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https://f1000research.com/articles/11-1163/v1
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11 Oct 22
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{
"type": "Research Article",
"title": "Characterization of virulence factors and antibiotic resistance pattern of uropathogenic Escherichia coli strains in a tertiary care center",
"authors": [
"Naveen Kumar M",
"Sevitha Bhat",
"Archana Bhat K",
"Vishwas Saralaya",
"Shalini Shenoy Mulki",
"Naveen Kumar M",
"Sevitha Bhat",
"Vishwas Saralaya",
"Shalini Shenoy Mulki"
],
"abstract": "Background: Urinary tract infections (UTI) are the most prevalent bacterial infection in humans. The uropathogenic E. coli (UPEC) expresses a range of virulence factors that contribute to their pathogenicity. The emergence of multidrug resistance (MDR)-associated UTI is increasing. This study monitors the distribution of virulence factors among UPEC strains to note the antibiogram, outcome and type of associated UTI. Methods: A prospective cross-sectional time-bound study of six months was done on clinically significant urinary isolates of Escherichia coli. Detection of haemolysin production and serum resistance was done by phenotypic methods. Genotypic characterization of the virulence genes (papC, iutA, hlyA, cnf1) was done by multiplex PCR. Demographic data, clinical history, antibiogram and type of UTI was collected from clinical case records. Results:75 E.coli isolates from patients with suspected UTIs were included. Females had a higher preponderance of UTI (66.7%). 93% of patients were adults and the remaining 7% were from paediatrics. 24 (32%) isolates showed haemolysis by plate haemolysis and all isolates were serum-resistant. Out of 75 isolates, 65 were positive for at least one of four targeted genes, while remaining ten isolates were negative for all four genes. Multidrug resistance was found in 40 (53.3%) isolates. 97.4% of the UTI cases had a favourable clinical outcome at discharge. Mortality due to urosepsis was 2.6%. Conclusion: Association of hemolysin production with resistance to imipenem and norfloxacin in UPEC strains was significant. Presence of hlyA gene is positively associated with ceftazidime resistance. Nitrofurantoin, piperacillin, tazobactam, and cefaperazone sulbactam are possible candidates for empirical therapy of UTIs. Drugs like aminoglycosides, carbapenems and fosfomycin may be used as reserve drugs in the treatment of MDR-UTI. However, inappropriate usage can increase antibiotic resistance. Hence proper selection of antibiotics in hospitals taking into account the local antibiogram is needed to reduce the emergence of antibiotic resistance.",
"keywords": [
"Virulence factors",
"Uropathogenic Escherichia coli",
"genes",
"antibiotic resistance",
"multiplex PCR"
],
"content": "Introduction\n\nBackground: Urinary tract infections (UTI) are the most prevalent bacterial infection in humans. Every year, globally about 150 million people are diagnosed with UTI.1 Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, Proteus mirabilis, Citrobacter spp., Staphylococcus spp., Enterococcus spp., are the most common species causing UTI. Escherichia coli is the most frequent pathogen in the human urinary tract and accounts for 75% of the UTI. 85% of the community acquired UTIs and 40% of the hospital acquired UTI are attributed to Escherichia coli.2\n\nThe term uropathogenic E. coli (UPEC) refers to the extraintestinal strains of E. coli that express a variety of virulence factors, contributing to their pathogenicity in comparison to commensal E. coli.3,4 The specific virulence genes present in strains of UPEC isolates are the genes that encode adhesins (e.g. Type I fimbriae and P fimbriae), mechanisms for acquisition of nutrients (e.g. siderophores), factors that help the UPEC to escape from host defence systems (e.g. lipopolysaccharide, capsule) and toxins (e.g., cytotoxic necrotising factor 1, hemolysin).3 The factors mentioned above equip the bacteria with the ability to colonize the periurethral region, ascend the urinary tract to reach the urinary bladder resulting in infections like cystitis, urethritis, pyelonephritis, and urosepsis.5 UPEC strains have acquired the virulence genes (chromosomal or plasmid mediated by horizontal transfer of DNA). The molecular based platforms aid in the detection and characterization of UPEC strains.4 The characterization of these virulence genes in UPEC strains will help in better understanding of pathogenesis and course of UTI.\n\nRecently there is an upsurge in UPEC strains that are multidrug-resistant (MDR), i.e., resistant to at least three or more classes of antibiotic agents.6 The emergence of MDR-associated UTI is increasing off late. Extended Spectrum β-Lactamase (ESBL) production among UPEC strains pose a therapeutic challenge. As a result, the therapeutic options available for the treatment of UTI are cut down which in turn is linked to treatment failure and increase in the economic burden of the community.7\n\nObjectives: The study was undertaken to monitor the distribution of virulence factors among UPEC strains, to note the antibiogram, outcome, type of UTI and to look for the association of genetic virulence traits with antibiotic resistance.\n\n\nMethods\n\nStudy design: Prospective cross sectional time bound study.\n\nStudy setting: The study was conducted in the Department of Microbiology, in a tertiary care center at Mangalore, India, for a duration of six months (Study period: January 2020 to May 2021).\n\nParticipants: The inclusion and exclusion criteria are as mentioned below:\n\nInclusion criteria: All clinically significant isolates of E.coli from urine. An isolate was considered significant if urine cultures had colony count ≥105 CFU/ml or ≥103 CFU/ml in symptomatic patients.1\n\nExclusion criteria: Urine samples with no growth, less significant counts of E.coli, growth of bacteria other than E.coli, isolates of E.coli from clinical samples other than urine.\n\nThe study was conducted after approval from the Institutional Ethics Committee, Kasturba Medical College, Mangaluru (Reg No. ECR/541/Inst/KA/2014/RR-17) Reference number IECKMCMLR-12/2020/408). The study was performed on isolates retrieved in the laboratory obviating the need for informed consent from the patients.\n\nSpecimen processing: Clean catch midstream urine samples received from suspected cases of UTI were processed within one hour of collection. The samples were inoculated onto MacConkey’s agar by semi quantitative method, Cystine-Lactose-electrolyte-deficient agar, UTI chrome agar. The culture plates were incubated for 37°C for 24 hrs. Urine samples with pure growth of E.coli, with a colony count of ≥105 CFU/ml or ≥103 CFU/ml in symptomatic patients, were considered significant. The study included 75 urinary isolates of E. coli. The isolates were identified based on colony morphology and standard biochemical tests. Antibiotic susceptibility testing was performed by the modified Kirby–Bauer disk diffusion/Vitek2 Compact (Biomerieux, France) system and interpretation was done as per the Clinical and Laboratory Standards Institute guidelines.\n\nVariables and data source: The phenotypic methods for haemolysin production, serum resistance and genotypic characterization of virulence genes in UPEC are explained below.\n\nPhenotypic methods for detection of haemolysin production and serum resistance:\n\nThe detection of α-haemolysin produced by E. coli was performed by plate haemolysis test. The presence of a zone of complete lysis of erythrocytes around the colony and clearing of the medium on 5% sheep blood agar, is suggestive of α-haemolysin production.8,9\n\nSerum resistance was studied by using fresh overnight culture of isolates as per the method described by Sharma et al.9 The UPEC strains were considered serum sensitive if viable count dropped to 1% of the initial value and serum resistant if ≥90% of organisms survived after 180 minutes.\n\nGenotypic characterization of virulence genes of UPEC:3,10\n\nDNA extraction was performed by boiling method. The spectrum of virulence genes in UPEC strains was detected using two sets of multiplex PCR as shown below. Table 1 shows the PCR mastermix preparation used. The primer sequence of the mentioned genes is shown in Table 2. PCR was performed in a final reaction volume of 50 μl. The program for amplification included a step of initial denaturation at 95°C for 3 min, followed by 25 cycles of 94°C for 30 s, 61°C for 30 s and 68°C for 3 min and a final extension step at 72°C for 3 min. The amplicons are visualized using the gel documentation system.\n\nThe required data was retrieved from the clinical case records and the cases of complicated and uncomplicated UTI were identified. Uncomplicated UTIs are those that occur in healthy individuals without any of the predisposing factors for UTI. Complicated UTIs occur in individuals with underlying functional or structural abnormalities of the genitourinary tract.11\n\nSample size: The sample size was calculated taking into account the data of the previously published article (2). Using the formula n=Z2pqd2, a sample size of total 75 is calculated. Where p=prevalence=75%, q=1-p, d=Effect size=10%, Z=1.96 at 80-95% confidence interval.\n\nThe sample size for the study was 75.\n\nAll the data was entered into an excel sheet and analyzed using IBM SPSS version 25. The continuous and categorical variables have been represented as mean ± standard deviation and frequency percentages respectively. The association between the variables were analyzed using the chi-square test.\n\n\nResults\n\nA total of 75 urinary isolates of E.coli from patients with suspected urinary tract infections were included. Females had a higher preponderance of UTI (66.7%) than males (33.3%). 93% (n=70) of the patients were adults and the remaining 7%(n=5) were from paediatric population. The majority of the female patients were in the age group 20-39 years.\n\nPhenotypic detection of serum resistance and hemolysin production exhibited by E.coli was 100% and 32% respectively. Multiplex PCR was performed for the detection of virulence genes papC, Cnf1, hlyA & iutA as shown in Figures 1 and 2. The distribution of virulence genes among the 75 UPEC isolates is as shown in Figure 3. Out of 75 isolates, 65 were positive for at least one of the four targeted genes as shown in Table 3, while the remaining ten isolates were negative for all 4 genes.\n\nL- ladder 1000+ bp, lane 1-6: test isolates, lane 7: Negative control.\n\nL: ladder 1000+ bp, lane 1-7: test isolates, lane 8: Negative control.\n\nIt was found that hlyA gene was found in a higher percentage in haemolytic isolates (41.7%) than non- haemolytic isolates (19.6%). p-value was statistically significant (p-value=0.044). Also, 50% of the cnf1 positive isolates harboured the hlyA (haemolysin) gene (p=0.003; statistically significant).\n\nThe antibiotic resistance pattern of the UPEC isolates are as shown in Figure 4. Out of 75 isolates, 38 (50.6%) isolates were ESBL producers. Multidrug resistance (resistance to three or more antibiotic classes) was found in 40 (53.3%) isolates. Our study revealed that 45 out of the 75 urinary isolates, possessed more than one virulence factor as shown in Table 5.\n\nThe distribution of virulence factors in antibiotic-resistant isolates were studied as shown in Table 4. Hemolysin production and resistance to imipenem, Norfloxacin was found to be significant (p≤0.05). The presence of hlyA gene and resistance to ceftazidime was found to be significant (p≤0.05). There was no statistically significant difference between the presence and absence of the other virulence genes with specific antibiotic resistance.\n\n* p≤0.05 statistically significant.\n\nAmong the 40 MDR E. coli isolates, 11 (27.5%) isolates produced haemolysis and all were serum resistant. iutA, papC, cnf1, hlyA genes were detected in 72.5% (n=29), 47.5% (n=19), 35% (n=14) and 27.5% (n=11) of the MDR isolates respectively.\n\nOut of the total 75 cases of UPEC studied, 60% (n=45) were complicated UTI and 40% (n=30) were uncomplicated UTI. Out of the complicated UTI cases, the common genes detected were iutA (83%) and papC (50%) followed by cnf1 (33%) and hlyA (10%) genes. Among the uncomplicated UTI isolates, iutA (77%), papC (55%) and cnf1 (23%) were the common genes detected. None of the isolates from uncomplicated UTI had hlyA. 77% of the complicated UTI were MDR and 33% of the uncomplicated UTI cases were MDR.\n\nOut of the total 75 cases of UPEC studied, majority (97.4%) had a favourable clinical outcome at discharge. Mortality due to urosepsis was noticed in two cases (2.6%).\n\n\nDiscussion\n\nUrinary tract infection is one of the infectious diseases which is most prevalent amongst the people of all age groups from neonate to geriatric age group. Studies from India have reported varying prevalence rates of E.coli associated UTI- 50%-, 75%.12 The bacterial pathogen accounting for the majority of community and hospital-acquired urinary infections is the UPEC. Depending on the virulence, these infections might range from mild uncomplicated UTI to complicated UTI.2 Characterization of UPEC isolates with respect to their antibiotic resistance patterns and virulence factors, will aid in the effective management of UTI.\n\nOur study revealed that 32% of the isolates produced haemolysin which is similar to the findings of Chhaya shah et al and Anuradha et al -25%, 28.07%, 32% & 47% respectively.13,14 The exotoxin implicated in the enhanced virulence and lethality of clinical infections among UPEC strains is Alpha-hemolysin (Hly) production.15 UTIs associated with Alpha-hemolysin may be associated with extensive kidney inflammation and injury due to it’s cytotoxic nature. The majority of hlyA-positive strains were identified in patients with pyelonephritis (> 70%) compared to from patients with cystitis (31–48%), ascertaining the role of hlyA as an important virulence factor in the pathogenesis of pyelonephritis.16\n\nSerum resistance is a property that provides a survival advantage to the bacteria. This makes UPEC resistant to killing by the alternative complement pathway in the normal human serum. Serum resistance in UPEC strains has been typically associated with pyelonephritis, cystitis and bacteraemia.7 In the current study, all 75 isolates showed resistance to serum bactericidal action. This is similar to the studies by Sharma et al and Shetty SK et al which reported 86.7% and 83% of serum resistance.9,17 However, study by Anuradha et al revealed 51% of serum resistance.7 In UPEC, capsule and the O antigen are polysaccharides that contribute to virulence. The extracellular polysaccharides are antiphagocytic and inhibit complement-mediated lysis.18 All the strains in this study on UPEC showed serum resistance indicating its significant association with UTI.\n\nIn the current study, the genes coding for adherence gene (papC), Cytotoxic necrotizing factor I (cnf1), α haemolysin (hlyA) and ferric aerobactin receptor (iutA) were detected by multiplex PCR.\n\nThe virulence gene iutA, is the gene for the siderophore ferric aerobactin receptor which helps the bacterial intake of iron and this enables the survival of bacteria in an atmosphere with limited concentrations of iron (urinary tract) This gene was the commonest gene detected in the UPEC isolates of our study(65%), thus proving its association with the virulence of UPEC. This finding supports the data published by Munkhdelger et al (62.2%),19 and Karam et al (66.4%).20\n\nThe rate of detection of adherence gene (papC) was 52%. This is in par with a study by Chakraborty A et al in 2017 in which nearly half of their isolates (49%) carried this gene.3 Firoozeh et al reported a lower rate of detection (34.6%) of papC gene in UPEC isolates.21\n\n27% of our isolates were positive for hlyA gene which was similar to the study by Gohar et al (26%).22 A lower rate (13.6%) of hlyA gene were seen by Daniela A et al study.23\n\nToxigenic strains of E.coli like necrotoxigenic E.coli-1(NTEC-1) produce Cytotoxic necrotizing factor 1 (cnf1).24 Our study showed that 29%(n=33) were NTEC -1 strains harbouring the gene cnf1. The distribution of cnf1 in our study is similar to the studies by Chakraborty A et al (29.5%) and Gohar et al (30%).3,22 NTEC -1 strains are emerging pathogens in India.24 Our study revealed that 50% of the cnf1 positive isolates harboured hlyA (haemolysin) gene, which is statistically significant. The combined production of several powerful toxins (haemolysin, CNF) and co-expression of various virulence genes by NTEC strains makes them potentially aggressive pathogens.24 Hence identification of these strains at an early stage, would prevent the complications associated with NTEC -1 strains.\n\nThe virulence genes studied are involved in the pathogenesis of UTI. However the absence of genes in 10 isolates (13.3%) could possibly be due to mutation of the gene Thus, a negative PCR result doesnot rule out the absence of virulence genes.\n\nVarying spectrum and rates of antibiotic resistance have been reported among the UPEC isolates and most studies have reported that amikacin, nitrofurantoin and imipenem are highly efficacious against such strains.20 In our study, a high percentage of resistance was noted to beta lactam group of antibiotics (ampicillin-75%, ceftriaxone-64.4%), fluoroquinolones (ciprofloxacin-63%, norfloxacin-50%), trimethoprim/sulfamethoxazole (49.3%). Lower rates of resistance was detected with respect to piperacillin/tazobactam(13.9%), carbapenems (ertapenem-1.4%, imipenem-6.4%), amikacin(2.7%) and nitrofurantoin (2.7%), Cefoperazone/sulbactam (2.9%) and fosfomycin (1.4%). Based on these findings, nitrofurantoin, piperacillin tazobactam and cefaperazone sulbactam maybe suitable candidates for empirical therapy of UTIs. Drugs like aminoglycosides, carbapenems and fosfomycin maybe used as reserve drugs in the management of MDR-UTI due to E. coli. These results are in par with a study which revealed that nitrofurantoin and carbapenems are suitable as empirical antibiotics in the treatment of UTIs in outpatients and fosfomycin can be used against highly resistant UPEC isolates.25 However, their inappropriate usage may gradually give rise to their increase in antibiotic resistance. This accentuates the need for local hospital data compilation and antibiotic resistance analysis to devise a suitable antibiotic policy for the hospitals.\n\nWe found that 51% were ESBL producers which is similar to studies by Shoba et al (19%-59.6%) & Chhaya et al (46%).26,27 In our study, 45 isolates expressed multiple virulence factors (Table 5), among which a majority (57.7%) were non ESBL producers. These results support the fact that the expression of virulence genes maybe inversely related to the presence of antibiotic resistance and ESBL production.\n\nThe distribution of virulence factors in antibiotic-resistant isolates showed that hemolysin production is significantly associated with resistance to imipenem, norfloxacin and ciprofloxacin (p≤0.05) at par with findings of Chhaya et al.27 The presence of hlyA gene is significantly associated with resistance to Ceftazidime (p≤0.05). The association of the presence of hlyA with resistance to third generation cephalosporins poses a therapeutic challenge.28 No other statistically significant difference was proved between the presence or absence of the other virulence factors, with any specific antibiotic resistance.\n\nMultidrug resistance was observed in 40 isolates (53.3%). This finding is comparable to the studies by Chhaya et al27 & Hasan et al29 in India, in which the prevalence of MDR E. coli was 51% and 52.9% respectively. However, this finding is in contrast to study by Munkhdelger et al20 which revealed a higher rate of MDR in UPEC (93.9%).\n\nIn our study, 27.5% (n=11) MDR isolates produced haemolysis and all the 40 MDR isolates showed serum resistance. Co-existence of MDR with hemolysis or serum resistance may contribute to the increased pathogenicity and nonresponse to therapy in cases of UPEC associated UTI. In our study, iutA, papC, cnf1, hlyA genes were detected in 72.5% (n=29), 47.5% (n=19), 35% (n=14) and 27.5% (n=11) of the MDR isolates respectively. iutA was the commonest gene detected in MDR isolates. This finding supports the fact that certain virulence genes like iutA is positively associated with MDR.30\n\nInappropriate use of broad-spectrum antibiotics, prolonged hospitalisation, poor hygiene are few major factors that contribute to increasing MDR infections. In our research, the percentage of MDR in complicated UTI was 77%; which was higher compared to uncomplicated UTI (33%). Our study supports the findings of a study by Johnson J R et al, which revealed that antibiotic resistance was higher in people with complicated UTIs than with uncomplicated UTIs.31\n\nIn our study, third generation cephalosporins (n=15, 37.5%), meropenem (n=12, 30%), piperacillin tazobactam (n=8, 20%) and nitrofurantoin (n=5, 12.5%) were the antibiotics used in the treatment of these MDR cases.\n\nOut of the total 75 cases of UPEC studied, majority i.e 60% (n=45) were cases of complicated UTI. Distribution of cnf1 gene was more in complicated UTIs compared to uncomplicated UTIs. hlyA gene detected in complicated UTIs was absent in isolates from uncomplicated UTIs. This difference in results, regarding the distribution of hlyA and cnf1 genes, maybe attributed to the fact hemolysin production and cnf1 are attributed to the dysfunction of local immune response and host tissue damage. Thus, probably there is increased expression of hlyA and cnf1 in complicated UTIs. There is no significant difference in the distribution of genes associated with adhesion (papC) and iron uptake (iutA). This finding is in contrast to the study by Takahashi et al, which revealed that the prevalence of papC was more in cases of uncomplicated UTI.32\n\nThe three isolates from patients with history of emphysematous pyelonephritis and urosepsis, were found to be positive for virulence genes papC (adherence) and cnf1 (cytotoxicity). cnf1 gene is associated with extensive tissue damage4 and this could have contributed to the emphysematous pyelonephritis in these three cases.\n\nMortality due urosepsis was noticed in two cases (2.6%). Isolates of both these cases had all the 4 genes, produced hemolysin, were serum resistant and MDR. This substantiates the contribution of hemolysin production, serum resistance and expression of the virulence genes in the increased pathogenicity of UPEC.\n\nLimitations of the study were that the study could have been performed on a larger sample size for better characterization of UPEC and also the difference in the virulence and antimicrobial drug resistance pattern of community acquired and healthcare associated UTI could have been studied.\n\n\nConclusion\n\nThe association of hemolysin production with resistance to imipenem and norfloxacin in UPEC strains was found to be significant and the presence of hlyA gene is positively associated with ceftazidime resistance, thus posing a therapeutic challenge. Nitrofurantoin, piperacillin tazobactam, cefoperazone/sulbactam, carbapenems, fosfomycin and amikacin were the antibiotics against UPEC which showed lower rates of resistance. Hence, nitrofurantoin, piperacillin tazobactam and cefaperazone sulbactam maybe suitable candidates for empirical therapy of UTIs. Drugs like aminoglycosides, carbapenems and fosfomycin may be used as reserve drugs in the treatment of MDR-UTI. However, inappropriate usage can gradually increase antibiotic resistance. Hence, proper selection of antibiotics in hospitals taking into account the local antibiogram is needed to reduce the emergence of antibiotic resistance. The data on distribution of virulence factors and antibiotic resistance helps in planning the management strategies in UTI in our setup, thus improving patient care.\n\n\nData availability\n\nDryad. Characterization of virulence factors and antibiotic resistance pattern of Uropathogenic Escherichia coli strains in a tertiary care center. DOI: https://doi.org/10.5061/dryad.q83bk3jmd\n\nThe full reference for data repository provided by dryad for access prior to publication, is shared using the unique URL: https://datadryad.org/stash/share/8Jp6sXknge83XG2LQqLY0nPRVbrjSjhQvvfxYFsDPkQ.\n\n\nAuthor contributions\n\n\n\n1. Mr Naveen Kumar M: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, SoftwareSupervision, Validation, Visualization, Writing & Editing\n\n2. Dr Sevitha Bhat: Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Supervision, Validation, Visualization, Writing – Review & Editing\n\n3. Dr Archana Bhat K - Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, ProjectAdministration, Resources, SoftwareSupervision, Validation, Visualization, Writing – Review & Editing\n\n4. Dr Shalini Shenoy M: Conceptualization, Project Administration, Resources, Supervision, Writing – Review & Editing\n\n5. Dr Vishwas Saralaya: Conceptualization, Project Administration, Resources, Supervision, Writing.",
"appendix": "Acknowledgments\n\nThe authors are grateful to Manipal Academy of Higher education for the support.\n\n\nReferences\n\nPardeshi P: Prevalence of urinary tract infections and current scenario of antibiotic susceptibility pattern of bacteria causing UTI. Indian J. Microbiol. Res. 2018; 5(3): 334–338.\n\nGaurav K, Mohan TS, Neeti M, et al.: Section: Microbiology Prevalence of Urinary Tract Infections in Elderly Patients Attending A Tertiary Care Hospital Section: Microbiology. Int. J. Contemp. Med. Res. 2019; 6(2): 16–19.\n\nChakraborty A, Adhikari P, Shenoy S, et al.: Molecular Characterisation of Uropathogenic Escherichia coli Isolates at a Tertiary Care Hospital in South India. Indian J. Med. Microbiol. 2017; 35(2): 305–310. PubMed Abstract | Publisher Full Text\n\nTarchouna M, Ferjani A, Ben-selma W, et al.: International Journal of Infectious Diseases Distribution of uropathogenic virulence genes in Escherichia coli isolated from patients with urinary tract infection. Int. J. Infect. Dis. 2013; 17(6): e450–e453. PubMed Abstract | Publisher Full Text\n\nKarimian A, Momtaz H, Branch S, et al.: Detection of uropathogenic Escherichia coli virulence factors in patients with urinary tract infections in Iran. Afr. J. Microbiol. Res. 2012; 6(October): 6811–6816. Publisher Full Text\n\nWolfensberger A, Kuster SP, Marchesi M, et al.: The effect of varying multidrug-resistence (MDR) definitions on rates of MDR gram- negative rods. Antimicrob. Resist. Infect. Control. 2019; 3(8): 1–9.\n\nBhrugubalda A, Penmetcha U, Yarlagadda P, et al.: A Study of Virulence Factors and Drug Resistance Pattern in Escherichia coli Isolated from Extra Intestinal Infections in a Tertiary Care Teaching. Int. J. Curr. Microbiol. App. Sci. 2016; 5(4): 140–158. Publisher Full Text\n\nArticle O: Phenotypic Study of Virulence Factors in Escherichia Coli Isolated From Antenatal Cases, Catheterized Patients, and Faecal Flora. J. Clin. Diagnostic Res. 2012; 6(10): 1699–1703.\n\nSharma S, Bhat GK, Shenoy S: Virulence factors and drug resistance in Escherichia coli isolated from extraintestinal infections. Indian J. Med. Microbiol. 2007; 25(4): 369–373. Publisher Full Text\n\nChakraborty A, Adhikari P, Shenoy S, et al.: Microbial Pathogenesis Molecular characterization and clinical signi fi cance of extraintestinal pathogenic Escherichia coli recovered from a south Indian tertiary care hospital. Microb. Pathog. 2016; 95: 43–48. PubMed Abstract | Publisher Full Text\n\nWagenlehner FME, Johansen TEB, Cai T, et al.: Definition and treatment of complicated urinary tract infections. Nat. Rev. Urol. 2020; 17(October): 586–600. PubMed Abstract | Publisher Full Text\n\nBhattacharyya S, Sarfraz A, Aftab M, et al.: Original Research Article Characterization and antibiogram of Uropathogenic Escherichia coli from a tertiary care hospital in Eastern India. Int. J. Curr. Microbiol. App. Sci. 2015; 4(2): 701–705.\n\nShetty AV, Kumar SH, Shekar M, et al.: Prevalence of adhesive genes among uropathogenic Escherichia coli strains isolated from patients with urinary tract infection in Mangalore.2014; 32: 175–8.\n\nShah C, Baral R, Bartaula B, Shrestha LB: Virulence factors of uropathogenic Escherichia coli (UPEC) and correlation with antimicrobial resistance.2019; 1–6.\n\nMay AK, Gleason TG, Sawyer RG, et al.: Contribution of Escherichia coli Alpha-Hemolysin to Bacterial Virulence and to Intraperitoneal Alterations in Peritonitis. Infect. Immun. 2000; 68(1): 176–183. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang C, Li Q, Lv J, et al.: Alpha-hemolysin of uropathogenic Escherichia coli induces GM-CSF-mediated acute kidney injury. Mucosal Immunol. 2020; 13: 22–33. PubMed Abstract | Publisher Full Text\n\nShetty SK, Venkatesha DT, Rao SP, et al.: Hemolysin and Serum Resistance among ESBL Producing Extraintestinal Pathogenic Escherichia coli Isolated from a Tertiary Care Hospital.2016; 5(1): 71–77.\n\nSarkar S, Ulett GC, Totsika M, et al.: Role of Capsule and O Antigen in the Virulence of Uropathogenic Escherichia coli. PLoS One. 2014; 9(4): e94786. PubMed Abstract | Publisher Full Text\n\nMunkhdelger Y, Gunregjav N, Dorjpurev A, et al.: Original Article Detection of virulence genes, phylogenetic group and antibiotic resistance of uropathogenic Escherichia coli in Mongolia. J. Infect. Dev. Ctries. 2017; 11(1): 51–57. PubMed Abstract | Publisher Full Text\n\nKaram MRA, Mehri Habibi SB: Osong Public Health and Research Perspectives Relationships between Virulence Factors and Antimicrobial Resistance among Escherichia coli Isolated from Urinary Tract. Osong. Public Health Res. Perspect. 2018; 9(5): 217–224. PubMed Abstract | Publisher Full Text\n\nFiroozeh F, Saffari M, Neamati F, et al.: International Journal of Infectious Diseases Detection of virulence genes in Escherichia coli isolated from patients with cystitis and pyelonephritis. Int. J. Infect. Dis. 2014; 29: 219–222. PubMed Abstract | Publisher Full Text\n\nGohar NM, Aly HF, Ayoub MI: Important Virulence Factors and Related Genes in Uropathogenic E. coli and their Relation to Fluoroquinolone Resistance. J. Pure Appl. Microbiol. 2018; 12(3): 1393–1403. Publisher Full Text\n\nLópez-banda DA, Carrillo-casas EM, Leyva-leyva M, et al.: Identification of Virulence Factors Genes in Escherichia coli Isolates from Women with Urinary Tract Infection in Mexico. Biomed. Res. Int. 2014; 2014: 1–10. PubMed Abstract | Publisher Full Text\n\nRahman H, Deka M: Detection & characterization of necrotoxin producing Escherichia coli (NTEC) from patients with urinary tract infection (UTI). Indian J. Med. Res. 2014; 139(April): 632–637.\n\nYazdanpour Z, Tadjrobehkar O: Significant association between genes encoding virulence factors with antibiotic resistance and phylogenetic groups in community acquired uropathogenic Escherichia coli isolates. BMC Microbiol. 2020; 20(241): 1–9. Publisher Full Text\n\nPrasada S, Bhat A, Bhat S, et al.: Changing antibiotic susceptibility pattern in uropathogenic escherichia coli over a period of 5 years in a tertiary care center. Infect. Drug Resist. 2019; 12: 1439–1443. PubMed Abstract | Publisher Full Text\n\nShah C, Baral R, Bartaula B, et al.: Virulence factors of uropathogenic Escherichia coli (UPEC) and correlation with antimicrobial resistance. BMC Microbiol. 2019; 19(204): 1–6. Publisher Full Text\n\nBischoff S, Walter T, Gerigk M, et al.: Empiric antibiotic therapy in urinary tract infection in patients with risk factors for antibiotic resistance in a German emergency department. BMC Infect. Dis. 2018; 18(56): 1–7.\n\nHasan AS, Nair D, Kaur J, et al.: Resistance Patterns Of Urinary Isolates In A Tertiary Indian Hospital. J. Ayub Med. Coll. Abbottabad. 2007; 19(1): 39–41.\n\nJohnson TJ, Logue CM, Johnson JR, et al.: Associations Between Multidrug Resistance, Plasmid Content, and Virulence Potential Among Extraintestinal Pathogenic and Commensal Escherichia coli from Humans and Poultry. Foodborne Pathog. Dis. 2012; 9(1): 37–46. PubMed Abstract | Publisher Full Text\n\nJohnson JR, Stell AL: Extended Virulence Genotypes of Escherichia coli Strains from Patients with Urosepsis in Relation to Phylogeny and Host Compromise.53–59.\n\nTakahashi A, Kanamaru S, Kurazono H, et al.: Escherichia coli Isolates Associated with Uncomplicated and Complicated Cystitis and Asymptomatic Bacteriuria Possess Similar Phylogenies, Virulence Genes, and O-Serogroup Profiles. J. Clin. Microbiol. 2006; 44(12): 4589–4592. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "153296",
"date": "31 Oct 2022",
"name": "Vignesh Ramachandran",
"expertise": [
"Reviewer Expertise Medical 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\nThe authors have planned, executed, and presented an important piece of work and the information from the findings adds so much value to the medical literature. The study findings are very significant and hope a much larger study will be planned based on these results.\nHowever, there are a few minor comments to be addressed by the authors.\nThe first line of the abstract and introduction part begins with, \"Urinary tract infections (UTI) are the most prevalent bacterial infections\". This statement is too strong and needs scientific backing. It would be appropriate to say \"one of the common bacterial infections\".\n\nThe references cited in numbers one and two are not from properly indexed journals and it would be better to cite references from reputed journals.\n\nReference number 31 is not cited properly - need to include the journal's name.\n\nIn the methodology section, need to give a reference for the CLSI method.\n\nThe second line of the results section starts with a numeral (93%), it has to start with the text.\n\nThere is no clear mention of the demographic characteristics of the study population. From the results, it is evident that the population is mixed including pediatrics as well as adults. It would add value to know about the study population. What if there were immunocompromised patients included and exposed to frequent antibiotics, the resistance patterns would be different in them. Moreover, the virulence characteristics are also different among those populations. How did the authors rule out other comorbidities and immune effects in the study population?\n\nHow many of the cases were community-acquired and how many were nosocomial? These factors have major implications in affecting the study results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "9055",
"date": "30 Nov 2022",
"name": "Archana Bhat K",
"role": "Author Response",
"response": "As per reviewer's suggestions, the changes mentioned below will be done accordingly in the updated text file of the manuscript and submitted to the journal. 1. The first line of the abstract and introduction part begins with, \"Urinary tract infections (UTI) are the most prevalent bacterial infections\". This statement is too strong and needs scientific backing. It would be appropriate to say \"one of the common bacterial infections\". Changes have been done in the first line of the abstract and introduction part as per reviewer suggestions. 2. The references cited in numbers one and two are not from properly indexed journals and it would be better to cite references from reputed journals. The references 1 and 2 have been updated. 3. Reference number 31 is not cited properly - need to include the journal's name. The journal's name has been added and updated in references and citation. 4.In the methodology section, need to give a reference for the CLSI method. In the methodology section, reference for the CLSI method has been cited. (Reference 8 ) References have been updated in serial order thereon. 5. The second line of the results section starts with a numeral (93%), it has to start with the text. Modified the second line of the results section. 6. There is no clear mention of the demographic characteristics of the study population. From the results, it is evident that the population is mixed including pediatrics as well as adults. It would add value to know about the study population. What if there were immunocompromised patients included and exposed to frequent antibiotics, the resistance patterns would be different in them. Moreover, the virulence characteristics are also different among those populations. How did the authors rule out other comorbidities and immune effects in the study population? Included this as a limitation of the study in the last paragraph of discussion. 7. How many of the cases were community-acquired and how many were nosocomial? These factors have major implications in affecting the study results Included this as a limitation of the study in the last paragraph of discussion."
}
]
},
{
"id": "154567",
"date": "17 Nov 2022",
"name": "Anusha Rohit",
"expertise": [
"Reviewer Expertise Antimicrobial resistance",
"infection 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\nThe manuscript describes the analysis of 75 isolates of UPEC for virulence factors and antimicrobial resistance. The virulence factors and their association with resistance was also discussed. The design of the study was prospective cross-sectional.\nAs 60% of the isolates were from complicated UTIs, can the authors explain why they suggest nitrofurantoin for therapy in the conclusion of the paper?\n\nWas any statistical analysis done for the association of the virulence factors detected and the resistance patterns of the isolates?\n\nWhy did the authors choose these genes for the detection of the virulence characterisation as many of these characteristics have multiple genes coding for them? The association between papC, iutA seemed to be the most common among the isolates.\n\nHow many of these isolates were from patients who developed CAUTI due to the presence of a urinary catheter?\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": "9056",
"date": "30 Nov 2022",
"name": "Archana Bhat K",
"role": "Author Response",
"response": "As per reviewer suggestions, the following changes will be done accordingly and updated in the revised text of the manuscript and uploaded. 1. As 60% of the isolates were from complicated UTIs, can the authors explain why they suggest nitrofurantoin for therapy in the conclusion of the paper? The authors have updated the discussion and conclusion in the paper . Owing to the lower rate of resistance and ease of administration, nitrofurantoin maybe an effective oral drug in outpatients with UTI (added in conclusion). However, the therapeutic utility of nitrofurantoin in complicated UTI compared to uncomplicated UTI was not studied.(added in discussion) 2. Was any statistical analysis done for the association of the virulence factors detected and the resistance patterns of the isolates? Statistical analysis (Chi square test ) for the association of the virulence factors detected and the resistance patterns of the isolates was done .The authors have added a sentence on the same. The results of significance is already mentioned in the content of discussion with reference to table 4. 3. Why did the authors choose these genes for the detection of the virulence characterisation as many of these characteristics have multiple genes coding for them? The association between papC, iutA seemed to be the most common among the isolates. The authors have updated the content in Background of the study-“Based on previously published literature, we aimed to look into the common genes papC and iutA and apart from them, other genes hly A and cnf1 were screened for epidemiological and virulence characterisation.” 4. How many of these isolates were from patients who developed CAUTI due to the presence of a urinary catheter? The authors have updated the results and added the sentence “Catheter associated UTI was seen in 33.3%(n=25) of the patients.”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1163
|
https://f1000research.com/articles/11-12/v1
|
07 Jan 22
|
{
"type": "Software Tool Article",
"title": "PhenoApp: A mobile tool for plant phenotyping to record field and greenhouse observations",
"authors": [
"Franco Röckel",
"Toni Schreiber",
"Danuta Schüler",
"Ulrike Braun",
"Ina Krukenberg",
"Florian Schwander",
"Andreas Peil",
"Christine Brandt",
"Evelin Willner",
"Daniel Gransow",
"Uwe Scholz",
"Steffen Kecke",
"Erika Maul",
"Matthias Lange",
"Reinhard Töpfer",
"Toni Schreiber",
"Danuta Schüler",
"Ulrike Braun",
"Ina Krukenberg",
"Florian Schwander",
"Andreas Peil",
"Christine Brandt",
"Evelin Willner",
"Daniel Gransow",
"Uwe Scholz",
"Steffen Kecke",
"Erika Maul",
"Matthias Lange",
"Reinhard Töpfer"
],
"abstract": "With the ongoing cost decrease of genotyping and sequencing technologies, accurate and fast phenotyping remains the bottleneck in the utilizing of plant genetic resources for breeding and breeding research. Although cost-efficient high-throughput phenotyping platforms are emerging for specific traits and/or species, manual phenotyping is still widely used and is a time- and money-consuming step. Approaches that improve data recording, processing or handling are pivotal steps towards the efficient use of genetic resources and are demanded by the research community. Therefore, we developed PhenoApp, an open-source Android app for tablets and smartphones to facilitate the digital recording of phenotypical data in the field and in greenhouses. It is a versatile tool that offers the possibility to fully customize the descriptors/scales for any possible scenario, also in accordance with international information standards such as MIAPPE (Minimum Information About a Plant Phenotyping Experiment) and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. Furthermore, PhenoApp enables the use of pre-integrated ready-to-use BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) scales for apple, cereals, grapevine, maize, potato, rapeseed and rice. Additional BBCH scales can easily be added. The simple and adaptable structure of input and output files enables an easy data handling by either spreadsheet software or even the integration in the workflow of laboratory information management systems (LIMS). PhenoApp is therefore a decisive contribution to increase efficiency of digital data acquisition in genebank management but also contributes to breeding and breeding research by accelerating the labour intensive and time-consuming acquisition of phenotyping data.",
"keywords": [
"Android app",
"plant phenotyping",
"digital data acquisition",
"LIMS",
"BBCH",
"FAIR principles"
],
"content": "Introduction\n\nClassical breeding of agronomical improved crops relies on crossing of desired genotypes, growing their offspring and performing genotypic and phenotypic selection on the various traits. Desired genotypes consist of elite breeding material as well as genetic resources that are characterized. Approximately 7.4 million accessions are stored in around 1750 ex-situ germplasm collections (genebanks) worldwide.1 These genebanks contain genetically and phenotypically diverse plant material and are excellent resources of novel traits useful for future plant breeding purposes in the context of changing demands.\n\nAlthough innovative breeding technologies like marker-assisted selection have dramatically evolved to improve selection accuracy and intensity during recent decades,2,3 only a small number of genotypes contributed directly to modern crop cultivars mainly due to the lack of sufficient phenotypic and genotypic characterization or limited evaluation of agronomic traits.4–6 The efficient use of germplasm collections as a source of genetic variation is time consuming and arduous and therefore still remains a challenging task. Thus, with the development and decreasing costs of genotyping and sequencing technologies, genebank phenomics display the current bottleneck for the utilization of genetic resources.7–9 Nevertheless, tremendous advancements in high-throughput phenotyping technologies during recent years are closing this gap.10–12 However, as long as these high-throughput phenotyping technologies are a limiting factor, e.g. due to missing technologies, infrastructure or funding, supporting tools for manual data acquisition and recording can accelerate and support the evaluation of genetic resources and can increase breeding efficiency.\n\nPlant phenomics is a multidisciplinary field developing novel sensing and imaging techniques for high-throughput phenotyping of plant genetic resources, and has applications in breeding.13–15 The research basis are morphological, agronomical, physiological and metabolic features, whereas the handling, processing and adequate utilization of data is still challenging. The big advantage of high-throughput platforms compared to manual plant phenotyping is its objectivity as well as the time and cost-effectiveness. However, the development is slow and a plethora of research needs to be done to provide further valuable screening tools with practical use in the future.16 With all these developments, the volume of data potentially usable for plant breeding has increased rapidly and will further increase in future. Therefore, the type of data generated range not only from agronomic and breeding-relevant phenotypic data, to results from quantitative and qualitative genetics, but can contain further information on fertilization, plant protection, field and soil conditions, geodata and weather data. Most data sets differ not only in their object of investigation, but also in their type, format and context of origin. The establishment of the FAIR principles (Findable, Accessible, Interoperable and Reusable) are therefore an important basis regarding harmonization and can increase the efficiency of plant breeding.17–19 Another requirement is the interoperability of data in terms of machine-readable access to support continuous data analysis flows. To address the resulting challenges, internationally recognized work has already been done in the area of metadata and the minimum information standard for plant phenotyping data - MIAPPE - has been developed.20 In addition, a large number of semantic resources exist, e.g. AGROVOC (word combination of agriculture and vocabulary)21 or the general ontologies of the Open Biological and Biomedical Ontology (OBO) Foundry.22 In the area of data structures, concepts for generalization have been proposed, such as Investigation-Study-Assay (ISA-TAB)23 or, more recently, the Core Scientific Dataset Model,24 which abstracts individual data structures to a self-describing generic data structure.\n\nTo ensure proper understanding of the content, we rely on common assessment and observation protocols, vocabularies and units. Many initiatives use their dedicated scoring scheme or, in the case of collaborative efforts such as genebanks, a commonly agreed set of observation protocols.25 Prominent examples for scoring schemes are Darwin Core (DwC),26 BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) for phenology27 and the International Union for the Protection of New Varieties of Plants (UPOV) lists for morphological traits. The manual acquisition of such field phenotyping data into local infrastructures is a first component in a data publication pipeline.\n\nA tool support for field phenotyping, i.e. observation scoring, enables the re-usability and fulfils the FAIR criteria. For this purpose, genebanks, research units, breeding companies or other stakeholder in plant phenotyping use not only simple, handwritten records, but also simple digital forms of recording. Microsoft Excel installations on mobile devices with or without voice input support, and solutions closely embedded in individual database infrastructures, such as the Genebank Information System/Bonitur (GBIS/B) at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)28 or recently published apps like vitisBerry,29 SeedCounter30 or Plant Screen mobile31 may address specific demands, but lack convenience or generalization. As an alternative to such proprietary, hand crafted and/or non-generic solutions for recording and transferring field-scoring data into a digital representation or even databases such as Lab Information Management Systems (LIMS), an in-field digitalization of observations on a general basis represents the initial process to advance the field-data acquisition process.\n\nIn the current manuscript, we present an easy-to-use Android app (PhenoApp) for recording field and greenhouse observations on mobile devices to relieve the labor intensive and time-consuming process of manual phenotyping. All evaluated descriptors/scales can be individually created with maximum customization, allowing a fast and seamless data transfer into a digital representation for further utilization in genebank management and/or breeding research.\n\n\nMethods\n\nData import and export\n\nAfter installation, the main directory contains an ‘in’ and ‘out’ folder. Input files need to be copied in the ‘in’ folder. Sample input files are then automatically displayed and selectable in the app entry page. The save button in the upper right corner of the app (Figure 1) creates an output Excel file saved in the ‘out’ folder.\n\nInput file with descriptor list\n\nThe first sheet of the input file (Locations) contains information on the specific plant locations with the columns plot, row, plant, accession name and number, variety number, genotype, mother, father, information and database-key. The last column (database-key) is not visible in the application and is used in the output file for better synchronization with the database. Only the first three columns or as alternative the fourth column with information on the exact plant locations are obligatory fields, all others are optional and implemented for better data handling and management as well as to give the user additional orientation and information.\n\nThe second sheet (Traits) contains all descriptors. These are described in the five columns which are shortcut (trait abbreviation), description, type, values and remark. The column type needs to be filled with 1 to 5 according to the format type of the recorded phenotypic data:\n\n1. Rating: For the acquisition of categorical data. The scale needs to be specified in the value column (for example, 1: none; 3: little; 5: medium; 7: strong; 9: very strong).\n\n2. Measured value: PhenoApp displays a numeric keypad for data entry.\n\n3. Date: PhenoApp displays selectable buttons for today, yesterday, day before yesterday, tomorrow, day after tomorrow and a button for an individual date selection. Data are stored in numerical date format.\n\n4. Text: PhenoApp opens a keyboard for free text input.\n\n5. BBCH: PhenoApp displays the pre-integrated BBCH scales for phenotyping of phenology.\n\nAn example input file is provided in Underlying data.35\n\nOutput file\n\nThe structure of the output file is the same as for the first sheet of the input file (specific plant locations) with additional columns for remarks and phenotyped data. Output format can be an Excel file or a csv (comma separated values) file for better machine readability. An example output file is provided in Underlying data.35\n\nImportant app functions\n\nPhenotyping phenology based on BBCH scales\n\nAs an additional mode for a convenient phenotyping of phenology over a certain time, PhenoApp provides pre-integrated BBCH scales without the need of own descriptors. Furthermore, if the option “BBCH question” is selected, each time PhenoApp is opened, it asks if the creation of a BBCH entry with the current date is desired. The integrated scales contain three list levels from species to principal growth stage to specific growth stage (Figure 1). The release version has the BBCH scales of apple, cereals, grapevine, maize, potato, rapeseed and rice already implemented.\n\nIf needed, the user can implement scales of other crops or add own scales using an Excel template (bbch_template.xls) located in the ‘bbch’ folder of the app main directory (see Software availability36). The first sheet is for the species as well as the principal growth stages and all further sheets for the specific growth stages. In addition, there is the option of adding sample images for each principal growth stage, which can be displayed in the app. To do this, the images need to be stored with the same filename as the stages in the app's ‘bbch’ folder together with the template file. The next time PhenoApp is started, the new BBCH scale will be imported to the internal database for further use and files are automatically deleted from the ‘bbch’ folder.\n\nDisplaying sample images of descriptors\n\nIf sample images of a descriptor with the same name as the descriptor shortcut are copied in the ‘descriptorPictures’ folder of the main directory, PhenoApp displays that image during phenotyping the same way as for BBCH scales.\n\nTaking pictures with the device camera\n\nThe user can take one or several photos at any time. Clicking on the camera icon automatically opens the device standard photo app. Once a desired photo has been taken, it is saved in the subfolder ‘fotos’ in the app’s main directory. The file name of the photo is a combination of the currently specified location, the actual time stamp and the variety name (if given).\n\nTaking general and location specific notes\n\nCentered in the upper half of the screen is a ‘REMARKS’ button, which opens a window with two text fields for the input of specific location information and any additional information on the current plant, respectively. The text entries of both fields are included in the output file in separated columns. This feature gives the user the possibility to take additional notes during phenotyping without the need for further apps or handwritten remarks.\n\nPartial selection of descriptors\n\nIt is possible to mark specific descriptors (square in the descriptor row, Figure 1) for selective data acquisition. Thus, the app only asks for indicated descriptors while all the others are skipped. This is particularly useful for phenotyping of multiple traits over time because it removes the necessity to manually skip descriptors not relevant at a specific time point.\n\nArrow keys displayed in the lower left corner\n\nThe arrow keys allow for a fast location jumping within a single row (up and down) or between rows (left and right).\n\nLanguage\n\nPhenoApp contains two language packages, English and German. The default language is English. If the global language setting of the mobile device is German, the language setting of the app changes automatically from English to German.\n\nImportant app settings\n\nZigzag mode\n\nThe app automatically jumps to the next listed descriptor after recording a data point, until the end of the descriptor list is reached. Then it moves directly to the first descriptor of the next location and so on. Logically, but quite unhandy in many practical cases, after reaching the end of a row, the app jumps to the first location in the next row (after the last row in a plot, it jumps to the next plot). To avoid walking unnecessary distances or the manual location correction, the app jumps in “zigzag” from the end of a row to the last location of the next row and counts backwards from there. This allows a continuous phenotyping while going through a field plot one row upwards and the next row backwards.\n\nArrow keys displayed in the top line give the direction of the next descriptor/location during phenotyping and are adaptable by a simple click on the button.\n\nFirst empty button\n\nThis is a button on the top line that allows the user to jump to the first/next empty entry in their records. This is particularly useful for phenotyping multiple traits over time because it allows a fast tracking of missing data points.\n\nAccession, passport, genotype, parents, collection no. and information\n\nDisplays the respective entry from the input file in the app if data are given.\n\nLeft-handed mode\n\nThe left-handed mode swaps the left and right side of the display for individual preferences.\n\nMultiple selection\n\nIf the descriptor is of type ‘rating’, this option allows the user to select multiple values for a single trait. Results are separated with a comma in the output file. The activation of this setting removes the automatic jumping of the app to the next descriptor/location.\n\nPhenoApp was developed with Java 8 using Google’s appcompat-v7 and Apache’s POI libraries. It works on mobile phones and tablets with android API-level 14, which stands for android version 4.0 (Ice Cream Sandwich), or higher and requires no internet connection. The software is open source under Apache 2.0 license (see Software availability36).\n\nIn general, PhenoApp is built as a simple interface to record phenotypic data. The app displays imported Microsoft Excel files containing a genotype and descriptor list and allows a data recording that can be saved and exported as Excel file for further use (Figure 2).\n\nA combined genotype-location and descriptor list is required as input. Post phenotyping, recorded data can be exported as a simple Microsoft Excel file. Minimal requirements are the PhenoApp on a mobile Android-based device and a computer with a spreadsheet software for data handling.\n\n\nUse cases\n\nFor most cases, PhenoApp can/will be used to digitally support phenotypic data acquisition in the course of specific projects or routine work. It only needs a computer with Microsoft Excel and a plant list (incl. locations), a defined scientific question that can be translated into a descriptor, and a mobile Android-based device. The data integration in superordinate structures or the descriptor adaptation according FAIR principles are desirable and emphasized, but not initially required.\n\nFor more than 10 years, IPK and the Julius Kühn Institute (JKI) have implemented a laboratory information management system (LIMS) as a universal platform for documenting and recording field, laboratory and bioinformatics data in order to establish a comprehensive system for research data documentation.\n\nFrom this starting point, in a collaboration of IPK and JKI, PhenoApp was integrated in the LIMS workflow to advance data acquisition by allowing a fast, user friendly and direct import and export of datasets without the need of further modifications (Figure 3). Using the well-defined, file based data exchange interfaces of PhenoApp, we embed the creation of necessary import files into the LIMS. Even a tight integration for an optimal data re-usability and interoperability was straightforward to implement, for example the storage and versioning of scoring methods. This, in turn, enabled mapping of scoring schemes for the same species across observation cycles and projects by linking various rating schemes with all scoring schema details and even reference images. In addition, a user-friendly input mask in the system provides the possibility of precisely documenting the locations of the corresponding plants. This enables the re-use and thus optimal interoperability across field phenotyping studies.\n\nThe data recorded by PhenoApp are exported as a well-structured CSV file and pictures taken stored into a specified folder. When a phenotyping run is finished, this enables an ad-hoc and consistent import into the LIMS database. The potential of such FAIR enabled field phenotyping is the pre-cursor to feed Web information systems (Figure 4), data publication pipelines and APIs.32 Currently, PhenoApp is used at the IPK within the barley pan-genome research project “SHAPE II”. Based on a defined so-called core set,33 representative barley genotypes were selected, grown in different years at IPK and scored with PhenoApp.\n\nHere, users will find a compilation of the data already registered in the laboratory information management system (LIMS), i.e. given descriptors and scales of the genebank as well as additional information such as specific contact persons. This offers a wide range of applications and enables quick and clear access to existing data and information for the development of new experiments and routine work.\n\n\nConclusions\n\nPhenoApp provides a convenient and free-of-charge interface for a manual, digital and mobile data acquisition of a diverse range of phenotyping data. The user can easily create and customize their own descriptors and phenology scales. A simple entry to the application is possible for every user with basic knowledge of handling an Android device and spreadsheet software like Excel, without the need of integration in data management systems, although this is possible as demonstrated. Adaptations according to FAIR data principles17 or international information standards like MIAPPE20 or EURISCO34 are possible without any restrictions. Furthermore, the resulting input and output files can easily be integrated in workflows of data management systems. The benefits can range from a facilitated project-specific phenotyping in the short term to a support during routine work in the medium term towards a complete harmonization of an institutional wide data infrastructure in the long term. In particular, datasets that have been uniformly collected and stored for years in genebanks or breeding facilities bear a huge potential to accelerate the efficient use of genetic resources and therefore the development of new adapted crop varieties that ensure future food security.\n\nThinking further, PhenoApp was initially developed for, but is not limited to plant phenotyping. The app is applicable whenever a manual data recording is required and a specific location is given. An input format of three separated parts (plot – row – individual) is required, but can easily be adapted or filled with placeholders to expand the application range.\n\n\nData availability\n\nZenodo: PhenoApp Input/Output files. https://doi.org/10.5281/zenodo.5760899.35\n\nThis project contains the following underlying data:\n\n- Input_example.xls (sample input file read in by PhenoApp. In addition, after installation, a sample input file will automatically be copied to the ‘in’ folder of the app main directory and no additional source data is required).\n\n- Output_example.xls (sample output file created by PhenoApp).\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\nSource code available from: https://gitea.julius-kuehn.de/JKI/pheno-app\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.552577936\n\nLicense: Apache-2.0",
"appendix": "Acknowledgements\n\nWe are grateful to Moritz Cappel, Teresa Claus and Claudia Vogel for ongoing testing, recommendations and bug report of PhenoApp during development.\n\n\nReferences\n\nYu X, Li X, Guo T, et al.: Genomic prediction contributing to a promising global strategy to turbocharge gene banks. Nat Plants. 2016; 2: 16150. PubMed Abstract | Publisher Full Text\n\nHickey LT, Hafeez AN, Robinson H, et al.: Breeding crops to feed 10 billion. Nat. Biotechnol. 2019; 37(7): 744–754. PubMed Abstract | Publisher Full Text\n\nNguyen GN, Norton SL: Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm. Plants (Basel). 2020; 9(7). Publisher Full Text\n\nNorton SL, Khoury CK, Sosa CC, et al.: Priorities for enhancing the ex situ conservation and use of Australian crop wild relatives. Aust. J. Bot. 2017; 65(8): 638–645. Publisher Full Text\n\nPilling D, Bélanger J, Diulgheroff S, et al.: Global status of genetic resources for food and agriculture: challenges and research needs. Genet. Res. 2020; 1(1): 4–16.\n\nTadesse W, Sanchez-Garcia M, Assefa SG, et al.: Genetic Gains in Wheat Breeding and Its Role in Feeding the World. Crop Breeding, Genetics and Genomics. 2019; 1(1): e190005.\n\nFurbank RT, Tester M: Phenomics–technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 2011; 16(12): 635–644. PubMed Abstract | Publisher Full Text\n\nHoule D, Govindaraju DR, Omholt S: Phenomics: the next challenge. Nat. Rev. Genet. 2010; 11(12): 855–866. PubMed Abstract | Publisher Full Text\n\nMorrell PL, Buckler ES, Ross-Ibarra J: Crop genomics: advances and applications. Nat. Rev. Genet. 2012; 13(2): 85–96. Publisher Full Text\n\nRebetzke GJ, Jimenez-Berni J, Fischer RA, et al.: Review: High-throughput phenotyping to enhance the use of crop genetic resources. Plant Sci. 2019; 282: 40–48. PubMed Abstract | Publisher Full Text\n\nYang WN, Feng H, Zhang XH, et al.: Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. Mol. Plant 2020; 13(2): 187–214. PubMed Abstract | Publisher Full Text\n\nKicherer A, Herzog K, Bendel N, et al.: Phenoliner: A New Field Phenotyping Platform for Grapevine Research. Sensors-Basel. 2017; 17(7). PubMed Abstract | Publisher Full Text\n\nTardieu F, Cabrera-Bosquet L, Pridmore T, et al.: Plant Phenomics, From Sensors to Knowledge. Curr. Biol. 2017; 27(15): R770–R783. PubMed Abstract | Publisher Full Text\n\nHaucke T, Herzog K, Barre P, et al.: Improved optical phenotyping of the grape berry surface using light-separation and automated RGB image analysis. Vitis 2021; 60(1): 1–10.\n\nRist F, Gabriel D, Mack J, et al.: Combination of an Automated 3D Field Phenotyping Workflow and Predictive Modelling for High-Throughput and Non-Invasive Phenotyping of Grape Bunches. Remote Sens-Basel. 2019; 11(24). Publisher Full Text\n\nZhao CJ, Zhang Y, Du JJ, et al.: Crop Phenomics: Current Status and Perspectives. Frontiers. Plant Sci. 2019; 10. Publisher Full Text\n\nWilkinson MD, Dumontier M, Aalbersberg IJ, et al.: Comment: The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3: 160018. PubMed Abstract | Publisher Full Text\n\nTian ZX, Wang JW, Li JY, et al.: Designing future crops: challenges and strategies for sustainable agriculture. Plant J. 2021; 105(5): 1165–1178. PubMed Abstract | Publisher Full Text\n\nWatt M, Fiorani F, Usadel B, et al.: Phenotyping: New Windows into the Plant for Breeders. Annu. Rev. Plant Biol. 2020; 71: 689–712. PubMed Abstract | Publisher Full Text\n\nPapoutsoglou EA, Faria D, Arend D, et al.: Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytol. 2020; 227(1): 260–273. PubMed Abstract | Publisher Full Text\n\nCaracciolo C, Stellato A, Morshed A, et al.: The AGROVOC Linked Dataset. Semant Web. 2013; 4(3): 341–348. Publisher Full Text\n\nSmith B, Ashburner M, Rosse C, et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007; 25(11): 1251–1255. PubMed Abstract | Publisher Full Text\n\nRocca-Serra P, Brandizi M, Maguire E, et al.: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010; 26(18): 2354–2356. PubMed Abstract | Publisher Full Text\n\nSrivastava DJ, Vosegaard T, Massiot D, et al.: Core Scientific Dataset Model: A lightweight and portable model and file format for multi-dimensional scientific data. PLoS One. 2020; 15(1): e0225953. PubMed Abstract | Publisher Full Text\n\nGermeier CU, Unger S: Modeling Crop Genetic Resources Phenotyping Information Systems. Front. Plant Sci. 2019; 10. Publisher Full Text\n\nEndresen DTF, Knüpffer H: The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets. Biodivers. Inform. 2012; 8. Publisher Full Text\n\nMeier U: Growth stages of mono-and dicotyledonous plants. Blackwell Wissenschafts-Verlag; 1997.\n\nOppermann M, Weise S, Dittmann C, et al.: GBIS: the information system of the German Genebank. Database-Oxford. 2015.\n\nAquino A, Barrio I, Diago MP, et al.: vitisBerry: An Android-smartphone application to early evaluate the number of grapevine berries by means of image analysis. Comput. Electron. Agric. 2018; 148: 19–28. Publisher Full Text\n\nKomyshev E, Genaev M, Afonnikov D: Evaluation of the SeedCounter, A Mobile Application for Grain Phenotyping. Front. Plant Sci. 2017; 7. PubMed Abstract | Publisher Full Text\n\nMüller-Linow M, Wilhelm J, Briese C, et al.: Plant Screen Mobile: an open-source mobile device app for plant trait analysis. Plant Methods. 2019; 15: 2. PubMed Abstract | Publisher Full Text\n\nGhaffar M, Schüler D, König P, et al.: Programmatic Access to FAIRified Digital Plant Genetic Resources. J. Integr. Bioinform. 2020; 16(4). PubMed Abstract | Publisher Full Text\n\nJayakodi M, Padmarasu S, Haberer G, et al.: The barley pan-genome reveals the hidden legacy of mutation breeding. Nature. 2020; 588(7837): 284–289. PubMed Abstract | Publisher Full Text\n\nWeise S, Oppermann M, Maggioni L, et al.: EURISCO: The European search catalogue for plant genetic resources. Nucleic Acids Res. 2017; 45(D1): D1003–D1008. PubMed Abstract | Publisher Full Text\n\nSchreiber T, Röckel F: PhenoApp Input/Output files (1.0) [Data set]. Zenodo. 2021. Publisher Full Text\n\nSchreiber T, Röckel F: PhenoApp (1.0). Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "119127",
"date": "25 Jan 2022",
"name": "Karin Köhl",
"expertise": [
"Reviewer Expertise plant phenotyping",
"data management",
"abiotic stress tolerance"
],
"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,\nYour manuscript describes a very useful tool for manual phenotyping based on mobile devices. However, the information on the tool need some amendments, especially for a user who is not familiar with the Limsophy-DB and wants to use it independently. I have some experience with using mobile devices for high-throughput phenotyping as we designed a similar tool for WinCE in 2015 (see reference).\n\nIs the plant identification done by selection from a pre-existing list or by free text entry? In the latter case, how do you make sure the plant exists in the database/LIMS? How do you deal with duplication of the location names: two independent experiments may use the same combination of plot row and plant I.D? If the system is used independent of a LIMS system: How do you ensure that controlled vocabulary is used for species/variety? And, how do you ensure that controlled vocabulary for descriptors are used in the entry excel file.\n\nUsing excel files as an entry format has risks. How do you avoid Excel reformatting numbers into dates? How do you avoid users messing up the file by accidentally including carriage returns and other control characters?\n\nFor the numeric data entry: where do you define the unit in which the measurement was done (e.g. m, cm for height)?\n\nHow many clicks do you need to enter the BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) information? Can you just enter the code or do you have to select from a list? The latter is very time consuming when you have to score a large number of plants.\n\nHow do you deal with multiple pictures of one BBCH stage, does the new image overwrite the old image or is it added?\n\nCan you store the specific selection of descriptors as a protocol for future use, to make sure that each time the same set of traits is phenotyped. Is it possible to store the protocol independent of the Limsophy-DB?\n\nCan you provide a reference for the Limsophy-DB?\n\nOutput excel file: how do you record the meaning of Sb and Bl if the system is not linked to a LIMS system? How do you maintain the link between input and output file?\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? Partly",
"responses": [
{
"c_id": "7867",
"date": "04 Mar 2022",
"name": "Franco Röckel",
"role": "Author Response",
"response": "First of all, we would like to thank the Reviewer who has provided us with many insightful comments and a chance to improve our work. To the review: Your manuscript describes a very useful tool for manual phenotyping based on mobile devices. However, the information on the tool need some amendments, especially for a user who is not familiar with the Limsophy-DB and wants to use it independently. I have some experience with using mobile devices for high-throughput phenotyping as we designed a similar tool for WinCE in 2015 (see reference). Is the plant identification done by selection from a pre-existing list or by free text entry? The PhenoApp is designed for phenotyping of previously defined material with given locations (e.g. breeding material in field) that is screened with defined descriptors. This information is provided to the App in an Excel file as described under “Data import and export” prior to the phenotyping. In the ”Locations” sheet, the material can be filled with the individual material, while in the sheet “Traits” the descriptors can freely be customised. Data to the Excel Import file can be (1) entered directly, (2) by copy & paste from pre-existing lists/files, or (3) from databases (like LIMS) using matching data export settings. In the latter case, how do you make sure the plant exists in the database/LIMS? There is no control via PhenoApp. If you use the PhenoApp independently of a database you can use the Excel output file with the data to feed every planned downstream application. For data import to a database/LIMS we highly recommend to use a script to create the input files and a second one that checks every entry during data import after phenotyping. This avoids errors a priori and gives full control over the clear allocation and completeness. How do you deal with duplication of the location names: two independent experiments may use the same combination of plot row and plant I.D? Each location (or plant) is linked to an experiment, so there are no problems if a location appears in several experiments. Thus, only the associated locations are used in each experiment. If a specific location is given multiple times in a single list with different names, all entries are displayed in PhenoApp, although only one is true and others are wrong. Users will recognize it and can then adapt the input file. If the system is used independent of a LIMS system: How do you ensure that controlled vocabulary is used for species/variety? And, how do you ensure that controlled vocabulary for descriptors are used in the entry excel file. We designed PhenoApp to be as customisable as possible. There is no controlling of common vocabulary for any descriptor. Nevertheless, we recommend using international standardised descriptor lists as mentioned in the text. The validation of the correct taxonomy rely on a central defined vocabulary or ontology. This central place should be a database that offer access and validation features. Nevertheless, there are spreadsheet based terminology validation features, e.g. RightField (DOI: 10.1093/bioinformatics/btr312). Furthermore, one may even implement MS-Excel macros that validate to a remote accessible list of valid species. Using excel files as an entry format has risks. How do you avoid Excel reformatting numbers into dates? Indeed this is a potential pitfall as reported already in Browman et al. (10.1080/00031305.2017.1375989) By following these rules, there have been no problems of this kind with Excel so far. After phenotyping, dates were displayed correctly. During development, Excel seemed to be the simplest and most used format for scientists to define their experiments independently. In the future, it is planned to support JSON as an alternative input format. Furthermore, csv file format can be used for export instead of xlsx. How do you avoid users messing up the file by accidentally including carriage returns and other control characters? So far, no problems of this kind were known and no controlling system is used. PhenoApp will display the special characters. In our institutes, the input files are mainly created directly by the LIMS to avoid these errors and where this is not possible, standardised input file templates are available. To a certain degree, users are responsible for the correctness of their own datasets. For the numeric data entry: where do you define the unit in which the measurement was done (e.g. m, cm for height)? This can be specified in the descriptor itself. We recommend defining the measurement including the used unit as precisely as possible in the “Remark” field of the “Traits” sheet in the input file. How many clicks do you need to enter the BBCH (Biologische Bundesanstalt für Land- und Forstwirtschaft, Bundessortenamt und CHemische Industrie) information? Can you just enter the code or do you have to select from a list? The latter is very time consuming when you have to score a large number of plants. Every pre-integrated BBCH scale has three list levels: species, macro stage and micro stage. Species and the macro stage need to be selected once in the beginning meaning that with every new plant entry both entries are kept. Only the micro stage needs obviously to be selected at every location entry. You need one click to open the micro stage menu and one additional click for the individual BBCH stage at every location. It is quite handy and approved. How do you deal with multiple pictures of one BBCH stage, does the new image overwrite the old image or is it added? There is only one image per stage/descriptor possible and a new image would replace the old one. If really two images are needed, users would have to merge them into one image file and then upload it. This has been done in the past. Can you store the specific selection of descriptors as a protocol for future use, to make sure that each time the same set of traits is phenotyped. Is it possible to store the protocol independent of the Limsophy-DB? We store our descriptor list in the LIMS database. This list is always used when an input file is created. Before we integrated the LIMS in the PhenoApp workflow, we created an empty input file (empty of plant locations) with a read-only descriptor list in Excel and saved it in an institutional-wide PhenoApp filesystem folder share for further use. Every new user was informed to rely on this standard list. Next to that, a user is free to adapt his individual descriptor list in the input file to only the relevant descriptors he is going to use in the given experiment or development state by deleting all others. Can you provide a reference for the Limsophy-DB? Ghaffar, M., Schuler, D., Konig, P., Arend, D., Junker, A., Scholz, U., Lange, M., 2020. Programmatic Access to FAIRified Digital Plant Genetic Resources. J Integr Bioinform; DOI: 10.1515/jib-2019-0060 Output excel file: how do you record the meaning of Sb and Bl if the system is not linked to a LIMS system? A detailed meaning of every descriptor can be given in the remark column, which is a free text field. We recommend defining records of individual rating systems here as precisely as possible including units for measured values, phenological state, organ positions etc. How do you maintain the link between input and output file? The complete location list of the input file is also copied to your output file independent of your phenotyping."
}
]
},
{
"id": "140861",
"date": "29 Jul 2022",
"name": "Andrew P. French",
"expertise": [
"Reviewer Expertise Automated image analysis in plant phenotyping"
],
"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,\nThis paper describes a potentially useful tool to address the issue of manual data collection from plant phenotyping experiments. Such a tool, if well executed, goes some way to providing for an information management system for collecting and recording phenotyping data in the field. I have more experience with automated data collection though analysis of images, but I do recognise the need and utility of a tool to assist with data capture by hand. The app seems to focus almost entirely on data collection, and as noted in a response to a previous review, this data can then be fed to further downstream processing outside the app as required. The app therefore seems to be a semi-constrained front end for entering data into an Excel/CSV format. Whilst a simple idea, I believe this is useful in practice. I have some comments below.\nIt is a shame that there is no enforcing of controlled vocabulary on some of the fields. In the previous response to authors it is noted that the use of internationally-recognised descriptors is recommended, so not having the option to enforce this in some scenarios feels like a missing feature which should be present. Related, a lot of emphasis is put on the input file, which I believe you use a lab information system to supply. How well practically do you see this working if the institute does not have a LIMS?\nI agree with the previous reviewer raising questions about Excel as a choice of data format. I think there are issues with this, and perhaps more flexible formats like JSON should be explored in the future (as you mention). However, there is no doubt Excel provides accessibility and readability of data in a form most phenotyping researchers will be familiar with.\nThe option of uploading images is welcome, especially as I can see the benefit in later using these alongside the manually collected data to support development of AI-based systems which can analyse the images. However, only allowing one image at a time seems like an oversight here. I am convinced it would be beneficial to allow users to upload as many images per entry as desired.\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? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "8783",
"date": "21 Oct 2022",
"name": "Franco Röckel",
"role": "Author Response",
"response": "First of all, we would like to thank the reviewer who gave us constructive comments and the opportunity to elaborate on certain aspects.To the review: \"Dear authors, This paper describes a potentially useful tool to address the issue of manual data collection from plant phenotyping experiments. Such a tool, if well executed, goes some way to providing for an information management system for collecting and recording phenotyping data in the field. I have more experience with automated data collection though analysis of images, but I do recognise the need and utility of a tool to assist with data capture by hand. The app seems to focus almost entirely on data collection, and as noted in a response to a previous review, this data can then be fed to further downstream processing outside the app as required. The app therefore seems to be a semi-constrained front end for entering data into an Excel/CSV format. Whilst a simple idea, I believe this is useful in practice. I have some comments below. It is a shame that there is no enforcing of controlled vocabulary on some of the fields. In the previous response to authors it is noted that the use of internationally-recognised descriptors is recommended, so not having the option to enforce this in some scenarios feels like a missing feature which should be present.\" We agree that a strict control of vocabulary and normed descriptors would be of outstanding importance. Nevertheless, the tool reflects the unsatisfactory situation that stakeholder, like funding agencies, publisher or international core database, implemented no mechanisms to ensure this. Rather, it is moved to the level of informal commitments in institutional strategies. But even those need proper review. In order to provide a commonly usable data recording tool, the decision was to implement the data consistency in the database layer, which implements site-specific rules. On any inconsistency, a data steward is then responsible to resolve these. PhenoApp was built to be as much as possible customizable for maximum user friendliness. We do not want to enforce the use of any specific descriptors and consequently exclude users with individual (not yet harmonized) use cases. The controlled use of certain descriptors can easily be supervised on the institutional-wide level with read-only descriptor lists as explained in more detail in the next comment. However, we recognize the possible benefit of such a feature. The integration of a common set of descriptors for specific species with a standardized vocabulary could be implemented in future updates. Steps to facilitate species-level descriptor management are the basis for such an option and are already under development. \"Related, a lot of emphasis is put on the input file, which I believe you use a lab information system to supply. How well practically do you see this working if the institute does not have a LIMS?\" At the beginning of the development, we did not use a LIMS either. We once created a common input file with a read-only descriptor list stored in an institutional-intern accessible folder. Therefore, users always used the same descriptor template and only added their specific plant list. It is more or less the same process as with a LIMS with a few more manual steps per user and without the automated LIMS database upload of the results after phenotyping. Since we use institutional-wide, standardized plant information (accession name, accession number, plant positions in the field etc.), the input files were completely standardized and the gathered information could be easily uploaded after the connection to our LIMS. To conclude, we already established the standardized, institutional-wide use before the implementation of a LIMS. This should be feasible for every institute/lab in comparable manners as described above. \"I agree with the previous reviewer raising questions about Excel as a choice of data format. I think there are issues with this, and perhaps more flexible formats like JSON should be explored in the future (as you mention). However, there is no doubt Excel provides accessibility and readability of data in a form most phenotyping researchers will be familiar with.\" Indeed the use of JSON as standardized, well-defined file format would have simplified the development of PhenoApp and ensured a robust file un-marshalling and data structure consistency per-se. As argued before, one aim is to support a wide range of application areas and institutional infrastructures where some need to support Excel as widely used and accessible solution for data acquisition, editing and exchange. We saw the risk of JSON in losing those data maintainers and producers, who rely on proprietary historic database backend systems and data management processes. E.g. some do not use databases at all and archive in folder systems of Excel files as primary storage. \"The option of uploading images is welcome, especially as I can see the benefit in later using these alongside the manually collected data to support development of AI-based systems which can analyse the images. However, only allowing one image at a time seems like an oversight here. I am convinced it would be beneficial to allow users to upload as many images per entry as desired.\" Please allow to clarfiy a potential misunderstanding. Only for a descriptor it is possible to upload one sample image. However, this should be sufficient to display representative images of rating schemes, phenological stages etc. in the app interface at the time of rating. Instead, for specific plant entries, it is not possible to upload images at all. However, we implemented the connection to the photo app of the devices used to take location-specific photos. There is no number limit for images per location here and naming is standardized based on the specified location, the actual timestamp and the variety name (if given) to ensure subsequent recognition. This allows clear allocation of the image to location/variety and if rating was performed for only one/few traits a clear allocation is possible even for the trait. Of course, these photos can be used for all downstream analysis without any restrictions."
}
]
}
] | 1
|
https://f1000research.com/articles/11-12
|
https://f1000research.com/articles/11-1395/v1
|
28 Nov 22
|
{
"type": "Research Article",
"title": "Anticancer and antiretroviral activities of methanolic extract from Theobroma cacao L pod husk: focusing on the ethyl acetate partition",
"authors": [
"Mustanir Yahya",
"Binawati Ginting",
"Nurdin Saidi",
"Binawati Ginting",
"Nurdin Saidi"
],
"abstract": "Background: Many researchers have paid attention to Theobroma cocoa pod husk for its bioactive phytoconstituents which have several medicinal benefits. Herein, we aim to evaluate the methanolic extract from T. cocoa pod husk and its partitions for their anticancer and antiretroviral activities. Methods: The T. cocoa pod husk was macerated using methanol, and then sequentially partitioned with n-hexane and ethyl acetate. MCF-7 and HeLa cells were used to assess the anticancer activities, while the simian retrovirus-2 (SRV-2)-infected A549 cells were used for antiretroviral study. The ethyl acetate partition (TCEA) was then fractionated and screened for in-vitro antioxidant and cytotoxicity. The most active fraction was sub-fractionated and analyzed using gas chromatography-mass spectroscopy (GC-MS). Results: The results suggested that TCEA had moderate and weak activities against MCF-7 (IC50=53.91 μg/mL) and HeLa cells (IC50=120.71 μg/mL), respectively. TCEA 125 μg/mL had higher anti-SRV-2 activity in comparison with lamivudine 25 μg/mL after 1—7 days of incubation. The GC-MS analysis of the polyphenol-predominated sub-fraction from the most active fraction revealed the presence of lupeol, syringaresinol, catechol, and squalene. Conclusions: TCEA derived from the methanolic extract of T. cacao pod husk had moderate activity against MCF-7 cells and weak activity against HeLa cells. Antiretroviral study suggests that TCEA 125 μg/mL had higher inhibitory activity against SRV-2 replication as compared to lamivudine 25 μg/mL.",
"keywords": [
"Cocoa pod husk",
"Simian retrovirus-2",
"MCF-7",
"HeLa",
"phytochemical profile"
],
"content": "Introduction\n\nTheobroma cocoa pod husk, a cacao by-product, has intrigued many researchers to study its potential as natural medicine. A review article has highlighted its bioactivities as an anticarcinogenic, antibacterial, antiviral, antidiabetic, neuroprotective, and anti-inflammatory agent.1 This is due to the fact that T. cocoa pod husk is rich in flavonoids and polyphenols which have been associated with a series of medicinal properties of plant extracts.2–4 Several methods to extract the active phytoconstituents have been carried out previously, including those using supercritical CO2 and microwave assistance.5,6 A simple maceration technique has also been carried out using different solvents namely methanol:acetone,7 ethyl acetate,8 and n-hexane solvents.9 In our recently published work, we extracted the T. cocoa pod husk using distilled water and found its potential as a source for dietary antioxidants.10 Nonetheless, the research on methanolic extract of T. cacao pod husk has been scarcely reported. Some studies suggest the methanolic extraction could attract a wide-range of bioactive compounds.11–13\n\nIn previous research, T. cacao was found to be active in inhibiting the growth of Caco-2 colon cancer, HL-60 leukemia, SH-SY5Y neuroblastoma, MCF-7 breast cancer, HepG2 hepatoma, and Int-407 intestinal cancer cell lines.2 Polyphenols from T. cacao were responsible for the downregulation of transcription factors nuclear factor-κB (NF-κB) and activator protein-1 (AP-1) that are involved in oncogenic process.14,15 Under the same light, the phytoconstituents of T. cacao may also have a role in immunomodulation. In fact, these biological activities have been utilized to reactivate latent human immunodeficiency virus type 1 (HIV-1).16 Herein, we investigated the methanolic extract from T. cacao pod husk and its partitions for their anticancer and antiretroviral activities. We used MCF-7 breast cancer and HeLa cervical cell lines to investigate the anticancer activities as these cells have been used for anticancer screening of natural products.17–20 Simian retrovirus-2 (SRV-2)-infected A549 cell line was used to study the antiretroviral activity as this method has been developed to culture the Indonesian strain.21 The active extract sample was fractionated for in-vitro antioxidant and cytotoxicity screenings and further sub-fractionated for phytoconstituents analysis.\n\n\nMethods\n\nMaterials used in this research included technical methanol, technical n-hexane, technical ethyl acetate, silica gel G60 F254, He gas, 2,2-diphenyl-1-picrylhydrazyl (DPPH) powder, ascorbic acid, pro-analytical methanol, gallic acid, and quercetin. Reagents used for the phytochemical screening included Folin-Ciocalteu reagent, Na2CO3 10%, AlCl3, and potassium acetate. Dulbecco’s Modified Eagle Medium (DMEM) from Gibco (Thermo Fisher Scientific, Waltham, MA, USA) was used for cell culture. In addition, NaHCO3, fetal bovine serum (FBS) (Invitrogen, USA), Penicillin-Streptomycin (Invitrogen, USA), trypsin (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), trypan blue (Sigma, USA), PBS (phosphate buffer saline) (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), dimethyl sulfoxide (Sigma, St. Louis, MO, USA), CO2 incubator, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) (Sigma, St. Louis, MO, USA), and pro-analytical ethanol (Merck, Germany) were also used. Kimwipes® tissue (Kimberly-Clark, Jawa Barat, Indonesia), Direct-zolTM RNA PreWash, RNA Wash Buffer, RNase-Free Water, primers SRV-2 5737 U19 and SRV-2 5943 L20, SSoFast Evagreen Mastermix (Bio-Rad Laboratories, Hercules, CA, USA), and nuclease-free water (NFW) were used for the real-time polymerase chain reaction (RT-PCR) protocol.\n\nTheobroma cacao L. specimen was collected from Desa Lawe Loning, Lawe Sigala-Gala District, Aceh Tenggara Regency, Aceh Province, Indonesia on 20 August 2021. The plant specimen was identified at the Department of Biology, Universitas Syiah Kuala, Indonesia with a voucher number of 795/UN11.1.28.1/DT/2008. The cocoa pod husk was washed with distilled water, cut into small pieces, and air-dried at 25±1°C for 7—10 days before crushed into powder.\n\nThe bioindicators MCF-7 cell line, HeLa cell, A549 cell, and Simian retrovirus-2 (SRV-2) were obtained from the Pusat Studi Satwa Primata-Lembaga Penelitian dan Pengabdian pada Masyarakat, Institut Pertanian Bogor (PSSP LPPM-IPB), Indonesia.\n\nPreviously prepared cacao pod husk powder (5 kg) was macerated using methanol for 24 h, performed repeatedly until the filtrate became clear. The methanolic filtrate was concentrated via rotary evaporation to produce the methanolic extract which was then labeled as TCM. Thereafter, the TCM was partitioned sequentially using n-hexane and ethyl acetate, where each sample was labeled as TCH and TCEA, respectively.\n\nMCF-7 and HeLa cancer cell lines (5x103 cells/well) were respectively grown in 96 well plate for 24 h (37°C; 5%CO2) with DMEM medium which had been priorly added with FBS 5% and Penicillin-Streptomycin 1% antibiotic. On the following day, each well was added with DMSO-dissolved extracts (TCM, TCH, and TCEA) with concentrations of 500, 250, 125, 62.5, and 31.25 μg/mL. The cell cultures were then incubated for 48 h before being added with 10 μL MTT and re-incubated for 4 h. Subsequently, as much as 100 μL ethanol 96% was added and optical density (OD) reading was carried out on a microplate reader (ELISA reader) at 595 nm. The procedure was performed in triplicate for each sample.\n\nThe concentration range for anti-SRV-2 studies was determined by MTT assay (as explained previously), but the non-infected A549 lung cancer cell line was used instead. For the antiretroviral study, SRV-2-infected A549 cell culture (50x103) was firstly sub-cultured in a 12-well plate and incubated for 24 h at 37°C, 5% CO2. Afterward, extract samples (2 mL) with a concentrations range that was non-cytotoxic against A549 cells (inhibition percentage < 50%) were added to each well (performed in duplicate). Cell receiving no treatment was taken as control. For the positive control, we used lamivudine at 25 μg/mL. Thereafter, the cells were incubated until day-7, where the supernatant was harvested on day-1, -3, -5, and -7. In each harvesting, the supernatant was taken as much as 500 μL, and into the cell culture, 500 μL sample solution was re-added. The harvested supernatant was stored at -80°C.\n\nThe viral RNA was extracted from the supernatant using QIAamp Viral RNA Mini Kits (Qiagen, Hilden, Germany) which was then reverse transcripted using SuperscriptTM III First-Strand Synthesis System for RT-PCR (Invitrogen) to obtain the viral cDNA. Primers used in the RT-PCR were SRV-2 5737U19 and SRV-2 5943L20 (collections of PSSP LPPM-IPB) which had been amplified with envelope gene gp70. As much as 1 μL of each primer was added to the master mix (PCR reaction mixture) containing 10 μL Sofast Evagreen Master Mix, 6 μL Nuclease Free Water dan 2 μL cDNA template. The PCR was performed in an iCycler Thermal cycler with iQ5 multicolor real time PCR detection system at 95°C for 30 seconds, followed by 40 cycles consisting of: denaturation (95°C; 30 second), annealing (47°C; 20 seconds), and DNA extension (72°C; 20 seconds). Standard used for the quantification of SRV-2 was SRV-2 plasmids with a concentration range of 101—106. This protocol was performed in duplicate, following the suggestion from a previously published study.22\n\nExtracts with anticancer and antiretroviral activities were further isolated using gravitational column chromatography with silica gel G60 F254. The extract was treated with gradient elution starting with non-polar solvent n-hexane (100%) up to semi-polar solvent ethyl acetate:methanol (1:1). Fractions with the similar patterns from the thin layer chromatography were combined into subfraction, and then tested for antioxidant and cytotoxic activities.\n\nThe subfraction was re-chromatographed using a column with silica gel G60 F254 based on gravitational force. The obtained subfraction was tested on thin layer chromatography and sprayed with vanillin sulfate and FeCl3 5% to identify the polyphenol contents. Subfraction with the most dominant polyphenol content was investigated on gas chromatography-mass spectroscopy (GC-MS) for phytoconstituents profiling.\n\nAntioxidant activities were based on the inhibition of DPPH radical (molecular weight=394.32 g/mol). As much as 11.82 mg DPPH powder was dissolved in methanol using 75-mL volumetric flask. The extract sample and positive control (ascorbic acid) were prepared in concentrations of 3, 6, 9, 12, and 15 μg/mL. Into each solution, DPPH 0.4 mM was drop-wised (1 mL), and the volume was increased with methanol until it reached 5 mL. The container was then sealed with aluminum foil to avoid the light exposure. Thereafter, the mixture was homogenized with vortex mixer and incubated for 30 minutes at 37°C. The mixture solution was measured for its absorbance at 517 nm using UV-vis spectrophotometer.\n\nThe cytotoxicity was determined by brine shrimp lethality test (BSLT) using Artemia salina larvae. The larvae (±50-100 mg) were firstly incubated in a covered container with saline water for 48 h. On the other hand, the extract sample (30 mg) was diluted with 3 drops of DMSO 5% and added with 30 mL saline water, and subsequently sonicated until homogenous. The concentrations of the prepared extract sample ranged from 1000 to 1 μg/mL, and a combination of saline water and DMSO 5% was taken as the negative control. A glass container was filled with the prepared extract sample and then added with 10 brine shrimps before incubated (24 h; room temperature). Dead brine shrimps were then counted in each glass container.\n\n\nResults\n\nTCH, TCEA, and TCM were screened for their anticancer activities against MCF-7 breast cancer and HeLa cervical cancer cell lines, where the results have been presented in Figure 1. At 31.25 μg/mL, TCH has a higher inhibition than TCEA (33.29% versus 18.93%). Meanwhile, no inhibition was observed in sample treated with TCM 31.25—62.5 μg/mL until its concentration increased to 125 μg/mL (inhibition=28.35%). Interestingly, at 250 μg/mL, TCM appeared to yield the highest inhibition (97.62%) as compared to TCEA (95.66%) and TCH (93.85%). Concentration-dependent increment of the MCF-7 inhibitions were observed when the extract concentrations ranged from 31.25 to 250 μg/mL. Hence, the IC50 values were calculated based on the polynomial regression on the concentration range of 31.25—250 μg/mL (Table 1). The calculation of the IC50 against MCF-7 revealed TCH as the most potent extract (IC50=45.36 μg/mL) among others (IC50=53.91 and 161.53 μg/mL for TCEA and TCM, respectively) (Table 1).\n\nA similar trend of anticancer activities was also observed for the HeLa cancer cell line, where highest to the lowest, the order was as follows: TCH, TCEA, and TCM with inhibition percentages of 44.15, 17.5 and 1.39%, respectively. For TCH and TCM, the increase of concentration from 31.25 to 62.5 caused a rapid elevation of inhibition. As for TCEA, the rapid increasing trend of inhibition percentage was observed until 125 μg/mL. Due to this nature of the curves, we employed polynomial regression for the IC50 calculation so that R2>0.90 could be obtained (Table 1). The lowest IC50 was obtained by TCH (82.44 μg/mL). Meanwhile, TCEA and TCM have IC50 against HeLa cervical cancer cell line of 120.71 and 272.58 μg/mL, respectively.\n\nScreening of anticancer activities revealed that TCEA and TCH fractions had higher activities as compared to TCM. Herein, we tested the antiretroviral activity of TCEA and further continued to analyze its subfractions along with antioxidant, cytotoxicity, and phytochemical screenings. The investigation on TCH fraction is currently being carried out and will be published separately later. For the antiretroviral investigation, we calculate the non-cytotoxic concentration of TCEA against A549 cell line since it was used for the viral replication (Figure 2). From the study, we obtained 438.99 μg/mL as the IC50 value which was then set as the cytotoxic concentration.\n\nThe antiretroviral activity of TCEA against SRV-2 with concentration range of 31.25—125 μg/mL has been presented in Table 2. On Day-1 the SRV-2-infected cells receiving TCEA 125 μg/mL and positive control experienced replication inhibitions, but not in TCEA 62.5 and 31.25 μg/mL groups. Viral replications of lower than that of the negative control (indicating the inhibitory activity) were significantly observed in TCEA 62.5 and 31.25 μg/mL only after 5 days of incubation. TCEA with a concentration of 125 μg/mL was considered as having more potent antiretroviral activity compared to lamivudine (positive control).\n\nAs many as 581 fractions were obtained from the column chromatography of TCEA, where those with the same stain patterns were combined one into a single subfraction. As many as 9 subfractions were obtained from the procedure and each of the subfractions was labeled with TCEA 1 to 9. The nine subfractions were analyzed with thin layer chromatography, and the results have been presented in Figure 3. Observation using vanillin sulfate revealed that the TCEA 1—4, TCEA 4—7, and TCEA 7—9 were predominated by terpenoids (purplish blue), flavonoids (yellow), and tannins (brownish color), respectively. Meanwhile, the FeCl3 5% confirmed the presence of polyphenols in all samples as indicated by the dark green color.\n\nFrom left to right: UV light at 254 nm; UV light at 366 nm; vanillin sulfate; and FeCl3 5%.\n\nAntioxidant activities of TCEA 1—9 based on the radical DPPH inhibition have been presented in Figure 4. TCEA was found to have the weakest antioxidant power with IC50 of the DPPH inhibition only reaching 137.511 μg/mL. TCEA 6 has the lowest 7.64 IC50 of 6.49 μg/mL, hence the most potent antioxidant among others. TCEA 5 was only seconds after TCEA 6 with IC50 of 7.64 μg/mL. It is worth noting that both TCEA 5 and 6 were obtained from column chromatography using n-hexane:ethyl acetate (3:7) eluent. Meanwhile, as a comparison, the IC50 obtained from the ascorbic acid was almost twice lower than TCEA 6 (3.25 μg/mL versus 6.49 μg/mL).\n\nThe cytotoxicity profiles of TCEA 1—9 based on the brine shrimp mortality are presented in Table 3. TCEA 8, 9, and 1 had the lowest LC50 with the values being 411, 394, and 252, respectively. Similar to the antioxidant test, we found TCEA 5 and 6 being the two most cytotoxic subfractions (LC50=5 and 2 μg/mL, respectively). The lethal cytotoxicity of these two subfractions could be observed even when the concentration was as low as 1 μg/mL (3 and 4% mortality for TCEA 5 and 6, respectively). TCEA 6 reached 100% mortality when the concentration was 500 μg/mL. Meanwhile, the same level of mortality was reached by TCEA 5 when its concentration was 1000 μg/mL. Other than TCEA 5 and 6, none of the subfractions could reach 100% mortality even when the concentration was as high as 1000 μg/mL.\n\nDue to its high antioxidant and cytotoxicity activities, TCEA 6 was selected for re-chromatography to obtain sample with higher purity. The re-chromatography was carried out using gradient elution of n-hexane and ethyl acetate combination resulting in another four subfractions (TCEA 6.1—6.4). The phytoconsituents of each subfraction were qualitatively analyzed using thin layer chromatography as presented in Figure 5. When sprayed using vanillin sulfate, the presence of flavonoids (yellow) was observed and more pronounced in TCEA 6.3 and 6.4. It was confirmed by FeCl3 5% test, where a dark green color was observed indicating the high content of polyphenols. We were interested in further analyzing TCEA 6.3 through GC-MS for phytoconstituents profiling due its green color being the most intense among others.\n\nFrom left to right: UV light at 254 nm; UV light at 366 nm; vanillin sulfate; and FeCl3 5%.\n\nA list of phytoconsituents identified by the GC-MS analysis from sample TCEA 6.3 has been presented in Table 4. As many as 39 compounds were identified from the 40 peaks in the chromatogram where benzoic acid, 4-hydroxy-3,5-dimethoxy- has the widest peak area (21.56%). Lupeol was identified twice, assigned for peaks 4 and 5, but the former had lower similarity than the latter (75.3 and 93.9%). Bioactive compounds which had been recognized for their anticancer and/or antioxidant activities were identified, namely lupeol, syringaresinol, catechol, and squalene. Among the four aforementioned compounds, catechol had the highest quantity (peak area = 9.29%) with similarity over 93.9%.\n\n\nDiscussion\n\nBased on the IC50 obtained herein, TCH was moderately active against MCF-7 and HeLa cancer line, whilst TCEA was only moderately active against MCF-7. Moderate activity could be ascribed to the presence of non-anticancer compounds in the extract, as suggested by a previous study investigating Calotropis gigantea extract against P388 leukemia cell lines.23 In our previous study, a moderate anticancer activity against MCF-7 cell lines was also obtained from n-hexane extract of Myristica fragrans Houtt roots, where a lignan compound was isolated and identified.20 The anticancer activity increased when the analysis was carried out on a fraction of the foregoing extract,19 indicating the activity is dependent on the bioactive compound concentrations. This is also the reason why TCEA and TCH were more active against the cancer cell lines than TCM because TCEA and TCH had higher purities as they were obtained from the fractionation of TCM.\n\nIn the case of T. cacao, its anticancer activities have been anticipated by researchers due to its rich content of dietary polyphenols.2 A review article has summarized these phenolic compounds that include catechin, 3′-O-methyl epicatechin, epicatechin, procyanidin B2, and polymer procyanidins.3 Our data is in an agreement with that from a previously published study, where the methanolic extract from T. cacao pod husk had lower IC50 on MCF-7 as compared to HeLa cell lines.24 Previously, BSLT cytotoxic activities of n-hexane extract from T. cacao pod husk have been documented to yield LC50<10 μg/mL.9\n\nIn this present study, the TCEA had a significantly higher inhibitory effect even when compared to lamivudine. Previous studies have reported that the NaOH extract from T. cacao pod husk mainly worked as antiviral by preventing the infection of human immunodeficiency virus (HIV) to the host immune cell including the syncytium formation.25 The lignin-carbohydrate complex derived from NaOH extraction in combination with acid precipitation of T. cacao pod husk had anti-HIV activity and immunomodulating activities.26 Moreover, the flavonoid compound from T. cacao could help the efficacy of antiretroviral therapy through the reactivation of latent HIV in human T-cells which was found correlated to NF-κB and MAPK signaling pathways.16 A review on the antiviral potential of T. cacao pod husk highlighted the inhibitory activity of its lignin fractions against cytopathic effects induced by influenza virus, in which this action could be synergized with ascorbic acid.1\n\nFollowing the investigation of the anticancer and antiretroviral activities, the TCEA was fractionated producing TCEA 1—9 fractions. The TCEA was revealed as the most potent antioxidant (IC50=6.49 μg/mL) and cytotoxic (LC50=2 μg/mL) fraction among others. This value is lower in comparison to that obtained from our previous study using aqueous extraction, where the highest antioxidant was IC50=9.61 μg/mL and the highest cytotoxicity – 74 LC50=μg/mL.10 However, more cytotoxically active compounds were obtained in the n-hexane extract of T. cacao pod husk with LC50 as low as 0.29 μg/mL.9 The bioactivities of T. cacao pod husk could be associated with the phenolic compound contained in the extract as suggested previously.10\n\nFurther purification of fraction TCEA 6 in this present study produced 4 subfractions (TCEA6.1—6.4), with TCEA 6.3 being the most predominated with polyphenol (based on FeCl3 5% test). The GC-MS analysis on subfraction TCEA 6.3 revealed its phytoconsituents consisted of bioactive compounds lupeol, syringaresinol, catechol, and squalene among many other compounds. The structures of the foregoing compounds are presented in Figure 6. Lupeol itself has been named as a novel anti-inflammatory and anti-cancer agent by a review article in 2009.27 Interestingly, lupeol has been found to specifically attack cell cancer in which a study reported its high toxicity against 451Lu and WM35 melanoma cells but not in normal human melanocyte cells.28 As an antiviral, lupeol has been found active against herpes simplex virus type 1 (HSV-1) and even its acyclovir-resistant strains.29 Syringaresinol isolated from Rhus javanica var. roxburghiana could inhibit the replication of tobacco mosaic virus.30 The ability of syringaresinol to induce cancer cell death has been documented in a study using HL-60 leukemia cells.31 However, a recent study revealed that syringaresinol was not cytotoxic towards HepG2 and HT29 cells.32\n\nCatechol and its derivatives have been recognized as broad-spectrum antiviral and anticancer agents.33,34 A study suggested that the antiviral and immunomodulating activities of catechol are dependent on the structure and position of the substituent group located on its aromatic skeleton.35 A reputable natural antioxidant, squalene has long been associated with anticancer activities especially in the case of the absence of cancer in sharks.36 Squalene has been witnessed to not only increase the toxicity of several commercial anti-cancers but also provide cytoprotective effect against normal cells.37 A recent report revealed that intravenous squalene BID could significantly improve COVID-19 conditions without any adverse effect.38,39 Taken altogether, the foregoing phytocompounds contained in TCEA 6.3 had a potential to act as anti-cancer and anti-retroviral agent.\n\n\nConclusions\n\nTCEA derived from the methanolic extract of T. cacao pod husk had moderate activity against MCF-7 cells and weak activity against HeLa cells. Antiretroviral study suggests that TCEA 125 μg/mL had higher inhibitory activity against SRV-2 replication as compared to lamivudine 25 μg/mL. Further fractionation using gravitational column chromatography yielded TCEA fractions with relatively high DPPH antioxidant and BSLT cytotoxic activities. The phytoconsituents of the subfraction revealed the presence of lupeol, syringaresinol, catechol, and squalene which have been reported previously as anti-cancer and anti-viral. The investigation on TCH for its anti-cancer and anti-retroviral activities is warranted.\n\n\nAuthor contributions\n\nConceptualization, M.Y. and B.G.; methodology, N.S.; validation, N.S.; formal analysis, M.Y.; investigation, B.G.; resources, M.Y.; data curation, B.G.; writing—original draft preparation, M.Y.; writing—review and editing, B.G. and N.S.; visualization, N.S.; supervision, M.Y.; project administration, B.G.; funding acquisition, M.Y. All authors have read and agreed to the published version of the manuscript.",
"appendix": "Data availability\n\nfigshare: ‘Anticancer and Antiretroviral Activities of Methanolic Extract from Theobroma cacao L Pod Husk: Focusing on the Ethyl Acetate Partition’. https://doi.org/10.6084/m9.figshare.21483096.v4 40\n\nThis project contains the following underlying data:\n\n- 1. MTT Test Design IC50 Calculation.xls [Table containing the raw data of the study].\n\n- 2. OD Value of MCF-7, HeLa dan A549 Cells MTT Test.xlsx\n\n- 3. Bar and Line Graphs represented MCF-7, HeLa & A549 Cells.xlsx\n\n- 4. Data qRT PCR SRV.xlsx\n\n- 5. TCEA Antioxidant Subfraction.xlsx\n\n- 6. TCEA Cytotoxic Subfraction.xlsx\n\n- 7. Supplementary Figures.zip [file containing supplementary figures of the study].\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 appreciate the assistance from the Head of Lembaga Penelitian dan Pengabdian Kepada Masyarakat, Universitas Syiah Kuala and the Dean of Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala. A special acknowledgment is granted to Reka Nurmania, Ayu Rahmadani who, at the moment of this manuscript preparation, were the students of the Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala.\n\n\nReferences\n\nRojo-Poveda O, Barbosa-Pereira L, Zeppa G, et al.: Cocoa Bean Shell—A By-Product with Nutritional Properties and Biofunctional Potential. Nutrients. 2020; 12. accessed. PubMed Abstract | Publisher Full Text\n\nMartin MA, Goya L, Ramos S: Potential for preventive effects of cocoa and cocoa polyphenols in cancer. Food Chem. Toxicol. 2013; 56: 336–351. PubMed Abstract | Publisher Full Text\n\nBaharum Z, Akim AM, Hin TYY, et al.: Theobroma cacao: Review of the Extraction, Isolation, and Bioassay of Its Potential Anti-cancer Compounds. Trop Life Sci Res. 2016; 27(1): 21–42. PubMed Abstract\n\nHarahap D, Niaci S, Mardina V, et al.: Antibacterial activities of seven ethnomedicinal plants from family Annonaceae. J. Adv. Pharm. Technol. Res. 2022; 13(3): 148–153. PubMed Abstract | Publisher Full Text\n\nMazzutti S, Rodrigues LGG, Mezzomo N, et al.: Integrated green-based processes using supercritical CO2 and pressurized ethanol applied to recover antioxidant compouds from cocoa (Theobroma cacao) bean hulls. J. Supercrit. Fluids. 2018; 135: 52–59. Publisher Full Text\n\nIbrahim NH, Mahmud MS, Nurdin S: Microwave-assisted extraction of β-sitosterol from cocoa shell waste. IOP Conference Series: Materials Science and Engineering. 2020; 991(1): 012106. Publisher Full Text\n\nMartínez R, Torres P, Meneses MA, et al.: Chemical, technological and in vitro antioxidant properties of cocoa (Theobroma cacao L.) co-products. Food Res. Int. 2012; 49(1): 39–45. Publisher Full Text\n\nUmri RJ, Maulana I, Ginting B: Antioxidant and cytotoxic activity of ethyl asetat extracts of cocoa pod husk (Theobroma cacao L). IOP Conference Series: Earth and Environmental Science. 2019; 364: 012026. Publisher Full Text\n\nMustanir N, Ginting B, Purnama A: Chemical composition and cytotoxic activities of n-Hexane extract from cacao pod husk (Theobroma cacao L.) Chemical Data Collections. 2020; 30: 100553. Publisher Full Text\n\nYahya M, Ginting B, Saidi N: In-Vitro Screenings for Biological and Antioxidant Activities of Water Extract from Theobroma cacao L. Pod Husk: Potential Utilization in Foods. Molecules. 2021; 26. accessed. PubMed Abstract | Publisher Full Text\n\nNurmilasari N, Ginting B, Helwati H: Isolation of antioxidant compounds of methanol extract of nutmeg leaves (Myristica fragrans Houtt). Jurnal Natural. 2017; 17(1): 49–57. Publisher Full Text\n\nAndalia N, Salim MN, Saidi N, et al.: Molecular Docking Reveals Phytoconstituents of the Methanol Extract from Muntingia calabura as Promising α-Glucosidase Inhibitors. Karbala International Journal of Modern Science. 2022; 8(3): 330–338. Publisher Full Text\n\nMustanir N, Ginting B: Antioxidant Activity and Phytochemical Identification of Annona Squamosa Leaves Methanolic Extracts. Pharm. J. 2021; 13: 1746–1750.\n\nGarcía-Mediavilla V, Crespo I, Collado PS, et al.: The anti-inflammatory flavones quercetin and kaempferol cause inhibition of inducible nitric oxide synthase, cyclooxygenase-2 and reactive C-protein, and down-regulation of the nuclear factor kappaB pathway in Chang Liver cells. Eur. J. Pharmacol. 2007; 557(2): 221–229. PubMed Abstract | Publisher Full Text\n\nWeng M-S, Chang J-H, Hung W-Y, et al.: The interplay of reactive oxygen species and the epidermal growth factor receptor in tumor progression and drug resistance. J. Exp. Clin. Cancer Res. 2018; 37(1): 61. PubMed Abstract | Publisher Full Text\n\nHori T, Barnor J, Nguyen Huu T, et al.: Procyanidin trimer C1 derived from Theobroma cacao reactivates latent human immunodeficiency virus type 1 provirus. Biochem. Biophys. Res. Commun. 2015; 459(2): 288–293. PubMed Abstract | Publisher Full Text\n\nTuama AA, Mohammed AA: Phytochemical screening and in vitro antibacterial and anticancer activities of the aqueous extract of Cucumis sativus. Saudi Journal of Biological Sciences. 2019; 26(3): 600–604. PubMed Abstract | Publisher Full Text\n\nNiksic H, Becic F, Koric E, et al.: Cytotoxicity screening of Thymus vulgaris L. essential oil in brine shrimp nauplii and cancer cell lines. Sci. Rep. 2021; 11(1): 13178. PubMed Abstract | Publisher Full Text\n\nBinawati G, Mustanir N, Maulidna M, et al.: Evaluation of Antioxidant and Anticancer Activity of Myristica fragrans Houtt.Bark. Pharm. J. 2021; 13(3).\n\nGinting B, Saidi N, Murniana M, et al.: Lignan compound isolated from n-Hexane extract myristica fragrans Houtt root as antioxidant and antitumor activities against MCF-7 cell lines data. Data Brief. 2020; 31: 105997. PubMed Abstract | Publisher Full Text\n\nSaepuloh U, Iskandriati D, Pamungkas J, et al.: Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey. Trop Life Sci Res. 2020; 31(3): 47–61. PubMed Abstract | Publisher Full Text\n\nBesson G, Kazanji M: One-Step, Multiplex, Real-Time PCR Assay with Molecular Beacon Probes for Simultaneous Detection, Differentiation, and Quantification of Human T-Cell Leukemia Virus Types 1, 2, and 3. J. Clin. Microbiol. 2009; 47(4): 1129–1135.\n\nHasballah K, Sarong M, Rusly R, et al.: Antiproliferative Activity of Triterpenoid and Steroid Compounds from Ethyl Acetate Extract of Calotropis gigantea Root Bark against P388 Murine Leukemia Cell Lines. Sci. Pharm. 2021; 89(2): 21. Publisher Full Text\n\nBaharum Z, Akim AM, Taufiq-Yap YH, et al.: In Vitro Antioxidant and Antiproliferative Activities of Methanolic Plant Part Extracts of Theobroma cacao. Molecules. 2014; 19: 18317–18331. accessed. PubMed Abstract | Publisher Full Text\n\nUnten S, Ushijima H, Shimizu H, et al.: Effect of cacao husk extract on human immunodeficiency virus infection. Lett. Appl. Microbiol. 1991; 13(6): 251–254. PubMed Abstract | Publisher Full Text\n\nSakagami H, Kawano M, Thet MM, et al.: Anti-HIV and Immunomodulation Activities of Cacao Mass Lignin–Carbohydrate Complex. In Vivo. 2011; 25(2): 229–236. PubMed Abstract\n\nSaleem M: Lupeol, a novel anti-inflammatory and anti-cancer dietary triterpene. Cancer Lett. 2009; 285(2): 109–115. PubMed Abstract | Publisher Full Text\n\nSaleem M, Maddodi N, Abu Zaid M, et al.: Lupeol Inhibits Growth of Highly Aggressive Human Metastatic Melanoma Cells in vitro and in vivo by Inducing Apoptosis. Clin. Cancer Res. 2008; 14(7): 2119–2127. PubMed Abstract | Publisher Full Text\n\nYe J, Wang Z, Jia J, et al.: Lupeol impairs herpes simplex virus type 1 replication by inhibiting the promoter activity of the viral immediate early gene α0. Acta Virol. 2021; 65(3): 254–263. PubMed Abstract | Publisher Full Text\n\nOuyang M-A, Wein Y-S, Zhang Z-K, et al.: Inhibitory Activity against Tobacco Mosaic Virus (TMV) Replication of Pinoresinol and Syringaresinol Lignans and Their Glycosides from the Root of Rhus javanica var. roxburghiana. J. Agric. Food Chem. 2007; 55(16): 6460–6465. PubMed Abstract | Publisher Full Text\n\nPark B-Y, Oh S-R, Ahn K-S, et al.: (–)-Syringaresinol inhibits proliferation of human promyelocytic HL-60 leukemia cells via G1 arrest and apoptosis. Int. Immunopharmacol. 2008; 8(7): 967–973. PubMed Abstract | Publisher Full Text\n\nKirsch V, Bakuradze T, Richling E: Toxicological testing of syringaresinol and enterolignans. Curr Res Toxicol. 2020; 1: 104–110. PubMed Abstract | Publisher Full Text\n\nMusial C, Kuban-Jankowska A, Gorska-Ponikowska M: Beneficial Properties of Green Tea Catechins. Int. J. Mol. Sci. 2020; 21. (accessed. PubMed Abstract | Publisher Full Text\n\nBotta G, Bizzarri BM, Garozzo A, et al.: Carbon nanotubes supported tyrosinase in the synthesis of lipophilic hydroxytyrosol and dihydrocaffeoyl catechols with antiviral activity against DNA and RNA viruses. Bioorg. Med. Chem. 2015; 23(17): 5345–5351. PubMed Abstract | Publisher Full Text\n\nLi R, Narita R, Ouda R, et al.: Structure-dependent antiviral activity of catechol derivatives in pyroligneous acid against the encephalomycarditis virus. RSC Adv. 2018; 8(63): 35888–35896. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMathews J: Sharks Still Intrigue Cancer Researchers. JNCI: Journal of the National Cancer Institute. 1992; 84(13): 1000–1002. PubMed Abstract | Publisher Full Text\n\nNakagawa M, Yamaguchi T, Fukawa H, et al.: Potentiation by squalene of the cytotoxicity of anticancer agents against cultured mammalian cells and murine tumor. Jpn. J. Cancer Res. 1985; 76(4): 315–320. PubMed Abstract\n\nEbrahimi M, Farhadian N, Amiri AR, et al.: Evaluating the efficacy of extracted squalene from seed oil in the form of microemulsion for the treatment of COVID-19: A clinical study. J. Med. Virol. 2022; 94(1): 119–130. PubMed Abstract | Publisher Full Text\n\nDas B, Yeger H, Baruchel H, et al.: In vitro cytoprotective activity of squalene on a bone marrow versus neuroblastoma model of cisplatin-induced toxicity: implications in cancer chemotherapy. Eur. J. Cancer. 2003; 39(17): 2556–2565. PubMed Abstract | Publisher Full Text\n\nYahya M: Anticancer and Antiretroviral Activities of Methanolic Extract from Theobroma cacao L Pod Husk: Focusing on the Ethyl Acetate Partition. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "216306",
"date": "19 Oct 2023",
"name": "Vijaya Anand Arumugam",
"expertise": [
"Reviewer Expertise Phytotherapeutics",
"Clinical Biolchemistry",
"Medical Genetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have put effort to evaluate the “Anticancer and antiretroviral activities of methanolic extract from Theobroma cacao L pod husk: focusing on the ethyl acetate partition”. The authors describe the research undertaken with this in an organized manner, emphasizing the results obtained by them. The article needs modification for better cohesion of information to achieve the goal and the shortcomings which need to be considered. Hence, the paper can be accepted after MAJOR REVISIONS are carried out.\nThe English need improvement since there are some grammatical and syntax errors in the manuscript. For example, the words “source for” may be as “source of”; “suggest the” as “suggest that the”; “in oncogenic” as “in the oncogenic”; “before crushed” as “before being crushed”; “with iQ5” as “with an iQ5”; “Standard” as “The standard”; “the similar” as “similar”; “75-mL” as “a 75-mL”; “the light” as “light”; “vortex” as “a vortex”; “brine” as “the brine”; “and added” as “added”; “in sample” as “in the sample”; “against HeLa” as “against the HeLa”; “on TCH” as “on the TCH”; “polynomial” as “the polynomial”; “against A549” as “against the A549”; “for the viral” as “for viral”; “with concentration” as “with a concentration”; “replications of” as “replications”; “as having” as “to have”; “results have been” as “results are”; “soluble of” as “soluble”; “6 being” as “6 are”; “obtain sample” as “obtain a sample”; “FeCl3 5%” as “the FeCl3 5%”; “due its” as “due to its”; “similarity over” as “a similarity of over”; “Moderate” as “The moderate”; “a moderate” as “moderate”; “that include” as “including”; “an agreement” as “agreement”; “as antiviral” as “as an antiviral”; “found correlated” as “found to correlated”; “Figure 5” as “in Figure 5”; “by influenza” as “by the influenza”; “of tobacco” as “of the tobacco”; “a potential” as “the potential”. The grammar mistakes which are not mentioned here are also to be checked and corrected properly.\n\nThere are some typing mistakes as well, and authors are advised to carefully proof-read the text. For example, the words “wide-range” may be as “wide range”; “sub-cultured” as “subcultured”; “Afterward,” as “Afterwards,”; “a concentrations” as “a concentration”; “real time” as “real-time”; “30 second” as “30 seconds”; “thin layer” as “thin-layer”; “extract sample” as “extracted sample”; “firstly incubated” as “first incubated”; “incubated” as “incubation”; “brine shrimps” as “brine shrimp”; “the rapid” as “the rapidly”; “Day-1” as “Day 1”; “phytoconsituents” as “phytoconstituents”; “review on” as “review of”; “cytoprotective effect” as “cytoprotective effects”; “retroviral agent” as “retroviral agents”; “investigation on” as “investigation of”. The typos not mentioned here are also to be checked and corrected properly.\n\nCheck the abbreviations throughout the manuscript and introduce the abbreviation when the full word appears the first time in the abstract and the remaining part of the manuscript (For example, simian retrovirus-2 (SRV-2), ethyl acetate partition (TCEA), DMSO, etc.,). Make a word abbreviated in the article that is repeated at least three times in the text, not all words to be abbreviated.\n\nThe full form of the species should be given when the first time appears in both the abstract and in the remaining part of the manuscript and it should be followed by only the first letter of the genus (For example, Theobroma cacao when the first time appear and followed by T. cacao).\n\nThe technical terms (Latin Phrase) \"in-vitro \" should be italic and it should be checked all over the manuscript.\n\nThe introduction part appears less informative about Theobroma cacao, thus this section should be indicated as detailed to understand the manuscript in clear since the main objectives is focused on Theobroma cacao. The botanical description, family name and different plants of the plant with it medicinal uses.\n\nThe authors may include the details of the quantity of fresh sample used and the quantity of the powder obtained (the ratio between fresh plant and powder) under the heading materials and methods.\n\nIn the materials and methods, the authors may cite references for standard protocol, instead of mentioning kid or manufacture instructions, if reference is given with it and the same should be added in the reference section.\n\nThe table and figure legends should be improved and a proper footnote should be given. All legends should have enough description for a reader to understand the tables and figures without and tables having to refer back to the main text of the manuscript. For example, the necessary abbreviations should be given.\n\nThe limitation of the present study may be given along with conclusion or under separate heading for understanding the concepts clearly.\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": []
},
{
"id": "232067",
"date": "11 May 2024",
"name": "Shinta Rosalia Dewi",
"expertise": [
"Reviewer Expertise Biomass valorisation",
"Bioactive extraction",
"Microwave extraction"
],
"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 very good research that will be very beneficial to researchers working in anticancer and antiviral areas, as well as medical studies. The valorization of cacao pod husk waste into anticancer and antiviral agents is a highly intriguing idea.\nThe research study has been carried out systematically and the results are written coherently in the article. The Abstract has been written clearly and reflects the manuscript's content. However, some improvements are still needed to ensure the information presented in the manuscript is clear. Possibly some English revision should also be done, and the following other comments can be addressed:\n1. English revision needs to be done to make the paper much pretty. For example, the term “as much as” is inappropriate (should be removed), or if required, replaced with “about”.\n2. Introduction: Please clarify the originality and research aim of this study in the Introduction section. The authors have explained the potential of cacao pod husk as a medicine for anticancer, antiviral, etc. Various extraction methods and solvents that are widely used have also been mentioned, including what had been previously studied (extraction using water). However, the authors did not elaborate to provide clear explanations for why the maceration with methanol solvent was then chosen for this study (the research gap analysis was unclear).\n3. Methods:\nMaterial: instead of using “technical methanol, technical n-hexane, etc”, it is preferable to use “methanol, n-hexane, etc (mention all), with technical grade quality”. Also, for “pro-analytical ethanol, methanol, etc”, I would recommend using “methanol, ethanol, etc, with extra pure or analytical grade quality. Cacao pod extraction: what is the solvent-to-sample ratio, number of repetitions, and total amount of solvent used? Introduce the abbreviation for the first time it appears in the manuscript: TCM, TCH.\n\n4. Results:\nPlease write the information clearly for readers to grasp. Compare the %inhibition with IC50 results to conclude the antioxidant activity. For example, how does the antioxidant activity of TCH, which has the highest %inhibition, correspond with the lowest IC50 value? Figure 1: Instead of placing the “MCF- and Hela” annotations within the picture, write the notations (a) and (b) in the figure title (bold text). Also, use consistent terminology: methanol extract, EA soluble, hexane soluble (all are extracts). Figure 2: provide number information (1,2, 3, 4, and so on) (possibly) under each figure.\n\n5. Discussion:\nPlease explain (based on the reference) the level of antioxidant activity (for example: very strong: <50 µg/mL; strong: 50-100 µg/mL, etc) to support your discussion. Additionally, compare your results to commercial antioxidant compounds, such as BHT, vitamin C, or others (included in Table 1) for a more interesting discussion. Also, to further highlight the anticancer potential of your extract, compare its anticancer activity to that of commercial anticancer drugs/compounds that are widely used. Paragraph 4: which TCEA fraction explains in this sentence: “The TCEA was revealed as the most potent antioxidant (IC50=6.49 μg/mL) and cytotoxic (LC50=2 μg/mL) among others” ? Figure 6: typo on GCMS, it should be “gas chromatography-mass spectroscopy”\n\n6. Conclusion means something else than summary, so please include recommendations for applying your extract, for example in the medical field where might it be used as a natural alternative treatment/drug/supplement (???)\n7. The is no statistical analysis or interpretation because the author did not explain the repetitions, either for experiments or analysis.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1395
|
https://f1000research.com/articles/11-1394/v1
|
28 Nov 22
|
{
"type": "Study Protocol",
"title": "Dynamic geographical accessibility assessments to improve health equity: protocol for a test case in Cali, Colombia",
"authors": [
"Luis Gabriel Cuervo",
"Ciro Jaramillo",
"Daniel Cuervo",
"Eliana Martínez-Herrera",
"Janet Hatcher-Roberts",
"Luis Fernando Pinilla",
"María Olga Bula",
"Lyda Osorio",
"Pablo Zapata",
"Felipe Piquero Villegas",
"Maria Beatriz Ospina",
"Carmen Juliana Villamizar",
"Ciro Jaramillo",
"Daniel Cuervo",
"Eliana Martínez-Herrera",
"Janet Hatcher-Roberts",
"Luis Fernando Pinilla",
"María Olga Bula",
"Lyda Osorio",
"Pablo Zapata",
"Felipe Piquero Villegas",
"Maria Beatriz Ospina",
"Carmen Juliana Villamizar"
],
"abstract": "This protocol proposes an approach to assessing the place of residence as a spatial determinant of health in cities where traffic congestion might impact health services accessibility. The study provides dynamic travel times presenting data in ways that help shape decisions and spur action by diverse stakeholders and sectors.\n\nEquity assessments in geographical accessibility to health services typically rely on static metrics, such as distance or average travel times. This new approach uses dynamic spatial accessibility measures providing travel times from the place of residence to the health service with the shortest journey time. It will show the interplay between traffic congestion, accessibility, and health equity and should be used to inform urban and health services monitoring and planning.\n\nAvailable digitised data enable efficient and accurate accessibility measurements for urban areas using publicly available sources and provide disaggregated sociodemographic information and an equity perspective.\n\nTest cases are done for urgent and frequent care (i.e., repeated ambulatory care). Situational analyses will be done with cross-sectional urban assessments; estimated potential improvements will be made for one or two new services, and findings will inform recommendations and future studies.\n\nThis study will use visualisations and descriptive statistics to allow non-specialized stakeholders to understand the effects of accessibility on populations and health equity. This includes “time-to-destination” metrics or the proportion of the people that can reach a service by car within a given travel time threshold from the place of residence.\n\nThe study is part of the AMORE Collaborative Project, in which a diverse group of stakeholders seeks to address equity for accessibility to essential health services, including health service users and providers, authorities, and community members, including academia.",
"keywords": [
"Health services accessibility",
"City planning",
"Urban health",
"Health inequality monitoring",
"Spatial Analysis",
"Residence characteristics"
],
"content": "Introduction\n\nEquitable accessibility is central to the United Nations Sustainable Development Goals and targets like universal health coverage and quality of care.1–5 A common definition of accessibility is the relative ease (travel time by car) by which a destination (health service) can be reached from a given location (residence).6–8 Equity assessments in geographical accessibility to health services typically rely on static metrics, such as distance or average travel times.9–11\n\nMeasuring equitable accessibility has several challenges. Accessibility studies assess distance or the shortest average travel time to the nearest facility; they seldom assess equity and are typically geared towards field experts. 12–14 These studies usually explore broad service categories without focusing on specific services people might need. They are lengthy, costly, and rarely address the dynamic temporospatial nature of accessibility, such as its links to traffic congestion. 6,15,16\n\nReliable data on equity of accessibility to urban health services has been elusive for most cities due to limitations in sampling techniques, extrapolations, and the use of complex methods to capture temporospatial variations associated with traffic congestion. Stakeholders, including urban and health service planners, have relied on indirect fixed assessments that fail to address the impact of traffic congestion on equity.6,9,15,17\n\nThese challenges were understandable because assessments were cumbersome and required detailed origin-destination studies with small samples from home surveys, traffic corridor speed cameras, or extrapolations from average traffic in selected corridors, with limited intersectoral and multistakeholder participation.6,16,18–26 Results would turn irrelevant given the rapid changes in conditions, including traffic congestion, populations, or infrastructure.27\n\nTravel times affect geographic accessibility and the quality of care.1,28,29 Poor accessibility can lead the most socially disadvantaged populations to pay the highest share to reach health services, an aberration of social justice known as the “inverse care law.” Lengthy travel times hurt people; they are detrimental to health, well-being, and family finances.28,30–35 Measuring travel times might reveal problems hiding in plain sight. Addressing accessibility might help people unable to choose a better place of residence overcome structural barriers to health.36\n\nTravel time assessments have been widely available for commodities and commerce and powered consumer apps. These developments have yet to translate into a systematic integration of dynamic equity assessments into urban and health services planning or public sector debates about land use and how to put health services within reach of the broadest population possible.\n\nMeasurements have proven difficult, and this project explores a new approach to making measurements feasible, scalable, and adaptable to urban sprawl and lengthening journeys. This new line of research explores if market forces and land use plans achieve service accessibility and if this holds for populations in situations of vulnerability.9,12,29\n\n\nThe need for this study\n\nThis proposal spurs the scaling up and replicating of accessibility analyses to health services in urban centers while promoting accessibility indicators based on dynamic travel times. The research demystifies the use of big data and analytics that reveal the needs of citizens, including the most vulnerable.37–42 The project will lay the basis for subsequent studies that assess the value and use of dynamic accessibility and equity assessments in urban and health services planning.\n\nThis project explores a new approach to making such measurements feasible, scalable, and adaptable to urban sprawl and long journeys. This new line of research examines whether market forces and land use planning achieve services’ accessibility and if this holds for populations in situations of vulnerability.29,43\n\nUsing reliable data that is systematically updated and publicly available could be a game-changer.6,37,44,45 This study tests a new approach for assessing dynamic accessibility to health services, providing an equity perspective and using digital data sources. 9,44,46\n\nUsing data readily available in the public domain allows these assessments to be completed in a shorter time and with a lower budget. When combined, the growing millions of measurements of travel times (big data) passively collected by mobile apps, the digitalized georeferenced sociodemographic data from the census, and the geolocation of health services, provide a dynamic assessment of accessibility that accounts for temporospatial variations related to traffic congestion.6,46,47 Big data provides millions of measurements that allow identifying unexpected correlations with a level of detail and accuracy that surveys and inferences cannot match.45\n\nThis study aims to overcome the limitations of regular accessibility assessments by prioritizing dynamic travel times and adopting recommended knowledge production and use practices. The following section details some key features and good practices that contribute to addressing present challenges:\n\n• Multistakeholder engagement: a diverse intersectoral team of stakeholders contributes to the AMORE Project throughout the research process, and their inputs also informed the AMORE Platform conceptualization and development.48–51 Contributors to the AMORE Project Collaborative Group represent the government, community, health service providers, and end users (consumers) who may directly or indirectly shape decisions, policies, plans, and programs.48,52–54,55\n\n• Measurement of dynamic travel times using “time to destination” is a universal and comparable metric used by urban dwellers and users of navigation and travel apps.44\n\n• Digitization and datafication by using anonymized publicly available georeferenced data of housing, people, and services, including disaggregated sociodemographic characteristics.6,27,37\n\n• Using analytics and modelling to obtain reasonable estimates and maintain efficiencies and affordability while still delivering valid and reliable forecasts.\n\n• Disaggregating sociodemographic data to deliver an equity analysis of accessibility.56–58\n\n• Scalability and replicability using sources increasingly available to low- medium, and high-income settings. The approach can be scaled, adapted, and replicated to other locations, transportation means, services, or sectors.\n\nSubsequent research will explore if revealing territorial inequities in urban and health services planning could catalyze intersectoral responses.30,59–63 Intersectoral collaborations rarely occur naturally and are challenged by the lack of consensus on issues and metrics. Using metrics and methods that all parties understand and facilitate direct communication could contribute to intersectoral action; assessing this will require additional research and is the subject of a separate proposal.9,60,64–68\n\n\nObjectives\n\nTo assess dynamic accessibility assessments for selected healthcare services in urban Cali, Colombia, and predict the maximum improvements possible if new services were added.\n\n\n\n• To assess the temporospatial characteristics of equity and accessibility to hemodialysis, radiation therapy (radiotherapy), and tertiary care emergency services when traveling by car in urban Cali, Colombia.\n\n• To provide dynamic assessments based on selected (arbitrary) travel time thresholds.\n\n• To assess if populations in a situation of vulnerability needing hemodialysis, radiotherapy, and tertiary care emergency services will likely incur longer journeys when traveling by car in urban Cali, Colombia.\n\n• To identify common variations of dynamic accessibility at two moments of the COVID-19 pandemic from an equity perspective.\n\n• Assess the magnitude of absolute and relative accessibility variations attributed to traffic congestion.\n\n• To estimate potential improvement for accessibility gained by expanding services.\n\nBox 1 provides a plain language summary of the project. The Extended data contains the goals of the AMORE project and previous versions of the protocol.69,70,71\n\nWhat is already known on this topic – dynamic travel times are not available for most cities, including Cali, and are not integrated into urban and health service planning; dynamic geospatial analyses reveal the effects of traffic congestion on health equity and accessibility to health services, a determinant of health.\n\nWhat this study adds – it will provide estimates of accessibility with an equity perspective using simple methods and metrics that concerned stakeholders might find familiar. This will test if dynamic accessibility assessments can be done with existing data. The study adds an approach to analyzing dynamic geographic accessibility by tapping into hundreds of thousands or millions of observations to analyze, predict, improve geographic accessibility to health services, and identify new correlations.\n\nHow this study might affect research, practice, or policy – This study will provide a new metric and data source to address inequities aggravated by poor accessibility offering new perspectives on land use and the expansion of health services. The study prioritizes travel times over distance, accounting for the temporospatial variations caused by traffic congestion. Subsequent examinations can explore stakeholders' valuing of the data and their communication of the methods and findings with peers and counterparts.\n\n\nProtocol\n\nThis health services quality improvement protocol will use anonymized coded secondary data sources from publicly available open records and will not include human subjects’ research.\n\nThis cross-sectional study will use a research design of GIS modelling applied to case studies based on analyses of publicly available secondary data. This study will conduct paired cross-sectional assessments comparing equity in health services accessibility from the 6th to the 12th of July 2020 and from the 23rd to the 29th of November 2020.\n\nReporting of study results will follow the STROBE Guideline for cross-sectional observational studies and incorporate elements from other guidelines, such as those on equity assessments (CONSORT-E and PRISMA-E equity extensions), public health and policy interventions (TIDieR-PHP), reporting of analytical models (e.g., SPIRIT-AI extension), and multistakeholder engagement with patient and public participation in research (GRIPP2).57,72–74\n\nThe study will be a proof-of-concept for implementation in Cali (estimated 2,258 million in 2020), the third largest and most populous city in Colombia and the dominant urban center of Colombia’s southwest and pacific regions (approx. 564 km2). The study includes the entire urban population. Nearly half of Cali’s population lives in low-income housing, 41% in medium income, and 9% in high-income housing. About 84% of the population identifies as white descent, and 14% identify as afro-descendent, with a small proportion identifying as Indigenous or Rrom.78–80\n\nThe COVID-19 pandemic severely impacted the local economy. By January 2021, unemployment rates in Cali rose to 23.2% for women and 14.6% for men, a one-year increase of 8.1% and 3.1%, respectively. The situation was worse for the youth, with an estimated 52% of women and 47.2% of men dependent on the informal economy. One in five people was unemployed, and unemployment rates were substantially higher for those living in lower socioeconomic areas. Cali absorbed 139,000 migrants from Venezuela over the past five years, with more than 25,000 in 2020.79,80\n\nFor the reports, contextual data will be obtained to provide an overview of the use and demand of services. Sources include reports and platforms such as the “Cuentas de Alto Costo.”82–84\n\nIn preparatory dialogues with contributors, we learned about plans to transform Cali into a Special District with its twenty-two communes converted into six to eight minor districts to be led by minor district mayors.85 This new political and administrative layout might raise interest in this topic as new authorities might want to discuss accessibility and equity issues with their constituents and in power-brokering negotiations, noting the equity implications of the concentration of health services in a few sectors of the city.\n\nThe study will use anonymized, aggregated data from the following data sources:\n\n• Microdata of Colombia’s National Census for Cali 2018 will be downloaded from the official public website of the National Department of Statistics– DANE.86 This will provide sociodemographic data of the populations at the block level for the entire city. The census population had a 28.1% adjustment estimated for 2020 to account for intercensal growth, under-registration, and migration.78,79,81,87\n\n• The city’s transportation analysis areas (TAZ) and census administrative sectorization for urban Cali will be obtained from the IDESC portal.88 This data allows linking TAZs with city blocks. TAZs are adequate to estimate travel times and less detailed than blocks, thus reducing the number of travel time measurements and adding anonymity to the population.\n\n• Approved health services relevant to the chosen scenarios, will be obtained from the National Special Registry of health services providers – REPS from the Ministry of Health and Social Protection. The services geolocation will be verified with Google Maps. Approved services were checked in June and October 2020 and January 2021, finding they remained unchanged. This protocol will assess accessibility to the entire city’s fourteen tertiary care hospitals with emergency services (REPS Code “Alta complejidad” + 501); eleven hemodialysis units totaling 370 chairs (REPS code 733); five radiotherapy services (REPS code 711).\n\n• Google’s Distance Matrix API provides big data measurements of travel times from the origin (TAZ for the residence) to the destination (TAZ of the health service). It allows the identification of travel time changes during the assessed weeks.\n\nSecondary data will be integrated into the AMORE Platform, a web-based digital platform developed with inputs and feedback from stakeholders and piloted by the AMORE Project.89–91 The Platform is hosted by IQuartil SAS. See https://www.iquartil.net/proyectoAMORE.\n\nThe AMORE Platform was developed and tested following a design-thinking approach between June and August 2020.49,92–95 The final version was completed in February 2022. The digital web-based platform was developed for this project by the principal investigator with input from experts in data science, public health, logistics, and mobility and a wide range of stakeholders (A description of the development and piloting phases of the AMORE Platform can be provided).\n\nFigure 1, Figure 2, and Figure 3 display examples of the AMORE Platform’s interface or “front-end” panels (presentation layers) with its zoomable choropleth maps and graphics that integrate multiple layers of data. Filters activated by tapping on the graphs act on sociodemographic variables, travel times, and health services to offer a descriptive analysis. The front-end has been developed with Microsoft's Power BI™ (v. 2.102.683.0). The back end (data access layer) is written in Python (v. 3.9.10)™ open-source software from the Python Software Foundation – PSF and in the Konstanz Information Miner – KNIME (v 4.5.1), a free and open-source data analytics, reporting, and integration platform.\n\nNorth to the right and west at the top. Source: AMORE Platform. ©Mapbox © OpenStreetMap\n\nSource: AMORE Platform. ©Mapbox\n\nSource: AMORE Platform. ©Mapbox\n\nReports will describe the people and percentages of the entire population able to reach services within a set threshold with peak and free-flow traffic conditions for each scenario. The variations in these accessibility figures will be disaggregated by sociodemographic characteristics such as sex, ethnicity, the socioeconomic stratum of housing, maximum education attainment, and marital status. These reports will contrast the statistics for peak and free-flow traffic conditions. These reports will use an arbitrary 15-minute threshold for accessibility by car to tertiary care emergencies and 20-minutes for hemodialysis and radiotherapy. Colombia’s census provides a binary sex classification (male-female) based on self-reporting.86,96\n\nGraphs will be used to present variations in accessibility as traffic congestion increases for different travel time intervals (e.g., 10-minute intervals vs. accessibility for each socioeconomic stratum), as shown in Figure 4. The contrast will be drawn between results obtained for July and November 2020. Reports will include the location(s) maximizing accessibility if one or two new services are added, contrasting predicted accessibility vs. measured accessibility for July and November 2020, and the recommended services locations. For an example, see Figure 3. All estimates in this test case use travel by car. Reports will include visualizations from the AMORE Platform, tables, and simple graphs with descriptive statistics.\n\nData and images for analyses will be obtained from the AMORE Platform and presented using descriptive statistics for absolute figures (people) and relative (percentage of population), as shown in Figure 2 and Figure 3.\n\nThe use of relatable and commonly used metrics (i.e., time to destination), descriptive statistics (percentage of a population that can reach the services within a travel time threshold), visualizations, and simple graphs (e.g., Figure 2, Figure 3, Figure 4) and maps (e.g., Figure 1) are chosen to allow non-specialized stakeholders to understand the effects of accessibility on populations and health equity.\n\nThe study will deliver (1) situational analyses of accessibility to a selection of urgent or frequent health care services scenarios in urban Cali, Colombia, and (2) predictions of potential improvements to the accessibility of adding services under changing assumptions.\n\nArbitrary travel-time points will be used (15 minutes for urgent care; 20 minutes for frequent care services); we found no standards for travel time thresholds.\n\nThe situational analyses of accessibility will consider the following study scenarios:\n\n1. Urgent care, assessing travel times to the health emergency department with the shortest journey by car, among the 14 hospitals with tertiary care emergency departments.\n\n2. Frequent care, assessing travel times to ambulatory services that require regular use. The analyses will investigate the shortest journey to five radiation therapy services and eleven hemodialysis units.\n\nFor these case studies, the project will deliver a:\n\n• Situational analysis uses descriptive and diagnostic analytics to assess accessibility under traffic conditions. Choropleth maps mark the boundaries of travel times Figure 1. The blocks building the map represent Traffic Analysis Zones (TAZ), and their height in the 3D choropleth map represents population density. By pointing to a TAZ, identification, population, and travel time to the nearest facility are displayed, and the sociodemographic characteristics of the people are presented in a dashboard (Figure 2). The dashboard also includes a choropleth map with the density of the population being analyzed.\n\nOptimization analysis using predictive and prescriptive analytics for modelling. Using heuristic techniques, the research will predict accessibility with different service schedules or when adding up to two new services in locations that maximize accessibility. Case studies will focus on hemodialysis and radiotherapy, which are used to treat high-cost conditions and must be accessed repeatedly for prolonged periods. For example, hemodialysis usually requires 3-5 weekly sessions, and radiotherapy may require daily sessions for weeks. Predicted accessibility with new services will be compared with measured accessibility (Figure 3).\n\nBeginning on 12th June 12 2020, interviews were conducted with key informants, local authorities, and experts to inform the project, assess feasibility, and develop a protocol. They provided verbal consent to participate. These interviews offered contextual insights and ideas for the AMORE Platform to address the needs of data users and stakeholders. Discussions helped identify contributors and provided valuable contextual information. They also revealed how stakeholders approached health equity and accessibility and the relationship to urban and health services planning and land use. Stakeholders offered insights into the elements and processes of urban and health services planning, public policy, and advocacy.\n\nInterviewees included:\n\n• Members of the SIGELO Project on vulnerability, accessibility, and logistics in the context of the COVID-19 pandemic, Universidad del Valle\n\n• Health equity and public health experts at the Bruyère Institute, University of Ottawa\n\n• Contributors to Cali’s Administrative Department of Municipal Planning (DAPM)\n\n• Advisors and staff working with Cali’s local government, including the secretariats of Health, Mobility, Urban planning, and Emergency response and preparedness.\n\n• Data Science for All Team33 and IQuartil SAS analysts.\n\n• Former local government and education authorities\n\n• Urban observatories, urbanists, and networks on urbanism, mobility, and public health.\n\n• Innovators and advisors working with health services and systems\n\n• Service providers, including managers and science advisors\n\n• Health services and accessibility data users\n\n• Doctoral and professional networks\n\n• Designers, graphic and science communications professionals, and artists\n\n• Researchers and research sponsors.\n\nOverall, 28 meetings were held with key informants and stakeholders between July 2020 and March 2022, when the advanced prototype of the AMORE Platform was completed. Like every doctoral thesis, this project is subject of yearly follow-up reviews by the Commission of the Doctoral Program on Research Methodology for Biomedical Research and Public Health of the Universitat Autònoma de Barcelona, since October 2020.\n\nDuring the preparatory phase, the project was also debated in international fora such as the Global Health Learning Network of the University of Ottawa, The 4th Urban Forum “Lima Cómo Vamos,” the CEDEUS-REDEUSLAC II International Symposium of Doctoral Candidates on Urban Development and Sustainability for Latin America, and the Caribbean (Chile), and with urban observatories (Cali, Bucaramanga).89,98,99\n\nThese interviews shaped the AMORE project and platform. The objectives and platform were discussed from a theoretical perspective. Once the prototypes of the AMORE Platform became available, tests and demonstrations were made as part of the validation.\n\nData downloads and sources were stored in a dedicated repository using CSV formats to adhere to data sharing and reuse good practices. They will be made public with the publication of relevant research reports. Similarly, the AMORE Platform hosted by IQuartil SAS is made accessible with the completion of non-disclosure agreements. We expect to make platform sections publicly available as relevant results are published.100\n\nThe fidelity of the AMORE Platform is based on data validation and verification exercises, comparing the findings from the AMORE Platform using the two data downloads and the two development teams.\n\nThe results of the platform will likely be optimistic for several reasons. For example, people do not always travel to the service with the shortest journey for known (e.g., lack of coverage from the insurance in the institution) and unexpected reasons (familiarity, poor navigation aids, reputation). The potential for improved accessibility would be accurate if all people were entitled to access those services.\n\nThe census includes respondent-reported data that is subject to interpretation. For example, variables like disability and health status are self-reported, and the question is unspecific.\n\nRespondents may not find a suitable response option. For example, ethnicity has no category for Caucasian or mestizo populations representing a substantial part of the population. People with mixed backgrounds may find no suitable option to represent them.\n\nThe census is still well suited for this study: the data has been digitized, and sociodemographic data are linked with the residential block. The place of residence is a common starting point for people undergoing hemodialysis or radiotherapy, children, the elderly, and those not engaged in formal employment.\n\nMobile phone data is impractical because it cannot be accurately tied to reliable sociodemographic data; coverage varies among the population and excludes those unregistered as users or without a phone. It also has technical limitations.101\n\nAccessibility and spatial equity have been studied in Cali by the Research Group on Transport, Transit and Roads (GITTV) of the Faculty of Engineering of the Universidad del Valle. Members of this group contributed to the validation of the AMORE Platform, and the preliminary findings of the AMORE Platform are consistent with those of the GITTV and other authors.102–107\n\nThis observational study addresses the impact of mobility on health equity without researching human subjects and by integrating anonymized coded secondary data obtained from openly available records.\n\nThe study does not involve human subjects’ research. The AMORE Platform and dynamic geospatial analyses expose social justice issues and potential solutions of benefit to society by enabling informed decisions relevant to policies, plans, and procedures for improving health equity. This data can also predict or monitor changes in urban accessibility. The data used is anonymized and publicly available. Under Colombian law, this component fits the definition of research without risk, as described in Resolution 008430-1993 of the Ministry of Health.108 This was corroborated on 25th July 2022, by the Research Ethics Committee of the School of Engineering of the Universidad del Valle, which declared the project “without risk” per Colombian law (Ref: CEIFI 010-2022). The project was cleared on September 16, 2022 by the Commission on Ethics in Animal and Human Experimentation (CEEAH), and the Vice-Rector for Research, Universitat Autònoma de Barcelona (Ref: CEEAH-6100) on September 20, 2022.\n\nThe study can challenge current thinking with data and disrupt traditional approaches to land use and health services planning that may perpetuate pervasive inequalities that could fuel social strife and corruption.102–105,109–115\n\nThe ethical approach of this study follows the broader principles and considerations of public health ethics and health systems ethics; it generates population data valuable to address inequity and social injustice, is helpful for accountability and is relevant to intersectoral action.116,117 The need for further guidance on these issues remains a challenge for cross-sectoral collaboration. It is part of the ongoing discussions on stakeholder engagement in global health.73,117\n\nAccessibility is a determinant of health on the supply side of health equity.119 Useful, valid equity assessments in accessibility matter to health systems and social justice. Having action-oriented data to challenge established thinking might contribute to various SDGs, such as improving good health and well-being (SDG 3), reducing inequalities (SDG10), having sustainable cities and communities (SDG11), improving infrastructure (SDG 9), and facilitating partnerships to achieve the SDGs (SDG17).3,48,52,60,116\n\nThese ideals are synergic with other urban development and planning initiatives on a human scale: Smart City, the 15-minute City, the Caring City, and the Committed City. Having data is the first step for technology to serve the needs of urban dwellers and inform public policy regularly or when facing health emergencies and pervasive inequities.52,120–122\n\nThe risks of this study are especially those associated with data science and artificial intelligence. Travel time data providers do not disclose the algorithms they use. These are empirically known to be accurate and are expected to be more accurate for the areas most travelled by people with network-engaged smartphones and sites where infrastructure and conditions remain stable; accuracy may vary across the city.27,123,124\n\nThere is a risk of errors in programming or labelling data; to control this risk, the validity of the data was tested, repeatedly reviewed, and found sensible by experts and local contributors. The chance that inaccuracies result from clustering traffic and times is low and is unlikely to change the overall picture the project analyzes.\n\nThe project reveals accessibility levels for populations and sectors of the city. It uses heuristic analysis to identify areas in which new services would significantly impact accessibility. These areas, like traffic conditions, may evolve. However, the data provided to inform decisions gives an overall idea of the locations that would optimize accessibility. It is unlikely that conditions and populations would change fast enough to make those broad estimations suddenly irrelevant. Regular updating of the AMORE Platform would allow for assessing these variations and would be the subject of further studies after this test case. Additional factors influence the use of a service, including insurance coverage entitlements. Exploring this would require different data layers and funding that exceeds the purpose and scope of the test case and would be a matter of subsequent implementation. There is an inherent risk of revealing social injustices or inequities that can lead to discomfort, alienation, or corrective action.\n\nAs part of the project, communication tools such as animations, infographics, videos, summaries, and logos were developed.\n\nThe research team seeks to publish its reports in open-access impactful journals and present them to diverse audiences, including observatories, networks, and intersectoral groups.\n\nThe planned reports include:\n\n• Accessibility of health services for the urban population of Cali, 2020: urgent care and frequent care\n\n• Predicted accessibility of health services for the urban population of Cali with the addition of health services in areas that would maximize accessibility (urgent care and frequent care scenarios) or changes in service schedules (frequent care)\n\n• Editorials and methodological articles.\n\nData extraction for research reports was initiated in January 2022 and is underway.",
