this variance.10\n\nThe majority of mothers who took part in the study thought that adolescents shouldn’t have access to information about sexual health, according to Mataraarachchi et al. (2023). Mothers in this study stated that they would feel more comfortable talking to their adolescents about sexual matters if they had previously received sex education in school. Research has already shown that when adolescents take part in sexual health education programmes at school, there is an increase in the amount of sexual communication that happens between parents and adolescent children.19\n\nKusheta et al. (2019) reported that only 35.0% of adolescents had conversations with their parents. This is lower than the percentage reported in research conducted in the Ethiopian cities of Debremarkos (36.9%), Sidama Zone (59.1%), Dire Dawa (37%), and Mekele (43.5%). The reason for the discrepancy could be attributed to the fact that 59.4% of participants reside in rural areas, potentially limiting their access to sexual and reproductive health information. Consequently, their less exposure probably made them less inclined to talk to their parents about these topics.14\n\nThe findings from this study could contribute significantly to implementing policies, interventions, and educational initiatives that promote better mother-daughter communication about reproductive health issues, ultimately leading to better adolescent health outcomes.\n\nIn this study we didn’t explore how mothers influence their adolescent daughters’ conversations with their mothers concerning reproductive health.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: STROBE checklist for ‘Exploring the status of mother and adolescent daughter communication on reproductive health: a cross-sectional study’. https://doi.org/10.6084/m9.figshare.25311223.v1. 20\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nParental knowledge and communication with their adolescent on sexual and reproductive health issues in Nepal - PMC.[cited 2023 Aug 17]. Reference Source\n\nReproductive health: [cited 2023 Sep 24]. Reference Source\n\nnina: UNICEF DATA. Women’s, children’s and adolescents’ health country profiles and dashboards.2022 [cited 2023 Sep 25]. Reference Source\n\nInvesting in sexual and reproductive health and rights: essential elements of universal health coverage.[cited 2023 Aug 20]. Reference Source\n\nAdolescent development and participation|UNICEF India: [cited 2023 Aug 28]. Reference Source\n\nUNFPA India|United Nations Population Fund: [cited 2023 Aug 28]. Reference Source\n\nVongxay V, Albers F, Thongmixay S, et al.: Sexual and reproductive health literacy of school adolescents in Lao PDR. PLoS One. 2019 Jan 16; 14(1): e0209675. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBekele D, Deksisa A, Abera W, et al.: Parental communication on sexual and reproductive health issues to their adolescents and affecting factors at Asella town, Ethiopia: a community-based, cross-sectional study. Reprod. Health. 2022 May 8; 19: 114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJerman P, Constantine NA: Demographic and Psychological Predictors of Parent–Adolescent Communication About Sex: A Representative Statewide Analysis. J. Youth Adolesc. 2010; 39(10): 1164–1174. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShiferaw K, Getahun F, Asres G: Assessment of adolescents’ communication on sexual and reproductive health matters with parents and associated factors among secondary and preparatory schools’ students in Debremarkos town, North West Ethiopia. Reprod. Health. 2014 Jan 8; 11: 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUNICEF DATA: Child and youth mortality data ages 5-24.[cited 2023 Sep 25]. Reference Source\n\nPatton GC, Sawyer SM, Santelli JS, et al.: Our future: a Lancet commission on adolescent health and wellbeing. Lancet Lond. Engl. 2016 Jun 11; 387(10036): 2423–2478. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarriers between mothers and their adolescent daughters with regards to sexual and reproductive health communication in Taunggyi Township, Myanmar: What factors play important roles? - PMC.[cited 2023 Aug 17]. Reference Source\n\nKusheta S, Bancha B, Habtu Y, et al.: Adolescent-parent communication on sexual and reproductive health issues and its factors among secondary and preparatory school students in Hadiya Zone, Southern Ethiopia: institution based cross sectional study. BMC Pediatr. 2019 Jan 7; 19: 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParent–adolescent communication on sexual and reproductive health and the utilization of adolescent-friendly health services in Kailali, Nepal - PMC.[cited 2023 Aug 17]. Reference Source\n\nManu AA, Mba CJ, Asare GQ, et al.: Parent–child communication about sexual and reproductive health: evidence from the Brong Ahafo region, Ghana. Reprod. Health. 2015 Mar 7; 12: 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBuffer or Brake? The Role of Sexuality-Specific Parenting in Adolescents’ Sexualized Media Consumption and Sexual Development. J. Youth Adolesc. [cited 2023 Sep 24]; 47: 1427–1439. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZakaria M, Xu J, Karim F, et al.: Reproductive health communication between mother and adolescent daughter in Bangladesh: a cross-sectional study. Reprod. Health. 2019 Jul 24; 16: 114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMataraarachchi D, Buddhika Mahesh PK, Pathirana TEA, et al.: Mother’s perceptions and concerns over sharing sexual and reproductive health information with their adolescent daughters- A qualitative study among mothers of adolescent girls aged 14–19 years in the developing world, Sri Lanka. BMC Womens Health. 2023 May 3; 23: 223. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKashyap V: STROBE checklist for Exploring the status of mother and adolescent daughter communication on reproductive health: A cross-sectional study. figshare. 2024. Publisher Full Text"
}
|
[
{
"id": "285004",
"date": "14 Jun 2024",
"name": "Sari Kistiana",
"expertise": [
"Reviewer Expertise Sexuality and Reproductive 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\nIntroduction, Rationale & Objective\n1. Consider narrowing the scope of the introduction to better align with the main research question, additional context about adolescents RH issues in India. Focus on information directly related to the research question\n2. The context of the study is well-established, but additional references about mother-daughter communication would enhance the background.\n3. The research aim is clearly stated, but ensure that the stated objectives align with the aim (could be more explicitly defined mother and daughter communication)\nMethods\n1. It would be helpful to provide a more detailed explanation to measure the outcome variables (knowledge and attitude), how these two will be categorised after giving the score in the analysis.\n2. Ensure that the stated aim align with the study outcome. Based on the aim of the study, should the outcome variable the quality of mother daughter communication? Please provide more detailed information measurement of mother-daughter communication\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? Not applicable",
"responses": []
},
{
"id": "284997",
"date": "29 Jun 2024",
"name": "Dilini Mataraarachchi",
"expertise": [
"Reviewer Expertise Adolescent health",
"sexual 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 study addresses an important issue in adolescent health, which is timely and relevant to the study context. The manuscript is generally well-organized and clearly written. Yet, some sections of the manuscript need more improvement.\nAbstract Accurately provides the content of the study.\nTitle The title should include the setting of the study and the study sample. Additionally, you assess mother-daughter communication, adolescents' sexual health knowledge and attitudes. These should be mentioned in the title.\nIntroduction and Justification Provide literature on any similar studies that have been carried out in the region. Similar studies are done in Sri Lanka and Bangladesh, which you may cite in your lit review. Have any similar topics been carried out in India?\nThe rationale is clear. Yet, you could give a more detailed description of why the particular study is needed in Wardha district.\nObjectives Objectives are clearly stated. Yet objective 3 needs rephrasing to clarify what you are measuring.\nMethodology Since this manuscript mainly provides the methodology of the study. Please provide a detailed description of each section.\nInclusion criteria: Why was the participants' age limited to 13-19? Any particular reason? When you say 'living with their biological mother', how did you decide the adolescents lived adequately to communicate a sensitive issue with their parents? Was any particular demarcation used to decide whether participants lived adequately with their mothers?\nSample size: Why was p taken as 50%? It is important that you keep a reserve for the non-respondents when you calculate the sample size.\nThe sampling method is not clear. Please give more details on how you selected the sample. Describe the procedure used to draw a random sample of adolescents from the district.\nElaborate more on how the questionnaire was pretested and validated.\nMentioning the methods to minimise potential bias is commendable. However, provide information on how you are planning to handle recaller bias.\nMention the measures you will take to improve adolescent participation in this study. How will you ensure the confidentiality of the information?\nDiscussion The discussion section is well written. However, it would be useful to provide information on how the findings of this research will be used to promote adolescent sexual health in the study setting.\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? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-196
|
https://f1000research.com/articles/13-195/v1
|
20 Mar 24
|
{
"type": "Research Article",
"title": "Effect of propolis on the mechanophysical properties of addition silicon dental impression material",
"authors": [
"Noor Falah Abdulaali",
"Shorouq Majid Abass",
"Shorouq Majid Abass"
],
"abstract": "Background Dental impressions should be disinfected to stop the transmission of germs among dental workers since they provide a risk of diseases. The aim of this study was to examine the effects of two disinfectants (16 mg/ml propolis and 5.25% sodium hypochlorite) on the detail reproduction, linear dimensional change, compatibility with gypsum products, wettability, and surface roughness of addition silicon material.\n\nMethods Ninety specimens were created using Addition silicon impression material, and they were then divided into three groups at random. Ten specimens from each test group were used in each test. Utilizing apparatus made in accordance with ISO 4823:2015, detail reproduction, linear dimensional change, and compatibility with gypsum products are assessed. A digital Profilometer was uutilized to evaluate surface roughness, and a Goniometer was utilized to evaluate wettability by taking the contact angle. Before testing, the specimens were immersed for 10 minutes each in two disinfection solutions: 16 mg/ml propolis and 5.25% NaOCL. The control group received no disinfection. One-way ANOVA tests and the Kruskal-Wallis test, which was statistically significant at a level of p 0.05, were used to examine the data.\n\nResults Comparing the linear dimensional change, surface roughness, and wettability of Addition silicon specimens immersed in 16 mg/ml propolis, 5.25% NaOCL, or the control group demonstrated statistically significant differences (p< 0.05), while details reproduction and compatibility with gypsum revealed statistically no significant differences (p > 0.05).\n\nConclusion Within the parameters of this study, the addition silicon can be immersed in 16 mg/ml propolis for 10 min. to disinfect it without compromising its dimensional accuracy, detail reproduction, compatibility with gypsum products, surface roughness, or wettability.",
"keywords": [
"Addition Silicon",
"Dental Impression Disinfection",
"Propolis",
"detail reproduction",
"linear dimensional change",
"compatibility with gypsum products",
"Surface Roughness",
"Wettability."
],
"content": "Introduction\n\nThe tooth form of the patient and how it relates to other oral features are precisely recorded and replicated using dental impressions.1 Upon contact between dental impressions and oral tissue covered in blood, plaque, or saliva, they become instantly contaminated with potentially dangerous microorganisms. As a result, contagious infections may be spread to laboratory workers, dental practitioners, and dental assistants, potentially leading to cross-contamination.2 Immersing or spraying impression material in a solution to disinfect it is standard procedure.3 However, as it allows for immediate contact with cleaning solutions on all impression areas, The immersion procedure is advised by the American Dental Association (ADA).4 Although Cross-infection risk is decreased by immersion disinfection, it has often been shown to change the dimensions of the impression materials and impair the quality of the cast that is generated.5,6 Therefore, it’s most likely that the accuracy of the dental cast prosthesis will alter, which will ultimately affect how well the final restoration fits.7 The Advisory British Dental Association Service advises that during ordinary dental operations, impression materials are often washed with tap water. Some of the germs adhering to the surface of a dental impression may be removed as a result of the halogenated substances found in some countries’ tap water, but a significant part remains.8 Nearly 90% of the microorganisms on the impression’s areas are eliminated by this process.9 However, significant amounts of the germs would remain. In light of the most recent guidelines, disinfection methods are recommended.10 Due to differing opinions on the best possible disinfection technique, it might be challenging to make an well-informed choice.11 The most often used disinfectants include chlorhexidine, hydrogen peroxide, alcohol, sodium hypochlorite, and glutaraldehyde.12 There is no single disinfectant suitable for all impression materials, thus it is crucial to choose one with potent antibacterial properties without affecting the dimensional stability or surface characteristics of the impression.13 Due to the wide range of branded impression materials (such as silicones, polyethers, polysulfides, and hydrocolloids that are both irreversible and reversible) and gypsum-based castings that were available on the market Additionally, a range of different impression materials and disinfection combinations can be used. The original dimensions of the impression material or gypsum model must be preserved while the disinfectant successfully kills microorganisms. It’s essential to do this if you want the finished product to fit correctly and function as planned. It is debatable if the disinfecting technique improves or worsens the impression.14 The many benefits of elastomeric impression materials make them popular. polyether and Polyvinyl siloxane are the two most widely used examples of these materials. Most frequently, they come into touch with human blood and saliva, which contaminates the stone cast.15 Addition impression material is a hydrophobic material. The ADA recommends using immersion, preferably in elastomers, due to its improved antibacterial effectiveness and capacity to compensate for polymerization shrinkage, which increases accuracy. Immersion is among the most effective ways to avoid cross-contamination.16\n\nSodium hypochlorite is an affordable, dependable disinfectant that is always available in dental clinics. Sodium hypochlorite is a water-soluble disinfectant that is used to disinfect surfaces and water. It produces hypochlorous acid when it dissolves in water, which then changes into oxygen atoms and hydrochloric acid, having a strong oxidizing impact.17 The American Dental Association (ADA) guidelines state that sodium hypochlorite offers a rapid, potent, and broad antibacterial effect.18 Following their immersion in 5.25% sodium hypochlorite to disinfect the silicone dental impressions, the disinfectant demonstrated strong antibacterial activity without significantly altering the materials’ three-dimensional structure.16 It therefore worked as a positive control in this study.\n\nPropolis is a dark resin that occurs naturally. Bees gather it from plant exudates and shoots for usage in building nests and modifying hives, most notably to close gaps in hives. For these purposes, bees combine wax and propolis. Ancient ages saw the use of propolis in traditional medicine.19 Propolis has antibacterial, antifungal, anti-inflammatory, hemostatic, and positive responses to superficial tissue remodelling properties, it is successfully used in dentistry.20,21\n\nIn a previous study, the effects of two disinfectants (16 mg/ml propolis for 5, 10, and 15 min and 5.25% NaOCL for 10 min) on the wettability and surface roughness properties of addition silicon (5 specimens for each group) were compared. The 16 mg/ml propolis immersion for 10 min. had an insignificant effect on the addition silicon’s wettability or surface roughness properties.22 The present study is undertaking according to the previous study.\n\nNull hypothesis stated that The immersion of the additional silicon impression material in propolis disinfectant solutions will have no significant effect on the properties of addition silicon impression material while Alternative Hypothesis stated that The immersion of the additional silicon impression material in propolis disinfectant solutions will have significant effect on the properties of addition silicon impression material.\n\n\nMaterials and methods\n\nFor preparation of 90 impression specimens, which were divided into three test groups with 30 specimens for each test group, addition silicon impression material (Zhermack, DC, Germany) was employed. The test groups were:\n\n• Control group (C group): this group represented the dental impression specimens without treatment.\n\n• Test group (Na group): this group represented the dental impression specimens disinfected with immersing in ready-made 5.25% sodium hypochlorite for ten minutes as a positive control and as recommended by ADA.\n\n• Test group (P group): this group represented the dental impression specimens disinfected with immersing in newly prepared 16 mg/ml propolis for ten minutes.\n\nten specimens for each test, each group undergo five tests.\n\nPropolis (1.6 grams) (Alsajad Beehives, Salah Aldeen in Iraq) were added to a container, and 100 ml of 96% ethanol was added to make propolis (16 mg/ml). The top was shut, for two weeks, the mixture was shaken twice a day in a dark, warm environment (room temperature). Then, the combination was filtered through a clear, incredibly fine paper filter (Qualitative Filter Paper 15 cm, China). The filtrate was a dark brown to slightly reddish liquid that was clear and pure. It was kept in airtight, clean, dark containers.23,24\n\nPutty Soft Addition Silicon Impression Materials (Zhermack, DC, Germany) were utilized To prepare the test impression specimens. Apparatus was created using the software program 3D max 2022 (1) and then printed using a 3D printer according to ISO 4823:2015 standard for testing elastomeric impression materials. The apparatus consists of four parts: the first is a ruled test block with five v-shaped lines etched into it. three vertical lines (A 50 m, B 20 m, and C 75 m) and two horizontal D1 and D2 with a depth of 75 m. The length of vertical lines between D1 and D2 is 25 mm, and this distance is used to measure the linear dimensional change. The second component is a ring mold that acts as a mold for a dental impression, and the third component is a riser. The slit mold used to test for compatibility with gypsum was the fourth component.\n\nIn order to normalize the test block’s temperature to intraoral temperature, it was immersed in a water bath at 35°C for 15 minutes.25,26 In accordance with ISO 4823:2015, impression material was injected and slightly overfilled the ring mold onto the test block, then covered with polyethylene sheet, the assembly was then placed back in a water bath to simulate oral temperature, a glass slab was placed on top, and a one kilogram of weight was added to the assembly to simulate the pressure of the hand on the tray.27 According to ISO 4823:2015 for lab testing, the specimens were taken out of the ring mold two minutes after the manufacturers recommended minimum removal time, and any excess was cut away using blade number 1526 and then washed for 15 seconds under running distilled water as directed by the manufacturer.\n\nIn the study of Oliveira et al. (2021) elastomeric materials and silane-containing alginate were molded using a stainless-steel cast. Three distinct approaches were used to measure the horizontal linear distances in the stainless steel cast: a measuring microscope, a digital caliper, digitization using a digital camera and measuring the distances using ImageJ software.\n\nDigital imaging was advised by Oliveira et al. (2021), this method showed insignificant difference from microscope measurements, which was frequently employed in investigations. The use of digitalized images for distance measurements using software provides a number of advantages over measuring using a microscope that should be highlighted, such as the reduced operational costs, the ability to store the photos for the measurements at any time the operator chooses, and the decrease in the average measurement time, To determine the distance between D1 and D2 on the specimen, this method was employed in this study.\n\nAfter the specimens had been photographed immediately following disinfection, line B between line D1 and Line D2 was measured using the ImageJ computer program (ImageJ 1.53k, National institutes of health USA).28 Three measurements were made for each impression specimen at various periods, and the means of those values were calculated. The test block was measured three times, with a mean length of 25 mm.\n\nThis value served as each specimen’s initial (pretreatment) measurement (L1). According to ISO 4823:2015, the calculation that was utilized to determine the percentage of linear dimensional change for each specimen was as follows:\n\nL1 is the reading of line B on the test block, and L2 is the reading of line B on the impression specimen following disinfection.\n\nElastomeric impression materials used to create precision castings must meet ISO 4823:2015’s requirement that they can replicate fine detail to a level of 20 m or less, which is a precise and comparable method. In this study, an ISO 4823:2015 standard apparatus was used to limit the variations associated with the uncontrollable factors, allowing for a more accurate and comparable assessment of the impression material’s capacity to replicate surface detail. The same image used to assess linear dimensional change was also utilized to assess details reproduction Figure 1, where line B was examined by two observers in order to determine the surface detail score using a ranking system developed by Owen to evaluate how well line B was reproduced in the specimens, The specimens were ranked using four scores29:\n\nScore 1: The whole line was sharply and clearly duplicated between the markings(D1 and D2).\n\nScore 2: The line is distinct for more than 50% of its length, less than 50% is unclear.\n\nScore 3: The line is obscure over 50% of its length, obscure over less than 50% of its length, or totally visible but rough and imperfect.\n\nScore 4: Disparate along the length and pitted, rough, or blemished.\n\nAfter preparation of the impression specimen, which was done in the same manner as for the first two tests stated, the impression specimen was then disinfected according to its group then rinsed with distilled water, then the impression specimen was secured to the ring mold, put over the riser, and gently squeezed to force the specimen up until the ruled surface of the specimen is level with the ring mold’s top. Then, the slit mold was attached to the ring mold. As advised by ISO 4823:2015, a slurry of type IV die stone (Zhermack, Italy) was poured over the impression. Following the manufacturer’s instructions, the gypsum slurry was created by mixing 25 ml of water with 100 g of stone for 60 seconds. After 45 minutes, the gypsum cast specimen was taken out of the mold.30\n\nEach gypsum specimen was removed from the mold, photographed, and the image was magnified Figure 2. all gypsum specimen was assessed using ISO 4823:2015 with a modification by assigning grades to all prepared gypsum specimens when assessing the 50 μm line on the gypsum.31\n\nScore 1: sharp continuous line, smooth cast surface\n\nScore 2: continuous line, loss of sharpness and small pits on the surface\n\nScore 3: deterioration of line detail, more extensive cast surface pits and porosity\n\nScore 4: rough appearance, loss of line continuity, pronounced porosity and deterioration of surface.\n\nThe employed mold was shaped like a disc, 2 mm thick, 20 mm in diameter.32 Following the guidelines provided by the manufacturers, thirty specimens of addition silicon impression materials were made for each test. Propolis (16 mg/ml, freshly made) and sodium hypoclorite (5.25%, AQUA, Turkey) were both used as disinfectants. The mold was set on a plate of clear glass before it was overfilled. A second plate of a comparable size was put on the apex of the mold, and pressure was applied for five seconds. After a specified period of time, the specimens were withdrawn from a water bath that was kept at 35 °C to aquivalent the temperature of the patient mouth.33\n\nAll specimen surfaces’ wettability was assessed using a VINO Contact Angle Goniometer (China, University of Babylon). The samples were positioned correctly on the goniometer’s mechanical stage. Using a needle that was already inserted and at room temperature, On the surface of each specimen, a single drop of distilled water was utilized. The dripping water could be seen by using optics equipment with a high resolution digital camera. Several photos were taken as soon as the drop of distilled water landed on the specimens’ surface. The contact angle was assesed directly following the drop landing and for one minute. We measured the contact angle of each drop twice, once on the left and once on the right of the image. Finally, The two values were averaged to determine the contact angle for each specimen.34\n\n\nEvaluation of surface roughness\n\nThe sample’s surface roughness was assessed precisely to within (0.001 m) using a stylus type, contacting surface roughness, digital roughness tester (Ra) measurement device (Profilometer, JIMEC, China) in the(Anwar Alrazi laboratory, Baghdad). Ra is an indicator of how rough the specimen’s average surface is.35 Throughout the assessment time, the specimen was putted on a stable, solid surface.36 A stylus diamond-tipped contact profilometer moved physically in the X, Y, and Z directions while remained in contact with the surface of specimen. The whole specimen’s surface was subjected to a measurement of surface roughness, and the mean value was then calculated.\n\n\nResults\n\nThe 20-μm line was clearly visible on the surface of impression specimens following their disinfection in 5.25% NaOCl and 16 mg/ml propolis, and it was identically replicated on the surface of every control addition silicon specimen. The 50-μm line was replicated sharply and completely on the gypsum surfaces over its whole length, demonstrating that the standards of ISO 21563 were met and that these two disinfectants have no effect on the surface quality of the addition silicon examined or their gypsum casts. All impression specimens displayed score (1).\n\nSince the data were homogeneous and consistent with the assumptions of normal distribution and revealed no significant difference (normal distribution of data, P˃0.05), one-way ANOVA statistics were selected.\n\n\nDiscussion\n\nFor the Liner dimensional change test the C-Na groups were showed insignificant difference, while C-P and Na-P groups showed significant difference, the propolis group had the least Liner dimensional change (%). All impression specimens at the three groups were showed score (1) in the Details reproduction and Compatibility with gypsum tests. The C-Na and Na-P groups showed significant difference, while the C-P groups were showed insignificant difference in the wettability test however, the Na group was improved the wettability property, while the mean of p group values was close to the mean of C group values. In the surface roughness test, the C-Na and Na-P groups were showed significant difference while the C-P groups were showed insignificant difference, where the mean of p group values close to the mean of C group values, while Na group was reduced surface roughness.\n\nAddition silicone is a synthetic elastomeric impression material that has been the preferred choice in numerous therapeutic situations due to its exceptional physical characteristics and handling qualities.37 It is advised that impression materials be assessed independently in order to give an appropriate disinfection technique and assess the disinfectant’s efficacy. The optimum method of disinfection is immersion since It makes sure that the entire impression and the impression tray will be covered in the disinfectant solution. Furthermore, the CDC and ADA recommend that elastomeric materials only undergo immersion disinfection for a maximum of 30 minutes.38 Finding a disinfectant that kills bacteria and is both convenient to use, reasonably priced, and undoubtedly won’t change the underlying characteristics of impression materials is important. Chemical agents are the only strategy that effectively eliminates bacteria from dental impressions as they cannot be sterilized by heat.39 Propolis is one of the materials used for disinfection in recent years.24 To compare how successfully propolis cleaned dental impressions contaminated with C. albicans, it was put up against various disinfectants. This solution was chosen in the current study because propolis in alcohol has beneficial antibacterial activity.24 Since the ADA recommends NaOCl as the optimum disinfection for addition silicon impression material, it was used in the current investigation as the gold standard. Its 5.25% concentration was used up in 10 minutes. This disinfectant has a number of advantages, including affordability, great efficacy, and the ability to clean tools and equipment,40 additionally quick response against a variety of pathogens.41 However, a drawback of its high contact angle was that it reduces wettability.42\n\nBecause there was a significant effect on the linear dimensional change property of addition silicone materials following immersion in Propolis disinfection (16 mg/ml) for 10 min, the alternative hypothesis was accepted and the null hypothesis was rejected.\n\nThere is a chance that the size of the impression could vary as a result of the disinfecting procedure, It can be brought on by a chemical reaction between the setting material and the disinfectant.43\n\nThe outcome can be attributable to the ongoing polymerization of the impression material or to the material’s volatile components evaporation.44,45\n\nThis outcome was consistent with research done by Mikaeel and Namuq26 the dental impression materials were employed: polyether,vinyl polysiloxane, and vinyl polyether siloxane. Each of the materials was disinfected using two ways, spraying and immersion, using Dettol, sodium hypochlorite, and Cavex Impresafe. According to the study’s findings, the dimensions of the vinyl polysiloxane material significantly changed after being immersed in sodium hypochlorite for ten min.\n\nAlso this study was consistent with Vrbova et al.31 study in which scanning electron microscopy, micro computed tomography, and Light microscopy were used to assess the dimensional changes. In comparison to the control group, it was found that the dimensional changes of the disinfection of the elastomeric impression materials in Aseptoprint Liquid and Zeta 7 solution increased significantly.\n\nThe null hypothesis was accepted based on this study’s findings, which demonstrated that 16 mg/ml propolis disinfected impression specimens provided detail reproduction that was comparable to the control specimens score (1).\n\nThis outcome was consistent with research done by Mikaeel and Namuq26 the dental impression materials were employed: polyether,vinyl polysiloxane, and vinyl polyether siloxane. Each of the materials was disinfected using two ways, spraying and immersion, using Dettol, sodium hypochlorite, and Cavex Impresafe. the study’s findings demonstrated that the surface detail reproduction was the same prior to and after disinfection and considered as the control group.\n\nAlso this study was consistent with Vrbova et al.31 study in which scanning electron microscopy, micro computed tomography, and Light microscopy were used to assess the dimensional changes. It was discovered that elastomeric impression materials have very good resistance to the disinfectants. Each of them replicated a 20-μm line.\n\nThe null hypothesis was accepted based on this study’s findings, which demonstrated that 16 mg/ml propolis disinfected impression specimens generated casts with comparable compatibility with gypsum as the control specimens score (1).\n\nThe hydrophobic and hydrophilic properties of the elastomeric material will dictate how well they interact with the gypsum slurry to create a void-free die.46\n\nThis outcome was consistent with research done by Vrbova et al.31 in which scanning electron microscopy, micro computed tomography, and Light microscopy were used to assess the dimensional changes. It was discovered that elastomeric impression materials have very good resistance to the disinfectants. Each of them, the entire length of a 50-μm line was sharply and clearly imprinted on the gypsum molds.\n\nAfter 10 minutes of immersion in a 16 mg/ml Propolis disinfectant, there was insignificant effect on the Wettability property of additional silicone materials, and the null hypothesis was accepted.\n\nThe increasing contact angle determines whether a surface may be wetted by a particular liquid. Higher contact angles increase the chance of air gathering on the surface, which could cause dies or voids in the impression. It is crucial to use a die stone to wet the impression surface since research has linked the amount of bubbles that form in the dies to the water’s contact angle with the impression surface.47 Before pouring the cast, the elastomeric (silicone) impressions need to be wetted down, typically with detergent, due to the hydrophobic nature of these impression surfaces.48\n\nThis outcome was consistent with research done by Anooz and Shorouq22 the addition silicon materials immersed into two disinfectant solutions: propolis (16 mg/ml) for 5,10,15 min and 5.25% NaOCL for 10 min. The addition’s wettability is not significantly affected by a 10-min immersion in 16% propolis.\n\nThe study of Kotha et al.49 was assessed how several important elastomer properties were affected by autoclave, microwave sterilization and chemical disinfection. Wetability was not significantly affected by any of the sterilizing or disinfection methods.\n\nAfter 10 minutes of immersion in a 16 mg/ml of propolis disinfectant, The surface roughness property of the addition silicone impression materials was not significantly affected, the null hypothesis was accepted.\n\nA rough, imperfect impression can be result in a cast that has a rougher surface than the imperfect impression. Therefore, sterilization and disinfection methods shouldn’t have an impact on the impression’s level of roughness. Any prosthesis should be less than 0.2 m in roughness since values greater than this threshold could indicate considerable plaque formation and values below could suggest additional food reduction or unpredicted plaque growth. The rougher surfaces of the prosthesis could easily cause inflammation in the soft tissues that support a prosthesis.50\n\nThis outcome was consistent with research done by Anooz and Shorouq,22 the addition silicon materials immersed into two disinfectant solutions: propolis (16 mg/ml) for 5,10,15 min and 5.25% NaOCL for 10 min. The addition’s surface roughness is not significantly affected by a 10-min immersion in 16% propolis.\n\nThe study of Kotha et al.49 was assessed how several important elastomer properties were affected by autoclave, microwave sterilization and chemical disinfection. The outcomes demonstrated that autoclave sterilization and chemical disinfection had no significant effect on surface roughness.\n\n\nConclusion\n\nWithin the parameters of this study, the addition silicon material can be immersed in propolis (16 mg/ml) for 10 min to disinfect it without compromising its dimensional accuracy, detail reproduction, compatibility with gypsum products, surface roughness, or wettability.",
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PubMed Abstract | Publisher Full Text\n\nMawlood ZS, Naji GA: Influence of addition of Bergamot Essential Oil on physico_mechanical Behavior of Heat Cure Acrylic Denture Base. Intern. Med. J. Jun 2021; 28(1): 21–25.\n\nPande NA, Parkhedkar RD: An evaluation of dimensional accuracy of one-step and two-step impression technique using addition silicone impression material: an in vitro study. J. Indian Prosthodont. Soc. 2013; 13: 254–259. PubMed Abstract | Publisher Full Text\n\nGeorge A, Chidambaram S, Muralidharan N, et al.: Current Overview for Chemical Disinfection of Dental Impressions and Models Based on Its Criteria of usage: a Microbiological Study. Indian J. Dent. Res. 2022; 33: 30–36. PubMed Abstract | Publisher Full Text\n\nBeyerle MP, Hensley DM, Bradley DV Jr, et al.: Immersion disinfection of irreversible hydrocolloid impressions with sodium hypochlorite. Part I: microbiology. Int. J. Prosthodont. 1994; 7: 234–238. PubMed Abstract\n\nMcGowan MJ, Shimoda LM, Woolsey GD: Effects of sodium hypochlorite on denture base metals during immersion for shortterm sterilization. J. Prosthet. Dent. 1988; 60: 212–218. Publisher Full Text\n\nHutchings ML, Vandewalle KS, Schwartz RS, et al.: Immersion disinfection of irreversible hydrocolloid impressions in pH-adjusted sodium hypochlorite. Part 2: effect on gypsum casts. Int. J. Prosthodont. 1996; 9: 223–229. PubMed Abstract\n\nCelebi H, Büyükerkmen EB, Torlak E: Disinfection of polyvinyl siloxane impression material by gaseous ozone. J. Prosthet. Dent. 2018; 120: 138–143. Publisher Full Text\n\nAhila S, Thulasingam C: Effect of Disinfection on Gypsum Casts Retrieved from Addition and Condensation Silicone Impressions Disinfected by Immersion and Spray Methods. J. Res. Dent. Sci. 2014; 5(3): 163–169. Publisher Full Text\n\nSakaguchi RL, Powers JM: Craig’s restorative dental materials. 13th ed. 2012; 293.\n\nWalker MP, Rondeau M, Petrie C, et al.: Surface quality and long-term dimensional stability of current elastomeric impression materials after disinfection. J. Prosthodont. 2007; 16(5): 343–351. PubMed Abstract | Publisher Full Text\n\nReddy NS, Reddy GV, Itttigi J: A Comparative Study to Determine the Wettability and Castability of Different Elastomeric Impression Materials. J. Contemp. Dent. Pract. 2012; 13(3): 356–363. PubMed Abstract | Publisher Full Text\n\nChandrakala S, Ramesh G, Nayar S: A Comparative Study to Determine the Wettability of Different Impression Materials. Indian J. Public Health Res. Dev. 2019; 10: 1183. Publisher Full Text\n\nLad PP, Gurjar M, Gunda S, et al.: The effect of disinfectants and a surface wetting agent on the wettability of elastomeric impression materials: an in vitro study. J. Int. Oral Health. 2015; 7: 80–83.\n\nKotha SB, Ramakrishnaiah R, Devang Divakar D, et al.: Effect of disinfection and sterilization on the tensile strength, surface roughness, and wettability of elastomers. J. Investig. Clin. Dent. 2017 Nov; 8(4). Epub 2016 Oct 26. PubMed Abstract | Publisher Full Text\n\nAbuzar MA, Bellur S, Duong N, et al.: Evaluating Surface Roughness of a Polyamide Denture Base Material in Comparison with Poly (methyl methacrylate). J. Oral Sci. 2010; 52: 577–581. PubMed Abstract | Publisher Full Text\n\nAbdulaali NF, Abass SM: Raw data for (EFFECT OF PROPOLIS ON THE MECHANOPHYSICAL PROPERTIES OF ADDITION SILICON DENTAL IMPRESSION MATERIAL). [Data set]. Zenodo. 2024. Publisher Full Text\n\nAbdulaali NF, Abass SM: Extended Data: Image for (Effect of propolis on the mechanophysical properties of addition silicon dental impression material). Zenodo. 2024. Publisher Full Text"
}
|
[
{
"id": "272917",
"date": "23 May 2024",
"name": "Zbigniew Raszewski",
"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\nInteresting article, but as a reviewer I have a few comments:\nAbstract ISO 4823:2015,- please use the new version of standard ISO 4823:2021 - Dentistry — Elastomeric impression and The purpose of impression disinfection is to eliminate bacteria and viruses from the surface of the disinfected material. Therefore, it would be good to add that further tests are necessary to determine how effective propolis is on the surface of silicone impression material.\nIntroduction As a result, contagious infections may be spread to laboratory workers, dental practitioners, and dental assistants, potentially leading to cross-contamination.2 Immersing or spraying impression material in a solution to disinfect it is standard procedure ( new thread of thought new line). The Advisory British Dental Association Service advises that during ordinary dental operations, impression materials are often washed with tap water. Some of the germs adhering to the surface of a dental impression may be removed as a result of the halogenated substances found in some countries’ tap water, but a significant part remains.8 Nearly 90% of the microorganisms on the impression’s areas are eliminated by this process.9 However, significant amounts of the germs would remain. - According to the instructions, you should always wash the material under running water to remove as much blood, saliva, etc. as possible. Only then disinfect it. The idea is that these residues do not deactivate the disinfectant\nThe ADA recommends using immersion, preferably in elastomers, due to its improved antibacterial effectiveness and capacity to compensate for polymerization shrinkage, which increases accuracy-Please read the O Brian Dental mateiral, it explains what bonding mechanisms occur in individual impression materials. Agar, alginates - OK, these change their dimensions under the influence of contact with water, but silicones do not exhibit water absorption, their binding involves the cracking of C=C double bonds and the attachment of a crosslinker containing Si-H groups.\noxygen atoms and hydrochloric acid- this is partially true look at this https://cdnsciencepub.com/doi/pdf/10.1139/v56-068\nNull hypothesis stated that The immersion of the additional silicon impression material in propolis disinfectant solutions will have no significant effect on the properties of addition silicon impression material while Alternative Hypothesis stated that The immersion of the additional silicon impression material in propolis disinfectant solutions will have significant effect on the properties of addition silicon impression material.- I have one thesis, it's about logical behavior. Propolis has no effect on silicone material - our thesis. Either it will be confirmed or we write that it has been refuted. Materials and methods addition silicon impression material (Zhermack, DC, Germany)- name of the material, city, , please add this info. Zhermack has Badia Polesine , Italy headquarters.\nTest group (Na group): this group represented the dental impression specimens disinfected with immersing in ready-made 5.25% sodium hypochlorite- please add the name, producer, citry, country.\nPropolis (1.6 grams) (Alsajad Beehives, Salah Aldeen in Iraq) were added to a container, and 100 ml of 96% ethanol was added to make propolis (16 mg/ml- 96% ethyl alcohol, which itself has bactericidal properties, may have a significant impact on your test. Secondly, it affects the surface of the silicone material. It is necessary that there are no propolis residues left on the surface of the silicone material, which affects the surface roughness?\nPutty Soft Addition Silicon Impression Materials- one or more materials? – It was Elite or other Putty material, As you know term putty is using for heavy body impression material from different manufactures.\npparatus was created using the software program 3D max 2022 (1) and then printed using a 3D printer according to ISO 4823:2015 standard for testing elastomeric impression materials. The apparatus consists of four parts: the first is a ruled test block with five v-shaped lines etched into it. three vertical lines (A 50 m, B 20 m, and C 75 m) and two horizontal D1 and D2 with a depth of 75 m. The length of vertical lines between D1 and D2 is 25 mm, and this distance is used to measure the linear dimensional change. The second component is a ring mold that acts as a mold for a dental impression, and the third component is a riser. The slit mold used to test for compatibility with gypsum was the fourth component. - what 3D printer was used for this purpose, name, manufacturer, country, city. What material was the block printed from? Honestly, I do this test 2-3 times a month, the ISO standard says that the block must be made of metal, I haven't really seen a 3D printer that can print 20 micron lines, because generally one layer of growth is 25-50 microns.\n\nThird thing, before the test, you would have to check the dimensions of this block (verification of the device). How did you check that it was 25 mm? As accurately as possible. I'm asking because the shrinkage of type A silicone materials (additioanl), which Zhermack's product belongs to, is about 0.15%....\nIn the study of Oliveira et al. (2021) elastomeric materials and silane-containing alginate- please add ref. Second there is no material calls silane containing alginate, Probably some make error during translation. Look at the material used by Oliveira.\nElastomeric impression materials used to create precision castings must meet ISO 4823:2015’s requirement that they can replicate fine detail to a level of 20 m or less, which is a precise and comparable method.- It depends on what material?\n\ntype IV die stone (Zhermack, Italy)- name of the product, please add. Table 1- no units in the table.\nDiscussion OK, I like it! It is also good to state what the limitations of your research are. Firstly, the impression material used for the research, secondly, propolis is a natural compound whose composition may vary depending on the region in the world, which affects its properties. Good luck in you further 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? 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": []
},
{
"id": "258077",
"date": "29 May 2024",
"name": "Mangala Patel",
"expertise": [
"Reviewer Expertise Dental materials scientist"
],
"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 focusses on the accuracy of addition silicone impressions and casts following disinfection in two media, conventional sodium hypochlorite and propolis. The latter has antimicrobial properties. Various properties were investigated and compared to the controls (no treatment group). These included linear dimensional change, surface roughness, detail reproduction (representing compatibility with gypsum products), and contact angle measurements. These methods are necessary in order to test the accuracy of the addition silicone following disinfection.\nThe comments provided below are to help the authors in substantially improving the quality of the manuscript and the data obtained.\nThe entire paper presents with poor language quality such that it is difficult to understand and follow logic. Capital letters appear in the middle of sentences as well. Furthermore, the experimental data obtained is not presented appropriately. The authors should look at other published work to see how their data can be displayed. Below are more specific comments/examples by section: Title The title refers to ‘mechanophysical properties’ of impression materials, but, in fact, no mechanical properties are performed. Abstract\nAlthough the abstract-method mentions the addition silicone impression material samples were immersed in 116 mg/ml propolis for 10 minutes, there is no mention of this in the Methods section. Introduction The introduction from ‘due to the wide range ……..all the way to the end of the Null Hypothesis becomes confusing and needs attention due to the way that it is written.\nThere are a number of issues with the methods and results that need to be clarified and addressed. Methods The methods lack detail eg preparation of sodium hypochlorite solution, after the specimens had been photographed immediately after disinfection – what camera was used? One equation is provided but there is no data given to show how this equation was used. Results\nOnly 2 figures are provided in the entire paper, and these need further annotation. Only the statistical analysis data (descriptive statistics, ANOVA and Post Hoc Tukey test) are presented in the results section (in three tables). It would be beneficial to see the data obtained from each test in tables that then contain columns with significance etc. Discussion In the discussion section the authors correctly attempt to compare their findings with published literature. However, since there was little data provided, apart from that given in the statistical tables, which were difficult for the reader to analyse, the discussion becomes redundant. Conclusion The conclusion will stand once the actual data and analysis is provided.\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? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "272920",
"date": "05 Jun 2024",
"name": "Anna Paradowska-Stolarz",
"expertise": [
"Reviewer Expertise dental materials",
"dentofacial anomalies",
"clefts",
"temporomandibular joint disorder"
],
"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, here are some comments of mine:\n1. In the introduction, state that disinfection should be the part of the process of impressions preparation - this is the matter of trust between Dentist and Laboratory. Please, add to that the fact of different methods of disinfection (refer 2) and the antimicrobial reaction and the aspect of influence of green dentistry, naturally driven dentistry and polymers such as chitosan and propolis in the bactericidal and anti-disease actions (refer 3, 4, 5)\n2. In M&M, please state how it happened that the same impression (I understand it so) underwent 5 tests each? Couldn't the previous test influence the properties of the sample before the next test? Is there any ISO regulation for that (it should be added, if so). Please, also state that the bioethical committee approval was not necessary because of the research design.\n3. When you add alcohol to propolis, I assume you make a solution of propolis (change the nomenclature)\n4. Check the punctation - some capital letters in the middle of the sentence are not correct\n5. Give the name of the 3 D printer, as well as all the information (country of origin, the light lenght etc). Give more details on preparation of the samples, especially the print.\n6. In the discussion, when checked the microscopic measurements, it would be nice if you added the information that other measurements could be done (such as fractal dimension analysis or texture analysis), which is an interesting way and novel trend in dentistry - you should add this aspect to the discussion, as well as think of the future studies on that.\n7. The language should be checked by the native speaker \"eliminating\" and \"killing\" bacteria sound to me too current\n8. Add to the discussion, the aspect of influence of disinfection on the properties of impression materials, especially silicones (refer 1). Could propolis act that way too? This should be discussed.\n9. In the discussion, you should also think of the influence of the larger or smaller solution of propolis on the material.\n10. Also, it would be mandatory to add to the discussion the new trend of scanning instead of using the impression materials. Would it solve some aspects? Is this a future?\n\n11. Add the limitation of the study - this is what authors should be aware of!\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": []
}
] | 1
|
https://f1000research.com/articles/13-195
|
https://f1000research.com/articles/12-1047/v1
|
29 Aug 23
|
{
"type": "Study Protocol",
"title": "Study protocol for supplementation of single high dose Vitamin D in deficient critically ill children and assessment of their short-term outcome: An open label randomized control trial",
"authors": [
"Keta Vagha",
"Sham Lohiya",
"Jayant Vagha",
"Sunita Vagha",
"Amar Taksande",
"Richa Chaudhary",
"Sham Lohiya",
"Jayant Vagha",
"Sunita Vagha",
"Amar Taksande",
"Richa Chaudhary"
],
"abstract": "Vitamin D is a fat-soluble vitamin and is classically considered to play a major role in bone metabolism and maintaining Calcium and phosphorus equilibrium. With progressing research, other roles of Vitamin D are surfacing. The pleotropic functions of Vitamin D regulate cell proliferation, differentiation, apoptosis, and angiogenesis. In critically ill children, Vitamin D deficiency is associated with poor outcomes in the form of increased PICU stay, increased duration of mechanical ventilation, higher rate of Ventilator Associated Pneumonias, increased incidence of sepsis, higher intensive care scores and increased incidence of end organ dysfunction. With this background, we aim to conduct an open label Randomized Control Trial to study the short-term outcome of Vitamin D deficient critically ill children after supplementation of a single high dose oral Vitamin D. This will be an open label randomized control trial conducted at a tertiary care hospital in central India. Children aged 1 month to 18 years, admitted in the pediatric intensive care unit with Serum Vitamin D level less than 20 ng/dL will be the study group. These children will be randomized into two groups as per the computer-generated randomization. Group A will receive standard treatment protocol with 10,000 IU/Kg to 400,000 IU (maximum) Vitamin D via mouth or nasogastric tube, whereas Group B will receive standard treatment protocol. Urinary calcium-creatinine ratio will be done on day 3 in Group A to check for hypervitaminosis D. The outcome of both the groups will be assessed. All the data will be added to a Microsoft Excel sheet. Results and interpretation will be determined on the basis of the obtained observation. Trial registration: CTRI/2022/10/046556.",
"keywords": [
"Vitamin D",
"Steroid hormone",
"Critically ill children",
"study protocol",
"Intensive care"
],
"content": "Introduction\n\nVitamin D is a fat-soluble vitamin and is classically considered to play a major role in bone metabolism and maintaining calcium and phosphorus equilibrium.1 With progressing research, other roles of Vitamin D are surfacing. This has been driven by the presence of Vitamin D receptors for cholecalciferol on most body tissues.2 The pleotropic functions of Vitamin D include regulation of expression of genes in many organs like immune cells, brain, colon, kidneys etc. which are of importance in critically ill children. These added functions of Vitamin D regulate cell proliferation, differentiation, apoptosis, and angiogenesis.3 These non-skeletal actions of vitamin D are similar to that of steroid hormones therefore Vitamin D is considered equivalent to a steroid hormone than just a vitamin.4 The majority of Vitamin D requirement is fulfilled by exposure to sunlight and lesser amount is obtained through diet. Despite sufficient sunlight in India, prevalence of Vitamin D deficiency is accounted to be 50% of critically ill children.5 In critically ill children, Vitamin D deficiency is associated with poor outcome in form of increased PICU stay, increased duration of mechanical ventilation, higher rate of Ventilator Associated Pneumonias, increased incidence of sepsis, higher intensive care scores and increased incidence of end organ dysfunction.5–10\n\nThere have been many studies conducted to determine the outcome of critically ill Vitamin D deficient children but there is a sparse data about the outcome of these children after supplementation of Vitamin D therefore we wish to take up this study. There are multiple dosing regimens and routes of administration of Vitamin D. In most of the studies, cholecalciferol was used from 200 to 540,000 IU in oral or intramuscular injection form either in single or multiple doses. The daily supplementation of Vitamin D takes months to replenish the body stores but there is a need of its rapid optimization in critically children if we desire its immunomodulatory function.11 A systematic review and meta-analysis conducted by Mc Nally et al. studied more than one hundred research studies, from which it was inferred that Vitamin D at a dose of 10,000 IU/Kg to maximum up to 400,000 IU is associated with no adverse effects. Therefore in our study we will be using this dosing regimen.12 With this background, we aim to conduct an open label Randomized Control Trial to study the short-term outcome of Vitamin D deficient critically ill children after supplementation of a single high dose oral Vitamin D.\n\nThe main objective of this study is to assess the short-term outcome of Vitamin D deficient critically ill children after supplementation of single high dose oral Vitamin D. Secondly, to determine the prevalence of Vitamin D deficiency in critically ill children in our area (Central India) and lastly, to assess the effect of single high dose oral Vitamin D supplementation on the immediate outcome.\n\n\nMethods\n\n\n\n1. Can supplementation of single dose Vitamin D orally, improve the short term outcome in critically ill children?\n\n2. What is the prevalence of Vitamin-D deficiency in critically ill children in our area (Central India).\n\n3. What is the effect of single high dose oral Vitamin D supplementation on the immediate outcome?\n\nThis will be an open-label randomized control trial. This study will be conducted at Acharya Vinoba Bhave Rural Hospital, a 1525 bedded tertiary care hospital located at Sawangi (Meghe), Wardha, Maharashtra in the duration of three years with total sample size of 100. The Insititutional Ethics Committee clearance has been obtained with reference number DMIMS (DU)/IEC/2022/207. This open label randomized control trial is also registered on the National Clinical Trial registration portal with reference number - CTRI/2022/10/046556.\n\nChildren aged 1 month to 18 years, admitted in the Pediatric Intensive care unit with Serum Vitamin D level less than 20 ng/dL will be included in this study.\n\nThe following will be excluded from the study.\n\n1. All the cases of Rickets (already diagnosed or diagnosed on this admission)\n\n2. Patients admitted in the PICU for monitoring purpose like post operative cases, for performance of a procedure like lumbar puncture, bone marrow aspiration etc.\n\n3. Patients who have received Vitamin D supplementation in the last 30 days.\n\n4. Patients with abdominal pathology.\n\n5. Patients requiring Intensive Care Unit stay less than 24 hours.\n\nParticipants: Children aged 1 month to 18 years, admitted in the Pediatric Intensive care unit with Serum Vitamin D level less than 20 ng/dL.\n\nIntervention: Single high dose Vitamin-D orally or via nasogastric tube.\n\nComparison: No supplementation of Vitamin-D.\n\nOutcome: Short term outcome in form of number of days of Paediatric Intensive Care Unit stay, duration of mechanical ventilation, occurrence of Hospital acquired infection like Ventilator Associated Pneumonia and Central Line Associated Blood Stream Infection, Acute Kidney Injury, Multiorgan dysfunction, maximum Vasoactive-Inotrope Score and mortality.\n\nAll the children admitted in the PICU will be screened using exclusion/inclusion criteria. After excluding those children, the Serum Vitamin D level of the study group will be measured in the hospital laboratory. Children with serum Vitamin D level less than 20 ng/dL will be included in the study. Children included in the study will undergo computer generated randomization into two groups: Group A receiving the Standard treatment protocol along with 10,000 IU/kg to maximum up to 4,00,000 IU single dose Vitamin D via mouth or through the nasogastric tube and Group B receiving the Standard treatment protocol. The participants will be registered after obtaining the written parental consent. Randomization will be carried out using the WINPEPI software, and the patients will be allocated a case number and randomized. All the children will be divided equally between the experimental or research group (Group A) and the control group (Group B).\n\nNutritional status assessment in both the groups will be done as per WHO criteria in which wasting is defined as weight for height (gender specific) to be less than -2 standard deviation on the growth chart and stunting is defined as height for age (gender specific) to be less than -2 standard deviation on the growth chart. The baseline blood investigations done in critically ill children like Complete Blood Count, Liver Function Test, Kidney Function Test and Serum Lactate levels, coagulation profile along with inflammatory markers such as C-Reactive Protein and Lactic Dehydrogenase will be sent on Day 0 (Day of admission) and Day 3 of admission of both the groups (before and after administration of Vitamin D in Group B). Urinary calcium-creatinine ratio will be done on day 3 in Group A to check for hypervitaminosis D. The multiorgan dysfunction will be assessed by Pediatric Logistic Organ Dysfunction Logistic- 2 scoring system on day 0 and day 3. The magnitude of requirement of ionotropic support will be assessed by Vasoactive-Ionotropic Score, the maximum score will be considered for comparison in both the groups. Acute Kidney Injury will be defined based on Urine Output and serum creatinine level as per Pediatric RIFLE criteria.\n\nThe outcome of both the groups in form of number of days of Paediatric Intensive Care Unit stay, duration of mechanical ventilation, occurrence of Hospital acquired infection like Ventilator Associated Pneumonia and Central Line Associated Blood Stream Infection, Acute Kidney Injury, Multiorgan dysfunction, maximum Vasoactive-Inotrope Score and mortality will be noted and compared in both the groups. End of the study will be considered at the day of discharge or mortality of the patient. Group B will receive the therapeutic dose of Vitamin D at the end of the study. All the data will be added to a Microsfot Excel spreadsheet. Results and interpretation will be determined on the basis of the obtained observation. The methodology is been depicted in a flowchart in Figure 1.\n\nSTATA 12 software will be used to analyse data. The graphs will be done using Microsoft Excel 2007. Numerical data will be summarized using means and standard deviations. The baseline measures will be compared using the paired-samples, two-sided t- test. PeLOd 2 scores and VIS across groups will be compared using the analysis of variance (ANOVA) test. Scheffe’s test will be used for post-hoc comparison to find out the presence of any significant differences between groups. P values <0.05 will be considered significant.\n\nThe recruitment of the children began on 01 April 2023. As of publication, 16 patients have been included and randomized into Group A and Group B.\n\n\nDiscussion\n\nIn literature, benefits of Vitamin D as a fat soluble vitamin in calcium and bone metabolism is well known but its pleotropic functions and its actions like a steroid hormone are lesser known. With recent research studies, these lesser known functions of Vitamin D are becoming evident. Vitamin D has a immunomodulatory function as it helps in regulating the cellular proliferation, differentiation, apoptosis and angiogenesis which can be crucial in a critically ill child. There have been many studies conducted to determine the outcome of Vitamin D deficient critically ill children but the outcome of these children on supplementation of Vitamin D is less studied upon.\n\nYung Wang et al.13 conducted a study with 150,000 IU supplementation of Vitamin D in the study group of Vitamin D deficient septic children and found that the group with supplementation had a better outcome. El Gendy et al.14 had a conducted a study like Yung Wang et al. where the study group was Vitamin D deficient septic children. Labib et al.,15 studied the outcome of supplementation of Vitamin D in deficient children with Pneumonia. These studies have categorised their study group to one particular ailment. But we want to include all the Vitamin D deficient critically ill children in our study and no one particular ailment. This is the research gap. We wish to determine the outcome in all the critically ill children irrespective of their illness.\n\nTherefore, we have taken up this study to determine the outcome in Vitamin D deficient critically ill children after its supplementation. The supplements of Vitamin D are easily available, well tolerated and cost effective therefore this can be a novel addition to our Paediatric Intensive Care unit protocol which can improve the short term outcome of these children.\n\n\nEthics approval and consent to participate\n\nThe institutional ethics committee has granted the permission to conduct the study with reference number - DMIMS (DU)/IEC/2022/207. Consent will be obtained from all the participants in the local language while enrolling them in the study.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nLan SH, Lai CC, Chang SP, et al.: Vitamin D supplementation and the outcomes of critically ill adult patients: a systematic review and meta-analysis of randomized controlled trials. Sci. Rep. 2020 Aug 31; 10(1): 1–7. Publisher Full Text\n\nNair P, Venkatesh B, Center JR: Vitamin D deficiency and supplementation in critical illness—the known knowns and known unknowns. Crit. Care. 2018 Dec; 22(1): 1–9. Publisher Full Text\n\nHolick MF: Vitamin D deficiency. N. Engl. J. Med. 2007 Jul 19; 357(3): 266–281. Publisher Full Text\n\nNorman AW: From vitamin D to hormone D: fundamentals of the vitamin D endocrine system essential for good health. Am. J. Clin. Nutr. 2008 Aug 1; 88(2): 491S–499S. PubMed Abstract | Publisher Full Text\n\nPonnarmeni S, Kumar Angurana S, Singhi S, et al.: Vitamin D deficiency in critically ill children with sepsis. Paediatr. Int. Child Health. 2016 Jan 2; 36(1): 15–21. PubMed Abstract | Publisher Full Text\n\nMadden K, Feldman HA, Smith EM, et al.: Vitamin D deficiency in critically ill children. Pediatrics. 2012 Sep 1; 130(3): 421–428. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArnson Y, Gringauz I, Itzhaky D, et al.: Vitamin D deficiency is associated with poor outcomes and increased mortality in severely ill patients. QJM. 2012 Jul 1; 105(7): 633–639. PubMed Abstract | Publisher Full Text\n\nBraun A, Chang D, Mahadevappa K, et al.: Association of low serum 25-hydroxyvitamin D levels and mortality in the critically ill. Crit. Care Med. 2011 Apr; 39(4): 671–677. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHan JE, Jones JL, Tangpricha V, et al.: High dose vitamin D administration in ventilated intensive care unit patients: a pilot double blind randomized controlled trial. J. Clin. Transl. Endocrinol. 2016 Jun 1; 4: 59–65. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSingh S, Sarkar S, Gupta K, et al.: Vitamin D Supplementation in Critically Ill Patients: A Meta-Analysis of Randomized Controlled Trials. Cureus. April 30, 2022; 14(4): e24625. PubMed Abstract | Publisher Full Text\n\nMcNally D, Amrein K, O’Hearn K, et al.: Study protocol for a phase II dose evaluation randomized controlled trial of cholecalciferol in critically ill children with vitamin D deficiency (VITdAL-PICU study). Pilot Feasibility Stud. 2017 Dec; 3(1): 1–3. Publisher Full Text\n\nMcNally J, Iliriani K, Pojsupap S, et al.: Rapid normalization of vitamin D levels: a meta-analysis. Pediatrics. 2015 Jan 1; 135(1): e152–e166. PubMed Abstract | Publisher Full Text\n\nWang Y, Yang Z, Gao L, et al.: Effects of a single dose of vitamin D in septic children: a randomized, double-blinded, controlled trial. J. Int. Med. Res. 2020 Jun; 48(6): 030006052092689. Publisher Full Text\n\nEl-Gendy FM, Khattab AA, Naser RG, et al.: Association between vitamin D deficiency and sepsis in pediatric ICU. Menoufia Med. J. 2021 Jan 1; 34(1): 210. Publisher Full Text\n\nLabib JR, Ibrahem SK, Ismail MM, et al.: Vitamin D supplementation and improvement of pneumonic children at a tertiary."
}
|
[
{
"id": "202369",
"date": "20 Sep 2023",
"name": "Tushar Jagzape",
"expertise": [
"Reviewer Expertise General Pediatrics",
"Ethics",
"Medical education"
],
"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 researchers are doing a randomized controlled trial (open label) to study the effect of single high dose of vitamin D in vitamin D deficient children admitted to the Pediatric intensive care unit. Following are my observations:\n\nThe authors have chosen a very wide age range (1 month to 18 years). The cause of morbidity and morbidity in different age groups is different. Hence the researchers should at least use stratified sampling or quota sampling in order to avoid skewed data.\n\nThe authors have not specified any severity of the illness, except that the patient should be in the ICU for more than 24 hours and not pre-operatively or post operatively. It would be better if a specific cut off of pSOFA score or PeLOd2 scores are used for inclusion and exclusion criteria.\n\nSample size calculation is not mentioned. Why only 100 patients are being studied?\n\nBetter to use block randomization.\n\nThe data analysis plan does not mention if it would be a per protocol analysis or intention to treat analysis.\n\nThe most important flaw in the study plan is withholding Vitamin D supplementation in the control group. At one place it has also been mentioned that the other group will be supplemented vitamin D at the end of the study (which is either discharge or death). It is ethically not correct to deny treatment, when it is available just for the research purpose.\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? No\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "11244",
"date": "04 Apr 2024",
"name": "Keta Vagha",
"role": "Author Response",
"response": "I would like to express my sincere appreciation for your thoughtful review of the manuscript. I would like to address a few misunderstandings regarding the drafting of the manuscript: 1. Regarding the impact of age on the modulation of immunity by Vitamin D at the cellular level, it is important to note that Vitamin D plays a significant role in cellular-level modulation across various diseases, rendering the age factor less influential. This aspect has been elucidated in the manuscript. 2. The sample size calculation was initially included in previous drafts but was subsequently edited out by preliminary editors. I acknowledge this oversight and assure you that it will be reinstated in the revised version. 3. Notably, the sampling technique has been refined and enhanced in the updated version of the manuscript. 4. Your ethical concern about the absence of vitamin D supplementation in the control group has been duly addressed. In the revised manuscript, a regular dose of vitamin D has been incorporated, assuaging the previously raised ethical concern. While it is disheartening that the manuscript was rejected due to misinterpretations, I acknowledge your genuine concerns. I regret any confusion and wish to highlight that the intent is not to challenge the decision but to offer clarifications and improvements. I understand your perspective on publishing the study protocol to solicit feedback from esteemed faculty. I appreciate your suggestion and am open to exploring such avenues in the future. Nevertheless, I am grateful for the time and consideration you have dedicated to the manuscript review. Thank you for your valuable insights, and I am committed to addressing the concerns raised in the revised submission."
}
]
},
{
"id": "205666",
"date": "05 Oct 2023",
"name": "Dayre McNally",
"expertise": [
"Reviewer Expertise 15 years of clinical trial experience including vitamin D supplementation in PICU"
],
"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 will add value to the field. Congrats to the team for identifying this question and seeking to help provide an answer.\n\nHowever, there are aspects of the report that warrant clarification. See comments below. In particular be clear what the primary clinical outcome will be AND how the sample size was calculated. I also did not follow the rationale for some of the statistical plan.\n\nAbstract\nCapitalization on words and phrases (was the intention to then provide an acronym)\n\nMake it more clear when you refer to vitamin D you are talking about cholecalciferol\n\nUrine calcium:creatinine levels are a poor marker/indicator of hypervitaminosis. Multiple pediatric and adult studies have not shown a relationship between receipt of high dose vitamin D and urine calcium levels. More related to critical illness and Lasix\n\nWhat does “the outcome of both groups will be assessed” mean. What is the primary?\n\nNo need to mention Microsoft excel sheet in abstract.\n\nAbstract should indicate proposed sample size\n\nThe line “Results and interpretation will be determined on the basis of the obtained observation.” Is not sufficiently clear. Remove or improve\nIntroduction\nRemove etc from the line” The pleotropic functions of Vitamin D include regulation of expression of genes in many organs like immune cells, brain, colon, kidneys etc”\n\nImprove on the line:” These non-skeletal actions of vitamin D are similar to that of steroid hormones therefore Vitamin D is considered equivalent to a steroid hormone than just a vitamin”\n\nWhat is meant by “higher intensive care scores “. Are you referring to PRISM, PIM etc? if so, consider providing examples\n\nAgree with the point of the sentence, but it needs improvement: “There have been many studies conducted to determine the outcome of critically ill Vitamin D deficient children but there is a sparse data about the outcome of these children after supplementation of Vitamin D therefore we wish to take up this study. “ consider changing to state sparse data on whether modifying vitamin D status, influences outcome. Remove the comment about “we wish to take up”\n\nClarify two points in the line: “A systematic review and meta-analysis conducted by Mc Nally et al. studied more than one hundred research studies, from which it was inferred that Vitamin D at a dose of 10,000 IU/Kg to maximum up to 400,000 IU is associated with no adverse effects.”. These were 100 interventional trials, and that the level would raise levels into the high normal range in 2-3 days\n\nFind a way to combine the following two sentences: Therefore in our study we will be using this dosing regimen.12 With this background, we aim to conduct an open label Randomized Control Trial to study the short-term outcome of Vitamin D deficient critically ill children after supplementation of a single high dose oral Vitamin D.\nMethods\nAre there three objectives or two? “The main objective of this study is to assess the short-term outcome of Vitamin D deficient critically ill children after supplementation of single high dose oral Vitamin D. Secondly, to determine the prevalence of Vitamin D deficiency in critically ill children in our area (Central India) and lastly, to assess the effect of single high dose oral Vitamin D supplementation on the immediate outcome.”\nDetermine prevalence\n\nDetermine whether supplementation influences short term outcome.\n\nIt is customary to be more clear what the primary outcome measure is for objective\n\nBe more clear the study is being conducted in India (say the country)\n\nBe more clear the vitamin D level you are referring to is 25 hydroxyvitamin D\n\nCan you be more clear what type of dosing you are referring to when you say: “Patients who have received Vitamin D supplementation in the last 30 days.” Also I do not see that it matters if they received vitamin D in the past, if they are vitamin D deficient at time of PICU admission\n\nCan you clarify whether it would be unacceptable for them to receive ANY vitamin D. In our setting it would be unacceptable for us to not allow ANY vitamin D supplementation as it is standard of care to receive 400-600 IU/day (which takes a month or more to raise levels)\n\nOutcome: While it would usual for a study to report on multiple outcomes, it is unusual for a study not to be clear on a primary, secondary and then a set a tertiary outcomes.\n\nPlease fix the error in the sentence: Group A receiving the Standard treatment protocol along with 10,000 IU/kg to maximum up to 4,00,000 IU single\n\nAs some of the patient are teenage, and the criteria do not clearly make it evident patients are intubated and/or incapacitated should consent and assent be considered as well\n\nProvide the reference or citation for the line: “Nutritional status assessment in both the groups will be done as per WHO criteria in which wasting is defined as weight for height (gender specific) to be less than -2 standard deviation on the growth chart and stunting is defined as height for age (gender specific) to be less than -2 standard deviation on the growth chart”\n\nPlease re-evaluate how the dates of blood collection are described. Is day zero the day of randomization or admission? Is day 3, day 3 of admission or after receipt of drug\n\nIn the description of group B, can it made be very clear whether they will receive a placebo or not.\n\nHypervitaminosis is usually measured using 25OHD. There is no clearly established threshold for definition\n\nWhen describing scores and states such as AKI and Inotrope score, provide citations so the reader can know precisely how you will approach measurement\n\n“End of the study will be considered at the day of discharge or mortality of the patient” Do you mean PICU or hospital?\n\nAgain no need to mention excel\n\nMain of your outcomes will NOT be normally distributed and reporting as means and analyzing using t test will not be appropriate\n\nI don’t understand the need for ANOVA in this two arm study. Are there three or more times points for analysis? Same re: Scheffe’s test\nDiscussion\nIn the discussion there is a paragraph: “Yung Wang et al.13 conducted a study with 150,000 IU supplementation of Vitamin D in the study group of Vitamin D deficient septic children and found that the group with supplementation had a better outcome. El Gendy et al.14 had a conducted a study like Yung Wang et al. where the study group was Vitamin D deficient septic children. Labib et al.,15 studied the outcome of supplementation of Vitamin D in deficient children with Pneumonia.” It is not clear which studies are interventional and which are observational. You are also missing details on the citation for the Labib study.\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? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "11242",
"date": "04 Apr 2024",
"name": "Keta Vagha",
"role": "Author Response",
"response": "I wish to express my sincere gratitude for your thoughtful review of the manuscript. Rest assured, I highly value your insights, and I am committed to incorporating all of your corrections diligently. The necessary adjustments will be made, and I am eager to resubmit the refined manuscript promptly. Thank you once again for your invaluable feedback."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1047
|
https://f1000research.com/articles/12-1361/v1
|
18 Oct 23
|
{
"type": "Study Protocol",
"title": "The effect of manual therapy on diaphragm function in adults with asthma: Protocol for a randomized controlled trial",
"authors": [
"Dimitrios Tsimouris",
"Eirini Grammatopoulou",
"Maria Papandreou",
"George Gioftsos",
"George Koumantakis",
"Eirini Grammatopoulou",
"Maria Papandreou",
"George Gioftsos",
"George Koumantakis"
],
"abstract": "Background: Diaphragm dysfunction is prevalent among individuals with asthma due to lung hyperinflation and hyperventilation in asthma paroxysm. This study was designed to evaluate the effect of the manual diaphragm release technique (MDRT) on diaphragm function in individuals with asthma.\nMethods: Adults with diagnosed stable asthma (n = 24), will be recruited from the General Hospital of Kifissia “Agioi Anargyroi” in Athens, Greece. The volunteers who meet the inclusion criteria will be randomly allocated to two groups: (a) the experimental group (n = 12) that will receive 12 sessions of MDRT in conjunction with breathing retraining exercises (BRE), and (b) the control group (n = 12) that will receive 12 sessions of BRE. Measurements will occur at three time points: before the initiation of treatment sessions (week 0), followed by 12 treatment sessions (week 6), and three months from the beginning of the trial (week 12). The main outcomes will be the diaphragm excursion (ultrasonography) and chest expansion (inch tape), with secondary outcomes the maximal respiratory pressures (digital pressure manometer), dysfunctional breathing (Nijmegen questionnaire), asthma control (ACT), dyspnea (Borg scale) and quality of life (SF-12v2).\nDiscussion: The proposed protocol is the first to examine the effectiveness of MRDT on diaphragm’s function in individuals with asthma. Manual Therapy (MT) is a low-cost alternative and supplementary therapy to standard treatment procedures that might improve the biomechanics of respiration in pulmonary rehabilitation.\nTrial Registration: Registered on Clinical Trials.gov (ID: NCT05709054)\nProtocol version: 29/09/2023",
"keywords": [
"Key Words: Asthma",
"Manual Therapy",
"Diaphragm",
"Breathing retraining exercises",
"Diaphragm mobility",
"Ultrasound"
],
"content": "Introduction\n\nDue to its anatomical structure and contribution to minute ventilation (60–80%), the diaphragm is the most important respiratory muscle. 1 – 3 An impaired diaphragm is associated with respiratory symptoms such as dyspnea, intolerance to exercise and sleep problems. 4\n\nChronic obstructive pulmonary disease (COPD) and asthma are umbrella terms for various conditions characterized by chronic airway disease. 5 COPD and asthma patients frequently experience diaphragmatic dysfunction (DD). 6 The diaphragm’s ability to raise and expand the lower ribcage within the zone of apposition (ZOA), where the lower ribcage directly interacts with the diaphragm becomes compromised due to mechanical challenges. This is due to the diaphragm functioning at a disadvantageous shortened position caused by air trapping, which hinders its contraction capacity and increases the respiratory workload. 7\n\nIn COPD, air progressively remains trapped in the lungs due to airway constriction. The architecture of the thoracic cage is disrupted by this clinical condition during exercise and rest, reducing the diaphragm’s physiological advantage. 8 , 9 Similarly, Individuals with moderate to severe asthma may have pulmonary overstretching (asthma paroxysm), which can cause functional problems because it reduces expiratory flow (early airway closure), activates inspiratory muscles at the end of expiration, and reduces lung flexibility. 10 – 12 Although the underlying mechanisms for these two lung conditions, COPD and asthma, differ, both cause secondary complications (pulmonary hyperinflation, hyperventilation syndrome). These features lead to similar pathological changes that impair the diaphragm’s ability to elevate and expand the lower ribcage. 13 Consequently, during inspiration, the lower ribcage’s transverse diameter may decrease. 14\n\nOver the past few decades, two research questions have emerged concerning how physiotherapy can enhance the mechanical efficiency of the thorax and the effectiveness of respiratory muscles during breathing in people with COPD. Researchers, from 1990 15 up to 2015, 16 have made several hypotheses and implemented physiotherapy interventions to find which procedure is more appropriate to improve the effectiveness of mechanical functioning of the thoracic cage in people with pulmonary diseases. Breathing retraining exercises (BRE) are a widely used, productive method, 17 – 19 simple, safe, accessible, with a high level of evidence-based efficacy. 20 – 22\n\nFinally, although specific diaphragm MT techniques have not been documented yet, recent studies have reported evidence for their positive effect on pulmonary rehabilitation (PR). 23 In particular, the manual diaphragm release technique (MDRT) aims to directly stretch the muscle fibers of the diaphragm, as detailed in Rochas’ research. 16 The study showed an improvement in diaphragm’s mobility, maximum inspiratory pressure (MIP), and exercise capacity (EC) in people suffering from COPD. 16 As for asthma, there is no data for the efficacy of diaphragm MT methods, except for one pilot study. 24\n\nThe primary objective of this study is to explore the impact of MDRT on the diaphragm’s function, particularly on the length-tension relationship and chest wall expansion (CWE) in people suffering from asthma. Secondary improvements are expected in the domain of dyspnea, asthma control and dysfunctional breathing. The MDRT in people with asthma may contribute to better disease management.\n\n\nMethods\n\nThe present RCT will be a single centric, two arm parallel equivalence randomized clinical trial. This RCT followed the SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) statement. 25 The completed SPIRIT checklist of the study is uploaded into an approved open repository (Reporting guidelines paragraph). The study’s flowchart is shown in Figure 1.\n\nThe laboratory of Advanced Physiotherapy at the Physiotherapy Department of the University of West Attica (UNIWA) in Athens will be responsible for coordinating the trial. The recruitment of the patients will be conducted from the Pulmonology Department of the General Oncology Hospital of Kifissia “Agii Anargiri” (GOHK) in Athens (Greece). The hospital’s research committee approved the protocol (4479/09-03-22). Interventions and assessments will take place individually (home-based treatment) in Athens (Greece).\n\nThe participants will be recruited from the GOHK. All participants will be out-patients with diagnosed stable asthma, referred by the director, pulmonologist, of the Pulmonary Department of the GOHK. The same pulmonologist will perform lung function testing on all participants (well-maintained and regularly calibrated equipment), will diagnose asthma and perform the measure of chest expansion. A radiologist will perform the ultrasonography (US) and a statistician will process the required analysis. Two separate physical therapists will implement the DMRT and BRE. All participants will read and sign the consent form. The declaration of consent refers to personal data privacy and participation protection. They will subsequently be informed about a) the objectives, methods, and details of the study, (b) that it will be the volunteers’ decision whether to take part or not, (c) they will always have the right to withdraw from the research even after signing, (d) they can also refuse to answer questions they will not wish or remain in the survey and (e) that the patient’s decision to participate will not affect the provision of our research services.\n\nFollowing the initial assessment, eligible volunteers will be randomly assigned to two experimental groups if they meet the inclusion criteria by the secretariat of the Pulmonology Department of the GCHAA. The randomization will be carried out using sealed envelopes. Individuals will have their allocation concealed through the use of sealed envelopes that are sequentially numbered and opaque. 26 The envelopes will be opened only by the primary researcher, who is responsible for the research project and coordination of the study. The pulmonologist who will perform lung function testing on all participants (well-maintained and regularly calibrated equipment), diagnose asthma and perform the measure of chest expansion, the radiologist who will perform the ultrasonography (US), and the two separate physical therapists, who will implement the DMRT and BRE will be unaware of the group allocation.\n\nThe pulmonologist of the trial will approach all eligible patients for recruitment into the study. They will be assessed through a set of questions to confirm eligibility. All patients will be requested to provide written informed consent (signed by the main researcher, the subject, and two witnesses) to participate in the study, including permission to publish results, with the understanding that they can withdraw at any time.\n\nAt least 24 adults will be recruited for the study.\n\nInclusion criteria: aged – 8-60 years, diagnosed with stable asthma 27 and correct use of the inhaler technique.\n\nExclusion criteria: Participation in other physical therapy methods, the presence of cardiopulmonary conditions, prior cardiothoracic or abdominal surgeries, recent chest wall or abdominal trauma, unstable hemodynamic parameters (systolic arterial pressure >140 mmHg and diastolic >90 mmHg), inability to comprehend verbal instructions required for outcome assessments, pregnancy, neurological ailments, and concurrent involvement in interventional programs.\n\nA pulmonologist of GOHK with years of experience diagnosing and treating asthma patients will examine the chest expansion, the pulmonary function, and diagnosis of asthma. The radiologist will perform the US assessment, and the secretariat of the GOHK will administer the questionnaires in a random order and collect all data.\n\nInterventions\n\nThe pulmonologist and the main researcher of the protocol will organize two online sessions with all the participants after the randomization. In one session, participants will be informed by the pulmonologist about (a) general asthma information, (b) asthma triggers, (c) recognition of asthma symptoms, (d) medication and proper use of asthma medications (inhaler techniques), (e) smoking, and (f) asthma control (symptom control/future risk domains/long-term goals). 28 As for the last domain (asthma control), information will be provided regarding, (i) the dynamic changes of asthma, (ii) the recognition of these changes based on PEF values and symptoms, (iii) the importance of early detection of clinical signs of worsening and the immediate initiation of appropriate medication.\n\nAt the second online session the participants will be informed by the main researcher about (a) the breathing pattern, (b) the pathological pattern of breathing that is developing both in stable phase and in paroxysm, 29 (c) the role of physiotherapy and specifically about the BRE in PR, (d) the formation of a trusting relationship between a person living with asthma and a medical professional (e) the importance of self-efficacy in asthma self-management 30 – 33 and (f) the self-efficacy enhancement process.\n\nFollowing the two online sessions, there will be a discussion between patients and health professionals (pulmonologist - main researcher) lasting approximately one hour, during which patients can share their objectives, values, apprehensions, support and commendations. The structure of the online session will be determined by a) the long-term objectives for asthma management 5 and b) the health belief model. 34 , 35 Regarding the treatment sessions, every participant will receive twelve sessions twice weekly for six weeks, lasting one hour per session. Individual sessions will be provided in patients’ homes under the same conditions (e.g., day, time of day, temperature, therapeutic bed, and patient’s position).\n\nPhysiotherapy intervention will be provided by two physical therapists, trained by the professor of chest physiotherapy and the professor of manual therapy respectively, at the Physiotherapy Department, UNIWA. Any departure from the administration of treatment sessions (such as missing more than one appointment) or any exacerbation of symptoms will lead to exclusion. Brief descriptions of the interventions planned for each group are provided below.\n\nIntervention Group: This group will receive MDRT plus BRE. MDRT is intended to stretch and mobilize the diaphragmatic muscle fibers indirectly. MDRT will be applied as described by Rocha and his colleagues. 16\n\nMDRT: Participants will be instructed to lie in a supine position with relaxed limbs. The therapist will be positioned at the patient’s head. Manual contact will be made using the hypothenar region and the last three fingers bilaterally, placed under the seventh to tenth rib costal cartilages. The therapist’s forearms will align towards the patient’s shoulders. During inhalation, the therapist will apply gentle pulling and lateral elevation of the ribs in the inspiratory phase at the points of contact. As the participant exhales, the therapist’s touch will deepen towards the inner costal margin while maintaining resistance. This connection will further deepen within the costal margin in subsequent respiratory cycles. The entire process will consist of two sets of 10 repetitions, separated by a 1-minute interval lasting 10 minutes. 36\n\nBRE: BRE will be conducted for 30 minutes. The primary objective of these exercises is to mitigate hyperventilation, hypocapnia, and dysfunctional breathing—common symptoms in individuals with asthma. 37 The initial step involves identifying and inhibiting an abnormal upper thoracic respiratory pattern and re-education of diaphragmatic and slow nasal breathing. Additionally, brief respiratory pauses will be introduced after each exhalation. 38 Subsequently, BRE aims to integrate the new breathing pattern into daily life. This stage focuses on incorporating diaphragmatic and slow nasal breathing into various daily activities, encompassing physical activities (e.g., speaking, swimming, walking, gardening), social activities (e.g., playing with children or pets), and work-related activities (e.g., managing work stress). 39\n\nThe phases of BRE will consist of: i) identification of the abnormal breathing pattern, ii) diaphragmatic breathing, ii) nose breathing, iii) slow breathing with controlled breath-holding at the end of exhalation, iv) adaptation of the new breathing pattern in everyday life activities and various positions (supine, semi-sitting, sitting), and v) breathing control in speech.\n\nControl Group: This group will receive only BRE, as mentioned in the intervention group.\n\nThe evaluations will take place at three time - points: prior to treatment (week 0), post-treatment (week 6), and three months subsequent (week 12). The primary outcomes will entail the measurement of diaphragm excursion using ultrasound 40 and chest expansion (CE) using a tape measure. 41 Secondary outcomes will also be employed: maximal inspiratory and expiratory pressures (MIP/MEP), 42 , 43 dysfunctional breathing (Nijmegen questionnaire – - NQ), 44 asthma Control (ACT), 45 , 46 quality of life (SF-12v2), 47 and dyspnea (Borg scale). 48 Table 1 illustrates the SPIRIT schematic protocol of the study along with the schedule of assessments.\n\nPrimary outcome measures\n\nDiaphragmatic excursion assessment with ultrasonography: Numerous studies have confirmed the effectiveness of the US to evaluate diaphragmatic function. Since 1970, 49 the US has been utilized to assess the diaphragm’s mobility. Modern medicine accepts its use as a completely safe method. The diagnostic US has 93% sensitivity and 100% specificity. 15 The examiners are not exposed to any radiation, and there is no need for special preparation, allowing for as many safe applications as required. The US offers the option of a dynamic inspection of the affected area in real time. The diaphragmatic excursion is measured in cm/mm.\n\nChest wall expansion (CWE): In clinical and research practice, the inch tape measure is an alternative method for assessing chest expansion. 50 By placing the tape measure at the level of the axilla (about the level of the sternal angle of Louis), the level of the xiphoid process, or between the xiphoid process and the umbilicus, the therapist identifies the upper, middle, and lower chest wall expansion, respectively. The therapist should repeat the measurement at least three times for each level for higher fidelity. 41 A tape measure (in centimeters) will assess the variance between values recorded during deep inhalation and exhalation, with greater values signifying improved results. 41 Norms have been developed according to age and sex. 51\n\nSecondary outcome measures\n\nNijmegen Questionnaire (NQ): The Nijmegen Questionnaire is a reliable and valid tool for assessing dysfunctional breathing in clinical practice and research. It is designed to identify the Hyperventilation Syndrome (HS). A score greater than 23 indicates the presence of HS in the general population. The NQ has shown 91% sensitivity and 95% specificity. 52 In previous research, NQ scores of 20, 22 and 23 have been used as cut-off scores to detect HS in subjects with and without asthma. 53 – 55 The NQ questionnaire has been validated in Greek adults with asthma, providing evidence of validity and reliability of measurements with a cut-off score of >17. 56\n\nAsthma control test (ACT): The ACT questionnaire is a valid and reliable clinical and research tool. 57 Its quick completion time is one of its key features. It has five items, all about the most recent four weeks. 57 , 58 The ACT evaluates the frequency of wheezing and other general asthma symptoms and the need for emergency control self-assessment. The score ranges from 5 (poor control of asthma) to 25 (good control of asthma). An ACT score >19 indicates controlled asthma. The ACT has been validated in the Greek population with asthma and has shown high indices of internal consistency (0.72) and test–retest reliability (IR = 0.85). 49\n\nSf-12v2 questionnaire: A simplified version of the SF-36 includes medications, and how well asthma affects daily functioning and overall asthma. The SF-12v2 is a practical, reliable, and valid way to assess physical and mental health. With one or two questions per domain, it assesses the exact eight health dimensions as the SF-36v2, which includes Physical Functioning, Role-Physical, Bodily Pain, General Health, Vitality, Social Functioning, Role-Emotional, and Mental Health. The SF-12 is a valid alternative to the lengthy SF-36 for the self-assessment of quality of life by assessing the health status of healthy and patient population groups. 59 Higher ratings indicate better physical and mental wellbeing, ranging from 0 to 100. 60 It has been suggested that a cut-off of 50 or less can be used to identify a physical condition, while a score of 42 or less may signify clinical depression. 60 The Sf-12v2 has been weighted in the Greek general population. 61\n\nBorg scale: The Borg dyspnea scale is a simple, non-proprietary scoring system. It is extensively used in clinical and research practice to evaluate symptoms of shortness of breath and provides valuable data. 62 , 63 It begins with 0 (no dyspnea), and goes up to 10 (extreme dyspnea). As a result, healthcare professionals must give patients enough time to learn and ensure they comprehend it before using it. 64\n\nThe study started in January 2023 and is scheduled to be completed in January 2024.\n\nSample size estimation was conducted using G*Power, version 3.1 software. For a study design involving two separate groups and three repeated measurements (pre-treatment, post-treatment, and one follow-up) to attain a statistical power of 0.80 for detecting an effect size (d) of 1.36 in the interaction effect (22), with a significance level of 5% (0.05), a minimum of 6 participants per group was determined as necessary. Accounting for a potential dropout rate of 10% and based on the calculated sample size, it was anticipated that approximately 12 individuals per group would need to be initially recruited. 65\n\nData collection methods\n\nData regarding the outcomes pre and post-intervention will be meticulously collected from the main researcher. The collected information will undergo a thorough examination to analyze the outcomes. Throughout the study, the professor of chest physiotherapy (supervisor) will closely oversee the main researcher administering the study’s data. To ensure the patient adheres to the study, timely messages will be sent to their mobile phones, providing information and reminders regarding upcoming sessions. A 10% drop-out rate has been considered in the sample size calculation, thus minimizing potential interference with the study results.\n\nData management\n\nEvaluation data will be sourced from a predefined spreadsheet containing baseline characteristics. A secure database will be employed to store all research-related data securely. Paper copies of evaluation forms signed informed consent forms, and other non-electronic documents will be securely stored in the study environment. A comprehensive backup of the data entries will be generated once a month until the conclusion of the trial.\n\nUpon completion of the study, the Excel spreadsheet will be published and forwarded to the statistician for the necessary analysis. A checklist will help prevent data loss from inefficient staff procedures. Given the extensive follow-up assessment for this experiment, participant retention and completion of follow-up assessments will be notably high. After six weeks from the end of interventions, the participants will be invited to a follow-up examination (12 weeks from the beginning of the trial).\n\nThe IBM SPSS software, specifically version 28, will be utilized for all data processing. The distribution of the data will be displayed using descriptive statistics. For each dependent variable independently (US, CWE, ACT, NQ, SF-12v2 and Borg scale), 2×3 ANOVA repeated measures, with Bonferroni adjustment will be used to examine the interaction between intervention (experimental and control group) and time (0, 6, and 12 weeks). The level of statistical significance was chosen at 0.05.\n\nMonitoring\n\nData monitoring\n\nA data monitoring committee of members from the UNIWA Physiotherapy Department will periodically review the accumulating data, determining if the trial should be modified or discontinued.\n\nHarms\n\nA clinical staff is going to supervise the entire procedure. Any adverse events will be immediately reported throughout the trial to the Physiotherapy Department of the UNIWA committee.\n\nAuditing\n\nAn evaluation of the experiment will be performed each month. Every deviation from the protocol will be recorded and addressed.\n\nEthics and dissemination\n\nResearch ethics approval\n\nThe Ethics Committee of the UNIWA in Greece approved this study under protocol 90853/04-10-2022. The study follows the Helsinki Declaration’s “Ethical Principles of Medical Research Involving Human Subjects.” Protocol modifications will be disclosed to the Ethics Committee as soon as possible. The trial has been proactively registered in the ClinicalTrials.gov database with the identification number NCT05709054.\n\nProtocol amendments\n\nThe study has already been modified and accepted in accordance with the Ethics Committee of the UNIWA in Greece suggestions. As a result, further modifications could not be made.\n\nConsent\n\nStudy participants will receive a translated version of the study protocol. Prior to participation, all individuals involved in the study will be fully informed, and written consent will be obtained from each participant.\n\nThe main researcher will collect personal data during the trial. A confidentiality statement on the permission form will be signed by the main researcher, the subject, and two witnesses. Whenever necessary to disclose information for the study, consent from the patients will always be obtained with utmost assurance of confidentiality.\n\nThe main researcher and the statistician will have access to the final trial datasheet.\n\nThe entire procedure will be conducted under the oversight of clinicians and the physiotherapy department of the UNIWA committee. After the trial sessions, the participants will be under supervision for about four weeks so that they can take care if there is any harm.\n\n\nDiscussion\n\nAlthough several studies assessing the efficacy of MT in obstructive lung diseases have been conducted, drawing definitive conclusions is challenging due to their conflicting results. 37 A review of the existing literature has outlined a model of how MT delays the onset of fatigue in respiratory muscles. 66 It reduces respiratory muscle effort by allowing them to function closer to their optimal length. 38 Remarkably, as of now, no RCT has explored the impact of manual therapy, specifically focusing on the zone of apposition (ZOA) of the diaphragm in individuals with asthma.\n\nThis is the first RCT endeavoring to investigate the influence of the manual diaphragm release technique on DE, CE, MIP, MEP, asthma control, dyspnea, and overall quality of life in individuals diagnosed with asthma. The study’s strength will be the high internal validity since this protocol is planned according to accepted methodology regarding randomization, concealed allocation, blinding of examiners, and appropriate sample size calculation. What sets this study apart is its original investigation into the mechanism of the MDRT on the ZOA of the diaphragm in individuals living with asthma.\n\nFinally, several significant constraints must be considered. The study sample is drawn exclusively from a single hospital, potentially limiting the generalizability of the findings. Additionally, the extended experimental period and the substantial number of sessions may lead to participant dropouts.\n\nThe study started in January 2023.\n\nThis work will be presented in International Conference Proceedings and published in an indexed journal.\n\n\nConclusions\n\nThis RCT will be innovative as it will, for the first time, provide evidence of the effect of the MDRT on diaphragm function in people with asthma. MT is a low-cost alternative and supplementary therapy to standard treatment procedures that might improve the biomechanics of respiration in pulmonary rehabilitation.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: SPIRIT checklist for ‘The effect of manual therapy on diaphragm function in adults with asthma: Protocol for a randomized controlled trial’, https://doi.org/10.6084/m9.figshare.24191106. 67\n\n\nReferences\n\nNason LK, Walker CM, Mc Neeley MF, et al.: Imaging of the Diaphragm: Anatomy and Function. Radiographics. 2012; 32(2): E51–E70. Publisher Full Text\n\nRicoya J, Rodríguez-Núnez N, Álvarez-Dobano JM, et al.: Diaphragmatic dysfunction. Pulmonology. 2018; 25: 223–235. Publisher Full Text\n\nRatnovsky A, Elad D: Anatomical model of the human trunk for analysis of respiratory muscles mechanics. Respir. Physiol. Neurobiol. 2005; 148(3): 245–62. 12. Publisher Full Text\n\nGibson GJ: Diaphragmatic paresis: pathophysiology, clinical features, and investigation. Thorax. 1989; 44: 960–970. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGlobal Initiative for Asthma: Global Strategy for Asthma Management and Prevention, 2023 Updated.2023. Reference Source\n\nRocha FR, Brüggemann AKV, de Souza Francisco D , et al.: Diaphragmatic mobility: relationship with lung function, respiratory muscle strength, dyspnea, and physical activity in daily life in patients with COPD. J. Bras. Pneumol. 2017; 43(1): 32–37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGreising SM, Ottenheijm CAC, O’Halloran KD, et al.: Diaphragm Plasticity in Aging and Disease: Therapies for Muscle Weakness go from Strength to Strength. J. Appl. Physiol. 2018; 125: 243–253. Publisher Full Text | Free Full Text\n\nDecramer M: Hyperinflation and respiratory muscle interaction. Eur. Respir. J. 1997; 10(4): 934–941. Publisher Full Text\n\nDe Troyer A: Effect of hyperinflation on the diaphragm. Eur. Respir. J. 1997; 10(3): 708–713. Publisher Full Text\n\nSilva IS, Fregonezi GAF, Dias FAL, et al.: Inspiratory muscle training for asthma. Cochrane Database Syst. Rev. 2013; 2013(9): CD003792. Art. No.: CD003792. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBurgel, et al.: Update on the roles of distal airways in asthma. Eur. Respir. Rev. 1980; 18(112): 80–95. Publisher Full Text\n\nMartin J, Powell E, Shore S, et al.: The Role of Respiratory Muscles in the Hyperinflation of Bronchial Asthma. Am. Rev. Respir. Dis. 2008; 121: 441–447. Publisher Full Text\n\nMauad T, Dolhnikoff M: Pathologic similarities and differences between asthma and chronic obstructive pulmonary disease. Curr. Opin. Pulm. Med. 2008; 14: 31–38. Publisher Full Text\n\nJean DA, Janssens P: The Pathophysiology of Respiratory Failure: Control of Breathing, Respiratory Load, and Muscle Capacity. Respiration. 2019; 97: 93–104. Publisher Full Text\n\nBoon AJ, Sekiguchi MDH, CaitlinM DJ, et al.: Sensitivity and specificity of diagnostic ultrasound in the diagnosis of phrenic neuropathy. Neurology. 2014; 83: 1264–1270. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRocha T, Souza H, Brandão DC, et al.: The Manual Diaphragm Release Technique improves diaphragmatic mobility, inspiratory capacity and exercise capacity in people with chronic obstructive pulmonary disease: a randomised trial. J. Physiother. 2015; 61(4): 182–189. PubMed Abstract | Publisher Full Text\n\nSantino TA, Chaves GS, Freitas DA, et al.: Breathing exercises for adults with asthma. Cochrane Database Syst. Rev. 2020; 3(3): CD001277. PubMed Abstract | Publisher Full Text\n\nYufan L, Peijun L, Ning L: Effects of Home-Based Breathing Exercises in Subjects With COPD. Respir. Care. (2020) Mar; 65(3): 377–387. Publisher Full Text\n\nMayer AF, Karloh M, Santos KD: Effects of acute use of pursed lips breathing during exercise in patients with COPD: a systematic review and meta-analysis. Physiotherapy. 2018; 104(1): 9–17. PubMed Abstract | Publisher Full Text\n\nGrammatopoulou E, Skordilis E, Stavrou N: The Effect of Physiotherapy-Based Breathing Retraining on Asthma Control. J. Asthma. 2011; 48(6): 593–601. PubMed Abstract | Publisher Full Text\n\nUbolnuar N, Tantisuwat A, Thaveeratitham P, et al.: Effects of Breathing Exercises in Patients with Chronic Obstructive Pulmonary Disease: Systematic Review and Meta-Analysis. Ann. Rehabil. Med. 2019; 43(4): 509–523. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBorge CR, Hagen KB, Mengshoel AM, et al.: Effects of controlled breathing exercises and respiratory muscle training in people with chronic obstructive pulmonary disease: results from evaluating the quality of evidence in systematic reviews. BMC Pulm. Med. 2014; 14(1). PubMed Abstract | Publisher Full Text | Free Full Text\n\nNair A, Alaparthi GK, Krishnan S, et al.: Comparison of Diaphragmatic Stretch Technique and Manual Diaphragm Release Technique on Diaphragmatic Excursion in Chronic Obstructive Pulmonary Disease: A Randomized Crossover Trial. Pulm. Med. 2019; 2019: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeonés-Macías E, Torres-Sánchez I, Cabrera-Martos I, et al.: Effects of manual therapy on the diaphragm in asthmatic patients: A randomized pilot study. International Journal of Osteopathic Medicine. Int. J. Osteopath. Med. 2018; 29: 26–31. Publisher Full Text\n\nChan AW, Tetzlaff JM, Altman DG, et al.: SPIRIT (2013) statement: defining standard protocol items for clinical trials. Ann. Intern. Med. 2013; 158(3): 200–207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChan AW, Tetzlaff JM, Altman DG, et al.: SPIRIT statement: defining standard protocol items for clinical trials. Ann. Intern. Med. 2013; 158(3): 200–207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGlobal Initiative for Asthma: Global Strategy for Asthma Management and Prevention.2023 Updated (2023). Reference Source\n\nPhysical Activity and Cardiovascular Health: NIH Consents Statement.1995 18-20; 13(3): 1–33.\n\nGrammatopoulou E, Skordilis E, Stavrou N, et al.: The effect to physiotherapy-based breathing retraining on asthma control. J. Asthma. 2011; 48: 593–601. PubMed Abstract | Publisher Full Text\n\nBandura A: Self-efficacy: Toward a unifying theory of behavioral change. Psychol. Rev. 1997; 84: 191–215. Publisher Full Text\n\nCampbell TS, Lavoie KL, Bacon SL, et al.: Asthma self-efficacy, high frequency heart rate variability, and airflow obstruction during negative affect in daily life. Int. J. Psychophysiol. 2006; 62: 109–114. PubMed Abstract | Publisher Full Text\n\nMancuso CA, Rincon M, McCulloch CE, et al.: Self-efficacy, depressive symptoms and patients’ expectations predict outcomes in asthma. Med. Care. 2001; 39(12): 1326–1338. PubMed Abstract | Publisher Full Text\n\nShortridge-Baggett LM: Self-efficacy: Measurement and intervention in nursing. Sch. Inq. Nurs. Pract. 2001; 15(3): 183–188. PubMed Abstract\n\nBecker MH: The health belief model and personal health behavior. Health Educ. Monogr. 1974; 2(4): 409–419. Publisher Full Text\n\nRosenstock IM, Strecher VJ, Becker MH: Social learning theory and the health belief model. Health Educ. Behav. 1988; 15: 175–183. Publisher Full Text\n\nBennett S, Siritaratiwat W, Tanrangka N, et al.: Effectiveness of the manual diaphragmatic stretching technique on respiratory function in cerebral palsy: A randomised controlled trial. Respir. Med. 2021; 184: 106443. PubMed Abstract | Publisher Full Text\n\nTatsios PI, Grammatopoulou E, Dimitriadis Z, et al.: The Effectiveness of Manual Therapy in the Cervical Spine and Diaphragm, in Combination with Breathing Reeducation Exercises, in Patients with Non-Specific Chronic Neck Pain: Protocol for Development of Outcome Measures and a Randomized Controlled Trial. Diagnostics. (2022) Nov 4; 12(11): 2690. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBruton A, Lee A, Yardley L, et al.: Physiotherapy breathing retraining for asthma: a randomised controlled trial. Lancet Respir. Med. 2018; 6(1): 19–28. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHolloway EA, West RJ: Integrated breathing and relaxation training (the Papworth method) for adults with asthma in primary care: a randomised controlled trial. Thorax. 2007; 62(12): 1039–1042. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVetrugno L, Guadagnin GM, Barbariol F, et al.: ULTRASOUND IMAGING FOR DIAPHRAGM DYSFUNCTION: A NARRATIVE LITERATURE REVIEW. J. Cardiothorac. Vasc. Anesth. 2019; 33: 2525–2536. PubMed Abstract | Publisher Full Text\n\nOlsén MF, Lindstrand H, Broberg JL, et al.: Measuring chest expansion; A study comparing two diferent instructions. Adv. Physiother. 2011; 13(3): 128–132. Publisher Full Text\n\nATS/ERS Statement on Respiratory Muscle Testing. Am. J. Respir. Crit. Care Med. 2002; 166(4): 518–624. PubMed Abstract | Publisher Full Text\n\nBlack LF, Hyatt RE: Maximal respiratory pressures: normal values and relationship to age and sex. Am. Rev. Respir. Dis. 1969; 99(5): 696–702. PubMed Abstract\n\nGrammatopoulou EP, Skordilis EK, Georgoudis G, et al.: Hyperventilation in asthma: a validation study of the Nijmegen Questionnaire–NQ. J. Asthma. 2014; 51(8): 839–846. PubMed Abstract | Publisher Full Text\n\nNathan R, Sorkenss CA, Kosinski M, et al.: Development of the asthma control test: a survey for assessing asthma control. J. Allergy Clin. Immunol. 2004; 113: 59–65. Publisher Full Text\n\nSchatz M, Sorkness CA, Li JT, et al.: Asthma Control Test: reliability, validity, and responsiveness in patients not previously followed by asthma specialists. J. Allergy Clin. Immunol. 2006; 117: 549–556. Publisher Full Text\n\nWare J, Sherbourne CD: The MOS 36-Item short-form health survey (SF-36): Conceptual framework and item selection. Med. Care. 1992; 30: 473–483. PubMed Abstract | Publisher Full Text\n\nBorg G: Borg’s Perceived Exertion and Pain Scales. Human Kinetics. 1998. 0-88011-623-4.\n\nHaber K, Asher M, Freimanis AK: Echographic evaluation of diaphragmatic motion in intra-abdominal diseases. Radiology. 1975; 114(1): 141–144. PubMed Abstract | Publisher Full Text\n\nMohan V, Dzulkifli NH, Justine M, et al.: Reliability of Chest Expansion using Cloth Tape Measure Technique. Bangladesh J. Med. Sci. 2012; 11(4): 307–311. Publisher Full Text\n\nÖzge İLLEEZMEMETOĞLU, Bülent BÜTÜN, İlhan SEZER: Chest Expansion and Modified Schober Measurement Values in a Healthy, Adult Population. Arch. Rheumatol. 2016; 31(2): 145–150. Publisher Full Text\n\nvan Dixhoorn J , Dulvenvoorden H: Efficacy of Nijmegen questionnaire in recognition of the hyperventilation syndrome. J. Psychosom. Res. 1985; 29: 199–206. PubMed Abstract | Publisher Full Text\n\nThomas M, McKinley R, Freeman E, et al.: Prevalence of dysfunctional breathing in patients treated for asthma in primary care: Cross sectional survey. Br. Med. J. 2001; 322: 1098–1100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHagman C, Janson C, Emtner M: A comparison between patients with dysfunctional breathing and patients with asthma. Clin. Respir. J. 2008; 2: 86–91. Publisher Full Text\n\nCourtney R, Greenwood K, Cohen M: Relationships between measures of dysfunctional breathing in a population with concerns about their breathing. J. Bodyw. Mov. Ther. 2011; 15: 24–34. PubMed Abstract | Publisher Full Text\n\nGrammatopoulou E, Skordilis E, Georgoudis G, et al.: Hyperventilation in asthma: A validation study of the Nijmegen Questionnaire - NQ. J. Asthma. 2014; 51: 839–846. Publisher Full Text\n\nNathan R, Sorkenss CA, Kosinski M, et al.: Development of the asthma control test: A survey for assessing asthma control. J. Allergy Clin. Immunol. 2004; 113: 59–65. Publisher Full Text\n\nGrammatopoulou E, Skordilis E, Stavrou N, et al.: The effect of physiotherapy-based breathing retraining on asthma control. J. Asthma. 2011; 48: 593–601. PubMed Abstract | Publisher Full Text\n\nKontodimopoulos N, Pappa E, Niakas D, et al.: Validity of SF-12 summary scores in a Greek general population. Health and Quality of LifeOutcomes. 2007; 5: 55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWare J, Kosinski M, Keller S: SF-12: How to score the SF-12 Physical and Mental Summary Scales. 2nd ed.Boston, MA: The Health Institute, New England Medical Center; 1995.\n\nKontodimopoulos N, Pappa E, Niakas D, et al.: Validity of SF-12 summary scores in a Greek general population. Health Qual. Life Outcomes. 2007; 5(1): 55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPfeifer KA, Pivarnik JM, Womack CJ, et al.: Reliability and validity of the Borg and OMNI rating of perceived exertion scales in adolescent girls. Med. Sci. Sports Exerc. 2002; 34: 2057–2061. Publisher Full Text\n\nSanjuas C, Alonso J, Ferrer M, et al.: Adaptation of the asthma quality of life questionnaire to a second language preserves its critical properties: The Spanish version. J. Clin. Epidemiol. 2001; 54: 182–189. PubMed Abstract | Publisher Full Text\n\nMitchell WH, Brubaker PH, Kaminsky LA, et al.: Validity of Rating of Perceived Exertion During Graded Exercise Testing in Apparently Healthy Adults and Cardiac Patients. J. Cardpulm. Rehabil. 1997; 17(4): 261–267. Publisher Full Text\n\nThomas JR, Nelson JK: Research methods in physical activity. Champaign, IL: Human Kinetics; 1996.\n\nRoh JA, Kim KI, Jung HJ: The efficacy of manual therapy for chronic obstructive pulmonary disease: A systematic review. PLoS One. 2021; 16(5): e0251291. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTsimouris D: SPIRIT_checklist.docx. figshare. Journal Contribution. 2023. Publisher Full Text"
}
|
[
{
"id": "216768",
"date": "25 Oct 2023",
"name": "Luis Vicente Franco Oliveira",
"expertise": [
"Reviewer Expertise PhD in Health Sciences",
"specialist in Respiratory Physiotherapy and Pulmonary Rehabilitation and Cardiorespiratory Sleep Disorders."
],
"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 RCT will be innovative as it will, for the first time, provide evidence of the effect of the manual diaphragm release technique on diaphragm function in people with asthma. Manual Therapy is a low-cost alternative and supplementary therapy to standard treatment procedures that might improve the biomechanics of breathing in pulmonary rehabilitation. Studies aimed at investigating intervention strategies that seek to improve the functioning of the main muscle of our breathing (diaphragm) are extremely important around the world. The authors propose a low-cost intervention strategy without any risk to patients. I believe that the results of this study protocol will make important contributions to Pulmonology and Respiratory Physiotherapy around the world. Below I describe some suggestions to improve the presentation of the study protocol.\nThe title of the study complies with the PICOS strategy, characterizing the proposal well. It is noteworthy that the study protocol is already registered at Clinical Trials.gov (ID: NCT05709054). The manuscript contains all sessions necessary for a study protocol. The abstract of the manuscript is well written and well designed, summarizing the study proposal very well.\nI suggest stating in the title of Figure 1. Design of the trial that the flowchart was prepared in accordance with the SPIRIT statement.\n\nIn the “Methods - Study design” section I suggest maintaining what is described about the SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) statement, in relation to the protocol design, however adding that the study will be a randomized controlled study conducted in accordance with the CONSORT statement.\n\nI suggest adding the acronym SPIRIT to the end of the title of Table 1.\n\nIn the primary outcome assessment item, add the commercial references of the ultrasound equipment that will be used to analyze the movement of the diaphragm. These details are important to allow other researchers to reproduce the study.\n\nI suggest improving the description of the statistical analysis, adding more details about the analyses. In this same item, please add the commercial description of the software to be used.\n\nThe study does not mention whether there are conflicts of interest between the authors. It would be interesting to mention if there is any type of conflict.\n\nI suggest that the authors standardize bibliographic references. There are some non-standard ones.\n\nI would also like to congratulate the authors for the brilliant proposal.\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": [
{
"c_id": "10457",
"date": "28 Nov 2023",
"name": "DIMITRIOS TSIMOURIS",
"role": "Author Response",
"response": "Dear Luis Vicente Franco Oliveira, I extend my sincere thanks for your meticulous evaluation of our study protocol and for providing valuable feedback that helped us improve our work's quality. Please be reassured that we will address all the issues mentioned and further improve the manuscript. We are excited to share our findings with the broader research community and hope they interest readers. The publication of our study will provide new insights and stimulate further research in this area. Yours sincerely, Mr Dimitrios Tsimouris -- PhD candidate Department of Physiotherapy University of West Attica Athens, Greece"
},
{
"c_id": "11152",
"date": "13 Apr 2024",
"name": "DIMITRIOS TSIMOURIS",
"role": "Author Response",
"response": "Dear Prof. Luis Vicente Franco Oliveira, We would like to thank you for allowing us to revise the manuscript. We appreciate the time and effort you put into this to improve our work further. We have responded to all the comments. Please find our replies below. Comment 1: «I suggest stating in the title of Figure 1. Design of the trial that the flowchart was prepared in accordance with the SPIRIT statement.» Thank you for the suggestion. The heading of Figure 1 has been changed. Comment 2: «In the “Methods - Study design” section, I suggest maintaining what is described about the SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) statement in relation to the protocol design, however adding that the study will be a randomized controlled study conducted in accordance with the CONSORT statement» Thank you for your comment. We apologize for the mistake you pointed out. We have now added that our study is a randomized controlled study conducted in accordance with the CONSORT statement. Comment 3: «I suggest adding the acronym SPIRIT to the end of the title of Table 1» Thank you for this suggestion. The acronym SPIRIT has been added to the end of the title of Table 1, as you suggested. Comment 4: «In the primary outcome assessment item, add the commercial references of the ultrasound equipment that will be used to analyze the movement of the diaphragm. These details are important to allow other researchers to reproduce the study.» Thank you for your comment. As you suggested, the commercial references to the ultrasound equipment were added to the main text. Comment 5: «I suggest improving the description of the statistical analysis, adding more details about the analyses. In this same item, please add the commercial description of the software to be used» Following your suggestion, we have improved the subsection on statistical analysis as requested. As you suggested, we have uploaded details about both the analyses and the commercial description of the software to be used. Comment 6: «The study does not mention whether there are conflicts of interest between the authors. It would be interesting to mention if there is any conflict.» Thank you for pointing out. Here and in the main text, we would like to disclose no conflicts of interest between the authors. Comment 7: «I suggest that the authors standardize bibliographic references. There are some non-standard ones.» Thank you for your comment. We apologize for the mistake you pointed out. We have now tried to upload the bibliographic references standardized to the best."
}
]
},
{
"id": "223569",
"date": "20 Feb 2024",
"name": "Ragab Elnaggar",
"expertise": [
"Reviewer Expertise Physical 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\nThis protocol for a prospective, randomized clinical trial will assess the effect of manual diaphragm release technique (MDRT) on diaphragm function in individuals with asthma. While, based on a brief search of the database, previous evidence on the effect of this intervention is likely scarce, there is, therefore, a need for more well-controlled trials, employing adequate methodology, to conclusively evaluate the role of MDRT for patients with asthma.\nI partially disagree with the assertion that “The proposed protocol is the first to examine the effectiveness of MRDT on diaphragm function in individuals with asthma”. There is a previous publication on the role of MRDT in pediatric patients with asthma (1).\n\nAsthma encompasses heterogeneous phenotypes that vary widely in terms of their underlying causes, triggers, clinical manifestations, and response to treatment. Furthermore, the severity of asthma can range from mild and intermittent symptoms to severe and persistent symptoms that require frequent medical intervention. Understanding the heterogeneity of asthma is important because it helps healthcare professionals tailor treatment approaches to individual patients. It is unclear in this protocol which type/severity of asthma would be considered.\n\nWhile reading the introduction section, I noticed that it lacks a comprehensive background on patients with asthma, their diaphragmatic function, and the potential benefits of MDRT in addressing this issue. I believe that including these key elements would greatly enhance the clarity and contextual understanding of the intended study. Providing a brief overview of the impact of asthma on diaphragmatic function, respiratory muscle strength, or altered breathing patterns, and emphasizing the potential of MDRT as a therapeutic intervention would help readers grasp the significance of the study and its potential implications for asthma management. I encourage the authors to consider revising the introduction accordingly to provide a more comprehensive background and set a firm foundation for the remainder of the study.\n\nThe significance of the study is not clear. Authors may need to justify the importance of their work, highlight the impact it has on the research field, and define its contribution to new knowledge.\n\nMore importantly, they need to pinpoint the research gap (in light of the related literature) and make it clear what drove them to conduct the study.\n\nAgain, the statement “As for asthma, there is no data for the efficacy of diaphragm MT methods, except for one pilot study” is not true and should be revised in light of the aforementioned publication.\n\nI have a concern regarding the study power. A sample size of 24 is a considerably small sample. The authors conducted an a priori power analysis to determine the minimum sample size necessary for detecting clinically significant results. They employed a substantial effect size (d = 1.36) and the minimum acceptable power level (80%) in their analysis. However, this approach may present challenges in detecting moderate or small changes in the outcome variable, potentially resulting in inconclusive findings and limiting the interpretability of the study conclusions.\n\nThe authors aim to recruit a minimum of 24 participants, encompassing a broad age range from 8 to 60 years. However, it is recommended that the authors consider prioritizing either pediatric or adult patients for a more focused investigation.\n\nIt is crucial to incorporate a thorough and detailed description of the pulmonary rehabilitation program within this protocol, as its current absence hinders the comprehensive understanding of the intervention being studied.\n\nThe data analysis plan is appropriate. The utilization of 2x3 repeated measures ANOVA with Bonferroni adjustment will be used to examine the interaction between intervention offer advantages for allowing for the examination of within-subject changes across multiple conditions or time points and accounting for the correlated nature of data within subjects.\n\nIn summary, the implementation of the study as outlined in this protocol has the potential to offer supplementary or corroborating evidence concerning the efficacy of MDRT in individuals diagnosed with asthma.\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? Not applicable",
"responses": [
{
"c_id": "11117",
"date": "13 Apr 2024",
"name": "DIMITRIOS TSIMOURIS",
"role": "Author Response",
"response": "Dear Ragab Elnaggar, Thank you for your thorough review and insightful feedback on our study protocol. Your contributions have significantly enhanced the quality of our work. We will meticulously address all the concerns raised and further refine our manuscript. Yours sincerely, Mr Dimitrios Tsimouris -- PhD candidate Department of Physiotherapy University of West Attica Athens, Greece"
},
{
"c_id": "11153",
"date": "13 Apr 2024",
"name": "DIMITRIOS TSIMOURIS",
"role": "Author Response",
"response": "Dear Prof. Ragab Elnaggar, We would like to thank you for reviewing our manuscript and giving us the opportunity to revise it. We appreciate the time and effort you put into this to further improve our work. Before presenting our responses to your comments, we deemed it important to clarify that our study will only focus on adults with mild to moderate severity of asthma. Unfortunately, we found a typographical error in the inclusion criteria of our study, where \"18\" was mistakenly written as \"8.\" We acknowledge that this significantly affected your assessment. Given the above, we here by provide our responses in the same order as you presented your comments. Please find our replies below: Comment 1: «I partially disagree with the assertion that “The proposed protocol is the first to examine the effectiveness of MRDT on diaphragm function in individuals with asthma”. There is a previous publication on the role of MRDT in pediatric patients with asthma (1).» Thank you for this comment. We agree that this part of the manuscript was a bit overstated. Following your suggestion, we decided to delete the sentence to improve the clarity of this section. Comment 2: «While reading the introduction section, I noticed that it lacks a comprehensive background on patients with asthma, their diaphragmatic function, and the potential benefits of MDRT in addressing this issue. I believe including these key elements would greatly enhance the clarity and contextual understanding of the intended study. Providing a brief overview of the impact of asthma on diaphragmatic function, respiratory muscle strength, or altered breathing patterns and emphasizing the potential of MDRT as a therapeutic intervention would help readers grasp the significance of the study and its potential implications for asthma management. I encourage the authors to consider revising the introduction accordingly to provide a more comprehensive background and set a firm foundation for the remainder of the study.» Thank you for this comment. We agree that this part of the manuscript was inadequate. Following your suggestion, we have modified the introduction, providing a more comprehensive background. We have added the text as follows: « It's also important to note that the mechanical disadvantage of the diaphragm in asthma can result in an increased workload for all inspiratory muscles, particularly during exercise, where dynamic hyperinflation may occur, leading to heightened dyspnea15,16» « Finally, although specific diaphragm MT techniques have not been documented yet, recent studies have reported evidence for their positive effect on pulmonary rehabilitation (PR). 25 In particular, the manual diaphragm release technique (MDRT) aims to directly stretch the muscle fibers of the diaphragm, as detailed in Rochas’ research. 18 The study showed an improvement in diaphragm’s mobility, maximum inspiratory pressure (MIP), and exercise capacity (EC) in people suffering from COPD. 18 We deem it pertinent to mention that previous studies have demonstrated that even a single MT session can have a positive effect on chest wall mechanics, dyspnea, and peripheral oxygen saturation (SpO2) in individuals with COPD. 26, 27 Therefore, dyspnea, being one of the primary symptoms of asthma, can adversely affect both exercise capacity (EC) levels and overall quality of life (QoL). 28-31 According to a study26 a single MT session of soft tissue and joint mobilization immediately improved dyspnea (Borg Scale 0-10, pre: 2.3 ± 0.8 vs 1.8 ± 0.5). The authors reported that the mechanism underlying this improvement could be the increase in respiratory muscle length and thoracic cage flexibility induced by MT, consequently reducing breathing effort and the development of dyspnea in individuals with COPD.32 As for asthma, there is currently no data regarding the efficacy of diaphragm MT methods, except for the pilot study conducted by Macias and colleagues24, and the study by Elnaggar and colleagues33, which investigated the efficacy of MDRT in children. Considering the growing clinical interest in asthma and the recent publications in the field, we believe that a randomized controlled trial (RCT) targeting intervention on the zone of apposition of the diaphragm using the MDRT in adults with asthma for outcomes assessment is warranted. .» Comment 3: «The significance of the study is not clear. Authors may need to justify the importance of their work, highlight the impact it has on the research field, and define its contribution to new knowledge.» Comment 4: «More importantly, they need to pinpoint the research gap (in light of the related literature) and make it clear what drove them to conduct the study.» Thank you for your suggestions. As requested, we highlighted the impact on the research field and the research gap at the discussion session. The text has been correspondingly modified as follows: “Although several studies assessing the efficacy of MT in obstructive lung diseases (OLD) have been conducted, drawing definitive conclusions is challenging due to their conflicting results.45 A recent systematic review (SR) of the existing literature aimed to identify indications that may underscore the need for differentiated manual therapy (MT) approaches targeting the zone of apposition (ZOA) of the diaphragm in individuals with OLD suffering from pathological adaptations of their chest wall or from respiratory symptoms. 76 This SR outlined a model illustrating how MT delays the onset of fatigue in respiratory muscles. Additionally, it demonstrated that there is no evidence supporting the effectiveness of MT on the diaphragm for treating individuals (adults) with asthma.76 It is noteworthy that two previous studies have examined how MT on the ZOA of the diaphragm hampers the diaphragm's function and pulmonary function in childhood asthma (RCT)33 and in adults with asthma24 (pilot study) accordingly. Up to this point, no RCT has comprehensively examined the impact of MDRT, in particular, on the ZOA of the diaphragm by MDRT in adults suffering from asthma. The primary objective of this RCT is to address the existing literature gap concerning the impact of MDRT on enhancing the functional parameters of individuals with asthma, thereby indicating the need for further research in this domain. Additionally, considering the prevalent pathological changes in the diaphragm muscle among individuals with asthma, it is crucial to determine which anatomical regions and hands-on therapy techniques are most effective for increasing diaphragm excursion in adults with asthma. The primary objective of this RCT is to address the existing literature gap concerning the impact of MDRT on enhancing the functional parameters of individuals with asthma, thereby indicating the need for further research in this domain. Additionally, considering the prevalent pathological changes in the diaphragm muscle among individuals with asthma, it is crucial to determine which anatomical regions and hands-on therapy techniques are most effective for increasing diaphragm excursion in adults with asthma. The protocol of this study is designed in accordance with accepted practices concerning randomization, concealed allocation, blinding of examiners, and appropriate sample size calculation. This rigorous approach ensures the reliability and robustness of the study's findings. What sets this study apart is its original investigation into the mechanism of the MDRT on the ZOA of the diaphragm in individuals living with asthma. Finally, several significant constraints must be considered. The study sample is drawn exclusively from a single hospital, potentially limiting the generalizability of the findings. Additionally, the extended experimental period and the substantial number of sessions may lead to participant dropouts. ” Comment 5: «Again, the statement “As for asthma, there is no data for the efficacy of diaphragm MT methods, except for one pilot study” is not true and should be revised in light of the aforementioned publication.» We believe that this comment has been addressed based on our previous replies. After clarifying that there was confusion due to the typographical error, we believe that this statement is now correct. Please do not hesitate to reach out for any further clarification. Comment 6: «I have a concern regarding the study power. A sample size of 24 is a considerably small sample. The authors conducted an a priori power analysis to determine the minimum sample size necessary for detecting clinically significant results. They employed a substantial effect size (d = 1.36) and the minimum acceptable power level (80%) in their analysis. However, this approach may present challenges in detecting moderate or small changes in the outcome variable, potentially resulting in inconclusive findings and limiting the interpretability of the study conclusions.» Thank you for your comment. We understand your concerns about the sample study calculation, and we would like to explain the rationale behind the participant number determined by our power analysis. In 2023, we conducted a systematic review (Is manual therapy of the diaphragm effective for people with Obstructive Lung Diseases? A Systematic Review, Respir Med Res. 2023 Jun:83:101002. doi: 10.1016/j.resmer.2023.101002. Epub 2023 Feb 15.) investigating the effects of specialized mobilization techniques applied to the zone of apposition of the diaphragm in patients with obstructive respiratory diseases, including asthma and COPD. The results of this study revealed a literature gap indicating that the applied techniques on the ZOA of the diaphragm have not been applied in people with asthma beyond, of course, your study (in the pediatric population) and that of Macias et al. 2018 (Effects of manual therapy on the diaphragm in asthmatic patients: A randomized pilot studyhttps://doi.org/10.1016/j.ijosm.2018.07.006). The two studies included in our research represented the closest in design to our own protocol (participants, manual therapy techniques of the diaphragm, diaphragm excursion measured by the US), thus necessitating the power analysis calculation based on them. For your convenience, we hereby provide the two studies in our research, which served as the basis for our study power. Rocha T, Souza H, Brandão DC, et al.: The Manual Diaphragm Release Technique improves diaphragmatic mobility, inspiratory capacity and exercise capacity in people with chronic obstructive pulmonary disease: a randomised trial. J. Physiother. 2015;61(4):182–189. 26386894 10.1016/j.jphys.2015.08.009 Nair A, Alaparthi GK, Krishnan S, et al.: Comparison of Diaphragmatic Stretch Technique and Manual Diaphragm Release Technique on Diaphragmatic Excursion in Chronic Obstructive Pulmonary Disease: A Randomized Crossover Trial. Pulm. Med. 2019;2019:1–7. 30719351 10.1155/2019/6364376 PMC6335861 These studies closely aligned with the design of our protocol and thus informed our power analysis calculation. The sample size calculation was based on an alpha (α) level of 0.01, a power (β) of 0.85, and a large effect size, Cohen's d, of 1.86 for a two-tailed independent t-test. This effect size was calculated based on the results reported by Rocha et al. (2015), specifically from the mean (SD) values of the control and experimental groups following six manual therapy intervention sessions. Furthermore, the calculation accounted for an anticipated attrition rate of approximately 15%, foreseeing the potential for participant dropout or exclusion. This comprehensive approach to sample size calculation ensures the robustness and reliability of the study's findings, enabling precise detection of the large effect size with high statistical confidence. This resulted in a total sample size of 24 people (12 per group), considering a withdrawal rate of 15%. Comment 7: «The authors aim to recruit a minimum of 24 participants, encompassing a broad age range from 8 to 60 years. However, it is recommended that the authors consider prioritizing either pediatric or adult patients for a more focused investigation.» We agree that this is a mistake. Thank you for pointing this out. We have modified the text according to your comment. Comment 8: «It is crucial to incorporate a thorough and detailed description of the pulmonary rehabilitation program within this protocol, as its current absence hinders the comprehensive understanding of the intervention being studied.» Thank you for prompting us to share the treatment regimen with our readers. It was an oversight, not to mention it in detail. The following paragraphs and Table 1. (Key parameters of the rehabilitation program) have been added to the manuscript (Interventions Section): “Regarding respiratory volumes, patients will be instructed to breathe progressively deeper from set to set, aiming for maximal diaphragmatic excursion and stretch. It is essential to ensure that the therapist's grip on the lower thoracic aperture is maintained throughout.” “The phases of BRE will consist of i) identification of the abnormal breathing pattern, ii) diaphragmatic breathing, ii) nose breathing, iii) slow breathing with controlled breath-holding at the end of exhalation, iv) adaptation of the new breathing pattern in everyday life activities and various positions (supine, semi-sitting, sitting), and v) breathing control in speech. The repetitions and sets of BRE are indicative, given that our priority was progression and individualization during the sessions. For instance, the first session may only include recognition of the abnormal breathing pattern exercise and practice diaphragmatic and nose breathing retraining exercise. At the beginning of every session, each participant will be assessed for their compliance concerning the exercises (use of a calendar or via questions about their exercise). If a patient has not comprehended or cannot perform the exercises correctly, the previous session will have to be repeated. Once they have fully understood the instructions and execution, they will proceed to the subsequent BRE.” Comment 9: «The data analysis plan is appropriate. The utilization of 2x3 repeated measures ANOVA with Bonferroni adjustment will be used to examine the interaction between intervention offer advantages for allowing for the examination of within-subject changes across multiple conditions or time points and accounting for the correlated nature of data within subjects.» Thank you for reviewing and confirming that our statistical approach is appropriate."