"appendix": "Data availability\n\nThe Data Sources section provides a list of publicly available data sources that will be used in this project. Relevant interfaces for each case study will be published with research results at https://www.iquartil.net/proyectoAMORE/.\n\nFigshare: Theory of Change for AMORE Project Protocol 2022 https://doi.org/10.6084/m9.figshare.20485404.v2. 69\n\nThis project contains the following extended data:\n\n- The 2022 goals of the AMORE project and how they will be achieved\n\nOpen Science Framework: Dynamic geographical accessibility assessments to improve health equity: protocol for a test case in Cali, Colombia. https://doi.org/10.17605/OSF.IO/ETPMA. 70\n\nThis project contains the following extended data:\n\n- 20220726 Protocol 5.5 AMORE Project_Approved CEII-UdelV Assembled.pdf\n\n- 20220726 Protocol 5.6.1 AMORE Project_Approved CEIIFI - CEEAH.pdf\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 following people contributed to the brainstorming preceding the writing of the protocol and approved this acknowledgment: Peter Tugwell and Vivian Welch (Campbell Collaboration and Cochrane Equity Group); Myriam Rosero and María Fernanda Tobar Blandón (Universidad del Valle); Alberto Concha-Eastman (Senior Advisor to the Secretary of Public Health of Cali); David Paredes Zapata (Hospital Clinic, Transplant and Organ Donation Section, Barcelona, Spain); Fredy Enrique Ágredo Lemus (Ph.D. student in Health, Universidad del Valle and advisor to the Secretary of Health of Cali); Crhistian García (Grupo de Aseguramiento y Desarrollo de Servicios e la Secretaría de Salud de Cali); Fernando R. Martínez A. (Departamento Administrativo de Planeación Municipal); and María Fernanda Merino. As a tutor for the Doctoral program at the Universitat Autònoma de Barcelona, Dr Xavier Bonfill I Cosp has provided guidance with the academic program and reports. We are grateful to contributors working for the Escuela de Escuela de Salud Pública and the Departamento de Administración y Organizaciones of the Universidad del Valle, the Secretaría de Movilidad, and the Centro Regulador de Urgencias y Emergencias del Valle.\n\nWe thank artist Adriana Cabal Aulestia for authorizing Cali-themed paintings to illustrate the presentations and graphic designers Ingrid Faber and Carlos A. Faber for preparing the infographics. Ingrid Faber was commissioned to develop the logo and animation.\n\nWe acknowledge the contributions of the Team33/DS4A members to developing the prototype of the AMORE Platform: Catherine E. Cabrera, Daniel Cuervo, Darío Mogollón, Juan P. Morales, Santiago A. Tovar, Stephanie A. Rojas, Juan G. Betancourt, Rafael E. Ropero.\n\nStephen Volante and Cristina Cuervo provided editing assistance for early versions of the protocol.\n\nAn earlier version of this article can be found on SSRN (doi: http://dx.doi.org/10.2139/ssrn.4175407).\n\n\nReferences\n\nFrenk J:The concept and measurement of accessibility.White K, editor. Health Services Research: an anthology. Washington DC:Pan American Health Organization/World Health Organization; 1992; p. 8–42855.Reference Source\n\nUnited Nations: About the Sustainable Development Goals. United Nations Sustainable Development; [cited 2020 Aug 22]. Reference Source\n\n53rd Directing Council: 66th Session of the Regional Committee of WHO for the Americas. Strategy for Universal Access to Health and Universal Health Coverage. Pan American Health Organization/World Health Organization;2014.Reference Source\n\n57th Directing Council of the Pan American Health Organization: 71st Session of the Regional Committee of WHO for the Americas. Strategy and Plan of Action to Improve Quality of Care in Health Service Delivery 2020-2025/Estrategia y plan de acción para mejorar la calidad de la atención en la prestación de servicios de salud 2020-2025. PAHO/WHO;2019.Reference Source\n\nCommission on Social Determinants of Health:Closing the gap in a generation: health equity through action on the social determinants of health: final report of the commission on social determinants of health. Combler Fossé En Une Génér Instaur Léquité En Santé En Agissant Sur Déterm Sociaux Santé Rapp Final Comm Déterm Sociaux Santé.2008 [cited 2022 Mar 19]; 247. Reference Source\n\nMoya-Gómez B, Salas-Olmedo MH, García-Palomares JC, et al.: Dynamic Accessibility using Big Data: The Role of the Changing Conditions of Network Congestion and Destination Attractiveness. Netw. Spat. Econ. 2018 Jun 1 [cited 2021 Jan 23]; 18(2): 273–290. Publisher Full Text\n\nLuo W, Wang F: Measures of Spatial Accessibility to Health Care in a GIS Environment: Synthesis and a Case Study in the Chicago Region. Environ Plan B Plan Des. 2003 Dec [cited 2020 May 10]; 30(6): 865–884. Publisher Full Text\n\nBureau of Transportation Statistics: Transportation Statistics Annual Report1997: mobility and access. US Department of Transportation;1997; 331. Reference Sourcex\n\nCuervo LG, Martínez-Herrera E, Cuervo D, et al.: Improving equity using dynamic geographic accessibility data for urban health services planning. Gac. Sanit. [cited 2022 Jun 11]; 36: 497–499. (ePublication ahead of print). PubMed Abstract | Publisher Full Text Reference Source\n\nNeutens T: Accessibility, equity and health care: review and research directions for transport geographers. J. Transp. Geogr. 2015 Feb 1 [cited 2022 Jan 20]; 43: 14–27. Publisher Full Text Reference Source\n\nKong X, Liu Y, Wang Y, et al.: Investigating Public Facility Characteristics from a Spatial Interaction Perspective: A Case Study of Beijing Hospitals Using Taxi Data. ISPRS Int J Geo-Inf. 2017 Feb [cited 2022 Jan 20]; 6(2): 38. Publisher Full Text Reference Source\n\nHiggins C, Palm M, DeJohn A, et al.: Calculating place-based transit accessibility: Methods, tools and algorithmic dependence. J. Transp. Land Use. 2022 Feb 1 [cited 2022 Feb 22]; 15(1): 95–116. Publisher Full Text Reference Source\n\nCarrasco-Escobar G, Manrique E, Tello-Lizarraga K, et al.: Travel Time to Health Facilities as a Marker of Geographical Accessibility Across Heterogeneous Land Coverage in Peru. Front. Public Health. 2020 [cited 2022 Apr 4]; 8. PubMed Abstract | Publisher Full Text\n\nBuzai GD, Santana Juárez MV: Condicionantes Socioespaciales de la Salud (CSS): bases y alcance conceptual. Annu Div Geogr. 2018; 2018(12): 15. Reference Source\n\nMalhotra S, White H; The Campbell Collaboration et al.: Evidence and gap map-studies of the effectiveness of transport sector intervention in low and middle-income countries. Centre for Excellence and Development Impact and Learning (CEDIL). 2022 Jun [cited 2022 Jul 11]. Reference Source\n\nAl-Taiar A, Clark A, Longenecker JC, et al.: Physical accessibility and utilization of health services in Yemen. Int. J. Health Geogr. 2010 Jul 21 [cited 2022 Jul 11]; 9(1): 38. PubMed Abstract | Publisher Full Text\n\nKajalić J, Čelar N, Stanković S: Travel Time Estimation on Urban Street Segment. Promet - TrafficTransportation. 2018 Feb 23 [cited 2022 Apr 20]; 30(1): 115–120. Publisher Full Text Reference Source\n\nHernández Gene FJ, Garnica BR: Accesibilidad física de la población a servicios de salud pública en San Pelayo y Cereté, Córdoba, Colombia, año 2015. Perspect Geográfica. 2017 Dec 19 [cited 2020 May 31]; 22(2). Publisher Full Text Reference Source\n\nGuagliardo MF: Spatial accessibility of primary care: concepts, methods and challenges. Int. J. Health Geogr. 2004 Feb 26 [cited 2020 May 7]; 3: 3. PubMed Abstract | Publisher Full Text Reference Source\n\nPáez A, Scott DM, Morency C: Measuring accessibility: positive and normative implementations of various accessibility indicators. J. Transp. Geogr. 2012 Nov [cited 2020 Jul 9]; 25: 141–153. Publisher Full Text Reference Source\n\nCurrie G: Quantifying spatial gaps in public transport supply based on social needs. J. Transp. Geogr. 2010 Jan 1 [cited 2020 Jun 11]; 18(1): 31–41. Publisher Full Text Reference Source\n\nLovett A, Haynes R, Sünnenberg G, et al.: Car travel time and accessibility by bus to general practitioner services: a study using patient registers and GIS. Soc Sci Med. 2002 Jul 1 [cited 2020 May 20]; 55(1): 97–111.PubMed Abstract | Publisher Full Text Reference Source\n\nRosero-Bixby L: Spatial access to health care in Costa Rica and its equity: a GIS-based study. Soc Sci Med. 2004 Apr 1 [cited 2020 May 20]; 58(7): 1271–1284. Publisher Full Text Reference Source\n\nTeach SJ, Guagliardo MF, Crain EF, et al.: Spatial Accessibility of Primary Care Pediatric Services in an Urban Environment: Association With Asthma Management and Outcome. Pediatrics. 2006 Apr 1 [cited 2020 May 7]; 117(Supplement 2): S78–S85. Publisher Full Text Reference Source\n\nAccessMod 5|Modelling physical accessibility to health care:accessmod. [cited 2021 May 3].Reference Source\n\nBanke-Thomas A, Wong KLM, Collins L, et al.: An assessment of geographical access and factors influencing travel time to emergency obstetric care in the urban state of Lagos, Nigeria. Health Policy Plan. 2021 Nov 1 [cited 2022 Jun 17]; 36(9): 1384–1396. PubMed Abstract | Publisher Full Text\n\nMayer-Schönberger V, Cukier K: Big data: a revolution that will transform how we live, work, and think. Boston, Mass:Houghton Mifflin Harcourt; 2013; 242 p. (An Eamon Dolan book).\n\nAlam K, Mahal A: Economic impacts of health shocks on households in low and middle income countries: a review of the literature. Glob. Health. 2014 Apr 3 [cited 2022 Jan 8]; 10(1): 21. PubMed Abstract | Publisher Full Text\n\nFullman N, Yearwood J, Abay SM, et al.: Measuring performance on the Healthcare Access and Quality Index for 195 countries and territories and selected subnational locations: a systematic analysis from the Global Burden of Disease Study 2016. Lancet. 2018 Jun 2 [cited 2020 Nov 11]; 391(10136): 2236–2271. PubMed Abstract | Publisher Full Text Reference Source\n\nHart JT: The inverse care law. Lancet. 1971 Feb 27 [cited 2021 Mar 28]; 297(7696): 405–412. Publisher Full Text Reference Source\n\nWhitehead M: The concepts and principles of equity and health. Health Promot. Int. 1991 Sep 1 [cited 2021 Mar 28]; 6(3): 217–228. Publisher Full Text\n\nNambiar D, Mander H: Inverse care and the role of the state: the health of the urban poor. Bull. World Health Organ. 2017 Feb 1 [cited 2021 Mar 28]; 95(2): 152–153. PubMed Abstract | Publisher Full Text Reference Source\n\nCookson R, Doran T, Asaria M, et al.: The inverse care law re-examined: a global perspective. Lancet. 2021 Feb [cited 2021 Mar 28]; 397(10276): 828–838. PubMed Abstract | Publisher Full Text Reference Source\n\nFiscella K, Shin P: The Inverse Care Law: Implications for Healthcare of Vulnerable Populations. J Ambulatory Care Manage. 2005 Dec [cited 2021 Mar 28]; 28(4): 304–312. Publisher Full Text Reference Source\n\nOECD: Health for Everyone?: Social Inequalities in Health and Health Systems. OECD; 2019 [cited 2021 Feb 11]. (OECD Health Policy Studies). Reference Source\n\nPineo H: Healthy Urbanism: Designing and Planning Equitable, Sustainable and Inclusive Places. London:Palgrave Macmillan;2022. Publisher Full Text\n\nAshford LS: Demystifying Big Data for Demography and Global Health. Popul. Bull. 2022; 76(1): 34. Reference Source\n\nAcosta A: Smart Cities & Inequidad: Forbes República Dominicana.2021 Jul 13 [cited 2021 Jul 17]; 82(julio-agosto 2021): 12. Reference Source\n\nBoeing G, Higgs C, Liu S, et al.: Using open data and open-source software to develop spatial indicators of urban design and transport features for achieving healthy and sustainable cities. Lancet Glob. Health. 2022 Jun 1 [cited 2022 May 12]; 10(6): e907–e918. PubMed Abstract | Publisher Full Text Reference Source\n\nd’Obrenan H v d B, Huxley R: Measuring what matters: supporting cities in tackling climate and health challenges. Lancet Glob. Health. 2022 Jun 1 [cited 2022 May 12]; 10(6): e788–e789. PubMed Abstract | Publisher Full Text Reference Source\n\nGiles-Corti B, Moudon AV, Lowe M, et al.: Creating healthy and sustainable cities: what gets measured, gets done. Lancet Glob. Health. 2022 Jun 1 [cited 2022 May 12]; 10(6): e782–e785. PubMed Abstract | Publisher Full Text Reference Source\n\nEvidence Aid: Factors affecting patients’ ability to access healthcare: overview of systematic reviews. Evidence Aid. Evidence Aid. 2022 [cited 2022 Jun 16]. Reference Source\n\nMartin: The Sustainable Development Agenda. United Nations Sustainable Development;[cited 2020 Aug 22].Reference Source\n\nŚleszyński P, Olszewski P, Dybicz T, et al.: The ideal isochrone: Assessing the efficiency of transport systems. Res. Transp. Bus. Manag. 2022 Jan 19 [cited 2022 Jan 27]: 100779. Publisher Full Text Reference Source\n\nArmstrong K: Big data: a revolution that will transform how we live, work, and think. Inf. Commun. Soc. 2014 Nov 26 [cited 2022 Apr 27]; 17(10): 1300–1302. Publisher Full Text\n\nJin T, Cheng L, Wang K, et al.: Examining equity in accessibility to multi-tier healthcare services across different income households using estimated travel time. Transp. Policy. 2022 Jun 1 [cited 2022 Apr 7]; 121: 1–13. Publisher Full Text Reference Source\n\nBimpou K, Ferguson NS: Dynamic accessibility: Incorporating day-to-day travel time reliability into accessibility measurement. J. Transp. Geogr. 2020 Dec 1 [cited 2022 Apr 21]; 89: 102892. Publisher Full Text Reference Source\n\nAbimbola S: Beyond positive a priori bias: reframing community engagement in LMICs. Health Promot. Int. 2020 Jun 1 [cited 2021 Apr 3]; 35(3): 598–609. PubMed Abstract | Publisher Full Text\n\nAbookire S, Plover C, Frasso R, et al.: Health Design Thinking: An Innovative Approach in Public Health to Defining Problems and Finding Solutions. Front. Public Health. 2020 [cited 2022 Jul 18]; 8. PubMed Abstract | Publisher Full Text\n\nBazzano AN, Martin J, Hicks E, et al.: Human-centred design in global health: A scoping review of applications and contexts. PLoS One. 2017 Nov 1 [cited 2022 Jul 18]; 12(11): e0186744. PubMed Abstract | Publisher Full Text\n\nBrown T Design Thinking. 2008.\n\nComprender para transformar, entrevista a Oriol Nel·lo.2018 [cited 2020 Aug 17]. Reference Source\n\nJull J, Giles A, Graham ID: Community-based participatory research and integrated knowledge translation: advancing the co-creation of knowledge. Implement. Sci. 2017 Dec 19 [cited 2021 Mar 25]; 12(1): 150. PubMed Abstract | Publisher Full Text\n\nPapa E, Coppola P, Angiello G, et al.: The learning process of accessibility instrument developers: Testing the tools in planning practice. Transp Res Part Policy Pract. 2017 Oct [cited 2021 Jan 23]; 104: 108–120. Publisher Full Text Reference Source\n\nCyril S, Smith BJ, Possamai-Inesedy A, et al.: Exploring the role of community engagement in improving the health of disadvantaged populations: a systematic review. Glob. Health Action. 2015 Dec 1 [cited 2021 Apr 2]; 8(1): 29842. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPROGRESS-Plus|Cochrane Equity:[cited 2020 Mar 23]. Reference Source\n\nJull J, Graham ID, Kristjansson E, et al.: Taking an integrated knowledge translation approach in research to develop the CONSORT-Equity 2017 reporting guideline: an observational study. BMJ Open. 2019 Jul 1; 9(7): e026866. PubMed Abstract | Publisher Full Text Reference Source\n\nWelch TF, Mishra S: A measure of equity for public transit connectivity. J. Transp. Geogr. 2013 Dec [cited 2021 Mar 4]; 33: 29–41. Publisher Full Text Reference Source\n\nRedman S, Greenhalgh T, Adedokun L, et al.: Co-production of knowledge: the future. BMJ. 2021 Feb 16 [cited 2021 Apr 23]; 372: n434. Publisher Full Text Reference Source\n\nChircop A, Bassett R, Taylor E: Evidence on how to practice intersectoral collaboration for health equity: a scoping review. Crit. Public Health. 2015 Mar 15 [cited 2020 Oct 10]; 25(2): 178–191. Publisher Full Text\n\nOrganización Panamericana de la Salud, Organización Mundial de Salud: Intersectorialidad y equidad en salud en América Latina: una aproximación analítica. Washington, D.C.:2015; 34. Reference Source\n\nGeurs KT, van Wee B : Accessibility evaluation of land-use and transport strategies: review and research directions. J. Transp. Geogr. 2004 Jun [cited 2020 May 10]; 12(2): 127–140. Publisher Full Text Reference Source\n\nUnited Nations: Multi-stakeholder partnerships and voluntary commitments. Department of Economic and Social Affairs.2020 [cited 2020 Dec 12]. Reference Source\n\nWhitty CJM: What makes an academic paper useful for health policy?. BMC Med. 2015 Dec 17 [cited 2022 Mar 24]; 13(1): 301. PubMed Abstract | Publisher Full Text\n\nHussain S, Javadi D, Andrey J, et al.: Health intersectoralism in the Sustainable Development Goal era: from theory to practice. Glob. Health. 2020 Feb 20 [cited 2021 Mar 28]; 16(1): 15. PubMed Abstract | Publisher Full Text\n\nOrganización Panamericana de la Salud:2016 [cited 2020 Aug 11]; Hoja de Ruta para el Plan de Acción sobre la Salud en Todas las Políticas. OPS; Reference Source\n\nPublic Health InstituteRudolph L, Caplan J, et al.: Health in All Policies: Improving Health Through Intersectoral Collaboration. NAM Perspect. 2013 Sep 18 [cited 2020 Sep 11]; 3(9). Reference Source\n\nde Kadt E : Making health policy management intersectoral: Issues of information analysis and use in less developed countries. Soc Sci Med. 1989 Jan 1 [cited 2020 Oct 10]; 29(4): 503–514. PubMed Abstract | Publisher Full Text Reference Source\n\nCuervo LG, Villamizar CJ, Jaramillo C, et al.:Theory of Change for AMORE Project Protocol 2022. figshare. figshare. [Dataset]2022 [cited 2022 Aug 13]. Publisher Full Text\n\nCuervo L, Molina CJ, Cuervo D, et al.:Dynamic geographical accessibility assessments to improve health equity: protocol for a test case in Cali, Colombia. [Dataset].2022, November 11. Publisher Full Text\n\nCuervo LG, Cuervo D, Hatcher-Roberts J, et al.: AMORE Project: Integrated knowledge translation and geospatial analysis to improve travel times to health services (accessibility) and health equity in Cali, Colombia: a proof of concept using mixed-methods research 2021. Publisher Full Text\n\nPetkovic J, Riddle A, Akl EA, et al.: Protocol for the development of guidance for stakeholder engagement in health and healthcare guideline development and implementation. Syst. Rev. 2020 Dec [cited 2021 Jan 3]; 9(1): 21. PubMed Abstract | Publisher Full Text\n\nPinnock H, Barwick M, Carpenter CR, et al.: Standards for Reporting Implementation Studies (StaRI) Statement. BMJ. 2017 Mar 6 [cited 2020 Jul 6]; 356. Reference Source\n\nCampbell M, Katikireddi SV, Hoffmann T, et al.: TIDieR-PHP: a reporting guideline for population health and policy interventions. BMJ. 2018 May 16 [cited 2020 May 7]; 361. Publisher Full Text Reference Source\n\nRivera SC, Liu X, Chan AW, et al.: Guidelines for clinical trial protocols for interventions involving artificial intelligence: the SPIRIT-AI extension. Lancet Digit Health. 2020 Oct 1 [cited 2020 Oct 30]; 2(10): e549–e560. PubMed Abstract | Publisher Full Text Reference Source\n\nStaniszewska S, Brett J, Simera I, et al.: GRIPP2 reporting checklists: tools to improve reporting of patient and public involvement in research. BMJ. 2017 Aug 2 [cited 2021 Mar 24]; 358: j3453. Reference Source\n\nKpokiri EE, Chen E, Li J, et al.: Social Innovation For Health Research: Development of the SIFHR Checklist. PLoS Med. 2021 Sep 13 [cited 2021 Sep 29]; 18(9): e1003788. PubMed Abstract | Publisher Full Text\n\nDANE: Información técnica y omisión censal 2018, aspectos conceptuales y metodológicos.2019 [cited 2020 Sep 10]. Reference Source\n\nDANE: Sistema Estadístico Nacional - SEN. Información del DANE para la toma de decisiones regionales: Cali - Valle del Cauca. Colombia - Cali:DANE; 2021 Mar [cited 2021 Apr 24]; p. 223. (La información del DANE en la toma de decisiones de las ciudades capitales). Reference Source\n\nDirección de Censos y Demografía - DCD: Departamento Administrativo Nacional de Estadística - DANE. COLOMBIA - Censo Nacional de Población y Vivienda - CNPV - 2018. Bogotá:Departamento Administrativo Nacional de Estadística - DANE; 2020 Feb; p. 124. (Microdatos). Report No.: DANE-DCD-CNPV-2018. Reference Source\n\nDANE: Sistema Estadístico Nacional - SEN. Información del DANE para la toma de decisiones de las ciudades capitales: Cali - Valle del Cauca. Colombia - Cali:DANE; 2020 Jan [cited 2021 Apr 24]; p. 79. (La información del DANE en la toma de decisiones de las ciudades capitales). Reference Source\n\nGamboa O, Cotes M, Valdivieso J, et al.: Estimation of the Need for Radiation Therapy Services According to the Incidence of Cancer in Colombia to 2035. Adv. Radiat. Oncol. 2021 Nov 1 [cited 2022 Jul 14]; 6(6): 100771. Publisher Full Text Reference Source\n\nde Vries E , Buitrago G, Quitian H, et al.: Access to cancer care in Colombia, a middle-income country with universal health coverage. J. Cancer Policy. 2018 May 1 [cited 2022 Jul 14]; 15: 104–112. Publisher Full Text Reference Source\n\nCuentas de Alto Costo - Fondo Colombiano de Enfermedades de Alto Costo: HIGIA - Enfermedad Renal Crónica, Indicadores de Riesgo Demográfico. - Diálisis Adultos y Niños en Cali. Cuenta de Alto Costo;2022 [cited 2022 Jul 15].Reference Source\n\nCali Distrito Especial tendría seis localidades:[cited 2021 Mar 31]. Reference Source\n\nCenso Nacional de Población y Vivienda 2018:[cited 2020 Jul 23]. Reference Source\n\nGrupo Interagencial sobre Flujos Migratorios Mixtos: Página de GIFMM Colombia|R4V.2022 [cited 2022 Jul 20]. Reference Source\n\nUnión Temporal UT SDG-CNC: Encuesta de movilidad de hogares Cali 2015: Producto 3. Ámbito y zonificación. Steer Davies Gleave.2015 [cited 2020 May 30]. Reference Source\n\nProyecto AMORE: mejorando la equidad en la accesibilidad (tiempos de viaje) a los servicios de salud: Prueba de concepto en Cali, Colombia. Sesión 01 Sala B: Ciudad Saludable, Smart Cities y Recursos Críticos. Santiago, Chile:Centro de Desarrollo Urbano Sostenible - Chile; 2022 [cited 2022 May 27].Reference Source\n\nAMORE Project - to improve health equity by reducing the travel time to essential health services. Bethesda, MD, USA;2021 [cited 2021 Sep 23].Reference Source\n\nDS4A Colombia 2020/Grand Finale:2020 [cited 2020 Aug 16]. Reference Source\n\nHendricks S, Conrad N, Douglas TS, et al.: A modified stakeholder participation assessment framework for design thinking in health innovation. Healthcare. 2018 Sep 1 [cited 2021 Apr 2]; 6(3): 191–196. PubMed Abstract | Publisher Full Text Reference Source\n\nBrown T, Wyatt J: Design Thinking for Social Innovation. Dev Outreach. 2012 Oct 3 [cited 2021 Apr 2]; 12: 29–43. Publisher Full Text\n\nAngotti T, Irazábal C: Planning Latin American Cities: Dependencies and “Best Practices.”. Lat. Am. Perspect. 2017 Mar 1 [cited 2021 Apr 1]; 44(2): 4–17. Publisher Full Text\n\nZurita I: Revisiting Urban Planning in Latin America and the Caribbean.2009 [cited 2021 Apr 1]. Publisher Full Text\n\nHeidari S, Babor TF, De Castro P, et al.: Sex and Gender Equity in Research: rationale for the SAGER guidelines and recommended use. Res Integr Peer Rev. 2016 May 3 [cited 2020 Mar 31]; 1(1): 2. PubMed Abstract | Publisher Full Text\n\nCuervo LG, Martinez-Herrera E, Osorio L, et al.: Dynamic accessibility by car to tertiary care emergency services in Cali, Colombia, in 2020: cross-sectional equity analyses using travel time big data from a Google API. BMJ Open. 2022 Sep 1 [cited 2022 Sep 1]; 12(9): e062178. Publisher Full Text Reference Source\n\nProyecto AMORE: Uso de Análisis Geoespacial para acceso a la Salud|4o Foro “Ciudades Cómo Vamos”. Lima:2021 [cited 2022 Jul 16].Reference Source\n\nGlobal Health Learning Network- Seminar on Digital app technology to assess equity: Spatial analysis and equity for health services:Ottawa; 2022 [cited 2022 Jan 22]. vol. 4. (Global Health Learning Network Seminar Series). Reference Source\n\nAnderson JA, Eijkholt M, Illes J: Ethical reproducibility: towards transparent reporting in biomedical research. Nat. Methods. 2013 Sep [cited 2022 Jul 16]; 10(9): 843–845. Publisher Full Text Reference Source\n\nAyesha B, Jeewanthi B, Chitraranjan C, et al.: User Localization Based on Call Detail Records. arXiv. 2021 [cited 2022 Jul 20]. Reference Source\n\nJaramillo C, Lizárraga C, Grindlay AL: Spatial disparity in transport social needs and public transport provision in Santiago de Cali (Colombia). J. Transp. Geogr. 2012 Sep 1 [cited 2020 Jun 4]; 24: 340–357. Publisher Full Text Reference Source\n\nGrindlay AL, Jaramillo C, Lizárraga C: Spatial relationships between mobility opportunities and constraints of transport disadvantages: the case of Santiago de Cali, Colombia. Rome, Italy:2017 [cited 2021 Nov 1]; 119–129. Reference Source\n\nRodríguez Mariaca DA, Vivas Pachecho H, Pinzón MA, et al.: Accessibility to the Employment Centers in Cali Through the Integrated System of Mass Transportation MIO. El Obs Reg. 2017 [cited 2021 Nov 1]; (34): 1–7. Publisher Full Text\n\nWilches Astudillo CA, Jaramillo C, Murillo-Hoyos J: Accesibilidad y equidad espacial al transporte público para pacientes con enfermedad neurodegenerativa en Santiago de Cali, Colombia. Investig Geográficas. 2021 May 13 [cited 2021 Jun 4]. Publisher Full Text Reference Source\n\nDelmelle EC: Casas I. Evaluating the spatial equity of bus rapid transit-based accessibility patterns in a developing country: The case of Cali, Colombia. Transp. Policy. 2012 Mar 1 [cited 2020 May 19]; 20: 36–46. Publisher Full Text Reference Source\n\nScholl L: Casos de estudio comparativos de tres proyectos de transporte urbano apoyados por el BID. Banco Interamericano de Desarrollo;2015 Jun [cited 2021 Nov 1].Reference Source\n\nMinisterio de Salud: Resolución 8430 de 1993: Normas científicas, técnicas y administrativas para la investigación en salud. República de Colombia; 1993.Reference Source\n\nWhitty CJM: What makes an academic paper useful for health policy?. BMC Med. 2015 Dec 17 [cited 2022 Mar 24]; 13(1): 301. PubMed Abstract | Publisher Full Text\n\nCurtis C, Scheurer J: Planning for sustainable accessibility: Developing tools to aid discussion and decision-making. Prog. Plan. 2010 Aug 1 [cited 2020 Jul 6]; 74(2): 53–106. Publisher Full Text Reference Source\n\nObservatorio de Sistemas de Ciudades: Resultados Índice de Ciudades Modernas 2019.2021 [cited 2021 Jan 16]. Reference Source\n\nCali emerges as epicentre of unrest in ongoing Colombia protests|Protests News|Al Jazeera.[cited 2021 Oct 11]. Reference Source\n\nColombia protests: UN “deeply alarmed” by bloodshed in Cali. BBC News;2021 May 4 [cited 2021 Oct 11].Reference Source\n\nCastro JES, González JDG: The relationship between corruption and inequality in Colombia: empirical evidence using panel data for the period 2008-2017. Rev Iberoam Estud Desarro Iberoam J Dev Stud. 2019 [cited 2021 Apr 26]; 8(2): 28–43. Publisher Full Text Reference Source\n\nColombia Corruption Index|1995-2020 Data|2021-2023 Forecast|Historical|Chart.[cited 2021 Apr 26]. Reference Source\n\nKrubiner CB, Hyder AA: A bioethical framework for health systems activity: a conceptual exploration applying ‘systems thinking.’. Health Syst. 2014 Jun 1 [cited 2021 Jan 1]; 3(2): 124–135. Publisher Full Text\n\nCash R, Wikler D, Saxena A, et al.: Casebook on ethical issues in international health research/edited by Richard Cash [… et al]. Estud Caso Sobre Ética Investig Int En Salud;2009 [cited 2021 Oct 30]; vol. 209. .Reference Source\n\nHEARD Project, USAID: Establishing Principles of Stakeholder Engagement in Global Health Implementation Science and Research|HEARD.[cited 2021 Jan 7]. Reference Source\n\nMcCollum R, Taegtmeyer M, Otiso L, et al.: Healthcare equity analysis: applying the Tanahashi model of health service coverage to community health systems following devolution in Kenya. Int. J. Equity Health. 2019 May 7 [cited 2021 Apr 23]; 18(1): 65. PubMed Abstract | Publisher Full Text\n\nVida urbana y proximidad – Carlos Moreno: Club de Lecturas.[cited 2021 Jul 18]. Reference Source\n\nBID I: Ciudades inteligentes en América Latina. Conexión Intal. 2018 [cited 2021 Jul 18]. Reference Source\n\nObservatorio de Sostenibilidad de Ciudades.[cited 2020 Oct 12]. Reference Source\n\nLuca M, Kleinberg J, Mullainathan S: Algorithms Need Managers, Too. Harv. Bus. Rev. 2016 Jan 1 [cited 2022 Jul 15]; Reference Source\n\nBanke-Thomas, Aduragbemi, Kerry L. M. Wong, Francis Ifeanyi Ayomoh, Rokibat Olabisi Giwa-Ayedun, and Lenka Benova. “‘ In Cities, It’s NotFar, but It Takes Long’: Comparing Estimated and Replicated Travel Times toReach Life-Saving Obstetric Care in Lagos, Nigeria.” BMJ Global Health 6, no. 1 (January 1, 2021): e004318. Publisher Full Text"
}
|
[
{
"id": "164257",
"date": "30 Mar 2023",
"name": "Airton Tetelbom Stein",
"expertise": [
"Reviewer Expertise I am a family physician and epidemiologist. My main interest in research is health service research",
"primary health care and clinical guidelines."
],
"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 proposes an approach to assessing the place of residence as a spatial determinant of health in cities where traffic congestion might impact health services accessibility. The study provides dynamic travel times presenting data in ways that help shape decisions and spur action by diverse stakeholders and sectors.\n\nThis is a very adequate protocol to discuss a valid equity assessment in accessibility to health system and social justice.\nIn the Introduction section, it could have a broader view and suggest to include this article for rationale - Hosking J, Braubach M, Buss D, Khayesi M, Filho VP, de Sá TH. Towards a global framework for transport, health and health equity. Environ Int. 2022 Nov;169:107472. doi: 10.1016/j.envint.2022.107472. Epub 2022 Aug 17. PMID: 36116365.\nThere is a need to include in the introduction an article discussing the PROGRESS-Plus strategy, such as: O'Neill J, Tabish H, Welch V, Petticrew M, Pottie K, Clarke M, Evans T, Pardo Pardo J, Waters E, White H, Tugwell P. Applying an equity lens to interventions: using PROGRESS ensures consideration of socially stratifying factors to illuminate inequities in health. J Clin Epidemiol. 2014 Jan;67(1):56-64. doi: 10.1016/j.jclinepi.2013.08.005. Epub 2013 Nov 1. PMID: 24189091.\nThere is a need to discuss this report - \"Integrating health in urban and territorial planning: A sourcebook for urban leaders, health and planning professionals\" - https://unhabitat.org/integrating-health-in-urban-and-territorial-planning-a-sourcebook-for-urban-leaders-health-and, in which it describes the need to build habitable cities on a habitable planet: Processes to guide the development of human settlements – in this document referred to as “urban and territorial planning (UTP)”; and concern for human health, well-being and health equity at all levels – from local to global, and from human to planetary health. As there is a need for a closer relationships between public health and spatial planning.\nPopulation ageing is one of the main demographic phenomena in Latin America and the Caribbean and in the world. This topic should also be addressed in this protocol, as this population has several disabilities due to chronic illness and inequity is something to manage based on this demographic transition.\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": []
},
{
"id": "175826",
"date": "17 Jul 2023",
"name": "Luiz Galvao",
"expertise": [
"Reviewer Expertise environmental and global 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 paper proposes a new approach to assessing the accessibility of health services in urban areas. The approach uses dynamic travel times, which take into account traffic congestion, to assess the ease with which people can reach health services from their homes. The paper also takes an equity perspective, assessing how the accessibility of health services varies for different populations. It argues that the traditional approach to assessing accessibility, which uses static metrics such as distance or average travel time, is no longer adequate in the context of urban sprawl and traffic congestion. Dynamic travel times provide a more accurate measure of accessibility, as they take into account the real-world conditions that people face when trying to reach health services.\nThe paper uses data from Cali, Colombia, to show that people in vulnerable populations, such as those living in poverty or those with disabilities, often have less access to health services than people in more privileged populations.\nThe conclusions includes a new framework for assessing dynamic accessibility to health services. The framework takes into account the following factors:\nThe location of health services The location of people's homes Traffic congestion The sociodemographic characteristics of the population\nThe paper argues that the framework can be used to identify areas where accessibility to health services is poor, and to target interventions to improve accessibility.\nOverall, the paper is a valuable contribution to the literature on accessibility to health services. The new framework proposed by the authors has the potential to improve the way that accessibility to health services is assessed and improved.\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/11-1394
|
https://f1000research.com/articles/11-154/v1
|
07 Feb 22
|
{
"type": "Research Article",
"title": "Demographical domains and clinico-radiological characteristics of study cohorts with simultaneous multiple intracerebral hemorrhages in a tertiary neurosurgical center in Nepal: a cross-sectional study",
"authors": [
"Sunil Munakomi",
"Dipak Chaulagain",
"Dipak Chaulagain"
],
"abstract": "Background: Spontaneous simultaneous multiple intra-cerebral hemorrhages (SMICHs) and its occurrences in different territories of arterial disposition has been viewed as uncommon clinical occurrences, since the pathophysiological and predisposing factors as mechanisms aren’t vividly defined. This research primarily aims for demographic stratification and dichotomization pertaining to risk factors, etiological classifications, anatomical distributions and outcome analysis by focusing on management strategies and pertinent stroke care. Methods: 40 patients presenting to the College of Medical Sciences, Chitwan, Nepal in the last two years were included in the study. The patients with two-or-more spontaneous SMICHs with affected arterial territories with similar tomographic density based profiling were chosen as samples. Regression analysis was chosen to test three hypotheses. Results: Among our study cohorts, cortical and cortical territory (60%) was the major anatomical patterns of involvement. A conservative approach was undertaken in nine patients (22.5%), whereas surgical intervention was needed in five others (12.5%). A total of 14(35%) patients leaving against medical advice and a further seven (17.5%) patients were referred for adjuvant oncologic care. Mortality was observed among five (12.5%) patients. Hypertension was seen as a significant variable in its pathogenesis. Male patients were more affected. Age groups comprising of 36-45years and 56-65 years were involved in 32.5% and 30% cases respectively. Conclusion: This study proves the need for a national stroke data bank pertaining to spontaneous SMICHs. This will help foster effective patient education during preoperative counselling; as well as formatting a management algorithm combating them.",
"keywords": [
"multiple strokes",
"simultaneous strokes",
"cause",
"patterns",
"pathogenesis",
"outcome"
],
"content": "Introduction\n\nSimultaneous multiple intra-cerebral hemorrhages (SMICHs) are characterized by intracerebral hemorrhages within the two-or-more distinct and non-contiguous intracranial vascular territories visualized in the initial radiological imaging (Wu et al., 2017). Generally intracerebral hemorrhage (ICH) connotes high odds of continuum morbidity and mortality (Laiwattana et al., 2014). Among ICH patients, approximately 5% (1:20) have been identified as SMICHs (Renard et al., 2020).\n\nStroke ripples affect patients with continuum multi-spectral consequences (Gokce et al., 2016). Literature scarcity pertaining to SMICH paves the way for further research on the entity. Better knowledge and in-depth information pertaining to the incidence and patterns of SMICHs can help formulate treatment algorithms as well as provide newer reforms in patient management system.\n\nThe research focused on pattern analysis on how the patients with SMICH are affected by applying age and gender as demographic variable and “hypertension” as the major risk variable.\n\nThus, three hypotheses were formulated:\n\n– Hypothesis 1:There exists an imperative association between age and SMICH;\n\n– Hypothesis 2:There exists an imperative association between gender and SMICH;\n\n– Hypothesis 3:There exists an imperative association between the hypertension and SMICH.\n\nThe primary aim was to examine risk factors in SMICH patients:\n\n– To analyze the demographic profile (age and gender)of SMICH patients;\n\n– To analyze pivotal factors that impact SMICH patients significantly, namely: hypertension, diabetes, etiological classifications, anatomical distributions and outcome analysis.\n\n\nMethods\n\nThe methodology for the research was focused to SMICH patients from the hospital medical record section of the College of Medical Sciences, in Bharatpur, Chitwan, Nepal, presenting between January 2019 to January 2021 (time we started recording and compiling data of patients with SMICHs). The outcomes were compiled to study the patterns through frequencies measures and analysis. The approval for the research conduction was obtained by the Institutional Review Committee (COMSTH-IRC/2021–56). Written informed consent was obtained from all the participants or their next of kin (in case their poor Glasgow coma scale did not allow taking consent from the patients themselves) at the time of their admissions.\n\nThe research mainly focused upon the SMICH patients as the independent variable and how it impacts the respondents under varied dependent variables like: age, gender and hypertension.\n\n40 patients from the College of Medical Sciences, Chitwan, Nepal with SMICH were included in this study. Data was retrieved from the medical record section of the hospital pertaining to patients presenting with SMICHs. The study size was arrived through convenience sampling.\n\nInclusion criteria\n\nAll patients presenting with SMICHs.\n\nExclusion criteria include:\n\nHistory of previous strokes;\n\nPatients with recurrent strokes;\n\nFailure to obtain consent for participation in the study.\n\nThe minimal necessary sampling for research has been estimated by Fischer’s formula (Charan & Biwas, 2013) as\n\nWhere:\n\na represents a value of 1.96 at the confidence-interval of 95%,\n\ns represents SMICH prevalence as 6%,\n\nr as 1-sand\n\nm represents the margin-of-error as 10%.\n\nThe final result through sampling estimation was calculated as 21.66 and the sample-size of40patientswas finalized for the research purpose.\n\nSMICH is the presence of two-or-more ICHs that affects different vascular territories with similar tomographic density-profiles. All findings were validated with radiologists.\n\nAll data was taken from patient medical records.\n\nEtiologic classification for the cause of ICH was stratified as per the SMASH-U classification into hypertensive angiopathy, cerebral amyloid angiopathy, structural vascular abnormalities, medication related, other systemic causes, and undefined causes respectively (Mosconi et al., 2021). The risk factors were defined as:\n\n1. Arterial hypertension if blood pressure was above 160/90 mm Hg for more than two readings at the time of admission, on antihypertensive drugs or previous medical history of hypertension.\n\n2. Diabetes mellitus if fasting glucose level was >120 mg/dL at the time of admission; hypercholesterolemia, and fasting cholesterol level >220 mg/dL.\n\n3. Vascular lesion with pertinent radiological imaging at the site of the ICH was classified as the primary cause of the hematoma.\n\n4. Cerebral venous sinus thrombosis was diagnosed on a cerebral venogram.\n\n5. Drug associated ICH was considered in a patient on warfarin with international normalized ratio ≥2.0, novel oral anticoagulants within three days, full-dose heparin, or on systemic thrombolysis.\n\n6. Cerebral amyloid angiopathy was classified in patients’ ≥55 years of age with predominant lobar bleeds with microbleeds on magnetic resonance imaging (MRI) sequences sparing the basal ganglion and the thalamus.\n\n7. Tumor associated strokes was considered among patients with proven primary lesions with a histological diagnosis following either the therapeutic hematoma evacuation or minimally invasive biopsies.\n\nThe images of the varied etiological causes of SMICH are demonstrated in the Figure 1–Figure 3.\n\nAll images are original, deidentified, and of our patients themselves.\n\nAll images are original, deidentified, and of our patients themselves.\n\nAll images are original, deidentified, and of our patients themselves.\n\nThe regression through analysis of variance (ANOVA) testing was adopted for examining the hypotheses formed as part of this research. Three hypotheses were tested and are analyzed in the following sections. The pertinent study variables of all 40 patients were retrieved and there were no missing data.\n\n\nResults\n\nThe patients’ demographics and clinico-radiological based outcomes are provided in Table 1 (Munakomi, 2022).\n\nAmong the cohort of 40 patients, the most common age group with 13(32.5%) patients was the 36–45 age group followed by 12(30%) in the 56–65 age group. The male to female gender ratio was 25:15 (62.5% vs. 37.5%).\n\nThe majority (75%) of the cohort had hypertension as the risk factor. Merely 10% of the respondents were affected by diabetes. The vast majority (97.5%) of patients lacked adherence to drug compliance. Cortical and cortical territory (60%) was the major anatomical patterns of involvement. Mortality was observed in 5 (12.5%) patients, and 14 (35%) patients left against medical advice.\n\nAge and SMICH. Age related to SMICH was verified against the SMICH patients in the first hypothesis through the regression technique. From Table 2b, the Regression analysis (R (0.116), R2 (0.013) and Adjusted R2 (-0.012) were found; Table 2b represents that the ANOVA outcome of the age analysis is found as ‘insignificant’ (p=0.476).\n\nThe regression equation used in analyzing the association between SMICH and age in patients was calculated through:\n\nSMICH = 3.692 + (-0.846 * AGE)\n\nThis equation is made from the beta values obtained from the above Table (2a)–Table (2c) after doing regression analysis.\n\nPredictors: (Constant), simultaneous multiple intracerebral hemorrhages\n\nDependent Variable: Age\n\nPredictors: (Constant), simultaneous multiple intracerebral hemorrhages\n\nDependent Variable: Age\n\nThe outcome is negative denoting that the hypothesis is invalid where age doesn’t impact the likelihood of SMICH.\n\nGender and SMICH. Gender was verified against the SMICH patients in the second hypothesis through the regression technique. From Table 3a, the R (0.207), R2 (0.043) and adjusted R2 (0.018) are shown; Table 3b suggests that the ANOVA outcome of the gender analysis is ‘insignificant’ (p=0.201).\n\nPredictors: (Constant), simultaneous multiple intracerebral hemorrhages\n\nDependent variable: Gender\n\nDependent Variable: Gender\n\nPredictors: (Constant), simultaneous multiple intracerebral hemorrhages\n\nTable 3c represents the association between SMICH patients and the gender factor. Regression equation in analyzing the SMICH patients and gender association was calculated through:\n\nSMICH = 0.718 + (0.641 * GENDER)\n\nThis equation is made from the beta values obtained from the above Table (3a)–Table (3c) after doing regression analysis.\n\nThe outcome denotes that the hypothesis is invalid wherein gender doesn’t impact SMICH patients.\n\nHypertension and SMICH. Hypertension as a factor affecting SMICH was verified, against the SMICH patients in the first hypothesis through the regression technique. From Table 4a, the R (0.000), R2 (0.000) and Adjusted R2 (0.000) were found; Table 4b represents that the ANOVA outcome of the hypertension analysis is found as ‘significant’ (p=0.000).\n\nPredictors: (Constant), simultaneous multiple intracerebral hemorrhages\n\nDependent variable: Hypertension\n\nDependent Variable: Hypertension\n\nPredictors: (Constant), simultaneous multiple intracerebral hemorrhages\n\nTable 4c represents the association between SMICH patients and the hypertension. Regression equation in analyzing the SMICH patients and hypertension association was calculated through:\n\nDependent Variable: Hypertension\n\nSMICH = .718 + (.641 * Hypertension)\n\nThis equation is made from the beta values obtained from the above Table (4a)–Table (4c) after doing regression analysis.\n\nThe outcome denotes that the hypothesis is valid where hypertension impacts SMICH patients.\n\n\nDiscussion\n\nIn a study by Yen et al. (2005), the mean age of the patients presenting with SMICH was 60.6 ±7.9 years with a male:female ratio of 1.5:1.The mean age of similar cohorts in another study was 68.5 ± 12.8 years (Yamaguchi et al., 2017). Comparatively, our study saw much younger patients with 32.5% of patients in the age groups of 36–45 years. The male to female ratio in our study was 1.66:1.\n\nContrary to single ICH, SMICH significantly showed lobar territorial preponderance (Wu et al., 2017) (Renard et al., 2020). Our study had cortical-cortical patterns of involvement in 60% of the patients and basal ganglion and thalamic involvement in 12.5% of cases. Putamen and thalamus patterns of involvement were the most common anatomical patterns of involvement in a study by Yamaguchi et al. (2017) whereas bilateral thalamic hemorrhages variants were the most common in a study by Yen et al. (2005).\n\nThe indication of surgery among patients with SMICH depends upon variables such as presenting GCS, location and size of the hematomas (Yi et al., 2013). Surgery has been advocated among patients with lobar or cerebellar hematomas (Yen et al., 2005). In a study by Yamaguchi et al. (2017), 35.3% of patients underwent craniotomy. Surgery was performed in only 12% of our cohort.\n\nThere are variables connoting clinical outcome among patients with SMICH. One study found low Glasgow Coma Scale (GCS) results, large hematoma and concurrent ventricular extension to be prognostic markers determining 90-day mortality (Wu et al., 2017). Unilateral supratentorial hematomas showed the most favorable outcomes (Zaorsky et al., 2019), while deep seated SMICH had the highest mortality (Renard et al., 2020). The SMICH mortality described in the literature is high, ranging from 37% to 50% (Wu et al., 2017) (Yen et al., 2005). The mortality in our study was comparatively low at 12%. 15% of the patients in our study were referred to appropriate oncology center while 35% of them left despite medical advice.\n\nHypertensive angiopathy and cerebral amyloid angiopathy accounted for more than 50% of cases in SMICH (Wu TY et al.) (Renard et al., 2020) (Stemer et al., 2010). They accounted for only 42.5% of the SMICH in our study. In total, 75% of our patients presenting with SMICH had a history of hypertension and were hypertensive on presentation. Paradoxically, 97.5% of diagnosed cases of hypertension lacked compliance to their medications.\n\nThe pathophysiology of SMICH was proposed to be due to degenerative alterations in the intraparenchymal arterioles caused by long-term, uncontrolled hypertension and the simultaneous rupture of bilateral charcot-bouchard microaneurysms (Yen et al., 2005). As per the “biphasic hypothetical mechanism,\" an initial ictal hematoma causes an adrenaline spike that disrupts the cerebral autoregulation thereby harbingering the rupture of already weakened arterioles (Yen et al., 2005). Primary SMICH characteristically showed high microhemorrhages burden of varying age in MRI studies. This also highlights the probable role of auto-regulatory dysfunction following the ictal bleed as the prime pathological genesis behind the SMICH (Stemer et al., 2010).\n\nThis real-world incidence, patterns and outcome of SMICH can only be validated following a nation-wide multicenter database study. Due to the location and specificity of our results they may not be generalizable to patients from other ethnic and geographic backgrounds. The recall bias (about the risk factors and the medical compliance by the patients when the information was provided by their kin) can be another limiting issue in this observational study.\n\n\nConclusions\n\nThis is one of the first observational studies pertaining to SMICH to be carried out within our subcontinent. This study proves the need fora national stroke data bank pertaining to SMICH. This will help foster effective patient education during preoperative counseling; as well as formatting a management algorithm combating them.\n\n\nData availability\n\nFigshare: Simultaneous multiple intracerebral hemorrhages. https://doi.org/10.6084/m9.figshare.19063982.v2 (Munakomi, 2022).\n\nThis project contains the following underlying data:\n\n- SIMS deep.xlsx (de-identified raw medical data)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\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\nGokce E, Beyhan M, Acu L, et al.: Computed tomography findings in multiple simultaneous intracerebral hemorrhages. Int J Clin Exp Med. 2016; 9(6): 10414–10423. Reference Source\n\nLaiwattana D, Sangsawang B, Sangsawang N: Primary Multiple Simultaneous Intracerebral Hemorrhages between 1950 and 2013: Analysis of Data on Age, Sex and Outcome. Cerebrovasc Dis Extra. 2014; 4(2): 102–114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMosconi MG, Paciaroni M, Agnelli G, et al.: SMASH-U classification: a tool for aetiology-oriented management of patients with acute haemorrhagic stroke. Intern Emerg Med. 2021; 16(1): 109–114. PubMed Abstract | Publisher Full Text\n\nMunakomi S: Simultaneous multiple intracerebral hemorrhages. figshare. Dataset. 2022. http://www.doi.org/10.6084/m9.figshare.19063982.v2\n\nRenard D, Castelnovo G, Ion I, et al.: Single and simultaneous multiple intracerebral hemorrhages: a radiological review. Acta Neurol Belg. 2020; 120(4): 819–829. PubMed Abstract | Publisher Full Text\n\nStemer A, Ouyang B, Lee VH, et al.: Prevalence and risk factors for multiple simultaneous intracerebral hemorrhages. Cerebrovasc Dis. 2010; 30(3): 302–7. PubMed Abstract | Publisher Full Text\n\nWu TY, Yassi N, Shah DG, et al.: Simultaneous Multiple Intracerebral Hemorrhages (SMICH). Stroke. 2017; 48(3): 581–586. PubMed Abstract | Publisher Full Text\n\nYamaguchi Y, Takeda R, Kikkawa Y, et al.: Multiple simultaneous intracerebral hemorrhages: Clinical presentations and risk factors. J Neurol Sci. 2017; 383: 35–38. PubMed Abstract | Publisher Full Text\n\nYen CP, Lin CL, Kwan AL, et al.: Simultaneous multiple hypertensive intracerebral haemorrhages. Acta Neurochir (Wien). 2005; 147(4): 393–9; discussion 399. PubMed Abstract | Publisher Full Text\n\nYi HJ, Shin IY, Hwang HS: Simultaneous multiple Basal Ganglia and cerebellar hemorrhage: case report. J Cerebrovasc Endovasc Neurosurg. 2013; 15(4): 316–319. PubMed Abstract | Free Full Text\n\nZaorsky NG, Zhang Y, Tchelebi LT, et al.: Stroke among cancer patients. Nat Commun. 2019; 10(1): 5172. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "122721",
"date": "07 Mar 2022",
"name": "Guo-Yi Gao",
"expertise": [
"Reviewer Expertise TBI"
],
"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 described the clinical features of simultaneous multiple intracerebral hemorrhages in a neurosurgical center in Nepal. The study was well designed and the data acquisition and analysis are both reasonable. The limitation, such as the sample size may influence the results, could be emphasized at the end of the manuscript thus to avoid an inadequate citing of the results in any other scenarios.\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": "153191",
"date": "14 Nov 2022",
"name": "Amit Thapa",
"expertise": [
"Reviewer Expertise Neurovascular"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors have studied 40 patients over a period of two years with spontaneous simultaneous multiple intra-cerebral hemorrhages (SMICHs). Being not so common, this entity demands more elaborate study. The present study evaluates the association of age, gender and presence of hypertension with SMICHs. Authors by using SMASH-U classification have simplified as well as standardized the etiological classification of ICH in this study.\nIt is suggested to add “spontaneous” to SMICHs to differentiate from traumatic conditions.\n\nThe formula for calculating sample size needs to be formatted to convey the correct method of identifying minimal necessary sample size.\n\nIt is pertinent to mention how the authors classified patients with mixed etiologies or when two or more factors exist without fulfilling the definition individually.\n\nTo identify the etiological factors, what were all investigations carried on each patient?\n\nTable 1 when mentioned in the text, is presented with a reference to figshare dataset. These two are however are different. This confuses the reader. It would be good to mention the dataset separately as done in the \"data availability\" section.\n\nMinor corrections like adjusting font size and style are required to allow proper spacing between the words and letters.\n\nBesides the above, it would have been great if the authors compared SMICHs with single ICH for the variables they have studied, from the available dataset. The incidence of SMICH among all ICH could also have been calculated in Nepalese cohort.\n\nThe fact that various researchers have found varied anatomical distribution of SMICHs demonstrate no territorial predilection for SMICHs.\n\nResults do not talk about who needed surgical treatment for SMICH and their outcome. However these datasets are discussed in Discussion.\nOverall the authors need to be commended to have properly conducted and presented nicely the findings of this little researched condition.\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/11-154
|
https://f1000research.com/articles/11-762/v1
|
08 Jul 22
|
{
"type": "Brief Report",
"title": "Growth kinetics of multiple Acinetobacter baumannii resistotype after meropenem-based antibiotic combination exposure",
"authors": [
"Erizka Rivani",
"Pepy Dwi Endraswari",
"Agung Dwi Wahyu Widodo",
"Erizka Rivani",
"Pepy Dwi Endraswari"
],
"abstract": "Background: Carbapenems are the treatment of choice for multidrug-resistant (MDR) and extensively drug-resistant (XDR) Acinetobacter baumannii infections, but the emergence of carbapenem-resistant A. baumannii (CRAB) has rendered it ineffective in the vast majority of cases. Combination therapy has grown in popularity over the last decade; this study aims to analyze A.baumannii growth kinetics after exposure to meropenem and ampicillin-sulbactam compared with meropenem and amikacin antibiotic combinations in clinically relevant concentrations. Methods: This experimental laboratory study was conducted on the A.baumannii ATCC 19606 isolate and three clinical isolates that were intermediate or resistant to tested antibiotics. Meropenem and ampicillin-sulbactam, as well as meropenem and amikacin, were tested at four different concentrations against isolates. Turbidity measurements were taken at predetermined time points of 0, 1, 2, 4, 6, 8, and 24 hours following exposure; bacterial concentration was enumerated using the agar plate method, with the results plotted in a time-kill curve.\n\nResults: A bactericidal effect was achieved in isolates that were intermediate to ampicillin sulbactam and resistant to meropenem after the administration of meropenem and ampicillin-sulbactam combination with a concentration of 4 µg/ml and 16/8 µg/ml, respectively. The combination of meropenem and ampicillin-sulbactam demonstrated bacteriostatic activity against isolates that were resistant to both antibiotics. Isolates treated with resistant antibiotics showed an increased growth rate compared to the growth control. Conclusion: The combination of meropenem and ampicillin-sulbactam could be a promising combination therapy in treating CRAB infections. The mechanism and degree of antibiotic resistance in the isolates affect the efficacy of antibiotic combinations; further research is needed to corroborate the findings of this study.",
"keywords": [
"Acinetobacter baumannii",
"antibiotic combinations",
"time-kill",
"meropenem",
"ampicillin-sulbactam",
"amikacin"
],
"content": "Introduction\n\nAcinetobacter baumannii is a Gram-negative rod that garners attention due to its role as a primary pathogen in healthcare-associated infections with a broad spectrum of antibiotic resistance1,2. Carbapenems are the preferred treatment for multidrug-resistant (MDR) A. baumannii infections. However, treatment options have dwindled due to high isolation rates of extensively drug-resistant (XDR) A.baumannii with concurrent carbapenem resistance3,4.\n\nThe discovery of new antibiotics is critical for treating MDR and XDR A.baumannii infections. Nevertheless, antibiotic studies take a long time to complete and are difficult to implement in developing countries with limited access to the latest antibiotics. The alternative strategy that has gathered the most interest is combination antibiotic therapy, which is theoretically supposed to boost antibiotic effectiveness compared to single antibiotics5–7.\n\nIn studies evaluating antibiotic combinations, isolates that are susceptible to at least one of the regimens are frequently used, whereas many A.baumannii clinical isolates frequently lack susceptibility to any antibiotic5,8. Additionally, because the antibiotic concentrations used in studies are typically multiple times of minimum inhibitory concentration (MIC) and are difficult to achieve during the administration of therapeutic antibiotic doses, the clinical application of study results is complicated5,9–11.\n\nMeropenem is one of the few remaining low-toxicity treatment options for MDR and XDR A. baumannii infections12,13. Sulbactam is a beta-lactamase inhibitor with intrinsic activity against A. baumannii, whilst amikacin is an aminoglycoside with relatively maintained efficacy against multidrug-resistant Gram-negative bacteria, including A.baumannii14–17. Ampicillin-sulbactam and amikacin are two antibiotics that are available and easy to obtain in Indonesia. A sole sulbactam regimen is not available; it is marketed in conjunction with ampicillin or cefoperazone. Ampicillin-sulbactam formulations were chosen because of the availability of breakpoints in CLSI M100 2022 and technical considerations such as affordability and convenience of access to the antibiotics.\n\nNumerous in vitro studies have demonstrated synergy between meropenem and ampicillin-sulbactam as well as meropenem and amikacin; thus, this study aimed to compare the growth kinetics of various A. baumannii strains exposed to these two antibiotic combinations at clinically relevant concentrations18–23.\n\n\nMethods\n\nExperiments were conducted on two MDR, one XDR clinical isolates from Clinical Microbiology Laboratorium Dr. Soetomo General Academic Hospital and one standard reference isolate (ATCC A.baumannii 19606 KWIK-STIKTM Microbiologics). All clinical isolates are meropenem resistant, conforming to the Clinical and Laboratory Standard Institute (CLSI) 2022 breakpoint for A.baumannii (MIC >8 μg/ml as determined by an automatic susceptibility test using BD Phoenix® ID/AST instrument). MDR 1 is resistant to meropenem and amikacin (MIC >32 μg/ml) but is intermediate to ampicillin-sulbactam (MIC 16/8 μg/ml); MDR 2 is resistant to meropenem and ampicillin-sulbactam (MIC >16/8 μg/ml) but is intermediate to amikacin (MIC 32 μg/ml). XDR exhibited resistance to all antibiotics tested.\n\nThis study was reviewed by the Ethics Committee of the Faculty of Medicine, Airlangga University (0758/LOE/301.4.2/I/2022).\n\nDrug concentrations were selected based on the CLSI breakpoint value for the susceptible category of tested antibiotics as it represents clinically achievable concentrations of drugs in human plasma following standard dosing. Fresh stocks of each antibacterial were prepared on the day of the experiment to achieve 0.5 MIC + 0.5 MIC, 1 MIC + 1 MIC, 2 MIC + 2 MIC, and 2 MIC + 0.5 MIC of meropenem + ampicillin-sulbactam and meropenem + amikacin (Sigma). Prior to the time-kill assay experiment, strains were subcultured onto blood agar (Oxoid CM0055 Blood Agar Base supplemented with 5% sheep blood) and incubated for 24 hours at 35°C. Mid-log phase growth suspension was obtained by inoculating isolated colony into cation-adjusted Mueller-Hinton broth (Oxoid CM0405 Mueller-Hinton Broth base) followed by 4 hours of incubation at 35°C. Static time-kill experiments were performed in sextuplicates on separate days at an initial inoculum of 6×105 CFU/ml with the combined antibiotic concentrations in the glass tube, incubated at 35°C. Samples were collected at 0, 1, 2, 4, 6, 8, and 24 h, measured for turbidity by nephelometer (BD PhoenixSpecTM Nephelometer), serially diluted in saline, plated on Mueller-Hinton agar (Oxoid CM 0337 Muelle-Hinton Agar base), and counted after 24 h of incubation for viable-cell counting. Enumeration was performed manually after 24 hours of incubation at 35°C. The limit of detection (LOD) was 102 CFU/ml. In the meantime, a control experiment was carried out simultaneously with the same procedure without antibiotic addition. Bactericidal activity was assessed as a ≥ 3 log10 reduction in a colony-forming unit (CFU)/mL over the period measured. Regrowth was defined as an initial decrease of turbidity or colony count followed by an escalation in the subsequent measurement hour.\n\n\nResults\n\nThe turbidity and colony count data did not follow a normal distribution (Shapiro-Wilk value 0.000). There were significant differences in mean turbidity between isolates of ATCC 19606, MDR 1, MDR 2, and XDR at 2, 4, 6, 8, and 24 hours following antibiotic exposure (p<0.05; Wilcoxon; CI 95%). There were significant differences in the mean colony count between isolates of ATCC 19606, MDR 1, MDR 2, and XDR at 6, 8, and 24 hours following exposure, (p = 0.001, p = 0.01, and p = 0.000; Wilcoxon; CI 95%). The full turbidity and colony count data can be found under Underlying Data24.\n\nIn MDR 1 isolates, sc. MDR isolates that were both carbapenem-resistant and intermediate to ampicillin-sulbactam, the bactericidal effect was achieved at a 2 MIC + 2 MIC concentration of meropenem and ampicillin-sulbactam, respectively (Figure 1). According to turbidity measurements, concentrations of 0.5 MIC + 0.5 MIC, 1 MIC + 1 MIC, and 2 MIC + 0.5 MIC were able to maintain growth under the rate of growth control during 0–24 hours. However, the turbidity was approximately indistinguishable at 48 hours (Figure 2). Changes in the number of colonies could not be observed at 0.5 MIC + 0.5 MIC and 1 MIC + 1 MIC concentration due to high colony count results. Exposure to a 2 MIC + 0.5 MIC concentration caused a transient inhibitory effect for up to 4 hours, but regrowth occurred at the hour of measurement thenceforth.\n\nMEM: meropenem, SAM: ampicillin-sulbactam, AK: amikacin, MIC: minimum inhibitory concentration. Acinetobacter baumannii’s MIC based on CLSI 2022 susceptible breakpoint: Meropenem 2 µg/ml, Ampicillin-Sulbactam 8/4 µg/ml, Amikacin 16 µg/ml.\n\nMEM: meropenem, SAM: ampicillin-sulbactam, AK: amikacin, MIC: minimum inhibitory concentration. Acinetobacter baumannii’s MIC based on CLSI 2022 susceptible breakpoint: Meropenem 2 µg/ml, Ampicillin-Sulbactam 8/4 µg/ml, Amikacin 16 µg/ml.\n\nAt 24 and 48 hours, MDR 2 isolates (isolates resistant to meropenem and ampicillin-sulbactam) treated to both antibiotics at concentration equivalent to or less than the MIC demonstrated higher turbidity compared to positive growth control. After four hours, at a concentration twice the MIC, there is a reduction in colony count followed by regrowth. XDR isolates which were also resistant to meropenem and ampicillin-sulbactam, did not show any regrowth phenomena during post-exposure monitoring except at a concentration of 1 MIC + 1 MIC, where regrowth occurred at 8 and 24 hours (Table 1).\n\nATCC: American Type Culture Collection, MDR: multidrug-resistant, XDR: extensively drug-resistant, MEM: meropenem, SAM: ampicillin-sulbactam, AK: amikacin, MIC: minimum inhibitory concentration\n\na: Meropenem MIC = 2 μg/ml; Ampicillin-Sulbactam MIC: 8/4 μg/ml; Amikacin MIC: 16 μg/ml\n\nb: Bactericidal: ≥ 3 log10 reduction in a colony-forming unit (CFU)/mL over the period measured. Bacteriostatic: < 3 log10 reduction in a colony-forming unit (CFU)/mL over the period measured\n\nc: Regrowth: initial decrease of turbidity or colony count followed by an escalation in the subsequent measurement hour\n\nd: Comparison of the colony count between the treatment group and growth control group of isolate. Growth control: isolate without antibiotic combination exposure\n\nMeropenem and amikacin had no bactericidal impact on intermediate and drug-resistant isolates; hence on all clinical isolates of A.baumannii in this study. The most significant reduction in the number of bacteria was observed following exposure to 2 MIC and 2 MIC; however, these concentrations had no effect on the number of colonies in XDR isolates when compared to the number of colonies at 0 hours measurement.\n\n\nDiscussion\n\nThis investigation discovered regrowth in clinical isolates from nearly all exposure groups. Regrowth is influenced by various factors related to the concentration of antibiotics and bacterial inoculum, as well as the susceptibility of bacteria25. Regrowth may occur when bacterial growth is not fully inhibited by exposure to antibiotics (due to insufficient antibiotic concentration or a resistant bacterial strain)26. Persistent/resistant bacterial subpopulations can also be inferred from time-kill curve regrowth27–29. Antibiotic degradation in the test suspension also plays a role; decreased active antibiotic amount during the final hours of testing may render inhibition ineffective, allowing regrowth to occur30.\n\nMeropenem and ampicillin-sulbactam are time-dependent beta-lactam antibiotics31. The synergism may be due to the distinct penicillin-binding proteins (PBP) binding mechanisms, hence enhancing the activity of beta-lactams in bacteria32. Meropenem has a high affinity for PBP 2, PBP 3, PBP 1a, and PBP 1b, ampicillin has a high affinity for PBP 4, and sulbactam has a high affinity for PBP 1 and 333,34. The downregulation of native and subsequent synthesis of altered PBPs is one of the mechanism behind A. baumannii's resistance to beta-lactam antibiotics35–37. In addition to its simultaneous action on PBP, sulbactam's beta-lactam inhibitory activity can boost meropenem's affinity and, consequently, activity38,39. Numerous investigations have demonstrated that subinhibitory concentrations of beta-lactam antibiotics can alter the shape of bacteria's cell walls. In theory, it has the potential to augment the intake of other antibiotics40,41.\n\nMeropenem in combination with ampicillin-sulbactam at a concentration twice the MIC was bactericidal against isolates intermediate to ampicillin-sulbactam. Moreover, it had a lower rate of regrowth than the meropenem and amikacin exposure groups. Differences in resistance levels are believed to have an effect on the efficiency of antibiotic combinations42–44 . It should be anticipated that the distinct resistance mechanisms held by various strains resulted in different responses to combination antibiotic exposure20,45,46.\n\nAdditionally, this study found that isolates treated at sub-MIC concentrations of antibiotics had a higher colony count than the growth control group. This finding merits additional investigation to ascertain the underlying mechanism. Antibiotics have a selection and inducer effect on antibiotic resistance, which demonstrates the importance of using them prudently.\n\n\nConclusions\n\nMeropenem in combination with ampicillin-sulbactam at a concentration twice the MIC was bactericidal against isolates resistant to meropenem and intermediate to ampicillin-sulbactam. Meropenem and ampicillin-sulbactam in combination demonstrated bacteriostatic activity against isolates resistant to both antibiotics. Meropenem and amikacin in combination had no bactericidal effect on isolates that were either intermediate or resistant to meropenem and amikacin. Combined administration of meropenem and ampicillin-sulbactam can be considered in cases of A. baumannii infection that is not susceptible to any antibiotics. Higher doses show better results and should be attempted when clinical circumstances allow.\n\n\nData availability\n\nFigshare: Colony Count and Turbidity Data from Time-Kill Assay of Acinetobacter baumannii exposed to Meropenem-based Antibiotic Combinations. https://doi.org/10.6084/m9.figshare.20024270.v224.\n\nThis project contains the following underlying data:\n\n- Colony Count Data.csv\n\n- Turbidity Data.csv\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 thank Dr. Soetomo General Academic Hospital and Department of Microbiology, Faculty of Medicine, Sriwijaya University, for providing all necessary support in this research and Daniel Edbert, MD, Clin. Microbiol., for editorial assistance.\n\n\nReferences\n\nLin MF, Lan CY: Antimicrobial resistance in Acinetobacter baumannii: From bench to bedside. World J Clin Cases. 2014; 2(12): 787. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee CR, Lee JH, Park M, et al.: Biology of Acinetobacter baumannii: pathogenesis, antibiotic resistance mechanisms, and prospective treatment options. Front Cell Infect Microbiol. 2017; 7: 55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKyriakidis I, Vasileiou E, Pana ZD, et al.: Acinetobacter baumannii antibiotic resistance mechanisms. Pathogens. 2021; 10(3): 373. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsif M, Alvi IA, Rehman SU: Insight into Acinetobacter baumannii: pathogenesis, global resistance, mechanisms of resistance, treatment options, and alternative modalities. Infect Drug Resist. 2018; 11: 1249–1260. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKarakonstantis S, Ioannou P, Samonis G, et al.: Systematic review of antimicrobial combination options for pandrug-resistant Acinetobacter baumannii. Antibiotics (Basel). 2021; 10(11): 1344. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnggraini D, Santosaningsih D, Saharman YR, et al.: Distribution of Carbapenemase Genes among Carbapenem-Non-Susceptible Acinetobacter baumanii Blood Isolates in Indonesia: A Multicenter Study. Antibiotics (Basel). 2022; 11(3): 366. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCoates ARM, Hu Y, Holt J, et al.: Antibiotic combination therapy against resistant bacterial infections: synergy, rejuvenation and resistance reduction. Expert Rev Anti Infect Ther. 2020; 18(1): 5–15. PubMed Abstract | Publisher Full Text\n\nSullivan GJ, Delgado NN, Maharjan R, et al.: How antibiotics work together: Molecular mechanisms behind combination therapy. Curr Opin Microbiol. 2020; 57: 31–40. PubMed Abstract | Publisher Full Text\n\nPeña-Miller R, Lähnemann D, Schulenburg H, et al.: The optimal deployment of synergistic antibiotics: a control-theoretic approach. J R Soc Interface. 2012; 9(75): 2488–2502. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnandan S, Jennifer L, Anandan S, et al.: Synergy testing between sulbactam and meropenem/colistin in MDR Acinetobacter baumannii-calcoaceticus complex isolated from ventilator associated pneumonia. J Infect Dis Ther. 2016; 4: 299. Publisher Full Text\n\nBremmer DN, Bauer KA, Pouch SM, et al.: Correlation of checkerboard synergy testing with time-kill analysis and clinical outcomes of extensively drug-resistant Acinetobacter baumannii respiratory infections. Antimicrob Agents Chemother. 2016; 60(11): 6892–6895. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJiang Z, He X, Li J: Synergy effect of meropenem-based combinations against Acinetobacter baumannii: A systematic review and meta-analysis. Infect Drug Resist. 2018; 11: 1083–1095. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSabet M, Tarazi Z, Griffith DC: Pharmacodynamics of meropenem against Acinetobacter baumannii in a neutropenic mouse thigh infection model. Antimicrob Agents Chemother. 2020; 64(4): e02388–19. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChu H, Zhao L, Wang M, et al.: Sulbactam-based therapy for Acinetobacter baumannii infection: a systematic review and meta-analysis. Braz J Infect Dis. 2013; 17(4): 389–394. PubMed Abstract | Publisher Full Text\n\nLevin AS: Multiresistant Acinetobacter infections: a role for sulbactam combinations in overcoming an emerging worldwide problem. Clin Microbiol Infect. 2002; 8(3): 144–153. PubMed Abstract | Publisher Full Text\n\nKaraiskos I, Lagou S, Pontikis K, et al.: The “old” and the “new” antibiotics for MDR gram-negative pathogens: for whom, when, and how. Front Public Health. 2019; 7: 151. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBassetti M, Peghin M, Vena A, et al.: Treatment of infections due to MDR Gram-negative bacteria. Front Med (Lausanne). 2019; 6: 74. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarie MAM, Krishnappa LG, Alzahrani AJ, et al.: A prospective evaluation of synergistic effect of sulbactam and tazobactam combination with meropenem or colistin against multidrug resistant Acinetobacter baumannii. Bosn J Basic Med Sci. 2015; 15(4): 24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu J, Shu Y, Zhu F, et al.: Comparative efficacy and safety of combination therapy with high-dose sulbactam or colistin with additional antibacterial agents for multiple drug-resistant and extensively drug-resistant Acinetobacter baumannii infections: A systematic review and network meta-analysis. J Glob Antimicrob Resist. 2021; 24: 136–147. PubMed Abstract | Publisher Full Text\n\nLenhard JR, Smith NM, Bulman ZP, et al.: High-dose ampicillin-sulbactam combinations combat polymyxin-resistant Acinetobacter baumannii in a hollow-fiber infection model. Antimicrob Agents Chemother. 2017; 61(3): e01268–16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Lima FCG, Oliveira-Júnior JB, Cavalcanti CDLB, et al.: Ultrastructural changes caused by the combination of intravenous immunoglobulin with meropenem, amikacin and colistin in multidrug-resistant Acinetobacter baumannii. Microb Pathog. 2020; 149: 104437. PubMed Abstract | Publisher Full Text\n\nLoho T, Sukartini N, Astrawinata DAW, et al.: In vitro antibacterial interaction of doripenem and amikacin against multidrug-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae isolates. Can J Infect Dis Med Microbiol. 2018; 2018: 1047670. PubMed Abstract | Publisher Full Text | Free Full Text\n\nScudeller L, Righi E, Chiamenti M, et al.: Systematic review and meta-analysis of in vitro efficacy of antibiotic combination therapy against carbapenem-resistant Gram-negative bacilli. Int J Antimicrob Agents. 2021; 57(5): 106344. PubMed Abstract | Publisher Full Text\n\nRivani E, Endraswari PD, Widodo ADW: Colony Count and Turbidity Data from Time-Kill Assay of Acinetobacter baumannii exposed to Meropenem-based Antibiotic Combinations. figshare. [Dataset]. 2022. http://www.doi.org/10.6084/m9.figshare.20024270.v2\n\nMartínez JL: Effect of antibiotics on bacterial populations: a multi-hierachical selection process. F1000Res. 2017; 6: 51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSulaiman JE, Lam H: Evolution of bacterial tolerance under antibiotic treatment and its implications on the development of resistance. Front Microbiol. 2021; 12: 617412. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBalaban NQ, Helaine S, Lewis K, et al.: Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol. 2019; 17(7): 441–448. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarth VC Jr, Rodrigues A, Bonatto GD, et al.: Heterogeneous persister cells formation in Acinetobacter baumannii. PLoS One. 2013; 8(12): e84361. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVogwill T, Comfort AC, Furió V, et al.: Persistence and resistance as complementary bacterial adaptations to antibiotics. J Evol Biol. 2016; 29(6): 1223–1233. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrouwers R, Vass H, Dawson A, et al.: Stability of β-lactam antibiotics in bacterial growth media. PLoS One. 2020; 15(7): e0236198. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEyler RF, Shvets K: Clinical pharmacology of antibiotics. Clin J Am Soc Nephrol. 2019; 14(7): 1080–1090. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKiffer CRV, Sampaio JLM, Sinto S, et al.: In vitro synergy test of meropenem and sulbactam against clinical isolates of Acinetobacter baumannii. Diagn Microbiol Infect Dis. 2005; 52(4): 317–322. PubMed Abstract | Publisher Full Text\n\nBreilh D, Texier-Maugein J, Allaouchiche B, et al.: Carbapenems. J Chemother. 2013; 25(1): 1–17. PubMed Abstract | Publisher Full Text\n\nWang L, Chen Y, Han R, et al.: Sulbactam Enhances in vitro Activity of β-Lactam Antibiotics Against Acinetobacter baumannii. Infect Drug Resist. 2021; 14: 3971. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRusso TA, MacDonald U, Beanan JM, et al.: Penicillin-binding protein 7/8 contributes to the survival of Acinetobacter baumannii in vitro and in vivo. J Infect Dis. 2009; 199(4): 513–521. PubMed Abstract | Publisher Full Text\n\nVashist J, Tiwari V, Das R, et al.: Analysis of penicillin-binding proteins (PBPs) in carbapenem resistant Acinetobacter baumannii. Indian J Med Res. 2011; 133(3): 332–8. PubMed Abstract | Free Full Text\n\nHan S, Caspers N, Zaniewski RP, et al.: Distinctive attributes of β-lactam target proteins in Acinetobacter baumannii relevant to development of new antibiotics. J Am Chem Soc. 2011; 133(50): 20536–20545. PubMed Abstract | Publisher Full Text\n\nPenwell WF, Shapiro AB, Giacobbe RA, et al.: Molecular mechanisms of sulbactam antibacterial activity and resistance determinants in Acinetobacter baumannii. Antimicrob Agents Chemother. 2015; 59(3): 1680–1689. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang Y, Fu Y, Lan P, et al.: Molecular epidemiology and mechanism of sulbactam resistance in Acinetobacter baumannii isolates with diverse genetic backgrounds in China. Antimicrob Agents Chemother. 2018; 62(3): e01947–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee CH, Tang YF, Su LH, et al.: Antimicrobial effects of varied combinations of meropenem, sulbactam, and colistin on a multidrug-resistant Acinetobacter baumannii isolate that caused meningitis and bacteremia. Microb Drug Resist. 2008; 14(3): 233–237. PubMed Abstract | Publisher Full Text\n\nLima LM, da Silva BNM, Barbosa G, et al.: β-lactam antibiotics: An overview from a medicinal chemistry perspective. Eur J Med Chem. 2020; 208: 112829. PubMed Abstract | Publisher Full Text\n\nJoly-Guillou ML, Decré D, Herrman JL, et al.: Bactericidal in-vitro activity of beta-lactams and beta-lactamase inhibitors, alone or associated, against clinical strains of Acinetobacter baumannii: effect of combination with aminoglycosides. J Antimicrob Chemother. 1995; 36(4): 619–629. PubMed Abstract | Publisher Full Text\n\nWang YC, Kuo SC, Yang YS, et al.: Individual or combined effects of meropenem, imipenem, sulbactam, colistin, and tigecycline on biofilm-embedded Acinetobacter baumannii and biofilm architecture. Antimicrob Agents Chemother. 2016; 60(8): 4670–4676. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOh S, Chau R, Nguyen AT, et al.: Losing the Battle but Winning the War: Can Defeated Antibacterials Form Alliances to Combat Drug-Resistant Pathogens? Antibiotics. 2021; 10(6): 646. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeck KR, Kim MJ, Choi JY, et al.: In vitro time-kill studies of antimicrobial agents against blood isolates of imipenem-resistant Acinetobacter baumannii, including colistin-or tigecycline-resistant isolates. J Med Microbiol. 2012; 61(3): 353–360. PubMed Abstract | Publisher Full Text\n\nLaishram S, Anandan S, Devi BY, et al.: Determination of synergy between sulbactam, meropenem and colistin in carbapenem-resistant Klebsiella pneumoniae and Acinetobacter baumannii isolates and correlation with the molecular mechanism of resistance. J Chemother. 2016; 28(4): 297–303. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "147379",
"date": "19 Aug 2022",
"name": "Sarunyou Chusri",
"expertise": [
"Reviewer Expertise Microbiology and 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 brief report by Erizka et al. demonstrated the bacteriostatic and bactericidal activities of meropenem in combination with ampicillin-sulbactam and amikacin. The finding showed that the meropenem + ampicillin-sulbactam provided the good activity against these isolates, which might be considered as an alternative treatment for A. baumannii infection, especially MDR and XDR strains. However, I have some comments to be addressed.\n\nMajor comments\n\nPage 6, in the results section: “XDR isolates which were also resistant to meropenem and ampicillin-sulbactam, did not show any regrowth phenomena during post-exposure monitoring except at a concentration of 1 MIC + 1 MIC, where regrowth occurred at 8 and 24 hours” – please verify these results again. I found that regrowth occurred not only at a concentration of 1 MIC + 1 MIC but also at a concentration of 0.5 MIC + 0.5 MIC and other concentrations. In addition, only 1 isolate of XDR was included in the study. Why did the authors write “XDR isolates” in this sentence?\n\nPage 6, in the results section: “Meropenem and amikacin had no bactericidal impact on intermediate and drug-resistant isolates; hence on all clinical isolates of A. baumannii in this study.” – according to Figure 1 and Table 1, not all concentrations of MEM + AK have no bactericidal effect on the clinical isolates. At twice MIC of this combination against MDR-1, it seems to provide ≥ 3 log10 reductions, which was considered to have bactericidal activity. Please rephrase this sentence.\n\nPlease carefully verify the combination activity (bactericidal and bacteriostatic) in Table 1, because there are some incorrect results.\n\nThe authors reported the bacteriostatic activity in the MEM 0.5 MIC + SAM 0.5 MIC against ATCC 19606 isolate, the MEM 2 MIC + SAM 0.5 MIC against MDR-1 isolate, the MEM 2 MIC + AK 2 MIC against MDR-1, and the MEM 1 MIC + SAM 1 MIC against XDR, whereas it seems to provide ≥ 3 log10 reductions (bactericidal), compared to the growth control (Figure 1). “Colony count higher than growth controld” – did the authors mean “Turbidity higher than growth controld”? Because the results seem to be received from Figure 2. If yes, please change the title and the description of this column.\n\nThe authors should recreate the supplementary tables (Colony Count Data and Turbidity Data) in data availability (underlying data). The information should be clearly and easily understood.\n\nMinor comments\n\nPage 1, in the abstract section, in a part of the results: “… that were intermediate to ampicillin sulbactam and …” – a hyphen between ampicillin sulbactam was missed.\n\nPage 2, in the keywords section: “Acinetobacter baumannii” should be italic.\n\nPage 3, in the methods section, in a part of the study design: “… ATCC A.baumannii 19606 …” – a space between genus and species was missed.\n\nPage 3, in the methods section, in a part of the study design: “… (CLSI) 2022 breakpoint for A.baumannii …” – again, a space between genus and species was missed, and please check this point throughout the manuscript.\n\nPage 3, in the methods section, in a part of the procedure: “… in a colony-forming unit (CFU)/mL over …” – “mL” should be replaced by “ml” as same as the other part of the manuscript.\n\nPage 4, in the results section: “In MDR 1 isolates, sc. MDR isolates that …” – what does the “sc.” mean?\n\nPage 4, in the results section: “In MDR 1 isolates, sc. MDR isolates that were both carbapenem-resistant and intermediate to ampicillin-sulbactam” – please rephrase this sentence.\n\nPage 5, in the results section: “At 24 and 48 hours, MDR 2 isolates (isolates resistant to meropenem and ampicillin-sulbactam) …” – did the authors mean the isolate that was coded as “MDR 2”? If yes, it might be better to change the code of “MDR 1” and “MDR 2” isolates. Because these codes make confusion between the code and the number of the isolates. As shown in this case, it also means 2 isolates of MDR bacteria. The authors could use other codes such as “MDR-1” and “MDR-2”.\n\nPages 6 - 7, in the results section: “… these concentrations had no effect on the number of colonies in XDR isolates when compared to the number of colonies at 0 hours measurement.” – according to Figure 1, the authors should also specify the type of antibiotic combination, because this phenomenon was only found in XDR against MEM + AK combination, but not XDR against MEM + SAM.\n\nPage 7, in the discussion section: “… sulbactam has a high affinity for PBP 1 and 3” could be replaced by “… sulbactam has a high affinity for PBP 1 and PBP 3”.\n\nPage 7, in the discussion section: “Numerous investigations have demonstrated that subinhibitory concentrations of beta-lactam antibiotics can alter the shape of bacteria’s cell walls” – please provide some references for this sentence.\n\nFigures 1 and 2: the color and the shape represented the results of “Growth Control” were similar to the results of “2 MIC + 0.5 MIC”. In the case of turbidity fluctuations in the MEM + AK combination against XDR isolate (Figure 2), the color and the shape represented the results of “Growth Control” were exactly the same as the results of “2 MIC + 0.5 MIC”. The authors probably use another color and shape (such as the star shape) to represent the results of “Growth Control”.\n\nHow many replications did the authors performed for time-kill assay?\n\nAccording to the description in Figure 1, Figure 2, and Table 1, why did the MICs not represent the exact MICs, but it represents the MIC at the susceptible breakpoint from CLSI guideline?\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? Yes\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": "8925",
"date": "24 Oct 2022",
"name": "Erizka Rivani",
"role": "Author Response",
"response": "Dear dr. Chusri, My co-authors and I were pleased to receive your response and the opportunity to resubmit a revised version of this manuscript. We would like to thank you for providing your constructive and detailed review comments on our manuscript. We have attempted to fully address comments in the revised manuscript; the reviewer's original comments are listed below, followed by our response to each comment. Edited text in the attached revised manuscript is visible as tracked changes under the markup mode of Microsoft Word that we've sent to Editor. All authors have read and approved the revised manuscript. We hope our resubmission is now suitable for acceptance, and we look forward to hearing from you. Major Revision 1. Page 6, Result “XDR isolates which were also resistant to meropenem and ampicillin-sulbactam, did not show any regrowth phenomena during post-exposure monitoring except at a concentration of 1 MIC + 1 MIC, where regrowth occurred at 8 and 24 hours” Please verify these results again. I found that regrowth occurred not only at a concentration of 1 MIC + 1 MIC but also at a concentration of 0.5 MIC + 0.5 MIC and other concentrations. Thank you for this observation. The second and third paragraphs of the Results section describe the measurement of the first antibiotic combination exposures, meropenem and ampicillin-sulbactam. The fourth paragraph discussed the results of meropenem and amikacin exposure. In XDR isolates exposed to meropenem and ampicillin-sulbactam, regrowth only occurred at a concentration of 1 MIC + 1 MIC. In XDR isolates exposed to meropenem and amikacin, regrowth did occur in all concentration groups.To clarify this conclusion, we attempt to rearrange the sentences. Only 1 isolate of XDR was included in the study. Why did the authors write “XDR isolates” in this sentence? Thank you very much for the reminder. We revised the sentence accordingly. 2. Page 6, Result “Meropenem and amikacin had no bactericidal impact on intermediate and drug-resistant isolates; hence on all clinical isolates of A. baumannii in this study.” According to Figure 1 and Table 1, not all concentrations of MEM + AK have no bactericidal effect on the clinical isolates. At twice MIC of this combination against MDR-1, it seems to provide ≥ 3 log10 reductions, which was considered to have bactericidal activity. Please rephrase this sentence. Thank you for pointing this out. According to the colony count of the MDR-1 isolate (attached in the Underlying Data), the colony count decreased by 2.83 log 10 CFU/ml following exposure to 2 MIC + 2 MIC concentrations of meropenem and amikacin (from 5.78 log 10 CFU/ml to 2.95 log 10 CFU/ml). Because the reduction in colony counts did not surpass 3 log 10 CFU/ml over the period measured, we categorized the activity as bacteriostatic. We will attempt to add column in table with Δ Log information to ensure that the findings are more easily discernible. 3. Table 1 “Bacteriostatic activity in the MEM 0.5 MIC + SAM 0.5 MIC against ATCC 19606 isolate, the MEM 2 MIC + SAM 0.5 MIC against MDR-1 isolate, the MEM 2 MIC + AK 2 MIC against MDR-1, and the MEM 1 MIC + SAM 1 MIC against XDR” Please carefully verify the combination activity (bactericidal and bacteriostatic) in Table 1, because there are some incorrect results. it seems to provide ≥ 3 log10 reductions (bactericidal), compared to the growth control. Thank you for the comment. As stated in Point 2, the reduction in colony count for the isolates mentioned did not reach 3 log 10 CFU/ml; therefore, it was classified as bacteriostatic (MEM 0.5 MIC + SAM 0.5 MIC against ATCC 19606 isolate: 2.87 log 10 CFU/ml, MEM 2 MIC + SAM 0.5 MIC against MDR-1 isolate: 2.71 log 10 CFU/ml, MEM 2 MIC + AK 2 MIC against MDR-1: 2.83 log 10 CFU/ml, MEM 1 MIC + SAM 1 MIC against XDR 2.48 log 10 CFU/ml). As it explains the growth of the isolates when exposed to antibiotics, the decrease in colony count of the isolates was compared to the time-to-time colony count of the isolates rather than to the growth control. We will attempt to add column in table with Δ Log information to ensure that the findings are more easily discernible. Title and description of Table 1 Thank you for the helpful reminder. We have made the necessary adjustments. 4. Data availability (Underlying Data) Recreate the supplementary tables (Colony Count Data and Turbidity Data) Revised accordingly. Minor Revision 1. Page 1, Abstract Results: “..… that were intermediate to ampicillin sulbactam and …”. A hyphen between ampicillin sulbactam was missed. Revised accordingly. 2. Page 2, Keywords “Acinetobacter baumannii” should be Italic We appreciate your pointing this out. Updated as required. 3. Page 3, Methods “… ATCC A.baumannii 19606 …” “… (CLSI) 2022 breakpoint for A.baumannii …”. A space between genus and species was missed. Thank you. Revised accordingly. 4. Page 3, Methods “… in a colony-forming unit (CFU)/mL over …”. “mL” should be replaced by “ml” as same as the other part of the manuscript. We concur. 5. Page 4, Results “In MDR 1 isolates, sc. MDR isolates that …”. What does the “sc” means? Thank you for your inquiry. The word “sc” in the sentence above is an abbreviation of scilicet, a contraction of Latin scire licet, meaning \"it is permitted to know.\" Sc. introduces additional information regarding something stated earlier, often in the form of a list to remove an ambiguity or supply a word omitted in the preceding text. We shall attempt to rephrase the sentence such that the meaning is more clearly apparent. 6. Page 4, Results “In MDR 1 isolates, sc. MDR isolates that were both carbapenem-resistant and intermediate to ampicillin-sulbactam”. Rephrase the sentence. We concur. 7. Page 5, Results “At 24 and 48 hours, MDR 2 isolates (isolates resistant to meropenem and ampicillin-sulbactam) …”. Use other codes such as “MDR-1” and “MDR-2” Thank you. Revised accordingly. 8. Page 6-7, Results “… these concentrations had no effect on the number of colonies in XDR isolates when compared to the number of colonies at 0 hours measurement.” According to Figure 1, the authors should also specify the type of antibiotic combination, because this phenomenon was only found in XDR against MEM + AK combination, but not XDR against MEM + SAM. We thank you for bringing this to our attention. As stated in Point 1.a, attempts are made to arrange the sentences. 9. Page 7, Discussion “… sulbactam has a high affinity for PBP 1 and 3” . Replaced with “… sulbactam has a high affinity for PBP 1 and PBP 3”. Revised accordingly. 10. Page 7, Discussion “Numerous investigations have demonstrated that subinhibitory concentrations of beta-lactam antibiotics can alter the shape of bacteria’s cell walls”. Provide some references for this sentence. We have made adjustments in accordance with the revision. 11. Page 4 and 5, Figure 1 and Figure 2 Use another colour and shape to represent the results of “Growth Control” We have made adjustments in accordance with the revision. 12. How many replications did the authors performed for time-kill assay? Experiments were conducted in six replications. 13. According to the description in Figure 1, Figure 2, and Table 1, why did the MICs not represent the exact MICs, but it represents the MIC at the susceptible breakpoint from CLSI guideline? Thank you for the question. The antibiotic concentration was based on the CLSI breakpoint since the susceptible breakpoint value was based on the patient's clinically standard dosing regimen. This study aims to identify clinically relevant, effective antibiotic combinations for patients with MDR and XDR A.baumannii infections; consequently, it is necessary to utilize antibiotic concentrations achieved through a standard dosing regimen. MDR and XDR A.baumannii are frequently resistant to the tested antibiotic, with MIC typically being multiple times that of susceptible isolates, which is difficult to achieve during the administration of therapeutic antibiotic doses, thereby complicating the clinical application of those kinds of studies."
}
]
},
{
"id": "149383",
"date": "07 Oct 2022",
"name": "Ardiana Kusumaningrum",
"expertise": [
"Reviewer Expertise antimicrobial resistance",
"MDRO"
],
"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 general, this article provides important in vitro data regarding the potential use of antibiotics combination in Acinetobacter baumannii infection management. The research method used is appropriate.\nHowever, there are several issues that need to be considered:\n1. Is there any preliminary examination to ensure that the antibiotic concentration used is as expected, at the beginning and also the end of observation time?\n2. How did the author confirm that the bacterial isolates being tested were in exponential growth period/log phase?\n3. Is it possible to conduct duplo testing to increase the strength of study method?\n4. Figure 1 --> is there any missing line on the picture? For example, at XDR colony count fluctuations, there are only 2 lines observed (growth control and MEM 0,5MIC + AK 0,5MIC)\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": "8926",
"date": "24 Oct 2022",
"name": "Erizka Rivani",
"role": "Author Response",
"response": "Dear Dr. Ardiana, My co-authors and I were pleased to receive your response and the opportunity to resubmit a revised version of this manuscript. We attempt to respond to reviewer questions with relevant information obtained from our research. 1. Is there any preliminary examination to ensure that the antibiotic concentration used is as expected at the beginning and end of observation time? Thank you for the question. There were two preliminary trials conducted before this study. The first preliminary trial was carried out to determine the appropriate colony measurement method for the test isolates exposed to the selected antibiotics for this study. The second preliminary study was carried out to determine the time required by the test isolates to reach the log phase of growth. We did not conduct a preliminary trial to ascertain the concentration of the test antibiotic because antibiotic exposure was performed for 24 hours (additional measurements were taken at 48 hours to collect post-antibiotic exposure data), which is comparable to the duration of antibiotic susceptibility tests conducted in clinical microbiology laboratory with antibiotic powders that were subjected to routine quality control. 2. How did the author confirm that the bacterial isolates tested were in the exponential growth period/log phase? Thank you for drawing attention to this. In the preliminary test, isolates were grown without antibiotic treatment in liquid media. This test is designed to determine the time required for the test isolate to reach the log phase under identical conditions to the actual test. After transferring isolated colonies from solid to liquid media, turbidity measurements and colony growth calculations were undertaken every 30 minutes. The data obtained was therefore plotted on a growth curve. According to the preliminary test results, all isolates entered the log phase after two hours of incubation, and six hours later, they began to reach the stationary phase. Therefore, in the actual experiment, isolated colonies were cultured in liquid media for four hours prior to the time-kill test (at the mid-log phase). 3. Is it possible to conduct duplo testing to increase the strength of study method? Thank you for the comment. The tests were carried out six times over the course of two days. On the first day of the trial, three replications were performed. On the second day, three additional replications were conducted, bringing the total number of replications to six. This experiment was repeated six times with four test isolates treated with two types of combination antibiotics at four different concentrations on each combination. 4. Figure 1 --> is there any missing line on the picture? For example, at XDR colony count fluctuations, there are only 2 lines observed (growth control and MEM 0,5MIC + AK 0,5MIC) We thank you for bringing this to our attention. Several lines in the figure are joined because they have the same value, so the end result gives the impression that some figures are missing lines (there are just two lines instead of five). We shall attempt to revise the graphic to ensure its meaning is more evident."
}
]
}
] | 1
|
https://f1000research.com/articles/11-762
|
https://f1000research.com/articles/11-1393/v1
|
28 Nov 22
|
{
"type": "Study Protocol",
"title": "Effectiveness of an mHealth application on remote monitoring and self-management of persons with hypertension in a coastal taluk of Udupi district: A study protocol",
"authors": [
"Prajwal L Salins",
"Suma Nair",
"Poornima P Kundapur",
"Akhilesh K Pandey",
"Bhageerathy Reshmi",
"Sabu K Mandapam",
"Prajwal L Salins",
"Suma Nair",
"Poornima P Kundapur",
"Akhilesh K Pandey",
"Bhageerathy Reshmi"
],
"abstract": "Background: Hypertension is the most important risk factor for cardiovascular disease, a major cause of death and disability globally. There is increasing evidence that demonstrates clinically relevant benefits from self-monitoring and self-management of blood pressure. Evidence suggests a reduction of systolic BP by 3.2 mm/hg through self-monitoring. The use of mHealth applications in health care monitoring and self-management can help in the timely delivery of health information. Around 33% of Indians use mHealth applications in their daily life. However, well-designed, user complied mHealth applications are essential to reach the masses and to be effective. A previously conducted study in India demonstrated that applications are not customized according to users' needs and expectations and lacked usability assessment by patients. Therefore, we aimed to develop and test a novel mHealth application on remote monitoring and self-management in hypertension.\nMethods: The study will be carried out in three phases. The first phase will be an in-depth interview to identify the required parameters to develop a customized mHealth android-based application to monitor hypertension. The second phase is to develop the customized application through the Agile development design using the android studio platform. In the third phase, a community-based cluster randomized trial will be carried out to assess the effectiveness of the mHealth intervention on the remote monitoring and self-management of people with hypertension. A sample of 236 people from 12 villages will be randomized and the mHealth application will be delivered to the intervention group and the standard regimen will be continued in the control group.\nResults: In the proposed study if the intervention is found to be helpful, then hypertension patients in the community can be encouraged to install the mHealth application. This application, if found effective can improve the health status, knowledge, and self-care approach among hypertensive patients. Registration: CTR India (CTRI/2022/03/041544).",
"keywords": [
"mHealth",
"remote monitoring",
"self-management",
"hypertension"
],
"content": "Introduction\n\nHypertension is a major public health concern worldwide and in India with a significantly growing prevalence in both urban and rural communities. It is one of the major causes of mortality and morbidity in elderly people, but hypertension is still a significant health problem (Karmakar et al., 2018). Approximately 13.5% of global premature deaths are due to increased blood pressure (Lawes et al., 2008). In low and middle-income nations, the age-adjusted systolic blood pressure (BP) is high and the mean age-adjusted systolic BP has drastically increased in developing countries like East Africa, and South and Southeast Asia. In addition, the number of persons with uncontrolled hypertension rose between 1980 and 2008 due to population growth and aging around the world (Danaei et al., 2011). Hypertension prevalence in India is enormous. Recent evidence shows a prevalence of hypertension in India of 30.7% (Ramakrishnan et al., 2019).\n\nHypertension leads to myocardial infarction, cerebral infarction, heart failure, and kidney disease (James et al., 2014). Early diagnosis is thus necessary for managing hypertension and preventing future risks (Dalal et al., 2020). Lifestyle modifications and drug treatment are the two primary types of hypertension care. Managing lifestyle is the primary step in hypertension care for patients over 18 years of age (James et al., 2014). Lifestyle management including exercise and diet helps in reducing blood pressure (Lackland & Voeks, 2014). Stress management including various relaxation techniques such as meditation, prayer, and yoga also helps in reducing systolic blood pressure (Dusek et al., 2008).\n\nThere is increasing evidence that demonstrates clinically relevant benefits from self-monitoring and self-management of blood pressure. Evidence suggests a reduction of systolic BP by 2-8 mm/hg (Chobanian et al., 2003; Tucker et al., 2017). In the recent era, user-friendly technology plays an important role in addressing the challenges with the dissemination of important and relevant health information to the public. mHealth refers to the provision of healthcare services by mobile communications devices (Santo & Redfern, 2019). The increase in the use of smartphones and tablets has been accompanied by an increase in the use of mHealth applications. The use of mHealth in the self-care of chronic diseases such as hypertension is becoming increasingly popular. Most mHealth apps are designed to assist persons with hypertension in self-management by providing self-monitoring tasks, alerts, personalized information, and feedback (Santo & Redfern, 2019).\n\nIn India, the awareness, medical treatments, and control of hypertension remain poor despite its substantial prevalence. Around 33% of Indians use some mHealth application in their daily life. Although few applications are available in the market, there are no adequate applications customized to the Indian population (Santo & Redfern, 2019). A recent study conducted demonstrated that applications are not customized according to Indian users’ needs and expectations in regional language and lacked usability assessment by patients (Alessa et al., 2018; Santo & Redfern, 2019). Most of the evidence that determines the effectiveness of mHealth applications has been conducted in developed countries with very little evidence from developing countries, specifically the South Asian region and India in particular.\n\nTherefore, there is a need to develop an application that meets the local health information needs, provides information in the local language, and is designed based on patient usability feedback. Further studying the effectiveness of the application on knowledge about the disease, self-care among the participants, and blood pressure status of the patients with hypertension will throw more light with regards to this.\n\nThus, we aim to develop a user-friendly mHealth application for remote monitoring and self-management in persons with hypertension and assess its effectiveness. Further, we propose to test this application for its effectiveness in improving the knowledge, self-efficacy, health status, and self-management of persons with hypertension.\n\n\nMethods\n\nThe approval has been obtained from Institutional Ethics Committee (IEC No: 587-2021), and written consent from the participants will also be obtained. The study has been registered in Clinical Trial Registry - India (CTRI/2022/03/041544).\n\nThe study is proposed to be conducted in three phases. The first phase of this study will be a qualitative one, to identify the needs and expectations of people with hypertension in the Udupi district, Southern India. This phase will be carried out in three steps:\n\n1. Focus group discussions (FGDs) with persons diagnosed with primary hypertension\n\n2. In-depth interviews with general physicians and cardiologists\n\n3. Development of educational material\n\nFocus group discussions\n\nFor the FGDs, we will be including persons diagnosed with primary hypertension and who are being medically managed (ICD 10 code: I10), between the age of 18 and 60, of either gender, and have access to smartphones (Android) with internet connectivity. The exclusion criteria are people with visual impairment, who cannot read and comprehend either English or Kannada, and who are dependent on self-care. We will also be including caregivers of hypertensive patients above 18 years of age, who have had experience for more than a year and can understand English or Kannada, and have access to Android-based smartphones with internet connectivity. For this FGD, we will have a sample size of 8 participants. This is as per previous studies.\n\nThe participants will be screened and recruited from health centers of Udupi district, Southern India. They will be contacted in person by the primary investigator and the written informed consent will be obtained from eligible participants after explaining the study. The recruited participants will be asked to take part in FGDs which will be carried out for the proposed objective. The moderator, who is the primary investigator, and the assistant will be introduced to the participants and the purpose of the FGD, as well as the guidelines, will be briefed to them. Before the FGDs, the screening questionnaire will be designed based on the objective of the study and validated by five experts in the field of community medicine and qualitative study experts. Subsequently, a moderator guide will be designed which includes the research rules, explanation of confidentiality, introductions to the FGD, questions, probes and follow-up questions, and conclusion. The FGDs will be audio recorded and conducted in the community health center till thematic saturation is achieved. We will be conducting thematic analysis using ATLAS.ti software version 9 and the report will be prepared. The process of the FGD has been depicted in Figure 1.\n\nIn-depth interviews\n\nAn in-depth interview guide will be prepared separately for physicians and an interview will be conducted to know their views, ideas, and opinions on the proposed mHealth application. A total of five physicians will be approached in person for the in-depth interview. Interviews will be conducted in the OPD by the primary investigator. The interview will be audio recorded. Thematic analysis will be carried out using ATLAS Ti version 9. The obtained information will be compiled and will be incorporated into the mHealth application. The process of in-depth interview is shown in Figure 2.\n\nDevelopment of educational information module on self-management for persons with hypertension\n\nEducational information material will be prepared based on the literature review and according to recommendations for the conception and efficacy of educational tools referring to content, language, organization, layout, illustration, learning, and motivation. The developed educational information material will be translated and back-translated to and from Kannada. The information will be content reviewed using PEMAT-A/V by five physicians and five health information professionals and any comments will be considered while preparing the final version (Shoemaker et al., 2014).\n\nThis phase of the study will be to develop a mHealth application for self and remote monitoring and self-management of hypertension and pilot test the application (to assess the acceptability, feasibility, usability, and user-friendliness of the app). Agile development design will be used to develop the application using Android studio (Moe et al., 2010).\n\nThe mHealth application will be developed in five steps as follows:\n\nRequirements analysis\n\nInformation based on end users' needs and expectations about the mHealth application will be captured as per the requirements to develop the mHealth application (data will be captured in phase 1 of the study).\n\nDesigning the requirements\n\nTeam members (i.e. Health Information Professionals, Physicians, Cardiologists, and Software developers) will be identified and the requirements of the end users will be discussed. Based on the requirements, high and low-level designing of the mHealth application will be done.\n\nDevelopment\n\nThe mHealth application will be developed based on the requirements specified by the end users. This step includes coding the application based on the design. Android Studio, an open source for Android software development will be used to develop the proposed mHealth application. The mHealth mobile application will connect to a backend database application (web-based) to help administration of content, visualization, and analysis of the data collected.\n\nTesting and quality assurance\n\nThe developed application will undergo standard testing and a quality assurance process to identify and rectify the issues and bugs.\n\nPilot testing and feedback\n\nA pilot test will be carried out once the application is developed and will be installed in Android-based smartphones among persons with hypertension to assess the acceptability, feasibility, usability, and user-friendliness of the application. Feedback from the end-users about the mHealth application would be obtained for necessary modifications in the application.\n\nDeployment\n\nThe developed application will be ready for use by persons with hypertension after pilot testing for acceptance and use for self-monitoring and self-management of hypertension.\n\nThe steps for the development of the software is shown in Figure 3.\n\nFigure 3 shows the process of android software development.\n\nFinally, requirement analysis will be carried out by the investigator along with experts by obtaining the requirements from the end-users. Based on the requirement, an investigator will design the mHealth application which includes various modules, layouts, tabs, widgets, and contents. The coding of the application will be done by the software developer with the help of an investigator. The developed application will be tested for quality assurance and will be pilot tested among the participants. The investigator will be involved in the front and backend process of software development.\n\nThe application will consist of blood pressure monitoring (Bluetooth enabled as well manually entered), weight, height, body mass index (BMI), medication reminder and physical activity (step count), and graphical reports of BP and weight. Weekly and monthly summaries (which can be converted into PDF and shared), abnormal warnings, Dietary Approaches to Stop Hypertension (DASH) diet plan, health education material, and recent updates on hypertension management will also be provided.\n\nAn open-label, parallel cluster randomized trial will be conducted from October 2023 to March 2025 with villages as the unit of randomization into the intervention and control arm with a 1:1 allocation. 12 villages in the Udupi district will be considered as the clusters included in the sampling frame and eligible for randomization. People diagnosed with hypertension within these clusters will be the targeted population. The eligibility criteria for the clusters include a hypertensive population strength ≥ 10. In case a cluster fails to have the prescribed strength, it will be clubbed with an adjacent cluster to achieve the required number. For the individual participants, the eligibility criteria would be people diagnosed with primary hypertension and on medical management (ICD 10 code: I10) for the last 5 years, of either gender, between the age of 18 and 60 years, who will be able to comprehend health messages in English or Kannada and have an access smartphone. We will be excluding people undergoing any other structured behavior change intervention and who are dependent for self-care.\n\nThe sample size was calculated based on the change in blood pressure status, which is the primary outcome variable, and was determined using the formula:\n\nWhere,\n\nn = number of subjects in each arm of the trial\n\nP1, P2 = success rates in the intervention and control groups respectively\n\nm = cluster size (For equal cluster size)\n\nρ = Intraclass correlation coefficient\n\n1+(m-1) ρ = Design effect\n\nConsidering a design effect of 1.45 (Intra class correlation coefficient for self-care in hypertension has been computed as 0.05 from literature) (Lee et al., 2020) and anticipating a 10% reduction in blood pressure readings attributable to the intervention, for a power of 90% at 5% level of significance for a 2-sided test, the required minimum sample in each arm is 118 distributed across 12 clusters of size 10. Therefore, the total sample size will be 236.\n\nRandomization will be carried out at the cluster level i.e. the villages would be the units of randomization. The entire process of randomization will be carried out by non-participating biostatistics faculty. Sequence generation will be done according to the block technique, with a block size of 4 for 2 allocation categories: 'A' for the new intervention and 'B' for the standard intervention, yielding 6 different combinations or sequences. Allocation concealment will be achieved through coded opaque sealed envelopes. Thereafter, the interventions will be allocated to the recruited clusters by the investigators strictly according to the sequence of the block. Each of the 3 steps of randomization, namely, sequence generation, allocation concealment, and implementation will be carried out by an independent faculty.\n\nFor the participants in the intervention group, the mHealth application will be installed on their smartphones, and the required data will be entered by the primary investigator. A demo of the application features will be provided. Participants from the intervention group will also be given automated BP apparatus and will be oriented on measuring blood pressure and the measurements will be updated in the mHealth application on the daily basis. The control group will receive standard care which includes advice to adhere to their prescribed medication and lead an active lifestyle. Baseline measurements like blood pressure, knowledge and practice of management of blood pressure, self-efficacy, and health status will be obtained from the recruited participants in both groups. Blood pressure will be measured with an electronic BP apparatus (Dr. Trust BP monitor-118), which will be calibrated periodically. Knowledge and practice will be assessed using a hypertension fact questionnaire. Self-efficacy using Medication Adherence Self-Efficacy Scale (MASES) and Self-Efficacy for Managing Chronic Disease 6-item Scale will be assessed and health status using SF-36 questionnaire will be assessed for pre and post-test (Fernandez et al., 2008; Lorig et al., 2001; Ware & Gandek, 1998). For any reason, if the participant is unable to use the application, we will be discontinuing the intervention regimen for that participant. Regular phone calls will be made to remind them to use the application and to track their BP. The participants will be allowed to withdraw from the study at any given time as per their decision. The consort flowchart of the phase 3 is shown in Figure 4.\n\nData will be entered and analyzed using SPSS version 22. The outcomes will be analyzed at the cluster and the individual level by intention-to-treat as well as per protocol analyses. Baseline data of all collected variables will be reported at both the individual as well as at the cluster level. The flow of participants and clusters through the various stages of the trial will be depicted through a flow diagram, giving the absolute number and reasons for non-inclusion, and non-adherence at various steps from the point of approach, recruitment, randomization, a follow-up to analysis, in both the arms. The effectiveness will be analyzed according to the principles of both intention-to-treat as well as per-protocol analysis.\n\nCluster-level analysis\n\nCategorical data will be summarized as proportions and quantitative data as means (or medians) and standard deviations (or interquartile range). Risk will be estimated as Relative Risk (RR). Chi-square test, repeated measures ANOVA (or Friedman's Test) will be used to compare the 2 groups and assess the significance of any difference therein. An estimate of the effect size for the various variables will be reported along with its precision as a 2-sided 95% confidence interval. A p-value of less than 0.05 will be taken as statistically significant. Regression models will be used according to standard protocols to find out significant factors affecting the intervention at the cluster level.\n\nIndividual-level analysis\n\nIt will be similar to that of the cluster-level analysis except for the fact that adjustments will be made for clustering. Hierarchical regression will be used according to standard protocols to find out significant factors affecting the intervention. In addition, the values of the intra-cluster correlation coefficient for the various outcome measures will also be reported. Subgroup analyses will be carried out and a multiplicity of analyses will be addressed.\n\nStudy status\n\nCurrently the focus group discussion and the in-depth interview is on-going. We plan to complete the analysis of Phase 1 by December 2022. Phase 2 of the study which is the application development will be commenced January 2023 and completed by September 2023. Phase 3 of the study which will be the determination of the effectiveness of the application will be conducted from October 2023 to March 2025.\n\nDissemination\n\nWe will be disseminating the results of the study in the form of conference presentations and as manuscripts.\n\n\nConclusion\n\nUse of mHealth applications for remote monitoring and self-management helps reduce the burden on health-service system. In the proposed research, we will be developing an mHealth application for people with hypertension to meet the local health information needs, provide information in regional language and will be designed based on patient usability feedback. The application will monitor blood pressure, physical activities, medication, diet, and provide recent updates on hypertension management. This application, if found effective, can improve the health status, knowledge, and self-care approach among hypertensive patients by installing the mHealth application. Additionally, it may even minimize the problems caused for accessing healthcare due to the recent pandemic and can be the solution to evade in-person sessions.\n\n\nAuthors’ contributions\n\nAll authors contributed to the ideas in this protocol. P.L.S., led the writing, and all authors approved the final version.",
"appendix": "Data availability\n\nNo underlying data are associated with this article.\n\nfigshare: FGD guide. https://doi.org/10.6084/m9.figshare.21463152.v1 (Salins, 2022a).\n\nfigshare: Interview guide.docx. https://doi.org/10.6084/m9.figshare.21485901.v1 (Salins, 2022b).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nfigshare: SPIRIT checklist for ‘Effectiveness of an mHealth application on remote monitoring and self-management of persons with hypertension in a coastal taluk of Udupi district: A study protocol’. https://doi.org/10.6084/m9.figshare.21485946.v1 (Salins, 2022c).\n\n\nReferences\n\nAlessa T, Abdi S, Hawley MS, et al.: Mobile Apps to Support the Self-Management of Hypertension: Systematic Review of Effectiveness, Usability, and User Satisfaction. JMIR Mhealth Uhealth. 2018; 6(7): e10723. PubMed Abstract | Publisher Full Text\n\nChobanian AV, Bakris GL, Black HR, et al.: Seventh report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure. Hypertension (Dallas, Tex.: 1979). 2003; 42(6): 1206–1252. Publisher Full Text\n\nDalal J, Sethi KK, Guha S, et al.: Screening for Hypertension in Asymptomatic Individuals in India: An Expert Consensus Statement. J. Assoc. Physicians India. 2020; 68(4): 73–79. PubMed Abstract\n\nDanaei G, Finucane MM, Lin JK, et al.: National, regional, and global trends in systolic blood pressure since 1980: Systematic analysis of health examination surveys and epidemiological studies with 786 country-years and 5·4 million participants. Lancet (London, England). 2011; 377(9765): 568–577. PubMed Abstract | Publisher Full Text\n\nDusek JA, Hibberd PL, Buczynski B, et al.: Stress management versus lifestyle modification on systolic hypertension and medication elimination: A randomized trial. J. Altern. Complement. Med. (New York, N.Y.). 2008; 14(2): 129–138. PubMed Abstract | Publisher Full Text\n\nFernandez S, Chaplin W, Schoenthaler AM, et al.: Revision and validation of the medication adherence self-efficacy scale (MASES) in hypertensive African Americans. J. Behav. Med. 2008; 31(6): 453–462. PubMed Abstract | Publisher Full Text\n\nJames PA, Oparil S, Carter BL, et al.: 2014 evidence-based guideline for the management of high blood pressure in adults: Report from the panel members appointed to the Eighth Joint National Committee (JNC 8). JAMA. 2014; 311(5): 507–520. Publisher Full Text\n\nKarmakar N, Nag K, Saha I, et al.: Awareness, treatment, and control of hypertension among adult population in a rural community of Singur block, Hooghly District, West Bengal. J. Educ. Health Promot. 2018; 7: 134. PubMed Abstract | Publisher Full Text\n\nLackland DT, Voeks JH: Metabolic syndrome and hypertension: Regular exercise as part of lifestyle management. Curr. Hypertens. Rep. 2014; 16(11): 492. PubMed Abstract | Publisher Full Text\n\nLawes CMM, Vander Hoorn S, Rodgers A, et al.: Global burden of blood-pressure-related disease, 2001. Lancet (London, England). 2008; 371(9623): 1513–1518. PubMed Abstract | Publisher Full Text\n\nLee YL, Lim YMF, Law KB, et al.: Intra-cluster correlation coefficients in primary care patients with type 2 diabetes and hypertension. Trials. 2020; 21(1): 530. PubMed Abstract | Publisher Full Text\n\nLorig KR, Sobel DS, Ritter PL, et al.: Effect of a self-management program on patients with chronic disease. Effective Clinical Practice: ECP. 2001; 4(6): 256–262. PubMed Abstract\n\nMoe N, Dingsøyr T, Dybå T: Agile Software Development. 2010.Reference Source\n\nRamakrishnan S, Zachariah G, Gupta K, et al.: Prevalence of hypertension among Indian adults: Results from the great India blood pressure survey. Indian Heart J. 2019; 71(4): 309–313. PubMed Abstract | Publisher Full Text\n\nSalins P:FGD GUIDE. figshare. Dataset.2022a. Publisher Full Text\n\nSalins P:Interview guide.docx. figshare. Dataset.2022b. Publisher Full Text\n\nSalins P:SPIRIT-Checklist. figshare. Dataset.2022c. Publisher Full Text\n\nSanto K, Redfern J: The Potential of mHealth Applications in Improving Resistant Hypertension Self-Assessment, Treatment and Control. Curr. Hypertens. Rep. 2019; 21(10): 81. PubMed Abstract | Publisher Full Text\n\nShoemaker SJ, Wolf MS, Brach C: Development of the Patient Education Materials Assessment Tool (PEMAT): A new measure of understandability and actionability for print and audiovisual patient information. Patient Educ. Couns. 2014; 96(3): 395–403. PubMed Abstract | Publisher Full Text\n\nTucker KL, Sheppard JP, Stevens R, et al.: Self-monitoring of blood pressure in hypertension: A systematic review and individual patient data meta-analysis. PLoS Med. 2017; 14(9): e1002389. PubMed Abstract | Publisher Full Text\n\nWare JE, Gandek B: Overview of the SF-36 Health Survey and the International Quality of Life Assessment (IQOLA) Project. J. Clin. Epidemiol. 1998; 51(11): 903–912. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "196811",
"date": "12 Dec 2023",
"name": "Blessing Onyinye Ukoha-kalu",
"expertise": [
"Reviewer Expertise disease management",
"clinical trials",
"mental health",
"evidence synthesis",
"mixed methods study"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this paper. I must commend the authors for taking the time to write down this protocol in a clear manner however, I have few comments which I believe will improve the clarity and reproducibility of the protocol.\nAbstract\nThe abstract is generally clear, but some sentences could be streamlined for improved readability. It is important that readers who are not in this field are able to understand how this research will be carried out. To enhance the impact of your opening statement, you might add some statistics or key figures related to the global prevalence of hypertension and its impact on health. In the \"Methods\" section, consider briefly explaining what Agile development design is, as this might not be familiar to all readers. You could mention the anticipated duration of each phase, providing a rough timeline for the study. Instead of stating the sample size as \"236 people from 12 villages,\" you might specify how many participants will be assigned to each group (intervention and control) to give a clearer sense of the distribution. Mention any criteria used for selecting these specific villages and participants.\n\nIntroduction\nWhen citing statistics or findings, consider including more recent sources, especially if available, to provide up-to-date information. Whenever possible, include a sentence or two explaining the findings or implications of the cited studies. It might be beneficial to briefly explain what kind of self-monitoring tasks, alerts, personalized information, and feedback mHealth apps provide to readers who might not be familiar with the concept. You could elaborate more on the challenges faced due to the lack of applications customized to the Indian population, including how this gap impacts hypertension management. Specify the key features of the mHealth application you plan to develop. For example, will it be available in regional languages? What specific features will it offer for hypertension self-management?\nMethods\nMention the name of the institution where the Institutional Ethics Committee approval was obtained. The study design could be reflected in the title of the study example: randomised clinical trial, mixed-methods, qualitative e.t.c When discussing FGDs, consider explaining the rationale behind involving caregivers of hypertensive patients in the discussions. Provide a brief explanation of Agile development design for readers who might not be familiar with this approach. Clarify whether the application development will occur continuously from January to September 2023 or if it will have distinct development periods. Elaborate on the randomization process at the cluster level, including how the blocks are assigned to intervention and control arms. Mention how many clusters will be in each arm after randomization. Clarify whether the pilot test and feedback phase will include both intervention and control groups or only the intervention group. Specify how missing data will be handled in the analysis. Provide a brief explanation of hierarchical regression and its role in the analysis. Kindly state the potential strenghts and limitations you may encounter while carrying out this study and how you intend to circumvent these.\nReferences I strongly encourage the use of more recent literature and citations.\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": "196844",
"date": "31 May 2024",
"name": "Kamakshi Lakshminarayan",
"expertise": [
"Reviewer Expertise Research in mHealth facilitated management of hypertension by engaging patients",
"post-stroke outcomes and post-stroke cognitive impairment."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper describes the protocol to develop and test a customized mHealth application to monitor HTN. The investigators describe a 3 step process including a needs and expectation assessment (phase 1), development and pilot testing a mHealth application for HTN management (phase 2), and conducting a cluster randomized trial to definitively test the mHealth application for HTN management (phase 3). DETAILED COMMENTS Introduction Improving HTN management is important since the prevalence of HTN is high (~30%). The authors state that the awareness of HTN, treatment and control are poor in India (para 4, line 1). However, they do not cite the numbers or references to back up this claim. Similarly, data sources or references for the fact presented that 33% of Indians use mHealth in daily life would be helpful. Methods Phase 1 In phase 1, the investigators will identify needs and expectations of people with HTN in Udupi using FGDs with patients, in-depth interviews with physicians and development of educational material. Re: the FGD, they propose a sample size of 8 participants total. Does this include patients and caregivers? Does this mean that they will have a single focus group of 8 participants? Re: sample size – a focus group size ranging from 5-8 is reasonable. However, literature also supports the use of multiple focus groups to reach thematic saturation with 3-6 individual focus groups (each group has multiple participants) needed to reach 90% saturation. (Guest G et al, 2017) [Ref 1]. Will the focus groups proposed by the authors encompass both genders? Be socioeconomically diverse? Overall the Focus Groups need to be re-evaluated in terms of being representative of the patient population (sex, age, education, socioeconomic status) which is hard to do with just a sample size of 8. Phase 2 In Phase 2, the team will develop a mHealth monitoring for self-monitoring and self-management of HTN. They also state that there is remote monitoring. Remote monitoring implies that the BP data are being transmitted to someone – a healthcare provider? If the data is being transmitted, this is not explained clearly. There insufficient information on development and it is hard to evaluate the experience of the development team and whether the implementation will be successful. How many patients will evaluate the pilot implementation. The application includes BP monitoring and weight / height / BMI and step counts and medication reminder. How is weight monitored? Is it a digital scale? How often is weight measured? Are they tracking weight and BMI as outcomes in addition to BP? Is there a fitbit application to perform step count? There are too many missing details. Phase 3 While the mHealth BP app is going to be developed – it is not clear that this is necessary. The BP monitor that they propose – Dr. Trust BP monitor has an App. The team will save time and resources by using the pre-existing App and perhaps only creating an app for medication reminders, nutrition support, and physical activity measurement. What are all the outcomes? Is it change in systolic and diastolic BP, change in BMI as well as changes in self-efficacy? This needs to be clearly specified. Overall, this protocol lacks sufficient detail and specification.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1393
|
https://f1000research.com/articles/11-1387/v1
|
25 Nov 22
|
{
"type": "Research Article",
"title": "Validation of an instrument in Latin America to measure fear perception of the consequences of a large-scale war (war-effect)",
"authors": [
"Christian R. Mejia",
"Renzo Felipe Carranza Esteban",
"Oscar Mamani-Benito",
"Luciana D Garlisi-Torales",
"Anthony Bautista-Pariona",
"Camilo Vega-Useche",
"Jamil Cedillo-Balcázar",
"Edilaine Braga-Souza",
"Carlos Jesus Iglesias Botello",
"Vanessa Ortiz",
"José Armada",
"Oriana Rivera-Lozada",
"Christian R. Mejia",
"Renzo Felipe Carranza Esteban",
"Oscar Mamani-Benito",
"Luciana D Garlisi-Torales",
"Anthony Bautista-Pariona",
"Camilo Vega-Useche",
"Edilaine Braga-Souza",
"Carlos Jesus Iglesias Botello",
"Vanessa Ortiz",
"José Armada",
"Oriana Rivera-Lozada"
],
"abstract": "Background: The Russia-Ukraine war brought immediate and delayed socio-economic consequences. In general, the repercussions caused fear all over the world. This study aims to validate an instrument for measuring fear perception caused by the consequences of a large-scale war in Latin American citizens. Methodology: An instrumental study in which 1705 residents of Bolivia, Colombia, Ecuador, Panama, Paraguay, Peru and other countries were surveyed through a virtual format. A literature search, expert judgment, preliminary (then exploratory and confirmatory) analysis, as well as reliability assessment were carried out. Results: The skewness and kurtosis values of the 13 questions did not exceed the range ± 1.5 and showed significant correlations (>0.30). The Kaiser-Meyer-Olkin index (0.962) and Bartlett's test (19558.5; df=78; p=0.001) had good indicators. The parallel analysis suggested a single factor, which explained 75.59% of the total variance. The confirmatory factor analysis generated an instrument with six items (χ2=47.33, df=9, p=0.001; RMR=0.010; GFI=0.990; CFI=1.00; TLI=0.990; and RMSEA=0.050), with an overall Cronbach's Alpha=0.949 (95% CI=0.94–0.95). Conclusion: A six-item instrument that measures the perception of fear caused by the consequences of a large-scale war was validated in half a dozen Latin American countries. This short and valid instrument can be administered to a broad population in Latin America.",
"keywords": [
"Latin America",
"War",
"Fear",
"Perception",
"Ukraine",
"Russian Federation."
],
"content": "Introduction\n\nThe coronavirus disease 2019 (COVID-19) pandemic is coming to an end, two years after it started in China and spread to practically all habitable territories in the world.1,2 During this time, it has generated material and human costs for most families in different countries worldwide. No one can deny the great economic, social, mental and general health repercussions that various populations have suffered as a result of this pandemic.3–9\n\nThis is the context in which another event that has had repercussions worldwide begun, the war between Russia and Ukraine. This conflict began to generate many repercussions at all levels in different countries.10 This is due to the possibility of an expansion of the war, especially due to the fact that the United States of America (USA) and its allies supported Ukraine, while China and its allies supported Russia.10–12 This led several people to think that there would be direct consequences generated by a war that would even reach far away regions, such as Latin America.13,14\n\nSubsequently, a series of consequences at the economic level started, since the USA and its allies imposed multiple sanctions on Russia. Russia did not want to be outdone and blocked all exports of oil, wheat and other products that they exported worldwide.15 This generated a series of repercussions for the economy, as there was an increase in prices in regard to oil and basic commodities, among many other items.16\n\nIn this panorama, many other repercussions have been foreseen, some acute, others that could last for several months.16 Therefore, it is important to measure the population's perception of the possible consequences of a war, not only in this context but also other possible war complications that may arise.10,16 It is important to validate an instrument in Latin America because it is a very diverse region and is still in the context of the pandemic, which means that the repercussions of the war are mixed with those of COVID-19. Therefore, the objective of the research was to validate an instrument to measure fear perception caused by the consequences of a large-scale war in Latin American citizens.\n\n\nMethodology\n\nObservational, analytical, instrumental and cross-sectional study.\n\nNon-probabilistic sampling was used to recruit 1705 participants. The participants came most frequently from Peru, Paraguay, Panama, Ecuador, Colombia and Bolivia. Citizens over 18 years of age and residing in a Latin American country during the days of the survey (first three weeks of the conflict between Russia and Ukraine) were included. Those who did not agree to participate in the research and those with surveys that were incompletely answered (fewer than 150) were excluded.\n\nThe questionnaire (war-effect) was administered. It was previously developed by the researchers and subjected to content and consistency evaluation procedures by experts. The initial instrument, which had 13 items, was administered to the participants virtually, using the most frequently used media (Facebook, WhatsApp and Instagram). It is worth mentioning that each of the questions had five response options formulated in accordance with the Likert format (from strongly disagree to strongly agree).\n\nAfter ethical approval, the war-effect questionnaire was analyzed and reviewed by the research team, before the evidence of content validity of the scale was analyzed. To this end, we requested the judgment of seven experts in different countries of Latin America (who were medical specialists, epidemiologists, teachers with master's or doctoral degrees, as well as some researchers with scientific publications). In this step, the relevance, representativeness and clarity of the items were analyzed.\n\nSubsequently, from 5th to 23rd March 2022, the administration of the balance was carried out virtually through Google forms, thanks to the participation of multiple collaborators in all the countries involved in this research. Before filling in the instrument, the participants were informed of the objective of the research and were asked to give their consent to proceed to respond. The participation was completely voluntary and anonymous.\n\nDescriptive analysis and exploratory factor analysis (EFA) were performed using the FACTOR Analysis program version 11.05. Thus, the mean, standard deviation, skewness and kurtosis of the 13 items of the scale were analyzed. Regarding the skewness and kurtosis coefficient, the value ± 2 was taken into account.17 For the EFA, the Kaiser-Meyer-Olkin coefficient (KMO) and Bartlett's test were considered. In addition, the estimation method we used was unweighted least squares with Promin rotation.18\n\nIn regard to the confirmatory factor analysis (CFA), the AMOS statistical program (version 21) was used, where structural equation modeling (SEM) was considered. The goodness-of-fit index (GFI), the Tucker-Lewis index (TLI) and the comparative fit index (CFI) were analyzed. Also, the parameters for the root mean square error of approximation (RMSEA) and the root mean square error index (RMR) were taken into account, following the criteria proposed by Hu & Bentler.19 These authors stated that the GFI, AGFI, TLI and CFI should be greater than 0.9 and the RMSEA lower than 0.08. Finally, the reliability of the scale was calculated using the SPSS statistical program (version 25.0) and its respective confidence intervals.20\n\n\nResults\n\nThe expert judgment shows that the 13 items received a favorable evaluation by the experts in the great majority of results (V>0.7). Only the relevance and clarity of Item 9 had a value of 0.7. In addition, we can see that almost all the values of the lower limit (Ll) of the 95% CI are appropriate (Ll>0.59). Also, these values were lower in the case of the relevance and clarity of Item 9. Despite this, as they were in the appropriate threshold, they entered the second stage of validation. Thus, the war-effect scale in Latin America reports evidence of content-based validity (Table 1).\n\nTable 2 shows the calculation of the mean, standard deviation, skewness and kurtosis (descriptive statistics) of the 13 items of the war-effect scale. It is observed that Item 1 had the highest mean score (M=3.66) and that Item 13 shows the highest variability (SD=1.07). The skewness and kurtosis values do not exceed the range ± 1.5.17 Moreover, the correlation between items were significant (all values>0.30).\n\nAn EFA was performed after calculating the Kaiser-Meyer-Olkin index (KMO=0.962) and Bartlett's test (19558.5; df=78; p=0.001), both of which were good. The unweighted least squares with Promin oblique rotation method and the parallel analysis were used to determine the factors, which suggested the extraction of a single factor. The factor reached explains 75.59% of the total variance of the scale and its factor loadings range from 0.785 to 0.896 (Table 3).\n\nA CFA was performed in order to analyze the evidence of validity, based on the internal structure of the war-effect scale. The results of the original model reported unsatisfactory goodness-of-fit indices. Therefore, through the index modification technique, two respecifications were performed. In the first one, Items 9, 10, 12 and 13 were eliminated, but a satisfactory fit was not achieved. In the second respecification, Items 1, 2 and 3 were eliminated and a satisfactory factor structure model was obtained (Table 4).\n\nThe FI show that the six-item single-factor model is adequate (χ2=47.33, df=9, p=0.001; RMR=0.010; GFI=0.990; CFI=1.00; TLI=0.990; and RMSEA=0.050) (Figure 1).\n\nThe scores of the war-effect scale are reliable (α=0.949; 95% CI=0.94–0.95). This instrument can be administered and we suggest, to determine those who have a greater perception of the repercussions of war, adding the scores (strongly disagree=1 point; disagreed=2 points; indifferent=3 points; agree=4 points; strongly agree=5 points). Having all the scores of the participants, those who are in the top tertile of the scores (33% of the best scores) should be considered those who perceive greater repercussions of a possible war (Figure 2).\n\n\nDiscussion\n\nIn this study, 1705 responses were collected from Latin American residents to validate the “war-effect” scale. According to the values obtained in the statistical analysis of the scale and each of its items, we can conclude that the scale is a reliable method to measure and compare, the perception of war and the approach within Latin America. The analysis performed is similar to that proposed by Yuchun Zhou et al, in their work on how to develop and validate scales.21 Optimal results were obtained at all phases, and it was executed in a large population of multiple countries during the most critical weeks of the conflict between Russia and Ukraine; therefore, this scale can be used in multiple contexts and countries.\n\nThe instrument designed and validated in this research (war-effect) can be used and administered in the current context of the armed conflict between Russia and Ukraine. Moreover, it is designed to have a wide margin of action so it can be applied in different scenarios of armed conflicts, regardless of their scope. This instrument allows us to evaluate fear perception of consequences resulting from war in different war scenarios and situations, due to the intrinsic adaptability of the variables established in the war-effect questionnaire. On the other hand, this questionnaire could be used along with other instruments and scales that allow the evaluation of other components of the population’s mental health, as well as other changes influenced by the war context.22–24\n\nWe have included questions that permit us to assess fear of the economic consequences of the conflict between Ukraine and Russia in the Latin American population. This is important because the economic and product exchange was stagnated between America and the conflict zone. This was not only due to the restrictions imposed, but also to the devaluation of the Russian currency, and the decrease in the supply of products, among others.25 This will affect the economy of many countries in our region. For example, a decrease of up to 90% of bananas, flowers, and shrimps is expected in Ecuador. In addition, in Paraguay and Colombia, it has caused a limitation in meat export. Furthermore, within the framework of this conflict, the price of oil in Paraguay has increased by up to 70%.26\n\nThese market changes are causing unemployment, strikes, and economic instability in Latin America. However, there could also be positive effects for some countries; for example, the limitation of fertilizer exports by Russia could benefit Bolivia by boosting its industry. In the case of Panama, this country remains neutral as long as the Panama Canal remains safe and open for the peaceful transit of ships of all nations on equal terms.27,28 This shows us that there could be several, very varied consequences in the countries on this side of the world, but that they must be evaluated with instruments that have passed a rigorous validation process.\n\nThere are questions that measure the direct repercussion for family/friends living near the conflict, with which we can measure how it affects mental health. In addition, it is known that there are almost 100 thousand immigrants in Ukraine, coming from diverse countries, including Latinos, who now face not only the problems of discrimination, but challenges generated while trying to escape the war.29,30 We can also mention the large group of migrants coming from Latin America, in recent years, not only because of the conflicts that have occurred in Venezuela, but also because of the poor situation in other countries such as Argentina and Peru. Therefore, it is necessary to have this type of instruments in order to determine whether there are relatives or people we know in that part of the world. In addition, this survey could be used for other wars or conflict, in general, occurring in other parts of the world.\n\nThe study’s limitation was the use of convenience sampling, which does not allow extrapolation of the results to the entire Latin American population or to the countries where it was administered. However, since it had a large population, this type of instrumental study does not require a random sampling; and more than 283 respondents were obtained for each of the six final questions. All in all, this research shows us an instrument that can be taken into account for different realities. Furthermore, it is the first instrument of its kind in the Latin American context. Additionally, it can be used for situations such as this Russian-Ukrainian war and in possible future warlike conflicts.\n\nTaking into account all that was generated in the research, it is concluded that a short instrument was validated in half a dozen Latin American countries in the context of the war between Russia and Ukraine. All the validation stages were satisfactory and with very acceptable indicators. Recommendations for analysis are also provided, using the tertiles after the addition of the scores.\n\n\nData availability\n\nDANS-EASY: Validation of an instrument in Latin America to measure fear perception of the consequences of a large-scale war (war-effect). https://doi.org/10.17026/dans-239-fyz5.31\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nEthical approval\n\nThis research project was approved by the Ethics Committee of Universidad Norbert Wiener (Ethics Committee Resolution No. 1649-2022).\n\n\nInformed consent\n\nAll respondents gave their written consent to participate in this study and fully answered the 13 initial questions of the previously created survey.",
"appendix": "References\n\nKhan M, Adil SF, Alkhathlan HZ, et al.: COVID-19: A Global Challenge with Old History, Epidemiology and Progress So Far. Mol. Basel Switz. December 23, 2020; 26(1): E39. Publisher Full Text\n\nRabaan AA, Al-Ahmed SH, Sah R, et al.: SARS-CoV-2/COVID-19 and advances in developing potential therapeutics and vaccines to counter this emerging pandemic. Ann. Clin. Microbiol. Antimicrob. September 2, 2020; 19(1): 40. PubMed Abstract | Publisher Full Text\n\nNicola M, Alsafi Z, Sohrabi C, et al.: The socio-economic implications of the coronavirus pandemic (COVID-19): A review. Int. J. Surg. Lond. Engl. junio de 2020; 78: 185–193. PubMed Abstract | Publisher Full Text\n\nLagos DG, Poulaki P, Lambrou P: COVID-19 and Its Impact on Tourism Industry. Adv. Exp. Med. Biol. 2021; 1318: 815–824. Publisher Full Text\n\nRasheed R, Rizwan A, Javed H, et al.: Socio-economic and environmental impacts of COVID-19 pandemic in Pakistan-an integrated analysis. Environ. Sci. Pollut. Res. Int. April, 2021; 28(16): 19926–19943. PubMed Abstract | Publisher Full Text\n\nHossain MM, Tasnim S, Sultana A, et al.: Epidemiology of mental health problems in COVID-19: a review. F1000Res. 2020; 9: 636. PubMed Abstract | Publisher Full Text\n\nJones EAK, Mitra AK, Bhuiyan AR: Impact of COVID-19 on Mental Health in Adolescents: A Systematic Review. Int. J. Environ. Res. Public Health. March 3, 2021; 18(5): 2470. PubMed Abstract | Publisher Full Text\n\nAfonso P: The Impact of the COVID-19 Pandemic on Mental Health. Acta Medica Port. May 4, 2020; 33(5): 356–357. PubMed Abstract | Publisher Full Text\n\nDong L, Bouey J: Public Mental Health Crisis during COVID-19 Pandemic. China. Emerg. Infect. Dis. July, 2020; 26(7): 1616–1618. PubMed Abstract | Publisher Full Text\n\nSheather J: As Russian troops cross into Ukraine, we need to remind ourselves of the impact of war on health. BMJ. February 25, 2022; 376: o499. Publisher Full Text\n\nQuinn VJM, Dhabalia TJ, Roslycky LL, et al.: COVID-19 at War: The Joint Forces Operation in Ukraine. Disaster Med. Public Health Prep. March 25, 2021: 1–8. PubMed Abstract | Publisher Full Text\n\nKoonin EV: Science in times of war: oppose Russian aggression but support Russian scientists. EMBO Rep. March 15, 2022; 23: e54988. Publisher Full Text\n\nStone R: War in Ukraine poses stark choices for scientists. Science. March 4, 2022; 375(6584): 942–943. PubMed Abstract | Publisher Full Text\n\nNott E: Ukraine invasion: Why I fear for Ukraine’s healthcare workers. BMJ. March 7, 2022; 376: o605. Publisher Full Text\n\nFernández Castañeda C: Medidas restrictivas en la Unión Europea: el nuevo régimen de sanciones contra las violaciones y abusos graves de los derechos humanos en el contexto internacional. Madrid:CEU Ediciones;2022 [cited on March 29, 2022]; vol. 2022. .Reference Source\n\nGrundberger S, Arellano Á, Coto A: El poder de Rusia en Latinoamérica. KONRAD-ADENAUER-Stift. 2022; 16.\n\nPérez E, Medrano L: Análisis factorial exploratorio: bases conceptuales y metodológicas. Revista Argentina de Ciencias del Comportamiento. 2010; 2(1): 58–66.\n\nLorenzo-Seva U, Ferrando PJ: FACTOR: A computer program to fit the exploratory factor analysis model. Behav. Res. Methods. 2006; 38(1): 88–91. Publisher Full Text\n\nHu L, Bentler PM: Cutoff criteria for fit indexes in covariance structure analysis: Conventional criteria versus new alternatives. Struct. Equ. Model. Multidiscip. J. 1999; 6(1): 1–55. Publisher Full Text\n\nDomínguez-Lara SA, Merino-Soto C: ¿Por qué es importante reportar los intervalos de confianza del coeficiente alfa de Cronbach? Rev. Latinoam Cienc. Soc. Niñez Juv. 2015; 13(2): 1326–1328.\n\nZhou Y: A Mixed Methods Model of Scale Development and Validation Analysis. Measurement: Interdisciplinary Research and Perspectives. 2019; 17(1): 38–47. Publisher Full Text\n\nPoikolainen K, et al.: Fear of nuclear war increases the risk of common mental disorders among young adults: a five-year follow-up study. BMC Public Health. 30 Sep. 2004; 4: 42. PubMed Abstract | Publisher Full Text\n\nBraquehais MD, Sher L: Posttraumatic stress disorder in war veterans: a discussion of the Neuroevolutionary Time-depth Principle. J. Affect. Disord. 1-3 2010; vol. 125: 1–9. PubMed Abstract | Publisher Full Text\n\nHarb GC, Schultz J-H: The nature of posttraumatic nightmares and school functioning in war-affected youth. PLoS One. 25 Nov. 2020; 15: e0242414. PubMed Abstract | Publisher Full Text\n\nStatista: Guerra de Rusia y Ucrania 2022 - Datos estadísticos.31 de marzo de 2022.Reference Source\n\nEkos: ¿Cómo afecta al sector bananero el conflicto entre Ucrania y Rusia?.12 de marzo de 2022.Reference Source\n\nBBC News Mundo: Rusia y Ucrania: cuánto depende el mundo del petróleo y el gas ruso (y cuál es la situación en América Latina).8 de marzo de 2022.Reference Source\n\nSanahuja JA, Stefanoni P, y Verdes-Montenegro FJ: “América Latina frente al 24-F ucraniano: entre la tradición diplomática y las tensiones políticas”, Documentos de trabajo n° 62 (2ª época). Madrid:Fundación Carolina;2022.\n\nOrganización de Naciones Unidas:6 de marzo de 2022. ONU pide fin de la discriminación contra los ciudadanos de terceros países que huyen de Ucrania.Reference Source\n\nExpansión Datos Macro: Inmigración en Rusia.2019.Reference Source\n\nMejia CR, Carranza RF, Mamani-Benito O, et al.: Validation of an instrument in Latin America to measure fear perception of the consequences of a large-scale war (War-effect). DANS;2022. Publisher Full Text"
}
|
[
{
"id": "228634",
"date": "28 Dec 2023",
"name": "Petri Karkkola",
"expertise": [
"Reviewer Expertise health psychology",
"work psychology",
"psychometrics"
],
"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 on: Is the work clearly and accurately presented and does it cite the current literature?\nThe work does not cite any previous attempts to develop scales to measure fear perceptions related to war (or its consequences). Is this scale really the first of its kind? Furthermore, there is no really a rationale given for the initial item development and selection. In the Discussion, the inclusion of some questions is discussed, but it is unclear whether this relates to the final item selection or initial development. Please clarify the whole development process and cite previous work on similar scales, if it exists.\nComments on: Are sufficient details of methods and analysis provided to allow replication by others?\nSection on data analysis lacks important details or some subjects entirely. How were skewness and curtosis values +-2 \"taken into account\"? What does it mean? What does it mean that KMO and Bartlett's test \"were considered\"? Were some cut-off values utilized? Criteria for CFA are reported considerably better, but clear criteria of factor extraction for EFA are not reported. Methods for determining \"expert judgement\" are not introduced at all. How is Aiken's V utilized? This has been completely omitted and results in confusion.\nMethod to drop items in CFA is unclear. The authors refer to index modification technique (and surely mean consulting modification indices). However, did they only consider numbers and not content of the items? How was model 1 different from original regarding item content? How was model 2 different from both of them? Did the authors consider multidimensional factor model? This problem compounds with mentioned vagueness of the initial item development. Altogether, it would be beneficial to consider item content more.\nThis may be self-evident for most, but what was the language of the scale?\nComments on: Are the conclusions drawn adequately supported by the results?\nI consider several of the conclusion too optimistic. It can be argued that the authors have initially validated the structure of a unidimensional scale, of which contents comprise mostly perceived economical consequences of war. They state that it can be used in multiple contexts and countries. However, the authors do not represent any measurement equivalence (invariance) information, so we can not conclude that the items are interpreted similarly in the different countries. The manuscript should be expanded by testing measurement invariance (configural, metric, scalar, residual) between groups.\nIt is laudable that the authors have collected samples from different countries and that the sample size is probably adequate for the aims of the study. It is true that random sampling for testing structural validity of a meausure shouldn't be required. Having said this, for criterion-related validity testing, representative samples are preferred. Suggesting cut-off scores based on this distribution is somewhat suboptimal, because we do not really know if people in the highers tertile are in more pronounced risk for adverse outcomes compared to people around other scores.\nFinally, the authors should discuss if the instrument can really be considered to measure general fear perceptions of the consequences of war. Its contents are far more restricted.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "251557",
"date": "21 Mar 2024",
"name": "Holger Mölder",
"expertise": [
"Reviewer Expertise Political science & International Relations & International Security"
],
"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 completed survey on several Latin-American countries, but its relevance in comparative prospective should be more elaborated and the results presented in more coherent manner. Particularly the mutual interdependence factor between the pandemics and the war in Ukraine needs clarification, at the moment looks artificially created. The general process of research and methods has been described but incompletely. The tables and figures provided should be explained in the text. The choice of sample should be more elaborated, why such sample has been built and what it should tell the potential reader. Right now I recognize, the research has been completed, but its findings and how it contributes to previous are not elaborated, so the analysis should be strengthened. There can be found missing data in some figures. Lack of coherency is my main concern after reading this report.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1387
|
https://f1000research.com/articles/11-1386/v1
|
25 Nov 22
|
{
"type": "Research Article",
"title": "Spatial association of land-use areas and disease occurred by pesticide poisoning in Thailand",
"authors": [
"Kittipong Sornlorm",
"Roshan Kumar Mahato",
"Withaya Polnakoo",
"Krissana Aunthakot",
"Kittipong Sornlorm",
"Withaya Polnakoo",
"Krissana Aunthakot"
],
"abstract": "Background: Thailand is one of the Asian countries where high pesticides use is common for agriculture. Therefore, this study aimed to determine the spatial association between types of land-use areas and diseases occurred by pesticide poisoning in Thailand. Methods: This study was conducted by using the data set of average prevalence of diseases occurred by pesticide pollution and the land-use areas between 2018-2020. A Moran’s I and local indicators of spatial association (LISA) were used to identify the spatial autocorrelation between each type of land use areas and diseases developed due to pesticide poisoning in Thailand.\nResults: This present study observed that the average prevalence of disease occurred from pesticide pollution between 2018-2020 was 13.17 (95% CI: 10.83 - 15.50) per 100,000 in Thailand. The results identified the spatial global autocorrelation of each type of land used and occurrence of diseases due to pesticide pollution, including rice field areas, field crops, fruit trees and perennials, vegetables and flowers, and other agriculture with Moran’s I 0.270, 0.144, 0.606, 0.135, and 0.324 respectively. A spatial association between various factors and average prevalence of pesticide pollutions with significant LISA analysis were; rice field areas with eight high-high clusters and nine low-low clusters, field crops areas with three high-high clusters and 11 low-low clusters, fruit trees and perennials areas with eight high-high clusters and 12 low-low clusters, and six high-high clusters and four low-low clusters vegetable and flower areas. Similarly, nine high-high clusters and nine low-low clusters of other agricultural areas had been observed with prevalence of diseases acquired by pesticide pollution.\nConclusions: There was significant spatial association between land-use areas and diseases acquired by pesticide pollution in Thailand. It should be controlled by new policy recommendations for pesticides use for agriculture., especially, in provinces with more land-use areas for each type of plant.",
"keywords": [
"land-use areas",
"pesticide poisoning",
"spatial association patterns",
"pesticide use in Thailand"
],
"content": "Introduction\n\nFarmers use agrochemicals extensively to obtain high yields as well as being able to harvest in a timely manner that meets the market demand for a high price.1 Pesticides are parts of the agrochemicals widely used in most agricultural areas. These chemicals are considered as safe when used under a limited level following the proper application procedures. Some chronic diseases such as cancer, diabetes, Parkinson’s, and Alzheimer’s are reported to have direct or indirect relationships with pesticide exposures and develop related diseases.2 The use of pesticides has shown varying detrimental effects on humans as well as the environment. Presently, enough evidence is available to suggest their misuse and overuse in last few decades in most of the developing nations. Primarily, due to the lack of education, they are endangering the lives of farmers as well as the entire population and environment.3\n\nThailand ranks third for herbicide use per area and fourth in annual insecticide use compared to 15 Asian countries4 as most Thai farmers are still using a lot of agricultural chemicals.5 Both farmers and people living around the production area with long-term exposure to pesticides can develop chronic health effects such as neurotoxicity, gastrointestinal tract inflammations and cardiovascular related diseases.2,6 The organophosphates used in pesticides affect the nervous system which is one of the most common problems among agricultural workers. Many farmers are still not using full range of personal protection standards.7 There is a lack of rigorous legislation and regulations to control pesticides use in developing countries.8 So, pesticide related disease is one of the major public health problems in Thailand.9 However, the spatial impact assessment of pesticide poisoning for further planning and policymaking to explore areas with a high risk of using chemicals is still underexplored in Thailand. Therefore, this study aimed to determine the spatial association of each type of land used and diseases associated with pesticide pollution in Thailand to provide comprehensive information to the policy makers and also provide recommendations related to health risk control which will further enhance the quality of life of the farmers.\n\n\nMethods\n\nThis study was approved by the Ethics Committee in Human Research of Khon Kaen University, Khon Kaen, Thailand (Reference no. HE652049).\n\nAll 77 provinces in Thailand were included which occupy an area of 514,000 square kilometers, which consists of 511,770 square kilometers of land and 2,230 square kilometers of water. Thailand shares borders with the following neighboring countries: Myanmar, Cambodia, Laos, and Malaysia.\n\nThe geographic coordinates of the administrative areas used in this study were collected from the DIVA-GIS (http://www.diva-gis.org/) online publicly available database.10 This cross-sectional analytical study used two datasets for analysis:1) A data set on status of patients with disease occurred by pesticide pollution and diagnosed on the basis of ICD10 code: T600, T601, T602, T603, T604, T608, T609 in January 2018-December 2020 from the occupational and environmental diseases report of Health Data Center (HDC), Thailand,11,12 and 2) Agricultural area distribution data on the agricultural statistics of Thailand report from the Office of Agricultural Economics, Thailand.13,14 There was no inclusion or exclusion criteria applied to the data accessed in these reports.\n\nThe independent variables of this study were types of land use areas for agricultural consisting of rice field areas, field crop areas (sugarcane, cassava, peanut, common tobacco, corn, and potato), fruit trees and perennial areas (including rubber trees, eucalyptus trees, and palm oil trees), vegetables and flower areas, and then other agriculture areas in the years 2018-2020, in Thailand. The dependent variable was the proportion of diseases related with pesticide pollution (insecticide and herbicide) in the provinces for the years 2018-2020 excluding Bangkok because data from Bangkok was not reported on the HDC.\n\nThis study used the Quantum GIS program (https://qgis.org/en/site/) to describe the spatial distribution patterns of agricultural areas and the proportion of patients infected with pesticide related diseases in the provinces of Thailand. The GeoDa program (https://geodacenter.github.io/) was used to analyze spatial autocorrelation by specifying XY-coordinates to automatically calculate distance between different points or centroids of polygons. It can further be specified for the threshold distance to determine the minimum distance for two units to be considered as neighboring provinces. For connecting as a criterion to identify groups which using the weight matrix to analyze spatial correlation.15,16\n\nMoran’s I spatial autocorrelation test statistic was performed to identify global autocorrelation within Thailand. The global autocorrelation statistics provide a single measure of spatial autocorrelation for an attribute in Thailand as a whole15,17 by an Empirical Bayes (EB) standardization as a means to correct Moran’s I spatial autocorrelation test statistic for varying population densities across observational units.\n\nThe reports of the Empirical Bayes Index (EBI) Moran scatter plot observed a plot with the spatially lagged variable on the y-axis and the original variable on the x-axis. Both variables were standardized and the graph was divided into four quadrants: high-high (HH) and low-low (LL) indicating positive spatial autocorrelation; and high-low (HL) and low-high (LH) indicating negative spatial autocorrelation. The slope of the linear fit to the scatter plot equals Moran’s I.15,18 The expected value of Moran’s I is -1/(n - 1), and the interpretation is similar to that of the product-moment correlation coefficient. Informally, +1 indicates strong positive spatial autocorrelation (i.e., clustering of similar values), 0 indicates random spatial ordering, and -1 indicates strong negative spatial autocorrelation (i.e., a checkerboard pattern).15,17 Then, a LISA was used to determine the local spatial autocorrelation patterns of the variables.17,19 This computes a measure of spatial association for each individual location.\n\nThe maps depict the locations with significant Local Moran statistics (LISA significance maps) and classify those locations by type of association (LISA cluster maps).15 The dark red is an indication of spatial clusters when having a high frequency of land used with a high frequency of patients infected with pesticides-induced diseases among the identified median of three neighboring provinces (high surrounded by high or hot-spot). The dark blue location is indication of spatial clusters when a low frequency of land used with a low frequency of patients acquired pesticides induced diseases in the identified province with neighboring provinces (low surrounded by low or cold-spot). By contrast, the light red and light blue are indications of spatial outliers (respectively, high surrounded by low, and low surrounded by high).15,19 The statistical significance level was 0.05. The simulation used 999 permutations to evaluate the sensitivity of the results (Figure 8 and Figure 11).\n\n\nResults\n\nThe average prevalence of pesticides-induced disease patients in the years 2018-2020 was 13.17 (95% CI: 10.83-15.50) per 100,000 population. We found that the highest average prevalence of pesticides-induced disease patients per 100,000 population in a province was between 25.39-55.28 when classified as decile in the Mae Hong Son, Uttaradit, Phitsanulok, Loei, Nong Bua Lam Phu, Nakhon Phanom, Nakhon Ratchasima, and Ang Thong provinces (Figure 1A). The highest average prevalence of pesticide-induced disease patients per 100,000 population were between 14.78-37.64 while classified on the basis of the insecticide (Mae Hong Son, Lampang, Uttaradit, Nakhon Phanom, Sakon Nakhon, Nakhon Ratchasima, Ang Thong, and Phetchaburi provinces) (Figure 1B). On the basis of herbicide, 6.36-16.14 per 100,000 population were having pesticide-induced diseases in the Mae Hong Son, Nan, Phetchabun, Loei, Nong Bua Lam Phu, Nakhon Ratchasima, Sa Kaeo, and Chai Nat provinces (Figure 1C).\n\nA: Distribution of the average prevalence of pesticide-induced patients per 100,000 population in years 2018-2020.\n\nB: Distribution of the average prevalence of insecticide-induced patients per 100,000 population in years 2018-2020.\n\nC: Distribution of the average prevalence of herbicide-induced patients per 100,000 population in years 2018-2020.\n\nRice field area was representing the average proportion of rice field when it has been classified as decile. We found that the province with the highest proportion of rice field areas (56.49-70.39%) was the Phichit, Maha Sarakham, Roi Et, Surin, Si Sa Ket, Sing Buri, Ang Thong, and Phra Nakhon Si Ayutthaya provinces (Figure 2). The highest average proportion of field crops areas (22.57-29.44%) were in the Kamphaeng Phet, Nakhon Sawan, Nakhon Ratchasima, Lop Buri, Saraburi, Suphan Buri, Sa Kaeo, and Chon Buri provinces (Figure 3). The highest average proportion of fruit trees and perennial area (44.03-64.65%) were identified in the Samut Songkhram, Rayong, Trat, Chumphon, Krabi, Trang, Pattani, and Narathiwat provinces (Figure 4). In addition, the highest average proportion of vegetable and flower areas (1.09-6.7%) were observed in the Ang Thong, Samut Songkhram, Samut Sakhon, Nakhon Pathom, Pathum Thani, Nonthaburi, Bangkok Metropolis, and Ratchaburi provinces respectively (Figure 5). Furthermore, the highest average proportion of other agriculture areas (6.19-21.34%) were in the Nakhon Nayok, Pathum Thani, Samut Songkhram, Samut Sakhon, Samut Prakan, Nakhon Pathom, Chachoengsao, and Chon Buri provinces (Figure 6).\n\nThe Moran’s I indicated clustering patterns of each type of land use density and the average prevalence of pesticide acquired diseases with statistical significance (p-value <0.05). The results illustrated that the proportion of rice field areas had a spatial autocorrelation with the distribution pattern in the same direction as the average prevalence of pesticide-related diseases with Moran’s I: 0.270. The average prevalence of pesticide-related diseases with high value surrounded by high value or risk areas (Hot spot or HH) were observed in eight provinces (Sing Buri, Saraburi, Nakhon Nayok, Phra Nakhon Si Ayutthaya, Samut Prakan, Nakhon Pathom, Pathum Thani, and Nonthaburi provinces). However, low value surrounded by low value (LL) were found in nine provinces (Chiang Mai, Lampang, Chumphon, Ranong, Surat Thani, Phangnga, Phuket, Krabi, and Phatthalung provinces) (Figure 7).\n\nA: Moran’s I scatter plot matrix of the rice field area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nB: LISA cluster map of the rice field area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nC: LISA significance map (p<0.05) of the rice field area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nIn addition, the average proportion of field crop areas found that there was a spatial autocorrelation with the distribution pattern in the same direction as the average prevalence of Pesticide associated diseases with the Moran’s I 0.144. Similarly, the average proportion of field crop areas and the average prevalence of pesticide-related diseases with high value surrounded by high value or risk areas (HH) were observed among three provinces (Sing Buri, Prachin Buri, and Rayong provinces). In contrast, low value surrounded by low value (LL) were found in 11 provinces (Chumphon, Ranong, Surat Thani, Nakhon Si Thammarat, Phangnga, Krabi, Trang, Phatthalung, Satun, Songkhla, and Pattani provinces) (Figure 8).\n\nA: Moran’s I scatter plot matrix of the field crops area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nB: LISA cluster map of the field crops area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nC: LISA significance map (p<0.05) of the field crops area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nSimultaneously, the average proportion of fruit tree and perennial areas were found to have spatial autocorrelation which has a distribution pattern in the same direction as the average prevalence of pesticide induced diseases with Moran’s I of 0.606 and high value surrounded by high value or risk areas (HH) were in eight provinces (Phangnga, Phuket, Krabi, Trang, Songkhla, Pattani, Yala, and Narathiwat provinces). Although, low value surrounded by low value (LL) were in found in 12 provinces (Phitsanulok, Phetchabun, Kamphaeng Phet, Phichit, Nakhon Sawan, Uthai Thani, Chai Nat, Lop Buri, Suphan Buri, Sing Buri, Ang Thong, and Phra Nakhon Si Ayutthaya provinces) (Figure 9). Furthermore, the average proportion of vegetable and flower areas in the province found a spatial autocorrelation which has a distribution pattern in the same direction as the average prevalence of pesticide-associated diseases with Moran’s I of 0.135, and found the high value surrounded by high value or risk areas (HH) were among six provinces (Nonthaburi, Pathum Thani, Nakhon Pathom, Samut Sakhon, Samut Songkhram, and Ratchaburi provinces). However, low value surrounded by low value (LL) were in four provinces (Uttaradit, Kalasin, and Yasothon provinces) (Figure 10).\n\nA: Moran’s I scatter plot matrix of the fruit trees and perennial area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nB: LISA cluster map of the fruit trees and perennial area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nC: LISA significance map (p<0.05) of the fruit trees and perennial area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nA: Moran’s I scatter plot matrix of the vegetables and flowers area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nB: LISA cluster map of the vegetables and flowers area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nC: LISA significance map (p<0.05) of the vegetables and flowers area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nFinally, we observed that the average proportion of other agriculture areas in the province showed spatial autocorrelation with the distribution pattern in the same direction as the average prevalence of pesticide-induced diseases with Moran’s I of 0.324. This signifies that the high value or risk areas (HH) were in nine provinces (Nonthaburi, Pathum Thani, Nakhon Pathom, Samut Sakhon, Samut Songkhram, Samut Prakan, Nakhon Nayok, Chachoengsao, and Chon Buri provinces). But, low value surrounded by low value (LL) were also in nine provinces (Chiang Mai, Lamphun, Lampang, Phrae, Uttaradit, Sukhothai, Phitsanulok, Kamphaeng Phet, and Phichit provinces) (Figure 11).\n\nA: Moran’s I scatter plot matrix of other agriculture area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nB: LISA cluster map of other agriculture area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\nC: LISA significance map (p<0.05) of other agriculture area and the prevalence of pesticide-induced diseases in 2018-2020, Thailand.\n\n\nDiscussion\n\nIn our setting, the overall average prevalence of pesticide-induced diseases was 13.17 per 100,000 population in year 2018-2020 in Thailand. However, the prevalence of pesticide-related diseases were lower than the overall study in Thailand for the years 2013 and 2014 which, were 11.62 and 12.25 per 100,000 population respectively in a previous study.20 This might be due to increase pesticide use in recent years.\n\nOur bivariate analysis of Moran’s I and LISA observed the spatial association between type of land-used and prevalence of pesticide induced patients. We found that areas with a higher proportion of rice fields showed a high prevalence of pesticide-induced cases especially in the Centre and Northeast of Thailand. The average proportion of field crop areas on the average prevalence of pesticide acquired cases in Thailand was found only in Central Thailand. The average proportion of fruit trees and perennial areas on the average prevalence of patients related with pesticide pollution was found only in the South of Thailand. And in the Centre of Thailand, the average prevalence of pesticide-induced cases was observed where the average proportion of land use was for the vegetables and flowers only.\n\nThose results might be obtained due to the geographical differences of Thailand with different land-uses. The risks of using chemical pesticides in each area were different as well. For example, the central and northeastern regions of Thailand have a lot of rice fields, which have a higher chance of using the herbicide.21 However, field crop areas and vegetable and flower areas, that were found in the Centre of Thailand have a greater chance of using insecticides.21 Similarly, in the south of Thailand, where people use other chemical pesticides, the fruit tree and perennial areas had a significant association with pesticide pollution.22 Therefore, policy formulations to prevent the use of pesticides, including limiting of pesticides chemical imports should consider for specific areas in order to plan effective control or prevention, such as herbicide and insecticide in the central region and herbicide in the northeast as well as other chemical pesticides in the fruit trees and perennial area in the south. However, this study described an initial assessment by bivariate analysis. Therefore, future studies should control co-variable for analysis to confirm the correct result.\n\n\nConclusions\n\nThis study allowed us to identify the average prevalence of pesticide-induced disease patients in the provinces of Thailand between 2018-2020. We observed the proportion of rice field areas had a spatial autocorrelation with the distribution pattern in the same direction as the average prevalence of pesticide-related diseases. In addition, areas with a higher proportion of rice fields showed a high prevalence of pesticide-induced cases especially in Central and Northeast Thailand. Therefore, policymakers should focus on the best means to control these cases and provide new policy recommendations for pesticide use for agriculture, especially, in the province with more land-use areas for each type of crop.",
"appendix": "Data availability\n\nZenodo: Occupational and environmental diseases by operating results report of 43 files from Health Data Center (HDC). https://doi.org/10.5281/zenodo.7233200. 12\n\nThis project contains the following underlying data:\n\n• Pe3all.xlsx. (Data used in this study were from the Health Data Center (HDC); permission to use these data can be requested from the Health Data Center (HDC), Ministry of Public Health Thailand. This study got approval from the Health Data Center (HDC) (reference no.0212-78) to use the data on pesticide pollutions (insecticide and herbicide) in provinces years 2018-2020 excluding Bangkok because data from Bangkok were not reported on HDC. Included pesticide poisoning from DIAGNOSIS_OPD and DIAGNOSIS_IPD files which used to DIAGCODE were ‘T600’,‘T601’,‘T602’,‘T603’,‘T604’,‘T608’,‘T609’ without the X68 code.).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: Land-use areas. https://doi.org/10.5281/zenodo.7233211. 14\n\nThis project contains the following underlying data:\n\n• Agri3all.xlsx. (Data used in this study were from the Office of Agricultural Economics Thailand. Land-use areas data from Agricultural statistics of Thailand are publicly available).\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\nAcknowledgement\n\nThis study was completed successfully with the support of occupational and environmental diseases report of Health Data Center (HDC) from the Ministry of Public Health, Thailand and the Office of Agricultural Economics, Thailand. We express our gratitude for supporting us with the advance data for analysis.\n\n\nReferences\n\nSekhotha MM, Monyeki KD, Sibuyi ME: Exposure to agrochemicals and cardiovascular disease: a review. Int. J. Environ. Res. Public Health. 2016; 13(2): 229. Publisher Full Text\n\nBaltazar MT, Dinis-Oliveira RJ, de Lourdes BM , et al.: Pesticides exposure as etiological factors of Parkinson’s disease and other neurodegenerative diseases—a mechanistic approach. JTl. 2014; 230(2): 85–103. Publisher Full Text\n\nDonkor J, Armenian P, Hartman IN, et al.: Analysis of gastric lavage reported to a statewide poison control system. J. Emerg. Med. 2016; 51(4): 394–400. Publisher Full Text\n\nTawatsin A: Pesticides used in Thailand and toxic effects to human health. Med. Res. Arch. 2015; (3). Publisher Full Text\n\nPetchuay C: Application of Agrochemicals in the Lower Mekong Basin.2017; 19(1): 111–122.\n\nMiah SJ, Hoque A, Paul A, et al.: Unsafe use of pesticide and its impact on health of farmers: a case study in Burichong Upazila, Bangladesh. Jc. 2014; 21(3): 22–30.\n\nCotton J, Edwards J, Rahman MA, et al.: Cholinesterase research outreach project (CROP): point of care cholinesterase measurement in an Australian agricultural community. Environ. Health. 2018; 17(1): 1–11. Publisher Full Text\n\nSapbamrer R: Pesticide use, poisoning, and knowledge and unsafe occupational practices in Thailand. New Solutions: A Journal of Environmental and Occupational Health Policy. 2018; 28(2): 283–302. Publisher Full Text\n\nTawatsin A, Siriyasatien P: Pesticides used in Thailand and toxic effects to human health.2015; 3.\n\nGeographic (GIS) data for any country in the world [database on the Internet]:2020 [cited 20/08/2020].Reference Source\n\nOccupational and environmental diseases by operating results report of 43 files, Health Data Center (HDC):2017 [database on the Internet]. 2020 [cited 20/08/2020].Reference Source\n\nSornlorm K:Occupational and environmental diseases by operating results report of 43 files from Health Data Center (HDC). [Data set]. 2022. Publisher Full Text\n\nAgricultural statistics of Thailand [database on the Internet]:2020 [cited 20/08/2020].Reference Source\n\nSornlorm K:Land-use areas. [Data set].2022. Publisher Full Text\n\nAnselin L, Syabri I, Kho Y: GeoDa: an introduction to spatial data analysis. Geogr. Anal. 2006; 38(1): 5–22. Publisher Full Text\n\nCliff AD, Ord JK: Spatial and temporal analysis: autocorrelation in space and time. Quantitative geography: a British view.1981; 1: 104–110.\n\nAnselin L: The Moran scatterplot as an ESDA tool to assess local instability in spatial association. WV:Regional Research Institute, West Virginia University Morgantown;1993.\n\nAnselin L: CHAPTER EIGHT The Moran scatterplot as an ESDA tool to assess local instability in spatial association. Spatial Analytical. 1996; 4: 121.\n\nAnselin L: Local indicators of spatial association—LISA. Geogr. Anal. 1995; 27(2): 93–115. Publisher Full Text\n\nDepartment of disease control: Report on the situation of diseases and health hazards from occupations and the environment in 2014. Department of disease control;2015 [cited 2020].Reference SourceReference Source\n\nChaimahawan M: An Approach on Soil Resources Management in Central Region for Increasing Agricultural Productivity. Land Development Department;2015.\n\nSaruno T: Basic information for research and development of plant production in the lower southern region. Agricultural Research and Development District 8, Songkhla Province.2015."
}
|
[
{
"id": "274131",
"date": "06 Jun 2024",
"name": "Qaiser Shakeel",
"expertise": [
"Reviewer Expertise Plant Pathology",
"Plant Disease Management"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study investigates the spatial distribution of pesticide-induced diseases in Thailand from 2018 to 2020, analyzing the association between these diseases and different types of agricultural land use. Utilizing cross-sectional analytical methods and spatial autocorrelation techniques, the study aims to identify regions with significant clustering of pesticide-induced health issues and to recommend policy measures for pesticide usage in agriculture. The study highlights regional differences in pesticide-induced disease prevalence related to the type of agricultural land use. For instance, central and northeastern regions, with extensive rice fields, show a higher prevalence of pesticide-related diseases. The central region’s field crop and vegetable areas also show significant associations. Southern regions, with fruit trees and perennials, similarly exhibit high prevalence rates. Conclusions: The study provides critical insights into the spatial patterns of pesticide-induced diseases in Thailand. It underscores the need for tailored policy interventions to manage pesticide use effectively in different agricultural regions. Recommendations include controlling pesticide imports and usage, particularly herbicides in rice fields and insecticides in field crop areas. Limitations Lack of control for potential confounding factors. Cross-sectional design limits causal inference. Data reliance on existing reports, which may have reporting biases. This study is a valuable contribution to understanding the spatial epidemiology of pesticide-induced diseases in Thailand. It provides essential data for policymakers to develop region-specific strategies to mitigate the health impacts of pesticide use. Future research should aim to build on these findings with more sophisticated analyses and broader datasets.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1386
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https://f1000research.com/articles/11-1384/v1
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25 Nov 22
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{
"type": "Case Report",
"title": "Case Report: Zen meditation-integrated CBT normalized the impaired brain function of a chronic low back pain patient—from the findings of brain blood flow SPECT imaging",
"authors": [
"Tetsumi Honda"
],
"abstract": "Background: Mindfulness meditation for chronic pain is popular globally, but evidence of its efficacy is limited. Moreover, there are no established methods on the objective evaluation of the effectiveness of interventions for chronic pain. In this study, a chronic low back pain patient was treated with traditional Japanese Buddhism meditation-integrated cognitive behavioral therapy and the pre- and post-intervention brain single-photon emission computed tomography (SPECT) images were compared. Case: A 45-year-old man was experiencing continuous back pain after a vehicular accident and experienced insufficient improvement after drug treatment. The patient underwent a 3-month outpatient mindfulness meditation-integrated cognitive behavioral therapy program executed by a multidisciplinary team: physician visits (once a week for 30 min), multidisciplinary medical and meditation education (Zen breath counting meditation and mantra), physiotherapy interventions (twice weekly), occupational therapy interventions (twice weekly), psychiatric occupational therapy interventions (twice weekly), and nutritional interventions (twice weekly). After treatment, the patient reported a decrease in subjective pain overall, based on whether or not a pain attack occurred. Brain SPECT imaging revealed an improvement in excess blood flow from the right temporoparietal junction to the inferior parietal lobe. Conclusions: These findings indicate that Zen meditation is an effective intervention method for chronic pain and SPECT is a useful tool for measuring its effectiveness.",
"keywords": [
"chronic pain",
"mindfulness",
"Zen meditation",
"cognitive behavioral therapy",
"brain single-photon emission computed tomography"
],
"content": "Introduction\n\nIn Japan, chronic pain is a highly prevalent (26.4%) major health care issue.1 In 2012, Ogawa et al. reported that 72.4% patients discontinue treatment provided by health care providers due to treatment ineffectiveness.1\n\nChronic pain is now considered a dysfunction of the central nervous system.2–4 A number of neuroimaging techniques developed to evaluate chronic pain have revealed reconstructions3,5 and changes in the networks3,6 of the brains of patients with chronic pain; however, data on the efficacy of neuroimaging techniques in real-life clinical conditions are scarce.7 It is important to conduct studies evaluating brain biomarkers of pain to assess their behavior at the individual level.7\n\nVarious therapeutic approaches, including cognitive behavioral therapy (CBT),8–11 exercise therapy,11,12 multidisciplinary approach,11–14 and mindfulness meditation11,15,16 have been shown to be effective for chronic pain, and combination treatment with these approaches has been recommended.17 However, none of these approaches have included the practice of Zen meditation in their programs.\n\nIn this case, we utilized single-photon emission computed tomography (SPECT) of the brain alongside Zen meditation-integrated CBT provided by a multidisciplinary team. We assessed the pre- and post-intervention changes in the brain scans as well as in physical, psychological, and quality of life (QoL) tests.\n\n\nCase report\n\nThe patient, a 45-year-old Japanese male taxi driver collided with a passenger vehicle in November 2015 and he bruised his back. Since then, he had been experiencing continuous back pain. Due to the frequent pain attacks, he sought relief through orthopedic surgery, massage, and osteopathy. In July 2019, he was referred to us by the rehabilitation department of a university hospital. The patient’s medical history included head trauma when he was 10 years old, bruising on the head, and 5-day hospitalization due to an unknown cause. He complained about cramp-like pain all over the paraspinal muscles on both sides of the back, which was centered on L4-5. There was no sensory impairment in the lower limbs, muscle atrophy, or the Lasègue’s sign, and the deep tendon reflex was normal. Simple lumbar spine radiographs and lumbar spine magnetic resonance imaging (MRI) showed no abnormalities.\n\nBased on the aforementioned clinical and imaging findings, the patient was diagnosed with nonspecific chronic low back pain.\n\nPre- and post-intervention evaluations included: (1) brain SPECT with 99mTc-ethyl cysteinate dimer and two-tailed view analysis using the easy Z-score imaging system (eZIS)18 (August 1, 2019 and April 10, 2020); (2) a pain diary in which the degree of pain was recorded using the Numerical Rating Scale (NRS) every hour for 1 week before the intervention and before/after the program (scores calculated as the daily average at the time of an attack and at the time of no attack); and (3) psychological, QoL, and physical strength examinations, including the Pain Catastrophic Scale (Japanese version),19 Pain Self-Efficacy Questionnaire (Japanese version),20 Beck Depression Inventory,21 12-item Short Form Health Survey (Japanese version),22 and physical strength examinations.23,24\n\nThe pre-intervention period was from October 3 to December 21, 2019. During the pre-intervention period, the effectiveness of pharmacotherapy was verified. Duloxetine has been tested in several randomized control trials (RCTs) for chronic low back pain25,26 and is strongly recommended in systematic reviews.27,28 In this case, duloxetine use was initiated from the initial consultation, with dosage increases each week from 20 mg/day to 60 mg/day. The patient was administered three tablets daily, ingested orally after each meal, starting with breakfast. As the drug administration alone did not lead to sufficient improvement, a 3-month Zen meditation-integrated CBT outpatient program was conducted. The intervention period was from January 8 to March 26, 2020. Before commencement of physician visits (once a week for 30 min), a brain SPECT eZIS image was obtained, and a treatment agreement was decided on with the goal of “normalization of brain function,” instead of healing of pain. During the program, drug administration was continued, and guidance was provided in terms of medical education about pain and breathing methods. The patient was advised to practice Zen breath counting meditation for 15 min twice a day with the following mantra “Leave pain alone. Do not fight against or escape from pain. Enjoy a bright and cheerful life” (Supplementary Video 1, which can be found as Extended data44). His physician was a certified rehabilitation doctor of the Japanese Association of Rehabilitation Medicine and a licensed Buddhism priest who had practiced meditation for 40 years. Twice weekly physiotherapy interventions, in addition to actual physical therapy sessions, provided guidance on stretches to be performed at home and on a training plan involving walking. During twice weekly occupational therapy sessions, guidance was provided on body mechanics as well as an activity for application (“bookshelf construction”). Counselling and yoga sessions were conducted twice a week by the psychiatric occupational therapy team. The Department of Nutrition conducted dietary checks twice a week and provided nutritional guidance. During the course of the treatment, a conference was held by the members of the multidisciplinary team once a week to present information and to allow for optimal patient support. Pre-intervention and post-intervention examples can be found as Supplementary Videos 2 and 3 in Extended data.44\n\nSubjective pain (NRS score) decreased both at the time of an attack and no attack. All test values were maintained or improved (Table 1).\n\nThe brain SPECT (eZIS) examination revealed that excess blood flow from the right temporoparietal junction (TPJ) to the inferior parietal lobe (IPL) had improved (Figures 1 and 2).\n\nBlood flow was decreased in the bilateral dorsolateral frontal lobe and increased in the IPL, anterior insula, and temporal lobe centered on the right TPJ. SPECT = single-photon emission computed tomography; eZIS = easy Z-score imaging system; IPL = inferior parietal lobe.\n\nThe brain SPECT (eZIS) examination revealed that excess blood flow from the right TPJ to the IPL has improved. SPECT = single-photon emission computed tomography; eZIS = easy Z-score imaging system; TPJ = temporoparietal junction; IPL = inferior parietal lobe.\n\nAt the follow-up visit to our clinic, the patient could walk without crutches after 3 months and could run after 4 months of the program (Supplementary Videos 4 and 5, which can be found as Extended data44).\n\n\nDiscussion\n\nMindfulness meditation for chronic pain is popular globally, but evidence of its efficacy is limited.16,29,30 In the case, Zen meditation-integrated CBT was found to be effective for improving chronic pain, as evidenced by improvements in excess regional cerebral blood flow and improvements in subjective pain scores.\n\nThe brain SPECT findings before the intervention showed decreased blood flow in the bilateral dorsolateral frontal lobe and extensive increased blood flow in the IPL, anterior insula, and temporal lobe, centered on the right TPJ. Previous studies on cerebral blood flow in chronic pain have highlighted hyperperfusion of the somatosensory cortex and hypoperfusion of the frontal, cingulate, medial temporal, and cerebellar cortices in patients with hyperalgesic fibromyalgia.31 We have previously reported decreased blood flow in the bilateral dorsolateral prefrontal cortex and increased blood flow in the parietal lobe and cerebellum in patients with chronic low back pain.32\n\nUsing MRI, decreased grey matter density in the prefrontal cortex and thalamus has been reported.5 The development of functional connectivity MRI has revealed that the right TPJ is the core region of the salience network (SN), and that the IPL is the core region of the default mode network (DMN).33,34 In chronic pain, the brain functional network at rest is impaired, and the DMN and SN are in a fused state.35 Additionally, Doll et al. reported that more mindful individuals show a stronger negative correlation between the DMN and SN.36 In this case report, improved clinical test results and normalization of cerebral blood flow in the right TPJ and IPL by SPECT are consistent with the aforementioned hypothesis.\n\nZen breath counting is a traditional Buddhism mindfulness practice in Japan and was integrated into the program. While practicing Zen breath counting meditation, the participants are trained to “Let random thoughts arise and vanish as they will. Do not dally with them and do not try to expel them, but merely concentrate on counting your breath” by the master.37 We reformed this mantra to “Leave pain alone. Do not fight against or escape from pain, but merely concentrate on enjoying a bright and cheerful life.”\n\nA common issue in pain management programs is the motivation of patients to engage in the program.38,39 From a behavioral therapy standpoint, the principle is that staff should be nonresponsive to the pain behavior to avoid reinforcing the patient's pain behaviors.40 However, this attitude often jeopardizes the therapist-patient relationship and leads to treatment interruptions.\n\nIn this program, we presented brain SPECT images to the patient before the start of the program and highlighted the overactivity of the right TPJ. To normalize the brain function and to reduce the unconscious focus of attention on pain, the staff advised against responding to the pain behavior. In addition to teaching, various skills including physical exercises, body mechanics to prevent pain, nutritional managements, and breath counting meditation, a multidisciplinary team support during the program resulted in the reduction of subjective pain, behavioral change, and improvement of brain function by increasing physical activity and development of the ability to practice applied activities by the patient in his daily life.\n\nIn terms of the limitations of the study, the improvement in the NRS score in this case was 0.8 at the time of no attack and 1.5 at the time of attack (Table 1). It has been noted that the change in the NRS score must be higher than or equal to 2 to objectively assess the improvement in pain41; however, this study did not include physical function as a marker of validity. According to the multifaceted model of pain,42 pain is composed of not only nociception from the peripheral tissue but also pain sensation in the nervous system, suffering in the brain, and pain behavior that the patient expresses. According to this model, verbal responses alone are not sufficient for objective assessment of pain, and improvements in physical activity should also considered. In this case study, the physical strength examination results showed significant improvement (Table 1); therefore, it is appropriate to judge that the intervention was effective, although the change in the NRS score was less than 2.\n\nChronic pain can last for 6 or more months.43 Because the pain is spread across all parts of the body, not all chronic pain presents with a uniform cerebral blood flow state. Differing findings on cerebellar blood flow on SPECT have been reported.31,32 The possibility that blood flow status may be altered by the period after the onset of chronic pain cannot be ruled out. Hence, it is necessary to investigate more cases in the future.\n\nIn addition to Zen meditation, the program included exercise therapy, rehabilitation, cognitive therapy, yoga, and a multidisciplinary approach in parallel. It is a challenge to explore the effectiveness of different therapy strategies for chronic pain patients by analyzing the effect of specific interventions on the brain morphologically and functional alternations, as well as on clinical measures of pain.3\n\nTo the best of our knowledge, this is the first report that has implemented Zen meditation to the therapy program for patients with chronic pain, and the first to use brain imaging for assessment of its effectiveness.\n\n“Before this program, my back hurt irregularly every day and I could not keep standing. I was in so much pain that I could not even walk. It was painful all over my body when the weather was bad. I could not carry anything heavy when I was shopping. I could not go out for a long period of time by myself.\n\nThe back pain that appeared irregularly every day was painful, and it was hard not knowing if it would ever go away. I thought that I would never get better; it was hard. I could not see the future. It hurt, because of which I tried to not do any activities and only lie on the bed as still as possible.\n\nHowever, after this program, I am only in pain once or twice a week, which is not as bad as before. Strong pain in the back appears once or twice a week. When the weather is bad, my body is sluggish, and my joints hurt.\n\nI can run a little bit. Overall, I am in a good condition. Now, I can go out on my own.\n\nIf I take the worst pain days as 100, my pain is 35 now.\n\nTo continue and to maintain the recovery I have had, I am aware of taking three meals regularly, losing weight, and continuing to walk and train daily. I am going to do my best without getting bogged down.\n\nWhen the back pain appears, I will start moving and find out what I can do, instead of staying still and putting up with the pain.”\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: Case Report: Zen meditation-integrated CBT normalized the impaired brain function of a chronic low back pain patient—from the findings of brain blood flow SPECT imaging. https://doi.org/10.6084/m9.figshare.21431493. 44\n\nThis project contains the following extended data:\n\n- Sample_video_1.mp4\n\n- Sample_video_2.mp4\n\n- Sample_video_3.mp4\n\n- Sample_video_4.mp4\n\n- Sample_video_5.mp4\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nI would like to thank Editage (www.editage.com) for English language editing. They have provided permission for acknowledgment.\n\n\nReferences\n\nOgawa S, Iseki M, Kikuchi S: A large-scale survey on chronic pain and neuropathic pain in Japan. The Journal of the Japanese Clinical Orthopaedic Association. 2012; 47: 565–574.\n\nBorsook D, Becerra L, Hargreaves R: Biomarkers for chronic pain and analgesia. Part 1: The need, reality, challenges, and solutions. Discov. Med. 2011; 11: 197–207. PubMed Abstract\n\nCoppieters I, Meeus M, Kregel J, et al.: Relations between brain alternations and clinical pain measures in chronic musculoskeletal pain: A systematic review. J. Pain. 2016; 17: 949–962. PubMed Abstract | Publisher Full Text\n\nPfannmöller J, Lotze M: Review on biomarkers in the resting-state networks of chronic pain patients. Brain Cogn. 2019; 131: 4–9. PubMed Abstract | Publisher Full Text\n\nApkarian AV, Sosa Y, Sonty S, et al.: Chronic back pain is associated with decreased prefrontal and thalamic gray matter density. J. Neurosci. 2004; 24: 10410–10415. PubMed Abstract | Publisher Full Text\n\nBaliki MN, Mansour AR, Baria AT, et al.: Functional reorganization of the default mode network across chronic pain conditions. PLoS One. 2014; 9: e106133. PubMed Abstract | Publisher Full Text\n\nMouraux A, Iannetti GD: The search for pain biomarkers in the human brain. Brain. 2018; 141: 3290–3307. PubMed Abstract | Publisher Full Text\n\nWilliams AC, Eccleston C, Morley S: Psychological therapies for the management of chronic pain a (excluding headache) in adults. Cochrane Database Syst. Rev. 2012; 11: CD007407. Publisher Full Text\n\nEccleston C, Fisher E, Brown R, et al.: Psychological therapies (internet-delivered) for the management of chronic pain in adults. Cochrane Database Syst. Rev. 2014; 2: CD01052. Publisher Full Text\n\nRichmond H, Hall AM, Copsey B, et al.: The effectiveness of cognitive behavioural treatment for non-specific low back pain: A systematic review and meta-analysis. PLoS One. 2015; 10: e0134192. PubMed Abstract | Publisher Full Text\n\nChou R, Deyo R, Friedly J, et al.: Nonpharmacologic therapies for low back pain: A systematic review for an American College of Physicians clinical practice guideline. Ann. Intern. Med. 2017; 166: 493–505. PubMed Abstract | Publisher Full Text\n\nVan Middelkoop M, Rubinstein SM, Verhagen AP, et al.: Exercise therapy for chronic nonspecific low-back pain. Best Pract. Res. Clin. Rheumatol. 2010; 24: 193–204. Publisher Full Text\n\nScascighini L, Toma V, Dober-Spielmann S, et al.: Multidisciplinary treatment for chronic pain: A systematic review of interventions and outcomes. Rheumatology (Oxford). 2008; 47: 670–678. Publisher Full Text\n\nGuzmán J, Esmail R, Karjalainen K: Multidisciplinary bio-psycho-social rehabilitation for chronic low back pain. Cochrane Database Syst. Rev. 2002; 1: CD000963. Publisher Full Text\n\nKabat-Zinn J: Full catastrophe living, random house 1990 translated by Yutaka Haruki. Mindfulness stress reduction methods. Kyoto:Kitaohji Publishing;2013; 199–218.\n\nHilton L, Hempel S, Ewing BA, et al.: Mindfulness for chronic pain: Systematic review and meta-analysis. Ann. Behav. Med. 2017; 51: 199–213. PubMed Abstract | Publisher Full Text\n\nYang S, Chang MC: Chronic Pain: Structural and functional changes in brain structures and associated negative affective states. Int. J. Mol. Sci. 2019; 20: E3130. Publisher Full Text\n\nMatsuda H, Mizumura S, Soma T, et al.: Conversion of brain SPECT images collimators and reconstruction process for analysis using statistical parametric mapping. Nucl. Med. Commun. 2004; 25: 67–74. PubMed Abstract | Publisher Full Text\n\nMatsuoka H, Sakano Y: Assessment of cognitive aspect of pain: Development, reliability, and validation of Japanese version of Pain Catastrophizing Scale. Jpn J Psychosom Med. 2007; 47: 95–102.\n\nAdachi T, Nakae A, Maruo T, et al.: Validation of the Japanese version of the pain self-efficacy questionnaire in Japanese patients with chronic pain. Pain Med. 2014; 15: 1405–1417. PubMed Abstract | Publisher Full Text\n\nNihon Bunka Kagakusha: Beck Depression Inventory. (accessed: 17 February 2020).Reference Source\n\niHope International: SF-12. (accessed: 17 February 2020).Reference Source\n\nMEXT: A new plan for testing physical strength. (accessed: 27 February 2020).Reference Source\n\nShimada H, Furuna T, Oobuchi S, et al.: Timed up and Go test is a useful assessment tool for community health in elderly people. Physical Therapy Japan. 2006; 33: 105–111.\n\nSkljarevski V, Zhang S, Desaiah D, et al.: Duloxetine versus placebo in patients with chronic low back pain: A 12-week, fixed-dose, randomized, double-blind trial. J. Pain. 2010; 11: 1282–1290. PubMed Abstract | Publisher Full Text\n\nKonno S, Oda N, Ochiai T, et al.: Randomized, double-blind, placebo-controlled phase III trial of duloxetine monotherapy in Japanese patients with chronic low back pain. Spine. 2016; 41: 1709–1717. PubMed Abstract | Publisher Full Text\n\nChou R, Deyo R, Friedly J, et al.: Systematic pharmacological therapies for low back pain. A systematic review for an American College of Physicians clinical practice guideline. Ann. Intern. Med. 2017; 166: 480–492. PubMed Abstract | Publisher Full Text\n\nUrquhart DM, Hoving JL, Assendelft WW, et al.: Antidepressants for non-specific low back pain. Cochrane Database Syst. Rev. 2008; 1: CD111703. Publisher Full Text\n\nBawa FL, Mercer SW, Atherton RJ, et al.: Does mindfulness impronve outcomes in patients with chronic pain? Systematic review and meta-analysis. Br. J. Gen. Pract. 2015; 65: e387–e400. PubMed Abstract | Publisher Full Text\n\nKabat-Zinn J: An outpatient program in behavioral medicine for chronic pain patients based on the practice of mindfulness meditation: Theoretical considerations and preliminary results.General Hospital Psychiatry.1982;4(1): 33-47. Publisher Full Text\n\nGuedj E, Taieb D, Cammilleri S, et al.: 99m Tc-ECD brain perfusion SPECT in hyperalgesic fibromyalgia. Eur. J. Nucl. Med. Mol. Imaging. 2007; 34: 130–134. PubMed Abstract | Publisher Full Text\n\nNakamura Y, Nojiri K, Yoshihara H, et al.: Significant differences of brain blood flow in patients with chronic low back pain and acute low back pain detected by brain SPECT. J. Orthop. Sci. 2014; 19: 384–389. PubMed Abstract | Publisher Full Text\n\nKucyi A, Hodaie M, Davis KD: Lateralization in intrinsic functional connectivity of the temporoparietal junction with salience- and attention-related brain networks. J. Neurophysiol. 2012; 108: 3382–3392. PubMed Abstract | Publisher Full Text\n\nKajimura S, Kochiyama T, Nakai R, et al.: Causal relationship between effective connectivity within the default mode network and mind-wandering regulation and facilitation. NeuroImage. 2016; 133: 21–30. PubMed Abstract | Publisher Full Text\n\nHemington KS, Wu Q, Kucyi A, et al.: Abnormal cross-network functional connectivity in chronic pain and its association with clinical symptoms. Brain Struct. Funct. 2016; 221: 4203–4219. PubMed Abstract | Publisher Full Text\n\nDoll A, Hölzel BK, Boucard CC: Mindfulness is associated with intrinsic functional connectivity between default mode and salience networks. Front. Hum. Neurosci. 2015; 9: 461.\n\nKapleau P: The three pillars of Zen. New York:Anchor Books, A Division of Random House;2000; 31–40.\n\nHeapy AA, Stroud MW, Higgins DM, et al.: Tailoring cognitive-behavioral therapy for chronic pain: A case example. J. Clin. Psychol. 2006; 62: 1345–1354. PubMed Abstract | Publisher Full Text\n\nJensen MP, Nielson WR, Kerns RD: Toward the development of a motivational model of pain self-management. J. Pain. 2003; 4: 477–492. PubMed Abstract | Publisher Full Text\n\nFordyce WE: Behavioral methods for chronic pain and illness. Saint Louis:The C.V. Mosby Company;1976; 150–156.\n\nSuzuki H, Aono S, Inoue S, et al.: Clinically significant changes in pain along the Pain Intensity Numerical Rating Scale in patients with chronic low back pain. PLoS One. 2020; 15: e0229228. PubMed Abstract | Publisher Full Text\n\nLoeser JD, Egan KJ:History and organization of the University of Washington multidisciplinary pain center.Loeser JD, Egan KJ, editors. Managing the chronic pain patient: Theory and practice at the University of Washington Multidisciplinary Pain Center. New York:Raven Press;1989; 3–20.\n\nMerskey H, Bogduk N: IASP Task Force on Taxonomy Classification of Chronic Pain. Seattle:IASP Press;2nd ed1994; 209–214.\n\nHonda T:Case Report: Zen meditation-integrated CBT normalized the impaired brain function of a chronic low back pain patient—from the findings of brain blood flow SPECT imaging. figshare. [Dataset]. 2022. Publisher Full Text"
}
|
[
{
"id": "267381",
"date": "07 May 2024",
"name": "Prem Venkatesan",
"expertise": [
"Reviewer Expertise chronic pain",
"rehabilitation"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Editor, Thanks for providing me the opportunity to review the manuscript titled: \" Case Report: Zen meditation-integrated CBT normalized the impaired brain function of a chronic low back pain patient—from the findings of brain blood flow SPECT imaging \" I really enjoyed reviewing the manuscript. But I have a few concerns which I am listing below.\nAbstract 1. Highlight the key findings. 2. Conclusion is inconclusive.\nIntroduction. 1. Currently huge body of evidence is available on the effects of mindfulness and brain (Mindfulness-based therapy improves brain functional network reconfiguration efficiency Transl Psychiatry. 2023 Nov 11;13(1):345. [Ref:1], hence what is the need to do case report 2. How Zen meditation is different from mindfulness therapy like above reference? 3. The introduction is written with facts but lacks continuity and hence not properly leading to the need of the study.\nMethods: 1.The presentation of case report is detailed but it creates a confusion while reading as the past history and present history are written together. 2. The study has examined a good number of parameters but what is the justification for not including the muscle strength assessment. 3. Can you provide details of exercise provided to patients- its type of exercise, intensity, time and progression. 4. Author can provide details about type of yoga, pranayamas, asanas and meditation practiced by the patients. Also duration, frequency and progression of yoga. The following study demonstrated effectiveness of yoga and Brain, hence how to justify improvement is due to Zen meditation and not due to components of yoga. (A feasibility study on yoga’s mechanism of action for chronic low back pain: psychological and neurophysiological changes, including global gene expression and DNA methylation, following a yoga intervention for chronic low back pain. Pilot Feasibility Stud. 2022; 8: 142) 5. Authors can provide details of the Nutrition. 6. Authors can provide details of Cognitive behavioral therapy. 7. Existing studies have provided evidence of CBT on the brain areas “Neural Effects of Cognitive Behavioral Therapy in Psychiatric Disorders: A Systematic Review and Activation Likelihood Estimation Meta-Analysis. Front Psychol. 2022; 13: 853804”, hence how do you justify the effect of Zen meditation. 8. Authors have addressed psychological tests and physical tests. 9. What is the hypothesis linking Zen meditation and physical tests improvement 10. The values pertaining to the blood flow in the areas of brain is missing and also it needs to be explained with the effect size so as to justify the result. 11. Details regarding the usage of any Guidelines for reporting Case Report is missing.\nDiscussion 1. A few terms has appeared in the discussion part which was nowhere mentioned in the introduction or in any part of the manuscript and hence it will be difficult for the readers to connect to the idea that the author tries to explain 2. Pain is the primary outcome and it has only been reduced below the effect size mark, hence the result of this technique has to be justified with a more evidences. 3. Although discussion is done on the key findings there is a need for more literature to support the findings.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? 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? No",
"responses": []
},
{
"id": "254953",
"date": "29 Aug 2024",
"name": "Arman Yurisaldi Saleh",
"expertise": [
"Reviewer Expertise Neurology"
],
"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 contents of the journal are short, concise and clear.\n\nThis research is rare and uses advanced technology. Even if it is only one research subject. It is worth considering so that similar research can be carried out in other settings to confirm the results they obtained\nBased on the abstract, the researcher explains quite concisely and clearly.\nMinor points that the future needs to be added are related to past history.\nIt can be concluded that in this case, the patient's pain complaints were more caused by neuropsychiatric disorders considering that the patient had a head injury when he was 10 years old, the type of head injury that had been experienced (degree of head injury) was not explained.\nWhile the results of the neurological examination were within normal limits and the results of the lumbar MRI did not find any abnormalities.\nThe major points of the advantages of this study are: The study conducted has the advantage that it is the first time it has been conducted on zen meditation practitioners with SPECT even though the subject is only 1 person (single trial), pre-post intervention can be proven valid.\nThe therapy schedule is such that it is carried out by multiple experts and can be carried out and imitated to confirm the results elsewhere so that it is replicable. The study can be used as an example for other researchers related to zen meditation.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1384
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https://f1000research.com/articles/11-1381/v1
|
25 Nov 22
|
{
"type": "Research Article",
"title": "Green taxes as ecosystem conservation: an analysis of the industrial sector's view in Peru",
"authors": [
"Walter Gregorio Ibarra Fretell",
"ROSARIO VIOLETA GRIJALVA SALAZAR",
"ROSARIO VIOLETA GRIJALVA SALAZAR"
],
"abstract": "Background: Environmental problems are becoming more recurrent nowadays, which is why many countries have acted on the matter, through different forms, laws and taxes that can contribute and reduce the polluting impact of companies at the time of manufacturing their products. One of the reforms has been environmental taxes, which are not only aimed at raising money, but also at taking corrective action on the behavior of companies that damage both the environment and the health of the population. The research is intended to finding out the opinion and interest of managers of different companies in the industrial sector on environmental taxes, also known as green taxes, and whether they consider it necessary to add green taxes to the current tax system. Method: For data collection of the research, 120 managers of small and medium-sized enterprises in the industrial sector were questioned about whether green taxes could have an influence on ecosystem conservation and several other questions. Results: 63.3% of the managers surveyed agree that the application of an environmental tax is necessary. Conclusion: It is concluded that managers are in favor of green taxes and approve that such taxes should be given as part of ecosystem conservation and environmental protection for all businesses, and that they promote businesses that do not generate any side effects or transformations to the environmental balance, thus improving the quality of life of residents.",
"keywords": [
"Environmental taxes",
"ecosystem",
"environmental problems",
"pollution",
"secondary effects."
],
"content": "Introduction\n\nThe greatest threat we are currently facing is climate change. The temperature has increased by 1.1°C in all these years and if this continues, the consequences could be catastrophic. Climate change constitutes a systemic risk that compromises the sustainability of all countries on the planet, however, although its contribution to global pollution is minimal, Peru and the Latin American region are the most vulnerable due to their rich biodiversity and their own endemism (Rivera, 2022).\n\nThe population depends on the existence, in the necessary quantities and quality of the environment, to use them for direct consumption or after conversion through industrial production. However, all these production processes cause pollution from transformation of organic matter to toxic substances (Bravo et al., 2021), which is partly due to the growth of sectors such as industry.\n\nThe growth that the industrial sector has had in recent times is imminent and this growth and the improvement in the quality of life of man have caused air, water and soil pollution directed towards, thus causing the depletion of natural resources and their degradation, negatively influencing either directly or indirectly on the welfare of the population (Evelia et al., 2019). That is why we need to reduce pollution, and a tool that can help combat climate change is green or environmental taxes.\n\nEnvironmental taxes, also called green taxes, have emerged as a useful and necessary tool to combat climate change, and their economic and social implications on tax behaviors that are harmful to the health of the planet in a way that favors sustainable development (Bedoya et al., 2022). Although there is consensus on its potential to curb climate change, the application of this is not so easy and on the contrary, faces resistance, as countries and industries have invested in traditional and polluting technologies.\n\nCountries in Latin America and the Caribbean (LAC) have so far been introducing such taxes. Among these countries, Costa Rica, and Colombia, recognized for their good environmental performance, stand out. The question is, what has Peru done for the introduction of environmental taxes?\n\nIn Peru, the government has introduced a tax on the consumption of plastic bags. Although more and more people are becoming aware of the environmental impact, the recycling culture is still far from the daily interest of Peruvian citizens, a fact that is far from the attention of other countries in Europe and even in the Asian continent, and the State has yet to define protocols that benefit the environment (Dávila & Mena, 2022).\n\nLima has one of the largest industrial sectors, where companies do not take into account the environmental costs generated by their operations, as the current rules aimed at correcting negative actions are scarce and have little or no effect, as the goods and services produced do not play the role that a socially responsible entity should have in protecting the environment, a vital characteristic today for any company. The research is justified from a socio-economic point of view, because there is a deterioration of the environment in all regions of Peru, caused by industrial activities. Studying the opinion of managers regarding green taxes can have an impact on regulating the activities that generate pollution with a tax that obliges businessmen to take responsibility for the activities they carry out, promoting a sustainable, responsible culture with reasonable use of resources.\n\nIn fact, reducing the impact and moving towards sustainable development requires an increasingly significant economic investment, and this action must be linked to the State's environmental policy and legislative action. Through this study we show interest in the need to incorporate green taxes into the Peruvian tax system. The combination of these taxes would provide multiple benefits by reducing existing pollution and making better use of resources, so the opinion of the industrial sector located in Lima on the issue of environmental taxes will be explored.\n\n\nMethods\n\nThe type of research conducted in this study was applied-descriptive (Hernández-Sampieri & Mendoza, 2018), quantitative and cross-sectional (Ñaupas et al., 2018).\n\nAccording to the report of the Instituto Nacional de Estadística e Informática (2018) there are 1, 106, 853 registered companies in Lima, of which only 5034 (8.5%) are located in South Lima (study scenario). Of this number, 458 (9.2%) are companies belonging to the industrial sector, the latter being the population to be considered for the study.\n\nTo determine the sample size, it was calculated based on a probability of success (p) of 0.88, a probability of failure of 0.12, and a confidence level of 95% (Z-value=1.96) and a margin of error of 5% distributed as follows:\n\nThe sample consisted of 120 company managers, which was obtained through simple random sampling where managers and/or owners of companies in the industrial sector were interviewed.\n\nThe collection and application of the instruments was carried out from 1st October to 15th December, 2021, and data processing was carried out from 20th December 2021, to 15th January 2022. Finally, the presentation and interpretation of results was carried out until 28th February 2022.\n\nThe data collection technique was the survey and the data collection instrument was a questionnaire.\n\nThe questionnaire consists of 14 items divided into three dimensions, with a polytomous response alternative, which aims to identify the opinion of the study sample on environmental taxes for the industrial sector.\n\n\n\n• Economic and social aspect - items 1, 2, 3, 4 and 5\n\n• Environmental policy - items 6, 7 and 8\n\n• Environmental impact - items 9, 10 and 11\n\n• Sustainable development - items 12, 13 and 14\n\nThe response alternatives were: (5) Strongly agree, (4) agree, (3) neither agree nor disagree, (2) disagree, (1) strongly disagree.\n\nThe researchers went directly to the management of each company and a questionnaire was administered to each manager. The managers were the ones who filled out the questionnaire freely and without the intervention of the interviewers. After the instrument had been applied to the 120 managers in the sample, all the information was passed directly to the SPSS version 25.0 statistical program (RRID:SCR_002865), all the descriptive data processing and analysis of the data obtained was carried out, and all the information was presented in the form of a frequency table, which provided a response to the objective of the study.\n\nIt should be noted that none of the managers surveyed refused to participate in the research, nor did they drop out of the questionnaire during or after the application of the questionnaire, so no data is missing from the research.\n\nThe Cronbach's Alpha test was used to measure the reliability of the instrument (α>0.7), obtaining a value of 0.791, concluding that the reliability of the instrument is high.\n\nThe study was approved in July 2021 by the Vice-Rector of Research of the Universidad César Vallejo, through registration No.190-2021-VI-UCV.\n\nWritten informed consent was obtained from all participants. Each manager and/or owner received a consent form disclosing all information related to the development of the questionnaire, which they were required to read and sign and then return to the researchers.\n\nThose who agreed to participate and signed the informed consent form were informed that their personal data would remain anonymous according to Law N° 29733-Law on the protection of personal data (Diario el Peruano, 2011).\n\n\nResults\n\nTable 1 shows that the industrial sector shows a tendency to be in favor of changes to help the environment; 63.3% of the managers surveyed agreed that the application of an environmental tax is necessary and that companies in the industrial sector have the economic capacity to pay an environmental tax (67.5%).\n\nThey also considered that it could be difficult for companies to internalize the environmental costs they generate in their production processes (36.6%) and indicated that the application of this tax would not reduce the degree of pollution of industrial companies (35.0%). The addition of a tax is not enough to solve the environmental problem but making this modification would help minimize the impacts. However, a large group considered that companies would prefer to invest in cleaner technology within their processes (62.5%), rather than paying a tax. For all the options, respondents considered that implementing them would allow for sustainable development within the country (50.8%).\n\n\nDiscussion and conclusion\n\nThe work did not present any major constraints that could affect its full development.\n\nIt is evident that the majority of the managers agreed (97.5%) with the implementation of an environmental tax, considering that the application and levying of a green tax could help the conservation of the environment, however, the tax alone would not reduce the pollution of the environment today. This must go hand in hand with state policies and collection by the government, all managed by a competent body that controls the systems of funds to be implemented. The idea is that green taxes should be a taxation tool that generates protection, production and conservation systems within the region, and as per Bedoya et al. (2022), “green taxation tools should be accompanied by fiscal incentives and facilitation of access to cleaner technologies, energy transition plans for industries and electricity generation and targeted social sustainability to mitigate the social impacts that these can cause” and that the placement of a tax like this should be taken as an opportunity to mobilize efforts and guidelines for the correct direction of the funds that are collected in all tax systems that a country has.\n\nIt is understood that the respondents considered that companies that have the economic capacity to pay an environmental tax, the payment of a levy would generate a greater awareness of pollution and that they could identify within their production processes those that generate more pollution, to the point that they internalize their environmental costs and expenditure on new, less pollution-causing technology. The aim is to be a less polluting and ecologically aware organization, all of which would benefit the surrounding agents (such as internal and external clients, competitors, local government and the community in general) by reducing the polluting agents that may arise from the economic activities they carry out.\n\nThere is still a long way to go for the government, as so far, it has not identified or designed any type of environmental tax within its public policies, and even more so when these green taxation tools must be accompanied by fiscal incentives and facilitation of access to cleaner technologies, energy transition plans for industries and electricity generation, and targeted social support to mitigate the social impacts that these can cause. This is an opportunity to mobilize efforts and identify from how the collection will be done to where the funds raised through these schemes should be directed.\n\nThe conclusion is that the managers of small and medium-sized enterprises in the industrial sector are positive about the introduction of green taxes within the Peruvian framework, which could help conserve the environment. However, this will not be achieved by simply collecting taxes, which will not improve the ecosystem, but must be accompanied by government policies that help to channel all these funds into environmental development and conservation works, generating a more balanced quality of life for the community and wildlife.",
"appendix": "Data availability\n\nZenodo. Green taxes as ecosystem conservation: an analysis of the industrial sector's view in Peru. https://doi.org/10.5281/zenodo.7302007 Vr2 (Ibarra & Grijalva, 2022).\n\nThis project contains the following underlying data:\n\n• Green taxes database.csv\n\n• Green taxes database.sav\n\nZenodo. Green taxes as ecosystem conservation: an analysis of the industrial sector's view in Peru. https://doi.org/10.5281/zenodo.7302007 Vr2 (Ibarra & Grijalva, 2022).\n\nThis project contains the following extended data:\n\n• Green taxes for environmental conservation questionnaire.docx\n\n• STROBE-checklist-v4-cross-sectional.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nBedoya C, Miranda P, Moreno L, et al.: Tributación ambiental, financiamiento climático y flujos ilícitos en América Latina. 2022. Reference Source\n\nBravo O, Osorio M, Loor X: La calidad del desarrollo industrial y su impacto en el medio ambiente. 2021.Reference Source\n\nDávila J, Mena J: Los impuestos verdes y su relación con el derecho fundamental a un medio ambiente saludable. TecnoHumanismo. Revista Científica. 2022; 2(3): 35–66.Reference Source\n\nEl Peruano D: Ley de protección de datos personales – Ley N° 29733. 2011.Reference Source\n\nEvelia L, Bernal P, Herrera A: Sustentabilidad y gestión Ambiental. 2019.Reference Source\n\nHernández-Sampieri R, Mendoza C: Metodología de la investigación. Las rutas cuantitativa, cualitativa y mixta. México:Grupo editorial Mc Graw Hill Education;2018.\n\nIbarra W, Grijalva R:Green taxes as ecosystem conservation: an analysis of the industrial sector's view in Peru. Vr.2. [Dataset]. Zenodo. 2022. Publisher Full Text\n\nInstituto Nacional de Estadística e Informática: Análisis de la Estructura Empresarial de Lima Metropolitana V. 2018. [Archive PDF].Reference Source\n\nÑaupas H, Valdivia M, Palacios J, et al.: Metodología de la investigación cuantitativa – cualitativa y redacción de tesis. 5ta ed.Colombia:Ediciones de la U;2018.\n\nRivera L: El cambio climático y la tributación ambiental en el Perú: la reforma pendiente. 2022.Reference Source"
}
|
[
{
"id": "170207",
"date": "04 May 2023",
"name": "Alex Borodin",
"expertise": [
"Reviewer Expertise social 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\nThe study was carried out on a topical issue. The issue of applying green taxes is relevant for both developing and developed countries. The article is a sociological study of the profile group of the population of Peru - entrepreneurs. It is gratifying that most of them are ready for \"green\" changes. However, it is noteworthy that, along with the readiness for change, there is also an impossibility, bias in the forecast costs for the \"green\" transformation.\nPerhaps a larger visualization of the data in graphical form would make it possible to more clearly present the results of the study.\nIn general, the article is a complete study with an appropriate style and composition. Therefore, it is recommended for 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? 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": "184513",
"date": "26 Jul 2023",
"name": "Shamal Chandra Karmaker",
"expertise": [
"Reviewer Expertise Statistical modeling",
"energy economics",
"econometrics",
"climate change"
],
"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 \"Green taxes as ecosystem conservation: an analysis of the industrial sector's view in Peru\" has been investigated in detail. The topic addressed in the manuscript is exciting, however, the authors should address the following issues:\n1. The authors should address the research gap and novelty of the study clearly.\n2. In this study, the sample (manager) was selected using simple random sampling. Is a simple random approach appropriate to ensure representativeness? Why not a stratified random sampling approach?\n3. The Introduction section needs to revise providing a more accurate and informative recent literature review. The authors should cite the following recent articles:\nKarmaker et al. (20211). Singha et al. (20222). Singha et al. (20233).\n\n5. The manuscript looks like a survey report. The authors should use extensive statistical analysis (Ordered logistic regression or other logistic regression) to ensure the study results.\n6. \"Discussion\" section should be added in a more highlighting, argumentative way. The authors should analyze the reason why the tested results are achieved.\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?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "184512",
"date": "27 Jul 2023",
"name": "Jarmo Vehmas",
"expertise": [
"Reviewer Expertise Sustainable development",
"futures studies",
"environmental and energy policies",
"sustainability evaluation",
"decomposition 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\nThe article is a nice generic opinion poll on environmental taxation. There are a few essential points to improve the paper.\nThe focus and design of a specific tax are much more important in the introduction and implementation process because then the real impacts of a proposed tax can be assessed. This perspective deserves to be mentioned in the article.\n\nThe list of references includes only publications in Spanish. The large literature available in English has not been used. In Western countries, environmental taxation has not been a major political issue recently. Therefore most of the scientific literature is rather old. However, important topics have been the ex-ante impacts of specific environmental tax instrument designs, and ex-post evaluations of the implemented environmental taxes, such as carbon/CO2 and energy tax systems.\n\nThe international context and differences between the Western countries and other parts of the World such as Latin America and Peru in particular could be brought out.\n\nAll background information of the respondent companies is missing in the article, and background questions cannot be found in the attached questionnaire data. This is the most serious problem in the article because differences in answers between various industrial branches cannot be assessed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1381
|
https://f1000research.com/articles/11-977/v1
|
24 Aug 22
|
{
"type": "Data Note",
"title": "Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence",
"authors": [
"Walaa Alshafie",
"Maryam Fotouhi",
"Irina Shlaifer",
"Riham Ayoubi",
"Aled M. Edwards",
"Thomas M. Durcan",
"Peter S. McPherson",
"Carl Laflamme",
"Walaa Alshafie",
"Maryam Fotouhi",
"Irina Shlaifer",
"Riham Ayoubi",
"Aled M. Edwards",
"Thomas M. Durcan",
"Peter S. McPherson"
],
"abstract": "TBK1 is a serine-threonine protein kinase that has been linked to a number of diseases including amyotrophic lateral sclerosis and frontotemporal dementia. Reproducible research on TBK1 has been hampered by the lack of well characterized antibodies. In this study, we characterized 11 commercial antibodies for TBK1 for use in immunoblot, immunofluorescence and immunoprecipitation, using an isogeneic knock-out cell line as a control. We identify antibodies that appear specific for all three applications but invite the readers to interpret the present findings based on their own scientific expertise and use this report as a guide to select the most appropriate antibody for their specific needs.",
"keywords": [
"TBK1",
"Uniprot# Q9UHD2",
"antibody characterization",
"antibody validation",
"Western blot",
"immunoblot",
"immunoprecipitation",
"immunofluorescence"
],
"content": "Introduction\n\nThe lack of robust characterization for research antibodies contributes to the reproducibility crisis.1 Given that there are more than five million antibodies on the commercial market (CiteAb.com), we hypothesize that with appropriate characterization criteria and testing, we should be able to identify high performing antibodies for many if not most proteins in the human genome.2\n\nTBK1 regulates autophagy through phosphorylation of Optineurin3 and the C9ORF72/SMCR8 complex.4 Of note, mutations in both Optineurin5 and the C9ORF72/SMCR8 complex6,7 cause monogenic forms of amyotrophic lateral sclerosis and frontotemporal dementia. Moreover, TBK1 also phosphorylates LC3C, GABARAP-L28 and AKT19 promoting autophagy.\n\nThe endogenous localization of TBK1 under the basal state and during autophagy remains to be determined. Moreover, TBK1 protein interactomes have been determined using overexpression systems, with the exception of one study.10 TBK1 antibodies are key to address these unknowns.\n\nTo explore the availability of high-quality antibodies for human proteins, we devised an antibody characterization strategy in which we use wild-type (WT) and isogenic knockout (KO) control cells to perform head-to-head comparisons of all available commercial antibodies in immunoblot (Western blot), immunoprecipitation and immunofluorescence applications.11 Here, we apply this approach to TBK1 and identify specific antibodies for all tested applications, enabling biochemical and cellular assessment of TBK1.\n\n\nValidation and discussion\n\nTo identify a cell line that expresses adequate levels of TBK1 protein to provide sufficient signal to noise, we examined the DepMap public proteomic database (depmap.org, RRID:SCR_017655). U2OS was selected as the expression of TBK1 protein level is in the average range of cancer cells analyzed,12 is easily amenable to CRISPR-Cas9 and is a rather flat cell line ideal for immunofluorescence studies. U2OS was modified with CRISPR/Cas9 to knockout the corresponding TBK1 gene (Table 1).13\n\nExtracts from wild-type and TBK1 KO cells were prepared and used to probe 11 commercial antibodies from 6 companies (Table 2) by immunoblot (Western blot) and immunoprecipitation. The profile of each of the antibodies is shown in Figures 1, 2 and 3.\n\nLysates of U2OS (WT and TBK1 KO) were prepared and 50 μg of protein were processed for immunoblot with the indicated TBK1 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 dilution used was 1/5000 for all tested antibodies. Predicted band size: ~83 kDa.\n\nU2OS lysates were prepared and IP was performed using 1.0 μg of the indicated TBK1 antibodies pre-coupled to either protein G or protein A Sepharose beads. Samples were washed and processed for immunoblot with the indicated TBK1 antibody. For immunoblot, ab40676, ab12116 and 67211-1-Ig were used. 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=immunoprecipitate.\n\nU2OS WT and TBK1 KO cells were labelled with a green or a far-red fluorescent dye, respectively. WT and KO cells were mixed and plated to a 1:1 ratio on coverslips. Cells were stained with the indicated TBK1 antibodies and with the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (WT), red (antibody staining) and far-red (KO) channels was performed. Representative images of the merged blue and red (grayscale) channels are shown. WT and KO cells are outlined with yellow and magenta dashed line, respectively. Schematic representation of the mosaic strategy used is shown on the bottom-right panel. Antibody dilution used: NB100-56705 at 1/1000; 28397-1-AP at 1/500; 67211-1-Ig at 1/1000; PA5-17478 at 1/1000; 703154 at 1/500; ab12116 at 1/1000; ab40676 at 1/1500; ab109735 at 1/500; GTX113057 at 1/700, 38066 at 1/500, 3504 at 1/500. Bars = 10 μm.\n\nAntibodies were screened by immunofluorescence using a mosaic strategy.11 WT cells were labelled with a green fluorescent dye, where as the KO cells were labelled with a far-red fluorescent dye. A third channel was used to image the primary antibodies. Plating WT and KO cells together and imaging both cell type in the same field of view reduces imaging and analysis biases.\n\nIn conclusion, we have screened TBK1 commercial antibodies by immunoblot, immunoprecipitation and immunofluorescence. The data provided can be used as a guide to purchase the most appropriate antibody for a researcher's needs.\n\n\nMethods\n\nAll TBK1 antibodies are listed in Table 2. Peroxidase-conjugated goat anti-mouse and anti-rabbit antibodies are from Thermo Fisher Scientific (cat. number 65-6120 and 62-6520). Alexa-555-conjugated goat anti-mouse and anti-rabbit secondary antibodies are from Thermo Fisher Scientific (cat. number A21424 and A21429).\n\nCell lines used are listed in Table 1. U2OS TBK1 KO clone was generated using an open-access protocol13 with an inducible Cas9 U2OS line.11 Two guide RNAs (purchased at Synthego) were used to introduce a STOP codon in the TBK1 gene (sequence guide 1: UUUGAACAUCCACUGGACGA, sequence guide 2: CAAAUUAUUUGCUAUUGAAG).\n\nCells 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\nImmunoblots were performed as described in our standard operating procedure.14 Lysates were sonicated briefly and incubated 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 immunoblot. BLUelf prestained protein ladder from GeneDireX (cat. number PM008-0500) was used.\n\nImmunoblots were performed with large 5-16% gradient polyacrylamide gels and transferred on nitrocellulose membranes. Proteins on the blots were visualized with Ponceau staining which is scanned at 300 dpi using a regular flatbed scanner to show together with individual immunoblot. Blots were blocked with 5% milk for 1 hr, and antibodies were incubated O/N 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 washes with TBST. Membranes are 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.15 Antibody-bead conjugates were prepared by adding 1.0 μg of antibody to 500 ul of PBS with 0.01% triton X-100 in a microcentrifuge tube, together with 30 μl of protein A- (for rabbit antibodies) or protein G- (for mouse antibodies) Sepharose beads. Tubes were rocked O/N at 4°C followed by several washes to remove unbound antibodies.\n\nU2OS WT were collected in HEPES buffer (20 mM HEPES, 100 mM sodium chloride, 1 mM EDTA, 1% Triton X-100, pH 7.4) supplemented with protease inhibitor. Lysates are rocked 30 min at 4°C and spun at 110,000×g for 15 min at 4°C. One ml aliquots at 1.0 mg/ml of lysate were incubated with an antibody-bead conjugate for ~2 hrs at 4°C. Following centrifugation, the unbound fractions were collected, and beads were subsequently washed three times with 1.0 ml of HEPES lysis buffer and processed for SDS-PAGE and immunoblot on a 5-16% acrylamide gel.\n\nImmunofluorescence was performed as described in our standard operating procedure.16 U2OS WT and TBK1 KO were labelled with a green and a deep red fluorescence dye, respectively. The fluorescent dyes used are from Thermo Fisher Scientific (cat. number C2925 and C34565). WT and KO cells were plated on glass coverslips as a mosaic and incubated for 24 hrs in a cell culture incubator. Cells were fixed in 4% PFA (in PBS) for 15 min at room temperature and then washed 3 times with PBS. Cells were permeabilized in PBS with 0,1% Triton X-100 for 10 min at room temperature and blocked with PBS with 5% BSA, 5% goat serum 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 TBK1 antibodies O/N at 4°C. Cells were then washed 3 × 10 min with IF buffer and incubated with corresponding Alexa Fluor 555-conjugated secondary antibodies in IF buffer at a dilution of 1.0 μg/ml for 1 hr at room temperature with DAPI. Cells were washed 3 × 10 min with IF buffer and once with PBS. Coverslips were mounted on a microscopic slide using fluorescence mounting media (DAKO).\n\nImaging was performed using a Zeiss LSM 880 laser scanning confocal microscope equipped with a Plan-Apo 40× oil objective (NA = 1.40). Resulting images were cropped and adjusted for brightness and contrast using the Zen navigation software (Zeiss, Zen blue 3.4.91.00000). All cell images represent a single focal plane. Figures were assembled with Adobe Illustrator (version 26.3.1).\n\n\nData availability\n\nZenodo: Antibody Characterization Report for Serine/threonine-protein kinase TBK1, https://doi.org/10.5281/zenodo.6402968.17\n\nZenodo: Dataset for the TBK1 antibody screening study, https://doi.org/10.5281/zenodo.6914815.18\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nWe thank Chetan Raina (YCharOS Inc.) for his important contribution to the creation of an open scientific ecosystem of antibody manufacturers and knockout cell line suppliers.\n\nA previous version of this article was published on bioRxiv: https://doi.org/10.1101/2022.06.03.494699.\n\n\nReferences\n\nBaker M: When antibodies mislead: the quest for validation. Nature. 2020; 585(7824): 313–314. PubMed Abstract | Publisher Full Text\n\nLaflamme C, et al.: Opinion: Independent third-party entities as a model for validation of commercial antibodies. New Biotechnol. 2021; 65: 1–8. PubMed Abstract | Publisher Full Text\n\nWild P, et al.: Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science. 2011; 333(6039): 228–233. PubMed Abstract | Publisher Full Text\n\nSellier C, et al.: Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death. EMBO J. 2016; 35(12): 1276–1297. PubMed Abstract | Publisher Full Text\n\nMaruyama H, et al.: Mutations of optineurin in amyotrophic lateral sclerosis. Nature. 2010; 465(7295): 223–226. Publisher Full Text\n\nRenton AE, et al.: A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD.2011; 72(2): 257–268.\n\nDeJesus-Hernandez M, et al.: Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron. 2011; 72(2): 245–256. PubMed Abstract | Publisher Full Text\n\nHerhaus L, et al.: TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease. EMBO Rep. 2020; 21(1): e48317. PubMed Abstract | Publisher Full Text\n\nXie X, et al.: IkappaB kinase epsilon and TANK-binding kinase 1 activate AKT by direct phosphorylation. Proc. Natl. Acad. Sci. U. S. A. 2011; 108(16): 6474–6479. PubMed Abstract | Publisher Full Text\n\nShang J, et al.: Quantitative Proteomics Identified TTC4 as a TBK1 Interactor and a Positive Regulator of SeV-Induced Innate Immunity. Proteomics. 2018; 18(2). Publisher Full Text\n\nLaflamme C, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8. PubMed Abstract | Publisher Full Text\n\nNusinow DP, et al.: Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell. 2020; 180(2): 387–402.e16. PubMed Abstract | Publisher Full Text\n\nShlaifer I, et al.: Generation of Knockout Cell Lines Using CRISPR-Cas9 Technology.February 24, 2020.Reference Source\n\nAyoubi R, McPherson PS, Laflamme C: Antibody Screening by Immunoblot.2021. Publisher Full Text\n\nAyoubi R, et al.: Antibody screening by Immunoprecitation.2021. Publisher Full Text\n\nAlshafie W, McPherson P, Laflamme C: Antibody screening by Immunofluorescence.2021. Publisher Full Text\n\nAlshafie W, Fotouhi M, Shlaifer I, et al.: Antibody Characterization Report for Serine/threonine-protein kinase TBK1.2021. Publisher Full Text\n\nLaflamme C: Dataset for the TBK1 antibody screening study [Data set]. Zenodo . 2022. Publisher Full Text"
}
|
[
{
"id": "148432",
"date": "06 Sep 2022",
"name": "Nicolas Charlet",
"expertise": [
"Reviewer Expertise 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\nIn this work, Laflamme and collaborators investigate the quality and specificity of various commercial antibodies directed against the TBK1 protein, an important kinase regulating immunity and which loss- or gain-of-function mutations cause Amyotrophic Lateral Sclerosis or Normal-Tension Glaucoma, respectively.\nImportantly, this work revealed that while most of the tested antibodies are suitable for classical immunoblot, only two of them are usable for immunoprecipitation. Similarly, only two, maybe three, TBK1-antibodies are specific in a well-controlled immunofluorescence assay. This is an extremely important result as the use of an incorrect antibody will undoubtedly result in the wrong interpretation of TBK1 localization by immunofluorescence and/or identification of erroneous interactants in immunoprecipitation followed by mass spectrometry analyzes.\nOverall, the text is clear and well written, experiments are well presented and technically extremely well performed and controlled, notably by the use of cells knockout for TBK1 expression, which is classical in immunoblot assays, but when mixed with WT cells is extremely well thought to test antibodies specificity in immunofluorescence. My only recommendation would be to include a table summarizing what antibody is best recommended for what usage, as the current “Invitation to the readers to interpret authors finding” will be a source of misinterpretation, especially in immunoprecipitation and immunofluorescence assays.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "9024",
"date": "24 Nov 2022",
"name": "Carl Laflamme",
"role": "Author Response",
"response": "We thank Nicolas Charlet (reviewer #1) for review of our manuscript. Dr. Charlet suggests we “include a table summarizing what antibody is best recommended for what usage” to avoid misinterpretation of our antibody characterization data. We have presented the YCharOS initiative on several occasions and have found that for the most part, scientists interested in our reports have the expertise to interpret the antibody characterization data. Moreover, we do not score/recommend antibodies because we tested the antibodies under one set of conditions, and the scoring/recommendation would be valid only under this precise experimental setup and in the cell line used. That said, YCharOS reports serve as an invaluable guide pointing scientists to appropriate antibodies for their experimental needs."
}
]
},
{
"id": "154820",
"date": "09 Nov 2022",
"name": "Simon L. Goodman",
"expertise": [
"Reviewer Expertise Antibody validation",
"IHC",
"integrins"
],
"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 researchers examine a set of 11 commercially available antibodies marketed as recognizing TBK1, a protein linked to several human neurological conditions, for reactivity in Western blot, immunoprecipitation, and fixed cell Immunofluorescence.\n\nThe specificity of the antibodies in the various techniques is shown beautifully, but not commented upon, which I find extremely strange. The YCharOs team follow a publication strategy of letting the results \"speak for themselves\".\nThe data is clearly presented in a standard format used by the YCharOs consortium, and detailed protocols are available online. I dislike the use of truncated gels in the IP data set (Fig2). It would improve the credibility if the whole IPs were shown, maybe as supplementary data?\nEspecially, the use of Table#2 including batch and RRID identifiers is an excellent example which all should follow. Would it be possible to have links in print for the RRIDs?\nI was rather puzzled by the choice of working concentrations, for the various techniques, which is not explained anywhere. Were all the reagents pre-titred in the techniques? Please, could the authors clarify a little?\nThe appalling situation with commercial antibodies being inadequately validated is now quite widely known, so YCharOs efforts are laudable, and to be encouraged. For the naive reader, the team at YCharos have an admirable mission to correctly and independently validate commercial tool antibodies. Their model involves external funding from antibody suppliers and the Canadian government.\nThis may be the source of my only criticism of the presentation method: it is a little odd, because the authors do not follow scientific traditions of discussing their data. One speculates that antibody providers, or managers within providers, of less-than-perfect antibodies might decide that negative commentary on their products was not worth the funding? But this does reduce the usability and accessibility of the data set. Can't the authors add a table summarizing the data sets (+ / - format stating apparent antibody specificity in each technology would do). Even without further detailed comment. I am perfectly well aware of why the authors have not chosen to do this; however, it is a little sad.\nRegardless: as a reviewer, I see that all the reagents WB well, but only 2-3 IP a band of an appropriate MW. And only 2 are some way specific in pfa-IF. Only one antibody, clone E813G, appears specific in all techniques.\nThis shows the power of the YCharOs approach, and the importance of their validation work - which should of course be published. This article could save the average researcher who need to find a specific TBK1 antibody for IF many thousands of dollars, and several weeks of frustrated effort, for example.\nSome minor points about the antibody table #2:\n108A429: this antibody has some 10 suppliers (CiteAb), but BioTechne is not one of them. Please clarify.\n2D7B1 = clone name also used by the supplier for another target specificity (TFF1).\nJM42-11 = anti- TFF1 from thermo fisher (and anti-TIA-1 from other companies) clone identifier and catalog number don't align. Catalog describes clone 12H60L39.\nMethods: IPs lysates: 110000g? Typo? g max? If not, please mention centrifuge used. \"Several washes\". Please specify wash buffer.\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": "9025",
"date": "24 Nov 2022",
"name": "Carl Laflamme",
"role": "Author Response",
"response": "We thank Simon Goodman (reviewer #2) for his review of our manuscript, and for summarizing the YCharOS effort. Dr. Goodman states “The specificity of the antibodies in the various techniques is shown beautifully, but not commented upon, which I find extremely strange. The YCharOs team follow a publication strategy of letting the results \"speak for themselves\". As discusses in respond to Dr. Chartrand, we believe that scientists interested in reading our reports have the expertise to interpret the antibody characterization data. Dr. Goodman mentions: “I dislike the use of truncated gels in the IP data set (Fig2). It would improve the credibility if the whole IPs were shown, maybe as supplementary data?”. We presented truncated gels in Figure 2 for space considerations. The complete lanes are shown in a collection of all raw data available to the public through the Zenodo open science repository. This link is also indicated in the article in the \"Data Availability\" section. This article was written under the \"Data Notes\" specification, and supplementary materials are not accepted. The posting of the supplementary materials on Zenodo was made in accordance with F1000's open data policy. Dr. Goodman states, “Especially, the use of Table#2 including batch and RRID identifiers is an excellent example which all should follow. Would it be possible to have links in print for the RRIDs?“ We thank Dr Goodman for his supportive comment. We have followed his recommendation and added the corresponding RRID link for each antibody to Table 2. Moreover, we confirmed that Novus (Bio-Techne) sells clone # 108A429 (cat# NB100-56705). We confirmed clone # 2D7B1 for Proteintech 67211-1-Ig. The clone number for Thermo 703154 is indeed 12H60L39 and not JM42-11 as originally indicated. This mistake was corrected in the revised version of the manuscript. Dr. Goodman mentioned to be “puzzled by the choice of working concentration”. We agree and have clarified how we selected antibody concentration. For WB, we follow the antibody manufacturer’s recommendations. Most TBK1 antibodies are recommended at 1/500 to 1/2000. For six TBK1 antibodies, the signal-to-noise ratio was satisfactory following manufacturers’ recommendations. However, the signal was too strong for 28397-1-AP, PA5-17478, 703154, ab40676 and ab109735 which we titrated at 1/10000. The figure legend has been updated in the revised version of the manuscript. For IF, we tested a dilution of 1.0 µg/ml for all antibodies. At this concentration, the signal from each antibody was in the range of detection of the microscope used. Dr. Goodman mentioned that “it is a little odd, because the authors do not follow scientific traditions of discussing their data”. In the F1000 Data Note format, discussion is not required, and we think it is not relevant for this presentation. Dr Goodman suggested “can't the authors add a table summarizing the data sets (+ / - format stating apparent antibody specificity in each technology would do”). We do not score/recommend antibodies because we tested the antibodies under one set of conditions, and the scoring/recommendation would be valid only under this precise experimental setup and in the cell line used. That said, YCharOS reports serve as an invaluable guide pointing scientists to appropriate antibodies for their experimental needs. Dr. Goodman speculates that “antibody providers, or managers within providers, of less-than-perfect antibodies might decide that negative commentary on their products was not worth the funding?” We can reassure Dr. Goodman and all readers and users of the YCharOS data that participating companies do not influence data presentation beyond informed scientific feedback. Every antibody tested is presented in the report, we omit no antibodies and never have. Prior to their release on Zenodo, each antibody characterization report is shared for technical review by a group of scientific advisors from academia and from participant antibody providers. Once the technical aspects have been reviewed, the reports, without edits, are uploaded without restriction on Zenodo. To date, antibody providers have actively removed sub-performing antibodies or modified recommendations after assessing our data. One TBK1 antibody has been already removed from the market, and recommendation has been modified for two TBK1 antibodies."