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https://f1000research.com/articles/12-1361
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https://f1000research.com/articles/12-602/v1
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05 Jun 23
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{
"type": "Research Article",
"title": "Study of anaemia in pregnancy and low birth weight in fluoride endemic area of Western Rajasthan: a cohort study",
"authors": [
"Pankaj Bhardwaj",
"Neha Mantri",
"Nitin Kumar Joshi",
"Praveen Suthar",
"Praveen Sharma",
"Purvi Purohit",
"Pratibha Singh",
"Shashank Shekhar",
"Shweta Khandelwal",
"Giribabu Dandabathula",
"Pankaja Ravi Raghav",
"Nikky Ramawat",
"Sanjeev Jain",
"Manoj Patil",
"Abhay Gaidhane",
"Zahiruddin Quazi Syed",
"Deepak Saxena",
"Pankaj Bhardwaj",
"Neha Mantri",
"Nitin Kumar Joshi",
"Praveen Suthar",
"Praveen Sharma",
"Purvi Purohit",
"Pratibha Singh",
"Shashank Shekhar",
"Shweta Khandelwal",
"Giribabu Dandabathula",
"Pankaja Ravi Raghav",
"Nikky Ramawat",
"Sanjeev Jain",
"Abhay Gaidhane",
"Zahiruddin Quazi Syed",
"Deepak Saxena"
],
"abstract": "Background: Fluoride is a noxious element known to destroy gastrointestinal mucosa, leading to erythrocytes' destruction and causing anaemia. The birth weight of newborn babies is a significant indicator of a child's vulnerability to the risk of childhood diseases and chances of existence. Methods: This prospective cohort study was planned to find linkages between fluorosis and the low-birth weight of newborn babies with anaemic mothers. Antenatal mothers until the 20th week of gestation were followed up till delivery in the Antenatal Clinic of a District Hospital in one of the known fluoride-endemic districts (Nagaur) and the other not-so-endemic district (Jodhpur) of Western Rajasthan. Results: Around 19% of the newborn in Jodhpur and around 22% in Nagaur had low birth weight. Mean fluoride values in water samples were measured to be 0.57 (range from 0.0 to 2.7 PPM) in Jodhpur and 0.7 (range from 0.0 to 3.4 PPM) in Nagaur. Conclusions: Thus, in fluoride endemic areas, other factors should be included besides iron and folic acid supplementation for improving anaemia in pregnant women. This calls for assessing the effectiveness of de-fluoridation activities along with the area's most common indigenous food practices.",
"keywords": [
"Newborns",
"Infant",
"Pregnancy",
"Fluoride",
"Low Birth Weight",
"Anemia",
"Geographic Information System"
],
"content": "Introduction\n\nMaternal and neonatal mortality rates are high in developing countries (Beck et al., 2010). Low birth weight (LBW) is the most common cause of neonatal mortality (Eshete et al., 2019; Watkins et al., 2016). The birth weight of newborn babies is a significant indicator of a child’s vulnerability to the risk of childhood diseases and chances of existence (Alemayehu et al., 2020). The World Health Organization (WHO) defines LBW as weight at birth less than 2.5 kg (“WHA Global Nutrition Targets 2025: Low Birth Weight Policy Brief,” n.d.). LBW may be an outcome of either preterm birth or retarded fetal growth. According to a report by UNICEF on “The State of the World’s Children 2008”, the highest percentage (43%) of LBW babies below five years of age are in India. The prevalence of LBW babies in South Asia is 42%, in developed countries 35%, in developing countries 26% and 25% in the rest of the world (Sachdev, 2001).\n\nIndia has been documenting the serious problem of anaemia in pregnancy, resulting in LBW (Batista Filho et al., 2008; Rahman et al., 2016; World Health Organization, 2015). The Ministry of Health and Family Welfare, Government of India, has launched the National Anaemia Prophylaxis Programme to combat anaemia. The decision to supplement iron along with folic acid (iron (60 mg) and folic acid (500 μg) orally for 90 days) to pregnant women visiting antenatal clinics (ANCs) during the first and second trimesters was implemented across the country. The Indian Council of Medical Research (ICMR) conducted a study in 11 Indian states in 1985–86 and discovered that the intervention did not affect pregnant women’s haemoglobin (Hb) levels. This resulted in the power of iron and folic acid tablets increasing to 100 mg and 500 mg, respectively, which has been popular since 1992 (Susheela et al., 2010).\n\nHowever, despite so many interventions to reduce anaemia during pregnancy, expected results have not so far been obtained (Beard, 2000; Kapil et al., 2019; Vijayaraghavan et al., 1990). So, another factor needs to be investigated, and one such factor is fluoride intake. Fluoride causes serious destruction to the gastrointestinal mucosa by destroying microvilli resulting in non-absorption of nutrients from the regimen (Das et al., 1994; Dhar and Bhatnagar, 2009; Susheela et al., 2018). Fluoride also destroys erythrocytes, thereby contributing to the loss of Hb and anaemia.\n\nFagin’s report on fluoride’s second thoughts in 2008 is a warning to all concerned, as he exposed the possibility of fluoride-producing diseases in the teeth, bone, brain, and thyroid gland (Fagin, 2008). Fluoride is a toxic substance that promotes thyroid hormone production in children when it is consumed during the intrauterine growth stage (Gedalia et al., 1964). As a result, the thyroid hormone status of married women before conception may need to be examined (McNeil and Stanford, n.d.).\n\nFluorides, like other elements, have both good and harmful properties that have a substantial impact on public health. Even though it is noted that an optimal dose of 1mg of fluoride per litre in drinking water is beneficial for the prevention of tooth decay, extended exposure to greater concentrations can lead to adverse effects on teeth and bones (Azami-Aghdash et al., 2013). A concentration of fluoride higher than 2 mg/l causes teeth corrosion to increase with fluoride intake, and this can occur in conjunction with other conditions or might increase certain risks (Susheela, 2013). In pregnant women, placental carriage of fluorides happens as early as the 19th week of gestation (Gedalia et al., 1964). Studies in a few countries have demonstrated linkages between dental fluorosis and LBW. However, there is a paucity of studies in the Indian context correlating exposure to fluoride and anaemia in mothers resulting in LBW infants (Guth et al., 2020). Therefore, this study was planned to find linkages between fluorosis, anaemia during pregnancy, and outcome regarding the birth weight of newborn babies.\n\n\nMethods\n\nFor years, Rajasthan has been one of the worst states impacted by fluorosis, which has had a significant impact on the health of the native people. According to assessment from the State Institute of Health and Family Welfare in 2004, all 32 districts of Rajasthan are fluoride endemic areas. From June 2017 to September 2018, a prospective cohort study was done in the Antenatal Clinics of a District Hospital in one of the known fluoride-endemic areas (Nagaur) and one not so endemic district (Jodhpur) in Western Rajasthan. The reporting was done in accordance with the checklist for Strengthening the Reporting of Observational Studies (STROBE) (Patil, 2023a).\n\nAll pregnant women until the 20th week of gestational age attending the ANC clinics from the month of initiation of study were enrolled for the study. Participants were enrolled based on consecutive sampling as they appear in the Out Patient Department (OPD). All participants were given a brief about the objectives of the study and were given choices for participation. After obtaining written informed consent, pregnant women were followed-up till delivery for estimating the birth weight of the new-born. For new-borns, consent was obtained from the parent/guardian. Those who did not give consent were excluded from the cohort. All participants were recruited till January 2018 and a ticket with the unique line listing number was provided to them with the dates for their next visit. The follow-up for each participant was conducted in the 2nd and 3rd trimester during their routine ANC check-up at the hospital and repeat test (Hb test, test for water fluoride and urinary fluoride) was conducted. To minimize loss-to-follow up, telephonic reminder was made to the enrolled participants and visits were planned according to their convenience. After the delivery, the new-born was enrolled and birth weight was estimated.\n\nEthical approval was obtained from the Institutional Ethics Committee of All India Institute of Medical Sciences, Jodhpur, Rajasthan, India on 20th August 2016 (Ref. AIIMS/RES (04)/2017/169). All participants were asked to sign an informed consent before enrolment.\n\nData was captured using a semi-structured questionnaire designed to elicit information on socio-demographic details, medical history, obstetric history, vital parameters, 24-hour diet, source of drinking water, medication history, dental and skeletal fluorosis (Patil, 2023b). The tool was pilot tested and refined based on experiences of the 20 participants who were not the part of the study. Appropriate measures were followed to minimize the potential bias at recruitment by providing a unique line listing number and concealing the identification details from the samples.\n\nHaemoglobin test – For the purpose of the study, we used the WHO Criteria for Anaemia as reference for pregnant women (pregnant women with haemoglobin levels less than 11.0 g/dl in the first and third trimesters and less than 10.5 g/dl in the second trimester were considered anaemic). A point-of-care instrument Haemocue 201+ analyser (Manufactured at HeamoCue AB, Sweden, Catalogue no. 1627013065)was used to measure haemoglobin level at three times – at enrolment, second visit and third visit. The trained research staff were appointed for conducting the procedure. All necessary PPE measures were used to avoid contamination during the procedure. After cleaning the puncture site with an alcohol swab (middle finger or ring finger of the either hand), a prick was made on the fingertip using a needle and 2–3 drops of blood was taken on a microcuvette and loaded in the analyser. The haemoglobin concentration was then displayed as a digital reading, in either g/dl or mmol/l in 15–45 seconds. Results were also mentioned in the patient summary sheet and necessary consultation with obstetrician was arranged if any intervention was required.\n\nFluoride test (water and urine) – All participants were given a 500 ml water sample sterile high-density polyethylene bottle for collecting water from their residence at the time of enrolment in the study. All enrolled participants were given a sterile polyethylene urine container (50 ml) by adding 0.2% Etheylenediaminetetraacetic acid (EDTA) [Orion Manufacturer] to bottles before collection during the visit to collect urine and were stored in refrigerator at 4°C to avoid bacterial contamination. The patient identification was concealed and all samples were labelled with unique line listing number and transported to the central laboratory for a test within 48 hours. Water and urine analysis was carried out in the biochemistry research unit, according to analytical protocol (NIOSH Manual of Analytical Methods, P&CAM, 2ND edition) using a Thermo Scientific Fluoride Ion Meter Model (Ion 85 Analyser Radiometer Copenhagen). As per NIOSH manual, Fluoride Ion is used as an analyte in Ion selective electrode (ISE) technique. A Fluoride standard was prepared and an electrode (Orion, 9609BNWP) was setup using TISAB III (Orion, 940911). Then, the urine sample was diluted with equal volume of TISAB III. The electrode was dipped in the sample and the reading was displayed on the screen. The instrument was calibrated with the reference electrode each time before running samples in a batch of 60–70 samples. The results were noted in the log book simultaneously with the line listing number.\n\nWe enrolled a total of 1440 pregnant women in the study. As per the reference article by Aditya et al. (Arun et al., 2022), Mean ± Std. Deviation of Water Fluoride (mg/L) in Low-birth-weight population = 0.54 ± 0.36.\n\nUsing the formula for minimal Sample size required-\n\nWhere Zα = 1.96 at a 5% level of significance\n\nAssuming a non-response of 10% and rounding off, the sample size was finalized to 1440.\n\nMicrosoft Excel v.2016 (Microsoft® Corp., Redmond, WA) was used to enter the data and was analysed using Statistical Packages for Social Sciences (SPSS) version 23 software (IBM Corp., Armonk, NY). The descriptive statistics (mean, percentages) were used to summarize quantitative data for the study outcomes. Chi-squared test was used to examine the differences between categorical variables and was considered significant when a p-value < 0.05. Further, to provide the graphical presentation, spatial mapping of the various variable like level of fluoride in urine and low birth weight in both the district was done using Arc GIS v 10.3(“ArcGIS 10.3,” n.d.).\n\n\nResults\n\nOut of 1440 pregnant women enrolled, 50% (n = 720) were from the Jodhpur district, and 50% (n = 720) were from the Nagaur district of western Rajasthan (Patil, 2023c, 2023d). The mean age of women from Jodhpur was 25.51 (±3.87) years, and from Nagaur were, 23.74 (±3.85) years.\n\nMean fluoride values in water samples were measured to be 0.57 (range from 0.0 to 2.7 PPM) in Jodhpur and 0.7 (range from 0.0 to 3.4 PPM) in Nagaur.\n\nThe excretion of mean fluoride value in the urine of pregnant females was found to be 1.4 (range from 0.0 to 12.7 mg/L) in the Jodhpur district and 2.2 (range from 0.1 to 13.7 mg/L) in the Nagaur district. Figure 1 depicts the urinary fluoride content in the Nagaur district, which is very high on the northern side. Figure 2 describes the level of urinary fluoride in the Jodhpur district. The level of fluoride is low compared to the Nagaur district. However, in the district’s central and southern regions, fluoride content is high in the urine as it is excessive in the groundwater.\n\nThe mean weight of newborns from the Jodhpur district was 2.8 kg (±0.56), and from Nagaur was 2.8 kg (±0.44). Around 19% of the newborns in Jodhpur and around 22% in Nagaur had LBW. As shown in Figure 3, the LBW babies were seen in the regions of the Nagaur district where the groundwater fluoride level was very high. However, in the context of the Jodhpur district (Figure 4), the low weight babies were seen in the southern part of the district where the groundwater fluoride level is low. This might be because of the consumption of the fluoride from the other sources.\n\nTable 1 illustrates the socio-demographic characteristics of western Rajasthan’s Jodhpur and Nagaur fluoride endemic districts. A significant association was seen between fluoride level in the water (p = 0.00001), Body Mass Index (BMI) (p = 0.00001), anaemia (p = 0.00001), and dental fluorosis (p = 0.00001). Table 2 illustrate the association of fluoride in water with BMI, anaemia and dental fluorosis among pregnant women.\n\nA significant association was also seen in dental fluorosis with birth weight and anaemia (p < 0.005). Table 3 illustrates dental fluorosis’s association with baby birth weight (normal birth weight (NBW) and LBW) and anaemia in pregnant women (no anaemia and anaemia). The excretion of fluoride in pregnant women’s urine and haemoglobin (Hb) has a statistically significant linear relationship. The direction of the relationship is negative, i.e., urine fluorosis and haemoglobin of pregnant women are negatively correlated. This illustrated that greater fluoride excretion is associated with lower haemoglobin levels (r = -0.2).\n\nUrine fluoride and newborn birth weight have a statistically significant linear relationship. The direction of the relationship is negative, i.e., urinary fluoride and newborn birth weight are negatively correlated. This illustrated that greater urinary fluoride is associated with birth weight (r = -0.01). The relative risk of LBW was 1.63 times more in high fluorosis cases. Also, the relative risk of anaemia among pregnant women was 2.2 times in high fluoride endemic areas.\n\nTea consumption was high in both districts, whereas tobacco/areca nut usage was high (55%) in the Nagaur district. It was observed that the consumption of black salt was around 38% in Nagaur and 28% in the Jodhpur district, and the consumption of churan/chat masala was 35.4% and 14.6% in Nagaur and Jodhpur districts, respectively. Table 4 shows drug consumption and selected dietary habits of pregnant women.\n\n\nDiscussion\n\nFluorosis is an endemic disease caused by excessive fluoride exposure from various sources. The element fluorine is a potent enzyme inhibitor, hormone disruptor, and neurotoxic, making it a double-edged sword that causes metabolic derangements (Susheela et al., 2018). Fluorosis manifests as a “linked disease” in many emerging Asian and African countries (Susheela and Toteja, 2018). In many countries throughout the world, high fluoride level in groundwater has become one of the most serious health-related geo-environmental challenges (Demelash et al., 2019; Johnston and Strobel, 2020). Fluorosis has affected 21 Indian states. The Fluorosis Research and Rural Development Foundation, India survey mentioned that more than 66 million people are affected by fluorosis in India (Susheela and Toteja, 2018).\n\nThe Bureau of Indian Standards (BIS) has specified fluoride levels in drinking water standards, with a maximum acceptable limit of 1.0 mg/L and an allowed limit of 1.5 mg/L in the absence of an alternative source (Puri and Kumar, 2012). In some areas of Rajasthan, people drink water with fluoride levels as high as 24 mg/l (Department of Environmental Engineering, Delhi Technological University, India et al., 2014). In our study, mean fluoride values in water samples were 0.57 (range 0.0 to 2.7 PPM) in Jodhpur and 0.7 (range 0.0 to 3.4 PPM) in Nagaur. A similar study was carried out in the Punjab district of Faridkot, India. The mean value of water fluoride content was discovered to be 2.4 mg/L, which was higher than the allowable limits (Goyal et al., 2020). Hence, this region’s exposure to fluoride from drinking water is of considerable concern.\n\nEven though low haemoglobin levels are frequently detected in clinical settings, they are rarely considered significant unless they are associated with the detection of a serious blood disease (Andezhath, 2010). The greatest concern is that ingesting fluoride (F–) through water and food could result in serious health consequences. In our research, there was a significant association between fluoride levels in water and anaemia (p = 0.00001). The highly detrimental F– damages the lining of the intestine and hinders nutritional absorption when it enters the body through food, water, habit-forming chemicals, and dental products (Susheela et al., 2018). Hillman et al. discovered anaemia in cattle due to F– poisoning and fluorosis in the 1980s (Hillman et al., 1979). Excessive fluoride may affect brain development in utero and lead to neurological abnormalities, according to evidence from several human studies (Grandjean, 2019; Guth et al., 2020).\n\nUrine has long been recognized as a significant diagnostic marker for fluoride intake since it is widely used, relatively easy to collect, and non-invasive (Idowu et al., 2019; Kumar et al., 2017). In our study, pregnant women’s excretion of fluoride in urine and haemoglobin (Hb) had a statistically significant linear relationship. The direction of the relationship is negative, i.e., urine fluorosis and haemoglobin of pregnant women are negatively correlated. Excretion of mean fluoride value in the urine of pregnant females was found to be 1.4 (range from 0.0 to 12.7 mg/L) in Jodhpur district and 2.2 (range from 0.1 to 13.7 mg/L) in Nagaur district. Females with high urine fluoride levels have a higher risk of pregnancy difficulties such as anaemia and poor fetal outcomes, according to a study by Goyal et al. (2020).\n\nAccording to AK Susheela et al., drinking fluoride-free water and eating fluoride-free food reduced preterm births by four times and LBW babies by two times (Susheela and Toteja, 2018).\n\nIn industrialized and developing countries, the burden of poor pregnancy outcomes (APOs), including preterm deliveries and LBWs, is significant (Blencowe et al., 2012; Lawn et al., 2006; Lee et al., 2013). Maternal anaemia was identified as a risk factor for low/insufficient birth weight in the current study, which was similar to findings from a prior study by Räisänen et al. (2014).\n\nIn India, anaemia affects 55.3 per cent of women aged 15 to 49 years old (Kulasekaran, 2012). Anaemia in women during pregnancy has been linked to underweight children. Mother and newborn mortality rates in India are still high due to poor haemoglobin levels. Furthermore, anaemic mothers frequently give birth to low-weight newborns (as low as 1.0 to 1.2 kg), with a high risk of developmental problems or infant mortality later in life (Andezhath, 2010).\n\nA study finds that maternal haemoglobin (Hb > 110 g/l) protects against the risk of APOs in the study populations, which is consistent with prior findings (Padhi et al., 2015). With anaemia in the first or second trimester, a recent systematic review and meta-analysis found a significantly greater risk of LBW (OR: 1.29; 95 percent CI: 1.09–1.53) and preterm birth (OR: 1.21; 95 percent CI: 1.13–1.30) (Haider et al., 2013). Preterm delivery and LBW are important factors of child survival, impairments, stunting, and long-term negative implications for the beginning of non-communicable diseases later in life. They necessitate effective public health interventions.\n\nThe precise mechanism that links maternal anaemia to LBW remains unknown. Only a few prospective cohort studies have examined the relationships between maternal anaemia and LBW (Bakacak et al., 2015; Figueiredo et al., 2019; Haider et al., 2013; Rahman et al., 2016). In Jodhpur, around 19 percent of newborns had a LBW, whereas, in Nagaur, nearly 22 percent had a LBW. According to another study, the relative risk of giving birth to LBW babies is 37% among the women with low haemoglobin levels (Figueiredo et al., 2019).\n\nAccording to other studies, factors such as diet, excessive tea consumption, other associated nutritional deficiencies, and the use of fluoridated toothpaste have also been linked to the occurrence and severity of fluorosis (Rao and Mahajan, 1990; Shruthi and Anil, 2018). The participants in our study mostly ate locally grown vegetarian cuisine daily and had a history of drinking tea and brushing their teeth with fluoridated toothpaste. In our study, there was a significant link between dental fluorosis and birth weight and anaemia (p > 0.005). Tea consumption was high in both districts, whereas tobacco/areca nut consumption was high (55 percent) in Nagaur. Black salt consumption was found to be roughly 38 percent in Nagaur and 28 percent in the Jodhpur district. In comparison, churan/chat masala consumption was found to be 35.4 percent and 14.6 percent in Nagaur and Jodhpur districts, respectively.\n\nThe prevalence of dental fluorosis was 13.17 percent in the study by Shruti et al., with a high fluoride level (Shruthi and Anil, 2018). Fluorosis is irreversible and only develops when the enamel is growing and exposed to fluoride. Fluoridated enamel is porous (objectionable secondary staining is common) and opaque rather than being a standard creamy-white translucent tint (Mahantesha et al., 2016). In our study, a significant association was also seen between fluoride level in the water and dental fluorosis (p = 0.00001) and baby birth weight (p = 0.000012) and LBW (p = 0.00001).\n\nThe presence of more than eight ppm of fluoride in drinking water over a long period might cause skeletal fluorosis (Reddy, 2009). As a result of the persistent poisoning, bone density gradually increases, and joints stiffen and become painful.\n\nSusheela et al.’s findings support the notion that iron and folic acid at current levels is beneficial in reducing the risk of LBW when combined with proper nutrition and reduced F– intake (Susheela et al., 2010). According to one study, efforts to raise Hb by iron and folic acid (IFA) supplementation through State and National Programs have yet to provide desired outcomes (Beard, 2000; Vijayaraghavan et al., 1990).\n\nThe use of validated instruments by previously trained researchers strengthens the internal validity of this study. A large sample size aids in extrapolating study findings to populations with similar geographies. In terms of the study’s weaknesses, the self-reported data may have resulted in calibration bias. Also, sample losses owing to missed follow-ups are a possibility.\n\nWith a coordinated effort to implement proper rules and procedures, the Millennium Development Goal of reducing early childhood mortality by two-thirds will be easier to attain (“Global nutrition targets 2025,” n.d.). Here are a few solutions that have been presented for better implementation.\n\nIn every policy design, Behavior Change Communication (BCC) intervention must be an integral part that focuses on each stakeholder (“tagged_ifas_participants_manual_for_healthcare_providers.pdf,” n.d.). Information, Education and Communication (IEC) initiatives must include educating pregnant women on the role of Hb and LBW children, as well as the do’s and don’ts of fluoride consumption in the diet, through media campaigns (“Dietary guidelines for Indians.pdf,” n.d.; Goyal et al., 2020). The role of dieticians and nutritionists must be escalated during ANC visits (Kominiarek and Rajan, 2016). Ascorbic acid improves iron absorption (vitamin C). This should be stressed throughout the diet counselling session, which includes a list of vital fruits and vegetables that contain vitamin C that should be consumed (Hallberg et al., 1989). Iron absorption is inhibited by phytic acid/sodium phytate in brown bread and tannin in tea. The resulting vitamin B12 and folic acid deficiencies may cause anaemias. Vitamin B12 is not often investigated but is a key constituent for Hb biosynthesis (Delimont et al., 2017). Withdrawing fluoride from the diet may have repaired damage to the gastrointestinal mucosa/loss of microvilli, allowing nutrients to be absorbed, resulting in increased Hb and correction of anaemias (Johnston and Strobel, 2020). This calls for assessing the effectiveness of de-fluoridation activities along with the most common food practices leading to high fluoride levels in pregnant women.\n\nFluoride assessment in body fluids is the primary criterion to know how much fluoride has entered the body. Regular monitoring of 24-hour urine samples and plasma samples may help researchers better understand the harmful effects of excessive fluoride exposure during pregnancy (Goyal et al., 2020). Thus, a monitoring and impact assessment must be part and parcel of future research related to fluoride and anaemic mothers.\n\n\nConclusion\n\nIn fluoride endemic areas, other factors should be included besides iron and folic acid supplementation for improving anaemia in pregnant women. This calls for an assessment of the effectiveness of de-fluoridation activities along with the most common indigenous food practices in the area. In India, the role of fluoride as a risk factor in pregnancy has not been documented. In this context, the current study has added a significant body of knowledge that can be further scaled up.",
"appendix": "Data availability\n\nZenodo: Jodhpur_Data File_anemia in Pregnancy_CSV.csv (Data of study participants from Jodhpur district on sociodemographic details, dietary habits and food consumption, addictions, drugs and medications consumed, drinking water sources, diseases, health parameters and anthropometric details) https://doi.org/10.5281/zenodo.7928263 (Patil, 2023c).\n\nZenodo: Nagaur_Data File_Anemia in Pregnancy_CSV.csv (Data of study participants from Nagaur district on sociodemographic details, dietary habits and food consumption, addictions, drugs and medications consumed, drinking water sources, diseases, health parameters and anthropometric details) https://doi.org/10.5281/zenodo.7928230 (Patil, 2023d).\n\nZenodo: Fluoride_studyQuestionnaire.pdf (Copy of blank Questionnaire used for data collection) https://doi.org/10.5281/zenodo.7962221 (Patil, 2023b).\n\nZenodo: STROBE checklist for ‘Study of anaemia in pregnancy and low birth weight in fluoride endemic area of Western Rajasthan: A cohort study’. https://doi.org/10.5281/zenodo.7780105 (Patil, 2023a).\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 acknowledge the support of study participants and all those who contributed directly and indirectly.\n\n\nReferences\n\nAlemayehu GM, Chernet AG, Dumga KT: Determinants of Child Size at Birth and Associated Maternal Factor in Gurage Zone.2020; 21: 8.\n\nAndezhath S: Anemia in pregnancy: An easily rectifiable problem. Fluoride. 2010; 43: 104–107.\n\nArcGIS 10.3: The Next Generation of GIS Is Here.n.d. (accessed 5.25.23). ArcGIS Blog. Reference Source\n\nArun AK, Rustveld L, Sunny A: Association between Water Fluoride Levels and Low Birth Weight: National Health and Nutrition Examination Survey (NHANES) 2013–2016. IJERPH. 2022; 19: 8956. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAzami-Aghdash S, Ghojazadeh M, Azar FP, et al.: Fluoride Concentration of Drinking Waters and Prevalence of Fluorosis in Iran: A Systematic Review.2013; 7: 7.\n\nBakacak M, Avci F, Ercan O, et al.: The effect of maternal hemoglobin concentration on fetal birth weight according to trimesters. J. Matern. Fetal Neonatal Med. 2015; 28: 2106–2110. PubMed Abstract | Publisher Full Text\n\nBatista Filho M, de Souza AI , Bresani CC: Anemia como problema de saúde pública: uma realidade atual. Ciênc. Saúde Coletiva. 2008; 13: 1917–1922. PubMed Abstract | Publisher Full Text\n\nBeard JL: Effectiveness and strategies of iron supplementation during pregnancy. Am. J. Clin. Nutr. 2000; 71: 1288S–1294S. Publisher Full Text\n\nBeck S, Wojdyla D, Say L, et al.: The worldwide incidence of preterm birth: a systematic review of maternal mortality and morbidity. Bull. World Health Org. 2010; 88: 31–38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlencowe H, Cousens S, Oestergaard MZ, et al.: National, regional, and worldwide estimates of preterm birth rates in the year 2010 with time trends since 1990 for selected countries: a systematic analysis and implications. Lancet. 2012; 379: 2162–2172. PubMed Abstract | Publisher Full Text\n\nDas TK, Susheela AK, Gupta IP, et al.: Toxic Effects of Chronic Fluoride Ingestion on the Upper Gastrointestinal Tract. J. Clin. Gastroenterol. 1994; 18: 194–199. PubMed Abstract | Publisher Full Text\n\nDelimont NM, Haub MD, Lindshield BL: The Impact of Tannin Consumption on Iron Bioavailability and Status: A Narrative Review. Curr. Dev. Nutr. 2017; 1: 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDemelash H, Beyene A, Abebe Z, et al.: Fluoride concentration in ground water and prevalence of dental fluorosis in Ethiopian Rift Valley: systematic review and meta-analysis. BMC Public Health. 2019; 19: 1298. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDepartment of Environmental Engineering, Delhi Technological University, IndiaJain A, Singh S, et al.: Prevalence of Fluoride in Ground Water in Rajasthan State: Extent, Contamination Levels And Mitigation. WPT. 2014; 2014: 50–57. Publisher Full Text\n\nDhar V, Bhatnagar M: Physiology and toxicity of fluoride. Indian J. Dent. Res. 2009; 20: 350. Publisher Full Text\n\nDietary guidelines for Indians.pdf: n.d.\n\nEshete A, Alemu A, Zerfu TA: Magnitude and Risk of Dying among Low Birth Weight Neonates in Rural Ethiopia: A Community-Based Cross-Sectional Study. Int. J. Pediatr. 2019; 2019: 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFagin D: Second thoughts about fluoride. Sci. Am. 2008; 298: 74–81. PubMed Abstract | Publisher Full Text\n\nFigueiredo ACMG, Gomes-Filho IS, Batista JET, et al.: Maternal anemia and birth weight: A prospective cohort study. PLoS One. 2019; 14: e0212817. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGedalia I, Brzezinski A, Zukerman H, et al.: Placental Transfer of Fluoride in the Human Fetus at Low and High F-Intake. J. Dent. Res. 1964; 43: 669–671. PubMed Abstract | Publisher Full Text\n\nGlobal nutrition targets 2025: low birth weight policy brief [WWW Document]: n.d. (accessed 11.23.22). Reference Source\n\nGoyal L, Bakshi D, Arora J, et al.: Assessment of fluoride levels during pregnancy and its association with early adverse pregnancy outcomes. J. Family Med. Prim. Care. 2020; 9: 2693–2698. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGrandjean P: Developmental fluoride neurotoxicity: an updated review. Environ. Health. 2019; 18: 110. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuth S, Hüser S, Roth A, et al.: Toxicity of fluoride: critical evaluation of evidence for human developmental neurotoxicity in epidemiological studies, animal experiments and in vitro analyses. Arch. Toxicol. 2020; 94: 1375–1415. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaider BA, Olofin I, Wang M, et al.: Anaemia, prenatal iron use, and risk of adverse pregnancy outcomes: systematic review and meta-analysis. BMJ. 2013; 346: f3443–f3443. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHallberg L, Brune M, Rossander L: The role of vitamin C in iron absorption. Int. J. Vitam. Nutr. Res. 1989; Suppl 30: 103–108.\n\nHillman D, Bolenbaugh DL, Convey EM: Hypothyroidism and Anemia Related to Fluoride in Dairy Cattle. J. Dairy Sci. 1979; 62: 416–423. PubMed Abstract | Publisher Full Text\n\nIdowu OS, Azevedo LB, Valentine RA, et al.: The use of urinary fluoride excretion to facilitate monitoring fluoride intake: A systematic scoping review. PLoS One. 2019; 14: e0222260. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohnston NR, Strobel SA: Principles of fluoride toxicity and the cellular response: a review. Arch. Toxicol. 2020; 94: 1051–1069. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKapil U, Kapil R, Gupta A: National Iron Plus Initiative: Current status & future strategy. Indian J. Med. Res. 2019; 150: 239–247. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKominiarek MA, Rajan P: Nutrition Recommendations in Pregnancy and Lactation. Med. Clin. North Am. 2016; 100: 1199–1215. Publisher Full Text\n\nKulasekaran R: Influence of mothers’ chronic energy deficiency on the nutritional status of preschool children in Empowered Action Group states in India. Int J Nutr Pharmacol Neurol Dis. 2012; 2: 198. Publisher Full Text\n\nKumar S, Lata S, Yadav J, et al.: Relationship between water, urine and serum fluoride and fluorosis in school children of Jhajjar District, Haryana, India. Appl Water Sci. 2017; 7: 3377–3384. Publisher Full Text\n\nLawn JE, Wilczynska-Ketende K, Cousens SN: Estimating the causes of 4 million neonatal deaths in the year 2000. Int. J. Epidemiol. 2006; 35: 706–718. PubMed Abstract | Publisher Full Text\n\nLee AC, Katz J, Blencowe H, et al.: National and regional estimates of term and preterm babies born small for gestational age in 138 low-income and middle-income countries in 2010. Lancet Glob. Health. 2013; 1: e26–e36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahantesha T, Dixit UB, Nayakar RP, et al.: Prevalence of Dental Fluorosis and associated Risk Factors in Bagalkot District, Karnataka, India. Int. J. Clin. Pediatr. Dent. 2016; 9: 256–263. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcNeil AR, Stanford PE: Reporting Thyroid Function Tests in Pregnancy 18.n.d.\n\nPadhi BK, Baker KK, Dutta A, et al.: Risk of Adverse Pregnancy Outcomes among Women Practicing Poor Sanitation in Rural India: A Population-Based Prospective Cohort Study. PLoS Med. 2015; 12: e1001851. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPatil M: STROBE-cohort_checklist_Anemia in Pregnancy.docx.2023a. Publisher Full Text\n\nPatil M: Fluoride_studyQuestionnaire.pdf.2023b. Publisher Full Text\n\nPatil M: Jodhpur_Data File_anemia in Pregnancy_CSV.csv.2023c. Publisher Full Text\n\nPatil M: Nagaur_Data File_Anemia in Pregnancy_CSV.csv.2023d. Publisher Full Text\n\nPuri A, Kumar M: A review of permissible limits of drinking water. Indian J. Occup. Environ. Med. 2012; 16: 40–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRahman MM, Abe SK, Rahman MS, et al.: Maternal anemia and risk of adverse birth and health outcomes in low- and middle-income countries: systematic review and meta-analysis. Am. J. Clin. Nutr. 2016; 103: 495–504. Publisher Full Text\n\nRäisänen S, Kancherla V, Gissler M, et al.: Adverse Perinatal Outcomes Associated with Moderate or Severe Maternal Anaemia Based on Parity in Finland during 2006-10: Anaemia and perinatal outcomes. Paediatr. Perinat. Epidemiol. 2014; 28: 372–380. Publisher Full Text\n\nRao KV, Mahajan CL: Fluoride content of some common South Indian foods and their contribution to fluorosis. J. Sci. Food Agric. 1990; 51: 275–279. Publisher Full Text\n\nReddy D: Neurology of endemic skeletal fluorosis. Neurol. India. 2009; 57: 7–12. PubMed Abstract | Publisher Full Text\n\nSachdev HPS: LOW BIRTH WEIGHT IN SOUTH ASIA.2001; 21: 19.\n\nShruthi M, Anil N: A comparative study of dental fluorosis and non-skeletal manifestations of fluorosis in areas with different water fluoride concentrations in rural Kolar. J Family Med Prim Care. 2018; 7: 1222–1228. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSusheela AK: Dental Fluorosis and its Extended Effects. Indian J. Pediatr. 2013; 80: 715–717. PubMed Abstract | Publisher Full Text\n\nSusheela AK, Mondal NK, Gupta R, et al.: Effective interventional approach to control anaemia in pregnant women. Curr. Sci. 2010; 98: 11.\n\nSusheela AK, Mondal NK, Gupta R, et al.: Fluorosis is Linked to Anaemia. Curr. Sci. 2018; 115: 692. Publisher Full Text\n\nSusheela AK, Toteja GS: Prevention & control of fluorosis & linked disorders: Developments in the 21st Century - Reaching out to patients in the community & hospital settings for recovery. Indian J. Med. Res. 2018; 148: 539–547. PubMed Abstract | Publisher Full Text | Free Full Text\n\ntagged_ifas_participants_manual_for_healthcare_providers.pdf: n.d.\n\nVijayaraghavan K, Brahmam GNV, Nair KM, et al.: Evaluation of national nutritional anemia prophylaxis programme. Indian J. Pediatr. 1990; 57: 183–190. Publisher Full Text\n\nWatkins WJ, Kotecha SJ, Kotecha S: All-Cause Mortality of Low Birthweight Infants in Infancy, Childhood, and Adolescence: Population Study of England and Wales. PLoS Med. 2016; 13: e1002018. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHA Global Nutrition Targets 2025: Low Birth Weight Policy Brief: n.d.\n\nWorld Health Organization: The global prevalence of anaemia in 2011. Geneva: World Health Organization; 2015."
}
|
[
{
"id": "179725",
"date": "05 Jul 2023",
"name": "Umesh Charantimath",
"expertise": [
"Reviewer Expertise Maternal child 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\nIt is one of the nicely written manuscript. It would be very nice if you add recent articles in the Introduction part rather than quoting a three decade old article. Low birth weight has multiple causes and in this article you have tried to enlist them, but how to minimize the confounding factors and prioritize fluoride still needs to be explained in detail.\n\nFluorosis is a very important public health problem in the LMICs. In this article the authors have clearly mentioned the importance of fluorosis in relation to anemia in pregnancy and LBW. There are many other reasons for LBW and anemia in pregnant women. How the fluoride content in the drinking water will have an adverse impact on maternal and child health has tried to be explained by the authors. What the impact fluorosis has on other age groups has to be addressed.\nI feel larger sample size should be looked into and along with that the multiple variables also need to be collected such as nutrition, obstetric history, other comorbidities etc. to come to a final consensus about at what level the fluorosis will have an adverse impact on maternal and child health.\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": "9872",
"date": "20 Jul 2023",
"name": "MANOJ PATIL",
"role": "Author Response",
"response": "Respected Sir, Thank you very much for taking time out of your busy schedule for this review. Also we are obliged for your valuable comments and suggestions on this manuscript and for approving the article. We are extremely thankful for bringing new insights for improving the manuscript. Please see below the reply to your comments for further perusal- Comment - Recent articles in the Introduction Response: Following are the recent references- 1. Fluorosis, an underestimated and sometimes debilitating condition, is being caused by high levels of fluoride in food and contaminated groundwater in India. Reference: Del Bello, Lou. Fluorosis: an ongoing challenge for India The Lancet Planetary Health,2020. Volume 4, Issue 3, e94 - e95 2. Interestingly, fluoride exposure during pregnancy was not significantly associated with fertility or birth outcomes, especially among women living in areas with levels of fluoride consistent with water fluoridation. Reference: Goodman C, Hall M, Green R, Hornung R, Martinez-Mier EA, Lanphear B, Till C. Maternal fluoride exposure, fertility and birth outcomes: The MIREC cohort. Environ Adv. 2022 Apr;7:100135. doi: 10.1016/j.envadv.2021.100135. Epub 2021 Nov 2. PMID: 36644332; PMCID: PMC9837859. 3. Contrastingly, other literatures have found increased risk of adverse birth outcomes in areas where fluoride levels in drinking water are high (> 1.5 mg/L) Reference: Goyal LD, Bakshi DK, Arora JK, Manchanda A, Singh P. Assessment of fluoride levels during pregnancy and its association with early adverse pregnancy outcomes. J Family Med Prim Care. 2020 Jun 30;9(6):2693-2698. doi: 10.4103/jfmpc.jfmpc_213_20. PMID: 32984109; PMCID: PMC7491833. Comment: How to minimize the confounding factors and prioritize fluoride still need to be explored. Response: The confounding factors included the exposure time to fluoride in drinking water, as well as the exposure to fluoride in age, obstetric history, supplements, diet, air, medication, water sources, cooking vessel etc. To minimize the confounding factors, we could have applied regression analysis to observe the impact of fluoride on maternal and child health. Further, recruitment of larger sample participants in a randomized manner could help in getting the impact of Fluoride on pregnant women (Limitation of Study). Comment: Impact of Fluorosis on other age groups It would be interesting to explore the impact of Fluoride on different age groups. Responses: Adolescents- A study conducted in the United States discovered that greater water fluoride concentrations were connected with a 3.3-month earlier age of menarche. Malin, A.J., Busgang, S.A., Garcia, J.C. et al. Fluoride Exposure and Age of Menarche: Potential Differences Among Adolescent Girls and Women in the United States. Expo Health 14, 733–742 (2022). https://doi.org/10.1007/s12403-021-00448-y Elderly- Further, cognitive skills in older adults living in high fluoride drinking water locations may be compromised. Ren C, Zhang P, Yao XY, Li HH, Chen R, Zhang CY, Geng DQ. The cognitive impairment and risk factors of the older people living in high fluorosis areas: DKK1 need attention. BMC Public Health. 2021 Dec 9;21(1):2237. doi: 10.1186/s12889-021-12310-6. PMID: 34886821; PMCID: PMC8656079. Children- A south Indian researcher discovered that nutritional status has an effect on the severity of fluorosis, with impoverished children being more affected by severe fluorosis. Mahantesha T, Dixit UB, Nayakar RP, Ashwin D, Ramagoni NK, Kamavaram Ellore VP. Prevalence of dental fluorosis and associated risk factors in Bagalkot District, Karnataka, India. Int J Clin Pediatr Dent. (2016) 9:256–63. doi: 10.5005/jp-journals-10005-1373 Comment: A larger sample size should be looked in and along with multiple variables such as nutrition, obstetric history, other co-morbidities to come to a final consensus to see the impact of fluoride on MCH. Response: However, we have collected data on variables like 24-hr diet recall to track nutrition aspects, past obstetric history, cooking vessels, medication, water sources and other co-morbidity like Blood pressure, diabetes etc. but we could not perform analysis to see their impact on MCH in fluoride endemic areas (Limitation of the study)."
}
]
},
{
"id": "232742",
"date": "22 Jan 2024",
"name": "Rungrote Natesirinilkul",
"expertise": [
"Reviewer Expertise anemia",
"bleeding disorders",
"thrombosis",
"blood transfusion"
],
"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 is interesting. However, a few issues are needed to be clarified more. 1.Please provide the exact mean number of hemoglobin level in each group apart from percentage of pregnant women with anemia. 2.Please provide the explanation why LBW neonates were more commonly found in Jodhpur district. 3.Several risk factors were different between both areas where this study was performed. How do we decrease the bias of the other risk factors causing anemia in this study as the mean levels of fluoride were not extremly high in both areas.\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": [
{
"c_id": "11258",
"date": "04 Apr 2024",
"name": "MANOJ PATIL",
"role": "Author Response",
"response": "We are extremely thankful to the Reviewer for bringing new insights for improving the manuscript. Reviewer Comments Response 1. Please provide the exact mean number of hemoglobin levels in each group apart from the percentage of pregnant women with anemia. The mean Hb (gm%) level in pregnant women in the Jodhpur district was 10.4gm% as compared to the Nagaur district (9.1gm%). 2. Please provide an explanation why LBW neonates were more commonly found in the Jodhpur district In our study, the mean weight of newborns from the Jodhpur district was 2.8 ± 0.56 kg, and from Nagaur was 2.8 ± 0.44 kg. Around 19% of newborns in Jodhpur and around 22% in Nagaur had LBW. However, there was no significant difference in LBW babies in both districts (p=0.151) 3. Several risk factors were different between both areas where this study was performed. How do we decrease the bias of the other risk factors causing anemia in this study as the mean levels of fluoride were not extremely high in both areas? In addressing the potential impact of various risk factors on anemia in the studied areas, we took measures to mitigate bias. Although the mean fluoride levels were not exceptionally high in both regions, we conducted a comprehensive assessment of potential contributors to anemia in pregnant women. This included the measurement of fluoride levels in both water and urine, acknowledging their role as risk factors. Additionally, we investigated other factors such as dietary patterns, excessive consumption of tea and black salt, concomitant nutritional deficiencies, and the use of fluoridated toothpaste. We also considered the source of drinking water, aiming to account for any potential effects on hemoglobin levels in pregnant women. The study also delved into iron and folate supplementation for pregnant women, exploring the correlation with the risk of low birth weight in both districts. However, there was no significant difference in LBW babies in both districts (p=0.151) It's important to note that the study has its limitations, and while we addressed a few risk factors, there may be several area-specific that were not thoroughly explored, contributing to potential bias in the assessment of anemia in pregnant women."
}
]
},
{
"id": "179723",
"date": "27 Jan 2024",
"name": "Apurvakumar Pandya",
"expertise": [
"Reviewer Expertise public health",
"anemia control",
"health behaviour change",
"public mental health",
"health technology assessment"
],
"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 is well carried out and nicely written. This prospective cohort study attempted to identify linkages between fluorosis and the low-birth weight of newborn babies with anaemic mothers. In this study, Antenatal mothers until the 20th week of gestation were followed up till delivery in the Antenatal Clinic of a fluoride-endemic district and not-so-endemic district of Western Rajasthan.\nConsidering current scenario, this study provides important insights. As this manuscript is well written, I have no comments for improvement.\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": "10961",
"date": "22 Mar 2024",
"name": "MANOJ PATIL",
"role": "Author Response",
"response": "Thank you very much for your appreciation. The authors are grateful for your timely response on this article and your valuable comments."
}
]
}
] | 1
|
https://f1000research.com/articles/12-602
|
https://f1000research.com/articles/13-193/v1
|
19 Mar 24
|
{
"type": "Research Article",
"title": "Unleashing the potential of digital twins: a new era with aeronautics 4.0 ",
"authors": [
"Mezzour Ghita",
"Benhadou Siham",
"Benhadou Mariam",
"Haddout Abdellah",
"Benhadou Mariam",
"Haddout Abdellah"
],
"abstract": "Abstract*\n\nIntroduction The aerospace value chain consists of several processes, and digitizing it first requires an assessment of these processes and their ability to be transferred to the fully integrated digital thread perspective of smart factories. A digital thread refers to the continuous flow of data and information related to a product throughout its life cycle, integrating and connecting all aspects of a product’s journey. Within this framework, digital twin technology, an essential element of Industry 4.0, comprises the implementation of a virtual presentation of a physical object, system, or process. It brings together the digital replica not only of the physical attributes but also of the behavioral performance of the physical twin.\n\nMethods To achieve a digital thread perspective for aeronautics, a research agenda is proposed, including all breakpoints in the current value chain through a PESTLE Analysis, which defines the value-added areas targeted by this transition to digital technology. An aeronautics 4.0 model Digital Thread Twin Smart Aeronautics D2TSAero is proposed, which provides a new perspective in the aeronautics field by integrating its main ecosystems into an interconnected model made possible by the integration of digital twin agent instances.\n\nProof of Concept A use case that deals with the dependability management of an aircraft fuel distribution system is presented. Based on these results, we can see that the proposed twin model can help in reducing real system parts down time, and it can also improve the management of maintenance across the system life cycle by offering a single source of trust for all stakeholders involved in the digital thread cycle of the real twin.\n\nConclusion A forward-looking perspective on the future of aeronautics with this integrated approach is presented, summarizing all the discussed points and the importance of digital twins in supporting the digitalization of the field.",
"keywords": [
"Aeronautics ecosystems",
"Digital Twin",
"Digital Thread",
"PESTLE Analysis",
"Smart agents"
],
"content": "1. Introduction\n\nThe rise in competitiveness among market actors from different industrial fields has resulted in an increase in systems engineering complexity and manufacturing process complications.1 Several years ago, the US Air Force in one of their publications on digital twins highlighted the concept of digital thread.2 Digital thread was introduced as a part of their framework for digital engineering in order to optimize defense system manufacturing and the engineering phase’s costs and delays. Digital threads were defined in their work as a scalable, configurable, and modular reference framework at the enterprise level for complex systems manufacturing and life cycle management across enterprise hierarchical levels.3 Based on the developed digital system model, the main purpose of the digital thread is to accelerate the sharing and transparency of authoritative interactions and exchanges of technical data, software, information, and knowledge in enterprise data, information, and knowledge systems in a smooth and controlled manner across the systems lifecycle. Second, heterogeneous and distributed data from different sources throughout the system life cycle are accessible to all system stakeholders and decision makers in order to integrate and transform them into actionable information.4 This concept contributes significantly to the deployment of end-to-end engineering reinforced by the Reference Architecture Model for Industry 4.0 RAMI 4.0 Vision.5 RAMI 4.0 is one of Germany’s reference architectures for the implementation of Industry 4.0, across factories. RAMI 4.0, which was proposed by the German Electrical and Electronic Manufacturers’ Association (ZVEI) and recognized by a large number of companies and research groups as a reference framework for the integration of Industry 4.0 within manufacturers to meet smart manufacturing requirements. RAMI 4.0 focus on the development of four main axes: horizontal and vertical integration, human intelligence integration with artificial intelligence and computing capacities, and smart end-to-end engineering.6 The digital twin that we defined according to our previous exploration of the concept background as a virtual image of living and non-living entities that incarnates real entities with complex internal structures and their behaviors with their evolving physical environment through the use of newly developed and highly connected technologies that take advantage of fusion between physical and virtual worlds within an interactive simulated environment for the establishment of smart data integration platforms and collaborative networks of intelligent and connected agents.7 Digital threads offer a single source of truth for digital twins, where all data from the real asset life cycle are stored and shared.8 However, it also presents some main challenges, one of which is discussed in this study.\n\nHow to deploy a secure, smart and resilient control command architecture to manage the horizontal and vertical integration of shopfloor and office floor within factories\n\nThe primary goal of this research is to comprehensively investigate the application and assess the impact of digital twin technology within aeronautical systems. In the aeronautics sector, a prominent transformation is unfolding through the integration of digital threads and twins.9 These concepts represent an innovative approach to information management and system analysis, presenting profound potential to revolutionize aircraft design, manufacturing,10 operation, and maintenance.11 We aim to explore how the implementation of digital twins in aircraft design, manufacturing, maintenance, and operational monitoring can optimize processes, enhance safety, reduce costs, and ultimately revolutionize the aeronautics industry. The remainder of the paper is organized as follows: Section 2 describes the current aeronautics aero value chain and its main activities from a macroscopic perspective, and the PESTELE analysis highlights the main breaking points for the integration of aero 4.0. In Section 3, the Digital Thread Twin for Smart Aeronautics DT2Aero 4.0, which portrays the new aeronautics value chain and ecosystems from a Digital Thread and Twin perspective, is discussed. Section 4 discusses the implementation of the proposed model with a proof of concept that deals with the implementation of digital twins for an aircraft fuel distribution system. The proposed use case aims to shed light on the potential value-added of digital twins for smart maintenance planning and operation optimization. Sections 5 and 6 summarize the contributions and limitations of the proposed solution and provide a further research axis.\n\n\n2. Methods\n\nThe aerospace value chain consists of a series of processes, and digitalizing it begins with an assessment of these processes and their potential for integration into the fully integrated, three-dimensional Industry 4.0 perspective of the smart factory. Through Figure 1. we attempt to frame all the aspects of the value chain.\n\nThe value chain is divided into three main parts:\n\n• Upstream activities: These activities involve obtaining the raw materials and components required to manufacture the product. This may include activities, such as procurement, logistics, and warehousing. This also includes a network of influencers, such as experts, universities, and the government, that can have an impact on the evolution of field regulations, standards, and structures in the long and short term. We also consider technology providers as they can present evolving solutions to initial product development phases and customer requirements as they evolve.\n\n• Core activities: These involve actual product manufacturing. This may include activities, such as production planning, assembly, and quality control. It includes all the main steps involved in system development and manufacturing from type to instances, as described for the digital thread concept.\n\n• Downstream activities: These activities involve obtaining the finished product from the customer. This may include activities, such as marketing, sales, and distribution. We add to these activities operations of reverse engineering, which are part of the new sustainable manufacturing perspective.\n\nFour main ecosystems are defined to frame the value chain of the aeronautics industry: development of engineering activities (study, design, research, and development), electrics and wiring (development of electrical systems and harnesses ….), assembly (mechanical equipment, electronic modules, wires and harnesses; structural parts …), and maintenance and repair operations (painting, component, and engine repair…). The mainstreaming of these improvements is achieved by leveraging Industry 4.0, technologies to support the realization, updating, and maturity enhancement of existing processes.\n\nTables 1, 2, 3, and 4 provide an overview of these tools and of the breaking points that we have defined as the value-added workstreams involved in this digital transition. The specification of these workstreams provides a clearer picture of the impact of digitalization on the value chain in the short and long terms. The representation of the current value chain in addition to the PESTEL analysis presented in Table 1, 2, 3, and 4 are used to define the targeted areas of improvement for each ecosystem in the selected business segment and find areas of added value for digital threads and digital twins.\n\n\n\n- Reinforced learning for collaborative maintenance\n\n\n\n- Internal Actors (control agents, production team, decision-makers)\n\n\n\n- Ontologies and linked data12\n\n\n\n- Actors Value chain Connected site\n\n\n\n- Supervised and unsupervised learning13\n\n\n\n- Customer network (Airline)\n\n\n\n- Cobots14\n\n\n\n- Supply chain 4.015\n\n\n\n- Social Digital twins16\n\n\n\n- Augmented and virtual reality17\n\n\n\n- Digital twins18\n\n\n\n- Distributed Ledgers Technology19\n\n\n\n- Configurable and integration of several aspects\n\n\n\n- Actors in the Supplier network\n\n\n\n- Adaptability and modularity of production line resources\n\n\n\n- Actors in the customer network\n\n\n\n- Horizontal identification and tracking of systems and components\n\n\n\n- Internal Actors (production team, business team, decision-makers)\n\n\n\n- Cognitive and physical ergonomics integration at the production system level\n\n\n\n- Semi-automatic or automatic quality control\n\n\n\n- Flexible and modular workstation\n\n- Self-assessment and context sensitivity\n\n- Connectivity and technical interoperability throughout the production chain\n\n- Integrated inventory management\n\n- Real-time KPI visualizations\n\n\n\n- Geospatial and business intelligence23\n\n\n\n- Artificial intelligence for demand prediction and game theory for balancing different design objectives\n\n\n\n- Blockchain through AAS24,25\n\n\n\n- Agile design and manufacturing26\n\n\n\n- Cyber Security\n\n- DLT\n\n- Cloud computing\n\n\n\n- Cyber Security\n\n- DLT\n\n\n\n- Business and geospatial intelligence\n\n\n\n- Responsiveness in waste management\n\n- Collaborative disassembly\n\n- Multidimensional modeling\n\n- Collaborative sharing of knowledge on the use and maintenance phase for adaptation, reuse and redesign\n\n\n\n- Expert system and intelligent recommendation system\n\n- Additive manufacturing\n\n- RFID technology\n\n- Object recognition using artificial intelligence\n\n- Cobots\n\n- Blockchain\n\nThe proposed solution D2TSAero, represented in Figure 2, consists of three key network elements: suppliers and influencers, digital twins and digital threads, customers, and their customers.\n\nNetwork of Suppliers and Influencers: The first network, namely that of suppliers and influencers, includes all parties with an influence on the operation of the main ecosystems, such as standardization or auditing organizations, which establish domain management procedures and define best practices; government; and its constituents, which manage the domain’s strategic development model and influence the local, national, and international organizational development of ecosystems.\n\nSecond, we identify all stakeholders involved in the production of the finished product and the supply of the main materials, elementary means for the development of the environment in which the finished product is produced, and the labor that completes this operation.\n\nThe field is classified as labor-intensive, and technological advances are reducing the number of complex or repetitive operations and helping the workforce improve its skills. The addition of universities and research organizations to this layer is intended to reinforce this aspect and thus continually update the sector’s various missing links for better integration. Each party in the network is represented by its AAS.\n\nThe AAS concept was introduced by the European Platform 4.0 coalition to ensure the deployment of Industry 4.0, within factories, and the implementation of the digital twin concept. It is the digital image of the entities within the virtual world, represented by the primary element encompassing the identification and domain information models of the entities, and the secondary elements constituted by the communication interfaces and management component enabling the various models and subsystems of the AAS to be managed.\n\nNetwork of Digital twins and Digital Thread: The second network is that of the digital twins and digital value chain and covers the new development model for the various production environments and ecosystems involved in the complete manufacturing of the finished product.\n\nEach ecosystem is represented by a global digital twin. Digital twin ecosystems communicate with each other and with the other two networks via dedicated application programming interfaces. The basic architecture of the digital twin ecosystems was developed according to the architecture shown in the figure and in compliance with the two standards ISO/IEC 30141:2018 for an Industrial Internet of Things reference architecture and ISO for the development of digital twins within manufacturing industries. The choice between these two standards is driven by our motivation to propose a generic and scalable architecture.\n\nWe have added a security layer to the base layer, made up of two actors: the first is that of intelligent contracts, developed on the basis of the description of network agents and their interactions, and monitored by intelligent encryption and artificial immunity algorithms; the second actor is based on Distributed Ledgers technology for managing exchanges and transactions between entities in the digital world. The interaction between these two elements makes it possible to build an immune interface between the different agents of the architecture given the criticality of the domain, despite the need to ensure horizontal and vertical integration between its players.\n\nThe basic twin architecture is composed of two layers: the digital twin layer and the service layer, which comprises three services: collaborative maintenance management, exploration of ecosystem entities, and quality management and continuous improvement.\n\nThe digital twin layer consists of twins and industrial entities as well as a workforce contributing to the creation of added value, its information perception and contextualization layer, and the intrinsic twin layer encompassing information models, physical entity simulation models, and twin functionality.\n\nCross domain functions: We also defined cross-domain functions for all parts of the architecture, such as security management, license management, and digital authorities. Communication between these different layers is ensured by communication protocols and mediating communication layers such as OPCUA, MT Connect, Automation ML, and OPCUA. The choice of protocol or integration depends on several criteria, including technical interoperability, cyber security, and deployment costs. The integration of standard data formats and information models within the architecture for semantic and syntactic interoperability is ensured by AAS directories developed based on an agile and collaborative engineering process provided by twin-type simulation, cloud platforms, and virtual prototyping.\n\nWithin the digital value chain model, logistics and reverse engineering are integral to the ecosystem development process. The digital twin’s reactivity to waste through optimization functionality enables the management of the non-value-added produced by each process. This non-value-added is communicated to the collaborative maintenance and continuous improvement departments for in-depth analysis, supported by the network of decision-makers. All modifications and improvements produced by the synergy of artificial and human intelligence were communicated to Ecosystem 1 and integrated into the new instance model of the twin types, thus facilitating reverse engineering and digitizing the process of testing new structures for improved performance. Meanwhile, waste management is handled by process twins, which integrate the reverse value chain into the overall ecosystem management.\n\nNetwork of Customers and their customers: The last layer of the architecture is that of customers and customers, represented by airlines, international manufacturers, and end-users who are customers of airlines. From a Lean management perspective, the aim is to create an interactive, dynamic interface with this network via the services in order to manage the entire development and engineering process in an optimized, end-to-end way, but also to offer this network the possibility of benefiting from the integration of digitalization tools within the value chain for triple synchronization of costs, deadlines, and quality.\n\n\n3. Proof of concept\n\nThe simulation is based on the model of an aircraft distribution system proposed by Ref. 28 for the monitoring of safety-related condition indicators, as shown in Figure 3(a). The choice of this particular use case was motivated by the first area of concern discussed previously, which extended the proposed framework discussed by the different developed DT instances and types. The remainder of the use case is based on the analysis of the dataset proposed for this system, which is considered to be produced data from the real system.\n\nThe proposed system is inspired by the system described in previous sections and is composed of three main components: tanks, five main pumps and valves, and a refuelling point. The central tank is connected to two valves that control the amount of fuel that flows to each of the two engine lines. The lines are connected to the front and rear engines by a main pump and a valve that controls, in addition to the pump, the flow of fuel through the engine. Each line is connected to a main tank provided with fuel from the central tank by means of a main pump and a valve for flow control. Different flow, pressure, temperature, and level sensors are installed to reinforce system safety and report measurements for flight control and for further analysis. A refuelling point is activated when the level of fuel crosses a minimum within the central tank.\n\nDT instances have the main mission of adapting system behavior to environmental changes by optimizing individual assets and collective performances. The proposed system consists of a set of complex systems that exhibit particular properties and models that relate to the areas of interest for decision makers and users’ operational and business teams. The two decision-making problems interact to achieve the two main defined sub-goals for DT agents: smart maintenance scheduling and control optimization. Decision-making problems are defined through States, Actions, Rewards and State-Action Transition matrices. In the context of this paper, we focus on defining smart maintenance scheduled through the proposed solution. Operation sequence control optimization will be included through the rewarding system and detailed in further work.\n\nDT Types work in parallel to help the instances perform best. DT Types continuously learn to reinforce their instances’ decision-making capabilities. For this purpose, we developed a simulated environment that helps simulate faulty and healthy scenarios from previous experience, but also results from random noise and conflicting situations. Real scenarios exploited from the proposed dataset for the use case were augmented with a newly developed dataset that aimed to integrate security threats affecting the three physical, cyber, and networking parts of each asset, particularly for the measurements and control system. As highlighted previously, we want to explore the situation of coordinated learning to resolve conflicting goals by integrating both security and safety concerns. Coordination completes the adaptive and smart monitoring loop of the system by evaluating the correlations between safety and security risks for implemented safety equipment and measurement systems, such as sensors and valves.\n\n\n\n• Centrifugal Pump Hydraulic Model for Type\n\nThe model was developed on the basis of the Pump Head and torque characteristic curve data interpolation according to the empirical model of the head and torque and pump Affinity Laws based on Eq. (1) and Eq. (2), respectively.\n\nHp,Q,w: head, Flow rate and speed for pump\n\nQ0,P0,H0: nominal head, Flow rate and speed for pump\n\nCoefficient approximation was performed on MATLAB Curve Fitting Tool according to selected operational points from the chose centrifugal pump for nominal speed:\n\n• Driver model for Pump Speed control model for Type\n\nThe dynamics of the electrical driver are modelled by speed variation across the shaft and pump torque evolution as a load for the motor represented by Eq. (3) and Eq. (4), respectively, and loss expressions are considered to reproduce real motor operation according to Eq. (5). The regulation pump speed through the diver was introduced by a PI regulator on the motor torque represented by Eq. (6).\n\nTe: Pump drive torque loss\n\nJ∆: Intertia for pump drive\n\nDω: Damping factor\n\nTp: Pump torque\n\nYs: Process variable\n\nus: Control output\n\nWs: Set point for control\n\nTo adapt the system to different operating scenarios, PID parameters were tuned according to a PSO Loop with system models of the plant. At each new goal plan for the agent, the PID function is called to provide agents with new optimized input variables. The activation of the Loop is Controller with a goal flowchart.\n\n• Tank model for Type\n\nThe dynamics of the tank are modeled by the tank volume, flow, and level evolution during the simulation according to Eq. (7), Eq. (8), Eq. (9) and Eq. (10). for level, fluid pressure, and flow, respectively. The flow at the outlet of the tank depends on the valve characteristics and the control signal to the valve-opening position. Eq. (11) describes the model tank level as an output variable for a control loop, which is discussed further for system fault modeling.\n\nAs Described earlier, the two DT networks of type and instance collaborate to achieve defined smart maintenance planning.\n\nTo achieve this goal, DT agents exploit their acquired capabilities and assigned roles by default. One of the main roles deployed by instance and type is Online and Offline learning.\n\nThe learning model for the two networks is defined by Reinforcement Learning RL quadruple StAtTsRt agent states within the environment, Actions, Transition probabilities, and rewards.\n\n- DT agents states within the environment:\n\nAgent States within the environment are defined by three dimensions that describe the main factors that orient agents’ decisions and actions.\n\nThe first dimension concerns Highly Critical Assets HCA states that can be considered as the main influencers of the overall system performance.\n\nThe second dimension is defined through the Asset Health Index, which portrays asset status by the combination of main asset deterioration and health evolution models and the impact of modifiers on this status. Three modifiers were considered: health, reliability, and operational modifiers.\n\nThe third dimension concerns failure evolution, which we define as the failure rate that can be linked to both deterioration modes and health index evolution to reduce the state-space dimension.\n\nInspired by Ref. 29, we define critical asset states as New, Deteriorating, Deteriorating critical, under PM, available to adjust, and failed. Asset’s criticality code that will be included in the Functional Safety Sub model will be assigned to assets based on a multicriteria analysis of asset health deterioration impact degrees, and this will be detailed throughout our further works. Several health index evaluation models have been proposed in the literature; for the purpose of this paper, and in order to reduce problem definition complexity referring to asset performance and deterioration modes, we define the Asset Health Index (AHI) Hit through flow and efficiencies, as proposed in the framework developed by.30 The choice of this framework is motivated by our interest in integrating different modifier factor impacts on asset performance and index-wide use in the aviation domain. The explicit representation of the states according to the health index and failure rates is given by Eq. (12) , Eq. (13) and Eq. (14). The failure rate in the context of this study was assumed to follow a probabilistic Weibull Distribution.\n\nSi: Asset state i at instant t.\n\nFRt, FEt,, FHt, FLt: Health, load, reliability, and environmental factors\n\nλjt: Failure rate for asset i at time t.\n\nβi,1d: Weibull distribution slope for Asset I.\n\nηi,2d: Weibull distribution scale for Asset I.\n\n- DT agents rewards:\n\nTo evaluate their performance in addition to asset state transitions, DT networks receive a reward at each decision epoch that helps them progress with their action plans through their operation.\n\nAgent rewards are defined by the maintenance policy value trajectories. The agents’ decision epochs are defined by several decision episodes at each decision episode agent across various states that are characterized by their values and impacts on maintenance value trajectory optimization. The usage costs of an asset are defined by Eq. (15). CO,Cenergy,Cm and CS represent the operation, energy, maintenance, and out-of-service costs, respectively, in Eq. (16), Eq. (17), Eq. (18) and Eq. (19). This cost was subtracted from the asset profit value to constitute the reward function represented in Eq. (20).\n\nThese costs are defined as the cumulative usage phase costs and reward for each agent within the network for each decision epoch. All usage-phase costs are considered in this case study to apprehend the benefits of the proposed architecture. The DT agent reward is defined by Eq. (21). Safety and satisfaction functions are represented by Eq. (22) and Eq. (23).\n\nWithin the cost function, we define three coefficients for preventive, corrective, and repair, and test costs ak, bk, ck respectively.\n\n- DT agents Actions:\n\nAction space consists of five main actions and their derivatives, which are defined through ISO 14624 definitions of major maintenance activities. Two categories are defined: the first includes one action, which is No Maintenance performed, and the second category, which focuses on different maintenance actions, includes four maintenance activities.\n\nCheck and adjust or Minor Maintenance, which consists of the execution of different inspection operations while maintaining asset operation; the second maintenance action within this category is Preventive Maintenance, which includes the set of planned checks for preventing asset operation and the adjustment of working parameters, the third action includes Corrective Maintenance actions that result from asset failure during its operation as a critical result for agent control. CM actions are defined according to the resulting failure modes, its causes, and effects, and their definition by architecture agents’ networks will be detailed further. The last action within this category is replacement, which transits assets to a new state and is considered the worst case for DT Types and instances network performance evaluation.\n\nAlgorithm 1 represents the agent’s capability for anomaly prediction and field interrogation based on the proposed model for Health Index estimation. The proposed algorithm processes time-series data related to asset conditions, extracts features, and uses a classifier to identify anomalies or normal behavior for each asset. It updates the failure probability and behavior label accordingly, and computes certain metrics based on the extracted data.\n\nInput:\n\nRawData Streams time series sequences for assetiPx1tPx2t……Pxnt\n\nAssset criticality code for assetiCic\n\nl:window lenght\n\nOutput:\n\nBehaviour labelyout̂ and corresponding deterioration mode for Maintainable items MI\n\nFik:Assetiestimated failure probabilityatstepk\n\nSHCA:HCAState\n\nInitialization\n\n1: SHCA←SNew\n\n2: λik←λik=0\n\n3: FR← 0\n\n4: FH← 0\n\n5: Fl← 0\n\n6: fork<T\n\n7 foriin1n\n\n8: Extract data stream sequence for condition varibales according to window sizel\n\n9: Construct Time series Features Matrix and generate condition indicators for asset\n\n10: Classify behaviour and determine extrcated sequences class basedonselected classifier\n\nIf anomaly mode i detected\n\nλik←∑1J∑1DλIdk\n\nyout̂←CNORMALm=i\n\n11: Else\n\nλik←0\n\nSHCA←Normal Behavior\n\nyout̂←CNORMALm=0\n\n12: End\n\n13: End\n\n14: Compute\n\nFH←∏1Hf1H\n\nFR←∏1Rf1R\n\nFL←∏1Lf1L\n\nAdd rule to set of behaviours rules and archive new scenario\n\nFinally, it adds the computed rule to a set of behavioral rules and archives the scenario for further analysis.\n\nClassification is performed based on a model pretrained by DT Types using a case base of healthy and faulty simulation results.\n\nAlgorithm 2 DT type capability for smart maintenance planning and action optimization based on RL logic.\n\nInput:\n\nStates\n\nHik:Assetihealth indexatstepk\n\nsik:AssetiStatusatstepk\n\nλik:Assetifailure rateatstepk\n\nActions\n\nNM: No Maintenance Actions; PM: Preventive Maintenance; CM: Corrective Maintenance; RA: Replacement Action; AA: Minor Maintenance and Adjustment Actions\n\nAction Execution interval tstarttend\n\nOutput:\n\nRewards\n\nR=rk+γrk+1+γ2rk+2+⋯+γK−krK\n\nInitialisation:\n\n1: R←0\n\n2: rk←0\n\n3: Si0←Sit //Random states for health index, status and failure rate extracted from model simulation at instant t\n\n4: k←0\n\n5: Repeat:\n\n6: for k < T\n\n7: a←πa //Actions Sequence according to chosen maintenance policy\n\n8: SikR←DTSika//Asset states and rewards according to Asset shadow feedback from the execution of action a at step k\n\n9: R←rk+γrk+1+γ2rk+2+⋯+γK−krK\n\n10: Update Qsaaccording to RL learning algorithm\n\n11: Sik←S′ik\n\n12: Until s is terminal\n\n13: Until criterion is reached\n\nAlgorithm 3 shows the DT-Instances Learning algorithm for Proactive Decision Making with the integration of collaborative learning between agents through the exploration of similar cases based on the agent’s own experiences and peers’ experiences.\n\nInput:\n\nStates\n\nRUL:Estimated Asset Remaining useful life\n\nHik:Assetihealth indexatstepk\n\nFikt:Assetifailure probabilityatstepk\n\nActions\n\nActions Sequences from heuristic search\n\nOutput:\n\nRewards\n\nR=rk+γrk+1+γ2rk+2+…+γK−krK\n\nInitialisation\n\n1: QtsaandHtsarandomly\n\n2: Formulate proposal joinpdescriptionscope //Description depends on failure probability and condition, scope with criticality code of neighbours\n\n3: Repeat:\n\n4: for each cycle step k:\n\n5: ComputeSimpcandCostadaptabilitypc //Explore for similar cases within knowledge base and according to network agent experiences\n\n6: if there is a case c that can be reused:\n\n7: ComputeHtsawith action policy proposedbythe selected cases\n\n8: a←xk.Ik.I+I−1 //Set policy based heuristic search extracted actions\n\n9: else\n\n10: Select actionausing∈−greedy policy\n\n12: Excute policy and observeRsa,S′ik\n\n13: UpdateQtsa\n\n14: Sik←S′ik\n\n15: Until s is terminal\n\n16: Until criterion is reached\n\nIn the context of the proposed use case, five runs with five operating points for each run were simulated to represent healthy conditions of the system. Faulty conditions were simulated using MATLAB by injecting faults at each epoch and their combination through the introduction of a Failure_Scenarios_Simulation () function that can be manipulated by system users to test, simulate, and generate ensemble fault data stores. Table 5 presents the experimental details for the heathy scenarios with different loads. We assume the initial condition that assets have been operating for 100h with 20 start-ups of the Front and Rear Pumps. The estimated flight time is considered to estimate the operational time of assets for the modifier estimation.\n\nThree main critical failure modes for assets, as well as one incipient and intermittent failure mode, were simulated to test different scenarios. Faults are modelled within MATLAB/SIMULINK using different fault models defined by StartTime, Duration, Fault_Value_Set, and Fault_Sevirity_Category. This section introduces Failure_Scenarios_Simulation () in MATLAB for the discussed use case. The fault mode sets are represented by different gains from Eq. (24)–(30), respectively.\n\n\n\nTable 6 presents the scenarios for the faulty behavior of the pump. Security faults arising from security threats are also considered.\n\nThe Weibull parameters estimated from a bibliographic review of aircraft fuel distribution reliability data enable the estimation of the probability parameters for different failure modes of the driven pumps within the system and their subunits. According to the Table above, α1 and β1, α2 and β2 are represented for the early and wear-out life phases of the pump unit Eq. (31) to Eq. (34).\n\n\n\nThe proposed reward function of the system was calculated based on the estimated maintenance costs of each subunit and its failure modes. The PM, CM, and RM costs for the subunit discussed in the context of this paper are presented in Table 8, and the failure mode costs and their respective necessary PM, CM, and RM duration are presented in Tables 7 and 9.\n\nAn example snapshot of the standard fault definition document for the fault submodel of digital twins in JSON format according to the standard definition of fault properties is presented in Table 10. The proposed type of fault model aims to fulfil the concept from digital thread to have a standard and sharable definition of maintenance main concepts that can be used by the DT network but also its stakeholders.\n\n\n4. Simulation Results\n\nThe simulation was executed based on the scenarios proposed in the previous sections.\n\nA set of six runs with 30 healthy scenarios and a combination of 30 faulty scenarios were proposed for the discussed use case to apprehend both DT benefits for the simulation of the systems and for testing different scenarios for DT agents. Simulations have focused on both normal and abnormal behavior of the system to work as an interface with the real twin and its stakeholders. Figure 4 (a), (b), (c), and (d) present the simulation results for the flow, pressure, head, and pump shaft torque in a normal scenario.\n\nFigure 5 (a) and (b) present the tank volumes and temperature evolution for the Central, Rear and Front tanks, respectively.\n\nFigure 6 and 7 (a) and (b) represent the simulation for some of the presented failure modes, such as the NOISE failure mode, BDR of pumps, and Structural Deficiency of the shaft that is simulated by the introduction of wear out into the shaft-produced torque.\n\nAuxiliary pumps are activated as a result in order to reproduce real system operational logic and dynamics. As we can see throughout the simulation with the introduction of noise into the speed sensor, deviations are reported to different system controllers that are impacted by the output of the speed sensor as instance flow control. This causes the entire system to deviate from its recommended nominal operating limits, which challenges both control logic and other safety equipment such as installed control valves and throttles.\n\nThe labeled data of the simulated faulty and healthy scenarios are exploited for system behavior classifications and system state reproduction for the type agent’s decision-making support. Simulation outputs were used to compute the asset health index, health modifiers, reliability modifiers, load modifiers, and failure rate estimation for failure story development. Failure stories are used by DT Instances for proactive decision-making and efficient maintenance policy selection in the event of abrupt failures. Figure 8 introduces the DT Instances interface for field interrogation, and Figure 9 introduces the interface for action selection and simulation based on selected policies.\n\n\n5. Discussion\n\nSimulation results for the use case showed that the proposed architecture can be used for both online and advanced offline learning because of the twin’s adaptability to the changes in environments that are either simulated or detected by the operation of the real system. The developed virtual environments for DT type agent learning and training can be easily exploited and adapted to users’ requirements, and learning can be transferred among different DT Types with various context constraints and conditions that enhance both DT types and instance awareness and reactivity. The introduction of the mediator agent for DT maintenance application use cases can help reinforce the testing of different policies and reduce the exploration space of the agents while reinforcing their information on the environment and other agents. Fusion between machine learning-based approaches and statistical analysis of faults by the introduction of estimations of failure rates based on similar equipment historical data can expand the scope of application of Digital twins through the maintenance field by taking advantage of approaches familiar to maintenance management teams and shared among different stakeholders, and can also help to establish real-time tracking of more advanced maintenance indicators for critical industrial domains and applications.\n\nIn this study, we hypothesize that the failure rate obeys a Weibull distribution with two-parameter estimation, and further studies will focus on the development of a database that serves as training samples for estimation, transmitting the focus on a larger scope that affects each failure mode with an adequate probability distribution according to a fleet of instances in different domains.\n\nThe proposed virtual environment can be enhanced by a direct connection with different types of engines and pumps. In this study, we focus on centrifugal pumps, electrical motors, Fuel Tanks, valves, and sensors as safety equipment failure modes. The focus is on centrifugal pump use, and safety systems were integrated into pump unit boundaries, which may have limited the overall impacts of fault simulation on overall system behavior changes. Security faults were integrated as a part of the noise in measurement systems, and further work will concentrate on the effective integration of these failures as a part of the smart supervision system introduced by mediator agents, as they constitute an integrated part of the system capability model.\n\nThe broader scope of the architecture was not developed through the paper as the use case was focused on an open ecosystem to apprehend the value added of the proposed model to the operation and maintenance perspective and provide an overview of how the concept of instances and types introduced by digital thread can facilitate the introduction of digital twins into the field and provide an improvement with regard to discussed break points by the PESTELE analysis presented.\n\n\n6. Conclusion\n\nAn approach based on the combination of digital thread and digital twin concepts and advanced simulation is proposed to develop a distributed and smart architecture for digital twins. Modeling, which is considered one of the main elements of the basic foundation of digital twins, is apprehended by a network of smart agents that, in addition to being structured and flexible, enables the integration of the organization concept, which is a major constraint for modern digital twin systems’ autonomy and interoperability. Reinforcement learning for individual digital twins has been tested throughout the literature, and the extension of RL scope to MAS systems by learning of collaboration takes organizational concepts into practical implementation within complex, highly constrained industrial environments. The things that we tried to concretize by the integration of several independent domain-based agent types and instances that create a cooperative behavior in order to achieve a set of defined goals and plans taking advantage of individual agents learning experience feedback offline environment states and rewards, and agents’ networks communicated observations and analyzed information.\n\nThe proposed approach was tested using an application use case that highlighted its efficiency for complex monitoring tasks within safety-constrained systems. The proposed Policy model for the presented architecture helps to establish a conceptual framework for the behavioral mapping of actions and operations during runtime mode, but also for offline learning tasks in which results are transmitted for online execution. The suggested implementation framework based on the simulation of DT agents in a virtual environment is intended to establish a monitoring interface for this policy-based verification mechanism for agents’ complex and unpredictable network behaviors.\n\nIn the following studies, we aim to explore the integration and runtime security verification policy aspects of the proposed architecture for highly critical industrial environments and work on the testing and simulation of the proposed architecture in real industrial environments for applications in complex systems life cycle management and implementation of DT2Aero in a real environment.",
"appendix": "Data availability\n\nZenodo: DT-MAS smart architecture for prescreptive maintenance of aircraft fuel distribution systems, https://doi.org/10.5281/zenodo.10649700. 31\n\nThis project contains the following underlying data:\n\n• Run1: 5 Scenarios with Healthy and Faulty Behaviors for pump, driver, Hydraulic Pump and Tank. Simulation of Fault Type from 1 to 5.\n\n• Run2: 5 Scenarios with Healthy and Faulty Behaviors for pump, driver, Hydraulic Pump and Tank. Simulation of Fault Type from 1 to 5 with combination of some failures.\n\n• Run3: 5 Scenarios with Healthy and Faulty Behaviors for pump, driver, Hydraulic Pump and Tank. Simulation of Fault Type 6 and 7. Change of operating conditions for Healthy scanrios.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nWolf M, Semm A, Erfurth C: Digital Transformation in Companies – Challenges and Success Factors. Springer International Publishing; 2018. Publisher Full Text\n\nWest TD, Blackburn M: Is Digital Thread/Digital Twin Affordable? A Systemic Assessment of the Cost of DoD’ s Latest Manhattan Project. Procedia Comput. Sci. 2017; 114: 47–56. Publisher Full Text\n\nMadni AM, Madni CC, Lucero SD: Leveraging Digital Twin Technology in Model-Based Systems Engineering.2021; 7: 1–13. Publisher Full Text\n\nVidal F, Alonso L, de Luca P , et al.: Development of a Digital Thread for Orchestrating Data Along the Product Lifecycle for Large-Part and High-Precision Manufacturing.2024; pp. 668–676. Publisher Full Text\n\nAnsari I, Barati M, Sadeghi Moghadam MR, et al.: An Industry 4.0 readiness model for new technology exploitation. Int. J. Qual. Reliab. Manag. 2023; (ahead-of-print). Publisher Full Text\n\nZezulka F, et al.: The Ideas of Industry 4.0: Seven Years after. IFAC-PapersOnLine. 2022; 55(4): 145–150. Publisher Full Text\n\nGhita M, Siham B, Hicham M, et al.: HT-TPP: A Hybrid Twin Architecture for Thermal Power Plant Collaborative Condition Monitoring. Energies. Jul. 2022; 15(15): 5383. Publisher Full Text\n\nZhang Y, Dong W, Wang J, et al.: The development of digital thread: the relations to digital twin and its industrial applications. Digit. Transform. Soc. Nov. 2022; 1(2): 147–160. Publisher Full Text\n\nSekera J, Novák A: The future of data communication in aviation 4.0 environment. INCAS Bull. 2021; 13(3): 165–178. Publisher Full Text\n\nZutin GC, Barbosa GF, de Barros PC , et al.: Readiness levels of Industry 4.0 technologies applied to aircraft manufacturing—a review, challenges and trends. Int. J. Adv. Manuf. Technol. May 2022; 120(1–2): 927–943. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKunju FKF, Naveed N, Anwar MN, et al.: Production and maintenance in industries: impact of industry 4.0. Ind. Rob. Apr. 2022; 49(3): 461–475. Publisher Full Text\n\nStojkovic M, Butt J: Industry 4.0 Implementation Framework for the Composite Manufacturing Industry. J. Compos. Sci. Sep. 2022; 6(9): 258. Publisher Full Text\n\nRaja Santhi A, Muthuswamy P: Pandemic, War, Natural Calamities, and Sustainability: Industry 4.0 Technologies to Overcome Traditional and Contemporary Supply Chain Challenges. Logist. Nov. 2022; 6(4): 81. Publisher Full Text\n\nAuledas-Noguera M, Liaqat A, Tiwari A: Mobile Robots for In-Process Monitoring of Aircraft Systems Assemblies. Sensors. Apr. 2022; 22(9): 3362. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang G, Yang Y, Yang G: Smart supply chain management in Industry 4.0: the review, research agenda and strategies in North America. Ann. Oper. Res. Mar. 2023; 322(2): 1075–1117. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsad U, Khan M, Khalid A, et al.: Human-Centric Digital Twins in Industry: A Comprehensive Review of Enabling Technologies and Implementation Strategies. Sensors. Apr. 2023; 23(8): 3938. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuo J, et al.: Design and application of digital twin system for the blade - rotor test rig. J. Intell. Manuf. 2021; 34: 753–769. Publisher Full Text\n\nLoaiza JH, Cloutier RJ, Lippert K: Proposing a Small-Scale Digital Twin Implementation Framework for Manufacturing from a Systems Perspective. Syst. Jan. 2023; 11(1): 41. Publisher Full Text\n\nPutz B, Dietz M, Empl P, et al.: EtherTwin: Blockchain-based Secure Digital Twin Information Management. Inf. Process. Manag. 2021; 58(1): 102425. Publisher Full Text\n\nAbu Salem K, Palaia G, Chiarelli MR, et al.: A Simulation Framework for Aircraft Take-Off Considering Ground Effect Aerodynamics in Conceptual Design. Aerosp. May 2023; 10(5): 459. Publisher Full Text\n\nDebnath B, Shakur MS, Tanjum F, et al.: Impact of Additive Manufacturing on the Supply Chain of Aerospace Spare Parts Industry—A Review. Logist. Apr. 2022; 6(2): 28. Publisher Full Text\n\nAl Rahamneh AA, et al.: The effect of digital supply chain on lean manufacturing: A structural equation modelling approach. Uncertain Supply Chain Manag. Dec. 2023; 11(1): 391–402. Publisher Full Text\n\nPonjavic M, Karabegovic A: Location Intelligence Systems and Data Integration for Airport Capacities Planning. Comput. Feb. 2019; 8(1): 13. Publisher Full Text\n\nArm J, et al.: Automated Design and Integration of Asset Administration Shells in Components of Industry 4.0. Sensors (Basel). Mar. 2021; 21(6): 1–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndrei AG, Balasa R, Costea ML, et al.: Building a blockchain for aviation maintenance records. J. Phys. Conf. Ser. Feb. 2021; vol. 1781(1): p. 012067. Publisher Full Text\n\nCiampa PD, Nagel B: AGILE Paradigm: The next generation collaborative MDO for the development of aeronautical systems. Prog. Aerosp. Sci. Nov. 2020; 119: 100643. Publisher Full Text\n\nXiong M, Wang H, Fu Q, et al.: Digital twin–driven aero-engine intelligent predictive maintenance. Int. J. Adv. Manuf. Technol. Jun. 2021; 114(11–12): 3751–3761. Publisher Full Text\n\nGheraibia Y, Kabir S, Aslansefat K, et al.: Safety + ai: A novel approach to update safety models using artificial intelligence. IEEE Access. 2019; 7: 135855–135869. Publisher Full Text\n\nMarais KB, Saleh JH: Beyond its cost, the value of maintenance: An analytical framework for capturing its net present value Beyond its cost, the value of maintenance: An analytical framework for capturing its net present value $.2018; (January). Publisher Full Text\n\nLitt JS: ONLINE MODEL PARAMETER ESTIMATION OF JET ENGINE DEGRADATION.2003; (August): pp. 1–17.\n\nMezzour G: DT-MAS smart architecture for prescreptive maintenance of aircraft fuel distribution systems (1.0). [DataSet]. Zenodo. 2024. Publisher Full Text"
}
|
[
{
"id": "290856",
"date": "19 Jul 2024",
"name": "Guillaume Renaud",
"expertise": [
"Reviewer Expertise Aircraft structures"
],
"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 must say that I am not that familiar with concepts related to Industry 4.0, PESTEL analysis, AAS, Internet of Things, etc. My experience is more on the digital twinning of specific components for life cycle management. That being said, I find this article a useful summary of the different aspects related to the digital transformation in the aerospace industry. Further, it proposed a detailed DT framework, along with a demonstration of the use of some of its aspects (training) for a concrete system problem. The paper is very well written but reads as a condensed version of what could be a much larger document. A lot of information is provided; it uses many terms and acronyms that are not defined. Defining these terms would help the non-expert readers.. One major negative aspect: the text in the figures is extremely difficult and sometimes impossible to read. The image conversion should be redone. Section 2 discusses the aeronautics value chain, divided in upstream, core and downstream activities, and defines four main ecosystems: engineering, electrics and wiring, assembly and maintenance/repair. These ecosystems are analyzed to identify added value and improvement areas related to the transition to digital threads/twins. A lot of information is packed in four tables and the key observations do not really stand out. The proposed very comprehensive digital thread/twin framework, D2TSAero, consists of three networks mapped to the aforementioned value chain activities. A lot of details are addressed, including aspects such as contracting, security, communication protocols, certification, etc. I am not in position to judge if anything is missing or how novel this specific architecture is. Section 3 is a proof of concept based on the simulation of an aircraft fuel distribution system, with the intend to use DT to define smart maintenance scheduling. For the paper, simulated environment, combining healthy scenarios, noise and conflicting situations, augmented with a focus on security threats in order to integrate safety and security concerns. Pump model: some parameters are not defined (Tp, ki, V, U, delta, x, etc.). Last sentence should be rewritten (The activation of the…). Tank/valve model: some parameters are not defined. DT network of type and instance collaborate to determine smart maintenance planning using online and offline learning – defined by agent states within the environment, actions, transition probabilities and rewards. More specifically:\n\nAgent states within the environment:\nHighly critical assets (states: new, deteriorating, deteriorating critical, under PM, available to adjust, failed) Asset health index (deterioration and health evolution + their impact) Failure evolution (rate)\n\nActions\nNo maintenance, check and adjust (minor maintenance), preventive maintenance, corrective maintenance, replacement Algorithm 1: Anomaly prediction and field interrogation Algorithm 2: Smart maintenance planning Algorithm 3: Proactive decision making\n\nThe objective is to determine the best maintenance actions based on costs (maintaining operations, maintenance, etc.). Section 4 present simulation results for healthy and faulty scenarios. Focus was put on normal and abnormal behavior of the system to work as an interface with the real twin. Healthy and faulty scenario data are used to train system state/health classification. Unfortunately, no demonstration using physical twin data is presented but the authors mention that it would be done in the future..\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/13-193
|
https://f1000research.com/articles/12-656/v1
|
13 Jun 23
|
{
"type": "Research Article",
"title": "Mango quality prediction based on near-infrared spectroscopy using multi-predictor local polynomial regression modeling",
"authors": [
"Millatul Ulya",
"Nur Chamidah",
"Toha Saifudin",
"Millatul Ulya",
"Toha Saifudin"
],
"abstract": "Background: pH and total soluble solids (TSS) are important quality parameters of mangoes; they represent the acidity and sweetness of the fruit, respectively. This study predicts the pH and TSS of intact mangoes based on near-infrared (NIR) spectroscopy using multi-predictor local polynomial regression (MLPR) modeling. Herein, the prediction performance of kernel partial least square regression (KPLSR), support vector machine regression (SVMR), and MLPR is compared. Methods: For this purpose, 186 intact mango samples at three different maturity stages are used. Prediction models are built using MLPR, KPLSR, and SVMR based on untreated and treated spectra. The best regression model for predicting pH is MLPR based on Gaussian filter smoothing spectra. Moreover, the TSS value is more accurately predicted using MLPR based on Savitzky–Golay smoothing. Results: The findings reveal that MLPR is highly accurate in estimating the pH and TSS of mangoes, with mean absolute percentage error (MAPE) values less than 10 %. In addition, the MLPR model has the best predictive performance with the lowest Mean Squared error (MSE) and root mean squared error (RMSE) values and the highest R2 value. Conclusions: The use of NIR spectroscopy in combination with multi-predictor local polynomial regression could provide a quick and non-destructive technique for predicting mango quality. Thus, the results of this study help support sustainable production as a sustainable development goal.",
"keywords": [
"NIR spectroscopy",
"mango",
"sustainable production",
"local polynomial regression"
],
"content": "Introduction\n\nIndonesia’s Gadung Klonal 21, commonly known as Avomango, is a popular mango cultivar owing to its thick flesh, low fiber content, and sweet flavor.1 Avomango can be eaten in the same way as an avocado. It was developed in Pasuruan Regency, East Java. Even now, fruit pickers hand-pick mangoes and must determine whether the mango is sufficiently mature for picking. Maturity indices determine the quality and shelf life of harvested fruits, and provide the necessary flexibility for transport and marketing.2 Harvest maturity is the stage of development in climacteric fruits, such as mangoes, when the fruit is harvest-ready and of an acceptable consumer grade. Consumer maturity is achieved when the fruit is ready for consumption or utilized in other ways. In climacteric fruits, consumer maturity is reached after harvest maturity.3 Mature mangoes have a low pH value and high Brix percentage; the pH value increases throughout the maturation period.\n\nFruit maturity indices can be estimated accurately using destructive methods. These methods are damaging, time-consuming, labor-intensive, and require manual loading.4 Furthermore, they are costly, require a long time for sample preparation, and are wasteful.5 Thus, rapid, non-destructive, and environment-friendly analytical methods are required. Hence, non-destructive techniques, such as visible imaging, colorimetry, visible and near-infrared (NIR) spectroscopy, computed tomography, hyperspectral imaging, fluorescence imaging, and multispectral imaging, have been developed to evaluate fruit maturity.3 NIR spectroscopy is the most widely used non-destructive technique in post-harvest fruit and vegetable quality determination.6 Moreover, NIR spectroscopy techniques have been used to overcome the limitations of destructive methods while maintaining the physicochemical attributes of food and agricultural products. In addition, using NIR spectroscopy technology helps support sustainable production as a sustainable development goal (SDGs).\n\nPhysicochemical, physical, and biological changes occur in mangoes during ripening. These changes differ depending on the mango variety. The color does not reflect the stage of maturity in Gadung Klonal 21 as the green color of the mature mango is similar to that of the raw mango. The texture of mature mangoes differs significantly; the tip of the fruit has a soft texture. A significant change is observed in the level of sweetness and acidity of mangoes, which can only be detected by destructive analysis. However, numerous studies have been conducted to predict the sweetness and acidity of mangoes using regression modeling based on spectral data from NIR spectroscopy.7–11\n\nStudies have been conducted to determine and forecast the maturity and quality of mangoes.7–12 Spectral data must be modeled using several regression methods, either as raw spectra or pre-processed spectral data, to estimate the internal quality of mangoes. Most of the previous studies have modeled spectral data using linear regression and nonlinear regression. Linear regression including partial least squares regression (PLSR) and principal component regression are the two most popular approaches for NIR calibration.13 Linear regression is commonly used in parametric regression techniques to predict the internal quality of fruit. Furthermore, nonlinear regression methods have the potential for such application. Forecasting changes in quality in agricultural products requires predictive modeling that considers the effectiveness of a nonlinear regression model.14 To predict the fruit quality, Nicolaï, Theron, and Lammertyn20 employed nonlinear regression analysis involving the kernel partial least squares regression method (KPLSR). Anderson, Walsh, Flynn, and Walsh15 reported using local PLSR to estimate the dry matter content of mango. The application of nonlinear regression to fruit quality prediction is relatively underexplored.\n\nA nonparametric regression approach can be used to model unpatterned data, including the nonlinear cases. Nonparametric regression for predicting the acidity level of mangoes was studied by Ulya and Chamidah.22,23 The prediction of the sweetness level of mangoes has been reported by Ulya, Chamidah, and Saifudin.16 These studies report that nonparametric regression based on local polynomial estimators, particularly, multiple polynomial regression (MPR), results in a better predictive model than the parametric regression approach.\n\nLocal polynomial regression can capture nonlinear patterns between the response and the predictor variables.17 This method looks at neighboring data for the specified bandwidth, matches separate piecewise regressions for each part, and combines them.18 The local regression fit is complete when all the data points are identified using the regression function values. Function calculation in local polynomial and local linear regression is performed locally at the point to be estimated.19 This is different from spline regressions.20–23 This local estimation technique captures nonlinearities that may exist without the influence of dataset outliers at each estimation stage.24 This method is data-based and easy to implement. It provides a flexible structure that can capture the nonlinear characteristics present in the data compared to multiple linear regression (MLR).25\n\nMango pH value prediction using multi-predictor local polynomial regression (MLPR) and MPR was investigated by Ulya et al.26 The results indicate that the MLPR method provides better predictive performance with a lower mean absolute percentage error (MAPE) value than the MPR method. However, some studies have attempted to overcome the problem of nonlinearity when predicting internal fruit quality based on NIR spectroscopy using KPLSR27 and support vector machine regression (SVMR).28,29 These two approaches perform better compared with MLR and PLSR. However, to date, no study has compared the predictive performance of nonparametric regression approaches, such as MLPR with KPLSR and SVMR, in predicting the internal quality of mangoes.\n\nThis study aims at comparing the performance of a mango pH and total soluble solid (TSS) prediction model based on MLPR with KPLSR- and SVMR-based models. MLPR was found to be the best regression model; it exhibited a predictive performance with the lowest mean squared error (MSE), root mean squared error (RMSE) and MAPE values, and the highest R2 value. The MLPR algorithm in this study is useful to design instruments to detect the acidity and sweetness of intact mango.\n\n\nMethods\n\nA total of 186 mangoes (Mangifera indica L, Gadung Klonal 21) were collected from a garden in Wonokerto Village, Sukorejo District, Pasuruan Regency, Indonesia. Mango samples weighing 250–300 g at varying stages of ripeness, ranging from unripe to ripe, were chosen. The mangoes were cleaned and air-dried before being wrapped in Styrofoam fruit netting, and were subsequently placed in boxes (approximately 12 mangoes). Fruit boxes were screened to avoid collisions.\n\nThe spectral data for intact mangoes was acquired using an NIR spectrometer (OtO Photonics. Inc.) in the range of 900–1650 nm at 7 nm intervals. The samples were scanned in reflectance mode to record the spectral data. The process of NIR spectra measurement was conducted by firing a halogen lamp on the sample, which was positioned at an angle of 45° to the sample, with the detector positioned at 45° to the sample. Each sample was scanned at three separate locations (the base, center, and tip of the fruit) and the obtained scans for each sample were averaged. The spectral data were originally presented in terms of the reflectance value (R) and were later converted to the absorbance spectra value (log 1/R).\n\nSpectral data pre-treatment\n\nBefore developing the prediction models, some pre-treatment methods can eliminate undesired effects, including random noise, high-frequency noise, light scattering, baseline shifts, and any other external effects caused by environmental or instrumental factors. Furthermore, smoothing effectively reduces the high-frequency noise. Among the numerous smoothing approaches in the field, Savitzky–Golay (SG) smoothing is one of the most widely used.30 Using SG can retain the signal properties, including the maximum and minimum relative values, and the width of the peak, which are lost when using other smoothing techniques. The present work pre-treated the spectra using SG smoothing generated with two-degree polynomials, Gaussian filter smoothing (GFS), and MSC.\n\nMeasurement of pH and TSS\n\nMango samples (10 g per sample) were blended with 40 ml of distilled water in a fruit blender. Mango juice was measured using a digital pH meter (Lutron pH-208). Triplicate measurements were performed to obtain average values. A small amount of mango juice was dropped onto a pocket digital refractometer (ATAGO PAL-1) to record TSS, expressed in terms of degree Brix (°Bx). The measurements were conducted at room temperature after spectral acquisition.\n\nThe pH, TSS, and spectral data was organized into matrices. The matrix rows represent the 186 samples, and the 114 columns represent the predictor (X) and response (Y) variables. The predictor variables were the wavelengths of 112 NIR spectra for each mango sample. The response variables described the measured pH and TSS values associated with each sample in the first and the second column, respectively.\n\nThe following steps were to perform dimension reduction using principal component analysis (PCA), detect outliers using Hotelling’s T2 ellipse method, and then analyze them using KPLSR, SVMR, and MLPR. The analysis was performed using calibration and validation models of the pH and TSS values. The Unscrambler X 10.4 software was used to perform spectral pre-processing and model development for pH and TSS values. The open-source software R was used to perform the MLPR method. The calibration and validation models' absorbance spectral data of the reference vs. predicted pH was plotted to investigate the nature of the spectral absorbance distribution.\n\nModeling using different calibration methods\n\nThe dataset was divided into two parts 80% as calibration data and the rest as validation data. For multivariate calibration, the data were modeled using a parametric regression method, including KPLSR and SVMR. Additionally, the data were modeled using the nonparametric regression method MLPR.26 Subsequently, predictions were conducted on the validation dataset based on the model developed for the calibration dataset. The prediction performance of the three methods was compared in this study.\n\nMulti-predictor local polynomial regression (MLPR)\n\nMLPR for predicting the internal quality of fruits was proposed by Ulya et al.16 The prediction was obtained using a nonparametric regression approach based on a local polynomial estimator with one response variable and multiple predictors. The MLPR model has a response variable y that depends on the sum of some functions of the predictor variable x and can be written as follows.\n\nβ̂∼ is the parameter estimator, which is performed by taking n pairs of samples xi1xi2…xipyi. The parameters were estimated using the weighted least squares (WLS) method by minimizing the following.\n\nIn addition, the optimum bandwidth (h) as a smoothing parameter in the estimation process must be determined using this method. If the bandwidth value decreases, the regression estimation becomes rougher and vice versa. The optimum bandwidth is the bandwidth with the minimum generalized cross-validation (GCV) value31 and is calculated using the following formula.\n\nModel evaluation\n\nSeveral methods have been used to assess the algorithm's performance in the prediction results. One such method is K-fold cross-validation, wherein the data is randomly divided into k parts before training a classifier with one part and testing it with another.32 This method can reduce sampling bias because the data is randomly divided into several (k) parts.33 The final accuracy of this process is the average accuracy of the number of processes.34 In this study, five-fold cross-validation was used (Figure 1). The 165 samples were split into calibration and validation data, with 80% used as calibration models and the rest as validation models.\n\nGenerally, in the studies on predicting the internal quality of fruits using NIR spectroscopy, the evaluation of the predictive performance and accuracy of the models is performed on the validation dataset. Previous studies have used R2 and RMSE to evaluate predictive models. However, this study evaluated the predictive model using MSE and MAPE values. The most frequently used forecasting accuracy measurement is MAPE.35 MAPE has some significant and desirable characteristics, including reliability, unit-free measurement, interpretability, clarity of presentation, statistical evaluation support, and utilization of all error information.36\n\nThe aforementioned four criteria are suitable for comparing the predictive performances of parametric and nonparametric regressions. Generally, a good model must have a high R2 value and low RMSE, MSE, and MAPE. The RMSE, R2,29 MAPE,36 MSE,37 and overall of RMSE, MSE, R2 and MAPE formulas can be defined using Equations (5)–(12).\n\nThe stages of developing the prediction models and measuring the predictive performance in this study are summarized in Figure 2.\n\n\nResults\n\nThe raw absorption spectra of 186 samples of three different types of mangoes acquired from a spectrometer of wavelength 900–1650 nm are shown in Figure 3(a). The spectral data were pre-treated with SG, a Gaussian filter, and MSC to reduce high-frequency noise, as shown in Figures 3(b)–(d). The MSC technique was used to correct the data by approximating the additive and multiplicative effects of the spectra.38\n\n(a) Raw spectra, (b) SG smoothing spectra, (c) Gaussian spectra, and (d) MSC spectra.\n\nAfter pre-processing the spectral data, the dimension of the absorbance spectra data was reduced by PCA using the singular value decomposition algorithm. Two latent variables representing 99.75% of the variance were selected. Spectral outliers were identified using PCA, subject to Hotelling’s T2 ellipse. In this study, 21 outliers were identified. These outliers were excluded because they could have a negative impact on the model. Sample outliers may provide helpful information, but they can also be non-representative samples that contribute to errors in a model.39 The final sample consisted of 165 observations, divided into two parts: calibration and validation datasets with five-fold cross-validation (see Figure 1). Each fold consisted of 132 calibration data samples and 33 validation data samples.\n\nThe descriptive statistical values for the measured pH and TSS are presented in Table 1. The robustness of the calibration models was evaluated using five-fold cross-validation. Three different calibration models (KPLSR, SVMR, and MLPR) were developed using the calibration dataset for each pre-treatment method (raw, SG smoothing, Gaussian filter, and MSC) to predict the pH and TSS values of the mangoes.\n\nTable 2 presents the calibration and validation results for the pH prediction using NIR. The three regressions provided robust models using GFS-treated spectra compared with untreated, SG smoothing, and full MSC spectra. Both calibration and validation in the MSC spectral model yielded higher MAPE values than those of the other two spectral treatments (SG and Gaussian smoothing). The raw spectra model was better than the MSC model but not better than the Gaussian and SG models. This result is similar; the raw spectra model had a worse predictive performance than the pre-treated spectra.\n\nMLPR is the best method for predicting the pH value of mangoes based on the three regression methods used for all spectral data. The prediction model's performance with MLPR had the highest R2 value and the lowest MSE, RMSE, and MAPE values compared with the KPLSR and SVMR methods.\n\nPredictive performance comparisons of the TSS values are listed in Table 3. Predictive models for TSS values have lower performance than predictive models for pH values. The performance of the pH prediction model was better than that of the TSS prediction model because it had a high R2 value with a low MAPE value (3.4–5.8%). The predicted pH value was closer to the observed pH value. Although the R2 value was high in the TSS prediction model, the MAPE value was also relatively high (6.4–8.1%). However, the MAPE value in the TSS model is still classified as highly accurate.36\n\nPre-processing spectra using SG smoothing for the TSS value parameter gave the best predictive model results, with the lowest RMSE, MSE, and MAPE values and the highest R2 value.\n\n\nDiscussion\n\nMLPR, SVMR, and KPLSR exhibited excellent predictions of the pH of mangoes. Overall, MLPR using GFS spectra provided the best overall model for pH prediction, with R2 = 0.832, RMSE = 0.187, MSE = 0.036, and MAPE = 3.389% (Table 2). All treatment spectra revealed that the best predictive model used MLPR, with the highest R2 value and the lowest RMSE, MSE, and MAPE values compared with the other regression methods. This is consistent with the results of the previous studies by Ulya et al.16,26\n\nMLPR is a novel method for predicting the internal quality of fruits developed by Ulya et al.16,26 This study confirms that the MLPR method can produce a robust predictive model for determining the internal quality of mangoes; MLPR (nonparametric regression) has predictive performance with a lower MAPE value than that of the MPR (parametric regression).\n\nAmong the three regression methods, MLPR exhibited lower MAPE values in all treatment spectra. With the Gaussian filter spectra calibration and validation data, MLPR provided the highest R2 and lowest RMSE, MSE, and MAPE compared with the other methods, as shown in Figure 4. Even with the overall data, the R2, RMSE, MSE, and MAPE values were better for MLPR than the those of the other methods, which indicates that the MLPR method provides an accurate prediction of all spectral data with MAPE <10%36 and low RMSE values. The predictive performance of the MLPR model also had a high R2 (0.82–0.9), thus indicating good predictive ability.40\n\nKPLSR method performed the worst in predicting the pH of mangoes. Only a few studies have predicted fruit characteristics using the KPLSR. Most studies use PLSR because of its simplicity and small calculation volume. Partial Least Square (PLS) is a linear method of data analysis.41 Based on untreated spectra, Nicolaï et al.27 used KPLSR to predict apple sugar content.\n\nThe prediction of the sugar content of Gannan Navel oranges based on several treated spectra was reported by Liu,39 where KPLSR, particularly the spline PLS model, was superior to others with an R2 of 0.87, RMSE validation of 0.47 °Brix, and standard deviation ratio of 2.34. Kernel PLS is suitable for dealing with nonlinear phenomena; this may be owing to the changes in the chemical interactions of the fruit matrix because unripe and ripe fruits have different structures and varieties.42\n\nThe best regression method for predicting the TSS value of mangoes was MLPR, based on SG smoothing. The calibration, validation, and overall models of the MLPR method based on all spectral treatments have higher R2 values and lower RMSE, MSE, and MAPE values than the other methods. The MAPE value is higher than that of the pH prediction model, but the MAPE value is still less than 10%, thus categorizing the method as highly accurate in forecasting.36 Figure 5 shows the MLPR predictive performance based on SG smoothing. Previous research has shown that a small set of reference attributes and spectral behavior changes influenced by cultivar, fruit size, and fruit origin significantly impact model robustness.6,43,44 Moreover, the prediction performance was affected by the lack of variability in the calibration model. When validated by samples outside the prediction model range, the prediction model performance in a study investigating the total acid content of Japanese plums decreased.43 Subedi, Walsh, and Owens45 reported that a TSS prediction model developed from fruits at late stages of ripening failed to predict the TSS of fruits at earlier stages of ripening.\n\nThe best pre-treatment spectral data for predicting the TSS value was SG smoothing. Overall, MLPR with SG smoothing spectra was the best model, with an R2 value of 0.805, RMSE value of 0.436, MSE value of 0.192, and MAPE value of 6.454. This is in agreement with the findings36 that the SG smoothing spectral model for predicting the tannin content of persimmon fruit is better than MSC. The R2 values for SG smoothing and MSC were 0.107 and 0.016, respectively.29 In contrast to,28 the prediction of the mangoes’ TSS values using SVMR based on extended MSC gave an R2 validation of 0.86 and an RMSE of 0.66.\n\nGenerally, all spectral treatment and regression methods on the calibration model have an R2 value higher than that of the validation model, with a small gap between them; this indicates that the k-fold cross-validation method can balance the prediction results of the calibration and validation datasets. The k-fold cross-validation method can reduce bias in sampling.33 If the test matrix method is used, the R2 of the validation models would be less than the R2 of the calibration model. Louw and Theron43 reported that the prediction model's performance for the total acid content of Japanese plums decreased when samples outside the prediction model range were validated.\n\n\nConclusions\n\nPrediction of the internal quality of mangoes, including pH and TSS, can be performed rapidly and non-destructively using NIR spectroscopy. Spectral pre-treatment, such as SG smoothing, GFS, and MSC, affects the ability of the prediction model to use KPLSR, SVMR, and MLPR. The best regression model for pH prediction is MLPR based on a GFS spectra. In addition, KPLSR, SVMR, and MLPR based on raw spectra, SG smoothing, and MSC also provided highly accurate prediction performance, with MAPE values of less than 10%, low MSE and RMSE, and high R2.\n\nThe best regression model for TSS prediction was MLPR based on SG smoothing. In addition, KPLSR, SVMR, and MLPR based on raw spectra, GFS, and MSC also provided highly accurate prediction performance, with MAPE values of less than 10%, low MSE and RMSE, and high R2. We believe that NIR spectroscopy can be used to determine the internal quality of mangoes. However, further research is required to improve the prediction model performance of TSS values using MLPR based on a combination of several pre-treatment spectra. In conclusion, NIR spectroscopy combined with nonparametric regression MLPR could become a rapid and non-destructive alternative method for predicting the internal quality of mangoes.",
"appendix": "Data availability\n\nOpen Science Framework: dataset avomango, https://doi.org/10.17605/OSF.IO/YMS7F. 46\n\nThis project contains the following underlying data:\n\n- datasets of 186 mangos Gadung Klonal 21.xlsx\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 Directorate General of Indonesian Higher Education, Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia, for funding this research through the BPPDN Scholarship 2019.\n\n\nReferences\n\nKarsinah, Rebin: Tasliah Varietas Unggul Mangga Gadung 21: Daging Buah Tebal, Berserat Rendah, Rasa Manis. Iptek Hortik. 2017; 13: 39–44.\n\nMir SA, Shah MA, Mir MM: Postharvest Biology and Technology of Temperate Fruits.2018. 9783319768434.\n\nSohaib ASS, Zeb A, Qureshi WS, et al.: Towards Fruit Maturity Estimation Using NIR Spectroscopy. Infrared Phys. Technol. 2020; 111: 103479. Publisher Full Text\n\nJie D, Xie L, Rao X, et al.: Using Visible and near Infrared Diffuse Transmittance Technique to Predict Soluble Solids Content of Watermelon in an On-Line Detection System. Postharvest Biol. Technol. 2014; 90: 1–6. Publisher Full Text\n\nSari HP, Purwanto YA, Budiastra IW: Prediction of Chemical Contents in ‘Gedong Gincu’ Mango Using near Infrared Spectroscopy. J. Agritech. 2016; 36: 294. Publisher Full Text\n\nNicolaï BM, Beullens K, Bobelyn E, et al.: Nondestructive Measurement of Fruit and Vegetable Quality by Means of NIR Spectroscopy: A Review. Postharvest Biol. Technol. 2007; 46: 99–118. Publisher Full Text\n\nJha SN, Chopra S, Kingsly ARP: Modeling of Color Values for Nondestructive Evaluation of Maturity of Mango. J. Food Eng. 2007; 78: 22–26. Publisher Full Text\n\nJha SN, Jaiswal P, Narsaiah K, et al.: Non-Destructive Prediction of Sweetness of Intact Mango Using near Infrared Spectroscopy. Sci. Hortic. (Amsterdam). 2012; 138: 171–175. Publisher Full Text\n\nJha SN, Narsaiah K, Jaiswal P, et al.: Nondestructive Prediction of Maturity of Mango Using near Infrared Spectroscopy. J. Food Eng. 2014; 124: 152–157. Publisher Full Text\n\nWatanawan C, Wasusri T, Srilaong V, et al.: Near Infrared Spectroscopic Evaluation of Fruit Maturity and Quality of Export Thai Mango (Mangifera Indica L. Var. Namdokmai). Int. Food Res. J. 2014; 21: 1073–1078.\n\nSchulze K, Nagle M, Spreer W, et al.: Development and Assessment of Different Modeling Approaches for Size-Mass Estimation of Mango Fruits (Mangifera Indica L., Cv.’Nam Dokmai’). Comput. Electron. Agric. 2015; 114: 269–276. Publisher Full Text\n\nRungpichayapichet P, Mahayothee B, Nagle M, et al.: Robust NIRS Models for Non-Destructive Prediction of Postharvest Fruit Ripeness and Quality in Mango. Postharvest Biol. Technol. 2016; 111: 31–40. Publisher Full Text\n\nAgussabti, Rahmaddiansyah, Satriyo P, et al.: Data Analysis on near Infrared Spectroscopy as a Part of Technology Adoption for Cocoa Farmer in Aceh Province, Indonesia. Data Br. 2020; 29: 105251. PubMed Abstract | Publisher Full Text | Free Full Text\n\nValipour M, Banihabib ME, Behbahani SMR: Monthly Inflow Forecasting Using Autoregressive Artificial Neural Network. J. Appl. Sci. 2012; 12: 2139–2147. Publisher Full Text\n\nAnderson NT, Walsh KB, Flynn JR, et al.: Achieving Robustness across Season, Location and Cultivar for a NIRS Model for Intact Mango Fruit Dry Matter Content. II. Local PLS and Nonlinear Models. Postharvest Biol. Technol. 2021; 171: 111358. Publisher Full Text\n\nUlya M, Chamidah N, Saifudin T: Predicting the Sweetness Level of Avomango (Gadung Klonal 21) Using Multi-Predictor Local Polynomial Regression. IOP Conf. Ser. Earth Environ. Sci. 2021; 733: 012009. Publisher Full Text\n\nChamidah N, Lestari B: Estimation of Covariance Matrix Using Multi-Response Local Polynomial Estimator for Designing Children Growth Charts: A Theoretically Discussion. J. Phys. Conf. Ser. 2019; 1397: 012072. Publisher Full Text\n\nDerkacheva A, Mouginot J, Millan R, et al.: Data Reduction Using Statistical and Regression Approaches for Ice Velocity Derived by Landsat-8, Sentinel-1 and Sentinel-2. Remote Sens. 2020; 12: 1–21. Publisher Full Text\n\nIslamiyati A, Chamidah N: Ability of Covariance Matrix in Bi-Response Multi-Prredictor Penalized Spline Model Through Longitudinal Data Simulation.2019; 3: 8–11.\n\nAdiwati T, Chamidah N: Modelling of Hypertension Risk Factors Using Penalized Spline to Prevent Hypertension in Indonesia. IOP Conf. Ser. Mater. Sci. Eng. 2019; 546: 052003. Publisher Full Text\n\nRamadan W, Chamidah N, Zaman B, et al.: Standard Growth Chart of Weight for Height to Determine Wasting Nutritional Status in East Java Based on Semiparametric Least Square Spline Estimator. IOP Conf. Ser. Mater. Sci. Eng. 2019; 546: 052063. Publisher Full Text\n\nLestari B, Fatmawati, Budiantara IN, et al.: Estimation of Regression Function in Multi-Response Nonparametric Regression Model Using Smoothing Spline and Kernel Estimators. J. Phys. Conf. Ser. 2018; 1097: 012091. Publisher Full Text\n\nHidayati L, Chamidah N, Nyoman Budiantara I: Spline Truncated Estimator in Multiresponse Semiparametric Regression Model for Computer Based National Exam in West Nusa Tenggara. IOP Conf. Ser. Mater. Sci. Eng. 2019; 546: 052029. Publisher Full Text\n\nGeorge J, Janaki L, Parameswaran Gomathy J: Statistical Downscaling Using Local Polynomial Regression for Rainfall Predictions – A Case Study. Water Resour. Manag. 2015; 30: 183–193. Publisher Full Text\n\nBlock P, Goddard L: Statistical and Dynamical Climate Predictions to Guide Water Resources in Ethiopia. J. Water Resour. Plan. Manag. 2012; 138: 287–298. Publisher Full Text\n\nUlya M, Chamidah N: Multi-Predictor Local Polynomial Regression for Predicting the Acidity Level of Avomango (Gadung Klonal 21). AIP Conf. Proc. 2021; 2329. Published. Publisher Full Text\n\nNicolaï BM, Theron KI, Lammertyn J: Kernel PLS Regression on Wavelet Transformed NIR Spectra for Prediction of Sugar Content of Apple. Chemom. Intell. Lab. Syst. 2007; 85: 243–252. Publisher Full Text\n\nAl-Sanabani DGA, Solihin MI, Pui LP, et al.: Development of Non-Destructive Mango Assessment Using Handheld Spectroscopy and Machine Learning Regression. J. Phys. Conf. Ser. 2019; 1367: 012030. Publisher Full Text\n\nCortés V, Rodríguez A, Blasco J, et al.: Prediction of the Level of Astringency in Persimmon Using Visible and Near-Infrared Spectroscopy. J. Food Eng. 2017; 204: 27–37. Publisher Full Text\n\nLuo J, Ying K, Bai J: Savitzky-Golay Smoothing and Differentiation Filter for Even Number Data. Signal Process. 2005; 85: 1429–1434. Publisher Full Text\n\nHastie T, Tibshirani R: Generalized Additive Models. Chapman & Hall; 1990. 9781351445962.\n\nAriyanto RA, Chamidah N: Sentiment Analysis for Zoning System Admission Policy Using Support Vector Machine and Naive Bayes Methods. J. Phys. Conf. Ser. 2021; 1776: 012058. Publisher Full Text\n\nArdhani BA, Chamidah N, Saifudin T: Sentiment Analysis Towards Kartu Prakerja Using Text Mining with Support Vector Machine and Radial Basis Function Kernel. J. Inf. Syst. Eng. Bus. Intell. 2021; 7: 119. Publisher Full Text\n\nAsrol M, Papilo P, Gunawan FE: Support Vector Machine with K-Fold Validation to Improve the Industry’s Sustainability Performance Classification. Procedia Comput. Sci. 2021; 179: 854–862. Publisher Full Text\n\nRen L, Glasure Y: Applicability of the Revised Mean Absolute Percentage Errors (MAPE) Approach to Some Popular Normal and Non-Normal Independent Time Series. Int. Adv. Econ. Res. 2009; 15: 409–420. Publisher Full Text\n\nMoreno JJM, Palmer Pol A, Sesé Abad A, et al.: El Índice R-MAPE Como Medida Resistente Del Ajuste En La Previsiońn. Psicothema. 2013; 25: 500–506. Publisher Full Text\n\nAkhlaghi YG, Ma X, Zhao X, et al.: A Statistical Model for Dew Point Air Cooler Based on the Multiple Polynomial Regression Approach. Energy. 2019; 181: 868–881. Publisher Full Text\n\nMagwaza LS, Opara UL, Nieuwoudt H, et al.: NIR Spectroscopy Applications for Internal and External Quality Analysis of Citrus Fruit-A Review. Food Bioprocess Technol. 2012; 5: 425–444. Publisher Full Text\n\nXie L, Ye X, Liu D, et al.: Prediction of Titratable Acidity, Malic Acid, and Citric Acid in Bayberry Fruit by near-Infrared Spectroscopy. Food Res. Int. 2011; 44: 2198–2204. Publisher Full Text\n\nWilliams P, Antoniszyn J, Manley M: Near Infrared Technology: Getting the Best out of Light. USA: Sun Press; 2019. 9781928480303.\n\nLiu Y, Sun X, Zhou J, et al.: Linear and Nonlinear Multivariate Regressions for Determination Sugar Content of Intact Gannan Navel Orange by Vis-NIR Diffuse Reflectance Spectroscopy. Math. Comput. Model. 2010; 51: 1438–1443. Publisher Full Text\n\nChauchard F, Cogdill R, Roussel S, et al.: Application of LS-SVM to Non-Linear Phenomena in NIR Spectroscopy: Development of a Robust and Portable Sensor for Acidity Prediction in Grapes. Chemom. Intell. Lab. Syst. 2004; 71: 141–150. Publisher Full Text\n\nLouw ED, Theron KI: Robust Prediction Models for Quality Parameters in Japanese Plums (Prunus Salicina L.) Using NIR Spectroscopy. Postharvest Biol. Technol. 2010; 58: 176–184. Publisher Full Text\n\nPeirs A, Tirry J, Verlinden B, et al.: Effect of Biological Variability on the Robustness of NIR Models for Soluble Solids Content of Apples. Postharvest Biol. Technol. 2003; 28: 269–280. Publisher Full Text\n\nSubedi PP, Walsh KB, Owens G: Prediction of Mango Eating Quality at Harvest Using Short-Wave near Infrared Spectrometry. Postharvest Biol. Technol. 2007; 43: 326–334. Publisher Full Text\n\nUlya M: dataset avomango. [dataset]. 2023, February 10. Publisher Full Text"
}
|
[
{
"id": "193780",
"date": "24 Aug 2023",
"name": "Kim Seng Chia",
"expertise": [
"Reviewer Expertise Machine Learning",
"Transfer Learning",
"Near Infrared Spectroscopy",
"Real-time Embedded System"
],
"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\nTitle: Mango quality prediction based on near-infrared spectroscopy using multi-predictor local polynomial regression modeling\n\nSummary of the study: This study shows that the use of nonparametric regression (i.e. multi-predictor local polynomial regression (MLPR)) outperformed kernel partial least square regression (KPLSR) and support vector machine regression (SVMR) in predicting the pH and total soluble solids (TSS) of \"Gadung Klonal 21\" mango fruits, which maturity stages cannot be visually classified as stated the introduction section - paragraph 3. 165 mangoes (three different maturity) were used (excluding 21 outliers) that appears sufficient to build the MLRP, KPLSR, and SVMR. 5-fold cross-validation was used to evaluate the performance of regression models.\nComments with respect to the questions (bolded) are as follows.\n1. Is the work clearly and accurately presented and does it cite the current literature?\n- No reference from 2023 and 2022 is cited and discussed. Authors shall discuss more related recent works (2019-2023) in the manuscript too. Suggestion: more than 50% of the cited works shall be published in last five years. Current manuscript only cited literature that published in 2021 (6 works), 2020 (3 works), 2019 (9 works), and other years (28 works).\n\n2. Is the study design appropriate and is the work technically sound?\n- Figure 3 suggests that only MSC was able to remove unwanted baseline/offset effects. This is questionable about why models with smoothing (that consisted of unwanted baseline shift effects) can outperform models with MSC preprocessing method. (p/s: please define the full name of MSC for its first use). Suggestion: author may try to use SG smoothing + MSC as Figure 3 (d) suggests that the spectra shall be smoothed first prior MSC.\n\n3. Are sufficient details of methods and analysis provided to allow replication by others?\nFour comments are as follows.\n(i) A figure to illustrate the actual spectral data acquisition setup shall be provided with details of the distances among sample, light source and spectrometer.\n(ii) From the manuscript, \"The following steps were to perform dimension reduction using principal component analysis (PCA), ...\" Why PCA was involved in this study? The use of PCA prior to KPLSR is not make sense as PLS does not need additional dimension reduction method to reduce dimension in general. Nevertheless, in the results section, PCA was used for outlier detection. Authors shall revise the description to avoid confusing.\n(iii) How were the data split during cross-validation (section Model evaluation)?\n\n(iv) Figure 4 and 5 are confusing. As cross-validation was used, authors shall provide performance of all folds instead of fold 4 and fold 1 in figure 4 and 5, respectively.\n\n4. If applicable, is the statistical analysis and its interpretation appropriate?\n- Table 1. Descriptive statistics shall detail the info for maturity stages - how many mangoes in each maturity stages and their descriptive statistics?\n\n5. Are all the source data underlying the results available to ensure full reproducibility?\n- Reproducibility concern: \"In this study, 21 outliers were identified. These outliers were excluded because they could have a negative impact on the model.\" Authors shall explain more about why more than 10% of data were outliers and how to avoid/minimize them in the future.\n- Additionally, which data were the outliers shall be stated clearly as the provided open dataset includes the 21 outliers.\n6. Are the conclusions drawn adequately supported by the results?\nConclusion content - in future, authors might consider to evaluate the robustness of the models using samples across different seasons as testing datasets.\n7. Other comments:\n- Authors shall use RMSECV instead of RMSEV as cross-validation was used in this study.\n- Figure 1 - please use Validation instead of Testing to align with the text.\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? Yes",
"responses": []
},
{
"id": "210564",
"date": "09 Oct 2023",
"name": "Jens Petter Wold",
"expertise": [
"Reviewer Expertise My areas of expertise are within NIR spectroscopy",
"food science and data modeling"
],
"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 compares different regression and pre-processing techniques of NIR spectra from mango fruits, where the reference values are sugar (TSS) and pH. Unfortunately, this is not a proper scientific study.\nNo consideration has been made on how to obtain a best possible match between NIR spectra and the target features TSS and pH.\n\nInternal quality features of mango are attempted modeled with surface measurements on the skin of the mangos.\n\nThe NIR spectra shown are extremely noisy. It is not clear what kind of noise this is. It is not commented on by the authors. Furthermore, the spectra are not in any way explained to the reader, what do we see, what are absorption bands of interest?\n\nThere is no interpretation of regression vectors or spectral features whatsoever to explain the results or to make probable that they rely on sound relations. It means that the models could rely on completely other features than TSS and pH, for instance pigments.\n\nBased on a data set that the authors clearly do not understand well, they compare different regression models. It does not make much sense.\nThis is an article that is more misleading than informative, and it should not be published unless major improvements can be made.\nOther comments:\n\nThe work is not clearly presented, see comments below. The work cites some relevant literature in the introduction, but almost no discussion of the results is done in relation to previous reported work.\n\nThe design of the study is very limited in terms of samples. All samples are from the same garden giving very little relevant bio-variation in the sample set. It is well known that fruit from different gardens can exhibit slightly different NIR signals, so a bigger data set should be made, especially when the aim here is to compare regression methods. A completely independent test set should also be used.\n\nThe NIR spectra are presented maybe as absorption spectra turned upside down? The quality of the spectra is very poor with a lot of noise. The noise seems to increase with increasing absorption. What is wrong here? This very high level of noise would obscure the calibrations, since e.g the absorption bands of sugar are very small and the variation very subtle.\n\nIt is well known that TSS can be measured with NIR spectroscopy, but not pH. The authors should argue and explain why they can measure pH. Which spectral features does the model rely on?\n\nA figure of the NIR measurement set-up should be included. Also showing where the samples for references were taken from each mango.\n\nDescription of data analysis is confusing. 5-fold cross validation is used. Still, they show predicted vs. Measured plots of calibration set and validation set. This does not make sense. It must be clarified.\n\nThe number of components in the models are not listed, they give an impression of the complexity of the models.\n\nThe differences in performance between the regression methods are small. A significance test should be conducted, to indicate if the RMSECV values are significantly different between the methods.\n\nMany outliers are taken out of the data set based purely on statistics. This is normally not acceptable. There must be a good reason for removing an outlier. E.g. that the measurement was done in a wrong way.\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": []
}
] | 1
|
https://f1000research.com/articles/12-656
|
https://f1000research.com/articles/12-75/v1
|
19 Jan 23
|
{
"type": "Research Article",
"title": "A cross-sectional study on exploring the antecedents of patient’s revisit intention: Mediating role of trust in the hospital among patients in India",
"authors": [
"Nahima Akthar",
"Smitha Nayak",
"Yogesh Pai P",
"Nahima Akthar",
"Yogesh Pai P"
],
"abstract": "Background: In the healthcare domain, patients’ trust in the hospital plays an instrumental role in determining the behavioral intention of the patient. This article attempts to investigate the impact of service quality perception on behavioral intention with the mediating effect of trust in the hospital and patient satisfaction. Methods: This research was carried out in multispecialty hospitals located in Bangalore Urban and Mysore districts of Karnataka during August 2021. This was a questionnaire-based study and the sample size was 242. Statistical Package for the Social Science (SPSS) 27.0 and SmartPLS 3.0 software was used to analyze the data. Results: The findings revealed that perceived service quality significantly influences trust through patient satisfaction (observed partial mediation) and patient satisfaction significantly impacts behavioral intention through trust (observed partial mediation). Conclusion: This study empowers hospital managers to understand the factors influencing behavioral intention. Healthcare professionals must ensure that good quality service is delivered to enhance patient satisfaction and trust in adverse services, which influence behavioral intention among the patients.",
"keywords": [
"Healthcare",
"service quality",
"satisfaction",
"trust",
"revisit intention",
"structural equation modeling",
"adverse services"
],