}
]
}
] | 1
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https://f1000research.com/articles/11-977
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https://f1000research.com/articles/11-1379/v1
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24 Nov 22
|
{
"type": "Research Article",
"title": "Factors influencing COVID-19 vaccine acceptance and hesitancy among pharmacy students in Bangladesh: a cross-sectional study",
"authors": [
"Debendra Nath Roy",
"Md. Mohabbot Hossen",
"Mohitosh Biswas",
"Ekramul Islam",
"Md. Shah Azam",
"Md. Mohabbot Hossen",
"Mohitosh Biswas",
"Ekramul Islam"
],
"abstract": "Background: In the wake of COVID-19 prevention, a growing attention has been devoted to administering vaccines among various sub-group populations including community health care providers. As a community health worker pharmacists and pharmacy students played a crucial role in patient-centered services for managing COVID-19. Examining pharmacy students’ vaccine acceptance intent has great potential in understanding how pharmacists’ perception impacts community people. This study investigated COVID-19 vaccine acceptance among pharmacy students in Bangladesh and identified the potential factors associated with their vaccine acceptance and hesitancy. Methods: An anonymous questionnaire was deployed online using Google forms in English and conveniently sent to 1190 pharmacy students at different universities between 15th October 2021 and 15th December 2021. The convenience sampling consisted of 1034 student pharmacists (response rate 86.9%) who participated in this study. Binary logistic regressions and Chi-squared test were used for rationalizing the study objectives. Results: The pooled COVID-19 vaccine acceptance rate was 908 (87.8%; 95% CI 85.8─87.8) among student pharmacists while 29.6% (95% CI 25.4─33.9) admitted the willingness to pay (WTP) for a COVID-19 vaccine. Out of 12 vital predictive factors, “safety,” “efficacy,” and “trust” had the strongest significant and positive association with vaccine acceptance (p=0.000). The logistic analysis also revealed that “communication” and “information sufficiency” had a significant positive association with vaccine acceptance (p=0.035 and 0.038, respectively) among student pharmacists. Although the odds of accepting the COVID-19 vaccine were found to be 1.1; an insignificant association between gender and vaccine acceptance was observed in the Chi-squared test. Conclusions: The prevalence of COVID-19 vaccine apprehension will reduce if vaccine-related information becomes more publicly available. Ensuring easy access to scientific information with evidence-based and tailored communication would enhance vaccine acceptance among pharmacy students. Implementation of multidisciplinary educational intervention would support the health care students to achieve adequate knowledge on vaccination consequences.",
"keywords": [
"COVID-19",
"vaccine acceptance",
"hesitancy",
"pharmacy students",
"Bangladesh"
],
"content": "Introduction\n\nThe coronavirus disease (COVID-19) has emerged as a recent health and humanitarian crisis and persisted with resurgent waves. COVID-19 has resulted in devastating consequences in human lives and has impacted the health care services provided in hospitals and community pharmacies. Since pharmacists and pharmacy students in training directly interact with patient-centered services in the health care industry and are, therefore, a group at high risk for COVID-19 exposure and transmitting the infection.1 To prevent rapid transmission and to protect a particular subset of the healthcare student from COVID-19 , vaccination is the most promising and effective therapeutic tool because the vaccine is delivered to curb the transmission of a contagious virus that saves millions of human lives every year.2 A growing number of vaccines to curb the COVID-19 pandemic have now been developed and distributed globally to fight against the novel coronavirus. Despite undeniable immunization success in the 21st century, a growing segment of people still distrusts vaccine safety and efficacy. In contrast, the doubtful attitude of the public towards accepting vaccines endangers massive public health threats and has been denoted as “hesitancy.”3 The World Health Organization (WHO) reported vaccine hesitancy as one of the ten top public health emergencies around the world.4\n\nThe complex nature of motives behind the COVID-9 vaccine hesitancy among the people varies widely depending on the context, way of measurement, and the pandemic stages.5 Recently, the magnitude of COVID-9 vaccine hesitancy has been found to differ significantly across the countries among different population sub-groups worldwide.6 Importantly, the prevalence of COVID-19 vaccines was also found to be predominant among students identified as 32% in Asian countries, 28.11% in the USA, 15.59% in Europe, and 55.93% in African regions, while the global pooled hesitancy rate in students was 29.8%.7 Students of representative health education sectors were potentially influenced by COVID-19; vaccine hesitancy reported 46% in Egypt8, 45% and 23% in the USA9, 30.5% in Malta10, 10.6% in India11, 17.8%inIsrael12, 62.7% in Uganda13, and 75.5% in Zambia.14 The most prevailing factors associated with distrust of corona vaccine receptivity that led to vaccine hesitancy among students follow the same pattern as they marked in frequencies around the world. A recent systematic review deduced that the most common concerns of COVID-19 vaccination decisions among students were side effects, safety, efficacy, trust, effectiveness, vaccine mandate, social influence, information sufficiency, conspiracy beliefs, and religiosity.7\n\nDue to the long-term existence of COVID-19 in Bangladesh, education is prey to collateral damage adding to the woes of the already hard-hit sector and its students. Although the government has sought to open educational institutions, but sudden unexpected worsening of the pandemic caused them to retract. The policymakers have started to work on a plan to include university students in the COVID-19 vaccine inoculation program on a priority basis to resume their regular physical activities in the classrooms and thereby comply with government decisions.15 To date, however, most of the studies conducted so far in Bangladesh focused on COVID-19 vaccination acceptability among the general people16,17 and rural community.18 However, to the best of our knowledge, there is a lack of exploratory study7 investigating COVID-19 vaccine acceptance among healthcare students, particularly pharmacy students in Bangladesh. This study thus aimed to assess COVID-19 vaccine acceptance among pharmacy students in Bangladesh and to explore the key factors associated with their vaccine acceptance and hesitance.\n\n\nMethods\n\nWe deposited step-by-step descriptions of the study protocols on protocols.io and the doi: dx.doi.org/10.17504/protocols.io.n2bvj88wngk5/v1.\n\nAn anonymous self-administered questionnaire was deployed online using Google form and conveniently sent to 1090 Bangladeshi university pharmacy students between 15th October 2021 and 15th December 2021, either via social media networks or personal emails. The investigators incorporated at the beginning of the questionnaire a separate paragraph describing the study and terms of consent. The permission to conduct this cross-sectional comparative study has been obtained from the “Ethical Review Committee” (IRC) of the author’s university. The detailed research protocol was reviewed and evaluated by the IRC before the study began. Data were collected via online mode and analyzed anonymously. No clinical intervention was applied on the subjects and the IRC approved this study as exempt. There was no external funding for the study.\n\nCurrently pharmacy students are studying at public or private university in Bangladesh. According to the latest census, out of 51 public and 108 privately funded universities in Bangladesh, 13 and 28 are providing Bachelor of Pharmacy (B.Pharm) education for students, respectively. These universities are approved by the University Grants Commission (UGC), and the B. Pharm education was approved by the Pharmacy Council of Bangladesh (PCB). This study did not harm the participants because and the individual was free to reject participation anytime\n\nThe study fixed some inclusion criteria to confirm the participant’s eligibility: (i) participants clearly understand and consent with the research objectives, (ii) willing to provide anonymous data on COVID-19 vaccine and vaccinations, (ii) pharmacy students of public or private universities in Bangladesh, and (iii) studying in junior (1st year) to masters, and research degree level. The study didn’t offer financial or in-kind reward for participating and submitting online survey.\n\nThe theoretical foundation of the potential factors associated with COVID-19 vaccine acceptance and hesitancy has been conceptualized from recent reviews.6,7 Accordingly, items of a multi-item’s questionnaire was adopted from theory analysis of the recent studies reflected COVID-19 vaccinations among the various students’ sub-groups globally.8–14 The questionnaire addressed multifaceted socio-psychological aspects and common concerns of COVID-19 vaccinations. The individual predictive items relating to vaccine receptivity were measured as a binary variable. Primarily we employed 5-point Likert scale: “definitely yes”, “yes probably”, “unsure”, “probably not” and “definitely not” to assess in-depth intention. The questionnaire was developed bilingually and the content of each item was validated for ensuring the relevance and clarity of the questionnaire.16,18 Furthermore, final version of the questionnaire was subsequently pre-tested on 20 student pharmacist, which were later excluded from final statistical analysis.\n\nThe survey instrument assessed (1) participants socio-demographic profile; (2) COVID-19 vaccine acceptance intention, (3) potential drivers of COVID-19 vaccine acceptance and hesitancy, and (4) WTP for vaccines.\n\nThe convenience sampling technique was used for systematic data gathering from online survey tools. This process created a survey to collect maximum insights from students’ sample of entities to develop quantitative variables of the attributes. The investigators distributed the online questionnaire among pharmacy students in almost all universities and encouraged them to participate in this study; thus, a potential source of non-response bias was avoided.\n\nFor analyzing responses in binary regression model, the categories “definitely yes” and “yes probably” responses were merged into binary variable (Yes=1) and the remaining three responses were combined into (No=0) response. Thus, vaccine acceptance was the response variable evaluated in binary response (1=Yes, 0=No). Respondent’s socio-demographic characteristics were also figured outby using suitable measurement scale. Predictive variables were dichotomized into (1=Yes and 0=No) response and thereby assessed the effects of these predictive factors on outcome variable. We used one item question to understand WTP and responses were measure by 1=Yes and 0=No scale.\n\nFor observational studies, a data of minimum of 500 considered the sample size compulsory to conduct binary logistic regression that characterizes the variable parameters. Another established thumbs rule explained an event per variable of 50 and the equation is expressed as; sample size (N) =100+50n, where n= number of predictor variables in the model.19 The average duration for survey completion and the clarity of instrument’s items were examined via pilot test (n=20). The possibility for generating missing data was minimized because the survey bars showed receiving any partial data, which ensured collection of complete response.\n\nThe descriptive statistics utilized weighted frequencies and percentage for expressing values of demographic profiles of the student participants. A non-parametric data analytical tool (binary logistic regression) was employed to explore the association mode between explanatory variables and response variable. The key assumptions were performed to adjust the suitability of binary regression analysis. Accordingly, the postulated model summary was evaluated and goodness of model fit was also examined. Raw data were inserted into the Microsoft excel (version 10) and imported to Statistical Package of Social Science (SPSS) software IBM SPSS Statistics, RRID: SCR_016479 for statistical analysis. We considered p<0.05 as statistically significant cut-point value.\n\n\nResults\n\nThe following table 1 represents the respondent’s demographic characteristics. We re-examined the participant’s inclusion criteria and in total, 1034 potentially eligible pharmacy students were included in this study. Participants not having digital devices had the possibility to skip participation in this study. According to the gender demographic profile, 50.5% (n=522) female and 49.5% (n=512) male students participated among which 87.1% (n=901) was the highest count of 20─24 years aged youth. However, the highest proportion 39.3% (n=406) pharmacy students studied in 4th year and 36.0% (n=372) of total participants are currently residing across Dhaka division. Most participants 87.9% (n=909) were Muslim by religion and 86.8% (n=898) of total respondents reported not being infected by COVID-19.\n\nFigure 1 shows the proportion of responses of COVID-19 vaccine behaviors among pharmacy students. Overall, 908 (87.8%; 95% CI 85.8─87.8) participants responded to the intent for vaccination, while 126 (12.2%; 95% CI 10.2─14.1) had the reservation to uptake it. By more specific breakdown, majority of the students responded “definitely yes” 701 (67.8%; 95% CI 64.9─70.7) followed by “yes, probably” 207 (20%; 95% CI 17.6─22.4). However, 64 (6.2%; 95% CI 4.7─7.7) admitted “probably not” response; 35 (3.4%; 95% CI 2.7─4.5) were“unsure” and 27 (2.6%; 95% CI 2.5─3.6) responded “definitely not”. However, 454 (87%; 95% CI 85.0─89.0) female and 454 (88.7%; 95% CI 61.3─91.4) male students had vaccine acceptance willingness and 29.6% (95% CI25.4─33.9) pharmacy students admitted WTP for COVID-19 vaccine. Since the online survey bars showed acceptance of any incomplete survey instrument, our postulated variable of interest produced no missing data.\n\nThe following table 2 displays the descriptive statistics of independent variables utilized in this study and the dependent variable (vaccine acceptance intention) as well.\n\n(1) Model summery\n\nThe value of Nagelkerke R Square and the Cox & Snell R square test were the best approaches employed to explain the model summery because these values together expressed the joint impact of predictive variables on the outcome variable shown in table 3. However, the Cox & Snell R square test result in our binary model showed that all predictive variables jointly 20%─38% explained the outcome variable in our binary model. The obtained result was satisfactory and confirmed to be at a good level.\n\n(2) Goodness of model fit\n\nGoodness of model fit is evaluated by Omnibus tests of model coefficients and Hosmer and Lemeshow test as displayed in table 4. The significance level for Omnibus tests of model coefficients was found significant (p<0.05) while the value was insignificant (p>0.05) for Hosmer and Lemeshow test. The results indicated a very good model fit for the binary logistic regression analysis.\n\nThe association pattern between independent variables and outcome variable (vaccine acceptance) is represented in the following table 5. Out of 12 key predictive factors listed out in table 5, “safety”, “efficacy” and “trust” had the strongest significant and positive association with vaccine acceptance (p=0.000). The binary logistic analysis also revealed that “communication” and “information sufficiency” had significant and positive association with vaccine acceptance (p=0.035 and p=0.038 respectively) among pharmacy students.\n\n** = significant at <0.01,\n\n* = significant at <0.05, level of significance\n\nTable 6 represented that Chi-squared test and Odds Ratio demonstrated no significant association between gender group-difference in response to accept COVID-19 vaccines. Although female group had a slight trend towards the willingness to accept vaccine (Odds Ratio=1.1), however, it was insignificant (p>0.05) according to Chi-Squared test. Hence, statistically no vaccine hesitancy risky group was found among young pharmacists in Bangladesh.\n\n\nDiscussion\n\nMassive vaccination is the only hopeful savior to curb the current pandemic. This study investigated COVID-19 vaccine acceptability among university pharmacy students in Bangladesh and identified the key factors associated with their vaccination decision. According to the study result, the pooled COVID-19 vaccine acceptance was 87.8%, while 12.2% students had the reservation to accept it. Although young pharmacy students are more inclined to get COVID-19 vaccinated; disagreements in enlisting the predictors potentially influenced their intention to accept vaccine or hesitance to receive. We observed that several societal, psychological, and vaccine related factors were associated with COVID-19 vaccine acceptance among student pharmacist. According to our analysis safety, efficacy, and trust had highly significant while communication and information sufficiency had significant association with vaccine acceptance and were identified as the most potential concerns.\n\nThis is the first study focused on COVID-19 vaccination and applied a new analytical approach to explore the key determinants of vaccine acceptance and hesitancy. Since misinformation and false news led to vaccine hesitancy, the significant impact of scientific reading in improving vaccine uptake has been identified. The preference for scientific resources other than traditional and social media was recognized, which would provide an important message to health academicians. The study addressed some limitations. Firstly, sampling method, scarcity of sample size and online data collection mode has been noted. Although we collected 1034 data a sample, the sample size was inadequate compared to the total number of pharmacy students in Bangladesh. Thus, a non-response bias may occur for individuals who did not participate and might have been more willing or refusal intention to take the COVID-19 vaccine. Secondly, the transformative behavioral nature of the respondents may be altered with the frequent changes in perceived health risk, newly promoted vaccines, and vaccine deployment. More specifically, the pattern of COVID-19 vaccine reluctance can alter over time in young adults, hence estimation of in-spot vaccine acceptance and hesitancy among the youth was challenging. Finally, sequential alteration and modification in associated factors of COVID-19 vaccinations would occur. This study did not explicitly define additional confounding factors that may also lead to vaccine hesitancy.\n\nEmpirical studies reported 76.4% COVID-19 vaccine acceptance intention among general Bangladeshi people17 and 84.3% among rural community18 included student participants in both surveys. In the Asian context, 89.4% of medical students had the willingness to uptake the COVID-19 vaccine reported in India.11 All these results are supportive of the current study findings. Even though there have been few studies16,17,20 that reported relatively high vaccine hesitancy rate among Bangladeshi people; however, this study found relatively low (12.2%) vaccine hesitancy among pharmacy students. These studies16,17,20 were conducted since COVID-19 vaccination was inaugurated to administer in priority groups of a few selective areas in Bangladesh. However, we collected data when the country-wide mass vaccination program was started among various population sub-groups. At the same time, people became more conscious about COVID-19 vaccinations and information communicated through different channels. We observed that safety and efficacy had a highly significant and positive correlation with corona vaccine acceptance. Results obtained from similar studies revealed that safety was one of the primary concerns among 10.6% of undergraduate medical students in India11, 17.8% of medical and nursing students in Israel12, 71.1% of pharmacy students in Zambia14, and 28.9% dental students in low and lower-middle countries (LMICs).21\n\nIt has been reported that the perceived efficacy varied between 50% and 95% for COVID-19 vaccines either approved by the Food and Drug Administration (FDA) or permitted for conditional approval in phase three trials.22 Efficacy has been identified as an essential determinant of COVID-19 vaccination decisions among 10.6% of medical students in India11 and 62.7% of medical students in Uganda.13 Public trust in vaccine safety and efficacy data to uptake it was one of the strongest forecasters of COVID-19 vaccine intention.23 Worldwide, side effects, safety, efficacy, trust, and information sufficiency were the most important predictors of COVID-19 vaccination decisions among students7 as well as in general population.6 Pharmacy students are well equipped to access scientific information and awakened to anti-vaccination rumors, thereby rejecting rumor-mongers associated with vaccine data. As a result, trust, communication, and information sufficiency were identified as critical predictors of vaccine acceptance among young pharmacists. Embracing the digital era and exposure to multimedia systems enabled university students to avoid misinformation, which positively built trust. It is thus necessary to provide adequate scientific resources for counteracting the anti-vaccination sentiment related to COVID-19 vaccinations.24 In our study, an insignificant association between side effects and vaccine acceptance was observed because mild symptoms were observed within 48 hours following administering the vaccine's first dose in Bangladeshi people, and no severity was reported to date.25 It has been evident that anti-vaccination sentiments such as conspiracy beliefs and religious beliefs were found to be critical determinants of COVID-19 vaccine acceptability among students7;follow-up consequences could build long term hesitancy. A roadmap to convey accuracy; however, these predictors were insignificant in our study. Information sufficiency and trust were impacted positively by COVID-19 vaccine acceptance, so the anti-vaccination belief was found insignificant. Association of conspiracy beliefs with vaccine origin, vaccine data, and post-administration information and strategic communications with community people would build public trust26 which in turn boosts vaccine confidence and reduces anti-vaccination beliefs.27 consequently; communication and trust were previously identified as a paramount concern of COVID-19 vaccination among general Bangladeshi people16, which are supportive of our findings. Although the COVID-19 vaccine is provided free of cost in Bangladesh, 29.6% of pharmacy students admitted WTP for COVID-19 vaccines if the government fixes the price value. It has been reported that several indicators that influenced the higher marginal WTP for vaccines, including socio-economic condition, affordability status, receiver occupations, and higher income level.28,29 This study has practical implications for policy support, practices, and future research. This study primarily benefits health policymakers and stakeholders in designing perfect vaccine promotion plans for mass vaccinations. The findings support overcoming the perceived vaccination barriers and facilitate pharmacists’ health engagement with the COVID-19 vaccination drive in near real-time, thus helping the governments to implement actionable strategies accordingly. The current study would act as a valuable scientific report for continuing further observational studies reflecting COVID-19 vaccine acceptance by re-examining additional confounding variables that impacted COVID-19 vaccine hesitancy, adding new value for scientific evaluation.\n\nWe collected a large data sample (1034) to ensure the external validity of our study outcomes. Respondent’s socio-demographic characteristics varied significantly. A large sample size ensured much strength to predict the generalizability of the study findings, reinforcing health engagement and boosting vaccine confidence among the general people. Since the pattern of COVID-19 vaccine reluctance can alter among young adults30, So the author suggests adopting a long-term surveillance study to evaluate more precisely the vaccination consequences among young pharmacists globally. Educational interventions highlighted vaccine readiness and pandemic preparedness materials would be imperative to improve people’s health engagement in the COVID-19 vaccination drive.31 Worldwide, pharmacists played a key role by offering advice and counseling to the public regarding ways to reduce COVID-19 contamination and suggesting potential treatments and preventive measures.32,33 Pharmacists were involved in vaccination programs to increase vaccine acceptance rate in a pandemic crisis.34,35 It is thus necessary to ascertain the potential drivers of COVID-19 vaccine acceptance and hesitancy among pharmacy students because they are the future pharmacists and custodians of medicine and vaccine development.\n\n\nConclusions\n\nPharmacy professional’s immunization act of COVID-19 was evaluated when the health policymakers launched a new vaccine vaccination throughout the country. The optimization of a large vaccine drive has already been proven to be effective in reducing coronavirus spread; however, at the same time, achieving a high uptake rate is a critical indicator of successful COVID-19 vaccination effort. This study explicitly defined the significance of positive behaviors regarding vaccine safety, efficacy, and trust in receiving a vaccine under any circumstances. The preference for academic knowledge and scientific reading had unique importance to counter rumors has been detected in this study. COVID-19 vaccine acceptance will improve if vaccine related data become more publicly available. Current study finding would be useful in planning adequate response and designing multi-disciplinary educational strategies for future pharmacist to encounter the future pandemic. Evidence-based and tailored health communication would reduce anti-vaccination sentiments, thus ensuring young pharmacist adherence in COVID-19 vaccination consequences.\n\n\nConsent\n\nThe authors confirm that, informed consent form was sent to participants with online questionnaire. The individuals were free to reject participation at any time.\n\n\nEthical statement\n\nThe Ethical Review Committee approved as exempt.\n\n\nAcknowledgements\n\nAll authors greatly acknowledge all student pharmacists who participated in this study.",
"appendix": "Data availability\n\nFigshare: “Factors influencing COVID-19 vaccine acceptance and hesitancy among pharmacy students in Bangladesh: a cross-sectional study” doi: 10.6084/m9.figshare.21368394.\n\n\nReferences\n\nBasheti IA, Nassar R, Barakat M, et al.: Pharmacists’ readiness to deal with the coronavirus pandemic: assessing awareness and perception of roles. Res. Soc. Adm. Pharm. 2021 Mar 1; 17(3): 514–522. PubMed Abstract | Publisher Full Text\n\nCenters for Disease Control and Prevention (CDC): Ten great public health achievements--United States, 2001-2010. MMWR Morb. Mortal. Wkly Rep. 2011 May 20; 60(19): 619–623.\n\nMarotta C, Raia DD, Ventura G, et al.: Improvement in vaccination knowledge among health students following an integrated extracurricular intervention, an explorative study in the University of Palermo. J. Prev. Med. Hyg. 2017 Jun; 58(2): E93–E98. PubMed Abstract\n\nHarrison EA, Wu JW: Vaccine confidence in the time of COVID- 19. Eur. J. Epidemiol. 2020; 35: 325–330. PubMed Abstract | Publisher Full Text\n\nLin C, Tu P, Beitsch LM: Confidence and receptivity for COVID-19 Vaccines: A rapid systematic review. Vaccine. 2021; 9(1): 16. Publisher Full Text\n\nRoy DN, Biswas M, Islam E, et al.: Potential factors influencing COVID-19 vaccine acceptance and hesitancy: A systematic review. PLoS One. 2022 Mar 23; 17(3): e0265496. PubMed Abstract | Publisher Full Text\n\nRoy DN, Hossen MM, Biswas M, et al.: Prevalence of COVID-19 vaccine hesitancy in students: A global systematic review. F1000Res. 2022 Aug 12; 11(928): 928. Publisher Full Text\n\nSaied SM, Saied EM, Kabbash IA, et al.: Vaccine hesitancy: Beliefs and barriers associated with COVID-19 vaccination among Egyptian medical students. J. Med. Virol. 2021 Jul; 93(7): 4280–4291. PubMed Abstract | Publisher Full Text\n\nKelekar AK, Lucia VC, Afonso NM, et al.: COVID-19 vaccine acceptance and hesitancy among dental and medical students. J. Am. Dent. Assoc. 2021 Mar 26; 152: 596–603. PubMed Abstract | Publisher Full Text\n\nGrech V, Gauci C: Vaccine hesitancy in the University of Malta Faculties of Health Sciences, Dentistry and Medicine vis-a-vis influenza and novel COVID-19 vaccination. Early Hum. Dev. 2020; 105258. PubMed Abstract | Publisher Full Text\n\nJain J, Saurabh S, Goel AD, et al.: COVID-19 vaccine hesitancy among undergraduate medical students: results from a nationwide survey in India. medRxiv. 2021 Jan 1.\n\nRosental H, Shmueli L: Integrating Health Behavior Theories to Predict COVID- Vaccine Acceptance: Differences between Medical Students and Nursing Students in Israel. medRxiv. 2021.\n\nKanyike AM, Olum R, et al.: Acceptance of the coronavirus disease-2019 vaccine among medical students in Uganda. Trop. Med. Health. 2021; 49(1): 1–11.\n\nMudenda S, Mukosha M, Meyer JC, et al.: Awareness and Acceptance of COVID-19 Vaccines among Pharmacy Students in Zambia: The Implications for Addressing Vaccine Hesitancy.\n\nTheDaily Star:August 2, 2021.Reference Source\n\nRoy DN, Hossen M, Ferdiousi N, et al.: Potential factors influencing COVID-19 vaccine acceptance and hesitancy among Bangladeshi people: a cross-sectional study. VirusDisease. 2022; 33: 251–260. Publisher Full Text\n\nAbedin M, Islam MA, Rahman FN, et al.: Willingness to vaccinate against COVID-19 among Bangladeshi adults: Understanding the strategies to optimize vaccination coverage. PLoS One. 2021; 16(4): e0250495. PubMed Abstract | Publisher Full Text\n\nRoy DN, Huda MN, Azam MS: Factors influencing COVID-19 vaccine acceptance and hesitancy among rural community in Bangladesh: a cross-sectional survey based study. Hum. Vaccin. Immunother. 2022 May 6; 1–9.\n\nBujang MA, Sa’at N, Bakar TM: Sample size guidelines for logistic regression from observational studies with large population: emphasis on the accuracy between statistics and parameters based on real life clinical data. The Malaysian journal of medical sciences: MJMS. 2018 Jul; 25(4): 122–130. PubMed Abstract | Publisher Full Text\n\nHossai E, Rana J, Islam S, et al.: COVID-19 vaccine-taking hesitancy among Bangladeshi people: knowledge, perceptions and attitude perspective. Hum. Vaccin. Immunother. 2021 Sep 24; 1.\n\nRiad A, Abdulqader H, Morgado M, et al.: Global Prevalence and Drivers of Dental Students’ COVID-19 Vaccine Hesitancy. Vaccine. 2021 Jun; 9(6): 566. PubMed Abstract | Publisher Full Text\n\nLi Y, Tenchov R, Smoot J, et al.: A comprehensive review of the global efforts on COVID-19 vaccine development. ACS Central Science. 2021 Mar 29; 7(4): 512–533. PubMed Abstract | Publisher Full Text\n\nQuinn SC, Jamison AM, An J, et al.: Measuring vaccine hesitancy, confidence, trust and flu vaccine uptake: results of a national survey of White and African American adults. Vaccine. 2019; 37(9): 1168–1173. PubMed Abstract | Publisher Full Text\n\nRzymski P, Borkowski L, Drąg M, et al.: The strategies to support the COVID-19 vaccination with evidence-based communication and tackling misinformation. Vaccine. 2021 Feb; 9(2): 109. PubMed Abstract | Publisher Full Text\n\nKhaleduzzaman HM, Mishu NJ: Frequency of Side Effects after First Dose of Vaccination against COVID-19 Among the People of Bangladesh. European Journal of Medical and Health Sciences. 2021 May 17; 3(3): 22–24. Publisher Full Text\n\nVergara RJ, Sarmiento PJ, Lagman JD: Building public trust: a response to COVID-19 vaccine hesitancy predicament. J. Public Health. 2021 Jun; 43(2): e291–e292. PubMed Abstract | Publisher Full Text\n\nBadur S, Ota M, Öztürk S, et al.: Vaccine confidence: The keys to restoring trust. Hum. Vaccin. Immunother. 2020 May 3; 16(5): 1007–1017. PubMed Abstract | Publisher Full Text\n\nWong LP, Alias H, Wong PF, et al.: The use of the health belief model to assess predictors of intent to receive the COVID-19 vaccine and willingness to pay. Hum. Vaccin. Immunother. 2020 Sep 1; 16(9): 2204–2214. PubMed Abstract | Publisher Full Text\n\nLin Y, Hu Z, Zhao Q, et al.: Understanding COVID-19 vaccine demand and hesitancy: A nationwide online survey in China. PLoS Negl. Trop. Dis. 2020 Dec 17; 14(12): e0008961. PubMed Abstract | Publisher Full Text\n\nXiao J, Cheung JK, Wu P, et al.: Temporal changes in factors associated with COVID-19 vaccine hesitancy and uptake among adults in Hong Kong: Serial cross-sectional surveys. Lancet Reg Health West Pac. 2022 Mar 29; 23: 100441. PubMed Abstract | Publisher Full Text\n\nShareef LG, Al-Hussainy AF, Hameed SM: COVID-19 vaccination hesitancy among Iraqi general population between beliefs and barriers: An observational study. F1000Res. 2022; 11: 11. Publisher Full Text\n\nRoy DN, Azam MS: An approach to integrate patient, pharmacist and quack physician in managing covid19 pandemic in bangladesh: A cloud based health management systems. Int. J. Pharm. Res. 2021; 502–513.\n\nAk M: Prospect of tele-pharmacists in pandemic situations: Bangladesh perspective. J Bio Med Open Access. 2020; 1(1): 72–77. Publisher Full Text\n\nHedima EW, Adeyemi MS, Ikunaiye NY: Community Pharmacists: On the frontline of health service against COVID-19 in LMICs. Res. Social Adm. Pharm. 2021; 17(1): 1964–1966. PubMed Abstract | Publisher Full Text\n\nCadogan CA, Hughes CM: On the frontline against COVID-19: Community pharmacists' contribution during a public health crisis. Res. Social Adm. Pharm. 2021; 17(1): 2032–2035. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "164150",
"date": "16 Mar 2023",
"name": "Russell Kabir",
"expertise": [
"Reviewer Expertise Suicide and Mental Health",
"Oral Health",
"Ageing and Healthcare",
"Violence against women"
],
"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 your manuscript. A published literature on the same issue is already from the same region. I was surprised that it was not even mentioned in the discussion part of the manuscript. I think you should consider using the following article in the discussion - http://dx.doi.org/10.3390/vaccines9050416\nIs there any particular reason for selecting pharmacy students?\nInclusion criteria numbering is wrong.\nIC (ii) is completely vague.\nWhat is the difference between IC (iii) and (IV), they can be merged.\nThe methods section does not clearly entail how many universities participated in this study.\nWhat does it mean 'RRID: SCR_016479'? This is not required.\nAny citation for this statement - 'For observational studies, a data of minimum of 500 considered the sample size compulsory to conduct binary logistic regression that characterizes the variable parameters'?\n\"Furthermore, final version of the questionnaire was subsequently pre-tested on 20 student pharmacist, which were later excluded from final statistical analysis.\"\nFor the above statement, how did you select them and how did you ensure that they are not part of the main research?\n\"This study did not harm the participants because and the individual was free to reject participation anytime.\"\nThe above statement is vague.\nAn anonymous self-administered questionnaire was deployed online using Google form and conveniently sent to 1090 Bangladeshi university pharmacy students between 15th October 2021 and 15th December 2021, either via social media networks or personal emails.\nFor the above, how did you ensure the quality of the data? Why social media was used? How did you receive the email addresses of all the students? How did you make sure that the participants recruited through social media are Pharmacy students?\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? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1379
|
https://f1000research.com/articles/11-1378/v1
|
24 Nov 22
|
{
"type": "Research Article",
"title": "Safety, quality, and nutritional aspect of smoked barracuda fish",
"authors": [
"Fronthea Swastawati",
"Putut Har Riyadi",
"Retno Ayu Kurniasih",
"Aninditya Artina Setiaputri",
"Defita Faridlotus Sholehah",
"Putut Har Riyadi",
"Retno Ayu Kurniasih",
"Aninditya Artina Setiaputri",
"Defita Faridlotus Sholehah"
],
"abstract": "Background: Barracuda fish has a superior nutritional content, so it can be utilized as raw material for smoked fish products. The smoking method most commonly applied in Indonesia is traditional smoking. The traditional smoking process implemented commercially in Indonesia still uses simple equipment and sanitation is typically not monitored. Traditional smoking used at high temperatures can cause contamination of the products, such as with chemicals and microbes. Liquid smoke can be used to overcome these disadvantages. The study aimed to evaluate the nutritional, chemical, and microbial content of fresh and smoked barracuda processed using different smoking methods, namely traditional and liquid smoke. Methods: Barracuda fish were smoked using different smoking methods, traditional and liquid smoke. The traditional method used a simple smoking furnace, while the liquid smoke method was carried out by immersing the fish in a 5% liquid smoke solution. Then, the smoked barracuda were analyzed with various methods, such as proximate, heavy metals, histamine, benzo[a]pyrene, and total microbes (TPC). Data was analyzed using ANOVA at significance level (p < 0.05) followed by Duncan’s test models using SPSS v.16. Results: Smoked fish treated with liquid smoke had a lower value of Arsenic heavy metal (As), at 0.73 mg/kg compared to the traditional method at 1.93 mg/kg; no histamine and carcinogenic polycyclic aromatic hydrocarbon (PAH) compounds were detected, namely benzo[a]pyrene; and liquid smoked fish can inhibit the growth of bacteria which can be seen from total bacteria value of 4.6 x 10 colonies/g Conclusions: Smoked fish processed using a liquid smoke was safer for consumption by the consumer.",
"keywords": [
"Barracuda fish",
"Heavy metals",
"Histamine",
"Polycyclic aromatic hydrocarbons",
"Smoked fish"
],
"content": "Introduction\n\nBarracuda fish can be processed into a smoked fish product. Barracuda fish production in Indonesia in 2017 was 22,118 tons.1 Despite their superior nutritional content, barracuda fish are prone to deterioration of quality, so adequate processing is needed. One kind of processing method is smoking. The smoking technique represents a series of chemical, thermal, and biochemical processes that occur in salted products. Currently, this technology is applied in various forms to process 40-60% of total meat products. Smoking is defined as the penetration of volatile materials resulting from the thermal damage of wood into the surface of fish.2 Smoking improves organoleptic characteristics, causes water loss, and prevents the growth of food microbes due to heat, aromatic substances, and bactericides from the smoke.3 The smoking method most commonly applied in Indonesia is traditional smoking.\n\nThe smoking process uses high temperatures, and the product is often dried first at a temperature of 40-50oC for 30 minutes to dry the surface of the product, followed by a smoking stage with a high temperature reaching 80-100oC.4 The traditional smoking process implemented commercially in Indonesia still uses simple equipment, and sanitation is typically not monitored; thus, sanitation efforts to prevent contamination during the smoking process require attention.\n\nTraditional smoking processes with high temperatures can cause contamination of the resulting products, such as chemical and bacterial. The danger of chemical contamination includes heavy metal and harmful polycyclic aromatic hydrocarbons (PAHs) contamination. The increase in heavy metal content in smoked fish products is due to contamination during the combustion of fuel in the smoking process;5 for example, the content of Pb in goldfish, rainbow trout, and northern pike was shown to increase after smoking when smoked fish and fresh fish were compared.6 The danger of contamination with pathogenic bacteria such as Escherichia coli, Staphylococcus aureus, Salmonella, and Bacillus aureus has also been detected in smoked fish products.7 Liquid smoke can be used as an alternative to replace the traditional smoking.\n\nLiquid smoke is a solution of compounds that are evaporated simultaneously during pyrolysis and condensed in cooling system. The chemical composition of liquid smoke depends on the type of wood used, the moisture content of the wood, the pyrolysis temperature, and the duration of smoke formation. Commercial liquid smoke has been shown to be effective against various types of putrefaction by pathogenic microorganisms.8,9\n\nA large amount of research on the application of liquid smoke in food has been reported. The application of liquid smoke from coconut shells at a concentration of 5% was shown to extend the durability of smoked skipjack tuna during storage for 4 days at room temperature.10 This study aimed to evaluate the nutrition, chemical and total bacteria of smoked fish processed using traditional and liquid smoke methods.\n\n\nMethods\n\n10 kg fresh barracuda fish (Sphyraena sp.) were procured deceased. All fish samples were purchased from the Fish Auction Hall at Fish Landing Area, located in Jepara, Central Java, Indonesia. The fish were then put into a Styrofoam box containing ice in fresh condition and were brought to the Fish Processing Laboratory, Universitas Diponegoro, Indonesia for smoking by the two different methods, traditional and liquid smoke.\n\nFresh barracuda fish were cleaned and washed using clean water. Then, the fish were gutted. All of the fish that were gutted were then washed and drained. The traditional smoking method used a smoking furnace for approximately ±15 minutes. The liquid smoke method was carried out by immersing the fish in a 5% liquid smoke for 30 minutes, drained for 30 minutes, then heated gradually, at a temperature of 40-45°C for 1 hour; 60-70°C for 1 hour; and 90°C for 1 hour.11\n\nThe process of making liquid smoke from coconut shell is carried out using a series of liquid smoke production equipment consisting of a pyrolysis reactor, heating tank, condenser, liquid smoke reservoir, and cooling system.\n\nThe proximate analysis of moisture, ash, and fat content was carried out according to the AOAC method.12\n\nThe moisture content analysis begins with drying porcelain dish in an oven at 105oC for 1 hour. The weighing porcelain dish is then placed in a desiccator and allowed to cool and then weighed. Sample weighing 3-4 g were weighed. The weighing porcelain dish with sample was put in an oven at a 105oC for 5-6 hours. The weighing porcelain dish was put into a desiccator and allowed to cool then weighed and repeated the procedure until a constant weight was obtained. The percentage of moisture content (wet basis) can be calculated by the formula:\n\nA: Weight of empty cup (g)\n\nB: Weight of cup filled with sample (g)\n\nC: Weight of cup with dried sample (g)\n\nAnalysis of ash content begins with drying the ashing dish in the oven for 1 hour at 105oC, then weighing it. A total of 5 grams of the sample was put into an ashing dish and ignited over a Bunsen flame until it no longer smoked, then put into an ashing furnace at 600oC until complete ash was obtained. After that, it was weighed until a constant weight was obtained. Ash content can be calculated by the formula:\n\nA: Weight of empty cup (g)\n\nB: Weight of cup filled with sample (g)\n\nC: Weight of cup with the sample has ash (g)\n\nFat content analysis begins with weighing 5 g of the sample (W1) and putting it into filter paper, then the wrapped sample is put into a fat flask that has been weighed with a fixed weight (W2) and connected to a Soxhlet tube. The fat sleeve was put into the Soxhlet tube extractor and rinsed with fat solvent. The extraction tube was mounted on a Soxhlet distillation apparatus and then heated at 40oC using an electric heater for 16 hours. The fat solvent in the fat flask is distilled until all the fat solvent has evaporated. When the distillation solvent is accommodated in the extractor chamber, then the solvent is removed and the fat flask is dried in an oven at 105oC, after which the flask is cooled in a desiccator to a constant weight (W3). Fat content can be calculated by the formula:\n\nStandard calibration curves for the determination of cadmium (Cd) and lead (Pb) were obtained by measuring the absorption of the standard solution of each element at the optimum condition of the element. The range of standard solutions of Pb is 0.1-2.5 mg/L, while Pb and Cd are prepared by varying their concentrations in the range of 0.01-1.5 mg/L. The calibration curve is obtained by making a curve between the concentration and absorption of each element.13\n\nAnalysis of heavy metals (Pb, Cd, Hg, Sn, As) was performed following the methods reported by National Standardization Agency for Indonesia (SNI 2354.5:2011).14 Sample 5 g was put in a closed container, then 5 mL of concentrated HNO3 and 5 mL of concentrated H2SO4 was closed and left for 24 hours. The solution is then heated at 60oC for 30 minutes, then heating was continued at 120-150oC until a black precipitate was formed. After its cooled, 10 mL of 10% nitric acid was added and shaken until the black precipitate dissolved. In the next step, 3 mL of H2O2 was added and shaken, then the solution heated again for about 15 minutes. The solution resulting from digestion after cooling was filtered through Whatmann filter paper No.42, and put in a 50 mL volumetric flask and diluted to the mark. After that it was put into a 200 mL beaker, then analyzed for lead (Pb), cadmium (Cd), tin (Sn), and mercury (Hg) measured by atomic absorption spectroscopy at 283,3 nm for lead (Pb), and 228.8 nm for cadmium (Cd).\n\nHistamine analysis began with making a p-phenyl diazonium sulfate reagent, by mixing 1.5 ml of cold 0.9% (w/v) sulfamic acid in concentrated HCl and 1.5 ml of 5% NaNO2, in a 50 ml standard flask. The mixture was kept in an ice bath for 5 minutes. The reagents stored in the ice bath were used 15 minutes after dilution with water and were stable for 12 hours. Next, the extraction step was carried out by weighing 5 g of fresh and smoked barracuda fish samples that were then homogenized with 20 ml of HCl solution and centrifuged at 3100 rpm for 10 minutes. The samples were then analysed spectrophotometrically. 5 ml of Na2CO3 was put into a test tube, and 2 ml of reagent was added slowly, mixed, and then added to a tube containing 1 ml of the residual solution collected in the extraction process. The absorbance of the resulting colour was measured immediately after 5 minutes using a UV-Vis spectrophotometer at a wavelength of 496 nm using distilled water as a blank. The histamine concentration in the sample was obtained from a standard curve according to the absorbance at 496 nm by regression analysis. The histamine concentration in the sample was calculated with the following formula:15\n\nA is the histamine value obtained in μg/ml from the standard curve.\n\nAnalysis of benzo[a]pyrene was performed following the methods reported by Ref. 16, 10 g of sample plus 10 g of anhydrous sodium sulfate was homogenized with 100 mL of n-heptane-ether, homogenized and centrifuged again. The second supernatant was mixed with the first supernatant and then put in an alumina column. The first 50 mL of eluent was discarded and then 50 mL of the second eluent was collected and calibrated on a spectrophotometer at an excitation wavelength of 295 nm and emission of 403 nm. Benzo[a]pyrene standard is used with a concentration of 0-10 mg/ml for calibration.\n\nMicrobiological analysis of fresh barracuda and smoked barracuda included determination of total plate count (TPC), Escherichia coli, Salmonella sp., and moulds.\n\nTotal plate count (TPC) determination was carried out on fresh and smoked barracuda fish samples using the Petri dish count method based on Indonesian National Standard number 01-2332.3-2006.17 The 25 g sample was added to 225 mL of Butterfield’s phosphate-buffered solution and homogenized for 2 minutes. This homogenate is a 10-1 dilution solution. Then, using a sterile pipette, 1 mL of the homogenate was taken and put into 9 mL of Butterfield’s phosphate-buffered solution to obtain a dilution of 10-2. A further dilution (10-3) is prepared by taking 1 mL of the sample from 10-2 dilution into 9 mL of Butterfield’s phosphate-buffered solution. Each dilution was shaken at least 25 times. Then the same thing was done for the dilution 10-4, 10-5, etc.\n\nAnalysis of Escherichia coli using the most probable number (MPN) method was based on Indonesian National Standard SNI 01-2332.1-2015.18 A sample of 25 g was homogenized with 225 mL of 0.1% buffer phosphate water (1:9) using a stomacher, then serially diluted 101-103. Samples were transferred by pipette 1 mL each from each dilution into 3 series of Lauryl Sulfate Tryptose Broth (LSTB) tubes containing Durham tubes. Samples were incubated at 35oC for 24-48 hours. The gas bubbles that appear are observed in the Durham tube. The test result is positive if there are bubbles. The estimation test was not repeated. In the confirmatory test, positive cultures were transferred from the assay with an Ose needle to an Echerichia coli Broth (ECB) tube, then incubated at 37oC for 24-48 hours. The gas formed was observed as a positive result. The MPN table was used to determine the positive MPN result of ECB as the number of Escherichia coli per g/per ml. In isolation and identification, samples from positive Escherichia coli Broth tubes were straked on Eosin Methylene Blue Agar (EMBA), incubation at 37oC for 24 hours. Escherichia coli colonies with a diameter of 2-3 mm were black/dark in the center of the colony with or without a shiny metallic green color on EMBA.\n\nDetermination of Salmonella sp. was based on the method of Indonesian National Standard number 01-2332.2-2006.19 50 g of samples were put into a sterile container and 450 mL of Lactose Broth solution was added. The solution mixture was homogenized for 2 minutes, then the solution was transferred to a sterile container and left at room temperature for 60 minutes in a closed container. The solution was shaken gently and if necessary determine to pH 6.8, then incubated for 24 h ± 2 h at 35oC ± 1oC. The next step is enrichment. 0.1 mL of the incubated solution was transferred to 10 mL of Rappaport-Vassiliadis (RV) medium and 1 mL of the incubated solution was transferred to 10 mL of Tetrahionate Broth (TTB). The RV medium was incubated for 24 h at 42oC ± 0.2oC. Then it was shaken using vortex and the TTB streak was incubated in Hectoen Enteric (HE) Agar, Xylose Lysine Desoxycholate (XLD) Agar, and Bismuth sulfite Agar (BSA). Scratch into the same medium from a Broth RV or Selenite Cystine Broth (SCB). BSA, HE, and XLD plates were incubated for 24 h at 35oC ± 1oC. Then, the possible presence of Salmonella colonies was observed.\n\nAnalysis of total mould colonies was performed according to Ref. 20 with slight modifications. All equipment was sterilized using an autoclave at 121oC and a pressure of 15 psi for 15 minutes. Potato dextrose agar (PDA) (approximately 3.9 g) was added to 100 ml of distilled water, and then brought to a boil. The mixture was sterilized in an autoclave at 121oC and a pressure 15 psi for 15 minutes. Test tubes were prepared and coded I to III. Each test tube was filled with 9 ml of 0.9% NaCl, and sterilized. In the next step, 10 g of sample was crushed and then put into a 250 ml Erlenmeyer flask containing 90 ml of sterile 0.9% NaCl solution to achieve a 10 fold dilution. A total of 1 ml of the solution was taken and transferred to test tube I with a pipette to obtain a (100-fold dilution). From the test tube, 1 ml of the solution was pipetted again and transferred to the second tube as 1000-fold dilution. From each dilution, 1 ml of the solution was taken aseptically and transferred into sterile Petri dishes, homogenized, and allowed to freeze. The Petri dish was then arranged upside down in an incubator at 25-30oC and incubated for 24-48 hours. The number of mould colonies growing on the agar medium in Petri dish was counted. The counted colonies amounted to 30-300 colonies. The total number of mould colonies counted was then multiplied by dilution factor.\n\nData obtained was reported as the mean of triplicates (n = 3) ± standard deviation. Statistical analysis was conducted using an ANOVA at significance level 5% (p < 0.05), followed by post hoc Duncan’s test. The data analysis was performed by SPSS software v. 16.0.\n\n\nResults\n\nThe moisture, total fat content, and histamine of fresh barracuda and smoked barracuda using different smoking methods are shown in Table 1, the heavy metals content are showed in Table 2, and the vitamins are showed in Table 3. The fresh barracuda fish’s moisture, total fat, and ash content were 74.27%, 0.54%, and 1.30%, respectively. The traditional smoked barracuda fish’s moisture, total fat, and ash content were 61.69%, 5.24%, and 3.68%, while smoked barracuda fish using liquid smoke were 64.46%, 5.63% and 1.04%, respectively. Based on the results of variance analysis, it was found that the traditional and liquid smoke methods had a significant effect (p < 0.05) on proximate composition (Tables 4-9).\n\n** For predator fish.\n\na R Squared = .965 (Adjusted R Squared = .954).\n\na R Squared = .834 (Adjusted R Squared = .779).\n\na R Squared = .658 (Adjusted R Squared = .545).\n\nThe heavy metals contents of fresh and smoked barracuda fish are shown in Table 2. The arsenic (As) of fresh barracuda and traditional smoked barracuda is higher than the liquid smoke method, at 3.88 mg/kg, 1.93 mg/kg, and 0.73 mg/kg, respectively. The mercury (Hg) of fresh barracuda fish, traditional smoked fish, and smoked barracuda fish using liquid smoke were 0.14 mg/kg, 0.08 mg/kg, and 0.11 mg/kg, respectively. The cadmium (Cd) in traditionally smoked barracuda was 0.13 mg/kg, while fresh barracuda fish and smoked fish processed using liquid smoke did not contain any cadmium (Cd). A small amount of Tin (Sn) was reported in liquid smoked fish (Table 2). Based on the results of variance analysis, it was found that two smoking methods had a significant (p < 0.05) effect on the levels of mercury (Hg) and arsenic (As) (Tables 10-13). The histamine content is shown in Figure 1; in the traditional method the level was 67.63 mg/kg, while in fresh barracuda fish and liquid smoke method, no histamine was reported.\n\na R Squared = .624 (Adjusted R Squared = .499).\n\na R Squared = .631 (Adjusted R Squared = .508).\n\nBarracuda fish processed using the traditional smoking method in this study showed a total benzo[a]pyrene content of 0.18 μg/kg, while fresh barracuda fish and barracuda fish treated with the liquid smoke method did not contain defectable levels of benzo[a]pyrene (Figure 2).\n\nThe total bacteria for fresh barracuda fish was 7.84 × 103 colonies/g, while those of barracuda fish smoked using the traditional method and the liquid smoke method were 4.2 × 102 colonies/g and 4.6 × 101 colonies/g, respectively. Other microbial contaminants, such as Escherichia coli and Staphylococcus aureus were observed at levels of < 3 APM/g and < 10 colonies/g, respectively (Table 3).\n\n\nDiscussions\n\nThe quality of fresh and smoked fish can be seen from the proximate content, including moisture content, total fat content, and ash content. Moisture content is the most important parameter because it greatly effects the shelf life of a product and also affects the growth of microorganisms. The moisture content of fresh barracuda fish decreased after the smoking process (Table 1) because the moisture content in the food material evaporated and was absorbed by the air in the traditional stoves and ovens. Smoked barracuda fish prepared with traditional and liquid smoke methods had a water content that still exceeded the maximum limit in the Indonesian National Standard for smoked fish, of 60%.21 However, liquid smoke has an antagonistic function, namely, it can kill bacteria at high moisture contents. The smoked fish has the lowest moisture content (9.6 ± 0.16%) of other smoking methods, such as the combination of sundried and smoke or the combination of salted and smoked methods.22 Tilapia fish chikuwa with liquid smoke addition has a lowest moisture content (63.54%).23 The moisture content of smoked fish processed using re-distilled liquid smoke ranges from 48.19% to 57.2%.24 The moisture content of barracuda fish decreases inversely proportional to the total fat content. The total fat content of barracuda fish increases along with the decrease of the moisture content because of heating in the smoking process.25\n\nThe total fat content of smoked barracuda fish in the traditional smoking method (5.24%) was lower than the total fat content in the fish smoked using liquid smoke (5.63%), which were not significantly different (p ≤ 0.05). Changes in fat levels in fish during processing can be caused by several factors such as processing, temperature, and reactions with chemical compounds in liquid smoke.23 Besides that, the distance between the heat source and fish in traditional stoves is very close; due to high smoking temperature, the fat in barracuda fish is damaged, and the total fat content decreases.26\n\nAnalysis of ash content needs to be performed because it is used to determine whether a food should be consumed. The ash content of the fish subjected to the traditional smoking method was higher than that of the sample subjected to the liquid smoke method (Table 1). The increase in ash content was inversely proportional to the decreasing moisture content. The ash content of smoked barracuda fish can be influenced by the salt used in the soaking process when preparing smoked fish. The changes in ash content were closely related to the NaCl content in the sample. The addition of NaCl increases the amount of sodium in a sample, resulting in an increase in ash content.27\n\nThe heavy metals lead (Pb), cadmium (Cd), mercury (Hg), arsenic (As), and tin (Sn) are dangerous and can cause poisoning in humans. Smoked barracuda fish prepared with either smoking method exhibited levels of cadmium (Cd) below the maximum limit of the Indonesian National Standard (Table 2), which is 0.5 mg/kg21, as well as relatively low levels of lead, mercury, and tin.\n\nThe level of the heavy metal arsenic in the fish subjected to the traditional smoking method exceeded the maximum Indonesian standard limit for smoked, while the liquid smoke method has met the Indonesian standard for smoked fish (maximum 1.0 μg/kg). Arsenic levels that exceed the maximum limit can cause toxicity in human body, and it can be harmful to the eyes, skin, blood, and liver. The effects of arsenic can interfere with vision and peripheral eye contractions, cause infection of the skin (dermatitis), cause bone marrow function failure and lead to a decrease in the number of peripheral blood cells. Prolonged exposure to arsenic can cause liver tissue to turn into connective tissue (liver cirrhosis), and can lead to the accumulation of fluid in the abdominal cavity (ascites). Arsenic exposure in the body can also cause kidney damage, especially renal damage (tissue damage).28\n\nHistamine is biogenic amine compound that plays an important role in physiological functions, but if the amount of histamine is excessive, it can cause poisoning in the consumer.29 As shown in Figure 1, histamine was not detected in fresh barracuda fish. This could be because the histamine levels were very low in the fresh barracuda fish. Fresh fish do not contain free histamine but contain the amino acid L-histidine. Histamine is formed in fish by certain bacteria capable of producing the enzyme histidine decarboxylase, which can convert free histidine into histamine.30\n\nThe histamine levels in barracuda fish increased after smoking using the traditional smoking method, reaching 67.63 mg/kg. The increase in histamine content was caused by unhygienic handling during the smoking process and the growth of histamine-producing bacteria. Significantly high amounts of biogenic amines are produced during seafood processing as a result of microbial contamination through decarboxylation of specific free amino acids by exogenous decarboxylase enzymes released by seafood-associated microorganisms.31\n\nIn smoked barracuda fish products processed using the liquid smoke method, no histamine was detected. This was caused by phenolic compounds and acetic acid, which act as antibacterial agents. Liquid smoke can slow the growth of microbes by lowering the pH. Histamine-forming bacteria can be halotolerant or halophilic, and some bacteria are better able to produce histamine at low pH levels. As a result, it is possible for histamine formation to occur during processes such as smoking, drying, and fermentation.32\n\nBased on the results of this study (Figure 1), it was found that the traditionally smoked barracuda fish product had a histamine content lower than the requirements of the Indonesian smoked fish standard (SNI 2725:2013), 100 mg/kg. This shows that smoked barracuda fish are safe for consumption. Consumption of foods that contain excess histamine can cause poisoning and disease. The human body can detoxify low histamine levels, but consuming foods containing histamine above 200 mg/kg can cause disease. After histamine is released into the bloodstream, various symptoms can be observed.33 The most common symptoms are tingling, rash, a drop in blood pressure, vomiting, headache, dizziness, nausea, diarrhea, heart palpitations, and respiratory distress.34 Various countries have set legal limits for the consumption of foods containing histamine such as 50 mg/kg35 and 100 mg/kg.36 At first glance the symptoms of histamine poisoning are similar to allergic symptoms that occur in general in people who have hypersensitivity to certain stimuli at doses tolerated by individuals.37\n\nBenzo[a]pyrene has the highest carcinogenic value compared to others PAHs. Benzo[a]pyrene contributes anywhere from 1%-20% of the total carcinogenic effects found in smoked products.38\n\nBarracuda fish processed using the traditional smoking method in this study showed a total benzo[a]pyrene content of 0.18 μg/kg, while fresh barracuda fish and barracuda fish treated with the liquid smoke method did not contain detectable levels of benzo[a]pyrene. The distance between fish and smoke sources in traditional smoking is also an important factor that must be considered. PAHs are bound to smoke particles. Longer distances between fish and the smoke source can reduce the number of PAHs in the fish.39 Benzo[a]pyrene content in coconut and paddy liquid smoke have been studied. Coconut shell and paddy liquid smoke did not have detectable levels, because the temperature of pyrolysis < 400oC was lowered in liquid smoke processing.40 Benzo[a]pyrene in smoked Nile tilapia using corn cob and coconut shells liquid smoke was not detected.41 The maximum acceptable level for benzo[a]pyrene is 5.0 μg/kg.21\n\nBenzo[a]pyrene can be carcinogenic; this is due to the nature of benzo[a]pyrene which is hydrophobic (does not like water) and does not have a methyl group as other reactive groups to be converted into more polar compounds. As a result, PAH compounds are very difficult to excrete from the body and usually accumulate in the liver, kidney, adipose tissue, or body fat. With molecular structures similar to nucleic bases (adenosine, thymine, guanine, and cytosine), PAH molecules can easily insert themselves into DNA strands. As a result, DNA function will be disrupted and if this damage cannot be repaired in cells, it will cause cancer.42\n\nThe principle of the fish smoking process is to suppress the growth of spoilage bacteria to extend the shelf life of the product. The comparison of microbial contamination of fresh barracuda fish with smoked barracuda is presented in Table 3. Smoked barracuda fish processed using the liquid smoke method had the lowest total plate count, due to ability of liquid smoke ton inhibit the growth of microorganisms by lowering the pH. The decrease in pH value is caused by the metabolism of lactic acid bacteria.35\n\nThe smoked barracuda fish products processed using the traditional and liquid smoke methods met quality standards because they had total plate count values below the maximum limit for the requirements of the Indonesian smoked fish (SNI 2725:2013). The maximum total bacteria limit for smoked fish consumed is 5.0 × 104 colonies/g or a log value of 4.6921; thus, based on this value, smoked barracuda fish using the traditional method and the liquid smoke method are suitable for consumption.\n\nBacterial contamination of smoked barracuda can occur through air, soil, or improper handling of fish. An increase in moisture content during storage and an increase in the supporting temperature can also trigger bacterial growth, such as the growth of Staphylococcus aureus bacteria, which grow well at temperatures of 30-37°C.43 Liquid smoke fumigation is more hygienic than traditional smoking using a furnace so that it can reduce the number of Escherichia coli and Staphylococcus aureus bacteria. Coconut shell liquid smoke can act as an antibacterial on Pseudomonas aeruginosa and Staphylococcus aureus.44 Corncob liquid smoke is also reported to be able to inhibit the growth of Escherichia coli, Staphylococcus aureus, Vibrio harveyi, and Vibrio parahaemolyticus bacteria.45\n\nFresh barracuda fish and smoked barracuda fish (traditional method and liquid smoke method) obtained negative results for the pathogenic bacteria Salmonella sp., so the products were safe for consumption. The quality standard for Salmonella bacteria is based on Indonesian smoked fish (SNI 2725:2013).21 The antimicrobial activity of liquid smoke is caused by the presence of phenol and acid components.46 The mechanism of antimicrobial activity of phenols and their derivatives includes reactions with the cell membranes that can increase cell membrane permeability and result in the loss of cell contents, inactivation of essential enzymes and functional inactivation of genetic material.47\n\nMould testing was carried out to identify and count the number of mould colonies that resulted in a decrease in product quality. A high amount of mould will cause a decrease in the quality of smoked fish, promoting rancidity.48 The results of the mould test (Table 3) show that both fresh barracuda fish and smoked barracuda fish (traditional methods and liquid smoke methods) met the requirements of the Indonesian smoked fish.21\n\nLiquid smoke is increasingly being used because it has a distinctive flavor and inhibitory effects on pathogens. The preservative effect of liquid smoke in these foods occurs because of the presence of antimicrobial and antioxidant compounds, such as aldehydes, carboxylic acids, and phenols.44 Therefore, liquid smoke has the potential to be used as a natural antimicrobial for food products. Liquid smoke also can make a product more flavoring.\n\n\nConclusions\n\nBarracuda fish have good potential to be processed into smoked fish. Smoked barracuda fish products using liquid smoke can guarantee nutritional needs and product safety because the content of heavy metals, histamine, and benzo[a]pyrene met the levels set in the Indonesian National Standard. Very low total plate count values were detected in the smoked barracuda fish and were within the Indonesian National Standard limits.\n\nFronthea Swastawati: Conceptualization, Project Administration, Resources, Supervision, Validation, Writing-Review and Editing.\n\nRetno Ayu Kurniasih: Conceptualization, Project Administration, Resources, Supervision, Validation, Writing-Review and Editing.\n\nPutut Har Riyadi: Conceptualization, Resources, Supervision, Validation, Writing-Review and Editing.\n\nAninditya Artina Setiaputri: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Resources, Validation, Writing-Original Draft Preparation, Visualization.\n\nDefita Faridlotus Sholihah: Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Resources, Validation, Writing-Original Draft Preparation, Visualization.\n\n\nData availability\n\nfigshare: Safety, quality, and nutritional aspect of smoked barracuda fish. https://doi.org/10.6084/m9.figshare.20201897.v149\n\nThis project contains the proximate analysis data.\n\nfigshare: Safety, quality, and nutritional aspect of smoked barracuda fish. https://doi.org/10.6084/m9.figshare.20201987.v150\n\nThis project contains the heavy metal analysis data.\n\nfigshare: Safety, quality, and nutritional aspect of smoked barracuda fish. https://doi.org/10.6084/m9.figshare.20202032.v151\n\nThis project contains the histamine and benzo[a]pyrene analysis data.\n\nfigshare: Safety, quality, and nutritional aspect of smoked barracuda fish. https://doi.org/10.6084/m9.figshare.20202011.v152\n\nThis project contains the microbiology analysis data.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nMinistry of Marine Affairs and Fisheries: Total production of barracuda fish in 2017. Jakarta, Indonesia:Ministry of Marine Affairs and Fisheries;2018. [in Indonesian]. Reference Source\n\nAdeyeye SAO, Oyewole OB: An overview of traditional fish smoking in Africa. J. Culin. Sci. Technol. 2016; 14(3): 198–215. Publisher Full Text\n\nYusuf KA, Ezechukwu LN, Faykoya KA, et al.: Influence of fish smoking methods on polycyclic aromatic hydrocarbons content and possible risks to human health. Afr. J. Food Sci. 2015; 9(3): 126–135. Publisher Full Text\n\nAhmad JI: Smoked foods/Applications of smoking. In Encyclopdia of Food Science and Nutrition. 2003: 5309–5316. Publisher Full Text\n\nCodex Alimentarius Commission: International food standards. FAO/WHO CAC/RCP 68-2009. Code of practice for the reduction of contamination of food with polycyclic aromatic hydrocarbons (PAH) from smoking and direct drying processes.2009.\n\nCieslik I, Migdal W, Topolska K, et al.: Changes in content of heavy metals (Pb, Cd, Hg, As, Ni, Cr) in freshwater fish after processing – the consumer’s exposure. J. Elem. 2018; 23(1): 247–259.\n\nIneyougha ER, Orutugu LA, Izah SC: Assessment of microbial quality of smoked Trachurus trachurus sold in some markets of three South-south States Nigeria. Int. J. Food Res. 2015; 2: 16–23.\n\nSimon R, de la Calle B , Palme S, et al.: Composition and analysis of liquid smoke flavouring primary products. J. Sep. Sci. 2005; 28: 871–882. PubMed Abstract | Publisher Full Text\n\nMilly PJ, Toledo RT, Ramakhrishnan S: Determination of minimum inhibitory concentrations of liquid smoke fractions. J. Food Sci. 2005; 70: M12–M17. Publisher Full Text\n\nLeha M: Application of liquid smoke as a bio preservative in food (smoked skipjack tuna).Proceeding of the National Seminar on Basic Science II. Faculty of Science and Mathematics Pattimura University Ambon, Indonesia.2010. 246–258\n\nSwastawati F, Cahyono B, Wijayanti I: Changes in the quality characteristics of tuna (Euthynnus affinis) with the traditional smoking method and the application of liquid smoke. Journal Info. 2017; 19(2): 55–64.\n\nAssociation of Official Analytical Chemist (AOAC): Official method on analysis of the association of official analytical of chemist. Arlington:The Association ion of Official Analytical Chemist, Inc.;2005.\n\nSupriatno L: Analysis of heavy metals Pb and Cd in fish and hellfih samples by atomic absorption spectrophotometry (Analisis logam berat Pb dan Cd dalam sampel ikan dan kerang secara spektrofotometri serapan atom). Jurnal Rekayasa Kimia dan Lingkungan. 2009; 7(1): 5–8. [in Indonesian].\n\nIndonesian National Standardization Agency (Badan Standardisasi Nasional): Determination of heavy metal levels of lead (Pb) and cadmium (Cd) in fishery products – SNI 2354.5:2011. Jakarta, Indonesia:Badan Standardisasi Nasional;2011.\n\nPatange SB, Mukudan MK, Ashok KK: A simple and rapid method for colorimetric determination of histamine in fish flesh. Food Control. 2005; 16(5): 465–472. Publisher Full Text\n\nHadiwiyoto S, Naruki S, Satyani S, et al.: Changes in protein solubility, lysine content (available), methionine and histidine milkfish presto during storage and re-cooking (Perubahan kelarutan protein, kandungan lisin, metionin dan histidin bandeng presto selama penyimpanan dan pemasakan ulang). Agritech. 2000; 19(2): 78–82.\n\nNational Standardization Agency for Indonesia: Determination of total plate count (TPC) on fishery products – Indonesian national standard number 01-2332.3-2006. Jakarta, Indonesia:National Standardization Agency for Indonesia (Badan Standardisasi Nasional);2006.\n\nNational Standardization Agency for Indonesia: Microbiological test method- part 1: Determination of Coliform and Escherichia coli in fishery products – Indonesian national standard number 2332.1:2015. Jakarta:National Standardization Agency for Indonesia;2015.\n\nNational Standardization Agency for Indonesia: Microbiological test method – part 2: determination of Salmonella in fisheries products – Indonesian national standard number 01-2332.2-2006. Jakarta, Indonesia:National Standardization Agency for Indonesia;2006.\n\nFardiaz S: Food microbiological analysis. Jakarta, Indonesia:Raja Grafindo Persada;1993.\n\nNational Standardization Agency for Indonesia: Smoked fish using hot smoking – Indonesian national standard number 2725:2013. Jakarta, Indonesia:National Standardization Agency for Indonesia;2013.\n\nMsusa N, Likongwe J, Kapute F, et al.: Effect of processing method on proximate composition of gutted fresh Mcheni (Rhamphochromis species) (Pisces: Cichlidae) from Lake Malawi. Int. Food Res. J. 2017; 24(4): 1513–1518.\n\nSwastawati F, Syakur A, Wijayanti I, et al.: Quality characteristics of chikuwa made from different species of fish. ARPN J. Eng. Appl. Sci. 2020; 15(24): 3056–3065.\n\nSwastawati F, Boesono H, Susanto E, et al.: Changes of amino acids and quality in smoked milkfish [Chans chanos (Forskal 1775)] processed by different redestilation method of corncob liquid smoke. Aquat. Procedia. 2016; 7: 100–105. Publisher Full Text\n\nSwastawati F, Susanto E, Cahyono B, et al.: Sensory evaluation and chemical characteristics of smoked stingray (Dasyatis blekeery) processed by using two different liquid smoke. Int. J. Biosci. Biochem. Bioinforma. 2012; 2(3): 212–216. Publisher Full Text\n\nSwastawati F, Surti T, Winarni TW, et al.: Quality characteristics of smoked fish processed using different methods and type of fish. Jurnal Aplikasi Teknologi Pangan. 2013; 2(3): 126–132.\n\nManurung H, Swastawati F, Wijayanti I: Effect of the addition of liquid smoke on the oxidation level of salted mackerel (Rastrelliger sp.) with different drying methods. Jurnal Pengolahan dan Bioteknologi Hasil Perikanan. 2017; 6(1): 30–37.\n\nZhuang P, Ye Z, Lan CY, et al.: Chemically assisted phyroextraction of heavy metal contaminated soils using three plant species. Plant Soil. 2005; 276(1-2): 153–162. Publisher Full Text\n\nChong CY, Abu BF, Russly AR, et al.: Mini review – The effects of food processing of biogenic amines formation. Int. Food Res. J. 2011; 18(3): 867–876.\n\nFood and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO): Public health risks of histamine and other biogenic amines from fish and fishery products. Meeting report.2013.\n\nLee Y-C, Lin C-S, Liu F-L, et al.: Degradation of histamine of Bacillus polymyxa isolated from salted fish products. J. Food Drug Anal. 2015; 23(4): 836–844. PubMed Abstract | Publisher Full Text\n\nTsai Y-H, Lin C-Y, Chien L-T, et al.: Histamine contents of fermented fish products in Taiwan and isolation of histamine-forming bacteria. Food Chem. 2006; 98: 64–70. Publisher Full Text\n\nLokuruka MN: Scrombotoxicosis in African fisheries-its implications for international fish trade: An overview. Afr. J. Agric. Nutr. Dev. 2009; 9: 1617–1634.\n\nLehane L, Olley J: Histamine food poisoning revisited. J. Food Microbiol. 2000; 58: 1–37. PubMed Abstract | Publisher Full Text\n\nFDA: FDA and EPA guidance levels. In fish and fishery products hazards and controls guide (pp. 245-248, Appendix 5). Washington, DC:Department of Human Health and Human Service, Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Seafood;1998.\n\nEuropean Commission: Commission recommendation of 10 January 2003 concerning a coordinated programme for official of foodstuffs for 2003 (2003/10/C). Off. J. Eur. Communities. 2003; 7: 76–81.\n\nEuropean Commission: Opinion of the scientific committee on food on the risk to human health of polycyclic aromatic hydrocarbons in food.2002. SCF/CS/CNTM/PAH/29/Finale.\n\nCodex Alimentrius Commission: Code of practice for the reduction of contamination of food with polycyclic aromatic hydrocarbons (PAH) from smoking and direct drying processes, CAC/RCP. Vol 68.July 2017.Reference Source\n\nMuratore G, Mazzaglia A, Lanza CM, et al.: Process variable on the quality of Swordfish fillets flavored with smoke spoilage potential and sensory profile associated with bacteria isolated from cold smoked salmon. Food Res. Int. 2007; 34: 797–806. Publisher Full Text\n\nSwastawati F, Darmanto YS, Sya’rani L, et al.: Quality characteristics of smoked skipjack (Katsuwonus pelamis) using different liquid smoke. Int. J. Biosci. Biochem. Bioinforma. 2014; 4(2): 94–99. Publisher Full Text\n\nSwastawati F, Surti T, Apriliani D: Analysis of thiobarbituric acid and benzo[a]pyrene value of smoked nile tilapoa (Oreochromis niloticus) using different liquid smokes. J. Coast. Dev. 2010; 12(3): 160–165.\n\nElisabeth J, Haryati T, Donald S: Polycyclic aromatic hydrocarbon (PAH) – The relation to palm oil and health.In PPKS News (Pusat Penelitian Kelapa Sawit): Medan, Indonesia. [Bahasa Indonesia].\n\nHadinoto S, Kolanus JPM: Evaluation of nutritional value and quality of round Scad (Decapterus sp) presto with addition liquid smoke and yeast. Majalah Biam. 2017; 13(01): 22–30.\n\nZuraida I, Sukarno, Budijanto S: Antibacterial activity of coconut shell liquid smoke (CS-LS) and its application on fish ball preservation. Int. Food Res. J. 2011; 18: 405–410.\n\nSwastawati F, Boesono H, Wijayanto D:Antimicrobial activity of corncob liquid smoke and its application of smoked milkfish (Chanos chanos Forsk) using electric and mechanical oven. International Proceeding of International Conference on Food Security and Nutrition IPCBEE. Singapore:IACSIT Press;2014; 67: 109–113.\n\nGomez-Estaca J, Montero P, Gimenez B: Effect of functional edible films and high pressure processing on microbial and oxidative spoilage in cold-smoked sardine (Sardina pilchardus). Food Chem. 2007; 105: 511–520. Publisher Full Text\n\nDavidson MP, Sofos JN, Branen AL: Antimicrobials in food. Third ed.Boca Rotan:CRC Press.\n\nFuadi A, Supriadi NR: Safety evaluation of smoke fish I EPIL I, District of Lais, Musi Banyuasin. Fishtech – Jurnal Teknologi Hasil Perikanan. 2015; 4(2): 148–157.\n\nSwastawati F, Riyadi PH, Kurniasih RA, et al.: Safety, quality, and nutritional aspect of smoked barracuda fish. figshare. [Dataset].2022. Publisher Full Text\n\nSwastawati F, Riyadi PH, Kurniasih RA, et al.: Safety, quality, and nutritional aspect of smoked barracuda fish. figshare. [Dataset].2022. Publisher Full Text\n\nSwastawati F, Riyadi PH, Kurniasih RA, et al.: Safety, quality, and nutritional aspect of smoked barracuda fish. figshare. [Dataset].2022. Publisher Full Text\n\nSwastawati F, Riyadi PH, Kurniasih RA, et al.: Safety, quality, and nutritional aspect of smoked barracuda fish. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "227497",
"date": "29 Dec 2023",
"name": "Bárbara Teixeira",
"expertise": [
"Reviewer Expertise seafood science and technology",
"seafood nutrition",
"seafood preservation",
"amino acids",
"chromatography methods"
],
"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 submitted presents results of proximate composition (protein not included), heavy metals contents (Pb, Cd, Hg, As, Sn), microbial contamination, histamine, and benzo[a]pyrene in fresh and smoked (traditional and with liquid smoke) barracuda fish.\n10 kg of barracuda fish was used, but it is not mentioned the size/weight of the individuals and the number of specimens used for each treatment. Also, the liquid smoke specifications should have been included in the manuscript, as well as details on the traditional smoking process. Some parts of the methods are extremely detailed (like proximate composition equations, dilutions in microbial analysis, etc) and should be deleted. In general, the methods are not clearly described (some temperatures and centrifuge conditions are missing, inconsistent range of concentrations for heavy metals, inconsistent wavelengths, missing concentrations, etc).\nThe results section is just a repetition of the values presented in tables and figures. There is a reference to vitamins, but those results are not presented in the manuscript. In figure 2, the size of the bar is not in accordance with the scale of the yy axis. The number of decimal units should be revised throughout the manuscript/tables/figures.\nThe discussion is very poor. Published research studies done with smoked fish (also using liquid smoke) should be included in the discussion. The conclusions mentions that smoked barracuda guarantee nutritional needs, but the nutritional results do not include proteins, amino acids, fatty acids, minerals, etc. The results presented should be complemented with sensory analysis results, and also with a preservation study. The manuscript should not be accepted for publication, due to its general low quality.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "227491",
"date": "16 May 2024",
"name": "Yénoukounmè Euloge Kpoclou",
"expertise": [
"Reviewer Expertise Food technology",
"Food safety 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\nReviewer comments Paper Title : Safety, quality, and nutritional aspect of smoked barracuda fish Comments Methodology Question 1: Authors have to specify the size of fish (e.g. 20 pieces/Kg) to ensure reproducibility of the study and ease of interpretation of the data. Question 2: For the traditional smoking process (15 min), How did the core temperature of the product evolve as a function of time during the heat treatments? What was the maximum temperature reached at the core of the product? Because if the heat treatment applied is not equivalent to pasteurization, it might not have any effect on the microbial load of the product. On the other hand, immersing the fish in liquid smoke is first and foremost a chemical treatment with a contact time (30 min) that is longer than that of traditional smoking (15 min). In addition to the action of the liquid smoke, the product is subjected to a heat treatment up to 4 times longer than traditional smoking duration. Therefore, the comparison of the safety of the both smoked fish from the different smoking method is not relevant. The authors should provide more details on the experimental set-up. Results and discussion Question 3: Table 1 shows that both treatments (traditional smoking and use of liquid smoke) significantly reduced the moisture of the product. This reduction in moisture was more pronounced with traditional smoking (74.27% - 61.69%) than with the liquid smoke treatment, which was more severe (74.27% - 64.46%), with 1 hour of exposure to heat compared with 15 minutes. How can the authors explain that? Question 4: The authors interpreted the ash content data by referring to the effect of adding NaCl, whereas in the study presented, the methodology does not mention adding this salt. Question 5: In view of the objective of the study as indicated by the authors, the data presented in table 2 do not show any significant difference in effect between the two processing treatments (traditional smoking and smoking with liquid smoke), contrary to the conclusion drawn in the summary of the study. These data show a trend towards a reduction in the concentration of heavy metals (Hg and As). How do the authors explain that? Question 6: Figure 1 shows an increase in histamine concentration which the authors have associated with the activity of positive decarboxylase microorganism. The authors should specify the time between the end of the processing trial and the analysis of the smoked fish to enable the extent of the microbial activity to be assessed, with details of the duration and the conditions under which the samples were stored before analysis. Question 7: The interpretation of Figure 2 (PAH content) is highly dependent on the fuels used for heat treatment. The methodology gives no details of the fuels used for each of the processing methods. Are fish's exposed to direct contact with combustion smoke? All the details on the factors conducive to PAH contamination in the context of this study must be provided. Furthermore, the analysis method is outdated. Recent methods use 1g of analysis samples and reveal more PAHs. Also, BaP is no longer the only indicator of the occurrence of PAHs in foodstuffs, the sum of 4PAHs (benzo[a]pyrene, chrysene, benzo[a]anthracene and benzo[b]fluoranthene) is recommended in addition to BaP.\nOverall assessment: The study has its shortcomings in its reproducibility. The analytical methods used to assess the safety of smoked fish lack precisions.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1378
|
https://f1000research.com/articles/10-951/v1
|
21 Sep 21
|
{
"type": "Case Report",
"title": "Case Report: An unusual case of small bowel volvulus associated with pneumatosis intestinalis",
"authors": [
"Alia Zouaghi",
"Dhafer Hadded",
"Mesbahi Meryam",
"Yazid Benzarti",
"Mona Cherif",
"Haithem Zaafouri",
"Khalil Ben Massoud",
"Chiraz Chamekhi",
"Anis Ben Maamer",
"Alia Zouaghi",
"Dhafer Hadded",
"Yazid Benzarti",
"Mona Cherif",
"Haithem Zaafouri",
"Khalil Ben Massoud",
"Chiraz Chamekhi",
"Anis Ben Maamer"
],
"abstract": "Pneumatosis cystoid intestinalis is a rare disease reported in the literature affecting 0.03% of the population. It has a variety of causes and its manifestation may change widely. It usually presents as a marginal finding resulting from various gastrointestinal pathologies. In the acute complicated form of pneumatosis intestinalis, management is challenging for physicians and surgeons. We present a case of a 60-year-old patient who was admitted to our surgical department with a symptomatology suggestive of small bowel occlusion. Computed tomography demonstrated ileal volvulus associated with parietal signs suffering and pneumoperitoneum. An emergent exploratory laparoscopy followed by conversion was performed demonstrating segmental ileal pneumatosis intestinalis secondary to a small bowel volvulus due to an inflammatory appendix wrapping around the distal ileum. Further, detorsion, retrograde draining, and appendectomy were performed because there were no signs of necrosis and the appendix was pathological. The postoperative course was uneventful. This case is exceedingly rare in the literature, because it was featured by the ileal volvulus due to appendicitis.This case report emphasizes the importance of surgical procedures in the management of symptomatic pneumatosis intestinalis.",
"keywords": [
"Pneumatosis cystoid intestinalis",
"small bowel volvulus",
"acute abdomen",
"case report"
],
"content": "Introduction\n\nPneumatosis cystoid intestinalis (PCI) is a low-incidence pathology defined by the existence of air in the small intestine or colon wall.1 PCI can affect any portion of the gastrointestinal tract and could be present in any layer such as the mucosa, submucosa, or subserosa.1–3 It can either be presented as a secondary form in 85% of cases or an idiopathic form in 15% of cases.1,2 The secondary pattern occurs more frequently in gastrointestinal causes such as bowel obstruction.3,4 The management of PCI is challenging to surgeons especially in symptomatic cases.5 We report a rare case of ileal pneumatosis cystoides associated with small bowel volvulus, presenting with acute abdominal pain. This case is exceedingly rare in the literature, because it was featured by the ileal volvulus due to appendicitis.\n\n\nCase report\n\nA 60-year-old retired, north African male patient without any medical or surgical history consulted the emergency department for 24 hours of abdominal pain, distension, and vomiting. The patient had experienced this pain a year earlier, but did not consult any doctor, and the pain faded away spontaneously. On physical examination, tachycardia and distended abdomen with mild tenderness were noted. White blood count was 8840 E/mm3 and C reactive protein was 36 mg/l (normal values: White blood count: 4000E/mm3, and C reactive protein: 1 mg/l). X-ray of thorax and abdomen showed dilated small bowel, multiple fluid levels and pneumoperitoneum (Figure 1).\n\nAn abdominal CT scan was performed, revealing distended small bowel loops upstreaming transitional levels like a ‘whirl sign’ (Figure 2), a bubbly pattern across the length of the small bowel associated with parietal suffering signs (Figure 3), abundant pneumoperitoneum (Figure 4), and a pathological meso-celiac appendix (Figure 5). The CT scan suggested a diagnosis of ileal volvulus due to the meso-celiac appendix.\n\nWe initially decided to perform laparoscopy. Intraoperatively, small bowel loops were much dilated not allowing intraperitoneal exploration. Gas-filled cystic lesions on small bowel serosa were identified. There was no evidence of perforation. We did choose to convert into midline incision for better and prudent exploration. A volvulus was found, involving a two-and-a-half clockwise turn around a long, pendulous small bowel mesentery, the strangled bowel was greatly congested (Figure 6). At the base of the volvulus, an inflammatory appendix was wrapped around the last loop of the ileum (Figure 7). Also, multiple gas-filled subserosal cysts, differently sized, on the wall of the ileum were encountered (Figure 8). When the ileum was re-rotated, small bowel loops had preserved vitality. The entire colon was normal. Detorsion, retrograde draining, and appendectomy were performed because there were no signs of necrosis and the appendix was pathological.\n\nPostoperatively, the patient completed a five-day course of intravenous metronidazole 500 mg three times a day. There were no postoperative complications. Anatomopathological examination revealed an inflammatory appendix without malignancy. A lower endoscopy was completed after surgery. It showed the presence of two polyps on the rectum and the transverse colon in low-grade dysplasia with no other lesions that were resected. There was no malignancy on the anatomopathological examination. The patient was monitored regularly, and the long-term post-operative course was uneventful.\n\n\nDiscussion\n\nPCI is an uncommon disease (0.03% of adults)6 and its pathogenesis is still not clear.7 According to its etiology, literature classifies this entity mainly as primary or secondary type.8 There is also an idiopathic type which usually affects the left colon and is rarely reported in the literature. We found that thirteen cases of primary PCI have been described in the international literature (Table 1). The secondary type frequently affects the small intestine and the right colon.9 Its pathogenesis is multifactorial and can be explained by 3 theories: mucosal disruption, bacterial theory, and pulmonary disease.1,7,10,11 The mucosal disruption is due to the dissemination of bowel gas through a mucosal defect into lymphatic channels.1,10 Wu et al.12 found that high altitude is a new theory explaining PCI’s pathogenesis. Highland areas induce passage of intraluminal gas into the submucosa damaging the mucosa. Mucosal damage can result from bowel occlusion, inflammatory process, and cytotoxic medical treatment.11 The pulmonary cause is confirmed in patients with asthma and chronic bronchitis. In these cases, the rupture of alveoli causes the migration of air bubbles from interstitial spaces through the mediastinum and from the retroperitoneum to the blood vessel of the intestinal wall.1,8,10 However, the bacterial theory is explained by entry of bacterial gas due to a defect on the bowel wall lymphoid tissue.8,10 This mechanism can justify the use of antibiotics.1 Chemotherapy or hormonal therapy, and systemic sclerosis were also reported in the literature as a cause of PCI.1 Finally, while keeping in mind these theories, their pathogenesis has not been yet fully clarified.1\n\nBesides, the disease’s location on the digestif tractus may be helpful to guide the etiology. So pyloric stenosis or gastric cancer can lead to a proximal pathology; however distant one might be due to mesenteric ischemia or diverticulitis.9\n\nPCI is a rare entity reported in the literature, but nowadays PCI reports’ number has been increasing because of the widespread use of CT scan and colonoscopy.9 This pathology is more frequently asymptomatic.1 Whereas in some cases, they may present with symptoms such as abdominal pain, constipation, distension, diarrhea, or bleeding.8,9 Incidentally PCI can induce surgical complications such as bowel obstruction, intestinal perforation, volvulus, intussusception, and bleeding, which require surgical intervention.13\n\nIntestinal obstruction can be a rare complication of PCI. This event depends on the size and number of the cysts which lead in certain cases to a reduction of the intestinal lumen, volvulus, perforation, and hemorrhage.7,11 In the literature, PCI associated with volvulus is much more uncommon. Besides this association, one of the highlights of our case is the long and hypermobile small bowel mesentery. Moreover, PCI is discussed to be a mechanical factor leading to irreversible volvulus, also it is disputed that volvulus contributes to ischemia which is an etiological factor leading to PCI.3,14\n\nImaging findings may be helpful to confirm PCI diagnosis, especially on CT scans.1,6 Computed tomography can show a grape cluster aspect within the wall of the intestine.1 Three patterns of pneumatosis have been reported in the literature using CT scan imaging: bubble cystoid, a linear pattern, and a circular pattern.1\n\nPneumoperitoneum can be explained by the rupture of the cyst on the wall intestine, without any evidence of peritoneal irritation or digestive perforation, like in our case. So that we should be wise to correlate clinical and radiographic findings, when free air is present below the diaphragm in chest X-ray.8,9 Pneumatosis intestinalis and portomesenteric venous gas (PVG) are generally debated independently in the literature. This association of radiological findings usually concludes to the presence of mesenteric infarction, but they may indicate occasionally nonischemic conditions. So that their presence should not be always regarded as signs of severity.13,15,16 Moreover, according to literature, the rare findings of PCI and PVG can be present in asymptomatic patients without ominous signs, as described in the series of Sooby et al.,17 including 88 patients with PCI/PVG of which 19 with benign PCI, and of these 19, 6 patients had both PCI and PVG. These patients were put under surveillance, and they had no uneventful recovery.\n\nThe management of PCI is not well established, there are no standard therapeutic rules.10 However, the mandatory in its management is to judge whenever it is benign or life-threatening.11 So that it is established that if a CT scan shows intestinal infarction, urgent surgery is mandated. If no signs of intestinal damage is found, a conservative treatment is regarded to be ideal.13 The common conservative procedure is to use metronidazole Antibiotics, which affects intestinal bacteria by the suppression of hydrogen production, and hyperbaric oxygen therapy.2,6,8,10 Nevertheless, a surgical procedure is indicated in complications such as peritoneal irritation or intestinal obstruction.2,10\n\nThe second particularity in our case is that the volvulus of the small bowel is due to acute appendicitis. This entity is explained by the wrapping of the appendix, due to its particular length, around the ileum occurring volvulus and strangulation.18,19 According to the literature, this mechanism resulted from adhesion of the inflamed appendix to the posterior peritoneum forming a turn of the spire of the ileum last loop resulting in volvulus.18,19 In summary, our case is exceedingly rare in the literature, featured by the ileal volvulus due to appendicitis.\n\n\nConclusion\n\nPCI is a rare disease whose diagnosis is offering a challenge for surgeons. This rare condition can often be associated with benign diseases or it can be proof of intestinal necrosis. Although surgery is mandatory in the complicated pattern, the treatment of asymptomatic forms is more likely conservative. Besides, both surgical and medical approaches can efficiently compete with these challenging diagnoses.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent was obtained from the patient regarding the publication of this case report.",
"appendix": "References\n\nSugihara Y, Harada K, Ogawa H, et al.: Pneumatosis Cystoides Intestinalis. 2018; 4.\n\nLing F, Guo D, Zhu L: Pneumatosis cystoides intestinalis: a case report and literature review. BMC Gastroenterol. déc 2019; 19(1):176. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiau S-S, Cope C, MacFarlane M, et al.: A lethal case of pneumatosis intestinalis complicated by small bowel volvulus. Clin J Gastroenterol . févr 2009; 2(1): 22–26. PubMed Abstract | Publisher Full Text\n\nArora R, El-Hameed AA, Harbi OA: Pneumatosis Intestinalis of Small Bowel in an Adult: A Case Report. Kuwait Med J. 2009; 3. PubMed Abstract | Publisher Full Text\n\nSlesser AAP, Patel PH, Das SC, et al.: A rare case of segmental small bowel pneumatosis intestinalis: A case report. Int J Surg Case Rep. 2011; 2(7): 185–187. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoyon FX, Molina GA, Tufiño JF, et al.: Pneumoperitoneum and Pneumatosis cystoides intestinalis, a dangerous mixture. A case report. Int J Surg Case Rep. 2020; 74: 222–225. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRachid MG, Sadok T, Narjis Y, et al.: Occlusive syndrome in intestinal cystic pneumatosis, medical treatment or surgery. PAMJ Clin Med. 2020 [cité 11 janv 2021]; 2. Publisher Full Text Reference Source\n\nÜstüner MA, Dalgıç T, Bostancı EB: Pneumatosis Cystoides Intestinalis: Three Case Reports. Indian J Surg . août 2020; 82(4): 690–692. Publisher Full Text\n\nFujiya T, Iwabuchi M, Sugimura M, et al.: A Case of Intussusception Associated with Pneumatosis Cystoides Intestinalis. Case Rep Gastroenterol. 12 sept 2016; 10(2): 494–498. Publisher Full Text\n\nDi Pietropaolo M, Trinci M, Giangregorio C, et al.: Pneumatosis cystoides intestinalis: case report and review of literature. Clin J Gastroenterol . févr 2020; 13(1): 31–36. PubMed Abstract | Publisher Full Text\n\nRathi C, Pipaliya N, Poddar P, et al.: A Rare Case of Hypermobile Mesentery With Segmental Small Bowel Pneumatosis Cystoides Intestinalis. Intest Res. 2015; 13(4): 346. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu L-L: A systematic analysis of pneumatosis cystoids intestinalis. World J Gastroenterol. 2013; 19(30): 4973. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrighi M, Vaccari S, Lauro A, et al.: “Cystamatic” Review: Is Surgery Mandatory for Pneumatosis Cystoides Intestinalis? Dig Dis Sci . oct 2019; 64(10): 2769–2775. PubMed Abstract | Publisher Full Text\n\nAlves SC, Seidi M, Pires S, et al.: Pneumatosis intestinalis and volvulus: a rare association.2.\n\nFurihata T, Furihata M, Ishikawa K, et al.: Does massive intraabdominal free gas require surgical intervention? World J Gastroenterol. 2016; 22(32): 7383. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWiesner W, Mortelé KJ, Glickman JN, et al.: Pneumatosis Intestinalis and Portomesenteric Venous Gas in Intestinal Ischemia: Correlation of CT Findings with Severity of Ischemia and Clinical Outcome. Am J Roentgenol. déc 2001; 177(6): 1319–1323. PubMed Abstract | Publisher Full Text\n\nSooby P, Harshen R, Joarder R: An unusual triad of pneumatosis intestinalis, portal venous gas and pneumoperitoneum in an asymptomatic patient. J Surg Case Rep. 8 avr 2015; 2015(4): rjv035–rjv035. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarrison S, Mahawar K, Brown D, et al.: Acute appendicitis presenting as small bowel obstruction: two case reports. Cases J. déc 2009; 2(1): 9106. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAssenza M, Ricci G, Bartolucci P, et al.: Mechanical small bowel obstruction due to an inflamed appendix wrapping around the last loop of ileum.6. PubMed Abstract\n\nRodríguez González M, de los Á Mejías Manzano M, Sobrino López AM, et al.: Primary or idiopathic intestinal pneumatosis: a rare casual endoscopic finding. Rev Esp Enfermedades Dig. 2021 [cité 6 juin 2021]. Reference Source\n\nTakahashi K, Fujiya M, Ueno N, et al.: Endoscopic Fine-Needle Aspiration Is Useful for the Treatment of Pneumatosis Cystoides Intestinalis With Intussusception. Am J Gastroenterol. janv 2019; 114(1): 13–13. PubMed Abstract | Publisher Full Text\n\nSuda T, Shirota Y, Wakabayashi T: Pneumatosis Cystoides Intestinalis. Clin Gastroenterol Hepatol . mars 2019; 17(4): A33–A34. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLin W-C, Wang K-C: Pneumatosis Cystoides Intestinalis Secondary to Use of an α-Glucosidase Inhibitor. Radiology. mars 2019; 290(3): 619–619. PubMed Abstract | Publisher Full Text\n\nRomano-Munive AF, Barreto-Zuñiga R: Pneumatosis cystoides intestinalis.1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFraga M, da Silva MJN, Lucas M: Idiopathic Pneumatosis Intestinalis, Radiological and Endoscopic Images. GE Port J Gastroenterol. sept 2016; 23(5): 270–2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTseng P-Y, Tarng D-C, Yang W-C, et al.: Benign Pneumatosis Intestinalis. Intern Med. 2014; 53(14): 1589–1590. PubMed Abstract | Free Full Text\n\nNagata S, Ueda N, Yoshida Y, et al.: Pneumatosis coli complicated with intussusception in an adult: Report of a case. Surg Today. mai 2010; 40(5): 460–464. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "95001",
"date": "12 Oct 2021",
"name": "Gennaro Martines",
"expertise": [
"Reviewer Expertise general 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\n'Pneumatosis intestinalis (PI), described by Du Vernoy in 1730, is a rare condition that refers to the presence of multiple gaseous cysts in the intestinal submucosa and subserosa with a reported incidence of 0.03%. It can be divided between a benign form and in a life-threatening condition requiring surgery.\nThe radiographic incidence of PI has been reported to be up to 0.37% of patients who have abdominal computed tomography (CT) scans. PI can be divided into the primary/idiopathic type (15%), which refers to air pockets that imply to a chronic and benign idiopathic etiology, and the secondary type (85%), which refers to radiological findings of linear, microvesicular, or more circumferential appearing intramural gas caused by several predisposing factors. The peak age at onset is 45.3 ± 15.6 years with a male to female ratio of 2.4: 1.' 1\nThis is an interesting paper which describes an unusual case of pneumatosis intestinalis. This situation is associated with many causes of bowel obstruction, and often requires a surgical approach in an emergency.\nThe manuscript is well described but I want to ask why the authors perform a laparoscopy. In these situations there is a distension of the bowel which does can make this kind of approach risky. Can they explain this decision as a surgical approach?\nAll the other parts are well described with adequate diagnostic steps.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "7556",
"date": "24 Nov 2022",
"name": "meryam meryam",
"role": "Author Response",
"response": "Dear Sir, I appreciate the time and effort that you and the reviewers have dedicated to providing your valuable feedback on my manuscript. I am grateful to the reviewers for their insightful comments on our paper. I have been able to incorporate changes to reflect most of the suggestions provided by the reviewers. Thank you, sincerely."
},
{
"c_id": "8906",
"date": "24 Nov 2022",
"name": "meryam meryam",
"role": "Author Response",
"response": "the first laparoscopic pathway was indicated in the first place as an easy and minimally invasive exploratory approach."
}
]
},
{
"id": "94998",
"date": "13 Oct 2021",
"name": "Jaques Waisberg",
"expertise": [
"Reviewer Expertise Gastrointestinal 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\nGeneral considerations:\nThe clinical relevance of pneumatosis intestinalis varies widely from benign to potentially fatal conditions, depending on the underlying cause of pneumatosis intestinalis, which can lead to high mortality if surgery is delayed when necessary. Mesenteric ischemia, intestinal obstruction, and intestinal necrosis represent the fatal causes of pneumatosis intestinalis. It is challenging to distinguish between those patients who require surgery and those who can be observed or treated conservatively with adequate treatment of the underlying disease. The diagnosis of intestinal pneumatosis is made by computed tomography or plain abdominal radiography. Computed tomography is the most sensitive imaging modality. A strong indicator of the presence of mesenteric infarction or ischemia is the association of pneumatosis intestinalis with gas in the portal venous blood.\nSurgery is not indicated in asymptomatic patients with radiographic signs of pneumatosis intestinalis but no signs of bowel obstruction or free peritoneal air. Intestinal ischemia is the most likely cause, and a delay in surgery will worsen the patient’s condition. When non-surgical treatment is initially performed, the patient must be re-evaluated later. Surgery must be performed if there is no response to conservative treatment or if the patient’s condition worsens.\nThis is an exciting manuscript about a rare case of pneumatosis intestinalis in an adult patient. The subject covered by the manuscript is required for clinical practice. This manuscript has scientific value due to the rarity of the case. However, this case report needs some adjustments.\nSpecific considerations:\nTitle – Appendix necrosis is identified as one of the contributing causes for the onset of pneumatosis intestinalis. As the authors themselves state in the text, appendicitis was the determining factor for small bowel volvulus. The title should include this information. The authors perform a literature review (Table 1 and 27 references), so the term “literature review” needs to be in the title.\nAbstract – The conclusion that “This case report emphasizes the importance of surgical procedures in the management of symptomatic pneumatosis intestinalis” needs to be contextualized according to the underlying disease, as this is precisely the dilemma that is faced with distinguishing the clinical or surgical approach in symptomatic cases of pneumatosis intestinalis.\nDiscussion – The terms “primary” and “idiopathic” pneumatosis intestinalis are equivalent, so I suggest unifying them. A thorough explanation of the theories of the pathogenesis of intestinal pneumatosis is not necessary for the case description. I also recommend not using the term “benign PCI,” just “PCI”. Is there a “malignant PCI”? What were the reasons for six patients with “benign” PCI and PVG “not having” or “having” an uneventful recovery? Please remove the term “Antibiotics” after the word “metronidazole”.\nFigures – The legends of figures 1 to 5 are incomplete, as they must be self-explanatory (Exam name, disease name). Highlights in the legend must be marked with arrows on the figure itself. In figures with arrows, the pointed structure must be indicated in the legend. Figures 6 and 7 are unnecessary, as they do not add relevant information to the report.\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? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No",
"responses": [
{
"c_id": "7555",
"date": "24 Nov 2022",
"name": "meryam meryam",
"role": "Author Response",
"response": "Dear Sir, I appreciate the time and effort that you and the reviewers have dedicated to providing your valuable feedback on my manuscript. I am grateful to the reviewers for their insightful comments on our paper. I have been able to incorporate changes to reflect most of the suggestions provided by the reviewers. Thank you, sincerely."
},
{
"c_id": "8907",
"date": "24 Nov 2022",
"name": "meryam meryam",
"role": "Author Response",
"response": "thank you for your efforts i made all the corrections"
}
]
},
{
"id": "94999",
"date": "20 Oct 2021",
"name": "Cristian Mesina",
"expertise": [
"Reviewer Expertise 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\n1. During the clinical examination of the abdomen it would have been better to explain what was found on the percussion of the abdomen.\n2. Digital rectal examination was to be included in the clinical examination of the patient.\n3. Biological paraclinical examinations should have been more extensive to highlight whether or not there existed the presence of toxic-septic shock.\n4. The intraoperative exploration of the peritoneal cavity, the cause of pneumoperitoneum, should have been better explained.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "7554",
"date": "24 Nov 2022",
"name": "meryam meryam",
"role": "Author Response",
"response": "Dear Sir, I appreciate the time and effort that you and the reviewers have dedicated to providing your valuable feedback on my manuscript. I am grateful to the reviewers for their insightful comments on our paper. I have been able to incorporate changes to reflect most of the suggestions provided by the reviewers. Thank you, sincerely."
}
]
}
] | 1
|
https://f1000research.com/articles/10-951
|
https://f1000research.com/articles/11-1377/v1
|
24 Nov 22
|
{
"type": "Systematic Review",
"title": "Towards achieving lightweight intrusion detection systems in Internet of Things, the role of incremental machine learning: A systematic literature review",
"authors": [
"Promise Ricardo Agbedanu",
"Richard Musabe",
"James Rwigema",
"Ignace Gatare",
"Theofrida Julius Maginga",
"Destiny Kwabla Amenyedzi",
"Richard Musabe",
"James Rwigema",
"Ignace Gatare",
"Theofrida Julius Maginga",
"Destiny Kwabla Amenyedzi"
],
"abstract": "While the benefits of IoT cannot be overstated, its computational constraints make it challenging to deploy security methodologies that have been deployed in traditional computing systems. The benefits and computational constraints have made IoT systems attractive to cyber-attacks. One way to mitigate these attacks is to detect them. In this study, a Systematic Literature Review (SLR) has been conducted to analyze the role of incremental machine learning in achieving lightweight intrusion detection for IoT systems. The study analyzed existing incremental machine learning approaches used in designing intrusion detection systems for IoT ecosystems, emphasizing the incremental methods used in detecting intrusions, the datasets used to evaluate these methods, and how the method achieves lightweight status. The SLR outlined the contributions of each study, focusing on their strengths and gaps, the datasets used, and the incremental machine learning model used. This study revealed that incremental learning approaches in detecting intrusion in IoT systems are in their infant stage. Over 12 years, from 2010 to 2022, a total of twenty-one (21) studies were carried out in IDSs using incremental machine learning, with eight (8) studies carried out in IoT systems. In addition to reviewing the literature, we offer suggestions for improving existing solutions and achieving lightweight IDS for IoT systems. We also discussed some problems with making lightweight IDS for IoT systems and areas where more research could be done in the future.",
"keywords": [
"Internet of Things",
"Incremental Machine Learning",
"Online Machine Learning",
"Intrusion Detection System",
"Anomaly Detection",
"Network Security"
],
"content": "Introduction\n\nThe past three decades have seen a massive paradigm shift in computing technology. This shift is mainly due to increased computing power and communication speed. The latter has enabled us to develop intelligent devices that can communicate with each other. These intelligent devices make up the Internet of Things (IoT) ecosystem. The IoT ecosystem is deployed in cities, healthcare, energy, agriculture, transportation, and industries. Moreover, the internet of things has become a household name because of its numerous benefits to the various domains it has been applied to. However, these benefits have made the IoT ecosystem attractive to cyber attackers. Over the years, security methodologies like encryption, authentication, data confidentiality, access control, and privacy have been proposed by several researchers to ensure security in IoT environments. Despite these security solutions, IoT systems are still vulnerable and highly susceptible to cyber-attacks. An alternative approach to fighting these attacks is to detect them using Intrusion Detection Systems (IDS). In traditional computer networks, IDS monitors the network’s activities. Although the concept of intrusion detection has been well explored in traditional computing and network systems as far back as the 1980s, the idea is in its infant stage in IoT security1. The computational constraints of IoT systems make it practically impossible to implement traditional IDS in IoT environments. Although many IDS solutions have been proposed, most use offline or batch machine learning models. This situation makes these models computationally expensive and difficult to deploy on IoT devices. An alternative to the above-mentioned the approach is to build IDS that learn from data streams, which can produce IDS with minimal computational usage. In this paper, the authors seek to present a systematic review of incremental ML-based IDS in IoT systems. Several surveys and review articles have been done in IDS for IoT. But to the best of our knowledge, none of these surveys or SLRs focuses on the role of incremental machine learning and how they can lead to lightweight IDS that are suitable for the IoT ecosystem. This study covers work done using incremental ML to develop IDS for IoT systems from 2010 to 2022. The period from 2010 to 2022 was adopted for this study because we wanted to analyze the research trend of incremental ML-based IDS in IoT systems since 2010. We used the methods identified by 2,3 to conduct our studies. This work differs from other existing studies by exploring how incremental machine learning methods achieve lightweight IDS that fit into the computational constraint nature of IoT systems. The study further considers some of the general potential problems facing the implementation of IDS in IoT environments. A total of 168 studies were returned based on our search criteria, but eight (8) studies were found to be IoT-based after applying our formulated inclusion and exclusion criteria. However, because the number was small, we decided to include studies that satisfied the inclusion criteria but were not IoT-based, which yielded 13 studies. This brought the total number of studies considered in this SLR to 21. However, most of our analyses were primarily focused on IoT-based studies since this study’s objective. The primary contributions of our study are as follows:\n\nConducting a comprehensive systematic literature review of incremental ML methods in designing IDS for IoT systems.\n\nThis work also provides a detailed analysis and discussion of how incremental ML models could effectively fit into real-time IDSs for IoT systems.\n\nFurthermore, the study analyzes the strengths and weaknesses of the IoT-based articles considered in this systematic literature review.\n\nThis work also identifies the most critical problems with IDS research in IoT systems and suggests future research.\n\nThe following is how the paper is structured. Sections 2 and 3 discuss related works and the research methodology employed. Sections 4 and 5 discuss the findings, challenges, and future research directions. Section 6 discusses validity threats, while Section 7 discusses the study’s conclusion.\n\n\nRelated works\n\nThis section presents some survey and review papers that are closely related to our study. We considered existing survey and review studies focusing on intrusion detection in IoT systems for the past five years, 2017–2022. We considered the past five years because most surveys and SLRs for IoT-based intrusion detection systems that are of interest to our study were done during this period.\n\nDuring their investigation, 4 conducted a comprehensive survey of the latest intrusion detection systems designed specifically for IoT systems. The study focused on the methods, features, and methods implemented in each study while providing insights into the various architectures used in IoT and some emerging vulnerabilities. The authors also looked at factors that affect the performance of IDS in intelligent environments. Some factors identified were detection accuracy, false positive rate, energy consumption, processing time, and the overall performance overhead.\n\nIn their research, 5 also presented a review of IDS for IoT environments, focusing on the techniques and deployment strategies used by each of the studies included in their work. The authors also considered the validation strategies and the datasets used in the respective works covered in their studies. Moreover, the study discussed some challenges facing intrusion detection in IoT systems.\n\nIn their work, 6 presented a survey that captures the practices and challenges facing intrusion detection systems in the internet of things. Benkhelifa et al.6 considered various IDS solutions used in IoT environments in their work. Each solution identified in the study was considered an improvement strategy to improve the detection methods.\n\nMishra et al.7 presented a study that compares models that detect and prevent distributed denial of service attacks. The study also discussed the different classifications of methods, models, and datasets used to build IDS. The study also looked at research challenges in IDS and proposed some solutions to mitigate these challenges. The authors presented some areas that can be considered studies for the future.\n\nIn their study, 8 provided an overview of the current security challenges of the IoT and how these challenges can be solved using IDS. The study also explored future challenges in IoT and how they can be addressed using intrusion detection.\n\nIn a similar study, 9 presented a review of machine learning-based intrusion detection systems in IoT environments, discussing various Machine Learning (ML) approaches used in designing IDS with emphasis on their advantages and disadvantages. The authors concluded their study by looking at some of the research challenges and possible future direction for work around IDS in IoT.\n\nArshad et al.10 conducted a comprehensive study on existing intrusion detection systems for IoT systems using three parameters, namely, computational overhead, energy consumption, and privacy implications. The study also identified some open challenges that exist in the area of their study.\n\nIn another study, 11 conducted a systematic review of the literature to examine existing works in anomaly-based intrusion detection that use deep learning techniques. The study also discussed the challenges faced by DL-based anomaly detection in the IoT domain and some areas that can be considered for future work.\n\nSimilarly, 1 conducted a survey of intrusion detection in IoT environments with a focus on the detection methods, placement strategy, security threats, and validation strategy.\n\nSeyfollahi et al.12 reviewed machine learning techniques used in designing intrusion detection systems for the Low-Power and Lossy Networks (RPL) protocol. The study also identified open issues and challenges related to their study’s domain.\n\nIn their study, 13 showed an overview of intrusion detection systems for IoT networks and presented some suggestions for future work that could help make IoT networks more secure.\n\nChaabouni et al.14 also conducted a survey that sought to classify IoT security threats and challenges. The study analyzed and compared the state-of-the-art NIDS in the context of IoT networks. The study considered the architecture, detection methodologies, validation strategies, and deployed algorithms.\n\nSaranya et al.15 evaluated the performance analysis of machine learning models used in the design of IDS for IoT systems. Besides the fact that none of the surveys or SLRs considered incremental ML-based IDSs in their studies, these studies had other gaps which have been considered in our study.\n\nA summary of the related literature is shown in Table 1 below.\n\n\nResearch method\n\nIn this section, we outlined this study’s method deployed by 2,3. We used general principles in conducting systematic reviews. The methodology proposed by 2 and 3 has five steps as follows:\n\nThe formulation of crucial research questions.\n\nThe formulation of the search process\n\nThe formulation of the general criteria for the selection of articles.\n\nThe data extraction process, and\n\nThe execution of analysis and classification\n\nThe following four research questions were considered in selecting the various papers used in this study.\n\nRQ1: What is the primary contribution of the paper?\n\nRQ2: What incremental or online machine learning algorithm was used in this study?\n\nRQ3: How does the proposed method handle data, feature, or concept drift?\n\nRQ4: How do the proposed IDS handle the computational constraints of IoT systems?\n\nRQ1 focuses on the primary contribution of each of the papers considered in our study. We looked at studies that used incremental or online machine-learning approaches to deploy intrusion detection in IoT environments. The goal is to provide readers and researchers with an overview of the problem and how it is addressed.\n\nRQ2 examines which incremental or online machine-learning algorithm was used in each study.\n\nRQ3 focuses on how the method proposed in RQ2 handles data, feature, or concept drift. Static models are generated by machine learning using historical data. However, once in production, ML models become unreliable, obsolete, and degrade over time. Changes in data distribution may occur during production, resulting in biased predictions. User behavior may have changed compared to the baseline data used to train the model, or there may have been additional factors in real-world interactions that influenced the predictions. Data drift is a significant cause of model accuracy deterioration over time.\n\nThe fourth research question (RQ4) aims to answer how the methods or models proposed in each of the studies handle the computation constraints of IoT devices. One limitation of IoT devices is their limited computational resources, which is one reason why traditional IDS cannot be deployed in IoT environments. It is in this regard that we looked at how each study handled the resource constraints of IoT systems while building an IDS for the same environment.\n\nThis work was conducted using the guidelines stipulated in the Preferred Reporting Items for SLRs and Meta-Analyses (PRISMA)16. To suite the guidelines proposed by PRISMA to Computer Science, we incorporated the PRISMA guidelines with the guidelines proposed by Kitchenham17. Figure 1 below shows the flow diagram of inclusion and exclusion process.\n\nIn this study, we considered articles published in peer-reviewed journals. In order for an article to be included in our study, it must fulfill seven criteria, which are elaborated on in Table 2.\n\nTo eliminate bias and to make our study easily reproducible, we used a quality assessment criteria procedure based on 17. Quality assessment criteria play a vital role in conducting systematic literature reviews. The concept of quality assessment criteria (QAC) is to use a process that improves the criteria for selecting research papers. The QAC was deployed using a set of quality assessment questions (QAQs). The QAQs were used to create a checklist against which we compared each paper to ensure that it met the QAC and answered our RQs. If a study answers a question from the QAC checklist, we mark it as \"Yes,\" and if it doesn’t, it is marked \"No.\" However, some papers partially answer some of the questions in the QAC. Such criteria are \"P\" to represent a partial response. Scores were assigned to each of the questions considered in the QAC. A \"Yes\" answer is worth one point, a \"No\" answer is worth zero points, and a \"P\" answer is worth 0.5 points. Each paper is evaluated against the QA, and the marks are summed. After awarding the mark to each QA, we decided to select papers whose summation was above 2.5. The value of 3.0 was chosen because we did not want to include papers that partially (50%) answered the quality assessment questions formulated for this study. Table 3 and Table 4 below show the quality assessment questions and the quality evaluation results we used in this study.\n\nWe manually searched for the articles included in this study in research six databases. The databases considered in this study are as follows;\n\nIEEE Xplore\n\nScienceDirect\n\nWiley\n\nACM Digital Library\n\nMDPI\n\nSpringer\n\nThe search process involved five keywords: incremental learning, online machine learning, internet of things, intrusion detection, and anomaly detection. The keywords were connected using the words \"AND\" and \"OR.\" Generally, the search terms were framed as \"Internet of Things AND Incremental Learning AND Intrusion Detection OR Anomaly Detection OR Online Machine Learning. The search terms were targeted at the author’s keywords provided in the paper.\n\n\nResults\n\nIn this section, we present the results of the systematic literature review carried out.\n\nIn Table 5, we looked at the research databases considered in our studies and the number of articles published in each journal during the period considered in our study before applying the inclusion and exclusion criteria. The search results returned a total of 159 articles. IEEE Xplore returned 68 results, Science Direct, returned 21 results, and Wiley returned 8 results. MDPI, Springer, and ACM returned 8, 44, and 10 results, respectively. Table 6 shows the number of articles considered in this study after applying our quality assessment criteria. A total of twenty-two (22) articles were selected from the six databases after applying the inclusion and exclusion criteria. IEEE Xplore had nine (9) publications, ScienceDirect had seven (7) publications meeting the QA criteria, MDPI had three (3) papers, Wiley had three (3) papers, and Springer and ACM Digital Library had 0 papers each.\n\nThe parameters considered in determining the contribution of a study are how these studies handle drift adaption, the lightweight status of models, the running time of models, and the memory consumption of models. The parameters considered for the contribution of the studies are shown in Figure 1 below.\n\nIn Table 7, we presented the contributions of each study based on the area of drift adaption, the lightweight status of models, the running time of models, and the memory consumption of models. Only the 8 IoT-based studies were considered in this analysis. Two of the eight (8) studies deployed solutions that could handle drifts in either data or concepts. Eight out of the nine studies focused on designing lightweight models. We also looked at how each of the studies handled computational complexity. Four (4) out of the eight (8) studies reported time complexity, while only two out of the eight (8) studies reported the space complexity of their proposed model. None of the eight IoT-based studies reports on the energy consumption of their proposed model.\n\nIn Table 8 and Table 9, we presented a summary of the strengths and weaknesses of the IoT-based intrusion detection studies are considered in our study. We chose to report on the strengths and weaknesses of the IoT-based IDSs because that is the core of our studies.\n\nThis study also considered the datasets used for experimental validation in the 8 IoT-based papers considered in this work. The datasets used in the IoT-based studies include N-BaIoT, NSL-KDD, KDD CUP 99, UNSW-NB15, IoTID20 and DS2OS traffic trace datasets. The rest are Intel Lab, sensorscope, and the secure water treatment dataset. Among the datasets used, N-BaIoT, Intel Lab, UNSW-NB15, and IoTID20 are datasets based on IoT traffic. Table 10 shows the summary of the datasets used in each study.\n\nIn this subsection, we analyzed the number of publications per year using our established quality assessment criteria. The number of publications per year is shown in Table 11. From Table 11 below, no publication met the criteria of our studies in the years 2010, 2012, 2016, and 2018. The years 2011, 2014, 2017, and 2019 recorded one publication each. The highest number of publications was recorded in 2020, when nine (9) publications were recorded. There were 2 publications in 2013 and 2021, and 3 publications in 2022. Drawing our attention to the IoT-based studies, there was one (1) publication in 2015, two (2) publications in 2020, 3 publications in 2021, and 2 publications in 2022.\n\n\nChallenges and directions for future work\n\nIn this section, we present some challenges we identified based on the analysis of our study. To begin with, we found out that 2 of the IoT-based studies used datasets (NSL-KDD and KDD CUP 99) that are no longer relevant when designing modern-day IDS.\n\nAdditionally, these datasets are non-IoT-based. Therefore, we recommend that future work use datasets from IoT environments to build and evaluate IDS for IoT systems. Secondly, from our studies, we discovered that seven (7) studies out of the 8 IoT-based studies designed lightweight IDS for IoT systems. However, only one reported on the proposed system’s memory consumption, and three (3) reported on the running time of the proposed methods. Only one study reported the computational complexity of the model used in designing their proposed IDS.\n\nAdditionally, in designing lightweight IDSs for IoT systems, parameters such as time and space complexity and power consumption of the proposed IDS should be evaluated. The portability of an IoT-based IDS is as important as its accuracy, precision, or recall. Therefore, we propose that future work include a performance matrix that measures the time and space complexity and power consumption of the proposed methods. Additionally, none of the IoT-based studies considered in this work deployed the proposed IDS on an IoT device. It is crucial not only to model IDSs for IoT ecosystems but these IDS models should be deployed on IoT devices. Deploying these models on real devices will help to evaluate parameters such as space complexity and energy consumption. Deployment models on real devices help to evaluate the model’s performance on drift adaptation and determine the model’s accuracy in production environments. We recommend that future studies on IDS for IoT systems incorporate model deployment on physical devices to evaluate how these models will perform in production environments.\n\nConcept Drift in Machine Learning refers to a situation in which the statistical properties of the target variable change over time. In other words, the meaning of the input data used to train the model has changed significantly over time, but the model in production is unaware of the change and thus cannot make accurate predictions. Although incremental machine learning has the advantage of detecting concept drifts, only 2 out of 8 IoT-based studies considered in this work considered concept drift adaption in their studies. Network traffic is usually dynamic, and attackers try to circumvent IDSs by changing the attack signatures of knowns, which leads to a change in the target variable. Future IDSs for the IoT ecosystem must focus on how to build IDSs that can detect drifts and learn from those drifts with minimal human intervention.\n\nFurthermore, the datasets used in the IoT-based studies and most datasets used in modeling IDSs are imbalanced, which gives these models higher accuracy but lower precision. To solve this challenge, more studies can be conducted on creating balanced datasets from IoT systems. Moreover, unlike traditional computing IDSs, which primarily focus on detection speed, precision, and accuracy, IDSs for the IoT ecosystem need a balance between accuracy, speed, precision, lightweight, and low energy consumption. Therefore, researchers must look at these parameters holistically to ensure that proposed IDSs for IoT systems can be deployed in such environments. It is recommended that future work in this domain should focus on using models that are not computationally intensive in designing IDSs for IoT systems.\n\nFinally, the results from the various experimental validations done in IoT-based studies considered in this SLR show that incremental learning is capable of achieving the lightweight IDS status that most IDS problems in IoT systems seek to attain. However, more studies need to be done using the approach mentioned above in the IoT ecosystem to determine the viability of incremental learning to solve the problem of high speed, high accuracy, low energy, and minimal space complexity IDS for IoT systems.\n\n\nThreats to validity of the study\n\nValidity threats hampered the data extraction process and the quality assessment of the papers chosen for this SLR protocol. Using the threats identified by 40, we divided the threats into validity. Internal, external, construct, and conclusion validity are the threats identified by 40. Each of the threats is briefly described in the preceding paragraphs.\n\nInternal validity: This threat focuses on implementing the SLR protocol, which includes search terms, the data extraction process, the method used for the research, and quality assessment criteria.\n\nConstruct validity: Construct validity is related to how search strings are constructed, the formulation of research questions, the online databases selected, and the inclusion and exclusion criteria. The search string used in this study was comprehensively formulated to answer the formulated research questions.\n\nExternal validity: External validity focuses on the degree that the SLR results reflect the topic under review. We mitigated this threat by repeating the procedure used in our study.\n\nConclusion validity: The nature of SLR makes it not possible to capture all relevant studies that answer the formulated research questions. There is a probability that some papers were missed. Using inclusion and exclusion criteria lessens the gravity of personal bias and subjectivity.\n\nWe will discuss some of the study’s limitations in this section. The research focused on a few carefully selected but highly referenced databases in the field of study. We admit that, like most SLRs, we had difficulty locating all of the papers associated with this study. We also admit that some papers were left out due to the difficulty in identifying all papers related to this study. The method used in this study is meant to help us with our research on incremental machine learning-based intrusion detection in IoT systems.\n\nThis study’s analysis is limited to incremental machine learning-based intrusion detection systems on the internet of things and does not represent the complete analysis of the individual papers. We made every effort in this regard to analyzing the papers presented in this work in order to provide answers to the research questions posed in this study.\n\n\nConclusion\n\nThis study comprehensively analyzed incremental machine learning-based intrusion detection systems in the internet of things. The aim of the study was to help us understand existing work in the domain of our study and provide suggestions on how future work in IDS for IoT systems can be enhanced. The Internet of Things (IoT) has not only become a household name through its application in smart homes but has also been used in domains like agriculture, healthcare, transportation, and cities and grid systems. Whereas the advantages of IoT cannot be downplayed; its computational constraints make it difficult to deploy security methodologies that have been deployed in traditional computing systems. The study examined the existing state-of-the-art incremental machine learning approaches used to design lightweight intrusion detection systems for IoT environments, as well as the datasets used and how these studies are designing IDS without overburdening IoT device computational resources. As the number of things connected to the internet increases, researchers must use various methods to ensure the security of these things. The application of ML and DL in intrusion detection has proven to be an effective mitigation strategy on traditional computers, and the trend of current research shows that it will become an effective mitigation strategy in detecting intrusions in IoT environments.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nThe completed PRISMA checklist of this study is found on a public repository with details as below: Figshare: PRISMA checklist for ’Towards achieving lightweight intrusion detection systems in Internet of Things, the role of incremental machine learning: A systematic literature review’, https://doi.org/10.6084/m9.figshare.21436152.v141.\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\nZarpelão BB, Miani RS, Kawakani CT, et al.: A survey of intrusion detection in internet of things. J Netw Comput Appl. 2017; 84: 25–37. Publisher Full Text\n\nStaffs Keele, Guidelines for performing systematic literature reviews in software engineering. Technical report, Technical report, ver. 2.3 ebse technical report. ebse, 2007. Reference Source\n\nPetersen K, Vakkalanka S, Kuzniarz L: Guidelines for conducting systematic mapping studies in software engineering: An update. Inf Softw Technol. 2015; 64: 1–18. Publisher Full Text\n\nElrawy MF, Awad AI, Hamed HFA: Intrusion detection systems for iot-based smart environments: a survey. J Cloud Comp. 2018; 7(1): 21. Publisher Full Text\n\nKhraisat A, Alazab A: A critical review of intrusion detection systems in the internet of things: techniques, deployment strategy, validation strategy, attacks, public datasets and challenges. Cybersecur. 2021; 4(1): 18. Publisher Full Text\n\nBenkhelifa E, Welsh T, Hamouda W: A critical review of practices and challenges in intrusion detection systems for iot: Toward universal and resilient systems. IEEE Communications Surveys & Tutorials. 2018; 20(4): 3496–3509. Publisher Full Text\n\nMishra N, Pandya S: Internet of things applications, security challenges, attacks, intrusion detection, and future visions: A systematic review. IEEE Access. 2021; 9: 59353–59377. Publisher Full Text\n\nHajiheidari S, Wakil K, Badri M, et al.: Intrusion detection systems in the internet of things: A comprehensive investigation. Computer Networks. 2019; 160: 165–191. Publisher Full Text\n\nAsharf J, Moustafa N, Khurshid H, et al.: A review of intrusion detection systems using machine and deep learning in internet of things: challenges, solutions and future directions. Electronics. 2020; 9(7): 1177. Publisher Full Text\n\nArshad J, Azad MA, Amad R, et al.: A review of performance, energy and privacy of intrusion detection systems for iot. Electronics. 2020; 9(4): 629. Publisher Full Text\n\nAlsoufi MA, Razak S, Md Siraj M, et al.: Anomaly-based intrusion detection systems in iot using deep learning: A systematic literature review. Appl Sci. 2021; 11(18): 8383. Publisher Full Text\n\nSeyfollahi A, Ghaffari A: A review of intrusion detection systems in rpl routing protocol based on machine learning for internet of things applications. Wirel Commun Mob Comput. 2021; 2021. Publisher Full Text\n\nAli Khan Z, Herrmann P: Recent advancements in intrusion detection systems for the internet of things. Security and Communication Networks. 2019; 2019. Publisher Full Text\n\nChaabouni N, Mosbah M, Zemmari A, et al.: Network intrusion detection for iot security based on learning techniques. IEEE Communications Surveys & Tutorials. 2019; 21(3): 2671–2701. Publisher Full Text\n\nSaranya T, Sridevi S, Deisy C, et al.: Performance analysis of machine learning algorithms in intrusion detection system: A review. Procedia Comput Sci. 2020; 171: 1251–1260. Publisher Full Text\n\nLiberati A, Altman DG, Tetzlaff J, et al.: The prisma statement for reporting systematic reviews and meta-analyses of studies that evaluate health care interventions: explanation and elaboration. J Clin Epidemiol. 2009; 62(10): e1–e34. PubMed Abstract | Publisher Full Text\n\nKitchenham B, Charters S: Guidelines for performing systematic literature reviews in software engineering. 2007. Reference Source\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The prisma 2020 statement: an updated guideline for reporting systematic reviews. Syst Rev. 2021; 10(1): 89. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGao J, Chai S, Zhang B, et al.: Research on network intrusion detection based on incremental extreme learning machine and adaptive principal component analysis. Energies. 2019; 12(7): 1223. Publisher Full Text\n\nQaiwmchi NAH, Amintoosi H, Mohajerzadeh A: Intrusion detection system based on gradient corrected online sequential extreme learning machine. IEEE Access. 2020; 9: 4983–4999. Publisher Full Text\n\nLiu L, Hu M, Kang C, et al.: Unsupervised anomaly detection for network data streams in industrial control systems. Information. 2020; 11(2): 105. Publisher Full Text\n\nDarem AA, Ghaleb FA, Al-Hashmi AA, et al.: An adaptive behavioral-based incremental batch learning malware variants detection model using concept drift detection and sequential deep learning. IEEE Access. 2021; 9: 97180–97196. Publisher Full Text\n\nTang Y, Li C: An online network intrusion detection model based on improved regularized extreme learning machine. IEEE Access. 2021; 9: 94826–94844. Publisher Full Text\n\nWu Z, Gao P, Cui L, et al.: An incremental learning method based on dynamic ensemble rvm for intrusion detection. IEEE Transactions on Network and Service Management. 2021; 19(1): 671–685. Publisher Full Text\n\nBaldini G, Amerini I: Online distributed denial of service (ddos) intrusion detection based on adaptive sliding window and morphological fractal dimension. Computer Networks. 2022; 210: 108923. Publisher Full Text\n\nReis LHA, Piedrahita AM, Rueda S, et al.: Unsupervised and incremental learning orchestration for cyber-physical security. Transactions on emerging telecommunications technologies. 2020; 31(7): e4011. Publisher Full Text\n\nTabassum A, Erbad A, Mohamed A, et al.: Privacy-preserving distributed ids using incremental learning for iot health systems. IEEE Access. 2021; 9: 14271–14283. Publisher Full Text\n\nYang L, Shami A: A lightweight concept drift detection and adaptation framework for iot data streams. IEEE Internet of Things Magazine. 2021; 4(2): 96–101. Publisher Full Text\n\nWahab OA: Intrusion detection in the iot under data and concept drifts: Online deep learning approach. IEEE Internet Things J. 2022; 9(20): 19706–19716. Publisher Full Text\n\nBosman HHWJ, Iacca G, Tejada A, et al.: Ensembles of incremental learners to detect anomalies in ad hoc sensor networks. Ad Hoc Netw. 2015; 35: 14–36. Publisher Full Text\n\nShao Z, Yuan S, Wang Y: Adaptive online learning for iot botnet detection. Information Sciences. 2021; 574: 84–95. Publisher Full Text\n\nMartindale N, Ismail M, Talbert DA: Ensemble-based online machine learning algorithms for network intrusion detection systems using streaming data. Information. 2020; 11(6): 315. Publisher Full Text\n\nYi Y, Wu JS, Xu W: Incremental svm based on reserved set for network intrusion detection. Expert Syst Appl. 2011; 38(6): 7698–7707. Publisher Full Text\n\nData M, Aritsugi M: T-dfnn: An incremental learning algorithm for intrusion detection systems. IEEE Access. 2021; 9: 154156–154171. Publisher Full Text\n\nChitrakar R, Huang C: Selection of candidate support vectors in incremental svm for network intrusion detection. Comput Secur. 2014; 45: 231–241. Publisher Full Text\n\nJiang F, Sui Y, Cao C: An incremental decision tree algorithm based on rough sets and its application in intrusion detection. Artif Intell Rev. 2013; 40(4): 517–530. Publisher Full Text\n\nTsai CW: Incremental particle swarm optimisation for intrusion detection. IET networks. 2013; 2(3): 124–130. Publisher Full Text\n\nNoorbehbahani F, Fanian A, Mousavi R, et al.: An incremental intrusion detection system using a new semi-supervised stream classification method. Int J Commun Syst. 2017; 30(4): e3002. Publisher Full Text\n\nGyamfi E, Jurcut AD: Novel online network intrusion detection system for industrial iot based on oi-svdd and as-elm. IEEE Internet Things J. 2022. Publisher Full Text\n\nWohlin C: Guidelines for snowballing in systematic literature studies and a replication in software engineering. In: Proceedings of the 18th international conference on evaluation and assessment in software engineering. 2014; 1–10. Publisher Full Text\n\nAgbedanu P, Musabe R, Rwigema J, et al.: Towards achievi ng lightweight intrusion detection systems in Internet of Things, the role of incremental machine learning: A systematic literature review.figshare. Online resource. 2022. http://www.doi.org/10.6084/m9.figshare.21436152.v2"
}
|
[
{
"id": "171434",
"date": "15 May 2023",
"name": "Yan Naung Soe",
"expertise": [
"Reviewer Expertise IoT",
"Cyber-security",
"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 authors conducted a review for the lightweight purpose of IoT-based introduction detection systems. It is interesting, but the following concerns have to be addressed.\nMany typos are found.\n\nIn the abstract, you mentioned that your review is based on the 21 IDS research works. It is not enough to review a specific work. There are many related works in recent years. More references are necessary.\n\nIn Table-5, the authors listed the sources/publishers of their references. Many lightweight IoT-IDS could be easily found by exploring these publishers' web sources. E.g., the authors can explore many articles in their sources, like MDPI, ACM Digital Library, and so on.\nIn Table-6, why can “only zero article in ACM” be considered as your quality assessment criteria?\n\nAccording to the title and abstract, you focus on the lightweight purpose in the detection systems, but you mentioned only 7 lightweight models.\nAlso, you have to check them again, are these really lightweight systems? The authors organized some lightweight models in Table 8, even if the referenced works are not deeply checked, the question arises, how could some of them be lightweight? E.g., in Table 8, in the reference [30], how it would be lightweight with computational complexity? And also, the reference [28], is it lightweight with memory consumption?\n\nAccording to your abstract, you mentioned that you analyzed the systems regarding 4 kinds of criteria. But your research questions almost did not reflect them. In addition, these are not also correct. In the abstract, the authors described \"The study analyzed 1) existing incremental machine learning approaches used in designing intrusion detection systems for IoT ecosystems, 2) emphasizing the incremental methods used in detecting intrusions, 3) the datasets used to evaluate these methods, and 4) how the method achieves lightweight status.\nIn the \"Research questions\" section, the authors generated 4-questions, such as RQ1: What is the primary contribution of the paper? RQ2: What incremental or online machine learning algorithm was used in this study? RQ3: How does the proposed method handle data, feature, or concept drift? RQ4: How does the proposed IDS handle the computational constraints of IoT systems?\nIs there any relation between these two parts? More importantly, even showing these facts in these parts, there is no significant explanation in this review, especially on the lightweight purpose. If so, why did the authors put the important concern in IoT-IDS, \"lightweight/handling the computational constraints\" in these parts, such as the title, abstract, and research questions?\n\nAccording to your references list, you put many published reviews and survey works. It would be better if you study them again how to arrange the contents in the review works.\n\nThe citation styles are also different. E.g., the reference numbers 7 and 8. Other references are also facing the same issue. In addition, the reference indexing style in tables is confusing.\n\nIn the conclusion, you describe that you analyzed comprehensively ML-based intrusion detection systems. However, in the current version, the manuscript seems just a report that you have studied.\nThe overall comment is that you have to improve your manuscript significantly, to be following the style of review works, to be focusing on the facts in the title and abstract, and be arranged as a well-structured manuscript.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1377
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https://f1000research.com/articles/11-1372/v1
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23 Nov 22
|
{
"type": "Research Article",
"title": "A short-term prospective study to evaluate the clinical performance of endosseous zirconia implants",
"authors": [
"Rakshith Hegde",
"Mridu Dubey",
"Manoj Shetty",
"Rakshith Hegde",
"Manoj Shetty"
],
"abstract": "Background: Endosseous zirconia implants have been established as an alternative to conventional titanium implants, especially in the aesthetic zone. This pilot study aimed to evaluate the outcome of rehabilitation with zirconia implants, in a subset of the Indian population, involving varying clinical scenarios. Methods: A total of 10 one-piece zirconia implants were placed in seven patients requiring rehabilitation of missing teeth. The survival rate and marginal bone levels were evaluated at six months and 12 months following implant placement. Results: Five implants were placed in the maxilla and five in the mandible, including well-healed sites, extraction sockets, a single cantilever in the lower anterior region, and a full-arch rehabilitation. During the observation period, two early implant failures were noted resulting in a survival rate of 80%. Mean marginal bone loss of 0.73mm was seen one year following implant placement, with maximum bone loss occurring in the first six months. Conclusion: The results of this study encourage the use of endosseous zirconia implants in diverse clinical scenarios with careful case selection. However, long-term studies are needed to further validate these findings.",
"keywords": [
"dental implants",
"clinical evaluation",
"marginal bone loss",
"implant survival",
"zirconia",
"immediate loading"
],
"content": "Introduction\n\nRehabilitation with dental implants has now become the mainstay of prosthetic care and greatly enhances the quality of life of patients undergoing replacement of missing teeth. For endosseous dental implants, titanium is considered the material of choice owing to its long-proven success and survival rates.1–3\n\nThe evolution of macro design and surface texture has resulted in the preferred use of rough surface implants, which contribute to increased primary stability and markedly reduced healing time.4 However, the rough surfaces of titanium are more prone to plaque accumulation and subsequent periimplantitis, as well as increased release of titanium particles and ions into the surrounding tissue.5–7\n\nAlthough the precise impact of the released titanium particles needs to be further explored, there have been concerns regarding hypersensitivity to titanium in a certain minority of the population, estimated to be 0.6%.8 Another noteworthy consideration is the greyish hue of titanium that reflects through the peri-implant tissue of patients with a thin gingival biotype and poses a threat to the aesthetic outcome, especially in patients with increased aesthetic demands or in those with a high smile line.9,10\n\nZirconia implants have recently been recommended as an aesthetic alternative to titanium implants. The resemblance to natural tooth colour, combined with excellent biocompatibility and reduced adhesion to dental plaque, favour its use as a dental implant biomaterial.11 They also exhibit favourable physical and mechanical properties.12 However, aging or low-temperature degradation of zirconia negatively impacts the properties of this biomaterial resulting in roughness and eventual degradation of the material.13,14\n\nEndosseous zirconia implants seem to be a preferred option in patients with a thin gingival biotype, or who express specific concern regarding the visibility of a greyish hue at the cervical margin, patients who may have sensitivity to titanium, or in those who insist on having “metal-free” dental therapy.15\n\nResearch has shown that the osseointegration of zirconia implants is similar to titanium implants.16 However, to the best of the authors’ knowledge, the clinical performance of zirconia implants has not yet been evaluated in the Indian population.16 Thus, this study was conducted to assess the short term treatment with endosseous zirconia implants in a subset of the Indian population.\n\n\nMethods\n\nThe study was designed as a prospective cohort investigation in a university setup (A B Shetty Memorial Institute of Dental Sciences) and was conducted following institutional ethical committee clearance (A B Shetty Memorial Institute of Dental Sciences; Cert no: ABSM/EC66/2017). Written informed consent was obtained from all participants in this study for publication of the data and their clinical images.\n\nAll seven patients who visited the clinic between June 2018 and February 2019 were included in the current study. Follow-up duration was set to six and 12 months after the placement of the implant. Participants were selected by following stated criteria:\n\n(i) Participants/source of data:\n\nA total of 10 endosseous zirconia implants were placed in seven patients who required rehabilitation of missing teeth.\n\n(ii) Inclusion criteria:\n\n‐ Age between 20 to 70 years\n\n‐ Good general condition\n\n‐ Single or extended edentulous spaces, preferably in the aesthetic zone\n\n‐ Adequate bone volume (Bone width ≥ 5 mm and Bone height ≥10 mm) as determined by preoperative cone-beam computed tomography (CBCT)\n\n(iii) Exclusion criteria:\n\n‐ Medically compromised patients\n\n‐ Patients with parafunctional oral habits\n\n‐ Adjacent teeth with non-treated periodontal disease or active infection\n\n‐ Smoking > 10 cigarettes per day\n\n‐ Implant sites requiring augmentation\n\nSintered and yttria-stabilised, one-piece, zirconia dental implants (WhiteSky, Bredent, Germany) were used in this study. These endosseous implants have a double cylindrical thread design. The portion of the implant surface that is intended to remain embedded in bone has a sandblasted surface, whereas the transmucosal portion is smooth, with a height of 2 mm. The abutment has a height of 6.8 mm which can be modified according to the clinical situation.17\n\nThe implants were placed according to the manufacturer’s instruction in a prosthetically determined 3D position. An immediate post-operative orthopantomogram (OPG)/intraoral periapical (IOPA) was taken to evaluate the positioning of the implants and to serve as a baseline for future bone level assessment.\n\nThe one-piece zirconia implants were immediately restored with a highly cross-linked acrylic proshell (Visiolign, Bredent) relined with composite resin (Comboline, Bredent). The restoration was kept out of centric and eccentric occlusion and served as a durable, long-term prosthesis. The marginal bone levels (MBL) were assessed at six months and 12 months following placement and mean MBL was calculated. Data was analysed by using SPSS version 23 (IBM SPSS Statistics, RRID:SCR_019096) (An open-access alternative is R Stats (R Project for Statistical Computing, RRID:SCR_001905)).\n\n\nResults\n\nFive implants were placed in the maxilla, out of which three were placed in well-healed sites, and two were placed following extraction (immediate and early placement, respectively). Five implants were placed in the mandible, among which one was used to replace two missing lower central incisors and the remaining four implants were used for an immediately loaded full-arch prosthesis. Two participants received implants in the mandible and five participants received implants in the maxilla.\n\nFigures 1, 2, and 3 show single tooth replacement in a well-healed edentulous site. Figure 4 shows a cantilever prosthesis using one implant in the anterior region. Figure 5 shows extraction and immediate placement. Figure 6 shows full arch rehabilitation.\n\n(a) Preoperative view; (b) Preoperative radiograph; (c) Implant insertion; (d) Immediate restoration; (e) Immediate post-op radiograph.\n\n(a) Preoperative view; (b) Preoperative radiograph; (c) Initial site; (d) Implant insertion; (e&f) Immediate restoration; (g) Immediate post-op radiograph; (h) Radiograph at 1-year post-placement.\n\n(a) Preoperative view; (b) Preoperative radiograph; (c) Implant insertion; (d) Immediate restoration; (e) Immediate post-op radiograph; (f) 1-year post-placement.\n\n(a) Preoperative view; (b) Preoperative radiograph; (c) Paralleling place; (d) Immediate restoration; (e) Immediate post-op radiograph.\n\n(a) Preoperative view; (b) Preoperative radiograph; (c) Implant insertion; (d) Implant insertion torque; (e) Immediate restoration; (f) Immediate post-op radiograph; (g) Radiograph 1 year post-placement.\n\n(a) Preoperative radiograph; (b) Implant insertion; (c) Immediate restoration; (d) Immediate post-op radiograph; (e) Radiograph 1-year post-placement.\n\nDiameter: Three implants of diameter 3.5 mm were placed in the lower anterior region and the remaining implants had diameters greater than or equal to 4 mm.\n\nTorque: A minimum torque of 25 Ncm was obtained during implant placement.\n\nSurvival rate: During the follow-up period which extended up to 12 months, two early implant failures were observed. Thus, the cumulative survival rate at the end of two years was 80%.\n\nMarginal bone loss: The present study showed a mean marginal bone loss (MBL) of 0.84 mm at one year following implant insertion, with maximum bone loss occurring in the first six months (0.73 mm) following placement (Table 1).18\n\n\nDiscussion\n\nThe present study evaluated the mean marginal bone loss and survival rate of 10 endosseous zirconia implants in various clinical scenarios, after 12 months of implant placement. Concern regarding the prevalence of hypersensitivity to titanium particles in peri-implant tissues, the impaired aesthetic outcome in patients with a thin biotype and increasing demand for “metal-free” therapy, have made zirconia implants a promising alternative to the conventional endosseous titanium implants.\n\nWhile the mechanical and optical properties of zirconia are the major factors supporting its use as an implant material, its biocompatibility and excellent soft-tissue response also have an important contribution to make in maintaining long term peri-implant health. Since zirconia implants emerged as a potential alternative to titanium, various studies have been conducted to assess its hard and soft tissue integration.18,19\n\nTo the best of the authors’ knowledge, this is the first study conducted in the Indian population to evaluate the performance of endosseous zirconia implants in a variety of clinical situations.\n\nOsseointegration of dental implants and long – term stability of marginal bone level remain the defining criteria for implant success.20 The present study showed a mean marginal bone level of 0.73 mm after one year, with maximum bone loss occurring in the first six months. This result is in accordance with previous studies conducted by Roehling et al., and Pieralli et al.,21,22 and following Albrektsson’s criteria of implant success.20 This may be credited to the high biocompatibility of zirconia, low plaque adhesion, and the absence of a micro gap between the fixture and abutment.23\n\nThe increased bone loss observed in the first six months is similar to the findings reported by Borgonovo et al.,23 and Balmer et al.,24 and can be attributed to the extensive bone remodelling following implant placement. Although in the present investigation, the mean MBL was 0.73 mm after one year, one implant showed MBL ≥ 2 mm. This was probably due to the greater initial implant insertion depth used in extraction sockets.\n\nOf the 10 implants, two implants showed early failure. One of these two implants was placed in the lower anterior region to replace two missing central incisors. The provisional restoration had a cantilever which could have caused an overload and increased micromovement leading to failure. The second implant which failed was placed in the maxillary canine region in a patient who had both upper and lower posterior teeth rehabilitated with removable partial prostheses. Failure of this implant may be attributed to the patient’s preference of incising with a fixed prosthesis. Thus, the cumulative survival rate of implants in this study was 80%, lower than those reported in a recently published systematic review25 and especially with the survival rate of titanium implants.26\n\nOf particular interest, was the reduced bone loss seen with the four implants placed in the mandible and immediately loaded with a fixed hybrid prosthesis, which can be attributed to the splinting effect of the prosthesis. However, this finding contrasted with the results of the study conducted by Borgonovo et al.,23 who observed no statistically significant difference in the marginal bone loss adjacent to free-standing vs. multiple splinted implants. Thus, while the results of this study were encouraging towards the use of endosseous zirconia implants in diverse clinical scenarios, due care and caution in case selection must be exercised. Long-term studies in this context are required.\n\n\nConclusion\n\nThe cantilever of an immediately loaded prosthesis can lead to implant failure. Missing posterior teeth and patients with a partial denture can lead to failure as the patients lend to bite with natural teeth. A minimum bone width of 5 mm is needed to place one-piece zirconia implants designed for immediate loading, to avoid simultaneous augmentation procedures. Splinting of zirconia implants in case of full arch reconstruction will reduce the resorption of bone.\n\n\nData availability\n\nFigshare: A short-term prospective study to evaluate the clinical performance of endosseous zirconia implants. https://doi.org/10.6084/m9.figshare.17163584.v6.18\n\nThis project contains the following underlying data:\n\n• Dataset.xlsx (region implant dimensions, insertion torque and MBL data)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nConsent\n\nWritten informed consent for publication of the patients’ details and their images was obtained from the patients.",
"appendix": "Acknowledgements\n\nThe authors thank Dr. Ganaraj Shetty, Dr. Nivya John and Dr. Athma Shetty for their guidance and help with the manuscript.\n\n\nReferences\n\nJung RE, Zembic A, Pjetursson BE, et al.: Systematic review of the survival rate and the incidence of biological, technical, and aesthetic complications of single crowns on implants reported in longitudinal studies with a mean follow-up of 5 years. Clin. Oral Implants Res. 2012; 23(Suppl 6): 2–21. PubMed Abstract | Publisher Full Text\n\nPjetursson BE, Thoma D, Jung R, et al.: A systematic review of the survival and complication rates of implant-supported fixed dental prostheses (FDP s) after a mean observation period of at least 5 years. Clin. Oral Implants Res. 2012; 23: 22–38. PubMed Abstract | Publisher Full Text\n\nHowe MS, Keys W, Richards D: Long-term (10-year) dental implant survival: A systematic review and sensitivity meta-analysis. J. Dent. 2019; 84: 9–21. PubMed Abstract | Publisher Full Text\n\nFerguson SJ, Langhoff JD, Voelter K, et al.: Biomechanical comparison of different surface modifications for dental implants. Int. J. Oral Maxillofac. Implants. 2008; 23(6): 1037–1046. PubMed Abstract\n\nSuárez-López del Amo F, Garaicoa-Pazmiño C, Fretwurst T, et al.: Dental implants-associated release of titanium particles: A systematic review. Clin. Oral Implants Res. 2018; 29(11): 1085–1100. PubMed Abstract | Publisher Full Text\n\nPettersson M, Pettersson J, Johansson A, et al.: Titanium release in peri-implantitis. J. Oral Rehabil. 2019; 46(2): 179–188. Publisher Full Text\n\nFretwurst T, Buzanich G, Nahles S, et al.: Metal elements in tissue with dental peri-implantitis: a pilot study. Clin. Oral Implants Res. 2016; 27(9): 1178–1186. PubMed Abstract | Publisher Full Text\n\nSicilia A, Cuesta S, Coma G, et al.: Titanium allergy in dental implant patients: a clinical study on 1500 consecutive patients. Clin. Oral Implants Res. 2008; 19(8): 823–835. PubMed Abstract | Publisher Full Text\n\nThoma DS, Ioannidis A, Cathomen E, et al.: Discoloration of the peri-implant mucosa caused by zirconia and titanium implants. Int. J. Periodontics Restorative Dent. 2016; 36(1): 39–45. PubMed Abstract | Publisher Full Text\n\nAndreiotelli M, Wenz HJ, Kohal RJ: Are ceramic implants a viable alternative to titanium implants? A systematic literature review. Clin. Oral Implants Res. 2009; 20: 32–47. PubMed Abstract | Publisher Full Text\n\nMöller B, Terheyden H, Açil Y, et al.: A comparison of biocompatibility and osseointegration of ceramic and titanium implants: an in vivo and in vitro study. Int. J. Oral Maxillofac. Surg. 2012; 41(5): 638–645. PubMed Abstract | Publisher Full Text\n\nManicone PF, Iommetti PR, Raffaelli L: An overview of zirconia ceramics: basic properties and clinical applications. J. Dent. 2007; 35(11): 819–826. PubMed Abstract | Publisher Full Text\n\nLughi V, Sergo V: Low temperature degradation-aging-of zirconia: A critical review of the relevant aspects in dentistry. Dent. Mater. 2010; 26(8): 807–820. PubMed Abstract | Publisher Full Text\n\nKohorst P, Borchers L, Strempel J, et al.: Low-temperature degradation of different zirconia ceramics for dental applications. Acta Biomater. 2012; 8(3): 1213–1220. PubMed Abstract | Publisher Full Text\n\nAfrashtehfar KI, Del Fabbro M: Clinical performance of zirconia implants: A meta-review. J. Prosthet. Dent. 2020; 123(3): 419–426. PubMed Abstract | Publisher Full Text\n\nSchultze-Mosgau S, Schliephake H, Radespiel-Tröger M, et al.: Osseointegration of endodontic endosseous cones: Zirconium oxide vs titanium. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2000; 89: 91–98. PubMed Abstract | Publisher Full Text\n\nBorgonovo AE, Censi R, Vavassori V, et al.: Zirconia implants in esthetic areas: 4-year follow-up evaluation study. Int. J. Dent. 2015; 2015: 1–8. Publisher Full Text\n\nHegde R, Dubey M: A short-term prospective study to evaluate the clinical performance of endosseous zirconia implants.Figshare. Dataset.2021. Publisher Full Text\n\nDepprich R, Zipprich H, Ommerborn M, et al.: Osseointegration of zirconia implants compared with titanium: An in vivo study. Head Face Med. 2008; 4: 30. PubMed Abstract | Publisher Full Text\n\nKohal RJ, Wolkewitz M, Hinze M, et al.: Biomechanical and histological behavior of zirconia implants: An experiment in the rat. Clin. Oral Implants Res. 2009; 20: 333–339. PubMed Abstract | Publisher Full Text\n\nAlbrektsson T, Zarb G, Worthington P, et al.: The long-term efficacy of currently used dental implants: a review and proposed criteria of success. Int. J. Oral Maxillofac. Implants. 1986; 1(1): 11–25. PubMed Abstract\n\nRoehling S, Schlegel KA, Woelfler H, et al.: Performance and outcome of zirconia dental implants in clinical studies: A meta-analysis. Clin. Oral Implants Res. 2018; 29: 135–153. PubMed Abstract | Publisher Full Text\n\nPieralli S, Kohal RJ, Jung RE, et al.: Clinical outcomes of zirconia dental implants: a systematic review. J. Dent. Res. 2017; 96(1): 38–46. PubMed Abstract | Publisher Full Text\n\nBorgonovo AE, Censi R, Vavassori V, et al.: Evaluation of the success criteria for zirconia dental implants: a four-year clinical and radiological study. Int. J. Dent. 2013; 2013: 1–7. Publisher Full Text\n\nBalmer M, Spies BC, Vach K, et al.: Three-year analysis of zirconia implants used for single-tooth replacement and three-unit fixed dental prostheses: A prospective multicenter study. Clin. Oral Implants Res. 2018; 29(3): 290–299. PubMed Abstract | Publisher Full Text\n\nCionca N, Hashim D, Mombelli A: Zirconia dental implants: where are we now, and where are we heading? Periodontology. 2017; 73(1): 241–258. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "292114",
"date": "26 Jun 2024",
"name": "Gustavo Vicentis de Oliveira Fernandes",
"expertise": [
"Reviewer Expertise Dental implant",
"Periodontics",
"Oral surgery",
"Biomaterial",
"Research."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear authors, I evaluated the article titled “A short-term prospective study to evaluate the clinical performance of endosseous zirconia implants”. The aim was “This pilot study aimed to evaluate the outcome of rehabilitation with zirconia implants, in a subset of the Indian population, involving varying clinical scenarios\". - Why pilot study? This topic, in the same setting, does not need of pilot study. It is not possible to say that it is in a specific population to justify the sample size. - Why only “10 endosseous zirconia implants were placed in seven patients who required rehabilitation of missing teeth.” - where is the sample size calculation? - Only 7 patients had the data collected. Please, increase the number of your sample. - why only short-term evaluation? the results are questionable in the short term… please, include data for long-term evaluation too, please. - please, revise and rewrite the conclusion.\n- I strongly suggest to include the 3 articles below in your introduction and discussion:\n\n1. Zirconia Implants and Marginal Bone Loss: A Systematic Review and Meta-Analysis of Clinical Studies -[Ref 1] 2. Histologic Osseointegration Level Comparing Titanium and Zirconia Dental Implants: Meta-analysis of Preclinical Studies -[Ref 2] 3. Clinical Performance Comparing Titanium and Titanium-Zirconium or Zirconia Dental Implants: A Systematic Review of Randomized Controlled Trials -[Ref 3]\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "292116",
"date": "26 Jun 2024",
"name": "Radwa M. K. Emera",
"expertise": [
"Reviewer Expertise Prosthodontics",
"CAD-CAM",
"Nanotechnology"
],
"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 short-term prospective study to evaluate the clinical performance of endosseous zirconia implants. The study is well-prepared and targets an important and updated point. However, more clarification is needed regarding the evaluated implant success criteria and 12-months period is not satisfactory for monitoring peri-implant marginal bone loss. long-term studies with different loading protocols and different prosthetic treatment options are recommended.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1372
|
https://f1000research.com/articles/11-149/v1
|
07 Feb 22
|
{
"type": "Research Article",
"title": "Knowledge about kitchen hygiene and associated factors in caregivers in a peri-urban area of Lima",
"authors": [
"Michelle Lozada-Urbano",
"Doris Miranda",
"Franklin Huamán",
"Jesus Chirinos-Cáceres",
"Oriana Rivera-Lozada",
"Doris Miranda",
"Franklin Huamán",
"Jesus Chirinos-Cáceres",
"Oriana Rivera-Lozada"
],
"abstract": "Background: The objective of this study was to identify the factors associated with caregivers’ knowledge of kitchen hygiene in San Juan de Lurigancho (SJL). Methods: This was a cross-sectional study. We surveyed 250 mothers at comedores populares (a sort of community kitchens which are very popular in Lima) and who were part of mothers' clubs in the areas of Huascar V and San Pablo, in SJL in Lima. The sample was selected through non-probability convenience sampling. A questionnaire with three dimensions (cleanliness, storage and contamination of children) was administered. Results: On average, in Huascar and San Pablo, most caregivers were the children’s mothers (93.2%); most of the caregivers were between 21 and 30 years old (54%); they had secondary level of education (70.4%); they were living in free union with their partners (69.2%); they were mainly housewives (80.4%); their houses were constructed with materials different from brick and cement (68.4%); and their houses had a bare floor (70.0%). They did not have drinking water in the kitchen (88.4%); they did not use a gas stove (88.4%), a refrigerator (50.0%), a radio (82.0%), or a microwave (16.4%). A good level of knowledge of food hygiene was found in 63.2% of caregivers. No predictive capacity of the assessed sociodemographic characteristics on the level of knowledge of kitchen hygiene was identified. Conclusions: This study determined that the assessed sociodemographic variables were not significantly associated with the level of knowledge about kitchen hygiene. It is necessary to improve mothers' knowledge about the handling and consumption of spoiled food and their effect on children's health.",
"keywords": [
"knowledge",
"food",
"kitchen",
"cleanliness",
"storage"
],
"content": "Introduction\n\nPoor food storage and handling as well as poor kitchen hygiene contribute to a large number of foodborne diseases (FDs).1 Up to 87% of food poisoning incidents originate at home due to improper food handling.2,3 FDs are a threat to public health in this century due to the role of the household in the transmission and acquisition of foodborne diseases. The most frequent causes are diarrheal pathogens,4 on contaminated surfaces such as kitchen towels5 and chopping boards in the kitchen6 as they can harbour a large number of coliforms. The most affected are children under 60 months old.7 In the event of diarrhoea in the child, mothers offer less food and the nutrients needed for growth decrease, and can result in malnutrition and make them more prone to illnesses,8 infections, and inadequate development.9\n\nIn many countries, hygiene and infant feeding processes become a highly vulnerable point due to poor handling,10,11 affecting 13.2% of children aged six to 60 months. Research in the peri-urban area of Lima showed that 21.8% of the children who required hospitalization were referred for diarrhoea.12\n\nDespite education efforts, consumers develop unsafe food storage and handling behaviours, contaminating sponges, kitchen towels, making them reservoirs and vectors of bacteria in the kitchen and contaminating other surfaces.13 Peru has a food sanitary regulation, according to the Dirección General de Salud Ambiental DIGESA,14 which regulates the products for sale and consumer defence code. The Health Ministry, Ministerio de Salud MINSA has published manuals on good food handling practices, aimed at restaurants, sale stores, but there are not any for mothers in the home.\n\nMothers play an important role in the prevention and control of FDs in regard to hygiene measures, including production, storage, food handling and hygienic practices.15 Dirty hands, stool remains, microbial load in water, flies, parasites, the presence of animals in the kitchen, poorly washed containers, and an unhygienic environment contaminate food.16 Studies in mothers in the rural jungle and highlands of Peru showed that only 20% of them washed their hands before touching food and only 6% of those who did used soap.17 In other countries, mothers have associated optimal cleaning of food products with preventing diseases, achieving a state of good health.18\n\nThere is information showing the economic and demographic aspects (e.g., rural living, poor access to water) related to mothers’ knowledge in regard to kitchen hygiene. In this study we proposed to establish whether the mothers’ sociodemographic characteristics were related to good knowledge about food management in the home or not, in a population of mothers in a peri-urban area of Lima. The results can be an opportunity to understand this group of mothers and their role in food management, since many of them are the main agent of the preparation of meals for their families.\n\n\nMethods\n\nWe conducted a cross-sectional observational study. The study was carried out in a peri-urban area in Lima, Peru in the human settlements of San Pablo and Huáscar V (SJL).\n\nThe population of interest was mothers with children, attending two comedores populares and/or mothers' clubs. This was a non-probability convenience sample.\n\nMothers were approached at the comedores populares and mothers' clubs. However, in the case of Huascar V, mothers who were at a health post were interviewed as well, to complete the sample. Two experienced field workers (MOC and MRR) helped with the face-to-face interviews.\n\nPermits were requested from the comedor populares and the health facility before surveying the mothers. The mothers were explained about the questionnaire and they were asked to sign the informed consent form. The interviewers mentioned that the mothers were suspicious when listing the appliances they had in their homes.\n\nA total of 250 women or caregivers were interviewed, distributed in the areas described (San Pablo = 125 and Huascar V = 125). Inclusion criteria were mothers who had a child under 60 months old and prepared food for them at home, and who voluntarily agreed to participate in the study by signing the informed consent form. Exclusion criteria were mothers or caregivers who had a child with a cognitive impairment.\n\nThe questionnaire had three dimensions: the first assessed the kitchen hygiene process; the second dimension evaluated the storage of products; and the last dimension examined the food-disease relationship based on the ingestion of spoiled products. A principal components analysis was applied; Kuder- Richardson (KR-20) was applied due to the dichotomous nature of variables, to define the internal validity; finally, the Kaiser-Meyer-Olkin (KMO) test and Barlet's test of sphericity were applied to define the validity of the test. The test results showed the following: KMO = 0.549; Barlet’s 591.678; gl =136, (p < 0.05). The three components (kitchen hygiene, product storage and disease from ingestion of spoiled foods) explained 66.75% of the total variance of the test.19 In this study, we need the sum of the questions of each dimension to calculate the total score, according to Table 1. As for the answers, yes (affirmative answer) and no (negative answer) were tabulated.\n\nThe knowledge variable was measured as follows:\n\nGood knowledge of food hygiene: If the participant had more than seven “YES” answers out of 10 questions, it was considered good knowledge of food hygiene in the home.\n\nNot so good knowledge of food hygiene: If the participant had fewer than or seven “YES” answers out of 10 questions, it was considered not so good knowledge of food hygiene in the home.20\n\nThe sample was obtained for convenience.\n\nThe sample was obtained with the following sampling proportion formula for a finite population.\n\nWhere:\n\nZ = confidence level = 1.96 α = 0.05\n\np = Probablility in favour = 50% of kitchen hygiene knowledge\n\nq = Probability against = 50% kitchen hygiene knowledge\n\nN = Universe\n\ne = estimation error\n\nn = sample size\n\nWe adopted a non-probabilistic sampling strategy to compare knowledge according to sociodemographic profile. The final sample for the study consisted of 250 mothers or caregivers who attended the comedores populares and mothers' clubs in the areas of San Pablo and Huáscar, where each area counted 125 participants.\n\nDependent variable (Y1): Knowledge of kitchen hygiene.\n\nIndependent variables (X1): Education level, occupation of the mother, marital status, caregiver (refers to the person who has a child, and takes care of it or can be just a caregiver), age of the mother, house building material, house floor material, drinking water, owning a gas stove, owning a refrigerator, a radio or television set, a microwave.\n\n\nResearch execution\n\nWe visited the mothers' clubs and comedores populares in Huáscar V and San Pablo, in SJL, to ask permission from the people in charge of these organizations and to inform them about the activities that were going to be carried out. This included approaching the mothers during the morning shift, very close to lunchtime. Only in Huascar V, the sample was completed with mothers who were interviewed at the health facility where mothers take their children for health checks, doctor appointments and vaccinations. Two field workers assisted with the face-to-face interviews (MOC and MRC). Prior to starting the questionnaire (as described in Table 1), the informed consent process was conducted. Detailed information about the study was provided to each potential participant, who was given the opportunity to ask questions and clarify doubts. After that, if they agreed to participate, they proceeded to sign the informed consent form. The questionnaires were completed in almost two months between April and May, 2018. Mothers were interviewed at the comedores or, if necessary, at home.\n\nThe analysis was conducted using Stata/SE 15.0 software for Windows, at the Universidad Peruana Cayetano Heredia (UPCH). Categorical variables were described as frequencies. The influence of sociodemographic variables or independent variables (education level, occupation of the mother, marital status, caregiver, age of the mother, house building material, floor material, drinking water, gas stove, refrigerator, radio or television set, microwave) on the dependent variable (knowledge of kitchen hygiene) was assessed through logistic regression analysis. Odds ratios (ORs) with 95% confidence intervals were reported. A p-value lower than 0.05 was considered statistically significant.\n\nThis study was approved by the Institutional Ethics Committee (IEC) of Universidad Peruana Cayetano Heredia. An informed consent form was prepared and signed by all the mothers and/or caregivers. Before signing, they were given information about the study, the use of the answers and how the information obtained will be kept under codes and that the questionnaires were anonymous. Finally, they signed the consent form if they decided to participate.\n\n\nResults\n\nA total of 250 caregivers were interviewed: 91.2% (114) of them were mothers in Huascar V and 95.2% (119) were from San Pablo. Fifty-four percent of the caregivers were between 21 and 30 years old. The highest education level achieved in Huascar V and San Pablo was secondary school (68.8% (86) and 72.0% (90), respectively). In Huascar V and San Pablo, the majority were in a free union (68.0%(85) and 70.4%(88), respectively), were housewifes (82.4%(104) and 78.4%(98), respectively), had brick and cement as house building material (68.0% (85) and 68.8%(86), respectively); they had a bare floor (70.4%(88) and 69, 6%(87), respectively), did not have drinking water (88.0%(110) and 88.8%(111), respectively), no gas stove (96.8%(121) and 96.0%(120), respectively), refrigerator (48.8%(61) and 51.2%(64), respectively), radio and TV set (79.2%(99) and 84.8%(106), respectively), and no microwave oven (82.4%(103) and 84.8%(106), respectively) respectively, see Table 2.\n\nTable 3 shows the percentage of questionnaire answers about knowledge of kitchen hygiene in Huáscar and San Pablo, where the mothers or caregivers were surveyed.\n\nThe caregivers from Huáscar responded affirmatively to the questions related to knowledge about cleanliness and storage in the kitchen (5, 6, 7, and 8) in a higher proportion than the caregivers in San Pablo.\n\nIn Table 4, we can see that the bivariate regression analysis did not identify any predictive capacity of any evaluated sociodemographic characteristic on the level of knowledge of kitchen hygiene.\n\nHowever, we can observe that in the age group older than 30, there was a higher proportion of caregivers with good knowledge of kitchen hygiene compared to the group aged 30 years or younger.\n\nIn addition, when the caregiver's role was filled by the grandmother or another person, most of them did not have a good level of knowledge of kitchen hygiene.\n\nFurthermore, when the caregiver had reached a secondary level of education, most of them showed a good level of knowledge about kitchen hygiene in contrast to the group with primary or higher education.\n\n\nDiscussion\n\nIn the investigated areas of SJL (San Pablo and Huáscar V), the surveyed mothers were mainly housewives and had a secondary education level. The vast majority of households lacked water and sewage services.\n\nAlthough no significant associations were identified between the variables studied and the level of knowledge of kitchen hygiene, the mothers’ education and age in other studies were associated with knowledge of safe food handling and consumption in the home.21 Years of school attendence could improve hygiene knowledge, as well as generating a larger social network in which mothers or caregivers interact. Likewise, having a radio in a large percentage of households can be a channel to increase mothers' knowledge and good practices and to obtain appropriate cooking behaviours, through hygiene educational programs. In other studies, mothers’ occupations (homemaker or work outside the home) was shown to be associated with more satisfactory hygienic practices in relation to food poisoning prevention.19,22\n\nMother with lower socioeconomic status have been found more likely to experience food products with a high microbial count.23 Our study presented the limitation of not including the microbial count. Studies such as Gil et al., 2014, have shown that this measure has been an accurate indicator to determine families’ household cleaning condition.24\n\nLikewise, demographic and socioeconomic factors may have contributed to unsafe food handling behaviours and microbial contamination risks during preparation.25 Poor food handling has been evidenced among low-income consumers.26\n\nThis study was conducted in a peri-urban area of Lima; some of our limitations may be due to the fact that the entire study population had the same socioeconomic status. Through an evaluation that includes heterogeneous populations, we could obtain complementary results regarding the influence of other variables not examined in the present study, that could improve our understanding of kitchen hygiene knowledge. It is important to highlight that data collection through interviews and surveys is prone to the possibility that the information revealed by the participants may be incomplete or not entirely truthful, which could directly impact the validity of the results.\n\n\nConclusions\n\nWe could not identify a predictive capacity in regard to the level of knowledge of kitchen hygiene in the evaluated sociodemographic characteristics in this sample.\n\n\nData availability\n\nFigshare: Knowledge about kitchen hygiene and associated factors, https://doi.org/10.6084/m9.figshare.16960207.v1.27\n\nThis project contains the following underlying data:\n\n- DB Depurada 07Oct21 ENG.xls (coded questionnaire responses and dictionary)\n\nFigshare: Kitchen hygene questionnaire, https://doi.org/10.6084/m9.figshare.17868758.v1.28\n\nThis project contains the following extended data:\n\n- Cuestionario ETA.docx (questionnaire in English)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nWorld Health Organization (WHO): WHO Estimates of the Global Burden of Foodborne Diseases: Foodborne Disease Burden Epidemiology Reference Group 2007–2015 Geneva, Switzerland: WHO; [cited on October 16, 2019]. 2015. Reference Source\n\nOgbo F, Page A, Idoko J, et al.: Diarrhoea and Suboptimal Feeding Practices in Nigeria: Evidence from the National Household Surveys. Paediatr. Perinat. Epidemiol. 2016. [Cited on October 16, 2019]; Jul; 30(4): 346–355. PubMed Abstract | Publisher Full Text\n\nCogan TA, Slader J, Bloomfield SF, et al.: Achieving hygiene in the domestic kitchen: the effectiveness of commonly used cleaning procedures. J. Appl. Microbiol. 2002. [Cited on October 16, 2019]; 92: 885–892. Publisher Full Text Reference Source\n\nBorrusso PA, Quinlan JJ: Prevalence of Pathogens and Indicator Organisms in Home Kitchens and Correlation with Unsafe Food Handling Practices and Conditions. J. Food Prot. 2017. [Cited on October 16, 2019]; 80(4): 590–597. Publisher Full Text Reference Source\n\nAmaya KS, Valle CS: Elaboración de un manual de limpieza y sanitización utilizando como parámetro la higiene de las mantas de cocina en hogares del Distrito 2 de San Salvador 2011. [Revista en internet]. [Accessed on Auguts 25, 2019]. Reference Source\n\nAlonso E: Estudio de la influencia del lavado en la reducción de la transferencia de escherichia coli en la cocina del consumidor 2013. [Journal on the Internet]. [Accessed on Auguts 25, 2019]. Reference Source\n\nRiveros M, Ochoa T: Enteropatogenos de importan cia en salud publica. Rev. peru. med. exp. salud publica [Internet]. 2015 Ene [citado 2022 Ene 22]; 32(1): 157–164. Reference Source\n\nOrganización Mundial de la Salud (OMS): Enfermedades diarreicas.2018. [cited on October 16, 2019]. Reference Source\n\nPenny ME, Creed-Kanashiro HM, Robert RC, et al.: Effectiveness of an educational intervention delivered through the health services to improve nutrition in young children: A cluster-randomised controlled trial. Lancet. 2005. [cited on October 16, 2019]; 365: 1863–1872. PubMed Abstract | Publisher Full Text . Reference Source\n\nFarthing M: Diarrea aguda en adultos y niños: una perspectiva mundial. Guía Práctica: Organización Mundial de Gastroenterología; 2012. [Jornal on the Internet] [Accessed on August 16, 2014]. Reference Source\n\nWorld Health Organization, WHO: Food and Nutrition Programme. Food Safety Unit. Contaminated food: A major cause of diarrhea and associated malnutrition among infants and young children. Facts Infant Feed. 1993. [Cited on October 16, 2019]; 1–4. Reference Source\n\nEhrenkranz P, Lanata C, Penny M, et al.: Rotavirus diarrhea disease burden in Peru: the need for a rotavirus vaccine and its potential cost savings. 2001. Rev Panam Salud Publica/Pan Am J Public Health. 2001. [Cited on October 16, 2019]; 10(4): 240–248. PubMed Abstract | Publisher Full Text Reference Source\n\nVan Asselt ED, de Jong AEI , de Jonge R , Nauta MJ: Cross-contamination in the kitchen: estimation of transfer rates from cutting boards, hand and knives. J. Appl. Microbiol. 2008. [cited on October 16, 2019]; 105: 1392–1401. Publisher Full Text Reference Source\n\nMinisterio de Salud: (Art. 25, (a) de la Ley del Ministerio de Salud, Ley 27657).Reference Source\n\nAngelillo I, Foresta M, Scozzafava C, Pavia M: Consumers and foodborne diseases: knowledge, attitudes and reported behavior in one region of Italy. Int. J. Food Microbiol. 2001 Feb 28. [Cited on October 16, 2019]; 64(1-2): 161–6. Publisher Full Text Reference Source\n\nWright J, Gundry S, Conroy R: Household drinking water in developing countries: A systematic review of microbiological contamination between source and point-of-use. Tropical Med. Int. Health. 2004. [Cited on October 16, 2019]; 9: 106–117. Reference Source\n\nPrisma: Estudio de comportamientos de lavado de manos con jabón en zonas urbano periféricas y rurales del Perú 2004. [Journal on the Internet]. [Accessed on September 11, 2013]. Reference Source\n\nUsfar A, Iswarawanti D, Davelyna D, et al.: Food and personal hygiene perceptions and practices among caregivers whose children have diarrhea: a qualitative study of urban mothers in Tangerang, Indonesia. J. Nutr. Educ. Behav. 2010 Jan-Feb. [Cited on October 16, 2019]; 42(1): 33–40. PubMed Abstract | Publisher Full Text Reference Source\n\nLozada-Urbano M, Rivera R, Miranda D, et al.: Validación de una escala para evaluar contaminación de alimentos en el hogar, estudio en la zona rural de Perú. Archivos de medicina. 2014. [Cited on October 19, 2019]; 10(1): 17. Reference Source\n\nOkugn A, Woldeyohannes D: Food hygiene practices and its associated factors among model and non model households in Abobo district, southwestern Ethiopia: Comparative cross-sectional study. PLoS One. 2018; 13(4): e0194391. PubMed Abstract | Publisher Full Text\n\nTalas C, Ucar A, Özfer Özçelik A: Attitudes of women towards food safety. Br. Food J. [Cited on 23, 2019], 2010; 112(10): 1115–1123. Publisher Full Text Reference Source\n\nZyoud S, Shalabi J, Imran K, et al.: Knowledge, attitude and practices among parents regarding food poisoning: a cross-sectional study from Palestine. BMC Public Health. 2019 May 16. [Cited on October 19, 2019]; 19(1): 586. PubMed Abstract | Publisher Full Text\n\nAyaz WO, Priyadarshini A, Jaiswal AK: Food Safety Knowledge and Practices among Saudi Mothers. Foods. 2018 Dec. [Cited on October 19, 2019]; 7(12): 193. PubMed Abstract | Publisher Full Text Reference Source\n\nGil AI, Lanata CF, Hartinger SM, et al.: Fecal contamination of food, water, hands, and kitchen utensils at the household level in rural areas of Peru. J. Environ. Health. 2014 Jan-Feb. [Cited on October 24, 2019]; 76(6): 102–6. Reference Source\n\nAl-Sakkaf A: Domestic food preparation practices: a review of the reasons for poor home hygiene practices. Health Promot. Int. 2015 Sep. [Cited on October 24, 2019];30(3): 427–37. Publisher Full Text Reference Source\n\nQuinlan JJ: Foodborne illness incidence rates and food safety risks for populations of low socioeconomic status and minority race/ethnicity: a review of the literature. Int. J. Environ. Res. Public Health. 2013 Aug 15. [Cited on October 19, 2019]; 10(8): 3634–3652. PubMed Abstract | Publisher Full Text Reference Source\n\nLozada-urbano M: Knowledge about kitchen hygiene and associated factors. figshare. Dataset. 2021. Publisher Full Text\n\nLozada-Urbano M: Kitchen hygiene questionnaire. figshare. Poster. 2022. Publisher Full Text"
}
|
[
{
"id": "135252",
"date": "11 May 2022",
"name": "Morad Guennouni",
"expertise": [
"Reviewer Expertise 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\nHygiene and food safety play a key role in the prevention of foodborne illnesses. In this context comes this article to assess knowledge about kitchen hygiene and associated factors in caregivers in a peri-urban area. The results of this study will encourage officials to provide these inhabitants with the necessary means to improve their living conditions.\nComments:\n\nAbstract:\nBackground:\nIt is better to start with a general statement before indicating the objective of this study.\n\nConclusions:\nYou said in conclusion that: “it is necessary to improve mothers' knowledge about the handling and consumption of spoiled food and their effect on children's health”. I think that you must add in result section that the limit level of mothers' knowledge about the handling and consumption of spoiled food.\n\nIntroduction:\n\nGood\n\nMethods:\nAdministration of the questionnaire:\nI want to know if the questionnaire is developed or adapted from a questionnaire already established.\nI want to know if you study the reliability (by Cronbach's α for example) and the reproducibility (by Intraca-calss for example) of the questionnaire with a small sample before the distribution of the questionnaire to the global sample.\nIt is preferable to indicate the number of item in each dimensions.\n\nResults:\nMore descriptions on the results presented in Table 3 are needed in the manuscript 5.\n\nDiscussion:\nThe discussion is quite limited. I think more details are needed.\n\nConclusion:\nThe conclusion is also quite limited. A paragraph about preventive and corrective actions is needed.\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? No",
"responses": [
{
"c_id": "8281",
"date": "23 Nov 2022",
"name": "Michelle Lozada-Urbano",
"role": "Author Response",
"response": "We thank the reviewer for his suggestions for improvement. Abstract: Background: It is better to start with a general statement before indicating the objective of this study. Answer: Food and kitchen hygiene are necessary conditions for safe food and prevent foodborne illnesses. Conclusions: You said in conclusion that: “it is necessary to improve mothers' knowledge about the handling and consumption of spoiled food and their effect on children's health”. I think that you must add in result section that the limit level of mothers' knowledge about the handling and consumption of spoiled food. Answer: Table 3 shows the results obtained for each of the questions in the questionnaire, according to the Huascar and San Pablo zones. Boundaries for Good knowledge of food hygiene: If the mother interviewed had more than seven answers out of 10 questions it was considered as good knowledge about food hygiene in the household. Not so good knowledge of food hygiene: If the mother interviewed had less than or equal to seven answers out of 10 questions it was considered as not so good knowledge about food hygiene in the household. This classification is found at the end of Table 1. Methods: Administration of the questionnaire: I want to know if the questionnaire is developed or adapted from a questionnaire already established. Answer: We apply the same questionnaire of a publication. I want to know if you study the reliability (by Cronbach's α for example) and the reproducibility (by Intraca-calss for example) of the questionnaire with a small sample before the distribution of the questionnaire to the global sample. Answer: The item Cleaning practices had a KR-20=0.722 storage practices and food contamination 0.518 and 0.5 respectively. Internal consistency. Test validity had a KMO=0.549 and a Barlet's test 591.678 , gl=136. It is preferable to indicate the number of item in each dimensions. Answer: Cleanliness has 4 statements Storage has 4 statements Contamination of the child: 2 statements. This answer can be found in table 1 Results: More descriptions on the results presented in Table 3 are needed in the manuscript 5. Answer: Ninety-five percent of mothers agree that sponges used to wash utensils may be contaminated, and 90.8% state that cloths used to clean surfaces may also contain bacteria and microorganisms. 93.2% consider that the garbage bag can be open as long as the utensils are protected or covered. 99.6% of chopping boards can cause contamination to other products. 74% consider that glass is of high quality for storage; 87.6% consider that utensils would be clean with dishwashing detergent; 84.4% state that food consumption can cause illness in children; 60% consider that if the table where the child consumes food is contaminated, it will also contaminate the food; 62% of mothers or caregivers consider that diarrhea and discomfort in children can have their origin in the food. Discussion: The discussion is quite limited. I think more details are needed. Answer: In the investigated areas of SJL (San Pablo and Huáscar V), More than half are between 21 and 30 years of age. Their marital status is free union in the majority. The surveyed mothers were mainly housewives and had a secondary education level. The vast majority of households lacked water and sewage services. Although no significant associations were identified between the variables studied and the level of knowledge of kitchen hygiene, the mothers’ education and age in other studies were associated with knowledge of safe food handling and consumption in the home.21 In this regard, studies in Africa have shown that caregivers, especially the younger ones, drop out of education or even abandon it, thus affecting their future 22. Another study developed in communities in Peru showed an intervention for handwashing in child feeding, where 12% of children were identified and this was increased to 32% 23. Years of school attendence could improve hygiene knowledge, as well as generating a larger social network in which mothers or caregivers interact. Likewise, having a radio in a large percentage of households can be a channel to increase mothers' knowledge and good practices and to obtain appropriate cooking behaviours, through hygiene educational programs. In other studies, mothers’ occupations (homemaker or work outside the home) was shown to be associated with more satisfactory hygienic practices in relation to food poisoning prevention.19,24 The WHO and the Food and Agriculture Organization of the United Nations mention that unsafe food affects the most vulnerable groups, and to promote the improvement of food safety, they should be kept informed, foodborne diseases can be prevented with optimal handling, some of the measures that we have assessed here in this study, are related to the cleanliness where food is prepared, including avoiding mixing raw and cooked food, the cooking of food should be complete, use of safe raw materials and use of potable water 25. Mother with lower socioeconomic status have been found more likely to experience food products with a high microbial count.26 Our study presented the limitation of not including the microbial count. Studies such as Gil et al., 2014, have shown that this measure has been an accurate indicator to determine families’ household cleaning condition.27 Likewise, demographic and socioeconomic factors may have contributed to unsafe food handling behaviours and microbial contamination risks during preparation.28 Poor food handling has been evidenced among low-income consumers.29 Hygiene education, improved treatment, storage and water connections are necessary 30. This study was conducted in a peri-urban area of Lima; some of our limitations may be due to the fact that the entire study population had the same socioeconomic status. Through an evaluation that includes heterogeneous populations, we could obtain complementary results regarding the influence of other variables not examined in the present study, that could improve our understanding of kitchen hygiene knowledge. It is important to highlight that data collection through interviews and surveys is prone to the possibility that the information revealed by the participants may be incomplete or not entirely truthful, which could directly impact the validity of the results. Conclusion: The conclusion is also quite limited. A paragraph about preventive and corrective actions is needed. Answer: We could not identify a predictive capacity in regard to the level of knowledge of kitchen hygiene in the evaluated sociodemographic characteristics in this sample. Caregivers in these communities should receive more education on treatment, food storage and achieve better health outcomes. Governments are called upon to join the efforts to accelerate efforts to lead education campaigns. We thank the reviewer for his suggestions for improvement."