"content": "Introduction\n\nThe service sector has a substantial influence on a country’s development and is increasingly driving economic transformation. The service sector accounted for approximately 55% of the gross domestic product (GDP) and 45% of employment in developing economies in 2019.1 The service sector constitutes diverse services like healthcare, banking, hospitality, consultancy, and entertainment, to name a few. In services like healthcare, customer undergoes stressful situation, in terms of treatment process etc., hence create an unpleasant experience for the customer.2,3 Healthcare service providers are leaving no stone unturned to create a positive servicescape to nurture an enabling environment for patients. Hence, service quality has attracted significant research and academic interest. Patient expectations for increasing levels of healthcare service quality are primarily triggered by rising healthcare demand and informed consumer decision-making.4–6\n\nResearchers have shown that healthcare services are evaluated based on service quality and medical efficacy.7–10 Service quality (SQ) is termed as the process of meeting consumers’ expectations by providing excellent services.11 Service quality evaluation helps to identify the unmet needs of the patients during the service encounter. In the healthcare landscape, SQ is crucial and it has a meaningful effect on patient satisfaction (PS).12–16\n\nPatients evaluate healthcare service quality based on their personal experiences, therefore a user-centered approach to healthcare delivery is critical for increasing overall patient satisfaction.4,17 Patients believe that the Health Care Organization (HCO) meets their expectations when they receive essential healthcare services, which results in a strong bond between the patients and the HCO.18 Patients’ perceptions of medical staff’s trustworthiness and the degree of satisfaction with the care they receive are directly related to each other. As a result, when patients require healthcare services again, they will seek the same facility and physician. Researchers have discovered that SQ is a precursor to PS, and satisfaction is an antecedent to trust.12,19\n\nWhen patients receive satisfactory medical care, they trust the hospital and return for future medical treatment.20–22 Patients shift to another hospital if the SQ of the hospital declines.4 Patients’ willingness to visit the hospital again for their treatment is referred to as “intent to revisit”.23 The effect of hospital SQ on PS and intent to return has been investigated by the researchers.24,25 Patients’ revisit intent and the services rendered by healthcare professionals are also studied in the past.16 This is in line with the service marketing literature, which reiterates the importance of trust in the service provider and trust in the brand of the service provider.26 The “Commitment-Trust Theory (CTT)” proposed by Morgan and Hunt (1994) has shown the relevance of trust and commitment in developing effective long-term partnerships in the service industry.27,28 Relationships are established on the foundation of mutual commitment in the services relationship marketing area.29 Customer commitment is defined as the customer’s long-term aim to create and maintain a connection with the supplier.30 Furthermore, commitment is a feature that has been widely identified in earlier studies as a key predictor of sustained usage. In addition, it was found that dedication had a considerable beneficial impact on consumers’ recommendations. Loyal consumers assume the role of company advocates by spreading favorable word of mouth and recommending the service to others.31\n\nIn the Jordanian setting, researchers have explored the association between perceived service quality (PSQ), PS, and trust in the service provider.12 They opined that trust in the service provider played an instrumental role in determining perceived service quality and patient satisfaction. The association of patients’ revisit intention has been researched with constructs like satisfaction, medical SQ, hospital brand image, assurance, and word-of-mouth.24,25,32 Researchers have explored the constructs such as PSQ, customer satisfaction, perceived value, brand trust, loyalty, and behavioral intention (BI) in various service sectors.33–36 However, literature on influencing BI through PSQ, PS, and trust in the hospital in the Indian context has received less attention. Therefore, this study proposes a conceptual framework and tests the relationship between the constructs in an attempt to bridge the gap. The objectives of the study are:\n\n• To investigate the mediating effect of patient satisfaction between perceived service quality and trust in the hospital\n\n• To examine the role of trust in mediating the relationship between patient satisfaction and behavioral intention\n\nThis research paper is structured as follows: First, a review of the literature and hypothesis development is explained. Secondly, the methodology adopted and results are presented. The report concludes with a discussion of the results, limitations, and useful implications, as well as recommendations for additional research.\n\n\nReview of Literature\n\nService quality (SQ) is regarded as a vital aspect of modern service firms.37 “SQ is the delivery of excellent or superior service relative to customer expectations”.11 “PSQ is defined as the consumer’s judgment about a product’s overall excellence or superiority”.38 In hospitals, SQ is appraised based on care provided by healthcare personnel, not only the technical aspect.6 Researchers have proposed that healthcare SQ acts as a mirror of PS.13 Also, SQ and consumer loyalty are strongly associated with each other.39,40 In addition, SQ is a key element to an effective consumer relationship.18,41\n\n“Satisfaction is defined as the consumer’s fulfillment response, a post-consumption judgment by the consumer that a service provides a pleasing level of consumption-related fulfillment including under or over fulfillment”.42 Like other services, customer or patient satisfaction is also considered to be a significant service outcome. PS is deliberated as one of the fundamental parameters of healthcare quality. Satisfaction among patients is a multi-dimensional concept.17 “PS is a patient’s sensation of joy or disappointment as a result of comparing a perceived service performance to his or her expectations”.43\n\nPS is a result of a patient’s experience of receiving medical services, and it displays a variety of functions concerning consumer relationships.17 Researchers have suggested that satisfaction is known as a global consumer response since it results from consumers’ pleasure levels.43 Healthcare professionals must ensure that they provide good quality services to meet patients’ anticipations thereby improving satisfaction. Therefore, hospitals must work consistently to meet their patient’s expectations.12,44\n\n“Trust is the client’s confidence that the service provider will fulfill his/her expectations by delivering what was promised explicitly and implicitly”.45 An organization must maintain customers’ trust, which will enhance competition and accomplishment of goals.46 A service provider is expected to work in favor of the patient when there is trust between them.47 “Trust is defined as a willingness to rely on an exchange partner in whom one has confidence”.48 Trust arises from faith and reliability. Hence, good relationships are developed and maintained.26 Positive behavioral intents are developed as a result of mutual trust among the partners. Trust inspires both parties to maintain the relationships.16,49 Through repeated encounters, trust is gradually created, and these interactions influence customers’ revisit intention.50\n\n“Patient trust is defined as patient’s belief that their doctors would act in their best interests and offer proper treatment and medical care”.51 Researchers have suggested that trust is essential since it serves as a foundation for upcoming associations. Patients usually evaluate the services provided by the healthcare professionals which leads to trust in the hospital brand.30,52 Customers revisit the service entity when they trust that service brand, which results in increasing the profit.52 Researchers have observed that building trust in the healthcare brand is very essential for selecting a hospital for treatment and continuing the treatment with the same hospital.16,53\n\n“BI can be defined as the likelihood that an individual will take part in a particular behavior and represents the level of effort that an individual is willing to make to secure a specific behavior”.54 BI concerns the hospital talks about the preparedness of patients to come back to the same hospital for their treatment. Retaining a client is very essential for the long-standing achievement of any service provider.25 Researchers have proposed that if a service is evaluated positively, then the desired BI of the client build up liaison with the provider. BI is divided into desirable and undesirable intentions. Clients with desirable BI think optimistically about the provider and recommend it to others.55\n\nThe key elements of BI are “SQ”, “customer satisfaction”, “perceived value”, and “customer loyalty”.56 Past research shows that client behavior is critical to the profitability and long-term viability of any service business.57 Customer satisfaction results from service contact having a direct impact on consumer behavior. Satisfied customers are more likely to experience positive behavior and stick to the same service provider. Client pleasure not only increases the company’s relationship with its customers but also aids in customer retention.58,59\n\n“Satisfaction is defined as an assessment of service experience, either specific or global, influenced by SQ among other factors”.60 The relationship between SQ and customer satisfaction (CS) is well-established by researchers from various sectors.24,61,62 Researchers view SQ as a precursor of CS.37,62,63 In HCO, the relationship between healthcare quality and PS is significant.25,43,63 When patients’ necessities and anticipations are equal to the quality services of the hospital, the patient will be satisfied.64,65 A linear liaison between SQ and PS (increased satisfaction level) is observed when the SQ is at a higher level.13,25 Hence, it is expected that there is a significant association between PSQ and PS.\n\nHI: PSQ is significantly related to PS.\n\nPatient satisfaction serves as a key factor when evaluating the quality of healthcare services.7,25,44 Based on an assessment of their impression and service outcome expectations, customers are either satisfied or dissatisfied.66 PS is a multi-faceted aspect of the healthcare industry that has an impact on patient trust.12,43 Trust is denoted as a key factor in any relationship. It is crucial since it is the most important part of any exchange connection.53,67\n\nAccording to past research, CS is critical for building customer trust and loyalty.45,68 Researchers have witnessed that satisfaction is a precursor of trust.69,70 Scholars have revealed that CS and trust play a crucial role in service sectors like tourism,45 retail,71 and public services.66 Trust can be developed over some time, based on CS.19,72 Customer trust is regarded as a crucial construct concerning satisfaction in marketing and consumer behavior research.21 Therefore, we propose that PS has a significant positive influence on trust in the hospital.\n\nH2: PS is positively related to trust in the hospital.\n\nPS results from healthcare SQ which leads to trust in the hospital. PS is a processing feature of trust.12 Perceived quality has a large and beneficial effect on consumer trust. SQ is a key precursor to customer trust.28,72 CS is a mediator in the relationship between SQ and consumer trust.12,19 Hence, we tend to establish that the liaison between PSQ and trust in the hospital is mediated by PS.\n\nH3: The link between PSQ and trust in the hospital is mediated by PS.\n\nThe effect of trust on BI has been exhaustively studied in the marketing literature.30,32,49,73 Customers’ BI can be developed and maintained with the use of trust.67,74 Trust and commitment are the main drivers of intent to return. Customers’ intentions to recommend the brand and make repeat purchases are also influenced by their degree of trust in the company.23\n\nIn service sectors, the association between brand trust and revisit intention is studied previously.75,76 Maintaining customer-provider relationships requires a high level of trust.16,49,74 Overall, past empirical research supports the idea that trust is important in the establishment of BI. The trust–BI relationship has received a lot of attention and support, especially in the context of the service sector.40,46 Hence, we propose that trust in the hospital significantly contributes to BI of the customer.\n\nH4: Trust in the hospital is positively related to BI.\n\nThe first research on healthcare trust concentrated on the interpersonal trust of the patient in their doctors.51 Scholars have investigated the impact of trust and assurance on “relationship marketing performance”.26 Trust has been studied as a mediator in other business entities.50,77,78 In a hospital, trust is important in the interaction between healthcare personnel and patients.16,79,80\n\nScholars have observed that a positive service evaluation (cognition response) has a favorable impact on patients’ trust in healthcare interactions.81 Trust has been established as a strong mediator among PSQ and intent to return to avail medical care.16 Patients’ perceptions of medical staff’s trustworthiness have an impact on their satisfaction level through the care they received. Studies have found that customers develop trust in the organization only if they are satisfied with the service provider.21,67 Hence, we tend to establish that the liaison between PS and BI is mediated by trust in the hospital.\n\nH5: The association between PS and BI is mediated by trust in the hospital.\n\nThe proposed conceptual framework (Figure 1) suggests that PSQ influences BI through PS and trust in the hospital.\n\n\nMethods\n\nThis research endeavor is quantitative by nature and has adopted a “cross-sectional research design”. The research philosophy deliberated in this study is “post-positivism”, which deals with the development of empirical approaches to interpret and study the behavior of people. This study explores the association between the independent, dependent, and mediating variables as proposed in the conceptual framework.\n\nThere is significant research evidence to indicate a strong relationship between human development index (HDI) and life satisfaction.82,83 Districts were ranked based on the HDI report of Karnataka state.84: 4 districts ranked high as per the HDI report namely, Bangalore Urban, Dakshina Kannada, Udupi, and Mysore. For this study, Bangalore Urban and Mysore Districts were selected through a simple random sampling approach. This research was undertaken in three multispecialty hospitals located in Bangalore Urban and one located in Mysore during 4th August 2021 to 26th August 2021.\n\nThe study comprised of patients within the 18-65 years of age group, who knew English or Kannada, and consulted the outpatient department at least two times. Medicine and medical specializations, as well as surgery and surgical specialties, were the outpatient departments (OPDs) studied. Pediatric and psychiatric OPDs were not included in the study.\n\nA structured questionnaire was used to gather the data. A copy of the questionnaire can be found in the Extended data.85 The survey included scales for assessing SQ perceptions,86,87 PS,42,88 trust,47 and BI.56 All the scales were scored on a “five-point Likert scale”. The questionnaire featured a total of 27 questions, 6 of which were about the participants’ demographics and 21 of which were about the study’s constructs. The questionnaire was developed in English and translated into the Kannada language in Microsoft Word 2013. The printed version of the questionnaire was utilized for data collection. Participation in the study was voluntary. The respondents were given a participant information sheet that explained the study’s purpose and procedures. After obtaining written agreement from the subjects, the investigator handed over the questionnaire to them. The research subjects were directed by the researcher to mark the right point on the questionnaire. The questionnaire was completed by all 242 participants; no partially completed questionnaires were acquired. The data were collected during 4th August 2021 to 26th August 2021.\n\nThis study adopted the purposive sampling method. A total of 242 respondents participated in this study. Respondents were contacted at the pharmacy, which was their last point of contact with the hospital for outpatient services.\n\nThe sample size was generated by multiplying the number of elements on the rating scale by ten89 i.e. 21*10 = 210. Considering 10% of the unanswered sample (i.e.21) gave rise to 231 (210+21=231). Finally, the researcher approached 242 participants to collect the data.\n\nThe preliminary analysis was performed using IBM SPSS statistics 27 (IBM SPSS Statistics, RRID: SCR_016479; Armonk, NY: IBM Corp). The frequency distribution of the demographic variables has been presented in the result section. SmartPLS 3 (smartPLS, RRID: SCR_022040) was used to test the proposed hypotheses and perform the mediation analysis. Partial least squares-structural equation modeling (PLS-SEM) was used to test linear and additive models. PLS-SEM is becoming more popular in healthcare research, as it is a suitable and reliable tool for analyzing composite models in empirical studies.90 In the following sections, the results are presented in the form of figures and tables.\n\nThe ethical approval (IEC: 868/2020) was granted by “The Institutional Ethics Committee (IEC) of Kasturba Medical College and Kasturba Hospital, Manipal”. The data were kept completely undisclosed and no participant identifiers are used.\n\nFinally, a pretest of the questionnaire was conducted on a sample of 47 outpatients in the Udupi area before the actual survey. There were no reported misconceptions or difficulties with the questions. The constructs had Cronbach’s alpha values of >0.7, specifying good levels of internal consistency such as BI (0.891), trust (0.875), PS (0.862), and PSQ (0.756). A main components analysis of the data was used to get a preliminary indication of construct validity. All factor loadings and communalities were considerably over 0.50, and “Kaiser–Meyer–Olkin and Bartlett’s test” was significant and >0.80.\n\n\nResults\n\nThe frequencies and percentages of the demographic variables were estimated using the software SPSS version 27 and the output is presented in Tables 1 & 2. The complete dataset is found in the Underlying data.85\n\nThe structural model evaluation is represented below (Figure 2).\n\nThe reliability and validity of constructs were investigated using outer loadings, composite reliability, average variance extracted (AVE), and variance inflated factor (VIF).89 The output is presented in the table below (Table 3). Composite reliability was used to examine the internal consistency reliability of constructs.91 The composite reliability of all the constructs is above the threshold value. In PLS, the indicators were placed in order based on their reliability. Cronbach’s alpha implies that all indications are equally reliable. Cronbach’s alpha value of all the constructs was above 0.7.92 AVE numbers were used to quantify convergent validity, which is the ability of a latent concept to elucidate a large portion of the variance in its indicators. The constructs’ AVEs were well above the threshold value of 0.5.93\n\n*** p<0.01,\n\n** <0.05,\n\n* p<0.1.\n\nThe guiding principle of VIF is considered to test the collinearity among the constructs.89 All the constructs exhibited VIF lesser than 5. This explains that there is no problem with collinearity in the structural model. Table 4, given below, demonstrates the VIF values that this study obtained while we tested the collinearity among independent variables against their respective endogenous constructs. The VIF values of this study were obtained when the collinearity was tested among all the constructs of the inner model of this study. The process of data analysis began with the objective to find out the probability of the presence of collinearity among exogenous constructs. No collinearity was found among the exogenous constructs of this study.\n\nTable 5 given below shows the VIF values of this study obtained when the collinearity was tested among all the indicators of the outer model of this study.\n\nAs the above tables demonstrate, there are no collinearity issues in the structural model of this research endeavor. Thus, there is no multicollinearity among either the constructs of the study (inner model) or indicators of the study (outer model). Multicollinearity is not an issue by the criterion VIF < 5.89\n\nCross-loadings (CL) of indicators constitute an additional method of assessing discriminant validity (DV). The outer loadings of indicators are expected to be greater than their CL on other constructs.89 The below-mentioned table (Table 6) demonstrates the presence of DV in the constructs of the study.\n\nAll exogenous latent variables’ effect sizes, f2, were estimated (Table 7). The magnitude of the variables’ influence is reflected by f2, regardless of the sample size.94 A strong effect is reported when the effect size exceeds 0.35; a moderate effect is given when the effect size is between 0.15 and 0.35, and a small influence is recorded when the effect size is less than 0.15 stated as a low effect. PSQ on PS (f2=2.375), PS on trust (f2=0.464), trust on BI (f2=0.352), and PS on BI (f2=0.368) are assessed to have substantial effect sizes in this study. The value of the standard root mean square residual (SRMR) is used to measure model fitness. The threshold value of SRMR is <0.8.95 This model’s SRMR rating is 0.066, indicating that it fits the data well.\n\n*** p<0.01,\n\n** <0.05,\n\n* p<0.1.\n\nBlindfolding is a technique for reusing samples. It allows you to calculate the Q2 value,96,97 which is an evaluation criterion for the PLS path model’s cross-validated predictive significance. Q2 values greater than zero suggest that your data is well rebuilt and the model is predictive. The Q2 values of the dependent and mediating variables are presented in the table below (Table 7).\n\nThis research endeavor includes two mediations. First, the latent variable PS is a mediator amongst the latent variables PSQ and trust in the hospital (Figure 3). A partial mediation has been observed and it is presented in the table below (Table 8). Second, the latent variable ‘trust in hospital’ is a mediating variable between the latent variables PS and BI (Figure 4). A partial mediation has been observed and it is presented below (Table 9).\n\n*** p<0.01,\n\n** <0.05,\n\n* p<0.1.\n\n*** p<0.01,\n\n** <0.05,\n\n* p<0.1.\n\nIPMA allows investigators to look at an item’s importance as well as its performance. The goal of this analysis is to determine the overall influence of the preceding constructs (PSQ, PS, and trust) in predicting the endogenous construct (BI).89 The total effect determines the construct’s relevance, while the performance is determined by the mean value of their score (from 0 to 100).98\n\nIPMA’s findings are shown in Figure 5 and Table 10. PS outperforms the other exogenous constructs in terms of performance (80.815), according to analyses. Furthermore, PS has a total effect on BI of 0.759, which is quite strong. As a result, a unit increase in PS performance from 80.815 to 81.815 results in a performance gain in BI from 80.046 to 80.805. The exogenous construct PSQ has a total effect of 0.787 and a performance of 79.916. As a result, a one-unit improvement in PSQ from 79.916 to 80.916 would boost BI’s performance from 80.046 to 80.833. Similarly, the exogenous construct trust has a total effect of 0.469 and a performance of 78.581. As a result, a one-unit increase in trust from 78.581 to 79.581 would result in an increase in BI to 80.515. PS has a robust and significant influence on BI, followed by PSQ and trust. This has significant implications for healthcare practitioners.\n\nFigure 6 shows the performance of the exogenous constructs. PS is high on performance whereas trust in the hospital is low on performance.\n\n\nDiscussion\n\nIn this research endeavor, the researchers observed that PS and trust in the hospital play a vital role in developing BI. In adverse services, PSQ and PS support building trust in the hospital. When a patient trusts the hospital, he/she intends to visit the hospital again for their treatment. PSQ, PS, and trust in the hospital are explored as an antecedent to BI. This study concludes that patient who is satisfied with the healthcare services received will develop trust in that hospital and continues to visit the hospital for treatment in the future.\n\nIn this study, a partial mediation relationship is observed between PSQ and trust in the hospital. Also, there is a partial mediating relationship between PS and BI. This study consists of a conceptual framework; the hypotheses were proposed based on the literature review explaining the association between the constructs. The proposed model is empirically tested, and validity and reliability of the constructs were estimated. Hypotheses testing and mediation analysis were done. IPMA was done to estimate the performance of endogenous variables through the exogenous variables.\n\nThe objective of this paper is to investigate the influence of PSQ on BI through PS and trust in the hospital. This paper includes a conceptual framework and hypotheses. The first hypothesis was that PSQ and PS are significantly related to each other. This hypothesis is in line with the literature that shows a significant relationship between healthcare quality and PS.43 Secondly, researchers hypothesized that PS is positively related to trust. It was shown by researchers in the past that PS is a multi-dimensional element of the healthcare sector that influences patient trust.12,43 Past literature has shown that satisfaction is an antecedent of trust.70 Further, it was hypothesized that the association between PSQ and trust in the hospital is mediated by PS. PS results from healthcare SQ which in turn leads to trust. PS is a processing feature of trust.12 In the service sector, the influence of SQ on building trust will be through consumers’ satisfaction.72\n\nThe next hypothesis states that trust in the hospital is significantly associated with BI. Past studies have explored the relationship between trust and BI in the marketing domain.26,30,49,73 Past empirical research recommended that trust is essential to establish BI, especially in service sectors.46,75,76 Scholars have suggested that building trust in any institution results in repeat business.29 Last, the researchers hypothesized that trust in the hospital acts as a mediator between PS and BI. Scholars have observed that trust plays a mediating role in service entities.50,77,78 Trust is exhibited as a mediator between perceived quality and intent to visit for medical treatment.16 IPMA determines that the performance of the construct PS is higher than the other exogenous constructs concerning BI. Trust in the hospital is low on performance. Therefore, it is important to build trust in the hospital and enhance behavioral intent.\n\nThe findings of the study imply a few managerial implications that are mentioned here. This study suggests that service providers should obtain customer input on the services received. Service providers should deliver error-free services to ensure satisfaction. It also aids in matching and comprehending customer expectations. The staff’s readiness to serve the patients is demonstrated by their willingness to provide service without being asked. Measurement of healthcare service quality should include factors such as personnel technical experience, availability of additional amenities such as medical equipment, and availability of various types of drugs. Hospitals should give effective training to all employees including nurses, doctors, and general staff to improve their communication so that they can deliver excellent service to patients. In a hospital, it is important to deliver the services to the best, which improves PS. Medical professionals should be consumer-oriented and deliver high-quality services with a human touch. Along with the quality of services, maintaining a patient-provider relationship is also very essential. This relationship becomes the base of developing trust in the hospital. This trust then influences repeat visits which aid in profitability. Therefore, trust in the hospital plays a vital role in enhancing the BI of a patient.\n\n\nConclusion\n\nThis study provides several insights for healthcare organizations to develop BI by enhancing trust in the hospital. A hospital can assure the satisfaction of patients when good quality services are rendered by healthcare professionals. Satisfied patients develop trust in the hospital and this becomes the influencing factor of revisit intention. PS has a significant mediating effect between perceived service quality and trust in the hospital. Trust in the hospital has a significant mediating effect between PS and BI. Thus, we can conclude that improving PS and trust in the hospital is essential to having a positive intention to revisit the healthcare organization.\n\nUnlike other studies, this study also has a few limitations which pave the way for future researchers. First, this study was conducted in outpatient departments of multispecialty hospitals. Future researchers would do a comparative study including both inpatients and outpatients. Second, the hospitals were situated in higher HDI districts. Future researchers would consider lower as well as higher HDI districts and carry out a comparative study.",
"appendix": "Data availability\n\nFigshare: Underlying data: A Cross-sectional study on Exploring the Antecedents of Patient’s Revisit Intention: Mediating role of Trust in the Hospital among Patients in India https://doi.org/10.6084/m9.figshare.21505641. 85\n\nThis project contains the following underlying data:\n\n• Dataset.csv\n\nThis project contains the following extended data:\n\n• Questionnaire.docx\n\n\nReferences\n\nNoland M, Park D, Estrada GB: Developing the service sector as engine of growth for Asia: an overview. Asian Development Bank Economics Working Paper Series. 2012 Nov; (320). Publisher Full Text\n\nBerry LL, Bendapudi N: Health care: a fertile field for service research. Journal of service research. 2007 Nov; 10(2): 111–122. Publisher Full Text\n\nHellén K, Sääksjärvi M: Happy people manage better in adverse services. International Journal of Quality and Service Sciences. 2011 Oct 18; 3: 319–336. 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Publisher Full Text\n\nZeithaml VA, Berry LL, Parasuraman A: The behavioral consequences of service quality. Journal of marketing. 1996 Apr; 60(2): 31–46. Publisher Full Text\n\nRyu K, Lee HR, Kim WG: The influence of the quality of the physical environment, food, and service on restaurant image, customer perceived value, customer satisfaction, and behavioral intentions. International journal of contemporary hospitality management. 2012 Mar 2; 24: 200–223. Publisher Full Text\n\nLadhari R: Service quality, emotional satisfaction, and behavioural intentions: A study in the hotel industry. Managing Service Quality: An International Journal. 2009 May 15; 19: 308–331. Publisher Full Text\n\nDolnicar S, Coltman T, Sharma R: Do satisfied tourists really intend to come back? Three concerns with empirical studies of the link between satisfaction and behavioral intention. Journal of Travel Research. 2015 Mar; 54(2): 152–178. Publisher Full Text\n\nLoureiro SM, Kastenholz E: Corporate reputation, satisfaction, delight, and loyalty towards rural lodging units in Portugal. International Journal of Hospitality Management. 2011 Sep 1; 30(3): 575–583. Publisher Full Text\n\nLee WI, Chen CW, Chen TH, et al.: The relationship between consumer orientation, service value, medical care service quality and patient satisfaction: The case of a medical center in Southern Taiwan. African Journal of Business Management. 2010 Apr 30; 4(4): 448–458.\n\nPanjaitan H, Djunaedi D: Product advantage, customer relationship marketing, and service quality on customer satisfaction of Bank Syariah Mandiri in Surabaya. International Review of Management and Marketing. 2017; 7(4): 122.\n\nSuhartanto D, Helmi Ali M, Tan KH, et al.: Loyalty toward online food delivery service: the role of e-service quality and food quality. Journal of foodservice business research. 2019 Jan 2; 22(1): 81–97. Publisher Full Text\n\nSrivastava S, Prakash G: Internal Service Quality: Insights from Healthcare Sector. Journal of Health Management. 2019 Jun; 21(2): 294–312. Publisher Full Text\n\nChahal H, Kumari N: Development of multidimensional scale for healthcare service quality (HCSQ) in Indian context. Journal of Indian Business Research. 2010 Oct 12; 2: 230–255. Publisher Full Text\n\nMelián-Alzola L, Martín-Santana JD: Service quality in blood donation: satisfaction, trust and loyalty. Service Business. 2020 Mar; 14(1): 101–129. Publisher Full Text\n\nBadri M, Al Khaili M, Al Mansoori RL: Quality of service, expectation, satisfaction and trust in public institutions: the Abu Dhabi citizen satisfaction survey. Asian Journal of Political Science. 2015 Sep 2; 23(3): 420–447. Publisher Full Text\n\nChang CS, Chen SY, Lan YT: Service quality, trust, and patient satisfaction in interpersonal-based medical service encounters. BMC health services research. 2013 Dec; 13(1): 1–1. Publisher Full Text\n\nKantsperger R, Kunz WH: Consumer trust in service companies: a multiple mediating analysis. Managing Service Quality: An International Journal. 2010 Jan 26; 20: 4–25. Publisher Full Text\n\nRasheed FA, Abadi MF: Impact of service quality, trust and perceived value on customer loyalty in Malaysia services industries. Procedia-Social and Behavioral Sciences. 2014 Dec 31; 164: 298–304. Publisher Full Text\n\nMoreira AC, Silva PM: The trust-commitment challenge in service quality-loyalty relationships. International Journal of Health Care Quality Assurance. 2015 Apr 20; 28: 253–266. PubMed Abstract | Publisher Full Text\n\nFernández-Sabiote E, Román S: The multichannel customer’s service experience: building satisfaction and trust. Service Business. 2016 Jun; 10(2): 423–445. Publisher Full Text\n\nPrameka AS, Do BR, Rofiq A: How brand trust is influenced by perceived value and service quality: mediated by hotel customer satisfaction. APMBA (Asia Pacific Management and Business Application). 2017 Apr 3; 5(2): 73–88. Publisher Full Text\n\nZboja JJ, Voorhees CM: The impact of brand trust and satisfaction on retailer repurchase intentions. Journal of services marketing. 2006 Oct 1; 20: 381–390. Publisher Full Text\n\nChiu JL, Bool NC, Chiu CL: Challenges and factors influencing initial trust and behavioral intention to use mobile banking services in the Philippines. Asia Pacific Journal of Innovation and Entrepreneurship. 2017 Aug 7; 11: 246–278. Publisher Full Text\n\nLimbu YB, Wolf M, Lunsford D: Perceived ethics of online retailers and consumer behavioral intentions: The mediating roles of trust and attitude. Journal of Research in Interactive Marketing. 2012 Jun 1; 6: 133–154. Publisher Full Text\n\nJung NY, Kim S, Kim S: Influence of consumer attitude toward online brand community on revisit intention and brand trust. Journal of Retailing and Consumer Services. 2014 Jul 1; 21(4): 581–589. Publisher Full Text\n\nVedel B, Gabarret I: The role of trust as mediator between contract, information and knowledge within business incubators. International Journal of Entrepreneurship and Small Business. 2014; 23(4).\n\nYu Y, Choi Y: Corporate social responsibility and firm performance through the mediating effect of organizational trust in Chinese firms. Chinese Management Studies. 2014 Oct 28; 8: 577–592. Publisher Full Text\n\nJambulingam T, Kathuria R, Nevin JR: How fairness garners loyalty in the pharmaceutical supply chain: Role of trust in the wholesaler-pharmacy relationship. International journal of pharmaceutical and healthcare marketing. 2009 Nov 20; 3: 305–322. Publisher Full Text\n\nMoliner MA: Loyalty, perceived value and relationship quality in healthcare services. Journal of service management. 2009 Mar 13; 20: 76–97. Publisher Full Text\n\nda Silva TM , dos Santos CP : Consumer trust in high-consequence decisions: a study of medical services. International Journal of Pharmaceutical and Healthcare Marketing. 2013 Jun 21. Publisher Full Text\n\nLeigh A, Wolfers J: Happiness and the human development index: Australia is not a paradox. Australian Economic Review. 2006 Jun; 39(2): 176–184. Publisher Full Text\n\nHall J, Helliwell JF, Helliwell JF: Happiness and human development. Occasional Paper, Human Development Report Office.2014.a\n\nKarnataka Human Development Index Report - 2015 (English).Pdf.\n\nAkthar N, Nayak S, Pai PY: Figshare: Underlying data: A Cross-sectional study on Exploring the Antecedents of Patient’s Revisit Intention: Mediating role of Trust in the Hospital among Patients in India. F1000Res. 2022 Nov. Publisher Full Text\n\nParasuraman A, Zeithaml VA, Berry L: SERVQUAL: A multiple-item scale for measuring consumer perceptions of service quality.1988; 64(1): 12–40.\n\nBrady MK, Cronin JJ Jr: Some new thoughts on conceptualizing perceived service quality: a hierarchical approach. Journal of marketing. 2001 Jul; 65(3): 34–49. Publisher Full Text\n\nGreenfield TK, Attkisson CC: Steps toward a multifactorial satisfaction scale for primary care and mental health services. Evaluation and Program Planning. 1989 Jan 1; 12(3): 271–278. Publisher Full Text\n\nHair JF Jr, Hult GT, Ringle CM, et al.: A primer on partial least squares structural equation modeling (PLS-SEM). Sage publications;2nd ed2017.\n\nAvkiran NK: An in-depth discussion and illustration of partial least squares structural equation modeling in health care. Health care management science. 2018 Sep; 21(3): 401–408. PubMed Abstract | Publisher Full Text\n\nWerts CE, Linn RL, Jöreskog KG: Intraclass reliability estimates: Testing structural assumptions. Educational and Psychological measurement. 1974 Apr; 34(1): 25–33. Publisher Full Text\n\nWong KK: Partial least squares structural equation modeling (PLS-SEM) techniques using SmartPLS. Marketing Bulletin. 2013 Jan 1; 24(1): 1–32.\n\nBagozzi RP, Yi Y: On the evaluation of structural equation models. Journal of the academy of marketing science. 1988 Mar; 16(1): 74–94. Publisher Full Text\n\nCohen J: Set correlation and contingency tables. Applied psychological measurement. 1988 Dec; 12(4): 425–434. Publisher Full Text\n\nHu LT, Bentler PM: Fit indices in covariance structure modeling: Sensitivity to underparameterized model misspecification. Psychological methods. 1998 Dec; 3(4): 424–453. Publisher Full Text\n\nStone M: Cross-validatory choice and assessment of statistical predictions. Journal of the royal statistical society: Series B (Methodological). 1974 Jan; 36(2): 111–133.\n\nGeisser S: A predictive approach to the random effect model. Biometrika. 1974 Apr 1; 61(1): 101–107. Publisher Full Text\n\nHock C, Ringle CM, Sarstedt M: Management of multi-purpose stadiums: Importance and performance measurement of service interfaces. International journal of services technology and management. 2010 Jan 1; 14(2-3): 188–207. Publisher Full Text"
}
|
[
{
"id": "176087",
"date": "20 Jul 2023",
"name": "Prof. (Ad.) Dr. Supaprawat Siripipatthanakul",
"expertise": [
"Reviewer Expertise Management (Business",
"Education",
"Healthcare) & Behavioural Analytics"
],
"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 should include patient satisfaction as another mediator. Please consider adding new citations and references because all previous studies are from 1974–1998 and 2006–2019. There are no recent studies for the years 2020–2023. It is hard to say that sufficient details of methods are provided due to the research design, which is necessary to be more straightforward for sample size determination. It is better to explain a definite or indefinite population of hospital outpatients. The data is from three multispecialty hospitals in Bangalore Urban and one in Mysore from August 4th, 2021, to August 26th, 2021. It means that it is a definite population, and it is necessary to calculate it from a known population of three hospitals. However, the sample size was 242; still, previous studies must support this number. In this case, the researchers did not use sample size determination calculations from a definite population. The statistical analysis and its interpretation are acceptable. The conclusion should summarize how a strategic planner could improve each variable, especially perceived service quality, because the researchers do not show the questions. The limitations could not be explained in the present because the data was collected in 2021, but now it is 2023 as current, and the data was explained in 2021, not now. It is necessary to mention this in the limitations section.\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": "10001",
"date": "29 Nov 2023",
"name": "Nahima Akthar",
"role": "Author Response",
"response": "Dear Sir, Many thanks for the review. We are hereby enclosing our response to your queries. Patient Satisfaction as a mediator: The mediating role of “patient satisfaction” as a construct is explored and presented in the manuscript. PLS SEM software is used to assess the mediating effect and the output is presented in Figure 3 and Table 8. References: This manuscript was conceptualized, and data collection was completed in 2021. Data cleaning, analysis, and drafting of the manuscript were undertaken in 2022 and the final version was submitted to the journal on November 5th, 2022. Hence, we have relied on the published literature until 2021. Sample size determination: we have incorporated this in our manuscript. The reference was not presented, which had been incorporated now. The explanation for the same is presented below: PLS-SEM is the software adopted to undertake the analysis. This investigation used a purposive sampling approach (non-probability by nature), which was adopted due to the absence of a sampling frame. Data was collected from 231 respondents. When the PLS-SEM is used for data analysis, Avkiran (2018) suggests that the sample size is determined by multiplying the number of items on the rating scale by 10. Hence 21 ( number of items) * 10 = 210. In addition 10% error of margin therefore 231. Ref: Avkiran NK: An in-depth discussion and illustration of partial least squares structural equation modeling in health care. Health care management science. 2018 Sep;21(3):401–408. 28181112 10.1007/s10729-017-9393-7 Implications: emphasized in the manuscript Limitation: change incorporated in the manuscript Regards, Authors"
}
]
}
] | 1
|
https://f1000research.com/articles/12-75
|
https://f1000research.com/articles/13-192/v1
|
15 Mar 24
|
{
"type": "Opinion Article",
"title": "Improving in vivo assays in snake venom and antivenom research: A community discussion",
"authors": [
"Amy E Marriott",
"Nicholas R Casewell",
"Elliot Lilley",
"José-María Gutiérrez",
"Stuart Ainsworth",
"Amy E Marriott",
"Nicholas R Casewell",
"Elliot Lilley",
"José-María Gutiérrez"
],
"abstract": "On the 26th January 2023, a free to attend, ‘improving in vivo snake venom research: a community discussion’ meeting was held virtually. This webinar brought together researchers from around the world to discuss current neutralisation of venom lethality mouse assays that are used globally to assess the efficacy of therapies for snakebite envenoming. The assay’s strengths and weaknesses were highlighted, and we discussed what improvements could be made to refine and reduce animal testing, whilst supporting preclinical antivenom and drug discovery for snakebite envenoming. This report summarises the issues highlighted, the discussions held, with additional commentary on key perspectives provided by the authors.",
"keywords": [
"Preclinical assays",
"Lethality",
"3Rs",
"NAMs",
"Antivenom",
"Venom"
],
"content": "Introduction\n\nSnakebite envenoming is a Neglected Tropical Disease (NTD) that causes extensive mortality and morbidity worldwide.1,2 Antivenom is the therapy of choice for treating envenomings and, if available, it can be a lifesaving treatment. However, antivenom is an unusual therapy as it is not routinely required to undergo the same level of scrutiny to demonstrate clinical effectiveness (i.e., clinical trials), as is routine with nearly all other medicines.3 Instead, prediction of antivenom efficacy in humans, except for a very small minority of products, is inferred through murine preclinical testing. Since the landmark achievement of snakebite envenoming being reinstated as an NTD by the World Health Organization (WHO) in 2017, much attention has been rightly focused on improving antivenom access, availability, quality, and applicability. However, the actual methodology by which antivenoms are assessed preclinically has received little attention.\n\nThe World Health Organisation (WHO) endorsed neutralisation of lethality assay has been the foundation of preclinical antivenom efficacy testing for over 40 years. However, the assay’s noted scientific shortcomings,4–6 the ethical, and in many locations legal, obligation to implement the 3Rs (Replacement, Reduction and Refinement) in animal experimentation, and the progression of next generation envenoming therapies towards human clinical use,7–9 has highlighted the need to refine this model to embrace advances in research and meet modern scientific and ethical standards. Consequently, a meeting of stakeholders in snakebite envenoming was convened to discuss the modernisation and improvement of preclinical models. This meeting was held virtually on the 26th of January 2023 and was attended by over 100 representatives from academic institutions, international health agencies, animal welfare groups, antivenom manufacturers, clinicians, and policy makers. This article details the areas of discussion held on the day, with additional commentaries from the authors, and outlines recommended steps for improving preclinical testing of snakebite envenoming therapies in the future.\n\n\nThe history of in vivo testing for snakebite envenoming therapeutics\n\nAn overview of the history of the development of the neutralisation of lethality murine models was presented by José María Gutiérrez (Instituto Clodomiro Picado, [ICP]). The very first recorded neutralisation of envenoming experiments were performed independently by Albert Calmette and Vital Brazil Mineiro da Campanha, among others, in the early 20th century – this work pioneered the use of antisera as a treatment for snakebite envenoming. In a manner in which many researchers in the field today would be familiar with, both experimenters developed pre-incubation models of mixtures of venom and antivenom prior to administration via different routes in various animal species including mice, rabbits, and pigeons.10–20 Both Brazil and Calmette noted that different results were obtained in different animal species, and that different pathologies were observed following different routes of venom administration.21,22 By the end of the 1930’s, the use of mice became commonplace to assess the ability of antivenoms to neutralise venom induced lethality.23\n\nOne of the first attempts to establish a universal standard for refinement of such testing was described by J. Ispen in 1938.24 With further refinements being made by Christensen,25,26 it was found that by using intravenous (i.v.) injections of antivenom and venom mixtures in mice, it was possible to standardise preclinical testing outcomes by expressing venom neutralisation as the mg of venom neutralised per ml of serum (antivenom). However, Ispen’s method was not universally adopted due to its technical complexity. A survey of existing methods to assess antivenom potency was later published by Grasset,27 who highlighted the heterogeneity in implemented methodology at the time. The need for a universally consistent method for analysis of antivenom efficacy was recognised by the WHO, which held key meetings to discuss standardisation and control of antivenoms in 197028 and 1979,29 with the first globally standardised form of the assay described in 1981.30 An additional meeting was held in 2001,31 which paved the way for the eventual publication of the first detailed WHO Technical Report Series (TRS) regarding antivenom production and regulation in 2008 (TRS964, annex 2), with a revision in 2017 (TRS1004, annex 5), ‘WHO Guidelines for the production, control and regulation of snake antivenom immunoglobulins’.3,32\n\n\nThe model today\n\nThe standardised murine ‘neutralisation of venom lethality assay’ (also known as the median effective dose [ED50] assay) has become the global standard for examining the efficacy of existing and new envenoming therapies.3,5,30,33 The assay is listed as a requirement by many national regulatory agencies, and national pharmacopoeia, as proof of antivenom efficacy before a product is approved for clinical use. The assay, as described in the WHO guidelines,3 is performed by mixing a fixed dose of venom with varying doses of a therapeutic agent. This dose of venom is typically three to six times the median LD50 (median lethal dose - the dose which induces death in 50% of mice within a group), to ensure 100% death. The mixture is then incubated for 30 minutes at 37 °C prior to i.v. or intraperitoneal (i.p.) injection into mice. Survival of the mice after a specified interval of time (24 or 48 hours, depending on route of administration) are recorded, and statistical analysis performed (Probits or Spearman-Karber) to calculate the ED50 –– the quantity of therapy resulting in survival of 50% of the injected mice. The median effective dose can be expressed as mg venom per mL antivenom (the most common), μL antivenom per ‘challenge dose’ of venom, or μL antivenom per mg of venom. This ED50 is used to predict the clinical efficacy of an antivenom against the venom for which it is indicated. More recently, the WHO has recommended that ED50 data be converted to potency (P), a metric which estimates the dose for complete neutralisation of lethality, rather than the ED50.34\n\n\nThe success of the neutralisation of venom lethality assay\n\nThere are several advantages to the neutralisation of lethality assay that have led to its long-standing use. Firstly, it is extremely easy to perform, not requiring any specialist equipment or expertise. Secondly, it is a ‘one model fits all’ approach, providing outputs (dead/alive) on therapeutic efficacy for all snake venoms and antivenoms despite the great diversity in venoms and their pathological effects (i.e. haemotoxicity, neurotoxicity, cytotoxicity, etc), so it can easily be applied to any new venoms being evaluated, and can generate efficacy data quickly. The success of the model has enabled substantial achievements in the field of snakebite envenoming. These include supporting the production of new antivenoms, identifying appropriate antivenoms for regions, whilst also providing evidence for serious shortcomings in antivenom provision in many regions, including sub-Saharan Africa, India, South-East Asia, and Latin America,35–38 and showing the potential use of certain antivenoms against snake species for which specific antivenoms do not exist.39,40\n\n\nThe limitations of the neutralisation of lethality assay\n\nDespite its success, the neutralisation of lethality assay has largely remained unchanged since its standardisation in the early 1980s. Its basic methodology, in place since the early 20th century, has also remained unchanged, all the while scientific technological and societal expectations of animal research has progressed significantly.41–44 There are three key issues with the neutralisation of lethality assay in its current form which make it problematic for widespread use in the 21st century: ethical concerns, scientific validity, and regulatory concerns.\n\nThe ethical use of animals in scientific experimentation is not the focus of this discussion, and we point readers to interesting articles45–47 and resources (e.g., www.understandinganimalresearch.org.uk, www.animalfreeresearchuk.org, www.nc3rs.co.uk) regarding this fundamental topic. Here, we are going to assume an understanding of the use of animals for development and quality control of antivenoms where non-animal alternatives are not currently available, or appropriately validated. There are two key ethical issues relating to the neutralisation of lethality assay: the number of mice used, and the level of suffering experienced, both to be taken in context of the additional ethical concern of the ultimate translatability of the obtained data (see scientific validity, below).\n\nMice used in the neutralisation of lethality assay often experience extreme pain, distress, fear, pathology (e.g. breathing difficulties, bleeding, organ damage, paralysis, etc) or ultimately death – like human snakebite victims. Due to the length of the protocol, suffering is often prolonged (up to 24 to 48 hours) and is often without analgesia, with the added distress of mice being left alongside dead cage mates. It should be noted that prolonged suffering without amelioration is specifically forbidden in some jurisdictions (for example in the United Kingdom and European Union) and so researchers have been required to adapt the assay to comply with relevant legislation (see regulatory issues, below).\n\nThe level of suffering is further put into context when the numbers of mice undergoing this procedure are considered. The neutralisation of lethality assay consumes a significant number of animals in order to demonstrate the preclinical efficacy of an envenoming therapeutic. Typically, the assay consumes at least 5 experimental groups of 5 mice (25 mice/venom or venom/antivenom mixtures). The statistical analysis (Probits or Spearman-Kaber) requires at least one group in which all mice succumb to venom injections (an all-death group) and one group where all mice group survive, along with multiple groups with varying numbers of survivors and deaths to allow the calculation of an ED50 value. As antivenoms are often designed to treat envenoming caused by multiple snake species (known as polyspecific antivenoms), the assay needs repeating for each different venom for which the antivenom is indicated for. Thus, it is not uncommon to subject hundreds of mice to this procedure to assess the efficacy of a single batch of antivenom.33 A study in 2020 assessing the published preclinical efficacy of antivenoms for sub-Saharan Africa estimated a figure of 3,980 mice used in the neutralisation of lethality assay across 18 publications.33 It is likely that manufacturers are required to use multiples of this number each year to assure the quality and undertake batch release of their antivenom products.\n\nNicholas Caswell (LSTM) presented an overview of the scientific shortcomings of the current model, highlighting that the primary issue in terms of scientific validity with the neutralisation of lethality model is that, like other preclinical models, it is not reflective of the human scenario. The high failure rate (>90%) of potential therapeutics that enter clinical trials is in part due to this, alongside other factors including key differences between humans and the model species used, the use of flawed or non-clinically reflective preclinical models, which combined lead to a lack of translatability in efficacy and toxicity outcomes in clinical trials.48 These have been well documented over the years,49–53 and are all relevant to the current neutralisation of lethality assay, albeit have often not been as well evidenced, as snakebite envenoming therapies have thus far largely avoided these issues due to the unusual regulatory approval framework associated with their clinical use, whereby they often bypass clinical trials.\n\nTo delve deeper into the scientific validity of the model, it is important to discuss the nature of the clinical envenoming scenario, and how this differs from the existing pre-clinical scenario. Human snakebite envenoming typically involves intra-dermal (i.d.), subcutaneous (s.c.) or intra-muscular (i.m.) venom injection, with antivenom administered i.v. hours later in a hospital. The current model is a an artificial ‘best case scenario’, whereby an artificially large and above lethal quantity of venom and therapy are premixed and incubated before injection directly i.v. or i.p. There are several key points that make this problematic in terms of predicting the therapeutic efficacy of snakebite treatments:\n\n1) The current murine administration routes, which entails of a single bolus injection, results in an instantaneous (i.v.) or rapid (i.p.) concentration of toxins in the bloodstream, as opposed to a steadier, sustained release of toxins from the bite site in patients.54–56 As such, whilst providing a readout of the capacity of an antivenom’s ability to neutralise a fixed dose of venom, the assay does not consider the pharmacokinetic or pharmacodynamic properties of either the venom or the therapy being tested.57–59\n\n2) The high dose of venom administered (above lethal) typically rapidly overwhelm the model (i.e., cause lethality in minutes) and so the model is unable to mimic delays in therapy administration which always occur in human treatment.\n\n3) Whilst many snake venoms can cause lethality, some medically important venoms do not. An obvious and commonly cited example is that of cytotoxic African spitting cobra venoms.5,33 These rarely cause fatalities in humans, although they do cause substantial local effects, i.e., dermonecrosis.60,61 It is likely that neutralization of lethality observed in experiments using spitting cobra venom in mice is inferring the neutralisation of a venom component which has very limited clinical translation. This poses the ethical question of when this assay should be employed, and whether it is appropriate to use a lethality assay for certain venoms which rarely cause human fatalities. It further emphasises the need to adapt animal models that are better representative the clinical manifestations of snakebite envenoming, which may in turn identify more appropriate treatments.\n\nUltimately, due to the fundamental issues above, the neutralisation of lethality assay is not appropriate to use to perform extrapolations to human envenoming contexts. However, influential documents and policies, such as the WHO Target Product Profiles (TPP) and antivenom risk benefit assessments, have recommended such extrapolation to inform antivenom choice and dose (albeit in the absence of a more appropriate model in which to do this).34 This approach ultimately does not take into consideration the reality of complex pharmacokinetic and pharmacodynamic interactions of individual venom components and therapies in complex multi-tissue and organ environments – henceforth, the current model is too simplistic to make such important, accurate dose predictions. Moreover, differences in the susceptibility to venoms of rodents and humans also question the validity of such extrapolations.62,63 It is notable that the complexity of envenoming is used as a justification of mouse use, in addition to testing the ‘worst case scenario’ (death), but this is overlooked when considering dose regimes.\n\nClearly an antivenom which fails to neutralise venom in the best-case scenario of venom and therapy co-incubation and administration in the neutralisation of lethality assay is not going to be suitable for treating envenoming clinically. However, it is imperative to stress that if an antivenom appears effective in this assay, it does not mean that this efficacy will translate to the clinical scenario, likely due in part to the scientific limitations limited listed above. The issues with the assay’s scientific validity in the context of the severe welfare costs, makes the ethical justification of the model increasingly challenging by today’s standards.\n\nRegulatory issues consider both experimental animal use regulations and pharmaceutical approval legislation. There is a push from many national funding agencies towards greater scientific scrutiny and justification of animal usage, which is in direct conflict with antivenom manufacturers, many of which are bound by pharmacopoeia or national regulatory agency guidelines that specify the use of the existing murine model and the current WHO guidelines. This is further compounded by the development of new generations of envenoming therapeutics which will likely be required to enter through the traditional clinical regulation pathways, and thus will require much more rigorous preclinical in vivo testing and data generation.64\n\nAnimal experimentation regulation\n\nAnimal experiment regulation standards vary substantially across the globe, with different levels of stringency depending on legislations in particular jurisdictions.65 The neutralisation of lethality assay in its basic form, as outlined in the current WHO guidelines,3 can no longer be used in several regions without substantial modification or adaptation. Under the UK Animals in Scientific Procedures Act 1986, and the EU Directive 10/63/EU,66 it is a legal requirement that death as an experimental endpoint and long-lasting pain and suffering which cannot be ameliorated, must be avoided as far as possible. In scenarios where death is considered unavoidable, such as the neutralisation of lethality assay, as inferred by its name, experiments must be designed to limit death resulting from the experiments, and should strive to end suffering as soon as feasible through the implementation of humane endpoints and euthanasia. These requirements have resulted in researchers being legally required to implement various modifications and adaptions in order to comply with local regulations (see “improvements to the standard model”, below). This in turn is contributing to an ever-increasing divergence from the global harmonisation of the assay which the WHO guidelines attempts to achieve.33 As improvements in animal research techniques and welfare continue at pace across the medical health research field, the continued justification of using the neutralisation of lethality model to both regulatory authorities, and increasingly funders, will continue to become ever more challenging and its use ever more restrictive.\n\nPharmaceutical regulation\n\nA major reason for the lack of revision of the neutralisation of lethality assay are requirements by geographical or national regulatory agencies specifying the use of the assay for a product to be registered. Changing assays is a laborious and costly process which requires detailed validation, and thus is not performed without a compelling justification. Ultimately, antivenoms are overwhelmingly produced by small-medium companies or public entities with restrictive budgets which generally do not have the resource or expertise to investigate alternatives. Academics developing new therapies and scrutinising existing therapies ultimately want to use similar models to the manufacturers to assist with translation of findings, so are disincentivised to using alternative models.\n\nHowever, regulators and manufacturers are committed (and bound by relevant national legislation) to implementing the 3Rs, which many examples of improved methodology have been adopted by pharmacopoeias in the recent past, most notably for biologics.67,68 This is reflected by some antivenom manufacturers actively investigating alternative efficacy models, including in vitro and non-regulated in vivo modes, for product release due to the ethical challenges and costs associated with conventional ED50 testing. Examples include the ongoing development of an embryonated egg model for testing by Seqirus,69–71 and approval in recent years of antivenomics (immunoaffinity chromatography) techniques for product release by a national regulator,72 and as screening test for antivenom efficacy before proceeding into mouse assays.3\n\nRegulation of next generation envenoming therapies\n\nDiogo Martins and Alethea Cope (Wellcome) provided an insight from a regulatory perspective, and highlighted how antivenoms are an anomaly in the therapeutic development pipeline. The standard pathway for drug development is complex, expensive, and lengthy (generally 10-15 years in duration), and depends on lead discovery, preclinical testing, clinical trial phases followed by National Drug Agency review and approval. This process requires the provision of appropriate information packages and dossiers which ensure a high-quality product. Historically (and even currently), many antivenoms have not been required to undergo Phase I-III clinical trials, meaning that the typical therapeutic development pipeline is truncated, with national drug association/regulation approval often occurring after initial preclinical testing. As >90% of novel drugs progressing through the standard therapeutic development pipeline fail in human clinical trials, blamed in part to unsuitable preclinical models, it is perhaps unsurprising that there have been occurrences of suboptimal antivenoms reaching patients and providing to be ineffective.73,74 Until very recently, there has been an expanding consensus that antivenoms should undergo clinical trials,75 however, due to the cost of such trials and regulatory shortfalls, this consensus has started to wane, with some stakeholders now in favour of Monitored Emergency Use of Unregistered and Investigational Interventions (MEURI) assessments,76 instead.\n\nHowever, next generation envenoming therapies, such as small molecule inhibitors and monoclonal or recombinant antivenoms, which are under development as possible alternatives or adjuncts to conventional antivenom therapy in recent years, are highly unlikely to be able to enter the same regulatory pipeline as antivenom. These new therapeutic candidates will likely be subjected to appropriate full therapeutic development and regulatory pipelines, being required to proceed through preclinical and clinical assessment before approval.62,64\n\n\nImprovements to the standard model: Refinement and Reduction\n\nWith the above issues in mind, several refinements to the standard neutralisation of lethality assay have been developed in recent times.\n\nGabriela Solano (ICP) described two modifications to the model which have recently been implemented at the antivenom manufacturer ICP. The first refinement was the use of analgesia for all in vivo envenoming assays, including the neutralisation of lethality assay, which is now common practice not only at ICP but at LSTM, too. The WHO guidelines “strongly recommends” the use of analgesia to reduce pain and distress in mice, however, it is not described in the methodology, and anecdotally seems to not be implemented widely. The analgesic of choice at ICP is tramadol, while morphine is used routinely at LSTM, with the choice of drug being dependent on availability and accessibility in specific countries, and all mice pre-dosed subcutaneously (s.c.) 15 minutes prior to venom administration. Importantly, the use of analgesia has been validated in the context of experimental outcome, with the results demonstrating analgesia use proved effective at reducing pain scores in mice, without adversely affecting lethality or neutralisation data.21,77,78\n\nThe second refinement was focused on the study design of the neutralisation assays. The current WHO guidelines for the neutralisation of venom lethality assay outlines a 24-hour timeframe for pre-mixed i.v. injections, or a 48-hour timeframe for pre-mixed i.p. injections. ICP investigated whether this timeframe could be shortened, reducing the length of time in which mice are suffering the effects of venom. The reduction in time was evaluated by calculating the LD50 of venoms and ED50 of antivenoms at 6-, 24-, and 48-hours post injection using a wide variety of venoms and two poly-specific antivenoms. The results demonstrated a significant correlation between LD50 and ED50 values estimated at the three observation times, with the majority of deaths occurring within the initial 6-hour timeframe.79 Based on similar observations, LSTM have also been using a reduced 6-7 hour model for all envenoming and neutralisation studies for over a decade.36,80\n\nTo our knowledge, very limited attempts have been made to reduce the number of animals used, with justification inferred due to the statistical requirement of specified numbers for analysis. However, a modified version of the neutralisation assay which substantially reduces the number of mice required to infer efficacy of an antivenom has been attempted in recent years and was presented by George Omandi (K-SRIC). In a 2017 study, a ‘gold standard’ approach to the neutralisation of lethality assay was used, which involved examining the ability of test antivenoms to prevent lethality at half, equal or 2.5 x the volume of the current antivenoms which provide 100 % venom neutralisation and survival (2 x ED50 dose volume).37 This approach, whilst still requiring the conventional neutralisation of lethality assay to determine the ED50 of the two arbitrarily chosen gold standard antivenoms, enabled an analysis of the efficacy of four regionally marketed antivenoms vs. six regional venoms using 75 % fewer the number of mice which would be required if using the standard assay (150 vs. 600).37\n\n\nRescue models\n\nThe use of post-envenoming (‘rescue’ or ‘challenge then treat’) models have increased in frequency in recent years as the limitations of the standard neutralization of lethality model have become more apparent. These models involve an initial injection of venom followed by an independent, and often time delayed, administration of therapeutic – a scenario much more reflective of human snakebite envenoming. The assay allows venom and therapeutics to be administered via different routes, allowing for a range of pharmacokinetic properties to be mapped and a more accurate output of potential therapeutic efficacy. As mentioned above, these models are especially useful for assessing the preclinical efficacy of next generation therapeutics, and thus represent a refinement in terms of scientific validity.6 However, the current drawback to rescue models is that they often still rely on lethality (unless specifically testing using a localised model) and still require death as an endpoint for determining effectiveness, and may possibly induce a greater degree of suffering (due to administration of venom with therapy withheld for a period).\n\nFurthermore, large differences in drug neutralizing potential can be observed in pre-incubation and rescue models, as demonstrated by Christoffer Sørenson (DTU). He explained that a candidate anti-myotoxin mAb was effective in reducing myotoxicity when pre-incubated with a myotoxin or B. asper venom, but potentiated myotoxicity, when administered in a rescue model of envenoming. i.e., after venom injection.81 This demonstrates clearly how the current standard neutralization of lethality assay can overestimate therapeutic potential, which may possibly lead to failure during clinical trials, and the potential utility and importance of rescue models, which attempt to better recapitulate a clinical envenoming, albeit with limitations. Perhaps of most concern, is that conventional antivenoms have scarcely been used in such rescue models, thus no benchmark yet exists what efficacy looks like using conventional treatment. and such models do not yet follow a universal standardised approach. In summary, rescue models must be performed with analgesia and careful monitoring, alongside the development and application of humane endpoints to avoid death and limit suffering.\n\n\nWhat future in vivo models of envenoming could look like: ending the reliance on lethality testing\n\nAn example of a condition which has a similar capacity to make a mouse as comparatively rapidly critically unwell as snakebite envenoming is sepsis. Lethality was once a common readout in sepsis models but there is a general consensus within the field that this is unjustifiable, due to the binary live/dead readouts not being useful for determining the clinical potential of a therapy, and the harm:benefit assessment of such studies.42 Manasi Nandi (Kings College London) described how technological advances in imaging and cardiac monitoring, and the implementation of biomarkers, have been established which allow comprehensive analysis of the efficacy of interventions in sepsis before mice become critically ill and long before they reach lethality in such models, whilst highlighting the wealth of data that can be obtained as compared to a simple death/survival result.42,82–85 This example demonstrates that the identification of appropriate surrogate markers can allow for the implementation of humane endpoints in animal models, which would otherwise progress to death as an endpoint, whilst still meeting the scientific aims and objectives of the study.\n\nAs there are several parallels with the previous sepsis mouse models, a fundamental rethink, and harm:benefit assessment of the current neutralisation of lethality assay is required. Is it essential that we need to assess the ability of an antivenom to prevent lethality specifically, when in fact the key question is to evaluate an antivenom’s ability to neutralise or reverse envenoming pathology which may lead to lethality if left to run its course, and thus, is death really required as an endpoint? Could a refined model be explored, and biomarkers be implemented at earlier stages negating the need to run studies until death, as has been done with the refined sepsis models? For example, if in the neutralisation of lethality assay, in which therapy and venom are premixed, a neurotoxic venom causes limb paralysis in the presence of antivenom, is that not an informative readout of the inefficacy of a therapy? Is it ethical to then leave an animal under study to further deteriorate and suffer from limb paralysis to severe respiratory distress, to eventual death in order to demonstrate therapy failure? A similar argument can be made in the context of haemotoxic envenomings and whether early murine readouts such as coagulopathy must progress to systemic internal (and lethal) haemorrhage to be viewed as ‘useful’ readouts. The latter is particularly relevant when considering that of the few robust clinical trials and studies of antivenom efficacy performed to date; several have used measures of coagulopathy as study endpoints,86–88 and would incorporating such markers into preclinical studies improve the translatability to clinical testing? Equally, if an experimental animal survives the duration of the study but is critically unwell at experiment end, is it appropriate to consider a therapy effective, based on a simplistic binary outcome of alive or dead? Similar questions have been asked in other fields, such as do vaccines need to prevent lethality or simply illness?89 Such questions call for novel, data-rich, informative approaches to assess venom toxicity and therapeutic efficacy, and a review of current practices.\n\nDue to legal requirements under UK legislation, humane endpoints have been established by researchers at LSTM and implemented for over a decade during neutralisation of lethality studies.90 Humane endpoints are put in place to prevent and minimise pain and distress, and as a substitute for death. Death as an endpoint is now rarely accepted, and researchers must present conclusive evidence to support the use of such an endpoint, and are essential in studies where potential severe suffering, or death, may occur, such as acute toxicity studies, infectious disease models, or models of cancer or neurodegenerative diseases.91 The endpoints used at LSTM during neutralisation of lethality studies are implemented when mice are severely moribund (e.g. loss of righting reflex, seizure, signs of external haemorrhage, dyspnoea) and enable a reduction of the duration for which prolonged suffering occurs during experimentation. Although a refinement to the model in the context of expeditiously ending animal suffering, the use of such endpoints in this model has proved more contentious, and have not been implemented in other settings. The primary reasoning for this is the concern over the subjective nature of implementing endpoints, and the potential for inaccurate reporting of an antivenom’s efficacy, and the consequent potential negative impact on human envenoming outcomes due to lack of clinical trials. Although termed ‘humane endpoints’, there is also the argument to be made that leaving an animal until a moribund state cannot be regarded as ‘humane’, as animals will still have suffered severe pain and distress to reach this state.92 Thus, a global standardisation of humane endpoints would improve animal welfare substantially.\n\nIt is clear from multiple clinical studies that different venoms cause different pathologies. Lethality may ultimately be a common pathology of envenoming caused by many snake species, but it is a result of the different toxic effects induced by individual venoms, which in turn consist of multiple toxins. Like cancer, snakebite should not be viewed as a single disease, but as a series of diseases with distinct pathologies under an umbrella term. Indeed, a recently published clinical outcome set for future snakebite therapy clinical trials,88 and a document outlining TPPs for conventional antivenoms for use in sub-Saharan Africa,34 detail pathology specific measurements that should be used as outcomes in clinical trials (such as international normalised ratio (INR) for coagulopathy) and clinical thresholds antivenoms should meet (such as persistence of coagulopathy after a defined time frame). Currently, pathology specific preclinical assays, when available, are described as ‘supplementary’ and typically overlooked, but would be useful in providing readouts of efficacy as opposed to only a live-dead phenotype, and provide a more informative data set prior to progression into clinical trials (discussed below).\n\nTo develop more appropriate pathology specific models, it would therefore be sensible to encourage a closer cross-talk between colleagues working on both sides of the preclinical/clinical divide, to facilitate development of preclinical testing methodologies to better support the development of initiatives like TPPs and clinical trial outcome sets. Below we briefly describe examples of what better developed models that avoid lethality, but could better support future antivenom development and assessment, could look like.\n\nEchis spp. venoms: It is clear from clinical studies that the main effects induced by Echis venoms are haemorrhage and coagulopathy.86,93 Therefore, instead of using the neutralisation of lethality assay, an alternative approach would be to assess neutralisation of venom induced coagulopathy and haemorrhage. The WHO listed minimum venom defibrinogenating (coagulopathy marker) and haemorrhagic dose assays are one hour and 2-3 hours, respectively, in duration and involve using comparatively lower doses of venom compared to the neutralisation of venom lethality assay, thus resulting in lesser suffering in mice.3 Although these tests are typically conducted with preincubation of venom and antivenom, they can be easily adapted to a rescue model format where needed, with appropriate validation.\n\nBothrops spp. venoms: Clinical observations have shown that relevant effects of many Bothrops envenomings are haemorrhage, coagulopathy, and myonecrosis.94 Thus, the assessment of haemorrhage and coagulopathy, as described for Echis, could potentially be applied, while myonecrosis can also be assessed in vivo, by measuring the increase in plasma creatine kinase activity as a surrogate marker for myotoxicity.95 Although this test involves pain, the duration of study is reduced to 3 hours, and analgesia can be used to reduce pain.\n\nCytotoxic African Naja spp. venoms: Clinically these venoms induce cutaneous necrosis (dermonecrosis), while lethality is less frequent.60 As has been repeatedly stated over the years, the use of the neutralisation of lethality assay is arguably inappropriate in this case; however, it persists due to the current guidelines and regulations. Instead, neutralization of local dermonecrosis would be more relevant. Similarly, to the minimum venom defibrinogenating dose assay, pathology specific assays for necrosis do exist (the neutralization of venom necrotizing activity) but are problematic in that they are extremely painful and prolonged. To develop clinically relevant neutralisation of venom dermonecrosis activity, much could be learnt from preclinical models in related fields, such as those studying necrotizing soft tissue infections, burns and hypoxia. Likewise, dermonecrosis may be modelled with cytotoxicity assays in cell culture models or organotypic models of human skin.60 However, care must be taken in this approach, as recent research has suggested that cell culture models do not accurately recapitulate dermonecrosis.96\n\nDaboia spp. venoms: The pathophysiology of envenomings by Daboia spp. is highly complex as it involves, in addition to lethality, a variety of effects such as haemorrhage, shock, coagulopathy, acute kidney injury and systemic capillary leakage syndrome.97 In addition to the tests for defibrinogenation and haemorrhage mentioned above, the systemic capillary leakage syndrome can be followed by determining haematocrit,98 and kidney injury can be assessed by quantification of serum creatinine and urea levels.99 In both cases, these tests can be done at early time intervals thus reducing the duration of animal experimentation.\n\nOur intricate knowledge of venom composition and pathophysiology has increased substantially in the past two decades. In vitro biochemical and cell-based assays, and more recently in silico assessments,58,100 are now routinely being developed and used based on our understanding of the main mechanisms of venom action, with the objective of rapidly assessing the neutralising capabilities of potential therapeutics in the context of clinically relevant bioactivities, and to improve the chances of progression to clinical use.101–105 The ideal setting would be the development of in vitro assays with direct correlation to outputs gained from in vivo lethality and venom neutralisation assays, which could potentially provide a replacement to in vivo models, or at the very least, a reduction in the number of animals subjected to the neutralisation of lethality assay. However, such approaches must be validated on a case-by-case basis since each venom-antivenom system behaves differently. In some cases, immunochemical assays have shown correlation with lethality.106 In other cases, neutralisation of in vitro venom activities (such as coagulant activity on plasma) correlate with lethality.107 Lethality induced by neurotoxic venoms with a post-synaptic mechanism of action can be modelled with an assay based on the inhibition of the venom binding to or activation of cholinergic receptors.101,102 In other cases, predictions of venom therapeutic efficacy made from in vitro assaying have not translated into in vivo preclinical venom neutralisation.108 Once validated appropriately, examples of such could be used as a first point testing call, made clear within policies to be prior to in vivo assays, and would facilitate in efforts to minimise animal use, or at the very least only allow for therapeutics with a high confidence of predicted efficacy in vivo, entering such studies.\n\n\nRisks of moving away from the neutralisation of lethality assay\n\nIt is easy to propose that models need to be better, more refined, and provide more data, in order to reduce the animal welfare cost and to increase the translatability of therapeutic efficacy into the clinic. However, the current realities of antivenom manufacturing must be taken into account. David Williams (WHO) emphasised that snakebite is a neglected tropical disease, that antivenom is an incredibly expensive drug to manufacture, and the economic incentives for private pharmaceutical companies are poor, whilst national public manufacturers, especially in resource limited settings, have limited budget or access to the highly skilled workforce required for performing such in vivo experiments, or indeed complex non-animal alternatives. Thus, any changes to the preclinical regulation of antivenoms must be proportionate, affordable, and sustainable and not inadvertently result in antivenom manufacturers withdrawing or being left unable to contribute to this already vulnerable and fragmented market.\n\n\nThe changing landscape of animal research and testing of biological therapeutics\n\nThis workshop was held against a background of considerable debate and change in the scientific community around the translational value of animal models.109,110 In parallel, there has been increasing research into novel non-animal methodologies/technologies (often referred to as NAMs and NATs) that have the potential to replace in vivo assays in a variety of area.49 There is widespread acknowledgement that transition towards non-animal approaches is not only ethically desirable but scientifically superior in many cases with generally lower variability and higher sensitivity. In vitro approaches are frequently more mechanistically relevant and quantitative than phenotypic, ‘black box’, mechanistically agonistic animal models. In the field of biologics, vaccines in particular, there has been considerable effort to transition away from animal models for quality control batch release testing. The European Pharmacopoeia took a considerable step towards encouraging the adoption of in vitro test methods with the publication of chapter 5.2.14 in January 2018.111 This chapter not only provides guidance to facilitate implementation of in vitro methods as substitutes for existing in vivo methods, but specifically indicates that because critical quality attributes for a given vaccine are likely to be assessed differently by in vivo and in vitro assays, it may not be scientifically justified to demonstrate agreement between these two approaches as part of the validation of an in vitro alternative assay. Given the current regulatory appetite for, and momentum towards, adoption of non-animal approaches in other biological therapeutics, coupled with the clear ethical issues with the current lethality assays, it is a good time to renew efforts to develop non-animal test methodologies for antivenom potency testing.\n\n\nConclusions and short-term suggestions\n\nIt was widely agreed amongst the contributors to the workshop that the existing snakebite preclinical development and testing approach needs substantial modernisation and improvement, and that in its current form is not suitable to support the development of the new generation of envenoming therapies. With drug development programmes for snakebite currently underway, and clinical trials for antivenom and alternative therapeutics on the horizon, it is evident that an updated in vivo models, and better in vitro and ex vivo alternatives, are urgently required to provide more information to support such developments and facilitate therapeutic candidate selection, in addition to improving the current harm:benefit assessment, and animal suffering encountered in the current model. An increased crosstalk between clinicians, experimental scientists, antivenom manufacturers and regulators is likely to benefit this field, catalysing the development of alternative ways to assess antivenom preclinical efficacy, that is more realistic and predictive of the clinical scenario. Moreover, as regulatory pressures increase, or as more countries modernise animal welfare regulation, the countries in which the lethality assays can be performed will decrease, thus underscoring the need for an acceleration of replacement, animal-free, alternative testing research for antivenoms. In the meantime, whilst possibly difficult for manufacturers to implement changes due to regulatory requirements for product release, there seems little justification to argue against the implementation of multiple small refinements to the neutralisation of lethality assay (analgesia at least, reduction in time and humane endpoints if possible), which will substantially increase animal welfare.112 We recommend these refinements are incorporated explicitly, within the sections describing the methodological details of this assay, in future revisions of the WHO guidelines.\n\nDespite the substantial animal costs outlined in this article, in the absence of the requirement for antivenoms to undergo the typical pathway for demonstrating clinical effectiveness through human clinical trials, the harm:benefit assessment these assays remains greatly skewed in the favour of human health benefit, rather than animal welfare. However, this does not mean improvements cannot be made. Ultimately, all snakebite envenoming stakeholders, from victims to manufacturers to researchers, owe a great deal to the consumption and fate of the tens of thousands of mice consumed in the neutralisation of venom lethality assay each year. The absolute minimum improvements that can be made as a community, for as long murine testing is necessary to demonstrate efficacy of envenoming therapies, is to try and reduce the severity of these studies and improve mouse welfare. It is important to note that refinements will not only improve the welfare of animals used in these experiments, but they are likely to also improve the quality and validity of the science being performed, and therefore improve outcomes for human snakebite victims, too.",
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Geneva: World Health Organisation; 2023.\n\nAbubakar SB, et al.: Pre-clinical and preliminary dose-finding and safety studies to identify candidate antivenoms for treatment of envenoming by saw-scaled or carpet vipers (Echis ocellatus) in northern Nigeria. Toxicon. 2010; 55: 719–723. PubMed Abstract | Publisher Full Text\n\nMenzies SK, et al.: Two snakebite antivenoms have potential to reduce Eswatini’s dependency upon a single, increasingly unavailable product: Results of preclinical efficacy testing. PLoS Negl. Trop. Dis. 2022; 16: e0010496. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarrison RA, et al.: Preclinical antivenom-efficacy testing reveals potentially disturbing deficiencies of snakebite treatment capability in East Africa. PLoS Negl. Trop. Dis. 2017; 11: e0005969. Publisher Full Text\n\nBogarin G, et al.: Evaluation of neutralizing ability of four commercially available antivenoms against the venom of Bothrops asper from Costa Rica. Toxicon. 1995; 33: 1242–1247. PubMed Abstract | Publisher Full Text\n\nWhiteley G, et al.: Defining the pathogenic threat of envenoming by South African shield-nosed and coral snakes (genus Aspidelaps), and revealing the likely efficacy of available antivenom. J. Proteome. 2019; 198: 186–198. PubMed Abstract | Publisher Full Text\n\nCastillo-Beltran MC, Hurtado-Gomez JP, Corredor-Espinel V, et al.: A polyvalent coral snake antivenom with broad neutralization capacity. PLoS Negl. Trop. Dis. 2019; 13: e0007250. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStrech D, Dirnagl U: 3Rs missing: animal research without scientific value is unethical. BMJ Open Sci. 2019; 3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLilley E, et al.: Refinement of Animal Models of Sepsis and Septic Shock. Shock. 2015; 43: 304–316. PubMed Abstract | Publisher Full Text\n\nHubrecht RC, Carter E: The 3Rs and Humane Experimental Technique: Implementing Change. Animals. 2019; 9: 754. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRobinson NB, et al.: The current state of animal models in research: A review. Int. J. Surg. 2019; 72: 9–13. Publisher Full Text\n\nPetetta F, Ciccocioppo R: Public perception of laboratory animal testing: Historical, philosophical, and ethical view. Addict. Biol. 2021; 26: e12991. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBailey J: Biomedical Research Must Change — But a Shift Toward Human-specific Research Methods Is Only Part of What Is Needed. Altern. Lab. Anim. 2021; 49: 69–72. PubMed Abstract | Publisher Full Text\n\nFerdowsian HR, Beck N: Ethical and Scientific Considerations Regarding Animal Testing and Research. PLoS One. 2011; 6: e24059. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Norman GA: Limitations of Animal Studies for Predicting Toxicity in Clinical Trials: Is it Time to Rethink Our Current Approach? JACC Basic Transl Sci. 2019; 4: 845–854. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarshall LJ, Bailey J, Cassotta M, et al.: Poor Translatability of Biomedical Research Using Animals — A Narrative Review. Altern. Lab. Anim. 2023; 51: 102–135. PubMed Abstract | Publisher Full Text\n\nLoewa A, Feng JJ, Hedtrich S: Human disease models in drug development. Nat. Rev. Bioeng. 2023; 1: 545–559. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSeyhan AA: Lost in translation: the valley of death across preclinical and clinical divide – identification of problems and overcoming obstacles. Transl. Med. Commun. 2019; 4: 18. Publisher Full Text\n\nPound P, Ritskes-Hoitinga M: Is it possible to overcome issues of external validity in preclinical animal research? Why most animal models are bound to fail. J. Transl. Med. 2018; 16: 304. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKnight A: Systematic reviews of animal experiments demonstrate poor human clinical and toxicological utility. Altern. Lab. Anim. 2007; 35: 641–659. PubMed Abstract | Publisher Full Text\n\nBoyer LV, et al.: Recurrent and persistent coagulopathy following pit viper envenomation. Arch. Intern. Med. 1999; 159: 706–710. PubMed Abstract | Publisher Full Text\n\nYap MK, Tan NH, Sim SM, et al.: Pharmacokinetics of Naja sumatrana (equatorial spitting cobra) venom and its major toxins in experimentally envenomed rabbits. PLoS Negl. Trop. Dis. 2014; 8: e2890. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSanhajariya S, Duffull SB, Isbister GK: Pharmacokinetics of Snake Venom. Toxins (Basel). 2018; 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorris NM, Blee JA, Hauert S: Global parameter optimisation and sensitivity analysis of antivenom pharmacokinetics and pharmacodynamics. Toxicon. 2023; 232: 107206. PubMed Abstract | Publisher Full Text\n\nMorris NM, Blee JA, Hauert S: Developing a computational pharmacokinetic model of systemic snakebite envenomation and antivenom treatment. Toxicon. 2022; 215: 77–90. PubMed Abstract | Publisher Full Text\n\nMorgan P, et al.: Can the flow of medicines be improved? Fundamental pharmacokinetic and pharmacological principles toward improving Phase II survival. Drug Discov. Today. 2012; 17: 419–424. PubMed Abstract | Publisher Full Text\n\nWarrell DA, Greenwood BM, Davidson NM, et al.: Necrosis, haemorrhage and complement depletion following bites by the spitting cobra (Naja nigricollis). Q. J. Med. 1976; 45: 1–22. PubMed Abstract\n\nWarrell DA: Handbook of clinical toxicology of animal venoms and poisons. Meier J, White J, editors. CRC Press; 1995; pp. 433–492.\n\nFernandez-Quintero ML, et al.: Assessing developability early in the discovery process for novel biologics. MAbs. 2023; 15: 2171248. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaduwage KP, Scorgie FE, Lincz LF, et al.: Procoagulant snake venoms have differential effects in animal plasmas: Implications for antivenom testing in animal models. Thromb. Res. 2016; 137: 174–177. PubMed Abstract | Publisher Full Text\n\nThumtecho S, Burlet NJ, Ljungars A, et al.: Towards better antivenoms: navigating the road to new types of snakebite envenoming therapies. J. Venom. Anim. Toxins Incl. Trop. Dis. 2023; 29: e20230057. Publisher Full Text\n\nBayne K, Turner PV: Animal Welfare Standards and International Collaborations. ILAR J. 2019; 60: 86–94. PubMed Abstract | Publisher Full Text\n\nCommission, E: Directive 2010/63/EU of the European Parliament and of the Council of 22 September 2010 on the protection of animals used for scientific purposes. Off. J. Eur. Union. 2010; 50: 33–79.\n\nAkkermans A, et al.: Animal testing for vaccines. Implementing replacement, reduction and refinement: challenges and priorities. Biologicals. 2020; 68: 92–107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLilley E, et al.: Integrating 3Rs approaches in WHO guidelines for the batch release testing of biologicals: Responses from a survey of National Control Laboratories and National Regulatory Authorities. Biologicals. 2023; 84: 101721. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSells PG, Ioannou P, Theakston RD: A humane alternative to the measurement of the lethal effects (LD50) of non-neurotoxic venoms using hens’ eggs. Toxicon. 1998; 36: 985–991. PubMed Abstract | Publisher Full Text\n\nSells PG, Laing GD, Theakston RD: An in vivo but insensate model for the evaluation of antivenoms (ED(50)) using fertile hens’ eggs. Toxicon. 2001; 39: 665–668. PubMed Abstract | Publisher Full Text\n\nVerity EE, Stewart K, Vandenberg K, et al.: Potency Testing of Venoms and Antivenoms in Embryonated Eggs: An Ethical Alternative to Animal Testing. Toxins (Basel). 2021; 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbd El-Aziz TM, Soares AG, Stockand JD: Advances in venomics: Modern separation techniques and mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2020; 1160: 122352. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVisser LE, et al.: Failure of a new antivenom to treat Echis ocellatus snake bite in rural Ghana: the importance of quality surveillance. Trans. R. Soc. Trop. Med. Hyg. 2008; 102: 445–450. PubMed Abstract | Publisher Full Text\n\nAlirol E, et al.: Antivenoms for Snakebite Envenoming: What Is in the Research Pipeline? PLoS Negl. Trop. Dis. 2015; 9: e0003896. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilliams DJ, et al.: Strategy for a globally coordinated response to a priority neglected tropical disease: Snakebite envenoming. PLoS Negl. Trop. Dis. 2019; 13: e0007059. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEmergency use of unproven clinical interventions outside clinical trials: ethical considerations. Geneva: World Health Organisation; 2022.\n\nHerrera C, Bolton F, Arias AS, et al.: Analgesic effect of morphine and tramadol in standard toxicity assays in mice injected with venom of the snake Bothrops asper. Toxicon. 2018; 154: 35–41. PubMed Abstract | Publisher Full Text\n\nGutierrez JM, Herrera C: The analgesics morphine and tramadol do not alter the acute toxicity induced by Bothrops asper snake venom in mice. Toxicon. 2014; 81: 54–57. Publisher Full Text\n\nDuran G, et al.: Assessing a 6-h endpoint observation time in the lethality neutralization assay used to evaluate the preclinical efficacy of snake antivenoms. Toxicon X. 2021; 12: 100087. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCasewell NR, et al.: Pre-clinical assays predict pan-African Echis viper efficacy for a species-specific antivenom. PLoS Negl. Trop. Dis. 2010; 4: e851. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSorensen CV, et al.: Antibody-dependent enhancement of toxicity of myotoxin II from Bothrops asper. Nat. Commun. 2024; 15: 173. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNandi M, et al.: Rethinking animal models of sepsis - working towards improved clinical translation whilst integrating the 3Rs. Clin. Sci. (Lond.). 2020; 134: 1715–1734. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSand CA, et al.: Quantification of microcirculatory blood flow: a sensitive and clinically relevant prognostic marker in murine models of sepsis. J. Appl. Physiol. 2015; 118(118): 344–354. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNirala S, Rui Tan X: Early markers of Sepsis Cardiomyopathy in Murine Models by Echocardiography. Curr. Med. Imaging. 2023; 20. PubMed Abstract | Publisher Full Text\n\nHoffman M, et al.: Myocardial Strain and Cardiac Output are Preferable Measurements for Cardiac Dysfunction and Can Predict Mortality in Septic Mice. J. Am. Heart Assoc. 2019; 8: e012260. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMion G, Larréché S, Benois A, et al.: Hemostasis dynamics during coagulopathy resulting from Echis envenomation. Toxicon. 2013; 76: 103–109. PubMed Abstract | Publisher Full Text\n\nAbubakar IS, et al.: Randomised Controlled Double-Blind Non-Inferiority Trial of Two Antivenoms for Saw-Scaled or Carpet Viper (Echis ocellatus) Envenoming in Nigeria. PLoS Negl. Trop. Dis. 2010; 4: e767. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbouyannis M, et al.: Clinical outcomes and outcome measurement tools reported in randomised controlled trials of treatment for snakebite envenoming: A systematic review. PLoS Negl. Trop. Dis. 2021; 15: e0009589. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSilverman J: Death as a study endpoint. Lab. Anim. 2008; 37: 345–345. Publisher Full Text\n\nBolton FMS: Incorporating the 3Rs (Refinement, Replacement and Reduction of Animals in Research) into the Preclinical Assessment of Snake Venom Toxicity and Antivenom Efficacy. United Kingdom: The University of Liverpool; 2017.\n\nHendriksen CFM, Morton DB , authors.\n\nFranco NH, Correia-Neves M, Olsson IA: How “humane” is your endpoint? Refining the science-driven approach for termination of animal studies of chronic infection. PLoS Pathog. 2012; 8: e1002399. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWarrell DA, et al.: Poisoning by bites of the saw-scaled or carpet viper (Echis carinatus) in Nigeria. Q. J. Med. 1977; 46: 33–62. PubMed Abstract\n\nOtero-Patino R: Epidemiological, clinical and therapeutic aspects of Bothrops asper bites. Toxicon. 2009; 54: 998–1011. PubMed Abstract | Publisher Full Text\n\nSegura A, et al.: Preclinical assessment of the neutralizing capacity of antivenoms produced in six Latin American countries against medically-relevant Bothrops snake venoms. Toxicon. 2010; 56: 980–989. PubMed Abstract | Publisher Full Text\n\nBartlett KE, et al.: Dermonecrosis caused by spitting cobra snakebite results from toxin potentiation and is prevented by the repurposed drug varespladib. bioRxiv. 2023. 2023.2007.2020.549878. Publisher Full Text\n\nWarrell DA: Handbook of clinical toxicology of animal venoms and poisons. Meier J, White J, editors. CRC Press; 1995; pp. 493–594.\n\nRucavado A, Escalante T, Camacho E, et al.: Systemic vascular leakage induced in mice by Russell’s viper venom from Pakistan. Sci. Rep. 2018; 8: 16088. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChaisakul J, et al.: Evaluation of the geographical utility of Eastern Russell’s viper (Daboia siamensis) antivenom from Thailand and an assessment of its protective effects against venom-induced nephrotoxicity. PLoS Negl. Trop. Dis. 2019; 13: e0007338. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorris NM, Blee JA, Hauert S: Global parameter optimisation and sensitivity analysis of antivenom pharmacokinetics and pharmacodynamics. Toxicon. 2023; 232: 107206. PubMed Abstract | Publisher Full Text\n\nPatel RN, et al.: An in vitro assay to investigate venom neurotoxin activity on muscle-type nicotinic acetylcholine receptor activation and for the discovery of toxin-inhibitory molecules. Biochem. Pharmacol. 2023; 216: 115758. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPruksaphon K, et al.: An in vitro α-neurotoxin—nAChR binding assay correlates with lethality and in vivo neutralization of a large number of elapid neurotoxic snake venoms from four continents. PLoS Negl. Trop. Dis. 2020; 14: e0008581. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLopes-de-Souza L, et al.: Development of a cell-based in vitro assay as a possible alternative for determining bothropic antivenom potency. Toxicon. 2019; 170: 68–76. PubMed Abstract | Publisher Full Text\n\nBhatia S, Blotra A, Vasudevan K: Evaluating Antivenom Efficacy against Echis carinatus Venoms—Screening for in vitro Alternatives. Toxins. 2022; 14: 481. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGutiérrez JM, et al.: In Vitro Tests for Assessing the Neutralizing Ability of Snake Antivenoms: Toward the 3Rs Principles. Front. Immunol. 2020; 11: 617429. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRial A, Morais V, Rossi S, et al.: A new ELISA for determination of potency in snake antivenoms. Toxicon. 2006; 48: 462–466. PubMed Abstract | Publisher Full Text\n\nPornmuttakun D, Ratanabanangkoon K: Development of an in vitro potency assay for antivenom against Malayan pit viper (Calloselasma rhodostoma). Toxicon. 2014; 77: 1–5. PubMed Abstract | Publisher Full Text\n\nAlape-Giron A, Miranda-Arrieta K, Cortes-Bratti X, et al.: A comparison of in vitro methods for assessing the potency of therapeutic antisera against the venom of the coral snake Micrurus nigrocinctus. Toxicon. 1997; 35: 573–581. PubMed Abstract | Publisher Full Text\n\nMonticello TM, et al.: Current nonclinical testing paradigm enables safe entry to First-In-Human clinical trials: The IQ consortium nonclinical to clinical translational database. Toxicol. Appl. Pharmacol. 2017; 334: 100–109. PubMed Abstract | Publisher Full Text\n\nBailey J, Balls M: Recent efforts to elucidate the scientific validity of animal-based drug tests by the pharmaceutical industry, pro-testing lobby groups, and animal welfare organisations. BMC Med. Ethics. 2019; 20: 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEuropean pharmacopoeia. EDQM; 2018.\n\nLilley E, Jennings M: Refinement: lessons from the 2012 Olympics. Altern. Lab. Anim. 2013; 41: P28–P29. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "259964",
"date": "29 Apr 2024",
"name": "Sébastien Larréché",
"expertise": [
"Reviewer Expertise toxinology",
"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\nThis opinion article summarizes the conclusions of an international webinar on modernizing and improving animal models in venom and antivenom research. This discussion seems indeed necessary in the context of the 3Rs aimed to improve animal welfare. A first chapter presented the history of lethality neutralization tests in mice, particularly during the discovery of passive immunotherapy which opened the way to the manufacture of antivenom. We recommend here that the authors recall that Phisalix and Bertrand were the first to report the transfer of immunity against viper venom from a previously immunized animal to another naive one, shortly preceding Calmette during the same session of the Society of Biology on February 10, 1894 (Ref-9). It is also worth noting that Calmette was the first to use antivenom in humans to treat snakebite envenomation. The median effective dose assay in mice as currently recommended by the WHO, and its advantages were then presented. The limitations were mentioned: ethical issues (important number of mice used, and level of suffering experienced), scientific validity and regularity issues. However, another limitation comes from the use of parametric statistical tests, which require a larger number of animals than non-parametric tests, but are unfortunately not yet accepted by drug regulatory authorities. Their use would make it possible to drastically reduce the number of animals used in neutralization tests. We noticed an error in the name of one of the contributor: “Caswell” instead of “Casewell” (at the bottom of page 4). Possible improvements regarding refinement and reduction, the rescue model and future developments were then presented. We fully agree with the authors’ suggestions. In addition, the potential interest of in vivo assays using large animals (i.e., sheep) deserves to be reported here as it allows to avoid certain limitations in the pharmacokinetics and pharmacodynamics of venoms and antivenoms mentioned in the webinar (Neri-Castro E,et.al., 2020 [Ref 1]) ; Paniagua D, et al.,2019 [Ref 2]). For the assessment of coagulopathy, it should be noted that the prothrombin time or INR must be measured according to a standard specific to the animal used. Alternatively, the use of viscoelastic tests such as TEG or ROTEM allows a global assessment of hemostasis, i.e., platelets, coagulation factors and fibrinolysis with a single test (Nielsen VG,et.al.,2023 [Ref 3]) ; Camacho E, et.al.,2023 [Ref 4]) ; Larréché S, et.al.,2023 [Ref 5]).\nLikewise, the study of the neutralization of venom procoagulant effect by an antivenom can be designed using an in vitro model, as has been demonstrated with Echis or Bothrops venoms (Rogalski A, et. al., 2017 [Ref 6]); Bourke LA, et. al.,2021 [Ref 7]).\nFinally, the authors should emphasize the urgent need for human clinical trials to validate the efficacy and safety of antivenoms, provided that standardized evaluation criteria are used (Abouyannis, et.al., 2023 [Ref 8]) .\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": []
},
{
"id": "259966",
"date": "02 May 2024",
"name": "Jarrod Bailey",
"expertise": [
"Reviewer Expertise Animal models",
"in vitro research methods",
"NAMs",
"molecular biology."
],
"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 are to be congratulated on putting together such a comprehensive, balanced, critical, constructive and well-referenced review of an ethically and scientifically difficult topic.\nThey deal admirably and honestly with an appraisal of the history and current use of animals in envenoming research, development and testing, including detailed issues with ethics and scientific validity, particularly with regard to the neutralisation of lethality assay.\nOf particular interest to the scientific community may be the lack of human relevance and translatability of snakebite envenoming research and related therapeutic development which, when combined with the severity of many of the procedures in which animals are used as experimental/testing subjects, raises a formidable case that the justification of animal use in these ways must be untenable.\nThe open and honest nature of the authors’ appraisal is of the type that can take some courage, particularly when it comes to critical views of established animal models. They also present a commendable and welcome account of ‘Three Rs’ approaches, which reflects a wider appreciation of the welfare issues they detail. The need for action, in terms of more focus on reduction, and most certainly on replacement, is also discussed.\nOf particular note in this regard is the section of the manuscript “What future in vivo models of envenoming could look like: ending the reliance on lethality testing.” Here, and in their Conclusions and Suggestions the authors deal well with the issues of Refining lethality testing, but do not shy away from discussing the need for more focus on Replacing in vivo assays, both for welfare/ethical and scientific/translational reasons. They cite examples of progress that have been made in this respect, and acknowledge the need to accelerate this progress in order to better address the animal welfare issues involved in in vivo methods. They also discuss the anticipation of regulatory pressures to replace animal testing in this field, based on increasingly stringent animal welfare regulations, which may increase the urgency for replacement. The authors could add a couple of notes to improve these discussions which I believe are pertinent, which would be relevant to their discussions of Refinement versus Replacement, and their assertions that any in vitro replacement methods should be validated on case-by base bases. In a paper I have currently in press (Ref [1]), I argue that focusing on Refinement, whatever the merits, can distract from and even discourage efforts on Replacement, which is significantly more urgent and preferable, both ethically and scientifically. Further, they might wish to briefly discuss the validation process. This process can take years, and is frustratingly and unnecessarily time consuming when there is an urgent need for a new, more translational and human-relevant method. Some argue that it is therefore important to ensure that the validation ‘bar’ is not set too high, and that an ethically superior method does not have to be perfect – it just has to match, or slightly improve on the performance of an animal based method to be acceptable.\n\nI highly recommend the approval of this manuscript without delay, so it can elicit important discussions within the field which should promise more ethical, human-relevant, predictive and rigorous science, as well as more generally in other biomedical areas.\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": []
},
{
"id": "265200",
"date": "14 May 2024",
"name": "Karen de Morais-Zani",
"expertise": [
"Reviewer Expertise Compositional and functional characterization of snake venoms."
],
"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 opinion article describes the topics presented and discussed at the meeting “Improving in vivo snake venom research” (2023), organized by the Center for Snakebite Research and Interventions of Liverpool School of Tropical Medicine (UK).\n\nIn the manuscript, the use of the murine model to determine the lethality of snake venoms and its neutralization by antivenoms was discussed, as well as suggestions for refining the model, with the aim of meeting the 3Rs principle in the use of animals. The authors also gather references that support the discussion of the topic and the proposed adaptations/modifications. This is a topic of great relevance not only for those directly involved in the area, but for the scientific community in general.\n\nMajor points: The authors describe the standardized murine model for neutralization of venom lethality and comment on the advantages of the assay that led to its success/widespread use. However, the manuscript focuses on discussing the limitations of the model, especially regarding its ethical issues and scientific validity. Refinements to the standard neutralization of lethality assay were described, as well as a modified version with reduced number of mice required. Importantly, the need and the challenges of the implementation of humane endpoints are discussed.\n\nMinor points: The authors give an historical overview of the development and standardization of the murine model for accessing the snake venom lethality and its neutralization. Additionally, authors give examples of alternatives to lethality model considering the pathophysiology of the envenomation caused by genera Echis, Bothrops, Naja and Daboia.\n\nI only suggest a review by the authors to amend some writing/typing mistakes.\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": []
}
] | 1
|
https://f1000research.com/articles/13-192
|
https://f1000research.com/articles/12-838/v1
|
17 Jul 23
|
{
"type": "Study Protocol",
"title": "A protocol for the development of PhyCaRe: An extension of the CARE guideline for physiotherapy using the Delphi method",
"authors": [
"Waqar M. Naqvi",
"Gaurav Mishra",
"Aishwarya A. Pashine",
"Sakshi P. Arora",
"Sonia Gupta",
"Chanan Goyal",
"Ashish R. Varma",
"Zahiruddin Quazi",
"Ramprasad Muthukrishnan",
"Praveen Kumar Kandakurti",
"Laxmikant Umate",
"Gaurav Mishra",
"Aishwarya A. Pashine",
"Sakshi P. Arora",
"Sonia Gupta",
"Chanan Goyal",
"Ashish R. Varma",
"Zahiruddin Quazi",
"Ramprasad Muthukrishnan",
"Praveen Kumar Kandakurti",
"Laxmikant Umate"
],
"abstract": "Background: Case reports are one of the important forms of documentation and publication of clinical physiotherapy presenting the first line of evidence in scientific literature. In order to provide a systematic and precise structure for reporting and presenting cases, the CARE guidelines were established in 2013. However, these guidelines present limitations as while reporting require items of specific specialties following the checklist. Authors from different specialities have developed CARE extensions specifying the characteristic features of corresponding fields, however, an extension dealing with physiotherapy assessment and line of management in the CARE guidelines is proposed as PhyCaRe. Method: After consulting with the advisors, a draft will be prepared of the specific elements that should be included in the PhyCaRe using Delphi methodology considering CARE statement as the source and SurveyMonkey will be used to undertake the Delphi questionnaire. The Delphi methodology will be assumed for three rounds and will be open to physiotherapists and others with substantial experience in reviewing case reports. Subsequently, an online consensus meeting, pilot testing, and submission of the CARE extension for physiotherapy will be conducted for publication. Dissemination: The 2010 \"Guidance for Developers of Health Research Reporting\" and instructions from the EQUATOR Network will be followed in the preparation of PhyCaRe guidelines. The guidelines will be propagated at different platforms and journals will be requested to adopt the guidelines. Registration: The reporting guideline under development is prospectively registered on the EQUATOR Network website on PhyCaRe – Reporting guideline for physiotherapy case reports.",
"keywords": [
"Case Report",
"CARE Guidelines",
"PhyCaRe",
"Physiotherapy",
"Physical Therapy",
"Reporting Guideline",
"Clinical Practice Guideline",
"CARE Extension"
],
"content": "Introduction\n\nThe basic publishable unit in the healthcare sector is a case report (CR) which provides a detailed clinical course description of an individual patient.1–3 A CR presents unusual signs and symptoms in rare diseases and syndromes with a novel and innovative approach of assessment and management. This avails the wide range of favourable or unfavourable outcomes of various approaches.4 The trend of publishing CRs can be traced back to the early twentieth century and has been increasing ever since.2,5\n\nPhysiotherapy or physical therapy (PT), is an integral part of healthcare sciences that deals with rehabilitation programs to relieve pain and restore functional independence, thus maximising the ability to participate.6 The primary aim of PT is to treat and prevent physical impairments associated with injuries and optimise the capacity of an individual.7 Physiotherapists evaluate, plan, and implement various rehabilitation programs by using a broad range of therapeutic techniques. Hence, they play a key role in restoring functional capacity of the patients and upgrading the quality of life.8\n\nPhysiotherapists follow a thorough assessment of structural and functional impairments of different conditions with a note on positive findings for tailoring patient-oriented treatment goals.9 However, from the assessment to the follow-up, the physiotherapeutic approach varies widely on the basis of confounding factors, the method of evaluation, frequency, intensity, time, and type (FITT) of the appropriate treatment as per individual needs.10 This emphasises the significance of CR in the research literature creating an awareness about the profession in the scientific community.\n\nIn order to provide a framework pertaining to the uniformity and accuracy in the CR presentation, CARE guidelines were developed in 201311 which consists of a 13-item checklist, thus satisfying the requirements of transparency as well as completeness in CRs.12 Authors are obliged to follow CARE guidelines or at least a part of it applicable for a case while writing CRs.13 There are over 10,000 published CRs in the PubMed database and more than 12,000 published CRs in the Scopus database, in accordance with the CARE guidelines and their present extensions.14 However, the contribution of physiotherapy CRs is comparatively limited as compared to other healthcare fields. It may be because of the presenting lacuna in the checklist which is unable to cover the different aspects of physiotherapeutic evaluation, treatment, and follow-up. Moreover, one of the major limitations of CARE guidelines was that the CARE guidelines may possibly require extensions to include information particular to different specialties, practitioners, and patients. As a result, multiple extensions were developed for surgery5; radiology13; endodontic15; therapeutic massage and bodywork16; and acupuncture.17 However, there is no such guideline specifying the checklist as per the needs of physiotherapeutic care.\n\nPhysiotherapists use different approaches for assessment as well as treatment like exercises,18 electrotherapy,19 manual therapy,20 hydrotherapy,21 and gamification22 wherein the effective dosage varies with patients to the manifesting conditions extensively necessitating the use of an associated format for effective documentation and presentation, so that the claims will benefit the researchers, academicians, and clinicians around the globe.3 Furthermore, this will provide an uniform, structured, and systematic way of presenting physiotherapeutic approach and efficacy in terms of FITT’s principle.10 This will enhance the reproducibility of assessment and management in clinical and/or community settings. This protocol aims at developing an extension dealing with PT assessment and line of management in the CARE guidelines as PhyCaRe by adding new items and adapting the current ones, adding to the EQUATOR Network’s guidelines while considering the 2010 “Guidance for Developers of Health Research Reporting”.\n\n\nMethods\n\nExecutive group\n\nThe executive group consisting of co-authors will supervise the conduction of the required assessment, drafting of primary items; arranging, and executing the Delphi method; concluding and finalising the draft; coordinating the preparations of the final manuscript and CARE extension for physiotherapy as PhyCaRe. The members of the Delphi panel will include physiotherapists, clinical practitioners, journal editors, peer reviewers, academic editors, researchers, statisticians, methodologists, epidemiologists, content experts, and professional medical writers who will be invited to attend at least three rounds of the Delphi process.23\n\nAdvisory group\n\nThis team will help with methodology enquiries, aid the executive team in recognizing key Delphi panel members, offer suggestions as required, and include experts in the field of PT, guideline development, and CR publishing. The patient representatives to the group will also be invited if possible. The key members of EQUATOR guidelines who have participated in reporting guideline development groups at least once in the past year will also be invited. Next, each member who accepted our invitation will be requested to suggest additional potential members (beyond those identified in our list).\n\nRegistration\n\nThe reporting guideline under development is now live on the EQUATOR Network website on PhyCaRe – Reporting guideline for physiotherapy case reports.\n\nLiterature review\n\nFor reviewing the existing literature, published PT CRs will be searched and extracted. After evaluating and assessing these CRs, the primary items for the Delphi survey method will be drafted.\n\nIdentify physiotherapy reporting standards\n\nThe data will be searched and extracted from six different databases: PEDro, PubMed-PubMed Central-MEDLINE, Scopus, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Google Scholar. Additional searches on the EQUATOR network website, as well as tracking of the citations and references of the acquired studies will be performed. Any previous version of the reporting guidelines will be excluded and PT reporting guidelines will be included in the process. A free and combination of keywords will be used to search for the required data. In order to conduct the process, the PRISMA-S guideline will be assigned and the search items will include, “CARE guideline, reporting, case report, case study, case presentation, physiotherapy, physical therapy, rehabilitation, exercises, electrotherapy, manual therapy, therapeutic exercise, exergaming, gamification, functional independence, quality of life, health intervention”.\n\nFinding recent physiotherapy case reports\n\nThe literature will be searched in the above mentioned databases with the use of selected keywords. CRs literature will be included whereas, non-clinical researches will be excluded from the study.\n\nDrafting of primary items\n\nThe executive group will search for the results and draft the primary elements specific to PT prior to the confirmation from the advisory committee. These primary specific elements will then be evaluated by the Delphi panel members.\n\nA survey will be conducted using standard Delphi methodology for which SurveyMonkey® (www.surveymonkey.com) will be employed to administer the Delphi questionnaire.5,1,3 All the stakeholders will complete the same questionnaire throughout the process. The Delphi questionnaire is supposed to comprise two sections. The respondents will be asked to rank the “importance” and “appropriateness” of each element in the first section. In the second section, the respondents will be asked to suggest new items or adaptations of the existing items in the CARE statement to fulfil the specific requirements of CRs in PT. Accordingly, the above mentioned suggestions will be included in the first round which will be oriented towards generating new items and adapting the current ones for PT.\n\nA nine-point Likert scale will be employed in each consecutive round wherein respondents will rank the relevance of each outcome’s reporting.5,1,3 The outcome of limited relevance is signified by 1 to 3; 4 to 6 signifies that the outcome is relevant but not essential; and 7 to 9 denotes a relevant and essential outcome. Only when at least 70% of respondents will rate an item 7 to 9 and less than 15% will rate it 1 to 3, the item will be promoted in the reporting standards. Similarly, if 70% or more of the respondents scored an item from 1 to 3 and 15% or less scored it from 7 to 9, such an outcome will be rejected from the reporting guidelines. Items with scores of 4 to 6 will be revised based upon the comments of the advisory group members for the next round of the Delphi methodology. Administration of the questionnaire as well as the sequential rounds will continue unless a comprehensive set of findings with concurred definitions is obtained. Due to the fact that there is no requirement set for number of Delphi rounds, the entire procedure will be carried out online. However, according to our expectations, at least three Delphi rounds will be required. Furthermore, the same procedure will be employed to get accepted definitions for the results.23\n\nFollowing the conclusion of each round, analysis will be conducted to determine if each item will be included, excluded, or forwarded for the next round. To determine which category suggested elements will be added, thematic analysis of the reviews will be done and descriptive statistics (median and interquartile range) will be used to analyse the Likert items.\n\nFollowing each round of the Delphi procedure, the executive group will collect the completed questionnaires, compile the results, and summarise the respondents’ comments and suggestions regarding any adaptations to the CARE guidelines and new items for the PhyCaRe. If no consensus will be reached, the Delphi exercise will be continued for another round. Once consensus will be reached, the executive group will prepare a list of items for consideration by the advisory group at the meeting.\n\nVenue and duration\n\nFace-to-face online consensus meetings will be held through a teleconference platform. The meeting participants will be anticipated to reach a consensus on the preliminary version of the PhyCaRe checklist in about one day. Therefore, a one-day online consensus meeting will be hold.\n\nAgenda\n\nThe executive group will develop an agenda for online meetings and circulate it in advance to all participants before the meeting. The overall framework of the agenda will include the PhyCaRe statement background, a preliminary version of the PhyCaRe reporting checklist, the process of the online consensus meeting, and a discussion on the possibility of developing a flow diagram for the PhyCaRe statement.\n\nOnline consensus meeting\n\nThe executive group will create a checklist of the included items after the Delphi process and will host an online consensus conference to review the outcomes. The meeting will be attended by the members of the Delphi panel who will be participating in each round of the Delphi procedure.\n\nIn order to set the stage for the discussion, first a brief outline of the background, methodology, and outcomes of the Delphi process will be provided. Second, a consultation to update each item on the checklist will be presented. Third, voting will be conducted on each suggested item and phrasing. The experts will review the checklist of items once more after the meeting to ensure that their inputs are properly received and taken into account. The CARE guideline and the EQUATOR template will then be used to generate the draft of the guideline.\n\nDrafting and finalising the checklist and developing guidance statement\n\nThe PhyCaRe executive group will begin to draft the final checklist immediately after the virtual meeting. The executive group will work in parallel on the PhyCaRe statement. In the PhyCaRe statement, an explanation will be provided on which parts of the PhyCaRe checklist have been taken unchanged from the original CARE checklist and which items have been modified or added in response to the specific requirements of PT.\n\nConsulting advisors\n\nTo further discuss, refine the terminology, and organisation of the checklist, the manuscript will be delivered to the advisory team for reviewing, and after receiving their feedback the amended version of the PhyCaRe will be employed for the pilot test.\n\nPilot test of the checklist\n\nA pilot test of the PhyCaRe checklist among potential users will be conducted for validation which include physiotherapists, clinicians, and editors of journals publishing CRs on PT, and intend to collect their feedback on the checklist. Using the PhyCaRe checklist, the reporting precision of a sample of CR will be evaluated which is published in 2022 with an intention to search for any specific issues with any of the presenting or missing elements. Additionally, an online survey of the CR’s corresponding authors for assessing the ease of execution with employment of PhyCaRe will also be conducted. The executive group will review the comments and incorporate them as appropriate into future revisions of the PhyCaRe checklist. A thorough critical appraisal will be undertaken to map the final draft of the guidelines after receiving feedback from piloting.\n\nElaboration of explanatory document\n\nTo enable accurate application of PhyCaRe, a comprehensive descriptive and explanatory material will be provided.\n\nDevelopment of publication strategy\n\nThe executive group will facilitate the journal submission and will work with the advisory group to discuss suitable journals, prepare a manuscript that all authors agree on, and submit the final manuscript to a set of journals for simultaneous publication. The executive group will communicate with the editors of corresponding journals before submission to facilitate multiple publications and will publish a comprehensive protocol, checklist, and background information on PhyCaRe in the form of an academic paper.\n\nReceiving the feedback and amending as appropriate\n\nFeedback on PhyCaRe will be received from different individuals, including those involved in establishing the guidelines, peer-reviewed journals that publish PT cases using PhyCaRe, clinical PT practitioners, researchers, etc.\n\nEncouraging guidelines endorsement\n\nThe editors of PT journals will be involved in the development of the PhyCaRe checklist to facilitate its endorsement by journals. PT journals that publish CRs will be recommended to include the PhyCaRe checklist in their guidance for authors, and fulfill the expectations regarding the requirements of PT CRs. Additionally, the reporting checklist on the EQUATOR website or library will be disseminated and recommended to the researchers to report CRs on PT through academic conferences or operational groups using PhyCaRe.\n\nSupporting adherence to the guidelines\n\nThe critiques and feedbacks will be continuously collected and reviewed about the precision and accuracy of PhyCaRe checklist. The suggestions will be used to maximise adherence to the purpose of the checklist by incorporating critical feedback and productive analysis into revisions of the updated checklist.\n\nMonitoring and evaluating the impact of reporting guidelines\n\nThe observation and evaluation of the impact of reporting guidelines will be conducted by following a three-step process. The first phase will detect how journals of the CR for PT will be accepting and listing in the journal policy. The second phase will involve estimation of the overall number of PT CRs that adhere to the PhyCaRe following a qualitative analysis of the CR. Third, CRs adhering to the PhyCaRe guidelines and CRs not adhering to the criteria will be compared. Further, a questionnaire-based survey will be carried out with stakeholders to find out their awareness and use of PhyCaRe.\n\nUpdating the guidelines\n\nOn the basis of stakeholders feedback and the findings of the monitoring and assessment of the PT statement after five years, a meeting or assembly of the relevant experts will be held with the goal of updating PhyCare.\n\n\nDiscussion\n\nThe purpose of this protocol is to develop a PT specific CARE guideline extension as PhyCaRe, by conducting a Delphi survey method in which collective opinions of a group of experts will be gathered to identify the reporting items and to develop reporting guidelines for CRs in PT.5,1,3 CARE guideline extensions have been developed and validated for various specialties and super specialities of healthcare sciences. Agha et al. developed the Surgical CAse REport (SCARE) guidelines using a consensus based approach with an aim of adding the surgical perspective while reporting a CR.5 Similarly, Nagendrababu et al. developed the Preferred Reporting Items for Case Reports in Endodontics (PRICE) guidelines as an extension of the CARE guidelines for specifying the endodontics application.15 Van Haselen developed the HOM-CASE guideline extension which substantially improved the quality of reporting homoeopathic clinical cases along with the consideration and follow up during the treatment.24 In addition, Munk et al. formed a Therapeutic Massage and Bodywork (TMB) CR template which has documented and presented the impact of the TMB.16 Furthermore, Duan et al. has also proposed a protocol for development of guidelines for accurate reporting of clinical cases of acupuncture.17\n\nReporting guidelines for specific areas could enhance the quality of the corresponding research and promote its dissemination and transparency but will only do so if the methods used to develop them are scientific, disciplined, and transparent.11 This protocol reports the methodologies that will be employed to develop PhyCaRe guidelines. The supporting systematic review is under process to recognize the lacuna in the existing reporting criterias. However, the methodologies, protocols, and content of the development of other extended versions of the CARE guidelines are reviewed and critically appraised for differentiating the required items in the PhyCaRe checklist. A face-to-face online consensus meetings will be hold for there is no set number of Delphi rounds, but it can be easily conuducted with an active involvement of the panel without offline meetings. A detailed description of the expert group is yet to be disclosed as it has not yet been assembled. However, these limitations will be considered as not to affect the quality of the PhyCaRe guidelines.\n\nCRs drafted in accordance with PhyCaRe will provide valuable evidence from the point of care, thus enhancing the accuracy and transparency of PT care for clinicians, patients, policy makers, researchers, and medical journals. Busy professionals would be encouraged to publish more CRs to share their unique experiences and encounters as PhyCaRe will save time in drafting manuscripts for publication targeting reputed journals.",
"appendix": "Data availability\n\nNo data associated with this article.\n\n\nAcknowledgements\n\nWe will be grateful to the members of the Delphi panel.\n\n\nReferences\n\nMoher D, Schulz KF, Simera I, et al.: Guidance for developers of health research reporting guidelines. PLoS Med. 2010; 7(2): e1000217. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMurad MH, Sultan S, Haffar S, et al.: Methodological quality and synthesis of case series and case reports. BMJ Evid-Based Med. 2018; 23(2): 60–63. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuidelines To Writing A Clinical Case Report. Heart Views Off J Gulf Heart Assoc. 2017; 18(3): 104–105. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMunn Z, Barker TH, Moola S, et al.: Methodological quality of case series studies: an introduction to the JBI critical appraisal tool. JBI Evid Synth. 2020; 18(10): 2127–2133. PubMed Abstract | Publisher Full Text\n\nAgha RA, Fowler AJ, Saetta A, et al.: A protocol for the development of reporting criteria for surgical case reports: The SCARE statement. Int J Surg Lond Engl. 2016; 27: 187–189. PubMed Abstract | Publisher Full Text\n\nMcGowan CM, Cottriall S: Introduction to Equine Physical Therapy and Rehabilitation. Vet Clin North Am Equine Pract. 2016; 32(1): 1–12. PubMed Abstract | Publisher Full Text\n\nNicholls DA, Gibson BE: Physiotherapy as a complex assemblage of concepts, ideas and practices. Physiother Theory Pract. 2012; 28(6): 418–419. Publisher Full Text\n\nWikström-Grotell C, Eriksson K: Movement as a basic concept in physiotherapy--a human science approach. Physiother Theory Pract. 2012; 28(6): 428–438. PubMed Abstract | Publisher Full Text\n\nKirkby Shaw K, Alvarez L, Foster SA, et al.: Fundamental principles of rehabilitation and musculoskeletal tissue healing. Vet Surg VS. 2020; 49(1): 22–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlves AJ, Wu Y, Lopes S, et al.: Exercise to Treat Hypertension: Late Breaking News on Exercise Prescriptions That FITT. Curr Sports Med Rep. 2022; 21(8): 280–288. PubMed Abstract | Publisher Full Text\n\nGagnier JJ, Kienle G, Altman DG, et al.: The CARE Guidelines: Consensus-based Clinical Case Reporting Guideline Development. Glob Adv Health Med. 2013; 2(5): 38–43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVernooij RWM, Alonso-Coello P, Brouwers M, et al.: Reporting Items for Updated Clinical Guidelines: Checklist for the Reporting of Updated Guidelines (CheckUp). PLoS Med. 2017; 14(1): e1002207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang M, Zhu Y, Luo X, et al.: Protocol for developing the reporting guidelines for radiological case reports: Case Report for Radiology statement. Ann Transl Med. 2022; 10(2): 107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCalvache JA, Vera-Montoya M, Ordoñez D, et al.: Completeness of reporting of case reports in high-impact medical journals. Eur. J. Clin. Investig. 2020; 50(4): e13215. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNagendrababu V, Jacimovic J, Jakovljevic A, et al.: A bibliometric analysis of the top 100 most-cited case reports and case series in Endodontic journals. Int Endod J. 2022; 55(3): 185–218. PubMed Abstract | Publisher Full Text\n\nMunk N, Boulanger K: Adaptation of the CARE Guidelines for Therapeutic Massage and Bodywork Publications: Efforts To Improve the Impact of Case Reports. Int J Ther Massage Bodyw. 2014; 7(3): 32–40.\n\nDuan Y, Chen Y, Chen J, et al.: Protocol for the development of consensus-based clinical case reporting guideline extension: CARE for acupuncture. Complement Ther Med. 2019; 45: 185–189. PubMed Abstract | Publisher Full Text\n\nTaylor NF, Dodd KJ, Shields N, et al.: Therapeutic exercise in physiotherapy practice is beneficial: a summary of systematic reviews 2002-2005. Aust J Physiother. 2007; 53(1): 7–16. Publisher Full Text\n\nTiktinsky R, Chen L, Narayan P: Electrotherapy: yesterday, today and tomorrow. Haemoph Off J World Fed Hemoph. 2010; 16(Suppl 5): 126–131. PubMed Abstract | Publisher Full Text\n\nHidalgo B, Hall T, Bossert J, et al.: The efficacy of manual therapy and exercise for treating non-specific neck pain: A systematic review. J Back Musculoskelet Rehabil. 2017; 30(6): 1149–1169. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKing MR: Principles and Application of Hydrotherapy for Equine Athletes. Vet Clin North Am Equine Pract. 2016; 32(1): 115–126. PubMed Abstract | Publisher Full Text\n\nSardi L, Idri A, Fernández-Alemán JL: A systematic review of gamification in e-Health. J Biomed Inform. 2017; 71: 31–48. PubMed Abstract | Publisher Full Text\n\nDiamond IR, Grant RC, Feldman BM, et al.: Defining consensus: a systematic review recommends methodologic criteria for reporting of Delphi studies. J Clin Epidemiol. 2014; 67(4): 401–409. PubMed Abstract | Publisher Full Text\n\nvan Haselen RA : Homeopathic clinical case reports: Development of a supplement (HOM-CASE) to the CARE clinical case reporting guideline. Complement Ther Med. 2016; 25: 78–85. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "188236",
"date": "27 Jul 2023",
"name": "Amna Khan",
"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 rationale, research question, and the need of the study has been presented with a precise description of limitations in the existing reporting guidelines corresponding to the Physiotherapy. This proposal identified and addressed an extension to the CARE checklist for Physiotherapy which went unnoticed till now and the initiative would bring a revolutionary change in reporting the efficacy and patient care aspect of the physiotherapy.\nThe methodology has described each and every step of undertaking of Delphi process concisely. The details have been provided with the planning, approach, conduction, and analysis of the outcome of Delphi procedure. The discussion has described the different aspects prompting to the need of this extension. The proposal is written with a perspective of determining the future implication of the extension too.\nFor critically appraising the article, the article sounds suitable for indexing.\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": [
{
"c_id": "11259",
"date": "04 Apr 2024",
"name": "Dr. Waqar Naqvi",
"role": "Author Response",
"response": "Dear Dr. Khan, Greetings, Thank you for your review. We have amended your suggestions in the protocol. Regards, Waqar"
}
]
},
{
"id": "197550",
"date": "29 Aug 2023",
"name": "Soheil Mansour Sohani",
"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 rationale, research questions, and the necessity behind this. The existing reporting guidelines for physiotherapy are outlined, along with their limitations. This proposal identified an overlooked opportunity to enhance the CARE checklist for physiotherapy, which has the potential to revolutionise the reporting of physiotherapy efficacy and patient care. Methodology section meticulously outlines the steps involved in the Delphi process. This covers the planning, approach, execution, and outcome analysis of the Delphi procedure. The discussion section delves into various aspects that underscore the need for this extension. Additionally, the proposal anticipates the future implications of this extension. Although I would like to suggest the authors if they can add the word “Web” to the Delphi process and it will be more suited for the methodology. There is one minor suggestion in the registration section of the manuscript. It would be better to replace “live” with registered words so that sentences are more scientifically sound. Upon critical assessment, the article is deemed scientifically suitable for publication.\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": [
{
"c_id": "11260",
"date": "04 Apr 2024",
"name": "Dr. Waqar Naqvi",
"role": "Author Response",
"response": "Dear Dr. Sohani, Greetings, Thank you for your review. We have amended your suggestions in the protocol. Regards, Waqar"
}
]
}
] | 1
|
https://f1000research.com/articles/12-838
|
https://f1000research.com/articles/12-1087/v1
|
01 Sep 23
|
{
"type": "Brief Report",
"title": "Methylation risk score in peripheral blood predictive of conversion from mild cognitive impairment to Alzheimer's Disease",
"authors": [
"Jarrett D. Morrow"
],
"abstract": "Background: Alzheimer’s disease (AD) is a neurodegenerative and heterogeneous disorder with complex etiology. Mild cognitive impairment (MCI) may represent an intermediate stage of AD, and the ability to identify MCI patients at greater risk of conversion to AD could guide personalized treatments. This study sought to develop a methylation risk score predictive of conversion from MCI to AD using publicly available blood DNA methylation (DNAm) data. Methods: Using blood DNA methylation data from an epigenome-wide association study of AD that included 111 subjects with MCI, a methylation risk score of MCI conversion was created using an elastic-net framework. The elastic-net model was trained with a high-variance subset of the DNAm data, age and sex as predictors. Results: The final model included four CpG sites: PNCK (cg01231576), SLC6A3 (cg09892121), and TRIM62 (cg25342005), with a fourth (cg17292662) near the genes ATP6V1H and RGS20. A significant difference (p < 0.0001, t-test) was observed in the scores for MCI stable subjects compared with MCI converters. No statistically significant difference was observed between AD subjects and controls, suggesting specificity of the risk score for susceptibility to conversion. Conclusions: The ability to identify MCI patients at greater risk of progression could inform early interventions and is a critical component in mitigation strategies for AD. This study provides insight into a potential role for epigenetics in the development of a multi-omic risk score of conversion.",
"keywords": [
"Alzheimer’s disease",
"cognitive decline",
"risk score",
"DNA methylation",
"epigenetics"
],
"content": "Introduction\n\nAlzheimer’s disease (AD) is a neurodegenerative and heterogeneous disorder with complex etiology and devastating impact on individuals and families. Although genome-wide association studies continue to provide insight into the genetic susceptibility to AD,1,2 epigenome-wide association studies (EWAS) and, in particular, studies of DNA methylation (DNAm) have the potential to capture signals related to environmental contributions.3 Mild cognitive impairment (MCI) may represent an intermediate stage of AD4 and the ability to identify MCI patients at greater risk of conversion to AD could guide personalized strategies for mitigation of decline, as the pathology of AD may be present years before onset of symptoms.5 Risk scores that provide predictive measures of AD susceptibility have been created using genetic6,7 and blood transcriptomic data.8 Epigenome-wide associations studies in peripheral blood have identified differentially methylated CpG sites associated with AD9–11 and AD progression.12–16 Associations between peripheral blood epigenetic age acceleration and cognitive function have also been examined.17,18\n\nThis study was focused on development of a methylation risk score (MRS) predictive of conversion from MCI to AD, using publicly available DNA methylation data9 and machine learning methods. This score was evaluated in cross-sectional data in AD subjects and controls in both the primary and a secondary datasets to help understand the relationship of the conversion risk score to overall disease severity. This study provides insight into the value epigenetics could provide in a multi-omic risk score of conversion.\n\n\nMethods\n\nTo create the risk score, blood DNA methylation (DNAm) data from an EWAS of AD in 300 subjects9 were obtained from the Gene Expression Omnibus (GEO: GSE144858). The cross-European AddNeuroMed study dataset includes 93 subjects with Alzheimer’s, 111 with MCI and 96 control subjects. Of the 111 MCI subjects, 68 were stable after one year, 39 converted to AD within one year and four converted at an unknown time. Roubroeks and colleagues9 extracted DNA from the blood samples and assayed DNA methylation levels using the Illumina Infinium Human Methylation 450K BeadChip array. After quality control analyses, they quantile-normalized the data using the dasen method from the R package wateRmelon to create a matrix of beta values (CpG sites in rows and subjects in columns). The data from the four subjects with unknown conversion date were excluded. Two MCI subjects less than 65 years of age, excluded from the study by Roubroeks et al.,9 were included in this study. Prior to the analyses in this study, any CpG site with a detection p-value >0 for any subject was excluded. Using the annotation from Zhou et al.,19 CpG sites with probe mapping issues or having a SNP with minor allele frequencies >1% within five bases were also removed. To reduce the influence of genetics on the prediction models, CpG sites with significant genetic associations (methylation quantitative trait loci: mQTL) in peripheral blood20 were also removed. The beta values for the remaining CG-annotated sites were retained for analysis. To identify possible sex mismatches, multidimensional scaling (MDS) plots were created using the cmdscale function in R and the X and Y chromosome data. MDS plots were also created using high variance DNAm data to observe batch effects. No sex mismatches or batch effects were observed.\n\nAn independent set of blood DNA methylation data from an epigenome-wide meta-analysis of neurodegenerative disorders21 was obtained from the Gene Expression Omnibus. The Australian Imaging, Biomarker & Lifestyle Flagship Study of Aging (AIBL) dataset of 726 subjects included 161 subjects with Alzheimer’s, 94 with MCI and 471 control subjects. Longitudinal information regarding conversion to AD is not available in this study. Nabais and colleagues21 assayed DNAm using the Illumina HumanMethylationEPIC BeadChip Array. Although data processed using functional normalization were publicly available, the methylated and unmethylated intensities were used to create a dataset normalized using dasen in the R package wateRmelon22 to create a matrix of beta values. Prior to normalization, CpG sites with a detection p-value >0 for any subject were excluded. CpG sites with probe mapping issues, nearby SNPs with minor allele frequencies >1%19 or a significant mQTL in peripheral blood20 were also removed. Following dasen normalization, no sex mismatches were observed in the MDS plot created using the X and Y chromosome data. The beta values for the remaining CG-annotated sites were retained for analysis.\n\nA methylation risk score of MCI conversion was created using an elastic-net binomial (classification) model via the R package glmnet.23 This regularized regression method combines the L1 and L2 penalties of the lasso and ridge methods and provides the ability to retain correlated features. To adjust model and feature selection performance, the contribution of each penalty is selected using the hyperparameter alpha. Using DNAm beta values, age and sex as predictors and the MCI outcome (stable or conversion to AD) as the response, a model was trained using a 10-fold cross-validation approach. Given the limited number of MCI subjects, all data were used in the training process. The alpha hyperparameter was chosen to minimize the cross-validation misclassification error. To compare the performance with a score based on demographics only, a binomial risk score model was created using the glm function in R with age and sex as predictors.\n\nReceiver operating characteristic (ROC) curves were created for each fold using the function roc.glmnet and for the final model with all training data using the function roc in the R package pROC.24 Risk scores were calculated using the final conversion risk score model via the predict function in the glmnet package.\n\n\nResults\n\nAfter quality control procedures, peripheral blood DNAm data were available for 251,491 CpG sites and 296 samples, including 93 AD subjects, 107 MCI subjects (68 stable, 39 converter) and 96 controls in the Roubroeks et al. (GSE144858) dataset (Table 1). Approximately 60% of the European subjects were female (52% female among MCI subjects).\n\n* Within one year.\n\nAn elastic net model was trained using the DNAm beta values (range: 0 to 1) for the MCI subjects. The beta values, age, and sex were included as possible predictors and the MCI outcome (stable or conversion to AD) was the response. Blood cell distribution values were not included in the model, seeking an epigenetic prediction model that may capture biology including shifts in cell abundance with conversion to AD. With a focus on more robust signatures, only CpG sites with variance in the top quartile (62,873 CpG sites) were included in the training set. After executing cross-validation for values of alpha from 0 to 1, an alpha value of 0.8 was observed to minimize cross-validation classification error (error = 0.34).\n\nThe final model from this process included four features, all CpG sites (Table 2). Three of the sites are annotated to the genes PNCK (cg01231576), SLC6A3 (cg09892121), and TRIM62 (cg25342005), with a fourth (cg17292662) near the genes ATP6V1H and RGS20. The distribution of the beta values for these sites are centered between 0.6 and 0.8 (Figures S1 to S4, Extended data). ROC curves were produced for each of the 10 folds (Figure S5, Extended data) with alpha=0.8 and the highest observed area under the ROC curve (AUC) was 0.635. A ROC curve was also created using the training data with the final model (Figure S6, Extended data) and the AUC was 0.877.\n\n# Genes with nearby TSS.\n\n* Illumina Infinium 450K BeadChip annotation from Zhou et al.19\n\nThe methylation risk score (predicted probability of conversion) was calculated using the final model and the DNAm beta values. A significant difference (p < 0.0001, t-test) in the score for MCI stable subjects compared with MCI converters may be observed in the box plots of the risk score (Figure 1). For MCI subjects, being above the mean MRS compared with below the mean equates to an odds ratio of 9.8 for conversion. Also included in Figure 1 are the scores for the AD subjects and controls. The seven controls and seven AD cases less than 65 years of age, excluded in the analyses by Roubroeks et al., were included in the MRS calculations in Figure 1. A nominal increase in MRS values may be observed with increased severity at baseline (Figure S7, Extended data), with no statistically significant difference between AD and controls (p = 0.83, t-test), perhaps suggesting specificity of the risk score for susceptibility to conversion. Box plots were created using the beta values for each of the four predictive sites across disease severity, stratified by sex (Figures S8 to S11, Extended data). The direction of effect for DNAm with respect to conversion in the MCI subjects is consistent across males and females.\n\nAfter processing, peripheral blood DNAm data were available for 601,732 CpG sites and 296 samples, including 161 AD subjects, 94 MCI subjects and 471 controls in the Nabais et al. (GSE153712) dataset (Table 1). Approximately 55% of the subjects were female. The MRS was calculated using the final conversion risk score model and the DNAm beta values in this secondary dataset. In the box plots across disease severity (Figure S12, Extended data), the MRS values increase with severity consistent with the discovery dataset. The MRS values are higher overall for the Nabais et al. data compared with Roubroeks et al. The secondary DNAm data were created using the Illumina HumanMethylationEPIC platform in contrast to the use of the Illumina 450K platform by Roubroeks et al.9\n\nFor the risk score created using only age and sex as predictors in the Roubroeks et al. dataset (Figure S13, Extended data), a significant difference was not observed between MCI stable and MCI converter (p = 0.2, t-test) and the AUC was 0.579 with the training data (Figure S14, Extended data).\n\n\nDiscussion\n\nIn this study, a methylation risk score was created to quantify susceptibility to conversion from MCI to AD. Highly variable CpG sites were selected for development of the score, seeking information to inform identification of robust biomarkers. In addition, the effects of genetics were suppressed by excluding sites previously associated with an mQTL or located near a common SNP. Using a modest set of 107 subjects with MCI, the model demonstrated predictive capabilities. The limited set of selected features, an AUC in the training data of 0.877, and a maximum AUC during cross-validation of 0.635 suggests both higher variance and bias. An MRS may find better utility as a component in a comprehensive conversion susceptibility prediction strategy.\n\nTwo of the four predictive CpG sites (cg17292662, cg25342005) were identified in the previous study by Roubroeks and colleagues.9 These two sites were their top two findings in the EWAS of MCI conversion, though neither site was statistically significant. The CpG site cg17292662 is within 6,000 bases of the transcription start sites for two genes: ATP6V1H and RGS20. A prior GWAS has identified a variant in ATP6V1H (ATPase H+ transporting V1 subunit H) influencing human cerebrospinal fluid (CSF) β-site APP cleaving enzyme (BACE) activity.25 Previous studies have suggested that elevated beta-site amyloid precursor protein-cleaving enzyme 1 (BACE1) levels in CSF may be an indicator of MCI and early-stage AD (Zong Arch Gen Psychiatry), with BACE1 a possible therapeutic target.26 The gene RGS20 (regulator of G protein signaling 20) has biased expression in the brain and has been found to be downregulated in AD astrocytes.27 The CpG site cg25342005 is within 1500 bases of TSS of the gene TRIM62 (tripartite motif containing 62), a gene expressed in the brain. The CpG site cg09892121 is located within the gene SLC6A3 (solute carrier family 6 member 3) and was among the top 500 findings in the study by Roubroeks et al.9 The gene SLC6A3 encodes a dopamine transporter and a genetic variant in the gene was previously identified that may confer greater risk of dementia and cognitive decline.28 The fourth predictive site (cg01231576) is within 1500 bases of the PNCK (pregnancy up-regulated nonubiquitous CaM kinase) transcription start site. This site was not among the findings of Roubroeks, as the authors of that study did not include the sex chromosome DNAm data. The gene PNCK has biased expression in the brain and in a recent brain RNA-sequencing study, expression was associated with cognitive trajectories in a sex-specific manner.29 The MRS model leverages DNAm differences in the TSS of PNCK that are concordant across females and males.\n\nLimitations of this study include the small population of MCI subjects with longitudinal outcomes for development of an MRS. Identifying a signature predictive of cognitive decline in peripheral blood presents many challenges with respect to signal and noise and a larger study population with longitudinal data would enhance future MRS creation efforts. The ability to effectively train an MRS model with 80% of the data, while holding out 20% of the data for validation, would provide an effective internal validation. Future efforts may also explore other machine learning frameworks, including deep learning, random forests and support vector machines. The secondary population for MRS evaluation lacked longitudinal outcome data. The disparity between MRS values for the training and secondary datasets may be due to the difference in assay platforms, as low correlations have been previously observed between Illumina 450K and EPIC DNA methylation data in blood for many CpG sites.30\n\nThe ability to identify MCI patients at greater risk of progression could inform early interventions and is a critical component in mitigation strategies for AD. This study is the first to develop a blood-based methylation risk score of conversion from mild cognitive impairment to Alzheimer’s disease. Although the predictive ability of the score is limited, this study demonstrates the potential value epigenetics would add to a risk score based on multi-omic and phenotypic data collected from the same patients.\n\n\nAuthor’s contributions\n\nJDM: conceptualization, methodology, formal analysis, interpretation of data, manuscript preparation and approval of the final version",
"appendix": "Data availability\n\nGene Expression Omnibus: An epigenome-wide association study of Alzheimer’s disease blood highlights robust DNA hypermethylation in the HOXB6 gene, https://identifiers.org/geo:GSE144858. 9\n\nGene Expression Omnibus: Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders, https://identifiers.org/geo:GSE153712. 21\n\nZenodo: Methylation risk score in peripheral blood predictive of conversion from mild cognitive impairment to Alzheimer’s Disease, https://doi.org/10.5281/zenodo.8189746.\n\nThis project contains the following extended data:\n\n- Methylation_Risk_Score_Supplemental.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\nBellenguez C, Küçükali F, Jansen IE, et al.: New insights into the genetic etiology of Alzheimer’s disease and related dementias. Nat. Genet. 2022 Apr; 54(4): 412–436. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWightman DP, Jansen IE, Savage JE, et al.: A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. Nat. Genet. 2021 Sep; 53(9): 1276–1282. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHannon E, Lunnon K, Schalkwyk L, et al.: Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. Epigenetics. 2015 Oct 12; 10(11): 1024–1032. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorris JC, Storandt M, Miller JP, et al.: Mild Cognitive Impairment Represents Early-Stage Alzheimer Disease. Arch. Neurol. 2001 Mar 1; 58(3): 397–405. PubMed Abstract | Publisher Full Text\n\nMarkesbery WR: Neuropathologic Alterations in Mild Cognitive Impairment: A Review. J. Alzheimers Dis. JAD. 2010 Jan; 19(1): 221–228. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeonenko G, Baker E, Stevenson-Hoare J, et al.: Identifying individuals with high risk of Alzheimer’s disease using polygenic risk scores. Nat. Commun. 2021 Jul 23; 12(1): 4506. PubMed Abstract | Publisher Full Text | Free Full Text\n\nManzali SB, Yu E, Ravona-Springer R, et al.: Alzheimer’s Disease Polygenic Risk Score Is Not Associated With Cognitive Decline Among Older Adults With Type 2 Diabetes. Front. Aging Neurosci. 2022 [cited 2023 Jul 26]; 14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPark YH, Hodges A, Simmons A, et al.: Association of blood-based transcriptional risk scores with biomarkers for Alzheimer disease. Neurol Genet. 2020 Dec 1; 6(6): e517. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoubroeks JAY, Smith AR, Smith RG, et al.: An epigenome-wide association study of Alzheimer’s disease blood highlights robust DNA hypermethylation in the HOXB6 gene. Neurobiol. Aging. 2020 Nov 1; 95: 26–45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVasanthakumar A, Davis JW, Idler K, et al.: Harnessing peripheral DNA methylation differences in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease. Clin. Epigenetics. 2020 Jun 15; 12(1): 84. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChouliaras L, Pishva E, Haapakoski R, et al.: Peripheral DNA methylation, cognitive decline and brain aging: pilot findings from the Whitehall II imaging study. Epigenomics. 2018 May; 10(5): 585–595. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi QS, Vasanthakumar A, Davis JW, et al.: Association of peripheral blood DNA methylation level with Alzheimer’s disease progression. Clin. Epigenetics. 2021 Oct 15; 13(1): 191. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFransquet PD, Lacaze P, Saffery R, et al.: Blood DNA methylation signatures to detect dementia prior to overt clinical symptoms. Alzheimers Dement. Diagn. Assess. Dis. Monit. 2020; 12(1): e12056. Publisher Full Text\n\nPérez RF, Alba-Linares JJ, Tejedor JR, et al.: Blood DNA Methylation Patterns in Older Adults With Evolving Dementia. J. Gerontol. Ser. A. 2022 Sep 1; 77(9): 1743–1749. PubMed Abstract | Publisher Full Text | Free Full Text\n\nManzali S, Ravona-Springer R, Jacob-Hirsch J, et al.: Blood DNA methylation biomarkers for cognitive decline in older adults with type 2 diabetes. Alzheimers Dement. 2023; 19(S2): e065120. Publisher Full Text\n\nLunnon K, Smith RG, Cooper I, et al.: Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus. Neurobiol. Aging. 2015 Mar 1; 36(3): 1600.e1–1600.e4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShadyab AH, McEvoy LK, Horvath S, et al.: Association of Epigenetic Age Acceleration With Incident Mild Cognitive Impairment and Dementia Among Older Women. J. Gerontol. Ser. A. 2022 Jun 1; 77(6): 1239–1244. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFransquet PD, Lacaze P, Saffery R, et al.: Accelerated Epigenetic Aging in Peripheral Blood does not Predict Dementia Risk. Curr. Alzheimer Res. 2021; 18(5): 443–451. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou W, Laird PW, Shen H: Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 2017 Feb 28; 45(4): e22. PubMed Abstract | Publisher Full Text\n\nMcRae AF, Marioni RE, Shah S, et al.: Identification of 55,000 Replicated DNA Methylation QTL. Sci. Rep. 2018 Dec [cited 2019 Mar 25]; 8(1): 17605. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nNabais MF, Laws SM, Lin T, et al.: Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol. 2021 Mar 26; 22(1): 90. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPidsley R, Wong CCY, Volta M, et al.: A data-driven approach to preprocessing Illumina 450K methylation array data. BMCGenomics. 2013; 14(14). Publisher Full Text\n\nFriedman JH, Hastie T, Tibshirani R: Regularization Paths for Generalized Linear Models via Coordinate Descent. J. Stat. Softw. 2010; 33(1): 1–22. PubMed Abstract\n\nRobin X, Turck N, Hainard A, et al.: pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011; 12: 77. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu H, Li H, Li J, et al.: Alzheimer’s Disease Neuroimaging Initiative. Genome-wide association study identified ATP6V1H locus influencing cerebrospinal fluid BACE activity. BMC Med. Genet. 2018 May 11; 19(1): 75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHampel H, Vassar R, De Strooper B, et al.: The β-Secretase BACE1 in Alzheimer’s Disease. Biol. Psychiatry. 2021 Apr 15; 89(8): 745–756. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPreman P, Alfonso-Triguero M, Alberdi E, et al.: Astrocytes in Alzheimer’s Disease: Pathological Significance and Molecular Pathways. Cell. 2021 Mar 4; 10(3): 540. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoussotte FF, Gutman BA, Hibar DP, et al.: Carriers of a common variant in the dopamine transporter gene have greater dementia risk, cognitive decline, and faster ventricular expansion. Alzheimers Dement. J. Alzheimers Assoc. 2015 Oct; 11(10): 1153–1162. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDavis EJ, Solsberg CW, White CC, et al.: Sex-Specific Association of the X Chromosome With Cognitive Change and Tau Pathology in Aging and Alzheimer Disease. JAMA Neurol. 2021 Oct 1; 78(10): 1249–1254. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLogue MW, Smith AK, Wolf EJ, et al.: The correlation of methylation levels measured using Illumina 450K and EPIC BeadChips in blood samples. Epigenomics. 2017 Nov; 9(11): 1363–1371. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "226564",
"date": "19 Dec 2023",
"name": "Adam Smith",
"expertise": [
"Reviewer Expertise Epigenetics",
"differential methylation."