}
]
}
] | 1
|
https://f1000research.com/articles/11-149
|
https://f1000research.com/articles/10-1287/v1
|
15 Dec 21
|
{
"type": "Research Article",
"title": "The “Rotten” matter in A Farewell to Arms: An Ecological Gothic reading",
"authors": [
"Lay Sion Ng"
],
"abstract": "This article uncovers the gothic tropes manifest in the “rotten” food, human bodies, landscapes, and rain in Ernest Hemingway’s A Farewell to Arms through an eco-gothic perspective. It demonstrates how the rotten food, the disjointed bodies, the broken landscapes, and the gothic rain can be viewed in the novel as counter-narratives against the narratives of war, the military, and modern medicine. The first part of this article suggests interpreting war as a form of cannibalism by exploring the representations of rotten food and the connection between eating and killing. Next, the author focuses on how the body is fragmented both metaphorically and literally by the discourse of war, the military, and medical science. The third part uncovers the non-anthropocentric consciousness embedded within the protagonist’s narrative, followed by the gothicizing and romanticization of nature in the fourth section. Here, the protagonist’s linking of the human body to the natural landscape, the descriptions of the gothic rain, and the romanticized snow—all these, as the author argues, can be interpreted as a collective resistance against industrial, anthropocentric warfare.",
"keywords": [
"eco-gothic",
"non-anthropocentrism",
"rotten food",
"deformed bodies",
"gothic rain",
"broken landscape",
"eco-resistance",
"anthropocentric warfare"
],
"content": "Introduction\n\nErnest Hemingway’s A Farewell to Arms depicts deformed and fragmented bodies, matters, and landscapes. In the novel, these aspects are embedded within the word “rotten,” which is used to depict the awful condition of the battlefields and war (AFTA, 29), the food (46), the combat life (63), romance (26), and luck (49). According to Oxford Learners’ Dictionaries, the word “rotten” is defined as “things—such as food or wood—that have decayed and cannot be eaten or used.” Macmillan Dictionary defines it as “terrible,” “unpleasant,” “looking, or feeling ill.” These implications—decaying, terrible, ill, unpleasant—embedded in the word “rotten” thus indicate a certain uncanny1 and grotesque2 quality. This article uncovers the gothic tropes manifest in rotten food, human bodies, landscapes, and rain in A Farewell to Arms. From an ecological gothic perspective, these elements serve as counter-narratives to the narratives of war, military, and modern medicine, making the egocentric delusion of the Great War visible.\n\nM. H. Abrams defines “gothic” as an “atmosphere of gloom and terror” that “represents events that are uncanny or macabre or melodramatically violent” (qtd. in Silviya and Immanuel, 25). Ecological Gothic is a relatively new field that merges two traditionally dissimilar fields, one with a biocentric focus and one that focuses on “humanity” and “human desires, fear, and trauma” (Deininger and Cox, 166).3 In his article, David Del Principe states, “the EcoGothic examines the construction of the Gothic body—unhuman, nonhuman, transhuman, posthuman, or hybrid—through a more inclusive lens, asking how it can be more meaningfully understood as a site of articulation for environmental and species identity” (1). The Ecological Gothic is thus a framework attempting to destabilize anthropocentrism by blurring or challenging the hierarchical boundaries between humans and nonhumans, the mind and the body, the self and the other.\n\nThe connection between Hemingway and the ecological gothic can be traced back to the author’s ambiguous relationship with nature. As Terry Tempest Williams notes, Hemingway’s relation to the natural world is shown in opposition: “hunting and loving. Physical and spiritual. Life and death. Controlling masculine and wild feminine” (Grimes, 104). This multidimensional perception of the natural world creates a possibility for an ecological gothic reading of his work. Moreover, the author’s high interest in “materiality” and sensitivity to “place-energies” are following the material ecocritical approach (Godfrey, 2016: 94, 95). Hemingway’s consciousness of the force, energy, and agency possessed by materials in places as well as sites themselves are shown in Williams’ description of him as “a powerful mentor, in terms of what it means to create a landscape impressionistically on the page, to make it come alive, pulse, breathe” (qtd. in Godfrey, 2006: 48).4\n\n\nResearch methodology\n\nIn this article, I utilize diverse analyses concerning the field of material ecocriticism, ecological gothic, the environmental history of The Great War, the previous ecocritical readings of Hemingway’s A Farewell to Arms, and biographical studies of Hemingway. More specifically, Andrew Smith and William Hughes’ edited collection EcoGothic (2013) and Serenella Iovino and Serpil Oppermann’s edited collection Material Ecocritism (2014) serve as the primary research methodology. Secondary literature used include David Del Principe’s “The EcoGothic in the Long Nineteenth Century” (2014), William Hughes, David Punter, and Andrew Smith’s edited book named The Encyclopedia of the Gothic (2015), Maria Concetta Dentoni’s “Food and Nutrition (Italy)” in International Encyclopedia of the First World War, Joseph P. Hupy’s “The Environmental Footprint of War” (2008), to name a few. Analyzing Hemingway’s work from the lens of eco-gothic is a relatively new thing. However, some previous studies help construct the arguments in this article. This includes Trevor Dodman’s “‘Going All to Pieces’: A Farewell to Arms as Traumatic Narrative” (2006), Gruber Laura Godfrey’s Hemingway Geographies (2016), David A. Rennie’s “The Real British Red Cross and Hemingway’s A Farewell to Arms” (2018), and so forth.\n\nThis article is divided into four sections. The first section examines the representations of rotten food as opposed to clean and fresh food in the novel. Here, the act of eating is juxtaposed with that of killing, leading to the argument that war is a grotesque form of cannibalism. Secondly, I concentrate on how the body is fragmented metaphorically and literally by the discourse of war, the military, and medical science. What does such fragmentation say about bodily boundaries and the integrity of the self? These questions are pondered in this section. The third part uncovers the non-anthropocentric consciousness embedded within Frederic’s narrative. Here, I see Frederic’s linking of the human body and the natural landscape as a form of eco-resistance against industrial warfare. Finally, I explore Frederic’s gothicizing and romanticization of nature in the novel and suggest that the gothicized rain/snow and romanticized rain/wind can also be seen as a counter-narrative to the anthropocentric war.\n\n\nThe rotten food\n\nThe rotten food in the novel serves as a storied5 matter that makes the war’s monstrosity visible. In the novel, the most representative rotten-food episode is in chapter nine. Prior to Frederic’s injury and Passini’s death, the ambulance team is having some “rotten” macaroni, cheese, and wine at the front (AFTA, 46). Here, the awful condition of the macaroni and wine (“It tasted of rusty metal” (46)), the dirty cheese (“its smooth surface covered with brick dust” (46)), the lack of any utensils (“I put thumbs and fingers into the macaroni and lifted” (46)), and the awkwardness of eating the macaroni (“They were all eating, holding their chins close over the basin, tipping their heads back, sucking in the ends” (46)) make a mockery of the ideal heroism of soldiers and the absurd glamor of war.\n\nFrederic’s linking of food to the war and its absurdity can be found in his description that “I had seen nothing sacred, and the things that were glorious had no glory and the sacrifices were like the stockyards at Chicago if nothing was done with the meat except to bury it” (AFTA, 161). To Frederic, the meaninglessness of human sacrifice is derived from the absurdity of war itself. Indeed, several instances show that warfare is absurd. For example, the military department decides to decorate Frederic with a “silver medal” (105) even though he has done nothing heroic during the fight: “I was blown up while we were eating cheese” (55). The military department does this to enhance its image for civilians; on seeing his medal, one may imagine that Frederic, who represents the Italian army, had “killed two hundred Austrians or captured a whole trench” during the fight (105). The system of military decorations is, therefore, a fraud. Another episode that shows the war’s absurdity is during the Caporetto retreat when the Italian military police begin to fire on their own people suspecting, in their fear, that the Germans have donned Italian uniforms to infiltrate themselves among the Italian soldiers. Aymo, a comrade of Frederic, is shot to death due to this. Moreover, to hide their own mistake, those frightened Italian battle police will have to kill more of their own people: “They’d have to shoot us all to prove they were right the first time” (185). Acknowledging these absurd incidents, Frederic concludes,\n\nThere were many words that you could not hear and stand to hear and finally only the names of places had dignity … Abstract words such as glory, honor, courage, or hallow were obscene beside the concrete names of villages, the numbers of roads, the names of rivers, the numbers of regiments and the dates.\n\n(AFTA, 161)\n\nIn addition to the military reward system, the food distribution system in the military is also problematic. This aspect is revealed in the conversation between Frederic and Gino before the Caporetto retreat. According to Gino, there is an issue regarding the distribution of food: “The regiments in the line get pretty good food but those in support don’t get so much. Something is wrong somewhere. There should be plenty of food” (AFTA, 160-61). “The dogfish are selling it somewhere else,” Frederic then concludes (161). Agreeing with Frederic, Gino states, “[i] t is very bad for the soldiers to be short of food. Have you ever noticed the difference it makes in the way you think?” (161). While Frederic’s statement confirms the corrupted food distribution system as rotten, Gino’s description foreshadows the important role food plays in times of war. In other words, insufficient food distribution leads to starvation, representing a form of physical and mental violence—among the soldiers, which ultimately results in defeat in war. Historically, after the Caporetto retreat, Silvio Crespi, the head of the Commission for Procurement and Consumption in the Italian army, decided to change the soldiers’ diet as he believed that the retreat was caused by the soldiers’ poor nutrition (Dentoni, 2014). From this respect, the rottenness of the food in the novel underscores the absurdity of war and the corruption of military systems during the era of World War One.\n\nIn contrast to the rotten food described in chapter nine, the food and drinks in Chapter Thirty-Four are fresh, clean, and delicious. After escaping from the Caporetto retreat, Frederic gets a room at the Grand-Hotel & des Isles Borromees before reuniting with Catherine. At the hotel’s bar, Frederic orders olives, salted almonds, potato chips, red wine, martini, cheese, bread, grappa, and sandwiches (AFTA, 213). After asking around about Catherine’s whereabouts, Frederic eats the sandwiches, drinks a couple more martinis, and claims, “I had never tasted anything so cool and clean. They made me feel civilized” (213). Here, Frederic’s linking of fresh food to civilization connects rotten food and barbarity. In the novel, the vicious quality of the war is emphasized in Rinaldi’s symbolic joke in Chapter Twenty-Five. During dinner time, Rinaldi sarcastically jokes that the meat-stew they are eating is the body of a “dead Austrian” (152). Here, the act of eating cooked meat is juxtaposed with the act of killing living humans, leading one to see warfare as a form of cannibalism (and hence, barbaric). It is under this implication that the food is claimed as rotten since barbarity has become the main component of it.\n\nAnother symbolic instance of cannibalism is reflected in Frederic’s repetition of the phrase “am cooked” seven times in chapter twenty-one. According to the Farlex Dictionary of Idioms, the term means physically ruined, mentally depressed, and emotionally traumatized. In his conversation with Rinaldi, Frederic claims, “[w] e are all cooked. The thing was not to recognized it. The last country to realize they were cooked would win the war” (116). Following this, the key to winning the war is to repress the trauma suffered by a nation because of the war. That is to say, to win the war for one’s country, one must cook (traumatize) oneself by cooking (killing) the other and then pretend that one is not yet cooked (ruined). Indeed, this method is beyond human limits. As Rinaldi reveals, “this war is killing me … I am very depressed by it” (146). War is, therefore, a slow-cook process that transforms one into both the eater and the eaten. It is in this sense that warfare can be seen as cannibalistic and hence, monstrous.\n\n\nThe rotten bodies\n\nBesides the rotten food, the wounded body represents another agentic matter that underlines the issue of war’s rottenness. In this case, it is necessary to explore the incident of Frederic Henry’s knee injury. Frederic gets injured when one of the Austrian’s trench mortar shells hits him during their mission to send four ambulances up to the river. When Frederic realizes that his comrade, Passini, is already dead and that the mortar shell has hit him on his knee, Frederic panics: “I looked at my leg and was very afraid”; “My knee wasn’t there. My hand went in, and my knee was down on my shin” (AFTA, 48). The uncanny out-of-body experience further enhances the panic Frederic had a moment ago: “I felt myself rush bodily out of myself and out and out and out and all the time bodily in the wind … I knew I was dead … Then I floated, and instead of going on I felt myself slide back” (47). Here, Frederic’s helpless condition—his out-of-body experience and witnessing Passini’s death—makes him realize that he has no control over his own body and possible death. Moreover, Frederic’s experience of derealization/depersonalization6 leads him to suffer from post-traumatic stress disorder (PTSD) in the latter part of the story.\n\nFrederic’s PTSD symptoms7 can be found in several aspects. For instance, he suffers from sleeping problems and a disturbing nightmare: “I slept heavily except once I woke sweating and scared and then went back to sleep trying to stay outside of my dream” (AFTA, 77). He also suffers from excessive drinking, causing him to have “jaundice” (124) and attempts to numb his emotions as a way to avoid being reminded of the traumatic event: “The head was mine, but not to use, not to think with … [and] not too much remember” (199). This leads him to depression.\n\nFrederic’s rejection of his wounded knee, his claiming its ownership to the doctor— “It was his knee all right. The other knee was mine” (199)—comes from his psychological disgust towards its foreignness. He begins to perceive the wounded knee as a grotesque Other after it is scanned by an X-ray machine and seen by the doctors. Through the “eye” of the device, Frederic notices that some “foreign bodies” have “invaded” and “penetrated” his body (AFTA, 82; Dodman 256). The doctor’s comment that “the foreign bodies were ugly, nasty, brutal. The Austrians were son of bitches” further indicates that his body had been penetrated by the enemy (82). Frederic’s bodily integration is hence undone not only by the trench mortar shell but also by the Austrians, the X-ray machine, and the Doctors; they represent the foreign Other that urge Frederic to reject his wounded knee.\n\nFrom a different perspective, Frederic’s disgust towards his wounded knee can be understood as self-defense against his “disabled” condition. In Consuming Gothic, Lorna Piatti-Farnell notes that “disgust is deeply connected to notions of normality and appropriateness” (50). “Disgust,” Piatti-Farnell continues to write, “signals the breakaway point from what is proper and acceptable, from the very notion of safety and propriety” (51). Frederic’s regard of his wounded knee as Other can thus be interpreted as his attempt to perceive himself as able-bodied rather than recognize that he has become “disabled” or somehow deficient.\n\nIn “Going All to Pieces,” Trevor Dodman stresses that the traumatic violence in the novel lies in the fragmentation of human bodies caused by weapons of mass destruction (249-256). Throughout the novel, a great variety of war weapons are introduced, which include artillery (AFTA, 158), rockets (47), big trench mortar shells (48), Skoda guns (47), grenades (106), rifles (106), pistols (130), naval guns (159), machine guns (162), iron shrapnel balls (162), cavalry (179), and so on. These destructive weapons blow Catherine’s ex-lover “all to bits” (17), injure Frederic’s knee, kill Passini, Aymo, and “one hundred and fifty thousand men on the Bainsizza plateau and on San Gabriele” and “forty thousand on the Carso” (116). Here, men’s bodies re spent in the war as if they hold little value: their bodies are fragmentized and their minds traumatized. This highlights industrial warfare’s fetishization of military technologies over human (living) bodies, leading to the massive production of destructive weapons and innumerable deaths.\n\nIn addition to military discourse, modern medical technologies (surgeries, x-rays) and doctors also play an essential role in creating fragmented disunity by imposing a mind-body dualism. As Emily Martin notes,\n\nMany elements of modern medical science have been held to contribute to a fragmentation of the unity of the person. When science treats the person as a machine and assumes the body can be fixed by mechanical manipulations, it ignores, and it encourages us to ignore, other aspects of our selves, such as our emotions and our relations with other people.\n\n(19-20)\n\nIn the novel, Frederic’s statement that “[d] octors did the things to you and then it was not your body anymore” reflects Martin’s critique above (AFTA, 199). Another instance that mirrors Martin’s idea can be found in the episode that explains Rinaldi’s depression. “All summer and all fall I’ve operated. I work all the time,” as the military surgeon tells Frederic (146). Here, one understands that Rinaldi is forcefully turned into an anomaly, working like a machine. Moreover, he loses the human capacity for fundamental emotions: “I never think. No, by God, I don’t think; I operate” (147). This mechanization of Rinaldi reveals the military medical system as oppressive and inhuman. Frederic’s alienation of his wounded knee and Rinaldi’s repression represent a counter-narrative to industrial warfare that imposes technological fetishism.\n\n\nThe rotten landscapes\n\nThe landscape of rotted and dead bodies represents another storied matter that showcases the horror of war. Unlike humans, who can speak for themselves, the natural world often remains a voiceless victim of war. Nevertheless, in A Farewell to Arms, a layer of non-anthropocentric consciousness resurfaces through the narrator’s descriptions, making the voices of nonhuman entities visible. Frederic’s non-anthropocentric consciousness is noticeable from the beginning of the novel. While observing Gorizia, Frederic states,\n\nThe river ran behind us and the town had been captured very handsomely but the mountains beyond it could not be taken and I was very glad the Austrians seemed to want to come back to the town some time, if the war should end, because they did not bombard it to destroy it but only a little in a military way.\n\n(AFTA, 5)\n\nAlthough the army has transformed Gorizia into a military town that includes hospitals, artillery, cafes, the shell-marked iron of the railway bridge, the smashed tunnel by the river, broken houses with plaster and rubble in the gardens, Frederic claims that he is “very glad” only because the town has not been ruined completely. (AFTA, 5-6). Here, the sense of happiness embedded in Frederic’s description shows his hope for the end of the war (“if the war should end”) and his relief that not all-natural landscapes, especially “the mountains,” have been transformed into battlefields (AFTA, 5).\n\nIn the novel, a counter-narrative on human-centrism can be found in Frederic’s association between the human body and the natural landscape. While observing Gorizia, Frederic claims, “the forest had been green in the summer when we had come into the town but now there were the stumps and the broken trunks and the ground torn up” (AFTA, 6). Here, as Victoria Addis (2018) points out, phrases such as “stumps” and “broken trunks” recall “the male body, and more specifically, with the injuries and amputations that resulted from fighting in the war.” This linking of human bodies to nonhuman entities equalizes the subjectivity and agency8 between the two, showing that both human and nonhuman bodies are victims of industrial warfare. According to anthropologist Joseph P. Hupy, the result of this first industrial-scale mechanized warfare is so devastating in terms of human loss of life and environmental cost that the war is regarded as an “anthropogenic disturbance” (418). In the novel, this anthropocentric destruction is committed by combatants who “marched as though they were six months gone with child” (4). Here, as Aime L. Pozorski notes, the phrase “to be gone with child” means “to be pregnant” (79). This linking of soldiers’ arms to maternal arms serves as an ironic representation that indicates the murder of children by the military arms. Frederic’s juxtaposition of soldiers’ arms and the maternal arms thus implies the front as a field of sterility. Historically, the French writer Henri Barbusse who fought on the Western Front also identified the battlegrounds as “‘fields of sterility’ where ‘frightful loads of dead and wounded men alter the shape of the plain’ and ‘everything appears turned over … full of rottenness and smelling of disaster’” (qtd. in Keller). As Joseph P. Hupy in “The Environmental Footprint of War” also notes, the environmental consequences of The Great War “obliterated forests” and “significantly altered the landscape” beyond recognition, creating “wide swathes of destruction, limited only by the range of artillery shells” (412). “Perhaps the best-known example of this swath of destruction,” Hupy continues to claim, “is the Western Front, a sinuous line of trenches craters, bunkers, and barbed wire averaging 20 km in width and stretching from the English Channel to the border of Switzerland” (413). Indeed, when Frederic looks at Biansizza after the war, he laments, “I had not realized it was so broken up” (159). This description recalls Barbusse’s claim that “‘[w] here there are not dead, the earth itself is corpselike”’ (qtd. in Keller). Frederic’s referring to the battlefield as “the picturesque front” thus indicates the wounded and dead human bodies and the broken, rotten, corpselike landscapes destroyed by modern destructive weapons (17).\n\nIn the novel, Frederic’s frustration toward the anthropocentric destruction further increases when he sees that Caporetto has shifted from a charming “white” and “clean little town” to a landscape of death and chaos with “many sick” (AFTA, 144).9 This enhances his desire to escape toward the undisturbed land to “forget the war” and to have “a separate peace” (211). As he states, “I wanted to go to Austria without war. I wanted to go to the Black Forest. I wanted to go to the Hartz Mountains” (31).\n\nFrederic’s impulse to escape the battlefields is linked to his witnessing the destruction of those towns. From the collapse of the older townscape to replacing the new landscape with fragmented and dead bodies, the whole process is mapped and set out as a visual geography of helplessness through Frederic’s eyewitness account. Here, the act of viewing is a “condition of passivity,” a form of violence one “can neither flee from nor defend against” (Nayar, 30). Furthermore, “[w] hat the eyewitness documents is a set of effects—primarily horror—and nothing beyond it. There is nothing intelligible about the events they see […] but what they apprehend is brutal, irreducible dying” (Nayar, 43). This, twinned with the fact that he is part of the destruction, makes Frederic feel extraordinarily helpless. Even after he flees the war with Catherine, this sense of helplessness continues to dominate him, making him think that he can never escape war: “I did not have the feeling that it was really over” (AFTA, 213). Here, Frederic’s case symbolizes not an individual but a collective post-war experience. All combatants and citizens who witness the landscapes of dead and dying bodies experience the collapse of recognition and intelligibility. The process of gazing at the dying landscapes and dead bodies on the battlefield strengthens the sense of helplessness through collapsing what is perceived as “normal” in oneself, confusing one’s recognition of the world. In other words, the documentation of an unmaking of the world leads to the unmaking of subjectivity, resulting in the formation of helplessness. From this respect, the monstrosity of war lies in the collapse of subjectivity caused by the forced view of the landscapes of dying and dead bodies.\n\n\nGothicized rain\n\nApart from food, bodies, and the landscapes, rain in the novel represents another storied matter worth exploring. In the novel, rain often creates a somewhat gothic atmosphere that is cold, dark, and chaotic and reflects and intensifies the feelings of helplessness, uncanniness, fear, and depression within the characters. This gothicized quality of rain can be found in the very first chapter of the novel, whereby rain corresponds directly with the coming of cholera and death: “[a] t the start of the winter came the permanent rain and with the rain came cholera” (AFTA, 4). Moreover, as referenced earlier, during their idyllic time in Milan, Catherine reveals to Frederic her morbid reaction to rain. Furthermore, the Italian retreat from Caporetto is covered by dark and cold rain: “[a] s we moved out through the town it was empty in the rain and the dark except for columns of troops and guns that were going through the main street” (169). During the retreat, Aymo is shot to death in the rainy mud. “He looked dead. It was raining,” as Frederic claims (185). Later, when Catherine is having a Caesarean section at the hospital, it starts raining. At last, after bidding farewell to his dead wife, Frederic walks back from the hospital to the hotel “in the rain” (284).\n\nThe association of rain with disease, death, and war leads Malcolm Cowley to call the rain “a conscious symbol of disaster” (16). Similarly, Philip Young regards the rain as a metaphor for death (1966: 88). Furthermore, Carlos Barker associates rain with suffering, war, death, irreligion, and low-lying plains, putting them into the “not-home” category; at the same time, elements such as mountains, health, happiness, good-life, and God belong to the concept of “home” (1972: 102).10 Thus, rain serves atmospheric and symbolic purposes in the novel. It is possible to argue that rain serves as a gothic “actant”11 that plots human relationships and alters the course of events in the novel. By emphasizing the destructive-creative agency of the rain (accompanied by snow and wind) in the novel, the notion of human domination over nature is called into question, suggesting an ecocritical awareness to challenge the anthropocentric perceptions that encourage the spread of war.\n\nThe destructive-creative agency of rain is clear from the beginning of the novel. Despite the coming of cholera when the permanent rain comes in winter, increasing sick and dead people, Frederic points out that, “in the end only seven thousand died of it in the army (AFTA, 4; italics added). The word “only” emphasizes that the number of deaths from the war is far more significant than those who died from cholera. This highlights the destructive impacts of warfare on humanity compared to that of the winter rain. In fact, the agency of rain is viewed as “destructive” only because it is not beneficial for the people at this point. However, the winter snow stops the war in the novel: “There will be no more offensive now that the snow has come” (7). This then allows Frederic to take a personal adventure on his own: “I went everywhere. Milan, Florence, Rome, Naples, Villa San Giovanni, Messina, Taormina” (10). When Frederic returns to the front in the spring, he sees that “the fields were green and there were small green shoots on the vines” (9). Thus, from a non-anthropocentric standpoint, the winter rainfall and the snow are significant for the revival of life in nature. In “Winter Precipitation and Forests,” it is stated that the “infiltration of water into the ground occurs most efficiently during times when the forest is dormant.” The rainwater and melted snow offer a slow and steady flow of water into the forest soil so that life will emerge again as the spring begins. In this sense, the winter rain and snow propel (non) human things into “new relationships and new material embodiments” (Duckert, 115).\n\nAnother instance that shows the rain’s destructive-creative agency can be found in the episode of the Caporetto retreat, which Frederic describes as “wet and sullen” (AFTA, 163). Historically, the Italian army did their best to contain the German assault under torrential rain and freezing fog during the retreat. As colonel Francesco Pisani noted, “[t] here was total confusion, the road was almost entirely blocked by a mass of troops, carts, horses, trucks, artillery pieces, mules, and supplies … in the chaos, the freezing fog and the rain” (Wilcox, para. 7). In the novel, a similar situation is shown in Frederic’s description that “along the crowded roads we passed troops marching under the rain, guns, horses pulling wagons, mules, motor trucks, all moving away from the front. There was no more disorder than in an advance” (163-64; italics added). Here, rain’s destructive agency is reflected in its intensification of the disorder, the chaotic situation existing alongside the feelings of horror and helplessness among the people. Interestingly, the incident of the Caporetto retreat also allows for the life-giving quality of rain. As Frederic notes, “I was certain that if the rain should stop and planes come over and get to work on that column that would all be over. All that was needed was for a few men to leave their trucks or a few horses to be killed to tie up completely the movement on the road” (173). With the rain, the retreat is plunged into chaos. However, the situation would have been even worse without the rain as more soldiers would have been wounded and killed. In this respect, rain “preserves life” (Rennie, 38).\n\nThe fact that rain (and snow) is attributed to both the destruction and preservation of life foreshadows its destructive-creative agency, indicating that rain exerts a subjectivity of its own, a type of existence indifferent to humanity. When it rains, it manifests “‘Thing-Power: the curious ability of inanimate things to animate, to act, to produce effects dramatic and strange” (qtd. in Duckert, 115). Rain’s ability to make things happen leads to the statement that “rain is not merely a metaphor for life, it is lively and a life, life defined in her own words” (Duckert, 115). In Vibrant Matter, Bennett also asks, “Does life only make sense as one side of a life-matter binary, or is there such a thing, a mineral or metallic life, or a life of the it in ‘it rains’?” (53). The fact that Hemingway, who was “depressed by rain” and “frequently complained about it,” constructed his novel heavily upon the agencies of rain seems to propose that rain is, indeed, a vibrant matter (qtd. in Grissom, 108).\n\nRain’s destructive-creative agency, together with its random, wild, and unsympathetic qualities, emphasizes the fact that “there is no such thing as getting above the rain” (Cathcart, 95). Indeed, rain appears not only in the realm of reality but also in the world of fantasy. While taking a short break during the retreat, Frederic falls asleep and dreams of Catherine being brought to him by the western wind and rain:\n\nBlow, blow, ye western wind. Well, it blew and it wasn’t the small rain but big rain down that rained. It rained all night. You knew it rained down that rained. Look at it. Christ, that my love were in my arms and I in my bed again. That my love Catherine. That my sweet love Catherine down might rain. Blow her again to me.\n\n(AFTA, 171-72)\n\nIn Frederic’s dream, the association between Catherine and rain is once more emphasized. However, rain is romanticized this time: “That my sweet love Catherine down might rain” (172). As Tait Keller points out, “[t] he war’s impact on the land horrified university-educated soldiers groomed in the romantic appreciation for nature.” Hence, the romanticization of the rain overturns the idea of nature as a passive background, which is an anthropocentric perception strengthened by the development of industrialization and mechanistic science (Merchant, 293, 294). In Frederic’s dream, the romanticized rain and wind are variable, creative, and lively. They save Frederic by blowing his lover to him and hence, blowing away the horror and pressure of being in war. Therefore, Frederic’s romanticization of the rain and wind is a result of his emotional resistance against the cruel, cold, lifeless war.\n\nIn the novel, Frederic’s mental resistance against the monstrosity of war is further reflected in his juxtaposition of the stormy weather and the weapons of war. Standing at the front line the day before the retreat begins, Frederic notes, “[i] t stormed all that day. The wind drove down the rain and everywhere there was standing water and mud” (AFTA, 161). Under this stormy weather, Frederic and the others fight “in the dark in the rain” (161). According to Frederic, “[t] here were much shelling and many rockets in the rain and machine-gun and rifle all along the line … and between the gusts of wind and rain we could hear the sound of a great bombardment far to the north” (162). Here, there are two kinds of war going on. While the storm is a nonhuman disturbance generated by wind and rain, the battle is an anthropocentric assault marked by machine guns, rifles, smoke balls, and bombardments. However, these forces possess a different nature and impact. Firstly, rain is indifferent, while guns and bullets, on the other hand, are often used to fulfill egoistic delusions of domination. Secondly, rain’s autonomous forces resist drawing “the separations between climate and culture, life and matter, and subject and object” (Duckert, 116). In the novel, rain not only blurs the boundary between fantasy and reality, allowing Frederic to reconnect with Catherine but also keeps on living its life: “It rained all night” (171). In contrast, war weapons are objects used to objectify, disconnect, and eradicate all forms of life. In this respect, Frederic’s juxtaposition of the stormy weather with war weapons seems to propose a non-anthropocentric view that highlights the egoistic nature of warfare.\n\nToward the end of the novel, rain further points toward the naturalist philosophy of human existence. After Catherine dies, Frederic leaves the hospital and walks back to the hotel “in the rain” (AFTA, 284). This recalls Catherine’s line, whereby she sees herself dead in the rain: “I’m afraid of the rain because sometimes I see me dead in it” (110). Nevertheless, there’s nothing intrinsically evil about the rain as Catherine’s hemorrhages occur randomly: “It’s just nature giving her hell” (274). After all, as Frederic comes to realize, whether, in war or love, his influence upon the outcome of events is insignificant.12 Eventually, the universe kills indifferently. “You died. You did not know what it was about. You never had time to learn. They … killed you gratuitously like Aymo. Or gave you syphilis like Rinaldi. But they killed you in the end. You could count on that. Stay around and they would kill you” (280). Here, Frederic’s use of the term “they” reveals his realization of one’s place in the more-than-human (their) world. More specifically, human agency is conditioned by the natural laws of cause and effect beyond humans, and nobody can transcend these forces.\n\nJust like one cannot stop the rain from falling, the death of Catherine will not stop the world from moving forward. “Things happen all the time. Everything blunts and the world keeps on … It never stops” (AFTA, “Appendix II” 312). As for Frederic, who is still alive, he understands that he must move forward in his life: “[t] he rest goes on and you go on with it” (312). However, in defiance, Frederic also writes, “you have to stop a story. You stop it at the end of whatever it was you were writing about” (312). Following this, the ending scene, whereby Frederic leaves the hospital and walks back to the hotel “in the rain,” embodies two layers of implication (284). On the one hand, it can be interpreted as Frederic’s attempt to move forward in his life, as stopping the story here involves moving on rather like the indifferent rain. On the other hand, the scene also reveals a difficulty to move on, as Frederic ends the story in a rather sudden, silent, and abrupt13 way, which might imply his inability to process his grief. However, ironically, since the living memory of Catherine is associated with rain, the only way not to forget about Catherine is, hence, to remain in the rain. Following this, while it seems to rain on Frederic’s behalf,14 it also rains indifferently. In fact, it simply rains when it rains.\n\n\nConclusion\n\nA Farewell to Arms is a novel about war, love, and trauma. But more than that, it is also a novel about material bodies. The rotten food, fragmented human bodies, broken landscapes, and the gothic rain—all these are storied matters. Yet, if we look closely enough, we can discover their narratives. By digging into the rotten, uncanny, and gothic representations of the food, bodies, landscapes, and rain in the novel, one comes to understand the absurd, dualistic, destructive, and cannibalistic aspects of industrial warfare. These posthuman narratives thus counteract the discourses of military and modern medical science, suggesting that warfare is the ugliest, darkest, and most disturbing aspect of humanity.\n\nThe suggestion that warfare is a grotesque form of cannibalism is emphasized in the “rotten food” chapter, whereby eating rotten food is juxtaposed with killing/cannibalizing human living bodies on the Western front. Moreover, if one sees the symbolic connection between the phrase “cooked” and “traumatized,” one understands that the four-year-long war represents a slow cook/traumatizing process that transforms one into both the eater (traumatizer) and the eaten (victim). Meanwhile, soldiers on the Western front are encouraged to fight for the absurd value of heroism and the glory of war without even filling their stomachs. It is the corrupted food distribution system in the army that causes starvation and death among these soldiers. Realizing this, Frederic cannot help but lament the absurdity of war that leads to the meaninglessness of human sacrifice.\n\nAnother monstrous characteristic of warfare lies in its objectification and fragmentation of living human bodies, which can be found in the episode of Frederic’s confrontation with his injured body part. In the novel, Frederic’s repudiation of his left knee is deeply associated with the objectification of his body by the doctors and the x-ray machine. Together with the foreign object inserted into his knee, these actions painfully penetrate Frederic and undo his bodily integrity. Frederic’s rejection of his knee is thus a self-defensive act. Another instance is shown in the case of Rinaldi, where the military surgeon is forced to work like a machine for months, causing him to suffer from mental health problems. Industrial warfare’s fetishization of medical/military technology over the living human body can be observed through these cases. Indeed, a variety of weapons are created for the sole purpose of destroying and killing. As a result, countless lives—including Catherine’s ex-lover—are blown “into bits” by weapons of war. In this sense, the fragmented bodies question the violent and violating objectification of living human beings by medical science and military technology.\n\nWar’s fondness for military technology further encourages the destruction of natural landscapes. Through industrial war, battlegrounds and towns are transformed into landscapes of wounded and dead bodies. Having witnessed this “picturesque” (AFTA, 17) transformation, Frederic feels frustrated as he is responsible for causing this anthropogenic disturbance . At the same time, he is also a victim based on his position as a passive, helpless viewer. Frederic then laments the ecological disaster caused by the war in his juxtaposition of the wounded human bodies with the broken landscapes. Here, Frederic’s anti-war consciousness shows that warfare is a destructive force that annihilates the subjectivity and agency of (non) human beings.\n\nThe dynamic narrative of the rain also plays a crucial role in revealing Frederic’s non-anthropocentric consciousness. In the novel, rain is a force that dominates human relationships and catalyzes events. While rain’s destructive agency, represented by the gothic rain in the novel, tends to destroy lives, its creative agency, expressed by the romanticized rain, reconnects relationships and preserves lives. After all, rain’s unpredictable, uncontrollable, and indifferent nature reveals that it holds a subjectivity of its own. In the novel, Frederic's promotion of this non-anthropocentric agency represents a counter-narrative to the human-centric war. Moreover, the connection between rain and Catherine’s sudden death urges one to acknowledge our place in this world. Humans are not as significant, influential, and independent as we assume; in fact, we are conditioned by indifferent forces and laws of nature. This conception is once again emphasized in the ending of the novel, where the rain seems to cry on Frederic’s behalf, but the fact is that it simply rains because it can. This points out the perception that the natural world is passive and feminized as human-centric and biased.\n\nSuppose we regard A Farewell to Arms as an ecosystem. In that case, this essay serves to demonstrate how industrial war has knocked the novel-as-ecosystem intensely out of balance and turned it into something distinctly “rotten.” Hence, an eco-gothic emphasis of the agentic roles played by the rotten food, the uncanny bodies, the deformed landscapes, and the gothic rain in the novel reminds us that we derive much of what we recognize as our power, creativity, and accomplishments from the material things around us. This mode of thinking explains what kind of beings we are: we, humans, are inextricably entangled with our worldly surroundings, biologically, psychologically, culturally, and spiritually. This mode of thinking is essential in the Anthropocene, whereby human capacity has overloaded the Earth, resulting in uncontrollable environmental, social, cultural, and political problems. Only by shifting our perspective to a non-anthropocentric direction can we overcome these problems and reduce the incidents of warfare in the world. In this sense, an eco-gothic reading of A Farewell to Arms becomes vital as it not only shows the destructive impacts of war but also encourages a more fluid, realistic, and ethical reconstruction of humanity.\n\n\nData availability\n\nAll data underlying the results are available as part of the article, and no additional source data are required.",
"appendix": "Acknowledgments\n\nThis research was presented at the 42nd Conference of the Southwest Popular/American Culture Association, February 23, 2021.\n\n\nReferences\n\nAddis V: Landscape and Masculinity in Ernest Hemingway’s A Farewell to Arms. U.S. Studies Online: Forum for New Writing. 13 November 2018. Accessed 20 July 2020. Reference Source\n\nam cooked: Farlex Dictionary of Idioms. Farlex, Inc.; 2015. 14 February 2020. Accessed 10 July 2021. Reference Source\n\nAlaimo S: Trans-corporeal Feminisms and the Ethical Space of Nature. Material Feminisms Alaimo S, Hekman S, editors. Bloomington: Indiana UP; 2008; pp. 237–64.\n\nBarker C: Hemingway: The Writer as Artist. Princeton: Princeton UP; 4th ed.1972.\n\nBarad K: Posthumanist Performativity: Toward an Understanding of How Matter Comes to Matter. Signs 2003; 28(3):801–831. Publisher Full Text\n\nBennett J: Vibrant Matter: A Political Ecology of Things. Durham and London: Duke UP; 2010.\n\nCathcart B: Rain. London: Granta Books; 2002.\n\nCohen JJ: Posthuman Environs. Environmental Humanities: Voices from the Anthropocene. Oppermann S, Iovino S, editor. London and NY: Rowman & Littlefield; 2017; pp. 25–44.\n\nDebeljak EJ: The Accidental Hero: Ernest Hemingway and Slovenia. Brick: A Literary Journal. 20 July 2015. Accessed 20 July 2021. Reference Source\n\nDeininger M, Cox NR: Different Shades of Green: Elizabeth Gaskell’s EcoGothic Short Fictions. Victorian Ecocriticism: The Politic of Places and Early Environmental Justice. Hall DW, editor. NY: Lexington Book; 2017.\n\nDentoni MC: Food and Nutrition (Italy). 1914-1918-online. International Encyclopedia of the First World War. Daniel U, Gatrell P, Janz O, et al.: Berlin: Freie Universität Berlin; 2014-12-18. Publisher Full Text\n\nDickerman L: Dada. Washington: National Gallery of Art; 2005.\n\nDodman T: ‘Going All to Pieces’: A Farewell to Arms as Traumatic Narrative. Twentieth-Century Literature 2006; 52(3): 249–274. JSTOR. Accessed 20 July 2021. Reference Source\n\nDuckert L: When It Rains. Material Ecocriticism. Iovino S, Oppermann S, editors. Bloomington: Indiana UP; 2014; pp.114–129.\n\nGodfrey GL: Hemingway’s Geographies: Intimacy, Materiality, and Memory. USA: Palgrave MacMillan; 2016.\n\nGrimes LE: Hemingway and the Natural World (Review). The Hemingway Review. 2000; 20(1): 104–108.\n\nGrissom CU: Fitzgerald and Hemingway on Film: A Critical Study of the Adaptations, 1924-2013. North Carolina: McFarland & Company, Inc; 2014.\n\nHemingway E: A Farewell to Arms: The Hemingway. NY: Scribner; Library ed.2014. First printed in 1929.\n\nHughes W, Punter D, Smith A: The Encyclopedia of the Gothic. UK: John Wiley & Sons; 2015.\n\nHupy JP: The Environmental Footprint of War. Environment and History. 2008; 14(3): 405–421.\n\nKeller T: Destruction of the Ecosystem. 1914-1918-online. International Encyclopedia of the First World War. Daniel U, Gatrell P, Janz O, et al., editors. Berlin: Freie Universität Berlin; 2014-10-08. Publisher Full Text\n\nMartin E: The Woman in the Body: A Cultural Analysis of Reproduction. Boston: Beacon Press; 1987.\n\nMerchant C: Feminism and the Philosophy of Nature. Environmental Ethics: The Big Questions. Keller DR, editor. Singapore: Wiley-Blackwell; 2010; pp. 291–300.\n\nNayar PK: Bhopal’s Ecological Gothic: Disaster, Precarity, and the Biopolitical Uncanny. London: Lexington Books; 2017.\n\nOldsey B: The Sense of an Ending. Ernest Hemingway’s A Farewell to Arms: New Edition. Bloom H, editor. NY: Infobase Publishing; 2009.\n\nOmbrophobia: Fear of Rain - Causes, Symptoms and Treatment. Healthtopia . Accessed 20 July 2021. Reference Source\n\nPiatti-Farnell L: Consuming Gothic: Food and Horror in Film. London: Palgrave Macmillan; 2017.\n\nPozorski AL: Modernism’s Ambivalent Beginnings: Infantry and Infanticide in A Farewell to Arms. The Hemingway Review 2004; 23(2): 75–98.\n\nPrescott M: ‘A farewell to Arms’: Memory and the Perpetual Now. College Literature 1990; 17(1): 41–52.\n\nDel Principe D : Introduction: The EcoGothic in the Long Nineteenth Century. Gothic Studies 2014; 16(1): 1–8.\n\nRabellino D, et al.: Altered Sense of Body Ownership and Agency in Posttraumatic Stress Disorder and Its Dissociative Subtype: A Rubber Hand Illusion Study. Front Hum Neurosci 2018; (12). Publisher Full Text\n\nRennie DA: The Real British Red Cross and Hemingway’s A Farewell to Arms. The Hemingway Review 2018; 37(2): 25–41.\n\nRotten: Oxford Learner’s Dictionaries 2020. Accessed 10 July 2021. Reference Source\n\nRotten: Macmillan Dictionary . Accessed 10 July 2021. Reference Source\n\nSilviya B, Immanuel SG, Raja.: Nature as Monster: Ecological Gothic and Biopolitical Uncanny in Amitav Ghosh’s The Hungry Tide. Bodhi International Journal of Research in Humanities, Arts and Science. 2019; 3(3): 25–28.\n\nSmith A, Hughes W: Ecogothic Manchester: Manchester UP; 2013.\n\nSullivan HW: Grotesque Purgatory: A Study of Cervantes’s Don Quixote, Part II Pennsylvania: Pennsylvania State UP; 1996.\n\nSymptoms: Post-traumatic Stress Disorder (PTSD): National Health Service. Accessed 12 July 2021. Reference Source\n\nThe Uncanny: Art Term, Art and Artist. TATE. Accessed 10 July 2021. Reference Source\n\nWilcox V: The Catastrophe at Caporetto. History Today. 24 October 2017. Accessed 20 July 2021. Reference Source\n\nWinter Precipitation and Forests: Was It Enough?: PennState College of Argricultural Sciences: Department of Ecosystem Science and Management 21 February 2017. Accessed 25 July 2021. Reference Source\n\nYoung P: Hemingway: A Reconsideration NY: Harcourt, Brace; 2nd ed.1966.\n\n\nFootnotes\n\n1 Drawing on TATE, the term “uncanny”—coined by the German psychiatrist Ernst Jentsch in The Psychology of the Uncanny in 1906—was referred to as “something new and unknown” that carries a negative implication. Sigmund Freud, however, repositioned the term in his essay The Uncanny (1919) as “the instance when something can be familiar and yet alien at the same time” (“Art Term: The Uncanny,” TATE). Uncanny, as Freud argued, was not just about the unknown but also “bringing out something that was hidden or repressed”; he called it “‘that class of frightening which leads back to what is known of old and long familiar’” (“Art Term: The Uncanny,” TATE).\n\n2 According to The Encyclopedia of Gothic, the grotesque is “a protean form that joins tragic, trivial, and serious elements in such a way that it can be monstrous, absurd, humorous, and contradictory” (Hughes and Punter and Smith 307). Similar to the Gothic that explores the combination of beings (dead and alive, human and nonhuman), the grotesque concerns the transgression of boundaries (for instance, between normality and abnormality). Both the Gothic and the grotesque are related to Julia Kristeva’s “abject” (“‘the in-between, the ambiguous, the composite’”), a concept dealing with “a disturbing identity that disrupts order and the given system” (qtd. in Hughes and Punter and Smith 309). The grotesque is also associated with the uncanny in the sense that they both deform what is familiar. The standard definition of the term “grotesque” is “‘[d] istorted, incongruous, or fantastically ugly in appearance or style; bizarre; outlandish’” (Sullivan 1996: 60). The term also carries the connotation of deformity and disability. After World War I, the prosthetic industry increased in a remarkable way which inspired the Dadaists to imagine a grotesque race of half-mechanical men (Dickerman 3-4). Alternatively, Ernst Friedrich, the founder of the Berlin Peace Museum and the author of War Against Peace (1924), used grotesque photographs of mutilated victims of World War I as a medium to promote peace.\n\n3 Ecological Gothic is an innovative research field led by Andrew Smith, William Hughes, Monika Elbert and others (Silviya and Immanuel 25). Notable publications regarding the research include Smith and Hughes’ edited collection EcoGothic (2013), a special issue of the journal Gothic Studies entitled “Introduction: The EcoGothic in the Long Nineteenth Century” (2014) by David Del Principe, and Dr. Pramod K. Nayar’s recent work, Bhopal’s Ecological Gothic (2017).\n\n4 Ford Maddox Ford, who wrote the first introduction to A Farewell to Arms, also claims, “Hemingway’s words strike you, each one, as if they were pebbles fetched fresh from a brook. They live and shine, each in its place” (qtd. in AFTA “Introduction” XV).\n\n5 I use the term “storied” to emphasize the agency and the narrative ability of nonhuman matter. In “Posthuman Environs,” Jeffrey Jerome Cohen draws on Serpil Oppermann and Serenella’s Iovino’s claim that “all matter is storied” and asks that “[m] ight ‘storied matter’ pulse in fundamental units—nouns, verbs, syllables, morphemes?”; “Might matter be inscribing us, rendering humans the record of a Disanthropoce that unfolds regardless of what epochs we declare?” (25). The term “storied” matter is thus a counter-narrative against the anthropocentric view that regards nonhuman matter as passive and lacking subjectivity.\n\n6 Traumatic experiences that involve the development of altered states of consciousness regarding “the sense of body ownership and agency” as well as “depersonalization (where parts of the body or the entire body itself is perceived as detached and out of control)” may lead to post traumatic stress disorder (PTSD) (Rabellino et al. “Abstract”).\n\n7 According to the National Health Service, common PTSD symptoms include, but are not limited to trauma re-experiencing (via nightmare, flashback, physical sensation), avoidance and emotional numbing, hyperarousal (anxious and difficulty to relax and concentrate), mental problems (depression, phobias), destructive behavior (drug or alcohol misuse), physical symptoms (headache, dizziness, stomachache, chest pain).\n\n8 Agency, as Stacy Alaimo emphasizes, is a performativity that “allows matter its due as an active participant in the world’s becoming, in its ongoing ‘intra-activity’” (2008, 248). “Agency,” more specifically, in Karen Baran’s words, “is not aligned with human intentionality or subjectivity”; it is a “‘doing’/ ‘being’ in its intra-activity”; it is “the enactment of interactive changes to particular practices through the dynamics of intra-activity” (2003, 827). Intra-action is a neologism created to emphasize “the mutual constitution of entangled agencies. That is, in contrast to the usual ‘interaction,’ which assumes that there are separate individual agencies that precede their interaction, the notion of intra-action recognizes that distinct agencies do not precede, but rather emerge through, their intra-action. It is important to note that the ‘distinct’ agencies are only distinct in a relational, not an absolute, sense, that is, agencies are only distinct in relation to their mutual entanglement; they don’t exist as individual elements” (Barad, 2007, 33).\n\n9 Historically, Colonel Francesco Pisani, who was ordered to Caporetto on 23 October 1917, also wrote in his official post-battle report that Caporetto was in a total mess, whereby the entire road was blocked by a mass of troops, trucks, artillery pieces as well as “the wounded […] who had been abandoned in the road” (Wilcox, 2017). Overall, the Italian army had forty thousand killed or wounded soldiers, followed by the two hundred and sixty-five thousands of prisoners and dispersed soldiers during the Caporetto retreat (Wilcox, 2017). Since then, the word “caporetto” functions as “a metaphoric expression for a contest where the defeated party is so thoroughly outplayed, outmaneuvered, and overpowered that it can do little more than dissolve into confusion and chaos” (Debeljak, 2015).\n\n10 According to Carlos Baker, A Farewell to Arms is organized connotatively around two poles: “the concepts of Home and Not-Home” (101). Baker links the Home-concept to “the mountains; with dry-cold weather; with peace and quiet; with love, dignity, health, happiness, and the good life; and with worship or at least the consciousness of God” (102). On the other hand, the Not-Home concept is connected to low-lying plains; with rain and fog; with obscenity, indignity, disease, suffering, nervousness, war and death; and with irreligion” (Baker 102).\n\n11 An “actant,” as Jane Bennet notes, is “a source of action that can be either human or nonhuman; it is that which has efficacy, can do things, has sufficient coherence to make a difference, produce effects, alter the course of events” (viii). Rain is thus a type of distributed agency that outstrips the rational, intentional agent of humanism.\n\n12 As Mary Prescott also points out, “Frederic’s sense of his lack of control and power in a world relentlessly indifferent to human suffering” is deeply linked to “the rain,” which is in association with the war, his trauma, and Catherine’s hemorrhages (45-6).\n\n13 As F. Scott Fitzgerald also wrote, “[w] hy not end the book with that wonderful paragraph on p. 241 [pp. 317-318 in print]. It is the most eloquent in the book and would end it rather gently and well” (qtd. in Oldsey 495).\n\n14 In his article, Kenneth Burke sees the raining scene as a reflection of Frederic’s inaudible cry. As he asks, “‘do you not find the very heavens are weeping on his behalf?’” (qtd. in Oldsey 499). To support his statement, he quotes Verlaine’s line “‘It rains in my heart as it rains on the town’” (qtd. in Oldsey 499)."
}
|
[
{
"id": "128703",
"date": "30 Mar 2022",
"name": "Scott Slovic",
"expertise": [
"Reviewer Expertise Ecocriticism",
"Interdisciplinary Environmental Humanities",
"American Literature",
"Comparative Literature",
"Environmental Communication"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is an exceptionally imaginative and convincing representation of the eco-gothic aspects of Hemingway’s famous novel. I am especially impressed by the way Lay Sion Ng draws parallels between the human and environmental facets of the narrative and between the violence of war and the unsettling aspects of normal human life, including the violence and mortal decay associated with eating and preparing food. The essay relies heavily on this strategy of establishing unexpected and jarring parallels, and this appears to be one of the goals of the author’s application of material ecocritical and eco-gothic methodologies and conceptual paradigms. But I find myself wondering whether establishing such parallels should be an end in itself or whether there might be additional, ulterior purposes for such a study.\nI see that one of the scholarly sources in this article, mentioned briefly in a footnote, is Pramod K. Nayar’s 2017 book Bhopal’s Ecological Gothic: Disaster, Precarity, and the Biopolitical Uncanny. Nayar’s study of the literature and art that have emerged following the 1984 industrial disaster in southern India also places heavy emphasis on surprising and unsettling connections and parallels. In “Conclusion: ‘Burial of an Unknown Child’ as Icon,” Nayar highlights the cognitive dissonance in this photograph by Raghu Rai, which the critic calls “gut wrenching.” The point of explaining this gut-wrenching application of gothic aesthetics to the representation of death and destruction caused by Union Carbide’s chemical spill in Bhopal is not merely to present an academic argument but to poignantly critique the social and environmental injustice associated with industrial activities. The exposure of children and other innocent people and organisms to deadly chemicals should be prevented—this is the moral core of Nayar’s work. At the outset of his book, in the Introduction,” he writes that “Literary-cultural studies embodying the ‘ethical turn’ have addressed human rights, democracy, torture and environmentalism in the past few years. Such studies enable us to see the rhetorical and discursive strategies employed in fields like Literature, films or comics that generate cultural models of victimhood, trauma, personhood, the Human, civilization or development” (xiv). I find that Professor Ng’s study does a very good job of illuminating the rhetorical and discursive strategies that Hemingway has intentionally or intuitively layered into his novel, but the ethical dimension of Hemingway’s eco-gothic “counter-narrative”—the anti-war critique—seems somewhat muted in this study and could perhaps be explained more directly and forcefully.\nAnother key aspect of recent ecocritical work that connects the human body to the natural landscape—and particularly to the vulnerability and mortality of nature—is the effort to overcome the myth of human exceptionalism. In my own analysis of Wilfred Owen’s World War I poem “Dulce Et Decorum Est” in the Routledge Handbook of Religion and Ecology (2017), I argued that Owen’s graphic portrayal of the brutality of war and the physical suffering it entails is not merely a critique of war itself but also a puncturing of the “old lie” that “humans often tell themselves. Humans are not presented here as being exceptional, or separate, from the natural order of things, from living and dying. The vivid portrayal of injured and dying human beings in this poem demonstrates that we are mortal, that we are animals” (360). More recently, in Ecocollapse Fiction and Cultures of Human Extinction (2021), Sarah E. McFarland writes, “At issue … is how to reject the impulse of human exceptionalism that pervades Western thought and much speculative fiction by exploring those few texts that engage with the potential of human species extinction…. Becoming attuned to the inseparability of human and nonhuman worlds—what Donna Haraway calls ‘entanglement’—thus insubstantiates the exceptionalism experienced as part of the Western human tradition” (3). It seems to me that perhaps Professor Ng could do a little bit more in this study of Hemingway to place this discussion in the context of other contemporary ecocritical projects that break down the separation between the human and the nonhuman in order to critique on a fundamental psychological and philosophical level the idea of human exceptionalism. Further, and this goes back to Nayar’s work on Bhopal and his broadening of this project in the 2019 volume Ecoprecarity: Vulnerable Lives in Literature and Culture, the point of representing the vulnerability of human bodies and minds and human communities is to reinforce the precariousness of our own lives and the planet we depend upon for our existence.\nI find Professor Ng’s study to be well written and thoroughly researched. The article is very effective in presenting important narrative details in Hemingway’s novel and in demonstrating how these details—especially the breaking and rotting of human bodies and the natural environment—contribute to a deeply moving and unsettling eco-gothic aesthetic in A Farewell to Arms. It might be helpful, though, to explain more fully the ethical urgency of such an anti-war and anti-human-exceptionalist perspective, as expressed in Hemingway’s work and in a contemporary analysis of such a novel. Linking this article to Nayar’s work on Bhopal literature and culture and to McFarland’s review of “ecocollapse fiction” might be helpful.\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "116255",
"date": "04 Aug 2022",
"name": "Hideo Yanagisawa",
"expertise": [
"Reviewer Expertise Ernest Hemingway",
"American literature",
"English-language",
"Representational 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\nThis paper is an attempt to reread Hemingway's A Farewell to Arms as a counter-narrative to anthropocentrism, using \"eco-gothic,\" the latest research method in environmental literary criticism. The originality of the attempt itself and its challenging attitude should be highly evaluated. However, I would like to point out two problems.\nIn the chapter \"The rotten food\", the author focuses on the food shortage during the war and points out the contradiction of civilized society that makes even the very primitive act of \"eating\" unfeasible. On the other hand, I find it contradictory that the author points out \"war = barbarism\" and \"civilization = healthy food control\" while pointing out in Frederic’s linking of fresh food to civilization from Chapter 34. In other words, the author should consider the fact that war itself is inseparably linked to civilization.\n\nIn the chapter \"Gothicized Rain,\" the author interprets Frederick's romanticization of rain to mean the restoration of people's romantic view of nature destroyed by war, and that this is Frederick's criticism of the anthropocentrism symbolized by war. However, the contradiction that the romantic view of nature itself is anthropocentric needs to be resolved.\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?\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/10-1287
|
https://f1000research.com/articles/11-1367/v1
|
23 Nov 22
|
{
"type": "Research Article",
"title": "Prevalence of anemia and its associated factors among women of reproductive age group attending Gaur Provincial Hospital: A cross-sectional study",
"authors": [
"Prem Shankar Chaurasiya",
"Shekhar Gurung",
"Saurab Karki",
"Krishna Chandra Mandal",
"Binod Mehta",
"Dipesh Kumar Rohita",
"Babli Mishra",
"Gopal Kumar Yadav",
"Surakshya Baral",
"Suhail Sapkota",
"Prem Shankar Chaurasiya",
"Shekhar Gurung",
"Krishna Chandra Mandal",
"Binod Mehta",
"Dipesh Kumar Rohita",
"Babli Mishra",
"Gopal Kumar Yadav",
"Surakshya Baral",
"Suhail Sapkota"
],
"abstract": "Background: Anemia is a principal public health concern. Worldwide one-third of women of reproductive age are affected. A 2016 survey showed that 41% of women in Nepal had anemia with the highest prevalence in Pradesh two. A complex interaction among socio-political, biological, and ecological elements determines anemia. Assessing the factors would help in minimizing anemia and its consequences. The study aimed to determine the prevalence of anemia in the reproductive age group and the factors affecting anemia.\n\nMethods: A hospital-based cross-sectional study was conducted among women of the reproductive age group (15–45) from 15th April to 15th June 2022 after ethical clearance was obtained from the Nepal health research council (Ref. 2737/2022). Regarding data collection, 375 women participants were selected via a simple random sampling technique. Participants underwent an interview after informed written consent followed by blood sample collection. Through a semi-structured questionnaire, the data was obtained. Then data entry and its analysis were performed via Microsoft Excel 2019 and Statistical Package for Social Sciences version 22.0.\n\nResults: The study showed that 229 (61.3%) females of the reproductive age group had anemia. Inadequate nutrition (OR 3.0, 1.9–5.0), breastfeeding (OR 7.3, 4.5–11.9), and rural place of residence (OR 4.2, 2.5–7.0) were significantly associated with anemia, with a corresponding odds ratio at 95% confidence each.\n\nConclusions: The prevalence of anemia was higher among women of the reproductive age group compared to provincial and national prevalence. The interventions should be focused on breastfeeding, nutrition, and rural women to combat anemia.",
"keywords": [
"anemia",
"breastfeeding",
"economic",
"prevalence",
"nutrition",
"regression",
"reproductive age",
"survey"
],
"content": "Introduction\n\nAnemia is a clinical condition with low hemoglobin levels in the blood, and hence, the oxygen-carrying capacity is compromised. With decreased iron levels being the most common in the developing world, iron deficiency anemia and anemia denote the same thing in this part of the world.1 A wide variety of factors are responsible in developing countries and hence dealing with this issue is a public health summons around the world.2 As per WHO and World Bank, the third paramount basis for disability-adjusted life years (DALY) loss among women of reproductive age accounts to iron deficiency anemia.2 Owing to excess loss of blood during menstrual flow as well as the fetus extracting more iron from the maternal pool, these females are most vulnerable to suffering.3 Further, in the developing world, the challenges in tackling the problems associated with iron deficiency anemia include and are not limited to a greater burden of the problem, more reliance on plant-based diets, concerns regarding cost and accessibility to iron-rich foods, and absence of extra supplementation or food fortification.2 Unable to address this issue, anemia can lead to multiple complications like dementia, fatigue, and impaired quality of life, along with adverse events during pregnancy including decreased productivity and physical abilities and even maternal deaths.4\n\nAnemia is a serious global public health obstacle. It is estimated that one in three women of the reproductive age group (WRA) are anemic worldwide. It is associated with a greater risk in terms of maternal as well as perinatal morbidity and mortality and thus a greater economic burden to society. A survey demonstrates 41% anemia prevalence among WRA in Nepal, and province two has the highest anemia prevalence at 58%. A complex interaction among socio-political, biological, and ecological elements ultimately regulates anemia and its prevalence among women that incorporates rural places of residency, younger age, inadequate nutrition, pregnancy, repeated childbearing, breastfeeding, and lack of hormonal contraceptives.5\n\nThe prevalence of anemia among the WRA group in our belt is significantly under-reported. Adequate reporting helps understand the true burden of anemia. It will help implement policies more effectively. The study also aimed to estimate anemia prevalence among the WRA group and to know the effects of associated factors among them.\n\n\nMethods\n\nThe ethical approval was obtained from Nepal Health Research Council (Reference no. 2737/2022) on 31st March 2022 after submitting the approval letter from the hospital. Informed verbal and written consent was taken before the study and confidentiality was maintained. In the case of a minor, we received assent from them as well.\n\nThis was a hospital-based cross-sectional study that was conducted in the Rautahat district of Nepal served by Gaur provincial hospital. The study was done with a target population (women of reproductive age 15–45 age group) of 375, attending regular out-patient department (OPD) visits at Gaur hospital. The hospital is located at the district headquarters of Rautahat, Nepal, in southern bordering India. It is a primary referral center for all health posts, primary health care (PHC), and local clinics located in the Rautahat district. The Ministry of Health and Population of Nepal has categorized it as a 75 bedded hospital with more than 80% occupancy. Now it is run under the government of province no 2.\n\nThe study followed the Strengthening the Reporting Observational Studies in Epidemiology (STROBE) guidelines.27\n\nAll women of the reproductive age group (15–45) visiting OPD at Gaur Hospital during the period of 15th April to 15th June 2022, were included in the study. The women who were seriously ill at the time of study and those taking iron supplements were, however, excluded from the study.\n\nAccording to the study by Sunuwar et al., the prevalence of anemia was 58% among WRA of Madhesh province.5 Considering the anemia prevalence of 58 % at a 95% confidence interval with a 5% allowable error, the calculated sample size was 375. The detailed elaboration is as follows:\n\nn = required sample size\n\nz = 1.96 at alpha 5% level of significance\n\np = prevalence = 0.58; q (compliment of prevalence) = 0.42\n\nE = allowable error, 5%\n\nThen women for this study were chosen through simple random sampling. A thorough physical examination was performed. Data regarding residency, pregnancy status, nutritional status, parity, breastfeeding status, nutrition, contraception, and income were collected through a semi-structured questionnaire. The questionnaires were developed after a full review of literature about anemia and the factor affecting it in women. Hemoglobin level was recorded from individual laboratory test reports.\n\nEach day, after proper consent and introduction, participants were asked about their name, age, address, marital status, religion, and nutritional status (adequate ≥ 1600 Kcal/day and inadequate < 1600 Kcal/day in single-day dietary recall of the preceding day), breastfeeding (not within 3 months of postpartum and ongoing breastfeeding for past 4 weeks was categorized as “yes” group), parity, contraception, residence (urban and rural), income per month per family (low < 20,000 NRs (Nepali Rupees), medium 20,000–40,000 NRs and high > 40,000 NRs) and hemoglobin level. A hemoglobin level of fewer than 12 g/dl was considered anemia, which was further graded into mild anemia (10–11.9 g/dl), moderate anemia (7–9.9 g/dl), and severe anemia (<7 g/dl) as per the recommendations of the World Health Organization.1\n\nAfter the interview, the individual participant was sent to the laboratory department. Approximately 1 ml of venous blood from each participant was taken from the arm via a sterile hypodermic syringe in a specific sterile EDTA tube. Samples were processed into an automated analyzer. The analyzer display showed the hemoglobin level, and the results were noted down.\n\nThe data was entered in to an Excel sheet (Microsoft Excel v16.0, WA, USA) and was analyzed using Statistical Packages for Social Sciences (SPSS), IBM SPSS® v21 (IBM, Armonk, New York).8 Frequency, percentage, mean, standard deviations, and/or interquartile range were used to express descriptive statistics as applicable. We described the categorical data in terms of frequency and proportions and continuous data in terms of mean ± standard deviation (SD) and interquartile range. Differences in participants’ characteristics were explored using the chi-squared test. The binary logistic regression was used to identify the association of anemia with the background characteristics of WRA. For binary logistic regression analysis, odds ratios (OR) and 95% confidence intervals (CI) were calculated.\n\n\nResults\n\nA total of 375 females of the reproductive age group participated in our study without a null response.27 Table 1 shows the mean age of participants was found to have 24.5±6.56 years. Most women belonged to the 20 to 34 age group (258 (68.8%)), followed by the less than 20 age group (78 (20.8%)). Most of the women were already married (94.9%) at the time of the interview.\n\n1 Single: divorced, separated, widowed.\n\n2 Income per month per family: Low<20,000 NRs (Nepalese Rupees); Middle: 20,000–40,000 NRs and High >40,000 NRs.\n\nMore than half of the women (207 (55%)) completed the primary level of education, followed by 103 (27.5%) who had informal education. The nutritional assessment revealed that two-thirds of the women (251 (66.9%)) had inadequate nutrition intake. Similarly, 192 (51.2%) women were engaged in breastfeeding at the time of the interview. Many women (173 (46.1%)) had one child whereas, 116 women had two children. More than half (214 (57.1%)) of the women were contraception users. Regarding residence, out of 375, 286 (84.3%) women lived in urban areas. Regarding monthly family income, most of the families belong to the low 183 (48.8%) and middle-income 173 (46.1%) categories.\n\nThe study showed that 231 (61.6%) women of the reproductive age group had anemia with an average hemoglobin level of 11.3 ± 1.8 g/dl. Among the 231 women, 148 (64.1%) belonged to a mild type of anemia, followed by moderate and severe anemia in 34.2% (79) and 1.7%4 women respectively [Table 2].\n\n1 Out of 231 participants.\n\nThe factors linked to anemia among females were analyzed using the binary regression model. Inadequate nutritional status was significantly associated with anemia (OR 3.0, 95% CI: 1.9-5.0). Similarly, breastfeeding women were significantly associated with anemia as compared to those currently not breastfeeding (OR 7.3, 95% CI: 4.5-11.9). Compared to urban dwellers, women living in the rural region were found to be statistically associated with anemia significantly (OR 4.2, 95% CI: 2.5-7.0) [Table 3].\n\n\nDiscussion\n\nOur study shows the overall prevalence of anemia among women under the reproductive age group was 231 (61.6%) and found it comparable to the prevalence of anemia in Province number two (58%). However, the figure is much higher if we compare it with the national data of Nepal in 2016 (41%) and the world. As per the reports of a study in East Africa, 34.85 (95% CI: 34.56–35.14) was the anemia prevalence in women of reproductive age.6 There is a complex interplay between various factors such as nutrition, infectious diseases, etc. which creates challenges and obstacles to addressing the population indicators leading to anemia.7 The study revealed that with poor nutritional status, the likelihood of having anemia was three times higher than those with good nutritional status. Likewise, the odds of anemia are two times higher if we compare data in province two of Nepal overall. This can partly be explained by the fundamental role of nutrition including micronutrients, iron in red blood cell (RBC) formation, and survival. The most frequently occurring anemia owes to iron deficiency. For a woman, iron loss from one’s body happens mostly either by the sloughing of cells from duodenal enterocytes or through blood loss following menstruation and postpartum, which results in deprivation of the iron from the circulatory pool. This iron is usually available for usage in different target organs and hence, it leads to the condition of functional iron insufficiency in the body.8 Although anemia can affect persons of any age group, the reproductive age group are more vulnerable due to busy timetables, inconsistent mealtimes, and working with longer schedules.9,10 It is a concern among the reproductive age-group females that anemia is supposed to have a massive impact on these groups of people like; loss of efficiency owing to decline in work capacity, impairment of perception and cognition, increased vulnerability towards infections due to its consequences on immunity, miscarriage or stillbirths, and maternal deaths.11 The consequences like having a preterm or low birth weight neonates, dry iron stores among new-borns, and overall increased infant/child mortality are an outcome among women suffering from anemia during their reproductive age.12 Every year, anemia leads to an excess of 115,000 maternal as well as 591,000 perinatal deaths around the globe.13 Prior studies had demonstrated that females from province number two had an increased likelihood to be arriving from a lower socioeconomic position with a lesser variety of the foods they consumed. The study demonstrates breastfeeding women are more than seven times more susceptible (OR = 7.3) to anemia as compared to non-breastfeeding. A study done in Myanmar, however, revealed there was no association between anemia with breastfeeding status.14 As the mothers are lactating, they are more likely to be anemic as their iron stores would have significantly depleted during breastfeeding in addition to the blood loss that had occurred at delivery.15 Additionally, the urban-rural residence also has a significant effect on the prevalence of this condition. In our study among women residing in rural places, they had 4.2 times more risk of having anemia. These women who live in rural sites have better access to nutrition along with health facilities. One study done in Ethiopia in 2016 demonstrates that the odds of suffering from anemia were significantly greater in women with low household wealth cohorts and those who lived in rural areas in comparison to females from the middle and higher household wealth cohorts who were from the urban area of residence (AOR = 1.37, 95% CI 1.14–1.65, P < 0.001).16 Similar studies have demonstrated that the status of anemia is greater among rural females (66%). Likewise, the odds of suffering from anemia are greater along with decreasing financial status and conditions whatever their address was, but it has been demonstrated that the odds are greater if a poor woman belongs to urban areas as compared to similar ones in rural places after covariates have been adjusted.17 According to a study conducted in Nepal, women living in rural parts of the country had 68.1% anemia as compared to only 31.9% among those women who live in urban areas.18 Although our study does not reveal an association with educational status, low educational standards do have a role in the higher prevalence of iron deficit.19 In addition, family income plays a significant role in anemia. The prevalent cases of anemia among women in their reproductive period are highest in low- and middle-income nations.20,21 Our study failed to show any association. The study reveals no correlation between hormonal contraception use and anemia. However, one study done in sub-Saharan countries elucidated that oral contraceptive pills (OCP) usage, prominently decreases the odds of having anemia by 38%.22 Similarly, another study’s result demonstrated the likelihood of anemia was decreased by around 40% as opposed to those who practiced the barrier method of contraception (OR=0.6,95% CI: 0.45 to 1.12).23 While mentioning parity, multiparous females were found to have reduced serum ferritin levels (and hence low hemoglobin) as compared to the controls, indicating that multiple pregnancies do play a role in the context of the iron content inside the body.24 Likewise, our study also had similar findings that the prevalence of anemia and iron deficiency was more among multiparous females as compared to nulliparous females.25 Women with high parity pregnancies had an increased risk of anemia than those women who had had a lesser number of pregnancies (risk ratio, RR = 2.92; 95% CI 2.02, 4.59). Also, the risk of anemia during pregnancy increased in a dose-response manner over multiple parity categories.26\n\nTo reduce the poor nutritional impact on anemia, The Ministry of Health and Population of Nepal has been delivering iron-folic acid (IFA) supplements to pregnant female cohorts and also to post-partum females since 1998 to reduce maternal anemia.\n\nThe sample was taken from the study population visiting Gaur Hospital. Therefore, its findings cannot be generalized to other hospitals/places. As this is a longitudinal study, different anemia-associated factors can’t establish causality. These were the limiting factors encountered during the study.\n\n\nConclusion\n\nThe prevalence of anemia was higher among women of the reproductive age group than in other studies done in a similar setting. Most of the women did not have knowledge and access to proper nutrition. Similarly, there should be the provision for additional nutrients and vitamins/minerals supplementation in breastfeeding women to counteract anemia. Special dietary awareness and interventions should be prioritized for multiparous women and women of rural areas to decelerate anemia and/or its possible consequences on women of reproductive potential. This fact might guide policy makers to target the above factors to decrease the prevalence of anemia and raise overall health.\n\n\nConsent\n\nWritten informed consent from all the participants was taken.",
"appendix": "Data availability\n\nFigshare: Prevalence of anemia and its associated factors among women of reproductive age group attending at Gaur Provincial Hospital: A cross-sectional study. https://doi.org/10.6084/m9.figshare.20378268. 27\n\nThis project contains the following underlying data:\n\n• Data anemia Rautahat v3wra.xlsx (raw data for the 375 individuals included in final analysis)\n\nFigshare: Prevalence of anemia and its associated factors among women of reproductive age group attending Gaur Provincial Hospital: A cross-sectional study. https://doi.org/10.6084/m9.figshare.20378268. 27\n\nThe project contains the following extended data:\n\n• Questionnaire updated.docx (tool used for data collection)\n\nFigshare: STROBE checklist for ‘Prevalence of anemia and its associated factors among women of reproductive age group attending Gaur Provincial Hospital: A cross-sectional study’. https://doi.org/10.6084/m9.figshare.20378268. 27\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors would like to thank Mr. Ram Prabesh, a lab technician at Gaur hospital and Gaur provincial hospital, Gaur following his permission for its support. They express their sincere gratitude to all participants who gave consent to conduct research.\n\n\nReferences\n\nTolentino K, Friedman JF: An update on anemia in less developed countries. Am. J. Trop. Med. Hyg. 2007; 77(1): 44–51. PubMed Abstract | Publisher Full Text\n\nYip R, Ramakrishnan U: Experiences and challenges in developing countries. J. Nutr. 2002; 132(4 SUPPL): 827S–830S. Publisher Full Text\n\nLevy JE, Jin O, Fujiwara Y, et al.: Transferrin receptor is necessary for development of erythrocytes and the nervous system. Nat. Genet. 1999 Apr [cited 2022 Oct 22]; 21(4): 396–9. PubMed Abstract | Publisher Full Text\n\nPrasanth R: Prevalence of Anemia in both Developing and Developed Countries around the World. World J. Anemia. 2017 Jun; 1(2): 40–43. Publisher Full Text\n\nSunuwar DR, Singh DR, Adhikari B, et al.: Factors affecting anaemia among women of reproductive age in Nepal: a multilevel and spatial analysis. BMJ Open. 2021 Mar 1 [cited 2022 Jul 11]; 11(3): e041982.Reference Source\n\nTeshale AB, Tesema GA, Worku MG, et al.: Anemia and its associated factors among women of reproductive age in eastern Africa: A multilevel mixed-effects generalized linear model. PLoS One. 2020 Sep 1 [cited 2022 Jul 11]; 15(9): e0238957. PubMed Abstract | Publisher Full Text\n\nBalarajan Y, Ramakrishnan U, Özaltin E, et al.: Anaemia in low-income and middle-income countries. Lancet. 2011 [cited 2022 Oct 22]; 378(9809): 2123–2135. Publisher Full Text Reference Source\n\nNegi PC, Dev M, Paul P, et al.: Prevalence, risk factors, and significance of iron deficiency and anemia in nonischemic heart failure patients with reduced ejection fraction from a Himachal Pradesh heart failure registry. Indian Heart J. 2018 Dec 1 [cited 2022 Jul 11]; 70(Suppl 3): S182–S188. Publisher Full Text Reference Source\n\nVibhute N, Shah U, Belgaumi U, et al.: Prevalence and awareness of nutritional anemia among female medical students in Karad, Maharashtra, India: A cross-sectional study. J. Family Med. Prim. Care. 2019 [cited 2022 Jul 11]; 8(7): 2369–2372. PubMed Abstract | Publisher Full Text\n\nRetnakumar C, Chacko M, Ramakrishnan D, et al.: Prevalence of anemia and its association with dietary pattern among elderly population of urban slums in Kochi. J. Family Med. Prim. Care. 2020 [cited 2022 Jul 11]; 9(3): 1533–1537. PubMed Abstract | Publisher Full Text\n\nTeshale AB, Tesema GA, Worku MG, et al.: Anemia and its associated factors among women of reproductive age in eastern Africa: A multilevel mixed-effects generalized linear model. PLoS One. 2020 Sep 1 [cited 2022 Jul 11]; 15(9): e0238957. PubMed Abstract | Publisher Full Text\n\nMawani M, Aziz AS: Iron Deficiency Anemia among Women of Reproductive Age, an Important Public Health Problem: Situation Analysis. Reprod. Syst. Sex. Disord. 2016; 5(3). Publisher Full Text\n\nTirore LL, Mulugeta A, Belachew AB, et al.: Factors associated with anaemia among women of reproductive age in Ethiopia: Multilevel ordinal logistic regression analysis. Matern. Child Nutr. 2021 Jan 1 [cited 2022 Jul11]; 17(1): e13063. PubMed Abstract | Publisher Full Text\n\nZhao A, Zhang Y, Li B, et al.: Prevalence of Anemia and Its Risk Factors Among Lactating Mothers in Myanmar. Am. J. Trop. Med. Hyg. 2014 May 5 [cited 2022 Jul 6]; 90(5): 963–967. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLakew Y, Biadgilign S, Haile D: Anaemia prevalence and associated factors among lactating mothers in Ethiopia: evidence from the 2005 and 2011 demographic and health surveys. BMJ Open. 2015 [cited 2022 Jul 8]; 5(4): e006001. Publisher Full Text | Free Full Text\n\nAbate TW, Getahun B, Birhan MM, et al.: The urban–rural differential in the association between household wealth index and anemia among women in reproductive age in Ethiopia, 2016. BMC Womens Health. 2021 Dec 1[cited2022Jul6]; 21(1): 311–318. PubMed Abstract | Publisher Full Text\n\nAwoleye AF, Alawode OA, Chima V, et al.: Rural-urban differentials in the relationship between household wealth index and maternal anaemia status in Nigeria.2022 [cited 2022 Jul 11]. Publisher Full Text\n\nAcharya D, Adhikari R, Simkhada P: Prevalence and Determinants of Anaemia among Women aged 15-49 in Nepal: A Trend Analysis from Nepal Demographic and Health Surveys from 2006 to 2016. Asian J. Popul. Sci. 2022 Mar 3; 32–48. Publisher Full Text\n\nYadav UK, Ghimire P, Amatya A, et al.: Factors Associated with Anemia among Pregnant Women of Underprivileged Ethnic Groups Attending Antenatal Care at Provincial Level Hospital of Province 2, Nepal. Anemia. 2021 [cited 2022 Jul 11]; 2021: 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStevens GA, Finucane MM, De-Regil LM, et al.: Global, regional, and national trends in haemoglobin concentration and prevalence of total and severe anaemia in children and pregnant and non-pregnant women for 1995-2011: a systematic analysis of population-representative data. Lancet Glob. Health. 2013 Sep [cited 2022 Jul 11]; 1(1): e16–e25. Publisher Full Text Reference Source\n\nDaru J, Zamora J, Fernández-Félix BM, et al.: Risk of maternal mortality in women with severe anaemia during pregnancy and post partum: a multilevel analysis. Lancet Glob. Health. 2018 May 1 [cited 2022 Jul 11]; 6(5): e548–e554. PubMed Abstract | Publisher Full Text\n\nGebremedhin S, Asefa A: Association between type of contraceptive use and haemoglobin status among women of reproductive age in 24 sub-Saharan Africa countries. BMJ Sex Reprod Health. 2018 Jan 1 [cited 2022 Jul 11]; 45(1): 54–60.Reference Source\n\nTeshome AA, Berra WG, Huryi AF: Modern Contraceptive Methods Predict Hemoglobin Levels Among Women of Childbearing Age from DHS 2016. Open Access J. Contracept. 2022 Jan [cited 2022 Jul 11]; 13: 1–8. PubMed Abstract | Publisher Full Text\n\nFarooq A, Rauf S, Hassan U, et al.: IMPACT OF MULTIPARITY ON IRON CONTENT IN MULTIPAROUS WOMEN. J. Ayub Med. Coll. Abbottabad. 2011; 23.Reference Source\n\nImai K: Parity-based assessment of anemia and iron deficiency in pregnant women. Taiwan. J. Obstet. Gynecol. 2020 Nov 1; 59(6): 838–841.\n\nAl-Farsi YM, Brooks DR, Werler MM, et al.: Effect of high parity on occurrence of anemia in pregnancy: A cohort study. BMC Pregnancy Childbirth. 2011 Jan 20 [cited 2022 Jul 11]; 11(1): 1–7. PubMed Abstract | Publisher Full Text\n\nChaurasiya PS, Gurung S, Karki S, et al.:Data anemia Rautahat v3wra.xlsx (Version 4). figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "240664",
"date": "05 Mar 2024",
"name": "Hugo G Quezada-Pinedo",
"expertise": [
"Reviewer Expertise fetal programing",
"anemia",
"iron deficiency"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review the study: “Prevalence of anemia and its associated factors among women of reproductive age group attending Gaur Provincial Hospital: A cross-sectional stud” The topic is a very interesting, given that anemia stands as a substantial global public health concern, impacting over 2 billion individuals worldwide. As current interventions failed to reduce this burden, there is an imperative for additional studies. These studies are essential to identify local factors contributing to anemia, allowing interventions to be tailored more effectively and addressing the disease burden at a local level.\nMajor comments:\nMethods The main limitation of the study is the absence of critical variables such as inflammation, (specially for hospital settings), comorbidities and BMI. Thus, I think the models did not adequately capture the complexity of anemia among women of reproductive age. For example, the model showed contradictory evidence between parity and breastfeeding and did not find evidence with important variables such as income, age and education.\n\nMinor comments: Methods Could the authors provide more details about the rationality / related mechanisms to include marital status, breastfeeding, contraception as potential explanatory variables?\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?\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": "240661",
"date": "24 Apr 2024",
"name": "Armando García-Guerra",
"expertise": [
"Reviewer Expertise Nutritional epidemiology",
"maternal and child nutrition",
"evaluation of social programs."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comment: This article presents an estimate of the prevalence of anemia and some associated factors in women of reproductive age. Due to the high prevalence of anemia reported in the region, it is of interest to know which characteristics are locally associated with anemia in this population. Comments or questions are invited in each section below to improve the presentation of this article. Introduction -In this section you could include the latest information on hemoglobin measurement. -In addition, you could include in the objective the scenario of the study and mention what kind of factors were measured, i.e. are they individual factors, residential structures, etc., this in order to know what the new contribution of this study is to the evidence on the subject. Methods The following information must be given or included: -Describe the inclusion criteria of the study population, e.g. whether pregnant women were excluded or not. -Describe the size of the population from which the study sample was drawn. -Describe the type of person who collected the information, took the blood sample and measured the hemoglobin concentration. -Indicate whether any adjustments were made to the hemoglobin concentration, e.g. for smoking, local altitude. Read the latest WHO publication on hemoglobin measurement. Results The main comment is that they present the estimates through a binary regression model. They did not run a multiple logistic regression model, which provides these associated variables and controls for other variables. Discussion -In general, in this section you need a little more order in the ideas and for the paragraphs to be shorter. -Interpret the findings, considering the population and setting of the study. -Include the limitations and strengths of the study. -Indicate why information on the delivery and consumption of iron and folic acid supplements was not collected or measured, as this is a delivery practice that has been in place in the region for many years. -Revise the paragraph before the conclusion section because it states that this is a longitudinal study, which it is not. Conclussion Once the pertinent adjustments have been made, they could rethink the conclusions and assess which of them can be granted based on the findings.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1367
|
https://f1000research.com/articles/11-1364/v1
|
22 Nov 22
|
{
"type": "Software Tool Article",
"title": "Chatbot to predict need of a stent in cardiac treatment",
"authors": [
"Krishna Chythanya Nagaraju",
"Narayana Murthy Jandhyala",
"Harika Konda",
"Fazilath Maheen",
"Reetica Rapolu",
"Alekhya Mudhunuri",
"Chaitanya Priya G",
"Narayana Murthy Jandhyala",
"Harika Konda",
"Fazilath Maheen",
"Reetica Rapolu",
"Alekhya Mudhunuri",
"Chaitanya Priya G"
],
"abstract": "Background: Every year, across the globe about 1,800,000 people suffers with heart attack and India has the highest rate in the world with almost 25% families having a member who suffered heart attack at least once. One of the solutions to reduce the heart attacks in patients is placing a stent. Once the blockage is identified, it is suggested that a stent with the required size is inserted into the coronary artery. The invasive device and its associated cost automatically leads to a dilemma for both the doctors as well as patients. The young practitioners of cardiology may face a dilemma sometimes whether to go for stent or not. The patients undergoing treatment for cardiac issues would be in a two state mind whether to go for stent or not. The above two dilemmas can be mitigated and confidence of both doctors and patients in decision making can be enhanced with the help of a technology driven application that suggests requirement of stent with a degree of confidence. Methods: The chatbot in our project shall help in taking textual and image based inputs of the information of the heart and coronary artery of a patient and predicts the requirement of stent being placed. The real time data of 50 patients was used in training the model with a data set consisting of 349 scanned images of angiogram. The model developed consists of sequential CNN model with 5 convolutional 2D layers and 5 Maxpool layers. Results: The model could achieve an accuracy of 81%. Conclusions: The authors have successfully developed and tested a machine learning based chatbot model to predict the need of a stent in cardiac treatment.",
"keywords": [
"Heart attack",
"Angiogram",
"Stent",
"Machine Learning",
"Chatbot",
"CNN",
"Treatment",
"Doctor",
"Patient."