],
"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\nMorrow develops a methylation risk score (MRS), based on publicly available blood DNA methylation data, with the aim to predict progression from mild cognitive impairment (MCI) to Alzheimer’s disease (AD). The author uses machine learning methodology and identifies methylation levels at four genomic loci that, in combination with age and sex, form the final MRS for conversion to AD. This study is novel and has the potential to elucidate a useful conversion susceptibility prediction method, either alone or in conjunction with other measures. However, at this stage there are considerable limitations and improvements that need to be addressed before I can recommend publication. Given the limitations including cohort size and lack of validation, the conclusions drawn are overstated. Major Revisions:\nDetection p value >0 led to exclusion of that probe. I would suggest that this is a typo or rounding error as a threshold of p>0 would yield 0 probes for downstream processing. Secondary dataset does not have suitable data to replicate model derived from primary data. The application of MRS onto this cohort gives little to no validation of the model. Further work is needed using an alternative dataset or splitting the initial cohort into a design vs. test approach to better validate the score. Para 13 – last line, “The MRS model leverages DNAm differences in the TSS of PNCK that are concordant across females and males.” This is incorrect looking at the beta vales presented in Figure S8, this site shows a beta difference of 0.05 (5%) in controls between males and females with a similar difference seen across disease states. This difference is considerably larger than the differences seen between disease states and is a strong argument for the removal of sex chromosomes from the analysis. Comment on the absence of age information in secondary cohort, was this information not needed for the final MRS calculation in this cohort?\n\nMinor Revisions:\nPara 1 – line 5, “stage of AD progression and the…” add \"progression\" to improve readability of this sentence . Para 2 – line 1, “on the development” add \"the\" to improve readability of this sentence. Para 7 – line 3, “seeking an epigenetic…” Suggest “To enable an epigenetic prediction model that is accurate despite shifts in cell abundance, blood cell distribution values were not included in the model.” Para 13 – line 2, “These two sites were their top two findings in the EWAS of MCI conversion, though neither site was statistically significant.” Sites were significant but did not reach multiple testing correction threshold. S6 ROC curve to be moved to main paper and legend expanded. Table 1 moved to supplementary. Table 2, “#genes with nearby TSS” – define nearby. Figure 1, a suitable legend is needed, with statistical significance quoted for all analyses.\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? I 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": [
{
"c_id": "11250",
"date": "04 Apr 2024",
"name": "Jarrett Morrow",
"role": "Author Response",
"response": "Reviewer 1: The comments and suggestions from Reviewer #1 have greatly helped to improve the manuscript and I hope the Reviewer finds the revised manuscript suitable for approval. Major Revisions: C1. Detection p value >0 led to exclusion of that probe. I would suggest that this is a typo or rounding error as a threshold of p>0 would yield 0 probes for downstream processing. R1. The Reviewer noticing this in the manuscript is appreciated. A significant percentage of the p-values in the detection p-value matrix had a value of zero. Therefore, any site having a p-value > 0 for any subject was considered of lower quality. The exclusion of these 82,090 sites is mentioned in the supplemental table (Table S1) added to the revised extended data that outlines the quality control process for the primary data. C2. Secondary dataset does not have suitable data to replicate model derived from primary data. The application of MRS onto this cohort gives little to no validation of the model. Further work is needed using an alternative dataset or splitting the initial cohort into a design vs. test approach to better validate the score. R2. The Reviewer is correct. The secondary dataset was not used to identify replication of the trends observed in the longitudinal primary data. This was mentioned in the limitations “The secondary population for MRS evaluation lacked longitudinal outcome data.”. However, to clarify this further, the fifth paragraph of Results was edited to note concordance of the score at baseline in the primary with the cross-sectional secondary data. Given the smaller dataset, a cross-validation approach was used to create within-cohort validation. In future studies within larger cohorts, an 80/20 split would be feasible as outlined in the discussion. With the predictive ability of the score limited, multi-omic scores in larger populations may be a better approach as mentioned in the conclusions. Please also note the updates to the methods and revised model described in the response to Reviewer #2. C3. Para 13 – last line, “The MRS model leverages DNAm differences in the TSS of PNCK that are concordant across females and males.” This is incorrect looking at the beta vales presented in Figure S8, this site shows a beta difference of 0.05 (5%) in controls between males and females with a similar difference seen across disease states. This difference is considerably larger than the differences seen between disease states and is a strong argument for the removal of sex chromosomes from the analysis. R3. These insightful comments from the Reviewer are appreciated. Based on reviewer comments, the model was revised and the model now includes three of the same CpG sites. However, the PNCK site is no longer included. Please see the response to Reviewer #2 for additional details. Constructing sex-stratified MRS models could be an effective approach to address similar issues in future studies. C4. Comment on the absence of age information in secondary cohort, was this information not needed for the final MRS calculation in this cohort? R4. The request for the clarification is appreciated. Subject age was not retained in the elastic-net model for the primary/discovery dataset, as mentioned in the third paragraph of the Results. Only the three CpG sites in Table 1 were included in the final MRS model. Minor Revisions: C1. Para 1 – line 5, “stage of AD progression and the…” add \"progression\" to improve readability of this sentence. R1. The sentence has been improved by this suggested revision. C2. Para 2 – line 1, “on the development” add \"the\" to improve readability of this sentence. R2. The sentence has been improved by this suggested revision. C3. Para 7 – line 3, “seeking an epigenetic…” Suggest “To enable an epigenetic prediction model that is accurate despite shifts in cell abundance, blood cell distribution values were not included in the model.” R3. The sentence has been improved by this suggested revision. C4. Para 13 – line 2, “These two sites were their top two findings in the EWAS of MCI conversion, though neither site was statistically significant.” Sites were significant but did not reach multiple testing correction threshold. R4. The revised manuscript includes a mention of multiple testing correction. C5. S6 ROC curve to be moved to main paper and legend expanded. R5. The revised Supplemental Figure S6 is now Figure 1 in the main document with additional information in the caption. C6. Table 1 moved to supplementary. R6. Table 1 is now Supplemental Table S2. C7. Table 2, “#genes with nearby TSS” – define nearby. R7. This information has been added to Table 1 (formerly Table 2). C8. Figure 1, a suitable legend is needed, with statistical significance quoted for all analyses. R8. A more detailed caption for Figure 2 (formerly Figure 1 – now updated using revised model) has been included in the revised manuscript."
}
]
},
{
"id": "235879",
"date": "06 Feb 2024",
"name": "Rachel Cavill",
"expertise": [
"Reviewer Expertise Data science applied to biological data",
"in particular",
"omics data."
],
"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 paper presents an interesting analysis of using methylation data to predict cognitive decline in alzheimers. However, I have serious concerns about the results, in particular with regard to over-fitting of the model.\nPotential indications of over-fitting:\n* Figure 1 shows the box-plot of the methylation risk scores (MRS) for the different groups of subjects. If this score was a real predictor of cognitive impairment and its development into alzheimers disease (AD), the a priori hypothesis would be that the subjects with AD would have more extreme scores than the mild-converters, this is not shown to be the case, with the AD group having intermediate scores between the mild-converters and the controls.\n* The MRS score is based off just 4 methylation sites. The initial full dataset contained >250,000 sites and therefore it would be very easy to find a small subset which is predictive by chance.\n* The cross validation AUC is significantly lower (0.635) than the training AUC (0.877), which is a sign of over-fitting the training set, given that the methods describe optimising the cross validation mis-classification error, it seems likely that the cross validation AUC is also over-fitted and an independent test set would display an even lower AUC.\n\n* The discussion that 2/4 CpG sites were previously identified is not evidence backing this up, as this result was obtained in a previous analysis of the same dataset. It would be unusual that two different analyses of the same dataset failed to find similar results (even when the analyses use different methods). A false positive CpG site in one analysis is likely to show up as a false positive in a different analysis on the same dataset.\nIndividually each of these indications is not conclusive, but put together they indicate a very strong likelihood of overfitting occuring.\n\n* The secondary dataset is not suitable to be used as an independent validation set, the study design is too different.\nAdditionally, I raise concerns about the description in the methods of \"any CpG site with a detection p-value > 0 for any subject was excluded\", this would surely exclude all detected CpGs, as a p-value of 0 for detection, surely indicates an undetected CpG site in that sample, and p-values can not go negative.\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? No\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": "11251",
"date": "04 Apr 2024",
"name": "Jarrett Morrow",
"role": "Author Response",
"response": "Reviewer 2: Updates to the manuscript prompted by the comments and suggestions from Reviewer #2 have greatly helped to improve the manuscript, through both a revised approach and more clarification regarding the limitations of the study. I hope the Reviewer finds the revised manuscript suitable for approval. C1. Figure 1 shows the box-plot of the methylation risk scores (MRS) for the different groups of subjects. If this score was a real predictor of cognitive impairment and its development into alzheimers disease (AD), the a priori hypothesis would be that the subjects with AD would have more extreme scores than the mild-converters, this is not shown to be the case, with the AD group having intermediate scores between the mild-converters and the controls. R1. These comments by the Reviewer regarding an a priori hypothesis are much appreciated. However, with the elastic-net model trained using longitudinal outcomes of decline instead of cross-sectional disease severity, the specific hypothesis proposed by the reviewer was not supported by the findings of the study. However, in the fourth paragraph of Results, a nominal increase in MRS values with increased severity at baseline was noted. While the observations suggest specificity of the risk score for susceptibility to conversion, a nominally higher score in AD provides evidence to support the spirit of the reviewer comment regarding AD and MCI scores. C2. The MRS score is based off just 4 methylation sites. The initial full dataset contained >250,000 sites and therefore it would be very easy to find a small subset which is predictive by chance. R2. This comment from the Reviewer is appreciated. An elastic-net model was the focus of the study, as this method seeks a model with fewer features to help avoid overfitting. In addition, to emphasize biological significance in the model, the variance of DNA methylation was considered. That is, the full set of methylation sites was filtered to approximately 63,000 sites based on variance, as low-variance sites may be less useful in practical applications. A predictive model leveraging a small number of features is not typically considered of lesser value. For example, a recent Nature Communications (2022) paper, van Breugel and colleagues (PMCID: PMC9715628) created a three CpG site predictor of allergic disease in a cohort of 348 subjects. This is one example of predictive models based on a limited set of features that have been developed in various tissues and complex diseases. C3. The cross validation AUC is significantly lower (0.635) than the training AUC (0.877), which is a sign of over-fitting the training set, given that the methods describe optimising the cross validation mis-classification error, it seems likely that the cross validation AUC is also over-fitted and an independent test set would display an even lower AUC. R3. I completely agree with this comment by the Reviewer and thank the Reviewer for the insight. The last sentence in the first paragraph of the Discussion states: \"The limited set of selected features, an AUC in the training data of 0.877, and a maximum AUC during cross-validation of 0.635 suggests both higher variance and bias. An MRS may find better utility as a component in a comprehensive conversion susceptibility prediction strategy.\" However, while revisiting the model development and results, prompted by the reviewer comments, the approach was modified to include mean squared error as the measure instead of misclassification error. With this change, an alpha of 1 now produced the lower error. In addition, lambda was chosen to reduce overfitting, leading to a three-site model. As a result, the AUC for the training data was 0.843, the average AUC across the ten folds was 0.752 and the out-of-fold AUC was 0.653. Revisions were made to the manuscript to reflect these methods changes. I found the updated results demonstrating improved performance encouraging and I hope the Reviewer also views these revised findings favorably. C4. The discussion that 2/4 CpG sites were previously identified is not evidence backing this up, as this result was obtained in a previous analysis of the same dataset. It would be unusual that two different analyses of the same dataset failed to find similar results (even when the analyses use different methods). A false positive CpG site in one analysis is likely to show up as a false positive in a different analysis on the same dataset. R4. These insightful comments from the Reviewer are appreciated. The discussion regarding the selected sites in the original study was not intended to justify the predictive model. However, the discussion of the two sites from the study by Roubroeks and colleagues is relevant to the current study, as it seemed unethical to omit these details and claim the sites as novel findings, particularly given the current study uses publicly available data linked to the Roubroeks et al. study. C5. The secondary dataset is not suitable to be used as an independent validation set, the study design is too different. R5. Although the particular aspects of the secondary data raising a concern were not noted by Reviewer #2, this appears to be similar to the second set of comments from Reviewer #1. With the secondary dataset not used to identify replication of score trends observed in the longitudinal primary data, clarifying text was added in the fifth paragraph of the Results to note concordance of the score at baseline in the primary data with the cross-sectional secondary data. C6. Additionally, I raise concerns about the description in the methods of \"any CpG site with a detection p-value > 0 for any subject was excluded\", this would surely exclude all detected CpGs, as a p-value of 0 for detection, surely indicates an undetected CpG site in that sample, and p-values can not go negative. R6. The reviewer noticing this in the manuscript is appreciated. As outlined in my response to Reviewer 1 (response #1), a significant percentage of the overall p-values in the detection p-value matrix had a value of zero. Therefore, any site having a p-value > 0 for any subject was considered of lower quality. The exclusion of these 82,090 sites is mentioned in the supplemental table (Table S1) added to the revised extended data that outlines the quality control process for the primary data."
}
]
}
] | 1
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https://f1000research.com/articles/12-1087
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https://f1000research.com/articles/12-612/v1
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06 Jun 23
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{
"type": "Research Article",
"title": "ERCP-induced perforation: review and revisit after half a century",
"authors": [
"Abdel Rahman A. A. Al Manasra",
"Zaid Mesmar",
"Tarek Manasreh",
"Hanan M . Hammouri",
"Anas Husein",
"Khaled Jadallah",
"Mohammed Bani hani",
"Niazy Abu Farsakh",
"Shatha K. Shahwan",
"Doaa Al-qaoud",
"Jehad Fataftah",
"Zaid Mesmar",
"Tarek Manasreh",
"Hanan M . Hammouri",
"Anas Husein",
"Khaled Jadallah",
"Mohammed Bani hani",
"Niazy Abu Farsakh",
"Shatha K. Shahwan",
"Doaa Al-qaoud",
"Jehad Fataftah"
],
"abstract": "Background: Endoscopic retrograde cholangiopancreatography (ERCP) is an invasive procedure. We aimed to investigate ERCP-induced perforations at our institution and conduct a comprehensive review of literature on ERCP-induced perforations (EIP) since the introduction of this procedure as a therapeutic intervention. Methods: This was a case-control study, in which charts of all patients diagnosed with ERCP-induced duodenal perforation were reviewed and compared to a control group without perforation. Patient’s sociodemographic and clinical data, including ERCP procedure-related data, were gathered. Results: A total of 996 ERCP procedures were performed; only 13 patients proved to have EIP. Obstructive jaundice was the most common indication for ERCP. The main predisposing factor was difficult cannulation (P = 0.003). In total, five patients required surgical treatment; the majority of them had type I perforation, whereas type IV was the most common in patients who were treated conservatively. The overall mortality rate was 15%, the surgical group had a slightly higher mortality rate. Conclusions: Fifty years after the introduction of ERCP for therapy, it remains an invasive procedure that carries significant morbidity and mortality, even in skilled hands or at high- volume units. Conservative management of perforation yields favorable outcomes in selected patients.",
"keywords": [
"ERCP",
"duodenal perforation",
"Stapfer classification",
"Obstructive jaundice",
"Choledocholithiasis"
],
"content": "Introduction\n\nEndoscopic retrograde cholangiopancreatography (ERCP) is one of the most commonly utilized procedures for both diagnostic and therapeutic indications. It was first developed in clinical practice in 1968 as a diagnostic tool.1 Cannulation of the ampulla and sphincterotomy were introduced in the early 1970s with consequent evolution of ERCP into a therapeutic procedure.1,2 Nowadays ERCP is almost exclusively indicated for the therapy of hepatobiliary disorders since other less invasive diagnostic modalities (for example: magnetic resonance cholangiopancreatography (MRCP)) which possess similar sensitivity, are widely available.\n\nIn spite of the valuable contribution of ERCP in patients’ management, it is not a complication-free intervention. The ERCP-related morbidity was estimated to be 6.9%; it also carries a mortality rate of 0.33%.3 The spectrum of complications includes pancreatitis being the most common, followed by cholangitis, bleeding and perforation. The incidence of severe complications is approximately four times higher in ERCP than in other endoscopic procedures.4\n\nOne of the most feared complications is ERCP-induced perforation (EIP). Although EIP is uncommon, it is potentially fatal. Moreover, the treatment of such complication is still controversial.\n\nThis study represents the first analysis of EIPs in Jordan. Along with this analysis, we aimed to conduct a comprehensive review of literature for ERCP-induced perforations since the introduction of this procedure as a therapeutic intervention.\n\n\nMethods\n\nThis was a retrospective study in which gastroenterology, surgery, anesthesiology, and intensive care data were collected from the electronic medical charts of patients who underwent ERCP during the period of January 2016 to June 2020.\n\nThe following information was extracted: patient demographics, comorbidities, indication for endoscopy, ERCP findings, presumed risk factors for difficult procedure (sphincterotomy versus precut, dilatation procedures, failed cannulation and relevant past anatomy-altering operation). In addition, clinical presentation of perforation, radiologic findings, time to diagnosis, as well as perforation type according to the Stapfer classification5 (Type I: lateral – free wall – or medial duodenal wall perforation, type II: peri-Vaterian injuries, type III: distal bile duct or pancreatic duct perforation, type IV: retroperitoneal air alone) were all documented. The treatment approach (conservative or operative), need for additional interventions (e.g. percutaneous drainage), length of hospital stay (LOS), morbidity, and mortality are also reported.\n\nSex and gender differences between participants were not taken into consideration, because in this study, the choice of design is little affected by implications of sex and gender. The sex of participants was defined based on self-report.\n\nPatients who were diagnosed to have endoscopic perforation (EP) either during ERCP or by imaging studies such as computed tomography (CT) were included. As a control group, 43 patients without ERCP-related complications were randomly selected from the same time period. The randomization process was done by selecting a control patient from every 23 patients after arranging the 966 patients chronologically by ERCP date.\n\nThe study protocol was reviewed and approved by the Institutional Review Board at King Abdullah University Hospital and by the Committee of Research on Human Subjects at the Jordan University of Science and Technology (Non-funded research No: 20200428). Patients’ data were kept anonymous and confidential. All study procedures were conducted according to the World Medical Association Declaration of Helsinki.\n\nThe management plan was dictated by the attending surgeon on call. Patients who were treated conservatively were kept nil per OS and received intravenous fluids, broad spectrum antibiotics and placement of a nasogastric tube. Failure to improve with conservative management, alarming CT findings and the presence of diffuse peritonitis were considered indications for operative treatment. Patients received percutaneous drainage for intra-abdominal collections and enteral or parenteral feeding as appropriate.\n\nData were managed and analyzed using JMP (version 15). Statistical summaries were presented. Q-Q plots were used to examine normality assumption for continuous variables. Afterward, significant differences in participants’ characteristics were analyzed using a t-test, Fisher exact test or logistic regression. Additionally, odds ratios were used for significant results. Alpha was set at 0.05.\n\n\nResults\n\nA total of 996 ERCP procedures were performed by three endoscopists. Thirteen patients (1.34%) were diagnosed with EIP. Additionally, 43 other patients who also underwent ERCP, but with no endoscopic induced perforation were randomly selected as a control group (Table 1).\n\na HTN, hypertension.\n\nb DM, diabetes mellitus.\n\nc IHD, ischemic heart disease.\n\nd NS, not Significant.\n\ne SD, standard deviation.\n\nEIP group: There were nine women (69%) and four men (31%) with a mean age of 52.6 years. Approximately two-thirds (69%) of patients had hypertension, 18.9% had diabetes mellitus while none were diagnosed to have ischemic heart disease. Only two patients (15%) had a history of abdominal surgery, both of which were laparoscopic cholecystectomy. One patient had pancreatic adenocarcinoma and another patient was known to have cholangiocarcinoma.\n\nERCP indications\n\nBy far, the most common indication for ERCP was obstructive jaundice (61%), followed by choledocholithiasis (23%). Other indications included gallstone pancreatitis and bile leak after cholecystectomy (Table 2).\n\na CBD, Common bile duct.\n\nb NS, not significant.\n\nc not applicable.\n\nd EIP, Endoscopic Induced Perforation.\n\nERCP characteristics\n\nDilated common bile duct (CBD) was observed in 31% of cases and 15% had a filling defect. Precut papillotomy was performed for 85% of the EIP group, 23% had a stone extracted during ERCP. Failure of cannulation was experienced in half of patients (six patients, 46%).\n\nPatient’s characteristics\n\nNotably, a higher number of patients had hypertension in the EIP group compared to the non-EIP group (69% versus 47%) but fewer had diabetes mellitus (18.9% versus 22.5%) with no statistical significance (Table 1).\n\nIndications for ERCP\n\nThe presence of obstructive jaundice and post-cholecystectomy bile leak were more common indications in the EIP compared to the non-EIP group (61% versus 53% and 7% versus 2% respectively). Choledocholithiasis (23% versus 28%), cholangitis (4% versus 0%) and gallstone pancreatitis (7% versus 11%) were more common indications in the non-EIP group. However, the observed differences in the ERCP indications did not reach statistical significance (Table 2).\n\nERCP characteristics\n\nFailure to cannulate the common bile duct showed significant association with EIP in contrast to the non-EIP (46% versus 6%; P = 0.003). Interestingly, patients who underwent CBD dilatation experienced substantially lower rates of EIP (31% versus 67%: P = 0.0214). The presence of CBD dilatation and filling defects was less common among the EIP group (31% versus 46% and 15% versus 26% respectively) but with no statistical significance. We found that the most significant risk factor and predictor of duodenal perforation during ERCP was failure of cannulation with an odds ratio of 11.4 (P = 0.003).\n\nDiagnosis and management\n\nThe majority of patients (11 patients, 84%) were diagnosed with EIP using CT scan while the remaining two patients (16%) were diagnosed during ERCP. One of the two patients developed extensive surgical emphysema during the operation while the other was diagnosed by directly visualizing the contrast extravasation through the duodenum. Of the patients diagnosed after the procedure, the most common symptom was abdominal pain (11 patients, 84%) with the remaining two patients (14%) presenting in the form of peritonitis.\n\nConservative treatment was preferred for eight patients (61%), while five patients (39%) were treated operatively; (Table 3). Operatively treated patients were of a younger age and had less comorbidities such as hypertension and diabetes, which might have influenced the choice of management. Moreover, half of the conservatively-treated group had a history of abdominal surgery, namely laparoscopic cholecystectomy, compared to only one patient (20%) in the surgical group, which could also have affected the surgeon’s choice of treatment. Conservatively managed patients had more dilated CBD as opposed to the surgically treated (37% versus 20%). Papillotomy, dilatation of CBD and stone extraction were much more commonly performed in the conservatively treated group (100% versus 60%, 50% versus 0% and 37.5% versus 0%, respectively). Otherwise, there was no significant differences in ERCP characteristics between the surgical and the conservatively treated groups (Table 3).\n\na HTN, hypertension.\n\nb IHD, ischemic heart disease.\n\nc DM, diabetes mellitus.\n\nd CBD, Common bile duct.\n\ne NS, not significant.\n\nf NA, not applicable.\n\ng SD, standard deviation.\n\nTreatment according to perforation type\n\nOverall, 75% of patients who had type I perforation were treated surgically whereas none of patients with type III or type IV perforation were operated. Type II perforation was divided between conservative treatment (two patients) and surgical management (one patient).\n\nPerforation type by treatment\n\nThe majority (80%) of the surgically treated patients had type I perforation. Of those treated conservatively, three had type IV perforation, two had type II perforation, two had type I perforation and 1 had type III perforation (Table 4).\n\na CBD, Common bile duct.\n\nb RP, retroperitoneal.\n\nc LOS, length of hospital stay.\n\nd SD, Standard deviation.\n\ne TPN, Total parenteral nutrition.\n\nf ICU, Intensive Care Unit.\n\nSurgically treated patients stayed longer in the hospital with an average of 24 days compared to 17.25 days for the conservatively treated group (Table 4). Additionally, ICU admission rates and the average LOS in the ICU were both higher among the surgically treated patients (60% versus 25% and 7.94 versus three days). Major complications were noted in slightly higher rates among the surgical group. Of those treated surgically, one patient (20%) suffered from an intra-abdominal abscess requiring drainage and another patient (20%) developed pneumonia. On the other hand, one patient (12.5%) among the conservatively treated patients had an intra-abdominal abscess requiring drainage and another patient (12.5%) sustained acute kidney injury. About half of the patients in both groups received enteral or parenteral feeding at some point of their hospital stay. The overall mortality rate was 15% with a slightly higher rate in the surgical group (20% versus 12.5%).\n\n\nDiscussion\n\nIn this study, we investigated the incidence rate of duodenal perforation among patients undergoing ERCP and compared patients’ and procedure’s characteristics to a control group. Our results revealed that perforations occurred in a comparable rate (1.34%) to published series. Our study also disclosed that failure to cannulate the CBD was the main predictor of perforation during ERCP.\n\nThe reported incidence of ERCP related perforations varied between 0.11% and 2.4%.6,7 In one large analysis of 21 prospective surveys of post-ERCP complications in adults (16,855 patients) between 1977-2006, 101 patients experienced perforation (0.60%). The mortality rate in that study was 9.9%.3 In another review of 18 (mainly retrospective) studies conducted between 2000-2014, the incidence rate of EIP was 0.39%, with an overall mortality of 7.8%.8 Surprisingly, published numbers did not seem to decline significantly over the last 20 years as ERCP became more popular and widely available.\n\nPublished data revealed that the incidence rate of ERCP perforations corresponds with volume of cases at each institution, as highes-volume centers (which perform more than 1000 ERCPs per year) reported lower incidence rates (Bill et al., 0.44%, Jin et al., 0.27%, Kim J et al., 0.61%, Howard et al., 0.6%, Dubecz et al., 0.09%),9–13 compared to the lower volume ones (less than 500 ERCPs per year) (Turner et al., 2.4%, Stapler et al., 1%, Miller et al., 1.65%, Rabie et al., 1.67%, Koc et al., 0.94%).5,6,14–16 The correlation between incidence of perforation and volume of ERCP cases needs further analysis to elaborate statistical significance. These observations, however, indicate that ERCP remains an invasive procedure which may carry significant morbidity and mortality, even in skilled hands or at high volume units.\n\n“Difficult cannulation” is a term employed to describe failure to gain access into the bile duct by the conventional cannulation technique. Factors that may contribute to this difficulty include presence of periampullary diverticula, altered anatomy and bulky papilla. In many studies, this situation has been defined as a leading cause of perforation.17 The risk is highest as precut papillotomy (or sphincterotomy) is attempted by the endoscopist to overcome this challenge. In Vezakis et al.’s review, endoscopic sphincterotomy was responsible for 41% of perforations.8 Another study by Stapfer and colleagues found that cannulation of the ampulla was considered difficult by the endoscopist in 10 of 14 patients who had perforations (out of 1413 ERCPs).5 In their review of 21 prospective reports of ERCP complications, Andriulli et al., found that the overall complication rate was significantly higher whenever therapeutic interventions were utilized during ERCP.3 Complications were also significantly higher in studies with a precut sphincterotomy rate of over 10%. Fifty years after the advent of therapeutic ERCP, difficult cannulation is still a frequently encountered condition, which may – although rarely – predispose to perforation and subsequent morbidity and death.\n\nThere appears to be a consensus on electing surgery for the treatment of free duodenal wall perforations (type I), which commonly present with signs of peritonitis.12,18–20 In our group of patients with perforation, surgery was required in 5/13(38%), 4/5 of the operated patients had type I (free wall) perforation. Surgical intervention is conducted in higher risk injuries that are more likely to progress into sepsis, which explains – in part – the higher morbidity observed in this subgroup. Because duodenal or duct wall defect identification during surgery might be very challenging, especially if diagnosis is delayed (>6 hours post ERCP),21,22 surgery can be limited to perform proper drainage and debridement of unhealthy tissue, which can reduce the risk of systemic manifestations and sepsis. Diversion surgeries (Roux-en-Y bypass) have been reported in management of large duodenal perforations.5 However, in ERCP most perforations are small, unless caused by the scope itself.\n\nEndoscopic repair of duodenal perforations, particularly small defects(<10mm) that are recognized during ERCP has been reported.23,24 The latter development of endoscopic clipping (through-the-scope clips), suturing and closure devices (ligation band, fibrin glue, and endo-loops) as well as covering luminal stents has made endoscopy more efficient in treating injuries similar to perforations and bleeding.25–31 With the growing body of evidence supporting the use of these techniques for the management of ERCP complications, endoscopist expertise, perforation type and diameter remain important predictors of the outcomes.\n\nIn other types of perforation, i.e. types I, II and IV, the injury is less likely to manifest as peritonitis, but rather as retroperitoneal (and to a less extent intraperitoneal) fluid or air accumulation. Conservative measures in such circumstances vary from simply restricting oral intake with parenteral nutrition, hydration and coverage with broad spectrum antibiotics to percutaneous drainage of collections under ultrasound or CT guidance.\n\nIt is critical to recognize if leakage has stopped after the endoscopy or is still ongoing, as the patient may have experienced transient fluid extravasation during the procedure due to duct or duodenal wall puncture. The presence of enlarging pockets of pus or fluid collections, especially in the retroperitoneal space, does not necessarily indicate an active leakage, which can usually be excluded utilizing CT scan with water soluble contrast (Gastrografin), or fluoroscopic imaging (meal). This may instead indicate inadequate drainage or persistent infection that mandates repositioning of the drain, upgrading the size of the drain or placing another drain. It may also be helpful to consider adding antifungals after submitting samples for cultures.\n\nThe following are literature-based guidelines which can be driven to conclude when and how to intervene in patient with suspected or proved ERCP-induced perforation:\n\n• Suspicion is raised whenever cannulation is difficult, the threshold for obtaining a post ERCP CT scan to exclude perforation has to be lowered, since early detection may improve outcomes.\n\n• Active intraperitoneal contrast extravasation from duodenal wall on CT scan is considered a reasonable indication for prompt operative exploration.\n\n• The main target of surgical exploration is to control sepsis by drainage of accumulated fluids. Repair of the defect, if identified, is another target with special attention to prevent occlusion of the ducts.\n\n• The presence of free fluids inside the peritoneum or in the retroperitoneal space is an indication for drainage; this can be achieved by interventional radiology (IR) under CT scan or ultrasound guidance, or by surgery if IR service is not available or the collection is not accessible.\n\n• Most bile duct perforations can be managed by internal biliary stents, along with drainage of any collection. External nasobiliary drainage is considered a valid alternative for internal stenting.\n\n• Failure of non-operative measures, which can be defined as the persistence of abdominal sepsis (significant pain, tenderness and ileus), as well as fever and continuous elevation of inflammatory markers (leukocytes, CRP, ESR, among others), indicates prompt conversion into surgical approach.\n\n• Prolonged restriction of oral intake may not be of any help if there is no evidence of an ongoing leakage.\n\n• ERCP perforation remains an event that has to be approached by both surgeons and endoscopists.\n\nThis study had some limitations. Firstly, it was a retrospective study. Secondly, the sample size of patients with EIP was relatively small to evaluate risk factors with statistical significance. Thirdly, we assume that a small group of patients with type IV perforation may have not been detected, due to lack of abdominal or systemic manifestations.\n\nIn conclusion, fifty years after introduction of ERCP for therapy, it remains an invasive procedure with certain complications that carry significant morbidity and mortality, even in skilled hands or at high volume units. Selection of patients for ERCP must be strict, it has to be done for therapeutic indications. Difficult cannulation is still a condition that is frequently encountered, and considered the main risk factor for perforation. Early diagnosis and appropriate surgical or percutaneous drainage yield favorable outcomes.\n\n\nAuthor contributions\n\nAM: investigation, methodology and project administration, ZM: resources, software, TM: software, analysis, HM: software, supervision, AH: methodology, resources, KJ: investigation, MH: methodology, NF: investigation, SS: resources, DA: resources, supervision, JF: methodology. All authors had substantial contribution to conception and design, interpretation of data, drafting, and revising the article. They all approved the final manuscript and agreed to be accountable for all aspects of the work.",
"appendix": "Data availability\n\nData supporting the study’s findings are available upon request from the corresponding author, Dr. Abdel Rahman A. Al Manasra, (request by email: Aaalmanasra@just.edu.jo). The data are not made public because they contain information that could jeopardize the privacy of research participants.\n\n\nReferences\n\nKozarek RA: The Past, Present, and Future of Endoscopic Retrograde Cholangiopancreatography. Gastroenterol Hepatol (NY). 2017; 13(10): 620–622. PubMed Abstract\n\nCotton PB: Cannulation of the papilla of Vater by endoscopy and retrograde cholangiopancreatography (ERCP). Gut. 1972; 13(12): 1014–1025. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndriulli A, Loperfido S, Napolitano G, et al.: Incidence rates of post-ERCP complications: a systematic survey of prospective studies. Am. J. Gastroenterol. 2007; 102(8): 1781–1788. PubMed Abstract | Publisher Full Text\n\nSieg A, Hachmoeller-Eisenbach U, Eisenbach T: Prospective evaluation of complications in outpatient GI endoscopy: a survey among German gastroenterologists. Gastrointest. Endosc. 2001; 53(6): 620–627. PubMed Abstract | Publisher Full Text\n\nStapfer M, Selby RR, Stain SC, et al.: Management of duodenal perforation after endoscopic retrograde cholangiopancreatography and sphincterotomy. Ann. Surg. 2000; 232(2): 191–198. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTurner RC, Steffen CM: Boyd P. Endoscopic duodenal perforation: surgical strategies in a regional centre. World J. Emerg. Surg. 2014; 9(1): 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKatsinelos P, Paroutoglou G, Papaziogas B, et al.: Treatment of a duodenal perforation secondary to an endoscopic sphincterotomy with clips. World J. Gastroenterol. 2005; 11(39): 6232–6234. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVezakis A, Fragulidis G, Polydorou A: Endoscopic retrograde cholangiopancreatography-related perforations: Diagnosis and management. World J. Gastrointest Endosc. 2015; 7(14): 1135–1141. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoward TJ, Tan T, Lehman GA, et al.: Classification and management of perforations complicating endoscopic sphincterotomy. Surgery. 1999; 126(4): 658–665. discussion 664-655. Publisher Full Text\n\nKim J, Lee SH, Paik WH, et al.: Clinical outcomes of patients who experienced perforation associated with endoscopic retrograde cholangiopancreatography. Surg. Endosc. 2012; 26(11): 3293–3300. PubMed Abstract | Publisher Full Text\n\nDubecz A, Ottmann J, Schweigert M, et al.: Management of ERCP-related small bowel perforations: the pivotal role of physical investigation. Can. J. Surg. 2012; 55(2): 99–104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJin YJ, Jeong S, Kim JH, et al.: Clinical course and proposed treatment strategy for ERCP-related duodenal perforation: a multicenter analysis. Endoscopy. 2013; 45(10): 806–812. PubMed Abstract | Publisher Full Text\n\nBill JG, Smith Z, Brancheck J, et al.: The importance of early recognition in management of ERCP-related perforations. Surg. Endosc. 2018; 32(12): 4841–4849. PubMed Abstract | Publisher Full Text\n\nMiller R, Zbar A, Klein Y, et al.: Perforations following endoscopic retrograde cholangiopancreatography: a single institution experience and surgical recommendations. Am. J. Surg. 2013; Aug 206(2): 180–186. PubMed Abstract | Publisher Full Text\n\nRabie ME, Mir NH, Al Skaini MS, et al.: Operative and non-operative management of endoscopic retrograde cholangiopancreatography-associated duodenal injuries. Ann. R. Coll. Surg. Engl. 2013; 95(4): 285–290. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoc B, Bircan HY, Adas G, et al.: Complications following endoscopic retrograde cholangiopancreatography: minimal invasive surgical recommendations. PLoS One. 2014; 9(11): e113073. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUdd M, Kylänpää L, Halttunen J: Management of difficult bile duct cannulation in ERCP. World J. Gastrointest Endosc. 2010; 2(3): 97–103. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChandrasekhara V, Khashab MA, Muthusamy VR, et al.: Adverse events associated with ERCP. Gastrointest. Endosc. 2017; 85(1): 32–47. Publisher Full Text\n\nErcan M, Bostanci EB, Dalgic T, et al.: Surgical outcome of patients with perforation after endoscopic retrograde cholangiopancreatography. J. Laparoendosc. Adv. Surg. Tech. A. 2012; 22(4): 371–377. Publisher Full Text\n\nKrishna RP, Singh RK, Behari A, et al.: Post-endoscopic retrograde cholangiopancreatography perforation managed by surgery or percutaneous drainage. Surg. Today. 2011; 41(5): 660–666. Publisher Full Text\n\nKumbhari V, Sinha A, Reddy A, et al.: Algorithm for the management of ERCP-related perforations. Gastrointest. Endosc. 2016; 83(5): 934–943. PubMed Abstract | Publisher Full Text\n\nPark SM: Recent Advanced Endoscopic Management of Endoscopic Retrograde Cholangiopancreatography Related Duodenal Perforations. Clin. Endosc. 2016; 49(4): 376–382. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEvans N, Buxbaum JL: Endoscopic treatment of ERCP-related duodenal perforation. Tech. Gastrointest. Endosc. 2019; 21(2): 83–90. Publisher Full Text\n\nDoğan ÜB, Keskın MB, Söker G, et al.: Endoscopic closure of an endoscope-related duodenal perforation using the over-the-scope clip. Turk. J. Gastroenterol. 2013; 24(5): 436–440. 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}
|
[
{
"id": "177536",
"date": "29 Aug 2023",
"name": "Hazem Hammad",
"expertise": [
"Reviewer Expertise Advanced endoscopic procedures"
],
"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\nThanks for submitting this excellent research project.\n\nPage #4 and table 2: Need to specify precut papillotomy vs papillotomy. Also need to look into how many patients actually received sphincterotomy (with length) and balloon sphincteroplasty (with diameter).\nPage #4: I am not why the status of having HTN or DM was looked at. Was this relevant?\nPage #5, Table 2.:\nFor the obstructive jaundice, were these all due to underlying malignancy such as HOP cancer? worth elaborating more.\n\nFor \"CBD balloon dilation\", did this mean CBD stricture balloon dilation or balloon sphincteroplasty?\n\nPage 6 and table 3: Please comment on stent placement (plastic/metal) in cases of EIP.\n\nPage #6: Worth mentioning if any patient had post ERCP pancreatitis and whether that could have affected the outcome.\n\nTable #4: I am not sure that comparing surgical and conservative groups help given that the main difference is likely the severity/type of perforation so may be comparing the outcomes of different types of perforation would have been more helpful.\n\nPage 8: \"In other types of perforations i.e types I, II and IV\"...was it meant to be \"type II, III and IV?\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": [
{
"c_id": "10549",
"date": "16 Nov 2023",
"name": "Zaid Mesmar",
"role": "Author Response",
"response": "Dear sir, Thank you very much for the time spent reviewing our manuscript. We have answered all your valuable comments one by one in the following table. Again, we highly appreciate your effort and we hope our response will meet your expectations. 1-The term papillotomy used in Table 2 refers to precut papillotomy, this has been discussed in the text following Table 2, “ERCP characteristics” paragraph. 2-Unfortunately, the length of the sphincterotomy and the diameter of the balloon were not included in the ERCP reports for most patients. So, this part was skipped in spite of the value that could be added to the analysis of outcomes. 3-The status of having HTN and DM, especially when uncontrolled, contributes significantly to the morbidity and mortality in hospitalized patients or in patients who undergo invasive procedures. It may also impact the optimal management plan for patients who sustain injury. 4-Obstructive jaundice proved to be secondary to cancer in 2/13 patients in the EIP group. The rest were secondary to benign strictures. 5-“CBD balloon dilatation” refers to CBD stricture balloon dilatation. This will be clarified in Table 2 6-The stent type used was plastic in EIP, the comment will be added to Table 3. 7- Correct, post-ERCP pancreatitis may affect outcomes in patients with EIP. However, it was not tracked in this analysis which focused on the types of perforation and outcomes in light of management choice, we may conduct a sub-analysis after revisiting patients’ data and gathering necessary details in future work. 8- The option of treatment correlates with the type of perforation, however, the outcomes have been discussed from a different perspective, which is the mode of treatment. The question raised initially was: do more invasive treatment options carry worse outcomes? The only approach to answer this was to review outcomes in the light treatment method. 9- Yes, sir, it was meant to be type II. III and IV, The editor is contacted so that the error will be corrected in the original manuscript."
}
]
},
{
"id": "238886",
"date": "05 Feb 2024",
"name": "Vaibhav Wadhwa",
"expertise": [
"Reviewer Expertise Interventional Endoscopy"
],
"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 submitting your detailed work to this journal. Authors present data on ERCP-induced perforation which serves as a helpful guide for gastroenterologists. There are some major revisions that are suggested:\nPatient demographic table. For standardizing the impact of comorbidities on the outcomes, it is recommended to use a standardized and validated comorbidity index such Charleson Comorbidity Index (CCI) (Ref 1, Ref 2 ). This will help in standardizing the comorbidity burden. Additionally, a sub-group analysis to see correlation with higher CCI to outcome (specifically between conservative and operative arm) can provide more information on case selection for intervention and increase generalizability of this study.\nFailure of cannulation: Since two patients (of the 13) were found to have a perforation during the procedure, it is assumed that the procedure was prematurely terminated. It should be considered to remove them from the analysis of ‘failed cannulation’ as that instills bias. In other words, in these two patients, perforation led to failed cannulation and not the other way around.\nLength of procedure and length to cannulation: It would be helpful to know if there was a difference in the two arms when it came to (1) total length of the procedure and (2) time to cannulation. These parameters are linked to post-ERCP pancreatitis and it would be useful to include them in analysis to see if they correlate with perforations (Ref 3).\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": []
},
{
"id": "235317",
"date": "15 Feb 2024",
"name": "Budhi Ida Bagus",
"expertise": [
"Reviewer Expertise Gastrointestinal Cancer",
"Colorectal Cancer",
"Acute Care Surgery",
"Immune-Oncology",
"Chemotherapy",
"Enhanced Recovery After 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\nGood written review manuscript. It might be better if you can described the criteria of endoscopist who performed the ERCP procedures (if possible). Please add the information whether the ERCP-induced perforation cases were occurred in the first or the second procedure of ERCP? Were there any information about the duration of each ERCP procedures which associated with perforation?\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": "11245",
"date": "04 Apr 2024",
"name": "Zaid Mesmar",
"role": "Author Response",
"response": "Dear sir, Thank you very much for the time spent reviewing our manuscript. We have answered all your valuable comments one by one . Again, we highly appreciate your effort and we hope our response will meet your expectations. 1- The criteria of endoscopist who performed the ERCP procedures are added to the text ( please see the result section , first paragraph) : board certified gastroenterologist, licensed to perform endoscopy after training in an accredited structured ERCP program. 2- The ERCP-induced perforation cases were occurred in the first time , this has also been clarified in the result section first paragraph. 3- Unfortunately , the duration of the procedure was not documented in the ERCP reports , neither stored on the patients electronic files."
}
]
}
] | 1
|
https://f1000research.com/articles/12-612
|
https://f1000research.com/articles/12-1160/v1
|
15 Sep 23
|
{
"type": "Study Protocol",
"title": "Barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of oral health policies in the WHO Africa region: A scoping review protocol",
"authors": [
"Alonso Carrasco-Labra",
"Francisca Verdugo-Paiva",
"Cleopatra N. Matanhire-Zihanzu",
"Emmett Booth",
"Iliana V. Kohler",
"Olivia Urquhart",
"Yuka Makino",
"Michael Glick",
"Francisca Verdugo-Paiva",
"Cleopatra N. Matanhire-Zihanzu",
"Emmett Booth",
"Iliana V. Kohler",
"Olivia Urquhart",
"Yuka Makino",
"Michael Glick"
],
"abstract": "Background: Evidence-informed oral health policies (OHP) can be instrumental in ending the neglect of oral health globally. When appropriately developed and implemented, OHP can improve the efficiency of healthcare systems and the quality of health outcomes. However, more than half of the countries in the World Health Organization (WHO) African region did not have an oral health policy or even the existence of a policy in need of additional and more national-specific OHP as part of non-communicable diseases and universal health coverage agendas. The objective of this protocol’s study is to determine the barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of OHP in the WHO Africa region. Methods: We will conduct a systematic search in Global Health, Embase, PubMed, PAIS, ABI/Inform, Web of Science, Academic Search Complete, Scopus, databases that index gray literature, and the WHO policy repositories. We will include qualitative, quantitative, or mixed-methods research studies and OHP documents published since January 1, 2002, which address stakeholders' perceptions and experiences regarding barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of OHP in countries part of the WHO African region. We will produce descriptive statistics (frequencies and proportions) for quantitative data and conduct descriptive content analysis for qualitative data. Discussion: To effectively establish evidence-based OHP in the WHO African region, it is crucial to recognize existing challenges and opportunities for progress. The findings of this review will be relevant for Chief Dental Officers at ministries of health, administrators of dental schools, or academic institutions in the WHO African region and will inform a stakeholder dialogue meeting in Kenya in November of 2023. Registration: Open Science Framework: https://doi.org/10.17605/OSF.IO/9KMWR",
"keywords": [
"Scoping review",
"WHO Africa region",
"Oral Health Policy",
"Barriers and Facilitators."
],
"content": "Introduction\n\nOral health is a topical health discipline neglected in global, regional, and national health matters.1 Oral diseases are among the most common non-communicable diseases (NCDs) in the African Region. In 2016, oral diseases affected approximately 45% of the population in the World Health Organization (WHO) African Region.2 In the previous 30 years, among all WHO regions, the African region has the largest increase in oral disease burden.1 In 2019, more than 70% of countries in the WHO African region spent less than USD 1 per person per year on oral health care. The region also has a long-term problem of a limited oral health workforce.1\n\nEvidence-informed policies can be instrumental in ending the neglect of oral health globally,3 since policies, when properly developed and implemented, can have the ability to improve the efficiency of healthcare systems and the quality of health outcomes.4 In 1998, the WHO African Region Committee proposed a strategy to strengthen countries’ capacity to improve community oral health by effectively using proven interventions to address oral health needs. At that time, only 14 countries in the WHO African Region (30%) had national oral health policies (OHP).5 Currently, several countries in the WHO African Region lack the necessary national OHP. By 2020, two decades later, only 19 countries confirmed having a national health policy plan when conducting the mid-term assessment of the latest regional strategy on oral health 2016-2025 to address oral diseases as part of NCDs and universal health coverage (UHC) agenda.6 The absence of evidence-informed OHP is a critical concern contributing to an increased oral disease burden, oral health workforce shortage, and inadequate oral health service provision.3\n\nThe FDI Vision 2030 Report,7 the Lancet Commission in Oral Health,3 the landmark 2021 WHO Oral Health Resolution,8 along with the WHO Global Strategy for Oral Health9 and its action plan have been highlighting an urgent need for immediate health systems enhancements, aiming to achieve UHC for oral health. The 2022 Global Oral Health Status Report notes that there is an pressing need to address the high oral disease burden and that policy-makers and various stakeholders will be instrumental in prioritizing oral health advocacy at a global, regional, and national level as part of NCDs and UHC agenda.1 To ensure the adoption and implementation of these frameworks in the African region, national OHP should be developed and aligned with global and regional strategies.\n\nTo accelerate the optimal creation, dissemination, implementation, monitoring, and evaluation of OHP in the WHO African region, understanding the current state of existing policies, including barriers and facilitators, is warranted. We present a protocol for a scoping review to determine what are the barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of oral health policies in the WHO Africa region.\n\n\nProtocol\n\nWe used the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P)10 and we will use the PRISMA-ScR extension for scoping reviews to present our findings.11\n\nOral health definitions\n\nAn article addressing oral health should cover aspects included in the following definitions:\n\n1. “Oral health is multi-faceted and includes the ability to speak, smile, smell, taste, touch, chew, swallow and convey a range of emotions through facial expressions with confidence and without pain, discomfort and disease of the craniofacial complex (head, face, and oral cavity).”12\n\n2. “Oral health is the state of the mouth, teeth and orofacial structures that enables individuals to perform essential functions, such as eating, breathing and speaking, and encompasses psychosocial dimensions, such as self-confidence, well-being and the ability to socialize and work without pain, discomfort and embarrassment.”9\n\nAs an extension, articles focusing on modifiable risk factors for oral diseases such as sugar consumption, tobacco use, alcohol use, and oral hygiene, and their underlying social and commercial determinants will also be included.\n\nHealth policy definition\n\nWe will consider a health policy any statement made by an organization, or a group of organizations, at the national or regional level (regions of the continent of Africa, e.g., Sub-Saharan Africa) that recommends or suggests a particular course of action or options related to health and directed to patients, caregivers, healthcare professionals, institutions, or organizations. In this review, a health policy may include a strategy (a long-term plan designed to achieve a particular goal) or an action plan (a scheme of course of action, which may correspond to a policy or strategy, with defined activities indicating who does what, when, how and with what resources to accomplish an objective).13\n\nInclusion criteria\n\nWe will include articles providing quantitative evidence or qualitative statements about barriers to and facilitators for creating, disseminating, implementing, monitoring, and evaluating OHP in the WHO African region.\n\nPopulation\n\nWe will include studies that focus on characterizing the perceptions and experiences of a variety of stakeholder groups, including policy-makers, healthcare managers, administrators, organizational leaders (including non-governmental organization leaders), healthcare professionals, researchers, and citizens. We will use the definition of citizens proposed by the Evidence Commission report, which includes all members of society (e.g., patients and caregivers, service users, parents, voters, community leaders, and workers).14\n\nSetting\n\nWe will include studies conducted in any of the 47 countries of the WHO African Region: Algeria, Angola, Benin, Botswana, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Cote d’Ivoire, Democratic Republic of Congo, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, Gabon, Gambia, Ghana, Guinea, Guinea Bissau, Kenya, Lesotho, Liberia, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mozambique, Namibia, Niger, Nigeria, Rwanda, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, South Africa, South Sudan, Togo, Uganda, United Republic of Tanzania, Zambia, and Zimbabwe.15\n\nType of evidence\n\nWe will include articles published since January 1, 2002, in English, French, or Portuguese, and falling between two types of publications addressing barriers to and facilitators for OHP:\n\n1. Research articles (systematic reviews, scoping reviews, umbrella reviews, primary studies, and conference proceedings):\n\n• Research articles that directly assess or measure barriers to and facilitators for OHP creation, dissemination, implementation, monitoring, and evaluation. The assessment of barriers and facilitators could have been done in a single dental clinic in the WHO Africa region at a national, regional (e.g., a province or territory), or community level (e.g., a village, a municipality).\n\n• Research articles exploring perceptions, experiences, perspectives, knowledge, or attitudes regarding oral health care services (financing, access, or provision) for strengthening healthcare systems in the WHO African region. The article can cover barriers or facilitators across several policies.\n\n• Research articles exploring perceptions, experiences, perspectives, knowledge, or attitudes related to specific interventions to diagnose, treat, or prevent oral diseases in the WHO African region. These studies will be included if the intervention is connected to an existing oral health policy or government program (the research article should report or reference in the introduction, methods, or discussion evidence of a connection between the study purpose and specific oral health policies or programs).\n\n2. Oral health policy-related documents (national policies, clinical practice guidelines, national strategies and plans, documents written by authors that are part of Ministries of Health or other policy-oriented governmental global and local organizations, policy briefs, and policy analysis):\n\n• Health policy documents are eligible if the document has a section or a sentence reporting barriers to or facilitators for oral health policy creation, dissemination, implementation, monitoring, and evaluation.\n\nExclusion criteria\n\nWe will exclude research articles and oral health policy-related documents meeting one of the following criteria:\n\n• Conference abstracts, commentaries, editorials, and protocols.\n\n• Articles assessing prevalence, burden of disease, or epidemiological data from oral diseases.\n\n• Articles assessing risk or protective factors for oral diseases.\n\n• Articles evaluating the effectiveness or safety of interventions to prevent, diagnose, or treat oral diseases.\n\n• Articles reporting economic evaluations of interventions to prevent, diagnose, or treat oral diseases.\n\n• Articles reporting only aggregated data on barriers and facilitators, including a combination of countries within and outside the WHO African region.\n\nWe will extract quantitative data and qualitative statements informing the existence of barriers and facilitators. We define a barrier as any practical, political, financial, or technical problem preventing or obstructing any OHP aspect. A facilitator corresponds to an entity, process, technology, legislation, or organizational structure that promotes or optimizes any aspect of an OHP.\n\nWe will classify barriers and facilitators according to the specific aspect of an OHP that is affected. First, an article classified as addressing issues of OHP creation should describe the development of a health policy for individuals, patients, caregivers, healthcare professionals, institutions, or organizations (e.g., studies or documents assessing stakeholder engagement in health policy development, use of research evidence in policy creation, researchers, policymakers, and other stakeholders’ involvement in health policy dialogue). These articles can also describe the adaptation or adoption of health policies, guidelines, or guidance developed elsewhere for local use, that is, the use of existing documents produced in one setting to be modified for use in another setting (e.g., studies reporting African guideline developers adopting existing recommendations from other countries).16 Articles describing plans and strategies to share, distribute and promote health policy content and ensure the audiences of interest are reached (e.g., translation into multiple languages, open-access publications, engagement of intermediaries, mass media campaign, email distribution) will be classified as describing issues of OHP dissemination. Articles relating interventions to apply the health policy content in the healthcare system, monitor policy implementation, evaluate its impacts or changes in healthcare organizations, the behavior of healthcare professionals, patients, caregivers, or the use of health services by healthcare recipients (e.g., printed educational materials, audit, and feedback, reminders, financial incentives, computer decision support systems) will be classified as addressing issues of implementation, monitoring, and evaluation. Second, we will also classify the barriers and facilitators based on the WHO building blocks pillars for health systems.17\n\nWe will search the following databases: Global Health, Embase, PubMed, Public Affairs Information Service Index (PAIS), ABI/Inform, Web of Science, Academic Search Complete, and Scopus. In addition, databases that index gray literature (Dissertations Global, Google Scholar) will be searched. To ensure the retrieval of relevant materials produced by WHO, additional sources of information will be searched (WHO’s Institutional Repository for Information Sharing (IRIS), Google, WHO Noncommunicable Diseases Document Repository, and the WHO’s African members’ oral health policies repository). Materials indexed in African regional databases such as Regional African Index Medicus and African Journals Online are covered in the databases mentioned above.\n\nThe specific search strategies for each database will be created by two information specialists with expertise in systematic review searching and health and social sciences. The search strategies will be developed by the specialists with input from the project team. The search strategies will be peer-reviewed by other information specialists not otherwise associated with the project. A link to the draft PAIS search strategy can be found in the extended data section.24 After the PAIS search strategy is finalized, it will be adapted to the syntax and thesauri of the other databases.\n\nPairs of reviewers will independently screen titles and abstracts against the eligibility criteria. Retrieved documents published in French or Portuguese will be designated to a research team member who comprehends each of these languages. We will obtain full reports for all records that appear to meet the eligibility criteria or require further analysis to decide their inclusion. A third review author will resolve any discrepancies. We will use Covidence18 to manage the screening process, upload search results, screen titles abstracts, and full-text articles, and resolve disagreements. We will record the reasons for citation exclusion at the full-text level.\n\nPairs of reviewers will independently extract data from each included article using a data extraction sheet specifically designed for this review. We will collect the following information: first author, publication year, type of article, country, setting, group or audience to which the policy was directed, participants’ characteristics, study objectives, study research methods, and key findings. We will also extract all relevant evidence regarding stakeholders’ perceptions and experiences regarding barriers and facilitators for the creation, dissemination, implementation, monitoring, and implementation of OHP. This includes qualitative, quantitative, or mixed data from participants’ quotes, narrative descriptive summaries, author hypotheses, theoretical frameworks, explanations and recommendations, themes, and sub-themes. The draft data extraction form will be modified and adapted as necessary during the extraction process. Modifications will be detailed as part of the methods of our review. We will discuss disagreements, and one arbiter will adjudicate unresolved discrepancies.\n\nWe will use descriptive statistics, including frequencies and proportions when analyzing quantitative data. Qualitative data will be analyzed using descriptive content analysis.19 Since this is the first review of its kind in oral health, we will combine two information sources to create a new taxonomy to classify identified barriers and facilitators. First, we will use taxonomies from previous systematic reviews addressing barriers and facilitators for health policies outside the scope of oral health.20 Second, in an iterative process, we will use statements identified from the included articles reflecting barriers and facilitators specific to oral health, and revise our taxonomy.\n\nAfter establishing an initial taxonomy, we will categorize the extracted data across the different categories. Two researchers will independently review and apply the coding to the included studies’ data and documents. The team will discuss discrepancies in coding to achieve consensus. Factors that affect OHP will be coded as barriers or facilitators against a predefined list of factors that will be iteratively updated and defined as new factors are identified. A summary of the data coded to barriers and facilitators will be presented in tables.\n\n\nDiscussion\n\nTo make the needed transformations to ensure rigorous evidence-based OHP in the WHO African region, it is essential to understand the current challenges and opportunities for their creation and implementation. Hence, this scoping review aims to identify and summarize the available research evidence and stakeholders’ perspective and experiences regarding the barriers and facilitators for OHP. This review will help to appreciate contextual factors, actors, stakeholders, policy processes, and other dynamics influencing the entire policy enterprise.21 In addition, it will help to identify challenges that have limited oral health system performance, particularly in low-resource settings such as the African context.22 Our findings can also assist in designing cost-effective initiatives to overcome the barriers, optimizing resource utilization, and enabling the effective adoption and implementation of the WHO Global Oral Health Strategy.23\n\nSome limitations of this review relate to the complexity in nature, design, and availability of articles to be retrieved. For example, preliminary piloting of potentially eligible articles proved that barriers and facilitators are widely reported, often not explicitly labeled as such, and rarely supported with references or data. The broad scope of our work warrants the application of a variety of quantitative and qualitative synthesis techniques. In addition, we expect that some eligible references may not be available in full text, even for members of the review team based in Africa. Our review’s strength relies on the comprehensive and multidisciplinary creation of a search strategy covering global and regional databases and considering policy-specific sources for Africa. Another strength is the collaboration with the Noncommunicable Diseases Management Team at the WHO Regional Office for Africa, whose input ensures that the review findings are relevant for stakeholders and other users.\n\nThe findings of this scoping review will be disseminated using a combination of strategies:\n\npublications in peer-review journals, abstract presentations in research and oral health policy related-conferences, circulation of executive summaries and policy briefs with Chief Dental Officers at ministries of health, deans of dental schools or academic institutions in WHO African region countries, and the organization of a stakeholder dialogue meeting in Kenya (November 2023), which this work will partially inform.\n\nCreation of the search strategy has been completed. Data collection has begun and analysis is expected to be completed by October 2023.\n\nAs there are no human participants involved, there will be no requirement for ethical approval. Patients and/or the public were not involved in the design of this protocol.",
"appendix": "Data availability\n\nNo underlying data are associated with this article.\n\nfigshare: Search strategy. Barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of oral health policies in the WHO Africa region, https://doi.org/10.6084/m9.figshare.23791923. 24\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 thank H. Austin Booth, Dean, Divisions of Libraries, New York University, for collaborating in creating the search strategy and identifying relevant databases and other sources of information.\n\n\nReferences\n\nWorld Health Organization: Global oral health status report: towards universal health coverage for oral health by 2030. Geneva: World Health Organization; 2023.\n\nRegional Office for Africa: Mid-term progress report on the implementation of the Regional oral health strategy 2016 –2025: Addressing oral diseases as part of noncommunicable diseases in the WHO African Region. Brazzaville: The World Health Organization (WHO); 2022.\n\nWatt RG, Daly B, Allison P, et al.: Ending the neglect of global oral health: time for radical action. Lancet. 2019; 394(10194): 261–272. PubMed Abstract | Publisher Full Text\n\nLanglois EV, Daniels K, Akl EA: Evidence synthesis for health policy and systems: a methods guide. Geneva: World Health Organization; 2018. Accessed June 2023. Reference Source\n\nRegional Committee for Africa, 48: Oral Health in The African Region: A Regional Strategy. World Health Organization; 1998. Accessed June 2023. Reference Source\n\nWorld Health Organization African Region: MID-TERM PROGRESS REPORT on the implementation of the Regional oral health strategy 2016–2025: Addressing oral diseases as part of noncommunicable diseases in the WHO African Region. Brazzaville, Africa: World Health Organization; 2022.\n\nGlick M, Williams DM, Ben Yahya I, et al.: Vision 2030: Delivering Optimal Oral Health for All. Geneva: FDI World Dental Federation; 2021.\n\nWorld Health Organization: Resolution WHA74/5. Oral health. Seventy-fourth World Health Assembly. Geneva: World Health Organization; 2021.\n\nWorld Health Organization: Draft Global Strategy on Oral Health. Follow-up to the political declaration of the third high-level meeting of the General Assembly on the prevention and control of non-communicable disease. Geneva: World Health Organization; 2022.\n\nMoher D, Shamseer L, Clarke M, 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\nTricco AC, Lillie E, Zarin W, et al.: PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation. Ann. Intern. Med. 2018; 169(7): 467–473. PubMed Abstract | Publisher Full Text\n\nGlick M, Williams DM, Kleinman DV, et al.: A new definition for oral health developed by the FDI World Dental Federation opens the door to a universal definition of oral health. Br. Dent. J. 2016; 221(12): 792–793. Publisher Full Text\n\nWorld Health Organization: Assessing national capacity for the prevention and control of noncommunicable diseases: report of the 2019 global survey. Geneva: World Health Organization; 2020.\n\nMcMaster Health Forum: Global Commission on Evidence to Address Societal Challenges. The Evidence Commission report: A wake-up call and path forward for decision-makers, evidence intermediaries, and impact-oriented evidence producers. Hamilton, ON, Canada: McMaster Health Forum; 2022.\n\nWHO African Region: WHO region country office for Africa. World Health Organization; 2022. Accessed June 2023. Reference Source\n\nSchünemann HJ, Wiercioch W, Brozek J, et al.: GRADE Evidence to Decision (EtD) frameworks for adoption, adaptation, and de novo development of trustworthy recommendations: GRADE-ADOLOPMENT. J. Clin. Epidemiol. 2017; 81: 101–110. Publisher Full Text\n\nWorld Health Organization: Draft Global Oral Health Action Plan (2023–2030). Geneva: World Health Organization; 2023. Accessed June 2023. Reference Source\n\nVeritas Health Innovation, Covidence systematic review software. Melbourne, Australia. Reference Source\n\nBoyatiz RE: Transforming Qualitative Information: Thematic Analysis and Code Development. Thousand Oaks, CA: SAGE Publications; 1998.\n\nOliver K, Innvar S, Lorenc T, et al.: A systematic review of barriers to and facilitators of the use of evidence by policymakers. BMC Health Serv. Res. 2014; 14: 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalt G, Gilson L: Reforming the health sector in developing countries: the central role of policy analysis. Health Policy Plan. 1994; 9(4): 353–370. PubMed Abstract | Publisher Full Text\n\nWalsh CM, Mwase T, De Allegri M: How actors, processes, context and evidence influenced the development of Malawi’s Health Sector Strategic Plan II. Int. J. Health Plann. Manag. 2020; 35(6): 1571–1592. PubMed Abstract | Publisher Full Text\n\nMatanhire-Zihanzu CN, Chambers S, Bagg J, et al.: Assessing Malawi’s recent development of a National Oral Health Policy – learning for the future. J. Glob. Health Rep. 2022; 6: 6. Publisher Full Text\n\nVerdugo F: Search strategy. Barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of oral health policies in the WHO Africa region. Dataset. figshare. 2023. Publisher Full Text"
}
|
[
{
"id": "207139",
"date": "16 Oct 2023",
"name": "Manu Mathur",
"expertise": [
"Reviewer Expertise Public health",
"oral health",
"health policy and systems research"
],
"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 protocol of a very interesting study. These are the water shed years for global oral health and this study will help in putting oral health at the forefront for the debates on strengthening health systems in Africa. There are a few bits and bobs that needs more elaborate work. Notably:\nIntroduction Line 2: Needs a reference.\n\nIntroduction: Africa is in a very nascent stage of building evidence on health policy and systems. Do you think that evidence informed policy is even feasible when the research is very sparse? I think it is important that you define what you mean by evidence informed policy making in the Introduction and then move forward.\n\nMethodology: Why 2002 is taken as a cut off date for inclusion of articles? This needs to be justified.\n\nType of evidence: Point Number 2: not entirely clear. Generally policy documents don’t have this information. Does that mean that all health policy documents will be excluded? Need some clarification.\n\nData Analysis: What sort of quantitative data are you expecting to obtain? This needs to be elaborated.\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": []
},
{
"id": "231587",
"date": "21 Feb 2024",
"name": "Mpho Molete",
"expertise": [
"Reviewer Expertise Oral health epidemiology",
"Child Oral Health",
"Implementation Science"
],
"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 important relevant enquiry as oral health in the African continent is neglected, not much funding goes into addressing its challenges, and yet 45% of the population living in the WHO African Region are affected by oral diseases. Therefore, effective policy processes are necessary for improving oral healthcare systems and outcomes around the continent. The proposal thus aims to undertake a scoping review that includes peer reviewed articles and grey literature as well. This is hoped to assist in addressing the gaps in terms of integrating oral health with NCD's and giving direction for Universal Health Coverage. The significance of the review is well highlighted, however there is concern that the objectives are too broad and may hinder the authors from obtaining rich insightful information. For instance, very little monitoring and evaluation information may be found as much literature has shown there to be paucity in M&E of not only of oral health policies but interventions across the continent. In terms of methodology, the inclusion criteria needs to be refined as it is ambiguous. There needs to be clarity on how each criterion is different from the other or else screening of the articles will be difficult. I also suggest that the overarching search strategy with the search terms used must be indicated in the protocol so that we have an idea on what was guiding the information specialist. There needs to be clarity on how many reviewers will be used to analyze papers in French and Portuguese. Lastly please check your use of tenses, particularly in the abstract.\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": "11255",
"date": "04 Apr 2024",
"name": "Alonso Carrasco-Labra",
"role": "Author Response",
"response": "Barriers to and facilitators for the creation, dissemination, implementation, monitoring, and evaluation of oral health policies in the WHO Africa region: A scoping review protocol. Peer review response We appreciate the input from Dr. Mpho Molete. Below, we provide our responses: Comment 1: This is an important relevant enquiry as oral health in the African continent is neglected, not much funding goes into addressing its challenges, and yet 45% of the population living in the WHO African Region are affected by oral diseases. Therefore, effective policy processes are necessary for improving oral healthcare systems and outcomes around the continent. The proposal thus aims to undertake a scoping review that includes peer reviewed articles and grey literature as well. This is hoped to assist in addressing the gaps in terms of integrating oral health with NCD's and giving direction for Universal Health Coverage. The significance of the review is well highlighted, however there is concern that the objectives are too broad and may hinder the authors from obtaining rich insightful information. For instance, very little monitoring and evaluation information may be found as much literature has shown there to be paucity in M&E of not only of oral health policies but interventions across the continent. Response: Thank you for your comment. Our review findings align with your description of a paucity of evidence regarding M&E. With the emergence of the new Global Oral Health Action Plan and the Regional Oral Health Strategy, which strongly focus on M&E, we considered it particularly necessary to bring to stakeholders’ attention the need to reinforce and promote research in these relevant aspects of the policy cycle. We hope the findings of this review can assist policymakers and leadership in public health in refocusing their efforts toward areas in policy development and enactment and that these findings can be used as advocacy tools. Comment 2: In terms of methodology, the inclusion criteria needs to be refined as it is ambiguous. There needs to be clarity on how each criterion is different from the other or else screening of the articles will be difficult. Response: We have conducted calibration exercises using the presented eligibility criteria in the protocol, and have obtained optimal levels of agreement between reviewers. Comment 3: I also suggest that the overarching search strategy with the search terms used must be indicated in the protocol so that we have an idea on what was guiding the information specialist. Response: The journal does not allow the submission of the search strategy as an appendix. To solve this issue, we included the search strategy in an external server that can be accessed and downloaded using a link. The link was provided with the submission and can also be found here: https://figshare.com/articles/dataset/Search_strategy_Barriers_to_and_facilitators_for_the_creation_dissemination_implementation_monitoring_and_evaluation_of_oral_health_policies_in_the_WHO_Africa_region_/23791923 Comment 4: There needs to be clarity on how many reviewers will be used to analyze papers in French and Portuguese. Response: Thank you for your comment. We have modified the language of the protocol to make this point explicit. Our modification: “Retrieved documents published in French or Portuguese will be designated to research team members who comprehend each of these languages, and will be screened in duplicate.” Comment 5: Lastly please check your use of tenses, particularly in the abstract. Response: We have modified the tenses in the manuscript abstract."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1160
|
https://f1000research.com/articles/12-834/v1
|
14 Jul 23
|
{
"type": "Method Article",
"title": "Agent-based models under uncertainty",
"authors": [
"Vladimir Stepanov",
"Scott Ferson"
],
"abstract": "Background: Monte Carlo (MC) is often used when trying to assess the consequences of uncertainty in agent-based models (ABMs). However, this approach is not appropriate when the uncertainty is epistemic rather than aleatory, that is, when it represents a lack of knowledge rather than variation. The free-for-all battleship simulation modelled here is inspired by the children’s battleship game, where each battleship is an agent. Methods: The models contrast an MC implementation against an interval implementation for epistemic uncertainty. In this case, our epistemic uncertainty is in the form of an uncertain radar. In the interval method, the approach occludes the status of the agents (ships) and precludes an analyst from making decisions about them in real-time. Results: In a highly uncertain environment, after many time steps, there can be many ships remaining whose status is unknown. In contrast, any MC simulation invariably tends to conclude with a small number of the remaining ships after many time steps. Thus, the interval approach misses the quantitative conclusion. However, some quantitative results are generated by the interval implementation, e.g. the identities of the surviving ships, which are revealed to be nearly mutual with the MC implementation, though with fewer identities in total compared to MC. Conclusions: We have demonstrated that it is possible to implement intervals in an ABM, but the results are broad, which may be useful for generating the overall bounds of the system but do not provide insight on the expected outcomes and trends.",
"keywords": [
"epistemic uncertianty",
"agent-based modelling",
"intervals"
],
"content": "Introduction\n\nAn agent-based model (ABM) is a model for simulating the actions and interactions of autonomous agents (either individual or collective entities such as organisations or groups) with the intention of observing the emergent behaviour of the whole system.1 ABMs are temporally explicit, usually with a fixed unit of time referred to as ticks. An ABM consists of its agents, with each agent being an autonomous discrete unit with its own aims, priorities and actions.1 Agents can also vary between themselves. The agents can be cooperative or prioritise their individual goals. An example of cooperative agents could be a coalition to lift a heavy object, while individualistic agents could be animals competing for scarce resources.\n\nABMs generally do not incorporate any epistemic uncertainty, such as imprecision or doubt about the agent’s properties or behaviours.2 It is argued that this kind of uncertainty can be modelled with distributions3 and Monte Carlo (MC) methods. With the MC approach, an ABM is executed a vast number of times with different parameters, which reflect the possible values that the parameter could take.4–7 This approach is computationally expensive, though there are strategies to reduce the number of computations, e.g., Latin hypercube sampling.8\n\nBesides attempts at reducing the computational cost of MC, some attempts try to reduce the computational cost of the model directly, e.g. in discrete event simulation, the introduction of “time buckets” which are intervals of time in which multiple events can occur.9 The equivalent strategy for an ABM would be a coarsening strategy that increases the fixed time step. This might be considered as introducing temporal epistemic uncertainty into an ABM, but as it handles this uncertainty in a simplistic way (in other words, by ignoring it) and with the simulation losing some of its detail depending on the magnitude of the time-step increase, which may not be desirable.10 As an example of losing detail, consider logging your position in daily life. If you log every 15 minutes, you might have 5 entries: home (0), travel (15), shop (30), travel (45) and home (60). However, if you log every hour, you will log: home (0) and home (60). Hence, you have lost detail, which in some applications may be critical.\n\nHowever, introducing non-time-based epistemic uncertainty into an ABM is not as simple as described above. For this implementation we will use intervals, which are arguably the simplest representation of epistemic uncertainty.11 The intervals will be used to model a free-for-all battleship simulation with uncertain radar ranges (inspired by the children’s game), showing that it is possible to use intervals to model battleship behaviour and status, but this approach occludes the status of the agents and precludes decision making about them.\n\nOne perspective against the use of intervals in ABM is that the parameters the intervals represent can be easily approximated with uniform distributions. However, this approach with uniform distributions acts as though the parameter is varying randomly, which may not be true.12,13 Though reasonable, there are some instances where combining two approximated intervals in this manner can cause problems, e.g., when A = [0.2, 0.4]; B = [0.3, 0.5], the product AB is [0.06, 0.02], but it will also indicate that there is a higher probability of it being a central value in the result if A and B are based on uniform distribution. Similarly, the sum of A and B will be [0.5, 0.9], but if approximated via uniform distributions it will also contain a central peak in this range. There is no justification for this higher central probability if the same calculation is performed without approximation but just utilising intervals.12,13 Thus, approximating with uniform distributions is not always appropriate.\n\nTherefore, it can be argued that a direct implementation of intervals in ABMs will avoid the above-mentioned problem. Additionally, a direct implementation should have a lower computational cost than MC and potentially avoid the problem that MC does not explore the full range of possibilities. Furthermore, it is argued that MC is poor at identifying extreme events, as can be observed in Figure 1, where it shows that most of the MC runs are concentrated in the central region of the outer bounds.2 However, the figure may exaggerate the convergence of the runs in respect to the outer bounds (indicated by the blue lines), but it helps to illustrate the centralisation effect of many random variables.\n\nReproduced with permission from original.\n\n\nModel configuration\n\nThe model is constructed in Python (v3)14 (RRID:SCR_008394), with the following packages: numpy15 (RRID:SCR_008633), enum,14 numbers,14 csv,14 matplotlib16 (RRID:SCR_008624), time,14 tqdm.14 The discrete simulation (global seed 0) can last up to 250 time-steps, during which the agents move about and interact with one another. The agents representing battleships are set in an X,Y grid (102 × 102) where the edges of the grid wrap-around so that a ship leaving the top of the grid reemerges at the bottom of the grid, and vice versa. Likewise, the right side wraps to the left side and vice versa, which is a toroidal or Pac-Man topology.17 The grid is randomly populated with 60 ships that will try to sink all other ships that they detect.\n\nEach ship is located in a grid cell, depicted as a dot in the grid, with the ship’s radar as a circle around the dot. The ships move at constant velocities during the simulation. Each ship is given a random velocity between 1 and 6 grid cells per time step. The initial direction of travel is random (determined by the movement generator with seed 2021), but each ship is turning in circular arcs across the grid, changing direction by π/30 radians at each time step. Each ship also has a maximum number of missiles, (uniformly) randomly generated from 10 to 60 missiles, that it launches at enemy ships whenever detected by radar whose range is (uniformly) randomly initialised for each ship between 2 to 27.5 grid units. Additionally, the ships are limited by the number of ships it can target in each time step (randomly generated from 2 to 16) ordered by proximity, with preference given to the ships closest to the ship firing the missiles. In an ideal world the declared radar range would always detect enemy ships within its boundaries. However, in a more realistic world a ship’s radar varies across its range. Close to the ship, the radar detects enemies perfectly (certain radar), but for enemies farther away, detection is uncertain. These two ranges are represented as two concentric circles: the inner certain radar range, and the larger uncertain radar range).\n\nAt each time step, each ship moves to another grid cell determined by its velocity, and from this new location detects other ships within its certain radar range and may detect those within its uncertain range. Once all targets are identified, the ship fires missiles at them as long as the lower bound of the interval for the missiles remaining is greater than zero. If the ship fires at a ship in the uncertain radar range, the ship fire is uncertain, i.e. the ship has both fired the missiles and not fired the missiles. Additionally, the ship can have less than the maximum number of targets and can even have zero targets if no other ships are located in it’s radar range. However, the number of missiles per target remains constant at three missiles, but if three missiles are not available, then the ship will fire any remaining missiles at the target. The ships’ actions are concluded by assessing any possible damage (hits) to itself that has been suffered due to the other ships having fired their missiles. Positive hits are determined from the missiles via a binomial distribution, with the chance of failure set as 0.5. If such hits sink the ship, its existence is negated. If the hits would surely not have sunk the ship, it continues to exist. If the hits could but might not sink it, the ship’s existence is represented as uncertain. The two states are depicted by the line type (solid line - ship exists; dashed line - ship with uncertain existence). Three certain missile hits will sink any ship.\n\nThe model code can be found on GitHub.18\n\n\nPossible model scenarios\n\nThe model keeps track of each ship’s state of existence and it’s remaining missiles. A ship is sunk when the number of missile hits exceeds the maximum possible hit threshold (3). There can be uncertainty about a ship’s existence, with this state a result of a missile from another uncertain ship increasing this ship’s hit count over the maximum possible hit threshold. The hit count is represented as an interval with the lower bound representing the total number of certain hits and the maximum bound representing the possible number of hits. Similarly, a ship’s missile count is represented as an interval once the ship has fired a missile at a ship located in its uncertain radar range. Here the upper bound represents the total number of certain missiles that the ship potentially has, while the lower bound represents the number of missiles it has left if it fired at the ship in the uncertain radar range.\n\nTo justify our decision on the interval implementation we have provided some scenarios to explain our reasoning. In our first scenario only one ship can fire at the other, while the second scenario shows the effect of uncertain existences. In these scenarios, the solid line within the Figures 2 represents the outer edges of the certain radar (if we see a ship here, we definitely see a ship), while the dashed line represents the outer range of the uncertain part of the radar (we are unsure that we have seen a ship there). We will represent missiles left as M, missiles fire as m, previous missiles hit as H, and missiles hit in this time segment as h. We will use subscripts to represent the ship that these values belong to.\n\nThe full line represents the certain radar range of the ship, while the dashed line represents the outer edge of its uncertain radar range.\n\nIt is shown in Figure 2a that only one ship (A) can fire missiles at the target ship (B). Thus ship A options can be listed as: it sees ship B, it does not see ship B; leading to ship A being able to fire and not fire its missiles, which would lead to an updated missile count for fire as M − m and not fire as M. We can summarise the missiles left for ship A with an interval [M − m, M]. It is important to note that if ship A does not exist, the outcome is equivalent to not firing the missiles as the argument is if the ship does not exist, then it cannot detect ship B, thus it will not be able to fire missiles. The other ship, Ship B, is the one that is getting fired upon by ship A, tracks the number of missiles h that have hit it. If the number of missiles that have hit the ship is zero, then the total number of hits remain unchanged at H (also true if ship A does not exist and so (ship A) does not have the capacity to fire missiles), otherwise the number of hits is H + h. Thus the total number of hits can be represented as [H, H + h]. As mentioned before, a ship’s existence is tied to the number of certain hits it has taken, which means that ship B will not sink as long as the existence of ship A is uncertain or the missiles are fired into the uncertain radar range of the attacking ship.\n\nIn the second scenario (Figure 2b) we explore the case where both ships are located in their certain range but the ships themselves are uncertain about their existence. Here the actions of ship A are mirrored for ship B, therefore only a detailed explanation for ship A will be provided. Ship A will fire its missiles if ship B exists, and it will not fire if ship B does not exist. Hence the remaining missiles for ship A will be MA−mAMA and the remaining missiles for ship B will be MB−mBMB. Ship A’s hit count will both increase by the number of missiles that hit ship A and stay the same as we are unsure if B has fired missiles as if B exists then surely it has fired the missiles, while if B does not exist then no missiles can be fired, thus HAHA+hA. As only the upper bound (of the hit count) is increased due to uncertainty, ship A will continue existing, no matter how high the upper bound gets. The same is true for ship B’s hit count HBHB+hB.\n\nIn summary, the scenarios demonstrate that an uncertain ship cannot sink a certainly existing ship, as when the upper bound for the hit counts exceeds the ship’s limit, the previously certainly existing ship becomes uncertain about its existence. This can be expanded to include that two uncertain ships cannot sink each other and that only a certainly existing ship can sink another certainly existing ship. Though the scenarios represent possible edge cases that can occur in the simulation, they can also illustrate the in-between states satisfactorily. These scenarios have been presented to aid in the understanding of the model; as the ships do not communicate with an external observer, thus we do not know the state of the ships or the number of missiles remaining.\n\n\nModel results\n\nThe emphasis of this investigation was to explore the effect of an imprecise radar range and how it could be propagated inside an ABM.19 To be able to propagate the effect of the imprecise radar range other uncertainties have to be added for the model to function, e.g. missile count and ship existence. We also varied the radar range for all the ships to explore the differences, while keeping the same seed for the random generator in all the experiments, in other words, we changed the parameter that affected the radar range while preserving the model architecture, with the results shown in Table 1.\n\nSquare brackets denote interval ranges. All results are shown for seed 0. Relative radar range 1 represents the original radar range.\n\nIn the first simulations, with no epistemic uncertainty, denoted Precise in Table 1, each ship’s original radar range was selected uniformly randomly to be between 2 and 27.5. This original setting is denoted by relative radar range of 1. Subsequent simulations collectively reduced or increased these ranges. For instance, for relative radar range of 2, the upper limit was doubled to 53. This meant that ships that originally had a relatively smaller radar range maintained their rank when their radar range was doubled. As the same seed was utilised, this ensured that multiple simulations were not needed. Additionally, even though the radar range was changed, the other parameters (starting number of missiles, initial velocity) were preserved. At the end of the simulation, with the original radar range, there are two ships and nine missiles remaining. Halving the range yields three ships with 53 missiles, while increasing the range by a factor of two gives one ship left with 24 missiles (Table 1). It can be seen that for the radar range of 0.75, the number of surviving ships is higher than for radar range 1, which is expected, but it is also higher than the number of surviving ships when the radar range is 0.5. The cause could be fewer ships sunk in the initial moments of the simulation as each ship sees fewer targets, leading to more initially surviving ships thus leading to more targeting in the simulation, in other words it is a consequence of the random number generator.\n\nWith an imprecise radar, the results are different as we get no definitive numbers but rather intervals (denoted by square brackets) for the possible solution (Table 1). With the original radar range we simulate that there are in the interval [0, 6] ships at the end and that they have [22, 234] missiles between them. Halving the radar range we increase the possible number of ships left to 15 [0, 15] with a larger possible number of missiles left [82, 660]. On the other hand increasing the radar range decreases the number of ships left [0, 4], but the overall possible number of missiles left [12, 254] is increased, though the interval starts with less fully known missiles.\n\nContrasting the two results, we observe that imprecise radar results are more ambiguous than their precise counterpart (for this particular seed) but they do follow the same general trend, i.e. as radar decreases there are more ships and missiles available. It is also important to note that as the imprecise radar decreases, the uncertainty increases in the number of ships and missiles remaining. This increase in uncertainty could be due to the increase in uncertain ships as they cannot be sunk and thus more uncertain ships mean there are more uncertain missiles fired.\n\nTable 1 shows that, although the current implementation of intervals is rather crude, it can also be argued that there is no feasible alternative for propagating epistemic uncertainty in an ABM. Thus, propagating with intervals is similar to propagating the worst-case and the best-case scenarios simultaneously. Given the available information, it is not possible to decrease the span of the results without additional knowledge. For example, consider a ship that has uncertainty about a target. The current model accounting for this epistemic uncertainty has the ship both firing and not-firing its missiles. Alternatively, the ship’s policy could be to fire a reduced number of missiles if it is unsure about a target, hence reducing the missiles’ interval. In such a case, if the modeller knows about the ship’s policy, the missile count interval and its epistemic uncertainty could then be reduced.\n\nThe results of Table 1 show that the imprecise (interval) implementation follows the same pattern as the precise results, but these results do not show that the interval implementation is a viable alternative, as the current precise radar results do not account for other possible radar ranges. Hence, for a more fair comparison, the precise radar ranges need to be varied to compensate for the uncertain radar range, which can be achieved via MC simulation. For simplicity we used the minimum (perfect radar range from the interval implementation) and maximum values (maximum possible radar range from the interval implementation) as the two possible ranges for the outer bounds of each uniform distribution from which each ship’s radar range is generated, as the MC implementation assumes ships see other ships perfectly in its entire radar range. The simulations were implemented in a straightforward MC approach, where the radar range varieties are produced in Python14 with the numpy.random.default_rng class with random seed 220 and the uniform function of this class. The model itself remains unchanged, with the same random generators and parameters.\n\nTo ensure a fair comparison between MC and the interval implementation, we must be able to generate the same sequence of events. Because the comparison is set between the results of the model, where each action in the model is determined by a random generator (e.g., the initial velocity of the ships, and the outcome that a fired shot found its target), a common strategy is to set the generator to repeat the list of random numbers in each run by setting the same start point for the generator at the simulation start. However, as this model is agent-based, this is not sufficient to guarantee that the actions taken by agents are the same when the ship’s radar ranges are varying. In other words, a ship may perform more actions as a result of a bigger radar range, thus requiring additional random numbers for the additional actions. As all the random numbers created from a set generator can be expressed as a list, this means more uses of the random generator leads to a longer list. Additionally, if each agent utilises the same generator, this means an additional action in the simulation by one agent can shift the random numbers used in other agents, thus possibly generating an alternative outcome as the agents may behave differently.\n\nTo prevent inconsistencies from divergences arising from such additional actions and to prevent unexpected path changes when varying the radar range, a predetermined path for each agent was generated. This was achieved by generating each path as if the simulation were being performed with each ship surviving for the full duration of the simulation time and recording these paths outside of Python. In our case, this is not a concern because ships all turn at a constant π/30 radians, as explained above. This framework using predetermined paths can be used in simulations where ship paths can include randomness. This framework ensures that the agents do not deviate due to shifting random values. However, divergence between our “All random” results and “Preset path, all missiles binomial hit” was observed, even though we are utilising a constant turn path. This was found to be due to a truncation effect from the recorded path values having fewer decimal points.\n\nThe final aspect that can change alongside the radar range changing is the outcome from the launched missiles: a ship with a larger radar range can fire earlier or detect a ship that it couldn’t detect beforehand. Thus, as there are more opportunities for the ship to fire missiles, the outcome of the barrage can shift, e.g. when before some particular missile may sink a particular ship now it may not, thus resulting in our previously generated random values to be used earlier and a demand for more random values to be generated. Thus, another measure that we have implemented to reduce the potential uncertainty lies in how a missile hit is determined. Our original implementation models missile hits binomially with 0.5 chance of failure. To reduce this uncertainty, we changed the original binomial to no longer have a failure state, thus ensuring that any missile fired always hits the target, i.e. the missiles fired can not miss. This modification is referred to as “all missiles fired hit”.\n\nWith these random generator control measures, the simulation results should only differ due to the ship radar range changes, thus allowing us to compare the two methodologies’ outcomes as equivalently as possible. Additionally, we have run the model without some of the control factors to demonstrate the variability without these control measures. The MC runs are collated as intervals into the Table 2 for easier comparison between the interval implementation (as this implementation outputs a pre-made interval) and the MC one.\n\nFrom the results, it can be seen that the interval implementation encompasses the MC one, with nearly all the Ship IDs found in the interval implementation occurring in the MC one.\n\nThe results in Table 2 show that the interval implementation encompasses the MC results for the total number of ships left. It is also important to note that the general pattern for the remaining number of ships is shared between the two implementations, i.e. more ships survive on a pre-set path with binomially distributed hits for the missiles; while the smallest number of ships survive with a random path and all missiles fired hit.\n\nAs a further review, the ship IDs are recorded to be compared between the two methods to ensure that the two methods simulate a similar outcome. Table 2 shows that the interval method has less variety in the possible ship’s ID compared to MC, as the interval method can only simulate one outcome under the set seeds. Thus, we need to check that the ship IDs generated from the interval method are found in the MC method to demonstrate that the ship ID outcomes are possible. Going back to Table 2, we can observe that nearly all the ship IDs found in the interval method can be found in the MC method, apart from Ship 13 (random path, all missiles fired hit) and Ship 32 (pre-set path, all missiles fired hit), but they may still be found present in the MC simulation if more MC runs were undertaken.\n\nIn this vein, as multiple iterations of the model are necessary for MC, there is additional data generated compared to the interval implementation (see endpoint results: Table 2), which can be collated to show the total number of occurrences for the number of ships that survived at the end of the simulation. This can be seen in Figure 3, where each sub-figure corresponds to one of the four previously discussed scenarios. Sub-figures (a) and (b) show that a predetermined path has a higher frequency for the number of surviving ships (with peak occurrence values at nine and five respectively) compared to their associated random path scenario (where both peak values are at one ship). Figure 3 also shows that the paths that the ships follow in the simulation have the greatest effect on the shape of the results; with a preset path ((a) and (b)) displaying results similar to a normal distribution, while a random path ((c) and (d)) coincides more with our expectations (one ship surviving and more ships surviving being less common). Another common factor shown in Figure 3 is that the number of surviving ships at the end of the simulation is higher when they are binomially distributed ((a) and (c)) compared to every missile fired hitting the target ((b) and (d)).\n\nIn summary, the results show that interval implementation encompasses the MC results for the high-level results (total number of ships left surviving), but there are fewer ship IDs in total compared to MC. Thus, the interval implementation may be good for finding the possible extreme values, while MC for the expected outcomes. However, it is important to note that extreme events may be more important as failure events are usually located in this region.\n\n\nConclusion\n\nWe have demonstrated that it is possible to implement and propagate intervals directly in an ABM, with the understanding that the interval endpoints represent the possible extreme values. Further, we show that MC is an ideal method for finding the expected outcomes and trends, as well as being simple to implement across various ABM models. However, in this case, it is poor at handling epistemic uncertainty due to assuming an interval can be represented as a uniform distribution but that is necessary for the MC method to work. Thus, other methods are needed for epistemic uncertainty, however they are also not without their drawbacks.\n\nOne of the drawbacks is that the answers may be vacuous (in the battleships example the answer is presented as an interval), while MC depends on how the results are collated at the end (e.g. enumerate the number of occurrences for 0 ships left; the number of times one ship is left…). Additionally, new rules may be added to the battleship interval implementation for some aspects to generate smaller intervals (e.g. how missiles are fired if they are uncertain about a target), but as the other aspects cannot be adapted it stands that the underlying problems with this type of implementation will still remain.\n\nTherefore, a direct implementation of intervals and propagating the uncertainty about a value with their use is not recommended as the results generated are rather broad and do not provide additional help in decision making, though it may be useful in generating the overall bounds of the system. Furthermore, depending on the model applications an interval model may be preferable as its computational time is lower compared to MC once the model is built.",
"appendix": "Data availability\n\nZenodo: Battleship Monte Carlo Results for comparison against Interval Implementation. https://doi.org/10.5281/zenodo.7990753. 19\n\nThis project contains the following underlying data:\n\n• PathsX.csv (Input file for X coordinates of ships using a predetermined path)\n\n• PathsY.csv (Input file for Y coordinates of ships using a predetermined path)\n\n• ResultsSPathBinMC.txt (contains the preset path and Binomially distributed hits)\n\n• ResultsRPathBinMC.txt (contains the random path and Binomially distributed hits)\n\n• ResultsSPathATMC.txt (contains the preset path and all missiles fired hits)\n\n• ResultsRPathAllTMC.txt (contains the random path and all missiles fired hits)\n\n• Scenario.txt (The minimum radar range for interval implementation)\n\n• ScenarioM.txt (The maximum radar range for interval implementation)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nBonabeau E: Agent-based modeling: Methods and techniques for simulating human systems. Proc. Natl. Acad. Sci. 2002; 99(suppl_3): 7280–7287. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFerson S, Sentz K: Epistemic Uncertainty in Agent-based Modeling. REC. 2016; 2016.\n\nMele FD, Guillén G, Espuña A, et al.: An agent-based approach for supply chain retrofitting under uncertainty. Comput. Chem. Eng. May 2007; 31(5-6): 722–735. Pergamon. 00981354. Publisher Full Text\n\nLux T: Estimation of agent-based models using sequential Monte Carlo methods. J. Econ. Dyn. Control. June 2018; 91: 391–408. 01651889. Publisher Full Text Reference Source\n\nWatson MD, Mesmer BL, Farrington PA: Engineering Elegant Systems: Theory of Systems Engineering.2020. Reference Section 5.6.2.\n\nBobashev GV, Morris RJ: Uncertainty and Inference in Agent-based Models. 2010 Second International Conference on Advances in System Simulation. 2010.\n\nMohammad Raoufi AM, Asce AR, Fayek PE, et al.: Fuzzy Monte Carlo Agent-Based Simulation of Construction Crew Performance. J. Constr. Eng. Manag. may 2020; 146(5). 0733-9364. Publisher Full Text Reference Source\n\nHilton J: Managing Uncertainty in Agent-Based Demographic Models. PhD thesis. 2017.\n\nChiang NY, Lin Y, Long Q: Efficient propagation of uncertainties in manufacturing supply chains: Time buckets, L-leap, and multilevel Monte Carlo methods. Operations Research Perspectives. January 2020; 7: 100144. Elsevier Ltd. 22147160. Publisher Full Text\n\nStepanov V: Modelling Epistemic Uncertainty in Agent-based Models. PhD thesis, University of Liverpool [Submitted]. 2023.\n\nOberkampf WL, Roy CJ: Verification and Validation in Scientific Computing. Cambridge University Press; 2010. Publisher Full Text\n\nFerson S, Ginzburg LR: Different methods are needed to propagate ignorance and variability. Reliab. Eng. Syst. Saf. 1996; 54(2-3): 133–144. 09518320. Publisher Full Text\n\nFerson S: What Monte Carlo methods cannot do. Hum. Ecol. Risk Assess. Int. J. 2008-12-02; 2: 990–1007. Taylor & Francis Group. Publisher Full Text\n\nVan Rossum G, Drake FL: Python 3 Reference Manual. Scotts Valley, CA: CreateSpace; 2009. 1441412697.\n\nHarris CR, Jarrod Millman K, van der Walt SJ , et al.: Array programming with NumPy. Nature. 2020; 585: 357–362. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHunter JD: Matplotlib: A 2d graphics environment. Comput. Sci. Eng. 2007; 9(3): 90–95. Publisher Full Text\n\nKruglyak L: The Topology of Pacman.2017. Accessed: 2023-06-20. Reference Source\n\nvvstepanov: vvstepanov/Battleship: Epistemic Battleship (v1.0a). [Source code]. Zenodo. 2023. Publisher Full Text\n\nStepanov V: Battleship Monte Carlo Results for comparison against Interval Implementation. [Data]. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "187524",
"date": "31 Jul 2023",
"name": "Vladik Kreinovich",
"expertise": [
"Reviewer Expertise Interval computations"
],
"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 problem that this paper solves is very ubiquitous. It is related to the fact that in many real-life situations, we need to make decisions under uncertainty. Sometimes, we know the probabilities of different alternatives; in this case, we can use usual Monte-Carlo simulation techniques. However, in many practical situations, we only have partial information about the corresponding probabilities. Frequently, all we know is the interval of possible values of some quantities, and we have no information about the probability of different values within this interval. In such situation of interval uncertainty, some practitioners assume that there is a uniform distribution on this interval, If the objective is to select a single distribution out of all possible distributions on the given interval, this assumption makes perfect sense: since we have no reason to believe that some values are more probable than others, it makes sense to assume that all the values are equally probable, i.e., that we have the uniform distribution. However, as is well known -- and as the authors convincingly show -- this assumption can lead to a drastic under-estimation of the resulting uncertainty. Instead, the authors propose to explicitly carry on intervals of possible values at each moment of the simulation -- and when moving to the next moment of time, consider all possible transitions which are consistent to the available interval information.\nThe authors illustrate this idea on the example of a battleship simulation inspired by the well-known children's game. The simulation is interesting and the results are interesting, but the text needs a few corrections and some clarification editing.\nMinor typo: on p. 3, 0.02 should be 0.20.\np. 4, first full paragraph, the ship fires only if the lower bound on the number of remaining missiles is larger than 0. This needs explanation, I did not expect it. We may not know during simulation whether the ship has any missiles left or not -- since in the previous moment of time, it was not clear whether the ship noticed the adversary and fired the missile. In this case, for us, the lower bound for the number of missiles is 0. However, in the actual run, the ship knows how many missiles it has left, so if a missile is left, it can fire it -- while this phrase seems to not allow this possibility.\nThe next phrase is even more confusing: the ship has both fired the missiles and not fired the missile. I know that everyone likes this confusing description of Schroedinger's cat that journalists use when they want to entertain the reader, but here the authors are trying to explain, so why not make it clearer. I think what the authors want to say is that in this case, when forming the state at the next moment of time, we take into account both possibilities: that the ship fires a missile and that the ship does not fire the missile.\nVery minor thing: the authors use it's when it should be its: e.g., its radar range (it's means it is, it is an exception to the general rule of adding apostrophe and s to a noun).\np. 5, last paragraph before the section titled \"Model results\", line 1: it is not clear why an uncertain ship cannot sink a certainly existing ship: uncertain ship means, e.g., that without our general description, in some possible histories, the ship is already destroyed. However, the fact that the ship is uncertain at this moment of the simulation means that in some possible histories, the ship is still there -- in which case it can sink another ship.\np. 5, line 3 from the bottom: I am not sure why the fact that the same seed was utilized, we do not need multiple simulations: using the same seed means that we select one random value out of many, if we selected a different seed and a different value, we could get a different result. In this case, the conclusions based on one simulation may not be applicable to other cases -- and to make general conclusions, we do need additional simulations. For the same reason, the last phrase in the first (incomplete) paragraph on p. 6 is not clear.\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? Yes\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? Yes",
"responses": [
{
"c_id": "10082",
"date": "31 Aug 2023",
"name": "Vladimir Stepanov",
"role": "Author Response",
"response": "Thanks to Prof Kreinovich for his thoughtful and careful comments. They have been valuable to us. We have numbered the points he has raised for easy reference. 1) Minor typo: on p. 3, 0.02 should be 0.20. Thank you. This has been corrected. 2)p. 4, first full paragraph, the ship fires only if the lower bound on the number of remaining missiles is larger than 0. This needs explanation, I did not expect it. We may not know during simulation whether the ship has any missiles left or not -- since in the previous moment of time, it was not clear whether the ship noticed the adversary and fired the missile. In this case, for us, the lower bound for the number of missiles is 0. However, in the actual run, the ship knows how many missiles it has left, so if a missile is left, it can fire it -- while this phrase seems to not allow this possibility. We have changed the word “lower” to “upper” in the confusing sentence. This allows for the possibility of firing missiles, as expected. 3)The next phrase is even more confusing: the ship has both fired the missiles and not fired the missile. I know that everyone likes this confusing description of Schroedinger's cat that journalists use when they want to entertain the reader, but here the authors are trying to explain, so why not make it clearer. I think what the authors want to say is that in this case, when forming the state at the next moment of time, we take into account both possibilities: that the ship fires a missile and that the ship does not fire the missile. We have changed the original sentence from: If the ship fires at a ship in the uncertain radar range, the ship fire is uncertain, i.e. the ship has both fired the missiles and not fired the missiles. To this: Due to uncertainty about the radar range, a ship may or may not detect a target ship within its firing range. In such a case, the firing of missiles is uncertain. If the ship detects the target it would fire, but if it does not detect the target it would not fire. This means that, when representing the state at the next moment of time, we consider both possibilities: that the ship fires a missile and that the ship does not fire the missile. In the former case, the ship’s complement of missiles decreases and the target may experience damage. In the latter, neither occurs. 4)Very minor thing: the authors use it's when it should be its: e.g., its radar range (it's means it is, it is an exception to the general rule of adding apostrophe and s to a noun). Corrected. 5)p. 5, last paragraph before the section titled \"Model results\", line 1: it is not clear why an uncertain ship cannot sink a certainly existing ship: uncertain ship means, e.g., that without our general description, in some possible histories, the ship is already destroyed. However, the fact that the ship is uncertain at this moment of the simulation means that in some possible histories, the ship is still there -- in which case it can sink another ship. We have clarified the paragraph that explains how a ship becomes uncertain about its existence by changing the explanation from: In summary, the scenarios demonstrate that an uncertain ship cannot sink a certainly existing ship, as when the upper bound for the hit counts exceeds the ship’s limit, the previously certainly existing ship becomes uncertain about its existence. To this: In summary, the scenarios demonstrate that an uncertain ship cannot sink a certainly existing ship, as the missiles fired from such a ship are uncertain. Thus only the upper bound of the hit count for the other ship is increased. When the hit count’s upper bound exceeds the ship’s upper existence limit, the previously certainly existing ship becomes uncertain about its existence, but it does not (certainly) sink. Recall that uncertainty about a ship’s existence means that we don’t know whether it has been sunk or not. 6)p. 5, line 3 from the bottom: I am not sure why the fact that the same seed was utilized, we do not need multiple simulations: using the same seed means that we select one random value out of many, if we selected a different seed and a different value, we could get a different result. In this case, the conclusions based on one simulation may not be applicable to other cases -- and to make general conclusions, we do need additional simulations. For the same reason, the last phrase in the first (incomplete) paragraph on p. 6 is not clear. We agree. We have modified the paragraph discussing the issue in two places: the middle and at the end. The additional part in the middle, explains why we have used one seed (we were testing the methodology and not the actual behaviour of those particular ships). Our edit at the end of the paragraph, clarifies that the simulation can still have variations even when using the same seed, leading to further testing explained at a later stage in the text. We hope that the changes improve clarity."
}
]
},
{
"id": "193841",
"date": "22 Aug 2023",
"name": "Josie McCulloch",
"expertise": [
"Reviewer Expertise Agent-based models",
"interval computations"
],
"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 an interesting method of using interval computations to understand epistemic uncertainty in an agent based model, with the goal of counteracting the problems with Monte-Carlo methods not being so suited to this kind of uncertainty.\nThe paper is well written, but there are a few points that could be better explained.\nIn the abstract, I'm not sure what the authors mean by \"the interval approach misses the quantitative conclusion\".\nOn page 4, why can a ship's radar reach 27.5 grid units? The text states that a ship occupies a grid cell, so it's not clear there's any advantage to being able to see half a cell.\nAlso on page 4, it states that a ship will fire a missile if the lower bound of the interval for the remaining missiles is above zero. Why does a ship have uncertainty in how many missiles it has? Is it the model that has uncertainty in how many missiles the ship has, and therefore what the ship then does? In addition, if there is another ship in uncertain radar range, then I don't think the current ship can be said to have both fired and not fired its missiles. I think it would be more accurate to say it may or may not have fired its missiles.\nAlso, a typo on page 4, it should be \"missiles fired as m\".\nOn page 5, the authors say the first simulations have no epistemic uncertainty. It would be useful to summarise how this is so. Do they have no uncertainty in their radar?\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? Yes\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? Yes",
"responses": [
{
"c_id": "10122",
"date": "31 Aug 2023",
"name": "Vladimir Stepanov",
"role": "Author Response",
"response": "Thanks to Prof McCulloch for her thoughtful and careful comments. They have been valuable to us. We have numbered the points she has raised for easy reference. 1)In the abstract, I'm not sure what the authors mean by \"the interval approach misses the quantitative conclusion\". We have changed “the” to “that” as we feel that helps to clarify that an interval implementation output is an interval. This interval may not be small, which may be unrealistic. 2)On page 4, why can a ship's radar reach 27.5 grid units? The text states that a ship occupies a grid cell, so it's not clear there's any advantage to being able to see half a cell. Thank you for pointing this out. As a result, we have changed the terminology from grid cell to grip point to better reflect the code implementation and to reduce confusion. 3)Also on page 4, it states that a ship will fire a missile if the lower bound of the interval for the remaining missiles is above zero. Why does a ship have uncertainty in how many missiles it has? Is it the model that has uncertainty in how many missiles the ship has, and therefore what the ship then does? In addition, if there is another ship in uncertain radar range, then I don't think the current ship can be said to have both fired and not fired its missiles. I think it would be more accurate to say it may or may not have fired its missiles. In addition to Vladik’s reply we have also added a clarifying statement that the ship doesn’t have uncertainty about how many missiles it’s fired, but the simulation does. That is, the analyst who is running the simulation. 4)Also, a typo on page 4, it should be \"missiles fired as m\". Corrected. 5)On page 5, the authors say the first simulations have no epistemic uncertainty. It would be useful to summarise how this is so. Do they have no uncertainty in their radar? We have added the following clarifying statement: “i.e. when the ships see other ships in their radar perfectly,” – to remove confusion."
}
]
}
] | 1
|
https://f1000research.com/articles/12-834
|
https://f1000research.com/articles/13-91/v1
|
01 Feb 24
|
{
"type": "Research Article",
"title": "Differentiation of invasive ductal and lobular carcinoma of the breast using MRI radiomic features: a pilot study",
"authors": [
"Sudeepta Maiti",
"Shailesh Nayak",
"Karthikeya D Hebbar",
"Saikiran Pendem",
"Sudeepta Maiti",
"Shailesh Nayak",
"Karthikeya D Hebbar"
],
"abstract": "Background Breast cancer (BC) is one of the main causes of cancer-related mortality among women. For clinical management to help patients survive longer and spend less time on treatment, early and precise cancer identification and differentiation of breast lesions are crucial. To investigate the accuracy of radiomic features (RF) extracted from dynamic contrast-enhanced Magnetic Resonance Imaging (DCE MRI) for differentiating invasive ductal carcinoma (IDC) from invasive lobular carcinoma (ILC).\n\nMethods This is a retrospective study. The IDC of 30 and ILC of 28 patients from Dukes breast cancer MRI data set of The Cancer Imaging Archive (TCIA), were included. The RF were extracted from the DCE-MRI sequence using a 3D slicer. The relevance of RF for differentiating IDC from ILC was evaluated using the maximum relevance minimum redundancy (mRMR) and Mann-Whitney test. Receiver Operating Characteristic (ROC) curve analysis was performed to ascertain the accuracy of RF in distinguishing between IDC and ILC.\n\nResults Ten DCE MRI-based RFs used in our study showed a significant difference (p <0.001) between IDC and ILC. We noticed that DCE RF, such as Gray level run length matrix (GLRLM) gray level variance (sensitivity (SN) 97.21%, specificity (SP) 96.2%, area under curve (AUC) 0.998), Gray level co-occurrence matrix (GLCM) difference average (SN 95.72%, SP 96.34%, AUC 0.983), GLCM interquartile range (SN 95.24%, SP 97.31%, AUC 0.968), had the strongest ability to differentiate IDC and ILC.\n\nConclusions MRI-based RF derived from DCE sequences can be used in clinical settings to differentiate malignant lesions of the breast, such as IDC and ILC, without requiring intrusive procedures.",
"keywords": [
"Invasive carcinoma",
"Radiomic features",
"MRI Sequences",
"Magnetic Resonance Imaging (MRI)",
"Noninvasive diagnosis"
],
"content": "Introduction\n\nBreast cancer (BC) is the most frequently diagnosed cancer among women worldwide. With an expected 2.3 million new cases, or 11.7% of all cancer cases worldwide in 2020, lung cancer has surpassed lung cancer as the most common cause of cancer incidence.1 According to epidemiological studies, by 2030, there will likely be roughly 2 million BC patients worldwide, according to epidemiological studies.2 Early and precise identification and characterization of cancers are crucial because of their incidence and therapeutic significance.\n\nMammography and Ultrasonography are frequently used for breast lesion detection, screening and diagnostic purposes.3,4 Breast Magnetic Resonance Imaging (MRI) is performed regularly to better detect primary and recurrent tumors, characterize them, and assess the patient’s response to therapy. Dynamic contrast-enhanced (DCE) MRI is an important component of the MRI-Breast protocol, which involves serial capture of strong T1 weighted images during intravenous administration of contrast. It provides information about tumor vascularity, and enhancement curves are frequently used to increase specificity (greater than 90%) for diagnosing cancer.5–8\n\nRadiomics is a popular area of study in the processing and analysis of medical images. Radiomics provides more information than the visual and qualitative patterns that radiologists can see with their unaided eyes by extracting a large number of quantitative imaging features from medical images. On routine imaging examinations performed in cancer patients, radiomic feature (RF) characteristics can non-invasively evaluate intratumoral variability.9,10 The use of RF in patients with BC is a novel and developing area of translational research. RF in BC has been extensively employed in research settings with the hope that it may eventually improve diagnosis and characterization.11,12\n\nThere are significant methodological variations in research involving RF and artificial intelligence (AI) techniques, such as machine learning (ML) based on radiomics, and there is potential for methodological advancement and standardization to improve study quality in BC. There is a lack of reproducibility and validation in radiomic studies.13 Our literature review revealed a few studies that used RF from the DCE sequence of breast MRI for differentiating malignant lesions such as invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC). Hence, our study investigated whether RF obtained from DCE-MRI would aid in the differentiation of IDC and ILC.\n\n\nMethods\n\nFirst, this was a retrospective study. The study was commenced upon approval from the Institutional Ethical Committee of Kasturba Medical College and Hospital, Manipal, India on 6th August 2022 (IEC 202/2022). Informed consent was waived since the data was collected from a publicly available database.\n\nPatients with confirmed histopathology diagnosis of IDC and ILC were included. The cases with artifacts on MRI images were excluded.\n\nPatients with confirmed histopathological reports of IDC (30) and ILC (28) from the Duke breast cancer MRI data set of the cancer imaging archive (TCIA) were included in this study14,15 (underlying data).16 The MRI breast dataset (IDC and ILC) used for this study is publicly available online at https://wiki.cancerimagingarchive.net/; https://doi.org/10.7937/TCIA.e3sv-re93). The Duke breast cancer dataset is composed of a retrospectively collected cohort of 922 biopsy-confirmed invasive breast cancer patients from a single institution (Duke Hospital, Durham, North Carolina, USA) with preoperative MRI from January 1, 2000 to March 23, 2014. The images were acquired using 1.5 Tesla GE (Signa Excite, Signa HDxt) and Siemens (Avanto) MRI scanners. The mean age (years) of the patients with IDC and ILC was 48 ± 11.15 and 59 ± 11 years, respectively. Demographic characteristics are shown in Table 1. Axial T1 dynamic post-contrast (DCE) sequence (gadolinium-based contrast of 15–20 ml) was performed using the image acquisition parameters listed in Table 2.\n\nThe DICOM MRI images of the Axial T1 DCE were uploaded into 3D slicer (version 4.10.2) and the regions of tumor were manually (slice by-slice) delineated by radiologist who had experience more than 10 years (Figure 1). The RF was extracted from the axial T1 dynamic contrast-enhanced sequence. ROIs were defined across the entire tumor using DCE-MRI images with the strongest enhancement phase. The observer specifically chose phase (3.92 ± 1.22-on average), to segment the analyzed lesions, out of the six or seven phases offered by the Axial T1 Dynamic contrast enhanced sequences, across different patients, where the breast mass was more visible than in the backdrop. The radiologist was blinded to histopathological reports.\n\nTo determine which RF was the most pertinent and least redundant, the maximum relevance and minimum redundancy (mRMR) approach was used.17 Fifteen RF features were selected for the subsequent analysis (Table 3).\n\nStatistical analyses were performed using Statistical Package for Social Sciences (SPSS-20.0) software. The maximum relevance and minimum redundancy (mRMR) approach was applied using Google Colab. The Mann-Whitney U-test was performed to identify significant features for differentiating IDC and ILC on Axial T1 dynamic contrast. Receiver Operating Curve (ROC) analysis was performed to determine the accuracy of RF in differentiating between IDC and ILC. Statistical significance was set at p < 0.001.\n\n\nResults\n\nIn our study, we analyzed the RF extracted from DCE-MRI. Our study extracted 107 features from the DCE-MRI sequence for each subject. The mRMR technique identified 15 RF features that were relevant for differentiating between IDC and ILC Table 3. Of the 15 selected features, 10 DCE MRI-based RF were significant for differentiating between IDC and ILC. A total of 58 cases were included in the study. The mean age (years) of the patients with IDC and ILC was 48 ± 11.15 and 59 ± 11 years, respectively.\n\nFor 3D DCE MRI sequence, Gray level dependence matrix (GLDM) gray level variance for IDC and ILC was 288.6 ± 136.4 and 1187.0 ± 342.5 (p < 0.001), Gray level co-occurrence matrix (GLCM) square for IDC and ILC was 118.5 ± 63.15 and 492.4 ± 277.6 (p < 0.001), GLCM difference average for IDC and ILC was 4.472 ± 2.694 and 20.45 ± 10.11 (p < 0.001), GLCM cluster tendency for IDC and ILC was 270.3 ± 81.47 and 1170.8 ± 145.5 (p < 0.001), GLCM interquartile range for IDC and ILC was 286.2 ± 52.8 and 1630.8 ± 332.9 (p < 0.001), first order robust-mean absolute deviation for IDC and ILC was 117.9 ± 18.2 and 403.5 ± 179.0 (p < 0.001), first order entropy for IDC and ILC was 4.776 ± 1.656 and 6.063 ± 1.697 (p < 0.001), first order variance for IDC and ILC was 44324.8 ± 3799.0 and 438604.1 ± 39979.8 (p < 0.001), Gray level run length matrix (GLRLM) gray level variance for IDC and ILC was 35.64 ± 31.20 and 741.40 ± 173.3 (p < 0.001) and GLRLM run entropy for IDC and ILC was 5.496 ± 1.677 and 6.814 ± 1.65 (p < 0.001) (Table 4 and Figure 2).\n\n(a) GLDM Gray Level Variance; (b) GLCM Sum Squares; (c) GLCM Difference Average; (d) GLCM Cluster Tendency; (e) GLCM Interquartile Range; (f) First Order RMAD; (g) First Order Entropy; (h) First Order Variance; (i) GLRLM Gray Level Variance; (j) GLRLM Run Entropy.\n\nThe accuracy measures of RF for differentiating between IDC and ILC are listed in Table 5. For 3D DCE MRI sequence, GLRLM gray level variance at cut off value of 42, had higher sensitivity (SN 97.21%), specificity (SP 96.2%), and area under curve (AUC 0.998; GLCM interquartile range at cut off value of 357 had higher SN (95.24%), SP (97.31%), and AUC of 0.968; and GLCM difference average at a cut off value of 6.5, had higher SN 95.72%, SP 96.34% and AUC of 0.983 compared to GLDM gray level variance (SN 91.02%, SP 89.72%), GLCM sum squares (SN 85.91%, SP 82.72%), first order variance (SN 81.54%, SP 82.72%), GLCM cluster tendency (SN 81.77%, SP 80.13%), first order RMAD (SN 80.12%, SP 79.23%), first order entropy (SN 75.24%, SP 72.23%), GLRLM run entropy (SN 75.47%, SP 77.83%) (Figure 3).\n\n(a) GLDM Gray Level Variance; (b) GLCM Sum Squares; (c) GLCM Difference Average; (d) GLCM Cluster Tendency; (e) GLCM Interquartile Range; (f) First Order RMAD; (g) First Order Entropy; (h) First Order Variance; (i) GLRLM Gray Level Variance; (j) GLRLM Run Entropy.\n\n\nDiscussion\n\nIn the current study, we explored the usefulness of DCE-based RF compared to MRI for differentiating malignant lesions of the breast, such as IDC and ILC. Breast MRI is superior to mammography and ultrasonography for early detection of BC. IDC and ILC are the most common subtypes of malignant cancer. Differentiation of ILC from IDC is quite difficult, as there are very few differences between them. The morphological and dynamic contrast kinetic characteristics of IDC and ILC did not differ considerably from each other. The correct identification of ductal and lobular carcinoma helps in the improved management and overall survival analysis of the patient.18,19\n\nPrevious studies have focused on differentiating benign and malignant lesions of the breast using radiomic models in MRI.20–22 However, few studies have been conducted to differentiate invasive carcinomas of the breast, such as IDC and ILC, using RF from dynamic contrast sequences. The integration of radiomic models in normal radiological practice will be extremely beneficial for non-invasive diagnosis and clinical management of invasive BC in the future.\n\nOur study found ten RF useful in differentiating IDC and ILC. We noticed that categories such as GLDM, GLCM, first order, and GLRLM showed significant differences in differentiating ductal and lobular carcinoma of the breast. Of these categories, GLRLM (Gray level variance AUC 0.998) and GLCM difference average) and interquartile range features were the best predictors for differentiation between IDC and ILC. GLCM features consider how pixels are arranged in space. These features describe the texture of a picture by calculating the frequency of pixel pairings with distinct values and a specific spatial relationship. GLRLM features are used to describe the length of successive pixels with the same grey level value in terms of pixels. GLCM and GLRLM are important markers for assessing tumor heterogeneity and for better characterization of malignant subtypes.\n\nWaugh et al.23 in their study noticed that all co-occurrence RF had higher accuracy (71.4% and AUC –0.745) in differentiating ductal and lobular carcinoma than entropy features (64.7% and AUROC –0.632). Holli et al.24 noticed that the co-occurrence RF of subtraction first images was more statistically significant than that of other features (Table 6). They also achieved a classification accuracy of 100% using first subtraction and contrast series using nonlinear and linear discriminant analyses. Our study also noticed that co-occurrence matrix features, such as sum squares, difference average, and cluster tendency, exhibited good accuracy in differentiating ductal and lobular carcinomas. In addition to co-occurrence matrix features, we also noticed additional categories showing statistically significant differences, which were not reported by Holli et al.24 and Waugh et al.23\n\nA study by Fusco et al.20 observed that kurtosis and skewness (AUC = 0.71) in X-ray mammography and range, energy, entropy, and gray-level non-uniformity (GLN) of the GLRLM from DCE-MRI were the best predictors for differentiating benign and malignant lesions. Niu et al.21 they studied the accuracy of RF extracted from digital mammography (DM), digital breast tomosynthesis (DBT), diffusion (DWI), and DCE MRI for the characterization of breast lesions and noticed that the RF extracted from DWI and DCE MRI yielded higher AUC, SN, and SP with DCE having the upper hand compared to DWI, and lower AUC, SN, and SP were noted from DM. Militello et al.22 reported that shape-based features such as least axis length, flatness, and elongation, GLCM-based features such as joint energy, GLRLM features such as short run emphasis, and Gray level size zone (GLSZM) of size-non-uniformity from DCE-MRI exhibited the highest SN and SP in characterizing breast lesions.\n\nA study by Lafci et al.25 noticed that Gray level zone length matrix (GLZLM) features had the highest accuracy (AUC = 0.718) in distinguishing Luminal A and B types of ductal carcinoma. They also noted that Luminal B tumors had a larger volume than luminal A tumors as they are aggressive and require intense chemotherapy, and observed shape-based features such as voxel volume showed significant differences between A and B. In our study, we also noted a larger voxel volume for ILC (5144 ± 306.5) than for IDC (3899 ± 684.3); however, we did not notice a statistically significant difference because of the smaller sample size. Literature suggests that ILC has a larger volume and is more aggressive compared to IDC.26\n\nOur study has the following limitations. First, we did not utilize machine learning and deep learning classifiers for the prediction of ductal and lobular carcinomas due to the small sample size. Second, longitudinal studies with large sample sizes and machine learning methods were used to further validate the results. Third, as the RF is obtained using manual segmentation, it is time-consuming and subjective.\n\n\nConclusions\n\nClassification of BC into histological subgroups is a dynamic process. Our study suggested an RF-based method for ductal and lobular carcinoma characterization using T1 dynamic contrast sequence, which might give radiologists additional value for decision making in a noninvasive method and could be utilized clinically for malignant BC classification.",
"appendix": "Data availability\n\nDuke breast cancer MRI data set used for this study are publicly available in the cancer imaging archive (14,15) at https://doi.org/10.7937/TCIA.e3sv-re93 under the terms of the http://creativecommons.org/licenses/by/3.0/ or the https://creativecommons.org/licenses/by/4.0/. There were no changes made to the dataset.\n\nFigshare: Underlying data for ‘Differentiation of invasive ductal and lobular carcinoma of the breast using MRI radiomic features: a pilot study’, ‘RF for IDC and ILC-F1000’, https://doi.org/10.6084/m9.figshare.24792693. 16\n\nThis project contains the following underlying data:\n\n- Demographic characteristics and RF of IDC and ILC (Spread Sheet)\n\n- MRI images (DICOM)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\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. Publisher Full Text\n\nDeSantis C, Siegel R, Bandi P, et al.: Breast cancer statistics. CA Cancer J. Clin. 2011; 61: 409–418.\n\nKolb TM, Lichy J, Newhouse JH: Comparison of the performance of screening mammography, physical examination, and breast US and evaluation of factors that influence them: an analysis of 27,825 patient evaluations. Radiology. 2002; 225: 165–175. PubMed Abstract | Publisher Full Text\n\nRomeo V, Cuocolo R, Apolito R, et al.: Clinical value of radiomics and machine learning in breast ultrasound: a multicenter study for differential diagnosis of benign and malignant lesions. Eur. Radiol. 2021; 31(12): 9511–9519. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDhillon GS, Bell N, Ginat DT, et al.: Breast MR Imaging: What the Radiologist Needs to Know. J. Clin. Imaging Sci. 2011; 1: 48. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSorace AG, Partridge SC, Li X, et al.: Distinguishing benign and malignant breast tumors: preliminary comparison of kinetic modeling approaches using multi-institutional dynamic contrast-enhanced MRI data from the International Breast MR Consortium 6883 trial. J. Med. Imaging (Bellingham). 2018; 5(1): 011019. PubMed Abstract | Publisher Full Text\n\nChen W, Giger ML, Bick U: A fuzzy c-means (FCM)-based approach for computerized segmentation of breast lesions in dynamic contrast enhanced MR images. Acad. Radiol. 2006; 13: 63–72. Publisher Full Text\n\nGhazala S: Characterization of suspicious breast lesions with dynamic contrast enhanced MRI in comparison to conventional mammography and ultrasonography. J. Cancer Prev. Curr. Res. 2016; 4: 00121. Publisher Full Text\n\nGillies RJ, Kinahan PE, Hricak H: Radiomics: images are more than pictures, they are data. Radiology. 2016; 278: 563–577. Publisher Full Text\n\nPapanikolaou N, Matos C, Koh DM: How to develop a meaningful radiomic signature for clinical use in oncologic patients. Cancer Imaging. 2020; 20: 33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nValdora F, Houssami N, Rossi F, et al.: Rapid review: radiomics and breast cancer. Breast Cancer Res. Treat. 2018; 169(2): 217–229. Publisher Full Text\n\nCrivelli P, Ledda RE, Parascandolo N, et al.: New Challenge for Radiologists: Radiomics in Breast Cancer. Bio. Med. Res. Int. 2018; 2018: 1–10. Publisher Full Text\n\nHoussami N, Lee CI, Buist DSM, et al.: Artificial intelligence for breast cancer screening: opportunity or hype? Breast. 2017; 36: 31–33. Publisher Full Text\n\nSaha A, Harowicz MR, Grimm LJ, et al.: Dynamic contrast-enhanced magnetic resonance images of breast cancer patients with tumor locations [Data set]. The Cancer Imaging Archive. 2021.\n\nSaha A, Harowicz MR, Grimm LJ, et al.: A machine learning approach to radiogenomics of breast cancer: a study of 922 subjects and 529 DCE-MRI features. Br. J. Cancer. 2018; 119(4): 508–516. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPendem S: RF for IDC and ILC-F1000. [Dataset]. figshare. 2023. Publisher Full Text\n\nPeng H, Long F, Ding C: Feature selection based on mutual information: criteria of max- dependency, max-relevance, and min-redundancy. IEEE Trans. Pattern Anal. Mach. Intell. 2005; 27(8): 1226–1238. PubMed Abstract | Publisher Full Text\n\nAlaref A, Hassan A, Sharma Kandel R, et al.: Magnetic Resonance Imaging Features in Different Types of Invasive Breast Cancer: A Systematic Review of the Literature. Cureus. 2021 Mar 12; 13(3): e13854. PubMed Abstract | Publisher Full Text\n\nMorris EA, Comstock CE, Lee CH, et al.: ACR BI-RADS Magnetic Resonance Imaging. Breast Imaging Reporting and Data System. 2013; 5.\n\nFusco R, Di Bernardo E, Piccirillo A, et al.: Radiomic and Artificial Intelligence Analysis with Textural Metrics Extracted by Contrast-Enhanced Mammography and Dynamic Contrast Magnetic Resonance Imaging to Detect Breast Malignant Lesions. Curr. Oncol. 2022; 29(3): 1947–1966. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNiu S, Wang X, Zhao N, et al.: Radiomic Evaluations of the Diagnostic Performance of DM, DBT, DCE MRI, DWI, and their Combination for the Diagnosis of Breast Cancer. Front. Oncol. 2021 Sep 10; 11: 725922. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMilitello C, Rundo L, Dimarco, et al.: 3D DCE-MRI Radiomic Analysis for Malignant Lesion Prediction in Breast Cancer Patients. Acad. Radiol. 2022; 29(6): 830–840. PubMed Abstract | Publisher Full Text\n\nWaugh SA, Purdie CA, Jordan LB, et al.: Magnetic resonance imaging texture analysis classification of primary breast cancer. Eur. Radiol. 2016; 26(2): 322–330. PubMed Abstract | Publisher Full Text\n\nHolli K, Laaperi AL, Harrison L, et al.: Characterization of breast cancer types by texture analysis of magnetic resonance images. Acad. Radiol. 2010; 17(2): 135–141. PubMed Abstract | Publisher Full Text\n\nLafcı O, Celepli P, Seher oztekin P, et al.: DCE-MRI Radiomics Analysis in Differentiating Luminal A and Luminal B Breast Cancer Molecular Subtypes. Acad. Radiol. 2023; 30(1): 22–29. PubMed Abstract | Publisher Full Text\n\nArpino G, Bardou VJ, Clark GM, et al.: Infiltrating lobular carcinoma of the breast: tumor characteristics and clinical outcome. Breast Cancer Res. 2004; 6: R149–R156. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "243253",
"date": "19 Feb 2024",
"name": "Avantsa Rohini",
"expertise": [
"Reviewer Expertise RADIO DIAGNOSIS AND 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\nThis is a very good article. The concept and idea of differentiating invasive ductal carcinoma and invasive lobular carcinoma prior to invasive test based on MRI radiomic features is interesting, and encouraging. The results of the study might encourage future studies and help in reducing the time gap between diagnosis and treatment of breast cancer.\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": []
},
{
"id": "243255",
"date": "28 Feb 2024",
"name": "Mubarak Taiwo Mustapha",
"expertise": [
"Reviewer Expertise Artificial Intelligence."
],
"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\nTitle and Abstract:\nThe title effectively summarizes the main objective of the study. The abstract provides a clear overview of the study's background, methods, results, and conclusions. It effectively communicates the main findings. However, it lacks specific details on the radiomic features analyzed and the statistical methods used.\n\nIntroduction:\nThe introduction provides relevant background information on breast cancer and the importance of early and precise identification of breast lesions. It effectively sets the stage for the study and highlights the potential clinical significance of the research. However, it could be improved by providing more context on the challenges in accurately diagnosing invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) and discussing the limitations of current diagnostic methods.\n\nMethods:\nThe methods section provides a detailed description of the study design, patient population, MRI imaging protocol, and radiomic feature extraction methods. The inclusion and exclusion criteria are clearly stated, and the data source is properly cited. However, the rationale for the sample size and radiomic feature selection criteria should be provided. The use of the mRMR approach and Mann-Whitney U-test for feature selection and statistical analysis is appropriate. However, more details on the statistical analysis methods used for ROC curve analysis would be beneficial.\n\nResults:\nThe results section presents the findings of the study, demonstrating significant differences in MRI radiomic features between IDC and ILC. The results are clearly presented, but more specific quantitative results, such as effect sizes, confidence intervals, and p-values, would enhance the interpretation of the findings.\n\nDiscussion:\nThe discussion interprets the findings in the context of existing literature and highlights the potential clinical implications of using MRI radiomic features to differentiate between IDC and ILC. The discussion acknowledges the limitations of the study but could be expanded to discuss potential biases, reproducibility issues, and future research directions in more detail.\n\nConclusion:\nThe conclusion summarizes the key findings of the study but could be strengthened by emphasizing the clinical significance of the results and suggesting potential implications for breast cancer diagnosis and treatment. It would be beneficial to provide a brief summary of the study's limitations and future research directions in the conclusion 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": "11247",
"date": "04 Apr 2024",
"name": "Saikiran Pendem",
"role": "Author Response",
"response": "Title and abstract 1.The title effectively summarizes the main objective of the study. Response: We would like to thank reviewer for positive comment regarding the title of the study. 2. The abstract provides a clear overview of the study's background, methods, results, and conclusions. It effectively communicates the main findings. However, it lacks specific details on the radiomic features analyzed and the statistical methods used Response: As per the suggestion, the specific details on the radiomic features analyzed and statistical methods used were addressed as below The RF categories such as shape based, Gray level dependence matrix (GLDM), Gray level co-occurrence matrix (GLCM), First order, Gray level run length matrix (GLRLM), Gray level size zone matrix (GLSZM), NGTDM (Neighboring gray tone difference matrix) were extracted from the DCE-MRI sequence using a 3D slicer. The maximum relevance and minimum redundancy (mRMR) was applied using Google Colab for identifying the top fifteen relevant radiomic features. The Mann-Whitney U test was performed to identify significant features for differentiating IDC and ILC. Introduction 3. The introduction provides relevant background information on breast cancer and the importance of early and precise identification of breast lesions Response: We would like to thank reviewer for positive comment regarding the introduction of the study. 4. It effectively sets the stage for the study and highlights the potential clinical significance of the research. However, it could be improved by providing more context on the challenges in accurately diagnosing invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) and discussing the limitations of current diagnostic methods. Response: As per the suggestion, the details regarding challenges in accurately diagnosing invasive ductal and lobular carcinoma and limitations of current diagnostic methods were provided as below: Accurately diagnosing invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) presents significant challenges, primarily due to overlapping clinical, radiological, and histological features. Diagnostic doubts are exacerbated by mammographic ambiguities, equivocal biopsy results, and challenges in differentiating between the two subtypes. The distinctive marker for ILC, E-cadherin, can be stained with immunohistochemically, butthe results can be ambiguous. Additionally, the genetic and molecular variability within each subtype makes classification even more difficult. Furthermore, the whole extent of the tumor may not always be captured by the diagnostic techniques used today, such as mammography, ultrasound, and biopsy, which could result in sample errors and incomplete assessments. These drawbacks highlight the necessity of continued research, thorough multidisciplinary approaches, and diagnostic technology developments in order to improve patient outcomes and increase the precision of IDC and ILC diagnoses. Methods 5. The methods section provides a detailed description of the study design, patient population, MRI imaging protocol, and radiomic feature extraction methods. Response: We would like to thank reviewer for positive comment regarding the methods of the study. 6. The inclusion and exclusion criteria are clearly stated, and the data source is properly cited. However, the rationale for the sample size and radiomic feature selection criteria should be provided. Response: As per the suggestion the rationale for sample size and radiomic feature selection criteria was provide as below: Sample size for the study was calculated using the formula of sensitivity and specificity for diagnostic test accuracy based on sensitivity and specificity and area under the curve. High-dimensional radiomic feature sets can lead to overfitting and increased computational complexity. Dimensionality reduction technique, such as maximum relevance and minimum redundancy (mRMR) is employed to retain the most informative features while reducing the risk of model overfitting. 7.The use of the mRMR approach and Mann-Whitney U-test for feature selection and statistical analysis is appropriate. However, more details on the statistical analysis methods used for ROC curve analysis would be beneficial. Response: Receiver Operating Characteristic (ROC) curve analysis, statistical methods were employed to evaluate the diagnostic performance /accuracy of RF in differentiating between IDC and ILC. Area Under the Curve (AUC), quantifies the discriminative ability of the RF for IDC and ILC. Sensitivity and Specificity, represents the true positive and true negative rates of IDC and ILC using RF Results 8.The results section presents the findings of the study, demonstrating significant differences in MRI radiomic features between IDC and ILC. Response: We would like to thank reviewer for positive comment regarding the results of the study. 9.The results are clearly presented, but more specific quantitative results, such as effect sizes, confidence intervals, and p-values, would enhance the interpretation of the findings. Response: The results have been clearly provided already in the table 4 and table 5 with Mean and standard deviation, p-value, area under curve, sensitivity, specificity and cutoff value. Discussion 10. The discussion interprets the findings in the context of existing literature and highlights the potential clinical implications of using MRI radiomic features to differentiate between IDC and ILC. Response: We would like to thank reviewer for positive comment regarding the discussion of the study. 11. The discussion acknowledges the limitations of the study but could be expanded to discuss potential biases, reproducibility issues, and future research directions in more detail. Response: As per the suggestion, a detailed discussion about potential biases, reproducibility issues, and future directions were provided in detail as below. The limited sample size of a pilot study may introduce biases into the study, which examined the use of MRI radiomic characteristics to distinguish between invasive ductal and lobular cancer of the breast. This would restrict the applicability of the findings. There is a chance that overfitting and inflated diagnostic accuracy will occur, so interpretation should be done carefully. Variations in imaging protocols, equipment, and radiomic feature extraction techniques between different institutions can lead to problems with reproducibility. Larger, multicenter studies should be prioritized in future research initiatives to improve generalizability and sample variety. The study's dependability will be increased by addressing potential biases through stringent statistical validation, using standardized imaging techniques, and using external validation datasets. Additionally, examining the influence of biological and molecular factors on radiomic features could lead to a more thorough comprehension of the distinction between invasive ductal and lobular carcinoma based on imaging, which could improve the accuracy and clinical applicability of breast cancer diagnosis. Conclusion 12.The conclusion summarizes the key findings of the study but could be strengthened by emphasizing the clinical significance of the results and suggesting potential implications for breast cancer diagnosis and treatment. Response: The clinical significance of the results and suggesting potential implications for breast cancer diagnosis and treatment is provided below in the conclusion.: Our study suggested an RF-based method for ductal and lobular carcinoma characterization using T1 dynamic contrast sequence, which might give radiologists additional value for decision making in a noninvasive method and could be utilized clinically for malignant BC classification. 13. It would be beneficial to provide a brief summary of the study's limitations and future research directions in the conclusion section Response: As per the suggestion, a brief summary of the study’s limitations and future research directions were included in the conclusion section as below: Due to potential biases and limited application, the pilot study's small sample size investigating MRI radiomic characteristics for differentiating between IDC and ILC cancer may be problematic. Cautious interpretation is necessary because of potential problems including overfitting and overstated diagnostic accuracy. Larger, multicenter studies are crucial for better generalizability since variations in imaging methods throughout institutions may present reproducibility issues. Future studies should focus on external validation datasets, standardized imaging methods, and rigorous statistical validation to improve reliability. They should also look into the influence of biological components to gain a more thorough understanding of breast cancer diagnosis."
}
]
}
] | 1
|
https://f1000research.com/articles/13-91
|
https://f1000research.com/articles/12-1251/v1
|
29 Sep 23
|
{
"type": "Research Article",
"title": "An overview of cybersecurity in Zimbabwe’s financial services sector",
"authors": [
"Vusumuzi Maphosa"
],
"abstract": "Background: As nations, businesses, and individuals rely on the Internet for everyday use, so are cybercriminals manipulating systems to access information illegally and disrupting services for financial gain. The global cost of cybercrime eclipsed one trillion US Dollars in 2020, with Africa losing US $3.5 billion. Methods: A quantitative research methodology was adopted to investigate factors affecting cybercrime in Zimbabwean financial institutions. The study focused on the technical aspects of cybersecurity. Data were collected from July 2022 to October 2022, targeting technology experts in the financial services sector. Participants were recruited from 13 institutions to rank cybersecurity constructs, frameworks, and challenges associated with cybersecurity. Data was collected using a questionnaire distributed to participants. Descriptive statistics were used to extract meanings from the responses that measure mean and standard deviation. Results: Network and data security were the most highly ranked cybersecurity constructs, while physical security was the least. The top three barriers are increasing sophistication of threats, limited skills and emerging technologies, while lack of executive support was the least. The top frameworks used are the Information Technology Infrastructure Library (ITIL) and Control Objectives for Information and Related Technologies (COBIT), while a fifth is yet to adopt cybercrime frameworks. Conclusions: The study proposes that financial institutions establish a cybersecurity culture to fight cybercrime, addressing cybersecurity barriers and following best practices. Financial institutions should invest in cybersecurity technologies, train security specialists, and employ a Chief Information Security Officer (CISO). The study’s small sample may affect the generalisability of the results. Financial institutions should implement strategies to raise awareness and collaborate with institutions to train cybersecurity security specialists to close the skills gap.",
"keywords": [
"cybersecurity",
"cybercrime",
"threats",
"barriers",
"frameworks"
],
"content": "Introduction\n\nThe internet supports today’s knowledge economy and affects every way of life. The internet is growing in volume and complexity, and without due care, it exposes private data and information to criminals. Businesses use information and communication technologies to drive production and automation, while consumers use technology for entertainment and services (Maphosa, 2022). The International Telecommunication Union (ITU) reports that fixed broadband access has increased globally. Decreasing data costs have fueled teleworking, electronic commerce (e-commerce), distance learning, remote entertainment, and telemedicine (Katz and Jung, 2021). The over-dependency on information technology (IT) systems and the rise of e-commerce make societies more vulnerable to cyber-attacks than ever. Nations, institutions, and individuals utilise cyberspace, a digital or virtual environment where they connect and access digital resources. Devices, networks, and systems that harness information and knowledge for economic development should be secured. Cyberattacks disrupt services and critical infrastructure such as electric grids, water supply and transport systems, banking, and social network systems. Cybersecurity breaches impact national security, economies, and individual livelihoods as attackers leverage the vulnerabilities on multiple devices connected to the internet.\n\nThe cost of cybercrime and cybersecurity in 2020 exceeded 1% of the world’s gross domestic product eclipsing one trillion US dollars (Sviatun et al., 2021). New forms of businesses purely mediated by the internet, such as crypto-currencies, virtual reality, and cloud computing, have emerged. The adoption of new technologies such as artificial intelligence, blockchain, and the Internet of Things (IoT), among others, offers the hacker community new methods and skills to breach and undermine the security of organisations that suffer irrecoverable losses (Radzikowski, 2015). When systems have been compromised, attackers may lock the data illegally and demand ransoms to restore compromised data. The internet provides significant advantages as customers can flip through virtual online systems to acquire goods and services. However, criminal elements are lurking, intercepting, and tracking these transactions for fraud. Industry experts report that IoT devices will surpass 75 billion units by 2025 (Hejase et al., 2021), offering more opportunities for cybercriminals to breach insecure systems and homes and access sensitive data.\n\nCyberspace comprises of three layers: infrastructure, software, and data. The infrastructure layer includes physical devices and network equipment, the software layer includes computer systems and applications, and the data layer includes the data held in storage devices. To reduce the impact of cyberattacks, institutions harden cyber resources through software upgrades and patches and train employees, constantly identify vulnerabilities, and mitigate effects through backups. Institutions deploy solutions to protect their cyber resources, from physical security to application and data security. Physical cybersecurity refers to using biometric controls, physical locks, alarm systems, human security guards, and video surveillance cameras to safeguard the tangible cyber assets of an organisation (Goldstein, 2016). Cybersecurity controls and measures are applied to an organisation’s cyber applications to reduce the risk of breach. Data cybersecurity protects the confidentiality, integrity, and availability of cyber data to meet the data user’s requirements. Network security safeguards systems against unauthorised access. Network cybersecurity refers to measures taken to protect data during transmission over interconnected networks (Awodele, Onuiri, and Okolie, 2012). Network cybersecurity entails enforcing policies and modifying the network architecture to include security controls such as firewall rules, intrusion detection, monitoring, and patch management.\n\nIdentity theft is the illegal use of another person’s private information for fraud. It involves impersonating an individual’s identity to steal personal information, including banking details, credit cards, and social security information (Arachchilage and Love, 2014). Phishing is a social engineering technique where an attacker seeks to access a legitimate user’s credentials illegally or personally sensitive information by impersonating electronic communications from a trusted source (Jakobsson and Myers, 2006; Jang-Jaccard and Nepal, 2014). During phishing, an unsuspecting victim is redirected to a malicious website after receiving an email with an embedded link using social engineering techniques (Gupta et al., 2015). Malware refers to software programs illegally installed on a victim’s computer to steal identifying information and cause malicious damage to cyberinfrastructure.\n\nAs banks go digital, customers use electronic devices to conduct banking services such as creating accounts, conducting financial transactions and paying bills anytime and anywhere, increasing exposure to cybercrime. Most of Africa’s economy is informal; therefore, cyberattacks target financial institutions and mobile network operators who drive the mobile money ecosystem (Mukiibi, 2019). Africa loses over four billion USD annually to cybercrime; other critical losses include data, intellectual property, reputation, and brand name (Weforum, 2022). The outbreak of the COVID-19 pandemic forced organisations to shift from the physical to the virtual environments to deliver services (Maphosa, 2021), putting a strain on cybersecurity. Cybercrimes continue to increase despite the availability of technical cybersecurity infrastructures such as firewalls, encryption, and antiviruses.\n\nDeveloping countries should strengthen cybersecurity measures as attacks on critical infrastructure are rising. According to the national cybersecurity index (CGI), a global tracker of countries’ progress in cybersecurity, Zimbabwe is ranked 129th due to a lack of policies that support the cybersecurity (NCSI, 2021). Cybersecurity breaches are rising in Zimbabwe due to a lack of a national cybersecurity implementation plan and strategy in Zimbabwe (NCSI, 2021). In a 2018 survey, 64% of industry leaders acknowledged that organisations had failed to manage cybersecurity risks; therefore, improvements were proposed (Deloitte, 2018). This calls for researchers to propose and evaluate technical cybersecurity solutions for combating cybercrime. The study aims to assess the state of cybersecurity in a developing country to raise awareness and compliance and fight cybercrime. The study also adds to the dearth of literature from developing countries on cybercrime.\n\nCyberspace is the fastest evolving technology in human history, where new emerging platforms such as IoT, social media, big data, and cloud computing provide new threats and opportunities. Despite the recent adoption of digital platforms in Africa, organisations still need to prioritise cybersecurity; unfortunately, only a few have developed comprehensive policies to improve security. Criminals have expanded their attacks as many systems are vulnerable due to lax cybersecurity practices in most African countries. Mukiibi (2019) reported that less than ten African countries have cybersecurity legislation. By 2022, 29 of the 54 African countries had cybersecurity legislation (Weforum, 2022). In 2018, only 13 of the 54 African countries had Computer Emergency Response Teams (CERT), and 14 had personal data protection laws (AUC, 2018). Mukiibi (2019) reports that only 18 countries have Computer Security Incident Response Teams (CSIRTs). As a result, many organisations are vulnerable, and assessment results revealed that only 52% of African companies could handle large-scale cyber-attacks (Weforum, 2022). In the 12 months ending February 2021, South Africa had 230 million attacks, followed by Kenya and Morocco, which recorded 72 and 71 million attacks, respectively (KPMG, 2022). Interpol reports that 90% of African businesses have no cybersecurity protocols to protect their businesses, leaving them vulnerable to threat actors (Scidenet, 2016). Zimbabwe and Libya had 90% of counterfeit and pirated software, the highest percentage, accelerating the spread of malware and system breaches (Scidenet, 2016; Kshetri, 2019).\n\nCybercrimes are known as crimes of the Internet; specifically, they refer to criminal activities perpetrated through computer-related devices in cyberspace (Kharb, 2017). As more workers took their computers to work from home during the COVID-19 pandemic, industry experts report that cyberattacks quadrupled (Menn, 2020). The World Economic Forum reports that cyberattacks increased to 125% globally in 2021, and indications show an upward increase in 2022 (Weforum, 2022). Ever since the outbreak of the COVID-19 pandemic, cybercrimes have increased by 300%, costing the world over six trillion USD (Hejase et al., 2021). Sviatun et al., (2021) reported that 87.6% of cybercrime attacks targeted the financial sector, with the retail industry coming second with 82.7%, while the communication and technology sector had 81.9%. African businesses face cyber threats such as online scams, ransomware, botnets and email compromise (KPMG, 2022). The most common cybercrimes in Zimbabwe are identity theft, hacking, email phishing, and malware victimisation (RBZ, 2015).\n\nA study carried out by Kahn and Roberds (2008) showed that identity theft was driven by the need to steal money on one side and the need to avoid being monitored. Alkhalil et al., (2021) postulated that phishers attack a technical system by tricking employees into clicking on malicious links or downloading harmful files to steal their private information required to commit fraud. Molinaro and Bolton (2018) highlighted the importance of the double lens model in preventing phishing attacks. Hacking has been attributed to low self-control (Kranenbarg, Holt, and Gleder, 2017). Odunze (2018) employed the differential association theory and the routine activity theory to explain hacking and found that women were more vulnerable to hacking than their male counterparts due to the prevalence of romance scams.\n\nCybersecurity combines procedures and processes to protect infrastructure, systems, and data from cyberattacks. Cybersecurity ensures data integrity and confidentiality by guarding against unauthorised access to sensitive information (Mukiibi, 2019). Cybercriminals exploit flaws and other vulnerabilities in emerging technologies to counter security offered by firewalls, antivirus scanners, and data encryption tools (Jang-Jaccard and Nepal, 2014). On average, organisations are paying US $3.6 million per attack, with ransomware attacks increasing by 151% as organisations witnessed a 31% increase in attacks (Bissell et al., 2021). A major cyber-attack on a power grid left over 1.4 million people without electricity in Ukraine (Knake, 2017). Financial institution systems have become a significant target for hacking, phishing, malware, and identity theft (Scidenet, 2016). Industry trends show exponential cyber-attack growth; Price Waterhouse Cooper (PWC) reported that 93% of financial institutions suffered security breaches in 2016 (Airehrour, Vasudevan, and Madanian, 2018). The financial services sector can become bankrupt after a security breach, with millions of dollars demanded to pay lawsuits and settle ransomware (Reddy and Reddy, 2014). After a phishing attack in 2017, the Bank of India lost US $170 million (Acharya and Joshi, 2020). Another bank in Brazil lost US $243 million to cyber criminals (Tabassum, 2020). Industry experts reported that Africa lost over US $3.5 billion in 2017, with Nigeria accounting for 18.5% (US $649m), Kenya losing 6% (US $210m), and South Africa losing 4.5% (US $157m) through cyberattacks (Kshetri, 2019). Klynveld Peat Marwick Goerdeler (KPMG) reported that Kenya’s interconnected supply chain networks had suffered ransomware attacks (KPMG, 2022). In contrast, its banking sector has suffered from distributed denial-of-service (DDoS) attacks. Cyber threats have disrupted South Africa’s maritime infrastructure, and its cities’ social services payment systems have suffered ransomware and data breach (KPMG, 2022). In 2018, over 4,000 cases of cybercrime were handled by Zimbabwean police, and the country lost US $40 million to cybercrime in 2018 (Bulawayo24, 2021).\n\nCybercriminals target and exploit technical vulnerabilities and pry on users with limited cyber training or ethics to breach systems. Physical security is achieved using human guards, video surveillance cameras, physical locks, and biometrics to protect cyberspace. Skopak and Sakanovic (2016) confirmed that physical security is necessary to protect information resources comprehensively. Kazemi (2018) asserted that physical security was among the factors helping to preserve confidentiality. This view was supported by Elnaim (2016), who found out that physical security helped to protect information against attacks. DiMase et al., (2015) highlighted the importance of physical security in denying access to hardware resources. Georgiadou et al., (2021) reported that it was easy to control machines as they were more predictable than humans. There is growing interest and broader emphasis on human factors in the fight against cybercrime.\n\nAs financial institutions move some of their services online, potential breaches and security attacks increase exponentially. Reaves et al., (2015) analysed branchless banking applications and reported increased cybersecurity threats. ENISA (2016) showed that application security influences cybersecurity. Elkhodr et al., (2012) proposed improving mobile banking’s application security in Australia and found that mobile application security significantly impacted cybersecurity. Ahluwalia (2016) postulated that biometrics were pivotal in mitigating cybersecurity breaches. Experimental results from a study conducted by Zhang and Wang (2010) showed that network security performance contributed to cybersecurity.\n\nGlobally, internet traffic increased by over 30%, with significant changes in geographic distributions of the connections from enterprise locations to residential access (Katz, 2020). As workers move to work from home due to COVID-19 and flexible working in line with 21st-century jobs, vulnerabilities intensify, and measures are required to protect data during transmission over interconnected networks. Gyabi and Shrivas (2016) used encryption to secure data in the rural bank of Ghana. A simulation analysis by Hossain et al., (2017) revealed that data security in the cloud could be achieved through encryption and a location-based salt algorithm. Durumeric et al., (2017) sought to avoid HTTPS interception through heuristics deployed on different networks. A study carried out by Subramanian and John (2017) revealed that a data security algorithm reduced malicious insider attacks. Kaiwartya et al., (2017) investigated biometric Internet security and found it suitable for Internet authentication. Tseng et al., (2015) realised the importance of internet security and proposed an anti-phishing-based video game to enhance the learners’ internet security.\n\n\nMethods\n\nThis study received ethical approval from the Lupane State University Institutional Ethics Committee (LSU00022). The online questionnaire explained the research objectives, participants' expectations, voluntariness and respondents’ anonymity. Participants gave their written consent before participating in the online survey.\n\nThe study applied a descriptive quantitative survey design. The comprehensive literature review identified critical technical factors influencing cybersecurity, such as physical security, data security, application security, network security, and internet security. These factors shaped the thrust of the study. The study’s questionnaire was adapted from the International Organization for Standardization (ISO)/International Electrotechnical Commission (ISOC/IEC) (ISOC/IEC, 2012). ISOC/IEC is a task force responsible for crafting and reviewing industry-wide cybersecurity standards after every five years. Since the targeted participants are professionals with post-secondary education, the questionnaire was administered in English, the country’s official language.\n\nA pilot study was conducted to verify the questionnaire’s appropriateness and completeness and gauge the meaning of the questions (Maphosa, 2023c). The instrument was piloted in June 2022 to six network and security personnel at the University. Participants made comments and suggestions on the online questionnaire, which the researcher captured. This ensured that the questions were not ambiguous, difficult to answer or prone to many interpretations, which could lead to biased responses. Before the survey instrument was disseminated, some questions were edited to ensure clarity and answerability, while some were re-arranged to improve the flow of responses. Other changes involved altering some binary responses ‘yes’ or ‘no’ to the Likert scale type and providing options to other questions.\n\nThe final questionnaire contained two key sections with 38 items based on the literature reviewed. Cybersecurity literature and security governance standards were contextualised to the Zimbabwean context to develop the questionnaire. Data were collected from early July 2022 to early October 2022. Section A contains the respondent’s age, financial institution’s name, and gender profile as shown in Appendix A. Section B consisted of the main questions on a five-point Likert scale ranging from 1 = Strongly Disagree to 5 = Strongly Agree (Maphosa, 2023b).\n\nThe study targeted IT experts from the country’s financial institutions comprising commercial banks, merchant banks, discount houses, building societies, and finance houses. The survey questionnaire for the study was self-administered to IT experts in the financial services sector to obtain an overview of cybercrime. Electronic mail was sent to personnel in the networks and infrastructure departments of the randomly selected financial institutions. Professional networks such as LinkedIn and Twitter and distribution lists such as the Computer Society of Zimbabwe and the Internet Society of Zimbabwe were used. Convenience sampling was used to recruit participants. The sample includes participants working in the networks and infrastructure department within their financial institutions. Data were collected electronically and stored in Google Drive, which was password encrypted.\n\n\nResults\n\nThe 76 responses received were from ICT managers (16), network security specialists (12), database and systems administrators (10), developers (28), and risk and compliance officers (10), giving an 84.4% response rate. Most (72%) respondents were male, while about a third were female. More than half of the respondents had an undergraduate degree, as shown in Table 1. The average age of the respondents was 29 years, while the IT experience in the financial services sector was 9.5. The respondents’ names and those of their financial institutions were kept anonymous (Maphosa, 2023a).\n\nThe study evaluated cybersecurity security constructs for initial threat areas from physical security to data security. The study used descriptive statistics and percentages to measure the constructs’ means and standard deviations (SD). The mean and the SD of the cybersecurity constructs are shown in Table 2. The mean values ranged between 3.699 and 4.854, while SD values ranged between 0.655 and 0.779. Participants ranked network security highly, with a mean of 4.854 and a standard deviation of 0.739. The following ranked construct was data security, with a mean of 4.739 and an SD of 0.655. The penultimate construct was identity theft, with a mean of 3.802 and an SD of 0.715. The last ranked construct was physical security, with a mean of 3.699 and an SD of 0.770. Physical security is easily fortified through security guards, CCTV, biometrics, electronic locks or other related devices.\n\nRespondents ranked the framework used by their financial institution; almost half (44.74%) used the Information Technology Infrastructure Library (ITIL), followed by Control Objectives for Information and Related Technology framework (COBIT), with 36.84% and about 10.53% of the institutions adopted other frameworks as shown in Table 3.\n\nFigure 1 shows the top cybersecurity barriers, which include increasing sophistication of threats (89.5%), limited technical skills (85.5%) and emerging technologies (81.6%). The least ranked barriers are lack of executive support (22.4%), lack of adequate budget (30.3%) and lack of cybersecurity policies (53.9%).\n\n\nDiscussion\n\nThis study confirmed the findings by Norris et al., (2019), who established that lack of skills, inadequate policies, limited funding and management support impacted cybersecurity. The results show that about a fifth (19.74%) of the financial institutions have yet to adopt cybercrime frameworks, worrying as public funds and investments are at risk. Institutions must balance the drive to increase revenues and reduce operating costs while ensuring compliance and investing in cybersecurity frameworks. The ranking of network security aligned with findings by Praveena and Smys (2017), who identified network security as a substantial concern in protecting financial information. Acharya and Joshi (2020) also contended that networks should be audited at fixed intervals to test for security breaches.\n\nBendovschi (2015) also ranked data security highly, noting that when organisations lose their data, they lose their market share and customer relationship. Figure 1 shows the barriers to cybercrime in line with Norris et al., (2019), who ranked cybersecurity management barriers as limited technical skills caused by the inability of institutions to pay competitive salaries. Verizon reports that 37% of security breaches resulted from identity theft, while social engineering or phishing accounted for 22% (Verizon, 2020). KPMG (2022) recommended that organisations perform penetration tests regularly and demonstrate response and readiness to evaluate the institution’s network security. The minimal technical skills mean institutions have limited capacity to secure networks and information systems, configure servers, recover data, and continuously scan for vulnerabilities and remediation.\n\nCavusoglu et al., 2004 lamented that most African countries needed meaningful budgets to support cyber security. The establishment of cybersecurity policies demonstrates management’s intent to create a culture and provide a guide to employees. Although management support was lowly ranked, none of the financial institutions had established a Chief Information Security Officer (CISO) to handle cybersecurity issues at a strategic level. Management support also influences budgetary allocations and prioritises cybersecurity issues within the institution. Richards (2014) noted that organisations had established the CISO to strengthen the institution’s cybersecurity portfolio, managing enterprise cybersecurity risks and mitigation measures to maintain the institutional brand.\n\nCybercriminals rely on sophisticated technologies that are difficult to detect and threaten even the savviest targets (Microsoft, 2020). The findings align with observations by the World Economic Forum, which reported that only 53.7% of African countries had cybersecurity policies (Weforum, 2022). The lack of policies hinders sharing cybersecurity information between institutions, resulting in fragmented knowledge across the domain. Caulkins et al., (2018) also identified a lack of cybersecurity personnel globally, affecting the availability of skilled and experienced staff who can handle cybersecurity tasks and challenges. Financial institutions should train and retain cybersecurity specialists to fight cybercrime.\n\nMicrosoft (2020) identified emerging threats, such as using AI-enabled capabilities to commit cybercrime and the increased adoption of IoT and teleworking. Such tools are available on the black market and online. Financial institutions can take practical steps to raise awareness and training and ensure that cybersecurity frameworks are adopted. Lack of cybersecurity awareness by employees can have devastating consequences on the organisation as they can quickly become a security loophole if they are not concentrating, are distracted, or are stressed. This aligns well with KPMG's (2022) recommendations, which suggested that institutions conduct cyber awareness and training, establish firewalls and maintain backup while ensuring their security systems have the latest patches. The top three barriers for this study are increasing sophistication of threats, limited skills and emerging technologies. Insufficient cybersecurity personnel, limited budgets, and executive support followed these. Financial institutions should adopt cybersecurity policies and engage in extensive end-user training programmes to fight cybercriminals.\n\nThe study has the following limitations. The small sample size impacts the generalisability of the findings; more responses would have improved the value of the study’s findings. Using a quantitative data collection approach may have restricted the probing of participants to elicit more information and further explain specific responses. The use of self-reported data raises fears that participants could have portrayed a positive outlook on the image of their institution since data breaches are sensitive in the financial services sector.\n\n\nConclusion\n\nLiterature shows that cybercriminals constantly attack financial institutions, yet results show that their cybersecurity practices are poor. As technology evolves, the means and opportunities to commit cybercrime also increase, and therefore, many organisations will suffer security breaches leading to irrecoverable losses. The study provides an overview of Zimbabwe’s cybersecurity landscape and threats while providing a roadmap to manage cybercrime in other developing countries with a similar socioeconomic environment. Research has been conducted to identify the motivations, techniques, and countermeasures to cybercrime; however, there is no single solution due to the heterogeneous nature of the attack vector. Financial institutions should embrace a strong awareness culture, invest in cybersecurity technologies, train security specialists, and employ CISOs and executives knowledgeable in cybersecurity.\n\nThe study established technical factors such as physical security, application security, data security, network security, and internet security. Network security and data security were the highly ranked cybersecurity constructs, while physical security was the least ranked. There are several barriers that financial institutions face in managing cybercrime. The top three barriers are increasing sophistication of threats, limited skills and emerging technologies. The top frameworks used by financial institutions are the ITIL and COBIT, while about a fifth are yet to adopt cybercrime frameworks. The study’s small sample may affect the generalisability of the results. The study focused on technical aspects of cybersecurity, and future studies could focus on social engineering aspects that compromise the security of systems. This study raises awareness of the ever-present cybersecurity threat in the financial services sector. The study provides a baseline on the state of cybercrime in developing countries. More research will be required to validate these findings by developing models and using advanced statistical analysis on independent and dependent variables to test for causality and correlation.\n\nThe Government should proactively provide an environment that supports cybersecurity research and reporting of cases so that institutions can learn from others and continuously improve their detection and protection systems. The study recommends developing a national cybersecurity framework for an improved cybersecurity strategy for protecting Zimbabwean financial institutions. This framework must include establishing a cybersecurity culture, addressing cybersecurity barriers and following best practices such as adopting frameworks and establishing the office of the CISO. This will improve the protection of critical assets, minimise service disruption and loss of resources and strengthen financial institutions’ public confidence and reputation. The practical implication of this study is improving cybersecurity risks, given the rising adoption of emerging technologies and frameworks that support participation in the global economy.\n\nFuture studies could investigate the effects of social media-based cybercrimes as emerging threats are predicted to increase significantly over the following years. The government should also implement and strengthen policies, laws and legislations that curb cybercrime to mitigate economic losses. Financial institutions must create strategies to raise awareness of cybercrime and collaborate with higher education institutions to introduce programmes addressing cybersecurity challenges to close the skills gap. Financial institutions can use social media platforms for cybersecurity literacy and awareness.",
"appendix": "Data availability\n\nZenondo: Cybersecurity. https://doi.org/10.5281/zenodo.7824605. (Maphosa, 2023a).\n\nThe project contains the following underlying data:\n\n• Cyber security survey.xlsx. (Anonymised responses from IT experts on cybersecurity in the financial services sector).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenondo: An Overview of Cybersecurity in Zimbabwe's Financial Services Sector. https://doi.org/10.5281/zenodo.7824658. (Maphosa, 2023b).\n\nThis project contains the following extended data:\n\n• Cybersecurity questionnaire.pdf. (Final version of the cybersecurity survey questionnaire in the financial services sector).\n\nZenondo: An Overview of Cybersecurity in Zimbabwe's Financial Services Sector. https://doi.org/10.5281/zenodo.7825562. (Maphosa, 2023c).\n\n• Questionnaire pilot.pdf (Pilot version of the Cybersecurity survey questionnaire in the financial services sector).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAcharya S, Joshi S: Impact of cyber-attacks on banking institutions in India: A study of safety mechanisms and preventive measures. PalArch's J. Archaeol. Egypt/ Egyptol. 2020; 17(6): 4656–4670.\n\nAhluwalia R: Banking’s biometric future. Biometric Technology Today. 2016; 2016(10): 7–9. Publisher Full Text\n\nAirehrour D, Vasudevan Nair N, Madanian S: Social engineering attacks and countermeasures in the New Zealand banking system: Advancing a user-reflective mitigation model. Information. 2018; 9(5): 1–18. Publisher Full Text\n\nAlkhalil Z, Hewage C, Nawaf L, et al.: Phishing Attacks: A Recent Comprehensive Study and a New Anatomy. Front. Comp. Sci. 2021; 3(563060): 1–23. Publisher Full Text\n\nArachchilage NAG, Love S: Security awareness of computer users: a phishing threat avoidance perspective. Comput. Hum. Behav. 2014; 38: 304–312. Publisher Full Text\n\nAUC: Cyber Security and Cybercrime Policies for African Diplomats. 2018. Reference Source\n\nBendovschi A: Cyber-Attacks – Trends, Patterns, and Security Countermeasures. Procedia Economics and Finance. 2015; 28: 24–31. Publisher Full Text\n\nBissell K, Fox J, LaSalle RM, et al.: How aligning security and the business creates cyber resilience. Accenture. 2021. Reference Source\n\nBulawayo24: Italy offers cyber security training in Zimbabwe. 2021, April 18. Reference Source\n\nCaulkins B, Marlowe T, Reardon A: Cybersecurity skills to address Today’s Threats.Ahram T, Nicholson D, editors. Advances in Human factors in Cybersecurity, AHFE 2018. Advances in Intelligent Systems and Computing. Springer; 2018; pp. 782–788. 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Publisher Full Text\n\nElnaim BME: The Impact Of Information Security Management For E- Banks Performance In Kingdom Of Sudi Arabia. Int. J. Eng. Res. Technol. 2016; 5(11): 266–271. Publisher Full Text\n\nEuropean Network and Information Security Agency (ENISA): NCSS Good Practice Guide Designing and Implementing National Cyber Security Strategies.2016. accessed on: 29 May 2019. Reference Source\n\nGeorgiadou A, Mouzakitis S, Askounis D: Detecting Insider Threat via a Cyber-Security Culture Framework. J. Comput. Inf. Syst. 2021; 62(4): 706–716. Publisher Full Text\n\nGoldstein P: Why Physical Security Should Be as Important as Cybersecurity. 2016. accessed 21 March 2021. Reference Source\n\nGyabi MO, Shrivas MK: Data Security in Rural Banking Sector: A Case Study in Ashanti Region. Internation Journal of Advanced Research in Computer Science and ETechnology. 2016; 4(2): 99–106. Reference Source\n\nGupta P, Srinivasan B, Balasubramaniyan V, et al.: Phoneypot: data-driven understanding of telephony threats. Proceedings 2015 network and distributed system security symposium. Reston, VA: Internet Society; 2015; 8–11. Publisher Full Text\n\nHejase H, Fayyad-Kazan H, Hejase A, et al.: Cyber Security amid COVID-19. Computer and Information Science. 2021; 14(2): 10–25. Publisher Full Text\n\nHossain MA, Al-Amin M, Hossain N, et al.: User Location Time and Entropy (ULTE) based Salt generation for Password Based Key Derivation Function (PBKDF) in Cloud Computing. Int. J. Sci. Eng. Res. 2017; 8(2): 1399–1408. Publisher Full Text\n\nInternational Organization for Standardization (ISO)/International Electrotechnical Commission (IEC): 2012 Information—Security Techniques—Guidelines for Cybersecurity, ISO/IEC 27032. 2012. Retrieved January 2023. Reference Source\n\nJang-Jaccard J, Nepal S: A survey of emerging threats in cybersecurity. J. Comput. Syst. Sci. 2014; 80(5): 973–993. Publisher Full Text\n\nJakobsson M, Myers S (editors): Phishing and countermeasures: understanding the increasing problem of electronic identity theft. John Wiley & Sons; 2006.\n\nKahn CM, Roberds W: Credit and identity theft. J. Monet. Econ. 2008; 55(2): 251–264. Publisher Full Text\n\nKaiwartya O, Prasad M, Prakash S, et al.: An Investigation on Biometric Internet Security. Int. J. Netw. Secur. 2017; 19(2): 167–176. Publisher Full Text\n\nKatz R: Economic impact of COVID-19 on digital infrastructure. Geneva: International Telecommunications Union; 2020. Reference Source\n\nKatz R, Jung J: The Economic impact of broadband and digitalization through the COVID-19 pandemic. International Telecommunication Union. 2021. Reference Source\n\nKazemi U: A Survey: Information Security Management System. Journal of Analog and Digital Devices. 2018; 2(3): 1–6. Reference Source\n\nKharb L: Cyber Crimes Becoming Threat to Cyber Security. International Journal of Engineering and Management Research. 2017; 7(2): 48–51. Reference Source\n\nKnake RK: A cyberattack on the US power grid. Council on Foreign Relations; 2017.\n\nKPMG: Africa Cyber Security Outlook. 2022, September. Reference Source\n\nKranenbarg MW, Holt TJ, Gleder J-L: Offending and Victimization in the Digital Age: Comparing Correlates of Cybercrime and Traditional Offending-Only, Victimization-Only and the Victimization-Offending Overlap. Deviant Behav. 2017; 40(1): 40–55. Publisher Full Text\n\nKshetri N: Cybercrime and Cybersecurity in Africa. J. Glob. Inf. Technol. Manag. 2019; 22(2): 77–81. Publisher Full Text\n\nMaphosa V: COVID-19 and the Digital Ecosystem: Using a Mobile App to Connect a Rural Community. Aqua. 2021; 5(1): ep21002. Publisher Full Text\n\nMaphosa V: Rethinking Sustainability: A Bibliometric and Visualisation of E-Waste Management in Africa. Journal of Higher Education Theory and Practice. 2022; 22(1): 123–135. 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Publisher Full Text\n\nNorris DF, Mateczun L, Joshi A, et al.: Cyberattacks at the grass roots: American local governments and the need for high levels of cybersecurity. Public Adm. Rev. 2019; 79(6): 895–904. Publisher Full Text\n\nOdunze D: Cyber Victimization by Hackers: A Criminological Analysis. Public Policy and Administration Research. 2018; 8(1): 8–15. Reference Source\n\nPraveena A, Smys S: Prevention of inference attacks for private information on social networking sites. 2017 International Conference on Inventive Systems and Control (ICISC). Coimbatore, India: IEEE; 2017; (pp. 1–7).\n\nRadzikowski S: Cybersecurity: Origins of the advanced persistent threat (APT). 2015. accessed on: 10 January 2020. Reference Source\n\nRBZ: Cybercrime in Zimbabwe and Globally. 2015. Reference Source\n\nReaves B, Scaife N, Bates A, et al.: Analysis of Branchless Banking Applications in the Developing World. 24th USENIX Security Symposium. 2015. Reference Source\n\nReddy GN, Reddy GJ: A study of cyber security challenges and its emerging trends on the latest technologies. arXiv preprint arXiv:1402.1842.2014; 1–5. Publisher Full Text\n\nRichards K: Has the CISO role changed under the spotlight? Inf. Secur. Mag. 2014; 2014: 56. accessed 21 March 2021. Reference Source\n\nSkopak A, Sakanovic S: Adoption of standards for information security ISO/IEC 27001 in Bosnia and Herzegovina. ICESoS. 2016; 2016. Reference Source\n\nSubramanian K, John FL: Enhanced Security for Data Sharing in Multi Cloud Storage (SDSMC). Int. J. Adv. Comput. Sci. Appl. 2017; 8(3). Reference Source\n\nSviatun O, Goncharuk O, Chernysh R, et al.: Combating cybercrime: economic and legal aspects. WSEAS Trans. Bus. Econ. 2021; 18: 751–762. Publisher Full Text\n\nTabassum L: State of Cyber Crime Safety and Security in Banking. Int. J. Sci. Res. Engineering Dev. 2020; 3(4): 72–76.\n\nTseng S-S, Yang T-Y, Weg J-F, et al.: Building a Game-Based Internet Security Learning System by Ontology Crystallization Approach. Int’l Conf. e-Learning, e-Bus., EIS and e-Gov. 2015. Reference Source\n\nVerizon: Data breach investigations report (DBIR) 2020. Verizon. 2020. Publisher Full Text\n\nWeforum: Global Cybersecurity Outlook 2022.2022. Reference Source\n\nZhang L, Wang Q: A Network Security Evaluation Method Based on Fuzzy and RST. 2nd International Conference on Education Technology and Computer (ICETC). Shanghai, China: 2010."
}
|
[
{
"id": "211331",
"date": "09 Oct 2023",
"name": "William Vambe",
"expertise": [
"Reviewer Expertise IoT",
"Fog Computing",
"Cloud Computing",
"ICT4D"
],
"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 present a very important aspect especially with the incoming of 4IR, internet and where everyone now use mobile, online and internet banking daily. I have few issues that I think might improve the paper.\nIntroduction\nIn the context of Zim, is this statement true, \"Decreasing data costs... \". Since the paper is about Zimbabwe, I think we need to contextualize why there is a rise in using online, mobile, internet banking.\n\nIn your write up, I propose you present state of cyber security in the context of Europe, Africa, Sadc countries, then Zimbabwe in particular since it is the study area. This gives us a clear view. Then you conclude this section by giving us the aim./ objective of this paper. Last paragraph should be a signpost to inform the reader what to expect in the whole paper.\nLiterature\nIn the literature/related work, I was expecting more focus and discussion to be on Zim not the world in general. Is there government policy, or financial organization policies pertaining to cybersecurity? What are the challenges and implications of implementing them? What does the current/literature say about cybersecurity in Zimbabwe? What are open gaps?\n\nThese discussions will help us to see why there was a need to do this research and will also helps us to link with the results section.\nResults\nI propose using graphs rather than tables as graphs show the comparison better.\n**Since you are an expert, based on your results, I propose you put a section Possible Solutions/ Significant Recommendations, where you articulate what as a researcher think can be done to address the challenges you got from literature and your results. This can be backed by literature on solutions that have been implemented in other countries almost similar to Zim.\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": "11042",
"date": "22 Feb 2024",
"name": "Vusumuzi Maphosa",
"role": "Author Response",
"response": "Developed countries have developed effective cybersecurity frameworks and policies to strengthen operations, raise awareness and support training programmes (Russell et al., 2017). Countries such as the United States of America, Australia, Canada and South Africa use cybersecurity to secure and fortify critical infrastructure which drives socioeconomic development (Catota et al., 2019). Developing countries lag in the adoption of cybersecurity despite the unprecedented adoption of ICTs over the last two decades. Only 11 African countries have cybersecurity policies (Kshetri, 2019). Kabanda (2019) noted that cybersecurity systems in Africa are underdeveloped due to limited infrastructure, lack of funding, inadequate policies and legislation, lack of education and awareness, and limited reporting and data-sharing platforms. In Zimbabwe, not much has been done in terms of cultivating a culture of cyber security and combating cybercrimes. Zimbabwe has a massive shortage of cybersecurity specialists and this is compounded by the lack of frameworks and policies to drive national implementation programmes. Kabanda (2019) notes in Zimbabwe, cybersecurity is regarded as an afterthought and is not part of the core business strategies and this is worsened by the unprecedented brain drain of skilled cybersecurity personnel. Zimbabwe faces challenges such as a lack of programmes and opportunities to equip the general public with skills, knowledge and awareness to fight cybercrime (Mutunhu et al., 2022). The Cyber Security and Data Protection Bill promulgation is a critical step in fighting cybercrime, but it has been widely criticised and viewed as a tool for the State to obstruct civil society, and the media in the fight against corruption (Transparency International, 2020). There is a need to include non-state actors in the development of the Bill. Zimbabwe mobile data prices have been decreasing over the past two decades from USD180.00 per giga byte in 2010 to USD15.50 in 2020 (POTRAZ, 2021). Recommendations More awareness and education are required for cyberspace users. A cybersecurity culture should be developed in the early stages of schooling such as at the primary school level. There should be a deliberate effort to grow cybersecurity skills which are extremely important to the financial services sector and are in short supply due to brain drain. The government and the private sector should partner to set up Computer Emergency Response Teams for the financial services sector and other sectors. The cybersecurity bill should be flexible to allow for continuous review by state and non-state actors and align with the dynamic threat levels. Tax rebates on cybersecurity equipment are required to ensure that organisations can afford basic cybersecurity equipment. Works Cited Catota, F.E; Morgan, M.G; Sicker, D.C. (2019). Cybersecurity education in a developing nation: the Ecuadorian environment. 1–19. DOI:10.1093/cybsec/tyz001 Kabanda, G. (2019). A Bayesian Network Model for a Zimbabwean Cybersecurity System. Orient. J. Comp. Sci. & Technol., 12(4), 147-167. Mutunhu, B; Dube, S; Ncube, N; Sibanda, S. (2022). Cyber Security Awareness and Education Framework for Zimbabwe Universities. A Case of National University of Science and Technology Proceedings of the International Conference on Industrial Engineering and Operations Management, Nsukka, Nigeria Russell, J.D; Weems, C.F; Ahmed, I; Richard III, G. (2017). Self-reported secure and insecure cyber behaviour: factor structure and associations with personality factors. J Cyber Secur Technol. 1 (3-4), 163-174. POTRAZ. (2021). Mobile data prices in Zimbabwe. cyber behaviour: https://t3n9sm.c2.acecdn.net/wp-content/uploads/2021/02/POTRAZ-Press-Statement-Mobile-Data-Prices-in-Zim-Final.pdf, Harare, Zimbabwe. Transparency International. (2020). Zimbabwe: Cyber Security and Data Protection Bill would restrict anti-corruption watchdogs. https://www.transparency.org/en/press/zimbabwe-cyber-security-and-data-protection-bill-would-restrict-anti-corruption-watchdogs-1"
}
]
},
{
"id": "211333",
"date": "20 Oct 2023",
"name": "Nomusa Dlodlo",
"expertise": [
"Reviewer Expertise IoT",
"Blockchain",
"ICT4D",
"ICT in Education",
"ICT in 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\nPlease refer to the attached file.\nWhat is the total population of the people who you could pull the participants from and how large is the sample you interviewed. ow did you identify the sample- is it purposive sampling / targetted sampling?\n\nWhat frameworks led to the questionnaire?\n\nBe specific on the numbers. How many questionnaires were distributed. ? How many responses did you get back? Are the responses an adequate representative sample of the total population of potential interviewees. How did you choose who to distribute the questionnaire to? Was it intentional or random?\n\nThe discussion can be approached in sub-sections where you explain the results under each subsection and then give a comparison of the results with other similar researches, e.g., Adoption of cybercrime frameworks, sophistication of threats, technical skills, etc. You already have that. You just need to add the subtopics.\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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "11041",
"date": "22 Feb 2024",
"name": "Vusumuzi Maphosa",
"role": "Author Response",
"response": "Population: The study targeted IT experts from the country’s financial institutions comprising commercial banks, merchant banks, discount houses, building societies, and finance houses. Sampling: Convenience sampling was used to recruit participants. Framework: The top frameworks used are the Information Technology Infrastructure Library (ITIL) and Control Objectives for Information and Related Technologies (COBIT), while a fifth is yet to adopt cybercrime frameworks. Questionnaire: The study’s questionnaire was adapted from the International Organization for Standardization (ISO)/International Electrotechnical Commission (ISOC/IEC) (ISOC/IEC, 2012). ISOC/IEC is a task force responsible for crafting and reviewing industry-wide cybersecurity standards every five years. Questionnaire: An online questionnaire was used and 76 responses were received. The data set is available to the public. The distribution was random. Discussion: The discussion is categorised into cybersecurity, security of data, security issues in developing countries, and emerging threats. A paragraph on frameworks has been added to the discussion section. Developing countries have rapidly increased access to cyberspace, without corresponding effort to fortify cyberspace and improve security measures. Developing countries face challenges in adopting cybersecurity frameworks and struggle to deter cybercrime (Muller, 2015). The most common cybersecurity frameworks in Zimbabwe are the ITIL and COBIT, while other frameworks like the NIST and ISO 27002 are quickly gaining recognition. Muller, L. P. (2015). Cyber security capacity building in developing countries: challenges and opportunities Norwegian Institute of International Affairs, Norway."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1251
|
https://f1000research.com/articles/13-190/v1
|
14 Mar 24
|
{
"type": "Study Protocol",
"title": "A study of behavioural problems in school going children in Wardha",
"authors": [
"Khushbu Chelak",
"Dr. Swarupa Chakole",
"Dr. Swarupa Chakole"
],
"abstract": "Introduction Behaviour problems like hyperactivity, lack of focus, temper tantrums, aggression, disobedience, conflicts with peers, nail-biting, thumb-sucking, and insomnia can happen during childhood or during the formative years of human development. The behavioural problem might not yet be categorised as a mental disorder, but it could develop into one. Although it could be challenging to spot these problems in young children. Schools are places where kids spend a lot of time and are active. Therefore, schools are the finest setting for young children’s mental and physical growth.\n\nObjective The study objective is to assess the prevalence of the behavioural problems among school-going children.\n\nMethods This cross-sectional observational study will be conducted on school going children in government school using a questionnaire, (which include questions based on socio-demographic and child behaviour characteristics). Sample population involved 172 school-going children aged 15-18 years old. Data will be collected by Google Form (using as a data collection tool) and Microsoft Excel (MS Excel 2010) will be used for the analysis.\n\nStudy implication Study interest will be identifying the factors influencing behavioural change in school-going children and to develop an intervention program to address these issues and development of effective interventions targeting behaviour-related problems in school-going children.",
"keywords": [
"Behavioural problems",
"prevalence",
"incidence",
"school",
"children",
"school going children",
"socio-demography",
"social media",
"mental health"
],
"content": "Introduction\n\nChildren between the ages of 5 and 16 who are enrolled in school make approximately 30% of India’s total population. This is a time of tremendous physical development and growth, as well as rapid mental, emotional, and social transformation for them.1 They could have mental diseases, particularly behavioural issues. Parents and educators are very concerned about behaviour issues in school-aged children because it is well established that these issues will have negative effects both now and in the future.2 The children behaviour problems may engage in violent or inappropriate behaviour. Such behavioural problems frequently result in criminal activity or drug dependence, which brings great financial stress and suffering in the community.3,4 These behavioural problems are thought to be influenced by a variety of factors, including family conflict, poverty, low academic achievement, and parental unemployment, rather than psychological and physiological health issues.3,5 Being a location where people are engaged, schools cannot be organised without taking the communities’ and parents’ active engagement into consideration. Parental involvement is crucial in the academic world since children with involved parents appear to have less behavioural issues and do academically considerably better than children with disinterested parents.6\n\nThere are many types of behavioural problems seen in the school going children. Firstly, Oppositional Defiant Disorder (ODD) – Oppositional defiant disorder causes children to create trouble repeatedly at the house, in the classroom, or among other siblings. Before the age of eight, the majority of children with ODD begin developing behavioural disorder signs. ODD typically signs as loose temper, arguing frequently with the elderly, denying complying with instructions, accusing others of their fault, feel offended. Secondly, Conduct Disorder (CD)- The term “conduct disorder” refers to a range of emotional and persistent actions that children and teenagers display. The rights of others, empathy, and adherence to social norms are often difficult for young people with CD. Kids with CDs could be categorised as “bad” or delinquent. They might also behave aggressively toward people or animals in the ways listed below: Fighting physically, abusing others, robbing them, intentionally injuring others, using weapons like sticks or bats against them, displaying no regret for their crimes, and damaging property be.7 Thirdly, Attention-Deficit/Hyperactivity Disorder (ADHD) – The children with attention-deficit/hyperactivity disorder acts impulsively or is more energetic than normal. Children with ADHD frequently experience difficulties focusing, which can cause problems in the classroom. When they are adults, many young persons with ADHD exhibit the same symptoms. The children with symptoms like, constantly daydreaming, talking constantly, struggling to get along with people, squirming when seated, displaying signs of forgetfulness or frequently losing things, taking unnecessary risks, frequently making mistakes due to forgetfulness, struggling to delay gratification may have ADHD.8\n\nAround twenty percent of children and adolescent experience difficulties because of different psychological diseases around the world.2 It is challenging to obtain exact number of child Psychological illnesses, but epidemiological data that are available shows that twelve to fifty one percent with approximately twenty-nine percent, of children around the world experience emotional and other psychological illnesses that require psychological health counselling.9,10 Children all together in this category that is around six to nine percent are required intensive psychological care because of severe emotional disturbances.9,11 Academic parental participation, which is defined as any parent-led action that might reasonably be anticipated to enhance a child’s performance or behaviour, is widely acknowledged.12 Parent participation includes interactions between parents and children, parents and teachers, and to some extent, parents and other parents.13 It describes actions that help children fulfil or exceed the expectations or standards of their role as a student.6\n\nSchool-going children are vulnerable to several health problems due to their active lifestyle and exposure to various environmental factors. One of the most common problems faced by school-going children is behaviour-related issues. The behaviour-related problems can affect a child’s academic performance, social interaction, and emotional well-being.\n\nThe aim of the study is to assess the prevalence of behavioural problems in school going children in the age of 15-18 years at Wardha.\n\n\nMethods\n\nThe study will be a community based cross sectional study among the school-going children in Wardha districts of Maharashtra.\n\nA study will be conducted to assess the prevalence of the behavioural problem in school going children of a government school in Wardha district, which is a part of Central India. District Wardha is located in Maharashtra’s vidarbha area. The districts of Amravati, Yavatmal, Chandrapur, and Nagpur are located on the west, north, south, and east, respectively, of the district. There are 6,310 sqkm in the district. 1,391,890 residents live in this area.\n\nThe school going children aged 15-18 years (both boys and girls) will be taken into consideration as mostly the youngsters have a behavioural problem.\n\nInclusion\n\nAll children who are 15-18 years of age are eligible to participate in the study. Those students who will be present on the data collection day will be included.\n\nExclusion\n\nThose participants who will show non-willingness to participate in the study and absent on the data collection day will be excluded.\n\nVariables:\n\nThe study tool will consist of a pre-designed, self-made questionnaire with a quantitative component for the data collection on socio-demographic variables and on the child behaviour of school going children. It will be divided into two sections (Table 1 shows data sources).\n\n\n\n1. Age\n\n2. Gender\n\n3. Medium of school\n\n4. Class\n\n5. Type of family\n\n\n\n1. Acts too young for their age\n\n2. Argues a lot\n\n3. Cries a lot\n\n4. Cruel to animals\n\nSection A: Self-made questionnaire related to socio-demographic details of the children such as name, age, gender, medium of school, standards, type of family.\n\nSection B: Self-made child behaviour checklist.\n\nMeasurement\n\nPrimary outcome measured will be prevalence of behavioural problem of the children and the secondary outcome will be common behavioural problem in children and factors influencing behavioural change in school-going children.\n\nThe data will be entered in Microsoft Excel (MS Excel 2010) and analysed by SPSS Version 22 (RRID:SCR_002865) (Statistical Product and Service Solutions). Frequencies and percentages will be presented in the form of tables, graphs.\n\nSome of the biases that may affect the study include:\n\nResponse bias: The children who participate in the study may be more motivated to report or exaggerate certain behaviours than others, leading to inaccurate data.\n\nRecall bias: Participants may not recall previous events or experiences correctly.\n\nSample size is calculated using the following formula:\n\nAlpha (α) = 0.05\n\nEstimated proportion of school going children (p) = 0.872\n\nEstimation error (d) = 0.05\n\nSample size = 172\n\nSample size calculated by using above formula with estimated proportion 0.872 with alpha error 0.05 and estimated error 0.05. Thus a sample size of 172 school going children will be used to collect data regarding the behavioural problems in school going children.\n\nThe study will be conducted using simple random sampling method, and two government schools in rural Wardha will be picked randomly. Random selection will be used to choose the first school for data collection. Another school will also employ this method of selecting. The study is open to students between the ages of 15 to 18 who are enrolled in school. The data will be gathered in the form of a Google form, information will be coded into a Microsoft Excel 2010 spread sheet. Statistical analysis will be done by using SPSS version 17 software. Descriptive statistics for Socio-demographic factors will be done using Microsoft office 2021 and data will be calculated in the form of percentages and frequencies. The data will be presented in the form of tables and graphs.\n\nEthical consideration\n\nEthical approval for this study (DMIHER (DU)/IEC/2023/640) was provided by the ethical committee of Datta Meghe Institute of Higher Education and Research (DMIHER) Sawangi (deemed to be University) on 11th February 2023.\n\nInformed written consent will be obtained from all study participants and data will be collected using a questionnaire.\n\nExpected outcomes and results\n\nThe key result will be finding the prevalence and factors influencing of the behavioural problems in school going children in the Wardha.\n\nStudy status\n\nThe data collection process has been completed, now the analysis will be started.\n\n\nDiscussion\n\nA 2017 study by Masare et al., on 304 secondary school students in the eighth and ninth grades, of both sexes, in municipal schools of a major city concluded that socio-demographic factors, the fathers’ occupation, and alcohol consumption were significantly associated with the study subjects’ behavioural issues.1 On the other hand, author Murata’s 2020 study found that children from households with lower socioeconomic status were more likely to exhibit behavioural problems, including violence, However, the study also suggests that supportive families and effective educational interventions can help to decrease these problems.3\n\nGupta et al. made two recommendations in their 2017 study report, highlighting the importance of routine school screenings to spot problems early and take preventative and corrective action on behavioural problems among school-going children, with an emphasis on anxiousness, hyperactivity, argumentativeness, and perfectionist beliefs.2 While authors Gedifew Sewenet and Yigzaw endorsed the idea that parents and school staff should work together to reduce disciplinary issues and encourage parental involvement in their children’s education, they also supported the idea that these two groups should work to improve school-family relations.6 Verma et al.’s concluding remarks in their study on 2001 stated that inadequate recognition of children’s mental health in some countries can cause serious harm to both the country’s economy and the health of the children; as a result, increasing awareness about the prevalence of behavioural problems in children should be strongly promoted.9\n\nStudy finding will give common behavioural problems with selected child behaviour and association of behavioural problems with selected demographic variables.\n\nThe study will be limited to children between the age group of 15-18 years. And sample size will be limited to 172.",
"appendix": "Data availability\n\nNo underlying data are associated with this article.\n\nZenodo: A study of behavioural problems in school going children in Wardha, https://doi.org/10.5281/zenodo.7994016. 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\nI would like to thanks Mr. Laxmikant Umate, statistician and member of research Guidance Unit, Research & Development Cell, DMIHER, for their contribution to the calculating sample size and statistical work in the research manuscript.\n\n\nReferences\n\nMasare MS, Bansode-Gokhe SS, Bansode-Gokhe SS, et al.: Shinde RR: A cross sectional study of behavioral problems of secondary school children and related socio-demographic factors. International. J. Res. Med. Sci. 2017; 5: 2760–2766. Publisher Full Text\n\nGupta AK, Mongia M, Garg AK: A descriptive study of behavioral problems in schoolgoing children. Ind. Psychiatry J. 2017; 26: 91–94. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMurata C: Behavioral Problems in Children.2020; 11–19. Publisher Full Text\n\nNair: Gadgets it’s use and stress on lifestyle. Accessed: May 12, 2023. Reference Source\n\nBlair RJR, Leibenluft E, Pine DS: Conduct Disorder and Callous-Unemotional Traits in Youth. N. Engl. J. Med. 2014; 371: 2207–2216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYigzaw GS: The Role of Parents in Improving the Behavior of School’s Students in Azena Primary School, Ethiopia. Int. J. Educ. Res. Rev. 2019; 4: 334–349. Publisher Full Text\n\nBabar V, Gedam SR, Manore S, et al.: Study of stress, anxiety, depression, coping, and associated factors among medical students from central India. J. Datta Meghe Inst. Med. Sci. Univ. Accessed: May 12, 2023. Reference Source\n\nAryal N, Regmi PR, van Teijlingen E , et al.: The Impact of Spousal Migration on the Mental Health of Nepali Women: A Cross-Sectional Study. Int. J. Environ. Res. Public Health. 2020; 17: 1292. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGupta I, Verma M, Singh T, et al.: Prevalence of behavioral problems In school going children. Indian J. Pediatr. 2001; 68: 323–326. Publisher Full Text\n\nSrinath S, Girimaji SC, Gururaj G, et al.: Epidemiological study of child & adolescent psychiatric disorders in urban & rural areas of Bangalore, India. Indian J. Med. Res. 2005; 14.\n\nMalhotra S, Kohli A, Arun P: Prevalence of psychiatric disorders in school children in Chandigarh, India. Indian J. Med. Res. 2002; 116: 21–28. PubMed Abstract\n\nIngole: Treatment-seeking behaviors of families for under five children in field practice area of jawaharlal nehru medical college. Wardha: Accessed: May 12, 2023. Reference Source\n\nThosar: Parental responses about sleep-disordered breathing and its association with mouth breathing in their children: A questionnaire-based study. Accessed: May 15, 2023. Reference Source\n\nChelak K: A study of behavioural problems in school going children in Wardha. Zenodo. 2023. Publisher Full Text"
}
|
[
{
"id": "321593",
"date": "17 Sep 2024",
"name": "Partha malakar",
"expertise": [
"Reviewer Expertise Child and Adolescent Psychology",
"Health Psychology",
"Indian Psychology."
],
"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\nReport are as follows- 1) Needed to mention in the objective which stage of development is being considered for the study. 2) In objective section authors should mention about the prevalence of the behavioral problems and how do these impact school going children. 3) Needed to write the criteria used for inclusion and exclusion. 4) Hypotheses of the study may be included for better understanding as this is a quantitative study. 5) More details regarding the study participants needed to include. 6) No information is provided regarding the standardization of the self made questionnaire. Self made questionnaire can never be used without standardization. 7) No discussion and implication is valid in quantitative study without without proper results or study findings. 8) Without demographic data, no quantitative data is available to check. Based on the above report I suggest that this article needs major revisions and authors must ensure that standardized tools are used for data collection.\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? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/13-190
|
https://f1000research.com/articles/12-1491/v1
|
21 Nov 23
|
{
"type": "Research Article",
"title": "A proposed equation for calculating the total horizontal distance in projectiles of varying launch and landing levels",
"authors": [
"hussein omer"
],
"abstract": "Background The projectile draws a path for the flight of the tool, a horizontal distance can be calculated according to the Galileo Galilei Law of Projectiles (GGLP), but only if the two points of the launch and fall of the tool are equal, otherwise we need an equation to be added to the (GGLP) to calculate the real distance that was generated due to the difference between the launch and fall points. There are several equations to calculate this, but they are complex and can be simplified.\n\nMethods The proposed equation was tested by exporting samples from three different throwing events (javelin, shotput, disc) data in track and field games, to calculate the horizontal throwing distance. The proposed equation was based on the basics of mathematics and geometry. The equation was tested in terms if the height is zero, the proposed equation is suitable even for projectiles with equal levels, and the credibility of the proposed equation with the previous equation was tested statistically.\n\nResults It was found that there were no differences between the two equations (p>0.05). and due to the relative ease of access of the proposed equation to very similar results, researcher suggests applying the proposed equation.\n\nConclusions The proposed equation contained the height factor in the previous equation, and when tested by several criteria, the proposed equation has proven its credibility, statistically and graphically. The ranges of theoretical achievement calculated by the proposed equation are often closer to the real achievements.",
"keywords": [
"track and field",
"different levels",
"biomechanics",
"launch angle"
],
"content": "Introduction\n\nThrowing activities are a part of track and field games activities, in which the achievement depends on the horizontal distance covered. It is cut off by the tool thrown from the shooter’s hand, and because the device is thrown, it is subject to the Galileo Galilei Law of Projectiles (GGLP). From a practical point of view, the shell draws a path for the flight of the projectile. Theoretically, it is possible to calculate the horizontal distance it will cover through three essential factors (height, angle and velocity of the projectiles). In GGLP there are only two factors that we can observe, namely the angle and velocity of throwing tools (Hall, 1995).\n\nWhere (v) velocity of release, (θ) angle of release, (g) acceleration due to gravity.\n\nGGLP measures the best angle to achieve the best horizontal distance (45 degrees) when the launch and landing levels are equal. However, in throwing events in track and field games, the initial starting height is always greater than the final height. Here the launch angle will vary, and the role of the third factor appears, which is the height difference between the throwing tool when launched, which requires that some adjustments be made to GGLP to calculate the horizontal distance to be accomplished theoretically. The resulting value is close to the measurement on the ground. The basis of the adjustments depends on adding a difference in the height of the launch from the landing to GGLP, to calculate the remainder of the distance. The case was treated according to the rule above (Hall, 1995).\n\nWhere (v) velocity of release, (θ) angle of release, (g) acceleration due to gravity, (h) height of release\n\nWe also see another formula for the additive equation, which is (Kinomura et al., 2013). The law has been written in several forms, including:\n\nWhere (x) initial horizontal, (v) velocity of release, (θ) angle of release, acceleration due to gravity, (y) height of release\n\nAmong the studies that dealt with analyzing the content of tournaments are Ariel et al. (1997); BADURA (15–23 August 2009); Abdel-Monsef Aly et al. (2012), and Mercadante et al. (2007).\n\nThe disc release angle varies in the effectiveness of the disc in normal conditions (36-38 degrees), meaning it is less than the best angle (45 degrees) due to the height of the shooting point. The best angle for the javelin (37-38 degrees) and the ideal angle (score 41-38) (Omer, 2018).\n\nThe aim of this study is to propose an equation to simplify the previous equation and reduce the steps required to reach the result.\n\nThe hypothesis of this research proves that the proposed equations have similar results compared with the previous equations.\n\n\nMethods\n\nSixteen Players from the Jung et al. (2012) and Woen-Sik Chae (2011) championships of javelin throwing events have been tested, males and females. Twenty eight players of the discus throw event (Panoutsakopoulos, 2008; Finals, 2011), males and females and thirty two players of the shotput throw event (Jung et al., 2012) males and females. These sources relied on video recordings and movement analysis using special software to extract velocity, angle, and height of projectile.\n\nThe studies from which the data were taken were used high-speed digital video camera and programs were used to analysis motions. The three variables to the projectile’s velocity, angle, and height were substituted into the proposed equation. Then the horizontal distance resulting from the two equations was compared statistically, as well as to the actual results that were measured on the, ground in those championships.\n\nThe height difference (h) between the launch of the projectile and its fall is the third factor of importance after the velocity and angle of release. The above equations are complicated (used velocity and gravity twice, sine and cosine also) and can be simplified while reaching the same results with high credibility; the simplification method depends on calculating the distance beyond the parabola and assuming that the launch angles are equal to the parabola angle of incidence.\n\nFigure 1 shows the hypothesis to simplify the equation added to the GGLP to calculate the remaining distance because the throwing tool (release) is higher than the level of its fall.\n\nThe proposed simplification method for calculating the remaining distance is based on a simple equation that we add to GGLP according to the following:\n\nWe need an angle to calculate the added horizontal distance because the vertical space is known from the launch height according to the law of triangles; given the opposite and adjacent, the other side’s value can be found using the tangent of the pitch. The contrast here is the height of the launch from the ground, and the adjacent is the added distance; the reason for our adoption of this angle is based upon; the falling angle at the moment of changing the path after the tool leaves the parabola path remains the same. Accordingly, the sequence of building the equation is as follows:\n\nThe proposed formula agrees with the following:\n\n1. The advantage of deleting the height. If the height is zero, the proposed procedure is valid even for equal projectiles that have the same shooting and falling heights without problems.\n\n2. To test the reliability of the proposed equation with the previous equation statistically, it has been applied to the data of activities throwing (disc, shotput, and Javelin), whose data has been approved by multiple championships. It is characterized by different heights, tool weights, velocities, and angles, and it was found that the differences were not significant.\n\n3. A virtual test of the graph of the differences between real achievement (measured on the ground) according to the common law and achievement that were also performed theoretically according to the proposed and previous equations. It turns out that the graphic curve of the two equations is harmonious and inverted.\n\n4. A comparison was made between the actual measurement recorded on the ground and the theoretical result from the common law of the proposed and previous equations.\n\n\nResults\n\nThe variables were compensated for GGLP and the proposed equation (Performance -Hussein), and the previous equation (Performance-Otto), and the graphs show the horizontal distance resulting from the GGLP and the two equations to observe the phenomenological differences through the raw data.\n\nTable 1 shows the differences in the actual achievement that was measured on the ground and the theoretical achievement that was produced using the general law and the proposed and previous equations in the release variables in the effectiveness of discus throw (n = 28).\n\nThere are some significant differences between the actual achievements and results from GGLP because the public law measures distance without calculating the difference between launch and fall position, and the two equations are designed to measure the horizontal lengths of projectiles by calculating the difference between launch and fall position. The difference between the two equations is less than (0.12 m.), and the difference between real achievement and Hussein equations is less than Otto equations.\n\nTable 2 shows the differences in the actual achievement that was measured on the ground and the theoretical achievement that was produced using the general law and the proposed and previous equations in the launch variables in the effectiveness of javelin throwing (n = 16)\n\nTable 3 shows the differences in the actual achievement that was measured on the ground and the theoretical achievement that was produced using the general law and the proposed and previous equations in the release variables in the effectiveness of shotput throwing (n = 32).\n\nTable 4 shows that the differences were not significant. Between the two activities, discus and javelin throwing, when conducting the theoretical calculation to measure the distance using GGLP and the two equations, the probability value was more significant than (p > 0.05), which means that the difference was random.\n\nAs for throwing the shotput, the differences were significant (p < 0.05) and the reason for that is the weight of the shotput, which causes a decrease in the velocity of its launch because the factor velocity, is squared in the equations.\n\nTable 5 shows least significant difference between the two equations were not significant. and that the distance measurement in the (GGLP) differs from what it is in the two equations.\n\nIt is noted from the Table 6 that the proposed equation has a probability value (p > 0.05) meaning that there are no significant differences between the two equations.\n\nIt is clear from Figures 2,3 and 4 that the results were very close between the previous equation and the proposed equation, which indicates that our use of the proposed equation is possible, and it is a less complicated equation than the previous equation. As for Figure 4 we notice a difference between the two curves, reviewing Table 3, we find that the differences with the measurements made on the ground and the equation used were in favor of our study. The reason is due to the importance of velocity in the law, it is square, and since the weight of shotput is greater than the other tools, their velocity is less.\n\nThe figure shows the difference between the actual achievement that was measured on the ground in the discus throws event (Atlanta, 2009 Berlin 2006 Athena, 1966 male, and female), according to common law without calculating the height factor and by calculating the height factor in the two equations (Otto and Hussein).\n\nThe figure shows the difference between the actual achievement that was measured on the ground in the javelin throw event (Diego 2011 males and females), according to common law without calculating the height factor and by calculating the height factor in the two equations (Otto and Hussein).\n\nFigure 7 shows the difference between the actual achievement that was measured on the ground in the Shotput throw event (2009 Berlin, 2011 Diego males and females), according to common law without calculating the height factor and by calculating the height factor in the two equations (Otto and Hussein).\n\nWe notice from Figures 5, 6 and 7 that when applying GGLP stripped of proposed equations, the samples will give us drawings that are inverted with the graphic curve for the same samples when we apply the two equations, which means that the proposed equation has the same components as the previous equation.\n\n\nDiscussion\n\nWhen analyzing the common law of projectiles, we see that the most critical factor on which the law depends is when the two launch points are equal. The launch (release) velocity, as it is squared, and although some tools are heavier than others, the law depends on the velocity, based on the power of the launch; the second factor is the angle of launch, and many experiments found that the release angle (45 degrees) is best when the launch and fall points are equal because this angle changes the magnitudes of the compounds the horizontal and vertical launch velocity is of secondary importance (Hamill et al., 2015), as the global rate may be vertical more than this process leads to the tool gaining a vertical distance more than the horizontal, as occurs in the effectiveness of high jump.\n\nTheoretically, achieving the best horizontal distance does not correspond to human bodies because they are designed for tools. Therefore, GGLP yields better results in throwing equipment compared to the long jump, or triple jump, and in all of these events, we notice that the center of gravity of the body emanates from a location different from the site of its descent, the shape or weight of the tool is not very large, and it also includes friction with the air or changing the direction of the wind. The law of events prevents recording some achievements due to the wind velocity that is expected to be the cause of the digital achievement. The critical factor is the height of the tool, and due to the lengths of the players being close, calculating the remaining distance is significant in this case, and as we observed in one of the figures, there must be an equation to calculate the remaining distance, because the common law will calculate the distance from the starting point to the point of fall parallel to the launch point.\n\nThe pervious equations put the same (v) velocity of release twice in the equation, it is incorrect to put the same value and perform other calculations on it once, we followed the same procedure for the same (θ) angle of release, we found that the sine and cosine is processed once mathematically.\n\nThe criticisms that can be directed at previous studies are that they considered the point at which the projectile reaches its initial level to be the end of the projectile, so they began with a new equation that was integrated with Galileo’s law. However, our study considered that the projectile’s reaching its launch level is the beginning of an angle that already exists, which is the launch angle. Considering that the height difference already exists, the proposed equation was formed according to this assumption.\n\nIn this study, we didn’t consider the case where the release point is lower than the landing point, as it occurs in High Jump or Basketball shooting, we need the horizontal displacement of performance events to calculate the horizontal displacement, this helps us control the three variables of the projectile for training purposes and to increase performance. However, we believe that the equation is still applicable in this case, because the terms used in the equation are the same. The equation, like its predecessors, did not address the weights of the tools used.\n\n\nConclusions\n\nThree important factors of projectiles were studied in three major throwing events of track and field events. These factors are (speed, angle, and height of the projectile). These factors were subjected to two types of equations for the purpose of finding the achievement, one of the equations is proposed in this study. The proposed equation was built on the basis that the angle of landing is the same as the angle of takeoff in the parabola, and from this we started to design the equation. This method prevented us from repeating the use of the three factors in the equation and the procedures of the computational operations again.\n\nThe results of the two equations were compared with the legal achievement that is measured on the ground as in competitions. We also used the Galileo Galilei Law of Projectiles as a second criterion to know the degree of convergence between the results of the two equations, as the Galileo Galilei Law of Projectiles is an important part of the equation designed by us.\n\nThe proposed equation has proven its credibility, statistically and graphically, and had high credibility when applied to (3) different activities in their velocity, weight and shape of throwing activities for track and field games, and the results are often closer to the real achievements.\n\nThe proposed equation is suitable for use as an alternative to Galileo’s law of projectiles with equal release and fall levels.\n\nThe importance of designing the equation comes from the fact that the three factors of the projectile can be important topics in the science of sports training for the development of achievement.\n\nIt is possible to conduct studies to compare with other equations, as we conducted a comparison with one equation. Such comparisons can also be conducted on events where the takeoff point is lower than the landing point (site of achievement calculation), as in high jump or shooting in basketball.",
"appendix": "Data availability\n\nZenodo. A proposed equation for calculating the total horizontal distance in projectiles of varying launch and landing levels. DOI: https://doi.org/10.5281/zenodo.8309822.\n\nThis project contains the following underlying data:\n\nData.xlsx(data obtained from real sports competition sources for the three variables: velocity, angle, height, and horizontal measurement on the ground for events) (Jung et al., 2012; Woen-Sik Chae, 2011; Panoutsakopoulos, 2008; Finals, 2011; Jung et al., 2012).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbdel-Monsef Aly R, Abdelhamid Salem M, Ismail El-Shaer O, et al.: Biomechanical Analysis of Top Discus Throwers Performance in Egypt. Journal of Applied Sports Science. 2012; 2(1): 21–28. Publisher Full Text\n\nAriel G, Finch A, Penny A: BIOMECHANICAL ANALYSIS OF DISCUS THROWING AT 1996 ATLANTA OLYMPIC GAMES. ISBS-Conference Proceedings Archive. 1997.\n\nBadura M: Biomechanical analyses.15–23 August 2009.\n\nFinals, M. s. S.-P: Biomechanics Research Project in the IAAF World Championships Daegu.2011.\n\nHall SJ: Basic Biomechanics. 2nd ed.1995.\n\nHamill J, Knutzen M, Derrick R: Biomechanical Basis of Human Movement. Fourt ed.Philadelphia, PA: Holters Kluwer Health; 2015\n\nJung J-H, Kim D-S, Kang H-Y, et al.: Kinematic analysis of the women’s javelin throw at the IAAF World Championships, Daegu 2011. ISBS-Conference Proceedings Archive. 2012.\n\nKinomura Y, Fujibayashi N, Zushi K: Characteristics of the long jump take-off as the novice increases the number of steps in the approach run. Procedia Engineering. 2013; 60: 313–318. Publisher Full Text\n\nMercadante LA, Menezes RP, Martini TP, et al.: 3D kinematical analysis of the hammer throw in competitions. ISBS-Conference Proceedings Archive. 2007.\n\nOmer HM: Analysis of Projectiles law for throwing events (Discus, Javelin, Shotput, and hammer) in track and field. Journal of Zankoy Sulaimnia part (B-for Humanities). 2018; 647–668.\n\nPanoutsakopoulos V: Biomechanical analysis of the men’s discus throw in the Athens 2006 IAAF World Cup in Athletics. In.2008.\n\nWoen-Sik Chae Y-TL: IAAF World Championships, Daegu KSSB Project Final Report (Javelin Throw - Men’s - Finals).2011."
}
|
[
{
"id": "224628",
"date": "14 Feb 2024",
"name": "Yasir Najah",
"expertise": [
"Reviewer Expertise Philosophy in physical education science Sports biomechanics and motor analysis"
],
"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 Editors of F1000Research, Regarding the evaluation of the attached article, there are some positive and negative points that have been found and I will tackle each point according to its priority:\nThe idea of proposing an equation for calculating varied levels of launching and landing is smart and creative specially because the researcher used a well – known geometrical system for simplifying this types of projectile’s equation a matter that makes this equation more simple to use and less complicated. The proposed equation cannot be generalized just because it was applied on three events in athletics for the following reasons:\n\nAll three events selected for the experiment have a higher launching level compared to the landing level and hence a question arises; should the same procedures be followed when the launching level is lower than landing level since the base of the drawn triangle will be in the launching side not the landing side? I would have preferred if the experiment covered two types of projectiles with different levels. According to my experience in biomechanics and gymnastics, within the same level that the researcher studied we find it difficult for most gymnasts to land from the horizontal bar with a smaller angle than landing angle and this does not match the researcher’s hypothesis concerning the proposed equation. The same is true concerning very high projectiles because their launching angle is smaller than their landing angle. In the first figure we find that angle (B) is smaller than angle (F) and this is the reason for differences in results otherwise the result should be identical according to the geometrical system. Therefor I would have preferred conducting more experiments to cover all variances so as to reach the final goal of generalizing this equation.\n\nIn the events that the researcher studied there are two distances; the actual throwing distance that is calculated manually according to the equation of the sport and the second distance is the mechanical distance calculated using projectile equation thus there are always differences in these distances based on launching point, calculation start line, landing point, and the last mark left on the ground. In this point it is difficult to decide which one is more accurate. Thus I propose, in order to generalize this equation, making further studies starting from the official distance for projectiles that are the same as the concluded mechanical distance calculated using projectile equation. The researcher recommended generalizing the proposed equation on throwing events in athletics only hoping for further generalization after conducting more researches on these points.\nThank you for your trust Professor Yasser Nejah (PhD)\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? Yes",
"responses": [
{
"c_id": "11071",
"date": "13 Apr 2024",
"name": "hussein omer",
"role": "Author Response",
"response": "The reviewer’s proposal is clear, and a simple comment will be made while explaining the equation, stating that it is designed for these three activities and may be suitable for application to other activities, and may be suitable for application at launch and landing levels opposite to what is in the equation."
}
]
},
{
"id": "224629",
"date": "14 Feb 2024",
"name": "Yarob Abdulbaqi Algaith",
"expertise": [
"Reviewer Expertise A specialist in the field of sports biomechanics and kinematic analysis of sports games"
],
"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 very well done and provides a suitable and easy way to measure the horizontal distance of a projectile in non-symmetrical levels. I have conducted an experiment on it and it has been shown to be effective and achieve results that are closer to the real distance and in a better way than what is available in the results of the computational averages in the tables. However, there are some values in the tables for the minimum and maximum columns that need to be reviewed and there are errors in them, especially in the differences between the results of the equations. I also recommend that an equation be found to calculate the time that accompanies such an equation. This is generally necessary, as the time must be calculated in an easier way than what is available to us currently. However, the required of the study has been achieved, especially in such sporting events, which is to achieve the best distance only regardless of the 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? 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": "11422",
"date": "29 Apr 2024",
"name": "hussein omer",
"role": "Author Response",
"response": "In V2, the comments of all peers were amended or included...with appreciation"
}
]
},
{
"id": "247956",
"date": "29 Feb 2024",
"name": "Basman Abdul Jabbar",
"expertise": [
"Reviewer Expertise Sports Biomechanics and Motion Analysis"
],
"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\nResearcher used the derivations through the projectiles equation to find the horizontal distance. The main equation that the researcher processed was Galileo’s equation for projectiles, and the research sample was appropriate by choosing three different throwing events in the arena and field. This is an innovative way to address the measurement problem in this type of activity.The main equation that the researcher processed was Galileo’s equation for projectiles, and the research sample was appropriate by choosing three different throwing events in the arena and field. The method was innovative to address the measurement problem in this type of activity. I suggested the possibility of comparison with more than statistical treatment of the same variables, or they could be added to the recommendations for the purpose of benefiting for the future.\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": "11179",
"date": "13 Apr 2024",
"name": "hussein omer",
"role": "Author Response",
"response": "The reviewer's proposal is clear, and a comment will be made on the possibility of using advanced statistical treatments for the purpose of making better use of the results of this study."
}
]
},
{
"id": "224631",
"date": "29 Jun 2024",
"name": "Uday CH Hasan",
"expertise": [
"Reviewer Expertise Movement Analysis",
"Sport Biomechanics",
"Sports Science"
],
"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 Helena The Editorial Team, F1000Research\nI hope you are fine. I would like to thank the editorial board for choosing us to be reviewer in \"F1000Research\" I accept the submission with the possibility of considering the proposed equation as a patent due to its ease of application and accuracy of calculation, and to be adopted in biomechanics curricula, I suggest that the following should be clarified: 1- Is the equation valid for calculating the horizontal distance at different levels (difference in the initial height and final height) in general, or is it valid only if the initial height is higher than the final height? 2- It is necessary to take into account the effectiveness of the javelin throw to calculate the initial and final height, especially the final height that is not at the level of the ground. Therefore, it is necessary to clarify the following in terms of the effectiveness of the javelin throw: total distance, achievement distance, and mechanical distance. To sum up, I endorse the article.\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/12-1491
|
https://f1000research.com/articles/8-1364/v1
|
06 Aug 19
|
{
"type": "Research Article",
"title": "Human TP53 gene polymorphisms among patients with hepatocellular carcinoma and chronic hepatitis B in Kenya",
"authors": [
"Missiani Ochwoto",
"Colins O. Oduma",
"Julius Oyugi",
"Dufton Mwaengo",
"Bartholomew N. Ondigo",
"James H. Kimotho",
"Alex K. Maiyo",
"Ruth M. Nyangacha",
"Gladys Chesumbai",
"Elijah Songok",
"Colins O. Oduma",
"Julius Oyugi",
"Dufton Mwaengo",
"Bartholomew N. Ondigo",
"James H. Kimotho",
"Alex K. Maiyo",
"Ruth M. Nyangacha",
"Gladys Chesumbai",
"Elijah Songok"
],
"abstract": "Background: Human TP53 is the gatekeeper for generation of human cells and is highly conserved. Any alteration/mutation to TP53 adversely affects the regulatory function of the protein, potentially resulting in cancer. This study investigated mutations in codons 7 and 249 of TP53, among patients with hepatocellular carcinoma (HCC) and chronic hepatitis B virus (HBV) infection at the Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya. Methods: In total, 33 HBV-positive patients attending MTRH hospital between September 2013 and July 2017 were purposely selected from medical records for the study; those with HCC were confirmed from the cancer registry. The patients were aged between 25-67 years, with a male-to-female ratio of 1.1:1. Blood samples were collected from the patients. DNA was extracted, amplified and sequenced using TP53 forward and reverse primers. Gene mutation detection and analysis was done on exons 4 and 7 Results: Of the 33 patients, 75.8% were chronically infected with HBV and had HCC; the rest were HBsAg positive without HCC. Homozygous proline was prevalent (54.5%) at exon 4 codon 72, followed by heterozygous Arg/Pro (33.3%) and lastly homozygous Arg/Arg (12.1%,). Pro/Pro allele was frequent in HCC group while Arg/Arg allele was common in patients without HCC. There was no significant association between the HCC and codon polymorphisms (p=0.12). In exon 7, codon 249, 24.2% of patients had an Arg-Ser mutation of which, 75.0% had HCC and 25.0% did not. There was no significant association between HCC patients and codon 249 mutation (p=0.15). Conclusion: TP53 is a gene gate keeper, the mutations under study may dependently play a role in HCC development. This study did not find any association or clear mutational pattern between P53 mutations and HCC development. Therefore, TP53 mutation is a poor indicator for prognosis and a tumor’s biological behavior among HBV-positive subjects in Kenya.",
"keywords": [
"p53 Gene mutation",
"Codon 249",
"Hepatocellular carcinoma",
"p53 Exon 4",
"p53 exon 7"
],
"content": "Abbreviations\n\nHCC: Hepatocellular carcinoma; MTRH: Moi Teaching and Referral Hospital; DNA: Deoxyribonucleic acid; PCR: Polymerase Chain Reaction; G: Guanine; T: Thymine; KEMRI: Kenya Medical Research Institute; EDTA: Ethylenediaminetetraacetic acid; BLAST: Basic Local Alignment Search Tool; NCBI: National Center for Biotechnology Information; MEGA: Molecular Evolutionary Genetics Analysis; IARC: International Agency for Research on cancer; HBV: Hepatitis B virus; HCV: Hepatitis C virus.\n\n\nIntroduction\n\nHepatocellular carcinoma (HCC) is the fourth most common malignancy according to the World Health Organization (2016). HCC is increasing in incidence and has a mortality incidence of 800,000 deaths globally per year (Stewart et al., 2016). Reported incidences of HCC vary worldwide, with the West, Asia and Africa having the highest incidence rates. According to report on the Global Burden of Disease Cancer Collaboration et al. (2017) HCC is the fifth and seventh most common cancer in men and women, respectively. There are various causes of HCC, of which the most common is chronic infection with hepatitis B virus (HBV) and hepatitis C virus (HCV). In Kenya, those infected with HBV constitute 78.0% of HCC cases (Mutuma et al., 2011).\n\nHCC is the primary liver cancer derived from uncontrolled multiplication of hepatocytes (Gomes et al., 2013). Just like in any other cancer, TP53 has a crucial role in HCC tumor suppression. The gene hampers progression of the cell cycle if DNA is damaged (Kruiswijk et al., 2015; Sasaki et al., 2011), a role that is inactivated in most cancers mainly through alteration to TP53, which can be caused by external agents (Gomes et al., 2013; Tokino & Nakamura (2000)). TP53 alterations are observed in most cancers (Kandoth et al., 2013; Levine, 2009) and they affect major regulators of various signaling pathways involved in tumor suppression.\n\nTP53 has ten coding exons, with mutations distributed in all of them, with a strong predominance in exons 4-9, encoding the DNA-binding domain of the protein (Rivlin et al., 2015). Studies have demonstrated that mutant TP53 contributes immensely to replication of damaged DNA and to tumor progression. These mutant proteins bind to TP53 response elements thereby weakening the process of DNA repair and TP53-mediated apoptosis (Carvajal et al., 2012; Maiuri et al., 2010). In exon 7, codon 249 (AGG→AGT, arginine to serine) has been identified as a “hotspot”. Differences in ethnicity and geographical location among other factors have varied impact on TP53 codon 249 (AGG→AGT) mutation profiles (Kandoth et al., 2013; Wen et al., 2016). In exon 4, an arginine to Proline substitution at codon 72 has been investigated as risk modifier in several cancer models; however, its role in cancer progression remains uncertain.\n\nThere is paucity of information on TP53 in Kenya. In this study we evaluated the presence of TP53 gene mutations in exons 4, 6 and 7 among HCC patients attending Moi Teaching and Referral Hospital (MTRH), in western region of Kenya.\n\n\nMethods\n\nThe samples were collected from jaundiced patients chronically infected with HBV attending Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya between September 2013 and July 2017. The patients were purposively selected from hospital records based on them being jaundiced and having HBV or HBV and HCC. Patients were then recruited in person. Those with HCC had their cancer status confirmed using the cancer registry of Eldoret hospital, Uasin Gishu, Kenya. A patient with HCC was defined as having liver cancer based on the patient’s medical record and cancer registry file. All patients with HCC were selected. Other patients’ medical records obtained from the hospital included gender and residential area. The MTRH was selected as it is one of the largest national referral hospitals in western Kenya, where rates of HBV infection are considered to be high (Ochwoto et al., 2016). The male-to-female ratio was 1.1:1 and the age range were from 25 to 67 years. None of the patients had received any viral HBV treatment by the time of sample collection.\n\nThe ethical approval to conduct the study was obtained from Institutional Research and Ethics Committee (IREC) of MTRH/Moi University (approval number 001002), from Kenya Medical Research Institute Scientific Ethics Review Unit (approval number KEMRI/SERU/CVR/001/3211) and from Eldoret Cancer Registry (approval number ECR/DRA/2017/001). Further, the participants consented for the study prior to blood draw.\n\nBlood samples were collected in vials anti-coagulated with EDTA. Plasma was separated at MRTH and thereafter the plasma tubes were shipped on dry ice to the KEMRI Production Unit in Nairobi. The samples were then stored in aliquots at -80°C until subsequent testing.\n\nScreening for hepatitis B virus surface antigen (HBsAg) and antibody to the core protein (anti-HBc) were was performed using the COBAS e411 platform (Elecsys; Roche Diagnostics, Quebec, Canada). Chronic hepatitis B (CHB) was determined by anti-HBc IgM--positive serology, as described previously (Park et al., 2015).\n\nCirculating DNA of Human TP53 tumor suppressor gene was extracted from 200 µl of plasma samples using QIAmp DNA mini-extraction kit (Qiagen Inc, USA) according to manufacturer’s instructions. The DNA was subsequently eluted in 60 µl of AE buffer and quantity measured by NanoDrop spectrophotometer (Thermo Scientific) and stored at -30°C until use.\n\nThree different primers targeting TP53 gene exons 4, 6 and 7 (Table 1) were used in amplification of the extracts using conventional PCR. The PCR mix targeting the three exons was similar except for the primer. Each PCR tube contained a total volume of 50 µl reaction mixture, with 5µl of human genomic DNA template, 5 µl of 10X PCR buffer 5 µl of 25 mM MgCl2, 5 µl of 1.25mM dNTP mix, 0.2 µl of 5U of Taq DNA polymerase (Qiagen Inc, USA), 1.25 µl each of a 20 uM stock of forward primer and reverse primer of sequences (Table 1).\n\nThe mix was loaded to a PCR machine (ABI systems). Amplification for exon 7 the PCR profile set at 95°C for 10 minutes initial denaturation and 35 cycles of denaturation at 95°C for 45 seconds, annealing at 58°C for 30 seconds and extension at 72°C 30 seconds. Final extension was at 72°C for 10 minutes. For exon 4 the PCR was set at 94°C for 12 minutes initial denaturation and 35 cycles of denaturation at 94°C for 40 seconds, annealing at 56°C for 30 seconds and extension at 72°C 30 seconds. Final extension was at 72°C for 10 minutes.\n\nAfter that, a 4-µl aliquot of PCR product was electrophoresed by using 2% agarose (Fisher Scientific), 2 µl of 5X Gelpilot DNA loading Dye (Qiagen Inc, USA) together with 100-bp Track DNA ladder (Invitrogen, California, US) in 1X TBE buffer containing SYBR-safe DNA gel stain (Invitrogen, California, US) and visualized using an ultraviolet trans-illuminator gel Doc-It2 Imager then viewed using Vision Works LS software v.7.1.\n\nFor exon 7, 5 μl of the all negative amplicons was used in the second nested PCR (forward primer exon 7b 5-AGGCGCACTGGCCTCCTT-3 and reverse primer exon 7b 5-TGTGCAGGGTGGCAAGTGGC-3). The master mix and the PCR profile of the nested PCR were similar to the first round profile. The amplicons were viewed following electrophoresis on a 2% agarose gel.\n\nAll PCR-positive amplicons were purified using the Qiagen Gel purification kit according to the manufacturers recommended protocol. The purified DNA was quantified using a Nanodrop spectrophotometer (Thermo Fisher Scientific), and purified DNA (50 ng) were send for sequencing at Macrogen, Inc. (Netherlands) using the first primer sequences and the manufacturer’s guidelines\n\nThe directly amplified sequences were assembled using GENETYX version 9.1.0 (GENETYX Co., Tokyo, Japan; PCAP is an open-access alternative) DNA sequence analysis software. The sequences were aligned to TP53 gene sequences using NCBI BLAST for identity confirmation. The contigs from GENETYX were then aligned to the TP53 gene reference sequence from the International Agency for Research on Cancer (IARC) database using Bioedit software version 7.2.5. Mutations to the sequences were analyzed using MEGA v.7.0 software bioinformatics editing tool.\n\nTest for statistical significance of mutation profile parameters were done using the χ2 test and Fisher’s exact test. P-values less than 0.05 were considered statistically significant. To examine possible associations between mutations in TP53 exons and hepatocellular carcinogenesis, we analyzed 2x2 tables using Fisher’s exact test. Odds ratios (ORs) were used to analyze two significant associations at 95% confidence interval (CI). Statistical analysis was performed using SAS version 9.4.\n\n\nResults\n\nThere were 33 subjects in total for whom results in exon 4, 6 and 7 were obtained. The characteristics of the subjects are shown in Table 2. The ratio of male to female was 51.5% to 48.5%. All the subjects were positive for HBsAg. Those who were chronically infected and had HCC were 75.8% (25/33), of which 48.0% were female and 52.0% were male. Among those (24.2%) that did not have HCC but were HBsAg positive, half were female and the other half male.\n\nThe total number of samples that were amplified with clear forward and reverse sequences for exon 4 codon 72 was 33. The majority (54.5%) of these had Pro/Pro (CCC) alleles, followed by heterozygous Arg/Pro (33.3%) and homozygous Arg/Arg (CGC) (12.1%) (Figure 1). All those homozygous for Arg/Arg were male.\n\nThere was statistically significant association between the sex of the subject and the polymorphism identity (Fisher test=5.4 and p=0.04), with all the homozygous Arg/Arg belonging to male patients, whereas more female patients had homozygous Pro/Pro than male (64.7% vs 35.3%) and more male had the heterozygous Pro/Arg than female (58.3% vs 41.7%). On the other hand there was no statistical significance between the HCC and the polymorphisms (Fisher test=3.58 and p=0.12); however, it is important to note that at codon 72 most of the patients with HCC had Pro/Pro alleles, followed by heterozygous Pro/Arg and lastly homozygous Arg/Arg (Table 3). The Pro/Pro allele was more frequent in the HCC group, whereas all patients wth Arg/Arg alleles did not have HCC (Table 4).\n\nThere was no significant association between HCC, gender and TP53 Arg72Pro/Arg when both HCC cases and the non-HCC cases were compared (P=0.57). Equally there was no significant association between HCC, gender and TP53 codon 72 Pro/Pro (P=0.40; Table 4)\n\nOut of the 33 subjects, eight (24.2%) had the Arg>Ser codon 249 mutation and the majority (75.8%) did not have the mutation. Serine 249 mutation was seen more in males (87.5%) than females (12.5%) and there was an association between the sex and mutation (Fisher's exact test =5.47, P-value =0.039) with male at higher risk compared to female (OR=10.5, 95% CI =1.1-98.9%) (Table 5).\n\nMutation: Guanine-to-thymine transversion in the third base of codon 249 of TP53 gene.\n\nThe majority (75.0%) of those with the serine 249 mutation had HCC; only 2 (25.0%) had the mutation without but not HCC. Similarly, among those without the mutation, 76.0% were had HCC and 6 (24.0%) did not have HCC. The findings showed no significant statistical association in the presence of codon 249 mutations between patients with and without HCC (p=0.15) at 95% CI (OR=0.52: 95% CI 0.054-4.773).\n\n\nDiscussion\n\nThe association between HCC and mutations at codon 72 or 249 of TP53 remains controversial. To our knowledge, this is the first information concerning TP53 exon 4, 6 and 7 mutation in Kenya. A number of studies have described two structurally different forms of wild-type p53 resulting from the substitution of a proline for an arginine at residue 72, with different biochemical and biological characteristics (Thomas et al., 1999). Different prevalence of this substitution has been reported in various studies. In this tufy, the HBV-positive Kenyan population, the homozygous Pro/Pro genotype is the most common (54.5%), and the least is homozygous Arg/Arg. This prevalence of allele is similar to Taiwanese (Mah et al., 2011), Egyptian (Neamatallah et al., 2014) and Chinese (Wang et al., 1999). We observed that patients with HCC had higher frequencies of Pro/Pro (88.2% Vs 11.8%) a similar observation made among Moroccan population (Ezzikouri et al., 2010) and Egyptian patients with HCV (Koushik et al., 2004; Neamatallah et al., 2014).\n\nThe association between TP53 codon 72 Pro/Arg gene polymorphism and cancer remains controversial, with some studies showing associations but others no association. Among the studies that show associations, Dong et al., 2018 found that the TP53 Pro allele and Pro/Pro genotype were associated with cancer risk, (Dong et al., 2018). In Egyptian patients with HCC, development of HCC was associated with Pro/Pro allele carriage as compared to Arg/Arg or Arg/Pr alleles (Neamatallah et al., 2014), This study did not find any association between polymorphisms and HCC among the HBV-positive patients. Other studies have shown similar findings (Eskander et al., 2014; Hu et al., 2014). The inconsistency in association and prevalence observed could be attributable to ethnic differences, since most study have been performed in Asian and Caucasian populations, while the current study was performed in an African population.\n\nOur findings show the presence of selective guanine-to-thymine transversion mutation in the third base of codon 249 of TP53 in DNA isolated from 8 out of 33 HCC patients. This mutation corresponds to arginine-to-serine substitution. Our findings corroborate data available among populations from Guangxi, Taiwan and The Gambia, where similar mutations were reported (Mah et al., 2011; Özdemir et al., 2010). However, evidence presented from a European population, which reported no mutation, is contrary to our findings (Kirk et al., 2000). According to a report by the Global Burden of Disease Cancer Collaboration et al. (2017), differences in geographical location, ethnicity, hereditary disorders, and excessive exposure to mutation-inducing agents as well as study size population offer explanation to the discordance observed in the reported findings between our study and European studies (Global Burden of Disease Cancer Collaboration et al., 2017). Our study found no significant association between codon 249 mutation and hepatocellular carcinogenesis (p=0.6821) at level of significance p<0.05. However, exposure to codon 249 mutation might be considered a predisposing factor for HCC (OR=0.5278; 95% CI 0.0584-4.7736). These findings are in agreement with finite data available in Taiwan, United states, Japan, Australia, Gambian and Guangxi populations (Kirk et al., 2000; Mah et al., 2011; Montesano et al., 2010; Özdemir et al., 2010; Stern et al., 2001). Likewise, array of literature is available implicating that the presence of this very mutation in HCC patients from developed countries including the United States, China, Japan and Australia is remarkably low (Bruix et al., 2011; Montesano et al., 2010; Özdemir et al., 2010).\n\nMales were overrepresented in the mutation positive categories in patients with and without HCC. This could be ascribed to possible occurrence of faster and more severe HCC in males than females (Li et al., 2017). However, there was there was an association between the sex and mutation (Fisher's exact test =5.47, P-value =0.039).\n\nCounter-intuitively, TP53 codon 249 mutations were observed not only in HCC patients but also in one the non-HCC patients, this corroborates earlier findings by Kirk et al. (2000) that reported codon 249 mutation presence in 3 of 53 control subjects (6%), and those of Ozturk et al. (1994), who reported codon 249 mutations in non-malignant liver tissues. A possible explanatory analysis for this finding is that mutations to codon 249 is generally known as a hotspot for aflatoxin B1 (AFB1)-driven modification. According to Özdemir et al. (2010), AFB1 induces codon 249 mutation among cancer patients residing in AFB1 high-risk regions, where chronic HBV and HCV infections are also endemic. Furthermore, among TP53 mutations described in human cancers and compiled in the IARC TP53 mutation database, 66% occur in patients with HCC originating from regions with a high incidence of HCC and high exposure to dietary AFB1. However, we did not perform aflatoxin exposure tests for the subjects to corroborate this. Additionally, published data from the Ministry of Health and the Gastroenterology Society of Kenya on guidelines for the treatment of HBV and HCV infections in Kenya (2015) suggested that 80% of HCC cases in the country are due to chronic infection with HBV (Ochwoto et al., 2016). This evidence perhaps indicates that the existence of the mutation in TP53 may be suggestive of an early genetic event in hepatocellular carcinogenesis. Consequently, it is argued that presence of a single mutation alone in DNA is unlikely to cause cancer, rather cumulative or multiple mutations in tumor suppressor genes are required (Adjiri, 2017).\n\nAlthough this study has investigated for the presence of TP53 mutation in exon 4, 6 and 7 hepatocellular carcinoma patients, there is a need to look at the remaining exons. However, this study was a cross-sectional study that involved 33 HBV-positive patients, of whom 25 had HCC, it was hard to compare the evolution of the mutations among the patients with HCC. The use of samples that only amplified the forward and reverse fragments of exon 7 and 4 could bias the mutational prevalence. The mutations reported in this study were found in samples taken from the patients’ blood and we did not obtain tumor tissues from the patients for verification.\n\n\nConclusion\n\nTP53 is a gatekeeper gene, and codon 72 and 249 mutations could play a role in HCC development. However, this study did not find any association or clear mutational pattern between TP53 mutations and HCC development. Equally the existence of multiple mutations in an individual was not associated with HCC. We therefore conclude that TP53 mutation is a poor Indicator for Prognosis and tumor’s biological behavior among HBV-positive subjects in Kenya. Other TP53 mutational sites may be considered and analysis of large numbers of cases may be an alternative option to allow specific use of the gene mutations in HCC development.\n\n\nData availability\n\nTP53 sequence data obtained from this study are available from GenBank, accession numbers MN119310 to MN119350.",
"appendix": "Grant information\n\nThis work was supported by KEMRI IRG grant from Kenya Medical Research Institute, protocol Number KEMRI/SERU/ CVR/001/3211 and IRG Number L057.\n\n\nAcknowledgments\n\nWe acknowledge the study participants and the staff of Moi Teaching and Referral Hospital.\n\n\nReferences\n\nAdjiri A: DNA Mutations May Not Be the Cause of Cancer. Oncol Ther. 2017; 5(1): 85–101. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBruix J, Sherman M, American Association for the Study of Liver Diseases: Management of hepatocellular carcinoma: an update. Hepatology. 2011; 53(3): 1020–1022. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCarvajal LA, Hamard PJ, Tonnessen C, et al.: E2F7, a novel target, is up-regulated by p53 and mediates DNA damage-dependent transcriptional repression. Genes Dev. 2012; 26(14): 1533–1545. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDong Z, Zheng L, Liu W, et al.: Association of mRNA expression of TP53 and the TP53 codon 72 Arg/Pro gene polymorphism with colorectal cancer risk in Asian population: a bioinformatics analysis and meta-analysis. Cancer Manag Res. 2018; 10: 1341–1349. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEskander EF, Abd-Rabou AA, Yahya SM, et al.: \"P53 codon 72 single base substitution in viral hepatitis C and hepatocarcinoma incidences\". Indian J Clin Biochem. 2014; 29(1): 3–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEzzikouri S, El Feydi AE, Afifi R, et al.: Polymorphisms in antioxidant defence genes and susceptibility to hepatocellular carcinoma in a Moroccan population. Free Radic Res. 2010; 44(2): 208–216. PubMed Abstract | Publisher Full Text\n\nGlobal Burden of Disease Cancer Collaboration, Fitzmaurice C, Allen C, et al.: Global, Regional, and National Cancer Incidence, Mortality, Years of Life Lost, Years Lived With Disability, and Disability-Adjusted Life-years for 32 Cancer Groups, 1990 to 2015: A Systematic Analysis for the Global Burden of Disease Study. JAMA Oncol. 2017; 3(4): 524–548. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGomes MA, Priolli DG, Tralhão JG, et al.: Hepatocellular carcinoma: epidemiology, biology, diagnosis, and therapies. Rev Assoc Med Bras (1992). 2013; 59(5): 514–524. PubMed Abstract | Publisher Full Text\n\nHu S, Zhao L, Yang J, et al.: The association between polymorphism of P53 Codon72 Arg/Pro and hepatocellular carcinoma susceptibility: evidence from a meta-analysis of 15 studies with 3,704 cases. Tumor Biol. 2014; 35(4): 3647–56. PubMed Abstract | Publisher Full Text\n\nKandoth C, McLellan MD, Vandin F, et al.: Mutational landscape and significance across 12 major cancer types. Nature. 2013; 502(7471): 333–339. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKirk G, Camus-Randon AM, Mendy M, et al.: Ser-249 p53 mutations in plasma DNA of patients with hepatocellular carcinoma from The Gambia. J Natl Cancer Inst. 2000; 92(2): 148–53. PubMed Abstract | Publisher Full Text\n\nKoushik A, Platt RW, Franco EL: p53 codon 72 polymorphism and cervical neoplasia: a meta-analysis review. Cancer Epidemiol Biomarkers Prev. 2004; 13(1): 11–22 . PubMed Abstract | Publisher Full Text\n\nKruiswijk F, Labuschagne CF, Vousden KH: p53 in survival, death and metabolic health: a lifeguard with a licence to kill. Nat Rev Mol Cell Biol. 2015; 16(7): 393–405. PubMed Abstract | Publisher Full Text\n\nLi Y, Li H, Spitsbergen JM, et al.: Males develop faster and more severe hepatocellular carcinoma than females in krasV12 transgenic zebrafish. Sci Rep. 2017; 7: 41280. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLv L, Wang P, Zhou X, et al.: Association between the p53 codon 72 Arg/Pro polymorphism and hepatocellular carcinoma risk. Tumour Biol. 2013; 34(3): 1451–1459. PubMed Abstract | Publisher Full Text\n\nMah YH, Hsu CS, Liu CH, et al.: Serum p53 gene polymorphisms and severity of hepatitis B or C-related chronic liver diseases in Taiwan. Hapatol Int. 2011; 5(3): 814–821. PubMed Abstract | Publisher Full Text\n\nMaiuri MC, Galluzzi L, Morselli E, et al.: Autophagy regulation by p53. Curr Opin Cell Biol. 2010; 22(2): 181–185. PubMed Abstract | Publisher Full Text\n\nMutuma GZ, Mbuchi MW, Zeyhle E, et al.: Prevalence of Hepatitis B Virus (HBV) surface antigen and HBV-associated hepatocellular carcinoma in Kenyans of various ages. Afr J Health Sci. 2011; 18: 53–61. Reference Source\n\nNeamatallah MA, El-Missiry MA, Said MA, et al.: TP53 polymorphism as a risk factor for hepatocellular carcinoma in hepatitis C virus-infected Egyptian patients. Egyptian Journal of Basic and Applied Sciences. 2014; 1(1): 9–15. Publisher Full Text\n\nOchwoto M, Kimotho JH, Oyugi J, et al.: Hepatitis B infection is highly prevalent among patients presenting with jaundice in Kenya. BMC Infect Dis. 2016; 16: 101. PubMed Abstract | Publisher Full Text | Free Full Text\n\nÖzdemir FT, Tiftikci A, Sancak S, et al.: The prevalence of the mutation in codon 249 of the P53 gene in patients with hepatocellular carcinoma (HCC) in Turkey. J Gastrointest Cancer. 2010; 41(3): 185–189. PubMed Abstract | Publisher Full Text\n\nOzturk M: p53 mutations in nonmalignant human liver: fingerprints of aflatoxins? Hepatology. 1995; 21(2): 600–601. PubMed Abstract | Publisher Full Text\n\nPark JW, Kwak KM, Kim SE, et al.: Differentiation of acute and chronic hepatitis B in IgM anti-HBc positive patients. World J Gastroenterol. 2015; 21(13): 3953–3959. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRivlin N, Koifman G, Rotter V: p53 orchestrates between normal differentiation and cancer. Semin Cancer Biol. 2015; 32: 10–17. PubMed Abstract | Publisher Full Text\n\nSasaki M, Kawahara K, Nishio M, et al.: Regulation of the MDM2-P53 pathway and tumor growth by PICT1 via nucleolar RPL11. Nat Med. 2011; 17(8): 944–951. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStern MC, Umbach DM, Yu MC, et al.: Hepatitis B, aflatoxin B(1), and p53 codon 249 mutation in hepatocellular carcinomas from Guangxi, People's Republic of China, and a meta-analysis of existing studies. Cancer Epidemiol Biomarkers Prev. 2001; 10(6): 617–625. PubMed Abstract\n\nStewart SL, Kwong SL, Bowlus CL, et al.: Racial/ethnic disparities in hepatocellular carcinoma treatment and survival in California, 1988-2012. World J Gastroenterol. 2016; 22(38): 8584–8595.PubMed Abstract | Publisher Full Text | Free Full Text\n\nThomas M, Kalita A, Labrecque S, et al.: Two polymorphic variants of wild-type p53 differ biochemically and biologically. Mol Cell Biol. 1999; 19(2): 1092–100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTokino T, Nakamura Y: The role of p53-target genes in human cancer. Crit Rev Oncol Hematol. 2000; 33(1): 1–6. PubMed Abstract | Publisher Full Text\n\nWang NM, Tsai CH, Yeh KT, et al.: P53 codon 72Arg polymorphism is not a risk factor for carcinogenesis in the chinese. Int J Mol Med. 1999; 4(3): 249–52. PubMed Abstract | Publisher Full Text\n\nWen X, Lu F, Liu S: Prognostic value of p53 mutation for poor outcome of Asian primary liver cancer patients: evidence from a cohort study and meta-analysis of 988 patients. Onco Targets Ther. 2016; 9: 7425–7433. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang Y, Xia T, Li N, et al.: Combined effects of p53 and MDM2 polymorphisms on susceptibility and surgical prognosis in hepatitis B virus-related hepatocellular carcinoma. Protein Cell. 2013; 4(1): 71–81. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "55172",
"date": "30 Oct 2019",
"name": "Lamech Mwapagha",
"expertise": [
"Reviewer Expertise Cancer Genomics"
],
"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\nIn this manuscript, Ochwoto et al. investigate mutations in TP53, among patients with hepatocellular carcinoma (HCC) and chronic hepatitis B virus (HBV) infection at the Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya. They conclude that TP53 mutation is a poor indicator for prognosis among HBV-positive persons in Kenya, due to a lack of association between TP53 mutations and HCC development.\nComments to Authors\nIn general, the manuscript owns some degree of novelty and clarifies previously existing hypothesis on the relationship between TP53 mutations and HCC. However, the study seems to have some glaring omissions with methodology and the results. The authors aimed to evaluate TP53 mutations in exons 4, 6 and 7, but there were no results shown for exon 6. Even though, this study didn’t find a significant relationship between TP53 mutations and HCC development in Kenya. It would have been ideal to include healthy subjects as part of the controls since previous studies have shown the presence of TP53 mutations in healthy cohorts albeit at much lower frequencies to HCC subjects, thus, it is difficult to make any inferences due to the lack of such controls. An interesting part of this study relies on the sequencing results, am referring to mutation detection and analysis. Accordingly, I think that the study would have greatly benefited from some experimental validation of this data e.g. Restriction endonuclease to validate the mutations.There are also no supporting results depicting the presence/lack of the said mutations i.e. Gel electrophoresis images and sequence electropherograms. Thus, making reproducibility of this work partly possible in validating the conclusions made.\nMinor Points\nOmitted results/typographical errors:\nStudy site and sample population, Page 3, line 6 “HBV or HBV” delete one. Serology testing, Page 3, line 2 “were was” correct the sentence. PCR mastermix, page 4, give the genomic DNA template concentration as opposed to a generic quantity. DNA sequencing, page 4, line 5 “were send” edit to were sent. Table 1, include the expected band sizes or mention these in the methodology. Include Exon 6 results. Figure 1 legend, not detailed and descriptive. Results, page 5, lines 2-3 delete word “more”. Results, page 5, paragraph 1 last line. The authors state “….all patients wth Arg/Arg alleles did not have HCC….” But both tables 3 and 4 show the presence of 2 (50%) HCC subjects with the polymorphisms. Codon 249 mutation and HCC, section is not clear, check for grammatical errors. Discussion, Page 6, line 3, no exon 6 results. Discussion, Line 9, “tufy” edit to study. Discussion, Paragraph 2, line 9, “most study” edit to most studies.\nSummary\nThis manuscript provides novel interesting data on TP53 mutation and HCC in Kenya. Subject to addressing the concerns raised, this work is scientifically sound and worthy of indexing.\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?\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? Yes",
"responses": []
},
{
"id": "55879",
"date": "06 Nov 2019",
"name": "Harris Onywera",
"expertise": [
"Reviewer Expertise Microbiome",
"Sexually Transmitted Infections",
"and Cancer"
],
"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 of the article by Ochwoto and colleagues\n\nThe article by Ochwoto and colleagues aimed to identify polymorphisms in the human TP53 gene among Kenyan patients with hepatocellular carcinoma (HCC) and chronic hepatitis B. TP53 is a gene that encodes tumour protein p53 that controls the cell cycle (division or proliferation), thereby suppressing tumorigenesis. Mutations in the TP53 impair the function of the tumour protein p53, causing the cells to proliferate uncontrollably. Ochwoto and colleagues examined mutations in codons 72 and 249, which exit in exons 4 and 7, correspondingly. They found that there was genetic heterogeneity in the nucleotide mutations in the TP53 gene, which resulted in either synonymous or nonsynonymous mutations. Further analyses found no association between p53 mutations and HCC, suggesting that mutations in the TP53 gene may not be good biomarkers for HCC, specifically among Kenyan patients with hepatitis B virus (HBV) infections.\n\nThere is paucity of data on the polymorphisms in the TP53 gene and their association, if there is any, with HCC on Kenyan cohort. Whereas the study by Ochwoto and colleagues adds knowledge to the existing literature, I approve it with sound reservations. First and foremost, they do not sufficiently address all their objectives. For instance, they indicate that they will investigate polymorphisms in specific codons found in exons 4, 6 and 7. However, they do not present any of the results for exon 6, yet they say in the “recommendations and limitations” section that they examined this. Besides, they detail (in the “methods” section) the primers that were used to amplify and sequence exon 6. What happened to exon 6 results? What codon positions in this exon were analysed? The authors do not consistently present their results. I mean, the way they present/tabulate their results for codon 72 (in exon 4) is totally different from codons 249 (exon 7). No PCR/sequencing and healthy controls were included in their study. There are sections in the manuscripts that have not been referenced. Ochwoto and colleagues do not adequately highlight findings of the literature that they use – as it is not clear what some of those studies reported. For example, in the discussion section (paragraph 1), they state: “Different prevalence of this substitution has been reported in various studies.” With this, they assume that the reader is aware of what those studies reported. To address this, they should give a range of the prevalence that these studies found, so that the reader can easily compare findings presented herein with/to what is already known. Another sentence would be in paragraph 2 (discussion), where they write, “This study did not find any association between polymorphisms and HCC among the HBV-positive patients. Other studies have shown similar findings (Eskander et al., 20141; Hu et al., 20142). The inconsistency in association and prevalence observed could be attributable to ethnic differences, since….” Could the authors kindly briefly highlight what some of these studies found? Apart from the aforementioned concerns, there are other concerns and a few typos and grammatical mistakes that need to be corrected. For example, the last sentence in paragraph 2 (discussion) is written as: “…since most study have been performed…” Study should be in plural.\n\nMy detailed review is as below:\n\nReviewer’s comments (according to manuscript section)\n\nTitle and author affiliations\n\nCould the authors add “infection” after “chronic hepatitis B” so that it reads “chronic hepatitis B”? The extra comma (,) in affiliation 2 should be removed.\n\nAbstract\n\nThe authors say in the background that “ANY” alteration/mutation in the TP53 gene adversely affects the regulatory function of the protein, potentially resulting in cancer. Synonymous mutations do not have this effect as the amino acids are not altered. Mutations in TP53 are not always associated with altered p53. The words “mutations to” should be changed to “mutations in”. Is “codon 7” supposed to be “codon 72”? The background does not provide motivation for the study and why it was conducted on a Kenyan cohort? Is it because there is paucity of data surrounding this topic, especially in Kenya? Is it because there are high rates of recurrent liver tumours/cancers?\n\nRemove the semi-colon (;) in the methods and put a full stop (.). Why do the authors say exons 4 and 7 were analysed yet in the manuscript they mention exon 6 too?\n\nIn the results, “12.1%,” should be “12.1%” and “Arg-Ser” should be “Arg/Ser”. They should be consistent when they present the mutations, either use forward slash (/) or hyphen (-) throughout the manuscript.\n\nPart of their conclusion in the abstract is not supported by their findings. The authors’ study is a cross-sectional one and test causal roles, it can only show an association between the polymorphism and HCC. It is thus inaccurate to say that the “mutations under study may dependently play a role in HCC development”. Moreover, they did not examine if other factors contributed to HCC development and whether the mutations they detected co-occurred with other mutations. The authors write, “TP53 mutation is a poor indicator for prognosis and a tumor’s biological behavior among HBV-positive subjects in Kenya.” The cross-sectional nature of their study does not permit them to assess this. They did not use a longitudinal study to study the mutation outcomes. In addition, they did not have information on tumour staging, response to treatment, survival rates (in comparison with healthy controls), vascular invasion (blood and/or lymph vessel invasion, LBVI), and Child-Pugh score. If Ochwoto and colleagues needed to examine the role of TP53 mutation on HCC development and whether these mutations could be indicators for prognosis, then they should have i) utilized a longitudinal study with important participant information, and ii) assessed where the mutations acted dependently (synergistically with other TP53 mutations) or independently to promote carcinogenesis in HCC. My last comment on the abstract, should it be “P53” or “p53” in the conclusion?\n\nKeywords\n\nWhy is “codon 249” included as keyword but “codon 72” is not? I am also curious why “p53 exon 6” was not included yet other exons were, despite the fact that the authors indicate that they examined mutations in codons in exon 6.\n\nAuthor roles\n\nAll authors are supposed to approve the final version of the manuscript. Based on the author contribution section, it appears like Maiyo AK and Chesumbaio G did not (review and edit the manuscript); hence, did not approve the final draft of the manuscript. Could the authors clarify if this was the case?\n\nAbbreviations\n\nThere are abbreviations in the manuscripts that need to be included in this part. For instance, “AE” buffer, “DNA”, “HBsAg”, “CHB”, “AFB1”, and so on.\n\nIntroduction\n\nParagraph 1: There should be a comma after “Global Burden of Disease Cancer Collaboration et al. (2017)”.\n\nParagraph 2: “Alteration to” should be “Alteration in”. The last sentence in this paragraph needs to be referenced as this is a fact that is being stated.\n\nParagraph 3: The first sentence is relatively long and needs to be split into two, that is, put as two sentences. This sentences need to be referenced: “In exon 7, codon 249 (AGG→AGT, arginine to serine) has been identified as a “hotspot”.” and “In exon 4, an arginine to Proline substitution at codon 72 has been investigated as risk modifier in several cancer models; however, its role in cancer progression remains uncertain.” In the latter sentence, “Proline” should appear as “proline”. In addition, the authors say that “codon 72 has been investigated as risk modifier in several cancer models”. What did these investigations find? Was there an association? Do their investigations suggest that mutation (Arg to Pro substitution) in codon 72 plays a role in cancer development? Or did the authors intend to say that those studies found mutation in codon 72 (Arg to Pro substitution) to be a risk factor for cancer?\n\nParagraph 4: there should be a comma after “In this study”. Although in paragraph the authors write, “TP53 has ten coding exons, with mutations distributed in all of them, with a strong predominance in exons 4-9,…” it is unclear why the authors chose to study mutations in only exons 4, 6, and 7 (as they state in paragraph 4). Why did they not examine exons 8 and 9? Is there another reason besides limited information on TP53 polymorphisms in Kenya that motivated the authors to conduct their study in Eldoret, Kenya?\n\nMethods\n\nStudy site and sample population: There is no need to write MTRH in full as this has been done before (in the last paragraph in the introduction section). The sentence “The MTRH was selected as it is one of the largest national referral hospitals in western Kenya, where rates of HBV infection are considered to be high (Ochwoto et al., 20163).” should come immediately after the first sentence. Regarding this sentence, the authors should state the rates of HBV infection that have been reported at MTRH. They should not assume that anyone reading the current paper is aware of this. The second sentence needs to be rephrased. Do the authors mean that they included only jaundice patients and that these patients were HBV-positive with and without HCC? It is not clear if the study by Ochwoto and colleagues is a cross-sectional one or a longitudinal study. They mention that after the patients were selected from the medical records, they “were then recruited in person.” Were the patients called and asked to participate in this study? Was it after this that samples were collected? The design of the study (whether cross-sectional or longitudinal) is somewhat confusing. If indeed it is a cross-sectional study, they should clarify and even acknowledge the fact that this was a retrospective study that depended on stored samples. The redundancy in the section, for instance, twice-mentioning that the study selected patients with jaundice, should be addressed/eliminated. “Eldoret hospital” should be “Eldoret Hospital”, and “age range were” should be “age range was”. What were the exclusion criteria in their study? Finally, the authors mention that information on “residential area” was abstracted from the health records. In spite of this, they do not use this information in their analyses. This information is not reported in their manuscript.\n\nEthical consideration: “The ethical approval to conduct the study was obtained from Institutional Research and Ethics Committee (IREC) of MTRH/Moi University (approval number 001002), from Kenya Medical Research Institute Scientific Ethics Review Unit (approval number KEMRI/SERU/CVR/001/3211) and from Eldoret Cancer Registry (approval number ECR/DRA/2017/001).” should be changed to “The ethical approval to conduct the study was obtained from the Institutional Research and Ethics Committee (IREC) of MTRH/Moi University (approval number 001002), from the Kenya Medical Research Institute Scientific Ethics Review Unit (approval number KEMRI/SERU/CVR/001/3211) and from the Eldoret Cancer Registry (approval number ECR/DRA/2017/001).” In line with my comments above (regarding the nature of the study), the authors say that “the participants consented for the study prior to blood draw.” The consent that the patient provided, was it an informed one? Was it a verbal or written consent? Were/Are the patients aware that this study in particular was being conducted? Did they receive any compensation/incentive?\n\nCollection and preparation of blood samples: The statement “Plasma was separated at MRTH and thereafter the plasma tubes were shipped on dry ice to the KEMRI Production Unit in Nairobi.” could be written as “Plasma was separated at MRTH and then shipped in plasma tubes on dry ice to the KEMRI Production Unit in Nairobi.”\n\nSerological testing: Remove the extra hyphen in “IgM--positive”.\n\nExtraction of DNA from plasma: Information on the source of the reagents (e.g., DNA mini-extraction kit) or equipment (e.g., NanoDrop spectrophotometer), which is bracketed, need to be comprehensive. Apart from including the name of the company, name of the city and country is required.\n\nPCR amplification of human TP53: The authors did not include any controls (negative and positive). How sure are they that their method is valid and that they did not get contamination during PCR? In the paragraph 1 of this section, “the extracts” should be written “the DNA extracts”. Moreover, there should be a space between “5” and “µl” so that it becomes “5 µl” instead of “5µl”. This statement “…of forward primer and reverse primer of sequences…” could be written as “…of forward and reverse primers…”. Table 1 could be put as part of the supplementary data. I am just curious, were the same primers used in PCR the same as those used for sequencing (putting into consideration that the authors mention there was an aspect of nested PCR)? Still in paragraph 1, “and” should be included between “… USA),” and “1.25 µl”. In paragraph 2, what is the model of the ABI PCR machine that was used? This sentence, “Amplification for exon 7 the PCR profile set at 95°C for 10 minutes initial denaturation and 35 cycles of denaturation…” does not makes sense. It needs to be corrected. Both the statements, “Final extension was at…” should be written as “Final extension was performed at…” Still regarding this paragraph (2), why did the authors opt not to give the PCR details for exon 6? The sentence in paragraph 3 is long and needs to be written as two or more sentences. “5X Gelpilot DNA loading” should be “5X Gelpilot DNA Loading”. For paragraph 4, why did the authors use “negative amplicons” in the second nested PCR? Is “negative amplicon” not a failed experiment according in their context? Why was this not performed for exons 4 and 6? Lastly, throughout this section (and the rest of the manuscript), the authors should include the information on the source of the reagents or equipment (which is bracketed) need to be comprehensive. Apart from including the name of the company, name of the city and country is required. This information should be furnished where appropriately, if possible even for the ultraviolet trans-illuminator gel Doc-It2 Imager, 5X Gelpilot DNA Loading Dye.\n\nDNA sequencing: The authors need to state that they used Sanger sequencing. There should be an apostrophe (‘) in the word “manufacturers”. It should be: manufacturer’s and not manufacturers. “send” should be changed to “sent”. There should be a full stop at the end of this paragraph.\n\nMutation detection and analyses: Is there any reason include the sentence “PCAP is an open-access alternative”? The authors should be specific about the BLAST they used. Was it BLASTn or BLASTp or both? “Bioedit” and “mutations to the” should be changed to “BioEdit” and “Mutations in”, respectively. Delete these words, “bioinformatics editing tool”. Lastly, about this section, the authors must reference BioEdit and MEGA software.\n\nStatistical analyses: What do the authors mean by “profile parameters”? The last sentence about SAS version 9.4 can be first sentence in this section. It is not clear what they mean by, “used to analyze two significant associations”? Did all the expected values in the 2x2 contingency tables warrant the use of Fischer’s exact text? Were all the expected value >5? If this was not the case, then Chi square test should be used in such scenarios. Odds ratios are used to measure the strength/magnitude of association. “P-values less” should be “P-values of less”.\n\nResults\n\nParticipant demographics: The authors do mention exon 6 yet these results are hugely lacking. No results regarding this are presented. Can the authors please provide the results for this? The sentence “Among those (24.2%) that did not have HCC but were HBsAg positive, half were female and the other half male.” should be written as “Among those that did not have HCC but were HBsAg positive (24.2%), half were female.” The title for Table 2 is not accurate. While the title says “clinical” and “molecular” characteristics, the variable “gender” does not fit in any of that (clinical or molecular). Gender is a demographic characteristic. The symbol % should be deleted in the numbers (e.g., 75.8%) in the last column as this (5) is already put in the column title. At the bottom of this table, ALL abbreviations (e.g., HCC, Arg, etc.) should be written in full (e.g., hepatocellular carcinoma, arginine, etc.). The same is required for Tables 3, 4 and 5. Furthermore, the numbers in Table 5 need to have spaces between them and opening brackets, e.g., it should be “6 (24.0%)” and not “6(24.0%)”. This should be done for the other numbers, where necessary. The comma in the title for Table 4 should be removed.\n\nTP53 exon 4, codon 72 polymorphism analysis: Paragraphs 2 and 3, the authors display the Fisher test value at differing decimal places; some are at 2 decimal places while others are at 1 decimal place. They must ensure that they are consistent. The same is true for the other sections entitled: “Mutations at exon 7, codon 249” and “Codon 249 mutation and HCC”. Check the number of decimal places for the p-values and CIs, throughout the manuscript (even in the tables). Paragraph 2 (of section titled: TP53 exon 4, codon 72 polymorphism analysis), there should be a full stop after “p=0.12)”. The next sentence should then be case sensitive (“However”). The last sentence of this paragraph, “The Pro/Pro allele was more frequent in the HCC group, whereas all patients wth Arg/Arg alleles did not have HCC (Table 4).” needs to be changed/revised. First, there is a typo (“with” is written as “wth”). Secondly, the statement is untrue. I see that there are HCC patients (2 males) who had Arg/Arg alleles. For Figure 1, it is not relevant to have a 3D-plot as the third dimension is meaningless. My last comments on results: In order to ensure consistency, the authors should decide if they want to write “P=value”, “p=value”, or “P-value”. Moreover, they should decide on whether to include space before/after the equal sign (=). I see in one place they have “Fisher test=3.58’ while in another they have “Fisher's exact test =5.47”. The other thing, is it “Fisher test” or “Fisher's exact test”. Ochwoto and colleagues do not consistently present (tabulate) their results for the mutations found in the codons that they studies. No results are presented for exon 6. Moreover, the way they presented the results for codon 72 is considerably different from those of codon 249. Why did they opt for this strategy?\n\nDiscussion\n\nParagraph 1: They indicate that to the best of their knowledge, this is the first time information concerning TP53 exons 4, 6, and 7 are presented in Kenya. They should say that this is among HBV-positive patients with and without HCC, as there are other investigators, who studied exons 6 and 7 (though in the context of oral squamous cell carcinoma). Ochwoto and colleagues do not present results for exon 6 yet they mention this exon in their discussion. They also have the sentence “A number of studies have described two structurally different forms of wild-type p53…”, yet they end up providing only one reference (Thomas et al., 19994).” There should be additional references then. This paragraph has a typo (“study” written as “tufy”). The prevalence values (of the specific mutations in different cohorts, e.g., Taiwanese, Chinese, etc.) should be provided. This should also be done for the part where they say, “Different prevalence of this substitution…”. A range should be provided in this case. This sentence “In this tufy, the HBV-positive Kenyan population, the homozygous Pro/Pro genotype is…” could be written as “In our present study, the homozygous Pro/Pro genotype was…”. The last sentence of this paragraph, they say “higher frequencies”, but they do not indicate what they compared these frequencies with. Higher than which comparison group? There should be a coma after “11.8%” and the abbreviation “Vs” put as “vs”.\n\nParagraph 2: The comma towards the end of the second sentence (“with cancer risk,” should be removed (and he words be “with cancer risk”). The next sentence, which starts with “In Egyptian patients…”, should have a full stop at the end, not a comma. It is also not clear if Ochwoto and colleagues are referring to their present results or other’s results when they state, “This study did not find any association between polymorphisms and HCC among the HBV-positive patients.” The authors should also give a few details about the studies by Eskander et al., 20141 and Hu et al., 20142. Otherwise, the reader is left to wonder what the other studies found when they simply say, “Other studies have shown similar findings”. The last sentence of this paragraph should have the words “most study” changed to “most studies”. Just to add on some of the reasons for inconsistencies in study findings, I believe heterogeneity in study methodology, sample (population) size, and specimen type could at least partly be contributing factors.\n\nParagraph 3: The authors should express the 8/33 as a percentage and go ahead and give us the exact rates that were reported on the cohorts from China, Taiwan and The Gambia. This sentence “However, evidence presented from a European population, which reported no mutation, is contrary to our findings (Kirk et al., 2000).” needs to be rewritten. This study5, done on an Egyptian cohort, should be included in this section and findings on rates of mutants in codon 249 reported. Another study would be this6, which found no mutation in codon 249 among HCC Korean patients. In manuscript by Ochwoto and colleagues, the part written, “offer explanation to” could be written as “could explain” as it is not certain what resulted in the discordance. Delete “(p=0.6821) at level of significance p<0.05”. Personally, I disagree with the fact that the authors think that based on the odds ratio (OR=0.5278; 95% CI 0.0584-4.7736), codon 249 might be a predisposing factor for HCC. The OR value do not support that as the values range from 0 to over 1. OR >1 indicates increased occurrence of an event whereas OR <1 indicates decreased occurrence of event (protective exposure).\n\nParagraph 4: The sentence could begin with, “We further found that males were overrepresented…”. The last sentence (However, there was there was an association between the sex and mutation (Fisher's exact test =5.47, P-value =0.039) needs to be rectified – as “there was” is repeated. The information on statistics (Fisher's exact test =5.47, P-value =0.039) should be deleted as they are already in the results section.\n\nParagraph 5: The authors need to present the rates (prevalence) rather than numbers so that their values can be compared to what is in the literature. This sentence (“TP53 codon 249 mutations were observed not only in HCC patients but also in one the non-HCC patient”) should have the prevalence so that the rates can be easily compared with/to others. Change “this corroborates earlier findings” to “thus, corroborating earlier findings”, “mutations to” to “mutation in”, and “A possible explanatory analysis…” to “A possible explanation…”. The authors mention that mutations in codon 249 are generally known as a hotspot for aflatoxin B1 (AFB1)-driven modification, and that AFB1 induces codon 249 mutation among cancer patients residing in AFB1 high-risk regions, where chronic HBV and HCV infections are also endemic. While they acknowledge that they did not perform aflatoxin exposure tests on their subjects, what makes them speculate that AFB1 could have an impact on their cohort? Can the authors please comment on the levels of aflatoxins in the region, Eldoret? Do the authors know if there are certain foods in the region that have AFB1 levels beyond the tolerated level? Do the authors think that other factors such as alcohol and smoking could have a similar influence on TP53 as AFB1?\n\nRecommendations and limitations\n\nIn this section, they mention exon 6, but no results were presented. The sentence “Although this study has investigated for” should be “Although this study investigated”. The sentence “However, this study was a cross-sectional study that involved 33 HBV-positive patients, of whom 25 had HCC, it was hard to compare the evolution of the mutations among the patients with HCC.” could be written as “The cross-sectional nature of the study limited our analysis. Thus, we were unable to perfume any analysis to determine the evolution of the TP53 mutations among the patients with HCC.”\n\nConclusion\n\nI tend to disagree with the authors’ conclusion as they do not write this section based on their findings. Their study was not a longitudinal one, which could/would enable them assess the role of polymorphisms (codons 72 and 249) in HCC development. Further, their study did not show that these mutations are poor indicator for prognosis.\n\nReferences\n\nThe authors need to present up-to-date information. Of all there >30 references, there is none for 2019, while there are only one, two, and three for 2018, 2017, and 2016, respectively. The rest are for the previous years, prior to 2016.\n\nOther comments\n\nNo PCR and sequencing controls were included in the study. Therefore, how sure are the authors that there were no contaminants in their study? How sure are they that they targeted the right gene? The authors do not mention anything about the size of the amplicon that they expected and whether they observed it.\n\nNo healthy human controls were included. Moreover, there was no information on tumour size, histopathological features, cancer staging, and treatment outcome. Thus, it is hard to infer speculate on the role of the TP53 mutations in their study.\n\nThe authors should not be too quick to generalize results as their sample size was relatively small, besides their study having other limitations.\n\nThe authors did not adjust their analysis for multiple comparisons. Moreover, they do not acknowledge other confounders.\n\nThe method they used for amplification and sequencing may have resulted in their ability to capture other mutations. They could have confirmed their findings using droplet digital PCR (ddPCR), restriction fragment length polymorphisms (RFLP), or polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP).\n\nWhat could be the implications of the TP53 mutations that the authors identified in their study? The implications should relate to their study cohort/population.\n\nThe study cohort/population is not sufficiently described. There is less information about the study cohort/population. Do the authors know the HIV status of the cohort? Other information that would have been relevant and important in their discussion would be HBV genotypes, other potential cancers, hereditary disorders and so on.\n\nThe results by Ochwoto and colleagues do not have the electrophoresis results. I recommend that they provide the results for band visualization?\n\nThe authors have information about the age of the study participants. One study on a small cohort of Hispanics7 associated TP53R249S mutation with a younger age (besides worse prognosis). The work by Ochwoto and colleagues has the potential to add more knowledge if they could stratify their participants by age (young vs old) and then examine if there is any association of the TP53 mutations with age.\n\nTo strengthen this finding (in the discussion) where they say “Our study found no significant association between codon 249 mutation and hepatocellular carcinogenesis…”, I suggest that they include this paper8 which does not support their findings. The suggested article found a strong association between TP53R249S in plasma and HCC Qidong patients.\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/8-1364
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https://f1000research.com/articles/10-1174/v1
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22 Nov 21
|
{
"type": "Research Article",
"title": "Correlations between components of the immune system",
"authors": [
"Yehudit Shabat",
"Yaron Ilan",
"Yehudit Shabat"
],
"abstract": "Background: No evidence of the possibility to alter a constituent of the immune system without directly affecting one of its associated components has been shown yet. Methods: A schematic model was developed in which two triggers, fasting and splenectomy, were studied for their ability to affect the expression of cell membrane epitopes and the cytokine secretion of out-of-body autogeneic and syngeneic lymphocytes. Results: Fasting decreased expression of CD8 and CD25 and increased TNFα levels. The effect of splenectomy as a trigger was investigated in non-fasting mice by comparing splenectomized and non-splenectomized mice. An increase in the CD8 expression and in TNFα, IFNg, and IL10 secretion was noted. The effect of splenectomy as a trigger was investigated in fasting mice by comparing splenectomized and non-splenectomized mice. Splenectomy had a significant effect on expression of CD25 and CD4 CD25 and on secretion of TNFα, IFNg, and IL10. To determine the effect of keeping the cells in an out-of-body location on the expression of lymphocyte epitopes, tubes kept on top of the cages of the fasting mice were compared with tubes kept on top of empty cages. A significant change in the CD8 expression was noted. To determine the effect of keeping cells in an out-of-body location on cytokine secretion, tubes kept on top of cages were tested for cytokine levels. A significant decrease was noted for the secretion of TNFα and IFNg. Conclusions: The data obtained from this study characterized a system for induction of correlations between two components of the immune system without a transfer of mediators. The study showed that a mouse could affect cells at a distance and alter the expression of surface markers and cytokine secretion following two types of triggers: fasting and/or splenectomy. Thus, an out-of-body correlation can be induced between two components of the immune system.",
"keywords": [
"complex systems",
"immune memory",
"information transfer",
"immune response",
"randomness"
],
"content": "Abbreviations\n\nIFNγ: interferon gamma\n\nIL10: interleukin 10\n\nOL: an independent control laboratory\n\nTGFβ: transforming growth factor beta\n\nTNFα: tumor necrosis alpha\n\n\nIntroduction\n\nMost living systems contain information. The more complex the system is, the higher the probability that it carries information. The immune system, similar to other biological systems, may optimize functionality, but it does not necessarily have perfect structure or symmetry. The irregularity that underlines some of the pathways of this system provides the opportunity to apply the concepts of physics to this biological system.1\n\nThe correlations between components of the immune system always involve reactions mediated by direct association between different elements of this system.2 Current paradigms of immune crosstalk between cells or at a subcellular molecular level are based on direct contact or on transfer of mediators in both health and disease.3–5 These elements serve as links for relocating associations between constituents of the immune system. No evidence for correlations between components of the immune system that alter a constituent of this system without directly affecting one of its associated parts has been reported.\n\nThe aim of the study was to develop a system in which a correlation exits between two separate components of the immune system without either a direct interaction or a transfer of mediators.\n\n\nMethods\n\nA total of 24 Male C57BL/6 healthy mice (11–12 weeks old, 30 gr.) were obtained from Harlan Laboratories (Jerusalem, Israel) and maintained in the Animal Core of the Hadassah-Hebrew University Medical School. Mice were administered standard laboratory chow and water ad libitum and kept in a 12-hour light/dark cycle. Mice were administered standard laboratory chow and water ad libitum and kept in a 12-hour light/dark cycle. Animal experiments were carried out according to the guidelines of the Institutional Committee for Care and Use of Laboratory Animals and with the committee’s approval. All efforts were made to ameliorate any suffering of animals by using mild anesthesia.\n\nSix groups of mice (Table 1) were studied, with four mice per group in each of the four experiments. Number of animals was determined based on statistical analysis. Data on all mice in each of the studies is included in the Underlying data.21 Groups were selected based on the different parameters tested with the appropriate controls.\n\nThe mice in groups A and B underwent splenectomy followed by fasting. Each mouse was kept in a cage with a tube containing its own autogeneic (group A) or syngeneic (group B) lymphocytes on top. The mice in groups C and D underwent splenectomy but did not fast, and they were kept in cages with tubes containing autogeneic (group C) or syngeneic (group D) lymphocytes on top. The mice in groups E and F did not undergo splenectomy and were kept in cages with a tube containing syngeneic lymphocytes on top. The mice in group E fasted, while that in group F did not fast. Tubes marked G and H contained lymphocytes harvested from syngeneic donors and were kept on top of empty cages. Controls were used for each of the experiments based on the parameter tested. Studies were repeated in an outside laboratory for verification of the effect. Studies were conducted in accordance with the Arrive guidelines.\n\nThe described system enabled us to study two types of triggers for the associations between two constituents of the immune system. Mice underwent splenectomy using standard procedure6 or fasting (21-24 hours). Each mouse was kept in a separate cage for the duration of the experiment. Autogeneic or syngeneic splenocytes were prepared from splenectomized mice and kept for 24 hours in a tube on top of the cage at a distance of 10-20 cm from the mouse itself. Control cells were kept in a tube placed on top of the cages containing either non-splenectomized or non-fasting naïve mice or were kept on top of empty cages without a mouse. In splenectomized mice, we tested the effect of splenectomy alone or splenectomy combined with fasting on either autogeneic or syngeneic cells. In naïve, non-splenectomized mice, we tested the effect of fasting on syngeneic cells. The effects of these triggers on the associations between immune components were examined by determining the expression of surface markers and cytokine secretion by the out-of-body lymphocytes. The study was replicated three times and for each study four mice per group were analyzed (marked 11A, 11B, and 11C). For epitope parameters, the experiment was repeated for the fourth time by an independent control laboratory (marked OL) for several of the parameters. Cytokine study was performed once in the controlled laboratory.\n\nSplenocytes were isolated as described previously.7 Flow cytometry was performed on splenocytes resuspended in 1 mL of Flow Cytometry Staining (FACS) buffer. Cells were stained with diluted antibodies (50 μL/sample). Cells were examined using FACS at times 0 and 24 hours for the expressions of epitopes, CD3, CD4, CD8, CD25, FoxP3, and NK1.1, on the lymphocytes (antibodies by BD Biosciences). Flow cytometry was performed using an LSR-II flow cytometer (BD Biosciences, DeNovo software). The following subsets were analyzed: CD4, CD25, CD4 CD25, Foxp3, CD4 Foxp3, CD4 CD25 Foxp3, CD4 CD25 Foxp3, CD8, CD8 Foxp3, CD8 CD25, CD8 CD25 Foxp3, CD8 CD25 Foxp3, CD3, NK1.1, and CD3 NK1.1. Full data of the study can be accessed from the Underlying data21 section.\n\nOne set of mice marked OL (n = 4) was analyzed in the control laboratory for serum levels of IFNγ, TNFα, IL10, and TGFβ. Determination of IFNγ, TNFα, and IL10 in supernatants was performed concurrently, using Flow Cytomix (Thermo Fisher Scientific (eBioscience)). TGFβ levels were determined separately using ELISA Quantikine (MB100B) (R&D Systems). Cytokine levels were determined according to the manufacturer’s instructions.\n\nThe Mann-Whitney SPSS test (software version 1.0) was performed for each experiment. Data of all individual mice in all studies is provided in the Underlying data.21 Only parameters that showed significant changes in two experiments or more, including changes in opposing directions, were used for the final analysis.\n\n\nResults\n\nThe effect of fasting and/or splenectomy on promoting correlations between immune systems was studied by determining the alterations in expressions of cell membrane epitopes and in cytokine secretion by out-of-body autogeneic and syngeneic lymphocytes.\n\nThe effect of fasting as a trigger for altering the association that can modify epitope expression on out-of-body lymphocytes kept in tubes on top of cages was investigated in splenectomized mice. The effect on autogeneic cells was determined by comparing groups A (fasting) and C (non-fasting). Figure 1A shows the effect of fasting on autogeneic lymphocytes; decreased expression of CD8 and CD25 was found in the mice in group A compared with mice in group C in experiments 11B (p = 0.02) and 11C (p = 0.019). Fasting exerted a significant effect on the cytokine secretion by the out-of-body syngeneic lymphocytes in non-splenectomized mice. Figure 1B shows a significant increase in the TNFα levels (p = 0.047) when comparing group E (fasting) to group F (non-fasting, the TNFα levels were undetectable in-group F). The data suggested that correlations can be induced between components of the immune system after fasting in splenectomized and non-splenectomized mice targeting both out-of-body autogeneic and syngeneic lymphocytes. Fasting had no effect on the syngeneic lymphocytes kept in a tube on top of the cages of splenectomized mice, as indicated by comparing groups B (fasting) and D (non- fasting).\n\nThe effect of fasting as a trigger on splenectomized mice was determined by comparing the syngeneic lymphocytes kept in tubes on top of the cages of the mice in groups B (fasting) vs. D (non-fasting). The effect of fasting as a trigger for an association that may alter the epitope expression and/or cytokine secretion of out-of-body lymphocytes kept in tubes on top of cages was determined by comparing the syngeneic lymphocytes of the mice in groups E (fasting) vs. F (non-fasting); there was a significant effect on the TNFα secretion.\n\nThe effect of splenectomy as a trigger for altering the association that can modify epitope expression and/or cytokine secretion from out-of-body syngeneic lymphocytes kept in tubes on top of cages was investigated in non-fasting mice by comparing groups D (splenectomized) and F (non-splenectomized). Figure 2A shows a significant increase in the CD8 expression (between time points 0 and 24 h) in experiments 11A (p = 0.021) and OL (p = 0.021) in-group D compared with that in-group F; however, the changes in CD8 expression in experiment 11A were opposite to those in experiment OL. The secretion of three cytokines, TNFα (p = 0.014), IFNγ (p = 0.021), and IL10 (p = 0.013), significantly increased in group D compared with group F, as shown in Figure 2B.\n\nThe effect was significant for CD8 expression and for TNFα, IFNγ, and IL10 secretion. The effect was also determined by comparing the syngeneic lymphocytes that were kept in tubes on top of the cages containing fasting mice from groups B (splenectomized) vs. E (non-splenectomized). It was significant for the expressions of CD25 and CD4 CD25, and for TNFα, IFNγ, and IL10 secretion.\n\nThe effect of splenectomy as a trigger for modifying the epitope expression and/or cytokine secretion of out-of-body syngeneic lymphocytes was investigated in fasting mice by comparing groups B (splenectomized) and E (non-splenectomized). Figure 2C shows that splenectomy had a significant effect on several parameters, as indicated by comparing the two groups in experiments 11B and 11C; however, the effects in group B were opposite to the effects in group E. The expression of CD25 (p = 0.02 and p = 0.03 for 11B and 11C, respectively) and CD4 CD25 (p = 0.021 and p = 0.034, for 11B and 11C, respectively) differed significantly between groups B and E. The secretion of TNFα (p = 0.021), IFNγ (p = 0.02), and IL10 (p = 0.02) was significantly higher in group B compared with that in group E, as shown in Figure 2D. The results suggested that a link can be induced between components of the immune system after splenectomy in fasting and non-fasting mice in syngeneic lymphocytes. No significant differences were observed when assessing differences between the effects on out-of-body autogeneic vs. syngeneic cells; these differences were determined by performing a group A (autogeneic) vs. B (syngeneic) comparison of the lymphocytes harvested from the fasting-splenectomized mice and by performing a group C (autogeneic) vs. D (syngeneic) comparison of the non-fasting splenectomized mice. The results suggested that the associations made for autogeneic cells did not differ significantly from that made for syngeneic cells.\n\nTo determine the effect of keeping the cells in an out-of-body location on the expression of lymphocyte epitopes, tubes kept on top of the cages of the fasting mice from groups A, B, and E were compared with tubes kept on top of empty cages (G), as shown in Figure 3. A significant change in the CD8 expression was noted by comparing groups B and G in 11B (p = 0.034) and OL (p = 0.043), as shown in Figure 3A; however, the changes in group B were opposite to those in group G. No significant effect was observed when comparing groups A and G.\n\nThe effect was significant for CD8 expression when comparing groups B and G (3A); for the secretion of TNFα and IFNγ when comparing groups A and G (3B); for the secretion of TNFα, IFNγ, and IL10 when comparing groups B and G (3C); for the expression of Foxp3 when comparing groups F and H (3D); for TNFα, IFNγ, and TGFβ secretion when comparing groups C and H (3E, 3F); for IFNγ, TNFα, and IL10 secretion when comparing groups D and H (3G); and for TNFα secretion when comparing groups F and H (3H).\n\nTo determine the effect of keeping cells in an out-of-body location on cytokine secretion, tubes kept on top of cages were tested for cytokine levels. A significant decrease was noted for the secretion of TNFα (p = 0.021) and IFNγ (p = 0.028) between groups A and G, as shown in Figure 3B. Similarly, a significant decrease was noted between groups B and G for the secretion of TNFα (p = 0.021), IFNγ (p = 0.021), and IL10 (p = 0.018), as shown in Figure 3C. No significant difference was observed between groups E and G for the epitope expression or cytokine secretion.\n\nTo determine the effect of keeping cells in an out-of-body location on the expression of lymphocyte epitopes, tubes kept on top of cages containing the non-fasting mice from groups C, D, and F were compared with tubes kept on top of empty cages (H). The Foxp3 expression significantly increased between groups F and H in all three experiments, as shown in Figure 3D (for 11A, p = 0.083; for 11B, p = 0.081; and for 11C, p = 0.083; p = 0.006 for all three; this parameter was not tested in OL). No significant difference was observed when comparing groups C vs. H and groups D vs. H.\n\nTo determine the effect of keeping cells in an out-of-body location for cytokine secretion, tubes kept on top of cages were assessed for cytokine levels. A significant decrease in the secretion of IFNγ, TNFα, and TGFβ was observed when comparing groups C and H, as shown in Figure 3E (p = 0.020) and Figure 3F (p = 0.43). A significant decrease in the secretion of IFNγ, TNFα, and IL10 was observed between groups D and H, as shown in Figure 3G (p = 0.021). A significant increase in the TNFα secretion was observed between groups F and H, as shown in Figure 3H (p = 0.047). The data suggested that the presence of a fasting or non-fasting mouse in a cage affects its connections with syngeneic cells.\n\n\nDiscussion\n\nThe present study presents measurements of parameters over a set of mutually unbiased states, which demonstrated an ability to induce a correlation between components of the immune system through an indirect effect in an isolated system. The described experiment showed that a mouse could affect cells at a distance and alter the expression of surface markers and cytokine secretion following two types of triggers: fasting and/or splenectomy. In the described laboratory setting only the measured observables, which are the result of this effect, can be detected. The effects were compared for cells kept on top of cages containing mice that did not undergo a splenectomy and did not fast with cells kept on empty cages.\n\nIn biological systems, different levels of associated states may be present. These levels might depend on the degree of comparison and/or correlation between donors and recipients that act simultaneously on various components of the immune system.3–5 In the present schematic model, a correlation between two systems, a cell, or other component of the immune system, allows for the recovery of a new state of a lymphocyte or cytokine-secreting cell.\n\nThe lymphocyte expression of cell surface markers and cytokine secretion involved different pathways.7–10 The “classical” transportation of immune signals is based on messages delivered by molecules (e.g., chemokines) secreted by different subsets of cells that transmit a direct signal to a target cell or to a subcellular organelle (e.g., receptor) through physical contact or a messenger molecule. The present data demonstrated that in an isolated system, a correlation can be induced independent of a direct interaction. The observed effects cannot be explained by classical immunology, and are, therefore, suggestive of a correlation-dependent phenomenon in the described system.\n\nThe effect that underlines the outcome observed in the present study on autogeneic cells can be explained by an inherent association between two components of the immune system, suggesting an undefined historical correlation between the two parts of the system. At the same time, the effects observed on syngeneic cells may imply a wave-dependent phenomenon between foreign components of the immune system.\n\nThe fidelity obtained in the current schematic model shows excellent adherence of properties of correlations when targeting the expression of cell membrane epitopes and cytokine secretion of lymphocytes. The results from each mouse in the described system suggest an inherent pattern that repeats itself. Each attempt for separate mice is viewed independent of all others. The use of a standard trigger, fasting or splenectomy, enables our protocol to succeed without filtering of results, and the effects are fairly reliable. The experiments were repeated in an independent laboratory, further supporting the feasibility of setting up isolated conditions, under which these effects can be measured.\n\nThe lack of effects for all parameters in all experiments (see Underlying data21) and changes in opposing directions for some of the measured observables may result from the multiple confounding factors that act simultaneously, which are hard to control, or from the disordered nature of the immune pathways and networks. These are inherent to any biological system.11–14 Nonetheless, the out-of-body correlation was significant for several of the investigated parameters in repeated experiments. For some of the observables, the changes were small and could be claimed to be a result of intra-test variability. However, each mouse was tested in a separate cage, and can be viewed as independent of the other mice. Only parameters that significantly changed in two separate experiments were used for the final data analysis.\n\nThe results described in the present study may support the presence of built-in memory in an isolated system, which is mandatory for such correlations to occur. Although the memory in immune systems is based on the direct delivery of mediators or messenger molecules secreted by immune cells,15,16 a “wave type of memory” is required at both the transmitting and receiving sites for such a correlation to occur. This type of an immune memory may explain some of the observations in the present study.\n\nThe effects observed in the present study may occur at a cellular or subcellular level and may act in accordance with theories that apply some of the principals of quantum physics to biological systems.11,17–19 A model using a non-natural computer-brain interface to induce an out-of-body effect has been reported, which showed non-invasive information transfer between the brains of different species.20 A translation of the intention of a human volunteer to stimulate the rat brain motor area responsible for tail movement has also been demonstrated. The data suggested the feasibility of a computer-mediated brain–brain interface that can link the neural functions between two biological entities.\n\nThe system described here provides a robust model for biological applications of correlations in immunology and biology. The model demonstrated here could also be used as an elementary constituent of a wave-type repeater in other biological systems. The state implemented in this protocol is based on complex systems, which enables modifying the surface markers and cytokine secretion of lymphocytes. Even with a relatively low success probability, this system can be scaled to more complex biological systems.\n\nOptimal function of the immune system may require an alliance between classical and correlative immunology. The present data shed light on several, not fully understood, biological phenomena, including inter-immune cells interactions, brain–immune component connections, environmental impacts, genotype-phenotype interfaces, and organism-host interactions. By enabling diagnostic and therapeutic procedures to be performed on out-of-body autogeneic or syngeneic tissues or organisms, these concepts may be applicable to the development of improved methods for diagnosis and treatment of immune-associated disorders.\n\nStudy limitations include the use of the defined model and extrapolations to other biological systems may require further studies.\n\n\nData availability\n\nDryad: Correlations between components of the immune system, https://doi.org/10.5061/dryad.prr4xgxn3.21\n\nThis project contains the following underlying data:\n\n- LDB_EM_Supplementary_File_1.5.xls\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nPLoS Biol: ARRIVE checklist for ‘Correlations between components of the immune system’, https://doi.org/10.1371/journal.pbio.3000411.22",
"appendix": "References\n\nBrizhik L, Foletti A:Nonlinear quantum phenomena and biophysical aspects of complexity related to health and disease. J. Biol. Regul. Homeost. Agents. 2014; 28(3): 357–66. PubMed Abstract\n\nBoehm T, Bleul CC:The evolutionary history of lymphoid organs. Nat. Immunol. 2007; 8(2): 131–5. PubMed Abstract | Publisher Full Text\n\nSeijkens T, Kusters P, Chatzigeorgiou A, et al.:Immune cell crosstalk in obesity: a key role for costimulation? Diabetes. 2014; 63(12): 3982–91. PubMed Abstract | Publisher Full Text\n\nWalsh JT, Watson N, Kipnis J:T cells in the central nervous system: messengers of destruction or purveyors of protection? Immunology. 2014; 141(3): 340–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChu H, Mazmanian SK:Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat. Immunol. 2013; 14(7): 668–75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIlan Y, Maron R, Tukpah AM, et al.:Induction of regulatory T cells decreases adipose inflammation and alleviates insulin resistance in ob/ob mice. Proc. Natl. Acad. Sci. U. S. A. 2010; 107(21): 9765–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCampbell DJ, Ziegler SF:FOXP3 modifies the phenotypic and functional properties of regulatory T cells. Nat. Rev. Immunol. 2007; 7(4): 305–10. PubMed Abstract | Publisher Full Text\n\nFeuerer M, Hill JA, Mathis D, et al.:Foxp3+ regulatory T cells: differentiation, specification, subphenotypes. Nat. Immunol. 2009; 10(7): 689–95. PubMed Abstract | Publisher Full Text\n\nOhkura N, Sakaguchi S:Regulatory T cells: roles of T cell receptor for their development and function. Semin. Immunopathol. 32(2): 95–106. PubMed Abstract | Publisher Full Text\n\nGor DO, Rose NR, Greenspan NS:TH1-TH2: a procrustean paradigm. Nat. Immunol. 2003; 4(6): 503–5. PubMed Abstract | Publisher Full Text\n\nBuiatti M, Longo G:Randomness and multilevel interactions in biology. Theory Biosci. 2013; 132(3): 139–58. PubMed Abstract | Publisher Full Text\n\nIlan Y:Randomness in microtubule dynamics: an error that requires correction or an inherent plasticity required for normal cellular function? Cell Biol. Int. 2019; 43: 739–48. PubMed Abstract | Publisher Full Text\n\nIlan Y:Generating randomness: making the most out of disordering a false order into a real one. J. Transl. Med. 2019; 17(1): 49. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIlan Y:Microtubules: From understanding their dynamics to using them as potential therapeutic targets. J. Cell. Physiol. 2019; 234(6): 7923–37. PubMed Abstract | Publisher Full Text\n\nFarber DL:Biochemical signaling pathways for memory T cell recall. Semin. Immunol. 2009; 21(2): 84–91. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWoodland DL, Kohlmeier JE:Migration, maintenance and recall of memory T cells in peripheral tissues. Nat. Rev. Immunol. 2009; 9(3): 153–61. PubMed Abstract | Publisher Full Text\n\nPenrose R:Uncertainty in quantum mechanics: faith or fantasy? Philos Trans A Math Phys Eng Sci. 2011; 369(1956): 4864–90. PubMed Abstract | Publisher Full Text\n\nHameroff S, Penrose R:Consciousness in the universe: a review of the 'Orch OR' theory. Phys Life Rev. 2014; 11(1): 39–78. PubMed Abstract | Publisher Full Text\n\nCraddock TJ, Friesen D, Mane J, et al.:The feasibility of coherent energy transfer in microtubules. J. R. Soc. Inter. 2014; 11(100): 20140677.\n\nYoo SS, Kim H, Filandrianos E, et al.:Non-invasive brain-to-brain interface (BBI): establishing functional links between two brains. PLoS One. 2013; 8(4): e60410. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIlan Y: Correlations between components of the immune system, Dryad. Dataset. 2021. Publisher Full Text\n\nPercie du Sert N, Ahluwalia A, Alam S, et al.: Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0. PLOS Biol. 2020; 18(7): e3000411. Publisher Full Text"
}
|
[
{
"id": "144783",
"date": "02 Sep 2022",
"name": "Suprabhat Mukherjee",
"expertise": [
"Reviewer Expertise Immunology of Inflammatory and 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\nApproval/reference number of the meeting of the Institutional Animal Ethics Committee for the Mice related experiments is required.\n\nFigures need to be revised.\n\nNames of the cytokines should be formatted correctly.\n\nPlease perform ANOVA following a post-hoc test to test the difference amongst the cytokine level.\n\nImmunofluorescence data may be added to strengthen the data of FACS and ELISA.\nThese changes are necessary to improve 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? 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": "10236",
"date": "28 Sep 2023",
"name": "Yaron Ilan",
"role": "Author Response",
"response": "Approval details were added. All figures were replaced with a more explicit version. Corrected. The Mann-Whitney SPSS test (software version 1.0) was used for revised statistical analysis. These were not performed in the current study and are subject to future experiments."