],
"content": "Introduction\n\nCardiovascular illnesses are the principal cause of fatality worldwide, with 17.9 million people dying each year. Low- and middle-income nations account for over 75% of all deaths related to cardiovascular disease. Every year, roughly 80,000 people suffer a heart attack at least once, with India having the highest rate in the world. Patients with obstructive arteries who have chest pain, tightness, or shortness of breath are at a higher risk of having a heart attack. One way the causality rate is handled is by administering stents. Stents of various sizes are advised to be positioned based on the size of the blockage inside the artery to treat them. The foremost important thing is to decide whether a stent is required or not. This decision is done by the cardiologist medical practitioner based entirely on observation and experience, which also includes the use of Human Intelligence. As a result, research into the possibilities of developing machine learning model-based fully agent to support human intelligence is considered in this work.\n\nA Chatbot is a computer program that can converse with humans in natural language. Chatbots can provide accurate and efficient info depending entirely on the user’s requirements. Chatbots are used in a variety of domains, including Customer Support, Virtual Assistance, Online Trainings, and Online Reservations, as well as for routine chats. The authors here proposed a Chatbot that interacts with users and provide them with a realistic experience of conversing with a medical expert. There are already a few Medical Chatbots; however, they don’t provide users with services such as determining heart stent requirement; instead, they link them to a medical question and answer forum and present them with similar solutions to their symptoms that medical doctors may have previously answered.\n\n\nLiterature review\n\nA study of different research works was done to elevate the methodologies earlier researchers followed and the success they obtained. The study was done in a progressive was on different aspects of usage of chatbot as general applications, applications specific to health care domain, works that could process only text in chatbot followed by the ones which can process text and images as well. The important observations made in the literature survey are given below with respect to each work considered.\n\nIn work,1 the real time data of 16,733 patients have been provided by the C.M.O. Centre. Different techniques like Deep learning algorithms, machine learning algorithms using Spark which provides fault tolerance features, implicit data parallelism and data storage have been used. The Spark.ML library also provides all the data-preparation functionalities and the machine learning algorithms to train the collected training data. The chat-bot has been designed to help patients in choosing the most proper disease prevention pathway by asking for different information. The data flows, from and to the patient, through the chat-bot interactions. The result shows that it has 86.78% accuracy. The shortcoming is that it is a text-based application and excludes spoken or visual input. Even in the present work author’s have not included voice based input and left it as a scope of extension to present work.\n\nIn work,2 the Reddit dataset has been used by the researchers to make a database for the chatbot. NLP techniques and deep learning methods like Convolution Neural Networks, deep learning library TensorFlow, Neural machine translation (NMT), Bidirectional Recurrent neural network (BRNN) and attention mechanisms have been used for the implementation. The Chatbot takes in the source sentence, understands and analyses it, and produces an output statement mapped to the particular problem or query of the user. With the inclusion of BRNN with Attention model it not only helps in short but also in longer tokens. The weakness of this research is that the chatbot knowledge is based on open domain and it requires further improvement for it to become domain specific (like healthcare, education, etc.).\n\nThe researchers of work3 used Radar profile images were used by the researchers as the dataset. The researchers used techniques like CNN-Based Image Recognition Using Deep Convolutional Generative Adversarial Networks, GAN framework, and models of ImageNet Champion, Image recognition, Radar profile recognition. Researchers designed a fresh model structure to generate examples which are tough to collect based on DCGAN’s high scalability and outstanding sample making competence. The research built a recognition framework based on CNN and matched enough sample generation to strengthen the training recognition model. Finally this could improve the accuracy of classification.\n\nIn research,4 real time data records of patients have been used by the researchers. Artificial intelligence, Machine learning algorithms like the NLTK library has been used for implementation. The research was used for thematic analysis on the qualitative data to identify the common trends and patterns. A mixed-method approach was used that helped in generating a multi-layered issue. The drawback of this research was that the entire sentences of the query inputs from the user are converted into lowercase which resulted in decline in accuracy of the result search process.\n\nResearchers in work5 dealt with image dataset of respective and CT perfusion techniques, Radlex playbook (tool) and various machine learning and image recognition techniques have been adopted for the implementation. Description of high-level features of reusable medical image datasets suitable to train and regulate ML products was done. Communication among medical imaging domain experts, medical imaging informaticists, academic clinical and basic science researchers, government and industry data scientists, and interested commercial entities were improved. The result of this research was that it helped in understanding the medical image datasets. The challenges found were that, it required highly centralized data security and different regulatory and legal environments.\n\nIn research of6 a medical knowledge database and user information database, conversation scripts are used by the researchers. For text understanding module pattern matching, ML Algorithms, XML, AIML, Decision Trees, Web services (Dialog Flow by google) are used. For Dialogue Management Pattern Matching, ML Algorithms have been used and for Text Generation ML and Deep Learning methods have been used by the researchers. This work was intended to support researchers of chatbot development for medical field by investigating different development strategies and connected technical characteristics. As a result the 4 technical aspects of the chatbot have been recorded. The problem is that, it only paid attention on text-based chatbot usage, where the input or output modality is only written.\n\nIn research7 the dataset of chest X-ray images, chest CT images was used by the researchers. “Automated Classification of COVID-19 from Chest X-Ray Images using Transform Learning with Deep Convolution Neural Network” to assist diagnosis is done. The network consists of risk factors of patients being considered in first layer followed by a convolution layer and risk prediction is done using softmax classifiers in the fully connected last layer. Risk prediction is done with output label as, P = P0,P1, where, P0 and P1 indicates the subject is at high risk and low-risk of COVID- 19, respectively. As a result, the 3 open research directions, classification of CXR images using ML techniques, and risk prediction are presented. The disadvantage observed is the generalizability of the ML model.\n\nIn work,8 Images from Pascal, ImageNet, SUN, and COCO were used as the dataset. The researchers have used object detection, image recognition techniques like Mask R-CNN. The chatbot was capable to identify objects in the image, tell about and make out the image, and was also able to answer the questions about the image. The underlying recognition framework for this work was an encoder-decoder network which is used for fusion of images and Resnet architecture for object detection and localization. The scope of improvement of this research was that still many necessary tests have to be carried out to prove whether the sample really has the characteristics of real data or not.\n\nThe researchers of work9 used the dataset includes the real time patient records. The research used the Food and Drug Administration (FDA) online database for premarket approval applications to identify the major regulatory approvals. It Used the World Intellectual Property Organization’s natural language search engine (TACSY version 2.1.1) to locate the appropriate International Patent Classification designation used by patent reviewers for classification of applications related to stents. Using a comprehensive database of patents, it identified all individuals and institutions that developed intellectual property related to stent technology early in its development process. The result of this research was that 245 granted patents were recorded. The drawback is that this study of patents and patent citations focused only on the years preceding the clinical introduction of artificial stents.\n\nIn work,10 brain MRI images containing tumors of different patients have been used as the dataset. The researchers used techniques like Threshold-based segmentation algorithm, Machine Learning algorithms such as clustering, fuzzy c-means clustering (FCM), K-means clustering, and expectation maximization (EM) and CNN. In order to segment brain images, the researches proposed a combination of morphological operations to develop a hybrid clustering algorithm. Outer membrane is removed in first step using morphological operations in algorithm thus reducing need of large number of clustering iterations and complexity of computation. In the clustering stage, the K-means++ clustering algorithm is exploited to initialize the clusters’ centroids which helps in solving the problem of unstable clustering. The drawback was that the noise present in the images greatly affected the segmentation of lesions and diagnosis of patient’s conditions.\n\n\nMethods\n\nThe block diagram of the overall idea can be seen in the Figure 1.\n\nThe user accesses the web application and inputs the concern regarding heart in the form of text data and scanned images of the artery. The entered text data is formatted using an AI - Natural Language Processing (NLP) technique.\n\nFigure 2 below shows the level-0 Use case diagram of the work carried out by authors of this paper.\n\nUsing the chatbot, the user can upload the scanned images of heart in jpeg format. The scanned images are processed using the Convolution Neural Networks (CNN) model which is an artificial neural network used in image recognition and image processing. CNN is a class of deep neural networks which is a subset and function of Artificial Intelligence. CNN module is composed of convolution layers and pooling layers to process input data. Various image processing techniques like image windowing, morphological operations, and object detection are used in procedure to identify the actual blockage part in a vein of the heart’s image that is uploaded.\n\nThe images used for this work are the Coronary Angiogram Reports and Angiogram images of real time data belonging to 20 patients provided by a well reputed Cardiac hospital in Hyderabad. The Angiogram data provided was in the form of DICOM images. DICOM is Digital Imaging & Communications in Medicine and used to supply interchangeability of medical information and images. “Syngo fast View” software enables to view DICOM images, apply image manipulation and convert them to bitmaps, JPEG, AVI. The images were provided along with the standalone viewing tool SYNGO fast View for visualization of DICOM images (series, studies, patients). For experimentation purpose these dicom images are converted to jpg using online available resources. The number of jpg images resulted is the number of frames consisting in the DICOM image. The required and useful images showing blockage in the coronary artery are separated manually and these useful images segregated forms the dataset of our project. The dataset considered consists of a total of 348 images of patients. To train the CNN model, 193 images having blockage and 155 images having no blockage were used.\n\nConvolution in mathematics is an operation of two functions that creates a third function, which shows how the form of one is changed by the other. The model built was sequential, 5 Convolution 2D layers and 5 Max Pooling layers are added to the model alternatively. The input shape is given 150 × 150 × 3 as the images are in the rgb format. The actual size of each image is 512 × 512. One flatten layer, dense layers and dropout layer is added to the model. The activation function used in these layers is ReLU. First, in relation to the dimensions of the input, the convolved function is reduced and the second type is used to minimize the padding. The rectified linear unit function “ReLU” activation is a piece-by-part linear function which reproduces the input directly if positive; otherwise it produces zero. The Pooling-Layer reduces the Convolved feature’s spatial dimension. It reduces the computational power necessary to process the data by reducing dimensionality. It is also used to extract dominant features that are invariant in rotation and position, thereby maintaining the model’s effective formation process. Max pooling returns “the maximum value in the kernel” area of the image. Max Pooling is called as a “Noise suppressant” because it discards the noisy activations and also performs de-noising along with dimensionality reduction. The flatten layer “converts the data into a 1-D array” for inputting it to the next layer. Flattening the output of the convolutional layers to create a long feature vector and then it is linked to the final classification model like ANN (Artificial Neural Networks) which is called a fully connected layer. The dropout rate is particular to the layer because the chances of placing every input to the layer to zero. The dropout rate is set to 0.2 in the experiments carried out. The dense layer’s neurons get input from output of each neuron of its previous layer, in which neurons of the dense layer carry out matrix-vector multiplication. The activation feature of this dense layer used was sigmoid. The CNN architecture used in experiments carried can be shown as in Figure 3.\n\nThe summary of model generated can be seen as given below in Figure 4.\n\nThe loss function “categorical crossentropy” is used. For the model developed, there are two classes NoStent and Stent to classify. Adam optimization is a stochastic gradient descent technique based on adaptive first and second order moment prediction. Adam has been specifically designed for the formation of deep-neural networks as an adaptive learning rate optimization algorithm. Adam optimizer was used during experimentation. The accuracy metrics have been used.\n\nA chatbot was created using flask techniques on deep learning algorithms. The chatbot was made to learn on the data which contains intents, pattern and responses. The chatbot was built using Flask, NLTK, Keras, Python, Punkt, wordnet package etc.\n\nAfter having training data ready, the model training was initialized. A 3-layer output model was used. There are hundred and twenty eight followed by a second layer having sixty four neurons having softmax, Relu activation function applied and the ultimate layer holds neurons matching with to be predicted number of intents. It was observed in work carried out that stochastic gradient descent with Nesterov accelerated gave acceptable results for this model.\n\nThe experimentation setup was done using a system of i5-7200U CPU, 2.7GHz, 4.00GB RAM, 64 bit operating system.\n\nThe implementation was done using Anaconda framework. Spyder environment of “conda” was used to setup the experiment environment. The software made use includes Python 3.6.5, Anaconda Distribution v5.1, Spyder 3.3.6, Flask etc. The packages such as tensorflow, keras are imported.\n\n\nResults\n\nThe results of application developed and experimentation done are shown in the Figures 5, 6, 7, 8 given. The series of screenshots shows the chat bot conversation and the decision given by the underlying trained model, whether stent is required or not for a patient based on image uploaded.\n\nFigure 8 below depicts the CNN training and Validation Accuracy for the model developed in order to predict whether stent is required or not.\n\n\nFuture scope\n\nThe experiment was carried out under a set of constraints and authors of this paper opine by modifying the parameters further and enhancing the dataset can result in high accuracy and most robust system. The research was carried out as a project work during final semester of engineering study of students resulting in time constraint for doing more iteration of experiments. The future scope of this project includes: application did not make use of voice based input, in next level audio based chat can be implemented. It was observed that the dataset used was not sufficient for model to learn the complete variations of blockages in images of heart. As researchers worked with only possible real time patient data of 459 images yet there is a good scope of improvement when using thousands of images the model may learn more accurately to classify stent required and not required heart images of patients. Data augmentation is one way we can try to overcome this problem. The low variance in the image set considered could be one reason of less model generalization achieved. If researchers can have as large as 10,000 data images with high variance we hope networks such as Variational-Auto Encoder combined with U-Net may give more better performance when run on GPUs.\n\n\nConclusion\n\nCoronary artery stenting is the remedy of preference for patients requiring coronary angioplasty. The quest for a perfect stent continues, however the decision of whether to go for stent or not is crucial. Using this work authors explored an easy to access chatbot based application that predicts the requirement of stent for the user based on scanned image of angiogram uploaded by user. The authors proposed a simple mechanism using chat bot to mitigate dilemma of young practicing doctors as well as patients in deciding whether stent is required or not. Authors made use of CNN model to classify the images having blockages in arteries. The sequential CNN model consists of 5 convolutional 2D layers and 5 Max Pooling Layers. It was observed that the model was giving an accuracy of 81%.\n\n\nAuthor contributions\n\nMr. Krishna Chythanya N was the brain behind this work and proposed as well guided the research with time to time code verification and suggesting team members. Dr. Jandyala N Murthy was instrumental in presenting the thoughts on paper in right way and also time to time evaluated the on going work suggesting where ever required. Ms. Harika Konda was instrumental in developing the required code to implement the work. Ms. Fazilath Maheen was playing the role of supporting Harika in code development. Ms. Rapolu Reetica was contributing in developing the chatbot module. Ms. Mudunuri Alekya played a pivotal role in contacting near by hospitals to get real time heart scan images of patients and also supported in coding as well as writing the technical paper. Ms. Chaitanya Priya played the role of tester and thoroughly tested the project besides helping in coding.\n\n\nData availability\n\nFigshare: Heart Image Data Set for chatbot to predict need of stent in cardiac treatment, https://doi.org/10.6084/m9.figshare.20252016.v1. This project contains the following underlying data:\n\n• trainset - NoStent and Stent JPEG\n\n• testset - NoStent and Stent JPEG\n\n\nSoftware availability\n\nZenodo: CHATBOT TO PREDICT NEED OF STENT IN CARDIAC TREATMENT, https://doi.org/10.5281/zenodo.6834504.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nConsent\n\nThe images data set used in this experimentation has been anonymised and such alterations have not distorted scientific meaning of the images. Hence, no consent was required.\n\n\nEthical approval\n\nThe ethical approval to use the dataset was given through email from the Hospital and the consent from the participants was waived by the organisation as the data would be anonymised for publication.",
"appendix": "Acknowledgements\n\nThe authors would like to acknowledge the support of Dr. Ramchandram, senior cardiologist, Holistics Hospital, Nizampet, Hyderabad, Telangana, India, for providing domain knowledge through his staff members which was very much required in developing this project.\n\n\nReferences\n\nAmato F, Marrone S, Moscato V, et al.: Chatbots Meet eHealth: Automatizing Healthcare.2017; pp. 40–49.\n\nDhyani M, Kumar R: An intelligent Chatbot using deep learning with Bidirectional RNN and attention model. Mater. Today: Proc. 2021; 34: 817–824. PubMed Abstract | Publisher Full Text\n\nFang W, Zhang F, Sheng VS, et al.: A Method for Improving CNN-Based Image Recognition Using DCGAN. Comput. Mater. Contin. 2018; 57(1): 167–178. Publisher Full Text\n\nKalla D, Samiuddin V: Chatbot for medical treatment using nltk lib. IOSR J. Comput. Eng. 2020; 22.\n\nKohli MD, Summers RM, Raymond Geis J: Medical Image Data and Datasets in the Era of Machine Learning–Whitepaper from the 2016 C-MIMI Meeting Dataset Session. J. Digit. Imaging. August 2017; 30(4): 392–399. PubMed Abstract | Publisher Full Text\n\nSafi Z, Abd-Alrazaq A, Khalifa M, et al.: Technical Aspects of Developing Chatbots for Medical Applications: Scoping Review. J. Med. Internet Res. December 2020; 22(12): e19127. PubMed Abstract | Publisher Full Text\n\nSomasekar J, Pavan Kumar P, Sharma A, et al.: Machine learning and image analysis applications in the fight against COVID-19 pandemic: Datasets, research directions, challenges and opportunities. Mater. Today: Proc. September 2020; S2214785320370620. Publisher Full Text\n\nShengyang S: Cs230-fall 2020 final project report conversational image recognition chatbot.2020.\n\nShuai X, Avorn J, Kesselheim AS: Origins of Medical Innovation: The Case of Coronary Artery Stents. Circ. Cardiovasc. Qual. Outcomes. November 2012; 5(6): 743–749. Publisher Full Text\n\nZhang C, Shen X, Cheng H, et al.: Brain Tumor Segmentation Based on Hybrid Clustering and Morphological Operations. Int. J. Biomed. Imaging. April 2019; 2019: 1–11. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "156342",
"date": "22 Dec 2022",
"name": "Jitendra Tembhurne",
"expertise": [
"Reviewer Expertise Deep Learning",
"Machine Learning",
"Parallel Computing and Information Security"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComments: Authors proposed the use of Chatbot for the prediction of need of a stent in cardiac treatment. The good attempt is tried.\nFormatting of manuscript needs to be checked, and typos and grammar errors need to be removed.\n\nHighlight the motivations and contributions in the Introduction section. Also, mention the organization of paper.\n\nWhat is the research gap identification after the literature review? Add the summary as a motivation towards the proposed work.\n\nWhat is the composition of CNN model used for the proposed work, and what is the novel contribution?\n\nWhat is the setup of training and testing/validation for the dataset at the time of model training? Also, mention the hyper-parameter setting at the time of training.\n\nDiscuss all the images with respect to the results obtained, any comparison with the existing literature?\n\nFuture scope should be the part of conclusion.\nThis article developed the deep learning based chatbot for heart patients. The authors investigated the methodology to reduce heart attacks in patients by placing a stent. Once the blockage is identified, a stent with the required size is inserted into the coronary artery.\nHere, the chatbot takes the textual and image inputs of the information of the heart and coronary artery of a patient and predicts the requirement of stent being placed. The 5 layer CNN model is developed for the proposed task with an accuracy of 81%.\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/11-1364
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https://f1000research.com/articles/11-1363/v1
|
22 Nov 22
|
{
"type": "Research Article",
"title": "Online learning during the COVID-19 pandemic: A qualitative study among final year medical students at the University of Zambia",
"authors": [
"Anthony Nsamba Limbumbu",
"Jane Chanda Kabwe",
"Andrew Kumwenda",
"Phyllis Chibuye Kasonkomona",
"Grace Mwila",
"Mwansa Ketty Lubeya",
"Anthony Nsamba Limbumbu",
"Jane Chanda Kabwe",
"Andrew Kumwenda",
"Phyllis Chibuye Kasonkomona",
"Grace Mwila"
],
"abstract": "Background Since the globe was faced with the COVID-19 pandemic in December 2019, numerous adjustments have been made in all sectors to curtail the spread of infection. Most elementary and tertiary schools were closed or suspended until the transmission rates dropped. Following the outbreak of COVID-19, medical schools in Zambia have sought ways to replace face-to-face medical learning with virtual clinical teaching. The objectives of this study were to explore the perceptions of online learning among University of Zambia medical students and understand the barriers and facilitators to effective online learning. Methods A qualitative descriptive approach was used, enrolling final year medical students from the University of Zambia; the consenting participants were sampled purposively and interviewed through virtual platforms until data saturation was reached upon interviewing the 11th participant. A total of 14 participants were interviewed, audio recorded, transcribed verbatim and data was analyzed using six steps of thematic analysis. Results Three broad themes arose from the interviews: online learning perceptions, facilitators and barriers to online learning. Regarding perceptions of online learning, they highlighted that the delivery was simple to understand, with convenient scheduling and the benefit of being able to refer back to the recorded lectures. Some barriers encountered during the online learning were poor network connection, frequent power outages, lack of patient-student interaction and challenges with learning space in their homes. The facilitators were self-paced learning, availability of lecturers and the desire to complete their training despite the lockdown being in effect. Conclusions Most medical students had positive perceptions of online learning despite its challenges. With the improvement in technology, online education should be incorporated into the traditional training of medical students to get the best outcomes.",
"keywords": [
"virtual learning",
"final year medical student",
"medical education",
"COVID-19 pandemic",
"quarantine"
],
"content": "Introduction\n\nWith the rise of the COVID-19 global pandemic, many learning institutions across the world had to shut down to slow the spread of the disease; an estimate of at least 1.5 billion children and youth were affected by the closures.1 To minimize interference in academic activities, online teaching and learning platforms were introduced in several countries with high levels of digital penetration.2 To curb the spread of the COVID-19 pandemic, the government in Zambia, through the Higher Education Authority, closed all the institutions. This prompted the University of Zambia (UNZA) to employ online teaching and learning via Moodle and ASTRIA to mitigate the impact of COVID-19 on academic activities.3 Moodle is a widely used, open-source learning platform that comes without a cost and enables educators to create interactive online courses. At the same time, ASTRIA is a paid service that provides several different management systems for the students and educators.4 Some lecturers used other platforms such as ZOOM, Google Meet and WhatsApp according to their preferences. This transition was made for all the programs offered at UNZA, including the Bachelor of Medicine and Surgery.\n\nOnline learning, also called virtual or e-learning, is the acquisition of knowledge through digital technologies and media, typically by accessing the internet or any electronically enabled learning.5 Online learning is variable among medical schools, and is more common in basic sciences than in clinical clerkship years. In clinical years, however, it has been used to increase the effectiveness of conventional face-to-face methods as it has its limitations.6 The discipline of medicine is about saving lives whilst upholding patient safety, and any significant alterations in how it is taught call for intensive consideration. Most of the activities and teaching in medical training are practical-based7 and require physical interaction with the patients, laboratories and theatres. This underscores the importance of social interactions in the constructivist learning theory, which is the philosophical underpinning principle of experiential learning.8 The UNZA had never taught medical students on a full-time digital platform. This meant that students needed to adapt to the new mandatory digital methods, including final year medical students who were soon to be interns and attending to patients as the first health professionals the patients would encounter in many hospitals in the country. Online teaching and learning were introduced at a time when the country was faced with challenges regarding consistent electricity supply countrywide. Some communities faced up to 15 hours of load shedding per day of electricity, with some parts of the country, such as rural areas, experiencing poor internet connectivity.9 During load shedding periods, the affected areas had no electricity supply from the country’s only power supply institution, meaning a total blackout.\n\nIn an integrative review conducted by O’Doherty et al., prior studies highlighted significant barriers to online learning that include: time constraints, attributed lack of incentives to engage in online education, deficits in technical skills, inadequate infrastructure like technology and quality of services, lack of institutional strategies and support as well as negative attitudes of the people involved.10 Some of the suggested solutions to these identified barriers include adopting digital tools that could free up some time, collaborating with relevant stakeholders and departments with the adoption of new approaches, as well as maintaining a positive attitude among all team players.\n\nThis study aimed to explore the experiences of final year UNZA medical students as they transitioned to online learning to complete their medical training program and highlight the barriers and facilitators.\n\n\nMethods\n\nWe used a descriptive qualitative approach to understand the experiences, barriers and facilitators of online learning among final year medical students for 2020 at the UNZA during the COVID-19 pandemic lockdown. Thus this study was imbedded within the interpretivism paradigm in trying to explore the perceived barriers and facilitators for the students’ online learning during the lockdown as the underlying philosophical approach because reality is deemed to be socially constructed.11 Since online learning is a fairly new concept in this setting, we adopted the individual facet of technology acceptance model (TAM) which has been used in other studies to show user acceptance of the technology based on the perceived usefulness and perceived ease of use.12\n\nEthics approval for this study was obtained from the University of Zambia School of Medicine Research Ethics committee (UNZASOMREC) on the 27th of July 2020 with Assurance No. FWA00000338 and the Dean of Students Affairs (DOSA) Ridgeway campus. Written informed consent was obtained from the students that participated in the study.\n\nThe target population was the final year medical students that were being trained at the UNZA during the time of the lockdown. A purposive sampling method was used with the criteria that the participants had to be in final year, at the UNZA and had participated in online learning at the time of selection. The participants were chosen irrespective of their residence of origin and were picked until saturation of data was achieved. This was considered attained upon interviewing 11 participants, however we interviewed three more participants making the total number of study participants 14. Data saturation is when enough data has been collected to replicate the findings, reached in this study after interviewing 11 participants.13 No participants refused to participate nor dropped out of this study.\n\nWritten informed consent was obtained from each participant. The participants signed the informed consent virtually which was sent and received back in PDF format through WhatsApp messenger. The data was then collected through scheduled in-depth interviews via the Zoom online platform and direct phone calls to minimize physical interactions with the participants. Three interviews were conducted by a medical student, male ANL together with an Obstetrics and Gynaecology specialist, female doctor MKL who is the corresponding author with several years of experience in research. The remaining 11 interviews were conducted by ANL supervised by MKL. This ensured that there was no power differential between the respondents and the researcher as it is easier to create a good research environment with a colleague and not withhold any information back for the purpose of the research. The interviews were conducted with videos turned off to facilitate good connectivity and ensure confidentiality as the interviews were being recorded. Other researchers have found the Zoom platform to be a good tool for collecting qualitative data because it is easy to use, cost-effective, and has good data management features and security options compared to other interviewing mediums like direct telephone and face-to-face.14 Telephone calls were done for two participants as they had poor internet connectivity in their residences. Interviews were conducted in English, audio-recorded and transcribed verbatim. The transcripts were returned to the participants to ensure there was no loss in information from audios, however three participants did not respond. The duration of each interview was 19–47 minutes.\n\nWe used an in-depth interview guide that was pre-tested and adjusted for clarity and ease of understanding; The questions were paraphrased in a simplified manner, ensuring the words were not too technical for the study participants. To avoid ambiguity, the questions were made to be concise, specific and relevant to the information required. The interview guide comprised open-ended questions with follow-up probes in instances where certain information was left out.15 Transcripts were then coded in preparation for analysis.\n\nThe data was coded through inductive coding approach and we employed the six steps of thematic analysis, a practical data analysis method used in qualitative research. It was advantageous since we explored participants’ experiences; it enabled us to develop a structured approach.16 Three researchers (JCK, AK, MKL) coded the transcripts based on the emerging themes from the respondents. We did not use any qualitative data analysis software during the analysis. All six researchers analyzed the data based on the codes generated and they expressed reflexivity throughout the entire process of this study.\n\n\nResults\n\nThe demographic characteristics of the participants are presented in Table 1 below.\n\nThe ages varied between 24 and 29, with all participants being single and unemployed. There were four female and ten male participants. The participants represented five of Zambia's ten provinces, including Copperbelt, Eastern, Central, Southern and Lusaka.\n\nWe considered the broad themes that affected the effectiveness of online learning during the COVID-19 lockdown: online learning perceptions, barriers and facilitators to online learning. Under these themes, we established sub-themes to provide a deeper understanding. Table 2 below shows the summary of the themes.\n\nTheme 1: Online learning perceptions\n\nThe participants' perceptions are discussed under three sub-themes: simplicity, scheduling, and self-directed learning or skills development. Overall, the participants' perceptions of online learning were generally positive, as some expressed their approval of this method, commending the University’s initiative of switching to online learning during the lockdown to facilitate the continuity of their studies.\n\nSimplicity\n\nThe first sub-theme we considered under this core theme was simplicity, where most participants stated to have been able to understand the presentations delivered as both lectures and notes with ease. When asked what they thought about the material that was provided online, one participant said:\n\n“Oh yeah, it was excellent. They (lectures) were readily available especially for the paediatrics course when they teach; they would make sure they upload, and also for the previous courses that I did they would make sure they upload all the lectures that they had uh done…” (p4)\n\nNot only was the material said to have been uploaded for easy accessibility, but the content was also excellent and sufficient according to the requirements of the students, as stated by participant 8 quoted below:\n\n“They (online lectures) were something new firstly, but uhm they were detailed, uh the doctors tried and were able to explain their material adequately, so they were great.” (p8)\n\nHowever, not all participants were satisfied by the lecture notes provided online; some expressed their disapproval of online learning, implicitly stating the need for further explanation of the lecture notes administered to them:\n\n“Uhm, the material was okay … it had enough content just that it lacked explanation, you know, it was just given (…) and (…)I had to read on my own, but the content was enough though you need an explanation to get something uh to a 100% uh level of understanding”\n\n(p11)\n\nScheduling\n\nThe lessons were delivered by sending lecture notes to the students to study at their convenience, and then they were assessed on this material. The assessment was done physically following the uploading of notes, thus combining traditional ways of evaluation with virtual methods of teaching. This was attested by the response below:\n\n“I think they tried their best as well; they sent notes like every- for everything on their lecture schedule was sent, they sent clinical scenarios, and they had to give us a physical test before the exams, so they did their best as well (…)”\n\n(p11)\n\nLectures were also delivered online in real-time, with interactions between the students and lecturers made possible by the Zoom platform.\n\n“Well, uh, we had lectures for about an hour in the morning, and an hour in the evening. And of course, with different doctors coming in and try to help out.” (p3)\n\n“(…)the fact that most of the lecturers were willing to let us ask questions, for me that was the major thing”\n\n(p12)\n\nFurthermore, as part of the training, the medical students were also assessed online through an assignment that required to be downloaded, answered and uploaded to complete the task.\n\n“The assignment was sent on Moodle (online learning platform), and we had to download, then we answer in a word document, then you send it back via Moodle (…)”(p2)\n\nSelf-directed learning\n\nSelf-directed learning (SDL), a strategy in which learners take responsibility for their learning, was yet another sub-theme that emerged, highlighting the participants’ willingness to augment their online learning. With medical training being a hands-on program, students need to learn certain skills to aid in patient management. A couple of examples are highlighted below how students were able to use their initiative to facilitate their learning:\n\n“so we had to make sure that we learnt the practical aspect as well as helping the patient on the ground and lessening the work of the doctors in our units and being available as always to follow up certain things in case uh one or 2 doctors were busy, yes, not forgetting the nurses as well…” (p6)\n\n“the day before or two days before our ward rounds we would clerk our patients then we would just come and present so that we facilitate the learning as we are presenting …”\n\n(p12)\n\nTheme 2: Barriers\n\nOnline learning had challenges; students and lecturers faced various difficulties with this method of sharing knowledge, such as the inability to navigate around the platform. We grouped the barriers encountered by the participants into four sub-themes: quality of internet and access, power outages, lack of patient-student interaction and lack of learning space at home. These barriers were beyond the students’ control and could not be easily overcome.\n\nQuality of internet and access\n\nInternet connectivity in the country depends on the network provider one subscribes to and the geographical location. The most prominent of these factors is the geographical location, where certain areas of the country struggle with internet connectivity more than others. Moreover, one needs to pay for internet access by buying data bundles to enable them to access online platforms. The University of Zambia offers internet access within the school premises through Wi-Fi routers; however, with the school’s closure, the students had to fend for themselves to have internet access because they were no longer on campus.\n\n“…At times you would find that the network is not good, so you are not able to get the lecturer clearly” (p13)\n\n“…I remember one time what happened I was just blocked out like network couldn’t log on, bundles were there I just couldn’t connect, so there is the issue of network …” (p3)\n\nWhile others struggled with internet connectivity, a few had challenges with access to the internet as they occasionally could not afford to purchase data bundles. These students would then be forced to abscond classes and either watch the lecture video if it was recorded or just read the lecture notes if and when they are made available. Some participants stated not to have always been able to afford data bundles to access online lectures.\n\n“Then sometimes there were issues of finances where you don’t have enough money for bundles (…)” (p2)\n\n“And also issues of finances coz we were expected to be spending a lot of money for us to be managing to learn online, so it was a bit difficult, so it set me back and when it came to catching up on things and understanding things it took an extra effort for me to do so.” (p4)\n\nPower outages\n\nZambia was experiencing load shedding in many regions to prevent excessive load on the main generating electric plant. With specific areas experiencing electricity power cuts for as long as 8 hours daily, such were the conditions that the final year medical students had to learn under as they were not exempted from these power cuts.\n\n“(…) Number two, we have what we call power cutting schedule, so sometimes they would put up lectures during the time that there is no power you should not- you haven’t charged your phone you would not be able to attend, so it was a setback.” (p4)\n\n“Then, of course, we also missed on several lectures, and as well as when online learning started (…) sometimes we would have load shedding where you are and all those things. Yeah.” (p2)\n\n“I think the issue may be that I had was maybe was with the load shedding (…) cause sometimes I would struggle to have a few of the lectures we were having online on the Zoom platform because of the load shedding issues that we would have from time to time (…)” (p14)\n\nLack of patient-student interaction\n\nTraditionally, clinical students learn most of their skills in the hospital wards, where they can interact with patients. Through these interactions, medical students are therefore able to practice therapeutic and diagnostic procedures as well as counselling patients. Virtual education resulted in the cessation of student-patient interactions, which affected the students.\n\n“Well, uh, you can’t learn medicine online, I think that’s my perception about it you can't do a lumbar puncture online” (p11)\n\nWith medical training being a hands-on program, the best place to train medical students remains at the patient’s bedside; despite being able to read various textbooks and presentations, a medical student's skills are best developed at the bedside through practical participation. Students need to learn specific skills to aid in patient management. The impact on the acquisition of skills that the lack of patient-student interaction brought was highlighted as follows:\n\n“It shattered my dreams of acquiring the basic skills that I needed to acquire, the things that I thought I would do in 7th year (referring to the final year of undergraduate medical training) that I didn't do in 5th year I didn't do in 6th year so I thought I would perfect on certain things in 7th year yeah so it shattered a lot on my side,” (p11)\n\n“For clinical students, I don’t think like online learning is enough you still need to have the practical part of it (… ) coz like they say diseases don't read textbooks so the textbook can explain to you as proper as possible, but when you go on the ward it will still look like something new something you had never heard before when you learnt about it (…) the negative part is that you don’t have the practical skills like for you to be able to see that on a patient, for you to be able to apply your knowledge, the application part of it lacks so I feel like yeah it’s okay, but I don’t think like it’s very appropriate or good enough for a clinical student” (p5)\n\nTo balance the practical aspect of the training with the theoretical one, some participants proposed methods in which students could do their theory work online and still find time to go to the ward for their practical training or even make use of the skills lab:\n\n“I think it can be a very positive thing to have lectures online, uh through Zoom like this discussion but still be expected to go to the ward for the practical sessions.” (p6)\n\n“At least if a way to keep us in school was found and a way of opening up maybe a skills laboratory so that in groups of small individuals with one or two lecturers (… ) you can now go and perform some of the things that you learnt online imagine you are being taught how to catheterize, how to cannulate I think it can make actually uh a good idea if students learnt in their hostel online doing their learning then afterwards have some time to perfect their skills (okay), even just for an hour, yes.” (p11)\n\nLack of learning space at home\n\nIn most homes, dependents are expected to help their guardians with chores that are usually routine and executed at specific time frames. With the medical students being sent home, they had to perform these chores as per custom. Furthermore, some houses’ setups have noisy environments or are too crowded to be impeccable for studying or attending online lectures. Moreover, none of them had designated places to enable participants adequately attend to their academic responsibilities. This was considered to be interfering with the learning process of some of the participants.\n\n“I had to factor those things chores, noise at home just it wasn’t a favourable environment, it wasn’t a favourable environment, so this is where you are sharing a bedroom, you can’t lock yourself up so such things had to come in and it was it was a huge challenge in terms of the way I live as an individual here (school)” (p11)\n\nLearning from home proved to be a barrier for most of the participants. When asked how the living arrangements fitted in with online learning, p3 and p12 had this to say:\n\n“Okay, uh, when we were back in school and learning from school, the living arrangements were okay, I would say okay, but then being home, coz at home you are not exactly a student. At home, you are a child, so you have to help out here and there, so it becomes very challenging cause one moment, of course, you are supposed to have classes at 9 (am), but then the parents want you to help out with something, so I found that challenging.” (p3)\n\n“They don’t fit at all. You know when I'm home, it’s a tiny place, so everyone is everywhere. I would inform them that I had class, and I would sit in the bedroom so that I would have some privacy, but everyone would come in, they’ll start calling me, and I had to remind them I was actually in class; they want to talk to me there and then and I am like, okay you people I am in class now. It's tough to even study from home, everyone expects you to work, prepare lunch, do the house chores, and then I have no time for my books because, by the time I finish everything, I am exhausted. I cannot touch a book, and you know how med school works like it requires a lot of time accorded to it to understand a certain concept, so home is not conducive at all.” (p12)\n\nTheme 3: Facilitators\n\nThree sub-themes emerged from the final core theme considered: self-paced learning schedules, support systems and prospects of completing school. These sub-themes expressed the factors that helped enhance the students’ learning experience.\n\nSelf-paced learning schedules\n\nAll participants regarded online learning as advantageous because they could easily refer back to the content given either during recorded lectures or in PowerPoint presentations. The participants revealed the following:\n\n“So, I think one thing I found interesting was that some of the lectures were recorded, meaning if you missed a lecture, you could easily just download and go through the lecture on your own time. Then the other good part was that since you have the downloaded lecture, meaning you can go through the lecture over and over so that you understand better, yes, so I think those were the positives.” (p2)\n\n“Okay, uhm, my experience was good, yes it was very good I was able to understand what the lecturer was saying … and uh and at least it was recorded, so I had a chance to be going through over and over again, it was a good experience” (p4)\n\n“So, what worked well for me was uh going back to the recorded uh lectures, yes it took a lot of time but at least it would help me understand what the uh lecturer was trying to tell me and also the fact that you know how when somebody is talking it’s rapid there are certain points that you would miss out but if you go back and listen to them it will be easier” (p5)\n\nSupport systems\n\nThe support systems of the students during this period were explored. Most respondents said they had not received any support from the University. In contrast, others considered the availability of lecturers during this period as a means of support from the University. Some of the participants’ verbatim regarding support from the University are highlighted below:\n\n“The university? Support? Uh no, not really. No, they didn’t.” (p7)\n\n“Uh, well, I think they tried to push our lecturers to do their work and also we had some Moodle lectures on how best you can use Moodle for you to be able to access the online lectures” (p5)\n\nOthers, however, allude to the support from colleagues as one of the facilitators.\n\n“Okay, so uh issues of uh maybe discussing, discussions, sorry, discussions with my friends online it gave room for me to get in touch with people, a good number of people from different courses and we’d hold a meeting effectively, so it was it was one good thing for me.” (p4)\n\n“(…) I asked some of my friends on how to go about it, activating the audio and everything, yeah it did improve with time at least I could easily join in and I was able to get the lecturer” (p2)\n\nProspects of completing school\n\nBeing at the verge of completing their undergraduate training and facing the closure of physical attendance of school, the medical students were fully receptive to the progression of lessons virtually.\n\n“I'm saying in a setting where we needed to learn and complete our studies, I think the online learning served well, yeah.” (p7)\n\n“(…) I think in as much as the online thing was forced on us, it was one way of helping us graduate, help us learn and catch up. I think there was a need for this online learning to continue (…).” (p11)\n\n“Firstly, I was able to continue my academic life despite the pandemic and complete my studies (…).” (p8)\n\n\nDiscussion\n\nThe study explored the experiences of final year medical students at the UNZA doing online learning during the COVID-19 pandemic. Online learning was delivered in a scheduled and simplified manner. However, there was unreliable internet connectivity and access, power outages and diminished patient-student interaction. Notwithstanding, positive online learning experiences were identified as self-paced learning, support systems and the thought of graduating from medical school.\n\nThe primary study findings are that their online learning was delivered in a scheduled and simplified manner, whilst they also had an element of self-directed learning. The notable barriers to this online learning were the variability in internet connectivity and access, power outages, and a lack of patient-student interaction impeding their acquisition of technical skills and a lack of learning space in their homes. On the other hand, highlighted facilitators to online learning include self-paced learning, having to support systems, and the prospects of completing medical school, which motivated them. Online learning provided the best available means for the students to continue their education during the lockdown, as the pandemic kept spreading with poor control globally, thus presenting an indefinite period of spread.17\n\nThe study participants were satisfied with the transition to online learning, commended the course delivery, and felt it was simple and convenient. Earlier studies also show that online learning was welcomed as the best alternative for continued education for the students given the circumstances.18 However, it was recommended that a combination of online learning and physical attendance in class should be used to maximize the benefits of education.19 Contrary to this welcomed initiative, a different study reported a general dissatisfaction by the students that led to a disruption of learning.20 It was also previously established that the student’s perception and ability to adapt to their learning environment were essential to achieving learning.21,22\n\nOnline learning was considered a platform that allowed students to set their own pace regarding learning. Our participants stated they were able to refer back to the recordings, and they could replay them as much as they would have loved to gain a deeper understanding. This student-centered advantage of online learning was also reported by Mukhtar et al. in that the students learned asynchronously during the day and also remotely from various locations across the country.23 Considering that it enabled these students to log in from various geographical locations, this was deemed beneficial to them as they could easily access lectures with great convenience.\n\nOne of our participants' negative learning experiences was the inability to develop skills through online learning. Participants felt that the practical aspect of the training was deprived and shattered the possibility of acquiring basic skills and needed supplementation with physical attendance to aid in skills development. Similar findings were reported in China, where some students in one study also thought it was necessary to reteach the topics physically to gain a comprehensive understanding.24 Similarly, Mukhtar et al. in 2020 found online learning inefficient and difficult to maintain academic integrity. Skills could not be taught; there was a lack of student feedback, poor attentiveness, lack of discipline and plagiarism during assessments.25\n\nAnother negative online learning experience that the students reported arose from their environment. They reported to have had challenges with internet connectivity, and the poor quality of internet access led to the students failing to log in and being logged out of lectures. This challenge was not unique to our study participants but has also been encountered by students in several other studies.26–28 According to the World Bank, many African countries already have substandard internet quality of less than 10mbps. With the institution of the COVID-19 lockdown, there was increased traffic on the internet which led to slow internet speeds with reductions of as much as -10%.29 Another challenge was frequent electricity power outages reported by some participants who missed some of the lessons as a result of the power challenges. Similarly, students in India also reported poor network and electricity power cuts as disturbing the online learning process.30 Electricity outages were coupled with the high demand on the electricity industry encountered during the lockdown, which immediately ameliorated with the lifting of the quarantine.31\n\nLack of learning space was yet another highlighted challenge some participants reported. There were various distractions to their learning schedule such as noise, chores and other competing demands. These findings were also reported by Ishita et.al. in 2021, whereby the students would encounter distractions that eventually affected their performance in exams.32 Other studies found mind wandering as one of the distractions to online learning33–35 but this phenomenon was not reported by any of our study participants.\n\nFurthermore, the students indicated that the absence of interaction with patients for their training during this period was a barrier to adequate learning. For instance, one participant alluded to how he needed to be able to put the theoretical knowledge into practice and be able to appreciate the theory on an actual patient. Singh described the importance of student-patient interaction as it aids in building social intelligence, confidence, communication skills, coming up with differential diagnoses following clinical examination and how the patient is the best teacher for the student than a book would be.36 Another study reports that students were not able to contribute to patient care anymore as a result of the closure.37\n\nSmith reported that some universities offered support for the students to cater for their mental health and financial support. Mental health assistance had always been there for these students, but with the arrival of the pandemic, it was now accessible through video call counselling sessions. More than half of their students had reported deterioration of their mental health during the lockdown. Although there was no financial support from the University that our participants reported, Smith reported a hardship fund that their students acquired from the institutions’ financial support services38 whose idea was also recommended recently by Rainbow and Dorji.39 Our participants considered the availability of lecturers and technical guidance on how to navigate the online platforms as the only support they received from the University.\n\nWe recommend a blended learning approach for medical students consisting of both physical and virtual training. This will make both the lecturers and students well oriented with the use of technology and the constant feedback from the users will compel faster improvements to the virtual platform developers. Furthermore, it would be preferred for the various learning institutions to develop or improve their own virtual learning platforms which should cater for the respective needs of various programs offered by the institution. This will call for increased engagement between the University management, lecturers, information communications technology (ICT) department and student representatives. We also recommend that in instances where physical attendance of training in large groups is not feasible, as it was during this pandemic, students be allowed to do their clinical placements in smaller groups. They can also achieve this by having the students be at liberty to do the placements at any hospital convenient for them provided they are guided on the basic learning requirements in order for them to graduate. This can be done through logbooks as is the case in their primary training institutions.\n\nThis study endeavored to highlight the online learning experiences of final year medical students during the COVID-19 pandemic which has not been previously reported. Further, the qualitative method provides a deeper understanding of the perceptions, barriers and facilitators of online learning thus enhancing the rigor of the study. The responses were transcribed verbatim and counter-checked to verify accuracy through an iterative process that was equally applied to the generation of themes hence adding to the credibility of the study. Whilst the results are not generalizable as is the case for qualitative studies,40 there is immense value in the themes identified which the University could put into consideration and inform policy when online learning is engaged for medical students as their learning needs are unique.\n\nThe limitation of this study lies in its lack of triangulation in that we only focused on one data collection tool which was the in-depth questionnaire administered to only the final year medical students from one institution and we did not use other tools such as focus group discussions (FGDs) and considered other academic years. However, with the COVID-19 restrictions, it was not feasible to have meaningful FGDs. Conducting interviews using a virtual platform without recording in order to increase the bandwidth or telephone meant we were not able to take into account the participants’ body language, which would have aided in a more comprehensive analysis. This study will have to be followed up with a quantitative study consisting of larger sample size, a validated study tool and the incorporation of different learning institutions.\n\n\nConclusion\n\nDespite its potential benefits, online learning cannot completely replace the traditional training of medical students. However, it could be considered supplemental to student clinical placements. As the information communications technology industry develops further, there is hope for future training to have better delivery virtually with better student satisfaction.\n\n\nData availability\n\nFigshare: Online learning during the COVID-19 pandemic: A qualitative study among final year medical students at the University of Zambia, https://doi.org/10.6084/m9.figshare.21086992.v1.41\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe would love to acknowledge the students that participated in this study and the Dean of Students Affairs (DOSA), Ridgeway campus, for allowing us to carry out this study on the students under their care. We are also delighted to acknowledge YES Zambia for their contribution to this study.\n\n\nReferences\n\nThis Is How COVID-19 Is Affecting The World’s Children. World Economic Forum. 2022. Accessed 23 May 2022.Reference Source\n\nNash Visctoria E: Coronavirus school closures impact 1.3 billion children – and remote learning is increasing inequality.2020. (Accessed: 17 June 2020).Reference Source\n\nSitali W: closure of the university of zambia (unza) due to COVID-19 pandemic.2020. (Accessed: 26 June 2020).Reference Source\n\nHimoonga R, Phiri J: Increasing the Use of E-Learning Platforms in Tertiary Learning Institutions for Blended Distance Programmes in Zambia. Open J. Soc. Sci. 2020; 08: 174–190. Publisher Full Text\n\nWhat is the Definition of E-Learning? - E-Student:2020. Retrieved 12 August 2022.Reference Source\n\nHuynh R: The Role of E-Learning in Medical Education. Acad. Med. 2017; 92(4): 430. Lippincott Williams and Wilkins. Publisher Full Text\n\nVonbank A, et al.: Toward a more professional and practical medical education: a novel Central European approach. Advances in Medical Education and Practice. 2015; 6: 459–467. Dove Medical Press Ltd. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYardley S, Teunissen P, Dornan T: Experiential learning: Transforming theory into practice. Med. Teach. 2012; 34(2): 161–164. PubMed Abstract | Publisher Full Text\n\nMulenga EM, Marbán JM: Is COVID-19 the Gateway for Digital Learning in Mathematics Education? Contemp. Educ. Technol. 2020; 12(2): ep269. Publisher Full Text\n\nO’Doherty D, et al.: Barriers and solutions to online learning in medical education - An integrative review. BMC Med. Educ. 2018; 18: 130. BioMed Central Ltd. PubMed Abstract | Publisher Full Text\n\nCohen L, et al.: Research Methods in Education. 5th ed.Taylor and Francis;2005.\n\nAl Kurdi B, Alshurideh M, Salloum S: Investigating a theoretical framework for e-learning technology acceptance. International Journal of Electrical and Computer Engineering (IJECE). 2020; 10: 6484–6496. Publisher Full Text\n\nWalker JL: The Use Of Saturation In Qualitative Research. Canadian Journal Of Cardiovascular Nursing = Journal Canadien En Soins Infirmiers Cardio-Vasculaires. 2012; 22(2). Accessed 23 May 2022. PubMed Abstract\n\nArchibald MM, et al.: Using Zoom Videoconferencing for Qualitative Data Collection: Perceptions and Experiences of Researchers and Participants. Int. J. Qual. Methods. Jan. 2019; 18: 160940691987459. Publisher Full Text\n\nHolloway 1997 States That At Its Roots Phenomenology Attempts To Describe|Course Hero. Coursehero. Com. 2022. Accessed 23 May 2022.Reference Source\n\nDawadi S: Thematic Analysis Approach: A Step by Step Guide for ELT Research Practitioners. J. NELTA. 2020; 1: 71.\n\nPreventing COVID-19 spread in poor areas - World Heart Federation.Accessed 27 May 2022.Reference Source\n\nShehata MH, et al.: Medical Education Adaptations Post COVID-19 - An Egyptian Reflection. Preprints. 2020. Publisher Full Text\n\nHongbin W, Leisi P: Does online learning work better than offline learning in undergraduate medical education? A systematic review and meta-analysis.2019. Accessed 17 June 2020.Reference Source\n\nRay I, et al.: Medical Student’s Perspective Regarding Undergraduate Surgical Education With Special Reference To Pandemic. Indian J. Surg. 2021; 1–5. Springer Science And Business Media LLC. Accessed 27 May 2022. PubMed Abstract | Publisher Full Text\n\nGijbels D, Van de Watering G, Dochy F, et al.: New learning environments and constructivism: The students’ perspective. Instr. Sci. 2006; 34(3): 213–226. Publisher Full Text Google Scholar\n\nEntwistle N, Tait H: Approaches to learning, evaluations of teaching, and preferences for contrasting academic environments. High. Educ. 1990; 19(2): 169–194. Publisher Full Text Google Scholar\n\nMukhtar K, et al.: Advantages, Limitations And Recommendations For Online Learning During COVID-19 Pandemic Era. Pak. J. Med. Sci. 2020; 36(no. COVID19-S4): S27–S31. Accessed 28 May 2022. PubMed Abstract | Publisher Full Text\n\nWang Y, Yu R, Liu Y, et al.: Students’ and Teachers’ Perspective on the Implementation of Online Medical Education in China: A Qualitative Study. Adv. Med. Educ. Pract. 2021; 12: 895–903. PubMed Abstract | Publisher Full Text\n\nMukhtar K, et al.: Advantages, Limitations And Recommendations For Online Learning During COVID-19 Pandemic Era. Pak. J. Med. Sci. 2020; 36(no. COVID19-S4): S27–S31. Accessed 23 May 2022. PubMed Abstract | Publisher Full Text\n\nBączek M, et al.: Students’ Perception of Online Learning During the COVID-19 Pandemic. Medicine. 2021; 100(7): e24821. Ovid Technologies (Wolters Kluwer Health). Accessed 28 May 2022. PubMed Abstract | Publisher Full Text\n\nAttardi S, Rogers K: Design and implementation of an online systemic human anatomy course with laboratory. Anat. Sci. Educ. 2015; 8: 53–62. PubMed Abstract | Publisher Full Text\n\nKhalil R, et al.: The Sudden Transition To Synchronized Online Learning During The COVID-19 Pandemic In Saudi Arabia: A Qualitative Study Exploring Medical Students’ Perspectives. BMC Med. Educ. 2020; 20(1): 285. Springer Science And Business Media LLC. Accessed 27 May 2022. PubMed Abstract | Publisher Full Text\n\nBank, World: The Effect Of COVID-19 Lockdown Measures On Internet Speed. Washington, DC;World Bank;2020. Accessed 28 May 2022.Reference Source\n\nSharma N, et al.: Perception Towards Online Classes During COVID-19 Among MBBS And BDS Students In A Medical College Of Nepal: A Descriptive Cross-Sectional Study. J. Nepal Med. Assoc. 2021; 59(235): 276–279. Accessed 29 May 2022. PubMed Abstract | Publisher Full Text\n\nImplications Of COVID-19 For The Electricity Industry: A Comprehensive Review. Ieeexplore. Ieee.Org. 2022. Accessed 29 May 2022.Reference Source\n\nRay I, et al.: Medical Student’S Perspective Regarding Undergraduate Surgical Education With Special Reference To Pandemic. Indian J. Surg. 2021. Springer. Science And Business Media LLC. Accessed 27 May 2022. Publisher Full Text\n\nKohan N, et al.: Self- Directed Learning Barriers In A Virtual Environment: A Qualitative Study. J. Adv. Med. Educ. Prof. 2017; 5(3): 116–123. Accessed 28 May 2022. PubMed Abstract Reference Source\n\nSzpunar KK, Khan NY, Schacter DL: Interpolated memory tests reduce mind wandering and improve learning of online lectures. Proc. Natl. Acad. Sci. 2013; 110(16): 6313–6317. PubMed Abstract | Publisher Full Text PMC free articlePubMedGoogle Scholar\n\nKoller D: Death knell for the lecture: Technology as a passport to personalized education. New York:New York Times;2011 [updated: 5 Dec 2011].Reference Source\n\nSingh A: The Impediment In Acquiring Clinical Skills By Medical Students During The COVID-19 Pandemic. J. Nepal Med. Assoc. 2020; 59(233): 98–99. Accessed 29 May 2022. PubMed Abstract | Publisher Full Text\n\nNolan H, Owen K: Qualitative Exploration Of Medical Student Experiences During The Covid-19 Pandemic: Implications For Medical Education. BMC Med. Educ. 2021; 21(1): 285. Springer Science And Business Media LLC. Accessed 29 May 2022. PubMed Abstract | Publisher Full Text\n\nSmith L: How Are Universities Supporting Students During The COVID-19 Pandemic? Patient. Info. 2022. Accessed 29 May 2022.Reference Source\n\nRainbow S, Dorji T: Impact Of COVID-19 On Medical Students In The United Kingdom. Germs. 2020; 10(3): 240–243. Asociatia Pentru Cresterea Vizibilitatii Cercetarii Stiintifice (ACVCS). Accessed 29 May 2022. PubMed Abstract | Publisher Full Text\n\nKabwe JC, et al.: Psychosocial issues and coping mechanisms of pregnant and postnatal women diagnosed with COVID-19: A qualitative study. Womens Health. 2022; 18: 174550572211113. PubMed Abstract | Publisher Full Text\n\nLimbumbu AN, Kabwe J, Kumwenda A, et al.: Online learning during the COVID-19 pandemic: A qualitative study among final year medical students at the University of Zambia. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "213506",
"date": "08 Nov 2023",
"name": "Forman Erwin Siagian",
"expertise": [
"Reviewer Expertise Parasitology",
"Mycology",
"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\nLimbumbu et al conducted a study regarding the effectivity of online learning exerience during COVID pandemic from the perspective of final year medical students (n=14); and even the number of participant is limited, but their qualitative approach gave us a more specific problems regarding their experiences, barriers and factors that can facilitate them to adjust or modify the problem1, and this showed us the benefit of using qualitative approach in limited setting2. Financial related infrastructure and temporal obstacles are always become the main problem for delivering good online teaching2. Zambia as a country also struggling economically, and this give big impact to other sector, including medical education3, and this perhaps became the \"silent iceberg phenomenon\" that caused \"poor quality internet access\" and \"poor supply and access to electricity\" that clearly mentioned by the participants ( also check the part of \"lack of learning space\").\nThese obstacles, more or less, actually also happened everywhere and many reports offer solution or at least ‘shortcut4,5. The data these investigators revealed showed us how they tried their best to adjust and even modify everything in order to make sure that at least minimum education delivered.\nOne of the shortcomings that also needs to be revealed is how the government react and support the medical institutions, because many of the roots of the problems are far beyond the reach of students, lecturers, academic staffs and institutions, but actually within the jurisdiction of the government.\nTo my opinion this article deserve compliment and worth to be read and studied in more depth; and I am grateful that this journal, in its high moral values, accepted this simple qualitative article to open our minds about the importance of support and equality for those in need.\nReferences\nSawatsky AP, Ratelle JT, Beckman TJ. Qualitative Research Methods in Medical Education. Anesthesiology. 2019 Jul;131(1):14-22. https://doi.org/10.1097/ALN.0000000000002728.\n\nRastogi A, Bansal A, Keshan P, Jindal A, Prakash A, Kumar V. Medical education in post-pandemic times: Online or offline mode of learning? J Family Med Prim Care. 2022 Sep;11(9):5375-5386. https://doi.org/10.4103/jfmpc.jfmpc_2305_21.\n\nU.S Department of State. 2023 Investment Climate Statements: Zambia. Downloaded from https://www.state.gov/reports/2023-investment-climate-statements/zambia/\n\nDaroedono E, Siagian FE, Alfarabi M, Cing JM, Arodes ES, Sirait RH, et al. The impact of COVID-19 on medical education: our students perception on the practice of long distance learning. Int J Community Med Public Health 2020;7:2790-6. https://doi.org/10.18203/2394-6040.ijcmph20202545\n\nGrafton-Clarke C, Uraiby H, Gordon M, Clarke N, Rees E, Park S, et al. Pivot to online learning for adapting or continuing workplace-based clinical learning in medical education following the COVID-19 pandemic: A BEME systematic review: BEME Guide No. 70. Med Teach. 2022 Mar;44(3):227-243. https://doi.org/10.1080/0142159X.2021.1992372.\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": "244781",
"date": "29 Aug 2024",
"name": "Nirav Nimavat K",
"expertise": [
"Reviewer Expertise public health",
"epidemiology",
"statistics",
"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\nThe qualitative study elaborates on the perceptions and barriers to medical education through an online portal. As this is a qualitative study, the methodology, results, and statistical analysis are different. The study gathers subjective feedback related to the thematic approach of the objectives. Points to be improved: 1. Grammatical errors and sentence should be formed appropriately as required, 2. The recommendation part requires modifications in terms of length. Also, recommendations should be based on the study 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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1363
|
https://f1000research.com/articles/11-379/v1
|
31 Mar 22
|
{
"type": "Research Article",
"title": "IL1B gene variants, but not TNF, CXCL8, IL6 and IL10, modify the course of cystic fibrosis in Polish patients.",
"authors": [
"Oliwia Zakerska-Banaszak",
"Joanna Gozdzik-Spychalska",
"Marcin Gabryel",
"Joanna Zuraszek",
"Marzena Skrzypczak-Zielinska",
"Ryszard Slomski",
"Agnieszka Dobrowolska",
"Tomasz Piorunek",
"Halina Batura-Gabryel",
"Joanna Gozdzik-Spychalska",
"Marcin Gabryel",
"Joanna Zuraszek",
"Marzena Skrzypczak-Zielinska",
"Ryszard Slomski",
"Agnieszka Dobrowolska",
"Tomasz Piorunek",
"Halina Batura-Gabryel"
],
"abstract": "Background: The main aim of this study was to evaluate whether selected polymorphic variants in genes from the inflammatory pathway can be predictors of pulmonary or digestive manifestation of cystic fibrosis, as well as of severity of lung disease. Materials and methods: Using pyrosequencing and sequencing we have genotyped 12 variants in TNF (rs361525, rs1800629), CXCL8 (rs4073, rs2227306, rs2227307, rs188378669), IL1B (rs16944, rs1143634, rs1142639, rs1143627), IL6 (rs1800795) and IL10 (rs1800896) genes in a cohort of 55 Polish patients with diagnosed cystic fibrosis and controls. In our study group, a pulmonary manifestation of disease revealed 44 of subjects (80%), and digestive symptoms dominated in 11 (20%) of analyzed individuals. Severe lung dysfunction has occurred in 20 (36.4%) of patients. Results: We proved, that two promoter variants of IL1B, rs1143627 (c.-118G > A) and rs16944 (c.-598T > C) are presented significantly more often in patients with severe character of lung disease compared to mild (82.5% vs. 62.8%, p-value 0.030, and 87.5% vs. 64.3%, p-value 0.008, respectively) in cystic fibrosis course. Haplotype AC formed by both changes had also a higher frequency (80%) in patients with severe course compared to the mild character (61.4%) of disease. However, the frequency of promoter variant TNF c.-308C > T (rs1800629) was presented at a significantly lower level in the patient’s group compared to healthy controls (2.7% vs. 15%, p-value 0.001). Furthermore, the presence of methicillin-resistant Staphylococcus aureus significantly correlated with the lower FEV1% in patients (p-value 0.01). Conclusions: Genetic variants, rs1143627 and rs16944, of IL1B are promising candidates as predictors of the severe character of lung disease in Polish patients with cystic fibrosis.",
"keywords": [
"cystic fibrosis",
"modifier genes",
"inflammatory mediators",
"IL1B"
],
"content": "Introduction\n\nRecent scientific outcomes confirm that the clinical phenotype of cystic fibrosis (CF) (OMIM: 219700) is determined not only by classes of mutations in the CFTR gene (cystic fibrosis transmembrane regulator) but in association with environmental factors and genetic variations in modifier genes.1–3 The hypothesis about the role of modifier genes in CF was born based on the observations, that patients with the same CFTR genotype presented diverse manifestations and course of the disease.4 Today, over 2000 different CFTR mutations have been reported and F508del is by far the most common.5 Although mutations in the CFTR gene are well known and classified, the contribution of modulatory genes in CF is currently still investigated. Among analyzed candidate genes are those involved in the inflammatory process, as well as in immunity and antioxidant molecules.6 However, the results of the majority of global research on modifier genes’ role in CF are inconclusive.\n\nCF is a multi-organ disease, whereas chronic pulmonary inflammation and respiratory failure consist of the main cause of death in those patients. There is evidence, that the inflammatory process in the lung is associated with an imbalance between pro- and anti-inflammatory mediators.7 Among important pro-inflammatory cytokines produced during the response are tumor necrosis factor-alpha (TNF-α), interleukins (IL) 8, 6, 1, and 1B, while among cytokines inducing the opposite effect are transforming growth factor-beta 1 (TGFB1) and IL10.8–10\n\nProteins, IL8 and TNF-α, play a crucial role in the pathophysiology of CF lung disease due to their participation in the recruitment and activation of neutrophils on the respiratory epithelial surface, which is a primary component of the innate immune response.11 Thus, genes CXCL8 and TNF coding for those cytokines, which expression is regulated by sequence variants, are highlighted as potential modifier genes in the severity of lung disease in CF. Although numerous polymorphic variants have been described in the CXCL8 gene, the association only between polymorphisms rs4073 (c.-251T>A), rs2227306 (c.781C>T), rs2227307 (c.396T>G), pulmonary function, and clinical severity markers in CF patients was confirmed in several studies.8,12 The most often analyzed changes in the TNF gene are located in the promoter region, such as c.-238G>A (rs361525) having a variable effect on gene expression and c.-308A>G (rs1800629) associated with increased gene transcription, worst pulmonary function, and early pulmonary symptoms in patients with CF.13,14 in contrast to studies performed by Schmitt-Grohé et al.15 and Khorrami et al.16 There is also proven, that some of TNF and CXCL8 polymorphisms are associated with Pseudomonas aeruginosa (PA) chronic colonization in CF patients.14,17 Furthermore, modulating effects on the CF also have shown IL1B and IL10 genes, where the most common SNPs were associated with severe lung disease in pediatric American and Australian populations.18,19 Whereas, in French and German pediatric CF patients those results were not shared.8\n\nResults of up to now performed studies, searching for genes that modify the course and phenotype of CF, mostly concern the association with pulmonary exacerbation. However, based on our long-term observations of CF patients we state, that around 20% of CF patients manifest a pronounced exacerbation of symptoms from the digestive system. We hypothesized, that this possibly may be predicted by polymorphic changes at immunologically relevant genes. Within this context, we have selected 12 polymorphisms located in five genes CXCL8 (rs4073, rs2227306, rs2227307, rs188378669), TNF (rs361525, rs1800629), IL1B (rs16944, rs1143634, rs1142639, rs1143627), IL6 (rs1800795), and IL10 (rs1800896) for correlation analysis, as candidate genetic modulators of the pulmonary or digestive manifestation and severity of the disease among Polish CF patients.\n\n\nMaterials and methods\n\nThe study was approved by the local Ethics Committee of the University of Medical Sciences in Poznan, Poland (resolution no. 675/15), and all experiments were performed following the relevant guidelines and regulations of this Committee. Written informed consent was obtained from each patient. 55 Polish patients (20 males and 35 females) between the ages of 20-52 with diagnosed CF were enrolled for this study. The patient group was collected in 12 months (from January to December 2016) in the Department of Pulmonology, Allergology and Lung Oncology of the Clinical Hospital of Poznan University of Medical Sciences in Poland. Diagnosis of CF in all patients was performed by sweat chloride test results (> 60 mmol/L) or/and identification of CFTR gene mutations. Detailed information about each patient including sex, age, BMI, age of diagnosis, presence of F508del mutation, pulmonary function parameters, function of internal organs, complications, and hospitalizations were recorded. Additionally, a control group of 50 healthy individuals was collected. A detailed characteristics of the study cohort with clinical and demographic data are presented in Table 1.\n\nPulmonary function tests, using Jaeger MasterScreen system (Erich Jaeger GmbH; Würzburg, Germany) were performed to assess lung function. All spirometric examinations were carried out with the subject seated, using a nose clip and a disposable mouthpiece. Using spirometric measurements, values of expiratory forced vital capacity (FVC) and forced expiratory volume in one second (FEV1%) were obtained and were expressed as the percentage of predicted values according to European Community for Steel and Coal.20\n\nAt the same time the body plethysmography for assessing residual volume (RV), total lung capacity (TLC), and diffusing capacity of the lungs for carbon monoxide (DLCO) were performed.\n\nSputum/bronchoalveolar lavage results for Pseudomonas aeruginosa according to Leed’s criteria, presence of other Gram-negative microorganisms (mostly Stenotrophomonas maltophilia and Alcaligenes xylosoxidans), and methicillin-resistant Staphylococcus aureus (MRSA) were obtained from microbiological reports for each patient.\n\nPatients were divided in the context of lung function impairment, based on the FEV1% values, 1 - within the norm (FEV1% ≥ 70) and mild pulmonary obstruction (FEV1% 40-70) (35 subjects in total), 2 - severe pulmonary obstruction (FEV1% ≤ 40) (20 subjects in total).\n\nIn an attempt to analyze the correlation between the genotype and manifestation of CF, patients were divided into two subgroups depending on the dominant symptoms - the group with the manifestation primarily from the respiratory system (44 individuals) and the group of patients with prevalent gastrointestinal symptoms (11 individuals). The division was made by the specialists from the pulmonology field conducting the patients, based on the clinical data and interview (including information about the presence or absence of glucose metabolism disorders, pancreatic exocrine insufficiency, chronic liver disease, malnutrition, pulmonary complications, and FEV1% values).\n\nIn correlation analysis of manifestation and severity of CF with genetic factors, the participation of F508del mutation as a differentiating factor was excluded because the frequency difference of this mutation in individual groups was under statistical significance (pulmonary – 81%, gastrointestinal – 73%, severe – 80%, mild – 68%).\n\nGenomic DNA of each patient was extracted from the peripheral blood samples (5 mL) using the standard method with guanidine isothiocyanate (GTC). Detection of the single nucleotide polymorphisms (SNPs) in five genes: CXCL8 (rs4073, rs2227306, rs2227307, rs188378669), TNF (rs361525, rs1800629), IL1B (rs16944, rs1143634, rs1142639, rs1143627), IL6 (rs1800795) and IL10 (rs1800896) was performed using pyrosequencing or Sanger sequencing. Primers for the pyrosequencing analysis were designed using PyroMark Assay Design Software (Biotage, Uppsala, Sweden) and for Sanger sequencing using Primer3Plus software. Primer details are shown in Table 2. Amplification of targeted DNA regions was carried out on Applied Biosystems 2720 Thermal Cycler (Applied Biosystems, Foster City, CA) on the total volume of 30 uL containing 0.75 U of FIREPol® DNA Polymerase, 2.5 μL 10× buffer, 2.0 μL dNTP mix (2.5 mM each dNTP), 1.5 mM MgCl2 solution, 80 ng DNA and 0.2 μM of each primer. All reagents were obtained from Solis BioDyne (Tartu, Estonia). The amplification products were analyzed in 1.5% agarose gels electrophoresis. Pyrosequencing was performed by the PSQ™ 96MA system (Qiagen) using PyroMark™ Gold Q96 Reagents (Qiagen GmbH, Hilden, Germany), according to the manufacturer instructions. Direct sequencing was performed using BigDye Terminator v3.1 Cycle Sequencing Kit (Thermo Fisher Scientific) on the Applied Biosystems 3500 and Series Genetic Analyzers.\n\n* Primers labelled with biotin for pyrosequencing.\n\nConformance of genotypes distribution of all analyzed polymorphisms with the Hardy-Weinberg equilibrium (HWE) was assessed using Fisher’s exact test. The pair-wise linkage disequilibrium (LD) of variants located in genes TNF, CXCL8, and IL1B was evaluated by Lewontin’s D′ using Haploview software version 4.2. The correlation analyses between genotypes and clinical data were performed using the chi-square test and Fisher’s exact test.\n\nFor all calculations, STATISTICA 12.0 software (Stat Soft, 2014) was used. The level of significance was set at p < 0.05.\n\n\nResults\n\nA total of 55 CF Polish patients and 50 healthy controls were successfully genotyped for selected 12 polymorphisms located in genes CXCL8, TNF, IL1B, IL6, and IL10. Genotypes distribution for all SNPs met the requirements of HWE. No relevant differences in variant allele frequency between both groups were demonstrated. Only TNF c.-308C > T variant was observed significantly less often in the patient group (2.7%) compared to controls (15%), where the p-value was 0.001. All obtained frequencies of each genotype and allele are presented in Table 3.\n\n** HWE – Hardy-Weinberg equilibrium (occurs when p > 0.05).\n\nOur haplotype analysis confirmed a strong LD (D' = 1, r2 = 0.928) between variants c.-251T > A (rs4073), c.781C > T (rs2227306) and c.396T > G (rs2227307) in the CXCL8 gene, forming four haplotypes: TCT, ATG, TCG and ACG observed in our CF patient group with frequency 54.6%, 41.8%, 1,8% and 1,8%, respectively. Furthermore, two polymorphic changes located in the promoter region of IL1B gene, c.-118G > A (rs1143627) and c.-598T > C (rs16944) were observed in high LD (D’ = 0.904, r2 = 0.75), constructing a haploblock, where haplotypes AC, GT, GC, AT frequency was 68.1%, 26.3%, 3.7% and 1.9%, respectively. Both haploblocks are presented on the Figure 1.\n\nFirst, we have analyzed all 12 variants in designated, based on clinical data, groups of patients - with different manifestations of CF (with pulmonary or digestive dominant symptoms) and with variable courses of disease (mild or severe) to examine possible association.\n\nOur study demonstrated that the presence of two polymorphisms, c.-598T > C (rs16944) and c.-118G > A (rs1143627), in IL1B gene significantly correlate with character of disease (Table 4). Higher frequency of variant allele c.-598C was observed in patients with severe character of CF, compared to patients with mild course of disease (87.5% and 64.3%, respectively, χ2 = 6.92; p = 0.008). Similarly, variant allele c.-118A occurred with higher frequency in subjects presented severe character of CF versus those with mild course of disease (82.5% vs. 62.8%, respectively, χ2 = 4.68; p < 0.05).\n\nConsidering the fact, that analyzed changes formed in our study two haploblocks (in CXCL8 and IL1B genes), an analysis of the haplotypes in the context of the course and manifestation of disease was performed. We proved, that only haplotype AC created by changes c.-118G > A and c.-598T > C in IL1B gene is significantly more often observed in group with severe course of CF in comparison with mild course (80% and 61.4%, respectively; χ2 = 4.055; p = 0.03).\n\nFurthermore, the presence of MRSA and PA in the context of manifestation and course of the disease was checked. Our research has shown that only MRSA was significantly often observed in patients with severe course of CF compared to the mild character of disease (25% and 2.9%, respectively; p = 0.02). Additionally, correlation analysis between MRSA presence and lung function in the whole patients group indicated lower FEV1% in patients with MRSA (p = 0.01) (Figure 2).\n\nThe presence of PA was observed with 72.7% and 54.5% frequency in groups with pulmonary and digestive symptoms, respectively (p > 0.05), while in patients with mild and severe lung impairment with frequency 60% and 85%, respectively (p > 0.05).\n\n\nDiscussion\n\nBecause CF is a multifactorial, life-shortening disorder, the determination of SNPs that would affect the general phenotype or course of the disease is essential, but also challenging due to previous inconclusive results. So far, most of the CF studies were focused on searching modifier genes responsible for the severe pulmonary phenotype of the disease. In our investigation we have analyzed the impact of selected 12 potential candidates of modulator changes, rs4073, rs2227306, rs2227307 and rs188378669 in CXCL8 gene, rs361525 and rs1800629 in TNF gene, rs16944, rs1143634, rs1142639 and rs1143627 in IL1B gene, rs1800795 in IL6 gene and rs1800896 in IL10 gene on CF phenotype in Polish patients, taking into account the severity of symptoms on the side of the digestive, but also, respiratory system. Our hypothesis was that candidate modulator changes may predict digestive character of CF.\n\nWe observed, that in most of our group of patients (80%) the dominating symptoms occurred from the respiratory system and only in 20% of CF patients from the digestive system. Severe character of lung disease, diagnosed based on the FEV1% values, was noted in 20 patients (36%) and mild in 35 individuals (64%). In those subgroups of patients, we have performed a correlation analysis with DNA changes. Obtained variant allele frequencies of analyzed genetic variants, did not much differ from reference values for European population in 1000 Genomes database, except change TNF c.-308C > T (rs1800629) which occurred in our patients group less often (2,7%) than in the database (13%). Also interesting is, that variant CXCL8 c.91G > T, p.Glu31Ter (rs188378669) globally noted with variant allele frequency < 0.1%, was detected in our CF patients at level 0.9% (one heterozygote detected in a cohort of 55 individuals). In our previous study, we proved, that this variant is significantly more common in patients with inflammatory bowel disease (MAF = 2.12%, 15 heterozygotes detected in a cohort of 353 patients) compared to healthy Polish population (MAF = 0.25%, 1 heterozygote identified in a cohort of 200 individuals of Polish population), what may suggest its association with inflammatory diseases (unpublished data). Therefore, studies on a larger group of patients are undoubtedly necessary to verify the participation of this variant in CF, especially since there are no data on the relationship with this disease.\n\nOur study revealed, that among all analyzed genetic changes two of them, c.-598T > C (rs16944) and c.-118G > A (rs1143627) located in the IL1B gene, are significantly associated with the severe character of lung disease in polish CF subjects. Allele C in locus -598 was observed with frequency of 87.5% in patients with severe lung disease compared to patients with mild lung dysfunction (64.3%, p = 0.008, OR = 3.88, C.I. = [1.351-11.190]), while allele A in locus -118 was observed with frequency 82.5% and 62.8% in both groups, respectively (p = 0.03, OR = 2.78, C.I. = [1.079-7.194]). We confirmed high LD between both changes (rs1143627 and rs16944) creating haplotypes AC, GT, GC and AT, where AC was significantly more often observed in subjects with severe course of CF in comparison to mild.\n\nOur findings concerning the impact of polymorphism rs16944 on CF phenotype are consistent with those obtained by de Vries et al.18 They also proved a significant correlation of the variant allele c.-598C of IL1B gene with severe pulmonary dysfunction in total of 152 Australian CF patients. Similarly, Levy et al.19 have reported that IL1B constitutes a clinically relevant modulator of CF lung disease in the study conducted among American patients. However, in their research other SNPs, rs1143634 and rs1143639 demonstrated a consistent association with severe pulmonary phenotype.\n\nIn contrast to those results, Corvol et al.8 did not find any correlation between variants c.-598T > C and c.-118G > A in IL1B gene and lung function assessed by spirometry in 329 Caucasian CF children from France and Germany. Additionally, they did not confirm any linkage disequilibrium between those polymorphisms.\n\nStudies mainly highlight the relationship between lung disease in CF and CXCL8 gene polymorphism.21–23 IL8 plays a crucial role in the pathophysiology of inflammation of the airways in CF patients caused by a deficiency or absence of the CFTR protein.24 Our study did not confirm this association among Polish patients.\n\nInterestingly, our research demonstrated that MRSA, but not PA presence, determine severe pulmonary phenotype of CF. So far, studies have shown PA presence as a risk factor of respiratory failure in CF patients. We did not find any SNP, which correlated with PA or MRSA colonization in CF patients, in contrast to results of Cutinho et al.14 who reported that AA genotype in the c.-308 position of the TNF gene is protective for early colonization with PA or Furlan et al.,12 which demonstrated association between PA presence and CXCL8 variants.\n\nWe are aware of several limitations of our research. Our study cohort included only 55 patients and 50 controls. In the next step, verification of our results should be performed on a larger group of patients. This may be crucial in the case of rare variants, as c.91G > T, p.Glu31Ter (rs188378669) in CXCL8 gene, candidate as a modifier of CF. Furthermore, other factors such as BMI, gender, or age of diagnosis was not taken into account in our statistical analyzes.\n\nWe should also highlight the strengths of our study. First, the study cohort was represented by detailed characterized patients and homogenous controls group. What is important, the effect of CFTR mutation F508del on the manifestation and course of CF in the studied patients was excluded because the frequency of mutations in the subgroups was similar.\n\nAlthough this study does not indicate any modulators of digestive manifestation of CF, it constitutes the first report of genes predicting the course of this disease in the Polish population.\n\nRecent studies indicate the important role of the microbiome in the course and manifestation of cystic fibrosis. Scientists underline that both, genotype and microbiome profiles are crucial interconnected factors in disease progression.25\n\n\nConclusions\n\nOur data have shown, that from all analyzed pro-inflammatory cytokine genes, only IL1B, but not TNF, CXCL8, IL6, or IL10 clearly play a crucial role in CF manifestation, determining the severe character of lung disease. This is a confirmation of major global results, as well as the first report concerning modulator genes of CF manifestation among Polish patients. Unfortunately, none of the analyzed genetic variants was found as predictors of digestive manifestation of CF disease, which may suggest the participation of also other modulator genes in the final phenotype of the disease.\n\n\nData availability statement\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
"appendix": "References\n\nMarson FAL, Bertuzzo CS, Ribeiro JD: Personalized drug therapy in cystic fibrosis: from fiction to reality. Curr. Drug Targets. 2015; 16(9): 1007–1017. PubMed Abstract | Publisher Full Text\n\nStanke F, Becker T, Kumar V, et al.: Genes that determine immunology and inflammation modify the basic defect of impaired ion conductance in cystic fibrosis epithelia. J. Med. Genet. 2011; 48: 24–31. PubMed Abstract | Publisher Full Text\n\nHull J, Thompson AH: Contribution of genetics factor other than CFTR to disease severity in Cystic Fibrosis. Thorax. 1998; 53: 1018–1021. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBronsveld I, Mekus F, Bijman J, et al.: Chloride conductance and genetic background modulate the cystic fibrosis phenotype of Delta F508 homozygous twins and siblings. J. Clin. Invest. 2001; 108(11): 1705–1715. PubMed Abstract | Publisher Full Text\n\nDe Boeck K: Cystic fibrosis in the year 2020: A disease with a new face. Acta Pediatr. 2020; 109(5): 893–899. PubMed Abstract | Publisher Full Text\n\nMerlo CA, Boyle MP: Modifier genes in cystic fibrosis lung disease. J. Lab. Clin. Med. 2003; 141(4): 237–241. Publisher Full Text\n\nTabary O, Corvol H, Boncoeur E, et al.: Adherence of airway neutrophils and inflammatory response are increased in CF airway epithelial cell-neutrophil interactions. Am. J. Physiol. Lung Cell. Mol. Physiol. 2006; 290(3): L588–L596. PubMed Abstract | Publisher Full Text\n\nCorvol H, Boelle PY, Brouard J, et al.: Genetic variations in inflammatory mediators influence lung disease progression in cystic fibrosis. Pediatr. Pulmonol. 2008; 43(12): 1224–1232. PubMed Abstract | Publisher Full Text\n\nJundi K, Greene CM: Transcription of interleukin-8: how altered regulation can affect cystic fibrosis lung disease. Biomolecules. 2015; 5(3): 1386–1398. PubMed Abstract | Publisher Full Text\n\nArkwright PD, Laurie S, Super M, et al.: TGF-beta(1) genotype and accelerated decline in lung function of patients with cystic fibrosis. Thorax. 2000; 55: 459–462. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDowney DG, Bell SC, Elborn JS: Neutrophils in cystic fibrosis. Thorax. 2009; 64(1): 81–88. PubMed Abstract | Publisher Full Text\n\nFurlan LL, Marson FA, Ribeiro JD, et al.: IL8 gene as modifier of cystic fibrosis: unraveling the factors which influence clinical variability. Hum. Genet. 2016; 135(8): 881–894. PubMed Abstract | Publisher Full Text\n\nActon JD, Wilmott RW: Phenotype of CF and the effects of possible modifier genes. Paediatr. Respir. Rev. 2001; 2(4): 332–339. PubMed Abstract | Publisher Full Text\n\nCoutinho CA, Marson FA, Marcelino AR, et al.: TNF-alpha polymorphisms as a potential modifier gene in the cystic fibrosis. Int. J. Mol. Epidemiol. Genet. 2014; 5(2): 87–99. PubMed Abstract\n\nSchmitt-Grohé S, Stüber F, Book M, et al.: TNF-alpha promoter polymorphism in relation to TNF-alpha production and clinical status in Cystic Fibrosis. Lung. 2006; 184: 99–104. PubMed Abstract | Publisher Full Text\n\nKhorrami A, Bonyadi M, Rafeey M, et al.: Association of TNF-α Gene Variants With Clinical Manifestation of Cystic Fibrosis Patients of Iranian Azeri Turkish Ethnicity. Iran. J. Pediatr. 2015; 25(1): e307. PubMed Abstract | Publisher Full Text\n\nYarden J, Radojkovic D, de Boeck K , et al.: Association of tumour necrosis factor alpha variants with the CF pulmonary phenotype. Thorax. 2005; 60(4): 320–325. PubMed Abstract | Publisher Full Text\n\nde Vries L , Griffiths A, Armstrong D, et al.: Cytokine gene polymorphisms and severity of CF lung disease. J. Cyst. Fibros. 2014; 13(6): 699–705. PubMed Abstract | Publisher Full Text\n\nLevy H, Murphy A, Zou F, et al.: IL1B polymorphisms modulate cystic fibrosis lung disease. Pediatr. Pulmonol. 2009; 44(6): 580–593. PubMed Abstract | Publisher Full Text\n\nQuanjer PH, Tammeling GJ, Cotes JE, et al.: Lung volumes and forced ventilatory flows. Report Working Party Standardization of Lung Function Tests, European Community for Steel and Coal. Official Statement of the European Respiratory Society. Eur. Respir. J. Suppl. 1993; 16: 5–40. PubMed Abstract\n\nHeinzmann A, Ahlert I, Kurz T, et al.: Association study suggests opposite effects of polymorphisms within IL8 on bronchial asthma and respiratory syncytial virus bronchiolitis. J. Allergy Clin. Immunol. 2004; 114: 671–676. PubMed Abstract | Publisher Full Text\n\nHillian AD, Londono D, Dunn JM, et al.: Modulation of cystic fibrosis lung disease by variants in interleukin-8. Genes Immun. 2008; 9(6): 501–508. PubMed Abstract | Publisher Full Text\n\nScarel-Caminaga RM, Kim YJ, Viana AC, et al.: Haplotypes in the interleukin 8 gene and their association with chronic periodontitis susceptibility. Biochem. Genet. 2011; 49(5–6): 292–302. PubMed Abstract | Publisher Full Text\n\nPoghosyan A, Patel JK, Clifford RL, et al.: Epigenetic dysregulation of interleukin 8 (CXCL8) hypersecretion in cystic fibrosis airway epithelial cells. Biochem. Biophys. Res. Commun. 2016; 476(4): 431–437. PubMed Abstract | Publisher Full Text\n\nFrançoise A, Héry-Arnaud G: The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes (Basel). 2020; 11(5): 536. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "135127",
"date": "16 May 2022",
"name": "Tadeusz Przybyłowski",
"expertise": [
"Reviewer Expertise Lung 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 is a very interesting paper in which the authors decided to evaluate whether selected polymorphic variants in genes encoding selected inflammatory mediators can predict pulmonary or digestive manifestation of cystic fibrosis and severity of lung involvement. Using advanced genetic engineering techniques they have genotyped 12 variants in TNF, CXCL8, IL1B, IL6 and IL10 genes in a group of 55 Polish patients with cystic fibrosis and 50 healthy controls. The most important outcome was the finding of significant differences in the frequency of two promoter variants of IL1B, rs1143627 (c.-118G > A) and rs16944 (c.-598T > C) in relation to the severity of lung involvement. It was also observed that AC haplotype was significantly more frequent in the group of patients with more advanced lung damage than in the group with milder disease progression. These results allowed the authors to conclude that genetic variants, rs1143627 and rs16944, of IL1B may be used as predictors of more severe respiratory involvement in the course of cystic fibrosis. Additionally, it should be noted that this is the first study of its type performed in a group of Polish patients.\nThe work was prepared very carefully, but in my opinion, 2 issues need re-evaluation.\nThe way of classifying patients into different stages of disease severity on the basis of FEV1 is not very clear to me. Why the cut-off points of 70% and 40% of predicted were used?. In this part of method description there should be information if it was arbitrary classification or if it is consistent with the generally accepted system of grading, and in this case reference to an appropriate publication should be given.\n\nThe paragraph concerning the occurrence of PA and MRSA in the studied group does not fit into the subject of the paper, does not add any new information, and may be omitted in the final version.\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": "8270",
"date": "23 May 2022",
"name": "Oliwia Zakerska-Banaszak",
"role": "Author Response",
"response": "Dear Reviewer, Prof. Przybyłowski, We thank you very much for your comments and all the valuable suggestions concerning our manuscript. According to Your questions: The way of classifying patients into different stages of disease severity on the basis of FEV1 is not very clear to me. Why were the cut-off points of 70% and 40% of predicted were used?. In this part of the method description there should be information if it was arbitrary classification or if it is consistent with the generally accepted system of grading, and in this case reference to an appropriate publication should be given. The paragraph concerning the occurrence of PA and MRSA in the studied group does not fit into the subject of the paper, does not add any new information, and may be omitted in the final version. Our response: In the literature on cystic fibrosis, disease severity is determined from FEV1 as follows: FEV1> 70% severe, 40-69% moderate, and <40% severe. Such a division was presented, inter alia, in the work: Yankaskas JR. Cystic fibrosis adult care: consensus conference reprt. chest 2004; 125: 1-39. The paragraph concerning the occurrence of PA and MRSA was omitted. Thank You very much. We hope our revised version of the manuscript will be correct now. Your sincerely, Oliwia Zakerska-Banaszak"
}
]
}
] | 1
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https://f1000research.com/articles/11-379
|
https://f1000research.com/articles/11-909/v1
|
08 Aug 22
|
{
"type": "Systematic Review",
"title": "A systematic review assessing the effectiveness of COVID-19 mRNA vaccines in chronic kidney disease (CKD) individuals",
"authors": [
"Soniya A. Malik",
"Kavindiya Modarage",
"Paraskevi Goggolidou",
"Soniya A. Malik",
"Kavindiya Modarage"
],
"abstract": "Background: SARS-CoV-2 is a coronavirus that has rapidly spread across the world with a detrimental effect on the global population. Several reports have highlighted an increased mortality rate and a higher severity of COVID-19 infection in chronic kidney disease (CKD) individuals. Upon the development of various SARS-CoV-2 vaccines, mRNA vaccines including BNT162b2 and mRNA-1273 were deemed safe, with a high efficacy in preventing COVID-19 in the general population. This review investigates whether SARS-CoV-2 mRNA vaccines are as effective in triggering an immune response in Dialysis Patients (DPs) and Kidney Transplant Recipients (KTRs) and if a third dose is required in this population. Methods: A systematic search employing the PRISMA criteria was conducted in several major databases, with the data being extracted from publications for the period January 2021 to May 2022 (PROSPERO: CRD42022338514, June 15, 2022). Results: 80 studies were included in this analysis with a total cohort number of 15,059 participants. Overall, 85.29% (OR = 17.08, 95% CI = 15.84-18.42, I2 = 98%) and 41.06% (OR = 0.52, 95% CI = 0.48-0.5, I2 = 95%) of DPs and KTRs included in this review showed positive seroconversion after two doses of either mRNA vaccine, respectively. A total 76% (OR = 6.53, 95% CI = 5.63-7.5, I2 = 96%) of the cohort given a third dose of an mRNA vaccine demonstrated positive seroconversion, with 61.86% (OR = 2.31, 95% CI = 1.95-2.75 I2 = 95%) of the cohort that was assessed for a cellular response displaying a positive response. Conclusions: This data emphasises a reduced incidence of a positive immune response in DPs and KTRs compared to healthy controls, albeit a better response in DPs than when compared to KTRs alone was observed. A third dose appears to increase the occurrence of an immune response in the overall DP/KTR cohort.",
"keywords": [
"Chronic Kidney Disease",
"COVID-19",
"Dialysis",
"IgAN",
"mRNA Vaccines",
"Kidney Transplant"
],
"content": "Introduction\n\nIn December 2019, an outbreak of atypical respiratory disease was reported in Wuhan, Hubei Province, China (Kumar et al., 2021). This was later confirmed to be caused by a novel coronavirus, formally recognised by the World Health Organisation (WHO) as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or Coronavirus Disease-2019 (COVID-19) (Tsang et al., 2021). SARS-CoV-2 rapidly spread across the globe, with WHO declaring it a Public Health Emergency of International Concern (PHEIC) on January 30, 2020 (Cucinotta and Vanelli, 2020). Shortly after, COVID-19 was declared a pandemic by WHO on March 11, 2020, with current data from WHO reporting a cumulative total number of 521,920,560 cases and 6,274,323 total deaths as of May 23, 2022 (Cucinotta and Vanelli, 2020; WHO Coronavirus (COVID-19) Dashboard).\n\nSARS-CoV-2 is a β-coronavirus; coronaviruses consist of enveloped, positive-sense, single-stranded RNA, and non-structural, structural and accessory proteins (Chan et al., 2020; Yadav et al., 2021). Each of these proteins play a crucial role in the process of viral-host invasion. In the initial stages of infection, the spike (S) protein is a crucial factor for viral entry. The S protein is composed of two functional subunits, S1 and S2. The S1 subunit of the S protein in SARS-CoV-2 is responsible for binding to the cellular ligand on Angiotensin Converting Enzyme 2 (ACE2) receptor on the host cell surface (Tsang et al., 2021; Yuki, Fujiogi and Koutsogiannaki, 2020; Hoffmann et al., 2020; Li et al., 2003). Following this interaction, transmembrane protease serine 2 (TMPRSS2) plays a crucial role in priming the S1/S2 cleavage site, leading to the stabilisation and subsequent cleavage of the S2 subunit (Hoffmann et al., 2020; Tsang et al., 2021; Belouzard, Chu and Whittaker, 2009). This presumably activates the S protein, facilitating the viral and host cell membrane fusion (Belouzard, Chu and Whittaker, 2009; Hoffmann et al., 2020; Ou et al., 2020). Upon cell entry, the replicase complex begins the process of transcription and translation, leading to the synthesis of new viral RNA and proteins. At this stage, the nucleocapsid (N) protein will begin virion assembly and bind new genomic RNA, whilst the S, envelope (E) and membrane (M) structural proteins, which comprise trafficking signal sequences, translocate to the endoplasmic reticulum (Chang et al., 2005; Chen, Liu and Guo, 2020; Yadav et al., 2021; Tsang et al., 2021). The M protein plays a crucial role in shaping virions and binding to the nucleocapsid, whilst the E protein then plays a direct role in viral pathogenesis, assembly and eventual release out of the cell via exocytosis (Neuman et al., 2011; Chen, Liu and Guo, 2020; Yadav et al., 2021).\n\nThe initial point of entry for SARS-CoV-2 is the respiratory tract, where the virus will enter and bind to nasal epithelial cells in the upper respiratory tract, via ACE2 (Sungnak et al., 2020). ACE2 is expressed in several organs including the heart, lungs and intestine (Tsang et al., 2021; Zou et al., 2020). Importantly, the highest levels of expression of ACE2 can be found in the kidneys, especially in renal tubular cells (Hamming et al., 2004). However, it has been reported that ACE2 expression can vary within kidney disease and renal transplant patients, with a reduced level of ACE2 expression also reported in diabetic nephropathy (Tikellis et al., 2003; Lely et al., 2004). Upon investigation, one in vivo study highlighted that chronic pharmacologic inhibition of ACE2 could worsen glomerular injury (Soler et al., 2007). Kidney cells also express TMPRSSs, a co-receptor to viral entry (Chen et al., 2021). Since the kidney is a target organ for SARS-CoV-2, viral invasion and consequent replication in kidney cells have the potential to trigger a cytokine storm, initiating possible organ damage in patients (Jin et al., 2020). Population studies revealed that older patients were more prone to a severe clinical outcome alongside those who were clinically vulnerable and suffered from conditions including but not limited to diabetes, cardiovascular disease (CVD) and chronic kidney disease (CKD) (Hu and Wang, 2021; Gansevoort and Hilbrands, 2020).\n\nDeveloping research has quickly recognised that CKD patients are more susceptible and prone to developing severe outcomes due to SARS-CoV-2 infection. High mortality risk was associated with CKD for patients with eGFR <30 mL/min/1.73 m2 (adjusted hazard ratio (aHR) 2.52), dialysis patients (aHR 3.69) and transplant patients (aHR 3.53), constituting some of the top risk categories in this study (Williamson et al., 2020). Similar to this, the 28-day mortality was 20.0% (95% confidence interval (CI) 18.7% - 21.4%) and 19.9% (17.5% - 22.5%) in 3285 dialysis patients (DPs) and 1013 kidney transplant recipients (KTRs), respectively (Jager et al., 2020). Another meta-analysis established a higher mortality rate in CKD patients with COVID-19 infection compared to those without COVID-19 infection (pooled OR 5.81 (95% CI 3.78 – 8.94)) (Cai et al., 2021).\n\nNearing the end of 2021, several SARS-CoV-2 vaccines have emerged for use with authorisation across the globe. According to WHO, as of May 17, 2022, a total of 12,186,798,032 vaccine doses have been administered (WHO Coronavirus (COVID-19) Dashboard). Despite several studies investigating the safety and efficacy of vaccinations, there is no conclusive evidence as to whether the SARS-CoV-2 vaccines provide the same level of immunity in CKD patients. Overall, it has been deemed safe to use the mRNA vaccines BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) in immunocompromised patients, including CKD patients (Windpessl et al., 2021). Clinical trials have detected a higher level of efficacy in mRNA vaccines compared to viral-vectored vaccines (95% for BNT162b2, 94.1% for mRNA-1273, 70.4% for ChAdOx1 nCoV-19) (Baden et al., 2021; Polack et al., 2020; Voysey et al., 2021). All three vaccines have got the ability to induce a strong S-specific antibody response followed by T-cell immunity after two parenteral injections (Folegatti et al., 2020; Jackson et al., 2020). However, since characteristics such as kidney disease, and dialysis treatment/transplantation could affect vaccination efficacy, this study will focus on investigating the evidence on whether the SARS-CoV-2 mRNA vaccines can indeed provide effective immunity to CKD individuals and if further action is required.\n\n\nMethods\n\nThis systematic review was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, published in 2020. See Reporting guidelines (Goggolidou, 2022) for the completed checklist. The study was registered in PROSPERO: CRD42022338514, on June 15, 2022 (Page et al., 2021). A preliminary search was first conducted on PubMed for publications detailing the efficacy of SARS-CoV-2 vaccination in CKD patients to validate the research question. This was followed by a systematic search by two independent reviewers which was last conducted on May 23, 2022 on PubMed, Google Scholar, Semantic Scholar, CORE, Science Open and BioMed Central using search terms and phrases of ‘efficacy of COVID-19 vaccine’, ‘immunogenicity of COVID-19 vaccine’, ‘chronic kidney disease’ and ‘COVID-19 booster’. Filters were applied whereby only studies published between January 2021 and May 2022 were included, with unpublished studies i.e. pre-prints also being included in this analysis. Inclusion and exclusion criteria were defined to ensure all relevant studies were identified. Only studies with an adult human cohort of any sex and published in any country were included. Patients under the age of 18 were excluded from this analysis. As well as this, studies or trials that specify the vaccine type including BNT162b2 and mRNA-1273 vaccinations were only included. Patients who received any other form of COVID-19 vaccine were excluded, since there was limited information available. The studies must have also mentioned at least the treatment regimen that patients were undertaking including dialysis or transplantation. If this was unclear, studies were excluded. Studies were grouped into categories according to the treatment regimen patients undertook and the vaccine that patients were given, including the number of doses. As well as this, studies were separated according to the type of analysis that was undertaken i.e., seroconversion and/or cellular analysis.\n\nStudies were grouped together as described above with two independent reviewers assessing whether they met the inclusion criteria (S.A.M, K.M). Studies were assessed and data was collected via Microsoft Excel 2016 by the same reviewers. The information extracted included sample size and sample groups, treatment regimen, number of doses, whether there is a history of COVID-19 and how long after vaccination any assessments took place. The effects and responses to the vaccination including humoral and cellular immunity responses after the second and third doses were also reviewed (the PRISMA flow diagram is given as Figure 1). Any disputes were overlooked by P. G. Studies with missing or unclear data were removed from the analysis. The risk of bias and heterogeneity were assessed with the Cochrane’s Q test and I2 test using RevMan (version 5.4) by two independent reviewers (S.A.M, K.M).\n\nTwo independent reviewers assessed studies for eligibility for each synthesis using Microsoft Excel 2016. Studies were grouped in accordance with data availability before being included in the synthesis, with those with missing data being excluded from analysis. Funnel plots, forest plots and statistical analysis were performed using RevMan (version 5.4). Odds ratios (OR) and 95% confidence intervals (CI) were calculated to evaluate the seroconversion and cellular response in DPs and KTRs after two and/or three doses of the BNT162b2 and mRNA-1273 vaccinations. The seroconversion is a measure of antibody response to SARS-CoV-2-specific antibodies including IgG, IgA, and IgM antibodies. The cellular response incorporated the number of patients that developed a T-cell response across the studies included in this analysis, including CD4+ and CD8+ T cells. The population was divided into subgroups i.e., dialysis patients and transplant recipients; two dose and three dose groups; seroconversion and cellular response group. A pooled 95% CI not including 1 for the OR was considered as statistically significant. Risk of bias/heterogeneity was assessed using RevMan (version 5.4) with the Cochrane’s Q test and I2 test and presented in funnel and forest plots. If a P value of < 0.1 and/or I2 was > 50%, heterogeneity was determined as significant.\n\n\nResults\n\nA total of 80 studies (76 published, 4 preprints) were included in this work, with an overall cohort number of 15,059 participants. Of these, 11,509 participants were recipients of the BNT162b2 vaccine, with 4,263 being KTRs and 7,246 participants being DPs. Separately, a total of 3,550 participants were vaccinated with the mRNA-1273 vaccine. Of these, 826 participants were KTR, and 2,724 participants were DP. Finally, 292 participants had been given the ChAdOx-1 nCoV-19 vaccination, with 11 participants being KTR and 281 participants being DP. Due to the lack of studies for ChAdOx-1 nCoV-19 vaccination in this population, this data was excluded from analysis and one study was ruled out (Meshram et al., 2021). Seroconversion and cellular response were assessed to investigate whether the mRNA vaccines were able to trigger a response in immunocompromised patients; to determine if a particular vaccine was more appropriate for DPs or KTRs; and to determine the ability of a third dose in inducing an antibody or cellular response in this population type.\n\n57 studies with a total of 9,913 participants were included to determine how effective two doses of the mRNA vaccines, including BNT162b2 and mRNA-1273, were in DPs. Overall, the mRNA vaccines prove to be effective in inducing seroconversion, with around 85.29% of participants positively seroconverting. All but five studies in this cohort favoured positive seroconversion with the remaining 14.71% of participants favouring no seroconversion response (OR = 17.08, 95% CI = 15.84-18.42, Figure 2A). Significant heterogeneity was observed (P < 0.00001, I2 = 98%, Figure 2B).\n\n(A) Forest plot comparison of the number of DPs who seroconverted or had no response after two doses of an mRNA vaccination (OR = 17.08, 95% CI = 15.84-18.42, P < 0.00001, I2 = 98%). (B) Funnel plot evaluating heterogeneity when comparing seroconversion response in DPs after two doses of an mRNA vaccine. Significant heterogeneity was observed (P < 0.00001, I2 = 98%).\n\nComparatively, 33 studies with a total of 4,822 participants were included to determine the effectiveness of two doses of the mRNA vaccines including BNT162b2 and mRNA-1273 in KTRs. Compared to the seroconversion rate in DPs, the mRNA vaccines were not able to effectively trigger a positive seroconversion in the KTR population. 41.06% of participants displayed positive seroconversion, with the remaining 58.94% of participants showing no response (OR = 0.52, 95% CI = 0.48-0.56, Figure 3A). Significant heterogeneity was observed (P < 0.00001, I2 = 95%, Figure 3B).\n\n(A) Forest plot comparison of the number of KTRs who seroconverted or had no response after two doses of an mRNA vaccination (OR = 0.52, 95% CI = 0.48-0.56, P <0.00001, I2 = 95%). (B) Funnel plot evaluating heterogeneity when comparing seroconversion response in KTRs after two doses of an mRNA vaccine. Significant heterogeneity was observed (P <0.00001, I2 = 95%).\n\nAside from this, 17 studies with a total of 1,513 participants were included to determine the effectiveness of three doses of the mRNA vaccines, consisting of either the BNT162b2 or the mRNA-1273 in both DPs and KTRs. Of the participants that were included in this assessment, 76% displayed seroconversion after three doses of an mRNA vaccine, with 24% of participants showing no response; multiple studies included in this analysis demonstrate a strong, positive seroconversion after a third dose of an mRNA vaccine (OR = 6.53, 95% CI = 5.63-7.58, Figure 4A). Significant heterogeneity was however observed (P < 0.00001, I2 = 96%, Figure 4B).\n\n(A) Forest plot comparison of the number of DPs and KTRs who positively seroconverted after three doses of an mRNA vaccine (OR = 6.53, 95% CI = 5.63-7.58, P < 0.00001, I2 = 96%). (B) Funnel plot evaluating heterogeneity when comparing seroconversion in DPs and KTRs after three doses of an mRNA vaccine. Significant heterogeneity was observed (P < 0.00001, I2 = 96%).\n\nFurther to this, 12 studies with a total of 978 participants were included for this analysis to determine how many DPs and KTRs developed a cellular response after being vaccinated with two doses of either the BNT162b2 or mRNA-1273 vaccines. Overall, in this cohort, 61.86% of participants favoured an effective cellular response with a further 38.14% of participants showing no cellular response (OR = 2.31, 95% CI = 1.95-2.75) (Figure 5A), nevertheless significant heterogeneity was observed (P < 0.00001, I2 = 95%; Figure 5B).\n\n(A) Forest plot comparison of the number of DPs and KTRs who developed a cellular response after two doses of an mRNA vaccine (OR = 2.31, 95% CI = 1.95-2.75, P < 0.00001, I2 = 95%). (B) Funnel plot evaluating heterogeneity when comparing cellular response in DPs and KTRs after two doses of an mRNA vaccine. Significant heterogeneity was observed (P < 0.00001, I2 = 95%).\n\nIt has also been reported that IgAN or other kidney diseases could be triggered as a response to the COVID-19 mRNA vaccinations in certain populations (Wisnewski, Campillo Luna and Redlich, 2021). IgA nephropathy (IgAN) is an autoimmune kidney disease characterised by the deposition of IgA in the glomerulus, which causes inflammation and damage in the kidney (Selvaskandan et al., 2019). We found five studies where it was reported that nine patients were diagnosed with IgAN or presented with hallmarks of IgAN, such as gross haematuria after having either the BNT162b2 or mRNA-1273 vaccine administered (Table 1). Of these, six patients had previously diagnosed IgAN, with a further two patients having no significant medical history besides gestational diabetes and hyperlipidaemia. The final patient also had no significant past medical history. Most of these individuals were female with an average age of ~42 years old, with one study not specifying the age of the female and instead, using the description ‘older woman’ (Perrin et al., 2021; Rahim, Lin and Wang, 2021; Tan et al., 2021; Sacker, Kung and Andeen, 2021; Negrea and Rovin, 2021). One case study reported the IgAN phenotype in a 22-year-old male (Perrin et al., 2021). Overall, five of these individuals were vaccinated with the BNT162b2 vaccine, with the remaining individuals having received the mRNA-1273 vaccination. There was a report of one separate case study where a 42-year-old woman who went into full remission after being diagnosed and treated for lupus nephritis class V in 2016, had relapsed a week after the first dose of the BNT162b2 vaccine. The patient went on to develop nephrotic syndrome with hyperlipoproteinemia and hypalbuminaemia (Tuschen et al., 2021). This data brings about the question as to whether there is a link between being vaccinated with an COVID-19 mRNA vaccine and the glomerulonephritis response and whether the COVID-19 mRNA vaccines are completely safe for use in certain vulnerable populations.\n\n\nDiscussion\n\nThis study set out to establish the efficacy of the COVID-19 mRNA vaccines in DPs and KTRs. The seroconversion and cellular response were assessed in 15,072 participants after either two or three doses of an mRNA vaccine. The vaccines that were included in this analysis include BNT162b2 and mRNA-1273, with ChAdOx-1 nCoV-19 being excluded due to lack of available data.\n\nOf the 9,913 DPs that were assessed for seroconversion after two doses of an mRNA vaccination, 85.29% showed positive seroconversion, with 14.71% of participants displaying no response. Comparatively, in the 4,822 KTRs that were assessed, the response was deemed ineffective when compared to DPs. 41.06% of KTRs displayed positive seroconversion, with the remaining 58.94% of participants showing no significant response to the vaccinations after two doses. We also assessed the seroconversion response after three doses of an mRNA vaccine. Of 1,513 participants, 76% of patients showed positive seroconversion with the remaining 24% of patients showing no response. When assessing cellular response in DPs and KTRs after two doses, 978 participants were included in the analysis, with a positive cellular response being observed in 61.86% of patients. The remaining 38.14% of participants showed no or little cellular response.\n\nThe BNT162b2 and mRNA-1273 vaccines both demonstrated a ~95% and ~94.1% efficacy at preventing COVID-19 in the general population respectively, during phase III clinical trials (ClinicalTrials.gov number: NCT04470427; ClinicalTrials.gov number: NCT04368728) (Polack et al., 2020; Baden et al., 2021). Comparatively, the seroconversion was also reported to be ~95% - 100% in healthy controls when fully vaccinated with either of the mRNA vaccines in four separate studies (Stumpf et al., 2021b; Ben-Dov et al., 2022b; Grupper et al., 2021; Sattler et al., 2021). Our findings have highlighted a reduced seroconversion rate when compared to healthy controls of 85.29% and 41.06% in DPs and KTRs, respectively, albeit a better response in DPs when compared to KTRs alone. This could be due to several factors that should be taken into consideration. For example, age may play a factor in individual response to the vaccinations, with some studies showing younger KTRs may respond better to vaccination (Broseta et al., 2021; Torreggiani et al., 2021). As well as this, it has also been highlighted that immunosuppression can impair immunity to COVID-19, with post-vaccination humoral response being inhibited by immunosuppressive therapy in KTRs (Rincon-Arevalo et al., 2021; Danthu et al., 2021; Rozen-Zvi et al., 2021; Deepak et al., 2021; Strengert et al., 2021). It is interesting to note that being fully vaccinated with BNT162b2 instead of mRNA-1273 was associated with a reduced immune response and yielded lower antibody titres in DPs and KTRs across several studies (Affeldt et al., 2021; Ionita et al., 2022; Haller et al., 2022; Broseta et al., 2021; Stumpf et al., 2021a).\n\nThis study also assessed whether a third dose of an mRNA vaccine generates an immune response in DPs and KTRs and whether this is stronger than the immune response observed after two doses. For this analysis, both DPs and KTRs were combined with 76% of the overall population favouring seroconversion after three doses compared to an average of 63.18% of DPs and KTRs favouring seroconversion after two doses. This strongly suggests an increase in the number of patients that display an immune response after a third dose of an mRNA vaccine. Further to this, there have also been some reports where it is noted that the immune response after two doses of an mRNA vaccine has declined, when reassessed at a later time point (Boedecker-Lips et al., 2022; Agur et al., 2021; Dulovic et al., 2022). From this, and since there appears to be an increase in the number of patients displaying an immune response in both DPs and KTRs after three doses, and no significant adverse side effects were reported, we do recommend administering a third dose to both population types.\n\nAs well as assessing seroconversion in DPs and KTRs, this study also looked at the cellular response upon being double vaccinated with an mRNA vaccine. Albeit a limited number of studies available, we found that 61.86% of 978 DPs and KTRs included in this assessment displayed a cellular response after two doses of an mRNA vaccine. This compares to ~97% - 100% of healthy controls displaying a positive cellular response in some studies (Espi et al., 2021; Strengert et al., 2021; Sattler et al., 2021; Bertrand et al., 2021b). There has also been reports of an overall weaker T-cell response in DPs and especially KTRs compared to healthy controls (Bertrand et al., 2021a; Espi et al., 2021; Strengert et al., 2021; Sattler et al., 2021). T-cell immunity is considered essential for long-lasting protection against infection, with reports of T-cell immunity being elicited after up to 17 years in patients who had recovered from Severe Acute Respiratory Syndrome (SARS) (Le Bert et al., 2020). Given that seroconversion or the antibody response can begin to wane overtime (Boedecker-Lips et al., 2022; Dulovic et al., 2022; Agur et al., 2021), eliciting a poor T-cell response can be associated with a worse prognosis for COVID-19 patients (Mann et al., 2020). With the production of broadly reactive T-cells, an individual may be able to develop better, long-term immunity, and the ability to better recognise potential variants in the future (Peng et al., 2020). Further work is now being undertaken to establish a mechanism to trigger broadly reactive T-helper cells and killer T-cells for an overall greater protective immunity to COVID-19 (Dolgin, 2022; Heitmann et al., 2022).\n\nSeparately, in the cohort that developed a glomerulonephritis response, albeit intriguing, it cannot be confirmed that the vaccination alone has triggered this response (Klomjit et al., 2021). Despite this, patients 1, 2, 3, 6, 8, and 9 had previously diagnosed IgAN with patients 4 and 5 having underlying medical health conditions, including gestational diabetes and hyperlipidaemia respectively. Upon investigation, both latter patients revealed previously undiagnosed IgAN and crescentic glomerulonephritis alongside patient 7, who also had a clear medical history revealing crescentic glomerulonephritis after examination. Further to this, patient 10 is the only case study with a relapse in lupus nephritis class V and II being reported, however, this further brings about the question as to whether the mRNA COVID-19 vaccines trigger a relapse in immune-mediated disease. Since it cannot be confirmed whether these relapses in disease are completely co-incidental due to the limited evidence highlighting this possible relationship, we recommend caution when administering COVID-19 mRNA vaccines in cases where glomerulonephritis may be present, with further investigation also being required for conclusive data.\n\nIt is important to note that there were certain limitations to this study. Firstly, the type of immunoassay used to evaluate seroconversion and cellular response was not standardised and thus, there may be some variation between studies and thresholds that were used to determine a positive test. It should also be considered that we were only able to assess whether there was an immune response rather than whether the immune response was sustained at different time points. In addition to this, across all the studies that met the inclusion criteria of this analysis, the type of reactive antibody measured to assess seroconversion was not standardised due to the variation between studies. Thus, upon evaluating the rate of seroconversion and antibody response after vaccination administration, we deemed it appropriate to group together the different antibody responses including IgG, IgA and IgM antibodies. One study also evaluated the number of detectable SARS-CoV-2-specific and receptor-binding domain (RBD)-specific antibodies (Tai et al., 2020). For similar reasons, the cellular response was also evaluated in a similar manner with the grouping of responses from different T-cell types, including CD4+ and CD8+ T cells. Further to this, although we had tried to limit our analysis to infection-naïve participants only, this was not always possible since some studies did not specify or clarify this information. There was also a great degree of variability between studies on the timing between doses and the timing between the last dose given and the assessment of the patients’ immune response to the vaccination. As a result, all studies were included, regardless of when the doses were given, and assessment was performed.\n\nFrom the analysis performed in this study, there appears to be some publication bias and significant heterogeneity amongst studies. It is important to note that systematic heterogeneity is inevitable in this type of analysis due to the nature of the studies being investigated. Both publication bias and heterogeneity, as well as the limitations reported above must be taken into consideration when interpreting the results reported in this study. Overall, we have still been able to highlight the efficacy of the BNT162b2 and mRNA-1273 vaccines in DPs and KTRs. In conclusion, our analysis has highlighted that the mRNA vaccines yield an immune response in fewer CKD patients than when compared to healthy controls, albeit a better immune response in DPs than when compared to KTRs. Further to this, a third dose appears to be well-tolerated in both DPs and KTRs, and thus we recommend a third dose being administered to this population type to boost and ensure longevity in the patient’s immune response.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nOpen Science Framework: PRISMA checklist for ‘A systematic review assessing the effectiveness of COVID-19 mRNA vaccines in chronic kidney disease (CKD) individuals’. https://doi.org/10.17605/OSF.IO/63PJX (Goggolidou, 2022).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nAffeldt P, Koehler FC, Brensing KA, et al.: Immune Responses to SARS-CoV-2 Infection and Vaccination in Dialysis Patients and Kidney Transplant Recipients. Microorganisms. 2021; 10(1). PubMed Abstract | Publisher Full Text\n\nAgur T, Ben-Dor N, Goldman S, et al.: Antibody response to mRNA SARS-CoV-2 vaccine among dialysis patients—a prospective cohort study. Nephrol. Dial. Transplant. 2021; 36(7): 1347–1349. PubMed Abstract | Publisher Full Text\n\nAgur T, Ben-Dor N, Herman-Edelstein M, et al.: Longevity of Humoral Response Six Months Following BNT162b2 Vaccine in Dialysis Patients. Front. Med. 2022; 9: 781888. PubMed Abstract | Publisher Full Text\n\nFucci A, Giacobbe S, Guerriero I, et al.: The DiaCoVAb study in South Italy: immune response to Sars-CoV-2 vaccination in dialysis patients. Kidney Blood Press. Res. 2022; 47: 467–474. PubMed Abstract | Publisher Full Text\n\nAngel-Korman A, Peres E, Bryk G, et al.: Diminished and waning immunity to COVID-19 vaccination among hemodialysis patients in Israel: the case for a third vaccine dose. Clin. Kidney J. 2022; 15(2): 226–234. PubMed Abstract | Publisher Full Text\n\nAttias P, Sakhi H, Rieu P, et al.: Antibody response to the BNT162b2 vaccine in maintenance hemodialysis patients. Kidney Int. 2021; 99(6): 1490–1492. PubMed Abstract | Publisher Full Text\n\nBaden LR, El Sahly HM, Essink B, et al.: Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. N. Engl. J. Med. 2021; 384(5): 403–416. PubMed Abstract | Publisher Full Text\n\nBelouzard S, Chu VC, Whittaker GR: Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proc. Natl. Acad. Sci. U. S. A. 2009; 106: 5871–5876. PubMed Abstract | Publisher Full Text\n\nBen-Dov IZ, Oster Y, Tzukert K, et al.: Impact of tozinameran (BNT162b2) mRNA vaccine on kidney transplant and chronic dialysis patients: 3-5 months follow-up. J. Nephrol. 2022a; 35(1): 153–164. PubMed Abstract | Publisher Full Text\n\nBen-Dov IZ, Tzukert K, Aharon M, et al.: Response to tozinameran (BNT162b2) booster in twice-vaccinated kidney transplant and maintenance dialysis patients. J. Nephrol. 2022b; 35(3): 761–763. PubMed Abstract | Publisher Full Text\n\nBenning L, Klein K, Morath C, et al.: Neutralizing Antibody Activity Against the B.1.617.2 (delta) Variant Before and After a Third BNT162b2 Vaccine Dose in Hemodialysis Patients. Front. Immunol. 2022; 13: 840136. PubMed Abstract | Publisher Full Text\n\nBenotmane I, Gautier G, Perrin P, et al.: Antibody Response After a Third Dose of the mRNA-1273 SARS-CoV-2 Vaccine in Kidney Transplant Recipients With Minimal Serologic Response to 2 Doses. JAMA. 2021a; 326(11): 1063–1065. PubMed Abstract | Publisher Full Text\n\nBenotmane I, Gautier-Vargas G, Cognard N, et al.: Low immunization rates among kidney transplant recipients who received 2 doses of the mRNA-1273 SARS-CoV-2 vaccine. Kidney Int. 2021b; 99(6): 1498–1500. PubMed Abstract | Publisher Full Text\n\nBensouna I, Caudwell V, Kubab S, et al.: SARS-CoV-2 Antibody Response After a Third Dose of the BNT162b2 Vaccine in Patients Receiving Maintenance Hemodialysis or Peritoneal Dialysis. Am. J. Kidney Dis. 2021; 79: 185–192.e1. PubMed Abstract | Publisher Full Text\n\nBertrand D, Hamzaoui M, Lemée V, et al.: Antibody and T Cell Response to SARS-CoV-2 Messenger RNA BNT162b2 Vaccine in Kidney Transplant Recipients and Hemodialysis Patients. J Am Soc Nephrol. 2021a; 32: 2147–2152. PubMed Abstract | Publisher Full Text\n\nBertrand D, Hanoy M, Edet S, et al.: Antibody response to SARS-CoV-2 mRNA BNT162b2 vaccine in kidney transplant recipients and in-centre and satellite centre haemodialysis patients. Clin. Kidney J. 2021b; 14(9): 2127–2128. PubMed Abstract | Publisher Full Text\n\nBoedecker-Lips SC, Lautem A, Runkel S, et al.: 'Six-Month Follow-Up after Vaccination with BNT162b2: SARS-CoV-2 Antigen-Specific Cellular and Humoral Immune Responses in Hemodialysis Patients and Kidney Transplant Recipients. Pathogens (Basel, Switzerland). 2022; 11(1). PubMed Abstract | Publisher Full Text\n\nBroseta JJ, Rodríguez-Espinosa D, Cuadrado E, et al.: Humoral Response after Three Doses of mRNA-1273 or BNT162b2 SARS-CoV-2 Vaccines in Hemodialysis Patients. Vaccines (Basel). 2022; 10(4): 522. PubMed Abstract | Publisher Full Text\n\nBroseta JJ, Rodríguez-Espinosa D, Rodríguez N, et al.: Humoral and Cellular Responses to mRNA-1273 and BNT162b2 SARS-CoV-2 Vaccines Administered to Hemodialysis Patients. Am. J. Kidney Dis. 2021; 78(4): 571–581. PubMed Abstract | Publisher Full Text\n\nButt AA, Talisa VB, Yan P, et al.: Real-world Effectiveness of the SARS-CoV-2 mRNA Vaccines in Preventing Confirmed Infection in Patients on Chronic Hemodialysis. Clin. Infect. Dis. 2022. PubMed Abstract | Publisher Full Text\n\nCai R, Zhang J, Zhu Y, et al.: Mortality in chronic kidney disease patients with COVID-19: a systematic review and meta-analysis. Int. Urol. Nephrol. 2021; 53(8): 1623–1629. PubMed Abstract | Publisher Full Text\n\nChan JF, Kok K, Zhu Z, et al.: Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg. Microbes Infect. 2020; 9(1): 221–236. PubMed Abstract | Publisher Full Text\n\nChang C, Sue S, Yu T, et al.: Modular organization of SARS coronavirus nucleocapsid protein. J. Biomed. Sci. 2005; 13(1): 59–72. PubMed Abstract | Publisher Full Text\n\nChang D, Lin M, Wei L, et al.: Epidemiologic and Clinical Characteristics of Novel Coronavirus Infections Involving 13 Patients Outside Wuhan, China. JAMA. 2020; 323(11): 1092–1093. PubMed Abstract | Publisher Full Text\n\nChen Y, Liu Q, Guo D: Emerging coronaviruses: Genome structure, replication, and pathogenesis. J. Med. Virol. 2020; 92(10): 2249. PubMed Abstract | Publisher Full Text\n\nChen Z, Hu J, Liu L, et al.: SARS-CoV-2 Causes Acute Kidney Injury by Directly Infecting Renal Tubules. Front. Cell Dev. Biol. 2021; 9PubMed Abstract | Publisher Full Text\n\nChukwu CA, Mahmood K, Elmakki S, et al.: Evaluating the antibody response to SARS-COV-2 vaccination amongst kidney transplant recipients at a single nephrology centre. PLoS One. 2022; 17(3): e0265130. PubMed Abstract | Publisher Full Text\n\nClarke C, Martin P, Gleeson S, et al.: Comparison of immunogenicity between BNT162b2 and ChAdOx1 SARS-CoV-2 vaccines in a large haemodialysis population. Medrxiv. 2021. Publisher Full Text\n\nCucinotta D, Vanelli M: WHO Declares COVID-19 a Pandemic. Acta bio-medica: Atenei Parmensis. 2020; 91(1): 157–160. PubMed Abstract | Publisher Full Text\n\nDanthu C, Hantz S, Dahlem A, et al.: Humoral Response after SARS-CoV-2 mRNA Vaccination in a Cohort of Hemodialysis Patients and Kidney Transplant Recipients. J Am Soc Nephrol. 2021; 32(9): 2153–2158. PubMed Abstract | Publisher Full Text\n\nDeepak P, Kim W, Paley MA, et al.: Effect of Immunosuppression on the Immunogenicity of mRNA Vaccines to SARS-CoV-2: A Prospective Cohort Study. Ann. Intern. Med. 2021; 174(11): 1572–1585. PubMed Abstract | Publisher Full Text\n\nDekervel M, Henry N, Torreggiani M, et al.: Humoral response to a third injection of BNT162b2 vaccine in patients on maintenance haemodialysis. Clin. Kidney J. 2021; 14(11): 2349–2355. PubMed Abstract | Publisher Full Text\n\nDolgin E: T-cell vaccines could top up immunity to COVID, as variants loom large. Nat. Biotechnol. 2022; 40(1): 3–4. PubMed Abstract | Publisher Full Text\n\nDucloux D, Colladant M, Chabannes M, et al.: Factors associated with humoral response after BNT162b2 mRNA COVID-19 vaccination in kidney transplant patients. Clin. Kidney J. 2021a; 14(10): 2270–2272. PubMed Abstract | Publisher Full Text\n\nDucloux D, Colladant M, Chabannes M, et al.: Humoral response after BNT162b2 mRNA COVID-19 vaccination in patients on haemodialysis depends on immune status. Clin. Kidney J. 2021b; 14: 2266–2267. PubMed Abstract | Publisher Full Text\n\nDulovic A, Strengert M, Ramos GM, et al.: Diminishing Immune Responses against Variants of Concern in Dialysis Patients 4 Months after SARS-CoV-2 mRNA Vaccination. Emerg. Infect. Dis. 2022; 28(4): 743–750. PubMed Abstract | Publisher Full Text\n\nDuni A, Markopoulos GS, Mallioras I, et al.: The Humoral Immune Response to BNT162b2 Vaccine Is Associated With Circulating CD19+ B Lymphocytes and the Naïve CD45RA to Memory CD45RO CD4+ T Helper Cells Ratio in Hemodialysis Patients and Kidney Transplant Recipients. Front. Immunol. 2021; 12: 760249. PubMed Abstract | Publisher Full Text\n\nEspi M, Charmetant X, Barba T, et al.: The ROMANOV study found impaired humoral and cellular immune responses to SARS-CoV-2 mRNA vaccine in virus-unexposed patients receiving maintenance hemodialysis. Kidney Int. 2021; 100(4): 928–936. PubMed Abstract | Publisher Full Text\n\nEspi M, Charmetant X, Barba T, et al.: A prospective observational study for justification, safety, and efficacy of a third dose of mRNA vaccine in patients receiving maintenance hemodialysis. Kidney Int. 2022; 101(2): 390–402. PubMed Abstract | Publisher Full Text\n\nFolegatti PM, Ewer KJ, Aley PK, et al.: Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet (London, England). 2020; 396(10249): 467–478. PubMed Abstract | Publisher Full Text\n\nFrantzen L, Cavaillé G, Thibeaut S, et al.: Efficacy of the BNT162b2 mRNA COVID-19 vaccine in a haemodialysis cohort. Nephrol. Dial. Transplant. 2021; 36(9): 1756–1757. PubMed Abstract | Publisher Full Text\n\nGansevoort RT, Hilbrands LB: CKD is a key risk factor for COVID-19 mortality. Nat. Rev. Nephrol. 2020; 16(12): 705–706. PubMed Abstract | Publisher Full Text\n\nGeorgery H, Devresse A, Yombi J, et al.: High response rate to BNT162b2 mRNA COVID-19 vaccine among self-care dialysis patients. Clin. Kidney J. 2021; 14: 2129–2131. PubMed Abstract | Publisher Full Text\n\nGiot M, Fourié T, Lano G, et al.: Spike and neutralizing antibodies response to COVID-19 vaccination in haemodialysis patients. Clin. Kidney J. 2021; 14(10): 2239–2245. PubMed Abstract | Publisher Full Text\n\nGoggolidou P: COVID-19 mRNA vaccine effectiveness in Chronic Kidney Disease. Dataset. 2022, July 1. Publisher Full Text\n\nGrant MC, Geoghegan L, Arbyn M, et al.: The prevalence of symptoms in 24,410 adults infected by the novel coronavirus (SARS-CoV-2; COVID-19): A systematic review and meta-analysis of 148 studies from 9 countries. PLoS One. 2020; 15(6). Publisher Full Text\n\nGrupper A, Katchman E, Ben-Yehoyada M, et al.: Kidney transplant recipients vaccinated before transplantation maintain superior humoral response to SARS-CoV-2 vaccine. Clin. Transpl. 2021; 35(12): e14478-n/a. PubMed Abstract | Publisher Full Text\n\nGrupper A, Rabinowich L, Ben-Yehoyada M, et al.: Humoral Response to the Third Dose of Sars-Cov-2 Vaccine in Kidney Transplant Recipients. Transplant. Proc. 2022. PubMed Abstract | Publisher Full Text\n\nHaller MC, Kaiser RA, Langthaler S, et al.: Comparison of mRNA-1273 and BNT162b2 SARS-CoV-2 mRNA Vaccine Immunogenicity in Kidney Transplant Recipients. Transpl. Int. 2022; 35PubMed Abstract | Publisher Full Text\n\nHamaya T, Hatakeyama S, Yoneyama T, et al.: Seroprevalence of SARS-CoV-2 spike IgG antibodies after the second BNT162b2 mRNA vaccine in Japanese kidney transplant recipients. Sci. Rep. 2022; 12(1): 5876. PubMed Abstract | Publisher Full Text\n\nHamming I, Timens W, Bulthuis MLC, et al.: Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesis. J. Pathol. 2004; 203(2): 631–637. PubMed Abstract | Publisher Full Text\n\nHeitmann JS, Bilich T, Tandler C, et al.: A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity. Nature. 2022; 601(7894): 617–622. PubMed Abstract | Publisher Full Text\n\nHod T, Ben-David A, Olmer L, et al.: BNT162b2 Third Booster Dose Significantly Increases the Humoral Response Assessed by Both RBD IgG and Neutralizing Antibodies in Renal Transplant Recipients. Transpl. Int. 2022; 35: 10239. PubMed Abstract | Publisher Full Text\n\nHoffmann M, Kleine-Weber H, Schroeder S, et al.: SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020; 181(2): 271–280.e8. PubMed Abstract | Publisher Full Text\n\nHsu CM, Weiner DE, Aweh GN, et al.: Seroresponse to SARS-CoV-2 Vaccines Among Maintenance Dialysis Patients. Am. J. Kidney Dis. 2022; 79(2): 307–310. PubMed Abstract | Publisher Full Text\n\nHu J, Wang Y: The Clinical Characteristics and Risk Factors of Severe COVID-19. Gerontology. 2021; 67(3): 255–266. PubMed Abstract | Publisher Full Text\n\nHuang C, Wang Y, Li X, et al.: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet (British edition). 2020; 395(10223): 497–506. PubMed Abstract | Publisher Full Text\n\nIonita C, Marcelli D, Nita C, et al.: Comparison of antibody response to two different mRNA Covid-19 vaccines in patients on hemodialysis. J. Nephrol. 2022; 35(1): 143–151. PubMed Abstract | Publisher Full Text\n\nJackson LA, Anderson EJ, Rouphael NG, et al.: An mRNA Vaccine against SARS-CoV-2 — Preliminary Report. N. Engl. J. Med. 2020; 383(20): 1920–1931. PubMed Abstract | Publisher Full Text\n\nJager KJ, Kramer A, Chesnaye NC, et al.: Results from the ERA-EDTA Registry indicate a high mortality due to COVID-19 in dialysis patients and kidney transplant recipients across Europe. Kidney Int. 2020; 98(6): 1540–1548. Publisher Full Text\n\nJahn M, Korth J, Dorsch O, et al.: Humoral Response to SARS-CoV-2-Vaccination with BNT162b2 (Pfizer-BioNTech) in Patients on Hemodialysis. Vaccines. 2021; 9(4). PubMed Abstract | Publisher Full Text\n\nJin Y, Yang H, Ji W, et al.: Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses. 2020; 12(4). PubMed Abstract | Publisher Full Text\n\nKaiser RA, Haller MC, Apfalter P, et al.: Comparison of BNT162b2 (Pfizer-BioNtech) and mRNA-1273 (Moderna) SARS-CoV-2 mRNA vaccine immunogenicity in dialysis patients. Kidney Int. 2021; 100(3): 697–698. PubMed Abstract | Publisher Full Text\n\nKitamura M, Takazono T, Yamaguchi K, et al.: Favorable Humoral Response to Third Dose of BNT162b2 in Patients Undergoing Hemodialysis. J. Clin. Med. 2022; 11(8): 2090. PubMed Abstract | Publisher Full Text\n\nKlomjit N, Alexander M, Fervenza F, et al.: COVID-19 Vaccination and Glomerulonephritis. Kidney International Reports. 2021; 6(12): 2969–2978. PubMed Abstract | Publisher Full Text\n\nKolb T, Fischer S, Müller L, et al.: Impaired Immune Response to SARS-CoV-2 Vaccination in Dialysis Patients and in Kidney Transplant Recipients. Kidney360. 2021; 2(9): 1491–1498. PubMed Abstract | Publisher Full Text\n\nKorth J, Jahn M, Dorsch O, et al.: Impaired Humoral Response in Renal Transplant Recipients to SARS-CoV-2 Vaccination with BNT162b2 (Pfizer-BioNTech). Viruses. 2021; 13(5). PubMed Abstract | Publisher Full Text\n\nKumar A, Singh R, Kaur J, et al.: Wuhan to World: The COVID-19 Pandemic. Front. Cell. Infect. Microbiol. 2021; 11: 596201. PubMed Abstract | Publisher Full Text\n\nKwiatkowska E, Safranow K, Wojciechowska-Koszko I, et al.: SARS-CoV-2 mRNA Vaccine-Induced Cellular and Humoral Immunity in Hemodialysis Patients. Biomedicines. 2022; 10(3): 636. PubMed Abstract | Publisher Full Text\n\nLabriola L, Scohy A, Regemorter EV, et al.: Immunogenicity of BNT162b2 SARS-CoV-2 Vaccine in a Multicenter Cohort of Nursing Home Residents Receiving Maintenance Hemodialysis. Am. J. Kidney Dis. 2021; 78: 766–768. PubMed Abstract | Publisher Full Text\n\nLacson E, Argyropoulos C, Manley H, et al.: 'Immunogenicity of SARS-CoV-2 Vaccine in Dialysis', Journal of the American Society of Nephrology. JASN. 2021; 32: 2735–2742. PubMed Abstract | Publisher Full Text\n\nle Bert N, Tan AT, Kunasegaran K, et al.: SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020; 584(7821): 457–462. Publisher Full Text\n\nLely AT, Hamming I, Goor H, et al.: Renal ACE2 expression in human kidney disease. J. Pathol. 2004; 204(5): 587–593. Publisher Full Text\n\nLi H, Liu S, Yu X, et al.: Coronavirus disease 2019 (COVID-19): current status and future perspectives. Int. J. Antimicrob. Agents. 2020; 55(5): 105951. Publisher Full Text\n\nLi W, Moore MJ, Vasilieva N, et al.: Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature. 2003; 426(6965): 450–454. Publisher Full Text\n\nLonglune N, Nogier MB, Miedougé M, et al.: High immunogenicity of a messenger RNA-based vaccine against SARS-CoV-2 in chronic dialysis patients. Nephrology, Dialysis, Transplantation: Official Publication of the European Dialysis and Transplant Association - European Renal Association. 2021; 36(9): 1704–1709. PubMed Abstract | Publisher Full Text\n\nLu R, Zhao X, Li J, et al.: Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet (London, England). 2020; 395(10224): 565–574. Publisher Full Text\n\nMalha L, Mueller FB, Pecker MS, et al.: COVID-19 and the Renin-Angiotensin System. Kidney international reports. 2020; 5(5): 563–565. PubMed Abstract | Publisher Full Text\n\nMann ER, Menon M, Knight SB, et al.: Longitudinal immune profiling reveals key myeloid signatures associated with COVID-19. Science Immunology. 2020; 5(51). PubMed Abstract | Publisher Full Text\n\nMassa F, Cremoni M, Gérard A, et al.: Safety and cross-variant immunogenicity of a three-dose COVID-19 mRNA vaccine regimen in kidney transplant recipients. EBioMedicine. 2021; 73: 103679. PubMed Abstract | Publisher Full Text\n\nMasset C, Kerleau C, Garandeau C, et al.: A third injection of the BNT162b2 mRNA COVID-19 vaccine in kidney transplant recipients improves the humoral immune response. Kidney Int. 2021; 100(5): 1132–1135. PubMed Abstract | Publisher Full Text\n\nMatsunami M, Suzuki T, Fukuda J, et al.: Comparison of antibody response following the second dose of SARS-CoV-2 mRNA vaccine in elderly patients with late-stage chronic kidney disease. Ren. Replace. Ther. 2022; 8(1): 13. PubMed Abstract | Publisher Full Text\n\nMatsunami M, Suzuki T, Terao T, et al.: Immune response to SARS-CoV-2 vaccination among renal replacement therapy patients with CKD: a single-center study. Clin. Exp. Nephrol. 2021; 26(3): 305–307. PubMed Abstract | Publisher Full Text\n\nMelin J, Svensson MK, Albinsson B, et al.: Humoral and cellular response to SARS-CoV-2 BNT162b2 mRNA vaccine in hemodialysis patients. BMC Immunol. 2021; 22(1): 70. PubMed Abstract | Publisher Full Text\n\nMeshram HS, Kute VB, Shah N, et al.: COVID-19 in Kidney Transplant Recipients Vaccinated With Oxford-AstraZeneca COVID-19 Vaccine (Covishield): A Single-center Experience From India. Transplantation. 2021; 105(9): e100–e103. PubMed Abstract | Publisher Full Text\n\nNacasch N, Erez D, Lishner M, et al.: Long-term Antibody Response to the BNT162b2 Vaccine Among Maintenance Hemodialysis Patients. Am. J. Kidney Dis. 2022; 79(1): 137–139. PubMed Abstract | Publisher Full Text\n\nNegrea L, Rovin BH: Gross hematuria following vaccination for severe acute respiratory syndrome coronavirus 2 in 2 patients with IgA nephropathy. Kidney Int. 2021; 99(6): 1487. PubMed Abstract | Publisher Full Text\n\nNeuman BW, Kiss G, Kunding AH, et al.: A structural analysis of M protein in coronavirus assembly and morphology. J. Struct. Biol. 2011; 174(1): 11–22. Publisher Full Text\n\nOu X, Liu Y, Lei X, et al.: Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat. Commun. 2020; 11: 1620. PubMed Abstract | Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ (Clinical research ed.). 2021; 372: n71. PubMed Abstract | Publisher Full Text\n\nPatecki M, Merscher S, Dumann H, et al.: Similar humoral immune responses in peritoneal dialysis and haemodialysis patients after two doses of the SARS-CoV-2 vaccine BNT162b2. Perit. Dial. Int. 2022; 42(1): 100–101. PubMed Abstract | Publisher Full Text\n\nPeng Y, Mentzer AJ, Liu G, et al.: Broad and strong memory CD4.sup.+ and CD8.sup.+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19. Nat. Immunol. 2020; 21(11): 1336–1345. PubMed Abstract | Publisher Full Text\n\nPerrin P, Bassand X, Benotmane I, et al.: Gross hematuria following SARS-CoV-2 vaccination in patients with IgA nephropathy. Kidney Int. 2021; 100(2): 466–468. PubMed Abstract | Publisher Full Text\n\nPolack FP, Thomas SJ, Kitchin N, et al.: Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N. Engl. J. Med. 2020; 383(27): 2603–2615. PubMed Abstract | Publisher Full Text\n\nRabi FA, Al Zoubi MS, Kasasbeh GA, et al.: SARS-CoV-2 and Coronavirus Disease 2019: What We Know So Far. Pathogens. 2020; 9(3). PubMed Abstract | Publisher Full Text\n\nRahim SEG, Lin JT, Wang JC: A case of gross hematuria and IgA nephropathy flare-up following SARS-CoV-2 vaccination. Kidney Int. 2021; 100(1): 238. Publisher Full Text\n\nRaj R: Analysis of non-structural proteins, NSPs of SARS-CoV-2 as targets for computational drug designing. Biochemistry and Biophysics Reports. 2021; 25: 100847. PubMed Abstract | Publisher Full Text\n\nRincon-Arevalo H, Choi M, Stefanski A, et al.: Impaired humoral immunity to SARS-CoV-2 BNT162b2 vaccine in kidney transplant recipients and dialysis patients. Sci. Immunol. 2021; 6(60): eabj1031. PubMed Abstract | Publisher Full Text\n\nRozen-Zvi B, Yahav D, Agur T, et al.: Antibody response to SARS-CoV-2 mRNA vaccine among kidney transplant recipients: a prospective cohort study. Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. 2021; 27(8): 1173.e1–1173.e4. PubMed Abstract | Publisher Full Text\n\nRusso G, Lai Q, Poli L, et al.: SARS-COV-2 vaccination with BNT162B2 in renal transplant patients: Risk factors for impaired response and immunological implications. Clin. Transpl. 2022; 36(1): e14495. PubMed Abstract | Publisher Full Text\n\nSacker A, Kung V, Andeen N: Anti-GBM nephritis with mesangial IgA deposits after SARS-CoV-2 mRNA vaccination. Kidney Int. 2021; 100(2): 471–472. PubMed Abstract | Publisher Full Text\n\nSantos-Araújo C, Mota Veiga P, Santos MJ, et al.: Time-dependent evolution of IgG antibody levels after first and second dose of mRNA-based SARS-CoV-2 vaccination in haemodialysis patients: a multicentre study. Nephrol. Dial. Transplant. 2022; 37(2): 375–381. Publisher Full Text\n\nSattler A, Schrezenmeier E, Weber UA, et al.: Impaired humoral and cellular immunity after SARS-CoV-2 BNT162b2 (tozinameran) prime-boost vaccination in kidney transplant recipients. J. Clin. Invest. 2021; 131(14). PubMed Abstract | Publisher Full Text\n\nSchrezenmeier E, Bergfeld L, Hillus D, et al.: Immunogenicity of COVID-19 Tozinameran Vaccination in Patients on Chronic Dialysis. Front. Immunol. 2021; 12: 690698. PubMed Abstract | Publisher Full Text\n\nSeija M, Rammauro F, Santiago J, et al.: Comparison of antibody response to SARS-CoV-2 after two doses of inactivated virus and BNT162b2 mRNA vaccines in kidney transplant. Clin. Kidney J. 2022; 15(3): 527–533. Publisher Full Text\n\nSelvaskandan H, Cheung CK, Muto M, et al.: New strategies and perspectives on managing IgA nephropathy. Clin. Exp. Nephrol. 2019; 23(5): 577–588. PubMed Abstract | Publisher Full Text\n\nShashar M, Nacasch N, Grupper A, et al.: Humoral Response to Pfizer BNT162b2 Vaccine Booster in Maintenance Hemodialysis Patients. Am. J. Nephrol. 2022; 53(2-3): 207–214. PubMed Abstract | Publisher Full Text\n\nShi H, Han X, Jiang N, et al.: Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Lancet Infect. Dis. 2020; 20(4): 425–434. PubMed Abstract | Publisher Full Text\n\nSimon B, Rubey H, Treipl A, et al.: Haemodialysis patients show a highly diminished antibody response after COVID-19 mRNA vaccination compared with healthy controls. Nephrology, Dialysis, Transplantation: Official Publication of the European Dialysis and Transplant Association - European Renal Association. 2021; 36(9): 1709–1716. PubMed Abstract | Publisher Full Text\n\nSoler MJ, Wysocki J, Ye M, et al.: ACE2 inhibition worsens glomerular injury in association with increased ACE expression in streptozotocin-induced diabetic mice. Kidney Int. 2007; 72(5): 614–623. PubMed Abstract | Publisher Full Text\n\nSpeer C, Göth D, Benning L, et al.: Early Humoral Responses of Hemodialysis Patients after COVID-19 Vaccination with BNT162b2. Clinical Journal of the American Society of Nephrology: CJASN. 2021; 16(7): 1073–1082. PubMed Abstract | Publisher Full Text\n\nStrengert M, Becker M, Ramos GM, et al.: Cellular and humoral immunogenicity of a SARS-CoV-2 mRNA vaccine in patients on haemodialysis. EBioMedicine. 2021; 70: 103524. PubMed Abstract | Publisher Full Text\n\nStumpf J, Siepmann T, Lindner T, et al.: Humoral and cellular immunity to SARS-CoV-2 vaccination in renal transplant versus dialysis patients: A prospective, multicenter observational study using mRNA-1273 or BNT162b2 mRNA vaccine. The Lancet Regional Health. Europe. 2021a; 9: 100178. PubMed Abstract | Publisher Full Text\n\nStumpf J, Tonnus W, Paliege A, et al.: Cellular and Humoral Immune Responses After 3 Doses of BNT162b2 mRNA SARS-CoV-2 Vaccine in Kidney Transplant. Transplantation. 2021b; 105(11): e267–e269. Publisher Full Text\n\nSungnak W, Huang N, Bécavin C, et al.: SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat. Med. 2020; 26(5): 681–687. PubMed Abstract | Publisher Full Text\n\nTai W, He L, Zhang X, et al.: Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine. Cell. Mol. Immunol. 2020; 17(6): 613–620. Publisher Full Text\n\nTan HZ, Tan RY, Choo JCJ, et al.: Is COVID-19 vaccination unmasking glomerulonephritis?. Kidney Int. 2021; 100(2): 469–471. PubMed Abstract | Publisher Full Text\n\nTikellis C, Johnston CI, Forbes JM, et al.: Characterization of Renal Angiotensin-Converting Enzyme 2 in Diabetic Nephropathy. Hypertension. 2003; 41(3): 392–397. PubMed Abstract | Publisher Full Text\n\nTorreggiani M, Blanchi S, Fois A, et al.: Neutralizing SARS-CoV-2 antibody response in dialysis patients after the first dose of the BNT162b2 mRNA COVID-19 vaccine: the war is far from being won. Kidney Int. 2021; 99(6): 1494–1496. PubMed Abstract | Publisher Full Text\n\nTsang HF, Chan LWC, Cho WCS, et al.: An update on COVID-19 pandemic: the epidemiology, pathogenesis, prevention and treatment strategies. Expert Rev. Anti-Infect. Ther. 2021; 19(7): 877–888. PubMed Abstract | Publisher Full Text\n\nTuschen K, Bräsen JH, Schmitz J, et al.: Relapse of class V lupus nephritis after vaccination with COVID-19 mRNA vaccine. Kidney Int. 2021; 100(4): 941–944. PubMed Abstract | Publisher Full Text\n\nVaiciuniene R, Sitkauskiene B, Bumblyte IA, et al.: Immune Response after SARS-CoV-2 Vaccination in Kidney Transplant Patients. Medicina (Kaunas). 2021; 57(12): 1327. PubMed Abstract | Publisher Full Text\n\nVillanego F, Cazorla JM, Vigara LA, et al.: Protecting kidney transplant recipients against SARS-CoV-2 infection: A third dose of vaccine is necessary now. Am. J. Transplant. 2022; 22(4): 1275–1276. PubMed Abstract | Publisher Full Text\n\nVoysey M, Clemens SAC, Madhi SA, et al.: Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. Lancet. 2021; 397(10269): 99–111. PubMed Abstract | Publisher Full Text\n\nWang D, Hu B, Hu C, et al.: 'Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus–Infected Pneumonia in Wuhan, China. JAMA. 2020; 323(11): 1061–1069. PubMed Abstract | Publisher Full Text\n\nWeigert A, Bergman M, Gonçalves L, et al.: Longitudinal analysis of antibody responses to the Pfizer BNT162b2 vaccine in Patients Undergoing Maintenance Hemodialysis. Medrxiv. 2021. Publisher Full Text\n\nWHO Coronavirus (COVID-19) Dashboard.Accessed: Nov 4, 2021.Reference Source\n\nWilliamson EJ, Walker AJ, Bhaskaran K, et al.: Factors associated with COVID-19-related death using OpenSAFELY. Nature. 2020; 584(7821): 430–436. PubMed Abstract | Publisher Full Text\n\nWindpessl M, Bruchfeld A, Anders H, et al.: COVID-19 vaccines and kidney disease. Nat. Rev. Nephrol. 2021; 17(5): 291–293. Publisher Full Text\n\nWisnewski A, Campillo Luna J, Redlich C: Human IgG and IgA responses to COVID-19 mRNA vaccines. PLoS One. 2021; 16(6): e0249499. PubMed Abstract | Publisher Full Text\n\nWrapp D, Wang N, Corbett KS, et al.: Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, N.Y.). 2020; 367(6483): 1260–1263. PubMed Abstract | Publisher Full Text\n\nYadav R, Chaudhary JK, Jain N, et al.: Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells. 2021; 10(4). PubMed Abstract | Publisher Full Text\n\nYahav D, Rahamimov R, Mashraki T, et al.: Immune Response to Third Dose BNT162b2 COVID-19 Vaccine Among Kidney Transplant Recipients-A Prospective Study. Transpl. Int. 2022; 35: 10204. PubMed Abstract | Publisher Full Text\n\nYanay NB, Freiman S, Shapira M, et al.: Experience with SARS-CoV-2 BNT162b2 mRNA vaccine in dialysis patients. Kidney Int. 2021; 99(6): 1496–1498. Publisher Full Text\n\nYau K, Abe KT, Naimark D, et al.: Evaluation of the SARS-CoV-2 Antibody Response to the BNT162b2 Vaccine in Patients Undergoing Hemodialysis. JAMA Netw. Open. 2021; 4(9): e2123622. PubMed Abstract | Publisher Full Text\n\nYau K, Chan CT, Abe KT, et al.: Differences in mRNA-1273 (Moderna) and BNT162b2 (Pfizer-BioNTech) SARS-CoV-2 vaccine immunogenicity among patients undergoing dialysis. Canadian Medical Association Journal (CMAJ). 2022; 194(8): E297–E305. PubMed Abstract | Publisher Full Text\n\nYi SG, Moore LW, Eagar T, et al.: Risk Factors Associated With an Impaired Antibody Response in Kidney Transplant Recipients Following 2 Doses of the SARS-CoV-2 mRNA Vaccine. Transplant. Direct. 2022; 8(1): e1257. PubMed Abstract | Publisher Full Text\n\nYuki K, Fujiogi M, Koutsogiannaki S: COVID-19 pathophysiology: A review. Clinical Immunology (Orlando, Fla.). 2020; 215: 108427. PubMed Abstract | Publisher Full Text\n\nZhou P, Yang X, Wang X, et al.: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798): 270–273. PubMed Abstract | Publisher Full Text\n\nZitt E, Davidovic T, Schimpf J, et al.: The Safety and Immunogenicity of the mRNA-BNT162b2 SARS-CoV-2 Vaccine in Hemodialysis Patients. Front. Immunol. 2021; 12: 704773. PubMed Abstract | Publisher Full Text\n\nZou X, Chen K, Zou J, et al.: Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different human organs vulnerable to 2019-nCoV infection. Front. Med. 2020; 14(2): 185–192. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "149323",
"date": "08 Sep 2022",
"name": "Marios Papasotiriou",
"expertise": [
"Reviewer Expertise Nephrology"
],
"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 systematic review the authors assessed the response rate and overall effectiveness of vaccination against Covid-19 with mRNA vaccines in patients on dialysis or patients after kidney transplantation.\nThe work overall is clearly presented and the most contemporary literature is cited. The design meets the standards of systematic reviews and analysis details are provided clearly in methods. The statistical analysis is appropriately performed, nevertheless some results need clarification. Firstly, it is stated that 17 studies with 1,513 participants were included to determine the effectiveness of 3 doses of the mRNA vaccines (either BNT162b2 or mRNA-1273) in both DPs and KTRs. In my opinion the seroconversion results after a third mRNA vaccine dose should be presented separately for DPs and KTRs. Moreover, it should be noted whether those patients, either DPs or KTRs, who did not show seroconversion with the 2nd dose, had a substantial increase in antibody production after the 3rd dose.\nIn general, although the authors describe in detail the seroconversion ratio of DPs and KTRs after Covid-19 vaccination with an mRNA vaccine, they do not discuss about the actual protective threshold of antibodies that is reached in these groups of patients. Thus, I would propose to mention apart from seroconversion ratio, the ratio of patients that have a titer that is actually protective against severe Covid-19 infection as well.\nFinally, the source data are reported to be available and the final conclusions of the study are sound and are supported from the original results.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "9035",
"date": "25 Nov 2022",
"name": "Paraskevi Goggolidou",
"role": "Author Response",
"response": "We thank the reviewer for their comments. In response to them, we have submitted a revised version of the article, with any amendments shown as tracked changes. Please note: 1) There were a limited number of studies available and thus, to perform statistical analysis, the percentage of patients displaying positive seroconversion for both DPs and KTRs after a third dose were grouped together. Despite this, our data shows that separately, 89.13% and 61.29% of DPs and KTRs displayed positive seroconversion after a third dose of an mRNA vaccine, respectively. 2) It was not confirmed in the studies whether antibody production/seroconversion after a third dose was compared to unvaccinated individuals or individuals who had received a second dose. Thus, in this study, we were unable to conclude whether there was an increase in antibody production after the third dose in those who did not show positive seroconversion after the second dose. 3)Not all studies published the antibody titre levels, therefore it was not possible to conclude what the exact protective threshold was in DPs and KTRs vaccinated against severe COVID-19. Nonetheless, we have provided in Table 1 the threshold over which an individual's test is scored as seroconverted. It is important to note that it is not possible to deem immunity levels or identify protective thresholds from antibody testing alone. Further to this, we can confirm there is no specific antibody titre for protection against severe COVID-19. Accordingly, the U.S. Food and Drug Administration (FDA) states that “antibody testing is not currently recommended to assess immunity after COVID-19 vaccination” because a result from currently authorized SARS-CoV-2 antibody tests is not an indication of a specific level of immunity or protection from SARS-CoV-2 infection after the person has received a COVID-19 vaccination."
}
]
},
{
"id": "151580",
"date": "10 Oct 2022",
"name": "Katherine Karakoula",
"expertise": [
"Reviewer Expertise Cancer genetics",
"immunological 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\nThe authors present a thorough systematic review on the effectiveness of mRNA vaccines for COVID-19 infection in DPs and KTRs patients.\nOverall, the review is well-presented with a detailed description of methods used for the analysis and good presentation of Figures. The review is highly cited with up-to-date references. The statistics used for the analysis are appropriate for systematic reviews and with sufficient details.\nThe results are presented nicely albeit some additional information would be beneficial for this review. The authors investigated the efficacy of the 2 COVID-19 mRNA vaccines in DPs and KTRs by analysis of the seroconversion and cellular response in patients after either 2 or 3 doses of an mRNA vaccine. The authors found that a third dose of mRNA vaccine increased seroconversion by 76% in both DPs and KTRs together compared to an average of 63.18% after two doses. It would be helpful if the authors could do a separate analysis per set of patients (DPs and KTRs alone) after administration of a third dose of mRNA vaccine rather than grouping them together and then compared each set with the ones after a second vaccine dose. I believe the results of this analysis would help to understand better the requirement or not of a third dose of vaccine in these groups of patients.\nThe discussion and conclusions support the results of this review.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "9036",
"date": "25 Nov 2022",
"name": "Paraskevi Goggolidou",
"role": "Author Response",
"response": "We thank the reviewer for their comments. We have taken their points on board and edits to the initial manuscript can be seen as tracked changes. Please note that unfortunately, there are a limited number of studies available and thus, to perform statistical analysis, the percentage of patients displaying positive seroconversion for both DPs and KTRs after a third dose were grouped together. Despite this, our data shows that separately, 89.13% and 61.29% of DPs and KTRs displayed positive seroconversion after a third dose of an mRNA vaccine, respectively."