}
]
},
{
"id": "197558",
"date": "11 Sep 2023",
"name": "Biswadeep Das",
"expertise": [
"Reviewer Expertise Biomedical genetics and diganostics"
],
"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 depicts the correlation of different components of the immune system in fasting and splenectomy scenarios. Though the topic is moderately interesting, and in context to metabolism and immune system cross-talk, the overall manuscript and the methods are inadequate to justify its claims.\nMajor issues:\nThe introduction is too small and does not involve the rationale behind selecting such a research work. Need to elaborate significantly.\n\nMethods are the major limitation: The selection of mice need to be well defined. Flow cytometry is very subtly written. The authors say that, \"The following subsets were analyzed: CD4, CD25, CD4 CD25, Foxp3, CD4 Foxp3, CD4 CD25 Foxp3, CD4 CD25 Foxp3, CD8, CD8 Foxp3, CD8 CD25, CD8 CD25 Foxp3, CD8 CD25 Foxp3, CD3, NK1.1, and CD3 NK1.1.\"\nHowever, this is just a random statement. How to classify the different immune cells without using a backbone flow cytometry, LCA? First major classification need to be done, followed by subset analysis. Where are the raw files of flow cytometry? What about autofluorescence and compensation? How did u confirm the expression of these markers using experimental and instrumental controls?\n\nWestern blot need to be done to confirm the existence of the markers in the given population. It is missing.\nResults:\nNo flow cytometry graph or quadrant analysis. Just a mere bar diagram does not prove the analysis. Western blot has to be shown for all the markers as confirmed by flow cytometer.\nIn view of these facts, I cant be more positive and have to opt for rejection, unless all these issues are addressed.\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?\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": "10237",
"date": "28 Sep 2023",
"name": "Yaron Ilan",
"role": "Author Response",
"response": "The Introduction section was revised as proposed for better clarity. The relevant references were inserted. A supplementary file is included with all the data of all experiments. The relevant section in the Methods was revised for better clarity. Western blots were not conducted in the present study and are subject to future studies. The data of all studies is included in the supplementary file. The graphs were not included as multiple analyses were conducted in these experiments."
}
]
}
] | 1
|
https://f1000research.com/articles/10-1174
|
https://f1000research.com/articles/11-1111/v1
|
28 Sep 22
|
{
"type": "Research Article",
"title": "Progression of chronic kidney disease in patients with hypertension or type 2 diabetes mellitus, can it be delayed?",
"authors": [
"Leena Sequira",
"Ravindra Prabhu A.",
"Shreemathi S Mayya",
"Shankar Prasad Nagaraju",
"Baby S Nayak",
"Ravindra Prabhu A.",
"Shreemathi S Mayya",
"Shankar Prasad Nagaraju",
"Baby S Nayak"
],
"abstract": "Background: In India, the number of patients with type II diabetes mellitus in 2006 was 40.9 million and is expected to increase by 2025 to 69.9 million. Annually 1,00,000 new patients get diagnosed with End-Stage Renal Disease and require maintenance dialysis. Diabetes Mellitus and hypertension were the usual triggers of Chronic Kidney Disease (CKD). A structured education program helps in the prevention of diabetes and hypertension related complications. Methods: This quasi-experimental study was conducted among 88 participants who had hypertension, diabetes mellitus, or both for five or more years with an objective to find the effect of a Disease Management Program on delaying progression of CKD in patients with hypertension or diabetes mellitus.\n\nThe baseline data were collected on demographic proforma, serum creatinine, blood pressure, and random blood sugar, and the patients were taught the management of hypertension and diabetes mellitus. In the fourth and the eighth month, blood pressure and blood sugar were reassessed. At one-year blood pressure, blood sugar, and serum creatinine were tested. Baseline and one-year follow-up blood pressure, blood sugar, and estimated Glomerular Filtration Rate were compared. Descriptive statistics and \"Wilcoxon signed-rank test\" were used to analyze the data.\n\nResults: In one year, the mean systolic blood pressure reduced by six mm of Hg and mean blood sugar by 24 mg/dl. The prevalence of CKD stage three and above (< 60 ml/min/m2) was nine (10.22%). The median decline in eGFR was 5 ml/min/m2 (Z= 5.925, P< 0.001). Conclusion: The Disease Management Program led to improvements in blood pressure and diabetes control and median progression of CKD was estimated at five ml/min/m2/year.",
"keywords": [
"Hypertension",
"Type 2 DM",
"Disease Management Program",
"estimated Glomerular Filtration Rate",
"Chronic Kidney Disease"
],
"content": "Introduction\n\nNon-Communicable Diseases (NCD) are the most remarkable cause of fatality in the world. The global predicted prevalence of diabetes among adults is 439 million by 2030 (Shaw, Sicree, & Zimmet, 2010). The estimated global prevalence of diabetes in 2019 is 9.3% expected to rise to 10.2% by 2030 (Saeedi et al., 2019). Stage 3 Chronic Kidney Disease (CKD) in people with diabetes is reported to be high (56%) in Cambodia (Thomas, van, Mehrotra, Robinson-Cohen, & LoGerfo, 2014). CKD was 10·8% in rural areas of China. Hypertension and diabetes were associated with CKD (Zhang et al., 2012). In the United States, 23.5% of individuals aged above 18 years, had CKD (McFarlane et al., 2011).\n\nThe studies conducted in India, on the prevalence of CKD especially among people with hypertension and type 2 DM. The occurrence of diabetes in adults has increased in India (Tandon et al., 2018). The prevalence of diabetes mellitus was 8.3%, with only 18% receiving treatment (Tripathy et al., 2017). Type 2 DM and hypertension were the usual triggers of CKD (Rajapurkar et al., 2012). Hyperglycemia is causing an increase of CKD cases in India. Programs are needed to reduce the risk factors of diabetes mellitus (Tripathy, 2018). CKD was found in 34.91% of the general population, aged above 18 years, from Varanasi, India (Rai, Jindal, Rai, Rai, & Rai, 2014). Screening programs are needed to identify CKD in a risk group (Ene-Iordache et al., 2016). The occurrence rate of stage 5 CKD was 151 per million population (Modi & Jha, 2006). Lack of knowledge about CKD was observed in people with diabetes (Fiseha & Tamir, 2020). Diabetes and hypertension were associated with low eGFR and proteinuria (Singh et al., 2009).\n\nScreening of high-risk populations for CKD helps in the initial detection of CKD (Bradshaw et al., 2019). It is observed that people are unaware of the complications of diabetes and hypertension. Educating the people is essential before they could land up with CKD (Hussain, Habib, & Najmi, 2019). The CKD was found to be 24.2% among people aged above 50 years in rural Pondicherry, India. The study suggests targeted screening of adults to prevent further progression of CKD (Kumar, Dongre, Muruganandham, Deshmukh, & Rajagovindan, 2019). A structured education program helps in the prevention of diabetes-related complications (Iqbal & Heller, 2018).\n\nThe National kidney foundation has defined five stages in CKD, and in the fifth stage, a patient needs dialysis or kidney replacement to live. GFR can be estimated by using the Chronic Kidney Disease – Epidemiology Collaboration (CKD - EPI) formula (Michels et al., 2010). Serum creatinine is widely used to measure the eGFR (Coresh et al., 2002). Detection of CKD at the beginning stages helps to slow down progress, which in turn reduces the financial load on individuals, families, and communities.\n\nStudies suggest that the prevalence of hypertension and diabetes is increasing in India and it is the main cause of CKD. There is a clear lack of knowledge about the risks associated with uncontrolled diabetes and hypertension. Most of the population are diagnosed with type 2 DM but are not rightly educated about the complications of negligence associated with it. So, this lack of knowledge has been identified as one of the major reasons for the progress of CKD. Hence the present study intends to look at this aspect and educate the population about the same and monitor their progress across one year period.\n\n\nMethods\n\nA quantitative approach with quasi-experimental, one group pretest- posttest design was used in this study. The aim of this study was to find the effect of a Disease Management Program (DMP) on delaying progression of CKD in patients with hypertension or type 2 diabetes mellitus.\n\nThe participants were the people diagnosed with hypertension and/or diabetes for five or more year's duration and treatment. People visiting rural health centers of Udupi District, Karnataka State, India, aged 30 years and above were the sampled population selected through enumerative sampling technique. Sample size calculated to reach statistical significance with a power of 0.8, a standard deviation of eight, decline in eGFR in one year of five, and significance level 0.05, the total sample required was 22 each in stages one, two, and three of CKD. Keeping a 5% nonresponse rate total sample estimated was 70. The Chronic Kidney Disease stage was known after the serum creatinine test and formula application; hence the total sample taken was 103. Out of 103, for one year, 15 participants failed to follow up and hence 88 samples were analyzed.\n\nThe data were collected using demographic proforma which includes, age, gender, height, weight, serum creatinine, blood pressure, RBS, hypertension, and diabetes mellitus status, and duration of illness. A calibrated weighing scale was used to measure the weight. New measuring tape, sphygmomanometer, and glucometer were used to assess the height, blood pressure, and blood sugar, respectively. The intervention, DMP, refers to educating the participants about the management of hypertension or diabetes mellitus on a one-to-one basis (explaining and giving leaflets) and follows up on every fourth month, till one year, with teaching reinforcement along with random blood sugar and blood pressure assessment, as well.\n\nDevelopment of the education module and leaflet about hypertension and diabetes mellitus was prepared by the researcher by reviewing the published and unpublished literature and validated by experts. The education module contains the meaning, causes and risk factors, signs and symptoms, diagnosis, and management. Management included nutrition, exercise, monitoring of blood sugar and blood pressure, pharmacologic therapy. An explanation about the disease is given in a simple, understandable way, and doubts raised by patients were cleared. Complications were explained to improve the compliance level. The importance of exercise, nutrition, and compliance with medication in controlling blood sugar and blood pressure were also explained.\n\nThe researcher filled the demographic proforma by collecting information from the participants and assessed height, weight, blood pressure, and Random Blood Sugar (RBS). Blood for serum creatinine was collected using serum vacutainer and assessed using the standard Jaffe method calibrated to Isotope Dilution Mass Spectrometry (IDMS). CKD-EPI formula was used to estimate GFR. Teaching was given about managing hypertension and diabetes mellitus, and a leaflet about the same was distributed during the baseline data collection. Fourth and eighth-month blood pressure and RBS were reassessed, and teaching was reinforced. At one-year blood pressure, RBS, and serum creatinine were tested.\n\nDemographic variables were age, gender, serum creatinine height, and weight. Teaching regarding management of Hypertension and Diabetes Mellitus is the independent variable. Blood pressure and RBS were the dependent variables that affect kidney function and eGFR is the key variable. Other variables are disease conditions (Diabetes Mellitus or Hypertension or both) and duration of illness.\n\nData were analyzed using SPSS. Continuous variables are summarized using mean or median whichever is applicable and categorical variables using proportions. Frequency and percentage were used to describe the participant characteristics. Blood pressure and RBS were the dependent variables that affect kidney function. Mean, standard deviation, and range were used to summarize blood pressure, RBS, and paired’t’ test to compare baseline and at one year follow up systolic blood pressure (SBP), diastolic blood pressure (DBP), and RBS. As per, kidney disease: Improving Global Outcomes (KDIGO) Guidelines CKD is classified into five stages. Stage 1 (GFR ≥ 90 ml/min), stage 2 (GFR = 60-89 ml/min), Stage 3 (GFR = 30-59 ml/min), Stage 4 (GFR = 15-29 ml/min), stage 5 (GFR < 15 ml/min). Cross table was used to explain the number of participants who improved, remained in the same stage of CKD, and progressed to a higher stage of CKD. “Wilcoxon signed-rank test” was used to find the effectiveness of DMP as data (eGFR) were not following normality. The difference between baseline and one-year follow-up GFR is done and categorized into ≤1 ml, 1-10 ml, and more than 10 ml.\n\nThe study protocol was approved by the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee. (IEC184/2011). The participant information sheet was given to the participants, and the study process was explained and informed written consent was obtained from the participants before data collection.\n\n\nResults\n\nDemographic characteristics of baseline and one-year follow-up are summarized in Table 1. About 87.5 % of them belong to the age group of 51 years, and above, 46.6% of them were hypertensive, and 35.2% of them had both hypertension and type 2 DM.\n\nTable 2 shows mean, standard deviation, range of blood pressure, and RBS at the four-month interval and results of paired t' test applied to compare baseline and at one year follow up systolic blood pressure (SBP), diastolic blood pressure (DBP) and RBS. At baseline, most (69.44%) of them had SBP of 141-220 mm of Hg, 29.78% of them had an RBS level of 201-400 mg/dl. Mean SBP reduced by 6 mm of Hg and mean RBS by 24 mg/dl at one year, follow-up. There was a significant reduction in blood pressure and RBS (p < 0.001) for one-year follow-up.\n\nTable 3 shows the baseline and one-year follow-up stages of CKD. At baseline, 47 participants had stage 2 CKD. Among them, four of them improved to stage 1, and 13 of them progressed to stage 3 CKD. At baseline, eight participants had CKD stage 3. Out of eight, two of them improved to stage 2, and one progressed to stage 4 CKD, and five remained in the same stage.\n\nTable 4 shows the effectiveness of the DMP. The pre and post-intervention eGFR data of participants was not following normality, hence median, median difference, and 'Z' value of pre and post-intervention eGFR were assessed. The median fall in GFR is 5 ml/min/m2/year and there is a significant difference in GFR change in one year follow up, which says the intervention is not effective. The intervention helped to delay renal function deterioration. Table 5 shows the progression of CKD for a one-year follow-up. About 36.4% of participants lost only less than 1ml of GFR for one year.\n\n\nDiscussion\n\nThe result of the present study shows that CKD stage 3 and higher amounts to 10.22% of the participants. There have been few large community-based studies looking at the prevalence of CKD among hypertensive and diabetic populations in India and other countries. A study done in India reported that among 6129 participants, 2578 are having hypertension and CKD is present in 23.5% of hypertensive patients (Farag et al., 2014). Another study done in China among 1039 patients diagnosed with type 2 DM aged over 30 years shows 32.8% of CKD stage 3-5 (Lu et al., 2008). Collectively the reflection indicates that Type 2 DM and hypertension are the important public health issues, and it is associated with kidney disease.\n\nThe present study shows, in a year, mean systolic blood pressure decreased by 6 mm of Hg. A few participants confided that they were skipping the medication as signs and symptoms of the disease were not evident, but due to DMP, they returned to regular medication. Studies done in other countries suggested that DMP and assessing blood pressure, blood sugar, and GFR helps to sensitize the patients about their disease condition and to seek nephrology references if needed. DMP leads to improved hypertension control and eGFR among participants with CKD stage four or five (Richards et al., 2008). A study done in India by kidney help to screen the entire population of one village and provide medication for hypertension and diabetes showed a decrease in the prevalence of CKD (Prabahar, Chandrasekaran, & Soundararajan, 2008). Another study done in Australia among patients with diabetes, CKD, and hypertension showed no significant improvement in the intervention group (n = 36) in terms of medication adherence and blood pressure control. However, there was a 6 mm Hg reduction in SBP (Williams, Manias, Walker, & Gorelik, 2012b). Another study showed no significant differences in drug adherence between the intervention and control groups (Williams, Manias, Liew, Gock, & Gorelik, 2012a). The study on the impact of eGFR reporting on referral rates shows that eGFR reporting was useful in reducing the late referral to nephrology services (Foote et al., 2014). Hence it is necessary to identify the early stages of CKD, educate them about the importance of disease management.\n\nThe present study reports that the rate of drop in eGFR in one year was 5 ml/minute/1.73 m2. At one year follow-up, 36.4% lost less than 1 ml, and 21.6% lost 1-10 ml of eGFR. However, there are no research studies done in India to compare the change in eGFR in one year. The fall in eGFR ranges from 2-20 ml/minute/1.73 m2/year (Snyder & Pendergraph, 2005). In a study done in the US among people with diabetes, the eGFR dropped at 2.8 ml/min/1.73 m2 per year (Hanratty et al., 2010). A study done among the Rural Diabetic Cambodian population shows, at a median of 433 days follow up, 32% of patients lost more than or equal to 5 ml/min/m2 of eGFR (Thomas, Pelt, Mehrotra, Robinson-Cohen, & LoGerfo, 2014). Further studies are required to find the rate of decline in GFR in normal individuals and individuals with comorbidities.\n\nGlomerular Filtration Rate was estimated and not measured. The control group was not used due to ethical reasons. Only patients with diabetes and hypertension aged 30 years and above, were studied.\n\n\nConclusion\n\nThe Disease Management Program led to improvements in blood pressure and diabetes control and median progression of CKD was estimated at 5 ml/min/m2/year. Regular assessment of eGFR of the risk group, sensitizes the patient about their renal function. Teaching about the management of hypertension and diabetes mellitus and checking blood pressure and RBS helps to know about their disease control and to take action to control blood pressure and blood sugar.\n\nPeople in the community are unaware of the seriousness of CKD. In the prevention and control of CKD, nurses can play an important role. In the outpatient department, nurses can educate the patients with hypertension and diabetes mellitus, and thus implement an effective DMP at the early stages of CKD. The nurse can work in the field with peripheral clinic workers for monitoring and evaluating each person by checking blood pressure and blood sugar and screening for CKD.\n\n\nData availability\n\nFigshare: Progression of chronic kidney disease in patients with hypertension or type 2 diabetes mellitus, can it be delayed? DOI: https://doi.org/10.6084/m9.figshare.20278266\n\nThe project contains the following underlying data:\n\n- Data file 1 (Sample size calculation)\n\n- Data file 2 (Education program handout)\n\n- Data file 3 (Raw Data)\n\nData are available under the terms of the Creative Commons Attribution 4.0 international licence (CC BY 4.0)",
"appendix": "Acknowledgement\n\nThe authors would like to express their sincere gratitude to all participants, who have cooperated in conducting this study.\n\n\nReferences\n\nBradshaw C, Kondal D, Montez-Rath ME, et al.: Early detection of chronic kidney disease in low-income and middle-income countries: development and validation of a point-of-care screening strategy for India. BMJ Glob. Health. 2019; 4(5): e001644. PubMed Abstract | Publisher Full Text\n\nCoresh J, Astor BC, McQuillan G, et al.: Calibration and random variation of the serum creatinine assay as critical elements of using equations to estimate glomerular filtration rate. Am. J. Kidney Dis. 2002; 39(5): 920–929. PubMed Abstract | Publisher Full Text\n\nEne-Iordache B, Perico N, Bikbov B, et al.: Chronic kidney disease and cardiovascular risk in six regions of the world (ISN-KDDC): a cross-sectional study. Lancet Glob. Health. 2016; 4(5): e307–e319. PubMed Abstract | Publisher Full Text\n\nFarag YM, Mittal BV, Keithi-Reddy SR, et al.: Burden and predictors of hypertension in India: results of SEEK (Screening and Early Evaluation of Kidney Disease) study. BMC Nephrol. 2014; 15(1): 42. PubMed Abstract | Publisher Full Text\n\nFiseha T, Tamir Z: Prevalence and awareness of chronic kidney disease among adult diabetic outpatients in Northeast Ethiopia. BMC Nephrol. 2020; 21(1): 1–7. Publisher Full Text\n\nFoote C, Clayton PA, Johnson DW, et al.: Impact of estimated GFR reporting on late referral rates and practice patterns for end-stage kidney disease patients: a multilevel logistic regression analysis using the Australia and New Zealand Dialysis and Transplant Registry (ANZDATA). Am. J. Kidney Dis. 2014; 64(3): 359–366. PubMed Abstract | Publisher Full Text\n\nHanratty R, Chonchol M, Miriam Dickinson L, et al.: Incident chronic kidney disease and the rate of kidney function decline in individuals with hypertension. Nephrol. Dial. Transplant. 2010; 25(3): 801–807. PubMed Abstract | Publisher Full Text\n\nHussain S, Habib A, Najmi AK: Limited knowledge of chronic kidney disease among type 2 diabetes mellitus patients in India. Int. J. Environ. Res. Public Health. 2019; 16(8): 1443. PubMed Abstract | Publisher Full Text\n\nIqbal A, Heller SR: The role of structured education in the management of hypoglycaemia. Diabetologia. 2018; 61(4): 751–760. PubMed Abstract | Publisher Full Text\n\nKumar P, Dongre A, Muruganandham R, et al.: Prevalence of chronic kidney disease and its determinants in Rural Pondicherry, India-A community based cross-sectional study. Open Urol. Nephrol. J. 2019; 12(1): 14–22. Publisher Full Text\n\nLu B, Song X, Dong X, et al.: High prevalence of chronic kidney disease in population-based patients diagnosed with type 2 diabetes in downtown Shanghai. J. Diabetes Complicat. 2008; 22(2): 96–103. PubMed Abstract | Publisher Full Text\n\nMcFarlane SI, McCullough PA, Sowers JR, et al.: Comparison of the CKD epidemiology collaboration (CKD-EPI) and modification of diet in renal disease (MDRD) study equations: prevalence of and risk factors for diabetes mellitus in CKD in the kidney early evaluation program (KEEP). Am. J. Kidney Dis. 2011; 57(3): S24–S31. PubMed Abstract | Publisher Full Text\n\nMichels WM, Grootendorst DC, Verduijn M, et al.: Performance of the Cockcroft-Gault, MDRD, and new CKD-EPI formulas in relation to GFR, age, and body size. Clin. J. Am. Soc. Nephrol. 2010; 5(6): 1003–1009. PubMed Abstract | Publisher Full Text\n\nModi GK, Jha V: The incidence of end-stage renal disease in India: a population-based study. Kidney Int. 2006; 70(12): 2131–2133. PubMed Abstract | Publisher Full Text\n\nPrabahar MR, Chandrasekaran V, Soundararajan P: Epidemic of chronic kidney disease in India-what can be done? Saudi J. Kidney Dis. Transpl. 2008; 19(5): 847–853. PubMed Abstract\n\nRai PK, Jindal PK, Rai P, et al.: Screening of chronic kidney disease (CKD) in general population on world kidney day on three consecutive years: A single day data. Int. J. Med. Public Health. 2014; 4(2): 167. Publisher Full Text\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(1): 10. PubMed Abstract | Publisher Full Text\n\nRichards N, Harris K, Whitfield M, et al.: Primary care-based disease management of chronic kidney disease (CKD), based on estimated glomerular filtration rate (eGFR) reporting, improves patient outcomes. Nephrol. Dial. Transplant. 2008; 23(2): 549–555. Publisher Full Text\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. Diabetes Res. Clin. Pract. 2019; 157: 107843. PubMed Abstract | Publisher Full Text\n\nShaw JE, Sicree RA, Zimmet PZ: Global estimates of the prevalence of diabetes for 2010 and 2030. Diabetes Res. Clin. Pract. 2010; 87(1): 4–14. PubMed Abstract | Publisher Full Text\n\nSingh NP, Ingle GK, Saini VK, et al.: Prevalence of low glomerular filtration rate, proteinuria and associated risk factors in North India using Cockcroft-Gault and Modification of Diet in Renal Disease equation: an observational, cross-sectional study. BMC Nephrol. 2009; 10(1): 1–13. Publisher Full Text\n\nSnyder S, Pendergraph B: Detection and Evaluation of Chronic Kidney Disease. Am. Fam. Physician. 2005; 72: 1723–1732. PubMed Abstract\n\nTandon N, Anjana RM, Mohan V, et al.: The increasing burden of diabetes and variations among the states of India: the Global Burden of Disease Study 1990–2016. Lancet Glob. Health. 2018; 6(12): e1352–e1362. PubMed Abstract | Publisher Full Text\n\nThomas B, van Pelt M , Mehrotra R, et al.: An estimation of the prevalence and progression of chronic kidney disease in a rural diabetic Cambodian population. PLoS One. 2014; 9(1): e86123. PubMed Abstract | Publisher Full Text\n\nTripathy JP, Thakur JS, Jeet G, et al.: Prevalence and risk factors of diabetes in a large community-based study in North India: results from a STEPS survey in Punjab, India. Diabetol. Metab. Syndr. 2017; 9(1): 8. PubMed Abstract | Publisher Full Text\n\nTripathy JP: Burden and risk factors of diabetes and hyperglycemia in India: findings from the Global Burden of Disease Study 2016. Diabetes Metab. Syndr. Obes.: Targets Therapy. 2018; 11: 381–387. PubMed Abstract | Publisher Full Text\n\nWilliams A, Manias E, Liew D, et al.: Working with CALD groups: testing the feasibility of an intervention to improve medication self-management in people with kidney disease, diabetes, and cardiovascular disease. Ren. Soc. Australas. J. 2012a; 8(2): 62–69.\n\nWilliams A, Manias E, Walker R, et al.: A multifactorial intervention to improve blood pressure control in co-existing diabetes and kidney disease: a feasibility randomized controlled trial. J. Adv. Nurs. 2012b; 68(11): 2515–2525. PubMed Abstract | Publisher Full Text\n\nZhang L, Wang F, Wang L, et al.: Prevalence of chronic kidney disease in China: a cross-sectional survey. Lancet. 2012; 379(9818): 815–822. Publisher Full Text"
}
|
[
{
"id": "153673",
"date": "27 Oct 2022",
"name": "Manohar Bairy",
"expertise": [
"Reviewer Expertise eGFR",
"CKD",
"Dialysis"
],
"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\nThanks for asking me to review.\nThis is an evaluation of an educational program implemented in a population with diabetes and hypertension with the objective to delay CKD progression.\n\nI have the following comments to make:\nCan the research question be more clearly elucidated? More specifically, was the study looking at whether the DMP impacted the eGFR change or whether the DMP impacted the BP and RBS? The assignment of BP and RBS as dependent variables suggests the latter was the study research hypothesis but the title suggests otherwise.\n\nThe abstract says that 100000 patients enter ESRD per year. Does this refer to the Indian population or the global population? In the second paragraph of the introduction, 'the occurrence rate of stage 5 CKD' is mentioned to be 151 per million population in India which amounts to around 200000 entering CKD5. Perhaps these statements could be coalesced and mentioned in the introduction for clarity.\n\nThe criteria used to diagnose CKD stages 2 and 1 could be clarified as nearly 90% of the participants were in this category. How were they diagnosed to have CKD as eGFR was above 60 - did they have evidence of structural damage (proteinuria, abnormal urine sediment, radiological abnormalities, hereditary diseases.)? As an example, an individual aged 40 with an eGFR of 100 does not have CKD stage 1 unless there is evidence of structural damage. Likewise, an individual with eGFR 78, aged 70 does not have CKD stage 2 unless there is evidence of structural damage. The eGFR is to be used merely for the staging of diagnosed CKD except when the eGFR is <60 when it is used for diagnosing CKD.\n\nA discussion of how using RBS by glucometer would compare with using HBA1C or FBS/PPBS as a measure of DM control would be relevant while discussing the strengths and limitations of the study as the RBS is the main dependent variable. Likewise, the method of BP measurement - number of attempts, device used, measured by whom, average of readings in a single sitting - is also worth discussing as the effect size was small (5mm hg of SBP, nil In DBP) and BP was the main dependent variable.\n\nI note that the eGFR was merely a key variable rather than the dependent variable. That diminishes the stated intent of the study.\n\nWould it be possible to include the eGFR at baseline and at the end of the study in Table 1 as it is not in the data collection sheet?\n\nIn the results section, in the paragraph headed 'Effectiveness of the DMP’ the author says: ‘The median fall in GFR is 5 ml/min/m2/year and there is a significant difference in GFR change in one year follow up, which says the intervention is not effective. The intervention helped to delay renal function deterioration.’ - this needs further clarification due to the contradictory nature of the two statements.\n\nIn the first paragraph of the Discussion section, it is worth commenting on whether the study sampling was considered representative of the population and hence comparable to the other studies referenced.\n\nIt appears there are missing values for BP – how they were dealt with could be mentioned.\n\nCould the fall in BP be attributed to starting antihypertensives during the course of the study or titration of dose as part of the standard of care rather than the DMP? The lack of a control group or historical data (BP, RBS, eGFR) for the same group of patients impacts the precision and validity of the study.\n\nIn the data collection sheet, the data collection time points mentioned are the 4th, 6th, and 12th month. Elsewhere, the 4th, 8th, and 12th month is mentioned.\n\nTable 3 suggests there was significant progression of CKD through the stages, for example, 15 individuals with stage 1 progressed to stage 2, and 13 progressed from stage 2 to stage 3 within the span of 1 year. eGFR data would help the reader visualise the continuous nature of the data.\n\nOverall, it is reasonable to conclude that a DMP program is feasible in a population with DM and hypertension attending rural health centres in India. Qualitative data on the impact of the education program would be useful in the absence of a control group or historical pre-test data.\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? No",
"responses": [
{
"c_id": "9391",
"date": "08 Mar 2023",
"name": "leena sequira",
"role": "Author Response",
"response": "Thank you for the detailed review. Please find the response for the comments. Title is modified - Effectiveness of a Disease Management Program (DMP) in controlling the progression of Chronic Kidney Disease among hypertensives and diabetics. Uncontrolled hypertension and diabetes were the main causes of CKD. Hence the researcher studied the people with hypertension and diabetes. The abstract was modified adding this sentence -The occurrence rate of stage 5 CKD was 151 per million population in India. Classification of CKD is done based on eGFR. Other diagnostic measures were not done. That is one of the limitations. For checking blood pressure calibrated sphygmomanometer with appropriate cuff size of 13.1 × 23.5 cm was used. Before blood pressure measurement was taken it was made sure that the samples has not consumed tea or coffee, smoked or exercised vigorously in the last 30 minutes. Blood pressure was measured in the sitting position on the upper arm with the arm supported, and sphygmomanometer at the level of the heart. The investigator checked blood pressure twice in one sitting and average of the two readings recorded. The researcher mainly focused on eGFR. Kidney function depends on Control of blood sugar and blood pressure also. eGFR is a dependent variable and Disease management program was the independent variable. Included in the data sheet. Statistically significant change in eGFR was observed. People with hypertension and diabetes, there will be more chances of decrease in eGFR. But intervention helped to delay the progression of GFR. The research design was not strong to prove this. Control group was not included, based on the experts suggestion. In the studies selected for the discussion , the study population was representative of the population. Blood pressure was checked for all patients and entered in data sheet only for patients with history of hypertension. Fall in BP could be due to the education and sensitization of the people about the complications of uncontrolled hypertension. Correction is done in the data sheet. Base line and at one year GFR included in the data sheet. Good suggestion."
}
]
}
] | 1
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https://f1000research.com/articles/11-1111
|
https://f1000research.com/articles/12-532/v1
|
23 May 23
|
{
"type": "Research Article",
"title": "Field study of parasitic contamination of fruits, vegetables and leafy greens in the Ecuadorian Andes",
"authors": [
"Luisa Carolina González-Ramírez",
"Pablo Djabayan-Djibeyan",
"José G. Prato",
"Cecilia Alejandra García Ríos",
"Julio César Carrero",
"María Trelis",
"Màrius Vicent Fuentes",
"Pablo Djabayan-Djibeyan",
"Cecilia Alejandra García Ríos",
"Julio César Carrero",
"María Trelis",
"Màrius Vicent Fuentes"
],
"abstract": "Background: Raw vegetables have been considered vehicles of enteroparasites. South American countries are among the most important exporters of fresh vegetables; Ecuador has tropical climates and soils rich in organic matter that allow it to harvest throughout the year for sale to different countries. The aim of the study was to assess the occurrence of the parasitic contamination of fruits, vegetables and leafy greens grown in an agricultural area of the Ecuadorian Andes. Methods: A field study, cross-sectional, snowball sampling was conducted on 1,416 samples (516 fruits, 488 vegetables, and 412 leafy greens). Each sample were washed with water, and the resulting solution after removing the vegetables, was subjected to 24-hour sedimentation. The concentrated sediment underwent microscopic analysis. Results: Parasites were detected in 63.4% of the samples, leafy greens were the most contaminated (76.9%) (P<0.0001), (vegetables 67.8% and fruit 48.4%), of these, cabbage (100%), onions (84%) and strawberries (60.2%) were the most contaminated. Protozoa were more frequent (49.6%) than helminths (15.5%) (P<0.0001). Blastocystis sp. (33.5%) was the highest, followed by Eimeria spp. (26.3%), Entamoeba spp. (10.3%), Giardia spp. (8.3%), Balantidium spp. (6.9%); Cryptosporidium spp. (6.6%), Cyclospora spp. (4.4%), Cystoisospora spp. (0.5%); Strongylida (15.5%) and Ascaris spp. (0.4%). Conclusion: The consumption of fruits, vegetables, and leafy greens from these crops is a possible source of infection to humans and animals in this area or in nonendemic areas where these products are marketed. This study establishes the need for strict hygienic measures in growing; this will be properly achieved by the treatment of the soil, manure and water used for cultivation.",
"keywords": [
"agricultural production",
"food",
"transmission",
"parasites",
"fruits",
"vegetables",
"leafy greens"
],
"content": "Introduction\n\nThe consumption of fruits and vegetables provides essential nutrients for a healthy diet; however, raw vegetables are among the main vehicles for enteroparasites (FAO/WHO, 2008; Punsawad et al., 2019; Al Nahhas & Aboualchamat, 2020), and contamination can occur at any stage of the food production and marketing chain (Trelis et al., 2022). Various studies have focused on cultivation and harvesting stages as a risk phase, due to inadequate farming hygiene, contact with soil contaminated with human and animal feces (by direct defecation on crops or their fertilization), and the use of contaminated water for irrigation, dilution of pesticides, or washing equipment (Pérez-Cordón et al., 2008; Efstratiou et al., 2017; Ercumen et al., 2017; Luz et al., 2017; Karshima, 2018; Trelis et al., 2022).\n\nAlthough parasites do not multiply in food, they can survive for months, and resistance to some chemical and physical inactivating agents aggravates the situation (Ramos et al., 2013), so parasites can infect individuals in areas far away from the production site (Dixon et al., 2013; Dixon, 2016; Caradonna et al., 2017; Machado-Moreira et al., 2019; Li et al., 2020).\n\nSouth American countries are among the most important exporters of fresh vegetables. Ecuador has a tropical climate and soils rich in organic matter that allow it to harvest fruits, vegetables, and grains throughout the year for sale to different countries. According to figures from the Agriculture and Livestock Ministry, during the period of 2014-2018, Ecuador raised more than $3,500 million by exporting 6,000,000 tons of fruits and vegetables, including 212 tons of bananas, 139 tons of baby bananas, 81 tons of pineapples, 74 tons of broccoli and 60 tons of mangoes (Ministerio de Agricultura y Ganadería Ecuador, 2020).\n\nImports of fresh produce from endemic countries have contributed to the spread of parasites to nonendemic countries; diarrhoea epidemics have been reported from the consumption of raspberries, tomatoes, peppers, onions, carrots and radishes (FAO/WHO, 2008; Dixon, 2016; Machado-Moreira et al., 2019; Li et al., 2020). The WHO highlights the importance of leafy greens (spinach, lettuce, cabbage, watercress, basil, mint, coriander and parsley) as vehicles for food-borne parasites (FAO/WHO, 2008), among which are Cyclospora cayetanensis, Cryptosporidium spp. and Giardia duodenalis, Toxoplasma gondii, Entamoeba histolytica, Blastocystis sp., Cystoisospora belli, Balantidium coli, Dientamoeba fragilis and geohelminths (Ramos et al., 2013; Gamble, 2015; Dixon, 2016; Caradonna et al., 2017; Karshima, 2018; Robertson, 2018; Trelis et al., 2022).\n\nIn Ecuador, there is a dramatic health situation that affects all rural Andean regions, especially those located at high altitudes, which are mostly inhabited by indigenous populations that have agriculture, livestock, and other animal husbandry as a means of subsistence (González-Ramírez et al., 2021, 2022). Moreover, it is important to note that farmers need to learn good agricultural practices since they may not have adequate training, confidence, or economic resources to maintain crops and animals with proper hygiene to guarantee food quality production.\n\nA review indicated that there are no studies carried out in other provinces of Ecuador; only one report evaluated the risk factors associated with parasite transmission and described a total of 70.6% contamination of fruits and vegetables grown in six rural communities in the parish of San Andres, Chimborazo province (González-Ramírez et al., 2022). Due to this alarming contamination figure, we proposed evaluating the parasitic contamination of all products (fruits, vegetables and leafy greens) grown in the capital of San Andres, an agricultural zone of the Ecuadorian Andes. The probable causes of produce contamination during the primary production phases are likely due to sanitary control during these stages of the production chain; these need to be analyzed to minimize the risk of infections, which will benefit exports with favourable consequences on the country’s economy.\n\n\nMethods\n\nThe study area was the community of San Andrés, Guano canton, Chimborazo province of Ecuador, located at 3,900 meters above sea level. The local temperature ranges between 5-18 °C, and rainfall varies between 500-1,000 mm/year. There are two rainy periods, February to May and October to November; the remaining months are transitional with moderate rains. Evapotranspiration affects the drought of the soil, which originates from volcanic ashes of variable textures, most of which are shallow silty loam, with a pH of 4.5 to 6.5. There are loamy soils in the areas with the highest agricultural production, but they are affected by chemical fertilizers. There are also sandy soils with low fertility because they do not retain moisture and nutrients; the latter and the action of steep slopes make them susceptible to erosive processes; consequently, crops and sowing grass are not abundant. However, agricultural activity is 34.5%, and cattle breeding activity is 50.4%; these two are the main means of financial income for the local population (PDOT San Andrés, 2015).\n\nGovernment records indicate that 47.9% of the rural population of Ecuador lives in poverty, with an average monthly family income of $84.05, and 27.5% living in extreme poverty, with an average income of $47.70. The province of Chimborazo has an illiteracy rate of 13.5%, and the community of San Andrés has an indigenous population of 36.9% (INEC, 2020). Hence, their training is based on habits and customs acquired from their ancestors, which may contribute to as a lack of basic hygiene and sanitary measures. The most remote communities have built septic tanks, and the communities closest to the capital have sewers; however, both drain wastewater into rivers and streams (PDOT San Andrés, 2015).\n\nA field study, cross-sectional, was carried out between May and December 2019 (1 month of rain/7 months of drought). The snowball sampling technique was applied, whereby a grower helped locate the nearest farm and so on. All types of products found were included in the sampling (1,416 samples in total); the inclusion criteria were that all agricultural products must come from San Andrés fields and those not cultivated in the community were excluded.\n\nThe total of 1,416 samples analyzed included 516 fruits of 8 types: Fragaria ananassa (strawberry), Rubus glaucus (blackberry), Physalis peruviana (uvilla), Prunus persica (peach), Citrus limon (lemon), Psidium guajava (guava), Ficus carica (fig), and Solanum lycopersicum (tomato); 488 vegetables of 9 types: Allium cepa var. rosum (red onions) and Allium cepa L (white onions), Solanum tuberosum (potato), Daucus carota (carrot), Raphanus sativus (radish), Beta vulgaris (beet), Capsicum annuum (sweet pepper), Capsicum frutescens (chili pepper), and Lupinus mutabilis (bean chochos) and 412 leafy greens of 8 types: Medicago sativa (alfalfa), Lactuca sativa (lettuce), Brassica oleracea (cabbage), Beta vulgaris (chard), Petroselinum crispum (parsley), Coriandrum sativum (cilantro), Apium graveolens (celery), and Nasturtium officinale (watercress).\n\nAll samples were obtained from the owners' fields and stored in hermetically sealed propylene bags. Each sample was labelled indicating the plant species name, origin, date, and time of collection. The samples were immediately transported in their containers with cooling gels to the Research Laboratory of the Faculty of Health Sciences, National University of Chimborazo, to be processed within one hour of collection.\n\nThe sampling was carried out with the appropriate permission of the Cantonal and Parochial Decentralized Autonomous Governments. All farmers collected samples of their own crops (as they always do), knowing that the study benefits the community, without compromising the health of the population with respect to bioethical principles.\n\nThe processing protocol for the parasitological analysis of all samples, previously described by Rivero de Rodríguez et al. (1998), was utilized. For the processing of the samples, 75 g of vegetables, fruits or green leaves were taken and added to 500 mL of previously filtered and boiled water. The contents were stirred with the help of a magnetic stirrer for 1 hour, the remains of the vegetable were removed and the solution was left to stand for 24 hours. Subsequently, the solution was decanted into a separatory funnel and the first fraction was collected in 15 mL tubes to be subjected to centrifugation for 5 min at 800 xg. Once the concentrate or sediment was separated, the supernatant was discarded and the precipitate was reconstituted in 400 μL of saline (0.85%). Each sample was observed under a light microscope (Nikon E200) using 10x and 40x objectives. In addition, iodized solution and the ocular micrometer were used when necessary, for stain parasitic structures or to measure the dimensions for their recognition. Additionally, a smear was made with one drop from the pellet and prepared for acid-fast staining (using a modified Zielh-Neelsen technique) for coccidia oocyst detection and identification after measurement, mainly Crytosporidium and Cyclospora, and subsequent microscopic assessment (100×) (García et al., 1983).\n\nThe database made in Microsoft Excel was exported to SPSS Statistic 26.0 software (IBM, New York, NY, USA). The difference in parasitic contamination between the various categories of plant products and the predominant parasite type in each plant species were compared using Pearson's chi-square test (χ2) and Fisher's exact test, when appropriate. A P value <0.05 was considered statistically significant.\n\n\nResults\n\nWhen analyzing the different crop products, a total of 898 (63.4%) were contaminated by parasites. A statistically significant difference between the overall contamination rates, the leafy greens (76.9%) were more contaminated than vegetables (67.8%) and fruits (48.4%) (P<0.0001). Also identified were 15 protozoa and 2 helminth nematodes, protozoa also had a higher prevalence (49.6%) than nematodes (15.5%) (P<0.0001). Blastocystis sp. was outstanding among protozoa (33.5%) (P<0.0001), followed by Eimeria spp. (26.3%), Entamoeba spp. (10.3%), Giardia spp. (8.3%) and Cryptosporidium spp. (6.6%). Between the nematodes, Strongylida were more frequent than Ascaris spp. (P<0.0001) (see Table 1).\n\nWhen comparing the percentages of contamination of fruits, vegetables and leafy greens by the different parasites, the statistical analysis determined that, in fruits, a higher prevalence of Blastocystis (37.4%) (P=0.0018), Cryptosporidium (7.6%) (P<0.0001), Cyclospora (6%) (P<0.0001) and Endolimax nana (6%) (P=0.0028) was found. Vegetables were mostly contaminated by helminths (24.2%) (P<0.0001), represented mainly Strongylida (23.6%) (P<0.0001). Finally, the leafy greens showed greater contamination by Eimeria (33.5%) (P=0.0002), Entamoeba spp. (16.7%) (P<0.0001), Balantidium (15.0%) (P<0.0001) and Giardia (12.6%) (P=0.0002), which comprised the highest contamination with protozoa (61.4%) (P<0.0001) and a total parasitic contamination of 76.9% (P<0.0001) (see Table 1).\n\nTable 2 summarizes the results obtained according to the type of fruit, the highest number of protozoa was found in strawberries (60.2%) (P<0.0001), with Blastocystis sp. (59.2%) (P<0.0001), E. nana (17.35%) (P<0.0001) and Cyclospora spp. (14.3%) (P=0.0011) in contrast to peaches, which were more often contaminated with helminths (30%) (P<0.0001).\n\nParasitic contamination in the different types of vegetables is detailed in Table 3, the highest was found in red (84%) and white (82.4%) onions, followed by chili pepper (78%) (P<0.0001). It is important to highlight the level of contamination detected in other vegetables that are eaten raw (carrot 66%, radish 72.1% and pepper 44%). In the analysis to contrast the total parasitic contamination between protozoa (47.1%) and helminths (24.2%), it was possible to verify a higher frequency of protozoa (P<0.0001).\n\nThe parasitic contamination in leafy greens was significantly different among types (Table 4); greater percentages of parasites were found in cabbage (100%), alfalfa (90.2%) and parsley (82.4%). It was possible to verify higher contamination of the cabbage with Eimeria (53.8%) (P<0.0001) and with Endolimax nana (13.5%) (P=0.0002), lettuce with Entamoeba spp. (36.2%) (P<0.0001), and parsley with Blastocystis (56.9%) (P=0.0071).\n\nComparative analysis of parasitic contamination rates detected between fruits and vegetables/leafy greens (Table 5) showed higher parasites percentages in vegetables/leafy greens, with significant differences in the total (72%) (P<0.0001), protozoa (53.7%) (P<0.0001) and helminths (20.9%) (P<0.0001). A higher prevalence of Eimeria (29%) (P=0.0027), Entamoeba spp. (13%) (P<0.0001), Giardia (10.2%) (P=0.0007), and Balantidium (10.2%) (P<0.0001) were found. In contrast, higher percentages of Blastocystis (37.4%) (P=0.0199) and Cyclospora (6%) (P=0.0313) were found in fruits.\n\nWhen parasitic contamination was compared between leafy greens (76.9%) and vegetables (67.8%), a statistically significant difference was found (P =0.0024) (see Table 6). This result was supported by the highest contamination of leafy greens with Blastocystis (35.9%) (P=0.0064), Eimeria (33.5%) (P=0.0063), Balantidium (15.1%) (P<0.0001), Entamoeba spp. (16.8%) (P=0.0021) and Giardia (12.6%) (P=0.0290). However, vegetables were found to be more contaminated by helminths than leafy greens (24.2%) (P=0.0082), determined by Strongylida (23.6%) (P=0.0150).\n\n\nDiscussion\n\nThe results of the present study prove that the fruits, vegetables and green leafy that are cultivated and harvested in the capital of San Andrés, the area with the highest agricultural production in the Ecuadorian Andes, present significant contamination with parasites. Multiparasitism in the samples analyzed reflects inadequate hygiene conditions during agricultural activities and the crops products thus obtained represent a possible vehicle for parasites when consumed without adequate sanitation. It is important to note that agricultural production is marketed locally, regionally, nationally, and internationally; therefore, the risk of contagion to individuals is extrapolated to non-endemic areas.\n\nDirect contamination with human and animal excrements is a potential source of contamination of anthroponotic and zoonotic parasites for vegetables, so their consumption constitutes an important risk factor associated with the transmission of infective forms. However, it is possible that free-living parasites (Strongylida), also contaminate these crop products, being considered an insignificant finding, in this population where our research group has detected parasite prevalence’s reaching 97.3% in humans (González-Ramírez et al., 2022) and 90.3% in animals (González-Ramírez et al., 2021).\n\nWhen contrasting the results of the present investigation carried out in the capital of San Andrés with those obtained in six different communities of the same parish, the total percentage of contamination is lower in agricultural products harvested in the capital (63.4%) compared to the other communities further away, located at higher altitudes and with a larger indigenous population (70.6%); likewise, fruits (48.4 versus 67.1%) and vegetables (67.8 versus 73.6%) (González-Ramírez et al., 2022). These differences may be present because the capital of San Andrés offers better environmental sanitation conditions and the farmers have a higher level of education and better access to the urban area.\n\nIn the present study, leafy greens were more contaminated (76.9%) than vegetables (67.8%) and fruits (48.4%), likely because these maintain contact with the soil and organic fertilizers from the beginning as seedlings until they are fully grown, and external leaves allow protection for internal plant parts in contact with contaminated soil. The greater parasitic contamination of leafy greens has been explained by the irregularities of their leaves and the roughness of their surface that allows the adhesion of infectious parasitic forms that persist in the environment (Vuong et al., 2007; Allende et al., 2017).\n\nVegetables were the second most contaminated products after leafy greens, which is explained by the greater contact they maintain with the soil. The rooted vegetables (tubercle) were found to be more parasitized by nematodes (24.3%), always being less than contamination by protozoa (47.1%), possibly because they grew under the ground. It is important to highlight that, onions, carrots and radishes are frequently consumed raw and can function as efficient vehicles for parasites.\n\nIn creeping fruits such as strawberries, a greater number of contaminating parasitic species was found, compared to those that grow on shrubs and trees, perhaps due to direct contact with irrigation water (Esteban et al., 2002; Daniels et al., 2016; González-Ramírez et al., 2020), organic fertilizer and the soil (Dixon, 2016; Rodríguez-Eugenio et al., 2019).\n\nIn addition, the roughness of its surface is a condition that can also influence in the contamination of blackberry and peaches (Resendiz-Nava et al., 2020). Although, these rough fruits do not come into contact with the soil, nor with irrigation water, the texture of their surface allows the adhesion of parasites dispersed by the wind, insects or the hands of farmers, as explained by Dixon (2016) and Machado-Moreira et al. (2019).\n\nAnimal faeces is a source of nutrients for the soil, fertilizing agro-systems at low cost (Daniels et al., 2016), but if this material does not receive prior treatment, it is highly polluting. Among the inappropriate agricultural practices detected in San Andrés, considered risk factors, the fertilization of crops with fresh excreta from parasitized animals, as well as the contamination derived from their displacement on the crops, dispersing viable parasitic infectious forms persist in the environment (Gutiérrez-Rodríguez and Adhikari, 2018; Julien-Javaux et al., 2019; Resendiz-Nava et al., 2020; González-Ramírez et al., 2021). Additionally, the contamination of soils with human fecal matter contained in septic tanks that overflow or leak is another important source of contamination (Daniels et al., 2016; González-Ramírez et al., 2022).\n\nOn the other hand, the irrigation of crops with water bodies conducted by channels or contained in artificial wells that receive runoff from rain should be considered a risk factor for parasitic dispersal, as has been verified by Machado-Moreira et al. (2019) and González-Ramírez et al. (2020). These artificial water resources carry a high risk to human health in relation to the spread and increased transmission of parasites as shown by Esteban et al., (2002). Our results question the rationality of irrigation projects through open channels that carry contaminated water and artificial wells from which the animals drink. Furthermore, this water is used for the dilution of fertilizers and fungicides, machinery and the washing of work equipment and utensils that increase the possibility of contamination of vegetables (Dixon, 2016; Machado-Moreira et al., 2019; Trelis et al., 2022).\n\nIn addition, aspects of the field that promote the dissemination of parasitic forms found in the soil include flooding, rain, and sprinkler irrigation that allow the transport of microorganisms from the soil to the plants, as confirmed by Efstratiou et al. (2017), or when water drops splash as explained by Dixon (2016).\n\nLikewise, the wind brings dust particles from the ground that aid adherence of parasitic forms to the vegetables or fruits of trees or shrubs (Dixon, 2016; Machado-Moreira et al., 2019), which explains the finding of Strongylida on the woolly surface of peaches. Additionally, insects, rodents, wild animals and the contaminated hands of farmers can spread parasites, as indicated by Dixon (2016), Machado-Moreira et al. (2019) and González-Ramírez et al. (2021).\n\nMoreover, various actions carried out by farmers can contaminate crop products, including handling of vegetables without hygienic measures by the personnel in charge of sowing and harvesting, as has been verified in various localities (Dixon, 2016; Machado-Moreira et al., 2019; Li et al., 2020). However, the transfer, storage, washing, packaging, distribution, and marketing activities that are carried out after harvest also contribute to food contamination (Etewa et al., 2017; Trelis et al., 2022).\n\nAfter becoming aware of the parasitic contamination of food grown in the area, consumers from any part of the world should be warned that they must properly sanitize fruits, vegetables and leafy greens before consuming them, especially those that are eaten raw, if its origin is unknown. Just as this alarming contamination has been detected in this agricultural area, it is likely that it also occurs in other rural areas, mainly in low-income countries where producers do not apply hygienic measures during their agricultural practices, as previously was demonstrated by Pérez-Cordón (2008) in the Andean zone of Peru.\n\nThe potential effects of primary production activities on food safety need to be considered. These include identifying any specific points where the probability of contamination may exist and taking specific measures to minimize them. Growers are required to implement measures to prevent contamination of air, soil, water, feed, fertilizers, pesticides, or any other agent used in production and to control animal health so that it does not pose threats. If programs are implemented and executed to guarantee sanitary control in the farms and the objectives of food security are achieved in primary production, exports would increase, translating to an increase in the economic income of the producing countries.\n\nThe considerable parasitic contamination in vegetables obtained in the field immediately after harvest in this zone might be one of the causes of the high parasitic prevalence in humans (98.2%), mechanical vectors (52.7%) (González-Ramírez et al., 2022), and animals (90.3%) (González-Ramírez et al., 2021), as well as the 100% contamination of man-made water resources (channels and wells) of these rural communities (González-Ramírez et al., 2020).\n\nThese results suggest the need to integrate protozoa and helminths into the list of contaminants that are handled in the microbiological criteria required by the Ecuadorian Technical Standard (INEN, 2016). Monitoring only Escherichia coli in vegetables and fruits is not a good indicator of the absence of faecal contamination, nor does it guarantee food safety. Protozoa, whose high resistance to temperatures and disinfectants (Ramos et al., 2013) and low infectious doses have been demonstrated constitute a significant risk for consumers.\n\nPolicy decisions should promote the development of mitigation plans that involve health and hygiene education programs for producers and consumers. In addition, more advanced technological procedures and treatments that contribute to contamination prevention, as well as the inactivation and elimination of infectious forms in contaminated fresh produce to improve the quality and safety of these foods in accordance with the standards of Caradonna et al. (2017), should be promoted.\n\nThe sedimentation technique, Ziehl Neelsen staining, and measurement with the ocular micrometer performed for parasitic detection in the present study allowed us to carry out a low-cost analysis, as long as, microscopic visualization is done by trained analysts, fresh plant products can be monitored in other endemics areas of developing countries, where biological analysis cannot be performed by molecular techniques because of its high cost. We are aware of the importance of determining the parasitic species by molecular methods for epidemiological control. However, for surveillance studies on the contamination of these products in poor countries, microscopic diagnosis (though insufficient) is relevant because it is the only thing available; these results provide the basis for food safety guidelines to reduce the risk of contamination and minimize the transmission of food-borne parasitic diseases.\n\nThe samples of vegetables and fruits were analyzed by light microscopy alone because of limited resources to perform molecular analysis and the difficulty in obtaining permission to transport the samples to a molecular laboratory, but the overall prevalence detected in this study was one of the highest described thus far. In this Andean region of Ecuador, the global contamination of agricultural products by parasites has a mean prevalence of 63.4 and 70.6% (González-Ramírez et al., 2022), which are higher than those described in Phnom Penh, Cambodia 56.0% (Vuong et al., 2007), Alexandria, Egypt 31.7% (El Said Said, 2012), Koforidua, Ghana 57.5% (Kudah et al., 2018), Arba Minch, Ethiopia 54.4% (Bekele et al., 2017), Nakhon Si Thammarat, Thailand 35.1% (Punsawad et al., 2019), and Damascus, Syria 34.4% (Al Nahhas and Aboualchamat, 2020).\n\nNevertheless, our results are similar to those found in Trujillo, Peru, where Pérez-Cordón et al. (2008) reported the presence of Giardia, Cyclospora, E. nana, Iodamoeba buetschlii, Blastocystis and Ascaris lumbricoides. Moreover, the prevalence values are similar to those reported in Mina Gerais, Brazil, by Luz et al. (2017), with 50.9% of vegetables contaminated, with a predominance of nematode larvae (36.5%), Entamoeba coli (26.0%) and eggs of hookworms/Strongyloides spp. (12.9%).\n\nOur results also differ from those obtained by Honório Santos et al. (2019) in Bahia, Brazil, with prevalence’s of 70% in fruits: guava (90%), lemon and apple (70%) and grape (50%). The highest prevalence in this study was of the helminths A. lumbricoides, Ancylostomids, Taenia spp., and Enterobius vermicularis, followed by the protozoa Balantidium coli and Entamoeba coli. These differences might be due to the high altitude of San Andrés, where the evolution of soil-transmitted helminths is limited.\n\nInterestingly, in San Andrés, there were significant differences between contamination in leafy green types, which is consistent with the results of other studies that indicate that the highest-contaminated vegetable is lettuce, reaching rates of 29.5% in Damascus (Al Nahhas and Aboualchamat, 2020), 54.2% in Ghana (Kudah et al., 2018), and 61.1% in Mina Gerais, Brazil (Luz et al., 2017).\n\nFood-borne transmission of protozoan parasites is an emerging issue in developed countries around the world. Giardia, Cryptosporidium and Cyclospora have been implicated in both human and animal illness: unpasteurized apple juice, unwashed onions, salad, mixed baby lettuce, basil, sandwiches, fruit salad and raspberries (Dixon, 2016). Rzezutka et al. (2010), in Lublin, Poland, detected Cryptosporidium sp. in 4.7% of fresh vegetables; in packaged salads, Italy revealed 4.2% contamination of the samples, and the prevalence of each species was for G. duodenalis 0.6%, T. gondii 0.8%, Cryptosporidium spp. 0.9%, C. cayetanensis 1.3%, B. hominis 0.5% and D. fragilis 0.2% (Caradonna et al., 2017). In contrast, Trelis et al. (2022) were able to prove higher contamination with G. duodenalis 23.3% and Cryptosporidium spp. 7.8% in green leafy vegetables marketed in the city of Valencia, Spain.\n\nInformation collected at each sampling point checked to field cultivation as the critical step for contamination (Luz et al., 2017). The high parasitic frequency is associated with the inadequate handling of crop products, as well as, to the inefficient sanitary conditions of the places where they are marketed. It is recommended to teach hygienic measures through sanitary education for farmers, merchants, and consumers (Honório Santos et al., 2019).\n\nIn these tropical countries, the highest records of parasitic contamination are in vegetables, so they are described as endemic for enteric parasites. From there, they are spread to other countries through fresh vegetables. Developing countries have not been able to control their enteric-parasitosis because of the low socioeconomic and hygienic-sanitary levels, inability to offer adequate sanitary infrastructures and the education that could change of habits in people and prevent soil, water, and food contamination.\n\nThe implementation of control measures in fresh produce preharvest and postharvest, as well as an adequate sanitary hygienic level of the producer, handler, and consumer, will be crucial to minimize the food transmission of protozoa and helminths. To control parasites at the time of cultivation and harvest, irrigation with properly treated water, monitoring the health and hygiene of agricultural workers, improving agricultural sanitation, and restricting access of livestock and other animals to crops and surface water bodies (building adequate drinking troughs) are needed. Additionally, proper construction and maintenance of septic tanks is important to prevent contamination by overflow.\n\nUnsafe agricultural practices, such as irrigation with untreated contaminated water and fertilization of the soil with improperly treated animal manure, are used very commonly by small farmers; mainly in developing countries, due to the export of agricultural products. To mitigate this problem, it is necessary to use treated water for irrigation, washing fresh produce, washing hands and equipment. Good hygienic practices by farm workers involved in the cultivation, harvesting and handling of fresh produce are another important means of reducing the likelihood of contamination at the farm level in endemic regions.\n\n\nConclusion\n\nThis research demonstrated the important parasitic contamination of fruits, vegetables, and leafy greens. Warns about the risk of consuming raw products from these crops, without proper hygiene can be infection source of enteroparasites to humans and animals in this area or in nonendemic areas where these products are marketed. This study establishes the need for strict hygienic measures in growing and harvest areas, which can be achieved by the treatment of soil, manure, and water used for the cultivation of vegetables and fruits, as well as proper disinfection before consumption.",
"appendix": "Data availability\n\nFigshare: Parasitic contamination of fruits, vegetables and leafy greens harvested in an Andean agricultural area, https://doi.org/10.6084/m9.figshare.22313335.v2 (González-Ramírez et al., 2023).\n\nThis project contains the following underlying data:\n\n• Data parasites fruits vegetables Ecuador.xlsx\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 give thanks to Universidad Nacional de Chimborazo by the for approval the Project (Diagnóstico de factores de riesgo asociados a enteroparasitosis, en población de 4 a 99 años, procedentes de la parroquia San Andrés, Guano, Chimborazo-Ecuador, periodo 2021-2023). 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}
|
[
{
"id": "221529",
"date": "19 Dec 2023",
"name": "Samar Al Nahhas",
"expertise": [
"Reviewer Expertise Parasitology",
"Protozoa",
"molecular diagnosis",
"infectious 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\nThis study addresses an important knowledge gap regarding the prevalence of enteric parasites on fruits, vegetables and leafy green in an agricultural area of the Ecuadorian Andes. The study also indicated the necessity of dealing with these materials, which are responsible for infection in humans and animals, by treating the soil as well as the water used in irrigation.\n\nI have previously reviewed this manuscript and gave my decision to accept 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": []
},
{
"id": "228642",
"date": "24 Jan 2024",
"name": "Papa Kofi Amissah-Reynolds",
"expertise": [
"Reviewer Expertise Zoology",
"Parasitology",
"Zoonosis",
"One-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\nGenerally, the manuscript is very good and relevant. However, the authors should consider the following:\nThe discussion can be revised as some aspects lack clarity and are difficult to read and/or understand. The conclusion seems not to address the aim of the study. Comment on the occurrence of parasites in the conclusion. Apart from using tables, can the authors consider other ways of presenting the results?\n\nFrom the discussion: Paragraph 3 (When constrasting ...) How does access to the urban area influence parasitic contamination?\nParagraph 8 (Animal faeces ...) Consider revising this paragraph. It is not easy to understand some aspects of this paragraph.\nParagraph 21 (Our results ...) How does altitude influence the evolution of soil-transmitted helminths? Can you provide a reference for this?\nParagraph 23 (Food-borne ...) Link the results from the developed countries you have stated to your work and explain any differences there may be.\nParagraph 24 (Information collected ...) What were the inadequate handling practices and insanitary conditions at the market? This article (Duedu et al., 20141) could be useful.\nParagraph 25 (In these tropical ...) Which tropical countries are you making reference to?\nParagraphs 26 & 27 There are no references in these paragraphs. This article could be relevant to your work (Amissah-Reynolds et al., 20202)\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? Partly",
"responses": [
{
"c_id": "11145",
"date": "13 Apr 2024",
"name": "LUISA CAROLINA GONZALEZ",
"role": "Author Response",
"response": "Revisor 2 We thank the reviewer for the importance has given to our research, the time spent correcting the manuscript, their knowledge, experience, and willingness to improve the article. Generally, the manuscript is very good and relevant. However, the authors should consider the following: Comment 1: 1. The discussion can be revised as some aspects lack clarity and are difficult to read and/or understand. Response 1: The discussion has been revised, incorporating straightforward language and addressing all the reviewer's recommendations. Comment 2: The conclusion seems not to address the aim of the study. Comment on the occurrence of parasites in the conclusion. Response 2: A comment regarding the occurrence of parasites in the samples examined has now been included in the conclusion section, as follows: This study uncovers significant parasitic contamination in fruits (48.4%), vegetables (67.8%), and leafy greens (76.9%), from San Andrés a principal agricultural hub in the Ecuadorian Andes, attributed to poor hygiene practices in agriculture. The detection of multiple enteric parasites in these foods highlight the potential risk of transmitting infections if consumed without adequate sanitation. The local, national and international distribution of these foods, amplifies the risk of disseminating parasites to non-endemic regions, thereby increasing the likelihood of disease outbreaks as it was shown in studies on leafy greens and berries (Tefera et al., 2018; Marques et al., 2020; Barlaam et al., 2021, 2022; Faria et al., 2023). When comparing the results of vegetable contamination from the San Andres capital, with an overall prevalence of 63.4%, (fruits 48.4% and vegetables 67.8%), was lower than the detected in provinces located at high altitudes and more indigenous populated with overall prevalence of 70.6% (fruits 67.1% and vegetables 73.6%) (González-Ramírez et al., 2022), this could be explained to the access of better methods of sanitation, cleaner restrooms with proper septic tanks and overall more preventive education and information on food handling (González et al., 2022). Comment 3: Apart from using tables, can the authors consider other ways of presenting the results? Response 3: We value the recommendation to enhance the article's dynamism. While we acknowledge the appeal of diversifying presentation, we have opted for tables due to their capacity to encapsulate detailed information on parasitic contamination, which may not be effectively conveyed through figures alone. Comment 4: From the discussion: Paragraph 3 (When constrasting ...) How does access to the urban area influence parasitic contamination? Response 4: Urban area used to have access to better methods of sanitation, cleaner restrooms with proper septic tanks, drinking water, and overall more preventive education and information on food handling than rural areas. This could explain why central town of San Andres showed lower percent of parasitic contamination in their vegetable products when compared to the contamination rate determined in products from rural provinces located at high altitudes (63.4% vs 70.6%) (González-Ramírez et al., 2022). Comment 5: Paragraph 8 (Animal faeces ...) Consider revising this paragraph. It is not easy to understand some aspects of this paragraph. Response 5: The paragraph was revised as suggested and now it can be read as follows: Animal feces are a nutrient-rich fertilizer for agricultural systems and offer a low-cost solution (Daniel et al., 2016). However, without prior treatment (composting, storage, chemical treatment, drying, fermentation), it is a vehicle for microorganisms (Amissah-Reynolds et al., 2020). This risk factor was identified in the agricultural practice of San Andrés. (González-Ramírez et al., 2021), suboptimal crop management practices, including open defecation near crops without handwashing by farmers due to a lack of portable toilets, irrigation of crops with contaminated water and persistent unsatisfactory sanitary conditions in the areas where they sell their products (González-Ramírez et al., 2021, 2022). Comment 6: Paragraph 21 (Our results ...) How does altitude influence the evolution of soil-transmitted helminths? Can you provide a reference for this? Response 6: Our results differ from those obtained in Brazil (Honório Santos et al., 2019), with prevalence of 70% in fruits: guava (90%), lemon and apple (70%) and grape (50%). The highest prevalence in this study was of the helminths A. lumbricoides, Ancylostomids, Taenia spp., and E. vermicularis, followed by B. coli and E. coli. These differences might be due to the high altitude of San Andrés (3,020–6,310 m above sea) could affect the evolution of soil-transmitted helminths due to the extreme environmental conditions such as low temperatures (0–19 ºC), intense solar radiation and low rainfall (250 and 500 mm/year). In addition, these conditions affect the soil composition which is constituted by very thin layers of lithic materials of volcanic origin (González-Ramírez et al., 2022). Effect of altitude on helminths has been reported elsewhere (Chammartin et al., 2013) Comment 7: Paragraph 23 (Food-borne ...) Link the results from the developed countries you have stated to your work and explain any differences there may be. Response 7: When comparing findings from agricultural products from industrialized nations with our study in Ecuador, we obtained a higher prevalence and diversity of human and veterinary parasitic species. For example, in Italy (Barlaam et al. 2021, 2022), Spain (Trelis et al., 2022); Portugal (Marques et al., 2020), Norway (Temesgen et al., 2022) and Sweden (Ahlinder et al., 2022), coccidia were mainly identified. Notably, species prioritized in Europe such as Echinococcus, T. gondii, Toxocara, and Fasciola were not detected in our research (Bouwknegt et al., 2018). However, European studies used to be done on fruits and vegetables from supermarkets, which are pre-washed or disinfected prior to sale, in contrast to our agricultural products directly obtained from farmers' fields. This is a factor that likely influences the observed prevalence rates. Comment 8: Paragraph 24 (Information collected ...) What were the inadequate handling practices and insanitary conditions at the market? Response 8: The clarification has been made. suboptimal crop management practices, including open defecation near crops without handwashing by farmers due to a lack of portable toilets, irrigation of crops with contaminated water and persistent unsatisfactory sanitary conditions in the areas where they sell their products (González-Ramírez et al., 2021, 2022). Comment 9: Paragraph 25 (In these tropical ...) Which tropical countries are you making reference to? Response 9: In Latin America there are the highest records of contamination in vegetables (Cazorla-Perfetti et al., 2013; Rodríguez et al., 2015; Polo et al., 2016; Luz et al., 2017; Benites Salcedo et al., 2019; Bracho et al., 2022; González-Ramírez et al., 2022; Lucas et al., 2023; Falcone et al., 2023), being countries endemic for parasites, from there they spread to other countries nonendemic, through fresh vegetables. Developing countries have not been able to control their parasites due to low socioeconomic and hygienic levels, and the inability to offer adequate health and education infrastructure that can change people's habits and prevent environmental pollution. Comment 10: Paragraphs 26 & 27 There are no references in these paragraphs. This article could be relevant to your work (Amissah-Reynolds et al., 2020) Response 10: It has been included. Animal feces are a nutrient-rich fertilizer for agricultural systems and offer a low-cost solution (Daniel et al., 2016). However, without prior treatment (composting, storage, chemical treatment, drying, fermentation), it is a vehicle for microorganisms (Amissah-Reynolds et al., 2020). This risk factor was identified in the agricultural practice of San Andrés. (González-Ramírez et al., 2021), suboptimal crop management practices, including open defecation near crops without handwashing by farmers due to a lack of portable toilets, irrigation of crops with contaminated water and persistent unsatisfactory sanitary conditions in the areas where they sell their products (González-Ramírez et al., 2021, 2022). The place sampling was identified as critical nodes for contamination (Lucas et al., 2023), this is linked to suboptimal crop management practices, including open defecation, the absence of handwashing due to a lack of portable toilets in the fields; and the use of fresh animal excrement as fertilizer (Amissah-Reynolds et al., 2020). Farmers neglect to sanitize work tools like shovels, picks, rakes, and wheelbarrows, facilitating the transfer of parasites between different crops. Furthermore, unsatisfactory sanitary conditions persist in the areas where they sell their products (González-Ramírez et al., 2022)."
}
]
},
{
"id": "228648",
"date": "24 Jan 2024",
"name": "Alessandra Barlaam",
"expertise": [
"Reviewer Expertise Parasitology",
"parasitic diseases",
"zoonoses",
"foodborne parasites",
"food safety"
],
"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 aim of the study was to assess the occurrence of the parasitic contamination of fruits, vegetables and leafy greens grown in Ecuador, one of the most important exporters of fresh vegetables. In total 63.4% of the samples were found positive for a variety of parasites which highlights the need to improve and look into the management of the products from farm to fork.\nAbstract: In the Abstract, Methods: “Each sample were washed” should be replaced with “Each sample was washed”. Abstract, Results: The English language should be revised as the paragraph is not as clear as it should be. In addition, some repetitions occur (the most contaminated) and the use of , and ; is confusing. Abstract, Conclusion: Delete “From these crops” given that it is a general concept regardless of the obtained results.\nIntroduction: Given the variety of fresh produce included in the study and the number of parasites detected, the introduction is too concise and should be enriched. In addition, the importance of leafy greens as vehicles of foodborne parasites is emphasized whereas the role vegetables and fruits, including berries (also analyzed in this study and for which relevant and recent publications are available) is completely overlooked.\nWhen discussing import of fresh produce from endemic countries and the spread of parasites to nonendemic ones the authors fail to include relevant and recent bibliography on the subject. There are, in fact, recent studies that show how fresh produce imported from countries endemic for certain parasites have been found contaminated in the importing country. These articles have been completely overlooked and should be included. I recommend:\nBarlaam et al. (20211); Temesgen et al. (20222); Barlaam et al. (20223).\n\nMethods: The data are quite old (the samples were collected four years ago) and so is the methodology used for processing the fresh produce. The detection is also not quite in step with the times. Specifically, in the present study, the occurrence of parasites in fresh produce was investigated by microscopy although it is not clear how the genera and species were verified. Nowadays, with molecular tools available it would be auspicable to use them not only to verify the microscopy results but also to gather more information on the detected parasites (pathogenicity, zoonotic relevance etc.). I would like to ask the authors whether the samples were not tested molecularly because of lack of equipment/resources or for different reasons.\nTables: In all the tables there is a line that refers to “Protozoa”. I don’t understand why given that the protozoa identified are listed individually. Please clarify. Abbraviations should be written in full at the bottom of the table (IC with a * that links the abbreviation and the extended form).\nDiscussions: The discussions are well organized and the key concepts regarding parasitic contamination of fresh produce are covered.\n\nFirst paragraph: See comment in the Introduction section about the risk that these products represent for people living in non-endemic areas. Please cite relevant literature. When discussing contaminated berry products and the surface of such products is discussed, the following paper should be taken into consideration: Tefera et al. (20184). The paragraph starting with “Food-borne transmission of protozoan parasites…” needs to be amended in order to clarify two different concepts: foodborne transmission of protozoan parasites and detection of foodborne parasites into fresh produce. When listing the cases in which parasitic contamination of fresh produce occurred, the authors do not use the most recent bibliography available. They include, in fact, older articles, but they overlook more recent publications on the subject (among others, Barlaam et al., 2021; Barlaam et al., 2022; Temesgen et al., 2022; Marques et al. (20205); Faria et al. (20236). Please update.\nConclusion: It may start from three paragraph above (“In these tropical countries,..”) since they are very general concluding paragraphs.\nReferences: In some parts of the manuscript as stated in the previous comments the references are rather dated. For many subjects the authors write about, in fact, they cite articles that are not among the most relevant and recent on the subject. I recommend doing another bibliographic research and going through the references again.\nEnglish: The use of the English language is generally good, however, some misspellings, inaccuracies and errors in the sentence structure have been spotted throughout the text and a further revision is highly recommended.\n\nTaking everything into account this study has some limitations and the manuscript has some flaws, however, these data shed light on an important matter which is parasitic contamination of fresh produce in developing Countries which play a key role in our economy as exporters. This means that such issue is not limited to the Country in topic but potentially threatening for the rest of the world. For this reason, I think that it’s important to share data as limited as they may be on the subject and raise awareness on the issue. Therefore, in my opinion the manuscript can be indexed after the points raised above are clarified and a thorough revision of the manuscript is made according to the revisions above.\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": "11146",
"date": "13 Apr 2024",
"name": "LUISA CAROLINA GONZALEZ",
"role": "Author Response",
"response": "Revisor 3 We thank the reviewer for the importance has given to our research, the time spent correcting the manuscript, and their knowledge, experience, and willingness to improve the article. Comment 1: Abstract: In the Abstract, Methods: “Each sample were washed” should be replaced with “Each sample was washed”. Response 1: We have done the change Comment 2: Abstract, Results: The English language should be revised as the paragraph is not as clear as it should be. In addition, some repetitions occur (the most contaminated) and the use of, and; is confusing. Response 2: The English in the Abstract and Result sections has been revised and improved. Comment 3: Abstract, Conclusion: Delete “From these crops” given that it is a general concept regardless of the obtained results. Response 3: The phrase has been deleted Comment 4: Given the variety of fresh produce included in the study and the number of parasites detected, the introduction is too concise and should be enriched. In addition, the importance of leafy greens as vehicles of foodborne parasites is emphasized whereas the role vegetables and fruits, including berries (also analyzed in this study and for which relevant and recent publications are available) is completely overlooked. Response 4: Thank you very much for these observations. The introduction has been enriched as suggested and the role of vegetables and fruits as parasitic foodborne carriers is now highlighted (see paragraphs 4, 5, and 6 in the new paper version). Comment 5: When discussing the import of fresh produce from endemic countries and the spread of parasites to nonendemic ones the authors fail to include relevant and recent bibliography on the subject. There are, in fact, recent studies that show how fresh produce imported from countries endemic for certain parasites have been found contaminated in the importing country. These articles have been completely overlooked and should be included. I recommend: • Barlaam et al. (20211); • Temesgen et al. (20222); • Barlaam et al. (20223). Response 5: They have been included as suggested (see paragraph 2 new version of paper). Comment 6: Methods: The data are quite old (the samples were collected four years ago) and so is the methodology used for processing the fresh produce. The detection is also not quite in step with the times. Specifically, in the present study, the occurrence of parasites in fresh produce was investigated by microscopy although it is not clear how the genera and species were verified. Nowadays, with molecular tools available it would be auspicable to use them not only to verify the microscopy results but also to gather more information on the detected parasites (pathogenicity, zoonotic relevance etc.). I would like to ask the authors whether the samples were not tested molecularly because of lack of equipment/resources or for different reasons. Response 6: 6.1. The data are quite old (the samples were collected four years ago) The samples were collected a few years ago; however, the hygienic and sanitary practices in the area persist, and the prevalence of infection within the human populations remains constant (98.2%). No educational interventions have been implemented to enhance crop management hygiene. Additionally, indigenous communities do not readily alter their ancestral customs, suggesting that significant changes in these results are unlikely. 6.2. The methodology used for processing the fresh produce are quite old The washing and sedimentation technique used in our study (Rivero de Rodríguez et al., 1998) has been widely used, even today (Al Nahhas et al., 2020; Devera et al., 2021; Falcone et al., 2023; Lucas et al., 2023; Yahia et al., 2023; Asfaw et al., 2023; El Safadi et al., 2023). These parasitological techniques are very useful in low-resource countries, such as our case in Ecuador, since the addition of coagulant or flocculant reagents would increase the overall cost of the process. 6.3. The detection is also not quite in step with the times Optical microscopy remains the most used method in laboratories for the diagnosis of coproparasitoscopic. Its limitation has to do with the expertise of the laboratory technician to identify parasitic species. We have extensive experience in this type of diagnosis. On the other hand, we have no other diagnostic option due to the economic and logistical limitations of the area. 6.4. The occurrence of parasites in fresh produce was investigated by microscopy although it is not clear how the genera and species were verified. The identification of parasitic elements (eggs, larvae, cysts, oocysts) was conducted by an expert in parasitic microscopy, boasting 33 years of experience, utilizing the dimensions of the forms (using an ocular micrometer) and morphological characteristics (WHO, 2019). Given the wide variety of human, animal, and free-living parasites recoverable from plant matter, coupled with the limitations of microscopy for precise species identification, we have reported them generically (e.g., Strongylida, Ascaris spp.) without specifying species. 6.5. Nowadays, with molecular tools available it would be auspicable to use them not only to verify the microscopy results but also to gather more information on the detected parasites (pathogenicity, zoonotic relevance etc.). Undoubtedly, employing molecular methods (PCR) would yield more precise results and enable molecular epidemiology, contributing to addressing the issue of parasitic contamination. However, as previously mentioned, the application of these techniques was unfeasible in our study, due to budget constraints. The parasitological findings from this study have unveiled significant insights into the environmental health of crops in the Ecuadorian Andean region. 6.6. I would like to ask the authors whether the samples were not tested molecularly because of lack of equipment/resources or for different reasons. Molecular techniques were not used by lack of equipment/resources as mentioned above. Comment 7: In all the tables there is a line that refers to “Protozoa”. I don’t understand why given that the protozoa identified are listed individually. Please clarify. Abbraviations should be written in full at the bottom of the table (IC with a * that links the abbreviation and the extended form). Response 7: In the protozoa section of the tables, we specify the frequency and percentage of contamination for fruits, vegetables, and leafy greens individually, rather than providing a cumulative count of protozoa. The same was done with the helminth section. This approach allows us to ascertain the prevalence of each category and facilitates meaningful comparisons between the two. Comment 8: Discussions: The discussions are well organized and the key concepts regarding parasitic contamination of fresh produce are covered. 8.1. First paragraph: See comment in the Introduction section about the risk that these products represent for people living in non-endemic areas. Please cite relevant literature. When discussing contaminated berry products and the surface of such products is discussed, the following paper should be taken into consideration: Tefera et al. (2018). Response 8.1: Relevant literature, including the reference suggested, have been incorporated. Please, see lines 8 to Tefera et al., 2018; Marques et al., 2020; Barlaam et al., 2021, 2022; Faria et al., 2023, in the new version of the manuscript. 8.2. The paragraph starting with “Food-borne transmission of protozoan parasites…” needs to be amended in order to clarify two different concepts: foodborne transmission of protozoan parasites and detection of foodborne parasites into fresh produce. When listing the cases in which parasitic contamination of fresh produce occurred, the authors do not use the most recent bibliography available. They include, in fact, older articles, but they overlook more recent publications on the subject (among others, Barlaam et al., 2021; Barlaam et al., 2022; Temesgen et al., 2022; Marques et al. (2020); Faria et al. (2023). Please update. Thank you for these observations. The paragraph has been modified in order to avoid confusion with the sense in which the term is used. In addition, the references suggested has been now included (Please, paragraph see 16 new version) Comment 9: Conclusion: It may start from three paragraph above (“In these tropical countries,..”) since they are very general concluding paragraphs. Response 9: We believe that with our results, we cannot conclude what occurs in other Latin American countries."
}
]
},
{
"id": "228641",
"date": "30 Jan 2024",
"name": "Zulbey Rivero",
"expertise": [
"Reviewer Expertise Parasitology",
"Diagnostic Techniques"
],
"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 meets the objective proposed from the beginning and the introduction is brief but clear enough. The methodology is well described, but there is something that needs to be clarified and about which I am asking the authors in the comments placed as stickers in the PDF file. The most important findings are highlighted in the results, however it would be interesting if the authors could report which morphotypes of Blastocystis sp were detected in the samples evaluated. In addition, they must indicate if samples were found that showed contamination by more than one parasitic species in the vegetable or fruit analyzed. The discussion is fine, but depending on what you answer regarding polyparasitism and Blastocystis, you may have to add some of this to the discussion.\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": "11147",
"date": "13 Apr 2024",
"name": "LUISA CAROLINA GONZALEZ",
"role": "Author Response",
"response": "Revisor 4 We thank the reviewer for the importance has given to our research, the time spent correcting the manuscript, their knowledge, experience, and willingness to improve the article. Comment: The article meets the objective proposed from the beginning and the introduction is brief but clear enough. The methodology is well described, but there is something that needs to be clarified and about which I am asking the authors in the comments placed as stickers in the PDF file. The most important findings are highlighted in the results; however it would be interesting if the authors could report which morphotypes of Blastocystis sp were detected in the samples evaluated. In addition, they must indicate if samples were found that showed contamination by more than one parasitic species in the vegetable or fruit analyzed. The discussion is fine, but depending on what you answer regarding polyparasitism and Blastocystis, you may have to add some of this to the discussion. Response Observations made in the text Investigation design A field study, cross-sectional, observational and descriptive, was carried out during 1 month of rain / 7 months of drought. The snowball sampling technique was applied, whereby a grower helped locate the nearest farm and so on. All types of products found were included in the sampling (1,416 samples in total); the inclusion criteria were that all agricultural products must come from San Andrés fields and those not cultivated in the community were excluded. A separatory funnel was not used; it has been a translation error The reviewer is right. We apologize for the writing mistake. The allusion to a funnel has been deleted (see line 6 paragraph 8) It would be interesting if the results indicated whether, in some samples, more than one parasitic species was obtained from the studied vegetables, lettuce, or fruit. Something akin to polyparasitism in humans. This is a very important observation of the reviewer as most samples already presented polyparasitism. We have now described this in our results as well as in the discussion section (please see lines ???? in the new version of the manuscript). Given that Blastocystis was the primary microorganism found, if the authors have the information, it would be important to indicate which morphotype was most frequently observed. The morphotype of Blastocystis identified in the samples is now indicated in the result section (please, see lines 9 and 10) I assume that leafy vegetables were combined to enable pairwise comparisons. If that is the case, it should be noted that, for statistical reasons, sample groups were combined The reviewer is right. We have now indicate that some groups were combined for statistical purpose."
}
]
}
] | 1
|
https://f1000research.com/articles/12-532
|
https://f1000research.com/articles/12-1197/v1
|
25 Sep 23
|
{
"type": "Research Article",
"title": "Prospective effect of linkers type on the anticancer activity of pemetrexed-monoclonal antibody (atezolizumab) conjugates",
"authors": [
"Faten Q. Ibraheem",
"Nidhal K. Maraie",
"Basma Talib Al-Sudani",
"Ayad M.R. Raauf",
"Nidhal K. Maraie",
"Basma Talib Al-Sudani",
"Ayad M.R. Raauf"
],
"abstract": "Background: Conventional chemotherapy results in severe toxic side effects due to affecting normal and cancer cells. The conjugation of chemotherapy with mAb will improve the chemotherapy selectivity towards cancer cells and at the same time will potentiate immune system to detect and kill cancer cells. The aim of the study was to prepare atezolizumab-pemetrexed conjugate using two types of linkers (linker conjugated with -NH2 of lysine amino acid in the mAb). Methods: This study utilizes (for the first time) the mAb atezolizumab (AtZ) to prepare a new, selective conjugate carrier for pemetrexed (PMX) by using gamma amino butyric acid (GABA) as linker for the first time in comparison to the commonly used linker polyethylene glycol (PEG) using carbodiimide (EDC) / N-hydroxysulfosuccinimide (Sulfo-NHS) zero length cross linker. Stepwise evaluation for PMX-linkers linkage as well as mAb conjugates was evaluated by FTIR, 1HNMR, DSC, LC-MS, gel-electrophoresis as well as the anticancer activity against lung cells A549. Results: The work revealed that two molecules of GABA combined with PMX, which in turn conjugated with an average ratio of 4:1 with mAb, while one molecule of PEG combined with PMX, which in turn conjugated with mAb in the same average ratio. The IC50 for the prepared PMX-GABA-AtZ conjugate was 0.048 µM, which was much lower than PMX alone, antibody AtZ alone as well as PMX-PEG-AtZ conjugate in a dose and time dependent manner. Conclusions: The potential use of such conjugate that selectively directed to the overexpressed lung cells antigen in a low dose leading to reduction of serious side effects of PMX and the cost of therapeutically AtZ mAb used.",
"keywords": [
"monoclonal antibody",
"antibody drug conjugate",
"pemetrexed"
],
"content": "Introduction\n\nThe beneficial effects of therapeutic monoclonal antibodies (mAbs) that are represented by selectivity, minimum toxicity, and immune system activation gave chance for protein in biotechnology, such as bispecific mAbs, antibody drug conjugate (ADC). The mAb developed for many indications, including cancer, autoimmune disorder, and infectious diseases.1,2 Each mAbs has high affinity to specific antigen (overexpressed for example in diseased cancer cells), mAb applied as a carrier for drug through chemical conjugation to ensuring minimal drug loss during the transit to the target site, protect the drug from metabolism and premature clearance, and retain the drug at the target site.3 ADCs consist of a monoclonal antibody, cytotoxic drug, and a linker to conjugate the drug with mAb.4 The mAb is a promising target in anticancer field therapy that offers other advantage of improving exhausted immune cells (T cells) capability to detect and destroy tumor.5,6 The interaction between the surface programmed death-1 (PD1) with its ligand (PDL1), which are expressed on the surface of T cells and tumor cells, respectively prevents immune mediated cancer killing. To enhance T-cells capability against cancer cells, several antibodies have been developed.7,8 Atezolizumab (AtZ) was approved by the US FDA in 2016 for urothelial and metastatic lung cancer, gained approval for the treatment of advanced bladder cancer in 2017.9,10 AtZ immunologically interrupts PDL1–PD1 binding and therefore prevents T cell exhaustion.11 Pemetrexed (PMX) disrupts cellular replication by directly incorporating into the DNA,12 approved by the FDA for treatment of advanced lung cancer13,14 but unfortunately the physicochemical characteristics act as a barrier in its pharmacokinetic, where PMX diacid is practically insoluble in water,15 while the PMX disodium salt fails in achieving high stability upon storage.16 The most important points associated with PMX are lack of selectivity by affecting normal and cancer cells and serious side effects such as hepatic and hematological toxicities.17 The aim of this work is to improve the selectivity and targeting of PMX towards lung cancer through conjugation with therapeutic mAb (AtZ) where both act for treatment of lung cancer cells and study the efficacy of conjugate using a new linker gamma amino butyric acid (GABA) in the conjugation in comparison to the commonly used linker polyethylene glycol (PEG). Such conjugation might reduce the serious side effects of PMX chemotherapy and reduce the high cost of using therapeutic mAb alone.\n\n\nMethods\n\nAtezolizumab (Tecentriq®, F. Hoffmann-La Roche Ltd), pemetrexed diacid (purity 98%) with MW 427.41 g/mol, Hydroxy -2, 5-dioxopyrrolidine -3-sulfonicacid sodium salt (Sulfo-NHS), EDC (1- ethyl-3- (3-dimethylaminopropyl) carbodiimide hydrochloride), all purchased from Baoji Guokang Bio-Technology Co., Limited. Amine-PEG4-COOH (α-amine-ω-propionic acid tetraethylene glycol) MW 265 g/mol, gamma-Aminobutyric acid (GABA) MW 103.12 g/mol purchased from Tunchem Pharm (Shanghai) Tech Co., Ltd. N, N-Dimethylformamide (<0.1% H2O) purchased from Sinopharm Chemical Reagent Co., Ltd. Thermo Scientific Slide -A- Lyzer Dialysis Cassettes 10K MWCOs., Thermo Scientific Zeba Spin Desalting Columns 40K MWCOs.\n\nDialysis was done to remove all the excipients included in the marketed AtZ mAb. The dialysis done according to Thermo Fischer scientific protocol for protein dialysis,18 using Slide-A-Lyzer® Dialysis Cassettes, 10K MWCO (Thermo scientific, Prod # 66810, Lot # 10001172, U.S.A.). A total of 20 ml from the supplied AtZ solution were withdrawn under sterile aseptic laminar flow cabinet and divided into two dialysis cassettes, each cassette immersed in 1 L of sterile phosphate buffer saline (PBS) pH 7.6 and left stirring using magnetic stirrer (Misung scientific, MS-300HS, Korea) at 50 rpm and 2-8°C for 4 hr, the buffer was replaced twice in each 2 hr with fresh 1L PBS pH 7.6 medium. After 4 hr of stirring, the medium was replaced with 1 L fresh one and left overnight in 2-8°C.18 The dialyzed antibody was transferred into an empty vial containing 4% (W/V) mannitol and 1% (W/V) sucrose then lyophilized.19 The lyophilization process was done for 8 hr (-55°C and 0.07 mbar) using a CHRIST lyophilizer (ALPHA 1-2 LD plus, Germany) and the obtained lyophilized powder stored at 2 to 8°C for later use.\n\nThe conjugation of PMX with AtZ mAb was done using two types of linkers (each one separately), the α-amine-ω-propionic acid tetraethylene glycol, which is NH2-PEG4-COOH and gamma-Aminobutyric acid (GABA). The procedure involved two steps: first; chemical conjugation of PMX with each linker to obtain PMX-linker conjugate and second; reacting the developed PMX-linker conjugate with the monoclonal antibody (AtZ), as shown in Figure 1.\n\nThis figure is an original figure produced by the authors for this article.\n\nSynthesis of PMX-linker conjugate (PMX linkage), the procedure involved activation of the carboxylic acid (carboxylic acids in general are not reactive enough to undergo nucleophilic addition directly) moiety in PMX using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and Hydroxy -2, 5-dioxopyrrolidine-3-sulfonicacid sodium salt (Sulfo-NHS) through the NHS ester formation, followed by reaction with a primary amine (in the linker molecule) to form an amide product.\n\nFor synthesis of PMX linkage with NH2-PEG4-COOH linker, PMX (0.04 mmol, 0.017 gm) was dissolved in 5 mL of dimethyl formamide (DMF) solvent, then EDC (0.06 mmol, 11 μl) and Sulfo-NHS (0.06 mmol, 0.013 gm) were added to pemetrexed solution in DMF. The solution was stirred by magnetic stirrer (Misung scientific, MS-300HS, Korea) at room temperature for 2 hr. Then NH2-PEG4-COOH (0.04 mmol, 0.010 gm) was added, and the mixture was stirred at room temperature for 2 days. The resultant solution was dialyzed in a dialysis bag (MWCO 3.5 kDa) against deionized water for 24 hrs with replacing the deionized water every 2 hr. Then, the obtained solution was freeze dried at (-55°C and 0.07 mbar) using a CHRIST lyophilizer (ALPHA 1-2 LD plus, Germany) to obtain the powder form of the PMX-NH2-PEG4-COOH linkage (symbol as PMX-PEG).16,20 This procedure was repeated to link PMX with other linker (gamma amino butyric acid; GABA) using (0.04 mmol, 0.00412 gm) of GABA, to get PMX-GABA linkage as a powder.\n\nFor conjugation of PMX linkage with AtZ mAb, synthesis done by taking 17 mg of each of the obtained product separately (dried PMX-PEG and PMX-GABA linkages) and placed in 5 ml DMF solution containing mixture of 9 μl EDC/0.01 gm Sulfo-NHS and stirred by magnetic stirrer at room temperature for 2 hr, then 17 mg of AtZ mAb was added and stirring continued gently at 6°C for 48 hr using magnetic stirrer. The resultant mixture purified by desalting column (Zeba TM Spin Desalting Columns, 40K MWCOs, 10 ml, Thermo scientific, REF 87772, LOT XG361556, U.S.A.)21 and the obtained products was freeze dried after adding 5% (W/V) mannitol: sucrose mixture (4:1), using a CHRIST lyophilizer.\n\nThe characterization of the entire conjugate (AtZ-PMX) was carried out step by step. First step is characterization of PMX with linkers and this include:\n\n1 Fourier transform infra-red (FTIR) analysis\n\n2 Differential scanning calorimetric (DSC) analysis\n\n3 Mass spectroscopy (MS) analysis\n\n4 Proton nuclear magnetic resonance (1HNMR) analysis\n\nThe second step is characterization of (PMX-linker-AtZ) which symbolled (AtZ-PMX) and this include:\n\n1 Gel electrophoresis\n\n2 Mass spectroscopy\n\nCharacterization of conjugation of PMX with linkers\n\nThe characterization of linkage of PMX with NH2-PEG-COOH and PMX with GABA linker involved the following:\n\nThe FTIR (Shimadzu 8400 S, Japan) was done using potassium bromide disc, wavelength (4000–500 cm-1) was used for PMX-PEG linkage, PMX-GABA linkage, pure PMX, pure PEG, pure GABA, physical mixture of PMX and PEG, and the physical mixture of PMX with GABA.22\n\nThe DSC analysis (DSC 131EVO, France) was done for pure PMX, PEG, GABA, PMX-PEG linkage, and PMX-GABA linkage, using aluminum containers containing 2 mg of each sample, under nitrogen atmosphere 50 mL per minute, and a heat rate of 5°C in minute in temperature of 25-300°C.23\n\nCompounds screening was done using Bruker Daltonik (Bremen, Germany) Impact II ESI-Q-TOF System by direct injection. Stock Solution for each sample (pure PMX, pure GABA, pure PEG, PMX-PEG linkage, and PMX-GABA linkage) was prepared by dissolving 1 mg of each compound in 700 μl MeOH and 300 μl water, 1 μL were injected to get appropriate signal in mass spectrometer,24 separation was done by UHPLC column (100 mm x 2.1 mm x 2.0 μm) Bruker solo2.0-C-18, flow rate of 0.51 mL in minute and temperature of 40°C.\n\nThe 1HNMR was done for PMX, PEG, GABA, PMX-PEG linkage, and PMX-GABA linkage using Bruker (BioSpin GmbH 500 MHz, Germany). 1H-NMR analysis performed using DMSO solvent and chemical shifts (δ) stated in parts per million.25\n\nThe prepared PMX-AtZ conjugate using either PEG or GABA as a linker were characterized by:\n\nGel electrophoresis\n\nThe SDS PAGE is a characterization tool for pure mAb, and the two PMX-AtZ mAb conjugates. SDS-PAGE gel assay kit (Elabscience®, U.S.A., Cat No. E-IR-R305) was used for gel preparation. The vertical electrophoresis system (Bio-rad, PowerPacTM Basic, Singapore) was used for gel electrophoresis.\n\nThe separating gel concentration used was 6% (for protein with MW 50-150 KDa), the constituents illustrated in Table 1. The separating gel was prepared as follows: water, 30% Acrylamide/Bis-acrylamide solution, and Separating Gel Mix, were mixed in a clean dry beaker. Then 10% Ammonium Persulfate, and Tetramethylethylenediamine were added, mixed gently to avoid bubbles, the prepared mixture poured immediately into a clean assembled gel mold and kept until solidified for approximately 30-60 minutes then ethanol (1-2 ml) was added to flatten the gel surface. Ethanol was removed after gel solidified and any residual liquid in the assembled gel mold was removed gently by using absorbent paper.\n\nThe 5% stacking gel was prepared (constituents illustrated in Table 1) by gently mixing in dry, and clean beaker the following components: water, 30% Acrylamide/Bis-acrylamide solution, and Stacking Gel Mix. Then 10% Ammonium Persulfate and Tetramethylethylenediamine were added and poured immediately into the previously prepared solidified separating gel. Comb teeth were inserted, and gel kept until solidified for 30-40 minutes.26,27 The solidified gel cassette fixed inside the electrophoresis tank; comb removed carefully. The electrophoresis tank filled with 1X Tris-Glycine buffer (Elabscience®, U.S.A.).\n\nSamples for gel electrophoresis (AtZ mAb, PMX-PEG-AtZ conjugate, and PMX-GABA-AtZ conjugate) were prepared by mixing 20 μl of each sample (concentration 0.5mg/ml) with 5 μl loading buffer (5X SDS Loading Buffer, Elabscience®, U.S.A. Cat No. E-BC-R288), samples mixed with (vortex mixer, Faithfull, model MX-S). The prepared samples were heated (dry block heater, jSR, model JSBL-01T, korea) at 95°C for 5 minutes (heating speed up protein denaturation by increasing sample molecular motion), then samples were cooled to room temperature before loading.\n\nA total of 10 μL of each sample loaded into the gel well (lane), 5 μL marker (pre-stained protein marker 10-180 KDa, Elabscience®, U.S.A. Cat No. E-BC-R273) was loaded into gel lane. In another gel mold, samples without heating (keeping the temperature 20-25°C to avoid denaturation) were loaded into the gel lane.\n\nThe electrophoresis system was run at voltage 120V for about 2-3 hours. At the end of experiment the gel was removed from the tank and transferred directly into 20 mL staining solution (mixture of 2 g Coomassie Brilliant Blue R-250, 300 ml methanol, 100 ml glacial acetic acid, and 600 ml distilled water) and gel left gently shaking (Human, HumaRock, Germany) for approximately 1 hr. After 1 hr the gel transferred into the de-staining solution (mixture of 300 ml methanol, 100 ml glacial acetic acid, and 600 ml distilled water) and left shaking gently overnight. The gel washed with distilled water and band visualized by using Bio-Rad Chemidoc XRS Gel Imaging System (RRID:SCR_019690), model No. Universal Hood II, U.S.A.\n\nA UHPLC Bruker (Bremen, Germany) was used for screening conjugates compounds. Stock Solution for each sample (unconjugated atezolizumab mAb, pemetrexed-PEG-mAb conjugate, and pemetrexed-GABA-mAb conjugate) was prepared by dissolving 7.25 mg in 50 ml ACN: water (1:1) and 0.1 formic acid, 125 ppm of sample injected (sample concentration) to get appropriate signal in mass spectrometer. The separation was performed using Bruker solo2.0-C18 UHPLC column (100 mm x 2.1 mm), flow rate 0.3 mL/min, column temp of 60°C, and dry gas temp 300°C.28\n\nCytotoxic activity of PMX-AtZ conjugates using two types of linkers PEG and GABA (each one separately) were studied using lung cancer cells (A549) in comparison to pure PMX, pure AtZ, PMX-PEG linkage, and PMX-GABA linkage. Lung cancer cell line (A549) was purchased from American Type Culture Collection ATCC (Middlesex, UK) and stored in the Cell Bank of the Biomedical Research Centre at Mustansiriyah university.\n\nThe viability of A549 cancer cells after exposure to various samples, including pure PMX, PMX-PEG linkage, PMX-GABA linkage, pure mAb, PMX-PEG-AtZ conjugate, and PMX-GABA-AtZ conjugate was determined by MTT assay.\n\nThe A549 cell suspensions were dispensed into 96-well flat plates in a concentration of 5 x 103 cells per well, incubated for 1 day under standard conditions; 4 x 103 cells per well, incubated for 2 days; and 3 x 103 cells per well, incubated for 3 days under standard conditions.29,30 Cells were treated with same concentration range 0.05-100 μM of each sample, control group with only growth medium included within plate and plate incubated. After a 24 h, 48 h, and 72 h incubation, the cell culture medium was removed (after each recovery period) and incubated with MTT solution (3-(4,5-Dimethyl thiazol-2-yl)-2,5 Diphenyl tetrazolium Bromide), the medium was removed and DMSO was added to plates (remained at room temperature in the dark for fifteen minutes). The absorbance was measured at 540 nm with background absorbance correction at a wavelength of 650 nm, optical density of the control wells was used to determine the cells viability.31,32 The dose response plotted over log concentrations and IC50 values calculated using Graph Pad Prism version 8.4.3 (RRID:SCR_002798), results represented standard error of the mean for triplicate data.33 R is an open source alternative software which could be used for this.\n\n\nResults and Discussion\n\nTwo types of PMX-AtZ conjugates were prepared using two types of linkers (each one separately) including PEG (the commonly used linker) and GABA, which was used for the first time in drug-antibody conjugation in this work. Both conjugates were characterized and evaluated.\n\nThe FTIR spectrum (Figure 2) of pure PMX displaced the characteristic stretching band O-H of COOH near 3400 cm-1, stretching NH2 at 3309.85 cm-1, stretching NH at 2970.38 cm-1, stretching C-H aliphatic at 2877.79 cm-1, C=O of COOH at 1689 cm-1, C=C aromatic at 1527.62 cm-1, and all these peaks similar to that reported.29\n\nThe α-amine-ω-propionic acid tetra ethylene glycol (NH2-PEG4-COOH) displaced characteristics stretching C=O of COOH at 1631.78 cm-1, stretching band O-H of COOH at 3514.30 cm-1.34 The mixture of PMX and PEG showed the same characteristics peaks observed in each ingredient separately with observable broadening in C=O of COOH at 1631.78 and 1697.36 cm-1, which are for C=O of COOH of the PEG and PMX, respectively. The spectrum of the chemically linked PMX-PEG displaced a new sharp peak at 1643.35 cm-1 and this not found neither in the physical mixture, nor in each molecule separately indicating chemical linkage and related to C=O of intended amide.\n\nGABA (Figure 3) showed aliphatic -CH peaks at 2951.09 cm-1, 3008.96 cm-1 and 2846.93 cm-1. There were also bands corresponding to asymmetrical and symmetrical stretching vibration of carboxylate group at 1573.92 cm-1 and 1396.47 cm-1, respectively, stretching band O-H of COOH 3402.43 cm-1 and 3506.59 cm-1. The GABA FTIR is in accordance with reported data.35 The physical mix of PMX and GABA showed the same characteristics peaks observed in GABA at 1338.6 and 783.1 cm-1 and others related to PMX at 3309.85 cm-1 and this appeared as a broad band with aliphatic -CH peaks of GABA. The chemically linked PMX-GABA displayed amide -NH stretching at 3360 cm-1, sharp intense peak at 1639.49 cm-1 related to C=O stretching of conjugated amide. The underlying data are available in a data repository.36\n\nCharacterization by DSC done for PMX, PEG, GABA, physical mix in equal amount of PMX and PEG, physical mix in equal amount of PMX and GABA, PMX-PEG linkage, and PMX-GABA linkage. The DSC results (Figure 4A) showed that PMX had a sharp narrow, intense endothermic peak at 252°C that represents melting point of the drug.15 PEG spectrum displayed a strong endothermic peak at 88°C.37 The physical mix of PMX and PEG displayed the two characteristics endothermic peaks of them, while the chemically linked one (PMX-PEG) displayed one new sharp intense endothermic peak at 164°C. GABA spectrum (Figure 4B) showed an intense endothermic peak at 205°C in accordance with the melting point of GABA.38 The physical mix of PMX and GABA displayed the two characteristics endothermic peaks, while PMX-GABA linkage spectrum had a new peak at 180°C, which is neither related to PMX nor to GABA, suggesting chemical linkage between drug and GABA linker. The underlying data are available in a data repository.39\n\n(B) DSC for GABA, PMX, PHM (physical mixture of PMX and GABA), PMX-GABA (pemetrexed-GABA linkage).\n\nLC-MS chromatograms of PMX, GABA, PEG, PMX-PEG linkage, PMX-GABA linkage is demonstrated in Figure 5, where the retention time for PMX at 4.7 min, GABA 0.55 min, PEG 1.4 min, PMX-PEG linkage 7 min, PMX-GABA linkage 5.2 and 6.2 min. It was obvious that the newly conjugated molecule (PMX-PEG and PMX-GABA) displayed different retention time of their pure molecules alone.\n\nMass divided by charge number (M/Z) represents the dividing mass number of ion by its charge, since the charge is almost equal to one, so the M/Z represents the molecular mass of the compound in the horizontal axis of chromatogram.40 The (M/Z) for pure PMX 428.159, (M/Z) pure GABA 104.0713, (M/Z) pure PEG 266.16, the PMX-PEG linkage displayed different and multiple (M/Z) due to possibility of side reaction or unreacted materials. Among these multiple (M/Z) is 674, which may represent the intended molecular weight of our target molecule PMX-PEG linkage (Figure 6). The final (M/Z) for PMX-GABA linkage displayed two main peaks 513.32 and 598.41, and it was concluded that the newly conjugated molecule may involve one GABA molecule conjugated by the α-COOH group of PMX to give the new entity with molecular weight 512 g/mol, while the second M/Z (598.4) may involve two molecules of GABA conjugated with the two α and γ COOH groups of PMX. Similar changes in M/Z in the LC-MS were observed in pegylated pemetrexed prodrug conjugated with amino acid linker.41 The underlying data are available in a data repository.42\n\nThe PMX-PEG linkage and PMX-GABA linkage were confirmed by 1HNMR spectra using DMSO as the solvent and all the results analyzed by MesterNova NMR analysis software and presented in Figure 7.\n\nThe 1HNMR spectrum of pure PMX gives a signal at 2.08–2.98, 3.31–3.41 ppm (−CH2−), 6.3 ppm (pyrrole −CH−), 7.2 and 7.7 ppm (aryl–CH), signal 10.15 ppm pteridine proton, 6.01 ppm aniline proton, and 10.62 ppm (-NH of pyrrole) and all agreed with reported values.43\n\nThe typical 1HNMR spectrum of PEG gives signal 3.3–3.7 ppm for the protons of PEG chain, other signals in good agreement with reported data.44\n\nThe 1HNMR spectrum of PMX-PEG linkage showed all the main characteristics peaks of pure PMX and showed all peaks presented with PEG linker with a slight shift in protons peaks that specifically involved in the linkage and amide bond formation. The 1HNMR spectrum for PMX-PEG linkage displaced the characteristics peaks for PEG after linkage at 2.86–3.9 ppm for the protons PEG chain, peaks spectrum of PMX after linkage showed all original PMX signal at 6.3 ppm (−CH− of pyrrole), 6.02 ppm for aniline protons of PMX,16 7.25 with 7.76 ppm (−CH aryl), 10.18 ppm for pteridine PMX proton, and 10.6 ppm (-NH of pyrrole).43 The -CH2 of PMX neighboring to the α -COOH shifted from 2.33–2.36 to 2.26 ppm after linkage, also its neighboring -CH2 shifted from 2.08 to 1.7 ppm. The 1HNMR spectrum of PMX-PEG linkage displaced a peak at 3.35 ppm corresponding to -CH2 of PEG neighboring to terminal -NH2 after linkage and this was at 2.89 ppm for pure unreacted PEG, disappearance of the broad -NH2 PEG peak at 6.04 ppm and the appearance of a peak at 7.89 ppm in the PMX-PEG linkage 1HNMR spectrum, which corresponds to (-NH) proton of amide is further confirmed the intended linkage.45\n\nThe 1HNMR spectrum of GABA displaced the characteristics GABA proton peaks at 1.23, 1.98, and 3.36 ppm (for −CH2−) as well as other peaks and all in good agreement with reported data.46 The 1HNMR spectrum for PMX-GABA linkage showed all main peaks of PMX and GABA. The -CH2 proton peak of PMX adjacent to the α-COOH of PMX appeared as one peak range with the -CH2 proton peak neighboring to terminal -COOH of GABA in the PMX-GABA linkage, also the -CH2 proton peak of GABA neighboring to -NH shifted to 3.5 ppm (it was at 3.36 ppm in pure GABA) after linkage affected by adjacent amide bond, in addition to the appearance of new peak between 7.78–7.80 ppm in the 1HNMR spectrum of PMX-GABA linkage indicating the success of linkage and formation of amide bond.47 Broadening of the -CH2 group of PMX in the 1HNMR spectrum, which is neighboring to the α- carboxyl group of PMX and appeared as broad peak at 3.93 ppm indicated reaction also occurred on the neighboring carbonyl group (conjugation of GABA with α-COOH of PMX). All other peaks appeared are correlated to PMX. These results of 1HNMR agreed with our results obtained with FTIR, DSC, and mass spectroscopy, which suggested two molecules of GABA linked by two amide bonds with two -COOH of PMX. The data of 1HNMR spectrum are available in a data repository.48\n\nThe successful linkage between PMX and each of PEG and GABA, proceeded by introducing the mAb (atezolizumab) to the prepared linkage to get two types of conjugates: PMX-PEG-AtZ mAb and PMX-GABA-AtZ mAb. Both conjugates were characterized.\n\nResults of gel electrophoresis for samples without heating the samples (AtZ mAb, PMX-PEG-AtZ conjugate, and PMX-GABA-AtZ conjugate) showed in Figure 8 (A) in which mAb showed band near 130 KDa and the two conjugates (PMX-PEG-AtZ and PMX-GABA-AtZ) showed band at 180 KDa and this confirmed the conjugation and the mAb was not affected by the experimental condition during conjugation. The same samples (unconjugated mAb and the two conjugates), which were heated 95°C for 5 minutes before being introduced into the wells of assembled gel (which is the common method applied for many proteins in PAGE49) showed no bands indicating unfolding of mAb by heating (Figure 8B), as atezolizumab had limited stability for only few hours at 20-25°C.50 These results were in agreement with other study in which antibody conjugated with maytansinoid and auristatin demonstrated that both unconjugated and conjugated antibody were unfolded properly by heating to 95°C.51 The data are available in a data repository.52\n\n(A) samples without heating where (1): pre-stained protein marker, (2) AtZ mAb, (3) PMX-PEG-AtZ conjugate, and (4) PMX-GABA-AtZ conjugate. (B): heated samples of conjugate and unconjugated mAb.\n\nThe LC-MS is beneficial tool for characterization of antibody and identification of antibody conjugate by detection of antibody mass.53 The total ion chromatogram (TIC) results of characterization of AtZ mAb, PMX-PEG-AtZ conjugate, and PMX-GABA-AtZ conjugate are shown in Figure 9 and revealed a change in chromatograms of conjugate in comparison to unconjugated pure antibody and represented the major conjugated molecules eluted after 15 minutes. These results are in accordance with another study in which trastuzumab conjugated to microtubule disrupting agent.54 The mass profile of AtZ-PMX conjugate were simplified (Figure 10) with only m/z values (results showed up to eight molecules of the PMX-PEG linkage and PMX-GABA linkage were conjugated to AtZ with increase in molecular mass of antibody), these results in accordance with Trastuzumab deruxtecan conjugate in which mAb conjugated 8 deruxtecan molecules through a maleimide based linker and gain approval for breast cancer.55 The drug: antibody ratio calculated as the average PMX linkage conjugated based on the sum of all intensities.56 The calculated drug: antibody ratio of PMX-AtZ conjugate using two types of linker PEG and GABA was 4 and 3.74, respectively. The obtained PMX-AtZ conjugation ratio agreed with that Ado-trastuzumab emtansine (first ADC approved) for malignancy in which emtansine conjugation with trastuzumab in average of 3 to 4 (emtansine molecules): 1 (mAb molecule) using stable thioether linker.57 The data are available in a data repository.58\n\nIn accordance with data obtained from the applied characterizations, the expected structure for 1:1 PMX-AtZ mAb conjugation is suggested in Figure 11, where in PMX-PEG-AtZ mAb conjugate one molecule of PMX linked to one molecule of PEG, which in turn linked with one molecule of mAb. While 1:1 of PMX-GABA-AtZ mAb conjugation, where one molecule of PMX linked to two molecules of GABA, which in turn conjugate with one molecule of mAb.\n\nThis figure is an original figure produced by the authors for this article.\n\nCells treated with increasing concentrations of AtZ mAb, pure PMX, PMX-PEG linkage, PMX-GABA linkage, PMX-PEG-AtZ mAb conjugate, and PMX-GABA-AtZ mAb conjugate.\n\nThe PMX-PEG linkage and PMX-GABA linkage showed lower IC50 (2.54, 1.814 μM, respectively) than that of pure PMX (2.67 μM) on cancer cell at different time (24, 48 and 72 h) (Figure 12). These results indicated that PMX-PEG linkage could potentiate drug cytotoxic activity due to enhancement of solubility and therefore enhances cell uptake and penetration, and this in agreement with other study demonstrated that the incorporation of PEG altered paclitaxel delivery mechanism and enhanced cytotoxic efficacy.59 The IC50 (1.814 μM) obtained with PMX-GABA linkage was significantly (P≤ 0.05) lower than pure PMX and PMX-PEG linkage due to the synergistic effect of conjugation, where a previous reported data assumed that GABA had a strong inhibitory effect on cell proliferation.60 In addition, the gene expression of GABA receptor is high in lung cancer and the proliferation index for such cancer is inversely correlated with GABA concentration when given exogenously, therefore GABA inhibits proliferation of the lung cancer in time and dose manner.61\n\nAtZ mAb gave IC50 0.817 μM (Table 2), which is similar to reported data,21 indicating that the lyophilized mAb kept its anticancer activity. The complete conjugation (PMX-PEG-AtZ mAb) and (PMX-GABA-AtZ mAb) showed potent cytotoxic effect where the IC50 was 0.0818 and 0.0485 μM for each, respectively (Figure 12). The two types of conjugation were significantly (P≤ 0.05) more cytotoxic activity than PMX alone and antibody alone, which demonstrated that hybrid effect of the final conjugates significantly enhanced cytotoxicity due to synergistic effect. The data are available in a data repository.62 Original data by Graph Pad Prism are available in a data repository in a pzfx and JPG format.63\n\nIt was noted that using GABA (as a linker) for PMX-AtZ mAb conjugation gave higher cytotoxic effect than using PEG as a linker, which could be attributed to the involvement of two molecules of GABA in the PMX-AtZ mAb conjugation that may cause further enhancement (≈ 2 folds) in cytotoxic effect of the final conjugate. According to our knowledge no previous work was reported on using GABA as a linker for drug-monoclonal antibody conjugation.\n\nThe dose-response curve showed that the cytotoxic activity of the two types of the prepared conjugates was dose and time dependent. Figure 13 shows that as the concentrations of the conjugates increased; their cytotoxic activity increased significantly (P≤ 0.05), where at concentration 12.5 μM; PMX-GABA-AtZ mAb and PMX-PEG-AtZ mAb conjugates gave 71.168% and 55.167% cell death, respectively, after 24 h in comparison to pure PMX, which gave 39.58% cell death and the cell death continued to reach 88.987% and 80% for the two conjugates as well as 69.43% for pure PMX at 100 μM concentration after 24 h and similar increase in response upon increasing concentration was observed after 48 and 72 h. This suggests that the higher percentage of cell death achieved by the two PMX-AtZ mAb conjugates attributed to the collaborative effect of PMX and AtZ mAb upon conjugation. The enhancement of cytotoxic activity of drug-mAb conjugation observed in this study agreed with reported enhancement observed upon conjugation of auristatin with trastuzumab and attributed to the synergistic effect of both the drug and antibody.64\n\nIn this study, it was observed that in all the working concentrations; the PMX-GABA-AtZ mAb conjugate showed a significantly (P≤ 0.05) higher anticancer effect against the lung cancer cells indicating the contribution of the inhibitory effect of GABA on these cancer cells.65 The data are available in a data repository in a pzfx and PDF format.66\n\nThe time response curve (Figure 14) shows that with 12.5 μM of pure PMX at 24 h gave (39.58% cell death), at 48 h (48.39% cell death) and 72 h (78.70% cell death) indicating the drug activity is time dependent, which agreed with reported data for PMX.29,67\n\nAtZ mAb with 12.5 μM concentration at 24 h lead to (52% cell death), at 48 h (63% cell death) and 72 h (85.14% cell death). which was also time dependent and agreed with reported data for AtZ,68 but it was significantly (P≤ 0.05) higher than PMX confirming the potency (as well as selectivity) of the mAb as anticancer agent.69\n\nThe PMX-PEG-AtZ mAb conjugate showed also time response and higher cytotoxic effect than PMX where it gave (with concentration 12.5 μM) cell death 52.16% at 24 h, 73.69% at 48 h, and 85.14% at 72 h, but it was not significantly higher than pure mAb.\n\nThe PMX-GABA-AtZ mAb conjugate (12.5 μM concentration) showed significant superior high percent of cell death with time than pure drug and PMX-PEG-AtZ mAb conjugate where it gave 71.16% cell death after 24 h, 83.69% after 48 h, and 95.17% cell death after 72 h. This confirms the contribution of GABA in enhancing the anticancer activity of both PMX and AtZ mAb in dose and time dependent manner. The data are available in a data repository in a pzfx and PDF format.70\n\n\nConclusions\n\nThis work succeeded to prepare pemetrexed-atezolizumab conjugation (for the first time) using two types of linkers PEG and GABA (each one separately) in an average ratio of 4 (pemetrexed molecules):1 (atezolizumab mAb) with significantly higher cytotoxic effects than each of pemetrexed and mAb alone indicating the potential use of such conjugates in a low dose leading to reduction of the serious side effect of pemetrexed that may be selectively delivered towards the lung cells where antigen is overexpressed as well as to reduction in the amount and cost of therapeutically mAb used. This work also revealed the efficacy of linkers used for such conjugation namely GABA, which was newly used in this work for drug-mAb conjugation where two molecules of GABA contributed and resulted in significantly higher cytotoxic effects compared to PEG (the commonly used linker in many drug-mAb conjugation). This may confirm that GABA molecule possesses anticancer effect which resulted in synergistic anticancer effect in the prepared pemetrexed-GABA-atezolizumab conjugate.",
"appendix": "Data availability\n\nZenodo: Figures of FTIR. https://doi.org/10.5281/zenodo.8132774. 36\n\nThis project contains the following underlying data:\n\n- FTIR figures (pdf ).\n\nZenodo: Figures of DSC. https://doi.org/10.5281/zenodo.8132703. 39\n\nThis project contains the following underlying data:\n\n- DSC figures (jpg).\n\nZenodo: Data for LC-Mass. https://doi.org/10.5281/zenodo.8132322. 42\n\nThis project contains the following underlying data:\n\n- Excel files contain figures for pemetrexed, PEG, GABA, pemetrexed-PEG conjugate, and pemetrexed-GABA conjugate represented the retention time for each one and molecular mass detection for each compound.\n\nZenodo: Figures of 1HNMR. https://doi.org/10.5281/zenodo.8180439. 48\n\nThis project contains the following underlying data:\n\n- 1HNMR figures (pdf ) for pemetrexed. PEG, GABA, pemetrexed-PEG conjugate, and pemetrexed-GABA conjugate.\n\nZenodo: Figure of gel electrophoresis. https://doi.org/10.5281/zenodo.8132813. 52\n\nThis project contains the following underlying data:\n\n- Gel electrophoresis figure (tif ).\n\nZenodo: Data of LC-Mass. https://doi.org/10.5281/zenodo.8132226. 58\n\nThis project contains the following underlying data:\n\n- Excel file for unconjugated antibody (atezolizumab)\n\n- Excel file for pemetrexed-PEG-atezolizumab conjugate\n\n- Excel file for pemetrexed-GABA-atezolizumab conjugate\n\nZenodo: Excel data for MTT assay by promega. https://doi.org/10.5281/zenodo.8132166. 62\n\nThis project contains the following underlying data:\n\n- Excel data for MTT assay\n\nZenodo: Data of IC50. https://doi.org/10.5281/zenodo.8243096. 63\n\nThis project contains the following underlying data:\n\n- IC50 data by Graph pad prism in a pzfx format.\n\n- IC50 data in a JPG format.\n\nZenodo: Figures of Dose response curve. https://doi.org/10.5281/zenodo.8243127. 66\n\nThis project contains the following underlying data:\n\n- Figures of Dose Response Curve by Grap Pad Prism in a pzfx format.\n\n- Figures of Dose Response Curve in a PDF format.\n\nZenodo: Figures of Time response curve. https://doi.org/10.5281/zenodo.8243151. 70\n\nThis project contains the following underlying data:\n\n- Time response curve figures by Grap Pad Prism in a pzfx format.\n\n- Time response curve figures in a PDF format.\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 Mustansiriyah University, Baghdad/Iraq for supporting this work.\n\n\nReferences\n\nCastelli MS, McGonigle P, Hornby PJ: The pharmacology and therapeutic applications of monoclonal antibodies. 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Al Mustansiriyah. J. Pharm. Sci. 2022; 22(2): 35–43. Publisher Full Text\n\nHami Z, Amini M, Ghazi-Khansari M, et al.: Doxorubicin-conjugated PLA-PEG-Folate based polymeric micelle for tumor-targeted delivery: Synthesis and in vitro evaluation. DARU, Journal of Pharmaceutical Sciences. 2014; 22(1): 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKırımlıoğlu GY, Yazan Y, Erol K, et al.: Gamma-aminobutyric acid loaded halloysite nanotubes and in vitro-in vivo evaluation for brain delivery. Int. J. Pharm. 2015; 495(2): 816–826. PubMed Abstract | Publisher Full Text\n\nIbraheem FQ, Maraie NK, Al-Sudani BT: FTIR Figures for pemetrexed, PEG, GABA, physical mixture of pemetrexed with PEG, physical mixture of pemetrexed with GABA, pemetrexed-PEG conjugate, and pemetrexed-GABA conjugate. [Dataset]. Zenodo. 2023. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nNagornov KO, Gasilova N, Kozhinov AN, et al.: Drug-to-Antibody Ratio Estimation via Proteoform Peak Integration in the Analysis of Antibody-Oligonucleotide Conjugates with Orbitrap Fourier Transform Mass Spectrometry. Anal. Chem. 2021; 93(38): 12930–12937. PubMed Abstract | Publisher Full Text\n\nPeddi PF, Hurvitz SA: Ado-trastuzumab emtansine (T-DM1) in human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer: Latest evidence and clinical potential. Therapeutic Advances in Medical Oncology. 2014; 6(5): 202–209. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbraheem FQ, Maraie NK, Al-Sudani BT: LC-MS results for unconjugated antibody (Atezolizumab (AtZ)), pemetrexed-PEG-Atezolizumab (PemPEG-AtZ conjugate), and pemetrexed-GABA-Atezolizumab (PemGABA-AtZ conjugate). [Dataset]. Zenodo. 2023. Publisher Full Text\n\nSteffes VM, Zhang Z, MacDonald S, et al.: PEGylation of Paclitaxel-Loaded Cationic Liposomes Drives Steric Stabilization of Bicelles and Vesicles thereby Enhancing Delivery and Cytotoxicity to Human Cancer Cells. ACS Appl. Mater. Interfaces. 2020; 12(1): 151–162. Publisher Full Text\n\nBrzozowska A, Burdan F, Duma D, et al.: γ-amino butyric acid (GABA) level as an overall survival risk factor in breast cancer. Ann. Agric. Environ. Med. 2017; 24(3): 435–439. PubMed Abstract | Publisher Full Text\n\nZhang X, Zhang R, Zheng Y, et al.: Expression of gamma-aminobutyric acid receptors on neoplastic growth and prediction of prognosis in non-small cell lung cancer. J. Transl. Med. 2013; 11: 102. Publisher Full Text\n\nIbraheem FQ, Maraie NK, Al-Sudani BT: Excel data for MTT assay by promega. [Dataset]. Zenodo. 2023. Publisher Full Text\n\nIbraheem FQ, Maraie NK, Al-Sudani BT: Figures of IC50 of each compound by graph pad prisim. [Dataset]. Zenodo. 2023. Publisher Full Text\n\nAxup JY, Bajjuri KM, Ritland M, et al.: Synthesis of site-specific antibody-drug conjugates using unnatural amino acids. Proc. Natl. Acad. Sci. U. S. A. 2012; 109(40): 16101–16106. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchuller HM, Al-Wadei HAN, Majidi M: Gamma-aminobutyric acid, a potential tumor suppressor for small airway-derived lung adenocarcinoma. Carcinogenesis. 2008; 29(10): 1979–1985. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbraheem FQ, Maraie NK, Al-Sudani BT: Dose Response curve figures by graph pad prism. [Dataset]. Zenodo. 2023. Publisher Full Text\n\nChen RS, Ko JC, Chiu HC, et al.: Pemetrexed downregulates ERCC1 expression and enhances cytotoxicity effected by resveratrol in human nonsmall cell lung cancer cells. Naunyn Schmiedeberg's Arch. Pharmacol. 2013; 386(12): 1047–1059. 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}
|
[
{
"id": "216712",
"date": "23 Oct 2023",
"name": "Ghazi Al Jabal",
"expertise": [
"Reviewer Expertise Drug design",
"Analytical analysis"
],
"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 research article explores the potential impact of different linkers on the anticancer activity of a pemetrexed-monoclonal antibody conjugate. The study successfully demonstrates the conjugation of pemetrexed (PMX) and atezolizumab (AtZ) using two distinct linkers: polyethylene glycol (PEG) and gamma-aminobutyric acid (GABA). Various analytical techniques were employed to evaluate the PMX-PEG and PMX-GABA conjugates with AtZ. Notably, the PMX-GABA-AtZ conjugate exhibited enhanced cytotoxic activity when compared to pure PMX, AtZ, and the PMX-PEG-AtZ conjugate. The study suggests that such a conjugate has the potential to reduce the side effects and costs associated with pemetrexed chemotherapy and therapeutic monoclonal antibodies.\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": [
{
"c_id": "11217",
"date": "04 Apr 2024",
"name": "faten ibraheem",
"role": "Author Response",
"response": "Thanks Dr. Ghazi for your valuable reviewing"
}
]
},
{
"id": "247798",
"date": "01 Mar 2024",
"name": "Khalid Kadhem Al-Kinani",
"expertise": [
"Reviewer Expertise Pharmaceutical nanotechnology and biotechnology including monoclonal antibody and antibody drug conjugates."
],
"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- Extensive amount of work and a very well written manuscript. - It would be better to make clearer that DSC analyses were done for the \"chemical parts' of the ADC but not the entire ADC (AtZ-PMX). Future studies could include DSC for the prepared ADC from stability point of view. - It might be better to delete table 1 since SDS-PAGE components are widely used and can be found very easily elsewhere. Instead, the authors can focus on the other interesting findings of this work which are plenty, according to my opinion. - UHPLC is not Mass spectroscopy. So, correct that in the methods section (Mass spectroscopy) accordingly and mention the full LC-MS setup. - SDS_PAGE gel, the experimental section needs to provide better description in terms of heated and non-heated samples to better explain panel B of Figure 8. Also, the statement \" atezolizumab had limited stability for only few hours at 20-25 C\" could not be very true since mAbs are fairly stable for many days if not months.\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? Yes",
"responses": [
{
"c_id": "11216",
"date": "04 Apr 2024",
"name": "faten ibraheem",
"role": "Author Response",
"response": "Thanks Dr. Khalid for your valuable review comments. We are going forward in our future research to discover more about Atezolizumab stability and specifically temprature effect. We appreciate your feedback."
}
]
}
] | 1
|
https://f1000research.com/articles/12-1197
|
https://f1000research.com/articles/13-70/v1
|
15 Jan 24
|
{
"type": "Study Protocol",
"title": "Effectiveness of multi-component modular intervention on screen-based and non-screen-based sedentary time among adolescents in an urban area of Mangalore: a school-based cluster randomised controlled trial-protocol",
"authors": [
"Soundarya Janani S",
"Nithin Kumar",
"Mithun Rao",
"Rekha T",
"Prasanna Mithra",
"Bhaskaran Unnikrishnan",
"Ramesh Holla",
"Saraswathy M Vikraman",
"Himani Kotian",
"Soundarya Janani S",
"Mithun Rao",
"Rekha T",
"Prasanna Mithra",
"Bhaskaran Unnikrishnan",
"Ramesh Holla",
"Saraswathy M Vikraman",
"Himani Kotian"
],
"abstract": "Background Behavioural risk factors are often present during adolescence and account for 70% of premature deaths during adulthood. Excessive sedentary behaviour and screen time have become significant concerns, especially among adolescents, due to their potential negative impact on physical and mental health. Adolescents with a high screen-based sedentary time are more likely to be physically inactive, have unhealthy body structure and poor academic performance. The objective of our study is to assess the effect of multi-component modular educational intervention on screen-based sedentary time (SST) and non-screen-based Sedentary time (NSST) among adolescents.\n\nMethods Ethical approval for the study has been obtained from the institutional Ethics Committee of Kasturba Medical College in Mangalore, India. This cluster randomized control trial will be carried out in schools located in the urban area of Mangalore. Using simple randomization, the eligible schools will be randomized into intervention and control arms, each consisting of 10 clusters. A multi-component modular educational intervention will be administered to participants in the intervention group at baseline, second and fourth month. The control group will receive the standard curriculum. Both the groups will be assessed at baseline and at second month, fourth month and sixth month of follow up for SST, NSST and level of physical activity. Anthropometric measurements like height, weight, waist circumference and hip circumference will be taken at baseline and sixth month of follow up.\n\nResults A comprehensive school-based modular educational intervention can have cumulative advantages by reducing screen- and non-screen-based sedentary time, and encouraging physical activity. Similar modular teaching can be incorporated into the curriculum, which will promote healthy life-style among the adolescents.",
"keywords": [
"Adolescent",
"Screen time",
"Sedentary behaviour",
"Modular intervention",
"Cluster randomized control trial."
],
"content": "Introduction\n\nNon-communicable diseases (NCDs) according to the World Health Organization (WHO) are long-lasting, non-infectious conditions with slow progression that are brought on by a confluence of genetic, physiological, environmental, and behavioral variables.1 Around 41 million deaths, viz seventy-four per cent of total deaths worldwide each year are attributed to NCDs. This number includes 14 million premature deaths from NCDs, the bulk of which are preventable. By 2030, it is anticipated that 55 million people will die annually from NCDs if immediate and appropriate interventions are not made.1\n\nBehavioural factors including lack of physical activity (PA) and unhealthy diet result in metabolic conditions like weight gain and obesity, high blood pressure, high cholesterol, and high blood sugar levels which are the main risk factors for NCDs. Rapid globalization and urbanization have resulted in the spread of unhealthy diets and poor lifestyles worldwide.2 Given that these behavioural factors contribute significantly to the development of the majority of non-communicable diseases (NCDs), their effects on health across the lifespan of an individual, especially during adolescence have gained considerable attention in recent times.3\n\nAccording to the WHO, adolescents are young people, aged 10 to 19, who are rapidly developing in terms of their bodies, minds, and social connections.4 It is also a crucial period for the establishment of health-related behaviours and lifestyle choices. Physical inactivity, substance use, unhealthy diet, being overweight and obesity are all risk factors for NCDs which are not seen as potential threats during adolescence. However, these health-related behavioural risk factors that begin during adolescence account for 70% of premature deaths during adulthood.5\n\nIn response to the WHO Global Action Plan for the Prevention and Control of NCDs, India developed a National Action Plan to reduce the number of premature deaths due to NCDs.6 However, until recently the discussion around NCD prevention strategies mostly overlooked adolescents and focused only on the adult population.7\n\nResearch involving sedentary time and sedentary behaviour has gained importance in recent times.8 Evidence demonstrates a strong link between excessive sedentary behaviour and poor health outcomes. Sedentary behaviour as an independent entity has drawn a lot of attention as a risk factor for poor physical and mental health outcomes in children and adults.9\n\nSedentary behaviour (SB) is any waking behaviour that involves sitting, reclining, or lying down while spending less than 1.5 metabolic equivalents of task (MET) of energy. It is seen in various domains in an adolescent’s life at home, at school, while using transport, and during free time. Examples include sitting in the school bus, playing board games, watching television, reading while sitting or lying down, and sitting in the classroom.8 Excessive sedentary behaviour and screen time have become significant concerns, especially among adolescents, due to their potential negative impact on physical and mental health.\n\nScreen time (ST) refers to the amount of time an individual spends engaged with screens, such as watching television, using computers, playing video games, or using smartphones and tablets.\n\nScreen-based sedentary time (SST) is the amount of time spent using a screen-based device while being sedentary in any setting (e.g., school, home, or recreation). Examples of such devices include smartphones, tablets, computers, and televisions. SST, and in particular the time spent viewing television, is thought to be a key proxy for sedentary behaviour in adolescents.9\n\nSedentary behaviour and screen time are closely related since screens often serve as the platform for various sedentary activities. The ease of accessibility and its utility for both academics and entertainment has led to a rise in screen time among children and adolescents. The recent COVID-19 pandemic led to significant changes in various aspects of our lives, including time spent using screens. Online classes and social isolation brought on by frequent lockdowns during the pandemic have also led to an increase in screen time among children and adolescents.10 Various research studies have generated evidence indicating the relation between excessive screen time and the development of depression, anxiety, inattention, poor sleep, and physical inactivity among children and adolescents.11\n\nNon-screen-based sedentary time (NSST) is time spent engaging in sedentary activities, that don’t include the use of a screen such as doing paper-based homework, reading a physical book, playing board games and time spent on car rides and studying.9\n\nAs per the recommendations by WHO and the American Academy of Paediatrics (AAP), children under the age of two should not spend any time seated in front of a screen (such as watching TV or videos or playing computer games), and children between the ages of two and five should restrict their screen time to no more than one hour (less is ideal).12 Adolescents who watch TV, use computers, or play video games for more than two hours a day (screen-based sedentary time) are more likely to have an unhealthy body structure, poor fitness, and poor academic performance. Despite this, more than 30% of adolescents in the majority of countries around the world engage in screen-related behaviour that lasts more than two hours per day.13\n\nAccording to the WHO’s recommendation on sedentary behaviour, children and adolescents should limit their time spent sitting, especially screen time for leisure.14\n\nOver the past ten years, considerable research interest has been generated due to the rise in screen time use and its detrimental effect on health. As a result, intervention studies targeting a variety of demographic groups and contexts have been conducted to reduce screen-based sedentary time.15–18\n\nInterventional studies to reduce screen time targeting adolescents in schools in various Western and Latin American countries have been shown to bring about a significant reduction. The interventions applied in these studies can be categorized into three distinct groups: interventions consisting of motivational/volitional components such as health education sessions on healthy lifestyle, interventions using mass media and other health promotion materials like posters, and newsletters, and interventions involving modification of physical environments like standing desks and policy modifications such as curriculum changes.19\n\nThis study aims to decrease screen-based and non-screen-based sedentary time in school-going teenagers through a multi-component modular educational intervention. Our study will indirectly focus on the third Sustainable Development Goal (SDG) ‘Good Health and Well-Being’ which aims to promote mental health and wellbeing while reducing premature mortality from noncommunicable diseases by one-third through prevention and early treatment.\n\nReducing screen time among school-aged children is an important public health goal, as excessive screen time has been associated with various negative health outcomes, including obesity, sleep problems, and reduced physical activity. School-based interventions can play a critical role in addressing this issue.\n\nHowever, a considerable knowledge gap still exists in this area. While some school-based interventions have shown promise in reducing screen time among students, there may be a lack of comprehensive understanding of the most effective strategies. Research is needed to identify whether the combination of interventions is most successful in different school settings, age groups, and populations. There has been a limited number of school-based intervention studies for adolescents to decrease screen and non-screen-based sedentary time using a multi-component approach.\n\nUnderstanding whether these interventions lead to sustained behaviour change and whether the benefits persist from adolescence through adulthood is also essential. It may be regarded as an effective method to encourage adolescents to self-regulate their screen use. However, there hasn’t been much experimental research in India looking at the effects of such interventions The current study aims to close a gap in the body of knowledge on the effectiveness of a multi-component modular intervention on sedentary behaviour involving screens and other devices in urban Mangalore’s teenage populations.\n\nIn a school-based cross-sectional study in Brazil carried out among 2874 high school students in the age group between 14 and 19 years, the prevalence of high screen time was 79.5%. A higher proportion of males were engaged in high screen time compared to female students (84.3% vs.76.1%). On multivariate analysis, students belonging to high socio-economic status had higher odds of prolonged screen exposure. The level of physical activity and nutritional status was not found to be associated with high screen time among adolescents in the study.20\n\nIn a cross-sectional study in Mumbai among 772 school-going adolescents in the age group between 10-15 years, screen time was high among girls compared to boys (218.21 min/d vs.165.3 min/d, p < 0.001). The combined prevalence of being overweight and obesity was 38.3%, low physical activity (PA) 38% and ST >120min/d was 85%. Clustering of high ST and low PA was seen in 69.2%. The odds of being overweight or obese in boys reporting low PA were 2.10 times higher, while the odds were 4.13 times higher in those with low PA+ST > 120 min/d. The study concluded that integrated interventions are necessary to allow greater reductions in obesity risk behaviours.21\n\nIn a cross-sectional study in China among 971 children, it was observed that children typically spent one hour per day engaging in screen-based sedentary activity (SST) and one hour per day engaging in non-screen-based activity (NSST). Children were more likely to be overweight if they spent more time in SST. There was no connection between time spent on the NSST and overweight children (P > 0.05). This study demonstrated no link between NSST and being overweight, however, a correlation was observed between children who spent more time in SST and their likelihood of becoming overweight.11\n\nIn a community-based cross-sectional study in New Delhi among 10 to 19-year-olds, the average daily screen time was calculated to be 3.8 hours. The majority of screen time—2.8 hours per day—is spent watching television. 68% of the teenagers admitted to watching television for more than the stipulated two hours a day.22\n\nIn a cluster-randomised trial carried out among 8th and 9th graders of 20 urban schools in Cuenca-Ecuador, behavioural intervention was administered in two stages. Stage one of the intervention included diet, physical activity and screen time, while stage two included only diet and physical exercise. The screen time was evaluated at baseline, at 18 months for stage one and 28 months for stage two. At the end of the 18th month of follow-up, lower TV time during weekday and weekends, and lower total screen time during weekday was observed among the intervention group. However, at the end of the 28th month of follow-up, the TV time and total screen time on weekdays increased in the intervention group. The study concluded that the intervention to reduce screen time worked only if the intervention was specifically targeted at reducing screen time.15\n\nIn an RCT carried out among 251 children aged 9 to 12 years in New Zealand, 127 children received intervention for 20 weeks which included training and educating the parent/caregiver on various strategies to reduce screen time. Screen time (TV) monitoring devices, mobility exercises, and support via online and newsletter were some of the interventions. The intervention group had more children participate in moderate-intensity physical activity (24.3 min/d; 95% CI: 0.94, 49.51; p = 0.06). No significant difference was observed in the BMI z score (−0.016; 95% CI: −0.084, 0.051; p = 0.64). The study concluded that home intervention to decrease screen time during leisure did not significantly reduce screen time or BMI.16\n\nA school-based cluster randomized control trial was conducted among 361 adolescents in the age group between 12-14 years in Australia which involved a 20-week intervention program. It included pedometers for self-monitoring physical activity, a smartphone app, a website, interactive seminars led by researchers, fitness equipment provided to schools, teacher-led physical education classes, lunchtime physical activity mentoring sessions, and newsletters for parents about screen time. The recreational screen time was recorded at baseline, 8th month and 18th month of intervention. Self-motivated screen time was significantly reduced by the intervention, while parental screen time guidelines were unaffected.17\n\nIn an umbrella review that included systematic reviews and meta-analyses of interventions among children and adults directed at reducing sedentary behaviour (screen time, sitting time, or sedentary time), the interventions were found to be more successful at reducing sitting time than either physical activity alone or physical activity and sedentary behaviour combination interventions. There were slight but significant differences in viewing time in six out of the eleven meta-analyses (reported in seven studies).18\n\nTo determine the effectiveness of a multi-component modular intervention on screen-based sedentary time and non-screen-based sedentary time in school-going adolescents in an urban area of Mangalore.\n\n\n\n1. To measure the screen sedentary time and non-screen sedentary time among the adolescent population.\n\n2. To develop a multicomponent modular intervention to reduce screen sedentary time and non-screen sedentary time among the adolescent population.\n\n3. To determine the effectiveness of the multi-component modular intervention on screen-based and non-screen-based sedentary time among adolescents.\n\n\nMethods\n\nMangalore is a major port city and the commercial headquarters of the district of Dakshina Kannada in the south Indian state of Karnataka. In comparison to the national average of 85%, the district has a high literacy rate of 93.4%.23 Mangalore is a leading educational hub owing to the plethora of educational institutions offering high-quality education. This interventional study will be carried out in the schools located in the urban area of Mangalore.\n\nThis will be a cluster randomized control trial. Consolidated Standards of Reporting Trials (CONSORT) will be used for reporting the trial.24\n\nThe Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) Guidelines are used to report the study’s protocol. A completed SPIRIT checklist is one of the prerequisites of the reporting guidelines.25\n\nStudents studying in 8th standard (middle school) in the selected schools in the urban area of Mangalore.\n\nJanuary 2023 - September 2024\n\nAssuming that the proposed intervention in this study will result in a reduction in the mean screen-based sedentary time by 0.9 hours (54 minutes) between intervention and the control groups, with 80% power and at a level of significance of 5%, the sample size was calculated to be 180 in each of the intervention and control arm. A design effect of 2 was assumed since this was a cluster randomized trial, and a sample size of 360 was determined for both the intervention and control groups. The final sample size was 400 in each arm, taking into account a maximum loss of 10% throughout the six-month follow-up period.\n\nThe sample size was calculated using the following equation ((1):\n\nWhere,\n\nZ1-α/2 = 1.96, Standard normal value at 5% level of significance\n\nZ1-β = 0.84, Standard normal value at 80% power\n\nσ = standard deviation = 3.025 hours13\n\nd = clinically significant difference = 0.9 hours\n\nAll the students of class 8 of the selected schools in the urban area of Mangalore will be eligible to participate in the study. Students whose parents do not give consent for their ward to participate in the study, students who do not assent to participate in the study and students who are not present on the day of baseline evaluation will be excluded from the study.\n\nThe list of schools situated in Mangalore will be obtained from the Block Education Officer/Deputy Director of Public Instruction. A comprehensive list of all eligible schools i.e., schools with classes 8 and above will be prepared. All the schools located within the limits of Mangalore City Corporation will be considered clusters. The study will employ cluster randomization, with clusters being allocated in a 1:1 ratio to the intervention arm and control arm. Randomization of schools will be done to accommodate 10 schools each in the intervention and control arm by simple randomization technique.\n\nThe study participants will be selected from the 8th standard of selected schools. In schools with multiple sections of the same class, a simple random sampling technique will be employed to select one section, assuming a batch size of 40 students in each section.\n\nThe selected schools in the intervention arm would receive the comprehensive multicomponent modular intervention and the control group would not receive any intervention from the investigator. The students in the control group will undergo routine physical health education as per the school curriculum. They will be offered the comprehensive modular intervention only after the end of the final data collection.\n\nThe intervention designed will be a combination of a health education session, distribution of information flyers, and an activity designed to promote self-motivated behaviour change.\n\nBased on suggestions from subject experts, a thorough literature assessment, and interaction with local stakeholders, a health education module will be created. This will be a multi-component educational module in English containing pertinent textual and illustrated/pictorial information curated according to the local context. The module has four main components:\n\n• Component 1: Sedentary behaviour\n\nThis will provide information as to what constitutes sedentary behaviour and the various activities which are considered sedentary in various settings including school and at home.\n\n• Component 2: Screen-based sedentary behaviour\n\nThis will introduce the participants to the concept of screen time and screen sedentary time. Activities constituting screen-based sedentary behaviour will be demonstrated using pictures.\n\n• Component 3: Effects of sedentary behaviour\n\nThis component will explain to the participants the harmful effects of excessive screen time and how screen time is associated with reduced physical activity and sedentary behaviour, unhealthy eating and poor quality sleep. The section will also introduce the participants to the health effects of sedentary behaviour on the body and mind.\n\n• Component 4: Reducing screen time and sedentary behaviour\n\nThis component will introduce participants to various methods designed to reduce screen time like setting screen time limits for a day, turning off notification sounds in their phones to avoid picking up their phone more often, practising screen-free time e.g. avoiding screen use during lunch breaks, avoiding using screens before going to sleep, encouraging a screen-free bedroom, avoiding the use of eBooks to read novels, and taking part in screen-free physical activities that they enjoy to promote a healthy lifestyle. Since classroom learning can account for the least active time of a child’s day, incorporating physically active learning in between classes can help in reducing the amount of time children spend sitting down each day. The component will introduce the students to the concept of ‘movement breaks’ where the students will be taught how to break continuous periods of sedentary behaviour during the school hours. They will be taught small activities that they can do while still inside the classroom that we call ‘chairobics’. They will also be taught about how movement helps to increase blood flow around the body and to the brain so that they can feel alert, concentrate better and are ready to learn and think during the class.\n\nThe selected schools in the intervention arm would receive the multi-component modular intervention. Along with the educational module, a flyer depicting the effects of excessive screen time, risks of sedentary behaviour and tips for reducing screen time will be distributed to all the students in the selected class. Each student will also be given a notebook to log the duration of screen time during school and non-school hours (screen time tracking) duration of physical activity and duration of sleep until the end of the intervention period. At the end of every week’s recording, students will be encouraged to write a reflection on challenges or difficulties they faced in following a healthy lifestyle and how to overcome them.\n\nThe class size of the selected schools is expected to be 40. The educational intervention will be delivered by the primary investigator. Three sessions at two monthly intervals will be conducted in the schools (Baseline, 2nd month and 4th month) selected to receive the modular educational intervention. The duration of each session will be 40 minutes.\n\nThe students in the schools selected for the control arm will not receive any intervention from the investigators. They will continue receiving the physical activity routine as per the school curriculum. The school will be offered the modular intervention only at the end of the final data collection.\n\nScreen time: This refers to how much time a person spends using screen-equipped electronic devices, such as computers, televisions, game consoles, cell phones, and tablets, irrespective of whether the activity is carried out when physically active or sedentary.26\n\nScreen-based sedentary time: This refers to the duration an individual spends engaged in sedentary activities while using electronic devices with screens in any context (e.g., school, work, recreation). Sedentary activities involve minimal physical movement or energy expenditure and typically involve sitting or lying down for extended periods.26\n\nRecreational screen time: This refers to the period during which an individual engages in screen-based activities for leisure, entertainment, or personal enjoyment. This includes the time spent using screen-equipped electronic devices, such as computers, televisions, game consoles, cell phones, tablets, and other similar devices, for activities that are not work or education-related.26\n\nNon-screen-based sedentary time: This refers to the amount of time spent engaging in sedentary activities that don’t use screens.26\n\nA pre-tested, content-validated semi-structured questionnaire will be used for data collection. The questionnaire was prepared after an extensive review of the literature and consultation with subject experts, and will include the following sections:\n\nSection 1: Socio-demographic details\n\nSection 2: HELENA (Healthy Lifestyle in European Adolescents) Screen-Time-Based Sedentary Behaviour Questionnaire27\n\nSection 3: Non-Screen-Based Sedentary Behaviour Questionnaire\n\nSection 4: Physical Activity Questionnaire for Adolescents (PAQ-A)28\n\nSection 5: Anthropometric measurements based on STEPS questionnaire29\n\nHELENA questionnaire will be used to assess the screen-associated sedentary behaviour among the adolescents. The questionnaire requires adolescents to report how much time they typically spend on a variety of sedentary activities on weekdays and weekends.\n\nThe sedentary activities captured by the questionnaire include:\n\n(i) Watching television\n\n(ii) Playing games on the computer\n\n(iii) Playing games on a console\n\n(iv) Academic web browsing\n\n(v) Nonacademic web browsing (E.g., Watching videos on YouTube)\n\n(vi) Browsing through social media (such as Facebook, Instagram, etc.)\n\nDepending on the time spent on these activities, the participants will choose one from the following options: (i) 0 hours (ii) < 1/2 hr (iii) ½ -1 hr (iv) 1-2 hrs (v) 2-3 hrs (vi) 3-4 hrs (vii) >4 hrs. Weekly time will be calculated by taking the mean time in the selected category and applying the formula: [(weekdays x 5) + (weekend x 2)] /7. A final screen-based sedentary score will be generated by adding the time reported for each category.27\n\nThis section of the questionnaire was prepared after an extensive review of the literature. It captures the duration of time spent by adolescents during school days and holidays, carrying out sedentary activities which do not involve the use of screens. The activities included are as follows:\n\n(i) Educational purposes: (number of hours sitting in the class, hours spent studying, doing homework, tuition class outside of school)\n\n(ii) Recreational purposes: (hours spent sitting and playing games such as chess, carrom board, playing a musical instrument, hours spent on hobbies while sitting down such as reading novels, painting, arts and crafts etc)\n\n(iii) Travel purposes: (hours spent in car, bus, school van etc.) and social purposes (talking with friends and family).\n\nDepending on the time spent on these activities, the participants will choose one from the following options: (i) 0 hours (ii) < 1/2 hr (iii) ½ -1 hr (iv) 1-2 hrs (v) 2-3 hrs (vi) 3-4 hrs (vii) >4 hrs. Weekly time will be calculated by taking the meantime in the selected category and applying the formula: [(weekdays x 5) + (weekend x 2)] /7. The time reported for each category will be added up to produce a final non-screen-based sedentary time.\n\nIt is an 8-item self-report questionnaire developed to assess the adolescents’ levels of physical activity over the previous 7 days. Each of the eight (PAQ-A) questionnaire items is scored between 1 and 5, and the mean score across all items is the total PAQ score. A score of 1 indicates low physical activity, whereas a score of 5 indicates high physical activity.\n\nThis is a structured process for gathering, examining, and sharing information on noncommunicable diseases (NCDs) and their risk factors. Anthropometry measurements will be taken as per the standard and protocol outlined in WHO-STEPs.\n\nThe Institutional Ethics Committee (IEC) of Kasturba Medical College, Mangalore, has accepted the protocol (IECKMCMLR-02/2023/57). The trial has been registered with the Clinical Trial Registry-India (CTRI) (REF/2023/04/066280). Before the commencement of the study, the Block Education Officer, Mangalore will be approached to obtain the list of schools in Mangalore and to get the necessary permission to conduct the study in schools.\n\nPermission to conduct the study in the selected schools will be obtained from the school administration. The school administration/Principal will be told the objectives of the study. On receiving the formal approval, the schools will be visited on a previously informed date. The study will be carried out among the students studying in class 8 of the selected schools. In case there are multiple sections for the same class, one of the sections will be selected for the study using simple random sampling.\n\nSince the participants in the study are under the age of 18 years, documented parental consent will be required before their enrollment in the study. The information sheet and consent form will be distributed to the students of the selected class on the first visit to be shared with their parents. On the second visit, a written assent will be taken from the students whose parents have consented and the questionnaire will be distributed.\n\nA self-administered questionnaire will be used to gather the demographic data, which includes information like age, gender, class, section, address, contact information, and the parents’ or guardians’ occupations. The study participants will be asked about their screen- and non-screen-based sedentary time as well as their physical activity. Anthropometric measurements like height, weight, waist and hip circumference will be collected using standardized techniques.29\n\nFollowing the collection of baseline data, the schools selected for intervention will receive the multi-component modular intervention. Three sessions at two monthly intervals will be conducted in these schools. (Baseline, second month and fourth month) Both groups will complete the questionnaires at baseline, and two, four and six months of follow-up. Anthropometric measurements will be taken at baseline and sixth month of follow-up) Outcome will be assessed at each point of time in both intervention and control arm students. Confidentiality and anonymity will be maintained throughout the study (Figure 1).\n\nMeasurement of weight\n\nA digital weighing scale will be used to measure weight. The patient will be requested to take off their shoes, socks, and any additional footwear they may be wearing before being instructed to place one foot on either side of the scale. The participant will be instructed to stand still, with their arms at their sides and their face front. The scale will record the weight in kilos to the nearest 0.1 cm. After each use, the scale will be reset to zero.29\n\nMeasurement of height\n\nA portable stadiometer will be used to measure the height. The participant will be directed to take off their shoes, slippers, and sandals in addition to their hat, cap, hair bows, comb, and ribbons. The participant will be instructed to face the investigator and stand on the board. He/She will be instructed to stand with their feet together, knees upright, and heels touching the backboard. He or she is instructed to maintain a straight-ahead gaze and to keep their eyes level with their ears. By lowering the measuring arm to the patient’s head, the reading will be measured to the nearest 0.1 cm.29\n\nBody mass index30\n\nBody Mass Index (BMI) will be calculated using the equation (2):\n\nThe presence of being overweight and obesity will be assessed by computing BMI for age z scores and comparing them to the age- and sex-specific BMI z score +1 cut-offs published by the World Health Organization.28 The interpretation of BMI z scores is as follows: The presence of being overweight and obesity will be assessed by computing BMI for age z scores and comparing them to the age- and sex-specific BMI z score +1 cut-offs published by the World Health Organization.28 The interpretation of BMI z scores is as follows:\n\nOverweight: >+1 SD (equivalent to BMI 25 kg/m2 at 19 years)\n\nObesity: >+2 SD (Equivalent to BMI 30 kg/m2 at 19 years)\n\nMeasurement of waist circumference\n\nWaist circumference will be taken halfway between the bottom of the last rib and the top of the iliac crest (hip bone), at the end of breathing, with arms at the sides using a measuring tape. The subject is instructed to put the tape over themselves. It will be instructed for the subject to stand with their feet together, their weight evenly spread over both feet, and their arms relaxed by their sides. Only one measurement will be made to the closest 0.1 cm.29\n\nMeasurement of hip circumference\n\nHip circumference will be calculated using a measuring tape. The participant must stand with their feet together, their weight evenly distributed over both feet, and their arms at their sides. The tape would be applied to the buttocks’ largest circumference. Measurements will be made to the nearest 0.1 cm at the level of the tape.29\n\n\n\n1. Mean screen sedentary time (SST) and non-screen sedentary time (NSST)\n\n2. Level of physical activity\n\n3. Association of BMI, waist circumference hip circumference and waist height ratio with screen sedentary time and non-screen based sedentary time\n\n4. Difference in the mean SST and mean NSST between the intervention and control group\n\nUtilizing IBM SPSS (Statistical Package for Social Sciences) Statistics for Windows Version 25.0, the gathered data will be coded, inputted, and analyzed. Armonk: IBM Corporation.31 The proformas will be checked for completeness and the participant will be contacted for any missing information. The data will be kept confidential and protected using encryption.\n\nProportions will be used to express the results. The interquartile range (IQR) and standard deviation (SD) associated with summary measures like mean and median will be reported for continuous variables. ITT analysis—intention to treat—will be used. The data will be represented by suitable tables and figures. The chi-square test will be used to compare variables between intervention and control groups. The baseline and post-intervention values across the intervention and control groups will be compared using the Mann-Whitney U test for non-normal data. (ST, SST, NSST) For data following normal distribution (WC, HC) independent t-test will be used and p < 0.05 will be considered to be statistically significant. Repeated measures of ANOVA will be used to compare the change scores (ST, SST, NSST) within the intervention and control groups and ’a p-value less than < 0.05 will be considered statistically significant.\n\nA comprehensive school-based modular intervention with an active behavioural change component like the one utilized in this study can have cumulative advantages by reducing screen- and non-screen-based sedentary time, encouraging physical activity, and promoting quality sleep to mitigate each factor’s individual effects on adiposity measurements in teenagers. It can be effective in promoting healthier habits and reducing the negative impacts of excessive screen time on academic performance, physical health, and overall well-being.\n\nThe Institutional Ethics Committee (IEC) at Kasturba Medical College, Mangalore has approved the study protocol.\n\nIf changes are made to the protocol after the commencement of the study, it will be resubmitted to the IEC for approval.\n\nThe trial has been registered with the Clinical Trial Registry-India (CTRI) (REF/2023/04/066280).\n\nRequired permissions will be obtained from the block educational officer and the school administration.\n\nWritten parental approval and informed assent will be obtained from the participants. The participant information data will be handled with the utmost confidentiality.\n\nAn interim analysis will be carried out after 3 months from the commencement of the study. There is no known adverse effect associated with this study. There will not be any committee formed for data monitoring. The selected schools in the control arm will be offered the modular intervention at the end of the final data collection.\n\nPresentations at scientific meetings and publications will be used to publicize the study’s findings. As stated in the methodology, we will report the study’s flow and results using the CONSORT principles. The Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) Guidelines are used to report the study’s protocol. As a result of the research data’s potential to compromise participants’ anonymity and the fact that they contain personal information, the IEC guidelines of the study institute forbid sharing research data with any other organization. However, the information can be obtained from the associated author upon personal request and with sufficient cause.\n\nThe study has not started recruiting participants.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nWe would like to thank the Department of Community Medicine, Kasturba Medical College, Mangalore, and Manipal Academy of Higher Education, Manipal for the support extended towards the publication of this protocol.\n\n\nReferences\n\nWorld Health Organization (WHO) 2023: Noncommunicable diseases: Risk factors.[cited 2023 Aug 28]. Reference Source\n\nKaur N, Gupta M, Malhi P, et al.: A Multicomponent Intervention to Reduce Screen Time Among Children Aged 2-5 Years in Chandigarh, North India: Protocol for a Randomized Controlled Trial. JMIR Res. Protoc. 2021; 10(2): e24106. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO) 2023: Noncommunicable diseases.[cited 2023 Aug 28]. Reference Source\n\nWorld Health Organization (WHO) 2023: Adolescent health.[cited 2023 Aug 28].Reference Source\n\nAkseer N, Mehta S, Wigle J, et al.: Non-communicable diseases among adolescents: current status, determinants, interventions, and policies. BMC Public Health. 2020; 20(1): 1908. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNon-communicable Diseases|National Health Portal Of India.[cited 2023 Jan 13]. Reference Source\n\nSawyer SM, Afifi RA, Bearinger LH, et al.: Adolescence: A foundation for future health. Lancet. 2012; 379(9826): 1630–1640. Publisher Full Text\n\nTremblay MS, Aubert S, Barnes JD, et al.: Sedentary Behavior Research Network (SBRN) - Terminology Consensus Project process and outcome. Int. J. Behav. Nutr. Phys. Act. 2017; 14(1): 75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYoung DR, Hivert MF, Alhassan S, et al.: Sedentary Behavior and Cardiovascular Morbidity and Mortality: A Science Advisory from the American Heart Association. Circulation. 2016; 134(13): e262–e279. Publisher Full Text\n\nSingh S, Balhara YPS: “Screen-time” for children and adolescents in COVID-19 times: Need to have the contextually informed perspective. Indian J. Psychiatry. 2021; 63(2): 192–195. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu R, Zheng H, Lu C: The Association Between Sedentary Screen Time, Non-screen-based Sedentary Time, and Overweight in Chinese Preschool Children: A Cross-Sectional Study. Front. Pediatr. 2021; 9: 767608. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO) 2023: [cited 2023 Aug 30]. To grow up healthy, children need to sit less and play more. Geneva: Reference Source\n\nAndrade S, Lachat C, Ochoa-Aviles A, et al.: A school-based intervention improves physical fitness in Ecuadorian adolescents: a cluster-randomized controlled trial. Int. J. Behav. Nutr. Phys. Act. 2014; 11: 153. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO) 2023: Guidelines on physical activity, sedentary behaviour, and sleep. Geneva: [cited 2023 Aug 30]; vol. 4. Reference Source\n\nAndrade S, Verloigne M, Cardon G, et al.: School-based intervention on healthy behaviour among Ecuadorian adolescents: effect of a cluster-randomized controlled trial on screen-time. BMC Public Health. 2015; 15: 942. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaddison R, Marsh S, Foley L, et al.: Screen-Time Weight-loss Intervention Targeting Children at Home (SWITCH): A randomized controlled trial. Int. J. Behav. Nutr. Phys. Act. 2014; 11: 111. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSmith JJ, Morgan PJ, Lonsdale C, et al.: Mediators of change in screen-time in a school-based intervention for adolescent boys: findings from the ATLAS cluster randomized controlled trial. J. Behav. Med. 2017; 40(3): 423–433. Publisher Full Text\n\nNguyen P, Le LK, Nguyen D, et al.: The effectiveness of sedentary behaviour interventions on sitting time and screen time in children and adults: an umbrella review of systematic reviews. Int. J. Behav. Nutr. Phys. Act. 2020; 17(1): 117. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBiddle SJ, O’Connell S, Braithwaite RE: Sedentary behaviour interventions in young people: a meta-analysis. Br. J. Sports Med. 2011; 45(11): 937–942. Publisher Full Text\n\nSchaan CW, Cureau FV, Bloch KV, et al.: Prevalence and correlates of screen time among Brazilian adolescents: findings from a country-wide survey. Appl. Physiol. Nutr. Metab. 2018; 43(7): 684–690. Publisher Full Text\n\nMoitra P, Madan J, Verma P: Independent and combined influences of physical activity, screen time, and sleep quality on adiposity indicators in Indian adolescents. BMC Public Health. 2021; 21(1): 2093. Publisher Full Text\n\nDubey M, Nongkynrih B, Gupta SK, et al.: Screen-based media use and screen time assessment among adolescents residing in an Urban Resettlement Colony in New Delhi, India. J. Family Med. Prim. Care. 2018; 7(6): 1236–1242. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPopulation census Census: 2011 [cited on 2023 Sep 07]. Reference Source\n\nConsort: The CONSORT Flow Diagram: [cited 2023 Sep 07]. Reference Source\n\nThe SPIRIT Statement: Standard Protocol Items: Recommendations for Interventions Trials.[cited 2023 Sep 07]. Reference Source\n\nStamatakis E, Hamer M, Dunstan DW: Screen-based entertainment time, all-cause mortality, and cardiovascular events: population-based study with ongoing mortality and hospital events follow-up. J. Am. Coll. Cardiol. 2011; 57(3): 292–299. Erratum in: J Am Coll Cardiol. 2011 Apr 19;57(16):1717. PubMed Abstract | Publisher Full Text\n\nRey-López JP, Vicente-Rodriguez G, Ortega FB, et al.: Sedentary patterns and media availability in European adolescents: The HELENA study. Prev. Med. 2010; 51(1): 50–55. Publisher Full Text\n\nKowalski KC, Crocker PR, Donen RM: The physical activity questionnaire for older children (PAQ-C) and adolescents (PAQ-A) manual.Reference Source\n\nWorld Health Organization (WHO) 2023: Noncommunicable Disease Surveillance, Monitoring and Reporting.[cited 2023 Sep 03]. Reference Source\n\nWorld Health Organization (WHO) 2023: BMI-for-age (5-19 years).[cited 2023 Sep 03]. Reference Source\n\nIBM Corp: IBM SPSS statistics for Windows, version 25.0. ArmonkNY: IBM Corp; 2017. Reference Source"
}
|
[
{
"id": "238233",
"date": "09 Feb 2024",
"name": "Sudhir Prabhu H",
"expertise": [
"Reviewer Expertise Immunization",
"Public 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\nThe research question addresses a very important public health issue of concern and the study design being an interventional study will be apt in addressing it. The Study tool used are extensive and comprehensive for addressing the research objectives. However, there are a few scientific and ethical concerns in the protocol. The scientific concerns to the protocol submitted include: 1. Why the study population is being restricted to 8th std students only? Any specific reasons can be mentioned in methods section. 2. Will there be adequate representation of primary sampling units in the school-based cluster (dual medium, dual lingual, type of curriculum, type of board etc.)? 3. A statement on how will screen based sedentary and non-screen based sedentary time be explained to students can be mentioned (since it's the primary objective of the study)\nEthical concern: A statement on informed parental consent being taken and its process can be mentioned.\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": [
{
"c_id": "11224",
"date": "04 Apr 2024",
"name": "Nithin Kumar",
"role": "Author Response",
"response": "Thank You sir for your suggestions to improve the manuscript. We have addressed your queries and incorporated the changes /modifications suggested by you. Why the study population is being restricted to 8th std students only? Any specific reasons can be mentioned in the methods section. Thank you, sir. We restricted our study population to students of 8th standard since the students will be available in the selected schools for the entire duration of the study and loss to follow-up is nil or minimal. Since the study has a one-year duration of follow-up, students from the 10th standard were not selected since they will complete their studies and shift to a different college. The same has been mentioned in the methods section. Will there be adequate representation of primary sampling units in the school-based cluster (dual medium, dual lingual, type of curriculum, type of board etc.)? Thank you, sir. The intervention will be carried out only in English medium schools. The primary sampling units will be selected ensuring adequate representation of private and aided schools and the type of boards (CBSC and state board) A statement on how will screen based sedentary and non-screen based sedentary time be explained to students can be mentioned (since it's the primary objective of the study) Thank you sir for the suggestion. We have included the same in the multi-component intervention section of the manuscript and incorporated it in the module as well. Ethical concern: A statement on informed parental consent being taken and its process can be mentioned. Thank you sir for the suggestion. We have incorporated the same in the data collection section of the manuscript."
}
]
},
{
"id": "238235",
"date": "20 Feb 2024",
"name": "Jay Sheth",
"expertise": [
"Reviewer Expertise Public health",
"epidemiology",
"research methodology",
"NCDs"
],
"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 first line should have ‘may’ instead of ‘can’\nMany sentences in the introduction, which have some numbers or major scientific documented facts, do not have any reference. Ideally, it has to be supported by appropriate recent and authentic references.\nThere is some duplication of information (e.g. related to risk factors of NCD) which should be avoided for a smooth flow of text and better understanding.\nAs the study aims to decrease SST and NSST, a hypothesis could have been added in the protocol.\nKnowledge gaps are well identified but some of the gaps are going beyond the focus and scope of the protocol. The authors may focus more on those gaps which the present protocol would be addressing scientifically.\nObjective1, Objective 2 & Objective 3 focuses on baseline, developing a modular intervention and Assessing its effectiveness in sequence. Here, after development, implementation of the multicomponent modular intervention may be added between objective 2 & objective 3. Alternatively, objective 2 may have “Develop and implement” as the action verb.\nThere is some difference between “eligibility criteria”, “study population” and “inclusion criteria”.\n\nWhat the authors have suggested after the first line under “eligibility criteria” are actually exclusion criteria. The flow should be “eligible criteria” followed by “study population”, followed by inclusion criteria and then the exclusion criteria.\nThe protocol assumes a batch size of 40 students for standard 8 of each school. However, if there are less than 40 (available, gives consent and enrolled) what is to be done to achieve the desired sample of 40 from the cluster, should have been included in the protocol. As this is a protocol, the authors should refrain from any assumption and prepare it thorough to address all possibilities, only then it can be easily adopted and replicated by others.\nComponents of multicomponent Modular intervention are clarified. Component 4 lists multiple activities and action points, however, it gives only an idea of the broad gamut it covers and conveys. It might be possible that this component is delivered differently in different clusters and by different investigators. Authors may consider streamlining and standardizing the component so that all investigators in all the intervention cluster apply it in a uniform manner. If this can be added and clarified, it will greatly improve the standard of intervention.\nWhether component 1,2 & 3 will be given but component 4 will not be addressed in control clusters? If there is no intervention in the control arm cluster, what the investigators will do there during follow up (after baseline)? I am unable to clearly understand this aspect.\nInstrument used for data collection is not available here. Without its availability detailed review of the tool is not possible.\nSince it's not a blinded study and intervention (educational intervention) is obvious, whether permission from school authorities (for the control cluster group) will be possible? Consider why and how the schools will give permission to be included in the control cluster. Even if they are not told, they will know that they are part of control cluster if nothing is done apart from bimonthly data collection after the baseline.\nInterim analysis at 3 month seems to be misfit. Why it can't be done or should not be done at first follow up at 2 months? What is the specific advantage of doing it at 3 months at the cost of an additional visit?\nThis is a protocol so dataset may not be applicable. But, study tool and details of multicomponent module may be included.\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? No",
"responses": [
{
"c_id": "11225",
"date": "04 Apr 2024",
"name": "Nithin Kumar",
"role": "Author Response",
"response": "Thank You sir for your suggestions to improve the manuscript. We have addressed your queries and incorporated the changes /modifications suggested by you. In the abstract, the first line should have ‘may’ instead of ‘can’ – Thank you sir for the suggestion. Many sentences in the introduction, which have some numbers or major scientific documented facts, do not have any reference. Ideally, it has to be supported by appropriate recent and authentic references Thank you Sir for the observations. Appropriate citations have been provided wherever applicable and the reference list updated. There is some duplication of information (e.g. related to risk factors of NCD) which should be avoided for a smooth flow of text and better understanding. Thank you Sir for the suggestion. We have made the appropriate changes in the manuscript. As the study aims to decrease SST and NSST, a hypothesis could have been added to the protocol. Thank you, sir. We have incorporated hypotheses under a separate heading in the manuscript. Knowledge gaps are well identified but some of the gaps are going beyond the focus and scope of the protocol. The authors may focus more on those gaps which the present protocol would be addressing scientifically. Thank you sir for the suggestion. We have modified the knowledge gap section as per your suggestion. Objective1, Objective 2 & Objective 3 focuses on baseline, developing a modular intervention and Assessing its effectiveness in sequence. Here, after development, implementation of the multicomponent modular intervention may be added between objective 2 & objective 3. Alternatively, objective 2 may have “Develop and implement” as the action verb. Thank you Sir for the suggestion. The Objectives have been modified as per your suggestion. There is some difference between “eligibility criteria”, “study population” and “inclusion criteria”.What the authors have suggested after the first line under “eligibility criteria” are actually exclusion criteria. The flow should be “eligible criteria” followed by “study population”, followed by inclusion criteria and then the exclusion criteria. Thank you sir. The changes have been made to the manuscript as per your suggestion. The protocol assumes a batch size of 40 students for standard 8 of each school. However, if there are less than 40 (available, gives consent and enrolled) what is to be done to achieve the desired sample of 40 from the cluster, should have been included in the protocol. As this is a protocol, the authors should refrain from any assumption and prepare it thorough to address all possibilities, only then it can be easily adopted and replicated by others. Thank you Sir. If the batch selected after simple random sampling has less than 40 students, the next batch will be selected by simple random sampling without replacement method, to reach the desired sample of 40 from the clusters. Components of multicomponent Modular intervention are clarified. Component 4 lists multiple activities and action points, however, it gives only an idea of the broad gamut it covers and conveys. It might be possible that this component is delivered differently in different clusters and by different investigators. Authors may consider streamlining and standardizing the component so that all investigators in all the intervention cluster apply it in a uniform manner. If this can be added and clarified, it will greatly improve the standard of intervention. Thank you for the question. The intervention will be carried out only by the primary investigator in all the intervention clusters making sure that there will be uniformity across all clusters. Whether component 1,2 & 3 will be given but component 4 will not be addressed in control clusters? If there is no intervention in the control arm cluster, what the investigators will do there during follow up (after baseline)? I am unable to clearly understand this aspect. Thank you for the question. All components of the module will be given to only the intervention cluster. The students in the schools selected for the control arm will not receive any intervention from the investigators. They will continue receiving the physical activity routine as per the school curriculum. The school will be offered the modular intervention only at the end of the final follow up data collection. Instrument used for data collection is not available here. Without its availability detailed review of the tool is not possible. Since the journal did not require us to upload the study instrument, we have not included it. The tool will be made available if required. Since it's not a blinded study and intervention (educational intervention) is obvious, whether permission from school authorities (for the control cluster group) will be possible? Consider why and how the schools will give permission to be included in the control cluster. Even if they are not told, they will know that they are part of control cluster if nothing is done apart from bimonthly data collection after the baseline. The schools in the control arm will be informed that the study will help in determining the screen time and sedentary time among their students. Since there has been an increase in mobile phone and gadget usage among adolescents over the years we hope to convince the school authorities that assessing the screen time behaviour among the students over a period of time may result in self introspection of the students regarding their screen usage and sedentary behaviour. Secondly, we hope to convince them since the anthropometric measurement of the students in the control arm will be measured. Also, at the end of the follow up period after assessing the effectiveness of the module, the modular intervention will be offered to all the schools in the control arm. Interim analysis at 3 month seems to be misfit. Why it can't be done or should not be done at first follow up at 2 months? What is the specific advantage of doing it at 3 months at the cost of an additional visit? Thank you Sir. Even though the follow up is at the end of 2 months for every school recruited, the interim analysis will be done at the end of 3 months after the start of the study to ensure sufficient number of schools have been recruited in the intervention and control arm. This is a protocol so dataset may not be applicable. But, study tool and details of multicomponent module may be included. Thank you Sir. The description of the multicomponent module is included under the multicomponent modular intervention section of the manuscript. The actual module will be made available to all if required by the journal."
}
]
}
] | 1
|
https://f1000research.com/articles/13-70
|
https://f1000research.com/articles/12-312/v3
|
11 Mar 24
|
{
"type": "Research Article",
"title": "Investigation of wine fermentation of three-leaf cayratia (Cayratia trifolia L.) using Saccharomyces cerevisiae 2.1",
"authors": [
"Doan Thi Kieu Tien",
"Le Doan Quoc Binh",
"Huynh Thi Ngoc Mi",
"Nguyen Ngoc Thanh",
"Bui Hoang Dang Long",
"Ngo Thi Phuong Dung",
"Ha Thanh Toan",
"Huynh Xuan Phong",
"Doan Thi Kieu Tien",
"Le Doan Quoc Binh",
"Huynh Thi Ngoc Mi",
"Nguyen Ngoc Thanh",
"Bui Hoang Dang Long",
"Ngo Thi Phuong Dung",
"Ha Thanh Toan"
],
"abstract": "Background\nCayratia trifolia has been extensively studied for its bioactive components and medicinal properties. This study was carried out to evaluate the fermentation ability of Saccharomyces cerevisiae 2.1 yeast to determine suitable fermentation conditions.\n\nMethods The initial sugar content for three-leaf cayratia fermentation and fermentation efficiency were calculated. The temperature for three-leaf cayratia fermentation, incubation time, and preliminary 1 liter of three-leaf cayratia wine fermentation were determined. All treatments showed that the total sugar content decreased after 9 days of fermentation compared to the initial level. Temperature during fermentation has a direct effect on yeast activity. Temperature increases the growth of yeast and speed of enzyme activity. The fermentation time changes depending on temperature, initial soluble solid contents, and yeast strains, leading to changes in the ethanol content after the end of fermentation.\n\nResults The results showed that the S. cerevisiae 2.1 was able to ferment at room temperature with an initial pH of 4.5, 24 °Brix, and a yeast density of 107 cells/mL. The appropriate fermentation conditions determined for S. cerevisiae 2.1 were 24 °Brix and incubation at room temperature (28-33°C) with a fermentation time of 11 days.\n\nConclusion In 1-L scale fermentation, three-leaf cayratia wine had 9.46% (v/v) and the fermentation efficiency was 90.34%. The wine produced had a unique color, flavor, and aroma that met the sensory evaluation of the Vietnamese national standard TCVN-3217:79.",
"keywords": [
"Cayratia trifolia",
"ethanol fermentation",
"Saccharomyces cerevesiae",
"three-leaf cayratia wine"
],
"content": "1. Introduction\n\nWine, an indispensable drink that contributes significantly to maintaining and supporting human health, is invested in various ingredients. In the past, France and Italy were the cradles of the wine industry. Countries like Australia and New Zealand have created wine brands with modern technology and high quality. In the Asian market, particularly in Vietnam, wine has been conquering the consumer thanks to its abundant production, competitive price, and novel taste. Wines are fermented alcoholic beverages made from various base ingredients, such as apple, banana, papaya, mango, apricot, pineapple, and jackfruit juice. These are classified as grape wine, fruit wine, berry wine, vegetable wine, plant wine, and raisin wine, as well as flavors from flowers and herbs. Typical wine, natural wines (9–14% alcohol), or dessert and appetizer wines (15–21% alcohol) contain ethyl alcohol, sugar, acids, higher alcohols, tannins, aldehydes, esters, amino acids, minerals, vitamins, anthocyanins (Amerine et al., 1980).\n\nThree-leaf cayratia (Cayratia trifolia) has been extensively studied for its bioactive components and medicinal properties. In particular, thanks to the abundant source distributed throughout the Mekong Delta of Vietnam, its antioxidant and polyphenolic compound contents were not significantly changed after fermentation (Doan et al., 2018d). Additionally, its color and flavor are specific to three-leaf cayratia wine, particularly proven in our previous studies (Doan et al., 2018d, 2019b), and C. trifolia berries are becoming an expected source of winemaking materials from grapes in Vietnam. However, the isolated thermotolerant yeast from C. trifolia berries is mainly used to ferment three-leaf cayratia wine. At the same time, non-thermotolerant S. cerevisiae is the primary source for winemaking at room temperature. Therefore, this study aimed to investigate and evaluate the fermentability of S. cerevisiae to three-leaf cayratia juice isolated from rice wine starters. In addition, 1 liter of C. trifolia juice was fermented to complete the larger-scale fermentation process of three-leaf cayratia wine.\n\nAccording to Ngo et al. (2005), 50 yeast strains have been isolated from wine yeast starters in the Mekong Delta, of which S. cerevisiae 2.1 has the highest fermentability. Since then, strain S. cerevisiae 2.1 has been selected for application in wine fermentation from three-leaf cayratia.\n\n\n2. Methods\n\nWine fermentation of three-leaf Cayratia (C. trifolia L.) using S. cerevisiae 2.1 was conducted between 12/04/2022 and 25/10/2022. Three-leaf cayratia samples were collected from shiny ripe, dark black, and undamaged berries in the Mekong Delta, Vietnam. The fresh berries were brought to the Laboratory of the Industrial Microbiology at the Institute of Food and Biotechnology, Can Tho University. The selected un-crushed ripe samples were washed several times with tap water, rinsed with distilled water, and squeezed out of flesh into juice to conduct further experiments.\n\nS. cerevisiae 2.1 strain was isolated from a rice wine starter and stored at the Laboratory of Industrial Microbiology at the Institute of Food and Biotechnology Institute, Can Tho University (Ngo et al., 2005). A single colony of yeast was inoculated in Yeast extract - Peptone - Dextrose (YPD broth) (yeast extract 0.5%, peptone 0.5%, D-glucose 2.0%; sterilized at 121°C for 15 min) and shaken at 180 rpm at 30°C to 109 cells/mL of yeast inoculum level (using Haemocytometer – Neubauer).\n\n2.2.1 Determination of initial sugar for three-leaf cayratia fermentation\n\nThree-leaf cayratia juice was added to NaHSO3 (140 mg/L) and left alone for 2 h after being adjusted to 20, 24, and 28 °Brix (using sucrose provided by Bien Hoa Sugar Joint Stock Company) and pH 4.5 (Doan et al., 2018b, 2018d). One mL of S. cerevisiae was inoculated to 99 mL of three-leaf cayratia juice (107 cells/mL after inoculation) in a 250 mL Erlenmeyer flask. The flask was sealed with a water lock and incubated at room temperature (in triplicate). The changes in pH, °Brix, and ethanol contents were measured after 9 days of fermentation Nguyen (2007). The total sugar content of the fermentation process was analyzed according to Nielsen (2010), and fermentation efficiency was calculated.\n\nFermentation efficiency is calculated according to ethanol fermentation efficiency on the amount of sugar used, H (%) = (Et°*0.789*10)/(S*0.5111) where H: fermentation efficiency; Et°: alcohol content obtained (% v/v); 0.789: density of ethanol (0.789 g/cm3); 10: conversion factor; S: the actual amount of sugar used in glucose (following the phenol-sulfuric method); 0.5111: the grams of theoretical ethanol obtained from 1 gram of glucose.\n\n2.2.2 Determination of temperature for three-leaf cayratia fermentation\n\nThree-leaf cayratia juice was prepared with °Brix, selected from a previous experiment. After inoculation with 1 mL yeast culture, three-leaf cayratia juice was fermented at 25°C, room temperature (28–33°C), and 35°C for 9 days. The changes in pH, °Brix, and ethanol contents were determined as described above.\n\n2.2.3 Determination of incubation time for three-leaf cayratia fermentation\n\nThree-leaf cayratia juice was prepared with °Brix selected from the experiment as mentioned in Section 2.2.1, and incubated at the selected temperature from the experiment in Section 2.2.2, on days 7, 9, 11, and 13. The changes in pH, °Brix, and ethanol content were determined (see Section 2.2.1).\n\n2.2.4 Preliminary 1 liter of the three-leaf cayratia wine fermentation\n\nThe initial sugar content, fermentation temperature, and fermentation time were determined based on the selective results of previous screening tests to ferment 1 liter of three-leaf cayratia juice (triplicate). Sensory evaluation of wine was based on the criteria of clarity, color, aroma, taste, and overall confidence according Vietnamese national standard 3217:79 (TCVN 3217:79), which is done through a sensory board consisting of 10 members at the Institute of Food and Biotechnology, Institute Can Tho University. The changes in pH, °Brix, ethanol content, and total sugar content were determined (see Section 2.2.1).\n\n2.2.5 Statistical analysis\n\nThe analyzed data were processed using Excel 2013 (RRID:SCR_016137) (Microsoft Inc., USA). The variance and the Lease Significant Difference (LSD) were analyzed using SPSS Version 27.0.1.0 (RRID:SCR_002865) and Statgraphics Centurion XV - https://www.statgraphics.com/ (Manugistics Inc., USA).\n\n\n3. Results\n\nThree-leaf cayratia fermentation processes were conducted with an initial pH of 4.5 and an initial sugar content of 20, 24, and 28 °Brix, respectively. As to the results, all treatments show that the total sugar contents decreased after 9 days of fermentation compared to the initial level (Table 1). The ethanol content was the highest at 7.17% v/v in the 24 °Brix treatment, which is a significant difference compared to the 20 and 28 °Brix treatments. When the sugar concentration is too high, yeast cells shrink and die, lowering the alcoholic fermentation efficiency. In principle, the rate of fermentation and the maximum amount of ethanol decreased when the sugar concentration was increased. However, a particular type of yeast strain can be selected, conditioned to grow at higher sugar concentrations (>30% sugar) and adapted (Matei & Kosseva, 2017).\n\nThe total sugar content of the samples was determined using the phenol-sulfuric acid method (Nielsen, 2010), measured at a wavelength of λ = 490 nm. The linear regression equation was y = 0.0095x + 0.0049. The total sugar content after fermentation reflected the fermentation efficiency of S. cerevisiae 2.1. The 24 °Brix treatment had the highest fermentation conversion efficiency of 91.00% produced by S. cerevisiae 2.1, 82.47% at 20 °Brix treatment, and 75.13% at 28°Brix treatment, which was significantly different from 5% (p<0.05). The fermentation conversion efficiency was proportional to the ethanol content (Table 2). The highest alcohol content (7.17%) was produced in the 24 °Brix treatment. S. cerevisiae strains are tolerant to low pH, high sugar content, and high ethanol concentrations compared to other species, thus reducing the risk of bacterial contamination during industrial fermentation (Nevoigt, 2008).\n\nThe ethanol content was significantly different depending on the incubation temperature (Doan et al., 2019a). Temperature during fermentation has a direct effect on yeast activity. In this study, the ethanol content was produced at 6.94% (v/v) at room temperature, higher than that of 25°C (6.16% v/v) and 35°C (4.28% v/v). The optimum temperature for the growth and multiplication of ordinary yeast is 30°C and is usually inhibited at temperatures higher than 32°C.\n\nTemperature increases the growth of yeast and speed of enzyme activity. Because of the increased membrane fluidity, cell sensitivity to the toxic effects of alcohol increases with temperature. Thus, yeast viability may rapidly decline at temperatures above 20°C during wine fermentation. Normal cider production occurs at 20–25°C and lasts for 1–4 weeks (Waites et al., 2001).\n\nThe fermentation time changes depending on temperature, initial soluble solid contents, and yeast strains, leading to changes in the ethanol content after the end of fermentation (Figure 1). The results showed the highest ethanol content at 11 days compared to 13, 9, and 7 days with 8.93%, 8.54%, 6.94%, and 6.23% v/v, respectively. There were no significant differences between 7 to 9 days and 11 to 13. However, these values were significantly different between days 7 and 11 (Table 3).\n\nThe end time of fermentation was inversely proportional to the degree of Brix after fermentation. The longer the time, the lower the °Brix, and the higher the ethanol concentration produced. Initially, when the ethanol concentration was quite low, the ethanol concentration began to increase, and the sugar content decreased.\n\nFermentability of fruit wine was tested with a volume of 1 liter, surveyed with a density of S. cerevisiae 2.1 at 107 cells/mL for 11 days at room temperature, and the juice was adjusted to pH 4.5 and 24 °Brix. From the above experiments, it can be seen that S. cerevisiae 2.1 produced an ethanol content of 9.49% (v/v), and the fermentation efficiency was quite high, reaching 90.34%.\n\nAfter fermentation, the sensory properties were evaluated according to the criteria of TCVN 3217:79. Three-leaf wine was evaluated as good in clarity, color, aroma, and taste, reaching 4.4, 4.2, and 3.8 points, respectively. Sensory evaluation results show that the wine had no strange, cloudy smell, and the color and odor were very specific to the product. Compared to the TCVN 3217:79, the sensory quality assessment of left-sided wine received a good rating.\n\n\n4. Discussion\n\nIn a previous study, we isolated 151 strains of yeast from 53 samples of C. trifolia in the Mekong Delta. Of these, 30 isolates were highly fermentative and produced ethanol concentrations between 6.0 and 9.9% (v/v) (Doan et al., 2018c). The fermentability of thermotolerant yeast isolates from three-leaf juice showed that the survey with 3.6 of the natural pH, 22 °Brix by adding sucrose, the initial yeast density of 106 cells/mL, and 7 days of incubation time at 37°C. Saccharomyces sp. CT3.2 has a fast filling time for the gas column in the Durham tube (after 12 h), and the ethanol content after fermentation was not high (5.4% v/v). In contrast, Saccharomyces sp. HG1.3 has a slower gas column filling time (after 18 h) but produces the highest ethanol content (9.9% v/v) (Doan et al., 2018b). Meanwhile, with initial fermentation conditions of pH 4.5, and 20 °Brix fermented at 35°C for 6 days, Saccharomyces sp. HG1.3 gave the ethanol content of post-fermentation three-leaf fruit wine 12.0% v/v (Doan et al., 2018d).\n\nThe fermentability of thermotolerant yeasts was investigated at pH 4.5, 22 °Brix, 107 cells/mL of the initial three-leaf juice, and at 37°C for 7 days. The ethanol contents of three-leaf wine produced by CM3.2, CM3.3, and BT1.2 were 8.95%, 7.01%, and 6.79% v/v, respectively (Torija et al., 2003; Doan et al., 2018a).\n\nThe fermentation of 1-liter results shows that the ethanol content met the Vietnam standard 6-3:2010/BYT of the Ministry of Health for wine (Vietnam National Standard 3217:79, 1979), which is also similar to fermentation studies on watermelon wine (Nguyen, 2010; Ngo et al., 2011), pineapple wine (Nguyen et al., 2013), and sim wine (Nguyen, 2010). However, the concentration value is lower than that of fruit wine fermented by a tolerant yeast strain isolated from fruit but aged at 35°C; for example, the strain S. cerevisiae AG2.1 is 11.36% (v/v) (Doan et al., 2018c), and S. cerevisiae CM3.2 is 12.46% v/v (Doan et al., 2019b).\n\nThe fermentation of 1 L results shows that the ethanol content meets the Vietnam Standard 6-3:2010/BYT of the Ministry of Health for wine, which is also similar to fermentation studies on watermelon wine (Ngo et al., 2011), pineapple wine (Nguyen et al., 2013), and sim wine (Nguyen, 2010). However, the concentration value is lower than that of fruit wine fermented by a tolerant yeast strain isolated from fruit but aged at 35 °C; for example, the strain S. cerevisiae AG2.1 is 11.36% (v/v) (Doan et al., 2018c), S. cerevisiae CM3.2 is 12.46% v/v (Doan et al., 2019b).\n\n\n5. Conclusion\n\nThis study aimed to test the fermentative capacity of the S. cerevisiae 2.1 strain isolated from a starter on three-leaf cayratia juice. However, microbiological and physicochemical criteria have not yet been implemented. The results showed that the S. cerevisiae 2.1 strain was able to ferment at room temperature with an initial pH of 4.5, 24 °Brix, and yeast density of 107 cells/mL. Preliminary 1 liter of fermentation for 11 days produced an ethanol content of 9.49% (v/v).\n\nThis study was approved by the research group at Can Tho University and Can Tho University of Technology, Vietanm. All authors mentioned in the manuscript have agreed to authorship, read and approved the manuscript, and provided consent for submission and subsequent publication of the manuscript. The authors declare no conflicts of interest.",
"appendix": "Data availability statement\n\nFigshare: Wine fermentation of three-leaf cayratia. figshare. Dataset, https://doi.org/10.6084/m9.figshare.22256188.v1 (Phong, 2023).\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 express their appreciation to QUVAE Research and Publications for their valuable aid in depositing raw data to the Figshare repository.\n\n\nReferences\n\nAmerine MA, Kunkee R, Ough KCS, et al.: The technology of wine making. 4th ed.Westport, Connecticut: AVI; 1980; 185–703.\n\nDoan TTK, Lu NH, Nguyen TN, et al.: Isolation and selection of thermotolerant yeasts for wine production from three-leaf cayratia (Cayratia trifolia L.), in Vietnamese. The Journal of Agriculture and Development. 2018a; 2: 55–64.\n\nDoan TTK, Vien YTH, Huynh PX, et al.: Selection of thermotolerant yeasts and application in wine production from three-leaf cayratia (Cayratia trifolia L.) in Hau Giang, in Vietnamese. Can Tho University Journal of Science. 2018b; 54(4B): 64–71.\n\nDoan TTK, Huynh THA, Nguyen TNM, et al.: Selection of thermotolerant yeasts for production of three-leaf cayratia (Cayratia trifolia L.) wine in Kien Giang, in Vietnamese. Science and Technology Journal of Agriculture and Rural Development. 2018c; 2: 54–62.\n\nDoan TTK, Huynh MTN, Nguyen DD, et al.: Total polyphenol content and antioxidant capacity of Cayratia trifolia (L) Domin berries before and after fermentation using thermotolerant yeast Saccharomyces cerevisiae HG1.3, in Vietnamese. Vietnam Journal of Science and Technology. 2018d; 60(8): 44–60.\n\nDoan TTK, Huynh PX, Yamada M, et al.: Characterization of newly isolated thermotolerant yeasts and evaluation of their potential for use in Cayratia trifolia wine production. Vietnam Journal of Science and Technology. 2019a; 61(1): 68–73. Publisher Full Text\n\nDoan TTK, Huynh MTN, Lu NH, et al.: Evaluation of total polyphenol and antioxidant capacity in wine fermentation of three-leaf cayratia from Ca Mau province using Saccharomyces cerevisiae CM3.2, in Vietnamese. Can Tho University Journal of Science. 2019b; 55(2): 285–291.\n\nMatei F, Kosseva MR: Chapter 2 - Microbiology of Fruit Wine Production. Science and Technology of Fruit Wine Production. Academic Press; 2017; pp. 73–103.\n\nNevoigt E: Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews. 2008; 72(3): 379–412. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNgo DTP, Ly HLH, Huynh PX: Isolation, selection of yeasts and determination of factors affecting watermelon wine fermentation, in Vietnamese. Can Tho University Journal of Science. 2011; 2011(18b): 137–145.\n\nNgo DTP, Rombouts FM, Nout MJR: Characteristics of some traditional Vietnamese starch-based rice wine fermentation starters (men). Food Science and Technology/LWT. 2005; 40: 130–135.\n\nNguyen VM: Biochemistry practice. HaNoi: Vietnam National University Press; 2007.\n\nNguyen TM: Stability and improvement of wine “sim” quality through chemical and biological method. Can Tho University Journal of Science. 2010; 14: 195–204.\n\nNguyen TV, Nguyen TM, Tran QT, et al.: Isolation, selection and identification of yeast strains for pineapple wine fermentation, in Vietnamese. Can Tho University Journal of Science. 2013; 25: 27–35.\n\nNielsen SS: Food Analysis Laboratory Manual. 2nd ed.New York: Springer; 2010.\n\nPhong H: Investigaton of wine fermentation of three-leaf cayratia (Cayratia trifolia L.) using Saccharomyces cerevisiae 2.1. figshare. Dataset. 2023. Publisher Full Text\n\nTorija MJ, Rozès N, Poblet N, et al.: Effects of fermentation temperature on the strain population of Saccharomyces cerevisiae. International Journal of Food Microbiology. 2003; 80(1): 47–53. Publisher Full Text\n\nVietnam National Standard 3217:79: Liquors, Sensory evaluation-Methodlogy Test by Means of Marking, in Vietnamese. Ha Noi, Viet Nam: Ministry of Science and Technology; 1979.\n\nWaites MJ, Morgan NL, Rockey JS, et al.: Industrial Microbiology. Blackwell Science Ltd.; 2001."
}
|
[
{
"id": "263138",
"date": "06 May 2024",
"name": "Javier Alonso-Del-Real",
"expertise": [
"Reviewer Expertise Laboratory scale wine fermentation by Saccharomyces cerevisiae"
],
"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 present paper aims to describe the suitability of a particular yeast strain isolated in a previous related work for the fermentation of Cayratia trifolia fruits. To that purpose authors conduct several fermentation experiments with different amount of initial sugars and temperature set up. Based on that, they determined the most suitable conditions in micro scale fermentation, and then scale up to pilot scale with a positive outcome.\nAlthough the manuscript harbors potential interest from a biotechnological point of view, several issues need to be addressed.\nFirst of all, some of the conclusions presented are not supported by the results or the experiments conducted. Also, The reader may have trouble finding the link between some of the conclusions and the results supporting them. The authors may find these cases detailed below so that they can improve this aspect.\nMoreover, authors should clearly explain the statistical treatment of the obtained data. In the paper, it is stated that three replicates have been used, but there is no indication about what are the values presented (presumably mean values). In addition, errors or standard deviations, as well as tests conducted to determine possible significant differences were not shown.\nAlso, the writing itself is an issue of concern, as it is sometimes difficult to follow. I would strongly recommend to consider a professional English editing service. Not only phrasing, but punctuation is confusing at some points. Also, the text is unnecessarily repetitive in some occasions, and ideas are not expressed in a cohesive and coherent way.\nSome particular comments reflecting these general considerations are the following:\n-In Abstract Methods section, the sentence \"The temperature for three-leaf cayratia fermentation, incubation time, and preliminary 1 liter of three-leaf cayratia wine fermentation were determined\" should be rephrased. Should \"preliminary\" be accompanying a noun?\n-In general, Abstract Methods section reflects a content more suitable for a results section. Please, modify that section accordingly.\n-The Conclusion Abstract section also has a content more suitable for a results section.\n- The first sentence of the introduction about the impact of alcoholic beverages on health is not in agreement with WHO, based on several recent studies such as Anderson BO et al, 2023 [Ref 2]\n\n-The word \"fermentability\" is used as a characteristic typical of yeast, but it would rather refer to a carbon source or a growth medium. Anyway, authors should provide an objective set of parameters defining quality of yeast in fermentation to justify the strain selection.\n-Some background about in vitro fermentation of three-leaf cayratia, their properties and biotechnological potential should be furthered commented. Otherwise, the work would remain quite out of focus.\n-In section 3.1, authors state that yeast die in the highest sugar concentration condition. However, results from a cell viability test should be provided to prove it. Anyway, another explanation would be a slower fermentation rate, probably because adjustment to higher sugar concentrations at the initial must normally requires a significant amount of time. In any case, it would be nice to have data of the dynamics of both the fermentation and the yeast growth.\n-In section 3.2, authors claim that ordinary yeast optimal temperature is 30ºC, but they probably refer to S. cerevisiae. There is a wide range of optimal growth temperatures for other yeast. Also, they state that their growth is inhibited above 32ºC, but this is simply not correct [Refer Ref 1]. After that, authors affirm that temperatures above 20ºC could provoke yeast viability to lower down, which seems contradictory. All in all, discussion of the results are not appropriated in its current state.\n-In section 3.3, the relationship between fermentation and temperature is introduced. However, the results presented do not correspond to anything about temperature. Also, the method to determine the end of the fermentation is not presented. It rather seems a serial sampling of the same fermentations at different time points.\n-Figure 1 relevance is hard to interpret.\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? 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": []
},
{
"id": "289555",
"date": "22 Jun 2024",
"name": "Susan Abdul Raheem Hasan",
"expertise": [
"Reviewer Expertise Microbiologist and expert in biological fermentation processes",
"with a particular focus on probiotics and plants."
],
"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 (Investigation of wine fermentation of three-leaf cayratia (Cayratia trifolia L.) using Saccharomyces cerevisiae 2.1) investigates the optimal conditions for the fermentation process. It discusses each condition and whether it was appropriate to meet the best efficiency (the aim of the study). This purpose was cleared in the context in detail. The materials were mentioned with their sources clearly and appropriate to their need and use in methods. Some methods details were not mentioned, but the source was written so the reader or researcher could follow the references for some unclear steps in the processes of this work. All following parts of the article were transparent and agreed or disagreed with the indexed sources and references for results and conclusion. It also mentioned some further criteria, such as microbiological and physiochemical to be studied. Some issues need to be solved or cleared to improve the article:\nMethod in abstract missing details such as (volumes, weights, etc.) that were tested, which then were cleared in the main part of the manuscript. It is crucial to emphasize the need for additional Statistical analysis, which will further strengthen the validity of the findings. It is essential to discuss the effect of a lower amount of sugar, as this could potentially significantly impact the fermentation process. Further information and details should be added to a conclusion as in the abstract.\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? Partly",
"responses": []
}
] | 3
|
https://f1000research.com/articles/12-312
|
https://f1000research.com/articles/12-817/v1
|
11 Jul 23
|
{
"type": "Research Article",
"title": "Clinical and seasonal pattern of dengue: Persistent hyper-endemicity of a vector borne disease from Southern-West Coastal India",
"authors": [
"Darshan BB",
"Ramesh Holla",
"Bhaskaran Unnikrishnan",
"Basavaprabhu Achappa",
"Robin Poovattil",
"Ashir Sharma",
"Shawna Simmy",
"Suryansh Prateek",
"Darshan BB",
"Bhaskaran Unnikrishnan",
"Basavaprabhu Achappa",
"Robin Poovattil",
"Ashir Sharma",
"Shawna Simmy",
"Suryansh Prateek"
],
"abstract": "Background: Dengue is an emerging global viral disease with an increase 30-fold in incidence in the past fifty years. In the past decade it was restricted to only few a states of South and Northern India but in the recent past it has affected almost all the states in India. The objective of this study was to assess the clinical profile, trends and outcome of dengue cases. Methods: This retrospective record based cross-sectional study was conducted in tertiary hospitals, Mangaluru in Southern India. The study population included all clinical dengue positive cases over a period of five years. Information from pre-recorded case sheets were used for data collection. The data collected was entered and analyzed in SPSS Version 20. Results were expressed in percentages, means and graphs. Results: The study included 401 dengue cases. Most cases were in the age range of 20-40 years with a male to female ratio of 3:2. Overall seropositivity rate was 23.94% with High IgM prevalence. Monthly distribution showed a maximum incidence in the months of June and July and minimum incidence in January and February. Among the study participants, 91.5% of patients recovered completely and 1.7% of patients had died. 8.7% of patients were discharged against medical advice. Conclusions: Dengue continues to be major public health problem which indirectly hints towards the hyper endemic nature of this disease in this part of the globe affecting mainly the working age group. Low seropositivity with High IgM prevalence makes dengue an important differential for febrile illness of vague nature and invokes the need for robust public health response to curb the hyper-endemicity.",
"keywords": [
"Dengue",
"Record based Study",
"Tertiary care Hospital",
"South India"
],
"content": "Introduction\n\nDengue is an emerging global viral disease with an increase in incidence of 30 times in the past fifty years. Nine countries were affected before the 1970s but now more than 100 counties have severely been affected with dengue epidemics with the Southeast Asian region and the Western Pacific region being the most severely affected. 390 million cases of dengue occur annually with 96 million showing clinical manifestation.1\n\nThe first case of dengue was reported by Benjamin Rush in 1789. Up until the middle of 20th century it was restricted to few geographical locations, but with the population movement during the Second World War there were recurrent epidemics with the re-emergence of the disease.2\n\nEven though the first epidemic of dengue was reported from Chennai in India, the virologically proven epidemic occurred in Kolkata in the 1950s. There were cases of dengue hemorrhagic fever and dengue shock syndrome in Delhi and Lucknow in the year 1996, thereafter with a cyclical pattern occurring every 2-3 years.2\n\nIn the past 20-30 years it was mostly restricted to only a few states of South and Northern India but in the last decade it has affected almost all the states of India.3\n\nDengue is viral vector borne disease spread by the day-biting endophilic Aedes mosquito. Its clinical features tend to be vague and nonspecific, ranging from fever to hemorrhage to shock with no specific treatment but supportive care.4,5\n\nGeographically, dengue is more prevalent in tropical countries like India. With that background understanding, we conducted our study in the coastal part of South India where developmental activities are on a rise with rapid urbanization where the study population is at a high risk of being affected with dengue. Our study was conducted to determine the socio-demographic and clinical profile along with the disease outcome of dengue patients. As information regarding the trend, burden and distribution of the disease is vital to plan disease control strategies and optimum utilization of the resources, our study aims to further contribute to the knowledge base regarding this disease.\n\n\nMethods\n\nRetrospective record-based Cross sectional study design\n\nThe study was conducted at Government Wenlock Hospital, a tertiary care teaching hospital affiliated to Kasturba Medical College, Mangalore.\n\nBeing a hospital which receives a confluence of patients from neighboring districts of Karnataka and from northern parts of Kerala, our study population well represents the burden of dengue in the South Western part of India.\n\nThe study population was dengue patients admitted to Government Wenlock Hospital within the time frame of five years from 2013 to 2017.\n\nInclusion criteria: Clinically confirmed Dengue cases admitted at the above-mentioned time period.\n\nExclusion criteria: All case sheets with inadequate or incomplete data were excluded from the study.\n\nThe IEC (Institutional Ethics Committee) of Kasturba Medical College, Mangalore (Manipal Academy of Higher Education) has reviewed the study and has granted approval prior to the onset of the study. Owing to the nature of study design as retrospective record based study, informed consent was waived by the Ethics Committee. Confidentiality of the present study data was maintained in accordance with the Declaration of Helsinki.\n\nCase sheets of Dengue positive patients fitting the inclusion criteria were carefully analyzed. Relevant demographical, clinical and biochemical parameters were recorded onto the data collection sheet.\n\nData collected was then analyzed with SPSS version 20. Results have been expressed in means, proportions and standard deviations.\n\n\nResults\n\nOur study was able to reinforce the prevalence of certain demographic trends that has been observed among patients affected with Dengue. Out of the 401 patients studied, 245 (61%) were males with a male to female ratio of 3:2. Majority of the cases fell under the age bracket of 20-40 years (169 cases, 42.1%) (Table 1). Certain demographic details such as occupation, marital status, place of residence were not available for all the patients and hence were not reported upon in our results.\n\nThe most common and consistent clinical feature with which most of the patients presented with was fever (398, 99.3%) proceeded by chills and rigor (256, 63.8%) followed by myalgia (194, 48.4%) (Table 2).\n\n* Multiple responses.\n\nIn line with expected trends, it was observed that most of our cases (n=368, 95.8%) had thrombocytopenia. 81.6% of patients had elevated SGOT and 48% had elevated SGPT enzyme levels indicating certain degree of hepatocyte injury during the acute phase of the infection.\n\nHowever, a closer look at the seropositivity rate amongst the study population posed some interesting queries. Out of the 401 cases, only 96 cases showed elevated IgG or IgM (total seropositivity rate of 23.94%). Separately, seropositivity rate of IgM was 22.9% and of IgG was 2.7%. Sex wise distribution shows 25.7% seropositivity in males and 22.72% seropositivity among females.\n\nBut amongst the seropositive patients 57.29% (55 cases) were female and 42.7% (41 cases) were male (Table 3).\n\nFrequency distribution of seropositive cases with respect to age showed that most cases (36, 37.5%) were in the age group of 20-40yrs followed by <20yrs (32, 33.3%).\n\nIn our study, it was observed that despite the state of presentation and clinical course the mass preponderance was towards recovery with a recovery rate of 91.5% (n=367). Case fatality rate was recorded to be 1.7% (Table 4).\n\nDengue being a vector borne disease was expected to boom in accordance with the monsoon seasons and our study was able to confirm this. As depicted by Figure 1 [Month wise distribution of dengue cases (n=401)], most of the cases were found to have been admitted during the months of June and July with a declining trend both pre- and post-monsoons. The months of January to April were shown to have a consistently low prevalence.\n\n\nDiscussion\n\nDengue is an upcoming and swiftly spreading vector borne disease that has taken strong hold in India.4 Owing to the complicated interplay between the host, agent, vector, and environmental conditions, the number of cases in India has consistently increased substantially over the past ten years.6 It is now even considered as a hyper endemic disease in certain parts of India. As Das et al. demonstrated in their study, the available data on dengue prevalence in India is just the tip of the iceberg and that further weighs down the preventive measures taken to reduce the brunt of the burden.7 Having recognized the need for comprehensive stratified data on dengue prevalence and its trends to further the knowledge database in Indian population, we focused our study to assess the various clinical, sociodemographic and climactic factors.\n\nOur study was able to demonstrate a significant male preponderance (male = 61%, females = 39%) in incidence with a male to female sex ratio of 1.5:1. Similar observations have been made by a multitude of studies, yet a conclusive reasoning has not yet been attributed to this trend.8 Doke and Pawar has attributed this finding to the nature of dressing among women which reduces the amount of skin exposure.9 Other studies have explained this as a product of reporting bias among females as it has been seen that traditional practitioners are the first point of contact for the large majority of symptomatic female population.10 A few studies even postulated that this disparity could be due to the skewed sex ratio leaning towards the side of males in the general population.11\n\nApart from the male preponderance, our research found that the productive working class aged 20-40 years was the age group most affected. Owing to the declining rate of incidence with advancing age, it could be said that infants, adolescents and young adults are at higher risk of developing dengue. Similar trend has been observed in other studies wherein they found that dengue is a disease that primarily affects the children and the young adults.3,12–15\n\nCombined, the age and sex distribution findings could be attributed to the complex interplay between outdoor nature of work (among men),9 dressing patterns (among women), skewed sex ratio and diurnal feeding habbits of Aedes aegypti.4\n\nMost of the cases were found to have occurred in the months of June and July, with the maximum being 120 cases. A study conducted by Kumar et al. in a coastal city of Karnataka revealed the maximum cases were found to have occurred in the month of September while a meta-analysis conducted by Ganeshkumar et al. found that most cases were seen in the monsoon and post monsoon seasons.13,16 The peri-monsoon seasonality of dengue has also been promptly emphasized by a number of studies which implicates that there is a strong correlation that exists between temperature and humidity to the favourable breeding conditions for the mosquitoes.3,13,14 During rainy season environmental changes such as artificial water stagnation, especially in low lying areas, labour settlements and small collection of water in tyres and flowerpots act as favourable breeding grounds for the vector which conclusively explains the precipitous climb of dengue cases during June to September.14\n\nThe clinical picture of patients in our study revealed that fever was present in almost all cases (99.3%) followed by chills and rigor (63.8%). Haematological symptoms included hematemesis and haematuria which were present in 12% and 7% of cases respectively. A meta-analysis conducted on a global scale on dengue outbreaks came to an almost similar picture with fever (98.1), chills (65.3), myalgia (64.2), arthralgia (53.6), body pain (67.2), vomiting (39.8) etc. with similar haematological symptoms like haematuria and hematemesis which were seen in 5% and 13.4% of cases respectively.17\n\nLiver functions test showed abnormal rise in almost 99% of patients of SGPT and SGOT levels but SGOT levels were more prominent in most patients as compared to SGPT, similar research done in Punjab in 2007 had similar results with 98.9% of patients showing a rise in either of SGPT or SGOT levels indicating a strong heptic predeliction for dengue virus.18 A dedicated study regarding dengue and hepatopathy also revealed similar results of elevated SGOT and SGPT with the former being more elevated than the latter.19\n\nThrombocytopenia is the most common laboratory finding in dengue patients and is referred to as an early marker and prognostic factor for the management and recovery of dengue fever.20 Of 384 dengue patients studied, 368 patients had thrombocytopenia (platelet count less than 100,000 per mm3).\n\nOur study revealed a seropositivity rate of 23.94% which is similar to another study conducted by Kalita et al. where they repoted a seropositivity of 14.85%.21 Along with having a low seropositivity rate, it was seen that High IgM prevelance was noted in our study. As concluded by Eshetu et al., high IgM prevelance is indicative of active transmission of dengue which could account for the hyperendemic status of dengue in Southern India.22\n\nOur study included 401 serologically confirmed dengue cases out of which 367 cases (91.5%) were found to have recovered completely. Seven deaths were recorded (1.7%), and 27 cases (6.7%) were found to have been discharged against medical advice. A meta-analysis conducted in India, found that the pooled CFRs of the studies was 2.6% which was in line with findings of the present study.16\n\n\nConclusion\n\nDengue remains to be a major public health problem which indirectly hints towards the hyper endemic nature of this disease in this part of the globe, affecting mainly the working age group. With vague nonspecific clinical features combined with low seropositivity rate, it is of paramount importance to keep dengue as a key differential when a patient presents with febrile illness of nonspecific nature. Clinical judgement with classical biochemical parameters involving platelets as demonstrated and reinforced by our study should take priority over serological status of the patient when it comes to making a diagnosis of dengue or excluding it. High IgM seropositivity also hints at the fact that a strong and robust vector control programme must be implemented to at least make a dent in the hyperendemic status of dengue especially during the monsoon seasons.",
"appendix": "Data availability\n\nFigshare: Data.xlsx (demographic and medical information of patients), https://doi.org/10.6084/m9.figshare.21257040.v1. 23\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: Dengue Control.Dengue/severe Dengue. FAQ.2017 [Updated on 2017 Jan 3; Cited 2018 April 26].Reference Source\n\nGupta E, Dar L, Kapoor G, et al.: The changing epidemiology of dengue in Delhi, India. BioMed. Central Ltd. 2006; 3: 92. Publisher Full Text\n\nChakravarti A, Arora R, Luxemburger C: Fifty years of dengue in India. Trans. R. Soc. Trop. Med. Hyg. 2012 May; 106(5): 273–282. Publisher Full Text\n\nWorld Health Organization: Media Centre. Dengue and severe dengue. Fact sheet.2017 [updated on 2017 Apr; cited 2018 Mar 9].Reference Source\n\nWali JP, Biswas A, Handa R, et al.: Dengue Haemorrhagic Fever in Adults: A Prospective Study of 110 Cases. Trop. Dr. 1999 Jan; 29(1): 27–30. PubMed Abstract | Publisher Full Text\n\nMutheneni SR, Morse AP, Caminade C, et al.: Dengue burden in India: recent trends and importance of climatic parameters. Emerg. Microbes Infect. 2017 Aug 9; 6(8): e70. PubMed Abstract | Publisher Full Text\n\nDas S, Sarfraz A, Jaiswal N, et al.: Impediments of reporting dengue cases in India. J. Infect. Public Health. 2017 Sep-Oct; 10(5): 494–498. PubMed Abstract | Publisher Full Text\n\nAgarwal R, Kapoor S, Nagar R, et al.: A clinical study of the patients with dengue hemorrhagic fever during the epidemic of 1996 at Lucknow, India. Southeast Asian J. Trop. Med. Public Health. 1999 Dec; 30(4): 735–740. PubMed Abstract\n\nDoke P, Pawar S: Profile of Dengue fever outbreaks in Maharashtra. Indian J. Community Med. 2000; 25(4): 170–176.\n\nGuha-Sapir D, Schimmer B: Dengue fever: new paradigms for a changing epidemiology. Emerg. Themes Epidemiol. 2005; 2: 1. PubMed Abstract | Publisher Full Text\n\nKumar A, Pandit VR, Shetty S, et al.: A profile of dengue cases admitted to a tertiary care hospital in Karnataka, southern India. Trop. Dr. 2010; 40(1): 45–46. PubMed Abstract | Publisher Full Text\n\nShobha, Lokanath H, Lokanath H, et al.: A retrospective assessment of dengue fever outbreak in Bangalore urban district, Southern India. Int. J. Med. Sci. Public Health. 2014; 3: 845–849. Publisher Full Text\n\nKumar A, Rao CR, Pandit V, et al.: Clinical manifestations and trend of Dengue cases admitted in a tertiary care hospital, Udupi district, Karnataka. Indian J. Community Med. 2010 Jul; 35(3);389–90.\n\nGunusekaran P, Kaveri K, Mohana S, et al.: Dengue disease status in Chennai (2006-2008): A Retrospective analysis. Indian J. Med. Res. 2011; 133: 322–325.\n\nRasul CH, Ahasan HA, Rasid AK, et al.: Epidemiological factors of dengue hemorrhagic Fever in bangladesh. Indian Pediatr. 2002; 39: 369–372. PubMed Abstract\n\nGaneshkumar P, Murhekar MV, Poornima V, et al.: Dengue infection in India: A systematic review and meta-analysis. PLoS Negl. Trop. Dis. 2018; 12(7): e0006618. PubMed Abstract | Publisher Full Text\n\nGuo C, Zhou Z, Wen Z, et al.: Global epidemiology of Dengue outbreaks in 1990-2015: A Systematic Review and Meta-Analysis. Front. Cell. Infect. Microbiol. 2017; 7: 317. PubMed Abstract | Publisher Full Text\n\nSoni A, Patel PM, Malhi NS, et al.: Spectrum of liver dysfunction in patients with dengue infection and the markers of severe disease: study from a tertiary care centre in Punjab. J. Liver Res. Disord Ther. 2017; 3(4): 95–98.\n\nKumar S, Lakhiwal R, Aswal V, et al.: A study of dengue and hepatopathy. Int. J. Res. Med. Sci. 2017; 5: 2625–2628. Publisher Full Text\n\nSingh K, Lale A, Eong OE, et al.: A prospective clinical study on the use of reverse transcription-polymerase chain reaction for the early diagnosis of Dengue fever. J. Mol. Diagn. 2006; 8: 613–616. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKalita JM, Aggarwal A, Yedale K, et al.: A 5-year study of dengue seropositivity among suspected cases attending a teaching hospital of North-Western region of India. J. Med. Virol. 2021 Jun; 93(6): 3338–3343. PubMed Abstract | Publisher Full Text\n\nEshetu D, Shimelis T, Nigussie E, et al.: Seropositivity to dengue and associated risk factors among non-malarias acute febrile patients in Arba Minch districts, southern Ethiopia. BMC Infect. Dis. 2020 Aug 31; 20(1): 639. PubMed Abstract | Publisher Full Text\n\nHolla R:Data.xlsx. figshare. [Dataset.]2022. Publisher Full Text"
}
|
[
{
"id": "187595",
"date": "25 Oct 2023",
"name": "Zinia Nujum",
"expertise": [
"Reviewer Expertise Neglected Tropical 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\nGeneral Comment The study is a single centre study done on a topic of public health relevance, but the information presented is not new. In order to bring in an analytic perspective, I would suggest classification of dengue cases into severe and not severe based on the need for hospitalization or shock and look at the determinants of severity. Since the number of deaths is small, they may also be included as severe dengue.\nSpecific comments\nTitle: The part \"persistent hyperendemicity\" may be taken off from the title. This study has not looked into the serotypes. It is better to keep the title simple as 'Clinical and Seasonal Pattern of Dengue in a tertiary care setting in South West India'.\nDiscussion: \"Our study was able to demonstrate a significant male preponderance (male = 61%, females = 39%) in incidence with a male to female sex ratio of 1.5:1\" - you cannot conclude on incidence from this study, you may say that there is a male preponderance in cases of dengue reporting to this hospital.\nResults:\nOverall IgM/IgG sero-positivity is only 23%. Then how was the diagnosis confirmed in rest of the cases?\n\nWhat proportion of cases were dengue, severe dengue (DHF, DSS, Dengue with organ involvement - expanded Dengue syndrome)?\nConclusions: The conclusions are vague and tend to be written as general statements than from the results of the study.\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": "11092",
"date": "13 Apr 2024",
"name": "Ramesh Holla",
"role": "Author Response",
"response": "Point to point response to Reviewer's comments: Dr. Zinia Nujum 1.Comment: Title: The part \"persistent hyperendemicity\" may be taken off from the title. This study has not looked into the serotypes. It is better to keep the title simple as 'Clinical and Seasonal Pattern of Dengue in a tertiary care setting in South West India'. Author’s Response: We agree with your comment. As per the suggestion title has been modified. Action Taken in the manuscript: As per the suggestion title has been modified. 2.Comment: Discussion: \"Our study was able to demonstrate a significant male preponderance (male = 61%, females = 39%) in incidence with a male to female sex ratio of 1.5:1\" - you cannot conclude on incidence from this study, you may say that there is a male preponderance in cases of dengue reporting to this hospital. Author’s Response: We value your suggestion. Necessary changes have been done in results and discussion section. Action Taken in the manuscript: Necessary changes have been done in results and discussion section. 3.Comment: Overall IgM/IgG sero-positivity is only 23%. Then how was the diagnosis confirmed in rest of the cases? Author’s Response: As a first line of diagnosis, patients were evaluated by using Dengue Non-structural Protein NS1 antigen test which is a rapid test kit. This has been used for the diagnosis in the remaining cases. Action Taken in the manuscript: Necessary changes have been done in results section. 4.Comment: What proportion of cases were dengue, severe dengue (DHF, DSS, Dengue with organ involvement - expanded Dengue syndrome)? Author’s Response: We concur that it is better to provide details regarding Dengue fever, DHF, DSS and Dengue with Organ involvement. As it is a hospital-based record-based study, we didn’t get all these details in the case record forms of the admitted patients. It is because of this reason we couldn’t analyse the data for determinants of dengue severity. Thus, this will be our study limitation. 5.Comment: Conclusions: The conclusions are vague and tend to be written as general statements than from the results of the study. Author’s Response: We are in complete agreement with your observation. Necessary changes have been done in the conclusion section of the manuscript. Action Taken in the manuscript: Necessary changes have been done in conclusion section."
}
]
},
{
"id": "187600",
"date": "25 Oct 2023",
"name": "Biju Soman",
"expertise": [
"Reviewer Expertise Epidemiology",
"Infectious Disease Modeling",
"GIS in public Health",
"Data Science",
"Health Technology 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\nThis is a good attempt at looking at the data from a prominent tertiary care hospital in Mangalore. However, the inference drawn by the authors conflicts with the hospital-based nature of the data. The manuscript should be rewritten as a hospital-based study, and the authors should refrain from giving statements on hyperendemicity, etc. The following detailed comments should be kept in mind while revising the paper.\n“The study population included all clinical dengue positive cases over a period of five years.” (p. 1) Give the exact period and the jurisdiction. If it is the Mangalore town, define it; if it is the district, specify it.\n\n“The data collected was entered and analyzed in SPSS Version 20” (p. 1) Please copy edit\n\n“Results were expressed in percentages, means and graphs.” (p. 1) Please copy edit\n\n“Among the study participants, 91.5% of patients recovered completely, and 1.7% of patients had died. 8.7% of patients were discharged against medical advice.” ( p. 1) Better round the decimal figures to 100%\n\n“Being a hospital which receives a confluence of patients from neighbouring districts of Karnataka and northern parts of Kerala, our study population well represents the burden of dengue in the South Western part of India.” (p. 3)\nThis assumption cannot be justified. Try to present this as a hospital study; at the most, you can claim this hospital as a sentinel hospital and suggest that the trend in this hospital could reflect what is happening in and around this location. However, please remember that Wenloc Hospital can no longer claim to cater to all or even a good majority of Dengue cases in the locality. There are many other government and private hospitals in the area. Also, it would help if you did a trend analysis to state the increase, decrease or other status of Malaria cases coming to the hospital. The Yearwise distribution should be used.\n\n“In our study, it was observed that despite the state of presentation and clinical course, the mass preponderance was towards recovery with a recovery rate of 91.5% (n=367).” ( p. 5) This sentence is also unclear; the manuscript will benefit from thorough copy editing.\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? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "11090",
"date": "13 Apr 2024",
"name": "Ramesh Holla",
"role": "Author Response",
"response": "Point to point response to Reviewer's comments: Dr. Biju Soman 1.Comment: Give the exact period and the jurisdiction. If it is the Mangalore town, define it; if it is the district, specify it. Author’s Response: We are in complete agreement with your observation. Our subset of patients are mainly residents of Dakshina Kannada district of Karnataka, Northern Kerala districts such as Kasargod, Kannur and Wayanad with a minority group of patients from other districts of Karnataka as well. Action Taken in the manuscript: Necessary changes have been done in the Materials and Methods section of the manuscript. 2.Comment: Better round the decimal figures to 100%. Author’s Response: We concur that it is better to round the decimal figures as pointed out. Action Taken in the manuscript: Figures have been rounded off to the nearest whole number. 3.Comment: This assumption cannot be justified. Try to present this as a hospital study; at the most, you can claim this hospital as a sentinel hospital and suggest that the trend in this hospital could reflect what is happening in and around this location. However, please remember that Wenlock Hospital can no longer claim to cater to all or even a good majority of Dengue cases in the locality. There are many other government and private hospitals in the area. Also, it would help if you did a trend analysis to state the increase, decrease or other status of Malaria cases coming to the hospital. The Year wise distribution should be used. Author’s Response: We agree that it would be better to represent our data as a hospital-based study that reflects the Dengue burden in the coastal districts of Kerala and Karnataka. We will also take into consideration the note to add year wise distribution of Dengue cases. Action Taken in the manuscript: Study title has been changed as per the suggestion. The results obtained have been rephrased to be a representation of a hospital-based survey. Year wise distribution of Dengue case load has been added as a graph. 4.Comment: This sentence is also unclear; the manuscript will benefit from thorough copy editing. Author’s Response: We agree that a thorough copy editing would help communicate the conclusions better to the reader. Action Taken in the manuscript: Necessary grammatical changes have been made 5. Comment: “The data collected was entered and analyzed in SPSS Version 20” (p. 1) Please copy edit Author’s Response: We agree that this statement could be rephrased better. Action Taken in the manuscript: This sentence has been rewritten 6. Comment: “Results were expressed in percentages, means and graphs.” (p. 1) Please copy edit Author’s Response: We agree that this statement could be rephrased better. Action Taken in the manuscript: This sentence has been rewritten"
}
]
}
] | 1
|
https://f1000research.com/articles/12-817
|
https://f1000research.com/articles/13-189/v1
|
11 Mar 24
|
{
"type": "Research Article",
"title": "Executive function and decision-making in Colombian patients with paranoid schizophrenia",
"authors": [
"JE Acosta-Lopez",
"M L Cervantes-Henriquez",
"S Téllez-Bustillo",
"Mostapha Ahmad",
"Manuel Sanchez-Rojas",
"C N Paredes-Manrique",
"J A Zegarra-Valdivia",
"M L Cervantes-Henriquez",
"S Téllez-Bustillo",
"Mostapha Ahmad",
"Manuel Sanchez-Rojas",
"C N Paredes-Manrique",
"J A Zegarra-Valdivia"
],
"abstract": "Background Schizophrenia (SCZD) is a mental disorder characterized by cognitive dysfunction, impaired decision-making abilities, abnormalities in brain functioning, and specific genetic markers. Ethnic and racial factors influence the development and presentation of schizophrenia, with different groups experiencing different levels of risk and exhibiting different patterns of mental disorders.\n\nObjective We sought to investigate the executive function and decision-making profile of Schizophrenia participants from Barranquilla, Colombia, which have a high genetic mixture and significant ethnic and racial diversity.\n\nMethods The sample consists of 40 individuals, 20 diagnosed with paranoid schizophrenia and 20 controls. We use the BANFE neuropsychological battery and the Iowa Gambling task to measure executive function and decision-making processes.\n\nResults The study found differences in cognitive performance, measured by the Neuropsychological Battery of Executive Functions and Frontal Lobes, in the medial orbit, anterior prefrontal, dorsolateral, and total executive function measures. In decision-making, as measured by the Iowa Gambling Test, there were also differences between the two groups, with those with schizophrenia performing worse and showing a preference for disadvantageous options. The study also found that there were no significant differences in socio-demographic characteristics between the two groups but that there were differences in terms of socio-economic status and educational level.\n\nConclusion This study found that individuals with paranoid schizophrenia had significant differences in their prefrontal cortex compared to those without the condition, specifically in the dorsolateral and orbital-prefrontal cortex. These differences may be linked to difficulties adjusting to their environment and processing reinforcement, leading to impaired learning and arousal disturbances.",
"keywords": [
"Schizophrenia",
"Colombia",
"neuropsychological assessment",
"executive function",
"decision-making."
],
"content": "Introduction\n\nSchizophrenia (SCZD) is a severe mental disorder that affects approximately 0.5-15 of the general population, occupying 0.9-3.8 cases per 1000 inhabitants.2 This disorder is associated with lasting effects on health, generating an impact on quality of life,3 presenting high costs for medical care, representing 1.1% of the total amount of national spending on health care4,5 in countries such as the United States (Charrier et al., 2013) China,4,6 Malaysia,7 India, England8,9 France,5 Germany,10 Switzerland11 and the rest of Europe.12 In Colombia,13 there is a significant variation in the interventions14 and the direct and indirect costs15 (i.e., employment rates, gender, salary, age, number of hospitalizations, pharmaceutical products, rehabilitation processes and monitoring of patients) compared to other countries.16\n\nNeurophysiology studies of schizophrenia report abnormalities in N200 and P300, functional connectivity measures17,18 electroencephalography EEG19 Quantitative association between the volume of gray matter and ventromedial prefrontal cortex (VMPFC),20 have evidenced alterations in the integration routes related to symptoms and cognitive dysfunction; as a fundamental characteristic of schizophrenia with substantial proportions of inheritability (h2 = 0.33-0. 85),21–25 which makes it possible to elucidate the mechanisms that lead from genes to psychopathology; therefore, genes such as Brain-derived neurotrophic factor (BDNF), Neurotrophic tyrosine kinase receptor 2 NTRK2,26–29 Cholinergic receptor nicotinic alpha 4 subunit (CHRNA4), cholinergic receptor nicotinic beta 2 subunit (CHRNB2), Brain-derived neurotrophic factor (BDNF), neurotrophic receptor tyrosine kinase 2 (NTRK2),30 Gamma-Aminobutyric Acid (GABA),28 Antagonists of receptors 5-hydroxitriptamine type 3 (5-HT3A),31 AKT serine/threonine kinase 1(AKT1),32 Neurogranin (NRGN)33; considered polygenic vulnerability markers34 with minor effects.35 Identifying these biomarkers could contribute to the diagnosis and treatment of schizophrenia.36 associated with neurocognitive deficits,37 inhibitory control, intellectual disability,38,39 working memory,40 visual and verbal memory, speed processing, attention,32,41–45 visual construction,46 social cognition,46 theory of mind,47–49 sensory processing, facial recognition deficits,50 and decision making.49,51 The identification of these markers could contribute to the diagnosis and treatment of schizophrenia36\n\nRegarding decision-making in patients with schizophrenia, most studies showed deficiencies in the Iowa Gambling Test (IGT), which suggests a preference for disadvantageous cards,52 which poses a reduced sensitivity to punishments, being unable to regulate their decision-making to implement practical strategies, even when the probabilities of winning or losing are explicitly revealed.53,54 In selecting and initiating action, through the integration of sensorimotor, cognitive, and motivational/emotional information.55\n\nThis work is of particular interest because Colombia is an ethnically diverse country presenting the highest levels in Latin America56,57 of mixtures by three groups (Indigenous/Amerindians, Spaniards, and Africans).58 The miscegenation process was selective to the point of having regions of African descent59–62 predominantly Caucasian or indigenous.63,64 Other prominent minority populations are concentrated on the Caribbean Coast.58,65 For example, the city of Barranquilla is the result of a mixture between the Afro-descendant population, white Europeans from Andalusia, Spain, Syrian Lebanese, Sephardic Jews, Germans, Italians and English.66–69 Colombia has one of the highest levels of genetic admixture of the three groups.70–72\n\nSignificant interactions have been found between race/ethnicity73,74 sociocultural traditions, education, linguistically different populations, developmentally presupposed behavioral stereotypes, typical patterns, and mental disorders73 in minority groups (i.e., Asian, Black, African American, White, Hispanic) who are at low risk for mental disorders, but not evenly across racial/ethnic groups or disorders.75\n\nThis study aims to characterize the executive function, specifically the decision-making of the people affected by the schizophrenia of a sample with these characteristics related to the demographic location.\n\n\nMethods\n\nWe recruited 40 participants for this study (20 controls and 20 Schizophrenia). Participants were selected according to the following The Diagnostic and Statistical Manual of Mental Disorders, fourth edition, text revision (DSM-IV-TR) criteria guidelines for paranoid schizophrenia. The control participants were recruited from the Health Services of Primary Attention and university students from Barranquilla City. The mean age of the sample was 33.80 ± 4.66 years old. 67.5% of the participants were females. Further details are provided in Table 1.\n\nRetrospective ex post facto study with two groups.76 Sampling was non-probabilistic and intentional. For the sample selection, we proceeded to request the respective permits in the hospital. Subsequently, informed consent was obtained from each participant. Controls were recruitment from Health Services of Primary Attention and the university. After approval, the participants were selected considering the following inclusion/exclusion points: a) the presence of any medical illness that prevents the evaluation; b) uncorrected sensory alteration (visual problems) that prevented the correct execution of the neuropsychological test; c) management and understanding of the tests instructions in the Spanish language; d) presence of psychiatric symptoms or severe cognitive alteration that prevented the evaluation, e) signed consent.\n\nThis study adhered to the ethical considerations for clinical trials, ensuring that all methods were conducted in accordance with the relevant guidelines and regulations of the Declaration of Helsinki. Participants were fully informed about the aims and potential risks of the study, and gave written consent. Ethical approval for the research was obtained from the Ethics Committee of the Universidad Simón Bolívar, created under internal regulation N° 00001 on 11/05/06 in Barranquilla, Colombia, which granted this research with the code CIE-USB-0075. Following approval by the ethics committee, participants were informed of the purposes of the study and their written consent was obtained.\n\nCrucially, all data collected during the research were stored anonymously in a database, ensuring the confidentiality and privacy of participants’ information. This additional measure reflects an ongoing commitment to the ethical principles outlined in the Declaration of Helsinki and safeguards the integrity of the research.\n\nBrief Psychiatric Rating Scale (BPRS): The Brief Psychiatric Rating Scale (BPRS) was created by Overall and Gorham77,78 and assesses symptomatologic changes in psychiatric patients. There is a validated Spanish version.79 It is currently used as a measure of severity and subtyping in schizophrenia. This assessment scale is probably the most widely used in psychiatry. This test initially consisted of 16 items, although there is also an expanded version with 24 items. It is carried out in the context of a semi-structured interview. It provides an overall score and scores in two sections: positive symptoms and negative symptoms. The Likert scale’s cut-off points offer three possibilities: absence of disorder, mild disorder or probable case, and severe disorder or specific case.\n\nThe Neuropsychological Battery of Executive Functions and Frontal Lobes (BANFE).80 The Battery of Executive Functions employed in this study, commonly known as BANFE (The Neuropsychological Battery of Executive Functions and Frontal Lobes), is indeed an instrument used in this research, acquired in compliance with ethical and legal considerations, along with the necessary licenses for its use. The required authorizations and licensing details have been secured by the psychometrics department of the institution, which is responsible for procuring materials and supplies while adhering to intellectual property regulations related to the use of the instrument.\n\nThis battery represents a detailed and appropriate neuropsychological assessment proposal for both children and adults; it evaluates the development of Executive Functions through high reliability and validity tests for assessing cognitive processes that depend on which are grouped into three specific areas: Orbit medial, Anterior Prefrontal, and Dorsolateral. The battery allows for obtaining not only a global performance index in the battery but also an index of the functioning of the three areas evaluated. It also has a performance profile in which a summary of the normalized scores corresponds to each subtest.81\n\nAs described somewhere else,82 the subtest includes the following a) prefrontal-dorsal-lateral (working memory verbal, ordering, Card Sorting Test (mental flexibility, Mazes (visuospatial planning), Tower of Hanoi (sequential planning), Consecutive Subtraction (reverse sequencing), Verb Generation (verbal fluency), b) Orbito-medial prefrontal (Stroop (inhibitory control), “Iowa” card test (processing risk-benefit), and mazes (following rules), and c) Anterior prefrontal (Generation of classifications semantics (productivity), comprehension and selection of proverbs (understanding the figurative meaning), the curve of meta-memory (metacognitive control, judgment, and monitoring). BANFE is a set of widely used neuropsychological tests applied to subjects with brain damage or neuropsychiatric diseases. These tests are supported by functional neuroimaging studies and are considered to have convergent and clinical validity in neuropsychology.\n\nIowa Gambling Task (IGT).83,84 It measures decision-making by risk-benefit election85 Participants were presented with four virtual decks of cards on a computer screen. They are told that each deck has cards that reward or penalize them using in-game money. The object of the game is to earn as much money as possible. The decks differ in the balance of reward vs. penalty cards. Therefore, some decks are “bad decks,” and other decks are “good decks” because some decks tend to reward the player more often than others decks.86\n\nMeasures of location and dispersion were employed to summarize continuous variables. Frequencies and proportions were estimated for categorical variables. Categorical variables were compared using a χ2 test. Variables meeting the assumptions of normality and homogeneity of variance were contrasted using the t-test for two independent samples or the nonparametric Mann–Whitney U test. Normality and homogeneity of variance were tested with the Shapiro–Wilks and the Bartlett tests, respectively. Uncorrected Cohen’s d was calculated to measure the effect size for all variables.87,88 To avoid the effect of potential confounding variables such as age, gender, and education, p-values were corrected using analysis of covariance (ANCOVA) and (MANOVA). Two-Way ANOVA followed by Sidak’s multiple comparisons tests was also performed. Statistical analysis was performed with Statistical Package for the Social Sciences version 24 (SPSS, Chicago, IL, USA) and Graph Path (version 9.5.0, San Diego, California, USA). Significant results are indicated with * p<0.05 and ** p<0.01.\n\n\nResults\n\nThe sample comprises 40 subjects residing in Barranquilla and its metropolitan area (Table 1). The subjects were organized into two groups made up of 20 adults diagnosed with paranoid schizophrenia (50.0%), of the diagnosed subjects (8[40%] male, 12 [60%] female). As expected, the distribution of diagnosis did not differ by gender (95% CI: 1.15-1.45). Subjects were under medication at the time of evaluation. While the control group with 20 subjects (50.0%), of which (5 [25%] were male and 15 [75%] were female). The mean age in the entire sample was 34.85±9.792 (range 18-50); As expected, the distribution by age found statistically significant differences (p<0.025) according to the SCZD status (affected 37.10±8.11, unaffected 30.50±10.17) regarding schooling, no statistically significant differences were found in the groups (SCZD 9.35±3.04, unaffected 9.70±2.59, p=0.568), regarding the stratum no significant differences were found.\n\nTable 2 presents the analysis results to determine the differences between individuals affected and not affected by SCZD in the sample of 40 subjects. Differences were found in the average performance registered by cases and controls in the medial orbit (p≤0.001; d=3.15), the Anterior Prefrontal (p≤0.001; d=1.99), Dorsolateral (p≤0.001) areas; d=3.02) and in Total Executive Functions (p≤0.001; d=3.39).\n\nThe analyzed results are presented to determine the differences (Table 3) between affected and unaffected individuals. After correcting for confounding variables, differences were found in the average performance recorded by cases and controls on the Iowa Gambling test (IGT) (p<0.012; d=0.96) with a medium effect size.\n\nFigure 1 shows the differences between the total amount obtained (cumulative earnings) by the control group vs. SCZD. Discrepancies in performance were found; even the SCZD group showed a more significant presence of economic losses, obtained by the absence of a pattern of adaptive responses or future myopia (t-test, Welch correction, p=0.0010**). The effect size through Cohen’s d is 1.032, which is considered a good effect. To avoid potential cofounders in this comparison, we use ANCOVA, including IGT total score as an independent variable, diagnostic as independent, and age, gender, and education years as covariables (see Supplementary Table 1). No effects were found for age (p=0.67), gender (p=0.402), and education years (p=0.405). The impact of diagnosis (control vs. patients) was still high (p<0.001, η2=0.243).\n\nFigure 2 shows the scores in groups of 20 stimuli through the different trials. Significant statistical differences are observed (Two-Way ANOVA, p≤0.0011 for the group, and p=0.03 for the interaction effect). From the second trial, it is observed that the learning pattern, guided by the positive/negative reinforcements in the choice of cards, shows that the SCZD group presents a poor performance, which is maintained throughout the trials, while the control group shows a straightforward learning process. Through multiple comparisons (Sidak’s test), the following differences were found trial 1 (p=0.0816), trial 2 (p=0.0050*), trial 3 (p=0.0053*), trial 4 (p≤0.0011**), and trial 5 (p≤0.0011**). To avoid potential cofounders in this comparison, we use MANCOVA, including IGT1 to IGT5 scores as dependent variables, diagnostic as independent, and age, gender, and education years as covariables (see Supplementary Table 2). No effects were found for age, gender, and education years. The impact of diagnosis (control vs. patients) was still high for each IGT score (IGT2: p=0.002, η2=0.206, IGT3: p=0.012, η2=0.146, IGT4: p=0.002, η2=0.203, and IGT5: p<0.001, η2=0.297) except for first trial block (IGT 1: p=0.1140, η2=0.060).\n\n\nDiscussion\n\nThe studies of schizophrenia related to cognitive deficits have gained great interest and have currently allowed us to identify and evaluate the altered cognitive dimensions in people with schizophrenia including executive functions; Especially, decision making. This study threw two aspects regarding the dimensions of the executive functions; The first aspect is a). The functions evaluated with the neuropsychological battery of executive functions and frontal lobes (BANFE) have solid evidence that support the presence of significant differences in areas belonging to the prefrontal cortex between affected and not affected by paranoid schizophrenia (Table 2) consisting of an altered activation To generate exploratory behaviors in uncertain reward environments affected with this disorder89,90 the sample belonging to the study presented poor performance in areas of the dorsolateral prefrontal cortex (DLPFC) particularly when the damage is in the right hemisphere and there are also difficulties In the working memory,91 in this sense there has been a marked deficit in decision making in patients with lesions in the orbitofrontal (COF) and ventromedial (CPFVM) regions of the prefrontal cortex (CPF) that is related to changes in the predictions of future and rewarding events; as well as, direct the behavior to the achievement of a goal, carry out adequate learning of the task and transfer the solution to similar tasks.92 Together, these findings can be unraveled through maladjustment and frequent outdated strategy.93–95\n\nOn the other hand and by the results, a continuous interpretation deficit was found based on its incentive value; The brain areas that underlie these processes have been identified as the medial and orbitofrontal,96 prefrontal regions, also related to functions such as the planning and anticipation of temporary signals, inhibition of erroneous behaviors, effectiveness in the solution of the task which It allows the constant update of the information regarding the time used to act, in addition to the processing of information, the regulation of the affective states, the control of the behavior and the decision making based on the estimate (risk-benefit), In uncertain, nonspecific or unpredictable situations, aspects present in patients with paranoid schizophrenia.\n\nThis result supports the tendency of those affected with the disorder to immediate gain, increasing the probability of remaining in the election due to the failure in the processing of the reward and the loss of avoidance91,96,97 presenting the association with the processing of the reinforcement of the reinforcement, Ability to transfer solutions to analogous situations could constitute the basis of learning deficits and their associated arousal alterations. Patients with schizophrenia have difficulties using feedback to guide future choices, generating a lower capacity to conceive alternatives in procedures, strategies, and responses to the same situations and preventing learning (risk-benefit) due to failures in value representations, The attribution of the importance of stimuli,98 evidencing an “emotional learning” that guides decision making. In addition, the probability-magnitude integration deficits were explicitly due to a failure in the representation of the magnitude of the reward.99 Therefore, those affected cannot avoid their preference for “bad” decks in the IGT (or, due to the “win-shed frequency” effect),97 which can explain myopic behaviors due to failed predictions of the consequences. Thus, as of inductive processes, the establishment of temporary connections between actions and their consequences, making it difficult to learn experiences, not being able to properly identify the advantageous and disadvantageous letters and their adjustment in real life because of their ability to Learning from reinforcement is affected,100 preventing the generation of behaviors that can organize prospectively.101 Consequently, a deficit in decision-making in paranoid schizophrenia can be assumed with an inability to move from initial preferences, that is, high risk, to a more profitable or low-risk strategy, with an initial selection of cards Without greater analysis. Again, this decision-making deficit seems to be specifically related to the paranoid schizophrenia subtype.91\n\nThe Iowa game task is an excellent method to evaluate ecological decision-making, since it mainly implies the anticipation of events, with rewards and losses. Neuroimaging studies in subjects who carry out the IGT demonstrate the importance of the dopaminergic system and wide areas of the orbit-medial prefrontal cortex and reward roads.102 In the case of subjects with schizophrenia, different studies have shown difficulties in decision-making based on the reward.103 This diminished response is likely because patients with schizophrenia cannot incorporate the experience obtained in successive past choices in the betting task,104 preventing an emotional-expensive categorization in similar situations, tasks, or circumstances. In its successive choices, this problem would be reflected in the lack of learning of negative decks (which imply more significant economic losses). It is interesting to think that the Iowa game task implies a “hot” cognitive reasoning task, distancing itself from “colder” executive function processes.105 It is possible that involving processes of effective anticipation of differential learning object/context/individual is more related to tasks of social cognition or theory of the mind.106\n\nAlthough these concepts have been traditionally linked to social interaction, many basic cognitive processes of social cognition imply the correct anticipation of events based on the experience and learning of contingencies related to a specific social context and the clear differentiation of objects and subjects. An especially striking characteristic of patients with schizophrenia is that show difficulties in these processes.106 On the other hand, studies that involve the analysis of Valencia Models of Perspective (PVL) highlight that the decision-making task would be linked to this model and the parameters of success/gain, actuality, and coherence. These parameters would reflect the degree of consistency in the choice of cards associated with low rewards in the SCZD.104",
"appendix": "Data availability\n\nSimon Bolivar University: XECUTIVE FUNCTION AND DECISION-MAKING IN COLOMBIAN PATIENTS WITH PARANOID SCHIZOPHRENIA, https://doi.org/10.17632/hsz66phhmf.1. 107\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 all the institutions and participants in this study.\n\n\nReferences\n\nNg MY, Levinson DF, Faraone SV, et al.: Meta-analysis of 32 genome-wide linkage studies of schizophrenia. Mol. Psychiatry. 2009 Aug; 14(8): 774–785. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcGrath J, Saha S, Chant D, et al.: A Concise Overview of Incidence, Prevalence, and Mortality. Epidemiol. Rev. 2008; 30(1): 67–76. PubMed Abstract | Publisher Full Text Reference Source\n\nSaarni SI, Viertiö S, Perälä J, et al.: Quality of life of people with schizophrenia, bipolar disorder and other psychotic disorders. Br. J. Psychiatry. 2010; 197(5): 386–394. 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PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nHernaus D, Frank MJ, Brown EC, et al.: Impaired Expected Value Computations in Schizophrenia Are Associated With a Reduced Ability to Integrate Reward Probability and Magnitude of Recent Outcomes. Biol. Psychiatry Cogn. Neurosci. Neuroimaging. 2019; 4(3): 280–290. PubMed Abstract | Publisher Full Text\n\nKoch K, Schachtzabel C, Wagner G, et al.: Altered activation in association with reward-related trial-and-error learning in patients with schizophrenia. NeuroImage. 2010; 50(1): 223–232. PubMed Abstract | Publisher Full Text\n\nGallistel CR: Conditioning from an information processing perspective. Behav. Process. 2003; 62(1): 89–101. Publisher Full Text Reference Source\n\nAram S, Levy L, Patel JB, et al.: The Iowa Gambling Task: A Review of the Historical Evolution, Scientific Basis, and Use in Functional Neuroimaging.2019. Publisher Full Text\n\nBetz LT, Brambilla P, Ilankovic A, et al.: Deciphering reward-based decision-making in schizophrenia: A meta-analysis and behavioral modeling of the Iowa Gambling Task. Schizophr. Res. 2019; 204: 7–15. PubMed Abstract | Publisher Full Text Reference Source\n\nKim MS, Kang BN, Lim JY: Decision-making deficits in patients with chronic schizophrenia: Iowa Gambling Task and Prospect Valence Learning model. NDT. 2016; 12: 1019–1027. Publisher Full Text Reference Source\n\nBuelow MT, Suhr JA: Construct validity of the Iowa Gambling Task. Neuropsychol. Rev. 2009; 19(1): 102–114. PubMed Abstract | Publisher Full Text\n\nZegarra-Valdivia JA: Funcionamiento ejecutivo, teoría de la mente y toma de decisiones en pacientes estabilizados con esquizofrenia paranoide del sur del Perú. Rev. Mex. Neuroci. 2016; 16(3): 13–26. Reference Source\n\nAhmad M, Acosta-Lopez J, Cervantes-Henriquez M: EXECUTIVE FUNCTION AND DECISION-MAKING IN COLOMBIAN PATIENTS WITH PARANOID SCHIZOPHRENIA. [Dataset]. Simon Bolivar University; 2023; V1. Publisher Full Text"
}
|
[
{
"id": "308640",
"date": "22 Aug 2024",
"name": "Indranath Chatterjee",
"expertise": [
"Reviewer Expertise Schizophrenia",
"neuroimaging",
"computational neuroscience."