}
]
}
] | 1
|
https://f1000research.com/articles/11-909
|
https://f1000research.com/articles/11-1362/v1
|
22 Nov 22
|
{
"type": "Research Article",
"title": "Financial distress, earning management, financial statement fraud and audit quality as a moderating variable: listed companies on the Indonesia Stock Exchange",
"authors": [
"Mukhtaruddin Mukhtaruddin",
"Widya Zahra Chairunnisa",
"Patmawati Patmawati",
"Yulia Saftiana",
"Widya Zahra Chairunnisa",
"Patmawati Patmawati",
"Yulia Saftiana"
],
"abstract": "Background: Accounting practices, profit bubbles, information manipulation and deception, and earning management are all examples of fraudulent financial statement cases. Companies create fraudulent financial statements for a variety of reasons, including financial challenges and debt payment delays. Financial fraud is created by five factors: pressure, opportunity, rationalization, capability, and arrogance. Methods: The purpose of this study is to see whether audit quality (AQ) has a moderating effect on the relationship between financial distress (FD) and earning management (EM) to financial statement fraud (FSF) in infrastructure, utility, and transportation companies listed on the Indonesia Stock Exchange during the years 2015 to 2019. The data sources are the www.idx.go.id and the company’s annual reports. Purposive sampling was used to collect data from thirty companies over the course of five years, totaling 150 observations. Moderating regression analysis (MRA) was used in data analysis. Result and conclusions: The hypothesis testing revealed that FD and EM have a significant impact on FSF. AQ is able to moderate the relationship between FD to FSF but unable to moderate the relationship between EM to FSF.",
"keywords": [
"Financial distress",
"earning management",
"audit quality",
"fraudulent financial statement"
],
"content": "Introduction\n\nA company’s financial report demonstrates how well a company has performed. If the company's financial accounts indicate a growth in earnings from year to year, the company is deemed to be performing well. However, when a company's situation is experiencing a revenue reduction, it presents a problem while generating financial accounts. It is conceivable that a corporation could find itseld tempted to modify the report in this situation; to maintain the positive image that the organization has established thus far. PT Garuda Indonesia has engaged in financial statement fraud (FSF) practices. PT. Garuda Indonesia is an Indonesia airline and state owned company. In 2018, PT Garuda Indonesia was accused of falsifying financial accounts by classifying outstanding receivables as revenue. PT. Garuda Indonesia had a profit of US$ 239.9 million, or Rp. 3.47 trillion (Rp 14,481 per USD exchange rate). Financial statements showed losses in 2017, while a profit of Rp. 72.69 billion was recorded at the end of 2018. PT. Garuda Indonesia, in fact, suffered a loss of IDR 1.6 trillion.1\n\nIn 2001, PT Kimia Farma, a state owned pharmautical company committed fraud in Indonesia; the corporation was suspected of creating a Rp. 132 billion profit markup.2 The next instance of deception came in 2006 after PT Kereta Api Indonesia, tbk, a state owned train company, generated a profit of Rp. 6.9 billion but should have lost Rp. 63 billion. The final case is PT. Waskita Karya, tbk, which occurred in 2009. From 2004 to 2007, the corporation made a miscalculation in recording net profits of roughly Rp. 400 billion.3 Cases of fraudulent financial statement presentation do not just occur in Indonesia; there have been a number of cases of financial reporting fraud globally, such as the Xeroc case in 2000, Enron in 2001, and Worldcom in 2002.4\n\nFinancial statement fraud refers to the practice of FSF presentation.5 Fraud is practice that involves the use of deception to acquire unfair or unlawful advantages by one or more individuals. This means that fraud is an act committed by specific people, whether intentionally or unintentionally, to benefit themselves and others. FSF, asset misappropriation, and corruption are three types of fraud.6\n\nFraudulent practices will become increasingly common without appropriate supervision and control. Financial distress (FD) is one of several characteristics or elements that contribute to fraudulent behavior. FD refers to a situation in which a corporation is having financial troubles. According to Fahreza, et al.,3 if a company runs into financial difficulties, it will be more likely to commit FSF and this will affect the investor’s behaviour. According to Bell & Carcello,7 fraud is motivated by financial difficulties or a high level of leverage. Zainudin and Hashim8 showed that leverage has an affect on identifying FSF. It means that a company is likely to commit FSF, if the company has a high level of leverage. This differs from Janrosl & Yuliadi,9 who found that leverage has no effect on FSF since even if leverage is large but not accompanied by a severe burden, the corporation can still pay off its debt.\n\nEarnings management (EM) is profit engineering carried out by managing revenues (cash inflows) and expenses (cash outflows) to ensure that the company's operations generate net operating profit. EM practices lead to fraud.10 According to Rashidah et al.,10 EM affects FSF. Managers tend to manage earnings because managers have the opportunity to do so. The practice of EM will decrease the financial statements' quality and credibility. However, in general, within recognized accounting rules, EM is permitted. In this scenario, a company does deply EM; an audit report would contain the proof of any FSF.11 As a result, audit quality (AQ) becomes a factor in detecting FSF, as well as an impact on financial statement presentation integrity. This study is unique in that it includes AQ as a moderating variable. This study re-examines the association between FD and EM on FSF by adding AQ as a moderating variable, due to the variations in the outcomes of the research stated above. Furthermore, what sets this study apart from previous research is the use of the f-score model to measure FSF. The f-score approach is based on a combination of two criteria, namely accrual quality and financial success. The use of this f-score model in financial statements can forecast the danger of fraudulent practices.12\n\n\nLiterature review\n\nJensen and Meckling13 proposed the agency theory. According to this view, the agent (management) and the principle (shareholders) have different interests. The difference in interest here refers to the fact that the agent must produce a profit in order for the principal to receive his return of capital. Agents/managers with the potential to meet profit targets will have an impact on the quantity of dividends paid to investors.\n\nManagers exhibit opportunistic behavior. Managers put their own interests ahead of those of the others. Managers look for rewards from their work, such as bonuses, for themselves. They disallow manipulating the company's profits to make the manager's performance appear strong in order to earn bonuses in gratitude for the work they do.14\n\nFurthermore, if the manager is confronted with a financial crisis or the organization is having financial issues, the manager will use all available resources to resolve the situation.15 Asymmetry information between the linked parties is created by the agent and principal's differing interests. The advent of asymmetric information creates an opportunity for agents, namely hiding certain knowledge that the principal is unaware of.16 As a result, the agent has the potential to perpetrate fraud without the principal's knowledge. It takes a third party, especially an auditor, to bridge these gaps. Financial auditing allows auditors to monitor the activities of agents. The auditor can determine whether the company has reported its financial accounts accurately and in compliance with generally accepted accounting principles based on the audit report's findings. If the audit quality is good, the financial statements of the organization can be trusted.17\n\nThe Association of Certified Fraud Examiners defines fraud as an intentional or inadvertent act of failing to disclose financial information. Acts of deception or omission by a company in the creation of items and amounts on a financial statement or in the disclosure of financial statements that are intended to deceive financial statement users. Financial statement fraud is when financial statements contain a major misstatement.18 Users of financial statements have doubts about the accuracy of the financial statements if there is fraud present. Users of these financial statements might make unwise decisions, which would harm the objectives that readers of financial statements are required to meet.19 This danger of falsifying financial statements increases when a company is having financial difficulty.20 If not addressed early, this fraudulent activity becomes a significant problem. Companies must be aware of the elements that can contribute to deceptive reporting. To interpret FSF signs, a method is required.\n\nFD is a circumstance in which a company's financial situation deteriorates to the point of bankruptcy.21 The inability to pay short-term loans that are due is an example of one of the many causes of financial troubles in businesses. This inability could be due to two factors: lack of company funds or waiting for assets to be disbursed, in order to pay off the short-term debt. The higher the debt, the greater of the companies risk, because companies assets are insufficient to cover its debts.\n\nAccording to Pratama,22 EM is an earnings presentation strategy in which profits are ordered depending on the interests of managers rather than actual situations. EM is a condition in which management participates in the presentation of financial statements in order to achieve certain objectives, hence reducing the fairness of a financial report.23 To summarize, EM is the practice of presenting earnings in financial statements that are not in conformity with the true state of the firm's profits, in order for the company to appear to have increasing profits from year to year. EM probabilities are made up of two components: (1) conversion or manipulation, and (2) concealment, or hiding/covering.1\n\nAn audit is a method of gathering data and determining whether financial accounts are presented fairly in conformity with generally accepted accounting rules. The audit is performed by someone that is competent and independent.24 An auditor may obtain evidence from observation activities and report if the auditee system has been violated.25 When evaluating a financial statement, AQ is crucial. If the AQ is good, it will generate trustworthy financial reporting.17 According to Tussiana & Lastanti,26 if the audit process is carried out in accordance with appropriate norms, the risk of fraud in reporting financial statements is reduced, and the financial statements' credibility is increased.\n\nPFT was introduced by Crowe Howard in 2011. According to PFT, the practices of FSF have five main aspects, namely pressure, opportunity, rationalization, competency, and arrogance.27 The PFT is a refinement of a prior idea, specifically Dr. Donald Cressy's fraud triangle theory (1953). Pressure, opportunity, and rationalization are the three indicators of deception in the fraud triangle. There is also Wolfe & Hermason's28 fraud diamond idea. The ability indicator was added by Wolfe & Hermason28 to the fraud triangle theory. PFT improved the fraud diamond theory by including an additional indicator; arrogance. A manager with a large ego will display arrogance because they believe they have a high position and play an essential role and are exempt from regulations and internal control systems.29 Arrogance in this context is defined as an attitude held by someone who believes they can commit fraud without being discovered by others.4 Crowe27 devised a pentagon fraud scheme that can be seen in Figure 1.\n\nSource: Crowe (2011).27\n\nFSF is built on five elements, including pressure, opportunity, rationalization capability, and arrogance, according to the fraud pentagon theory. This pressure can be caused by a variety of factors, such as the company's financial difficulties or that the public's perception of the company will be harmed by its insecure state.15 This pressure can encourage managers to commit fraud in order to restore normalcy to the company's operations.15 Managing profit, or EM, is one of the acts that management might do. The manager’s action is moderated by audit quality. The framework of thought in this study, based on the explanation above, can be seen in Figure 2.\n\nThe effect of financial distress on financial statement fraud\n\nIf a company's financial situation has deteriorated, shareholders may be encouraged to replace company executives.21 As a result, the worth of the company's controlling manager decreases. This encourages executives to manage earnings in such a way that their image remains positive and they retain control of the business.19 If a company is getting losses or lower profit, the company faces the financial diffucties. This situation can cause the company to be unable to fulfill its obligations. This condisions arise the practice of FSF.\n\nAccording to the fraud pentagon theory, financial troubles become a factor causing fraud, forcing the firm or management to do everything possible, such as manipulating financial statements to make the company's condition look excellent in order to attract an investor or maintain its existence.3 Poor financial conditions, according to Bell & Carcello,7 drive management to simulate these FD problems by producing reports that are better than the original. A hypothesis can be stated based on the preceding description; H1= Financial distress has a significant effect on financial statements fraud.\n\nThe effect of earning management of financial statement fraud\n\nAccording to agency theory, management operates as an agent in the management of a corporation, with aims in finance, sales, and several other areas. If management fails to meet targets, particularly in terms of profits, management will likely play the profits that have been earned so that it can be seen that the profit has reached the point or is on track.30 Because it does not provide true financial statements, EM is a form of manipulation. Bisogno & De Luca31 found a link between EM and FSF in their investigation. The finding of this study found that the higher profit, and the greater the risk of fraud. EM will impair the integrity of financial statements.30\n\nThe practice of EM on the one hand is an act of manipulation because it does not present real financial statements. In line with research conducted by Bisogno & De Luca31 found that there is a relationship between EM and FSF. The results of this study indicate that the higher the management performs the distribution of profits, the higher the chance of fraud. Putra & Muid (2007) argued that EM will affect the integrity of financial statements. The second research hypothesis is formulated as: H2= Earning management has a significant effect on financial statements fraud.\n\nThe effect moderating of audit quality towards financial distress on financial statements fraud\n\nAccording to Bell & Carcello,7 financial diffuclties can drive management to enhance or distort financial statistics to make them appear more appealing to users. Fraud protects businesses that are suffering financial difficulties. The audit report is critical in determining if the financial statements were prepared in compliance with generally accepted accounting principles. Financial statements that have been audited will have more credibility and will reduce fraudulent activity.25 The third hypothesis in this investigation is based on this explanation H3= Audit quality moderates financial distress on financial statements fraud.\n\nThe effect moderating of audit quality towards earning management on financial statement fraud\n\nBecause financial statements are not presented in accordance with the company's circumstances, EM behavior is a form of manipulation.14 As a result, the company's financial statements cannot be relied upon. Managers typically perform this EM action in order to meet defined targets and earn bonuses.10\n\nThe audit process is required to ensure that a company's financial statements have been prepared in line with the current situation and widely recognized accounting rules. According to DeAngelo,17 a good AQ makes the financial statements given credible. Hardiningsih32 demonstrates that the higher the AQ, the more trustworthy the financial statements are. The fourth hypothesis is H4 = Audit quality modeartes earning management to financial statements.\n\n\nResearch methods\n\nThe study's subjects are companies in the infrastructure, utilities, and transportation sectors that have been listed on the Indonesia Stock Exchange during five years observation. The purporsive sampling approach was used to select samples. The sample was chosen based on several criteras. The 30 companies were chosen based on criteria for a period of five years; 2015 – 2019.\n\nFinancial statement fraud\n\nThe f-score model is used to determine whether a financial statement is fraudulent. There are two components in the f-score model's calculation: accrual quality and financial performance,33 hence the equation is as follows:\n\nAccrual quality is proxied by RSST Accrual,34 which was developed by Richardson, Sloan, Soliman, and Tuna and has the following formula:\n\nWhere as: WC (Working Capital) = (Current Assets – Current Liability), NCO (Non Current Operating Accrual) = (Total Assets–Current Assets–investment and Advances) - (Total Liabilities – Current Liabilities – Long Term Debt), FIN (Financial Accrual) = Total Investment –Total Liabilities and ATS (Average Total Assets) = (Beginning Total Assets + End Total Assets)/2.\n\nChanges in receivables, inventory, cash sales, and profits before interest and tax (EBIT) are all used to measure financial success.33 If a corporation has more than one fraud score model, it is assumed that it will commit fraud.\n\nFinancial distress\n\nLeverage is a proxy for financial distress. Leverage is a ratio that depicts a company's ability to meet its obligations. The company's high degree of leverage is thought to have the potential to violate borrowing processes, as well as limit the company's capacity to obtain more capital by borrowing money from creditors.8 By comparing total debt to total assets, Brazel, et al.,35 shows that leverage is a proxy for FD.\n\nEarning management\n\nEM is classified as a form of fraud. According to Kurniawansyah,36 EM practices satisfy the elements of conversion (manipulation) and concealment, meaning hiding/covering up even when it is not directly beneficial to oneself, but financial statements must be provided factually. The discretionary accruals (DACC) value or the Jones Modified Model's discretionary accruals37 are used to calculate EM. The following formula is used to calculate DACC:\n\nAudit quality\n\nAQ is a moderating variable that influences the link between financial distress and EM on FSF. The moderating variable will influence the relationship between the independent variable on the dependent variable. It might strengthen or weaken its relationship.38 Brazel, et al.,35 divided public accounting firm’s (PAF) into two categories: big four and non-big four. According to Brazel et al,35 good AQ results prevent fraudulent behavior. The auditor's reputation determines the quality of the audit. If the company has been audited by the PAF big four, it is given 1; otherwise, it is given 0.\n\nRegression modet testing\n\nThe data analysis method, namely multiple regression analysis, was utilized to examine the association between the independent and dependent variables. The following are the equations applied in this study:\n\nWhere as: αα = constant, ββ = coefiesient regression, F-Score = Fraudulent financial statement, LEV = Total debt/Total asset, DACC = Earning Management, AQ = Audit Quality and εε = eror.\n\nFollowing the multiple regression analysis, a moderating regression analysis was conducted. This analysis was done to investigate if the moderating variable in this study had any effect on the link between the independent and dependent variables, either weakening or strengthening it. If the test findings demonstrate a significant effect, the moderating hypothesis is adopted.39 The moderating regression equation is as follows:\n\nWhere as αα = constant, ββ = coefiesient regression, F-Score = Fraudulent Financial Statement, LEV = Total Debt/Total Asset, DACC = earning management, AQ = Audit Quality, LEV*AQ = Interaction between leverage and audit quality, DACC*AQ = Interaction between earning management and audit quality and εε = eror.\n\nThe stages to determine the moderation nature of AQ quality, according to Solimun, et al.,40 are shown in Table 1.\n\nHypothesis testing\n\nCoefficient determination (R Square)\n\nThe coefficient of determination (R2) is used to determine how much the independent variable influences the dependent variable. If R2 equals 0, the independent variable has no effect on the dependent variable. Meanwhile, if the R2 value is 1, the independent variable has a 100% influence on the dependent variable.41\n\nPartially test\n\nThe influence of each independent variable on the dependent variable must be tested using hypothesis testing (t-test). Several assumptions are used to determine whether the hypothesis is accepted or rejected, including (a) the level of significance = 0.05, (b) degrees of freedom (df = n – k), and (c) the t table results. After applying these assumptions, the following conditions can be used to derive conclusions: (a) significance = 5%, the hypothesis is accepted; (b) significance = 5%, the hypothesis is rejected.\n\n\nResults and discussion\n\nThe influence of the independent variables on the dependent variable was tested using a multiple regression model analysis. Table 2 shows the results of the multiple regression model tests.\n\na Dependent Variable: Fraudulent Financial Statement.\n\nBased on the above table, multiple regressions equal is as following:\n\n1. The constant is 0.258, indicating that the FSF is 0.193 if FD and EM are both zero. FSF does not occur in the research sample since the F-score is less than 1.\n\n2. The FD coefficient is 0.791, which means that if the level of FD rises by one, the level of FSF rises by one as well.\n\n3. EM's coefficient is 0.830. This means that if the management uses EM, the possibility of FSF will increase by 0.830.\n\n4. AQ has a coefficient of -0.168. This means that if the AQ produced is satisfactory, the possibility of FSF will be reduced by -0.168.\n\nRegression model analysis in the form of moderated regression is a regression equation that contains elements of interaction (multiplication of two or more independent variables). The results of the moderation regression model test can be seen in Table 3.\n\na Dependent Variable: Fraudulent Financial Statement.\n\nModerating regression model can be descripted by the following equation:\n\n1. The constant is 0.159, indicating that if FD and EM are both zero, the FSF will be 0.159. FSF does not occur in the research sample since the F-score is less than 1.\n\n2. The FD coefficient is 0.909, meaning that when the level of FD raises, the level of FSF rises by 0.909.\n\n3. EM's coefficient is 1.403. This suggests that if the manager executes EM, the likelihood of FSF increases by 1,403 percent.\n\n4. AQ's coefficient is -0.213. This suggests that as the quality improves the likelihood of FSF decreases by -0.213.\n\n5. The moderating regression coefficient of FD and AQ is -0.542, indicating that increasing the level of FD followed by increasing the level of AQ reduces FSF.\n\n6. The moderating regression coefficient of EM and AQ is -2,026. This means that increasing EM followed by increasing AQ reduces FSF.\n\nPartially test\n\nThe results of partially test of every variable are descripted in Table 4.\n\nThe findings of the t-test hypothesis can be accepted if the significance level is less than 0.05, as shown in the table above, and can be interpreted as follows:\n\n1. The effect of FD on FSF is 0.000000001 less than 0.05. H1 is accepted. This demonstrates that FD has a large and positive impact on FSF.\n\n2. The effect of EM on FSF is 0.020 less than 0.05. H2 is acceptable. This indicates that EM has a positive and significant impact on FSF.\n\n3. AQ has a significance of 0.042, which is less than 0.05. H3 is rejected. On FSF, AQ has a negative influence or weakens FD. Pure moderation is how AQ is classified. Because AQ interacts with the FD and cannot be an independent variable, it is clearly a strictly moderating variable.\n\n4. AQ is 0.092 more than 0.05. H4 is rejected. When AQ is used to moderate the effects of EM on FSF, it becomes a moderating homologiser variable or a possible moderator with no substantial link to FSF and no interaction with EM.\n\nCoefficient of determination\n\nThe result of coefficient determination can be seen in Table 5.\n\na Predictors: (Constant), X2Z, Financial Distress, AQ, X1Z, EM.\n\nb Dependent Variabel: FSF.\n\nThe adjusted square in the table above shows that the coefficient of determination is 0.290 or 29 percent. This suggests that FD and EM can predict FSF in 29% of cases, whereas the remaining 71% is impacted by other factors.\n\nThe effect of financial distress on financial statement fraud\n\nThe test results found that FSF has a positive and significant influence on FSF. H1 is accepted. FD's significance is 0.000 less than the 0.05 significance level. This means that the higher the company's FD level, the higher the FSF level. The positive impact of FD on FSF demonstrates that a company in financial distress will be under pressure to remedy the situation. According to the PFT, financial statement fraud is caused by five reasons, one of which is pressure. The opening of the possibility to take action supports a person who is under pressure to take whatever action to return the situation to its original state. The same is true for businesses. When a firm is facing financial difficulties and there is a chance to conduct fraud, the company is more likely to do so.\n\nThe findings of this study correlate with Zainudin & Hashim,8 who indicated that the higher the level of FSF, if a company has characteristics such as a high degree of leverage or financial distress with an unbalanced capital structure. Similar findings were found by Utami & Pusparini,15 specifically that FD had a positive effect on FSF. In contrast, Janrosl & Yuliadi9 found that financial difficulties have no impact on FSF in the banking industry. This suggests that infrastructure, utility, and transportation sectors have higher debt levels than the banking industry, putting them under alot of strain and making them vulnerable to fraud.\n\nThe effect of earning management on financial statement fraud\n\nThe second hypothesis test revealed that EM has a positive effect on FSF. H2 is acceptable. The effect of EM on FSF is 0.020 less significant than 0.05. According to the findings of this research, EM increases the act of FSF. This is because EM is the practice of showing earnings that do not reflect the true state of the company, where profit is increased or decreased depending to market conditions. The agent and the principal have opposing interests, according to agency theory. Their interests are the agent's main concern. They run the business to maximize profits. The greater corporate image—in this example, managers—is a result of the bigger profit. In addition, the management want a sizable bonus for the job well done. Meanwhile, shareholders expect a company to pay the dividend and the shareloder welfare increase. This competion of interest causes information asymmetry, which provides chances for FSF, including the adoption of EM techniques.30\n\nThe findings of this study support Rashidah, et al.,10 who suggested that companies with fraud indicators take EM steps. This is because management is under pressure to meet the company's goals in order for the principal to receive a return on their investment. This differs from Kurniawan et al.,14 who looked into FSF in the industrial industry. The disparities in the study's findings suggest that each company's EM practice is unique. Manufacturing organizations have minimal EM practices because they rarely face losses, but the infrastructure, utility, and transportation sectors frequently experience losses and select EM strategies to better their financial situation. The discrepancies in the studies are attributable to the different goals of adopting EM techniques.\n\nThe moderation effect of audit quality towards financial distress on financial statement fraud\n\nThe third hypothesis was tested, and the results show that audit quality diminishes the link between financial difficulty and financial statement fraud. This demonstrates that H3 is acceptable.\n\nThe significant value is 0.042 lower than the 0.05 threshold. It means that AQ has an impact on relationship between FD to FSF. This means that if the company has a good AQ, fraudulent actions induced by FD will be reduced. The findings of this study are consistent with agency theory, which states that a third party is required to bridge the gap between the agent's and principal's interests. An auditor is the third party in question. Auditors can oversee a firm's operations, particularly if it is suffering financial difficulties; the auditor will be responsible for determining whether the company can overcome these challenges without engaging in fraudulent tactics. As a result, financial difficulties can be resolved.\n\nThis study is supported by Himawan,2 who states that companies used the high quality of PAF to produce high-quality financial reports and provide financial statements in conformity with generally accepted accounting principles. This PAF has an international reputation and experience. As a result, auditors can predict whether the company is having FD issues or engaging in fraudulent behavior. FSF can be reduced by using the services of the PAF big four. According to the findings of Achmad,42 AQ has no effect on FSF in all companies listed on the Indonesia Stock Exchange. The differences in this study's findings are related to differences in the research object. The risk levels of financial difficulties for every industry are very different, not specific to one industry. In the infrastructure, utilities, and transportation sectors, AQ can moderate the influence of AQ on FSF. Variation of research results is described by Achmad,42 stating that the extent of financial difficulty varies greatly across enterprises. The difference in results is caused by the different industry objects. In the industry that has a high probability of FSF, AQ can moderate the relationship between FD and FSF.\n\nThe moderation effect of audit quality towards earning management on financial statement fraud\n\nThe fourth hypothesis was tested, and the results revealed that AQ reduces the link between EM and FSF. As a result, H4 was rejected. AQ modulating EM has a significance of 0.092, which is larger than 0.05. According to the findings of this investigation, AQ was unable to moderate EM on FSF. Because there are many various forms of EM practices, and organizations can utilize different EM practices from year to year for their company, the ability to identify EM is minimal if a large PAF size is not accompanied with high auditor skill. This finding is supported by Luhgiatno,43 who states that companies audited by the PAF big four have not been able to reduce EM practices. When a firm decides to go public, it uses EM to ensure that its financial performance is attractive to potential investors. As a result, auditors have a tough time detecting EM. This EM practice continues to be misunderstood. On the one hand, EM activity is permissible, but on the other hand, this action can also be highly problematic if the company does not produce financial statements that fully reflect the company's current condition.36\n\nThis is consistent with agency theory, which maintains that the principal and agent are distinct. According to this hypothesis, if management has its own interests as well as the principal's, the resulting discrepancies might lead to information asymmetry. The company's overall goal is to keep a positive image, and potential investors are interested in investing. In general, investors consider the company's ability to generate profits per year to be positive. Earnings in financial accounts are frequently falsified in the practice of EM. If a company's profit is good, then its performance in the eyes of investors is also good, and investors will opt to invest in it, resulting in the company generating more profits as a consequence of EM practices. In contrast to Rashidah, et al.,10 who found that, a significant number of small and medium businesses engage in FSF through EM actions. The difference between Rashidah’s study and our study, are due to the different research samples. The sample in this study is infrastructure, utility, and transportation corporations that used EM practices while adhering to generally accepted accounting principles. The focus of the study by Rashidah, et al.,10 was small to medium Malaysian firms, where EM practices in Malaysian companies change every year depending on the company's conditions, and each company will utilize various methods.\n\n\nConclusion\n\nFSF in infrastructure, utilities, and transportation businesses listed on the Indonesia Stock Exchange between 2015 and 2019 may have occured as a result of FD and EM practices, according to our findings. Because EM practices are still difficult to identify by auditors and EM practices still have pros and cons in their use in accounting, AQ can only regulate FD to FSF, but not EM to FSF.\n\nThe adjusted square for this study is 0.290, or 29 percent, indicating that FD and EM are relatively low in explaining their effect on FSF, and the subject of this study only focuses on infrastructure, utility, and transportation businesses that listed on the Indonesia Stock Exchange between 2015 and 2019. The research sample comprised only thirty companies, with a total of 150 observations, which is considered a small sample.\n\nBased on the findings and limitations, it is suggested that additional variables that may play a role in the occurrence of FSF be investigated, as well as the utilization of a larger research sample to broaden research on financial statement fraud practices.",
"appendix": "Data availability\n\nFigshare: Fraudulent of Financial Statement: The Effect of Financial Distress, Earning Management and Audit Quality as Moderating Variable, https://doi.org/10.6084/m9.figshare.20113889.v1. 44\n\nThis project contains the following underlying data:\n\n• Data of Earning Management.xlsx\n\n• Data of Fraudulent Financial Stement.xlsx\n\n• Data of Leverage.xlsx\n\n• Data of Quality Audit.xlsx\n\n• Result Test.docx\n\n• Samples Data.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\nWe would like to express our special thanks for Professor Dr. Mohamad Adam as The Dean of Economics Faculty Universitas Sriwijaya, Arista Hakiki, M. Acc and Dr. E. Yusnaini as the head and secretary of Accounting Department, Economics Faculty, Universitas Sriwijaya were supporting our research teams to do the research and publish article. We are really thankful to them.\n\n\nReferences\n\nRiyanti EC, Putri WHC, Artadi W, et al.: Pengaruh Kualitas Audit Terhadap Fraudulent Financial Reporting Dengan Komite Audit Sebagai Variabel Moderasi (Studi Empiris Pada Perusahaan Manufaktur yang terdaftar di BEI tahun 2016 – 2018). Prosiding Seminar Nasional Cendekiawan. 2019; 2–278. Publisher Full Text\n\nHimawan FA: Analisis Pengaruh Good Corporate Governance, Profitabilitas dan Leverage Terhadap Integritas Laporan Keuangan Dengan Moderasi Kualitas Audit Pada Perusahaan Manufaktur yang Terdapat di Bursa Efek Indonesia Periode 2013-2017. ESENSI: Jurnal Manajemen Bisnis. 2019; 22(3): 289–311. Publisher Full Text\n\nFahreza MB, Guritno Y, Lastiningsih N: Analisis Faktor Faktor Mempengaruhi Fraudulent Fianacial Statement pada Perusahaan Pertambangan. Jurnal Equity. 2020; 23(1): 43–62. Publisher Full Text\n\nApriliana S, Agustina L: The Analysis of Fraudulent Financial Reporting Determinant through Fraud Pentagon Approach. Jurnal Dinamika Akuntansi. 2017; 9(2): 154–165. Publisher Full Text\n\nTessa C, Harto P: Pengujian Teori Fraud Pentagon Pada Sektor Keuangan Dan Perbankan Di Indonesia. Simposium Nasional Akuntansi XIX, Lampung. 2016; 1–21. Reference Source\n\nAssocation of Certified Fraud Examiner: Report To The Nations On Occupational Fraud and Abuse. 2016.Reference Source\n\nBell TB, Carcello JV: A Decision Aid for Assessing the Likelihood of Fraudulent Financial Reporting. Auditing: A Journal of Practice and Theory. 2000; 19(1): 169–184. Publisher Full Text Reference Source\n\nZainudin EF, Hashim HA: Detecting Fraudulent Financial Reporting Using Financial Ratio. Journal of Financial Reporting and Accounting. 2016; 14(22): 266–278. Publisher Full Text\n\nJanrosl VSE, Yuliadi.: Analisis Financial Leverage, Likuiditas dan Profitabilitas Terhadap Financial Statement Fraud Pada Perusahaan Perbankan. Jurnal KRISNA: Kumpulan Riset Akuntansi. 2019; 11(1): 40–46. Reference Source\n\nRashidah AR, Sulaiman S, Fadel ES, et al.: Earnings Management and Fraudulent Financial Reporting: The Malaysian Story. Journal of Modern Accounting and Auditing. 2016; 12(2): 91–101. Publisher Full Text\n\nMaryulianti H: Determinasi Kualitas Audit Dan Pengaruhnya Terhadap Fraud Detection Pada Laporan Keuangan. Jurnal Bisnis Dan Ekonomi. 2015; 6(1): 1–16. Reference Sourcef\n\nRini VY, Achmad T: Analisis Prediksi Potensi Risiko Fraudulent Financial Statement melalui Fraud Score Model. Diponegoro Journal of Accounting. 2012; 1(1): 1–15. Reference Source\n\nJensen MC, Meckling WH: Theory of The Firm: Managerial Behavior, Agency Costs and Ownership Structure. Journal of Financial Economics. 1976; 3(10): 305–360. Publisher Full Text\n\nKurniawan AA, Hutadjulu LY, Simanjuntak AM: Pengaruh Manajemen dan Corporate Governance Terhadap Kecurangan Laporan Keuangan. Jurnal Akuntansi & Keuangan Daerah. 2020; 15(1): 1–14. Publisher Full Text Reference Source\n\nUtami ER, Pusparini NO: The Analysis Of Fraud Pentagon Theory And Financial Distress For Detecting Fraudulent Financial Reporting In Banking Sector In Indonesia (Empirical Study Of Listed Banking Companies On Indonesia Stock Exchange In 2012-2017). Advances in Economics, Business and Management Research. 2019; 102(5): 60–65. Publisher Full Text\n\nNurbaiti Z, Hanafi R: Analisis Pengaruh Fraud Diamond Dalam Mendeteksi Tingkat Accounting Irregularities. Jurnal Akuntansi Indonesia. 2017; 6(2): 167–184. Publisher Full Text\n\nDeAngelo LE: Auditor Size and Audit Quality. Journal of Accounting and Economics. 1981; 3(3): 183–199. Publisher Full Text\n\nAyu M, Pratiya M, Susetyo B, et al.: Pengaruh Stabilitias Keuangan, Target Keuangan, Tingkat Kinerja, Rasio Perputaran Aset, Keahlian Keuangan Komite Audit, dan Profitabilitas Terhadap Fraudulent Financial Statement. PERMANA. 2018; 10(1): 257–272. Publisher Full Text\n\nDarmansyah: Pengaruh Financial Distress terhadap Kualitas Laporan Keuangan dengan Pemoderasi Prudence: Study Empiris pada Industri Tejstil dan Garment yang Terdaftar di Bursa Efek Indonesia. Jurnal Ekonomi. 2016; 7(2): 135–148. Publisher Full Text\n\nArifin B, Nofianti N, Kautsar HF: Pengaruh Likuiditas, Solvabilitas, Profitabilitas, Nilai Pasar dan Pemanfaatan Aset Terhadap Financial Statement Fraud. Ekonomika. 2016; 11(2): 255–279. Reference Source\n\nSulastri S, Anna YD: Pengaruh financial distress dan leverage terhadap konservatisme akuntansi. Jurnal Akuntansi. 2018; 14(1): 58–68. Publisher Full Text\n\nPratama MY: Pengaruh Ukuran Perusahaan, Leverage, Kebijakan Dividen, Kepemilikan Institusional dan Kepemilikan Manajerial Terhadap Manajemen Laba. Jurnal Online Mahasiswa Fakultas Ekonomi. 2016; 3(1): 2342–2356. Reference Source\n\nSetiawati L, Naim A: Manajemen Laba. Jurnal Ekonomi Dan Bisnis Indonesia. 2000; 15(4): 424–441. Reference Source\n\nAgoes S: Auditing: Petunjuk Praktis Pemeriksaan Akuntan Oleh Akuntan Publik. 5th ed.Jakarta:Salemba Empat;2016.Reference Source\n\nIrawati L, Fakhruddin I: Pengaruh Dan Kualitas Audit Corporate Governance Terhadap Integritas Laporan Keuangan. Kompartemen. 2016; 14(1): 90–106. Publisher Full Text\n\nTussiana AA, Lastanti HS: Pengaruh Independensi, Kualitas Audit, Spesialisasi Industri Auditor Dan Corporate Governance Terhadap Integritas Laporan Keuangan. Media Riset Akuntansi, Auditing Dan Informasi. 2017; 16(1): 69–78. Publisher Full Text\n\nCrowe H: Why The Fraud Triangle Is No Longer Enough. In Horwath, Crowe LLP.2011.Reference Source\n\nWolfe DT, Hermanson DR: The Fraud Diamond: Considering The Four Element of Fraud. CPA J. 2004; 74.12: 38–42. The Fraud Diamond: Considering The Four Elements of Fraud. The New York State Society of CPAs. Reference Source\n\nSeptriani Y: Mendeteksi Kecurangan Laporan Keuangan dengan Analisis Fraud Pentagon. Jurnal Akuntansi, Keuangan Dan Bisnis. 2018; 11(1): 11–23. Reference Source\n\nPutra DST, Muid D: Analisis Pengaruh Independensi, Mekanisme Corporate Governance, Dan Kualitas Audit Terhadap Integritas Laporan Keuangan. Jurnal Akuntansi Dan Ekonomi. 2007; 1(1): 1–11. Reference Source\n\nBisogno M, De Luca R: Financial Distress and Earnings Manipulatiom: Evidence from Italia SMEs. Journal of Accounting and Finance. 2015; 4(1): 42–51. Reference Source\n\nHardiningsih P: Pengaruh Independensi, Corporate Governance, dan Kualitas Audit Terhadap Integritas Laporan Keuangan. Kajian Akuntansi. 2010; 2(1): 61–76. Reference Source\n\nSkousen CJ, Twedt BJ: Fraud score analysis in emerging markets. Cross Cultural Management: An International Journal. 2009; 16(3): 301–316. Publisher Full Text\n\nRichardson SA, Sloan RG, Soliman MT, et al.: Accrual Reliability, Earning Persistence and Stock Prices. Journal of Accounting and Economics. 2004; 39(3): 1–65. Publisher Full Text\n\nBrazel JF, Jones KL, Zimbelman MF: Using Nonfinancial Measures to Assess Fraud Risk. Journal of Accounting Research. 2009; 47(5): 1135–1166. Publisher Full Text\n\nKurniawansyah D: Apakah Manajemen Laba Termasuk Kecurangan?: Analisis Literatur. Jurnal Riset Akuntansi Dan Bisnis Airlangga. 2018; 3(1): 341–356. Publisher Full Text\n\nDechow PM, Hutton AP, Kim JH, et al.: Detecting Earnings Management: A New Approach. Journal of Accounting Research. 2012; 50(2): 275–334. Publisher Full Text\n\nSugiyono: Metode Penelitian Kuantitatif, Kualitatif dan R&D. Bandung:Alfabeta;2018.Reference Source\n\nLiana L: Penggunaan MRA dengan Spss untuk Menguji Pengaruh Variabel Moderating terhadap Hubungan antara Variabel Independen dan Variabel Dependen. Jurnal Teknologi Informasi DINAMIK. 2009; 9(2): 90–97. Publisher Full Text\n\nSolimun S, Achmad AR, Nurjannah N: Metode Statistika Multivariat Pemodelan Persamaan Struktural (SEM) Pendekatan WarpPLS. UB Press;2017.Reference Source\n\nKuswantoro A: Pendidikan Administrasi Perkantoran Berbasis Teknologi Informasi Komputer. Jakarta:Salemba Empat;2014.Reference Source\n\nAchmad T: Pengaruh Kualitas Audit dan Auditor Switching terhadap Kecurangan Pelaporan Keuangan: Kepemilikan Institusional sebagai Variabel Moderating. Jurnal Akuntansi Dan Bisnis. 2019; 18(2): 110–125. Publisher Full Text\n\nLuhgianto L: Analisis Pengaruh Kualitas Audit terhadap Manajemen Laba (Studi Pada Perusahaan yang melakukan IPO di lndonesia). Jurnai Akuntansi Riset, Prodi Akuntansi UPI. 2010; 2(1): 319–334. Publisher Full Text\n\nMukhtaruddin M: Fraudulent of Financial Statement: The Effect of Financial Distress, Earning Management and Audit Quality as Moderating Variable. figshare. Conference contribution.2022. Publisher Full Text"
}
|
[
{
"id": "178309",
"date": "30 Jun 2023",
"name": "Gatot Soepriyanto",
"expertise": [
"Reviewer Expertise Fraud Examination",
"Accounting and Auditing Research",
"Corporate Tax Avoidance",
"Capital Market Research in Accounting."
],
"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 investigate whether financial distress, earnings management and audit quality as determinants/moderating variable for financial statements fraud in Indonesian listed firms during 2015 to 2019 period. The authors focused on infrastructure, utility and transportation sectors.\nIn general, the study has been designed adequately to tackle the research questions and issues posed by the authors.\nHowever, there are some elements need to be addressed to improve the paper:\nWhilst the study provide adequate research background and institutional setting, it did not mention on why the study focuses on infrastructure, utility and transportation sectors? Is there any specific issues on that sector that related to financial statements fraud? In addition to that, why the study chooses 2015-2019 period?\n\nThe study should also discuss the reason choosing F-Score as its main measure for financial statement fraud. Why, for example, the study did not use, Beneish M-Score? Or other accounting irregularities measures in the literature?\n\nThe study needs to provide descriptive statistics table, so the reader can gauge and understand the dataset better. This should be provided before the authors arrive with the hypothesis discussion;\n\nGiven the study uses panel data (multi years, across different firms), is there any attempt to mitigate the issues of panel data regression? For example, using year-fixed effects or even using panel data regression analysis?\n\nThe manuscript need to be checked in terms of the quality of English write up. The title for example, is a little bit confusing, as it did not really represent what the study want to achieve in general.\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": []
},
{
"id": "250245",
"date": "25 Mar 2024",
"name": "Toni Šušak",
"expertise": [
"Reviewer Expertise Forensic Accounting",
"Accounting",
"Audit",
"Corporate Finance",
"Corporate Governance",
"Corporate Law"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDespite the interesting idea for research, the paper has its shortcomings: ** The title of the paper is too long, it should be shortened. ** Throughout entire paper (including the title) the term “earning management” is used instead of “earnings management”. ** [Page 1] “Accounting practices, profit bubbles, information manipulation and deception, and earning management are all examples of fraudulent financial statement cases”. – Earnings management is not necessarily fraudulent behavior. Why are accounting practices and profit bubbles listed as fraudulent? ** [Page 1] The website www.idx.go.id cannot be reached. The better option was to write the name of the source instead of a website. ** [Page 3] The name of the company is not Xeroc, it is Xerox. ** [Page 3] “Fraud is practice that involves the use of deception to acquire unfair or unlawful advantages by one or more individuals. This means that fraud is an act committed by specific people, whether intentionally or unintentionally, to benefit themselves and others.” – How can a fraud be unintentional? ** [Page 3] “Earnings management (EM) is profit engineering carried out by managing revenues (cash inflows) and expenses (cash outflows) to ensure that the company's operations generate net operating profit.” – Revenues are not synonym of cash inflows, nor are expenses synonym of cash outflows. ** [Page 3] F-score should be written with capital F. ** [Page 3] “Principal” should be written instead of “principle”. ** [Page 4] “Asymmetric information” or “Information asymmetry” should be written instead of “Asymmetry information”. ** [Page 4] “Donald Cressey” should be written instead of “Donald Cressy”. ** [Page 6] “Financial statements” should be written instead of “financial statistics”. ** [Page 6] “The study's subjects are companies in the infrastructure, utilities, and transportation sectors that have been listed on the Indonesia Stock Exchange during five years observation.” – What is the reason for choosing these sectors? ** [Page 6] If panel regression model is used, methodology and applied tests should be elaborated. ** [Page 6] RSST Accrual formula has duplicated content. ** [Page 6] “If a corporation has more than one fraud score model, it is assumed that it will commit fraud.” – Should it be written “If a corporation has F-score value more than one…”? ** [Page 7] “EM is classified as a form of fraud.” – Earnings management is not necessarily fraudulent behavior. ** [Page 7] DACC formula has duplicated content.Instead of DACCit = TAit/Ait-1*TAit/Ait-1 - NDACCit it should be written DACCit = TAit/Ait-1 - NDACCit. TAit/Ait-1 is duplicated in the formula.\nThe same remark is applicable to: ** [Page 6] RSST Accrual formula has duplicated content. ** [Page 7] Jones model formula should be included in the paper and elaborated. ** [Page 7] “Big Four” should be written with both capital letters (not “big four”). ** [Page 7] α, β, and ε is doubled in the explanations of formulas. ** [Page 8] Besides test variables, it is advisable to include additional control variables in the multiple regression model. ** [Page 8] “1. The constant is 0.258, indicating that the FSF is 0.193 if FD and EM are both zero. FSF does not occur in the research sample since the F-score is less than 1.” – Instead of “if FD and EM are both zero” it should be written “if all other variables are zero” given that AQ is also part of the model. ** [Page 8] “2. The FD coefficient is 0.791, which means that if the level of FD rises by one, the level of FSF rises by one as well.” – Instead of “the level of FSF rises by one as well” it should be written “the value of FSF rises by 0.791”. Ceteris paribus assumption should be stated. ** [Page 8] “3. EM's coefficient is 0.830. This means that if the management uses EM, the possibility of FSF will increase by 0.830.” – Instead of “if the management uses EM, the possibility of FSF will increase by 0.830.” it should be written “if the value of EM increases by 0.1, the value of FSF will increase by 0.083”. Ceteris paribus assumption should be stated. ** [Page 8] Variable explanations for moderating regression should be revised according to the previous three comments. ** [Page 10] “Industrial industry” should be corrected. ** Paper lacks descriptive statistics of the research sample. ** Robustness analysis could be conducted using alternative fraud measures. ** This paper would benefit from some closer proofreading. It may be useful to engage a professional English language editor. There is abundance of grammatical and typo errors (e.g. “diffucties”, “condisions”, “modeartes”, “criteras”, “coefiesient”, “shareloder” etc.).\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
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https://f1000research.com/articles/11-1362
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https://f1000research.com/articles/11-1361/v1
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22 Nov 22
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{
"type": "Case Report",
"title": "Case Report: Reversal and subsequent return of optic disc cupping in a myocilin (MYOC) gene-associated severe Juvenile Open-Angle Glaucoma (JOAG) patient",
"authors": [
"Hani El Helwe",
"Sandy Samuel",
"Sanchay Gupta",
"Cameron Neeson",
"Marika Chachanidze",
"David A. Solá-Del Valle",
"Hani El Helwe",
"Sandy Samuel",
"Sanchay Gupta",
"Cameron Neeson",
"Marika Chachanidze"
],
"abstract": "To our knowledge, this case report describes the first instance of reversal of glaucomatous optic nerve cupping in a young adult with a rare form of juvenile open-angle glaucoma (JOAG) associated with a novel variant of the myocilin gene (MYOC). This 25-year-old woman with severe-stage MYOC-associated JOAG presented with blurry vision and intermittent pain in her left eye. She had a strong family history of glaucoma in multiple first-degree relatives with an identified novel variant of MYOC. Examination revealed intraocular pressures (IOPs) of 10 mmHg OD and 46 mmHg OS, with cup-to-disc ratios of 0.90 and 0.80. The patient experienced substantial reversal of optic disc cupping OS following dramatic IOP reduction with trabeculectomy, and subsequently experienced a return of cupping after an IOP spike 15 months postoperatively. The reversal of cupping did not correspond to any changes in the patient’s visual field. After an initial decrease in retinal nerve fiber layer (RNFL) thickness, RNFL remained stable for over 2 years after trabeculectomy as seen on Optical Coherence Tomography (OCT). This case suggests reversal of cupping can occur well into adulthood in a MYOC-associated JOAG patient, and it demonstrates the potential bidirectionality of this phenomenon. Moreover, it suggests that these structural changes may not correspond to any functional changes in visual fields or RNFL thickness.",
"keywords": [
"Reversal of optic nerve head cupping",
"Juvenile open-angle glaucoma",
"Myocilin gene",
"glaucoma filtration surgery"
],
"content": "Introduction\n\nThe myocilin gene (MYOC) is located within the glaucoma locus GLC1A present on chromosome 1q21-q31.1 It encodes an extracellularly-secreted matrix protein expressed by many tissues throughout the body but only found to cause disease at the level of the trabecular meshwork (TM).2 MYOC mutations have been implicated in 8-36% of cases of familial juvenile open-angle glaucoma (JOAG) which is characterized by very high intraocular pressures (IOPs), optic disc cupping, and visual field loss at a young age (<40 years).3,4 The exact mechanism by which MYOC exerts its function isn’t fully understood, but it is believed to be intimately involved in dictating TM stiffness and resistance to flow.5,6 There are currently 280 identified MYOC mutations, 37.86% of which have been associated with the development of glaucoma.6–8 These mutations are thought to cause aqueous outflow obstruction at the level of the TM. Missense mutations make up 85.9% of glaucoma-related MYOC mutations, most of which arise within the olfactomedin (OLF) domain present on exon 3 of MYOC.9 One such mutation carried by the patient presented in this report is Glu385Lys. This mutation was initially discovered in her sibling and was later found to be present in all her family members affected by glaucoma and absent in those unaffected by the disease. Glu385Lys exchanges a highly-conserved negatively-charged glutamic acid for a positively-charged lysine amino acid.7 This substitution causes a conformational change at the level of the OLF domain, which disrupts proper processing and delivery of the MYOC protein to the extracellular matrix. Studies hypothesize that misfolded MYOC proteins are then retained within the endoplasmic reticulum (ER) of TM cells.10–14 These retained MYOC proteins trigger a stress response within the ER that eventually leads to the apoptosis of the TM cells.12,15,16 These morphological changes impact TM biomechanics causing increased stiffness and reduced drainage capability, which give rise to JOAG.\n\nPreviously described in other JOAG patients, reversal of optic disc cupping refers to the improvement in the appearance of the optic nerve head in response to a marked decrease in IOP, often following surgical intervention.17 While this structural phenomenon is widely recognized as an indicator of successful treatment in pediatric glaucoma patients, it is less commonly described in adults.18,19 Moreover, there is controversy as to whether these structural improvements correspond to any functional improvements in patients’ visual fields and optical coherence tomography (OCT).20,21\n\nThis case report describes reversal of optic disc cupping in a 25-year-old woman with severe-stage MYOC-associated JOAG, and eventual return-of-cupping following a period of less tightly controlled IOP. Additionally, using fundus photos, Humphrey Visual Field (HVF), and OCTs, we suggest these structural changes did not appear to correspond to functional disease changes.\n\nTo the best of our knowledge, this is the first time this phenomenon has been described in a MYOC-associated JOAG patient.\n\n\nCase presentation\n\nThe case involves a 25-year-old Puerto Rican woman with severe-stage MYOC-associated JOAG (first diagnosed at age 20) who presented to the Massachusetts Eye and Ear Glaucoma Clinic in February 2018 with blurry vision and intermittent pain in the left eye (OS). She had a strong family history of glaucoma in multiple first-degree relatives, and she was found to share a novel variant of the MYOC gene (NM_000261.2: c.1153G>A, p.Glu385), as described above, with her father, sister, and brother under a research protocol completed at the Yale Center for Genome Analysis.7 The patient had previously undergone successful trabeculectomy with mitomycin C in the right eye (OD) in 2014 and selective laser trabeculoplasty (SLT) in the left eye in early 2018 that failed to significantly lower her IOP. Her maximum recorded IOP was 40 mmHg OD and 46 mmHg OS.\n\nOn examination in February 2018, the patient’s best corrected visual acuity (BCVA) was 20/25 OD and 20/30 OS. Her IOP was 10 mmHg OD off glaucoma medications and 46 mmHg OS on dorzolamide twice a day (bid), timolol bid, brimonidine bid, and bimatoprost at night (qhs).\n\nExamination of both optic nerves revealed diffuse thinning of the disc without hemorrhage bilaterally with a cup-to-disc ratio of approximately 0.90 OD and 0.80 OS. HVF analysis revealed constriction with central island OD and superior arcuate more than inferior arcuate OS. OCT revealed diffuse thinning of the retinal nerve fiber layer (RNFL) OU (shown in Figure 1).\n\na. Optic nerve head OD (2/16/2018). b. Optic nerve head OS (2/16/2018). c. OCT ONH and RNFL Analysis OU (2/13/2018). d. HVF OD (2/13/2018). e. HVF OS (2/13/2018).\n\nGiven the extremely elevated IOP in her left eye despite receiving close to maximally tolerated medical therapy (MTMTx), the patient underwent an urgent trabeculectomy with mitomycin-C (concentration of 0.4 mg/mL) in February 2018. The patient’s IOP and BCVA OD have remained stable since her initial presentation, ranging from 10-12 mmHg and 20/20 to 20/25, respectively. Subsequent discussion is therefore focused primarily on her left eye with relevant visit data for the left eye provided in Table 1. On postoperative day one, her IOP was 05 mmHg OS off glaucoma medications. Her slit lamp and fundus exam revealed a deep anterior chamber, cornea without Descemet’s folds, and a flat macula. The anterior chamber showed 1+ cell. Three days following her procedure, a leak was seen along the limbus and a bandage contact lens (BCL) was placed in the office. Anterior chamber inflammation resolved by her one-week postoperative follow-up. At this time the BCL was removed, and the leak along the limbus became evident again. Due to persistent leakage along the conjunctiva superiorly the patient underwent a revision where 8-0 Vicryl mattress sutures were used to repair the leak. One day after the first revision, a slow leak persisted along the superonasal aspect of the peritomy, and the patient’s IOP dropped to 02 mmHg. This was the only instance when IOP was in the hypotonous range, although a deep central anterior chamber, absence of corneal Descemet’s folds, and a flat macula were noted. This necessitated a second bleb revision in March 2018 with more 8-0 Vicryl and several 10-0 Nylon mattress sutures. Her IOP was subsequently noted to be 06 mmHg with no signs of hypotony or leak.\n\nIn April 2018, a reliable macula OCT revealed normal values for central subfield thickness, cube volume, and cube average thickness, indicating absence of macular folding or signs of macular hypotony even when the cup-to-disc ratio was noted to be 0.35 (shown in Figure 2). Eight months after the initial surgery her BCVA was 20/25 OD and 20/40 OS, and IOP measurements were 10 mmHg OD and 05 mmHg OS off glaucoma medications. Her exam continued to show no signs of hypotony. Photographs of the left optic disc eight-months postoperatively demonstrated substantial reversal of cupping with a reduced cup-to-disc ratio of 0.45 (shown in Figure 3). Although the patient’s first postoperative OCT showed a decrease in RNFL thickness from 71 μm OS preoperatively to 56 μm OS, this thickness remained stable throughout her follow-ups. It is also worth noting that the patient’s average neuro-retinal rim thickness was higher at the October 2018 visit compared to preoperative measurements, further corroborating reversal of cupping of the nerve head (shown in Figure 3).\n\na. Optic nerve head OS (10/11/2018). b. OCT ONH and RNFL Analysis OU (10/11/2018).\n\nIn May 2019, the patient’s IOP OS spiked to 23 mmHg and her cup-to-disc ratio increased to 0.70, indicating a return to cupping of the nerve. After the IOP spike, the patient was placed on timolol OS, and her IOP has been controlled at subsequent follow-ups. It is worth noting that the RNFL and HVF remained stable after the nerve became cupped again in May 2019 (shown in Figure 4). From her November 2019 follow-up to her most recent follow-up in January 2022, her cup-to-disc ratio has remained steady at 0.70 throughout all visits. Additionally, her average neuro-retinal rim thickness returned to below normal levels and has remained there, as seen in Figures 5 and 6. In contrast, her RNFL remained stable at 53 μm compared to 56 μm in October 2018 (shown in Figure 6). Additionally, her HVF has remained stable throughout the preoperative and all postoperative follow-ups, with a maximum deviation of -1.32 dB from baseline. These fluctuations are within the expected test-retest variability range and will be explained in the discussion. For the patient’s follow-ups after November 2019, her IOP has been stable, ranging from 09-11 mmHg OS. At her latest follow-up in January 2022, the patient’s BCVA was 20/30 OS, with an IOP of 07 mmHg OS. The patient is currently on timolol bid OS.\n\na. Optic nerve head OS (11/14/2019). b. OCT ONH and RNFL Analysis OU (11/14/2019). c. HVF OS (11/14/2019).\n\n\nDiscussion\n\nThe current case describes the reversal of optic disc cupping after substantial IOP reduction in an adult patient with severe-stage MYOC-associated JOAG. We also describe a significant return towards the patient’s preoperative cup-to-disc ratio following an IOP spike. The patient’s cup-to-disc ratio was noted to be 0.70 in their May 2019 follow-up and has remained consistent for over two years. Corresponding HVF and OCT analyses do not appear to show significant corresponding functional changes. Reversal of cupping has been described in only a select few adult patients following substantial reductions in IOP. Specifically, Pederson et al. reported five adult cases (31-62 years of age) where reversal of cupping was observed after an IOP reduction of 68% following filtration surgery.19 Similar to this case, one of these patients experienced an IOP spike 10 months later that led to a return of cupping to preoperative size. In addition, Esfandiari et al. showed a positive correlation between the degree of cupping reversal and the magnitude of IOP reduction (regression coefficient = 0.251, P = 0.02).22 Interestingly, the authors found a negative correlation between the extent of cupping reversal and age (regression coefficient = -0.224, P = 0.04) as well as cup-to-disc ratio (regression coefficient = -0.212, P = 0.05). In short, a larger IOP reduction and younger age were correlated with larger reversals of cupping and degrees of functional improvement in the HVF.\n\nSome authors suggest that macular hypotony after glaucoma surgery may trigger ocular changes that mediate optic nerve cupping reversal in such cases.23,24 However, exam and imaging findings from our patient’s postoperative follow-up visits suggest that macular hypotony is not a significant driver for her cupping reversal as her IOP was below 05 mmHg only once for a day without ocular signs of hypotony. Her exams were notable for a deep central anterior chamber and absence of significant Descemet membrane folds while macular OCT demonstrated normal central subfield thickness with no evidence of choroidal or retinal folding (shown in Figure 2).\n\nIn the current case, we did not observe any functional changes on HVF or OCT that would correspond to the structural changes observed at the optic nerve head. Horani et al. and Tan et al. quantified the test-retest variability of HVF and OCT imaging, reporting mean variability among repeat tests of 2.44 dB on HVF and 4.89 μm on Cirrus OCT.25,26 Table 1 shows stability in the patient’s HVF over all follow-ups with median deviations from baseline falling within the expected ±2.44 dB range. Although RNFL thickness decreased after the initial surgery from 71 μm OS to 56 μm OS in October 2018, BCVA and HVF were virtually unchanged over this interval and average RNFL thickness has remained stable in the mid-50s for over two years in subsequent reliable OCTs. Interestingly, Kim et al. found that patients with a high preoperative peak IOP (≥37 mmHg) exhibited significant average RNFL thinning after IOP lowering surgery compared to their preoperative average RNFL thickness.27 We hypothesize that the higher preoperative RNFL value in this case may have been artificially elevated in the setting of extremely high IOP (46 mmHg) and appears to subsequently stabilize after surgery. Furthermore, when the patient experienced cupping reversal, her average neuro-retinal rim thickness increased from preoperative baseline (compare Figures 1 and 3). The neuro-retinal rim is the area of the optic disc occupied by the retinal nerve fiber axons. Analyzing its changes in pattern of thickness and thinning are important for detecting the extent of disc damage. When the patient’s optic nerve cupped again, her average neuro-retinal rim thickness returned to below normal levels and has remained there in subsequent follow-ups, consistent with nerve cupping (shown in Figures 5 and 6).\n\nIn contrast, Leung et al. reported reversal of cupping in a 20-year-old woman with corresponding functional improvements in RNFL thickness.28 However, the duration of these structural and functional improvements was not reported. Notably, adult cases of cupping reversal are limited to patients in the early stages of glaucoma, unlike the current severe-stage patient. For instance, all the patients reviewed by Pederson et al. were in the early stages of glaucoma and Leung et al. described a case of mild JOAG.19,28 None of these patients were known to have glaucoma associated with an identified genetic mutation.\n\nTo the best of our knowledge, this is the only case to report reversal of cupping in an adult patient with MYOC-associated severe JOAG. While we are unable to infer a causal link between the MYOC variant and this patient’s cupping reversal after trabeculectomy, this case may shed light on the structural and functional consequences of IOP changes in patients with this genetic mutation.\n\nTo conclude, this case reflects the responsiveness of the optic nerve head to IOP-lowering surgery in a patient with a rare form of MYOC-associated severe JOAG. Furthermore, it describes a return of optic nerve cupping corresponding to a resurgence in IOP. This highlights the bidirectional quality of this phenomenon, and the relatively short timescale in which cupping can resume after a period of suboptimal IOP control. Moreover, HVF and OCT testing did not seem to reveal a corresponding functional change in the patient’s disease, suggesting that such a structural change may not indicate any significant functional disease changes in MYOC-associated JOAG.\n\nEthical approval was not required for this study in accordance with local or national guidelines. Written informed consent was obtained from the patient for publication of the details of their medical case and any accompanying images. A copy of the written consent is available for review by the Editor of the journal.\n\n\nAuthor contributions\n\nDr. Hani El Helwe, Sandy Samuel, and Sanchay Gupta contributed equally to this work as co-first authors. These authors substantially acquired, analyzed, and interpreted the data for this work. Additionally, they drafted and revised the work to be as up to date as possible. They have read and approved of the final version to be published and agreed to be accountable for all aspects of the work. Dr. Marika Chachanidze, and Cameron E. Neeson initiated this case report, performing the initial data acquisition, analysis, and manuscript drafting. They have read and approved the final draft to be published and agreed to be accountable for all aspects of the work. Dr. David A. Solá-Del Valle is the corresponding author, who has full access to all the data in the study and takes responsibility for the integrity of the data, the accuracy of the data analysis, and the decision to submit for publication.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nAll the mentioned individuals have given their permission for their names and affiliations to be included in this work. With grateful appreciation to Mr. Joseph Leitch, Mrs. Cathey S. Leitch, Mr. Chad Gifford, Mrs. Anne Gifford, and Mr. Stephen Traynor for their philanthropic support of this work. We also would like to acknowledge Mohammad Al-Alkaidib and Emma Klug, who contributed to initial data collection, drafting, and literature review of this manuscript.\n\n\nReferences\n\nStone EM, Fingert JH, Alward WL, et al.: Identification of a gene that causes primary open-angle glaucoma. Science. 1997 Jan 31; 275(5300): 668–670. PubMed Abstract | Publisher Full Text\n\nBorrás T: The effects of myocilin expression on functionally relevant trabecular meshwork genes: a mini-review. J. Ocul. Pharmacol. Ther. 2014 Mar-Apr; 30(2-3): 202–212. PubMed Abstract | Publisher Full Text\n\nWiggs JL, Allingham RR, Vollrath D, et al.: Prevalence of mutations in TIGR/Myocilin in patients with adult and juvenile primary open-angle glaucoma. Am. J. Hum. Genet. 1998 Nov; 63(5): 1549–1552. PubMed Abstract | Publisher Full Text\n\nSouzeau E, Burdon KP, Dubowsky A, et al.: Higher prevalence of myocilin mutations in advanced glaucoma in comparison with less advanced disease in an Australasian disease registry. Ophthalmology. 2013 Jun; 120(6): 1135–1143. PubMed Abstract | Publisher Full Text\n\nResch ZT, Fautsch MP: Glaucoma-associated myocilin: a better understanding but much more to learn. Exp. Eye Res. 2009 Apr; 88(4): 704–712. PubMed Abstract | Publisher Full Text\n\nWang H, Li M, Zhang Z, et al.: Physiological function of myocilin and its role in the pathogenesis of glaucoma in the trabecular meshwork (Review). Int. J. Mol. Med. 2019 Feb; 43(2): 671–681. PubMed Abstract | Publisher Full Text\n\nCriscione J, Ji W, Jeffries L, et al.: Identification of a novel MYOC variant in a Hispanic family with early-onset primary open-angle glaucoma with elevated intraocular pressure. Mol. Case Studies. 2019 Dec 1; 5(6): a004374. PubMed Abstract | Publisher Full Text\n\nFan W, Li W, Duan C, et al.: Characterization of a novel mutation in the MYOC gene in a Chinese family with primary open-angle glaucoma. Mol. Med. Rep. 2020 Oct; 22(4): 3263–3270. PubMed Abstract | Publisher Full Text\n\nHewitt AW, Mackey DA, Craig JE: Myocilin allele-specific glaucoma phenotype database. Hum. Mutat. 2008 Feb; 29(2): 207–211. Publisher Full Text\n\nVollrath D, Liu Y: Temperature sensitive secretion of mutant myocilins. Exp. Eye Res. 2006 Jun; 82(6): 1030–1036. PubMed Abstract | Publisher Full Text\n\nLiu Y, Vollrath D: Reversal of mutant myocilin non-secretion and cell killing: implications for glaucoma. Hum. Mol. Genet. 2004 Jun 1; 13(11): 1193–1204. PubMed Abstract | Publisher Full Text\n\nYam GH, Gaplovska-Kysela K, Zuber C, et al.: Aggregated myocilin induces russell bodies and causes apoptosis: implications for the pathogenesis of myocilin-caused primary open-angle glaucoma. Am. J. Pathol. 2007 Jan; 170(1): 100–109. PubMed Abstract | Publisher Full Text\n\nCaballero M, Borrás T: Inefficient processing of an olfactomedin-deficient myocilin mutant: potential physiological relevance to glaucoma. Biochem. Biophys. Res. Commun. 2001 Apr 6; 282(3): 662–670. PubMed Abstract | Publisher Full Text\n\nAroca-Aguilar JD, Sánchez-Sánchez F, Martínez-Redondo F, et al.: Heterozygous expression of myocilin glaucoma mutants increases secretion of the mutant forms and reduces extracellular processed myocilin. Mol. Vis. 2008; 14: 2097–2108. PubMed Abstract\n\nJoe MK, Sohn S, Hur W, et al.: Accumulation of mutant myocilins in ER leads to ER stress and potential cytotoxicity in human trabecular meshwork cells. Biochem. Biophys. Res. Commun. 2003; 312: 592–600. PubMed Abstract | Publisher Full Text\n\nAnholt RR, Carbone MA: A molecular mechanism for glaucoma: endoplasmic reticulum stress and the unfolded protein response. Trends Mol. Med. 2013 Oct; 19(10): 586–593. PubMed Abstract | Publisher Full Text\n\nHarju M, Saari J, Kurvinen L, et al.: Reversal of optic disc cupping in glaucoma. Br. J. Ophthalmol. 2008 Jul; 92(7): 901–905. Publisher Full Text\n\nLesk MR, Spaeth GL, Azuara-Blanco A, et al.: Reversal of optic disc cupping after glaucoma surgery analyzed with a scanning laser tomograph. Ophthalmology. 1999 May 1; 106(5): 1013–1018. PubMed Abstract | Publisher Full Text\n\nPederson JE, Herschler J: Reversal of Glaucomatous Cupping in Adults. Arch. Ophthalmol. 1982 Mar; 100(3): 426–431. PubMed Abstract | Publisher Full Text\n\nParrish RK, Feuer WJ, Schiffman JC, et al.: Five-year Follow-up Optic Disc Findings of the Collaborative Initial Glaucoma Treatment Study. Am. J. Ophthalmol. 2009 Apr; 147(4): 717–724.e1. PubMed Abstract | Publisher Full Text\n\nKatz LJ, Spaeth GL, Cantor LB, et al.: Reversible optic disk cupping and visual field improvement in adults with glaucoma. Am J. Ophthalmol. 1989 May 15; 107(5): 485–492. PubMed Abstract | Publisher Full Text\n\nEsfandiari H, Efatizadeh A, Hassanpour K, et al.: Factors associated with lamina cribrosa displacement after trabeculectomy measured by optical coherence tomography in advanced primary open-angle glaucoma. Graefes Arch. Clin. Exp. Ophthalmol. 2018 Dec; 256(12): 2391–2398. PubMed Abstract | Publisher Full Text\n\nKao ST, Lee SH, Chen YC: Late-onset Hypotony Maculopathy After Trabeculectomy in a Highly Myopic Patient With Juvenile Open-angle Glaucoma. J. Glaucoma. 2017; 26(4): e137–e141. PubMed Abstract | Publisher Full Text\n\nThomas M, Vajaranant TS, Aref AA: Hypotony Maculopathy: Clinical Presentation and Therapeutic Methods. Ophthalmol. Ther. 2015; 4(2): 79–88. PubMed Abstract | Publisher Full Text\n\nHorani A, Frenkel S, Blumenthal EZ: Test-retest variability in visual field testing using frequency doubling technology. Eur. J. Ohthalmol. 2007 Mar-Apr; 17(2): 203–207. PubMed Abstract | Publisher Full Text\n\nTan B, Natividad M, Chua KC, et al.: Comparison of retinal nerve fiber layer measurement between 2 spectral domain OCT instruments. J. Glaucoma. 2012 Apr-May; 21(4): 266–273. PubMed Abstract | Publisher Full Text\n\nKim WJ, Kim KN, Sung JY, et al.: Relationship between preoperative high intraocular pressure and retinal nerve fibre layer thinning after glaucoma surgery. Sci. Rep. 2019; 9(1): 13901. PubMed Abstract | Publisher Full Text\n\nLeung CK, Woo J, Tsang MK, et al.: Structural and functional recovery in juvenile open angle glaucoma after trabeculectomy. Eye (Lond.). 2006 Jan; 20(1): 132–134. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "209578",
"date": "03 Nov 2023",
"name": "Bryan Ang",
"expertise": [
"Reviewer Expertise Glaucoma",
"Glaucoma Progression",
"Glaucoma Surgery"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, this is a well-written manuscript describing an interesting case that deserves sharing with the wider scientific community. The authors should also be congratulated for successfully managing this difficult case, which has done well despite what appears to be a stormy immediate postoperative course.\nI have a few queries/comments regarding this case, and some points for the authors' consideration.\nPg 3 - “This is the first time this phenomenon has been described in a MYOC-associated JOAG patient.” A suggestion to the authors is to consider a more nuanced statement. This phenomenon has indeed been described in JOAG patients. While previous studies may not have definitively elucidated the MYOC mutation, it may be well plausible many were MYOC-related JOAG cases - particularly given the high overall prevalence of MYOC mutation among JOAG eyes.\n\nThe reliability indices for the various tests seem to have been omitted. This case report relies heavily on investigation and imaging findings. It may be useful to include these indices for better contextualization of the results – e.g. indication of the signal strength for OCT scans, and the reliability indices for HVFs.\n\nDid any of the patient's siblings with the MYOC variant have a similar clinical picture? Did any of them undergo surgery with reversal of cupping as well? If this is known, it will be of interest and should be mentioned in this case report as well.\n\nPg 11 - “In the current case, we did not observe any functional changes on HVF or OCT that would correspond to the structural changes observed at the optic nerve head. Horani et al. and Tan et al. quantified the test-retest variability of HVF and OCT imaging, reporting mean variability among repeat tests of 2.44 dB on HVF and 4.89 μm on Cirrus OCT.” Authors can consider explaining the rationale for mentioning the test-retest variability of HVF and OCT imaging. Are authors suggesting that the apparent absence of corresponding changes in the HVF and OCT versus those in the degree of cupping/neuroretinal rim thickness may be confounded by the test-retest variability? While this may be conceivable for the HVFs, the direction of change in OCT findings (which does not correspond with the change in cupping/neuroretinal rim thickness) appears to be well out of the test-retest variability range.\n\nRepeatability of tests – as a related point, were the tests repeated to confirm the readings/measurements? The postoperative OCTs and HVFs are likely representative and reproducible, given the consistent longitudinal readings over several visits. But how about preoperative investigations? Only one set of preoperative results appears to be presented here. It may be useful to include reliability indices (as per my previous comment (2) ) or include a mention that the results were similar for repeated tests.\n\nPg 12 - “We hypothesize that the higher preoperative RNFL value in this case may have been artificially elevated in the setting of extremely high IOP (46 mmHg)”. Why should this be? Kindly explain this association.\n\nPg 12 - “Notably, adult cases of cupping reversal are limited to patients in the early stages of glaucoma, unlike the current severe stage patient”. It appears that Esfandiari et al’s paper (reference 22 in the manuscript) may also have described cupping reversal in patients with advanced disease.\n\nWhat was the preoperative duration of symptoms/duration of high IOP preoperatively for the left eye? Could this also be a factor that may influence the “reversibility” of cupping/neuroretinal rim thickness before and after surgical intervention?\n\nThroughout the manuscript, OCT changes/findings have been repeatedly described as being “functional” in nature. However, OCT changes may perhaps be considered more structural in nature.\n\nWas the axial length of the eye measured for this case? Axial length is correlated with RNFL thickness, as well as with IOP. If known/measured, it would be of interest and useful to mention in this case report.\n\nThe inconsistency/non-correspondence in findings between cupping/neuroretinal rim thickness/area versus RNFL thickness appears to be a key point of interest in this case report and may deserve further elaboration/explanation.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "277956",
"date": "11 Jun 2024",
"name": "Nader Bayoumi",
"expertise": [
"Reviewer Expertise Glaucoma",
"childhood glaucoma"
],
"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 a case of MYOC-associated JOAG managed by a combination of surgical and medical treatments and demonstrated optic nerve cupping reversibility with treatment. The manuscript is generally well written and highlights the importance of genetic testing in cases of JOAG and childhood glaucoma in general. Specific comments for improvement of the manuscript include:\n\n\"To the best of our knowledge, this is the first time this phenomenon has been described in a MYOC-associated JOAG patient.\" Reversibility of ON cupping is reported following successful IOP control in JOAG. However, genetic analysis of JOAG patients is not routinely performed. This may account for the relative paucity of published reports about MYOC associated JOAG. Hence, please rephrase to reflect this issue; the need for routine genetic analysis of JOAG patients.\n\n\"the patient underwent an urgent trabeculectomy with mitomycin-C\" Please explain why an angle procedure was not performed given the reported high success rate of angle procedures (in isolation or combined to filtering surgery) in JOAG.\nTable 1: Please present information on the bleb appearance over time (given the fluctuation of IOP).\nPlease comment on the health of the neural rim (colour, pallor, etc) throughout the follow up period, before, during and after the reported reversibility of cupping.\nWas a VF performed at the time when the cup reversibility was noted? In other words, was the reversibility of cupping noted clinically correlated with the function of the ON? The presented VFs demonstrate improvement of PSD & MD between 2018 & 2019 visits (although the VFI deteriorated).\n\"In May 2019, the patient’s IOP OS spiked to 23 mmHg and her cup-to-disc ratio increased to 0.70, indicating a return to cupping of the nerve.\" The patient was subsequently prescribed Timolol and the IOP control was regained. Did the patient demonstrate repeated reversal of the ON cupping with subsequent reduction of IOP? Please explain (or at least hypothesise) why not.\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/11-1361
|
https://f1000research.com/articles/11-1360/v1
|
21 Nov 22
|
{
"type": "Systematic Review",
"title": "Rapid review on monkeypox policies among the G20 nations: relevance to policy and practitioner",
"authors": [
"Viola Savy Dsouza",
"Sanjay Pattanshetty",
"Rohit Raj",
"Anupama DS",
"Nachiket Gudi",
"Helmut Brand",
"Viola Savy Dsouza",
"Rohit Raj",
"Anupama DS",
"Nachiket Gudi",
"Helmut Brand"
],
"abstract": "Background: Monkeypox has been declared as a Public Health Emergency of International Concern (PHEIC) by the WHO Director General (WHO-DG). Most of the G20 nations have reported Monkeypox outbreak. Policies developed and implemented in G20 countries for the prevention and control of monkeypox preparedness and response have global consequences. This rapid review aimed to map the monkeypox prevention and control policies planned and implemented in G20 nations in line with temporary recommendations issued by the WHO-DG. Methods: We mapped monkeypox prevention and control policies in G20 nations based on the WHO-DG recommendations. Medline (through PubMed), Scopus, and ProQuest Health and Medical Complete were searched to understand G20 preventative, diagnostic, and therapeutic policies. We also performed an extensive gray literature search through the Ministry of Health websites and newspaper through Google. The documents/ studies that had an information on prevention, control and management guidelines/policies and published through journal, news articles and health ministry websites of G20 nations on monkeypox were included. We excluded the editorials, opinion, and perspective papers and studies published prior to May 6, 2022. Results: We obtained 671 articles with 10 articles included in the review. Additionally, we identified 55 documents from the gray literature. We included national guidelines of the 18 countries on the control, prevention, and management of monkeypox. National guidelines were compared with the WHO guidelines in terms of implementing coordinated response, engaging and protecting communities, surveillance and public health measures and international travel, clinical management and infection, prevention and control (IPC) measures and medical countermeasures research. Depending on the availability of resources, some recommendations are followed by nations while others are not. Conclusions: Coordinated response among states is key to contain the transmission of monkeypox. To bring a coordinated response, G20 nations are following temporary recommendations that are context specific to their nation.",
"keywords": [
"Monkeypox",
"G20 nations",
"Rapid review",
"Monkeypox policy"
],
"content": "Introduction\n\nMonkeypox is a viral zoonotic disease. Monkeypox virus is an enveloped double-stranded DNA virus that belongs to the Poxviridae family's Orthopoxvirus genus.1,2 Monkeypox was first identified in humans in 1970.3 Monkeypox had been recorded in various Central and Western African nations prior to the 2022 outbreak.4\n\nMonkeypox symptoms typically last 2-4 weeks and are self-limiting. In recent years, however, the case fatality ratio has hovered around 1-10%.5 Human cases of monkeypox have been reported in 11 African countries since 1970.4 Nigeria documented 446 suspected cases and 199 confirmed cases from 18 States during 2017 to 2021.6 Monkeypox was first detected in the United States of America (USA) in 2003.7 Monkeypox was recorded among Nigerians travelling to Israel, the United Kingdom (UK), Singapore, and the United States between 2018 and 2021.8–11 However, many instances of monkeypox were discovered in several non-endemic countries in May 2022.12\n\nSince January 1, 2022, 92 Member States from all six World Health Organization (WHO) regions have reported cases of monkeypox to WHO. A total of 57,995 laboratory confirmed cases including 18 deaths, had been reported as of September 12, 2022. Since May 13, 2022, a large majority of these cases have been reported from countries where monkeypox transmission has not previously been documented.12\n\nDespite the fact that the WHO emergency committee voted against declaring monkeypox a public health emergency of international concern (PHEIC), the WHO Director General (WHO- DG) vetoed it during the second meeting of the International Health Regulations (2005) (IHR) Emergency Committee.13\n\nAccordingly, in relation to the multi-country outbreak of Monkeypox, temporary recommendations were issued by the WHO-DG. Temporary recommendations were made based on the burden of disease, and the country's ability to Prevent, Detect and Respond.13 According to the recommendation, states with no history of monkeypox in the human population or no detection of a case of monkeypox for more than 21 days would be classified as group 1, while states with recently imported cases of monkeypox in the human population and/or otherwise experiencing human-to-human transmission of monkeypox virus, including in key population groups and communities at high risk of exposure, would be classified as group 2. States Parties with known or suspected zoonotic transmission of monkeypox, including those where it appears or has been reported, those where monkeypox virus has been documented in any animal species, and those where infection of animal species in countries may be suspected, including newly affected countries categorized as group 3 and group 4 countries with manufacturing capacity for medical countermeasures.13\n\nWHO assesses the global risk as “Moderate”. Regionally, WHO assesses the risk in the European Region as “High” and as “Moderate” in the “African Region, Region of the Americas, Eastern Mediterranean Region and the South-East Asia Region”. The risk in the Western Pacific Region is assessed as Low-Moderate.\n\nThe 10 most affected countries globally (as on 02/09/2022) are: United States of America (n = 21,984), Spain (n = 6,749), Brazil (n = 6,033), France (n = 3,785), Germany (n = 3,533), The United Kingdom (n = 3,484), Peru (n = 1,808), Canada (n = 1,321), Netherlands (n = 1,195), and Portugal (n = 871). Together, these countries account for 88.9% of the cases reported globally.\n\nMost of the G20 nations have reported monkeypox outbreak. European Union, USA, Germany, France, UK, Brazil, India, Canada and Spain are part of the G20 countries. Together, the G20 members represent more than 80% of the world’s Gross Domestic Product (GDP), 75% of international trade, and 60% of the global population. Policies framed and implemented in G20 countries for the prevention and control of monkeypox preparedness and response would have implications on rest of the world. Investment in prevention, diagnostics, therapeutics and vaccine is pivotal to achieve equity and solidarity globally.\n\nThis rapid review aims to map the monkeypox prevention and control policies planned and implemented in G20 nations in line with temporary recommendations issued by the WHO-DG.13\n\n\nMethods\n\nAn initial scoping of literature was conducted to understand the various prevention and control measures to respond to the disease.14 Since the research question is broad, we did not follow the typical PICOS or the PCC framework and the approach has been demonstrated previously.15,16 We could not register the rapid review protocol as the review was completed in six days timeframe. We have reported this review based on the “Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) extension for Scoping Reviews”.17,18,61\n\nA comprehensive search was conducted through Medline (through PubMed), Scopus, and ProQuest Medical library to understand the various policies on prevention, diagnostic and treatment modalities implemented among the G20 nations. Since our initial scoping pointed towards few published studies, we performed an extensive Gray literature search through the Ministry of Health websites and online newspapers through Google. Documents found on the government website other than English language were translated using Google translator. Relevant government advisories and guidelines was also searched. We included articles and advisories published between 06/05/2022 and 15/08/2022 as the first case of the disease was reported on the May 6, 2022. A detailed search strategy is presented in the Extended data.61\n\nThe screening process was streamlined to provide timely evidence.19 Screening for the Title-Abstract (Ti-Ab) stage and the full-text stage was conducted by VD, NG, and RR in Rayyan.ai. software. Articles were initially screened by NG and later cross verified by VD and RR. Conflicts regarding the inclusion of the articles was resolved through consensus. At the Ti-Ab stage, we included articles when we were categorising them as “Maybe”. Articles retrieved from the Gray Literature was screened by VD and RR together. The following selection criteria was used to guide our inclusion and exclusion. Conflicts regarding the inclusion of articles at the full text stage was arbitrated by SP.\n\nWe included studies and/or documents that met the following criteria:\n\n• Prevention, control and management guidelines/policies published through journal, news article and health ministry website on monkeypox\n\n• Countries limited to G20 nations (“Argentina, Australia, Brazil, Canada, China, France, Germany, India, Indonesia, Italy, Japan, Republic of Korea, Mexico, Russia, Saudi Arabia, South Africa, Turkey, the United Kingdom, the United States, and the European Union”)\n\nWe excluded:\n\n• Studies published prior to May 6, 2022 on monkeypox.\n\n• Editorials, opinion, and perspective papers\n\nData extraction was conducted using a pre-designed Data Extraction Sheet (DES). Data extraction was carried out by VD and RR independently to ensure minimal loss of information. We consolidated the available evidence in different forms (policies, guidelines and clinical practice guidelines). Data was extracted from the Government website, journal articles and newspapers for the following: country, implementing coordinated response, engaging and protecting communities, surveillance and public health measures, clinical management and infection prevention and control (IPC) measures, medical countermeasures research and information on international travel. In case of missing details, we have not attempted to contact agencies or authors for the details. A detailed DES is presented in the Extended data.61\n\n\nResults\n\nWe obtained 671 articles from the three databases (Medline through PubMed, Scopus and ProQuest), with 10 articles included in the review. Additionally, we identified 55 documents from the Gray literature. Figure 1 depicts an overview of the included literature.\n\nThis review provides a description of monkeypox-related guidelines/policies/recommendations, as well as their implementation strategies/response indicators; we have categorized G20 nations into two groups based on their epidemiological status, transmission patterns, and capacities13 (Table 1). We found that the guidelines included information on vaccine, diagnosis, transmission mechanisms, risk minimization and communication strategies, travel advisory, surveillance and public health initiatives, clinical management, and infection prevention and control in the Extended data.61\n\n* No guidelines available.\n\nTable 1 depicts the national guidelines of the 18 countries on the control, prevention, and management of monkeypox, most of which belonged to group 2 countries. However, we couldn’t retrieve guidelines from China and Argentina during our search.\n\nThe actions under implementing coordinated response included targeted risk communication (lesbian, gay, bisexual, transgender, queer, or questioning [LGBTQ] community and other vulnerable populations), case detection, supported isolation of cases and treatment, contact tracing, and targeted immunization.\n\nAs mentioned in Table 2, few countries have launched public health campaigns and health authority websites to create awareness of monkeypox among the public and health care professionals. Some countries included strategies to focus on LGBTQ communities such as advertising on social media and dating apps, improved coordination and communication with gay and bisexual men.22–24 Contact tracing of the people who travelled or had contact with the confirmed case was implemented in most of countries.21,25–28 Also, few countries-initiated immunization strategies to support high-risk populations.29–39 The available countries' guidelines specified that MPX is confirmed by real-time PCR (polymerase chain reaction) laboratory testing (Table 2).\n\nEngaging and protecting communities includes raising awareness against transmission, engaging with organizers of gatherings, target risk communication and community engagement using digital platform and strategies to avoid stigma.\n\nSome countries emphasized that the awareness initiatives on monkeypox are toll-free information services, massive awareness campaigns, public messaging services and the formation of task force.40–43 In addition, efforts were taken to educate people on sexual health during mass gatherings in few countries. Also, digital social media and dating apps were utilized to create awareness among the queer community. Furthermore, the countries with a higher burden of cases have also emphasized methods for preventing stigmatization of particular groups of people (Table 3).\n\nAs mentioned in Table 4, tracking the monkeypox cases began in 11 countries. Each states have their own monitoring and surveillance system, for instances, the European Surveillance System (TESSy) for European countries, the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing in Russia, and the CDC National Wastewater Surveillance System in the USA.20,44,45\n\nAll the available guidelines recommend isolation of the confirmed cases either in-home or a hospital setting if needed. However, India and UK recommend 21 days of isolation for the contact of the cases.22,29,46 Vaccine recommendations also varied among the countries.30,31 The Modified vaccinia Ankara (MVA) vaccine is the preferred vaccine in Australia, Canada, EU, Saudi Arabia, UK and USA.33,47 ACAM2000TM is another vaccine considered in Australia, EU and USA. Although the LC16 vaccine for monkeypox has been approved in Japan, it is not widely available. In India and Brazil, no vaccine is yet available for monkeypox.\n\nThe travel advisory is developed in most countries. As per the advisory, passengers must pay attention to monkeypox symptoms such as fever, a distinctive rash, swollen lymph nodes, and to seek medical attention immediately if they have been exposed or have symptoms.48 Some guidelines specifically advised the use of facemask and social distancing and suggested hand hygiene and nasal hygiene.49 Canadian guidelines indicate travelers or specific groups of travelers (for example, pregnant women, campers, and people visiting friends and relatives) to an increased risk and reminds them to take extra precautions.\n\nMajority (13) of the countries in their guidelines provide detailed information on the confirmed case, probable case, and suspected case. Screening and triage were explained in two countries guidelines.50 All the guidelines suggested isolation of the confirmed and probable cases i.e., avoiding exposure to body fluids and any materials, hand hygiene, use of face mask, avoidance of sexual contact, and avoiding contact with infected animals are recommended. Use of N95 masks and personal protective equipment (PPE) kits in health care settings is advised in some countries according to the risk assessment of exposure to the body fluids.29,30 Treatment modalities are divided into two categories: supportive management and prescribing existing antiviral agents. Among which, tecovirimat is the preferred treatment for severe monkeypox virus in some countries.30,33,51 No specific treatment is available for monkeypox (Table 5).\n\n\nDiscussion\n\nMonkeypox was declared as Public Health Emergency of International concern (PHEIC) by WHO during the second meeting of IHR.13 PHEIC is notified when an outbreak spreads across borders and necessitates a coordinated international response to contain it. States have a legal duty to respond to PHEIC in a reasonable timeframe under the 2005 International Health Regulations (IHR). In this context, states have a responsibility to design contextual and internationally coherent policies to prevent and control monkeypox globally. This review was planned to understand monkeypox prevention and control - policy adherence in line with temporary recommendations issued by the WHO-DG, and policy similarities/actions among countries to explore if there are any inter-country cooperation strategies that are planned for coordinated international response, and also to document the inter-country differences in policy implementation among G20 nations.13 Most of the G20 nations have reported a monkeypox outbreak. G20 nations adherence to the recommendations of WHO sets the commitment for global solidarity as G20 members represent more than 80% of the world’s GDP, 75% of international trade, and 60% of the global population. Policies framed and implemented in G20 countries for the prevention and control of monkeypox preparedness and response would have implications on prioritization of investments in manufacturing capabilities, enhancing the capacity of developed and developing nations in prevention, diagnosis, therapeutics and vaccines.\n\nCoordinated response among states is the key component to contain the transmission of monkeypox. Depending on the availability of resources, some recommendations are followed by nations while others are not. Adhering to the recommendations given by the standard setting organizations like the WHO would facilitate in timely detection, response, and control of monkeypox. To bring a coordinated response, G20 nations are following temporary recommendations that are context specific to their nation. For instance, most of the G20 nations are following recommendations in case detection, contact tracing, surveillance, clinical care protocols, risk communication, IPC, distribution of PPE kits and vaccination (Table 6).\n\nVaccination is one of the most effective measures to avoid the transmission of monkeypox. Few countries such as the UK, USA, and Australia, have the capability in manufacturing vaccines, therapeutics, and advanced diagnostics for the disease.52,53 However, there is a large gap exists worldwide in vaccination production and availability. Currently, some of the countries like South Africa, Brazil and India do not have any vaccines available. Furthermore, some countries are initiating actions for vaccine manufacturing and procurement, for instance, India has initiated vaccine production efforts, and endemic countries such as Africa seek help from WHO for the procurement of the vaccine.54,55 Historical evidence also suggests that illness or poor health among the population has always shifted the balance of power, suggesting that world politics has had a significant impact on PHEICs.56 For example, it wasn't until the devastating Ebola outbreak in West Africa in 2014-2016 spread throughout the population of rich countries that authorities ultimately accelerated the licensing of an Ebola vaccine, capping a decades-long endeavor.57 To bridge the vaccine inequality gap among states, we need a coordinated global response from state parties in which additional resources are made available to support the management of monkeypox as a global concern. The resources for vigorous surveillance and training activities must also be provided to the endemic countries. During the coronavirus disease 2019 (COVID-19) discussion, Mr. Guterres, the United Nations Secretary-General stated, “history will judge the efficacy of the response not by the actions of any single set of government actors taken in isolation, but by the degree to which the response is coordinated globally across all sectors for the benefit of our human family”.58\n\nIn addition, States Parties have always undermined the IHR's effectiveness by being non-compliant towards their proposed guidelines in accordance with agreed during previous outbreaks.59 Hence, the G20 nations should set an example by complying to IHR recommendation as well as to support each other during a crisis by advocating for sharing PPE kits, vaccines, data-sharing technology, and risk-communication channels to curb the spread of disease. Also streamline the regulatory standards and procedures to procure medical countermeasures. Developed countries are responsible for funding research and facilities in developing countries, as well as supporting information exchange as outlined in the new pandemic treaty.60 In this context, states have a responsibility to design contextual and coherent policies to prevent and control monkeypox globally in line with temporary recommendations issued by the WHO Director General.13 G20 nations advocating for inter-country cooperation will lead to coordinated international response and interruption of transmission of monkeypox. To best of our knowledge, this is the first review to collate the national guidelines published among the G20 nations and comparing them with WHO recommendations. Though we extensively searched for the eligible studies and gray literature, we only included the guidelines available on the public domain.\n\n\nConclusion\n\nCooperation among the G20 nations is important in the context of building international health system resilience especially in the context of pandemics and sharing of information. Some of the countries are following the WHO recommendations who have resources, and some are not following. It's important for the countries to support each other during the crisis as we are not safe until everybody is.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nOpen Science Framework: Rapid review on monkeypox policies among the G20 nations: relevance to policy and practitioner. https://doi.org/10.17605/OSF.IO/WA3K7.61\n\nThis project contains the following extended data:\n\n- Appendix 1. Search strategy (information about the searches, including full search strategies)\n\n- Appendix 2. Data Extraction Sheet (DES)\n\nPRISMA checklist for ‘Rapid review on monkeypox policies among the G20 nations: relevance to policy and practitioner’. https://doi.org/10.17605/OSF.IO/WA3K7.61\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 would like to acknowledge Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, for the logistics and administrative support.\n\n\nReferences\n\nMoore MJ, Rathish B, Zahra F: Monkeypox. StatPearls. Published online July 16, 2022. Accessed September 13, 2022.Reference Source\n\nAlakunle E, Moens U, Nchinda G, et al.: Monkeypox Virus in Nigeria: Infection Biology, Epidemiology, and Evolution. Viruses. 2020; 12(11). PubMed Abstract | Publisher Full Text\n\nLadnyj ID, Ziegler P, Kima E: A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo. Bull. World Health Organ. 1972; 46(5): 593. Accessed September 13, 2022. Free Full Text\n\nBeer EM, Bhargavi RV: A systematic review of the epidemiology of human monkeypox outbreaks and implications for outbreak strategy. PLoS Negl. Trop. Dis. 2019; 13(10): e0007791. PubMed Abstract | Publisher Full Text\n\nBunge EM, Hoet B, Chen L, et al.: The changing epidemiology of human monkeypox—A potential threat? A systematic review. PLoS Negl. Trop. Dis. 2022; 16(2): e0010141. PubMed Abstract | Publisher Full Text\n\nPembi E, Awang S, Salaudeen SO, et al.: First confirmed case of monkeypox in Adamawa State, Nigeria: a clinico-epidemiological case report. Pan Afr. Med. J. 2022; 42: 38. PubMed Abstract | Publisher Full Text\n\nReed KD, Melski JW, Graham MB, et al.: The detection of monkeypox in humans in the Western Hemisphere. N. Engl. J. Med. 2004; 350(4): 342–350. PubMed Abstract | Publisher Full Text\n\nVaughan A, Aarons E, Astbury J, et al.: Two cases of monkeypox imported to the United Kingdom, September 2018. Eurosurveillance. 2018; 23(38). PubMed Abstract | Publisher Full Text\n\nErez N, Achdout H, Milrot E, et al.: Diagnosis of Imported Monkeypox, Israel, 2018. Emerg. Infect. Dis. 2019; 25(5): 980–983. PubMed Abstract | Publisher Full Text\n\nYong SEF, Ng OT, Ho ZJM, et al.: Imported Monkeypox, Singapore. Emerg. Infect. Dis. 2020; 26(8): 1826–1830. PubMed Abstract | Publisher Full Text\n\nRao AK, Schulte J, Chen TH, et al.: Monkeypox in a Traveler Returning from Nigeria - Dallas, Texas, July 2021. MMWR Morb. Mortal. Wkly Rep. 2022; 71(14): 509–516. PubMed Abstract | Publisher Full Text\n\nThornhill JP, Barkati S, Walmsley S, et al.: Monkeypox Virus Infection in Humans across 16 Countries — April–June 2022. N. Engl. J. Med. 2022; 387(8): 679–691. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Second meeting of the International Health Regulations (2005) (IHR) Emergency Committee regarding the multi-country outbreak of monkeypox.Published 2022. Accessed August 25, 2022.Reference Source\n\nMahase E: Monkeypox: Healthcare workers will be offered smallpox vaccine as UK buys 20 000 doses. BMJ. 2022; 377: o1379. PubMed Abstract | Publisher Full Text\n\nMunn Z, Stern C, Aromataris E, et al.: What kind of systematic review should I conduct? A proposed typology and guidance for systematic reviewers in the medical and health sciences. BMC Med. Res. Methodol. 2018; 18(1): 5. PubMed Abstract | Publisher Full Text\n\nGudi N, Kamath P, Chakraborty T, et al.: Regulatory Frameworks for Clinical Trial Data Sharing: Scoping Review. J. Med. Internet Res. 2022; 24(5): e33591. PubMed Abstract | 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\nKelly SE, McGowan J, Barnhardt K, et al.: Paper 4: a review of reporting and disseminating approaches for rapid reviews in health policy and systems research. Syst. Rev. 2022; 11(1): 152. PubMed Abstract | Publisher Full Text\n\nTricco AC, Langlois E, Straus SE, et al.: Rapid Reviews to Strengthen Health Policy and Systems: A Practical Guide. World Health Organization;2017.\n\nTASS Russian News Agency: No new confirmed cases of monkeypox in Russia - sanitary watchdog.Published July 23, 2022. Accessed September 2, 2022.Reference Source\n\nDaily Sabah with agencies: Turkey reports first monkeypox case.Published June 30, 2022. Accessed September 2, 2022.Reference Source\n\nWise J: Monkeypox: UK to run out of vaccine doses by next week. BMJ. 2022; 378: o2053. PubMed Abstract | Publisher Full Text\n\nCBC News: PHAC urges gay, bisexual men to practise safe sex as monkeypox spreads.Published July 27, 2022. Accessed September 2, 2022.Reference Source\n\nFrance 24: France to mobilise extra support for monkeypox vaccines as 1,700 infected.Published July 26, 2022. Accessed September 2, 2022.Reference Source\n\nANTARA Indonesian News Agency: Indonesia monitoring monkeypox outbreak.Published August 6, 2022. Accessed September 2, 2022.Reference Source\n\nRadwan R: Should Saudi Arabia be worried about monkeypox? Arab News. Published August 7, 2022. Accessed September 2, 2022.Reference Source\n\nReuters: WHO says more than 18,000 cases of monkeypox globally, most in Europe.Published July 27, 2022. Accessed September 2, 2022.Reference Source\n\nDreher A: Monkeypox spreading in United States. Axios.Published June 7, 2022. Accessed September 2, 2022.Reference Source\n\nMahase E: Monkeypox: Healthcare workers will be offered smallpox vaccine as UK buys 20 000 doses. BMJ. 2022; 377: o1379. PubMed Abstract | Publisher Full Text\n\nRizk JG, Lippi G, Henry BM, et al.: Prevention and Treatment of Monkeypox. Drugs. 2022; 82(9): 957–963. PubMed Abstract | Publisher Full Text\n\nKwon SL, Ban S, Shin J, et al.: Monkeypox Vaccination in the Republic of Korea: Identifying the High-Risk Target Group. J. Korean Med. Sci. 2022; 37(29): e239. PubMed Abstract | Publisher Full Text\n\nKupferschmidt K: Monkeypox vaccination plans take shape amid questions. Science. 2022; 376(6598): 1142–1143. PubMed Abstract | Publisher Full Text\n\nO’Shea J, Filardo TD, Morris SB, et al.: Interim Guidance for Prevention and Treatment of Monkeypox in Persons with HIV Infection - United States, August 2022. MMWR Morb. Mortal. Wkly Rep. 2022; 71(32): 1023–1028. PubMed Abstract | Publisher Full Text\n\nSpecialist Reporting Team’s Nick Sas: Third-generation monkeypox vaccines secured, with gay and bisexual men in “high-risk” categories targeted for first rollout. ABC News. Published 2022. Accessed September 2, 2022.Reference Source\n\nReuters: Gay men, some trans people and sex workers should be vaccinated against monkeypox, French health body says.Published July 8, 2022. Accessed September 2, 2022.Reference Source\n\nThe Local: German vaccine panel recommends monkeypox jab for risk groups.Published June 9, 2022. Accessed September 2, 2022.Reference Source\n\nThe Local: Italy begins monkeypox vaccination drive in four regions.Published August 9, 2022. Accessed September 2, 2022.Reference Source\n\nCollis H: Countries with most monkeypox cases receive first EU-bought vaccines. Politico.Published June 28, 2022. Accessed September 2, 2022.Reference Source\n\nKimball S: Monkeypox: U.S. to provide vaccines for Pride, other events attended by gay men. CNBC.Published August 18, 2022. Accessed September 2, 2022.Reference Source\n\nDW Made for minds: Monkeypox spread can be ′contained′ with vaccination.Published July 27, 2022. Accessed September 2, 2022.Reference Source\n\nDesai S: Monkeypox cases in France exceed 2,000. Anadolu Agency. Published online August 3, 2022. Accessed September 2, 2022.Reference Source\n\nThe New Indian Express: Check out the Health Ministry’s guidelines for battling Monkeypox outbreak.Published August 3, 2022. Accessed September 2, 2022.Reference Source\n\napa: Over 400 monkeypox cases registered in Italy.Published July 24, 2022. Accessed September 2, 2022.Reference Source\n\nThe White House: FACT SHEET: Ongoing U.S. Monkeypox Research Activities to Speed Science for Impact.Published August 11, 2022. Accessed September 2, 2022.Reference Source\n\nFatima S: Second in Gulf, Saudi Arabia reports first case of monkeypox. The Siasat Daily. Published July 15, 2022. Accessed September 2, 2022.Reference Source\n\nMint: Monkeypox patients to isolate for 21 days, keep lesions covered: Govt issues guidelines.Published July 27, 2022. Accessed September 2, 2022.Reference Source\n\nRao AK, Petersen BW, Whitehill F, et al.: Use of JYNNEOS (Smallpox and Monkeypox Vaccine, Live, Nonreplicating) for Preexposure Vaccination of Persons at Risk for Occupational Exposure to Orthopoxviruses: Recommendations of the Advisory Committee on Immunization Practices - United States, 2022. MMWR Morb. Mortal. Wkly Rep. 2022; 71(22): 734–742. Publisher Full Text\n\nWhitmore G: August 2022 Covid-19 And Monkeypox Travel Restrictions. Forbes. Published online August 2, 2022. Accessed September 2, 2022.Reference Source\n\nWego Travel Blog: Monkeypox Travel Bans and Restrictions: What We Know So Far.Published August 19, 2022. Accessed September 2, 2022.Reference Source\n\nIacobucci G: Monkeypox: Doctors in England will have to notify local agencies of all suspected cases. BMJ. 2022; 377: o1413. PubMed Abstract | Publisher Full Text\n\nal Jurdi A , Kotton CN: Monkeypox in Transplant Recipients: No Breaks Between Outbreaks. Transplantation. Published online August 2022. Publisher Full Text\n\nU.S. Department of Health and Human Services: HHS Facilitates Agreement to Accelerate Delivery of Additional Smallpox and Monkeypox Vaccines Using New U.S. Production Line.Published August 18, 2022. Accessed September 3, 2022.Reference Source\n\nThe Guardian: Australia secures 450,000 doses of monkeypox vaccine.Published August 4, 2022. Accessed September 3, 2022.Reference Source\n\nKumar P: 8 Firms In Race To Develop Monkeypox Vaccine In India: Sources. NDTV.Published August 13, 2022. Accessed September 3, 2022.Reference Source\n\nKew J: Monkeypox Outbreak: Africa Falling Behind on Vaccines as Virus Spreads. Bloomberg.Published July 28, 2022. Accessed September 3, 2022.Reference Source\n\nPattanshetty S, Brand H, Dsouza V, et al.:COVID-19 and International Relations (IR): A Global Perspective.Balint G, Antala B, Carty C, et al., editors. World Focus. 2022; 43(507): 21–28. Publisher Full Text\n\nKaner J, Schaack S: Understanding Ebola: The 2014 epidemic. Global Health. 2016; 12(1). PubMed Abstract | Publisher Full Text | Free Full Text\n\nUnited Nations: UN launches COVID-19 plan that could ‘defeat the virus and build a better world’||UN News Global perspective Human stories.Accessed August 30, 2022.Reference Source\n\nHabibi R, Burci GL, de Campos TC , et al.: Do not violate the International Health Regulations during the COVID-19 outbreak. Lancet. 2020; 395(10225): 664–666. PubMed Abstract | Publisher Full Text\n\nPerehudoff K, Hoen E’t, Mara K, et al.: A pandemic treaty for equitable global access to medical countermeasures: seven recommendations for sharing intellectual property, know-how and technology. BMJ Glob. Health. 2022; 7(7): e009709. PubMed Abstract | Publisher Full Text\n\nDsouza VS, Pattanshetty S, Raj R, et al.: Rapid review on monkeypox policies among the G20 nations: relevance to policy and practitioner. [Dataset].2022, September 14. Publisher Full Text"
}
|
[
{
"id": "156670",
"date": "13 Dec 2022",
"name": "Chandrakant Lahariya",
"expertise": [
"Reviewer Expertise Primary healthcare",
"COVID-19",
"emerging and re-emerging diseases",
"neonatal health",
"stillbirth",
"diabetes",
"hypertension",
"obesity."
],
"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\nIntroduction part is far too long. The authors may cite some of the recently published review articles as well as WHO page link and can come directly to objectives of this paper (two possible references which captures much of this information are listed below1,2) as. If there is a strongly felt need, some quantitative data used in introduction section can be put as annex or box.\n\nMethods are fairly well written and detailed.\n\nThe table 1 is not needed. In any case, there is paragraph describing table. Alternatively, an easy and simple box as right hand side column has all countries doing it and left side only a few countries implementing the strategy.\n\nThe manuscript need to reflect a bit more about inequity in access to epidemic and pandemic response tools and about vaccine related discussions. There is also need to contextualize a few learnings which should taken forward by G-20 countries for any disease emergence or outbreak.\n\nLimitations of the current review can also be included.\n\nIn short, a very well written manuscript, which has a lot many new points and will be important contribution to this field.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
},
{
"id": "156296",
"date": "14 Dec 2022",
"name": "Shyam Sundar Budhathoki",
"expertise": [
"Reviewer Expertise Global Health and Health Systems research in LMICs"
],
"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 report is well written and the report is presented well. The abstract is a good summary of the main text and has sufficient details in the methods section. The article is very timely. The introduction section provide a good summary of key statistics and has set the background for the paper in an useful manner. There is a good attempt to provide a justifiable rationale for the study. However there is some scope for the authors try and make more clear arguments around what gap still exists in literature that this paper will help fill in terms of evidence.\nThe methods is generally well presented. However some areas may benefit with more clarifications. You mention that the ‘research question is broad.’ However, the paper does not explicitly mention the research question but rather has presented the aims. Could you try and rephrase the sentence about research question by talking about the scope of the paper instead?\nYou have mentioned about including documents in languages other than English, using google translate, but the paper does not mention later how many such documents where included. Could you either mention this information or, if no document other than in English language was used, remove the line from methods.\nThe list of countries in tables could be arranged in alphabetical order if possible.\nThe discussion section is well written generally in terms of the contents and the relevant literature. Some improvements could still be done to improve the storyline. The table 6 presented in discussion section could be moved to results as it is fits more as results that could be further discussed in this section.\nThe first paragraph of the discussion section could be revised to provide a clear summary of the key findings from this review rather than read as a concise version of introduction. The paragraph also mentions, ‘this review was planned to understand…’. I advise this sentence to be rewritten in a manner that reflects that the study is conducted and what it aims to achieve rather than why it was planned.\nThe conclusion currently is too generic. It would be more meaningful to have a few sentences summarising what exists as common themes and what differences/what is lacking exist in the policies that need to be considered further (you have tried to mention the latter but could work on the former a little).\nAs you can see that I only have minor suggestions which may take very little time to revise. Otherwise very timely and relevant research that can be indexed immediately after considering my comments.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1360
|
https://f1000research.com/articles/11-101/v1
|
26 Jan 22
|
{
"type": "Research Article",
"title": "Students’ Satisfaction Of Online Learning In Oman",
"authors": [
"ALHAM RASHID AAMIR AL-OMAIRI",
"SOON HIN HEW",
"ALHAM RASHID AAMIR AL-OMAIRI"
],
"abstract": "Background: Due to the development facilitated by modern technology, the world has become a small village with instantly changing methods of education. Online education has become an alternative method for course delivery used by colleges and universities globally.\n\nMethods: The population of this study was N=564 students enrolled in asynchronous online learning at the College of Sharia Sciences in the Sultanate of Oman for the academic year 2020-2021. The survey instruments from “The Student Satisfaction Survey” developed by Strachota (2006) were utilized in this study. The survey included items in the following categories: demographics, learner instructor's interaction, learner-peer interaction, and lastly general satisfaction. The researcher reformulated the questions to suit the target group and some questions were changed to suit the target audience. Results: Remarkably, the data show that there is no direct relationship between demographic factors and student satisfaction with asynchronous online learning. On the other hand, there is a strong and noticeable relationship between students' satisfaction with asynchronous online learning and student-instructor interaction. There is also a correlation between students' satisfaction with asynchronous online learning and student-peer interaction.\n\nConclusions: The students of the College of Sharia Sciences are on the whole very satisfied with asynchronous online learning; they consider it a very successful experience and recommend its use by students in other educational institutions.",
"keywords": [
"Asynchronous online learning",
"Oman",
"Students’ Satisfaction"
],
"content": "Introduction\n\nSingh Kaurav, Rajput, and Baber (2019) emphasise that online learning is the replacement of traditional methods of teaching and the absorption of technology where students have the independence to learn at their own pace and space. Two main types of online education are cited: synchronous learning and asynchronous learning. According to Staff (2018), synchronous learning occurs in real-time, which means that students, their classmates, and their instructors interact in a particular virtual location through a specific online medium at a specific time. Asynchronous learning, on the other hand, occurs according to individual students’ schedules. While the course instructor provides reading materials, presentations of lectures, assignments, and assessment tests, students can reach and fulfill these requirements in a flexible time framework. According to Dziuban et al. (2015), higher education institutions and universities emphasize the importance of student's satisfaction with the educational experience as it is considered one of the main elements in determining the quality of academic programs. Educational institutions seek good reputations reflected in the impression and view of students about their academic experience in these institutions. Accordingly, academic institutions in the Sultanate of Oman need to encourage students to use online learning and to increase the number of students who enroll in asynchronous courses, as it depicts the latest and optimal method of learning with the advent of technology and its effect in different spheres of our life. Since there is no consensus on specific elements that measure the degree of satisfaction with online learning, it is very important to study the effect of different demographic characteristics in students’ satisfaction on online learning, as well as the effect of the students’ interaction with the instructor and other students involved in online learning. Thus, this study will serve to be a reference for the College of Sharia Sciences in particular, and higher education institutions in the Sultanate of Oman in general, regarding the benefits of online learning. The results this study yields will also enable faculty members and administrators in the College of Sharia Sciences to enhance students’ satisfaction with the online learning environment, which should lead to improvements in student retention in online courses.\n\n\nMethods\n\nThe researcher used a quantitative research method for data collection - an electronic survey. According to Goertzen (2017) quantitative research methods are concerned with collecting and analyzing structured and digitally represented data, as one of their central goals is to build accurate and reliable measurements that allow statistical analysis. Saleh and Bista (2017) reported that in the past three decades, online surveys have become the dominant method for attracting participation in academic research for an easy response, rapid response, and low cost. Thus, surveys allow the researcher to collect information related to the subject of the survey, when the researcher is not able to directly observe the phenomena, when the study sample is located in a remote location, or when the researcher faces difficulty in directly communicating with the study sample. Consequently, this study is based on an online survey in order to obtain high response rates, and thus reliable and generalizable results.\n\nThe researcher chose to conduct this study at the College of Sharia Sciences because it is the only college in the Sultanate of Oman that teaches asynchronous online learning. The researcher chose this university because it facilitated the process of data collection; it allowed the researcher to obtain data on the number of students who enrolled in online learning and was ready to spread the invitation to participate in the research study through the college’s online learning unit and using the college’s platform. The sample was drawn from all students who enrolled in asynchronous online learning. Samples were taken from the various degrees offered by the college, namely diploma, bachelor's and master's, in order to find out if there is a difference between these groups with regard to their satisfaction with the asynchronous online learning environments. The total number of students in the college involved in online learning for the 2020-2021 academic year is 3649 male and female students, 463 of which are diploma’s degree students, 3022 are bachelor’s degree students and 164 are master’s degree students. Students (see Appendix 1) are given two weeks to complete the survey. The questionnaire link was sent via an SMS message by the college's online learning unit, uploaded to the college’s platform, and the questionnaire was also published on the college's social media sites.\n\nThe survey instruments from “The Student Satisfaction Survey” developed by Strachota (2006) were utilized in this study. At the beginning of the survey, the Researcher included a statement on ethics approval and consent to ensure all participants agree to be part of this study. The survey included items in the following categories; demographics (added to the survey by the researcher), learner-instructor interaction, learner-peer interaction, and general satisfaction. The researcher added the sentence “I am satisfied with online learning because” before each section of interaction to ensure students understood the survey. In the last section of the survey, “general satisfaction”, the researcher also reformulated the questions to suit the target group. Some questions have also changed to suit the target audience.\n\n\nResults and analysis\n\nTable 1 shows Gender, age, marital status, employment obligations, student status, and current academic program were the main demographic factors investigated using descriptive analysis in this research. Gender as the first demographic factor reveals that males (89.9%) were a little more (7.5%) satisfied with online learning than females (82.4%). There were also a few differences between different age groups in regards to satisfaction with online learning. Students above 45 years (92.6%) were the most satisfied with online learning. The students least satisfied with online learning were students between 17 to 25 years of age (79. 1%). Marital status shows a slight difference in percentage (11.1%) between married (88.5%) students’ satisfaction with online learning as opposed to single (students (77. 4%). With regard to employment obligations, there is a 0.2% difference in percentage between full-time employed (88.7%) students' satisfaction with online learning and that of part-time students (88.5%). Similar to employment obligations, student status reveals a slight difference (1.5%) in percentage between full-time students' satisfaction with online learning (86.5%) compared to part-time students (85.0%). The sixth and final demographic factor, current academic program, shows that Masters’ students (91.8%) were the most satisfied with online learning. Students pursuing their Bachelor Degrees come next (85.3%) with a 0.4% difference in percentage from Diploma students (84.9%).\n\nTable 2 shows that most of the students (82.6%) were satisfied with online learning because the instructor had been an active member of the discussion group and provided guidance for the posted comments, while only 5.3% of students were dissatisfied on this measure. Also, it shows that most of the students (76.4%) were satisfied with online learning because the comments from the instructor regarding assignments, projects, and any queries were timely in this online learning, (6.5%) dissatisfied). It showed that most of the students (57.5%) were satisfied with online learning because learners were able to obtain individual attention from the instructor when needed, (14.8%) dissatisfied). It also showed that most of the students (73.1%) were satisfied with online learning because the instructor always gives him valuable feedback on the subject and the tasks that they must complete, (8.7%) dissatisfied). Also, most of the students (77.6%) were satisfied with online learning because the teacher acted as a facilitator of the course by constantly encouraging communication, (8.5%) dissatisfied). It showed that most of the students (78.1%) were satisfied with online learning because although they saw the teacher in limited online discussions, they didn't feel isolated, (7.4%) dissatisfied). Most students (79.3%) were satisfied with the level of instructor interaction that happened in this online learning, (5.7%) dissatisfied). Also, the majority of the students (62.1%) were satisfied with online learning because the online discussion board provided an opportunity to solve problems with peers, while (13.0%) were dissatisfied). Also, it showed that most of the students (73.2%) were satisfied with online learning because online courses created a sense of community among peers, (9.8%) dissatisfied). Moreover, it showed that most of the students (76.8%) were satisfied with online learning because students were able to discuss their thoughts and ask clarification from peers when needed, (9.6%) dissatisfied). Most of the students (68.6%) were satisfied with online learning because they received timely (within 24-48 hours) feedback from peers in this online class, (11.7%) dissatisfied). Also, most of the students (76.3%) were satisfied with online learning because this online learning encouraged them to discuss ideas and concepts with peers, (9.7%) dissatisfied). It showed that most of the students (60.6%) were satisfied with online learning because, in this online learning teamwork was an essential part of their activities, (19.2%) dissatisfied). Also, most students (77.7%) were satisfied with the level of peer interaction that happened in this online learning, (7.8%) dissatisfied). The majority of the students (85.8%) were satisfied with online learning, while (4.7%) of students were dissatisfied with online learning. It is important to note that (82.6%) of learners would recommend the online course to someone else, while only (5.9%) of learners will not.\n\n\nDiscussion\n\nThis study identified the following questions:\n\n1. Do demographic characteristics (Gender, Age, Marital status, Employment obligations, Student status, and Current Academic Program) affect students’ satisfaction with online learning from the viewpoint of students at the College of Sharia Sciences in Oman?\n\n2. Do students’ interactions with instructors and peers affect students’ satisfaction with online learning from the viewpoint of students at the College of Sharia Sciences in online learning in Oman?\n\nRemarkably, the data show that there is no direct effect between demographic factors and students’ satisfaction with online learning. Students, irrespective of their demographic factors, were mostly satisfied with their experience in online learning. On the other hand, the results of the study revealed that student-instructor interaction and student-peer interaction had the greatest impact on enhancing students' satisfaction with online learning. It plays a key role in increasing students’ satisfaction with online learning and thus their recommendation to others to enroll in courses offered via online learning.\n\n\nConclusion\n\nThis study details the extent of students' satisfaction with asynchronous online learning. We present an analysis of the questionnaire distributed to students at the College of Sharia Sciences in the Sultanate of Oman to measure the degree of student satisfaction with online learning. Remarkably, the data show that there is no direct effect between demographic factors and student satisfaction with online learning. On the other hand, there is a strong and noticeable effect between students' satisfaction with online learning and students'-instructor interaction and students'-peer interaction. The students of the College of Sharia Sciences are on the whole very satisfied with asynchronous online learning. They consider it a very successful experience and recommend it to others.\n\n\nData availability\n\nFigshare: A study of students’ satisfaction in asynchronous online learning dataset. https://doi.org/10.6084/m9.figshare.18152690 (Al-Omairi & Hew, 2022).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nEthics and consent\n\nEthical Approval was granted by the Research Ethics Committee of Multimedia University (approval number EA2812021).\n\n\nParticipant consent\n\nConsent was obtained from all participants written (signed) and verbally involved in the study.",
"appendix": "Acknowledgements\n\nMany thanks go to all the people in the College of Shari'a Science whose assistance was crucial in the completion of this research. It facilitated the process of data collection; it allowed the researcher to obtain data on the number of students who enrolled in online learning.\n\n\nReferences\n\nDziuban C, Moskal P, Thompson J, et al.: Student Satisfaction with Online Learning: Is It a Psychological Contract?. Online Learning. 2015; 19(2): n2. Publisher Full Text\n\nGoertzen MJ: Introduction to Quantitative Research and Data. Library Technology Reports. 2017; 53(4): 12–18.\n\nSaleh A, Bista K: Examining Factors Impacting Online Survey Response Rates in Educational Research: Perceptions of Graduate Students. Online Submission. 2017; 13(2): 63–74.\n\nSingh Kaurav RP, Rajput S, Baber RJSAJ: Factors Affecting the Acceptance of E-learning By Students: A Study of E-learning Programs in Gwalior, India.2019; 26(1).\n\nStaff, T: 2018. Synchronous Learning vs. Asynchronous Learning in Online Education.Reference Source\n\nStrachota E: The use of survey research to measure student satisfaction in online courses. Paper presented at the Midwest Research to Practice Conference in Adult Continuing and Community Education, University of Missouri-St. Louis. 2006.\n\nAl-Omairi ARA, Hew SH: A study of students satisfaction in asynchronous online learning … دراسة رضا الطلاب عن التعلم غير المتزامن عبر الإنترنت.xlsx. figshare. Dataset. 2022. Publisher Full Text"
}
|
[
{
"id": "121388",
"date": "04 Mar 2022",
"name": "M. Khalid M. Nasir",
"expertise": [
"Reviewer Expertise Area of specialization in Computer Education",
"Educational Technology",
"Instructional Technology & Community of Inquiry (CoI) in Online learning. A Certified Professional Technologist as acknowledged by Malaysian Board of Technologists (MBOT) in the field of Information & Computing Technology (IT)",
"and A Master Trainer by Malaysia Digital Economy Corporation (MDEC) in 2019."
],
"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 of this article \"Students’ Satisfaction Of Online Learning In Oman\" with the aim to determine the relationship between demographic variables, interactions with instructors and peers with regards to students’ satisfaction was interesting. It could contribute to the literature in this field. However, the authors need to cite more current literature (e.g. 2018-2022). The Pearson correlation analysis is recommended instead of percentages, and the r and R square result should be the main focus of the discussion as well as the effect size.\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? Yes",
"responses": []
},
{
"id": "136631",
"date": "30 May 2022",
"name": "Norah Mansour Almusharraf",
"expertise": [
"Reviewer Expertise Dr. Norah Almusharraf is an Assistant Professor at the Linguistics and Translation Department at Prince Sultan University",
"Riyadh",
"KSA. She is currently leading three leading roles: the Research Director of the College of Humanities and Sciences",
"the leader of the Educational Research lab (ERL)",
"and the Director of the writing and Tutoring center (WTC) at the same institution. Dr. Almusharraf received her Ph.D. degree in Foreign and Second language Education from the University at Buffalo. Her professional and research interests focus on English as a foreign language (EFL) learning pedagogics",
"inquiry-based teaching and learning",
"project-based learning and content-based instruction",
"cultural magnitudes of foreign/second language teaching and learning classroom",
"multimodal assessment and teaching strategies",
"technology implantation in the EFL English classrooms",
"teacher professional development using class critique and through professional learning community (PLC)",
"qualitative research methods: dialogic classroom discourse & comparative case studies",
"and computing implementations in statistical 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\nA decision of “Approved with revisions” has been rendered for the manuscript. The main reasons are listed as follows:\nThe manuscript should be synthesized in a cohesive manner.\n\nThe manuscript is lacking a central argument for the submitted work.\n\nThe research questions need to be linked to the aim, analysis, and findings.\n\nThe reference is not up to date and there are not cited from peer-reviewed journals.\n\nThe design of the method is not justified as well as the analysis.\n\nThe Discussion needs to discuss future implications and significance to future work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-101
|
https://f1000research.com/articles/10-1177/v1
|
22 Nov 21
|
{
"type": "Case Study",
"title": "Explaining the unexpected COVID-19 trends and potential impact across Africa.",
"authors": [
"Daniel Oduro-Mensah",
"Ebenezer Oduro-Mensah",
"Peter Quashie",
"Gordon Awandare",
"Laud Okine",
"Ebenezer Oduro-Mensah",
"Peter Quashie",
"Gordon Awandare",
"Laud Okine"
],
"abstract": "Official COVID-19 case counts and mortality rates across Africa are lower than had been anticipated. Research reports, however, indicate far higher exposure rates than the official counts in some countries. Particularly in Western and Central Africa, where mortality rates are disproportionately lower than the rest of the continent, this occurrence may be due to immune response adaptations resulting from (1) frequent exposure to certain pro-inflammatory pathogens, and (2) a prevalence of low-grade inflammation coupled with peculiar modifications to the immune response based on one’s immunobiography. We suggest that the two factors lead to a situation where post infection, there is a rapid ramp-up of innate immune responses, enough to induce effective defense and protection against plethora pathogens. Alongside current efforts at procuring and distributing vaccines, we draw attention to the need for work towards appreciating the impact of the apparently widespread, asymptomatic SARS-CoV-2 infections on Africa’s populations vis a vis systemic inflammation status and long-term consequences for public health.",
"keywords": [
"COVID-19",
"Immunobiography",
"Inflamm-aging",
"Inflammation",
"Long COVID"
],
"content": "List of abbreviations\n\nCOVID: coronavirus disease\n\nLGI: low-grade inflammation\n\nPASC: post-acute sequelae of COVID-19\n\nSARS-CoV-2: severe acute respiratory syndrome coronavirus 2\n\n\nIntroduction\n\nDespite predictions of being among the worst affected globally, the trajectory of COVID-19 in Africa has been radically different, with far lower morbidity and mortality figures than recorded in the United Kingdom, India, Brazil, the Americas, and across Europe.1 By July 2021, Africa contributed approximately 2 % of global COVID-19 case reports.2 Considering Africa’s relatively ill-resourced healthcare settings, mainly across sub-Saharan Africa, it seems to follow that COVID-19 patients who require hospital admission are disproportionately more likely to die.3 However, Africa’s 16.72 % share of the global population4 contributed only up to 3.5 % of global COVID-19 mortality by July 2021.1,5 From December 2020 when emerging SARS-CoV-2 variants fueled second and third waves of COVID-19 across the globe6–11 from December 2020, Africa’s case reports declined steadily from January to mid-May 2021, climbed up sharply and started another decline at the end of June 2021.1,12–14 Interestingly among Africa’s five regions, countries in Western and Central Africa appear to be least affected by the COVID-19 pandemic (Figure 1).15 As of September 2021, the two regions which make up 43.5 % of Africa’s 1.4 billion population16 contributed only 13 % of Africa’s COVID-19 morbidity and 8 % of mortality figures.\n\nSources: https://www.statista.com/, https://covid19.who.int/; Accessed September 8, 2021.\n\nAttempts at explaining Africa’s trends include suggestions that not enough testing has been done in the region,17,18 that Africa has a relatively young population,19,20 the systematic use of antimalarials in parts of Africa21 and that the third-world conditions across most of the region may mean that people have previously been exposed to viruses molecularly similar to SARS-CoV-2.22–25 Others have suggested that exposure to similarly inflammatory conditions/pathogens may have led to a situation where individuals have adapted to the effects of inflammation and so are less sensitive to the SARS-CoV-2-induced inflammatory events which are the main drivers of COVID-19 pathogenesis.26–29 Here,1 we discuss evidence in support of the modification of the immune response due to frequent exposure to inflammatory pathogens, citing malaria, and2 present a second reason to explain why most parts of Africa have been relatively spared the worst of COVID-19.\n\nApproximately 85 % of global malaria incidence is in Africa.30 Of Africa’s five regions, Western and Central Africa are reported to have the highest malaria incidence, contributing up to 71 % of Africa’s total. In 2017, an inverse relationship between the pro-inflammatory response and exposure to malaria was reported.31 Contrastingly, naïve individuals exhibited a more pro-inflammatory response with higher circulating levels of pro-inflammatory immune mediators.32,33 Individuals residing in malaria endemic zones often harbor Plasmodium spp. infections but are clinically immune.34,35 Pro-inflammatory mediators are important in expressing the clinical presentation of malaria. It has been suggested that repeated episodes of febrile malaria alter the immune response, resulting in a blunted inflammatory response which shows low levels of pro-inflammatory cytokines and appears to be dominated by anti-inflammatory cytokines.36 This likely plays a significant role in the apparent immunologic tolerance manifesting as clinical immunity to malaria.34,35,37 In addition, there appears to be upregulation of certain components of the innate immune response, including phagocytes and interferon-gamma, in frequently exposed individuals.36,38,39 We suggest that this altered immune response, characterized by low pro-inflammatory mediator levels, high anti-inflammatory mediator levels and up-regulated innate immune components, offers some protection against SARS-CoV-2-induced inflammation.\n\nIn individuals with the altered response due to frequent malaria exposure, SARS-CoV-2 infection may be met by a heightened innate response which overwhelms the reported blocking of some innate immune response pathways by the virus.40–44 Our submission, therefore, is that although this heightened innate response is limiting to the virus, it does not elicit enough of a pro-inflammatory adaptive response which could lead to the classical COVID-19-associated hyperinflammation. Consequently, the result of SARS-CoV-2-induced inflammation is not the cytokine ‘storm’ that occurs in severe COVID-19, but a milder cytokine ‘drizzle’ that minimizes the deleterious effects of the inflammatory response. This is contrary suggestions, including that by Kusi et al.,27 that the innate response may be negatively associated with the observed immunopathology of COVID-19. We maintain that viral load would effectively be suppressed by the innate response, consistent with suggestions by Stertz and Hale,43 with a slow ramp-up in inflammatory cytokine production due to the blunted pro-inflammatory adaptive response. Therefore, patients would only experience mild COVID-19 symptoms, or even have asymptomatic infections. A study on patients in China with asymptomatic COVID-19 revealed that they had relatively lower levels of serum alanine aminotransferase (ALA) and C-reactive protein.45 Previously, it has been shown that ALA may correlate negatively with T cell and natural killer cell activity.46 This supports the suggestion that in individuals with asymptomatic infection, there may be a sharper cell-mediated innate response which significantly moderates the progression to a pro-inflammatory, adaptive immune response.\n\nIt is striking how patterns of malaria endemicity appear to contrast COVID-19 mortality patterns in several places across Africa. Countries with the least malaria are the most affected by COVID-related mortality (Figure 1). Only one (Nigeria) of the top ten malaria endemic countries in Africa was in the top ten of country reports on Africa’s COVID-19 mortality rates as of September 2021. This is likely to be because Nigeria has Africa’s largest population by far. Outside Africa, using Brazil as an example, only one of the top ten malaria endemic areas, Goias, was in the country’s top ten COVID-19 mortality count, at 8th place as of September 2021.47,48 Meanwhile, Brazil was the world’s second most affected country by COVID-19 mortality at the time.49\n\nIn addition to Plasmodium spp., other pro-inflammatory pathogens including helminths and human coronaviruses as may be common and/or endemic in many parts of Africa could potentially have similar effects.27,50–52 It is unclear, however, whether their effects may be as protective as the malaria effect we allude to. Human coronaviruses (HCoV), for example, has been suggested to play a role in the apparent protection from SARS-CoV-2 due to observed cross-reactivity between HCoV-exposd sera and SARS-CoV-2 antigen.25,53 However, a contrasting observation suggests that pre-exposure to certain HCoV variants correlates positively with severity of COVID-19.54\n\nLow-grade inflammation (LGI) is a state of persistent, low level systemic inflammation marked by approximately 2–4-fold increases in circulating immune pro-inflammatory markers.55–58 LGI may be due to chronic exposure to stimulatory environmental and lifestyle factors including stress, asymptomatic infections, bad oral hygiene practices, bad diet, obesity, traumatic injury, sedentary behavior, and smoke inhalation.59–61 The third world living conditions across much of Africa have long fueled a suspicion that LGI might be a relatively widespread phenomenon. Recently, this suspicion has been backed by the increasing reports of full-blown chronic inflammatory diseases among Africa’s populations.62,63 In individuals with LGI, changes in the immune response may include (1) reduced macrophage function, (2) decreased cytokine production in response to immune challenge, (3) decreased number of naïve T and B cells, (4) altered toll-like receptor expression and signaling, and (5) diminished response to antigen or mitogen stimulation.64 These changes suggest that both the innate and adaptive pro-inflammatory response would be at lower levels relative to individuals without LGI.\n\nAt the start of the pandemic, it was predicted that individuals with underlying chronic disease conditions that have systemic inflammation as a common feature would be prone to more severe forms of COVID-19.65–67 The expectation was that due to the pre-existing immune inflammatory dysfunction, the inflammatory response of such individuals would quickly spiral into hyperinflammation in response to SARS-CoV-2 infection. The situation would be similar for people with low grade inflammation or inflamm-aging but who did not yet have full-blown chronic diseases.68–70 This, however, appears not to have been the case. Looking at obesity for example, which is a model for LGI, a recent study on patients in America reported that in the first few days after diagnosis, levels of selected inflammation markers were lower in obese COVID-19 patients than in non-obese patients.71 Previous studies on influenza had reported that obese individuals (with LGI) mounted a slow pro-inflammatory response to the respiratory virus, with impaired pathogen-induced and lung-specific responses.72,73 This impaired adaptive pro-inflammatory response was suggested to contribute to the worse COVID-19 clinical outcomes in obese patients.74–76 In contrast, we suggest that the delayed response is rather protective, much like in the case of malaria exposure previously described. The worse COVID-19 outcomes in obese patients are more likely found in those with underlying chronic inflammatory diseases77–80 and are probably due to a combination of factors including extensive dysfunction and dysregulation of the inflammatory response.71,81–84 We suggest that, after an inflammatory response is mounted, appropriate metabolic regulation of the response is easily overwhelmed in patients with LGI-related comorbidities. In individuals with only LGI, however, the dysfunction is present but is not so extensive as to have caused organ damage and subsequent chronic disease. Relative to other persons, the already higher circulating levels of inflammatory mediators in LGI individuals feed an immune response, but escalation of the response is impaired. Therefore, there is a slow ramp-up of the pro-inflammatory response coupled with appreciable inflammatory response regulation, a combination which tends to be protective against COVID-19 progression.\n\nOur suggestion is backed by the observation that with the start of vaccination against COVID-19, literature from outside Africa suggest that older adults are less likely to report adverse effects after vaccination.85–87 Our interpretation of this is that the phenomenon of inflamm-aging, which has characteristics similar to low grade inflammation,58,88–91 appears to protect against vaccine side effects. This implies that the combination of higher systemic levels of inflammatory mediators, a blunt pro-inflammatory adaptive immune response, and an apparently impaired innate immune response are useful against COVID-19. In the African population, however, our thinking is that the innate response is not impaired. Rather, as described in the previous section, the history of frequent exposure to pro-inflammatory pathogens leaves the innate response at a higher level relative to individuals from other populations. This may explain why even older Africans appear to have better protection from the virus than older adults from elsewhere. This imprint of immune history on the specific modifications to an individual’s immune response would be consistent with the concept of immunobiography,58,92 which suggests close links between human health, longevity and individual immune system modifications.58,92–95\n\n\nOutlook\n\nThe focus on COVID-19 characterization and management had been on the clinical presentation of acutely ill patients. Only approximately 14 % of COVID-19 cases are severe enough to require hospital admission.96 References to the 86 % majority who experienced only mild/moderate or asymptomatic COVID-19 usually had to do with the tracking of the infection rate and transmission dynamics. Given the indications that an individual’s systemic inflammation state is altered post SARS CoV-2 infection, there had been the suspicion that even people with asymptomatic infection or mild COVID-19 symptoms would experience some sort of post-acute syndrome. Reports from across the world have indicated such a situation, showing that up to 50 % of non-hospitalized patients who experience mild or moderate COVID-19 continue to have symptoms up to six months and beyond after recovery.97–100 This has since been termed post-acute sequelae of COVID-19 (PASC). Health issues associated with PASC include fatigue, exercise intolerance, cognitive impairment, anxiety/depression, organ damage, impaired mobility, and reduced quality of life,101–104 all of which are also associated with LGI and inflamm-aging.58,105\n\nThe prevailing social and environmental conditions across Africa likely mean that the spread of SARS-CoV-2 has been rather extensive. This is supported, for example, by the observation of a 13–27 % average seroprevalence of SARS-CoV-2 antibodies in randomly sampled individuals across Ghana,106 compared to official figures of approximately 0.41 % for cumulative total infection rate as of September 2021.107 Similar situations have been reported in other African countries.108,109 Interestingly, the 60+ age group showed the highest seropositivity rate 106. Keeping in mind that the antibody test kit used had shown up to 66 % sensitivity and at least 94 % specificity,106 the report suggested that the observation of low sensitivity of antibody test kits may be due to generally low production of antibodies by infected persons rather than a failure of the kits used. The low sensitivity is interesting, particularly when some studies report significant cross-reactivity between other human coronaviruses antibodies and SARS-CoV-2 antigens.25 The likely underestimation of seropositivity106 suggests that far more people than officially reported are likely to have had SARS-CoV-2 infections which are unaccounted for. Such a phenomenon would lend support to our suggestion that some populations in Africa may exhibit a blunted, pro-inflammatory adaptive response to SARS-CoV-2 infection. Currently, ongoing works across the 16 administrative regions of Ghana report a SARS-CoV-2 antibody seroprevalence range of approximately 26–57 % as of October 2021 (unpublished work from Rockefeller Foundation Grant Number: 2021 HTH 006).\n\nPost-acute sequelae of COVID-19 lends credence to the suggestion that SARS-CoV-2 infection alters the inflammatory state. Alongside efforts to procure vaccines, therefore, it is just as important that Africa appreciates the potential impact of the apparently common but asymptomatic infections which likely have resulted in widespread natural inoculation. It is necessary to understand what changes in inflammatory state occur post SARS-CoV-2 infection in our populations, to help to characterize and preempt the effects on public health.\n\n\nData availability\n\nNo data are associated with this article.\n\n\nAuthors’ contributions\n\nDaniel Oduro-Mensah: Conceptualization, Writing – original draft, Writing – review and editing. Ebenezer Oduro-Mensah: Writing – original draft, Writing – review and editing. Peter Quashie: Writing – review and editing. Gordon Akanzuwine Awandare: Writing – review and editing. Laud Kenneth Okine: Writing – original draft, Writing – review and editing.",
"appendix": "Acknowledgements\n\nThe authors acknowledge the contributions of Nana Tawiah Ghunney and Stephanie Nanelle Hammond to the preparation of this manuscript.\n\n\nReferences\n\nWHO Coronavirus (COVID-19) Dashboard|WHO Coronavirus (COVID-19) Dashboard With Vaccination Data. Accessed June 23, 2021. Reference Source\n\nAfrica ‘has highest COVID-19 death rate of critically ill’ - Sub-Saharan Africa. Accessed June 23, 2021. Reference Source\n\nBiccard BM, Gopalan PD, Miller M, et al.: Patient care and clinical outcomes for patients with COVID-19 infection admitted to African high-care or intensive care units (ACCCOS): a multicentre, prospective, observational cohort study. Lancet. 2021; 397(10288): 1885–1894. Publisher Full Text\n\nWorld Population Clock: 7.9 Billion People (2021) - Worldometer. Accessed March 15, 2021. Reference Source\n\nCoronavirus deaths by country in Africa 2021|Statista. Accessed June 23, 2021. Reference Source\n\nGermany declares a Covid “third wave” has begun; Italy set for Easter lockdown. Accessed March 16, 2021. Reference Source\n\nEurope is struggling to contain the third wave of the epidemic. - CNN. Accessed March 16, 2021. Reference Source\n\nThird Covid wave sweeps across EU and forces new restrictions|Coronavirus|The Guardian. Accessed March 16, 2021. Reference Source\n\nFrance Battles a Third Wave of COVID Infections|Voice of America - English. Accessed March 16, 2021. Reference Source\n\nRisk of COVID-19 surge threatens Africa’s health facilities|WHO|Regional Office for Africa. Accessed July 4, 2021. Reference Source\n\nAfrica faces steepest COVID-19 surge yet|WHO|Regional Office for Africa. Accessed July 4, 2021. Reference Source\n\nCoronavirus cases by country in Africa 2021|Statista. Accessed March 12, 2021. Reference Source\n\nCOVID19_Cases. Accessed March 12, 2021. Reference Source\n\nWHO Coronavirus (COVID-19) Dashboard|WHO Coronavirus (COVID-19) Dashboard With Vaccination Data. Accessed July 4, 2021. Reference Source\n\nCoronavirus Disease 2019 (COVID-19) – Africa CDC. Accessed August 16, 2021. Reference Source\n\nPopulation of Africa (2021) - Worldometer. Accessed July 11, 2021. Reference Source\n\nNapoli PE, Nioi M: Global Spread of Coronavirus Disease 2019 and Malaria: An Epidemiological Paradox in the Early Stage of A Pandemic. J. Clin. Med. 2020; 9(4): 1138. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMbow M, Lell B, Jochems SP, et al.: COVID-19 in Africa: Dampening the storm?. Science (New York, N.Y.). 2020; 369(6504): 624–626. PubMed Abstract | Publisher Full Text\n\nDiop BZ, Ngom M, Biyong CP, et al.: The relatively young and rural population may limit the spread and severity of COVID-19 in Africa: a modelling study. BMJ Glob. Health. 2020; 5(5): e002699. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAdams J, MacKenzie MJ, Amegah AK, et al.: The Conundrum of Low COVID-19 Mortality Burden in sub-Saharan Africa: Myth or Reality?. Global Health: Science and Practice. Published online July 30, 2021; 9: 433–443. Publisher Full Text\n\nGendrot M, Duflot I, Boxberger M, et al.: Antimalarial artemisinin-based combination therapies (ACT) and COVID-19 in Africa: in vitro inhibition of SARS-CoV-2 replication by mefloquine-artesunate.Published online 2020; 99: 437–440. Publisher Full Text\n\nWhy Africa’s COVID-19 Outbreak Isn’t So Bad|Time. Accessed March 12, 2021. Reference Source\n\nCoronavirus in Africa: Five reasons why Covid-19 has been less deadly than elsewhere - BBC News. Accessed March 12, 2021. Reference Source\n\nNjenga MK, Dawa J, Nanyingi M, et al.: Why is there low morbidity and mortality of COVID-19 in Africa?. Am. J. Trop. Med. Hyg. 2020; 103(2): 564–569. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTso FY, Lindege SJ, Pena PB, et al.: High prevalence of pre-existing serological cross-reactivity against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in sub-Saharan Africa. International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases. 2021; 102: 577–583. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWhy Africa’s experience with COVID-19 has been atypical so far. Accessed March 12, 2021. Reference Source\n\nKusi KA, Frimpong A, Partey FD, et al.: High infectious disease burden as a basis for the observed high frequency of asymptomatic SARS-CoV-2 infections in sub-Saharan Africa. AAS Open Research. 2021; 4: 2. Publisher Full Text\n\nFonte L, Acosta A, Sarmiento ME, et al.: COVID-19 Lethality in Sub-Saharan Africa and Helminth Immune Modulation. Front. Immunol. 2020; 11: 2459. Publisher Full Text\n\nNaidoo P, Ghazi T, Chuturgoon AA, et al.: SARS-CoV-2 and helminth co-infections, and environmental pollution exposure: An epidemiological and immunological perspective. Environ. Int. 2021; 156: 106695. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMalaria cases: estimated country share 2018|Statista. Accessed July 5, 2021. Reference Source\n\nAdemolue TW, Aniweh Y, Kusi KA, et al.: Patterns of inflammatory responses and parasite tolerance vary with malaria transmission intensity. Malar. J. 2017; 16(1): 145. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoncunill G, Mayor A, Jiménez A, et al.: Cytokine and Antibody Responses to Plasmodium falciparum in Naïve Individuals during a First Malaria Episode: Effect of Age and Malaria Exposure. Beeson JG, ed. PLoS One. 2013; 8(2): e55756. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJagannathan P, Kim CC, Greenhouse B, et al.: Loss and dysfunction of Vδ2+γδ T cells are associated with clinical tolerance to malaria. Sci. Transl. Med. 2014; 6(251): 251ra117. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDoolan DL, Dobaño C, Baird JK: Acquired immunity to Malaria. Clin. Microbiol. Rev. 2009; 22(1): 13–36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchofield L, Mueller I: Clinical Immunity to Malaria. Curr. Mol. Med. 2006; 6(2): 205–221. PubMed Abstract | Publisher Full Text\n\nPortugal S, Moebius J, Skinner J, et al.: Exposure-Dependent Control of Malaria-Induced Inflammation in Children. Kazura JW, ed. PLoS Pathog. 2014; 10(4): e1004079. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFarrington L, Vance H, Rek J, et al.: Both inflammatory and regulatory cytokine responses to malaria are blunted with increasing age in highly exposed children. Malar. J. 2017; 16(1): 499. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBoström S, Giusti P, Arama C, et al.: Changes in the levels of cytokines, chemokines and malaria-specific antibodies in response to Plasmodium falciparum infection in children living in sympatry in Mali. Malar. J. 2012; 11: PubMed Abstract | Publisher Full Text | Free Full Text\n\nD’Ombrain MC, Robinson LJ, Stanisic DI, et al.: Association of early interferon-γ production with immunity to clinical malaria: A longitudinal study among Papua New Guinean children. Clin. Infect. Dis. 2008; 47(11): 1380–1387. PubMed Abstract | Publisher Full Text\n\nLei X, Dong X, Ma R, et al.: Activation and evasion of type I interferon responses by SARS-CoV-2. Nat. Commun. 2020; 11(1): 1–12. Publisher Full Text\n\nSARS-CoV-2 delays interferon signaling in host cells. Accessed March 12, 2021. Reference Source\n\nWei JH, Nan ZH, Feng MQ, et al.: SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cell. Mol. Immunol. 2020; 17(9): 998–1000. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStertz S, Hale BG: Interferon system deficiencies exacerbating severe pandemic virus infections. Trends Microbiol. Published online 2021; 29: 973–982. Publisher Full Text\n\nZhang Q, Liu Z, Moncada-Velez M, et al.: Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science. 2020; 370(6515) PubMed Abstract | Publisher Full Text | Free Full Text\n\nYu C, Zhou M, Liu Y, et al.: Characteristics of asymptomatic COVID-19 infection and progression: A multicenter, retrospective study. Virulence. 2020; 11(1): 1006–1014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChoi YH, Jin N, Kelly F, et al.: Elevation of alanine aminotransferase activity occurs after activation of the cell-death signaling initiated by pattern-recognition receptors but before activation of cytolytic effectors in NK or CD8+ T cells in the liver during acute HCV infection. PLoS One. 2016; 11(10): e0165533. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTrindade Bezerra JM, Soeiro Barbosa D, Rogerlândio Martins-Melo F: Changes in malaria patterns in Brazil over 28 years (1990–2017): results from the Global Burden of Disease Study 2017.Published online 2020. Publisher Full Text\n\nBrazil: number of COVID-19 deaths, by state 2021|Statista. Accessed July 12, 2021. Reference Source\n\nCoronavirus cases worldwide by country|Statista. Accessed July 12, 2021. Reference Source\n\nHong M, Bertoletti A: Tolerance and immunity to pathogens in early life: insights from HBV infection. Semin. Immunopathol. 2017; 39(6): 643–652. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYap GS, Gause WC: Helminth infections induce tissue tolerance mitigating immunopathology but enhancing microbial pathogen susceptibility. Front. Immunol. 2018; 9(Oct): 2135. Publisher Full Text\n\nKing IL, Li Y: Host-parasite interactions promote disease tolerance to intestinal helminth infection. Front. Immunol. 2018; 9(Sep): 2128. Publisher Full Text\n\nMa Z, Li P, Ji Y, et al.: Cross-reactivity towards SARS-CoV-2: the potential role of low-pathogenic human coronaviruses. The Lancet Microbe. 2020; 1(4): e151. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuo L, Wang Y, Kang L, et al.: Cross-reactive antibody against human coronavirus OC43 spike protein correlates with disease severity in COVID-19 patients: a retrospective study. Emerging Microbes and Infections. 2021; 10(1): 664–676. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRönnbäck C, Hansson E: The Importance and Control of Low-Grade Inflammation Due to Damage of Cellular Barrier Systems That May Lead to Systemic Inflammation. Front. Neurol. 2019; 10(MAY): 533. Publisher Full Text\n\nLeón-Pedroza JI, González-Tapia LA, del Olmo-Gil E , et al.: Low-grade systemic inflammation and the development of metabolic diseases: From the molecular evidence to the clinical practice. Cirugía y Cirujanos (English Edition). 2015; 83(6): 543–551. Publisher Full Text\n\nKrabbe KS, Pedersen M, Bruunsgaard H: Inflammatory mediators in the elderly. Exp. Gerontol. 2004; 39(5): 687–699. PubMed Abstract | Publisher Full Text\n\nCalder PC, Bosco N, Bourdet-Sicard R, et al.: Health relevance of the modification of low grade inflammation in ageing (inflammageing) and the role of nutrition. Ageing Res. Rev. 2017; 40: 95–119. PubMed Abstract | Publisher Full Text\n\nCastro AM, Macedo-de la Concha LE, Pantoja-Meléndez CA: Low-grade inflammation and its relation to obesity and chronic degenerative diseases. Revista Médica del Hospital General de México. 2017; 80(2): 101–105. Publisher Full Text\n\nMinihane AM, Vinoy S, Russell WR, et al.: Low-grade inflammation, diet composition and health: Current research evidence and its translation. Br. J. Nutr. 2015; 114(7): 999–1012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRönnbäck C, Hansson E: The Importance and Control of Low-Grade Inflammation Due to Damage of Cellular Barrier Systems That May Lead to Systemic Inflammation. Front. Neurol. 2019; 10(May): 533. Publisher Full Text\n\nThe Rise and Rise of Chronic Diseases in Africa - Sanofi. Accessed March 14, 2021. Reference Source\n\nde-Graft Aikins A, Addo J, Ofei F, et al.: Ghana’s burden of chronic non-communicable diseases: future directions in research, practice and policy. Ghana Med. J. 2012; 46(2 Suppl): 1–3. Accessed March 19, 2021. Reference Source\n\nMoro-García MA, Mayo JC, Sainz RM, et al.: Influence of inflammation in the process of T lymphocyte differentiation: Proliferative, metabolic, and oxidative changes. Front. Immunol. 2018; 9(Mar): 1. Publisher Full Text\n\nCiornei RT: Prevention of Severe Coronavirus Disease 2019 Outcomes by Reducing Low-Grade Inflammation in High-Risk Categories. Front. Immunol. 2020; 11: 1762. Publisher Full Text\n\nChiappetta S, Sharma AM, Bottino V, et al.: COVID-19 and the role of chronic inflammation in patients with obesity. Int. J. Obes. 2020; 44(8): 1790–1792. Publisher Full Text\n\nHuizinga GP, Singer BH, Singer K: The collision of meta-inflammation and SARS-CoV-2 pandemic infection. Endocrinology (United States). 2020; 161(11): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKim J, Nam JH: Insight into the relationship between obesity-induced low-level chronic inflammation and COVID-19 infection. Int. J. Obes. 2020; 44(7): 1541–1542. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTskhay A, Yezhova A, Alibek K: COVID-19 Pandemic: Is Chronic Inflammation a Major Cause of Death?.Publisher Full Text\n\nAkbar AN, Gilroy DW: Aging immunity may exacerbate COVID-19. Science. 2020; 369(6501): 256–257. PubMed Abstract | Publisher Full Text\n\nMostaghim A, Sinha P, Bielick C, et al.: Clinical outcomes and inflammatory marker levels in patients with Covid-19 and obesity at an inner-city safety net hospital. Zivkovic AR, ed. PLoS One. 2020; 15(12): e0243888. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHonce R, Schultz-Cherry S: Impact of obesity on influenza A virus pathogenesis, immune response, and evolution. Front. Immunol. 2019; 10(May): 1071. Publisher Full Text\n\nGreen WD, Beck MA: Obesity impairs the adaptive immune response to influenza virus. Ann. Am. Thorac. Soc. 2017; 14(Suppl 5): S406–S409. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDicker D, Bettini S, Farpour-Lambert N, et al.: Obesity and COVID-19: The Two Sides of the Coin. Obes. Facts. 2020; 13(4): 430–438. PubMed Abstract | Publisher Full Text | Free Full Text\n\nObesity and COVID-19 Severity in a Designated Hospital in Shenzhen, China A total of 383 consecutively hospitalized patients with COVID.Published online 2020. Publisher Full Text\n\nGreen WD, Beck MA: Obesity impairs the adaptive immune response to influenza virus. Ann. Am. Thorac. Soc. 2017; 14: S406–S409. PubMed Abstract | Publisher Full Text | Free Full Text\n\nContributor: Links Between COVID-19 Comorbidities, Mortality Detailed in FAIR Health Study. Accessed March 16, 2021. Reference Source\n\nGupta R, Agrawal R, Bukhari Z, et al.: Higher comorbidities and early death in hospitalized African-American patients with Covid-19. BMC Infect. Dis. 2021; 21(1): 78. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAge, sex, comorbidities impact outcomes after COVID-19 hospitalization. Accessed March 16, 2021. Reference Source\n\nD’ascanio M, Innammorato M, Pasquariello L, et al.: Age is not the only risk factor in COVID-19: the role of comorbidities and of long staying in residential care homes. BMC Geriatr. 2021; 21(1): 63. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMostaghim A, Sinha P, Bielick C, et al.: Clinical outcomes and inflammatory marker levels in patients with Covid-19 and obesity at an inner-city safety net hospital. PLoS One. 2020; 15(12 December): e0243888. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPatients with COVID-19 and obesity have poor outcomes not driven by inflammation|EurekAlert! Science News. Accessed March 12, 2021. Reference Source\n\nKooistra EJ, de Nooijer AH , Claassen WJ, et al.: A higher BMI is not associated with a different immune response and disease course in critically ill COVID-19 patients. Int. J. Obes. 2021; 45(3): 687–694. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPizarro-Sánchez MS, Avello A, Mas-Fontao S, et al.: Clinical Features of Asymptomatic SARS-CoV-2 Infection in Hemodialysis Patients. Kidney Blood Press. Res. 2021; 46(1): 1–9. Publisher Full Text\n\nPolack FP, Thomas SJ, Kitchin N, et al.: Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N. Engl. J. Med. 2020; 383(27): 2603–2615. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRamasamy MN, Minassian AM, Ewer KJ, et al.: Safety and immunogenicity of ChAdOx1 nCoV-19 vaccine administered in a prime-boost regimen in young and old adults (COV002): a single-blind, randomised, controlled, phase 2/3 trial. Lancet. 2020; 396(10267): 1979–1993. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnderson EJ, Rouphael NG, Widge AT, et al.: Safety and Immunogenicity of SARS-CoV-2 mRNA-1273 Vaccine in Older Adults. N. Engl. J. Med. 2020; 383(25): 2427–2438. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSanada F, Taniyama Y, Muratsu J, et al.: Source of Chronic Inflammation in Aging. Front. Cardiovasc. Med. 2018; 5: 12. Publisher Full Text\n\nFranceschi C, Campisi J: Chronic inflammation (Inflammaging) and its potential contribution to age-associated diseases. J. Gerontol. A Biol. Sci. Med. Sci. 2014; 69: S4–S9. Publisher Full Text\n\nPanda A, Qian F, Mohanty S, et al.: Age-Associated Decrease in TLR Function in Primary Human Dendritic Cells Predicts Influenza Vaccine Response. J. Immunol. 2010; 184(5): 2518–2527. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuarner V, Rubio-Ruiz ME: Aging and Health-A Systems Biology Perspective. Interdiscipl Top Gerontol Basel, Karger. 2015; 40: 99–106. Publisher Full Text\n\nGrignolio A, Mishto M, Caetano Faria AM, et al.: Towards a liquid self: How time, geography, and life experiences reshape the biological identity. Front. Immunol. 2014; 5(Apr): 153. Publisher Full Text\n\nSalvioli S, Monti D, Lanzarini C, et al.: Immune System, Cell Senescence, Aging and Longevity - Inflamm-Aging Reappraised.\n\nFranceschi C, Capri M, Monti D, et al.: Inflammaging and anti-inflammaging: A systemic perspective on aging and longevity emerged from studies in humans. Mech. Ageing Dev. 2007; 128(1): 92–105. PubMed Abstract | Publisher Full Text\n\nMorrisette-Thomas V, Cohen AA, Fülöp T, et al.: Inflamm-aging does not simply reflect increases in pro-inflammatory markers. Mech. Ageing Dev. 2014; 139(1): 49–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDaher A, Balfanz P, Aetou M, et al.: Clinical course of COVID-19 patients needing supplemental oxygen outside the intensive care unit. Sci. Rep. 2021; 11(1): 2256. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKlein H, Asseo K, Karni N, et al.: Onset, duration and unresolved symptoms, including smell and taste changes, in mild COVID-19 infection: a cohort study in Israeli patients. Clin. Microbiol. Infect. 2021; 27: 769–774. Publisher Full Text\n\nCarvalho-Schneider C, Laurent E, Lemaignen A, et al.: Follow-up of adults with noncritical COVID-19 two months after symptom onset. Clin. Microbiol. Infect. 2021; 27(2): 258–263. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStavem K, Ghanima W, Olsen MK, Gilboe HM, et al.: Persistent symptoms 1.5-6 months after COVID-19 in non-hospitalised subjects: A population-based cohort study. Thorax. Published online December 3, 2020; 76: 405–407. Publisher Full Text\n\nLadds E, Rushforth A, Wieringa S, et al.: Persistent symptoms after Covid-19: qualitative study of 114 “long Covid” patients and draft quality principles for services. BMC Health Serv. Res. 2020; 20(1): 1144. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuang C, Huang L, Wang Y, et al.: 6-month consequences of COVID-19 in patients discharged from hospital: a cohort study. Lancet. 2021; 397(10270): 220–232. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGarrigues E, Janvier P, Kherabi Y, et al.: Post-discharge persistent symptoms and health-related quality of life after hospitalization for COVID-19. J. Infect. 2020; 81(6): e4–e6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChopra V, Flanders SA, O’Malley M, et al.: Sixty-Day Outcomes Among Patients Hospitalized With COVID-19. Ann. Intern. Med. Published online November 11, 2020. Publisher Full Text\n\nCarfì A, Bernabei R, Landi F: Persistent symptoms in patients after acute COVID-19. JAMA. 2020; 324(6): 603–605. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLasselin J, Magne E, Beau C, et al.: Low-grade inflammation is a major contributor of impaired attentional set shifting in obese subjects. Brain Behav. Immun. 2016; 58: 63–68. Publisher Full Text\n\nQuashie PK, Mutungi JK, Dzabeng F, et al.: Trends of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody prevalence in selected regions across Ghana. Wellcome Open Res. 2021; 6: 173. Publisher Full Text\n\nCOVID-19 Situation Dashboard|Ghana. Accessed September 28, 2021. Reference Source\n\nAdetifa IMO, Uyoga S, Gitonga JN, et al.: Temporal trends of SARS-CoV-2 seroprevalence during the first wave of the COVID-19 epidemic in Kenya. Nat. Commun. 2021; 12(1): 3966–3966. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChisale MRO, Ramazanu S, Mwale SE, et al.: Seroprevalence of anti-SARS-CoV-2 antibodies in Africa: A systematic review and meta-analysis. Rev. Med. Virol. Published online July 6, 2021. Publisher Full Text"
}
|
[
{
"id": "146899",
"date": "30 Aug 2022",
"name": "Sankha Shubhra Chakrabarti",
"expertise": [
"Reviewer Expertise COVID vaccines",
"Geriatric pharmacovigilance",
"Geriatric neuropsychiatry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting hypothesis article. There are some minor grammatical errors. Please correct those.\nExample: \"From December 2020 when emerging SARS-CoV-2 variants fueled second and third waves of COVID-19 across the globe6–11 from December 2020, A\" - Here, \"From December 2020\" is repeated twice. Go through the entire text and check carefully.\nMy other suggestions are:\n1. Mention low vaccine coverage as a possible reason. Though it may seem unusual, the data for most countries with high vaccination rates such as Israel or South Korea show rising cases post-vaccination and even after boosters.\n\n2. The preferred abbreviation for alanine aminotransferase is ALT. Please correct.\n3. The part about obesity and low reactogenicity of vaccines in the elderly as support for the authors' hypothesis is unclear and does not seem convincing. More proof and clarity is needed, or better to delete.\n4. \"Interestingly, the 60+ age group showed the highest seropositivity rate 106. Keeping in mind that the antibody test kit used had shown up to 66 % sensitivity and at least 94 % specificity,106 the report suggested that the observation of low sensitivity of antibody test kits may be due to generally low production of antibodies by infected persons rather than a failure of the kits used. The low sensitivity is interesting, particularly when some studies report significant cross-reactivity between other human coronaviruses antibodies and SARS-CoV-2 antigens.25 The likely underestimation of seropositivity106 suggests that far more people than officially reported are likely to have had SARS-CoV-2 infections which are unaccounted for.\" - This part needs to be re-written for clarity. Also, reference 106 at the end of the first sentence is not linked as a reference. Please correct.\n5. The final part (last two paragraphs) are not written in synchrony. The authors have mixed up some important points they wish to make. Please re-write for clarity.\nOverall, the authors start off well but they have not separated the valid points they wish to make clearly in the rest of the article which makes it difficult to understand.\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? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\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? Partly",
"responses": [
{
"c_id": "8775",
"date": "21 Nov 2022",
"name": "Daniel Oduro-Mensah",
"role": "Author Response",
"response": "The authors sincerely appreciate the time and effort the reviewer has spent to make the report better. We take note of the reviewer’s comments and respond as follows: We appreciate the reviewer’s suggestion in comment 1 to add to our explanations in the manuscript. However, we believe that it would be a full discussion for another platform. Our thinking about vaccination, as relates to what is presented in this manuscript, has been touched on briefly in the conclusion section. The abbreviation has been corrected to ALT. Thank you very much for the notice in reviewer’s comment 2, that was an oversight. The authors remain committed to the suggestions and inferences the manuscript makes in the section referred to in reviewer’s comment 3. The section has been rewritten and strengthened with further evidence as the reviewer suggested. The section referred to in reviewer’s comment 4 has be rewritten for clarity as suggested by the reviewer. The last two paragraphs have been rewritten as suggested in reviewer’s comment 5. A portion has been broken off to make a conclusion section."