],
"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\nAs a reviewer assessing the paper, I have focused on several critical points and thus suggesting some major revisions to ensure clarity, robustness, and relevance of the findings presented. Here are my comments and suggestions: 1. The study utilizes a relatively small sample size of 40 individuals. A power analysis should be conducted to determine if this sample size has sufficient power to detect a significant effect, particularly given the complex nature of schizophrenia and its cognitive impacts. 2. While the paper states no significant differences in socio-demographic characteristics between groups, differences in socio-economic status and educational levels were noted. given the study’s emphasis on the high genetic mixture and significant ethnic and racial diversity of the sample from Barranquilla, Colombia, it is critical that the manuscript include an analysis or discussion on how these factors specifically influence the cognitive profiles observed. 3.The methods section briefly mentions the use of the BANFE neuropsychological battery and the Iowa Gambling Task but lacks detail on why these specific measures were chosen and how they relate to the constructs of executive function and decision-making in schizophrenia. 4. The paper should specify the inclusion and exclusion criteria for participants in both the schizophrenia and control groups. This information is vital for assessing the generalizability of the study. 5. If available, discuss how your findings compare with other studies, particularly those that might have contradictory results. This comparison can help in understanding the context and implications of your results within the broader field of research. 6. The discussion should more thoroughly address the limitations of the study, including potential biases, the effects of medication on cognitive performance, and the generalizability of the results to other populations with schizophrenia.\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?\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/13-189
|
https://f1000research.com/articles/11-307/v1
|
14 Mar 22
|
{
"type": "Research Article",
"title": "Interactive Learning System for Learning Calculus",
"authors": [
"Md Asifur Rahman",
"Lew Sook Ling",
"Ooi Shih Yin",
"Md Asifur Rahman",
"Ooi Shih Yin"
],
"abstract": "Background: IT tools assist in creating a more participative and independent learning environment. They have brought a new perspective to collaborative learning where students do not just sit in a chair and swallow lecture content but instead participate in creating and sharing knowledge. However, interactivity promoted through the implementation of technology is limited in many cases.\n\nPurpose: This research develops an interactive application for learning calculus that promotes human-system interaction via augmented reality (AR) and human-human interaction through chat functions. The study examines the effect of both interactivities on learning experience and how that learning experience affects the performance of learning.\n\nMethods: The research adopted a quasi-experimental study design and pre-post test data analysis to evaluate the effect of interactivities on learning experience and consequently the effect of learning experience on learning performance. The subjects were exposed to the developed application for learning the calculus chapter ‘Revolution of Solids” in a controlled environment. The study validated its research framework through partial least squares path modelling and tested three hypotheses via pre-and post-test evaluation.\n\nConclusions: The results found that both interactivities affect learning experience positively; human-human interactivity has a higher impact than human-system interactivity. It was also found that learning performance as part of the learning experience increased from pre-test to post-test.",
"keywords": [
"Interactive learning system",
"augmented reality",
"learning experience",
"learning performance"
],
"content": "Introduction\n\nIn traditional classroom environments, there exists a problem with student participation.1 It is also stated that the traditional method is inefficient as it is mostly spoon-feeding, and students’ analytical processes are absent due to a lack of peer interaction.2 Although some studies have addressed the issues of student interaction with the system there is still a lack of teacher-student or student-student interaction in interactive learning systems.1–3 Many systems have promoted a single type of interactivity.4–10\n\nCalculus is one of the core subjects in computer science studies. Malaysian students pursuing diplomas and degrees in Information Technology take calculus subjects that include differentiation, and integration. Application of integration is one of the chapters in Calculus that requires spatial visualization and the 2D medium of the traditional classroom does not provide a proper solution.11–13\n\nIn understanding the revolution of solids around an axis, visualization of the solid in-question is very important. Spatially related 3D images cannot be drawn on a 2D board or projected over a computer. These hinder students in visualizing the solid and result in difficulties in conceptualizing the concept. Although researchers have implemented AR to assist in visualization, they are mainly focused on human-system interaction, either through haptic or non-haptic interaction.14–17 Besides, agility is another issue that some systems could not address as they are desktop-based systems.17–19 As such, developing an interactive AR application that facilitates both human-human and human-system interactivities and assists in conceptualizing and understanding math better is needed.\n\nThe use of interactive technology in pedagogy has become very common in the last decade. Interactive technology has made learning more personalized and kept students engaged through various applications.20 Abykanova et al. also suggested that interactive technology can make learning more active, and intensive for students where students can communicate easily with each-others and also with the teacher.20 Game-based learning, multimedia lectures and labs, and electronic study guides are some examples of the most common interactive technologies in the pedagogy sector. Recently implementation of Augmented Reality (AR) in pedagogy has been adopted by many researchers where the emphasis has mainly been kept on 3D visualization. Many have implemented AR in geometry for school students14,19,21 while some others implemented it for calculus.12,13 In both cases, the authors have focused on the immersive learning experience through AR that allows students to comprehend and conceptualize learning content.\n\n\nLiterature review\n\nImplementation of interactive learning systems in class to engage students in learning has become a common focus in the pedagogical arena. A system that promotes interpersonal interaction and provides a sense of others’ presence can be considered as an interactive system.4\n\nIn an attempt to increase class interactivity different types of technologies have been implemented in class. These can be categorized as synchronous and asynchronous mediums of interaction.22 Synchronous is used as a medium of interaction during class, especially when participating in in-class discussions, whereas asynchronous is for facilitating learning remotely, which may happen after the class. Examples of synchronous learning tools include interactive whiteboards2 and virtual-reality-based systems for learning language.4 An example of an interactive learning system for asynchronous learning is an AR-based interactive book.5 On the other hand, interactivity can also be categorized as human-system and human-human, as technologies are allowing both in a learning environment.3 Human-human interactivity is further divided into teacher-student and student-student interactivity. Table 1 shows promoted interactivities by different studies. These studies focused primarily on human-system interactivity while a few provided human-human interactivities.\n\nAR has become a trending technology in the pedagogical sector to provide students with an immersive experience. AR provides a real and virtual experience together to allow users real-time interaction.16 3D representation of a virtual object in a real environment can make learning more engaging as it provides a visual learning experience. This can be helpful to the majority of students as studies have found that there are more visual learners compared to auditory or kinesthetic learners.23 Besides, haptic interaction happens when users are allowed to interact with the 3D object through AR technology24 which also address kinesthetic learners as they learn through physical involvement. Table 2 depicts the interactivities promoted by different AR studies.\n\nFrom the studies depicted in Table 2, five papers adopted mobility in their AR system except the three that were desktop-based. This table also shows that the systems solely focused on interaction through AR and not on implementing any human-human interactivity.\n\nThe learning experience can be defined as the experience a learner goes through while learning content set by an institution.25 Including active engagement and collaboration as a part of it affects learning performances26,27 Furthermore, implementation of technology in class affects the learning experience positively.28\n\n\nMethods\n\nA pre-test and post-test quasi-experimental research design was adopted. The data was collected through a personally administered questionnaire survey. As the study was designed to be conducted using a pre-and post-test methodology, a longitudinal time horizon was adopted since the study was comparing students’ learning experience and performance before and after using the application.\n\nSample size calculation was done by following the 10 times rule, where the sample size is required to be 10 times larger than the maximum number of structural paths directed towards a latent variable.30 As such the minimum sample for this study is supposed to be larger than 20 as two paths are directed towards the latent variable. The sample size for this research was 59, but after eliminating missing data and straight-line answers the data was analyzed from 55 respondents. The respondents were students from a Malaysian university taking Calculus. At the end, the data was analyzed and hypotheses were accepted or rejected based on the p-values. Figure 1 illustrates the research design of this study.\n\nThis research has identified two types of interactivities, human-human and human-system. Figure 2 depicts the research framework of this study.\n\nAn interactive learning system based on AR was developed. Human-system and human-human interactivities were included as part of application functions. Human-system interaction was promoted by haptic interaction based on marker-based AR technology whereas human-human interactivity was implemented through a function of discussion platform. The framework was developed to find how these two interactivities affect the learning experience, the first dependent variable, and lastly how the learning experience incurred by the promoted interactivities affects students’ academic performance.\n\nThis study hypothesizes:\n\nHuman-system interaction is positively associated with students’ learning experience.\n\nHuman-human interaction is positively associated with students’ learning experience.\n\nImprovement of learning experience improves the performance of learning\n\nThis research was conducted into three phases, in the first phase the students were asked to answer a pre-questionnaire and a quiz before using the application, in the second phase they used the application and explored AR, and lastly, in the third phase, they answered a post-test questionnaire.\n\nFigure 3 shows students exploring the AR function of the application.\n\nThe survey questionnaire was divided into segments of three. The first section (A) was demographic questions; the second section (B) evaluated the two independent variables and one dependent variable, and in the third section (C) dependent factor learning performance was evaluated through a quiz developed by the subject expert.\n\nSection A comprises of six questions regarding participants’ general information that included gender, ethnicity, age and whether they have used any educational AR application before or not. All the questions in this section were self-designed.\n\nSection B evaluates the variables of the research framework comprised of self-developed and adopted questions from multiple sources. Independent variable human-human interaction measurement questions were self-developed. Human-human interaction questions were formed based on the idea of peer-peer interaction and student-teacher interaction shown in Table 3.\n\nFor the second independent variable human-system interaction the questions were adapted from Sumadio and Rambli30 and are depicted in Table 4.\n\nThe learning experience variable was evaluated based on the adopted questionnaire from31 shown in Table 5 and also from the self-developed questionnaire listed in Table 6.\n\nSection C was developed by a calculus subject expert in evaluating learning performance via a quiz. The quiz included True/False and formative questions.\n\n\nResults\n\nThis study conducted two types of analysis through Smart PLS 3.0 and SPSS 22 (IBM SPSS Statistics, RRID: SCR_019096) for conducting structural model assessment and pre-and post-test comparison of variables respectively. R is an open-source alternative software (R Project for Statistical Computing, RRID: SCR_001905) for Smart PLS.\n\nDemographic profile\n\nThis study collected 55 valid responses from the selected sample of 59 students from a Malaysian private university (Table 7). Out of 55 respondents, 46 were male (83.6%) while 9 were female constituting 16.4% of total respondents. The result is in line with other research findings as the gender ratio significantly skews towards males in the technology field.32,33 Among the three main ethnicity groups 43 students were Chinese (78.2%), followed by six Malay and six Indians constituting 10.9% each. As the sample was from pre-university students, the age range was from 18-22. The majority of students were 19 years old (60%) where 18 and 22 were the smallest age groups, constituting 3.6 % each.\n\nStudents’ experience of using similar types of applications in learning provides an indication of whether users are experienced in using this type of application or not. It is found that none of the students had used an AR application before.\n\nThe study adopted a PLS_SEM approach to maximize the variance of the defined framework’s endogenous construct.34 Structural model analysis was used to test the hypotheses along with its predictive accuracy and effect size. All the constructs were measured with five or more indicators. As the model is reflective, the constructs are reflective too. “Internal consistency reliability”, “convergent validity” and “Discriminant Validity” are the three criteria used to assess the constructs.\n\nInternal consistent reliability\n\nTo evaluate the same source biasedness coefficient variation, Internal consistency reliability is used to investigate the reliability of indicators that measure a latent variable. From Table 8, each construct satisfied the criteria of composite reliability (CR) of ≥ 0.7.35 As such it can be concluded that the constructs met the internal consistency reliability criteria.\n\nConvergent validity\n\nConvergent validity is measured by the indicator of Average Variance Extracted (AVE) and factor loading.35 AVE indicates what percentage of the variance of a construct is defined by a marker.35 The acceptable value of AVE for each construct must be ≥ 0.5. From the AVE value depicted in Table 8, all constructs satisfied the convergent validity criteria. Factor loading of each indicator ≥ 0.6 is acceptable.36\n\nDiscriminant validity\n\nDiscriminant validity is measured by the Fornell and Larcker Criterion (FLC), cross-loading comparison and HTMT technique.37 Table 9 shows that all constructs satisfied FLC criteria, where the square roots of AVEs for the reflective constructs of HHI (0.751), HSI (0.726) and LE (0.711) are larger than the correlation for all other constructs diagonally.\n\nFrom Table 10 of cross loading, all indicators load high on their own constructs compared to others. This confirms that the constructs are distinct from each other indicating discriminant validity as a result.\n\nThe HTMT mechanism of assessing discriminant validity requires the value of HTMT to be lower than 0.85 for stringent criterion and 0.9 for conservative criterion.37 From Table 11, all the constructs satisfy the above criteria confirming discriminant validity thereof.\n\nFrom all the criteria of confirmatory factorial analysis, the research model is adequately fitting to be accepted. As such this designated measurement model with specified latent variables has been analyzed with SEM criteria.\n\nStructural model assessment\n\nPath analysis was performed to find the hypothesized relationship. The results for collinearity assessment and hypothesis are shown in Table 12.\n\nBoth latent variables Human-Human Interaction (HHI) and Human-System Interaction (HSI) have positive effects on Learning Experience (LE). The variance inflation factor (VIF) results in Table 12 show that the lateral multicollinearity meets the criteria of being above the threshold of 0.2 and below the threshold of 5, implying collinearity was not an issue in the structural model.35\n\nA study by35 suggested that for a one-tailed test “t-values” for a significant level of five per cent (α = 0.05) are required to be greater than 1.645. The result indicated that both exogenous constructs HHI and HSI have a “t-value” of >1.645 for a significant level of five per cent (α = 0.05). From the results, both latent variables have a positive relationship with LE, HHI being the stronger predictor than HSI.\n\nPredictive accuracy, effect size and relevance\n\n“Predictive accuracy” is evaluated through the “coefficient of determination, R2”. R2 values imply the predictive power of exogenous constructs over endogenous ones. From the analysis construct LE’s R2 value is found as 0.576 which means exogenous constructs substantially explain 57.6% of LE’s variance as predictive power can be considered as substantial if it is greater than 0.26.38 Although35 has stated R2 value less than 0.67 is moderate.\n\nTo evaluate the effect size of exogenous constructs Cohen’s f2 value was obtained from the model analysis.38 stated that the f2 value of 0.35 is considered a substantial effect whereas 0.15 is considered moderate. From Table 12 it can be seen that the HHI construct has a substantial effect on LE (0.463) and HSI has a moderate effect (0.157).\n\nIn addition, the Q2 value of endogenous construct LE was found at 0.269 indicating moderate “predictive relevance”.35 Besides, as the Q2 value is larger than 0, it can be concluded that HHI and HIS exogenous constructs have “predictive relevance” for the endogenous construct LE.39\n\nPre-test post-test\n\nFor understanding the significance of pre-and post-test performance of student paired sample t-test was carried out and the result is shown in Table 13. From Table 13 it can be concluded that there is a significant relationship between the results of the pre-and post-tests as the P<0.05.29 The post-test mean implies that students’ performance results in the post-test are higher than the pre-test one signifying a positive improvement in the performance of learning.\n\n\nDiscussion\n\nFrom the result of the hypotheses, two hypotheses, H1 and H2 were supported – the human-human factor has a larger impact than the human-system factor.\n\nHuman-human interaction through the application has a mean of 3.92 compared to human-human interaction without the application with a mean of 3.70. Human-human interaction affects the learning experience positively which is in line with results found by.1,2,3,40\n\nHuman system interactivity from AR has also affected learning experience positively in line with the related research.14,16,24,41 The learning experience mean score is 3.42 prior to application usage whereas later it turned to 3.68.\n\nFrom the pre-and post-test results, the learning experience has increased the mean score of students’ performances. Learning experience, because of these interactivities, has affected performance positively similarly to results found in other studies.3,15\n\n\nConclusions\n\nThe role of interactivity in the learning experience has been established by many studies before, but implementing both human-human and human-system interactivities in an augmented reality application was overdue. This research had done exactly that and analyzed the effectiveness of the research framework by using PLS. From the results, it can be concluded that the model was fit to analyze the research framework with substantial predictive accuracy and a moderate effect size of the exogenous variable with a moderate relevance on endogenous variable LE. All three hypotheses are confirmed as P values for all three are at a satisfactory level. These results imply that human-human and human-system interactions positively affect learning experience and performance of learning as a result of an enhanced learning experience.\n\n\nCompeting interests\n\nThis article has obtained public disclosure approval from Multimedia University. The authors declare that there is no conflict of interest.\n\n\nEthical considerations and consent\n\nAll the procedures performed in this study involving human participants were in adherence to the ethical policies of the University as approved by the Technology Transfer Office of Multimedia University under ethical approval number: EA0702021.\n\nWritten consent was also obtained from all individual participants involved in the study. Personal data from individuals was promised to be kept confidential and strictly restricted for use in this study only.\n\nThis research is funded and supported by Multimedia University under the MMU Graduate Research Assistant (GRA) Scheme with Grant Reference Number: MMUI/170099. Md Asifur Rahman is the appointed GRA for this grant.\n\n\nData availability\n\nZenodo: IARA LP Dataset. https://doi.org/10.5281/zenodo.574496042\n\nThis project contains the following underlying data:\n\nDataset IARA LP 01122021.xlsx (The file contains two sheets. The first one contains the indicators of three variables; Learning Experience, Human-Human Interaction and Human-System Interaction which were used for framework analysis. The second sheet includes the results of students' performance before and after using the learning system as pre-test and post-test).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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Educational Assessment, Evaluation and Accountability. 2012.\n\nFreeman S, Eddy SL, McDonough M, et al.: Active learning increases student performance in science, engineering, and mathematics. Proceedings of the National Academy of Sciences. 2014; pp. 8410–8415.\n\nKrishnasamy S, Sook-Ling L, Tan C-K: Information Technology Capabilities for Mathematics Education in High School: Conceptual Framework. Adv. Sci. Lett. 2017; 23: 8013–8016. Publisher Full Text\n\nSekaran U, Bougie R: Research Methods for Business. Chichester: John Wiley and Sons, Ltd; 2009.\n\nSumadio DD, Rambli DRA: Preliminary Evaluation on User Acceptance of the Augmented Reality. 2010 Second International Conference on Computer Engineering and Applications, Bali Island. 2010.\n\nSerio ÁD, Ibáñez MB, Kloos CD: Impact of an augmented reality system on students’ motivation. Comput. Educ. 2013; 68: 586–596. Publisher Full Text\n\nReinking A, Martin B: The Gender Gap in STEM Fields: Theories, Movements, and Ideas to Engage Girls in STEM. Reinking, Anni & Martin, Barbara. (2018). The gender gap in STEM fields: Theories, movementsJournal of New Approaches in Educational Research. 2018; 148–153.\n\nWang M-T, Degol J: Gender Gap in Science, Technology, Engineering, and Mathematics (STEM): Current Knowledge, Implications for Practice, Policy, and Future Directions. Educ. Psychol. Rev. 2016; 29: 119–140. Publisher Full Text\n\nHair JF, Black W, Babin BJ, et al.: Multivariate Data Analysis: A Global Perspective. Upper Saddle River: Pearson; 2010.\n\nHair JF, Hult GTM, Ringle CM, et al.: A Primer on Partial Least Squares Structural Equation Modeling (PLS-SEM). Sage Publication; 2017.\n\nByrne BM: Structural Equation Modeling With AMOS Basic Concepts, Applications, and Programming. Routledge; 2016. Publisher Full Text\n\nRamayah T, Cheah J, Chuah F, et al.: Partial Least Squares Structural Equation Modeling (PLS-SEM) using SmartPLS 3.0: An Updated and Practical Guide to Statistical Analysis, Kuala Lumpur: Pearson Malaysia Sdn. Bhd.2018.\n\nCohen J: Statistical Power Analysis for the Behavioral Sciences. New York: Routledge; 1988.\n\nGeisser S: A Predictive Approach to the Random Effect Model. Biometrika. 1974; 61: 101–107. Publisher Full Text\n\nLin H-C, Chiu Y-H, Chen YJ, et al.: Continued use of an interactive computer game-based visual perception learning system in children with developmental delay. Int. J. Med. Inform. 2017; 107: 76–87. PubMed Abstract | Publisher Full Text\n\nChang R-c, Yu Z-s: Application of Augmented Reality Technology to Promote Interactive Learning. Proceedings of the 2017 IEEE International Conference on Applied System Innovation IEEE-ICASI 2017 - Meen, Prior & Lam (Eds). 2017.\n\nLing LS: IARA LP Dataset [Data set]. Zenodo. 2021.\n\nKing A: Using Interactive Games to Improve Math Achievement Among Middle School Students in Need of Remediation. ProQuest Dissertations and Theses. 2011."
}
|
[
{
"id": "127477",
"date": "28 Mar 2022",
"name": "Yong Wee Sek",
"expertise": [
"Reviewer Expertise My research interest is in educational technologies",
"technology acceptance and information system"
],
"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 paper, the authors introduced the interactive learning system for learning Calculus. There is a great deal of good work in this paper. However, it does require a significant overall revision to make the best of this and present the work in a clear and well-structured way, particularly on the literature review, methodology, research design and procedures used in this study, measurement instruments, and data analysis techniques in order to achieve the research objectives. Additionally, the discussion section is not exhaustive enough to provide good attempt to explain many of the study results. In fact, the discussion is not aligned with the research objectives.\nAbstract\nBackground – the problems of the interactive system are not clear. The authors should point out the existing problems of the interactive system in learning mathematics, particularly in learning Calculus.\nPlease include the main objective(s) or research question(s) of this study in this section. The research objectives/research questions are not clear.\nIntroduction\nThis section should include the following information:\nWhat are the existing problems in learning Calculus?\n\nWhy is “Revolution of Solids” proposed in this research?\n\nWhy is an interactive approach proposed to overcome these problems?\n\nWhat are the existing interactive methods that have been proposed to solve Mathematics problem, in particular Calculus (Revolution of Solids)?\n\nWhat are the weaknesses of existing interactive methods in solving mathematics (Calculus - Revolution of Solids) problems?\n\nHow are the proposed interactive methods (augmented reality and chat functions) able to solve the existing problem in learning Revolution of Solids?\n\nPlease include the main objective(s)/research questions of this study in this section.\nInclude a brief description of the methodology and system used in this study.\n\nLiterature review/Background study\nIn this section, discussion on the following should be included:\nThe major problems in learning calculus (visualization)\n\nHow are the interactive activities able to solve the existing problem in learning calculus?\n\nWhat are the existing interactive methods proposed to overcome these problems? Should discuss the advantages and disadvantages of the existing methods.\n\nWhat are the major issues of the existing interactive methods?\n\nWhy are AR and chat functions introduced in learning calculus?\n\nMethodology\nThe author may consider sub-dividing this section as suggested below:\nStudy design and procedures\n\nThe design and development of the interactive methods\n\nParticipants\n\nMeasurement scales\n\nData analysis techniques\n\nStudy design and procedures – you should discuss the choice of quantitative research method in this research, what is the quasi-experimental design? Why is quasi-experimental design used in this research? What are the procedures used to conduct this research?\nA discussion on the design and development of the interactive methods should be presented here.\nParticipants – this study uses quasi-experimental design, the participants should be assigned into control and experimental group. This information is not available. How did you assign participants into these groups? How did you select the participants for this study?\nFor measurement items, what are the scales used in this study? Please list the sources. For the self-developed items, reliability and validity tests should be conducted and reported.\nWhat is the structural equation modelling (SEM)? Why is SEM used in this research? How did you conduct the data analysis? You should also discuss the data analysis for longitudinal study using SEM.\nResults\nAs the measurement items were adopted from many different sources, instrument reliability and validity tests using Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) should be conducted and reported.\nFor self-developed items, procedures to establish instrument reliability and validity should be presented.\nThe result section needs to do a major revision with appropriate analyses. Please include relevant Table(s) with appropriate details such as paired t test results, significant value, etc. for each of the test conducted.\nDiscussions\nThe author(s) should discuss/relate/compare the findings with prior relevant studies. Please also explain how the results in this study relate to previous findings, whether in support, contradiction, or simply as added data. The discussion should be aligned with the research objectives.\nAdditional comments:\nPage 5, figure 1. Research design - Causal not casual relationship\n\nThe development of research hypotheses is missing.\n\nDid not justify the adopted questionnaire.\n\nDid not specify the questions for the quiz. Are the same or different sets of questions used for pre and post? How many questions?\n\nDid not mention if measurement model and structural model were assessed based on data collected in the first phase or the third phase?\n\nEnsure consistency in reporting the number of decimals throughout the manuscript (including in Tables).\n\nPlease provide information about the ethical applications\n\nPlease refer to the article entitled \"Designing and evaluating a high interactive augmented reality system for programming learning\"1. This paper will provide some ideas on how to conduct quasi-experimental design, research procedures, and how the discussion was presented.\n\nFor the article entitled \"Primary school students' perceptions of scaffolding in digital game-based learning in mathematics\"2, This paper can give some information about the process of the research experiment, ethical considerations, and how the discussion was presented.\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": [
{
"c_id": "11004",
"date": "13 Apr 2024",
"name": "Sook Ling Lew",
"role": "Author Response",
"response": "Comment 1: In this paper, the authors introduced the interactive learning system for learning Calculus. There is a great deal of good work in this paper. However, it does require a significant overall revision to make the best of this and present the work in a clear and well-structured way, particularly on the literature review, the methodology, the research design and procedures used in this study, measurement instruments and data analysis techniques to achieve the research objectives. Additionally, the discussion section is not exhaustive to provide good attempt to explain many of the study results. In fact, the discussion is not aligned with the research objectives. Response 1: We have revised the manuscript carefully based on all the comments and issues raised. Comment 2: Abstract Background – the problems of the interactive system are not clear. The authors should point out the existing problems of the interactive system in learning mathematics, particularly in learning Calculus. Please include the main objective(s) or research question(s) of this study in this section. The research objectives/research questions are not clear. Response 2: Existing problems of the interactive system in learning mathematics, particularly in learning Calculus are added as follows: However, calculus learning augmented reality application has limitation in promoting a human collaboration in learning. The main objective is included in Purpose and Introduction: This research develops an augmented reality application that promotes interaction and spatial visualization for learning calculus and evaluates the effect of the interactive learning system on the performance of learning. Comment 3: Introduction This section should include the following information: Response 3: The existing problems in learning Calculus are included Introduction – Paragraph 1, 2, 3, Literature Review – Interactivity - Paragraph 1 & Paragraph 2; as follows: Comment 4: What are the existing problems in learning Calculus? Response 4: 1. Lacking Human-Human interactivity. Although there are some studies that have addressed the issues of student interaction with the system there is still a lack of teacher-student or student-student interaction in interactive learning systems [1, 2, 3]. Many systems have promoted a single type of interactivity [4, 5, 6, 7, 8, 9, 10]. Past studies in Table 1 shows promoted interactivities by different studies. These studies focused primarily on human-system interactivity while a few provided human-human interactivity. Past studies in Table 2 depicts that most systems solely focused on interactivity through AR and not implementing any human-human interactivity. 2. Lacking Spatial Visualization Application of integration is one of the chapters in Calculus that requires spatial visualization and the 2D medium of the traditional classroom does not provide a proper solution [11, 12, 13]. After consulting with the subject teacher on what the student struggle most in learning calculus, it was suggested that students face difficulties in understanding solid of revolution through traditional classroom method as it requires 3D visualization. Comment 5: Why “Revolution of Solids” is proposed in this research? Response 5: The reasons of “Revolution of Solids” are included as follows: In understanding revolution of solids around an axis, visualization of the solid in-question is very important. Spatially related 3D images cannot be drawn on a 2D board or projected over a computer. These hinder students in visualizing the solid and result in difficulties in conceptualizing the concept. After consulting with the subject teacher on what the student struggle most in learning calculus, it was suggested that students face difficulties in understanding solid of revolution through traditional classroom method as it requires 3D visualization. Comment 6: Why interactive approach is proposed to overcome these problems? Response 6: The reasons of interactive approach are included as follows: Although researchers have implemented AR to assist in visualization, they are mainly focused on human-system interaction, either through haptic or non-haptic interaction [14, 15, 16, 17]. Besides, agility is another issue that some systems could not addresses as they are desktop-based systems [17, 18, 19]. Under the theory of learner constructing their knowledge Lev Vygotsky theorized that learning occurs through personalization and socialization [20]. So it is crucial to provide the function to interact among the learners. Comment 7: What are the existing interactive methods have been proposed to solve Mathematics problem in particular Calculus (Revolution of Solids)? Response 7: The existing interactive methods are focused on providing content visualization and included in the Introduction as follows: Unfortunately, majority of the AR learning application only focused on providing content visualization resulting in not a holistic application in learning that promote both type of interaction [14, 15, 21, 22]. As such, developing an interactive AR application that facilitates both human-human and human-system interactivities and assists in conceptualizing and understanding math better is needed. Comment 8: What are the weaknesses of the existing interactive methods in solving mathematics (Calculus- Revolution of Solids) problems? Response 8: The weaknesses of the existing interactive methods are included in Introduction – Paragraph 4 as follows: Recently implementation of Augmented Reality (AR) in pedagogy has been adopted by many researchers where the emphasis has mainly been kept on 3D visualization. Many have implemented AR in geometry for school students [14, 19, 24] while some other implemented it for calculus [12, 13]. In both cases the authors have focused on the immersive learning experience through AR but no human-human interaction function was provided. Comment 9: How are the proposed interactive methods (augmented reality and chat functions) able to solve the existing problem in learning Revolution of Solids? Response 9: Introduction – Paragraph 3 So, it is crucial to provide the function to interact among the learners. Unfortunately, majority of the AR learning application only focused on providing content visualization resulting in not a holistic application in learning that promote both type of interactions. The interactive methods (augmented reality and chat functions) are proposed as follows: 1. AR – to implement Spatial Visualization 2. Chat – to improve Human-Human interactivity. Comment 10: Please include the main objective(s)/ research questions of this study in this section. Response 10: Main objectives are included as follows: This research aims to develop an interactive AR application for learning calculus that promotes human-system interaction via AR and human-human interaction through chat functions. Comment 11: Include a brief description of the methodology and system used in this study. Response 11: A brief description of the methodology and system used in this study are included as follows: Pre-test and post-test data from students learning calculus in the classroom using the AR interactive learning system were gathered using a questionnaire and a quiz to evaluate the impact of the developed AR system. Comment 12: Literature review/Background study In this section, discussion on the following should be included: Major problems in learning calculus (visualization) Response 12: Discussion on the major problems in learning calculus (visualization) are included as follows: 1. Lacking Human-Human interactivity. 2. Lacking Spatial Visualization Comment 13: How are the interactive activities able to solve the existing problem in learning calculus? Response 13: Under the theory of learner constructing their knowledge Lev Vygotsky theorized that learning occurs through personalization and socialization [20]. So, it is crucial to provide the function to interact among the learners. Unfortunately, majority of the AR learning application only focused on providing content visualization resulting in not a holistic application in learning that promote both type of interaction [14, 15, 21, 22]. Comment 14: What are the existing interactive methods proposed to overcome these problems? Should discuss the advantages and disadvantages of the existing methods. Response 14: The existing interactive methods proposed to overcome these problems are included as: AR based interactive book [5] is a tool used in asynchronous learning. Past studies in Table 1 shows promoted interactivities by different studies. These studies focused primarily on human-system interactivity while a few provided human-human interactivity. Advantages of the existing methods are included as: Interactive technology has made learning more personalized and kept students engaged through various applications [23]. This paper also suggested that interactive technology can make learning more active, and intensive for students where students can communicate easily with each-others and also with the teacher [23]. Disadvantages of the existing methods are included as: Recently implementation of Augmented Reality (AR) in pedagogy has been adopted by many researchers where the emphasis has mainly been kept on 3D visualization. Many have implemented AR in geometry for school students [14, 19, 24] while some other implemented it for calculus [12, 13]. In both cases the authors have focused on the immersive learning experience through AR but no human-human interaction function was provided. Comment 15: What are the major issues of the existing interactive methods? Response 15: Unfortunately, majority of the AR learning application only focused on providing content visualization resulting in not a holistic application in learning that promote both type of interaction [14, 15, 21, 22]. Past studies in Table 2 depicts that most systems solely focused on interactivity through AR and not implementing any human-human interactivity. Comment 16: Why are AR and chat functions introduced in learning calculus? Response 16: The interactive AR application facilitates both human-human and human-system interactivities and assists in conceptualizing and understanding math better. Comment 17: Methodology The author may consider sub-dividing this section as below: i. Study design and procedures ii. The design and development of the interactive methods iii. Participants iv. Measurement scales v. Data analysis techniques Response 17: We have re-arranged the sub-sections with the suggested sections such as Study design and procedures, Research Framework, Survey Design and Procedures and Data Analysis Techniques in Methodology. Comment 18: Study design and procedures – you should discuss the choice of quantitative research method in this research, what is the quasi-experimental design? Why is quasi-experimental design used in this research? What are the procedures to conduct this research? Response 18: The reason of Quantitative research method was used are added in Research Design and Participants as follows: Quantitative research designs include quasi-experiments, true experiments, causal-comparative research, surveys research and experiments research. Quantitative research is likely to test theories by investigating the relationships among variables [37]. Therefore, the primary research method for this study was quantitative. Comment 19: A discussion on the design and development of the interactive methods should be presented here. Response 19: A discussion on the design and development of the interactive methods is included as follows: Interactivity can also be categorized as human-system and human-human, as technologies are allowing both in a learning environment [3]. The framework for interactive learning application is developed based on these two types of interactions. Comment 20: Participants – this study uses quasi-experimental design, the participants should be assigned into control and experimental group. This information is not available. How did you assign participants into these groups? How did you select the participants for this study? For measurement items, what are the scales used in this study? Please list the sources. For the self-developed items, reliability and validity tests should be conducted and reported. Response 20: Additional information of participants is added in Research Design and Participants as follows: One of the numerous forms of quasi-experimental design is pre- and post-test research. \"Quasi\" refers to something that resembles experimental study. Studies evaluating a curriculum for education, a treatment system or a simulation training commonly apply pre- and post-test evaluation [33]. Since this study is to compare students' learning experiences and academic performance before and after using the AR system, a pre- and post-test quasi-experimental research method was chosen. Convenience sampling is a nonprobability or non-random sampling in which it is able to conveniently reach and recruit members of the target population for the study [34]. Usually, convenience samples of university students are used in academic surveys [35]. Since the respondents were students from a Malaysian university taking Calculus subject, a non-probability convenience sampling method was used for this study. For measurement items, the scales used in this study are included in Survey Design and Procedures - Section B as follows: All the questions for the aforementioned variables were measured through 5-point Likert scale. For the self-developed items, reliability and validity tests were conducted and included in Internal consistent reliability, as follows: All the self-developed questions under human-human interaction variables satisfied the reliability as the loading is >0.6 [33]. For the three self-developed questions (LE 10, LE11, and LE12) under learning experience variable two of the questions LE11, LE12 also satisfy this criterion. Comment 21: What is the structural equation modelling (SEM)? Why is SEM used in this research? How to conduct the data analysis? You should also discuss the data analysis for longitudinal study using SEM. Response 21: Structural equation modeling (SEM) combines multiple regression and factor analysis. It is employed to examine the relationships between a group of observable variables and latent concepts. There are two main types of the SEM. In this study, instead of using the traditional Covariance-Based-SEM (CB-SEM), Partial Least Squares-SEM (PLS-SEM). PLS-SEM is chosen to analyze the data based on its capability to handle complex models and small sample sizes. Data analysis using PLS-SEM was employed by defining clear research objectives and hypotheses, data preparation, structural model analysis, hypotheses testing, structural model assessment and predictive accuracy, effect size and relevance evaluation [36]. PLS-SEM is often chosen for longitudinal studies due to its effectiveness in handling small sample sizes, which are common in these studies, especially when compared to cross-sectional studies [36]. Comment 22: Results As the measurement items were adopted from many different sources, instrument reliability and validity tests using Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA) should be conducted and reported. Response 22: CB-SEM and PLS-SEM are two widely accepted second generation data analysis approaches. PLS-SEM is used to analyze the data as the objective of the study is to confirm the hypotheses to explain the relationship between the exogenous and endogenous constructs for the following reasons [39]: PLS-SEM can be applied for exploratory research—when “theory is less developed”. PLS-SEM can handle complex cause-effect structural models. Additionally, data characteristics, such as small sample size and non-normal data, can be some of the reasons to choose PLS-SEM. Comment 23: For self-developed items, procedures to establish instrument reliability and validity should be presented. Response 23: For the self-developed items, reliability and validity tests were conducted and included in Internal consistency reliability, as follows: All the self-developed questions under human-human interaction variables satisfied the reliability as the loading is >0.6 [33]. For the three self-developed questions (LE 10, LE11, and LE12) under learning experience variable two of the questions LE11, LE12 also satisfy this criterion. Comment 24: The result section needs to do a major revision with appropriate analyses. Please include relevant Table(s) with appropriate details such as paired t test results, significant value, etc. for each of the test conducted. Response 24: Tables 8 to 13 are included to report the results of paired t test results, significant value and other tests conducted. Comment 25: Discussions The author(s) should discuss/relate/compare the findings with prior relevant studies. Please also explain how the results in this study relate to previous findings, whether in support, contradiction, or simply as added data. The discussion should be aligned with the research objectives. Response 25: The discussion was rewritten with comparisons from previous studies and aligned with the research objectives as follows: The study aims to develop an augmented reality application that promotes interaction and spatial visualization for learning calculus and evaluates the effect of the interactive learning system on the performance of learning. Human-human interaction is evaluated as part of the chat function of application and human-system interaction is analysed as part of augmented reality implementation through mobile application. The first hypothesis was accepted as human-system interactivity positively affected the learning experience factor. As this study developed an augmented reality application for learning calculus, here human-system interaction is related to the interactivity promoted by the augmented reality application. Studies implementing augmented reality in improving learning experience founds that the didactic experience of this technology make students more engaged and hence providing an enriched learning experience [12, 14, 16, 21, 27]. This study has also found that among the human-system interaction all students univocally cancelled out disagreement that it provided them with real world 3D object feelings. The study using similar questionnaire have also found that it has significant impact on the learning experience in general and motivation in particular [39]. So, the result of this study is aligned with the prior relevant studies. The second hypothesis result found that human-human interaction significantly influences learning experience. The implication from this hypothesis acceptance indicate that learning experience is shaped by human-human interaction which can comes from student-teacher or student-student. In the study design both student-teacher and student-student interaction facilities were provided via application chat function. So, it can be said that both type of human-human interactions are associated positively with learning experience. This result is in line with the findings where both types of interaction led to learning satisfaction [47]. Another study found that human-human interactivity increases learning engagement [1, 2, 3]. In addition to that another study has also claimed that learning confidence as part of learning experience has also increased through interaction with peers and teachers [1]. From the findings of these research, it can be concluded that the result of human-human interaction affecting learning experience is in line with existing research. The third hypothesis of the study was tested by using paired sample “t-test” where learning performance’ means were compared from ‘pre-test’ to ‘post-test scenario. The result shows that there is significant relation between the score and “post-test” mean is higher than the ‘pre-test’ one. Other studies have also found that learning experience as result of human-system and human-human interactivity increase learning performance [3, 15, 47]. So, it can be claimed that in terms of hypothesis acceptance, this study is in line with existing literature. Comment 26: Additional comments: Page 5, figure 1. Research design - Causal not casual relationship The development of research hypotheses is missing. Did not justify the adopted questionnaire. Did not specify the questions for the quiz. Are the same or different sets of questions used for pre and post? How many questions? Did not mention if measurement model and structural model were assessed based on data collected in the first phase or the third phase? Ensure consistency in reporting the number of decimals throughout the manuscript (including in Tables) Response 26: In Figure 1, Casual Relationship is changed to Causal Relationship. The development of research hypotheses is included in Section Methods - Research Framework. Justifications were added in Survey Design and Procedures - Section B. Additional information for the quiz is included as follows: The quiz included five True/False and one formative questions on solid of revolution chapter. The quiz was used in pre- and post-test evaluation for measuring learning performance factor. To avoid question biases, the same questions were used. Order of true-false questions were changed to make sure students did not just follow the similar pattern of answer from the pre-test. 5. Phase three is included in Methods - Data Analysis Techniques as follows: The structural model was analyzed based on the data collected in phase three from post-test. 6. Done consistency in reporting the number of decimals. Comment 27: Overall: This paper requires a significant revision to make the best of this and present the work in a clear and well-structured way, particularly on the literature review, the methodology, the research design and procedures used in this study, measurement instruments and data analysis techniques. Additionally, the discussion section is not exhaustive to provide good attempt to explain many of the study results. In fact, the discussion is not aligned with the research objectives. Response 27: We have revised the manuscript carefully based on all the comments and issues raised."
}
]
},
{
"id": "127478",
"date": "12 Apr 2022",
"name": "Affandy Affandy",
"expertise": [
"Reviewer Expertise My research interest is in software engineering education",
"software visualization",
"and project 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 explores the benefits of human interaction in interactive learning systems with visualization through augmented reality. The subject exposed is calculus on the topic \"Revolution of Solids\". The research compares the impact of human-system interaction support with human-human interaction support on student learning experiences.\nIn this paper, the author presents information that is quite valuable, however, several important things need to be detailed to get a more comprehensive point of view.\nIntroduction:\nIn this section, explanations related to the following things need to be explained to construct a more complete research motivation:\nWhat problems are still encountered in the application of learning media based on 3D visualization with AR technology?\n\nWhat systems currently exist to support learning calculus using AR and what are their weaknesses?\n\nWhat are the existing systems that support visualization and interaction and what are the problems with these systems?\n\nLiterature study:\nThe paper needs to include an explanation of the following points to add clarity to the problem and state-of-the-art research on learning using visualization:\nUtilization of AR technology in calculus learning.\n\nVarious interaction models exist in learning applications and their advantages and disadvantages.\n\nWhy visualization systems must be supported by human-human interaction in learning applications?\n\nWhat prevents current AR applications from providing student-student and teacher-student interaction?\n\nMethodology:\nTo ensure the homogeneity of the sample, it was mentioned in the paper that none of the students had ever used AR applications before. However, the student's initial level of understanding in the area studied before they used the provided AR applications is unknown. Different starting points have the potential to provide different endpoints as well.\nDiscussion:\nIn the discussion section, the author should not only emphasize the findings obtained from the statistical approach that has been carried out. A more in-depth study to find out what aspects make human-human interaction give better student performance results than human-system interaction needs to be presented with comparisons from previous studies.\nUsing previous studies as a reference in the discussion/comparison of research results will provide clarity on the contribution of research in this field of study.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "11005",
"date": "13 Apr 2024",
"name": "Sook Ling Lew",
"role": "Author Response",
"response": "Comment 1: This research explores the benefits of human interaction in interactive learning systems with visualization through augmented reality. The subject exposed is calculus on the topic \"Revolution of Solids\". The research compares the impact of human-system interaction support with human-human interaction support on student learning experiences. In this paper, the author presents information that is quite valuable, however, several important things need to be detailed to get a more comprehensive point of view. Response 1: We have revised the manuscript carefully based on all the comments and issues raised. Comment 2: Introduction: In this section, explanations related to the following things need to be explained to construct a more complete research motivation: What problems are still encountered in the application of learning media based on 3D visualization with AR technology? Response 2: The problems are included as follows: (1) Lacking Human-Human interactivity. Introduction – Paragraph 1: Although there are some studies that have addressed the issues of student interaction with the system there is still a lack of teacher-student or student-student interaction in interactive learning systems [1, 2, 3]. Many systems have promoted a single type of interactivity [4, 5, 6, 7, 8, 9, 10]. Literature Review – Interactivity - Paragraph 1: Past studies in Table 1 shows promoted interactivities by different studies. These studies focused primarily on human-system interactivity while a few provided human-human interactivity. Literature Review – Interactivity - Paragraph 2: Past studies in Table 2 depicts that most systems solely focused on interactivity through AR and not implementing any human-human interactivity. (2) Lacking Spatial Visualization Introduction – Paragraph 2: Application of integration is one of the chapters in Calculus that requires spatial visualization and the 2D medium of the traditional classroom does not provide a proper solution [11, 12, 13]. Introduction – Paragraph 3: After consulting with the subject teacher on what the student struggle most in learning calculus, it was suggested that students face difficulties in understanding solid of revolution through traditional classroom method as it requires 3D visualization. Comment 3: What systems currently exist to support learning calculus using AR and what are their weaknesses? Response 3: Literature Review – Interactivity - Paragraph 1: The existing interactive methods proposed to overcome these problems are included as: AR based interactive book [5] is a tool used in asynchronous learning. Past studies in Table 1 shows promoted interactivities by different studies. These studies focused primarily on human-system interactivity while a few provided human-human interactivity. Introduction – Paragraph 4: Advantages of the existing methods are included as: Interactive technology has made learning more personalized and kept students engaged through various applications [23]. This paper also suggested that interactive technology can make learning more active, and intensive for students where students can communicate easily with each-others and also with the teacher [23]. Disadvantages of the existing methods are included as: Recently implementation of Augmented Reality (AR) in pedagogy has been adopted by many researchers where the emphasis has mainly been kept on 3D visualization. Many have implemented AR in geometry for school students [14, 19, 24] while some other implemented it for calculus [12, 13]. In both cases the authors have focused on the immersive learning experience through AR but no human-human interaction function was provided. Comment 4: What are the existing systems that support visualization and interaction and what are the problems with these systems? Response 4: Introduction – Paragraph 3: Although researchers have implemented AR to assist in visualization, they are mainly focused on human-system interaction, either through haptic or non-haptic interaction [14, 15, 16, 17]. Besides, agility is another issue that some systems could not addresses as they are desktop-based systems [17, 18, 19]. Under the theory of learner constructing their knowledge Lev Vygotsky theorized that learning occurs through personalization and socialization [20]. So it is crucial to provide the function to interact among the learners. Comment 5: Literature study: The paper needs to include an explanation of the following points to add clarity to the problem and state-of-the-art research on learning using visualization: Utilization of AR technology in calculus learning. Response 5: Advantages of the existing methods are included as: Interactive technology has made learning more personalized and kept students engaged through various applications [23]. This paper also suggested that interactive technology can make learning more active, and intensive for students where students can communicate easily with each-others and also with the teacher [23]. Disadvantages of the existing methods are included as: Recently implementation of Augmented Reality (AR) in pedagogy has been adopted by many researchers where the emphasis has mainly been kept on 3D visualization. Many have implemented AR in geometry for school students [14, 19, 24] while some other implemented it for calculus [12, 13]. In both cases the authors have focused on the immersive learning experience through AR but no human-human interaction function was provided. Comment 6: Various interaction models exist in learning applications and their advantages and disadvantages. Response 6: Under the theory of learner constructing their knowledge Lev Vygotsky theorized that learning occurs through personalization and socialization [20] . So it is crucial to provide the function to interact among the learners. Unfortunately, majority of the AR learning application only focused on providing content visualization resulting in not a holistic application in learning that promote both type of interaction [14, 15, 21, 22]. Comment 7: Why visualization systems must be supported by human-human interaction in learning applications? Response 7: Under the theory of learner constructing their knowledge Lev Vygotsky theorized that learning occurs through personalization and socialization [20] . So it is crucial to provide the function to interact among the learners. Comment 8: What prevents current AR applications from providing student-student and teacher-student interaction? Response 8: The current AR applications emphasized on immersive learning experience through AR that lacking in providing student-student and teacher-student interaction. The information is included as follows: Recently implementation of Augmented Reality (AR) in pedagogy has been adopted by many researchers where the emphasis has mainly been kept on 3D visualization. Many have implemented AR in geometry for school students [14, 19, 24] while some other implemented it for calculus [12, 13]. In both cases the authors have focused on the immersive learning experience through AR but no human-human interaction function was provided. Comment 9: Methodology: To ensure the homogeneity of the sample, it was mentioned in the paper that none of the students had ever used AR applications before. However, the student's initial level of understanding in the area studied before they used the provided AR applications is unknown. Different starting points have the potential to provide different endpoints as well. Response 9: Homogeneity of the sample is included as follows: Methods-Research Design and Participants This study conducted a pre-assessment evaluation of the respondents' knowledge, skills, or understanding in the AR area related to the system before they started using it [32]. Descriptive Statistics-Demographic Profile It is found that the students scored the same grades in this pre-assessment, indicating that they had the same initial level of understanding in the studied area before using the system. Comment 10: Discussion: In the discussion section, the author should not only emphasize the findings obtained from the statistical approach that has been carried out. A more in-depth study to find out what aspects make human-human interaction give better student performance results than human-system interaction needs to be presented with comparisons from previous studies. Response 10: The discussion was rewritten with comparisons from previous studies as follows: The study aims to develop an augmented reality application that promotes interaction and spatial visualization for learning calculus and evaluates the effect of the interactive learning system on the performance of learning. Human-human interaction is evaluated as part of the chat function of application and human-system interaction is analysed as part of augmented reality implementation through mobile application. The first hypothesis was accepted as human-system interactivity positively affected the learning experience factor. As this study developed an augmented reality application for learning calculus, here human-system interaction is related to the interactivity promoted by the augmented reality application. Studies implementing augmented reality in improving learning experience founds that the didactic experience of this technology make students more engaged and hence providing an enriched learning experience [12, 14, 16, 21, 27]. This study has also found that among the human-system interaction all students univocally cancelled out disagreement that it provided them with real world 3D object feelings. The study using similar questionnaire have also found that it has significant impact on the learning experience in general and motivation in particular [39]. So, the result of this study is aligned with the prior relevant studies. The second hypothesis result found that human-human interaction significantly influences learning experience. The implication from this hypothesis acceptance indicate that learning experience is shaped by human-human interaction which can comes from student-teacher or student-student. In the study design both student-teacher and student-student interaction facilities were provided via application chat function. So, it can be said that both type of human-human interactions are associated positively with learning experience. This result is in line with the findings where both types of interaction led to learning satisfaction [47]. Another study found that human-human interactivity increases learning engagement [1, 2, 3]. In addition to that another study has also claimed that learning confidence as part of learning experience has also increased through interaction with peers and teachers [1]. From the findings of these research, it can be concluded that the result of human-human interaction affecting learning experience is in line with existing research. The third hypothesis of the study was tested by using paired sample “t-test” where learning performance means were compared from ‘pre-test’ to ‘post-test scenario. The result shows that there is significant relation between the score and “post-test” mean is higher than the ‘pre-test’ one. Other studies have also found that learning experience as result of human-system and human-human interactivity increase learning performance [3, 15, 47]. So, it can be claimed that in terms of hypothesis acceptance, this study is in line with existing literature. Comment 11: Using previous studies as a reference in the discussion/comparison of research results will provide clarity on the contribution of research in this field of study. Response 11: The discussion was rewritten with comparisons from previous studies as above in Response 10."
}
]
}
] | 1
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https://f1000research.com/articles/11-307
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https://f1000research.com/articles/12-954/v1
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08 Aug 23
|
{
"type": "Method Article",
"title": "Ex-vivo drug screening of surgically resected glioma stem cells to replace murine avatars and provide personalise cancer therapy for glioblastoma patients",
"authors": [
"Hannah Gagg",
"Sophie T. Williams",
"Samantha Conroy",
"Katie N. Myers",
"Connor McGarrity-Cottrell",
"Callum Jones",
"Thomas Helleday",
"Juha Rantala",
"Ola Rominiyi",
"Sarah J. Danson",
"Spencer J. Collis",
"Greg Wells",
"Hannah Gagg",
"Sophie T. Williams",
"Samantha Conroy",
"Katie N. Myers",
"Connor McGarrity-Cottrell",
"Callum Jones",
"Thomas Helleday",
"Juha Rantala"
],
"abstract": "With diminishing returns and high clinical failure rates from traditional preclinical and animal-based drug discovery strategies, more emphasis is being placed on alternative drug discovery platforms. Ex vivo approaches represent a departure from both more traditional preclinical animal-based models and clinical-based strategies and aim to address intra-tumoural and inter-patient variability at an earlier stage of drug discovery. Additionally, these approaches could also offer precise treatment stratification for patients within a week of tumour resection in order to direct tailored therapy. One tumour group that could significantly benefit from such ex vivo approaches are high-grade gliomas, which exhibit extensive heterogeneity, cellular plasticity and therapy-resistant glioma stem cell (GSC) niches. Historic use of murine-based preclinical models for these tumours has largely failed to generate new therapies, resulting in relatively stagnant and unacceptable survival rates of around 12-15 months post-diagnosis over the last 50 years. The near universal use of DNA damaging chemoradiotherapy after surgical resection within standard-of-care (SoC) therapy regimens provides an opportunity to improve current treatments if we can identify efficient drug combinations in preclinical models that better reflect the complex inter-/intra-tumour heterogeneity, GSC plasticity and inherent DNA damage resistance mechanisms. We have therefore developed and optimised a high-throughput ex vivo drug screening platform; GliExP, which maintains GSC populations using immediately dissociated fresh surgical tissue. As a proof-of-concept for GliExP, we have optimised SoC therapy responses and screened 30+ small molecule therapeutics and preclinical compounds against tumours from 18 different patients, including multi-region spatial heterogeneity sampling from several individual tumours. Our data therefore provides a strong basis to build upon GliExP to incorporate combination-based oncology therapeutics in tandem with SoC therapies as an important preclinical alternative to murine models (reduction and replacement) to triage experimental therapeutics for clinical translation and deliver rapid identification of effective treatment strategies for individual gliomas.",
"keywords": [
"Glioblastoma",
"ex vivo drug screening",
"functional precision medicine",
"glioma stem cells",
"cancer therapeutics",
"GliExP"
],
"content": "\n\n\n\nScientific benefit(s)\n\n\n\n• Rapid analysis of drug responses within primary tumour cells\n\n• Can be used with specific tumour niches post-surgery\n\n• Drug responses can be tested alongside SoC therapies in patients as a clinical validation of the platform\n\n• Facilitates potential drug repurposing\n\n• Can be adapted for drug discovery/development\n\n• Pre-printed drug plates can be tested against multiple different cancers once optimised\n\n• Ideal model to investigate differential drug responses observed due to inter/intra tumour heterogeneity\n\n3Rs benefit(s)\n\n\n\n• Offers a significant reduction in use of animal-based preclinical models\n\n• Replace the use of mouse orthotopic/cranial resection models currently rated as severe under ASPA Faster readouts of patient-specific drug responses\n\n• Facilitates drug combination testing without the use of high numbers of animals\n\nPractical benefit(s)\n\n\n\n• Fairly easy to set up with standard commercially available equipment and image analysis software\n\n• Facilitates preclinical research questions to be tested in a rapid time frame\n\n• Scalability, many aspects could be readily automated\n\n• Brings together scientific and clinical teams\n\nCurrent applications\n\n\n\n• Rapid identification of potential patient/tumour-specific therapeutic strategies for improved treatment responses\n\n• Assessment of mono-therapeutic strategies, novel drug combinations and additions to current SoC treatments\n\n• Currently in the academic setting but moving towards clinical trial/intervention-based platforms\n\nPotential applications\n\n\n\n• Implementation within a clinical trial/intervention setting to direct patient treatment\n\n• Use within the commercial sector to assess novel therapeutics as well as drug discovery/development\n\n• Expandable technology to potentially other solid cancers and/or those with a defined stem cell niche.\n\n\nIntroduction\n\nBrain tumours kill more children and adults under 40 than any other cancer, with high-grade glioblastomas being the most common cancers arising within the brain, contributing to ~200,000 deaths/year globally.1,2 These tumours demonstrate large amounts of both inter- and intra-tumoural heterogeneity,3–6 however our increasing understanding of the genetic diversity present within these tumours has not yet led to any tangible improvements in patient survival rates, which have stagnated over the last 40-50 years.3,4,6–10 Additionally, these tumours harbour difficult-to-treat glioblastoma stem cell-like (GSC) subpopulations,11,12 which possess regenerative potential and enhanced DNA repair capabilities.13–15 As such, the majority of glioblastoma patients receive aggressive debulking surgical tumour resection followed by DNA-damaging radiotherapy and chemotherapy, which represents the current global standard-of-care (SoC) treatment for these currently incurable tumours. The mainstay chemotherapy is the DNA alkylating agent temozolomide (TMZ)16 and around half of glioblastomas exhibit promoter methylation of the dealkylating enzyme MGMT. Although MGMT is an established predictive biomarker of TMZ effectiveness/clinical response, there is currently no superior alternative treatment for patients with an unmethylated MGMT promoter (MGMT ‘positive’), and survival for all patients receiving current SoC therapy remains around 12-15 months post-diagnosis. These current SoC treatment regimens have changed little in over a decade with high levels of innate and acquired treatment resistance giving rise to mean disease recurrence of around seven months, resulting in less than 10% of patients surviving more than five years.3,16–18 Because of this, glioblastomas have been recognised globally as a cancer of unmet need that urgently requires new therapeutic interventions and approaches to improve treatment and patient survival.2,3\n\nCancer studies using mice to provide personalised drug screening generally involve harsh tumour implantation, either orthotopically (i.e. at the same anatomical site as the corresponding patient) or subcutaneously within the hind limb flank.19 Since these studies usually assess response to various treatments, implanted tumours are permitted to grow to a pre-specified size/volume before starting treatment. Despite treatment, many mice will still experience symptomatic cancer progression, prior to the inevitable death/cull of all mouse participants. Consequently, such animal studies are classed as ‘moderate-severe’ depending on xenograft location, highlighting inherent animal distress, discomfort and non-survival. Murine-based preclinical models such as tumour flank models using established cell lines and patient-derived xenografts (flank and orthotopic) have traditionally been used for glioblastoma research because of their accessibility and because they share physiological characteristics and around 80% genetic homology to humans.20 However, there is debate within the field as to whether or not the currently used plethora of murine preclinical models can accurately predict therapeutic responses in humans,3 which is an important consideration given the high risk, cost and attrition rate associated with drug discovery/development. Such failure of these models is most likely due to several factors including the ability of tumour models to reflect the properties of post-surgical tumour cells (i.e. residual disease), differences in pharmacokinetics, and the extreme cellular heterogeneity of gliomas not being recapitulated.21 As such, oncology has the lowest possibility for success in drug development programmes.22,23 The various advantages and disadvantages of commonly used glioblastoma models for preclinical drug screening including within drug development are discussed in more detail in our recent review article.19 Additionally, using such models (as described in more detail below), a limited drug discovery study using patient-specific xenograft (PDX) models may require over 35 mouse avatars to provide individualised recommendations from a shortlist of five treatment strategies for one patient. Even using a single avatar model, typically at least 5-10 mice are required to test a single treatment. Consequently, time, cost, and ethical considerations limit the number of treatments that can feasibly be tested using PDX avatars for a single patient (usually less than 50).19\n\nThere are three main types of in vivo models for primary brain tumours; chemically induced, genetically modified and xenograft (based either on established cell lines or more recently on patient-derived cells/tissue).24 Traditional xenograft models involve the transplantation of human cancer cells into immunocompromised mice. Multiple established glioma cell lines such as U87, U251 and LN18 have been successfully xenografted. These models have advantages of high engraftment, reliable disease growth and progression, high growth rates with good reproducibility for investigating glioblastoma. Immortalised cell lines can be easily expanded in vitro, to yield large numbers of tumour cells for experimental use.25 Despite this, cell line xenografts often do not resemble the complex clinical characteristics of the original tumour they are presumed to model.26,27\n\nMore clinically relevant in vivo glioblastoma models include patient-derived xenografts (PDX), where surgically removed tumour biopsies or spheroids are implanted orthotopically or subcutaneously into immunocompromised mice. There are two main methods for establishing PDX models: the first involves the direct injection of biopsy tumour tissue, and the second is injection of cultured tumour spheres or cells harvested from monolayer cultures. Both methods can maintain the genetic and phenotypical features of the original patient tumour. Nevertheless, injecting biopsy tissue may be more clinically relevant as the architecture of original tissue is maintained, along with endothelium, extracellular matrix and resident macrophages.28 However, one major caveat of PDX models is unsuccessful engraftment due to tumour sample size, aggressiveness, and low viability. PDX models are highly reliant on large tumour samples with good viability, to achieve successful engraftment, which is not always possible following surgical resection. This makes it increasingly difficult to model: lower grade gliomas such as oligodendrogliomas which proliferate much slower than high grade tumours; the invasive component of tumours which are more difficult to resect surgically and more likely to be left-behind; and small tumours in general, where less material is available for research. Once engraftment is successful it can take between 2-11 months for sufficient tumour growth,29 which does not synergise with the rapid time frames required for guiding personalised therapy regimes given the rapid disease progression observed in aggressive cancers such as glioblastoma.\n\nEarly preclinical research in glioblastoma involved the use of both cell line and PDX xenograft models. Prior to TMZ approval as a SoC therapy, its use was investigated alone and alongside BCNU in three different cell line xenograft models: SNB-75, SF-295 and U251, with this study alone using a total of ~600 xenograft models.30 Further preclinical investigations into TMZ utilised PDX xenograft models, where a total of ~280 murine models were used.31 Another preclinical study investigated interstitial localised delivery of BCNU into controlled release polymers, which used a total of 344 9L gliosarcoma rat models,32 which later led to the FDA approval of Carmustine wafers (Gliadel) that can be implanted into the surgical cavity following tumour removal as a complimentary treatment to TMZ; although it is not widely adopted due to marginal survival gains and a modified risk profile including increased wound breakdown and infection.33 More recently, an ongoing clinical trial using the microtubule-destabilising drug lisavanbutin is showing potentially promising results (NCT02895360).19 This is based on preclinical research showing the ability of the drug to penetrate the blood brain barrier (BBB) and increased survival fraction alone and alongside RT or RT/TMZ. This was determined using 14 different GBM PDX lines established as orthotopic xenografts, with each group containing 9-10 models giving a total count of up to 140 PDX models used.34 As such, although various murine-based models can be an important preclinical validation step to promising clinical trials and potential subsequent clinical approval, more rapid and high-throughput clinically relevant preclinical drug screening approaches are required.\n\nWe therefore present here the development and optimisation of a high-throughput ex vivo drug screening platform for glioma stem cell populations: GliExP, that can be used to rapidly assess both preclinical and experiential therapeutics on an individual tumour basis, including intratumoural spatial heterogeneity and difficult-to-treat post-surgical/residual disease. By developing such an alternative ex vivo screening platform, we aim to reduce and replace a meaningful proportion of murine model use, which we estimate based on comprehensive analysis of the current global ex vivo solid tumour studies utilising murine avatars (see Table 2 within our recent review article)19; this could amount to 2,000 mice per year not being used in preclinical high-grade glioma research, with the potential to impact on the current use of murine models for other solid tumours (e.g. bladder, kidney etc). This is based on our analysis that on average, around 400 mice are used per study, and ~20,000 mice were used globally in this setting over the last five years. This estimate increases significantly when one considers our future plans to further develop GliExP to combine multiple therapeutics and in tandem with current SoC radiation and TMZ treatments.\n\n\nMethods\n\nPreparation of GSC ‘stem’ culture media:\n\nHere we describe the procedure used to prepare 500 mL of GSC media used to maintain stem-like cell populations. Reagents used are listed in Table 1.\n\n1. Under sterile conditions add 1% B27, 0.5% N2, 1% L-glutamine, 1% Penicillin-streptomycin, 0.1% amphotericin B, 4 ug/mL heparin to 500mL bottle of advanced DMEM F12 media.\n\n2. Manually pipette solution up and down to ensure components are fully mixed.\n\n3. Prepare stocks of 0.1 mg/mL epidermal growth factor (EGF) and 0.1 mg/mL fibroblast growth factor (FGF) by dissolving in sterile PBS, aliquot into 20-40 μL stocks and store at -20°C until further use.\n\n4. When media is required, transfer an appropriate volume into upright separate sterile T75 flasks prewarmed to 37°C in an incubator.\n\n5. Add 20 ng/mL EGF and FGF to media, this is made fresh daily to avoid degradation of growth factors.\n\nPreparation of GSC ‘bulk’ culture media:\n\nHere we describe the procedure used to prepare 500 mL of differentiating ‘bulk’ media, the added serum induces differentiation of GSC cultures.\n\n1. Under sterile conditions add 10% FCS, 1% L-glutamine, 1% penicillin-streptomycin and 0.1% amphotericin B to a 500 mL bottle of MEM media.\n\n2. Manually pipette solution up and down to ensure components are fully mixed.\n\n3. No extra growth factors required so can use media directly from bottle stock.\n\nProtocol for coating plasticware with basement membrane:\n\nHere we describe the procedures used to coat plasticware with basement membrane extract (BME) (Cultrex), this allows GSC populations to grow as adherent monolayers. Concentrations and volumes used are listed in Table 2. To avoid any batch-to-batch variation of this product, sufficient volumes were purchased to cover the entirety of the project.\n\n1. Add BME Cultrex (5-10 mL) stock into ice bucket and thaw overnight in the fridge at 4°C.\n\n2. Under sterile conditions aliquot Cultrex into 1mL stocks and store at -80°C until further use (work on ice or work rapidly to prevent solidification of BME).\n\n3. When required thaw a Cultrex aliquot overnight as per step one.\n\n4. Dilute 1 mL of Cultrex with 39 mL (1:40) cold advanced DMEM F12 (without supplements and growth factors) gently pipette up and down to mix with a pre-chilled pipette.\n\n5. At room temperature, pipette onto plasticware at appropriate volumes (see Table 2) then gently tilt in all directions to ensure even coverage of liquid.\n\n6. Place coated plasticware into incubator set at 37°C for 30 minutes to polymerise.\n\n7. Gently tilt plasticware and remove excess media using a pipette, ensure flasks lids are securely fastened and 6 well plates are taped shut.\n\n8. Cultrex-coated plasticware can be stored in the fridge at 4°C for up to 14 days.\n\nProtocol for coating 384-well drug plates with basement membrane:\n\nHere we describe the procedures used to coat pre-treated 384 drug plates with basement membrane extract (BME; Cultrex™).\n\n1. Add 1mL BME aliquot into ice bucket and thaw overnight in the fridge at 4°C.\n\n2. Dilute 1mL of BME with 19 mL (1:20) cold advanced DMEM F12 (without supplements and growth factors) gently pipette up and down to mix.\n\nNote – BME 1:20 dilution used for drug plate coating to account for dilution when added the wells pre-coated with 5 μl drug.\n\n3. Pour diluted BME into a 50 mL reagent reservoir.\n\n4. Using an automated 16 channel E1-ClipTip and pre-chilled tip, pipette 5 μL per well into 384 well drug plate.\n\n5. To ensure even coverage of BME centrifuge plate for 30 seconds at 800 RCF at room temperature.\n\n6. Place coated drug plate into incubator set at 37°C for 30 minutes to polymerise.\n\n7. Once polymerised drug plates were used immediately to avoid degradation of drug.\n\nHere describes the protocol used for the 384-well drug plate printing. Drug compounds can be purchased as either pre diluted liquids or solids and diluted in DMSO (or water for platinum-based compounds such as cisplatin) to stock working concentrations of 5-10 mM and stored in -80°C. All compounds used in this study are listed in Table 3 with their concentrations.\n\n1. Store compounds purchased as liquid according to manufacturer’s instructions, to avoid any extra freeze thaw cycles thaw and aliquot as appropriate on day of drug plate printing.\n\n2. Dilute all compounds to 10X their top concentration (see Figure 1 below) and add to a 96-well master plate in duplicate, ensure duplicates are not in a similar region of the plate (to avoid any plate effects).\n\n3. This plate layout can be designed and known by the user prior to any subsequent analysis. Only use 77 wells, leaving row A and column 1 empty.\n\nInitially, compounds were diluted to ××10 the top concentration to be used and added to their corresponding wells on the ×10 master plate. Drugs from this plate were then serially diluted down 1:2 into ×5, ×2.5 and ×1.25 master plates. Vehicle control (DMSO) and positive controls (Staurosporine and aphidicoline) were added to the plate independently at single concentrations.\n\nNote – Row A and column 1 are left empty as these will correspond to the outer wells of the final 384 drug plate, which are left empty due to plate evaporation effects.\n\n4. Serially dilute this master plate into three separate 96 well master plates using a 1:2 dilution, to give four plates total with 10X, 5X, 2.5X and 1.25X dilution factor examples shown in Figure 1.\n\n5. Following this, add negative vehicle control; DMSO (n=24) and positive controls; staurosporine (n=8), and aphidicolin (n=8) independently. If using water soluble drugs such as cisplatin water should also be added as negative vehicle control.\n\n6. Rotate the 5X and 1.25X plates 180 degrees prior to transfering to 384 well format to ensure all four dilutions are not next to each other. Create the master plate layout ensuring all drug repeats, dilutions and controls are spread across the innermost 308 wells of a 384-well plate (Perkin Elmer 384 Cell Carrier Ultra) this avoid any bias resulting from edge evaporation effects or well positioning.\n\n7. Using a ThermoFisher Scientific Matrix Platemate Plus, dispense 5μL from the four master plates onto the allocated 384-well plate well, in addition to any vehicle control wells. Once the 384-well plates are printed, briefly centrifuge for 30 seconds at 800 RCF and seal with a non-permeable cover and immediately store at -80oC.\n\nFresh treatment-naïve glioblastomas were collected from patients who provided informed consent undergoing surgery at Sheffield Teaching Hospitals NHS Foundation Trust (Ethical approval: Yorkshire & The Humber – Leeds East REC (11-YH-0319/STH15598). Fresh glioblastoma tissue surplus to histological requirements resected by the operating surgeon was collected intraoperatively whilst surgery was ongoing, pseudonymised/assigned a unique sample identifier and then rapidly transferred to the ex vivo laboratory within <30 minutes within a dry sterile specimen pot (NHS) at room temperature. Tumour samples were taken from both male and female patients across a range of ages within the parameters associated with the prevalence for this disease and the local gender/age consenting at Sheffield’s Royal Hallamshire Hospital and anonymised to the ex vivo screening team.\n\nHere we describe the protocol used for the dissociation and seeding of tissue specimens onto pre-coated 384-well drug plates.\n\n1. Prior to collection of tissue ensure to pre-warm stem media, Accutase and PBS to 37°C.\n\n2. Place tumour sample into 50-100 mm petri dishes depending on the tissue size and wash thoroughly with pre warmed phosphate buffered saline (PBS)\n\n3. Aspirate all excess PBS, measure tissue specimens with a sterile metal ruler, divide any tissues larger than 20×20×20 mm into half or a third using a scalpel into separate petri dishes in order to model intratumoural heterogeneity (e.g. GBM1 sample A, B, C).\n\n4. Further divide these sections into smaller 2×2×2 mm regions prior to dissociation. Add 10-20 mL of pre-warmed stem media, without growth factors to immerse sample.\n\n5. Mechanically dissociate the sample using forceps and a p1000 pipette tip using pulling motions. For more calcified solid tumours dissociate using a scalpel.\n\n6. For smaller samples not modelling heterogeneity carefully divide the total tissue homogenate equally using a plastic Pasteur pipette into 4-6 15 mL falcon tubes to give a maximum of ~0.5 pellet of tissue per tube.\n\nTip – If the tissue homogenate is too large to be picked up with Pasteur pipette, repeat mechanical dissociation. Be careful when using pipette as tissue can suck up into bulb.\n\n7. Split larger tissues modelling intratumoural heterogeneity into appropriately labelled 15mL falcon tubes (e.g. Sample A, B, C) using ~4-6 tubes per sample.\n\nTip – It is possible to derive smaller samples with 1-2 ~0.5 mL pellets, however samples screened in this study are usually in excess, therefore we find it important to dissociate the majority of tissue to give accurate representation of cells in entire the tumour.\n\n8. Centrifuge the 15mL tubes at ~180 RCF for 3 minutes at room temperature, after which carefully remove the supernatant. If the residual pellet contains a large red blood cell (RBC) layer, then add pre-warmed PBS to each tube, agitate using a Pasteur pipette and leave to settle for 10 mins.\n\n9. Centrifuge tubes at 180 relative centrifugal force (RCF) for 30 seconds at room temperature, carefully aspirate supernatant with plastic Pasteur pipette.\n\n10. Add 3mL Accutase warmed to 37°C to each individual tube and the pipette suspension up and down to provide further disaggregation prior to agitated incubation using ThermoMixer C (Eppendorf) set at 37°C 750 rpm for 30 minutes. Repeat this enzymatic dissociation step until cells are well dissociated with the majority as single cells (typically 45-60 minutes). Check dissociation under a brightfield microscope using glass coverslips.\n\n11. Add 7 mL stem cell media to each falcon tube and mixed well using a 10/5 mL stripette. Centrifuge cell suspensions at ~180 RCF at room temperature, then remove supernatant.\n\n12. Resuspend pellets in 3 mL stem media, mix well then filter through a 70 μM cell strainer into a 50 mL falcon tube.\n\n13. At room temperature, divide cell solutions equally into 15 mL falcon tubes (one per every 2×2 mm tissue sample) and then centrifuge for 5 minutes at ~180 RCF, if a RBC layer is still present on the pellet, add 5 mL of ACK lysing buffer per tube, mix well and leave for 5 minutes before further centrifugation at ~180 RCF for 5 minutes.\n\n14. Following aspiration of the supernatant, resuspend cells in 5 mL PBS, mix well and centrifuge again at ~180 RCF for 5 minutes at room temperature, aspirate the supernatant aspirated and resuspended pellet in stem media including growth factors (EGF and FGF).\n\n15. Count and viability test the cells with trypan blue using Cellometer Mini (Nexcelom Bioscience) cell counter.\n\nNote – Viability was typically between 20-40% for these methods.\n\n16. Using the live cell count, dilute cells in stem media containing growth factors into a 50mL falcon tube to give an appropriate density (usually 5-10k cells per well in 384 well).\n\n17. Using the E1-clip 16 channel pipette and a 50 mL reagent reservoir dispense 40 μL of the resulting suspension to all but the outer wells of the pre-loaded drug ECM coated drug plates, making the total volume 50 μL.\n\n18. Fill the empty outer wells of the plate with 100 μL media before sealing the plate with “breathe easy” sealing membrane to help with any evaporation effects.\n\n19. Place drug plates within an incubator (37°C in 5% CO2) for a 4–8-day incubation period, which was set based on previous publications using similar techniques.35,36\n\nNote – End users should test different incubation periods to optimise appropriate incubation times for their specific needs/cell populations.\n\n20. Label samples with unique identifier e.g. p-GBM1a, prefix ‘p’ represents primary dissociated tissue\n\n21. For follow up experiments it is important to culture primary samples in tandem with drug screening, this is described in detail in the following section.\n\nHere we describe the protocol used for the culturing of GliExP samples for relevant follow up experiments:\n\n1. Place any residual cell solution into an upright T25 flask (non-adherent conditions) and place into an incubator (37°C in 5% CO2) 24-48 hours to facilitate the formation of primary neurospheres.\n\n2. Collect and transfer into BME-coated flasks to form primary monolayer\n\n3. Once adhered gently wash with PBS to remove residual RBCs and any cell debris\n\n4. Replace the stem media (with growth factors) every 3 days\n\n5. Once confluent transfer cells to two T25 flasks or one T75 flask to generate a secondary monolayer. Continue to expand cells and cryopreserve aliquots for long-term stocks and future experiments as needed\n\n6. Label flasks and cryovials with appropriate GBM identifier (without ‘p’ prefix as this represents freshly dissociated tissue rather than established GSC models)\n\nNote – for the purpose of this paper unless the ‘p’ prefix is used, the GSCs are derived from matched dissociated tissue. Furthermore, although well-established in our laboratory, to confirm that our GSC growth media appropriately maintained GSC niches within the 384-well format, we compared known GSC marker expression in matched GSC CX18 cell line populations grown in bulk and stem enrichment media and that GSC plasticity was maintained (Figures 2 and 3 respectively).\n\nExpression levels of all three GSC markers mRNA were higher within passage matched GSC populations compared to their bulk equivalent cells. Data represents the 25th and 75th percent quartiles (box) median (middle line). The lower and upper whiskers show the smallest and largest values within 1.5x of the interquartile range below the respective 25th and 75th percentile. Data shown is derived from two independent biological repeats from separate passages of the same patient derived cell line, with each repeat including three technical replicates for each marker condition. Statistical significance was calculated using the Mann-Whitney-U test (**P<0.002).\n\nSerum differentiated CX18 GSCs show the ability to revert to a de-differentiated state re-expressing stem markers SOX2 and Nestin, when bulk cells are cultured back in stem growth conditions, thus demonstrating and confirming GSC plasticity.\n\nStaining of drug plates\n\nHere we describe the protocol used for the immunofluorescent staining of 384-well drug plates for microscopy imaging to evaluate treatment response. These fixing, washing and staining steps have been optimised to reduce the number of tumour cells being washed away.\n\n1. Following a 4-8 day incubation, place drug plates into a class II laminar flow hood and remove breathable membranes.\n\n2. Using a E1-clip 16 channel pipette and a 50mL reagent reservoir add 40 μL cold 4% paraformaldehyde (PFA) containing 0.6% Triton-X to each well then incubate at room temperature for 30 minutes before aspirating fully.\n\n3. Using a different reagent reservoir add and remove 30μL of PBS to wash each well.\n\nTip – At this stage it is possible to add another 30μL of PBS and store the plate at 4°C for up to 48hrs or proceed directly with staining steps.\n\n4. If proceeding with staining make up antibody solutions using PBS, Tween-20 (0.05%) and bovine serum albumin (3%), all antibodies used, concentrations and their suppliers are listed in Table 4. Use DAPI as a marker for cell nuclei at a concentration of 1 μg/mL.\n\nTip – where possible implement conjugated antibodies to reduce washing steps and retain cell population on plates.\n\n5. Add 10 μL of antibody solution to each well (ensure the PBS has been removed). Cover plates with foil and incubate overnight at 4°C.\n\n6. The following day wash cells and resuspended in 30 μL PBS ready for microscopy analysis.\n\nTip – If not proceeding with microscopy immediately, plates can be wrapped in foil and stored in the fridge at 4°C. It is recommended to image the plates within a week of staining to avoid degradation of antibodies.\n\n7. If using unconjugated antibodies such as CD133, the primary antibody and DAPI should be added as described in step 5. On the following day, wash wells with PBS, then add appropriate secondary antibody made up in PBS (see Table 4 for dilutions) at room temperature for 1 hour. Wash cells and add 30μL PBS ready for microscopy analysis or store in the fridge at 4°C.\n\nGlioblastoma stem and bulk cells from early passage primary tumour samples (Rominiyi et al., under revision) were seeded at a density of 3×105 cells per well onto BME-coated coverslips inside a six-well tissue culture dish. Cells were then incubated at 37°C in 5% CO2 for 48 hours without treatment. The cells were then fixed and permeabilised using cold 4% PFA and 0.6% Triton X-100 (500 μL) for 10 minutes, followed by three PBS washes (5 minutes each). Cells were then blocked for 1 hour at room temperature in PBS containing BSA (3%). Conjugated and primary antibodies used were diluted in PBS containing Tween (0.05%) and bovine serum albumin (3%), 500μl of required antibody was added to each well at appropriate concentration (Table 4) and incubated overnight at 4°C in the dark. The following day the primary/conjugated antibodies were then aspirated before 3 additional washes with PBS. Next 500 μL of DAPI and/or secondary antibody was added for one hour at room temp on a gentle shaking platform in the dark to prevent photobleaching, the antibodies were aspirated and washed with PBS (5 minutes each). Following the final wash, coverslips were mounted onto labelled microscope slides using ProLong Gold Antifade Mountant (Thermo Scientific). Slides were then stored in the dark to drug overnight, before being stored in the fridge at 4°C. Antibodies for GSC markers were CD133, Nestin and SOX2, with Vimentin used as a marker of differentiation and DAPI used to identify cell nuclei.\n\nDrug plate imaging\n\nHere describes the protocol used for the microscopy imaging of sample drug plates, all plates in this study were imaged using a Cell Discoverer 7 microscope using Zen Blue 3.1 software.\n\n1. If drug plates have been stored in the fridge, remove and leave at room temperature for half an hour to remove condensation.\n\n2. Wipe bottom of 384-well plate clean with 70% industrial methylated spirit (IMS) and lint free tissue and insert onto microscope stage\n\n3. Select the appropriate channels based on the excitation of the conjugated antibodies used, along with brightfield and DAPI as the reference channel.\n\n4. Select the lens, this study used a 10× magnification using the 20×, 0.5 lens.\n\n5. Calibrate the software using the brightfield channel as a reference to set the peripheral wells and ensure the plate is positioned correctly.\n\n6. Select the tile strategy for plate, which by default set a non-overlapping five-tile strategy chosen by software, however on plates with reduced numbers of cells (common with freshly dissociated cells) increase this number to 9-12 tiles per well to increase the imaged area per well (5 tile = 28.6%, 9 tile = 51.5%, 12 = 68.7% of individual 384 well area).\n\n7. Set up the focus using DAPI as the reference channel, any of the additional antibody markers from this reference adding any offset values to the appropriate channels tab.\n\n8. Complete image capture by running experiment, this usually takes between 2-4 hours depending on the number of channels and density of cells. The default order at which the images are captured is left to right, top to bottom per well, and a serpentine pattern for the 384 well plate, left to right, down, right to left, down, and repeat.\n\nImaging of microscope slides was performed on an LSM-980 confocal microscope all images were taken using the Photometrics sCMOS Prime BSI imaging camera using 40x objective. Images were captured using the Zeiss Blue (3.0) software package with all settings (laser power, digital gain, digital offset) kept constant between experimental conditions and repeated measures.\n\nAll image analysis was performed using Zeiss Zen Blue 3.5 analysis software. Using the processing tab, an image subset from the initial image file was extracted selecting approximately 30 individual tiles, which included a selection of wells from positive, Staurosporine and negative DMSO control wells along with any wells containing significant debris or artifacts. This subset was then selected to train the software using the Zen Intellesis machine learning module, which allows segmentation of images based on the user training distinguishing between object and background. Objects (DAPI positive nuclei) were manually labelled using the labelling options tab with the brush option, background including artifacts were labelled the same way. The setting dropdown box was set to 50 features, as this enables Zen Intellesis machine learning module to full access the computer GPU, reducing the time taken to fully analyse the images (Figure 4). The supervised learning had to be done independently for each sample as every sample is very heterogeneous, therefore the model could not be transferred between different GBM samples. Once the Intellesis training model was completed a sample specific image analysis program was then created.\n\nPrimary glioblastoma positively DAPI stained nuclei were identified as objects by the algorithm for scoring purposes (yellow outlines).\n\nPlate layout templates were designed which contained compound name, concentration and well number it corresponded to. Using RStudio software version 4.2.2 the output CSV files that were produced by Zen Blue were initially concatenated using the summarise function by dplyr to obtain a DAPI frequency count per well. This file was then merged with the plate layout template by well number, so that each well corresponded to DAPI frequency, drug and concentration. Any data visualisation drug response plots were produced using the ggplot2 package. In order to obtain cell metrics such as LD50 values and AUC, a package called GRmetrics was used. GRmetrics files for each sample was then imported back into RStudio to generate a heatmap representing AUC values. This was performed using the pheatmap package.\n\nFor RNA extraction, Bulk/stem cells were seeded into Cultrex coated 6-well plates and incubated until 70% confluent before harvesting. Qiagen RNeasy Mini Kits were used to extract RNA. Initially, media was aspirated from cultured cells and cells were washed twice with PBS. PBS was then aspirated and 350 μL RLT buffer was added to each well and cells were then dislodged using a cell scraper and transferred to labelled QIAshredder columns before being centrifuged at 8000 RCF for 2 minutes. The purple columns were discarded and 350 μl of 70% ethanol was added to the supernatant, this solution was then transferred to a RNeasy Minispin column and centrifuged for 15 seconds. The flow through was discarded and 700 μl RW1 buffer was added to each column and centrifuged for another 15 seconds at 800 RCF. This process was then repeated again twice but with 500 μl RPE buffer, the first instance centrifuged for 15 seconds and the second for 2 minutes, discarding the flow through for each step. Excess ethanol was then removed by centrifuging the column for 1 minute, before adding 50 μl of RNase free water and centrifuging again for another 1 minute to elute the RNA. Total RNA was then quantified for each sample using Nanodrop 200 spectrophotometer, which quantifies absorbance at wavelength at 260 nm to establish the concentration of RNA in each sample, and the ratio of sample absorbance at 260/280 was used to confirm purity (absence of contaminants such as protein or phenol, which absorb strongly at/near 280 nm) with ratios of ~2 deemed to represent ‘pure’ RNA. After quantification RNA samples were either used immediately or stored at -80°C. RNA samples were reverse transcribed using High-Capacity RNA-to-DNA Kit (Applied Biosystems). The RT reaction was prepared on ice in order to obtain a 30 μl sample of cDNA for downstream qPCR. Volumes of sample equivalent to 1μg of RNA were added to reagents in the kit after 15 μl buffer and 3 μl of enzyme and made up to 30 μL using RNase-free water. Samples were then reverse transcribed using a Biorad thermal cycler T100 using cycling parameters 37°C for 1 hour, 95°C 5 minutes to convert RNA into cDNA. Each resulting cDNA sample was analysed in triplicate for each individual probe within a 384-well PCR plate with GAPDH used as a control ‘housekeeping’ gene for each sample. Each reaction consisted of: 2 μL cDNA, 5 μL TaqMan Universal PCR Mastermix, 2.5 μL ddH2O and 0.5 μL of probes (provided in Table 5). The plate was sealed using optical adhesive film (MicroAmp) and loaded onto a 7900HT Fast Real-Time PCR System to perform quantitative PCR. The system was set to report 18S FAM with repeats of 40 cycles. Cycling conditions involved an initial 95°C hold for 10 minutes followed by 40 cycles of 15 second 95°C denature step and finally 60°C for 1 minute in order to anneal and extend. Double delta Ct (2-ΔΔCt) analysis was used to determine relative gene expression using an average Ct value from the triplicate runs. For example, to detect differences in expression between primary, patient derived glioblastoma stem cells grown in stem conditions and bulk differentiated cells: ΔCt = Mean Control (GAPDH) Probe Ct – Mean Gene Probe Ct, and ΔCt Expression = 2-ΔCt. Then, to calculate fold-change expression in GSCs relative to bulk cells: ΔΔCt = ΔCt Expression (Stem)/ΔCt Expression (Bulk).\n\nFor immunoblotting glioblastoma (bulk/stem) cells were seeded into Cultrex-coated 6-well plates and incubated at 37°C in 5% CO2 for 48 hours without any treatments. Before media removal, cells were washed twice in ice-cold PBS. Cells were then lysed with the addition of 100 μL lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 1 mM DTT and 1 mM EDTA supplemented with 50 U/μL benzonase (Novagen), protease and phosphatase inhibitors (Sigma). Cells were immediately harvested using a cell scraper and transferred to labelled Eppendorf tubes on ice. Each sample was then vortexed for 10 seconds before being placed on ice for 15 minutes. Samples were vortexed again following a final 15-minute incubation on ice and one final vortex. Samples were then centrifuged at 14,000 × g for 15 min at 4°C. Gel electrophoresis was performed using NuPage system (Invitrogen). Samples were resolved on 4-12% Bis-Tris gels in MOPS buffer, transferred to Protran nitrocellulose membranes (0.1 μm pore size), which were then probed for proteins of interest using antibodies diluted in 5% BSA (details of antibodies shown in Table 6 below).\n\nShapiro-Wilk normality tests were performed to assess the datasets prior to statistical analysis to decide the correct tests to perform. In order to confirm differences between two groups Mann-Whiney U-test was performed on non-parametric datasets or Students t-test on parametric datasets, p-values less than 0.05 would determine whether the differences in results were significantly different. All normality tests and statistical analysis was performed using R package stats version 4.2.2. As the current study is not comparing ex vivo drug responses to any clinical indications, normal power calculation or simulation studies were not used to determine the sample size at this time.\n\n\nResults\n\nGlioblastoma cultures grow as neurospheres unless a BME is provided, giving structural support for the cells, thus providing a dense layer of extracellular matrix (ECM) to allow them grow as adherent monolayers. For the purpose of high throughput screening, monolayer growth is attractive as it will facilitate a rapid examination of cell-drug interactions using automated high-content microscopy. However, the requirement to pre-coat plates with a basement membrane that can only be stored for a couple of weeks once used, introduces a level of complexity compared with standard 2D established cell line-based monolayer drug screening. To keep the process as streamlined as possible, drug plates would ideally be pre-printed, stored at -80°C, then on the day of surgery the plates thawed and coated in ECM ready for GSC sample seeding directly from the clinic. Using the glioblastoma SoC drug Temozolomide (TMZ) we therefore determined if the order by which the ECM, compounds and cells affected drug efficacy (Figure 5), using primary GSCs derived from a patient tumour. The LD50 values for TMZ in Conditions 1 and 2 were consistent within both the four-day and eight-day incubation periods, highlighting that when TMZ was seeded underneath the ECM it still has the same efficacy as if it was seeded above. However, within both the four-day and eight-day incubation Condition 2 showed much higher variation for percentage inhibition within repeats, suggesting this method of drugging may lead to discrepancies between repeated measures. Additionally, Condition 3 showed an increased LD50 compared to the other 2 conditions, which may be a consequence of higher cell adherence and cell cycling, by allowing the cells to adhere to basement membrane prior to drugging. Despite Condition 3 being the most representative model of patient tumour treatment, for logistical reasons described above around the critical need for ex vivo screening of clinical samples with short notice requiring the use of pre-printed drug plates, we therefore proceeded to adopt condition 1 for future GliExP development.\n\nA: Diagrammatic representation of the three different drug, cell and ECM alternations tested to ensure drug efficacy within the screening platform. B: TMZ dose response curves for CX18 GSCs following 4-day drug incubation using the different plating conditions. C: Same as (B) but following an 8-day TMZ incubation/growth period. For both datasets, mean data derived from 3 independent biological repeat experiments is shown with their respective SDs. Condition 1 average LD50 = 18.95 ± 3.45 μM, condition 2; 16.28 ± 6.22 μM, and condition 3; 56.60 ± 50.15 μM for 4 days TMZ incubation/growth. For 8 days, Condition 1 average LD50 = 9.61 ± 4.9 μM, condition 2; 6.07 ± 0.87 μM, and condition; 23.04 ± 4.04 μM.\n\nTo further confirm that our ex vivo screening platform was able to give robust and accurate readouts of TMZ sensitivity, we tested its ability to predict MGMT promoter methylation status; a well-established clinical feature of around 40-50% of all glioblastomas that epigenetically silences the expression of the key O6-methylguanine detoxifying enzyme MGMT.37\n\nTMZ sensitivity was therefore assessed in an MGMT+ (unmethylated) GSC (Ox5) and a clinically determined MGMT methylated GSC (CX18). Note that CX18 has been deem as “equivocal” methylation status based on 10.7% exhibiting methylation across all CpG islands analysed (clinical data not shown), and therefore could be considered on the weaker side of MGMT methylation and subsequent TMZ sensitivity. However, GliExP was able to distinguish significant TMZ sensitivity between OX5 and CX18 GSC which correlated with their MGMT methylation status (Figure 6A). Importantly, when analysis of further primary GSCs was carried out before clinical MGMT status was known, the resulting TMZ sensitivity allowed us to predict with 100% accuracy the MGMT status (Figure 2B).\n\nA: Comparing the temozolomide (TMZ) LD50 values of OX5 (MGMT+/unmethylated) and CX18 (MGMT-/methylated) GSCs with differential MGMT methylation as defined by clinical methylation sensitive pyrosequencing of the MGMT gene promoter in parental tumour tissue. MGMT methylated CX18 GSCs exhibited a significant increased sensitivity to TMZ. Data shown represent median and the 25th and 75th percent quartiles (box) median (middle line). The lower and upper whiskers show the smallest and largest values within 1.5x of the interquartile range below the respective 25th and 75th percentiles. Median LD50 are 46.13 ± 60.5 μM (standard deviation) compared to MGMT unmethylated GSCs; LD50 = 385.72 ± 102.5 μM (standard deviation). Data shown is derived from three independent biological repeats from two different patient derived GSC models from separate passages (each containing four technical replicates); CX18 and OX5. B: Heatmap showing AUC responses to TMZ alone or in combination with 2Gy IR for 6 different tumours assessed by GliExP. Also shown is their MGMT methylation status which was subsequently determined clinically. GliExP was able to accurately predict the MGMT status for all these tumours based solely on TMZ sensitivity prior to MGMT status being known.\n\nIn addition to TMZ, the current post-surgical SoC regimen for glioblastomas involves a course of radiotherapy (typically 60Gy over six weeks in 2Gy fractions).16 We are fortunate, and in the minority of research laboratories, in that we have access to an experimental ionising radiation (IR) source within our research facility (~2Gy/min 137Cs irradiator; CIS Bio International IBL437c). However, many places that may wish to adopt an ex vivo drug screening platform as an alternative to animal-based preclinical models may not have such facilities. We therefore assessed the potential use of the radiomimetic agent bleomycin within GliExP as this can simply be added in a similar manner to small molecule compounds by comparing a dose range against known ionising radiation doses within our experimental Cs137 facility (Figure 7). For future use and for the benefit of groups that do not have access to a radiation source, we calculated that a concentration of around 6.85μM Bleomycin was equivalent to a 2Gy dose of IR (Figure 7).\n\nA: Cell frequency measured using DAPI positive cells. B: Calculated percentage growth inhibition derived from the same data. The response readout (DAPI count) was collected using automated IF microscopy, the counts were normalized using positive and negative controls on each dose plate to provide the response measure (relative inhibition %). Bleomycin LD50 = 6.85 μM which is equivalent to LD50 IR – 2Gy. Data shown is the mean derived from 3 independent biological repeats with respective SDs.\n\nAs the current SoC for glioblastomas involves a course of radiotherapy alongside TMZ for patients deemed well enough to receive this, we combined IR with TMZ within GliExP. Encouragingly, we were able to determine the combined cytotoxic effects of IR on top of concomitant TMZ across all primary GSC tested to date (Figure 8).\n\nA: Box plot comparing the median and interquartile AUC values calculated by GliExP for the indicated GSCs treated with TMZ ± 2Gy IR. Samples shown in green represent methylated MGMT status while red represents unmethylated. B: Line graphs for the same data showing % growth inhibition. All data shown is derived from 3 independent biological repeats (with 4 technical replicates from the same patient derived cell line) with their respective SDs.\n\nGiven the encouraging development and optimisation data around GliExP (see Figures 4-8), we proceeded to carry out an initial proof-of-concept drug screening. This consisted of creating an initial pre-printed drug plate consisting of just over 30 therapeutic and pre-clinical compounds. The dose ranges for the initial batch of pre-printed GliExP plates we based on existing literature around LD50 values across a range of cell lineages, including data from our own laboratories and consisted of four concentrations + a vehicle control for each compound. Using this batch of plates, we proceeded to screen GSCs derived from 18 individual patients taken straight from surgery, including a couple of multi-region samples to assess potential differential drug response associated with spatial heterogeneity, a known driver of therapeutic resistance in the clinic (Figure 5).\n\nThis initial set of encouraging data demonstrates that GliExP is able identify potential differential drug sensitivity for a given individual tumour using freshly derived GSC populations from surgically resected tumour within a week of surgery taking place. The limited number of multi-region samples on this initial screening plate also suggests that GliExP is able to determine differential drug sensitivity within a given tumour, further highlighting how spatial heterogeneity can lead to therapeutic resistance. It is important to note that the perceived universal inhibitory effects of the EGFR inhibitor are likely an artifact of the EGF-conditioned media used to enrich/grow GSCs. Encouragingly, we observe that some GSCs are sensitive to a number of compounds with related targets, such as GBM21 being sensitive to both WEE1 and Aurora kinase inhibitors, and GBM19 being sensitive to both PARP1 and PARG inhibitors (Figure 9). However, moving forward, longer incubation times and extended concentration ranges would be beneficial for certain compounds to allow a deeper assessment of inhibitory effects and calculation of more accurate LD50 values (see Discussion section for further details).\n\nScale shown represents cell death as 0 (blue) and cell survival as 1 (red). Larger samples such as GBM10 (A, B and C) and GBM20 (A and B; indicated in bold) were sectioned into multiple regions and screened independently in order to highlight the intertumoral heterogeneity of the disease. AUC values were calculated from 2 technical replicates following 96hr drug incubations using R package GR metrics and the heatmap was constructed using R package pheatmap as detailed in the methods section. Note, due to the fact that this was performed on limited fresh clinical material, biological repeats were not performed.\n\nFinally, in order to further develop GliExP to be able to identify potential GSC-specific compound cytotoxicity within the cell milieu, we have carried out initial staining optimisation of the GSC markers Sox2, Nestin and CD133 using direct fluorescent conjugated antibodies. To determine GSC specificity of the staining, we cultured CX18 cells as either tumour bulk or GSC-enriched populations (see methods section) prior to staining (Figure 10). Across multiple optimisation experiments, we found that the most robust of these GSC markers within GliExP were Sox2 and Nestin (Figure 10A and 10B), and that these correlate with mRNA expression levels (Figure 2). It is interesting that in our hands, CD133 was not as robust a GSC marker as one would have predicted based on mRNA expression data (Figure 2). However, there is evidence within previous studies that CD133-negative cells can be labelled incorrectly due to specific antibodies only targeting the AC133 specific epitope, which is located in one of the extracellular domains of membrane-bound CD133 (Barrantes-Freer et al., 2015). We therefore would need to test additional CD133 antibodies within our platform to ascertain if this is indeed the case. However, the robust ability of both Sox2 and Nestin to distinguish GSC-enriched populations gives us confidence that these could be implemented in future iterations of GliExP.\n\nA: Left panel; violin plots showing mean fluorescence intensity of Sox2 expression (pixels/cell) in both bulk and stem enriched CX18 GSCs. Right panel; example images. B: and C: Same as in A but showing data for Nestin and CD133 respectively. Data shown are means derived from three independent biological repeat experiments from separate passages of matched ‘bulk’ and ‘stem’ derived CX18 cells with their respective SDs. Each biological repeat experient contained analysis of 100 individual cells. Statistical analysis was performed using Man-Whitney U test to highlight significant differences GSC marker staining intensity between bulk and stem populations (p < 0.001).\n\n\nDiscussion\n\nThe devastating prognosis of patients with glioblastoma has not improved significantly over the last 50 years despite the use of cell lines, more complex co-culture/microenvironment systems, and a range of animal-based models.3 This highlights a need to explore novel strategies such as ex vivo drug screening to try and improve treatment outcomes for these patients.19 Considering the extreme intertumoral heterogeneity of the disease, it seems impossible to expect a one-size-fits-all treatment regime to be successful to treat all glioblastomas. As such, ex vivo drug screening aims to discover successful individualised niche treatments for patients and embed assessment of intra- and intertumoural heterogeneity early within preclinical drug evaluation. Such compounds can include well-established/safe therapeutics used to treat other cancers and diseases, but ex vivo platforms also facilitate the rapid assessment of novel preclinical agents as a potentially superior replacement (speed, affordability, tissue-sparing, human-specific and more humane) for traditional preclinical animal models.\n\nCurrent clinical regimens treat all glioblastoma patients with TMZ and/or IR irrespective of MGMT status, even though around half of glioblastomas are unmethylated and may not significantly benefit from TMZ when overall survival rates are considered.38 Indeed, within clinical trials it has been shown acceptable to remove TMZ from the treatment regimes in unmethylated MGMT patients, as long as the patient is offered an alternative treatment method.39 Ex vivo drug screening has the potential to be adopted for such patients to help guide this ‘alternative treatment’ regime, discovering patient/tumour specific drug sensitivities. As shown here, GliExP has the potential to rapidly identify TMZ responsive/non-responsive tumours (Figure 6) and can even be used to identify potential alternative treatment strategies alongside existing SoC therapies such as radiotherapy (Figure 8), that would often be a pre-requisite of a clinical trial in the setting of newly diagnosed glioblastoma.\n\nA major benefit of ex vivo drug screening is its speed, where results can be obtained within a week of surgery, which is within the clinically relevant window to a patient’s first line of treatment following surgery. Potential drug hits can be then evaluated by a multi-disciplinary team (MDT)/clinical decision board (consisting of oncologists, pharmacists, pathologists, and clinical scientists) alongside discussion of the formal histopathological diagnosis and subsequently prescribed depending on the safety and patients health condition, similar to previous work achieved in haematological cancer.40 Due to the classification as moderate-severe under the Animals in Scientific Procedures Act, it could be deemed unethical for PDX models to be generated on such a large scale when any potential drug hits could not subsequently be confirmed clinically, considering the average life expectancy of glioblastoma (12-18 months) and turnaround time for successful PDX engraftment of between four to eight months.37,41 Advances into Mini-PDX models, which are generated through injection of patient tumour cells into immunocompromised mice within special hollow capsules in order to increase turnaround and reduce complexity, could however circumvent these issues and deliver such data in a much sorted time frame than traditional PDX models (~one week).42–44 However, the ethical issues around the volume of animals needed in order to assess a large range of therapeutics alone or indeed in combination still remain. Ex vivo screening platforms such as GliExP could therefore facilitate new individualised treatment regimens to be implemented straight away, alongside and or replacing current standard of care therapy.\n\nAlthough extremely promising, and with some exciting proof-of-concept studies recently completed, we are still in the early stages of ex vivo screening platform development, certainly for solid tumours.19 To our knowledge, the work presented here represents the first such attempts to develop a robust ex vivo drug screening platform for gliomas using freshly dissociated tumour tissue. We believe that we have optimised the seeding order/conditions, growth, imaging and analysis to allow us to screen almost all glioma samples received from the clinic either against bespoke drug plates or current SoC treatments (Figures 8 and 9). We believe that we are now at a stage where we can also start to combine drug plate screening with SoC therapies such as IR (untreated plate versus 2Gy treated plate) to mimic how these tumours are treated in the clinic and within clinical trials (certainly if TMZ can be removed from the treatment strategy for identified MGMT unmethylated tumours; see above). As we move forward with further iterations of GliExP, we are hoping to further refine multi-channel imaging to allow us to identify compounds/treatments that exhibit specific potency against the GSC population whilst sparing other cell types (Figure 10). In tandem with this, we are also working with computer scientists and artificial intelligence experts to try and develop machine learning AI technologies that can further automate and enhance speed/efficiency at which GliExP can operate. Additionally, we are working within the larger Ex vivo determined cancer therapy (EVIDENT; NCT05231655) team with Sheffield (based at the University and Hospital sites) to knowledge share our ex vivo experiences to help develop additional animal-sparing ex vivo screening platforms for other solids tumours (e.g. bladder, kidney, head and neck etc).\n\nFrom a 3Rs perspective ex vivo has the potential to become a preclinical alternative, replacing and reducing the requirement for murine avatars for testing experimental therapeutics, not only in glioblastoma but for many other solid malignancies. Our first-generation drug plates contain 35 different therapeutics which have been used to screen 18 different patient samples (Figure 9). Feasibly it would be impossible to create the numbers of avatars needed per patient to obtain all 35 different drug response profiles using traditional PDX models. On average 5-10 mice are required to test one single treatment, to recreate this work in vivo a minimum of 3,150 PDX models would be required (175 models per patient). This is an especially large sample, and the time and cost of serially transplanting into multiple cohorts of mice would be astronomical, and extremely time consuming. Additionally genetic drift of the tumours through multiple cohort passages has resulted in engraftment being restricted to 10 or fewer passages,45 therefore limiting the drug screening capability of PDX models.\n\nBased on a comprehensive analysis of current global ex vivo studies utilising murine avatars (see Table 2 of our recent review article19), together with data obtained from the GlobalData database around the current therapeutic development for glioma, we estimate that around 400+ mice are used per study, and ~20,000+ mice were used globally in this setting over the last 5 years. We therefore believe the application of GliExP could replace the use of ~2,000 mice per year, with the potential for expansion to other solid tumour types. This estimate increases significantly when one considers our plans to combine multiple therapeutics in tandem with current SoC radiation and TMZ treatments. To facilitate this, we are currently in discussions with our research ethics and Healthcare Gateway teams at the University and Royal Hallamshire Hospital to explore how we could develop GliExP into a research, clinical and commercial service given recent positive conversations with drug development companies.",
"appendix": "Data availability\n\nFigshare: Ex-vivo drug screening of surgically resected glioma stem cells to replace murine avatars and provide personalise cancer therapy for glioblastoma patients, https://doi.org/10.15131/shef.data.c.6710475.v1. 46\n\nThis collection contains the following underlying data projects:\n\n- IF Mean Intensity files for markers CD133, Nestin, SOX2 and Vimentin (Datasets)\n\n- CX18 Bulk vs Stem qPCR Analysis\n\n- CX18 Bulk Vs Stem CD133 IF image files\n\n- CX18 Bulk Vs Stem Nestin IF Image Files\n\n- CX18 Bulk Vs Stem SOX2 IF Image Files\n\n- CX18 Bulk Vs Stem Vimentin IF Image Files\n\n- Western blots for CX18 undifferentiated (primary stem), differentiated (bulk) and de-differentiated (secondary stem)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAlexander BM, et al.: Adaptive Global Innovative Learning Environment for Glioblastoma: GBM AGILE. Clin. Cancer Res. 2018; 24(4): 737–743. PubMed Abstract | Publisher Full Text\n\nBrain, G.B.D. and C.N.S.C.C. Other: Global, regional, and national burden of brain and other CNS cancer, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Neurol. 2019; 18(4): 376–393.\n\nAldape K, et al.: Challenges to curing primary brain tumours. Nat. Rev. Clin. Oncol. 2019; 16(8): 509–520. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBergmann N, et al.: The Intratumoral Heterogeneity Reflects the Intertumoral Subtypes of Glioblastoma Multiforme: A Regional Immunohistochemistry Analysis. Front. Oncol. 2020; 10: 494. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPiccirillo SGM, et al.: Genetic and functional diversity of propagating cells in glioblastoma. Stem Cell Rep. 2015; 4(1): 7–15. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSottoriva A, et al.: Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics. Proc. Natl. Acad. Sci. U. S. A. 2013; 110(10): 4009–4014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrennan CW, et al.: The somatic genomic landscape of glioblastoma. Cell. 2013; 155(2): 462–477. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpiteri I, et al.: Evolutionary dynamics of residual disease in human glioblastoma. Ann. Oncol. 2019; 30(3): 456–463. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStupp R, Lukas RV, Hegi ME: Improving survival in molecularly selected glioblastoma. Lancet. 2019; 393(10172): 615–617. PubMed Abstract | Publisher Full Text\n\nVerhaak RG, et al.: Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010; 17(1): 98–110. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPrager BC, et al.: Glioblastoma Stem Cells: Driving Resilience through Chaos. Trends Cancer. 2020; 6(3): 223–235. 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Publisher Full Text\n\nOstrom QT, et al.: Adult Glioma Incidence and Survival by Race or Ethnicity in the United States From 2000 to 2014. JAMA Oncol. 2018; 4(9): 1254–1262. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStupp R, et al.: Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol. 2009; 10(5): 459–466. PubMed Abstract | Publisher Full Text\n\nWilliams ST, et al.: Precision oncology using ex vivo technology: a step towards individualised cancer care? Expert Rev. Mol. Med. 2022; 24: e39. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMouse Genome Sequencing, C et al.: Initial sequencing and comparative analysis of the mouse genome. Nature. 2002; 420(6915): 520–562. Publisher Full Text\n\nRominiyi O, Al-Tamimi Y, Collis SJ: The ‘Ins and Outs’ of Early Preclinical Models for Brain Tumor Research: Are They Valuable and Have We Been Doing It Wrong? Cancers (Basel). 2019; 11(3). PubMed Abstract | Publisher Full Text | Free Full Text\n\nJardim DL, et al.: Factors associated with failure of oncology drugs in late-stage clinical development: A systematic review. Cancer Treat. Rev. 2017; 52: 12–21. PubMed Abstract | Publisher Full Text\n\nWong CH, Siah KW, Lo AW: Estimation of clinical trial success rates and related parameters. Biostatistics. 2019; 20(2): 273–286. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAkter F, et al.: Pre-clinical tumor models of primary brain tumors: Challenges and opportunities. Biochim. Biophys. Acta Rev. Cancer. 2021; 1875(1): 188458. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuszthy PC, et al.: In vivo models of primary brain tumors: pitfalls and perspectives. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nPlowman J, et al.: Preclinical antitumor activity of temozolomide in mice: efficacy against human brain tumor xenografts and synergism with 1,3-bis(2-chloroethyl)-1-nitrosourea. Cancer Res. 1994; 54(14): 3793–3799. PubMed Abstract\n\nFriedman HS, et al.: Activity of temozolomide in the treatment of central nervous system tumor xenografts. Cancer Res. 1995; 55(13): 2853–2857. PubMed Abstract\n\nTamargo RJ, et al.: Interstitial chemotherapy of the 9L gliosarcoma: controlled release polymers for drug delivery in the brain. Cancer Res. 1993; 53(2): 329–333. PubMed Abstract\n\nTabet A, et al.: Designing Next-Generation Local Drug Delivery Vehicles for Glioblastoma Adjuvant Chemotherapy: Lessons from the Clinic. Adv. Healthc. Mater. 2019; 8(3): e1801391. PubMed Abstract | Publisher Full Text\n\nBurgenske DM, et al.: Preclinical modeling in glioblastoma patient-derived xenograft (GBM PDX) xenografts to guide clinical development of lisavanbulin-a novel tumor checkpoint controller targeting microtubules. Neuro-Oncology. 2022; 24(3): 384–395. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArjonen A, et al.: Image-based ex vivo drug screen to assess targeted therapies in recurrent thymoma. Lung Cancer. 2020; 145: 27–32. PubMed Abstract | Publisher Full Text\n\nMakela R, et al.: Ex vivo assessment of targeted therapies in a rare metastatic epithelial-myoepithelial carcinoma. Neoplasia. 2020; 22(9): 390–398. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRubio-Viqueira B, et al.: An in vivo platform for translational drug development in pancreatic cancer. Clin. Cancer Res. 2006; 12(15): 4652–4661. PubMed Abstract | Publisher Full Text\n\nHegi ME, et al.: MGMT gene silencing and benefit from temozolomide in glioblastoma. N. Engl. J. Med. 2005; 352(10): 997–1003. PubMed Abstract | Publisher Full Text\n\nWick W, et al.: Phase II Study of Radiotherapy and Temsirolimus versus Radiochemotherapy with Temozolomide in Patients with Newly Diagnosed Glioblastoma without MGMT Promoter Hypermethylation (EORTC 26082). Clin. Cancer Res. 2016; 22(19): 4797–4806. PubMed Abstract | Publisher Full Text\n\nSnijder B, et al.: Image-based ex-vivo drug screening for patients with aggressive haematological malignancies: interim results from a single-arm, open-label, pilot study. Lancet Haematol. 2017; 4(12): e595–e606. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang F, et al.: Characterization of drug responses of mini patient-derived xenografts in mice for predicting cancer patient clinical therapeutic response. Cancer Commun (Lond). 2018; 38(1): 60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhao P, et al.: Personalized treatment based on mini patient-derived xenografts and WES/RNA sequencing in a patient with metastatic duodenal adenocarcinoma. Cancer Commun (Lond). 2018; 38(1): 54. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu X, et al.: Individualized therapy based on the combination of mini-PDX and NGS for a patient with metastatic AFP-producing and HER-2 amplified gastric cancer. Oncol. Lett. 2022; 24(5): 411. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhan M, et al.: Guided chemotherapy based on patient-derived mini-xenograft models improves survival of gallbladder carcinoma patients. Cancer Commun (Lond). 2018; 38(1): 48. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMattie M, et al.: Molecular characterization of patient-derived human pancreatic tumor xenograft models for preclinical and translational development of cancer therapeutics. Neoplasia. 2013; 15(10): 1138–1150. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGagg H, Williams S, Conroy S, et al.: Ex-vivo drug screening of surgically resected glioma stem cells to replace murine avatars and provide personalise cancer therapy for glioblastoma patients. [data set]. The University of Sheffield. Collection 2023. Publisher Full Text"
}
|
[
{
"id": "195888",
"date": "31 Aug 2023",
"name": "Natividad Gomez-Roman",
"expertise": [
"Reviewer Expertise Glioblastoma",
"preclinical in vitro and in vivo models of cancer",
"high-throughput assays"
],
"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\nA meticulously crafted manuscript delineates a high-throughput screening platform designed for the assessment of novel treatment combinations employing ex vivo patient-derived glioma tumours. The document is well-written, furnishing a comprehensive exposition of the methodology.\nSome minor aspects necessitate revision:\nRegarding all drug dose-response curves: a) It is imperative to incorporate the control value (no drug) in these graphs. As 'X' employs a logarithmic scale, this can be indicated by a disjointed line, creating a visual gap between the 0 drug value and the first lowest dose. b) The provision of confidence intervals is indispensable for all LD50 data. c) The exhibited curves are not intrinsically fitted to the dose-response model. Although I acknowledge that the AUC is derived from these graphs, for precise LD50 calculations accompanied by confidence intervals, I propose appropriately fitting the data for both presentation and LD50 calculation. My recommendation is to employ a 4-parameter dose-response curve, utilizing the 'drc' package in R (version 3.6.3), available at (https://www.R-project.org).\n\nIn Fig. 8 – Could you specify the concentration of TMZ utilized for the box plots in section A?\n\nGiven the intricate cellular composition of freshly excised tumour biopsies, encompassing tumour cells along with associated elements like microglia, it is imperative to acknowledge that the cellular populations within GliExP would manifest heterogeneity. This factor could potentially introduce confounding variables to the outcomes of the screening, as responses may emanate not solely from glioblastoma cells, but also from the surrounding glioblastoma-associated cells. Could the authors kindly furnish insights into the viability of other cell types, such as microglia, within the GliExP models? If these cell types are indeed present, it would be valuable if the authors could provide an estimate of the percentage representation of each cell type cultivated in the GliExP model.\n\nWith reference to the CSC markers, could the authors elucidate the proportion of cells retaining these markers, and subsequently, establish a correlation with the characteristics of the biopsied material? Is there a discernible correlation between these values?\n\nRectification is required in the legend of Fig. 10 – a typographical error is apparent in the penultimate sentence, where 'experiment' is misspelt. Kindly effect the necessary correction.\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? Yes\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? Partly",
"responses": [
{
"c_id": "11212",
"date": "22 Mar 2024",
"name": "Spencer Collis",
"role": "Author Response",
"response": "Responses to reviewer comments for Gagg et al (f100research-12-954-V1; doi: 10.12688/f1000research.135809.1) We wish to thank both reviewers for the time taken to provide their insights and constructive comments on our F1000 methods paper. We have addressed comments to both reviewers and highlighted subsequent revisions to the manuscript below as well amending as the minor typographical errors that were also highlighted by the reviewer within the revised manuscript. Reviewer 1 A meticulously crafted manuscript delineates a high-throughput screening platform designed for the assessment of novel treatment combinations employing ex vivo patient-derived glioma tumours. The document is well-written, furnishing a comprehensive exposition of the methodology. Some minor aspects necessitate revision: Regarding all drug dose-response curves: a) It is imperative to incorporate the control value (no drug) in these graphs. As 'X' employs a logarithmic scale, this can be indicated by a disjointed line, creating a visual gap between the 0 drug value and the first lowest dose. b) The provision of confidence intervals is indispensable for all LD50 data. c) The exhibited curves are not intrinsically fitted to the dose-response model. Although I acknowledge that the AUC is derived from these graphs, for precise LD50 calculations accompanied by confidence intervals, I propose appropriately fitting the data for both presentation and LD50 calculation. My recommendation is to employ a 4-parameter dose-response curve, utilizing the 'drc' package in R (version 3.6.3), available at (https://www.R-project.org). Thank you for highlighting this, we have replace the original graph with appropriate DRC curves for the data mention (revised Figures 5 and 7), although we have maintained figure 8 in its original format, as this was more focused on the AUC as the main output. In Fig. 8 – Could you specify the concentration of TMZ utilized for the box plots in section A?. The dose range concentration of temozolomide has been added into figure 8B figure legend. Given the intricate cellular composition of freshly excised tumour biopsies, encompassing tumour cells along with associated elements like microglia, it is imperative to acknowledge that the cellular populations within GliExP would manifest heterogeneity. This factor could potentially introduce confounding variables to the outcomes of the screening, as responses may emanate not solely from glioblastoma cells, but also from the surrounding glioblastoma-associated cells. Could the authors kindly furnish insights into the viability of other cell types, such as microglia, within the GliExP models? If these cell types are indeed present, it would be valuable if the authors could provide an estimate of the percentage representation of each cell type cultivated in the GliExP model. This is an excellent observation; and at this stage we are focused on the stem cell population and are still validating the markers used. We do plan to try and validate further markers to provide insight into other populations, but this is current work in progress and we hope to share further details in due course. With reference to the CSC markers, could the authors elucidate the proportion of cells retaining these markers, and subsequently, establish a correlation with the characteristics of the biopsied material? Is there a discernible correlation between these values? We have undertaken multi-region sampling and found GBM surgical samples to be highly heterogeneous across the tumour at the phenotypic and genetic level between regions (see Derby et al 2023 doi: 10.1093/neuonc/noad210 and Jones et al doi.org/10.3390/cancers16050863 2024 for some examples), so it would be challenging to match the region from the GliExP to subsequent samples used for histology. Based on this we would expect to see differences, and thus once the markers are further validated, we would undertake this for our multi-region samples to validate the heterogeneity observed."
}
]
},
{
"id": "195890",
"date": "03 Oct 2023",
"name": "Anke Brüning-Richardson",
"expertise": [
"Reviewer Expertise Glioblastoma",
"pre-clinical models",
"drug development"
],
"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 Gagg et al. clearly describes a novel ex-vivo drug screening platform for personalised cancer therapy for glioblastoma patients. The authors are making a strong case to reduce animal-based pre-clinical models and replace mouse orthotopic/cranial resection models to ascertain drug responses in patient-derived glioma stem cell populations.\n\nThere are a few points to consider for further discussion.\nCan the authors further comment on the problems associated with the use of PDX models in terms of different methodologies and protocols used by researchers in the field? Unified protocols and sharing of the same resources (i.e. patient-derived cell lines) would generate more meaningful data, but this is currently not common practice.\n\nApart from the described novel ex vivo drug screening platform I think it would be worth mentioning that there are also additional, advanced 3D in vitro models and microfluidic Lab-on-a-chip technologies which may complement the research described here, which will help reduce the number of animals used in glioblastoma research.\n\nCan the authors comment on published data from in vivo models and the outcomes of research into some of the drugs they were investigating here, if available? How do the two models compare?\n\nJust some minor typos or inconsistencies in the text:\nPage 11: 2 'pre warmed' should be 'pre-warmed'. Page 11: 2.. Full stop after 'PBS'. Page 13. 20. Full stop after 'tissue'. On page 13, follow on instructions, for consistency there should be full stops after each sentence. Also at the end of the note, so after 'GSC'. Page 15: 2 Full stop after 'stage'. Page 18 - Results section - 'condition 1' should be 'Condition 1', to keep it consistent, so capital letters for this. Page 19. Figure 5 figure legend: 'condition 3' should be 'Condition 3'. Figure 6 figure legend - Temozolomide should be TMZ as already mentioned previously.\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? Yes\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? Yes",
"responses": [
{
"c_id": "11213",
"date": "22 Mar 2024",
"name": "Spencer Collis",
"role": "Author Response",
"response": "Responses to reviewer comments for Gagg et al (f100research-12-954-V1; doi: 10.12688/f1000research.135809.1) We wish to thank both reviewers for the time taken to provide their insights and constructive comments on our F1000 methods paper. We have addressed comments to both reviewers and highlighted subsequent revisions to the manuscript below as well amending as the minor typographical errors that were also highlighted by the reviewer within the revised manuscript. Reviewer 2 The article by Gagg et al. clearly describes a novel ex-vivo drug screening platform for personalised cancer therapy for glioblastoma patients. The authors are making a strong case to reduce animal-based pre-clinical models and replace mouse orthotopic/cranial resection models to ascertain drug responses in patient-derived glioma stem cell populations. There are a few points to consider for further discussion: Can the authors further comment on the problems associated with the use of PDX models in terms of different methodologies and protocols used by researchers in the field? Unified protocols and sharing of the same resources (i.e. patient-derived cell lines) would generate more meaningful data, but this is currently not common practice. Based on the reviewer’s suggestion and for completeness, we have added some additional information on this in the introduction section of the revised manuscript. Additionally, we have summarised below a fuller response to the Reviewer’s question around PDX models: PDX model generation typically involves transplantation of patient tumour sample (cells or tissue fragments) into immunocompromised mice, either orthotopically (i.e. at the same anatomical site as the corresponding patient) or subcutaneously within the hind limb flank (Williams et al., 2022, DOI: 10.1017/erm.2022.32). This subsequently involves the serial transplantation of tumours into consecutive cohorts of mice in order to achieve a sufficient number of models for downstream analysis. There are however discrepancies in the agreed protocols for establishment of PDX models. Firstly, is site of tumour transplantation, orthotopic or subcutaneous (SC). Whilst orthotopic is the most desirable for generation of glioblastoma PDX models, it is often more cost-effective and less labour intensive to produce subcutaneous models. A recent study (Alcaniz et al., 2023, DOI:10.3389/FONC.2023.1129627) compared the drug responses of matched subcutaneous and orthotopic PDX models, which revealed compounds bevacizumab and everolimus showing minimal efficacy within the orthotopic grown tumours. Responses to irinotecan was dependent on tumour site, some showing similarities while others differential responses compared to the SC models. The SoC drug TMZ showed pronounced efficacy towards the orthotopic models within all four transplanted tumours, which they concluded was due to the BBB, restricting the diffusion of compounds towards the tumour site. Another discrepancy within agreed PDX generation is the use of patient’s dissociated tumour cells, or tumour fragments. The advantage of maintaining the original tumour as fragments is maintaining some of the original architecture and cell-cell interactions thus mimicking the original microenvironment. On the other hand, the use of single cell suspensions prevents any sampling bias, avoiding any spatially enriched subclones (Williams et al., 2013, DOI: 10.1038/LABINVEST.2013.92), however mechanical and enzymatic dissociation steps can affect cell viability and therefore success of engraftment. Another variable effecting reproducible results is the availability of multiple different mouse strains with variable degrees of immunosuppression, due to presence of natural killer cells. Mouse strains with higher immunosuppression possess more favourable success of engraftment (Hidalgo et al., 2014, DOI: 10.1158/2159-8290.CD-14-0001). Some studies follow the protocols for PDX engraftment by Giannnini et al. This work describes initial dissociation of patient tumour specimens to enable draw through a 16-gauge needle, followed by 1:1 mixing with BME extract Matrigel. The Matrigel-tissue mixture was then injected subcutaneously into mice until desired tumour volume was reached. These mice were then harvested to obtain the tumour, followed again by mincing and injection into consecutive cohorts of mice, before being suitable for intracranial injection (Giannini et al., 2005, DOI: 10.1215/S1152851704000821; McCord et al., 2022, DOI: 10.3390/CANCERS14225494). This study described the establishment of 4 glioblastoma PDX models however, one of the main issues from this protocol was the variable subcutaneous tumour passage used (between 4-10), prior to suitable intracranial injection. Other reports followed similar protocols but do not specify the use of BME extract, rather that the required volume of PDX tumour material (1cm3) is required prior to harvesting (William et al., 2017, DOI: 10.1186/S12967-017-1128-5). Finally, another study specified the short-term culturing (5-14 days) of these harvested subcutaneous PDX tumours, prior to orthotopic xenograft injection (Sarkaria et al., 2007, DOI: 10.1158/1535-7163.MCT-06-0691). We hope this information adds further detail requested by the reviewer. Apart from the described novel ex vivo drug screening platform I think it would be worth mentioning that there are also additional, advanced 3D in-vitro models and microfluidic Lab-on-a-chip technologies which may complement the research described here, which will help reduce the number of animals used in glioblastoma research. We acknowledge this as a highly relevant comment. Although the published article is purely a methods paper, we are happy to expand on this as follows: With regards to the implementation of GliExp with more advanced 3D in-vitro models such as organoids on chips; these are microfluidic devices which permit the culturing of cells on micrometre-sized chambers which are continually perfused (Bhatia and Ingber, 2014, DOI: 10.1038/nbt.2989). They can be designed to mimic interfaces between different tissues such as the BBB (Cecchelli et al., 2014, DOI: 10.1371/JOURNAL.PONE.0099733; Vatine et al., 2019, DOI: 10.1016/J.STEM.2019.05.011). Successful BBB in-vitro microarray models have been used to assess drug toxicity, BBB permeation and intracellular transport mechanisms within the early stage of drug discovery (Moya et al., 2021, DOI: 10.3390/PHARMACEUTICS13060892). They have also been directly integrated into drug screens into the investigation of nanoparticles for treating CNS diseases such as epilepsy (Hou et al., 2022, DOI: 10.1039/D1NR05825H). As such, the incorporation of such models may be advantageous to combine within our GliExp platform to evaluate the ability of novel or repurposed compounds to penetrate the BBB, evaluate relevant pharmacokinetic (PK) and pharmacodynamic (PD) profiles to reduce the number of animals used within pre-clinical studies. Can the authors comment on published data from in vivo models and the outcomes of research into some of the drugs they were investigating here, if available? How do the two models compare? We acknowledge this is a highly relevant comment and the addition of these models will help to reduce the number of animals. We have recently reviewed ex vivo screening as well as an range of other ex vivo drug screening approaches (see Williams et al, 2022; doi: 10.1017/erm.2022.32), and as such, we consider this out of scope for this method specific paper. Whilst a direct comparison is challenging when dealing with patient tissue as alternate models would have to be generated on the same tissue in the same lab. We are currently looking at matched primary derived GBM and patient derived cell cultures. One study has done this directly investigating 2D and 3D and used different analysis techniques. Both 2D and 3D assays were suitable at highlighting drug hits within MAPK pathway, this was further confirmed by an activating KRAS mutation (Mäkelä et al., 2020, DOI: 10.1186/s12885-020-07092-w)."
}
]
}
] | 1
|
https://f1000research.com/articles/12-954
|
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