}
]
}
] | 1
|
https://f1000research.com/articles/10-1177
|
https://f1000research.com/articles/11-717/v1
|
29 Jun 22
|
{
"type": "Study Protocol",
"title": "Effectiveness of a peanut ball device during labour on maternal and neonatal outcomes: protocol for a randomised controlled trial",
"authors": [
"Pratibha Kamath",
"Muralidhar Pai",
"Revathi Shenoy",
"Sushmitha Karkada",
"Sonia D’souza",
"Judith Noronha",
"Pratibha Kamath",
"Revathi Shenoy",
"Sushmitha Karkada",
"Sonia D’souza",
"Judith Noronha"
],
"abstract": "Frequent positional changes and movements during labour is one of the recommendations by the World Health Organization (WHO) to prevent prolonged labour, thereby avoiding cesarean sections. However, labour induction, continuous fetal monitoring in supine position and immobilising the women during labour are standard practices in most private hospitals. To combat these problems and to implement WHO recommendations, the peanut ball is an effective device through which frequent positional changes will be achieved without disrupting the labour procedures. The current study aims to evaluate the effectiveness of the peanut ball device during labour on maternal and neonatal outcomes and assess the stress response induced by labour in terms of maternal and neonatal cortisol in low-risk primigravid women. The study is a prospective, block randomised controlled trial with parallel arms. A total of 768 study participants will be randomised to the peanut-ball group (intervention) and standard care group (control). The intervention group will receive different peanut ball positions during labour at or after 4 cm of cervical dilatation. The primary outcomes of the study are maternal outcome that includes measurement of duration of the active and the second stage of labour, stress level as measured by serum cortisol level at 3–4 cm and at 10 cm of cervical dilatation, mode of delivery, perception of pain, behavioural response during the active stage of labour and neonatal outcomes, which includes the pattern of fetal heart rate, APGAR score, birth injuries, and umbilical serum and salivary cortisol level. The collected data will be compared between the intervention and control groups.\n\nTrial Registration: This research is registered under the CTRI (Clinical Trials Registry of India) (CTRI/2019/08/020802) (21/8/2019).",
"keywords": [
"Study protocol",
"Randomized controlled trial",
"Labour",
"Peanut ball",
"Maternal and neonatal outcome",
"Stress",
"Cortisol"
],
"content": "Abbreviations\n\nAPGAR: Appearance, Pulse, Grimace, Activity, and Respiration\n\nCS: Cesarean section\n\nQACE: questionnaire on assessing the childbirth experiences\n\nWHO: World Health Organization\n\n\nIntroduction\n\nEven after the strong recommendations of the World Health Organization regarding mobility and upright positions to prevent delay in the first stage of labour, increase in induction during labour, and continuous fetal monitoring (Calik, Karabulutlu, & Yavuz, 2018) made position changes challenging during labour. Even if a mother is constrained to bed, frequent changes of maternal positions that facilitate pelvic movements should be given during labour (Lawrence, Lewis, Hofmeyr, & Styles, 2013). The absence of changes in the position of the mother during labour can lead to prolonged labour and increases the chance of cesarean birth due to failure to progress or descend (Zwelling, 2010; Akyıldız, Coban, Gör Uslu, & Taşpınar, 2021). The peanut ball is considered an effective intervention to overcome this obstacle and promote the different positions during labour.\n\nThe peanut ball is an alternative to the conventional birth ball. The birthing ball is preferably used during the pregnancy period (Ghasab, Kohan, Firoozehchian, & Ebrahimi, 2019; Mirzakhani, Hejazinia, Golmakani, Sardar, & SHakeri, 2015), whereas the effectiveness of the peanut ball is elicited even during labour (Outland & Alvarado, 2019). The peanut ball is a curved peanut-shaped ball that has a middle indentation that allows the women to place the ball between and below the knees for allowing either the lateral, supine or sitting position, which increases pelvic dimensions, promotes progressive fetal rotation and descent during second-stage labour and ultimately promote the progress of labour (Zwelling, 2010; Roth, Dent, Parfitt, Hering, & Bay, 2016). Several studies have shown a reduction in either the length of labour (Roth, Dent, Parfitt, Hering, & Bay, 2016; Tussey CM, 2015 Jan) or a reduction in the cesarean birth (Outland & Alvarado, 2019) with use of the peanut ball in immobile women.\n\nIn 2015, Tussey et al. reported in a randomised controlled trial that effective utilisation of peanut ball during labour in the epidural woman has shortened the second stage of labour by 11 minutes and reached clinical significance in decreasing the length of time of the second stage of labour by 29 minutes. In addition, only 10% of those women who delivered with a peanut ball had a caesareans birth compared to 21% in the control group (p < .05) (Tussey CM, 2015 Jan).\n\nRoth and his colleagues in the year 2016 demonstrated in a randomised controlled study that the first stage of labour was significantly reduced for the nulliparous women (p = .018), but not for the multiparous women after the use of peanut ball. But no statistically significant difference was found in the length of the pushing stage for either nulliparous or multiparous women (Roth, Dent, Parfitt, Hering, & Bay, 2016). These findings were supported by the quasi-experimental study done by Hickey & Savage, and they found out that peanut ball use during labour substantially (50%) decreased the rate of cesarean sections among women (164) labouring with epidurals (Hickey & Savage, 2019) However, these studies’ results are not statistically significant to prove that the peanut ball alone has decreased the labour duration (Outland & Alvarado, 2019; Roth, Dent, Parfitt, Hering, & Bay, 2016; Tussey CM, 2015 Jan; Hickey & Savage, 2019).\n\nFurthermore, Ahmadpour and team concluded in their systematic review and meta-analysis that the 645 women who used the peanut ball during labour have no statistically significant difference between the two groups in cesarean section rate and the length of the first stage of labour. Therefore, the study recommended conducting more rigorous randomised controlled trials to evaluate the effectiveness of the peanut ball during labour (Ahmadpour, Mohammad-Alizadeh-Charandabi, Doosti, & Mirghafourvand, 2021).\n\nEven the Grenwik, et al., study in 2019 supported the statement in their systematic review and summarised that more research is needed to prove the statistical significance in decreasing labour duration after the peanut ball use (Grenwik, et al., 2019).\n\nIn the Indian research literature, there have been no randomised studies conducted on the peanut ball interventions (Jayasudha, Lakshmi, Priscilla, Anitha, & Priya, 2021). That is why we, the researchers, through the randomised clinical trial, aimed at evaluating the effectiveness of a peanut ball device during labour on maternal and neonatal outcomes and assessing the stress response induced by labour in terms of maternal and fetal cortisol in low-risk primigravid women. If found to be effective, the proposed large-scale clinical trial, the peanut ball intervention can be implemented routinely in maternal healthcare settings for safe and comfortable delivery, which can ultimately prevent prolongation of labour and decrease the proportion of postpartum hemorrhage and stress level among the mother.\n\n\nResearch objectives\n\nThe following objectives are formulated:\n\n1. To determine the effectiveness of the use of a peanut ball device during labour in terms of following maternal outcomes:\n\n✓ Duration of the active stage of labour\n\n✓ Duration of the second stage of labour\n\n✓ Nature of delivery\n\n✓ Need for pain medications\n\n✓ Perception of pain\n\n✓ An occurrence of postpartum haemorrhage\n\n2. To determine the effectiveness of the use of a peanut ball device during labour in terms of following neonatal outcomes.\n\n✓ Fetal heart rate patterns\n\n✓ Neonatal Intensive Care Unit (NICU) admissions\n\n✓ APGAR score (Appearance (skin colour), Pulse (heart rate), Grimace (reflex irritability), Activity (muscle tone) score and Respiration) at the time of birth at one minute and five minutes.\n\n✓ Birth injuries\n\n3. To identify and compare the behavioural response, stress level, childbirth experience and maternal satisfaction among low-risk primigravid women during the active stage of labour between the experimental and control group.\n\n4. To identify and compare the stress level of neonates between the intervention and control.\n\n\nHypotheses\n\nThe trial is designed to test the hypotheses at a 0.05 level of significance. The following hypotheses were formulated.\n\nH1: There will be a significant difference in the maternal and neonatal outcomes during labour between the intervention and control group.\n\nH2: There will be a significant difference in the behavioural response score between the intervention and control group.\n\nH3: There will be a significant difference in the maternal cortisol levels between the intervention and control group.\n\nH4: There will be a significant difference in the neonatal cortisol levels between the intervention and control group.\n\nH5: There will be a significant difference between the childbirth experience score between the intervention and control group.\n\n\nMethods\n\nA prospective block randomised controlled trial with parallel groups is the research design adopted for the study. Block randomisation of 64 blocks with a block size of 12 each is generated using a Research randomiser, an online random number generator by a study statistician. A senior nurse who is working in the labour ward and who is not directly involved in the study will be generating the sequence. Concealment allocation will be achieved using a sequentially numbered opaque and sealed envelope (SNOSE), where participants will be assigned randomly either to receive the peanut ball intervention or standard care.\n\nAll study materials can be found as Extended data (Kamath, 2022a–f). The study will adhere to the Consolidated Standards of Reporting Trials (CONSORT) guidelines (Figure 1) (Sally Hopewell, 2008) and the protocol follows the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) guidelines (Kamath, 2022g).\n\n*PIH: Pregnancy Induced Hypertension, *GDM: Gestational Diabetes Mellitus, *VAS: Visual Anologue scale, WHO: World Health Organization. *SNOSEs: Sequentially Numbered Opaque and Sealed Envelopes, *QACE: Questionnaire on Assessing the Childbirth Experiences.\n\nThe study is funded by the Indian Council of Medical Research (ICMR), Government of India, (File No:5/7/58/MH/Adhoc/2019-0146/RBMCH) and is approved by Manipal Academy of Higher Education, Institutional review board (Reg no. ECR/146/Inst/KA/2013/RR-16). An estimated 768 low-risk primigravid women will be recruited from the selected tertiary care hospital of southern district of Karnataka. This research is registered under the CTRI (Clinical Trials Registry of India) (CTRI/2019/08/020802) (21/8/2019).\n\nThe eligibility criteria include low-risk primigravid women who are aged between 18 to 40 years, singleton pregnancy and in cephalic presentation, gestational age of 37.0 to 41.6 weeks, well-controlled pre-eclampsia, and gestational diabetes mellitus, history of abortions, well-controlled/moderate anaemia, history of mild intrauterine growth restriction (IUGR), willing to use the peanut ball during the first stage of labour and preferring a vaginal delivery.\n\nThe exclusion criteria include women who are known to have any major fetal anomalies and very low and late preterm, a high-risk antenatal mother with any pregnancy-related complications like severe pre-eclampsia/eclampsia, preterm labour, placenta praevia, malpresentation during the study, contraindication for vaginal delivery, multigravida, multiple pregnancies, had any sort of fracture of leg/any major problem in the past and having weight more than 90 kg.\n\nThe expected variations in the research outcome variable determines the sample size for the study; n=2Z1−α2+Z1−β2σ2/d2 (where n is the sample size per group, Z1−α2= 1.96 at α = 0.05, Z1−β = 0.84 (power at 80% power), σ = standard deviation of the primary outcome variable stress level of the mother as measured by serum cortisol level = 2.58 μg/dl (Stjernholm, Nyberg, Cardell, & Höybye, 2016), d = clinically significant difference = 0.55 μg/dl. The sample size, calculated with an anticipatory attrition rate of 10%, is 768.\n\nAll the low-risk primigravid women at or after 37 weeks of gestation attending the outpatient services at tertiary care hospitals for an antenatal check-up will be oriented about the implementation of peanut ball during labour by using the peanut ball positions chart prepared by premier birth tools and by showing the video on peanut ball during labour prepared by the researcher.\n\nThereafter, the mothers will be screened in the labour room based on the inclusion criteria. The research team will explain the research purpose and procedure to the eligible mothers and, if they are willing to participate, informed written consent will be taken.\n\nSubsequently, the low risk primigravid women at 2–3 cm of cervical dilatation preferring a vaginal delivery will be block randomised to peanut ball intervention group or standard care control group by an external member (labour room nurse) with the help of SNOSEs. The research assistant and research nurse carrying out data collection, data entry, and data analysis will be blinded to group allocation.\n\nThe peanut ball positioning is done at or after 4 cm of dilatation by a trained nurse-midwife whenever the mother is lying or sitting on the bed. Peanut balls are available in four sizes: 40 cm, 50 cm, 60 cm, and 70 cm to fit different participants as reported by Grant & Clutter in 2014. The researcher will make sure that the suitable size of the ball is given to the woman as recommended by the premier birth tools as per the height of the mother, that is: 40 cm for women whose height is under 5′3″, 50 cm is the most common size and exclusivly used for women with 5′3″ to 5′ 6″ height, 60 cm for women 5′7″ or taller or overweight women, and 70 cm used only to sit on and straddle on the peanut ball as reported by Grant C in 2015. All the sizes of peanut balls will be available in the labour room (Figure 2) to use during labour and will be covered with clean peanut ball covers. A suitable peanut ball will be provided to the mother to give four main peanut ball positions: sitting, semi-sitting, side-lying, and tuck position until the mother is ready to push during the second stage of labour.\n\nAdherence to intervention protocols and procedures will be done continuously by research assistants throughout the intervention by being with the patient and educating and comforting the mother.\n\nThe control group of women will receive the standard/routine care provided in the labour room of the tertiary care setting.\n\nParticipants will be recruited only after informed written consent. Participants participation in this study is voluntary and they can withdraw their participation at any time, without giving any reasons. They will still get the usual routine care during labour, and non-participation will not have any negative consequences on their subsequent medical treatment or relationship with the treating obstetrician and midwife. If the participant withdraws from the study before data collection is completed, their data collected till the withdrawal will be used in the study report.\n\nMaternal and neonatal outcomes will be measured by the research assistants at different points of time and compared between the intervention and control groups. The maternal outcome includes measurement of the duration of the active stage of labour, duration/pushing effort in the second stage of labour, mode of delivery, the need of pain medications, perception of pain, behavioural response during the active stage of labour, serum analysis of cortisol level, the proportion of postpartum hemorrhage, and neonatal outcome includes a pattern of fetal heart rate, APGAR score (Apgar V, 1958), birth injuries, and salivary cortisol level.\n\nDuring the active stage of labour blood samples will be collected twice from the mothers in both groups for serum cortisol analysis. The 1st sample will be collected when cervical dilatation is 3–4 cm and the 2nd sample will be collected after full dilatation of the cervix and these will be sent to lab for analysis. An umbilical cord blood sample will be collected from the newborn at the time of birth to check the serum cortisol level, and salivary cortisol will be collected from the newborn within one hour of birth to check the salivary cortisol level. An observational record on the progress of the labour will be done for both the groups once they reach 4 cm of cervical dilatation by using the WHO partograph Both the groups will be observed for their behavioral responses for any two hours during the first stage of the labour with the cervical dilatation ranging from 4–7 cms by using the behavioral response observational checklist (Karkada et al., 2010) Both the neonatal and maternal outcomes will be recorded by using the outcome of the labour assessment tool (Kamath, 2022f) and WHO Partograph, and during postnatal period before getting discharged from the hospital, ie., 3–4 days after the delivery, women from both of the groups will be assessed for their childbirth experience by using a questionnaire for assessing the childbirth experience (QACE) tool (Carquillat, P. et al., 2017). Maternal satisfaction regarding assistance provided during labour/delivery will be measured by using VAS (visual analogue scale) patient satisfaction score (Hayes and Patterson, 1921).\n\nThe researcher prepared a record of the outcome of labour to document maternal and neonatal outcomes. The maternal outcome consists of 18 items, such as duration of labour, nature of delivery, need of pain medications, objective assessment of pain, evaluation of maternal and fetal cortisol levels and postpartum hemorrhage etc. The neonatal tool includes details of APGAR score at birth, weight of the newborn, neonatal injuries during birth and particulars of NICU admission etc. (Kamath, 2022f).\n\nBlood samples will be collected twice during labour to determine the stress level. The first blood sample will be collected when cervical dilatation is 4–5 cm, and the second will be collected when cervical dilatation is of 10 cm from both groups and these will be sent to the biochemistry lab for analysis. After complete coagulation, the blood sample will be centrifuged, and then the serum will be separated for analysis of cortisol concentration. A blood sample from the umbilical cord will be taken at the time of birth to check the serum cortisol level of the baby, and saliva will be collected within one hour of birth by using swab stick by keeping it in baby’s mouth for two minutes to check the salivary cortisol level. The serum will be separated by centrifuging the cord blood. Using the principles of electrochemiluminescence immunoassays, cortisol levels will be measured in serum and cord blood using the Cobas -602 e-immunoassay analyser. Assay reagents are obtained from Roche Diagnostics. The saliva samples will be immediately frozen at 20° C until analysis. The free cortisol will be determined by ELISA.\n\nThis observation checklist, prepared by Karkada EC et al., is used in this study by obtaining permission from the author to assess the behavioural responses of low-risk primigravid women during the first stage of labour. A behavioural response checklist has three areas of observation, i.e., the behavioural response in between contractions which has 20 items, facial response during a contraction, which contains eight items; behavioural responses during contractions, which includes 20 items; and lastly, physiological parameters, which have two items. Overall, the tool includes 50 items. The study encompasses negative and positive responses (Karkada, Noronha, & Dsouza, 2010).\n\nCarquillat, P. et al., developed the QACE questionnaire, and it is self reporting tool screens for any negative experiences during child birth. It consists of six main thematic categories. These thematic categories are expectations (three items), sensory experiences (two items), perceived control (six items), relationship with caregivers and the midwife (four items), emotions (seven items), and the first moments with the baby (three items). Additional ten and the other three items are to measure causal indicators that potentially influence the childbirth experience. The response format is a 4-point Likert scale, ranging from “Totally”, “In part”, “Not so much”, and “Not at all” (Carquillat, P. et al., 2017).\n\nThe researchers modified the VAS into a patient satisfaction scale to assess the satisfaction level of low-risk primigravid women during labour. It is a 10 cm scale with smileys indicating expression of satisfaction, with the scoring: 0 – indicates no satisfaction and score ranging between 1–3 – mild level of satisfaction, 4–7 – moderate level of satisfaction, and 8–10 – high level of satisfaction (Hayes and Patterson, 1921).\n\nThe validity (item Content Validity Index (I-CVI) and Scale Content Validity Index (S-CVI/Ave) and reliability (Table 1) of the study tools were established by giving the tools, along with the criteria checklist, to a panel of nine experts from different fields, such as the women and child health department of physiotherapy, department of statistics, department of Obstetrics and Gynecological Nursing, and experts from OBG department, Kasturba Hospital Manipal to review the study tools. Content validity is established in terms of relevancy, accuracy, and appropriateness. The item Content Validity Index (I-CVI) and Scale Content Validity Index (S-CVI/Ave) of the tools were calculated based on recommendations by Polit and Beck (2012).\n\n*I-CVI- Item - content validity index, *S-CVI- Scale level - content validity index.\n\nThe research assistant will do coding and data entry. The primary investigator will review the data entered for any discrepancies such as data entry errors, missing values etc. One of the co-authors will check the data entry errors by randomly selecting data sheets. A separate laptop will be used for the project store data and can be accessed only by the research assistant and primary investigator.\n\nStatistical analysis will be performed using SPSS software version 16. The data analysis will be done based on the objectives and hypotheses of the study. We will follow the intention to treat analysis (ITT). The sample characteristics are measured using descriptive statistics. Two independent samples t-test/Mann-Whitney U-test (based on normality of data) will be used to determine the effectiveness of the usage of peanut ball on the maternal outcomes of labour. Associations among the variables will be computed using the Chi-square test (for categorical variables) and two independent samples t-test/Mann-Whitney U-test or one-way ANOVA/Kruskal Wallis test (for continuous variables). A comparison of behavioural response and stress level of low-risk primigravid women among experimental and control groups will be done using repeated measures of ANOVA. A comparison of childbirth experiences will be done using an independent t-test.\n\nData monitoring committee will be formed, which includes methodology experts, subject experts and statistician.\n\nApproval has been obtained from Head of the Unit - Obstetrical and Gynecological department and Medical Superintendent Kasturba Hospital Manipal for this study. Ethical clearance for the study was obtained from the Kasturba Medical College and Kasturba Hospital, Institutional Ethics committee Manipal (Reg No: ECR/146/1nst/KA/2013/RR-16). The trial is registered under the Clinical Trial Registry of India (CTRI/2019/08/020802). A written participant information sheet (Kamath, 2022b) will be given regarding the details of the study, and it will be explained to all low-risk primigravid women before enrolment to the study. Their involvement benefits and harm (none) as well as whom to contact in case of doubt will be explained to the participants. Written informed consent (Kamath, 2022c) from the participants will be obtained before involving them in study.\n\nConfidentiality of the research data collected will be maintained strictly as per the ethical standards. Only the research assistants and the researchers will have access to the participants’ data in the study. The data and results from this study may be presented at conferences and published in scientific journals without revealing the identity of the participants.\n\nDuring the study period, if any medical problem arises as a direct result of the study intervention, the researchers will be responsible for ensuring proper medical care is provided to the participant. Suppose a participant suffers from any injury (physical/mental) or disease/illness as result of the correctly implemented study procedures. In that case, the researcher is responsible for that unless the injury or disease relates to the mothers negligent or reckless act.\n\nThe time of sharing data is within one year after completion of the trial. The findings will be disseminated to participants, healthcare professionals, the public, and other relevant groups by attending scientific conferences and publishing in reputed journals.\n\n\nDiscussion\n\nLabour is a complex phenomenon in which the passenger (fetus) goes through the passage (pelvis) using the power (contractions) to deliver a healthy neonate (Michelle & Gayle, 2020). In order to accelerate the labour a series of interventional strategies has been adopted, and one among them is use of peanut ball during labour. Utilisation of peanut ball has proven effective in reducing cesarean section rates (Tussey CM, 2015 Jan), and even lowered the rates of instrumental births, including forceps and vacuum, and decreased the incidence of third- and fourth-degree perineal lacerations during vaginal deliveries. By widening the pelvic outlet to increase the progress of labour and thereby facilitate the descent of the fetal head.\n\nGlobally, the peanut balls are extensively utilised by midwives to deliver the women through vaginal mode, but in India it is underutilised. Jayasudha, et al. in the year 2021, did the quasi-experimental study in India, in which peanut ball use during the first stage of labour is explored (Jayasudha et al., 2021). The study lacks a controlled setting; the stakeholders consider methodologically rigorous research evidence to make a decision related to policymaking. Therefore, a clinical trial with block randomisation to investigate the effectiveness of peanut ball in improving maternal and neonatal outcomes is planned in the Indian context to make the appropriate clinical decision.\n\nFor the study the participant recruitment began in February 2020. To date, we have enrolled and randomised 550 low-risk primigravid mothers. Out of the total, 225 mothers were recruited to the intervention and 225 mothers were recruited for the control group. Mothers’ unacceptance to utilise the peanut ball during labour is a challenge faced during the initial part of the study. To encounter this, all the primigravid women at or after 37 weeks of gestation attending antenatal outpatient units were given informational material about the “Peanut ball use during labour”. This educational material has oriented and familiarised the mothers with peanut ball and its uses during labour which ultimately increased the rate of peanut ball acceptance and use during labour.\n\nAlong with that, coronavirus disease 2019 (COVID-19) imposed a lockdown, and after that, institutional restrictions to resume research activities to mitigate new cases of infection had made the study come to a halt. Recruitment for the study was stopped, and we lost participants for around five months. Due to this situation, we have fallen behind the recruitment timeline. To combat this, we utilised this duration to initiate a systematic review that will bring new evidence to implement peanut ball during labour.\n\nBesides these challenges, there are two possible limitations in this study, first, ascertainment bias, as the investigators are aware of the intervention the participants are receiving. In this project, the investigator and participants will know the allocation group for the women, as the woman will either utilise the peanut-ball or not, so they cannot be blinded. The strategy implemented to reduce the ascertainment bias is allocation concealment using SNOSEs by the labour room senior nurse on duty. The research assistant and research nurse carrying out data collection, data entry, and data analysis will be blinded to group allocation. The second limitation is compliance with the intervention during labour. To tackle this, a trained nurse will be present throughout the labour process and encourage and motivates the mothers to use the peanut ball continuously.\n\nDespite these possible limitations, this novel approach will be a promising intervention to promote labour progress and prevent unnecessary caesarean section and instrumental birth during the second stage of labour.\n\n\nConclusion\n\nIn this paper, researchers described the study design and the methodological approach adopted to evaluate the effectiveness of peanut ball during labour. Moreover, this study can be used as a guide to implement peanut ball use in the labour rooms of tertiary health care settings in the Indian context.\n\n\nData availability\n\nNo underlying data is associated with this article.\n\nThis project contains following extended data:\n\nFigshare: Demographic proforma.docx. https://doi.org/10.6084/m9.figshare.19122233 (Kamath, 2022a)\n\nFigshare: Participant Information Sheet.docx. https://doi.org/10.6084/m9.figshare.19122230 (Kamath, 2022b)\n\nFigshare: 18 Informed Consent English.doc https://doi.org/10.6084/m9.figshare.19122242 (Kamath, 2022c)\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: Screening Tool.docx. https://doi.org/10.6084/m9.figshare.19122239 (Kamath, 2022d)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Tool III modified partograph.docx. https://doi.org/10.6084/m9.figshare.19122236 (Kamath, 2022e)\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: Structured observational record on outcome of the labor.docx https://doi.org/10.6084/m9.figshare.19122227 (Kamath, 2022f)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReporting guidelines\n\nRepository: SPIRIT checklist for ‘Effectiveness of a peanut ball device during labour on maternal and neonatal outcomes: protocol for a randomised controlled trial’. https://figshare.com/s/5e8db2fc8dee7a7e06e5 (Kamath, 2022g)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAhmadpour P, Mohammad-Alizadeh-Charandabi, Doosti R, et al.: Use of the peanut ball during labour: A systematic review and meta-analysis. Nurs. Open. 2021; 8: 2345–2353. PubMed Abstract | Publisher Full Text\n\nAkyıldız D, Coban A, Gör Uslu F, et al.: Effects of Obstetric Interventions During Labor on Birth Process and Newborn Health. Florence Nightingale J. Nurs. 2021; 29(1): 9–21. PubMed Abstract | Publisher Full Text\n\nCalik KY, Karabulutlu O, Yavuz C: First do no harm - interventions during labor and maternal satisfaction: a descriptive cross-sectional study. BMC Pregnancy Childbirth. 2018; 18: 415. PubMed Abstract | Publisher Full Text\n\nGhasab SM, Kohan S, Firoozehchian F, et al.: Experience of Childbirth With Birth Ball: A Randomized Controlled Trial. Int. J. Women’s Health Reprod. Sci. 2019; 7(3): 301–305. Publisher Full Text\n\nGrenwik JM, Rosenthal E, Saccone G, et al.: Peanut ball for decreasing length of labor: A systematic review and meta-analysis of randomized controlled trials. Eur. J. Obstet. Gynecol. Reprod. Biol. 2019; 242: 159–165. Publisher Full Text\n\nHayes MHS, Patterson DG: Experimental development of the graphic rating method. Psychol. Bull. 1921; 18: 98–99.\n\nHickey L, Savage J: Effect of Peanut Ball and Position Changes in Women Laboring With an Epidural. Nurse Womens Health. 2019; 23(3): 245–252. PubMed Abstract | Publisher Full Text\n\nJayasudha A, Lakshmi GS, Priscilla K, et al.: Effectiveness of Peanut Ball On Outcome of First Stage of Labour Among Primi Mothers in Selected Tertiary Care Hospital, Coimbatore. International Journal of Research in Engineering, Science and Management. 2021; 4(3): 73–75.\n\nKamath P: Tool III modified partograph.docx. figshare. Figure. 2022a. Publisher Full Text\n\nKamath P: Participant Information Sheet.docx. figshare. Dataset. 2022b. Publisher Full Text\n\nKamath P: 18 Informed Consent English.doc. figshare. Dataset. 2022c. Publisher Full Text\n\nKamath P: Screening Tool.docx. figshare. Dataset. 2022d. Publisher Full Text\n\nKamath P: Tool III modified partograph.docx. figshare. Figure. 2022e. Publisher Full Text\n\nKamath P: Structured observational record on outcome of the labor.docx. figshare. Dataset. 2022f. Publisher Full Text\n\nKamath P: SPIRIT checklist for ‘Effectiveness of a peanut ball device during labour on maternal and neonatal outcomes: protocol for a randomised controlled trial’.2022g.Reference Source\n\nKarkada EC, Noronha JA, Dsouza SR: Preparing Primigravid Women for Childbirth: Behavioral Responses to Labour Pain and Outcome of Labour. Manglore, Karnataka, India:International Journal of Nursing Education Scholarship;2010; vol. 2.\n\nLawrence A, Lewis L, Hofmeyr GJ, et al.: Maternal positions and mobility during first stage labour. Cochrane Database Syst. Rev. 2013, Aug 20. PubMed Abstract | Publisher Full Text\n\nMichelle LM, Gayle MH: Labor and Delivery Nursing: A Guide to Evidence-Based Practice. (2nd ed.).Springer publishing company;2020. Publisher Full Text\n\nMirzakhani K, Hejazinia Z, Golmakani N, et al.: The Effect of Birth Ball Exercises during Pregnancy on Mode of Delivery in Primiparous Women. J. Midwifery Reprod. Health. 2015; 3(1): 269–275. Publisher Full Text\n\nOutland L, Alvarado Y: Preventing cesareans with peanut ball use. J. Nurs. Educ. Pract. 2019; 10(1): 107–112. Publisher Full Text\n\nRoth C, Dent SA, Parfitt SE, et al.: Randomized Controlled Trial of Use of the Peanut Ball During Labor. MCN Am. J. Matern. Child Nurs. 2016; 41(3): 140–146. PubMed Abstract | Publisher Full Text\n\nSally Hopewell MC:2008, January 22. CONSORT for reporting randomised trials in journal and conference abstracts. Plos Medicine, Group. Lancet. 2008 Jan 26; 371(9609): 281–283. PubMed Abstract | Publisher Full Text\n\nStjernholm YV, Nyberg A, Cardell M, et al.: Circulating maternal cortisol levels during vaginal delivery and elective cesarean section. Arch. Gynecol. Obstet. 2016; 294(2): 267–271. PubMed Abstract | Publisher Full Text\n\nTussey CM, Botsios E, Gerkin RD, et al.: Reducing Length of Labor and Cesarean Surgery Rate Using a Peanut Ball for Women Laboring With an Epidural. J. Perinat. Educ. 2015; 24(1): 16–24. Publisher Full Text\n\nVaijayanthimala M: Effecttivenness of Birthball Usage During Labour on Pain and Child Birth Experience Among Primi Parturient Mothers: A Randomized Interventional Study.July 2014. Publisher Full Text\n\nZwelling E: Overcoming the Challenges: Maternal Movement and Positioning to Facilitate Labor Progress. MCN Am. J. Matern. Child Nurs. 2010; 35(2): 72–78. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "150084",
"date": "17 Oct 2022",
"name": "Vidya Seshan",
"expertise": [
"Reviewer Expertise women's Health",
"Maternal Health",
"teaching stratergies"
],
"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: Effectiveness of a peanut ball device during labor on maternal and neonatal outcomes: protocol for a randomized controlled trial This is a study to see the effect of peanut ball devices during labor. It’s a proposal written by the researcher to the journal. Well-structured methodology. Needs some minor revisions:\nThe reference style is not followed consistently in the introduction.\n\nThe introduction is more of a literature review than an explanation related to the study. The researcher has quoted the funding under study setting and population; this is not required to be in this section, it should be written at the end related to funding.\n\nThe setting is not explained well. Only one sentence about the settings. Needs more explanation of the study setting for the readers to understand. Eligibility criteria and exclusion criteria need a separate heading. The discussion and conclusion are very shallow.\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": "8953",
"date": "04 Nov 2022",
"name": "Pratibha Kamath",
"role": "Author Response",
"response": "Dear Madam, Thank you very much for reviewing the article and for your suggestions, I will incorporate and upload again. With Warm Regards Pratibha PI of the project"
}
]
},
{
"id": "153356",
"date": "27 Oct 2022",
"name": "Sabitha Nayak",
"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 is an interventional/RCT study where the investigators could find out the effectiveness of peanut ball device during labour on maternal and neonatal outcomes is a novel study in Indian settings. The study protocol seems good enough with clear cut objectives and appropriate methodology as mentioned. The tools used are also appropriate. There seems to be no harm on the mother or the fetus. The study results may be of help to generalise as the sample size is large. It can be implemented as a clinical practice by all the health professionals mainly midwives and obstetricians working in the labour unit.\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": "8952",
"date": "04 Nov 2022",
"name": "Pratibha Kamath",
"role": "Author Response",
"response": "Dear Madam, Thank you so much for reviewing. With Warm Regards Pratibha PI of the project"
}
]
}
] | 1
|
https://f1000research.com/articles/11-717
|
https://f1000research.com/articles/10-635/v1
|
22 Jul 21
|
{
"type": "Research Article",
"title": "Comparison of mobile health education messages verses face-to-face consultation for weight reduction among overweight female adolescents in Thailand",
"authors": [
"Supim Wongtongtair",
"Sompoch Iamsupasit",
"Ratana Somrongthong",
"Ramesh Kumar",
"Khemika Yamarat",
"Sompoch Iamsupasit",
"Ratana Somrongthong",
"Ramesh Kumar",
"Khemika Yamarat"
],
"abstract": "Background: Obesity is considered a significant public health problem in Thailand. This study was conducted to compare the impact of mobile health education messages verses face-to-face consultation on weight reduction among overweight female university students. Methods: This comparative cross-sectional study comprised three groups: a control group, a group receiving mobile health education, and a group receiving face-to-face consultation. Each group contained 26 participants taking part over a period of 12 weeks, with a 12-week follow-up thereafter. The data analysis used two-way repeated measures ANOVA with least significant difference testing. The study was ethically approved at Chulalongkorn University, Thailand. Results: The results revealed that the group receiving mobile health education had the lowest average body mass index and waist–hip ratio after intervention (p < 0.05). In addition, both intervention groups significantly improved their health belief, social support, and health behavior scores in comparison to the control group (p < 0.001). The results show that the average scores for social support for eating and exercise at baseline were significantly lower than at post-intervention or follow-up (p < 0.001). In addition, the results of both aspects of social support showed that the average social support score at post-intervention was significantly higher than at follow-up. Furthermore, the health behavior score measured post-intervention was higher than at follow-up. There was a statistically significant difference in average metabolism during physical activity (p < 0.001) but no statistical difference in average eating behavior score. Conclusion: The study found that the use of mobile health education to deliver health programs facilitates communication between the healthcare provider and individual, and can empower adolescent females in their pursuit of weight loss by improving their attitudes and knowledge, leading to better health behavior.",
"keywords": [
"Electronic health education",
"Facebook",
"health education",
"health belief model",
"social support",
"obesity",
"Thailand",
"health behaviors"
],
"content": "Introduction\n\nBeing overweight or obese is known to be an important factor in many serious health issues, and approximately 10% of global health expenditure is spent on fighting obesity.1,2 Nearly one-third of Thai university students are reported to be overweight, and Thailand was ranked second highest for obesity in the Southeast Asia region in 2013.3 Studies have proposed face-to-face consultation interventions for weight loss among obese adolescents across the globe based on the health belief model (HBM) and social support theories in different parts of the globe.4,5 Such intervention requires significant funding and, over the last decade, the Thai government spent around five billion Baht on the health problem caused by obesity6; face-to-face activity spent more than 50% of their budget for food expenditure. Two particularly effective programs aimed at controlling obesity involved sending informative health education messages to smartphones.7,8 The younger section of the population, especially students, regularly use smartphones to interact on social networks, such as Facebook.9–11 It has been demonstrated that using social networks can be a useful approach in research and can strengthen disease prevention interventions and health promotion programs for control of weight and obesity.12 Mobile health education (MHE) is a simple means of supporting interactions with an individual and represents a cost-effective intervention approach. Thus, MHE has been used as tool to promote better health.13,14 The HBM states that the perception of a personal health behavior influences the consequences of a particular health problem.15 The HBM has been used to explain and predict preventative health behavior that can influence an individual’s decision making, which can be measured.16 Social support networks are present in relationships involving healthcare behaviors, especially among groups of women. It has been shown that women are more satisfied if their networks are wide, whereas men are more satisfied if their networks are small.17\n\nMHE could positively influence an individual's behavior based on HBM and social support theory. Therefore, this study used MHE to deliver a weight management program to adolescent females in Thailand and compared this method with a face-to-face health education (FHE) activity.\n\n\nMethods\n\nWritten informed consent was obtained from participants prior to the start of the study. Ethical approval was granted by the Ethics Review Committee for Research Involving Human Subjects of Chulalongkorn University, Thailand (COA No. 142.1/60).\n\nThis was a comparative cross-sectional pre–post study with three groups: face-to-face consultation (FHE), mobile health education message (MHE) and an observation (control) group.\n\nParticipants were invited through open advertisement on faculty boards at Srinakharinwirot University, Thailand and were screened according to the inclusion and exclusion criteria. Participants in the two test groups received a health education in the form of a weight management program either via Facebook or through face-to-face consultation; the control group received neither and was only observed (Figure 1). A sample size of 90 (including 20% drop out) was calculated with G*Power,18 using a power of 0.80, alpha value of 0.05, and a correlation between pre- and post-intervention of 0.5 was assumed. Each group was allocated 30 participants through simple random method by allocating an equal number in each group. Four participants from each group were unable to complete the end line assessment due to their personnel reasons. However; the response rate was 87% in this study. Inclusion criteria was the faculty members from one of three faculties at Srinakharinwirot University with BMI ≥ 23 and < 25; and for the Facebook group only they also had to have access to Facebook at least once per day. Those were excluded from the study who were disabled, physically inactive, had an underlying disease that could cause abnormal weight loss or gain; or (3) had participated in any other weight management program/trial within the previous six months.\n\nData collection\n\nThe dependent variables of this study were weight, body mass index (BMI, calculated as the weight [kilograms-kg] of a participant divided by the square of their height [meters-m]), waist–hip ratio (WHR, measured at the midpoint between the lower margin of the least palpable rib and the top of the iliac crest, using a stretch resistant tape that provided a constant 100 g tension), health beliefs, social support, and health behavior (eating and physical activity). Health beliefs were measured by using the HBM questionnaire,19 which contains six modules, and social support was measured with a questionnaire20 containing two modules. Physical activity was assessed by using the Global Physical Activity Questionnaire (GPAQ) developed by the World Health Organization (WHO) which comprised three domains: activity at work, travel to and from places, and recreational activities. The results describing participants’ physical activity were expressed as metabolic equivalents (METs), which reflected the intensity of physical activities as MET-minutes per day,21 and eating behavior was recorded through a self-evaluation questionnaire on eating behavior developed by the Department of Health (Thailand).22\n\nThe weight management program focused on weight loss. It presented information via an infographic message because it was easier to understand and recognize.23 The information provided was about being overweight, diet and exercise for weight loss, the severity of obesity, and the benefits of losing weight as described by the Thai Health Promotion Foundation.24 In the MHE group, infographics were posted to Facebook once a day, whereas question and answer activities took place biweekly via private messaging in Facebook for 12 weeks. In the FHE group, participants received a health information booklet and took part in biweekly group activity that included an individual test and an interactive discussion, for 12 weeks. The third group (control) was just observed and compared with the MHE and FHE groups at the end of 12 weeks and again at the total 24 week study period by all assessment (weight, BMI, WHR and questionnaire).\n\nStatistical analysis\n\nTwo-way repeated measures ANOVA tests and Fisher’s least significant difference (LSD) post hoc tests were used to analyze the data. Data was expressed as mean ± SD; statistical significance was considered at p < 0.05.\n\n\nResults\n\nThe average age of participants was 18.23 ± 0.42 years in the control group, 18.17 ± 0.37 years in the MHE group, and 18.20 ± 0.4 years in the FHE group. The baseline values for all variables, including weight, BMI, WHR, the six HBM modules, two social support modules, and two health behavior modules, are summarized in Table 1.\n\nAfter the 12 weeks intervention period, all variables were tested for interaction between group and time. When a variable showed p < 0.05 then that variable had to test pairwise as described in Table 2. The results from the two-way repeated ANOVA test showed statistically significant differences between the intervention and control groups, within group and the interaction effect taken at the start and end of the study.\n\n* The mean difference is significant at the 0.05 level.\n\nAccording to the analysis, there were no significant differences between groups for weight and eating behavior. Therefore, pairwise testing was conducted for all other variables (BMI, WHR, all HBM modules, both social support modules, and MET physical activity; Table 3).\n\n* The mean difference is significant at the 0.05 level.\n\nFrom the pairwise group analysis, the mean BMI and WHR in the MHE group were significantly lower than the control group. There was no significant difference in weight change between groups, but BMI and WHR showed significant differences in each group. The pairwise results revealed that the BMI of the control group was significantly higher than that of the MHE group but lower than the FHE group with no statistically significance. The average BMI of the MHE group was significantly lower than the average BMI of the FHE group. Whereas the average WHR of the control group was significantly higher than the MHE group and also higher than the FHE group, no significant difference was found. Moreover, the average WHR of the FHE group was higher than the MHE group but not significance.\n\nThe pairwise analysis of the HBM modules showed significantly different average scores between the control group and both intervention groups, with the exception of HBM 2 (perceived benefits of weight loss), which showed no significant difference between the control and MHE groups but did show a significant difference between the MHE and FHE groups (p < 0.001). The average scores for the HBM 1, HBM 3, HBM 4, HBM 5 (eat) and HBM 5 (ex) modules of the MHE and FHE groups were significantly higher than those of the control group. However, the average scores on the HBM 1, HBM 4 and HBM 5 (ex) modules for the FHE group were higher than those of the MHE group, but not statistically significantly so. Meanwhile, the average scores on the HBM 2, modules for the MHE group was significantly higher than those of the FHE group.\n\nThe average scores of social support exercise modules of the intervention groups were significantly higher than the average score from the control group. While the average score of social support eating module showed significance higher than control group only in MHH group. The MHE group showed a significantly higher score of social support (eating behavior) than the FHE group. Whereas the social support (exercise behavior) score of the FHE group was higher than that of the MHE group, it was not statistically different. The pairwise analysis between groups revealed that the average MET scores of both intervention groups were significantly higher than that of the control group. The MHE group averaged a higher MET score than the FHE group, but this difference was not statistically significant.\n\nWhen the differences between time points were analyzed, WHR was the only variable that was not statistically significantly different across the study period. Therefore, pairwise testing was conducted for all other variables (weight, BMI, all HBM modules, both social support modules and both health behavior modules; Table 4).\n\nWhen comparing the results at different points in the study, the analysis showed that average weight and BMI measured at baseline were significantly higher than at post-intervention and follow-up, but there were no significant differences between post-intervention and follow-up. There were no statistically significant differences in average WHR between baseline measurements and either post-intervention or follow-up.\n\nA comparison of the HBM scores at different time points revealed that the baseline of all HBM modules differed significantly between the intervention period and the follow-up period (p < 0.001). However, there was no significant difference between the end of the intervention period and the follow-up period, except for HBM 2.\n\nThe pairwise analysis of the three study phases (baseline, post-intervention and follow-up) showed that the average scores of HBM 1, HBM 4, HBM 5 (eat), and HBM 5 (ex) measured at baseline were significantly lower than those measured post-intervention and at follow-up. Although the average score of the HBM 2 module measured at baseline was significantly lower than the score post-intervention, it was significantly higher than the score at follow-up. The average score of HBM 3 at baseline was significantly higher than post-intervention and at follow-up. HBM 2 was only HBM module for which the post-intervention score was significantly higher than at follow-up, whereas the other HBM modules showed no significant differences between post-intervention and follow-up.\n\nA pairwise comparison of social support at the different study points showed that the average scores for social support for eating and exercise at baseline were significantly lower than at post-intervention or follow-up (p < 0.001). In addition, the results of both social support modules showed that the average scores post-intervention were significantly higher than at follow-up. The pairwise comparison of study points revealed that the average MET and average eating behavior scores at baseline were significantly lower than post-intervention or at follow-up. Moreover, the average MET and average eating behavior scores measured post-intervention were higher than at follow-up. There was a statistical difference in average MET (p = 0.039) but no statistical difference in average eating behavior score.\n\n\nDiscussion\n\nAs expected, the baseline characteristics among the three groups in this study were similar. The average weight of both intervention groups decreased after both the initial period and at follow-up. This is consistent with the findings of previous studies, which found that social media can encourage people to lose weight through social interactions on online notice boards or forums.25,26 Likewise, BMIs at post-intervention and follow-up were significantly lower than at baseline, a finding consistent with previous studies.27,28 Pairwise comparisons of the three groups revealed that the MHE group had the highest average scores for perceived benefits, barriers, and self-efficacy in dietary life. The FHE group showed the highest score in perceived threat, cues to action, and self-efficacy in exercise. These findings are consistent with those of a previous study, which found that print or electronic media (an external cue) impacted BMI through the HBM (specifically, perceived benefit, perceived barriers, and perceived threat or severity).29\n\nThe FHE group had the highest average score for the perceived threat of being overweight, cues to action for weight loss, and perceived self-efficacy in exercise. These are modules that require motivation to participate in activities such as face-to-face meetings (e.g., counseling) or planned exercise with another person.30 In addition, the perceived threats for adolescents, is about acceptance by their peers, and the participants expressed higher satisfaction if they participated in activities with friends. Previous studies found that female high-school and college students who had a role within their team changed their behavior when they perceived a threat or severity.29,31\n\nSocial support was consistent with the results of the HBM in the self-efficacy module; the MHE group had a lower score in the exercise module but a higher score for diet behavior. There was a significant difference in physical activity between groups because behavior modification is different from awareness or belief. Although awareness occurred, behavior might not have changed. This is consistent with previous research that found that online social support had a much greater influence on eating behavior than for exercise behavior.32\n\nHowever, the results revealed that both intervention groups showed significantly higher average MET scores than the control group. When considering the interaction between the time point of HBM, social support, and health behavior, most of the variables had similar average scores post-intervention, which were higher than baseline and at follow-up. This corresponds well to the findings of previous studies that found that intervention via EHE serves as information support, which is needed to be a successful weight loss program.32 In addition, a previous study revealed that participants who took part in a campaign of physical activity based on self-efficacy via EHE showed significant increasing medium MET scores compared with other groups that received printed brochures.33 The findings of another study revealed that motivation decreased when intervention ceased, resulting in reduced friend support and confidence to action because participants lack the ability to share and be supported by friends.34\n\nSome participants were still in growing up age; therefore, their height has an effect on BMI which could be stable or decrease despite of no change in weight and health behavior. Besides, the intervention has short-term effects because the follow up showed a trend of decreasing health belief, social support, and health behavior but showed an increasing trend in anthropometric assessment. Hence this study cannot be generalized in the whole country due to the limited nature of the population involved.\n\n\nConclusions\n\nThe data suggests that mobile health education is an effective approach for improving behavior towards weight reduction among obese adolescent females studying at Thai universities. Especially, in a condition where all activities must be based on principles of social distancing, using online social network sites to access activities or programs can stimulate feelings by inducing personal satisfaction. In addition, the program or information provided online should encourage participants to participate frequently in order to promote social support similar to what they receive from face-to-face activities.\n\n\nData availability\n\nOpen Science Framework. Comparison of mobile health education messages verses face-to-face consultation for weight reduction among overweight female adolescents in Thailand. OSF 2021. https://doi.org/10.17605/OSF.IO/4KPJ9.35\n\nThis project contains the following underlying data:\n\n• Source data for all table. (Raw data of each table)\n\n• Raw data Supim.xlsx (Deidentified raw data in excel file pattern)\n\n• Raw data Supim.sav (Deidentified raw data in SPSS file pattern)\n\nOpen Science Framework. Comparison of mobile health education messages verses face-to-face consultation for weight reduction among overweight female adolescents in Thailand. OSF 2021. https://doi.org/10.17605/OSF.IO/4KPJ9.35\n\nThis project contains the following extended data:\n\n• Questionnaire Supim.pdf. (the questionnaire used in this study).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReporting guidelines\n\nOpen Science Framework. STROBE checklist for ‘Comparison of mobile health education messages verses face-to-face consultation for weight reduction among overweight female adolescents in Thailand’. https://doi.org/10.17605/OSF.IO/4KPJ9.35\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Competing interests\n\n\n\nNo competing interests were disclosed.\n\n\nGrant information\n\nThis work was supported by the 100th Anniversary Chulalongkorn University Thailand Fund for Doctoral Scholarship [21/2556]. RK acknowledges support from the Rachadapisek Sompote Fund for Postdoctoral Fellowship, Chulalongkorn University, Thailand.\n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\n\nReferences\n\nWithrow D, Alter DA: The economic burden of obesity worldwide: a systematic review of the direct costs of obesity. Obes Rev. 2011; 12(2): 131–141. PubMed Abstract | Publisher Full Text\n\nThiabpho C, Changbumrung S, Soonthornworasiri N, et al.: Intensive lifestyle modification program on weight loss and metabolic syndrome risk reduction among obese women in rural areas of Thailand. J. Health Res. 2018; 32(3): 203–216. Publisher Full Text\n\nNg M, Fleming T, Robinson M, et al.: Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet. 2014; 384(9945): 766–781. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSuksanan P, Choptong S, Pranprawit A: Effects of a weight reduction program with application of self-regulations and social support among village health volunteers. Southern College Network J Nurs Public Health. 2015; 3(1): 46–59.\n\nKliemann N, Vickerstaff V, Croker H, et al.: The role of self-regulatory skills and automaticity on the effectiveness of a brief weight loss habit-based intervention: secondary analysis of the 10 top tips randomised trial. Int J Behav Nutr Phys Act. 2017 Dec 1; 14(1): 119. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHealth Systems Research Institute (Thailand): NCD crisis. HSRI forum. 2014; 3(1): 1–16. Reference Source\n\nCasey M, Hayes PS, Glynn F, et al.: Patients’ experiences of using a smartphone application to increase physical activity: the SMART MOVE qualitative study in primary care. Br J Gen Pract. 2014; 64(625): e500–e508. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJeon E, Park H: Development of a smartphone application for clinical-guideline-based obesity management. Healthc Inform Res. 2015; 21(1): 10–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChobdamrongtham N, Adisornprasert W, Yansomboon S: The influence of advertising on online social network to consumer response process. Srinakharinwirot Research and Development (Journal of Humanities and Social Sciences). 2011; 3(6): 12–26. Reference Source\n\nPhillips BJ, Grosch M, Laosinchai P: Mobile media usage by undergraduates and implications for m-learning instructional design. Int J Mobile Learn Organisat. 2014; 1, 8(1): 1–15. Publisher Full Text\n\nKheokao J, Yingrengreung S, Siriwanij W, et al.: Media use of nursing students in Thailand. 2015 4th International Symposium on Emerging Trends and Technologies in Libraries and Information Services; 2015, January 6-8; Bangkok. Thailand; 2015. p. 123–127. Publisher Full Text\n\nKoehly LM, Loscalzo A: Peer reviewed: Adolescent obesity and social networks. Preventing chronic disease. 2009 Jul; 6(3): 1–8. Reference Source\n\nKoehly LM, Loscalzo A: Peer reviewed: Adolescent obesity and social networks. Prev Chronic Dis. 2009 [cite 2017 March 8]; 6(3). Reference Source\n\nPark BK, Nahm ES, Rogers VE: Development of a teen-friendly health education program on Facebook: Lessons learned. J. Pediatr. Health Care. 2016; 30(3): 197–207. PubMed Abstract | Publisher Full Text\n\nZheng Y, Klem ML, Sereika SM, et al.: Self-weighing in weight management: A systematic literature review. Obes. 2015; 23(2): 256–265. PubMed Abstract | Publisher Full Text\n\nBandura A: Self-efficacy. In: Ramachaudran VS (Ed.), Encyclopedia of human behavior New York: Academic Press; 1994; Vol. 4. . p. 71–81.\n\nKaplan KRM: Social Support and Social Health. In: Sarason IG, Sarason BR (eds) Social Support: Theory, Research and Applications. NATO ASI Series (D: Behavioural and Social Sciences). Dordrecht: Springer; 1985: vol 24. . Publisher Full Text\n\nFaul F, Erdfelder E, Buchner A, et al.: Statistical power analyses using G* Power 3.1: Tests for correlation and regression analyses. Behav Res Methods. 2009 Nov 1; 41(4): 1149–1160. PubMed Abstract | Publisher Full Text\n\nPark DY: Utilizing the Health Belief Model to predicting female middle school students' behavioral intention of weight reduction by weight status. Nutr Res Pract. 2011; 5(4): 337–348. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSallis JF, Grossman RM, Pinski RB, et al.: The development of scales to measure social support for diet and exercise behaviors. Prev. Med. 1987; 16(6): 825–836. PubMed Abstract | Publisher Full Text\n\nArmstrong T, Bull F: Development of the world health organization global physical activity questionnaire (GPAQ). J. Public Health. 2006; 14(2): 66–70. Publisher Full Text\n\nKitvorapat W: Guide to conquer the obese and remove the belle (6th ed.), Self-assessment of eating behaviors.Nonthaburi: Department of Health, Ministry of Public Health Thailand; 2013. p. 26–27. Reference Source\n\nGrady CL, McIntosh AR, Rajah MN, et al.: Neural correlates of the episodic encoding of pictures and words. PNAS. 1998; 95(5): 2703–2708. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThai Health Promotion Foundation: 2015 [cite 2016 Feb 8]; Reduce Belly, Reduce disease: The guideline. Bangkok: Thai Health Promotion Foundation. Reference Source\n\nHwang OK, Ottenbacher AJ, Green AJ, et al.: Social support in an Internet weight loss community. Int. J. Med. Inform. 2010; 79(1): 5–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nReynolds M, Driver S, Bennett M: The social network–using social media to support individuals with traumatic brain injury participating in a pilot study weight-loss program. Brain Inj. 2018; 32(12): 1450–1454. PubMed Abstract | Publisher Full Text\n\nZheng Y, Klem ML, Sereika SM, et al.: Self-weighing in weight management: A systematic literature review. Obes. 2015; 23(2): 256–265. PubMed Abstract | Publisher Full Text\n\nMohorko N, Černelič-Bizjak M, Poklar-Vatovec T, et al.: Weight loss, improved physical performance, cognitive function, eating behavior, and metabolic profile in a 12-week ketogenic diet in obese adults. Nutr Res. 2019; 62: 64–77. PubMed Abstract | Publisher Full Text\n\nMcArthur LH, Riggs A, Uribe F, et al.: Health belief model offers opportunities for designing weight management interventions for college students. J Nutr Educ Behav. 2018; 50(5): 485–493. PubMed Abstract | Publisher Full Text\n\nDas BM, Evans EM: Understanding weight management perceptions in first-year college students using the health belief model. J Am Coll Health. 2014 Oct 3; 62(7): 488–497. PubMed Abstract | Publisher Full Text\n\nLagampan S, Lapvongwatana P, Tharapan C, et al.: Health belief model teaching program for thalassemia education in high school students. Chula Med J. 2004 [cite 2018 March 31]; 48(11): 725–735. Reference Source\n\nBallantine PW, Stephenson RJ: Help me, I'm fat! Social support in online weight loss networks. J Consum Behav. 2011 Nov; 10(6): 332–337. Publisher Full Text\n\nCheevasuntorn K, Watanapa B, Funilkul S, et al.: Factors influencing teenagers behavior on posting and sharing messages via EHE. 2nd International Conference on Information Technology. Bangkok, Thailand: 2017, November 2-3; pp. 1–4. Publisher Full Text\n\nProchaska JO, DiClemente CC: Transtheoretical therapy: toward a more integrative model of change. Psychol Psychother. 1982; 19(3): 276. Publisher Full Text\n\nWongtongtair S: Comparison of mobile health education messages verses face-to-face consultation for weight reduction among overweight female adolescents in Thailand. OSF. 2021. Publisher Full Text"
}
|
[
{
"id": "90391",
"date": "18 Aug 2021",
"name": "Umer Farooq",
"expertise": [
"Reviewer Expertise Epidemiology",
"Health Statistics",
"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\nThe study covers an important topic and provides evidence based results regarding an important intervention.\n\nMost of the references used are more than 6 years old. The author may look for some more studies recently done and include them in the write up.\n\nThis is a cross sectional study. Why it was not planned as an experimental study? The researchers are doing the intervention then why wasn't it planned as an experimental study?\n\nThe researchers have done a good analysis and have explained the results well as of a cross sectional study.\n\nThe external validity of the study is very limited as it applies only to the girls of that university.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "8131",
"date": "29 Apr 2022",
"name": "supim Wongtongtair",
"role": "Author Response",
"response": "Reviewer: The study covers an important topic and provides evidence based results regarding an important intervention. Response: Thank you for understanding our efforts. Reviewer: Most of the references used are more than 6 years old. The author may look for some more studies recently done and include them in the write up. Response: I agree for this and adding some recently study already but can only change some references because this work was done in 2018. Therefore some data which used as rational or theory of the study cannot changed. However, after this editing reference more than 75% will be in period of 2017-2021. Reviewer: This is a cross sectional study. Why it was not planned as an experimental study? The researchers are doing the intervention then why wasn't it planned as an experimental study? Response: This issue is in line with our concern too. Because 3 groups of this study was done in same university. Therefore we try to decrease contamination by specify faculty which less likely to encounter each other. However, we choose faculties where students have similar academic and social characteristics. For the reasons mentioned above, we therefore use the cross sectional design with pre –post study. Reviewer: The researchers have done a good analysis and have explained the results well as of a cross sectional study. Response: Thank you for the compliment. Reviewer: The external validity of the study is very limited as it applies only to the girls of that university. Response: It's an issue that we used to be afraid of. However, this study is based on HBM and social support principle which the universal theory to use for weight management in adolescent. Moreover, our results were also consistent with similar previous research as you seen in discussion."
},
{
"c_id": "8445",
"date": "30 Jun 2022",
"name": "supim Wongtongtair",
"role": "Author Response",
"response": "Reviewer: The study covers an important topic and provides evidence based results regarding an important intervention. Response: Thank you for understanding our efforts. Reviewer: Most of the references used are more than 6 years old. The author may look for some more studies recently done and include them in the write up. Response: I agree for this and adding some recently study already but can only change some references because this work was done in 2018. Therefore some data which used as rational or theory of the study cannot changed. However, after this editing reference more than 75% will be in period of 2017-2021. Reviewer: This is a cross sectional study. Why it was not planned as an experimental study? The researchers are doing the intervention then why wasn't it planned as an experimental study? Response: This issue is in line with our concern too. Because 3 groups of this study was done in same university. Therefore we try to decrease contamination by specify faculty which less likely to encounter each other. However, we choose faculties where students have similar academic and social characteristics. For the reasons mentioned above, we therefore use the cross sectional design with pre–post study. Reviewer: The researchers have done a good analysis and have explained the results well as of a cross sectional study. Response: Thank you for the compliment. Reviewer: The external validity of the study is very limited as it applies only to the girls of that university. Response: It's an issue that we used to be afraid of. However, this study is based on HBM and social support principle which the universal theory to use for weight management in adolescent. Moreover, our results were also consistent with similar previous research as you seen in discussion."
}
]
},
{
"id": "150532",
"date": "26 Sep 2022",
"name": "Kulnipa Kittisakmontri",
"expertise": [
"Reviewer Expertise Pediatric 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\nThe findings of this study are interesting, but the manuscript need major revision to meet the standard requirement of scientific research.\n\nSubstantial considerations:\n1) Study design\nIt was unusual to call a cross-sectional study in case that some interventions were given to the study population.\n\nI wonder whether simple randomization by lottery method adequately allocated participants in each groups? If the answer is yes, why did the authors called the study RCT? It was very confusing when the manuscript mentioned this study as the 'cross-sectional study' but the flow chart showed that participants were allocated in each group by simple randomization.\n2) Sample size calculation\nI didn't understand the method used to determine sample size. What did the correlation pre- and post mentioned by authors for example, correlation of body weight or BMI or behavioral scores? More importantly, it needed a reference for the number used in calculation - where did the correlation of 0.5 come from? It was very unclear to me how this formula was used to determine sample size could relate to main research questions of this study.\n3) Study population\nThe inclusion criteria were unclear. Which were the three faculties that authors had mentioned? Was there any selection bias if the authors had selected the MHE from a population who frequently used the Facebook than others? It might be assumed that the frequent users of Facebook would use variety of Social media platforms that could expose them to more knowledge of weight loss information or motivation from famous actress or models they admired. At least this issue should be discussed as a limitation of the study.\n4) Methodology\nThe authors should describe more details of the interventions and questionnaires used in this study. The validation of those questionnaires should be mentioned to confirm their accuracy and reproducibility.\n\n5) Results\nIn general, I suggest the authors to seek advices from the medical statistician for the presentation of research findings. I was very confuse with the presentation of the results. All tables should stand alone with clear messages. For those figures and tables, the titles and all abbreviations should be clarified. I suggest the authors should extensively revise all figure and tables. Moreover, the reported numbers should be consistent with specific decimal. If two decimal was used, the authors should write all reported number in two decimal.\n\nTable 2 - it was very unclear to me what the authors would like to present. The authors should clarify what time point that those results came from (at post intervention?). Basically, I think table 2 and 3 could be integrated into one table when the authors showed the results of all variables divided by groups and showed the post hoc p-value of each pairs. If the post hoc analysis show significant results, thus it can assume the significant p-value of the repeated ANOVA.\n\nTable 4 - I didn't know the population of this analysis whether only intervention groups were counted or all participants were included.\n\n6) Discussion\nThe discussion section should be intensively organized. I found some repetition of some sentences mentioning the same statement. Furthermore, there were many limitations that should be mentioned, for example, as I said before the selection bias of the MHE group, the nature of the study especially in case the authors were not sure with their random allocation, thus the authors cannot infer the causality between the interventions and outcomes because the study was not the RCT.\n\n7) Abstract\nThe sentences mentioning that 'the group received MHE had the lowest BMI and WHR' shouldn't be included in the abstract as these could lead to misunderstanding that the MHE groups clearly had benefit from the intervention while the results presented in the manuscript did not demonstrate that.\nMinor concerns:\nPlease check repetition of the sentences and typos carefully.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8932",
"date": "21 Nov 2022",
"name": "supim Wongtongtair",
"role": "Author Response",
"response": "Study design It was unusual to call a cross-sectional study in case that some interventions were given to the study population. I wonder whether simple randomization by lottery method adequately allocated participants in each groups? If the answer is yes, why did the authors called the study RCT? It was very confusing when the manuscript mentioned this study as the 'cross-sectional study' but the flow chart showed that participants were allocated in each group by simple randomization. Response: This was Quasi-experimental study design, We have corrected this mistake. 2) Sample size calculation I didn't understand the method used to determine sample size. What did the correlation pre- and post mentioned by authors for example, correlation of body weight or BMI or behavioral scores? More importantly, it needed a reference for the number used in calculation - where did the correlation of 0.5 come from? It was very unclear to me how this formula was used to determine sample size could relate to main research questions of this study. Response: We assumed 50% difference after the intervention, as we were unable to find out the exact difference in score in other interventional studies. Moreover, we have revised this sentence for more clarity. 3) Study population The inclusion criteria were unclear. Which were the three faculties that authors had mentioned? Was there any selection bias if the authors had selected the MHE from a population who frequently used the Facebook than others? It might be assumed that the frequent users of Facebook would use variety of Social media platforms that could expose them to more knowledge of weight loss information or motivation from famous actress or models they admired. At least this issue should be discussed as a limitation of the study. Response: We have included this in the limitation as per the guidance. 4) Methodology The authors should describe more details of the interventions and questionnaires used in this study. The validation of those questionnaires should be mentioned to confirm their accuracy and reproducibility. Response: We have added this information in method section as per the guidance. 5) Results In general, I suggest the authors to seek advices from the medical statistician for the presentation of research findings. I was very confuse with the presentation of the results. All tables should stand alone with clear messages. For those figures and tables, the titles and all abbreviations should be clarified. I suggest the authors should extensively revise all figure and tables. Moreover, the reported numbers should be consistent with specific decimal. If two decimal was used, the authors should write all reported number in two decimal. Response: We have corrected as per the guidance Table 2 - it was very unclear to me what the authors would like to present. The authors should clarify what time point that those results came from (at post intervention?). Basically, I think table 2 and 3 could be integrated into one table when the authors showed the results of all variables divided by groups and showed the post hoc p-value of each pairs. If the post hoc analysis show significant results, thus it can assume the significant p-value of the repeated ANOVA. Response: We have merged the table 2 as per the guidance. Table 4 - I didn't know the population of this analysis whether only intervention groups were counted or all participants were included. Response: We have included final 26 participants in the analysis. 4 from each group who did not complete the intervention were excluded in the analysis. 6) Discussion The discussion section should be intensively organized. I found some repetition of some sentences mentioning the same statement. Furthermore, there were many limitations that should be mentioned, for example, as I said before the selection bias of the MHE group, the nature of the study especially in case the authors were not sure with their random allocation, thus the authors cannot infer the causality between the interventions and outcomes because the study was not the RCT. Response: Agreed and revised as per the suggestions. 7) Abstract The sentences mentioning that 'the group received MHE had the lowest BMI and WHR' shouldn't be included in the abstract as these could lead to misunderstanding that the MHE groups clearly had benefit from the intervention while the results presented in the manuscript did not demonstrate that. Response: Revised as per kind guidance. Minor concerns: Please check repetition of the sentences and typos carefully."
}
]
}
] | 1
|
https://f1000research.com/articles/10-635
|
https://f1000research.com/articles/11-720/v1
|
30 Jun 22
|
{
"type": "Research Article",
"title": "Trends in prevalence and patterns of use of a heated tobacco product (IQOSTM) in Japan: A three-year repeated cross-sectional study",
"authors": [
"Karina Fischer",
"Martha Bajec",
"Nelly Mainy",
"Suzana AlMoosawi",
"Marius Sieverding",
"Bertram Zwisele",
"Nathalie Camille",
"Pierpaolo Magnani",
"Steve Roulet",
"Martha Bajec",
"Nelly Mainy",
"Suzana AlMoosawi",
"Marius Sieverding",
"Bertram Zwisele",
"Nathalie Camille",
"Pierpaolo Magnani",
"Steve Roulet"
],
"abstract": "Background: Numerous smoke-free tobacco or nicotine-containing product (TNP) alternatives have been introduced to support individual- and population-level harm reduction relative to continued cigarette smoking. This article details the nationwide prevalence and patterns of TNP use between 2016 and 2019 in Japan following the commercialization of IQOSTM, a smoke-free heated tobacco product (HTP). Methods: Cross-sectional surveys were conducted over a period of three study years (2016/2017, 2017/2018, and 2018/2019) in representative samples of the Japanese general adult population and samples of Japanese adult IQOS users registered in the IQOS owner database of Philip Morris International’s affiliate in Japan. Results: Across the three study years (Y1-Y3), the prevalence of overall current TNP use (Y1-Y3: 18.5%, 18.9%, and 18.2%) and overall TNP use by age and sex remained similar. However, there was a growing shift from cigarette smoking to smoke-free TNP use across the three study years. While the cigarette smoking prevalence (Y1-Y3: 17.6%, 17.3%, and 16.0%) decreased, the use prevalence of smoke-free TNPs, including the HTP IQOS (Y1-Y3: 1.8%, 3.2%, and 3.3%) and e-cigarettes (Y1-Y3, 0.7%, 1.6%, and 2.0%) increased. At the same time, TNP initiation, TNP relapse, and TNP reinitiation with IQOS were all very low across the three study years. Across Y1-Y3, exclusive use of only one type of TNP (Y1-Y3: 82.3%, 75.0%, and 70.4%) decreased, while dual use of two types of TNPs (Y1-Y3: 14.3%, 17.2%, and 16.7%) increased, and poly-TNP use (Y1-Y3: 2.1%, 6.1%, and 10.0%) increased markedly. Moreover, the majority of adult IQOS users were exclusive IQOS users. Conclusions: These findings suggest that current IQOS use behavior trends are in line with the principles of tobacco harm reduction and that HTPs are effective tools for complementing current tobacco control measures.",
"keywords": [
"Tobacco harm reduction",
"heated tobacco",
"smoke-free",
"IQOS",
"use patterns",
"prevalence",
"smoking initiation",
"smoking reinitiation"
],
"content": "Introduction\n\nIt is well established that cigarette smoking can lead to numerous negative health outcomes, including premature and preventable death1. The burden of smoking on individual and population health has driven health authorities and regulatory bodies to recommend and implement various tobacco control policies2. Never initiating or quitting smoking are the most direct ways to alleviate the health burden of smoking3. However, strategies aimed at preventing smoking and promoting cessation continue to face numerous challenges, including smokers who are not motivated to quit or who relapse/reinitiate smoking after a period of abstinence2,4,5. While smoking prevalence has declined over the last decades, over 1 billion people globally continue to smoke combustible tobacco products today1,6, and cigarette smoking continues to be responsible for the largest number of preventable deaths worldwide7,8.\n\nTo complement tobacco control efforts9, tobacco harm reduction strategies have been introduced around the world10,11. Tobacco harm reduction includes prevention of tobacco or nicotine-containing product (TNP) use initiation and reinitiation2,11,12 while ensuring that adult smokers switch completely from combustible TNPs to less harmful smoke-free (i.e., non-combustible) TNPs13,14.\n\nUnlike cigarettes, which burn tobacco and produce a complex mixture of harmful and potentially harmful constituents (HPHC) through combustion, IQOSTM, a smoke-free heated tobacco product (HTP) developed by Philip Morris International (PMI), heats a specifically engineered tobacco stick (i.e., HEETSTM/HeatSticksTM) to temperatures below the level of combustion15. As a consequence, smokers who switch completely to IQOS use are exposed to much lower levels of HPHCs than those who continue smoking cigarettes16–20.\n\nAs part of PMI’s commitment to a smoke-free future, IQOSTM was introduced in Japan in 2014 and is now available in more than 70 countries worldwide, with an estimated 21 million adult users globally21. The availability and demand for IQOS as an alternative to cigarettes has raised the need to monitor IQOS use prevalence and use patterns with the aim of informing public health authorities locally and worldwide. Such findings will further enable regulators to delineate the role of IQOS in harm reduction as a viable substitute for cigarettes2,22.\n\nBuilding on the reporting of Afolalu et al.23, the aim of the current study was to analyze the temporal trends in TNP use in nationally representative samples of the Japanese general adult population (JGAP) and, separately, in samples of Japanese adult IQOS users (JAIQOS) from PMI’s adult IQOS owner database in Japan across three recent years (2016/2017, 2017/2018, and 2018/2019).\n\n\nParticipants and methods\n\nCross-sectional surveys in representative samples of the Japanese general adult population (JGAP) and, separately, in samples of Japanese adult IQOSTM users (JAIQOS) registered in the IQOS owner database of Philip Morris International (PMI)’s affiliate in Japan were initiated in December 2016 and repeated annually over three full calendar years from 2016/2017 to 2018/2019 (Figure 1). Considering that IQOS was relatively new on the Japanese TNP market in 2016, the IQOS use prevalence in the JGAP was expected to be low. Therefore, additional surveys among JAIQOS were conducted alongside the JGAP surveys to obtain reliable estimates of IQOS use patterns among Japanese adult IQOS users23.\n\nAbbreviations: ICF, informed consent form; JAIQOS, sample of adult Japanese IQOS users from PMI’s IQOS™ owner database in Japan; JGAP, representative sample of the Japanese general adult population; PMI, Philip Morris International.\n\nStudy participants\n\nTo be included in the JGAP or JAIQOS samples, individuals had to be of legal age for purchasing TNPs in Japan (i.e., ≥20 years), current residents of Japan, and fluent in Japanese. Those included in the JAIQOS samples also had to have used >100 HEETSTM/HeatSticksTM in their lifetime24, be a current user of IQOS with HEETS/HeatSticks, have access to the internet, and not be currently employed by PMI or its affiliates.\n\nJGAP — Sampling, sample size, and survey mode\n\nThe JGAP samples were obtained via a syndicated (Omnibus) survey overseen and coordinated by Ipsos UK Ltd (London, UK). The fieldwork provider in Japan was Central Research Services Inc (Tokyo, Japan). The Omnibus surveys employed a three-stage stratified proportional sampling strategy that included the whole country. In stage 1, sampling points in the 12 Japanese administrative regions were allocated on the basis of their share of the population25. Households within each sampling point were identified in Stage 2 by using an electronic residential map, from which about 40 households were randomly selected. In the final stage 3, participants who met the inclusion criteria were selected from within the sampled households. Within each sampling point, quotas on age and sex were set to ensure the representativeness of the Japanese population.\n\nThe annual JGAP sampling consisted of four approximately equal-sized waves spaced throughout each study year to account for potential seasonal differences (Figure 2). A sample size of 5,000 participants per year was sufficient to estimate an IQOSTM use prevalence of 5.0% with 95% confidence and a precision of ±0.6% units. In the third year, six survey waves (7,000 participants) were conducted to increase the sample size and improve the accuracy of the estimates.\n\nAbbreviations: JAIQOS, sample of adult Japanese IQOS™ users from PMI’s IQOS owner database in Japan; JGAP, representative sample of the Japanese general adult population; PMI, Philip Morris International; W, survey wave.\n\nThe JGAP surveys were conducted at participants’ homes through in-person face-to-face pen-and-paper interviews. However, to avoid any bias on basis of social desirability of their response regarding their personal TNP use, the participants were handed the “Tobacco Use Prevalence” questionnaire section for self-completion. For completing the Omnibus questionnaires, each participant was given a coupon for JPY 500 (approximately USD 4).\n\nJAIQOS — Sampling, sample size, and survey mode\n\nUpon purchasing an IQOSTM device, users were invited to register in the PMI Japan IQOS owner database, which included about 350,000 adult IQOS owners in July 2017 and reached close to six million in 2019. Considering the demographic age-sex distribution of the database, individuals were randomly selected from the database and invited by email to participate in the survey for each wave.\n\nA sample size of 2,000 participants per year was sufficient to estimate a 50% proportion of exclusive IQOS use with 95% confidence and a precision of ±2.19% units. Each annual IQOS user sample consisted of four approximately equal-sized waves spaced throughout each study year to account for potential seasonal differences (Figure 2), with the aim of recruiting 500 adult participants per wave. The JAIQOS surveys were conducted entirely online through computer-assisted self-interviewing. For completing the online survey, participants were given a gift code valued at JPY 500 (about USD 4). The existing standard TNP use questions are available in the literature.\n\nSurvey questionnaires\n\nFor the present study, the “Tobacco Use Prevalence” questionnaire was developed on the basis of several existing standard TNP use questions available in the literature to capture information about TNP use; the questionnaire was not specifically validated. In both the JGAP and JAIQOS samples, the same questionnaire was used. However, while for the JGAP samples a pen-and-paper self-completion survey mode was used, for the JAIQOS samples an online mode was applied. The survey questions can be found in the Extended data.\n\nEthical conduct of the study\n\nAll subjects gave informed consent for inclusion in the study prior to participation. The participants of the JGAP samples gave verbal consent that was recorded by the interviewers as part of the Omnibus interviews, while the participants of the JAIQOS samples provided written consent. The study was conducted in accordance with the ethical principles that have their origin in the Declaration of Helsinki and were consistent with Good Epidemiological Practice (GEP)26. The study protocol, including the procedures of providing informed consent, were approved by the Hakata Clinic Institutional Review Board (Reference ID: J-186) in Fukuoka, Japan.\n\nAnalytical methods\n\nAnalyses were conducted using SAS v9.4 (or higher; SAS Inc., Cary, North Carolina, USA). For both the JGAP and JAIQOS samples, data were analyzed and summarized descriptively for each study year. For participant characteristics and outcome measures, continuous data are presented as mean and standard deviation (SD) or 95% confidence intervals (CI) and categorical data as number and percentage (95% CI) for the total samples and/or stratified by age and sex. Missing data were not included in the statistical analyses.\n\nThe following definitions were applied: “Use/never use” of cigarettes or IQOSTM with HEETSTM/HeatSticksTM: having/not having used 100 cigarettes or 100 HEETS/HeatSticks in the lifetime, to differentiate established cigarette or IQOS users from triers or experimenters24. “Current use”: daily or nondaily use of a TNP at the time of the survey. “Exclusive”, “dual”, and “poly” use: current use of only one type, two types, or three or more types of TNPs, respectively. “Initiation”: the time point at which a participant started established use/smoking of a TNP. “Initiation rate”: proportion of initiation in the last 12 months among never TNP users. “Relapse” and “reinitiation”: restarting TNP use following a period of quitting all TNPs for ≤12 months and >12 months, respectively.\n\nPrevalence of current TNP use for overall TNPs or by TNP category (cigarettes, IQOS, e-cigarettes, etc.) was calculated in the JGAP samples. For both JGAP and JAIQOS samples, the following was calculated: response rates, sample characteristics, and patterns of TNP use (JGAP: exclusive, dual, and poly use; JAIQOS: exclusive IQOS use and IQOS use with combustible or smoke-free TNP) as well as frequency (past 30-day use), intensity (average daily consumption), and history (JGAP: initiation, relapse, and reinitiation with IQOS; JAIQOS: previous cigarette smoking history before starting IQOS use) of TNP use.\n\n\nResults\n\nRegarding survey dispositions and outcome rates (Figure 3), the JGAP samples had a response rate of >30% in each of the three study years (Y1-Y3), which resulted in sample sizes of 4,878, 4,791, and 7,236 for Y1-Y3 of the Omnibus survey, respectively. In the Y1-Y3 JAIQOS samples, response rates of 19.4%, 4.7%, and 2.0% yielded sample sizes of 2,000, 2,044, and 2,013, respectively.\n\nAbbreviations: JAIQOS, sample of adult Japanese IQOS™ users from PMI’s IQOS owner database in Japan; JGAP, representative sample of the Japanese general adult population; n1-n3, sample sizes for study years 1–3, respectively; PMI, Philip Morris International.\n\nSample characteristics\n\nJGAP samples\n\nOverall, the demographic characteristics of the JGAP samples were similar across Y1-Y3 (Table 1) and comparable with those of the Japanese adult population25. The mean (±SD) ages of the Y1-Y3 samples were 53.8 (±17.9), 54.5 (±17.6), and 54.8 (±17.8) years, respectively, and each of the samples included slightly more women (Y1-Y3: 51.9%, 53.3% and 53.2%) than men (Y1-Y3: 48.1%, 46.7%, and 46.8%), mirroring the female skew in the actual Japanese population25.\n\nAbbreviations: CI, confidence interval; JAIQOS, sample of adult Japanese IQOS™ users from PMI’s IQOS owner database in Japan; JGAP, representative sample of the Japanese general adult population; NA, not applicable; PMI, Philip Morris International; SD, standard deviation.\n\n*Source: Statistics Bureau of Japan (2015) Source on Education: Statistics Bureau of Japan (2010) Source on Occupation: Public Opinion Survey on the Life of the People (23 June - 10 July 2016).\n\nIn each of Y1-Y3, a larger proportion of the sample was based in a major city (Y1-Y3: 27.4%, 28.1%, and 28.6%) than in rural areas (Y1-Y3: 10.0%, 9.3%, and 8.8%). Across Y1-Y3 (Table 1), most of the samples reported high school (Y1-Y3: 49.1%, 50.8%, and 49.8%) or college/university (Y1-Y3: 40.6%, 40.0%, and 41.0%) as the highest level of education, and the most common occupations were homemaker (Y1-Y3: 24.8%, 24.5%, and 24.8%), manual employee (Y1-Y3: 21.8%, 22.8%, and 21.6%), and clerical employee (Y1-Y3: 19.0%, 17.6%, and 17.8%).\n\nJAIQOS samples\n\nOverall, the demographic characteristics of the JAIQOS samples were similar across Y1-Y3 (Table 1). The mean (±SD) ages of the Y1-Y3 samples were 38.5 (±9.7), 39.7 (±10.1), and 39.9 (±9.9) years, respectively, and in each of the samples there were more men (Y1-Y3: 81.6%, 80.3%, and 79.9%) than women (Y1-Y3: 18.4%, 19.7%, and 20.1%).\n\nAcross Y1-Y3 (Table 1), most of the participants reported completing college/university (Y1-Y3: 56.8%, 54.4%, and 53.9%) or high school (Y1-Y3: 36.3%, 36.8%, and 37.0%), and the most common occupations were manager (Y1-Y3: 20.7%, 21.1%, and 19.8%) and self-employed/small business owner (Y1-Y3: 16.5%, 17.0%, and 17.6%).\n\nTNP use in JGAP samples\n\nPrevalence of overall TNP use\n\nAcross Y1-Y3, the prevalence of overall current (Y1-Y3: 18.5%, 18.9%, 18.2%) former (Y1-Y3: 18.7%, 16.3%, 16.9%), and never (Y1-Y3: 62.9%, 64.8%, 64.9%) TNP use as well as of TNP use by age and sex were similar (Table 2).\n\nAbbreviations: CI, confidence interval; JGAP, representative sample of the Japanese general adult population.\n\nPrevalence of individual TNP use\n\nCigarette smoking prevalence decreased from 17.6% in Y1 to 16.0% in Y3, while the use prevalence of other TNPs, including HTPs and e-cigarettes, increased (Table 3). The use prevalence of all HTP brands (i.e., IQOS™, Ploom/Ploom Tech, and glo) increased across Y1-Y3, and, of all HTP brands surveyed, IQOS had the highest use prevalence (Y1-Y3: 1.8%, 3.2%, 3.3%). The use prevalence of e-cigarettes increased from 0.7% to 1.6% to 2.0% during Y1-Y3.\n\nAbbreviations: CI, confidence interval; JGAP, representative sample of the Japanese general adult population; TNP, tobacco or nicotine-containing product.\n\n*Year 1 (2016/2017), Year 2 (2017/2018), and Year 3 (2018/2019)\n\n**Cigarettes include hand-rolled cigarettes\n\nIn each of Y1-Y3, cigarette smoking was more prevalent among men (Y1-Y3: 28.2%, 28.4%, and 26.3%) than women (Y1-Y3: 7.9%, 7.7%, and 7.0%) and was highest among 40–49-year-olds (Y1-Y3: 24.6%, 22.2%, and 20.4%). The IQOS use prevalence in each of Y1-Y3 was higher among men (Y1-Y3: 3.0%, 5.1%, and 5.4%) than women (Y1-Y3: 0.6%, 1.5%, and 1.5%) and was highest among 20–29-year-olds (3.8%) in Y1, but shifted to be highest among 30–39-year-olds in Y2 (8.7%) and Y3 (9.0%). In both Y1 (1.7%) and Y2 (3.0%), e-cigarette use prevalence was highest among 20–29-year-olds, but in Y3 shifted to be highest among 30–39-year-olds (3.9%; Table 3).\n\nPatterns of TNP use\n\nAcross Y1-Y3 (Table 4), exclusive use of only one type of TNP decreased (Y1-Y3: 82.3%, 75.0%, and 70.4%), while dual use of two types of TNPs increased (Y1-Y3: 14.3%, 17.2%, and 16.7%) and poly-TNP use increased markedly (Y1-Y3: 2.1%, 6.1%, and 10.0%).\n\nAbbreviations: CI, confidence interval; JGAP, representative sample of the Japanese general adult population.\n\n*Cigarettes include hand-rolled cigarettes\n\nAcross Y1-Y3 (Table 4), the greatest proportion, although declining, of participants who reported TNP use were exclusive cigarette smokers (Y1-Y3: 79.5%, 68.1%, and 63.0%), while conversely, the proportion of exclusive IQOSTM users increased (Y1-Y3: 2.5%, 4.8%, and 5.3%), and that of exclusive e-cigarette users remained low (Y1-Y3: 0.3%, 1.1%, and 0.5%).\n\nFrequency and Intensity of TNP use\n\nAmong the participants in the JGAP samples in Y1-Y3 who were currently using cigarettes (Y1-Y3: n=852; n=825; and n=1,150), the average number of cigarettes smoked per day (over the last 30 days) appeared to be stable (Y1-Y3: 16.0, 15.7, and 15.5) (Table 5).\n\nAbbreviations: CI, confidence interval; JAIQOS, sample of adult Japanese IQOS™ users from PMI’s IQOS owner database in Japan; JGAP, representative sample of the Japanese general adult population; PMI, Philip Morris International\n\n* Year 1 (2016/2017), Year 2 (2017/2018), Year 3 (2018/2019)\n\nTNP initiation/relapse/reinitiation\n\nAmong the participants who were never TNP users 12 months prior to the survey (Y1-Y3: n=3,066; n=3,109; and n=4,685), TNP use initiation with cigarettes in the preceding 12 months was considerably higher (Y1-Y3: 0.2%, 0.3%, and 0.2%) than initiation with IQOS™ (Y1-Y3: 0.03%, 0.1%, and 0.1%) (Table 6).\n\nAbbreviations: CI, confidence interval, JAIQOS, sample of adult Japanese IQOS™ users from PMI’s IQOS owner database in Japan; JGAP, representative sample of the Japanese general adult population; NA, not applicable; PMI, Philip Morris International; TNP, tobacco or nicotine-containing product.\n\n*Year 1 (2016/2017), Year 2 (2017/2018), and Year 3 (2018/2019)\n\n** Cigarettes include hand-rolled cigarettes\n\nNote: Initiation with e-cigarettes was not measured as part of the study.\n\nAmong current TNP users in Y1-Y3 (Y1-Y3: n=894; n=900; and n=1,304), in each year only one participant reinitiated TNP use with IQOSTM (Y1-Y3: 0.1%, 0.1%, and 0.07%). No relapse to IQOS use was reported in any of the three study years (Table 7).\n\nAbbreviations: CI, confidence interval; JGAP, representative sample of the Japanese general adult population; TNP, tobacco or nicotine-containing product.\n\n*Year 1 (2016/2017), Year 2 (2017/2018), and Year 3 (2018/2019)\n\nTNP use in the JAIQOS samples\n\nPatterns of TNP Use\n\nAcross Y1-Y3, a decreasing majority of participants in the samples used IQOSTM exclusively (Y1-Y3: 63.4%, 52.3%, and 49.4%), while the proportion who used IQOS together with other smoke-free TNPs increased (Y1-Y3: 7.6%, 17.7%, and 27.0%) and the proportion who used IQOS together with combustible TNPs decreased (Y1-Y3: 28.4%, 25.4%, and 23.6%). Consequently, by Y3, a greater proportion of participants used IQOS together with other smoke-free TNPs than IQOS together with combustible TNPs (Table 8).\n\nAbbreviations: CI, confidence interval; JAIQOS, sample of adult Japanese IQOS users from PMI’s IQOS™ owner database in Japan; JGAP, representative sample of the Japanese general adult population; PMI, Philip Morris International; TNP, tobacco or nicotine-containing product.\n\n*Year 1 (2016/2017), Year 2 (2017/2018), and Year 3 (2018/2019)\n\nFrequency and intensity of TNP use\n\nIn each of Y1-Y3 (Table 5), the average number of days of IQOSTM use in the last 30 days (Y1-Y3: 29.1, 28.9, and 28.8) and the average number of HEETSTM/HeatSticksTM used on the days of IQOS use in the last 30 days (Y1-Y3: 16.2, 16.5, and 15.9) were relatively stable. Thus, the average daily HEETS/HeatSticks consumption (over the last 30 days) across Y1-Y3 was similarly stable (Y1-Y3: 15.9, 16.1, and 15.5).\n\nHistory of TNP use\n\nIn each of Y1-Y3, the majority of the JAIQOS sample participants had a smoking history before starting IQOSTM use (Y1-Y3: 98.0%, 98.7%, and 99.3%), while only a few were never smokers (Y1-Y3: 2.0%, 1.3%, and 0.7%) before starting IQOS use.\n\n\nDiscussion\n\nThe present study is the first to report data on the prevalence and patterns of TNP use in samples of the Japanese general adult population (JGAP) and samples of Japanese adult IQOS users (JAIQOS) over the same three consecutive years (2016/2017, 2017/2018, and 2018/2019). The findings of this study are consistent with the trends observed by other surveys that have examined the prevalence and patterns of TNP use since the introduction of the HTP IQOSTM in Japan in 201427–31.\n\nIn the JGAP samples, the prevalence of overall TNP use was stable (~18%) across the study years. However, there was a trend towards a declining prevalence of cigarette smoking concurrent with an increase in smoke-free TNP and total HTP use, especially in the case of IQOSTM use (from 1.8% in 2016/2017 to 3.3% in 2018/2019).\n\nIt can, therefore, be concluded that the introduction of smoke-free TNPs does not lead to an unintended increase in overall TNP use in the general population, but rather drives a shift in TNP use patterns from cigarettes to smoke-free TNPs. When considered alongside the low TNP initiation rates with IQOSTM, the present findings further imply that introduction of smoke-free TNPs does not lead to an unintended increase in TNP use among non-users. This hypothesis is partially supported by the findings of other studies32,33 and is consistent with the findings of Cummings et al.4, who reported an accelerated reduction in cigarette sales in Japan concurrent with the introduction and increase in HTP sales. In agreement with Cummings et al.4 and others30,31, the total HTP use prevalence in year 3 of the present study was over 5%. A previous study had reported a total HTP use prevalence of 11%34. The prevalence of cigarette smoking observed in each year of the present study was in agreement with the prevalence data from the Japan National Health and Nutrition Survey for 2017 (18.8%)27, 2018 (18.9%)28, and 2019 (17.7%)29. Additionally, the present cigarette and overall TNP use data were well in line with those from other contemporaneous surveys30,31,35,36. Tabuchi et al.32 reported an IQOS use prevalence of 3.6% in 2017, which is higher than that observed in the present study (1.8%) for the same year. For 2018, Sutanto et al.37 reported an any-brand HTP use prevalence (i.e., IQOS, glo, and Ploom/Ploom Tech) of 2.7%, which is less than that observed in our study (3.2%) for IQOS use alone. These discrepancies are likely due to methodological differences (i.e., cross-sectional vs. longitudinal design or in-person vs. online interview) as described previously23.\n\nIn the JAIQOS samples, the age and sex distribution observed in each study year as well as the current HTP use patterns are in line with the Japan National Health and Nutrition Survey results for the same years27–29. Similarly, in agreement with the Japanese national survey27–29, the results presented here indicate that the majority of HTP users are using HTP exclusively. The average number of HEETSTM/HeatSticksTM used per day (Y1-Y3: 15.9, 16.1, and 15.5, respectively) in the JAIQOS samples was relatively stable across the study years and comparable with the 14.3 HEETS/HeatSticks used per day reported in Japan by Jones et al.31 in 2019. Moreover, the HEETS/HeatSticks consumption per day in the JAIQOS samples was very close to the average number of cigarettes consumed per day (Y1-Y3: 16.0, 15.7, and 15.5, respectively) among cigarette smokers in the JGAP samples, suggesting that IQOS users are not increasing their daily consumption upon switching from cigarettes to IQOS.\n\nTNP initiation, relapse, and reinitiation rates observed with IQOSTM in the present study were relatively low in all three years, indicating that IQOS uptake was limited to existing smokers who had switched to IQOS. Similarly, Sutanto et al.37 concluded that “virtually all HTP users were current cigarette smokers (67.8%) or former smokers (25.0%); and that only 1.0% of HTP users were never smokers.” Jones et al.31 observed that HTP uptake in 2019 occurred “almost exclusively among current tobacco users in Japan, with negligible uptake among never tobacco users.” In both samples in the present study, nearly all current IQOS users had started TNP use with cigarette smoking. These findings suggest that IQOS uptake is occurring among current adult smokers, which is in alignment with both the principles of harm reduction and the United States Food and Drug Administration’s (FDA) conclusion that IQOS has “potential benefit to population health.”20\n\nMajor strengths of this study, among those previously described23, include the annual repeated data collection using the same sampling framework and methods, face-to-face interviews, and nationally representative samples. The limitations of the current study include all biases typically associated with self-reported measures, such as recall, social desirability, or response bias as well as sampling and selection bias. To overcome these limitations, particularly in the JAIQOS sample, the response rates were monitored and compared against preestablished quotas on the basis of age and sex.\n\n\nConclusions\n\nWhile cigarette smoking remains the most prevalent way of consuming TNPs in Japan, a significant and growing number of adult Japanese smokers have switched to smoke-free alternatives such as IQOSTM, with the majority using these products exclusively. Additionally, there has been low initiation with IQOS among TNP never and former users. Taken together, the findings of the present study on the prevalence and patterns of IQOS use indicate that IQOS use behavior trends are in line with the principles of tobacco harm reduction and that HTPs are effective tools for complementing current tobacco control efforts14.\n\n\nData availability\n\nINTERVALS: YEAR 1–3 DATA (SAS DATASETS, CC-BY 4.0), https://doi.org/10.26126/intervals.r35iml.138\n\nThis project contains the following underlying data:\n\n▪ SAS datafiles in the Clinical Data Interchange Standards Consortium (CDISC) Analysis Data Model (ADaM) structure (www.cdisc.org/standards) for each of the study years 1–3.\n\n○ The ADSL (adsl_y1_jp.sas7bdat, adsl_y2_jp.sas7bdat, and adsl_y3_jp.sas7bdat,) datasets are the Subject Level Analysis Datasets and contain the main information on participants identifier, demographics, and tobacco and/or nicotine product use groups and patterns to facilitate analysis and interpretation of analysis.\n\n○ The ADQS (adqs_y1_jp.sas7bdat, adqs_y2_jp.sas7bdat, and adqs_y3_jp.sas7bdat) datasets are the Questionnaire Analysis Datasets and contain specific information on the study survey, i.e., all questions and items answered by participants in the survey.\n\n○ The ADEX (adex_y1_jp.sas7bdat, adex_y2_jp.sas7bdat, and adex_y3_jp.sas7bdat) datasets are the Exposure Analysis Datasets and contain specific information on the TNP use exposure, i.e., all questions and items answered by participants in the survey related to their product use.\n\n○ The ADAM Metadata Files (ADaM_PMX01JP_AnY1_Metadata, ADaM_PMX01JP_AnY2_Metadata, and ADaM_PMX01JP_AnY3_Metadata) contain the datasets and variable labels and definitions, code lists to decode the variables names, terms and values, and the methods and computational algorithms to derive the analytical datasets.\n\n▪ Study Year 1 Data and Metadata: https://doi.org/10.26126/intervals.8ybcxu\n\n▪ Study Year 2 Data and Metadata: https://doi.org/10.26126/intervals.hxaf2v\n\n▪ Study Year 3 Data and Metadata: https://doi.org/10.26126/intervals.6jbifs\n\nINTERVALS: Tobacco Use Prevalence Questionnaire. https://doi.org/10.26126/intervals.rxhx4a.138\n\nThis project contains the following extended data:\n\n▪ Tobacco Use Prevalence questionnaire (Tobacco Use Prevalence Questionnaire_engl_jap.pdf) is the questionnaire administered in the general population and IQOS user surveys (English and Japanese version).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThis study followed the STROBE reporting guideline.\n\nINTERVALS: STROBE checklist and flow chart for “Trends in Prevalence and Patterns of Use of a Heated Tobacco Product (IQOS™) in Japan: A 3-Year Repeated Cross-Sectional Study”, are available: https://doi.org/10.26126/intervals.dluspw",
"appendix": "Acknowledgements\n\nThe authors would like to thank all those who participated in this study. The authors also would like to thank Antonio Ramazzotti for reviewing and providing insightful comments on this publication.\n\n\nReferences\n\nWest R: Tobacco smoking: Health impact, prevalence, correlates and interventions. Psychol Health. 2017; 32(8): 1018–1036. PubMed Abstract | Publisher Full Text | Free Full Text\n\nInstitute of Medicine Committee to Assess the Science Base for Tobacco Harm R: Clearing the Smoke: Assessing the Science Base for Tobacco Harm Reduction. Washington (DC): National Academies Press (US); 2001. Reference Source\n\nGeneral OotS: Smoking cessation: a report of the Surgeon General. In: Services USDoHaH, ed. Rockville, MD: Public Heath Service; 2020. Reference Source\n\nCummings KM, Nahhas GJ, Sweanor DT: What Is Accounting for the Rapid Decline in Cigarette Sales in Japan? Int J Environ Res Public Health. 2020; 17(10): 3570. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLe Houezec J, McNeill A, Britton J: Tobacco, nicotine and harm reduction. Drug Alcohol Rev. 2011; 30(2): 119–123. PubMed Abstract | Publisher Full Text\n\nNg M, Freeman MK, Fleming TD, et al.: Smoking Prevalence and Cigarette Consumption in 187 Countries, 1980-2012. JAMA. 2014; 311(2): 183–192. PubMed Abstract | Publisher Full Text\n\nTobacco. Paris: OECD Publishing; 2020. Reference Source\n\nGowing LR, Ali RL, Allsop S, et al.: Global statistics on addictive behaviours: 2014 status report. Addiction. 2015; 110(6): 904–919. PubMed Abstract | Publisher Full Text\n\nWarner KE: How to Think-Not Feel-about Tobacco Harm Reduction. Nicotine Tob Res. 2019; 21(10): 1299–1309. PubMed Abstract | Publisher Full Text\n\nPrevention CDC: Best Practices for Comprehensive Tobacco Control Programs. In: Department of Health and Human Services CDC, Prevention National Center for Chronic Disease Prevention and Health Promotion, Office on Smoking and Health, eds. Atlanta, GA, USA, 2014. Reference Source\n\nGottlieb S, Zeller M: A Nicotine-Focused Framework for Public Health. N Engl J Med. 2017; 377(12): 1111–1114. PubMed Abstract | Publisher Full Text\n\nAbrams DB, Glasser AM, Pearson JL, et al.: Harm Minimization and Tobacco Control: Reframing Societal Views of Nicotine Use to Rapidly Save Lives. Annu Rev Public Health. 2018; 39: 193–213. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeitsch MC, Polosa R, Proctor C, et al.: Next-generation tobacco and nicotine products: Substantiating harm reduction and supporting tobacco regulatory science. Toxicol Res Appl. 2018; 2. Publisher Full Text\n\nHatsukami DK, Carroll DM: Tobacco harm reduction: Past history, current controversies and a proposed approach for the future. Prev Med. 2020; 140: 106099. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSmith MR, Clark B, Lüdicke F, et al.: Evaluation of the Tobacco Heating System 2.2. Part 1: Description of the system and the scientific assessment program. Regul Toxicol Pharmacol. 2016; 81 Suppl 2: S17–S26. PubMed Abstract | Publisher Full Text\n\nLüdicke F, Picavet P, Baker G, et al.: Effects of Switching to the Tobacco Heating System 2.2 Menthol, Smoking Abstinence, or Continued Cigarette Smoking on Biomarkers of Exposure: A Randomized, Controlled, Open-Label, Multicenter Study in Sequential Confinement and Ambulatory Settings (Part 1). Nicotine Tob Res. 2018; 20(2): 161–172. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLüdicke F, Picavet P, Baker G, et al.: Effects of Switching to the Menthol Tobacco Heating System 2.2, Smoking Abstinence, or Continued Cigarette Smoking on Clinically Relevant Risk Markers: A Randomized, Controlled, Open-Label, Multicenter Study in Sequential Confinement and Ambulatory Settings (Part 2). Nicotine Tob Res. 2018; 20(2): 173–182. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaziza C, de La Bourdonnaye G, Donelli A, et al.: Reduction in Exposure to Selected Harmful and Potentially Harmful Constituents Approaching Those Observed Upon Smoking Abstinence in Smokers Switching to the Menthol Tobacco Heating System 2.2 for 3 Months (Part 1). Nicotine Tob Res. 2020; 22(4): 539–548. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaziza C, de La Bourdonnaye G, Donelli A, et al.: Favorable Changes in Biomarkers of Potential Harm to Reduce the Adverse Health Effects of Smoking in Smokers Switching to the Menthol Tobacco Heating System 2.2 for 3 Months (Part 2). Nicotine Tob Res. 2020; 22(4): 549–559. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFDA: FDA Authorizes Marketing of IQOS Tobacco Heating System with ‘Reduced Exposure’ Information. FDA. 2020. Reference Source\n\nCostanzo R, Baker G: Are heated tobacco products (HTPs) a public health opportunity? Medical Word. 2020; 1: 95–100. Reference Source\n\nAdministration FDA: Guidance for industry - Modified risk tobacco product applications - Draft guidance. In: Services United States Department of Health and Human Services, eds. Center for Tobacco Products; Silver Spring, MD, USA, 2012. Reference Source\n\nAfolalu EF, Langer P, Fischer K, et al.: Prevalence and patterns of tobacco and/or nicotine product use in Japan (2017) after the launch of a heated tobacco product ( IQOS ®): a cross-sectional study [version 2; peer review: 2 approved]. F1000Res. 2021; 10: 504. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNHIS: Adult Tobacco Use - Glossary. 2019. Reference Source\n\nStatistics Bureau of Japan: Japan 2015 Population Census. 2015. Reference Source\n\nHoffmann W, Latza U, Baumeister SE, et al.: Guidelines and recommendations for ensuring Good Epidemiological Practice (GEP): a guideline developed by the German Society for Epidemiology (DGEpi). Eur J Epidemiol. 2019; 34(3): 301–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWelfare MoHLa: Summary: The Japan National Health and Nutrition Survey. In: Innovation NIoB, Nutrition NIoHa, eds. Japan, 2017. Reference Source\n\nWelfare MoHLa: Summary: The Japan National Health and Nutrition Survey. In: Innovation NIoB, Nutrition NIoHa, eds. Japan, 2018. Reference Source\n\nWelfare MoHLa: Summary: The Japan National Health and Nutrition Survey. In: Innovation NIoB, Nutrition NIoHa, eds. Japan, 2019. Reference Source\n\nAdamson J, Kanitscheider C, Prasad K, et al.: Results from a 2018 cross-sectional survey in Tokyo, Osaka and Sendai to assess tobacco and nicotine product usage after the introduction of heated tobacco products (HTPs) in Japan. Harm Reduct J. 2020; 17(1): 32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJones JD, Adamson J, Kanitscheider C, et al.: Cross-sectional Survey to Assess Tobacco and Nicotine Product Use since the Introduction of Tobacco Heating Products in Japan: Wave 1. Tob Regul Sci. 2021; 7(3): 210–220. Publisher Full Text\n\nTabuchi T, Gallus S, Shinozaki T, et al.: Heat-not-burn tobacco product use in Japan: its prevalence, predictors and perceived symptoms from exposure to secondhand heat-not-burn tobacco aerosol. Tob Control. 2018; 27(e1): e25–e33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMatsuyama Y, Tabuchi T: Heated tobacco product use and combustible cigarette smoking relapse/initiation among former/never smokers in Japan: the JASTIS 2019 study with 1-year follow-up. Tob Control. 2022; 31(4): 520–526. PubMed Abstract | Publisher Full Text\n\nHori A, Tabuchi T, Kunugita N: Rapid increase in heated tobacco product (HTP) use from 2015 to 2019: from the Japan 'Society and New Tobacco' Internet Survey (JASTIS). Tob Control. 2020; 30(4): 474–475. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJapan Tobacco Inc.: Japan Tobacco Annual Survey. 2017. Reference Source\n\nJapan Tobacco Inc.: Japan Tobacco Annual Survey. 2018. Reference Source\n\nSutanto E, Miller C, Smith DM, et al.: Prevalence, Use Behaviors, and Preferences among Users of Heated Tobacco Products: Findings from the 2018 ITC Japan Survey. Int J Environ Res Public Health. 2019; 16(23): 4630. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFischer K, Bajec M, Mainy N, et al.: Trends in Prevalence and Patterns of Use of a Heated Tobacco Product (IQOS™) in Japan: A 3-Year Repeated Cross-Sectional Study. YEAR 1-3 DATA. (Year1: https://doi.org/10.26126/intervals.8ybcxu, Year 2: https://doi.org/10.26126/intervals.hxaf2v, Year 3: https://doi.org/10.26126/intervals.6jbifs). 2022. http://www.doi.org/10.26126/intervals.r35iml.1"
}
|
[
{
"id": "142791",
"date": "28 Jul 2022",
"name": "Mohamadi Sarkar",
"expertise": [
"Reviewer Expertise Tobacco regulatory 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\n17/10/22: The reviewers' COI statement, \"The reviewers are employees of Altria Client Services LLC.\", was updated to include more detail on the potential link between the funders of this research and the reviewers, which was not fully declared at the time of publishing of this report.\nWe read the manuscript submitted by Fischer et al in F1000Research with great interest. The authors report results from cross-sectional surveys conducted over a period of three in representative samples of the Japanese general adult population and samples of Japanese adult IQOS users registered in the IQOS owner database. The authors conclude that the trend towards declining prevalence of cigarette smoking concurrent with an increase in smoke-free TNP and total HTP use, especially in the case of IQOSTM use are in line with the principles of tobacco harm reduction and that HTPs are effective tools for complementing current tobacco control measures. We have the following major and minor comments as listed below. We recommend that the authors address each comment and accordingly modify the manuscript.\nMajor comments\nThe authors report results from the general population survey among Japanese adults, which given the representativeness is appropriate to compare over time. However, the IQOS user survey was based on a convenience sample, and comparing trends over time is less robust. Therefore, comparing the results across the two surveys is not ideal. The authors should discuss this as a limitation of their approach. Instead of a direct comparison of the survey results between the general population and IQOS sample the authors should have considered characterizing IQOS sample tobacco use behaviors and benchmark that to the current adult tobacco users from the general population survey.\n\nWe were confused by the individual TNP use prevalence values among the general population reported in Table 3. The overall prevalence for cigarettes ranges from 17.6, 17.3, and 16 % each year. If add the prevalence values for IQOS and e-cigarettes, results in total TNP prevalence of 20.1, 22.1, and 21.3% for each year. These values differ from the overall TNP prevalence of 18.5, 18.9, and 18.2 reported for each year in Table 2. Perhaps the authors can offer an explanation for this discrepancy\n\nWhile we agree that this evidence supports or does not contradict that switching to a smoke-free product like IQOS supports harm reduction, we suggest that the authors should be careful in drawing broader conclusions like “IQOS use behavior trends are in line with the principles of tobacco harm reduction”. Tobacco harm reduction cannot be viewed only in the narrow perspective of switching. An important consideration of unintended consequence is not only initiation among adults but also among youth. Additionally, as pointed in our comment above, the total TNP prevalence as calculated by us does not indicate a reduction in total tobacco product use, on the contrary, appears to increase over time. The authors should provide some context regarding these observations. Therefore, the authors should consider modifying the conclusions as “The use behavior trends suggest that IQOS has the potential to switch adult smokers from cigarettes to smoke-free products, which presents a harm reduction opportunity.”\n\nWe caution the authors to avoid making causality inferences based on association. The authors should consider revising the conclusion - “The introduction of smoke-free TNPs does not lead to an unintended increase in overall TNP use in the general population, but rather drives a shift in TNP use patterns from cigarettes to smoke-free TNPs.” to reflect association rather than causation.\n\nThe survey lacks an appropriate characterization of quitting behavior among IQOS users. The survey does not present evidence regarding the likely interception of smokers who may have otherwise quit using TNP. If the survey did not assess this domain, the authors should cite this as a limitation. This further warrants a revision of the conclusions from not being so definitive but reflect the limitations of the survey results.\n\nThe authors should include an explanation of the drop in response rates for JAIQOS samples from 19.4% in Y1 to 4.7% and 2.0% in Y2 and Y3. Given that the IQOS users changed significantly, from 350,000 to 6 million, the IQOS population likely changed over the course of the 3 surveys. The authors should consider accounting for the change in IQOS population by adjusting either during recruitment or during the data analysis.\n\nThe authors only present descriptive analyses of survey findings, however, they may want to consider including some trend analysis or other statistical testing to determine whether the changes over time are significant. Perhaps such an analysis may not yield robust findings from a three-year survey and authors may consider providing more statistical rigor in future reports.\n\nWe understand that the focus of this manuscript was among adults age >20 years. However, an important consideration is the impact of IQOS and other smoke-free products among youth, which is an important public health concern. The authors should mention that this manuscript only addresses adult use behavior and either briefly describe data for youth use based on published literature or national surveys. Some indication of initiation among different age groups of youth and young adults would have provided useful insights in the overall harm reduction potential of IQOS and other smoke-free products.\n\nMinor comments\nThe authors should consider including the supporting literature citations in the statement – “The existing standard TNP use questions are available in the literature.”.\n\nThe authors should provide a possible explanation of the discrepancy in the reported total HTP use prevalence of 11% by Hori et al (ref 34) which is almost twice of that reported in the current manuscript. This discrepancy cannot be solely explained by methodological differences.\n\nIn this manuscript, the IQOS sample could have been better characterized. Given that the authors had access to the IQOS user database, they could have followed transition behavior over time rather than indirectly comparing changes in average smoking prevalence against increase in IQOS user prevalence. Moreover, they may also report transitions between dual use to exclusive switching behavior. Perhaps in future reports, the authors can include more detailed analyses of transition behaviors.\n\nWe believe that the title for Table 6 should include JGAP not JPAG. Please correct the typo.\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": "8985",
"date": "30 Nov 2022",
"name": "Karina Fischer",
"role": "Author Response",
"response": "Author Responses to Comments of Reviewers We thank Reviewer 1 and Reviewers 2 for their critical and comprehensive review as well as their constructive suggestions to improve the manuscript. We addressed all comments by point-to-point responses and referred to the related updates in the manuscript by page and line numbers (Note: page and line numbers reflect the tracked changes version 2 of the manuscript, not the edited version that reviewers will receive. Reviewers may have to additionally request the tracked changes version). Reviewers 2: Mohamadi Sarkar, Center for Research and Technology, Altria Client Services LLC, Richmond, VA, USA Brendan Noggle, Center for Research and Technology, Altria Client Services LLC, Richmond, VA, USA Reviewers 2 comments We read the manuscript submitted by Fischer et al in F1000Research with great interest. The authors report results from cross-sectional surveys conducted over a period of three years in representative samples of the Japanese general adult population and samples of Japanese adult IQOS users registered in the IQOS owner database. The authors conclude that the trend towards declining prevalence of cigarette smoking concurrent with an increase in smoke-free TNP and total HTP use, especially in the case of IQOS™ use are in line with the principles of tobacco harm reduction and that HTPs are effective tools for complementing current tobacco control measures. We have the following major and minor comments as listed below. We recommend that the authors address each comment and accordingly modify the manuscript. Major comments Reviewers 2 Major Comment 1. The authors report results from the general population survey among Japanese adults, which given the representativeness is appropriate to compare over time. However, the IQOS user survey was based on a convenience sample and comparing trends over time is less robust. Therefore, comparing the results across the two surveys is not ideal. The authors should discuss this as a limitation of their approach. Instead of a direct comparison of the survey results between the general population and IQOS sample the authors should have considered characterizing IQOS sample tobacco use behaviors and benchmark that to the current adult tobacco users from the general population survey. Authors’ Response Major Comment 1. As stated at the end of the introduction, we used the “convenience” JAIQOS samples (random samples from about 350,000 IQOS users in 2017 and 6 million IQOS users in 2019 registered in the adult IQOS owner database of PMI’s affiliate in Japan) alongside the representative JGAP samples because in the first and second year IQOS was relatively new on the Japanese tobacco market, and thus, the IQOS use prevalence in the representative JGAP samples was expected to be low. Therefore, to obtain reliable estimates of the use patterns of IQOS (e.g., exclusive IQOS use, IQOS use with combustible tobacco products, and IQOS use with non-combustible tobacco products, the differentiation of which is important regarding the impact on tobacco harm reduction), additional surveys among IQOS users were conducted. Although we presented the results of both samples in the results section, we only directly compared the study results on age and sex distribution, intensity of use, initiation, relapse, and reinitiation between the two samples because we believe it was important to show the study results of the two independent samples. Because we are well aware of the limitations of the IQOS user (JAIQOS) samples, most of the results presented are based on the representative JGAP samples (Tables 1 [demographics] and Tables 2-7) and the related text in the results section. Only the results presented in Table 1 [demographics], Table 5 [frequency and intensity of use] and Table 8 [IQOS use patterns] are also presented for the IQOS user samples. We amended the discussion to highlight the limited generalizability of the IQOS user (JAIQOS) samples (page 24, lines 389-392). Reviewers 2 Major Comment 2. We were confused by the individual TNP use prevalence values among the general population reported in Table 3. The overall prevalence for cigarettes ranges from 17.6, 17.3, and 16 % each year. If add the prevalence values for IQOS and e-cigarettes, results in total TNP prevalence of 20.1, 22.1, and 21.3% for each year. These values differ from the overall TNP prevalence of 18.5, 18.9, and 18.2 reported for each year in Table 2. Perhaps the authors can offer an explanation for this discrepancy. Authors’ Response Major Comment 2. We thank Reviewers 2 for this question on prevalence that often creates confusion when individual TNP prevalence values are shown that do not sum up to the overall TNP prevalence reported. Prevalence data for different tobacco product categories (e.g., cigarettes, HTPs, and e-cigarettes) can only be directly summed up to a higher-level use prevalence group (e.g., total prevalence of cigarette, HTP, and e-cigarette use) if each person only uses one category of tobacco product (e.g., only cigarettes, only HTPs, or only e-cigarettes). As soon as the same person uses more than one category (i.e., dual or poly use of different tobacco product categories), the person would be counted twice (dual use) or even more (poly use) in the higher-level prevalence group if the individual prevalence values would just be summed up, while correctly the person should only count once in the higher-level prevalence group (total prevalence of cigarette, HTP, and e-cigarette use). Reviewers 2 Major Comment 3. While we agree that this evidence supports or does not contradict that switching to a smoke-free product like IQOS supports harm reduction, we suggest that the authors should be careful in drawing broader conclusions like “IQOS use behavior trends are in line with the principles of tobacco harm reduction”. Tobacco harm reduction cannot be viewed only in the narrow perspective of switching. An important consideration of unintended consequence is not only initiation among adults but also among youth. Additionally, as pointed in our comment above, the total TNP prevalence as calculated by us does not indicate a reduction in total tobacco product use, on the contrary, appears to increase over time. The authors should provide some context regarding these observations. Therefore, the authors should consider modifying the conclusions as “The use behavior trends suggest that IQOS has the potential to switch adult smokers from cigarettes to smoke-free products, which presents a harm reduction opportunity.” Authors’ Response Major Comment 3. We thank Reviewers 2 for this comment. As suggested by Reviewers 2, we rephrased the conclusion section in the abstract (page 3) and discussion (page 24, lines 405-409) to make this point clearer. Regarding the overall TNP prevalence we reported, please see our response and explanations to Reviewers 2 Major Comment 2. Reviewers 2 Major Comment 4. We caution the authors to avoid making causality inferences based on association. The authors should consider revising the conclusion - “The introduction of smoke-free TNPs does not lead to an unintended increase in overall TNP use in the general population, but rather drives a shift in TNP use patterns from cigarettes to smoke-free TNPs.” to reflect association rather than causation. Authors’ Response Major Comment 4. We agree with Reviewers 2 that because our study results are based on cross-sectional and descriptive data only, cause-effect inference cannot be drawn. We consider this limitation as a well-known fact inherent to cross-sectional studies. However, to make this point clearer, we amended the discussion (page 22, lines 305-308) and limitation section (page 24, lines 382-384) with regard to the limitations of the cross-sectional design. Reviewers 2 Major Comment 5. The survey lacks an appropriate characterization of quitting behavior among IQOS users. The survey does not present evidence regarding the likely interception of smokers who may have otherwise quit using TNP. If the survey did not assess this domain, the authors should cite this as a limitation. This further warrants a revision of the conclusions from not being so definitive but reflect the limitations of the survey results. Authors’ Response Major Comment 5. We agree with Reviewers 2 that without addressing quitting behavior in our manuscript, we do not cover the information whether switching from cigarettes to IQOS may have prevented cigarette smokers from quitting all TNP. However, assessing quitting behavior was not in the scope of our manuscript. We still added the information that quitting behavior was not investigated to the limitation section of the discussion (page 24, lines 394-396). Reviewers 2 Major Comment 6. The authors should include an explanation of the drop in response rates for JAIQOS samples from 19.4% in Y1 to 4.7% and 2.0% in Y2 and Y3. Given that the IQOS users changed significantly, from 350,000 to 6 million, the IQOS population likely changed over the course of the 3 surveys. The authors should consider accounting for the change in IQOS population by adjusting either during recruitment or during the data analysis. Authors’ Response Major Comment 6. The decline in response rates across the three study years observed for the JAIQOS samples can be explained by the fact that over time, the IQOS users increasingly received email invitations to various PMI surveys which might have generated a lower willingness to participate in our surveys. We included the explanation for the decreasing response rates related to the JAIQOS surveys in the discussion section (page 24, lines 374-377). As stated in the limitations section of the discussion (page 24, lines 386-389), because during the study years, we continuously monitored the response rates and compared them against pre-established quotas on the basis of age and sex, there was no need for further adjustment during recruitment or the data analysis because we still had sufficient samples (500 completed surveys) in each survey wave available. Reviewers 2 Major Comment 7. The authors only present descriptive analyses of survey findings, however, they may want to consider including some trend analysis or other statistical testing to determine whether the changes over time are significant. Perhaps such an analysis may not yield robust findings from a three-year survey and authors may consider providing more statistical rigor in future reports. Authors’ Response Major Comment 7. We thank Reviewers 2 for this valid comment. Our statistical analysis plan for this 3-year study did only foresee descriptive analysis. For future studies, we are considering using more sophisticated trend analysis based on statistical methods. Reviewers 2 Major Comment 8. We understand that the focus of this manuscript was among adults age >20 years. However, an important consideration is the impact of IQOS and other smoke-free products among youth, which is an important public health concern. The authors should mention that this manuscript only addresses adult use behavior and either briefly describe data for youth use based on published literature or national surveys. Some indication of initiation among different age groups of youth and young adults would have provided useful insights in the overall harm reduction potential of IQOS and other smoke-free products. Authors’ Response Major Comment 8. We agree with Reviewers 2 and amended the discussion (page 23, lines 363-365) and limitation section (page 24, lines 396-398), mentioning that our manuscript is based on Japanese adult participants only and that with regard to tobacco harm reduction, tobacco use prevalence among youth should be taken into consideration. The available literature suggests that tobacco initiation with IQOS/HTPs and prevalence of IQOS/HTPs among youth in Japan is low (pages 23-24, lines 365-373). Minor comments Reviewers 2 Minor Comment 1. The authors should consider including the supporting literature citations in the statement – “The existing standard TNP use questions are available in the literature.”. Authors’ Response Minor Comment 1. We thank the Reviewers 2 for this valuable comment. In the methods section, we included the links to the (i) CDC Adult Tobacco Use Questions of the National Health Interview Survey (NHIS), (ii) WHO/CDC/CPHA Questions of the Global Adult Tobacco Survey (GATS), (iii) NIH/FDA PATH Study questionnaires, and (iv) MHLW Tobacco Questions of the Japan National Health and Nutrition Survey (page 6, lines 107-112). Reviewers 2 Minor Comment 2. The authors should provide a possible explanation of the discrepancy in the reported total HTP use prevalence of 11% by Hori et al (ref 34) which is almost twice of that reported in the current manuscript. This discrepancy cannot be solely explained by methodological differences. Authors’ Response Minor Comment 2. We believe that there are multiple conceptual and methodological differences that may have contributed to the lower overall HTP use prevalence (>5%) in our study than that observed by Hori et al. (11%). These differences between our study and the Hori et al. study, respectively, include i.a., (i) cross-sectional vs. longitudinal design, (ii) age ≥20 years vs. age range 15-69 years, (iii) no weighting methods vs. inverse probability weighting, (iv) no adjustments vs. multiple adjustment of the data, (v) definition of current use [at the time of the survey vs. past 30 days], and (vi) lifetime use criterion [100 tobacco sticks] vs. no lifetime use criterion to qualify as a HTP user. Of all these aspects, we believe that the difference in the age groups included in both studies (i.e., age ≥20 year in our study vs. 15-69 years in the Hori et al. study) had the largest impact on the difference in the observed overall HTP prevalence between our study and the study of Hori et al. In our study, we included also older age groups above 69 years, so the age distribution was skewed towards older age groups among whom, however, the IQOS use prevalence was very low with only about 1 %. We added this information to the discussion section (page 23, lines 327-337). Reviewers 2 Minor Comment 3. In this manuscript, the IQOS sample could have been better characterized. Given that the authors had access to the IQOS user database, they could have followed transition behavior over time rather than indirectly comparing changes in average smoking prevalence against increase in IQOS user prevalence. Moreover, they may also report transitions between dual use to exclusive switching behavior. Perhaps in future reports, the authors can include more detailed analyses of transition behaviors. Authors’ Response Minor Comment 3. We thank reviewers 2 for this important comment. Because the present study provides only cross-sectional but not longitudinal data of the same participants follow-ed up over time, investigating transition behaviors was not intended in this study. However, in future studies, we will consider analyzing transition behaviors based on prospective/longitudinal data. Reviewers 2 Minor Comment 4. We believe that the title for Table 6 should include JGAP not JPAG. Please correct the typo. Authors’ Response Minor Comment 4. We thank Reviewers 2 for spotting this typo. We have corrected it."
}
]
},
{
"id": "144380",
"date": "21 Sep 2022",
"name": "David T. Levy",
"expertise": [
"Reviewer Expertise Modelling and empirical 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 provides interesting results on trends in IQOS use as related to smoking and vaping. The methodology and results are well presented. With regards to data underlying the results, I don’t recall that the authors provided for data transferred to others. While desired, there may be issues of confidentiality. Using cross-sectional data, their results show increasing use of IQOS with and without e-cigarettes and a decline in smoking. Their results, however, in the Discussion section, I had problems with the failure to adequately discuss the limitations of the study and the author’s generalization of the results.\nThe limitations of the study merit further attention in the Discussion section. The authors fail to recognize the limited nature of their sample. In particular, the sample is limited to IQOS users and the sample is based on IQOS users who chose to register on the PMI website, thus presenting the potential problem of selection bias. Indeed, IQOS was the first and has a dominant share in Japan and may not represent other HTP use and its relationship to smoking. These limitations should be clearly recognized and discussed. It wasn’t clear to me whether there was a switching between IQOS and other HTPs. The use of cross-sectional rather than longitudinal data also merits discussion.\nIn addition, the authors attempt to generalize the results for IQOS and e-cigarette use in their sample to the rest of the Japanese population by comparing to NHNS and other samples. As currently presented, I did not feel that the conclusions, ie. Upward exclusive use of IQOS as cigarette use decline, are well supported. The authors do compare some trends, but the comparisons are not rigorous. It would be useful to compare relative changes over time in their sample to relative changes other more representative samples (e.g., NHNS, JASTIS), and provide direct comparisons by age and gender in a table. The authors may then be able to compare whether the trends related to IQOS and cigarette use are the same or different. Given the potential for selection bias, which should be made explicit, these comparisons are important.\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? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "8986",
"date": "30 Nov 2022",
"name": "Karina Fischer",
"role": "Author Response",
"response": "Author Responses to Comments of Reviewers We thank Reviewer 1 and Reviewers 2 for their critical and comprehensive review as well as their constructive suggestions to improve the manuscript. We addressed all comments by point-to-point responses and referred to the related updates in the manuscript by page and line numbers (Note: page and line numbers reflect the tracked changes version 2 of the manuscript, not the edited version that reviewers will receive. Reviewers may have to additionally request the tracked changes version). Reviewer 1: David T. Levy Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA. Reviewer 1 comments Reviewer 1 Comment 1. This study provides interesting results on trends in IQOS use as related to smoking and vaping. The methodology and results are well presented. With regards to data underlying the results, I don’t recall that the authors provided for data transferred to others. While desired, there may be issues of confidentiality. Authors’ Response 1. We thank Reviewer 1 for this comment. All data and extended data underlying the results and conclusions of this study as well as the questionnaire and reporting guideline related information (Strobe Checklist) have already been made publicly available on the INTERVALS platform as part of the manuscript submission to F1000Reserach (see Data Availability section [pages 25-26] of the manuscript). Therefore, all data and information underlying the manuscript, are publicly available on the INTERVALS platform and have a Digital Object Identifier (DOI) that directs to the related data/information on INTERVALS. Reviewer 1 Comment 2. Using cross-sectional data, their results show increasing use of IQOS with and without e-cigarettes and a decline in smoking. Their results, however, in the Discussion section, I had problems with the failure to adequately discuss the limitations of the study and the author’s generalization of the results. Authors’ Response 2. We agree with Reviewer 1 to highlight the limitations of the study in more detail. We amended the discussion (page 22, lines 305-308) and limitation (page 24, lines 382-384) section with regard to the limitations of the cross-sectional design, as well as the limitation section in view of the limited generalizability of the results from the IQOS user (JAIQOS) samples (page 24, lines 389-392). Reviewer 1 Comment 3. The limitations of the study merit further attention in the Discussion section. The authors fail to recognize the limited nature of their sample. In particular, the sample is limited to IQOS users and the sample is based on IQOS users who chose to register on the PMI website, thus presenting the potential problem of selection bias. Indeed, IQOS was the first and has a dominant share in Japan and may not represent other HTP use and its relationship to smoking. These limitations should be clearly recognized and discussed. It wasn’t clear to me whether there was a switching between IQOS and other HTPs. The use of cross-sectional rather than longitudinal data also merits discussion. Authors’ Response 3. We would like to clarify that In each of the three study years, the study included both (i) representative samples of the Japanese General Adult Population (JGAP samples based on three-stage stratified proportional random sampling covering the whole of Japan) as well as (ii) “convenience” samples of Japanese adult IQOS users registered in the IQOS owner database of Philip Morris International’s affiliate in Japan (JAIQOS samples randomly selected from about 350,000 IQOS users in 2017 and 6 million IQOS users in 2019 registered in the Japanese adult IQOS owner database). As stated at the end of the introduction, we used the IQOS user samples (JAIQOS samples) alongside the representative JGAP samples because in the first and second year of the study IQOS was relatively new on the Japanese tobacco market, and thus, the IQOS use prevalence in the general population (representative JGAP samples) was expected to be low. Therefore, to obtain reliable estimates of the use patterns of IQOS (i.e., exclusive IQOS use, IQOS use with combustible tobacco products, and IQOS use with non-combustible tobacco products, the differentiation of which is important regarding the impact on tobacco harm reduction), we conducted additional surveys among IQOS users. Because we are aware of the limitations of the JAIQOS samples, most of the results presented in our study are based on the representative JGAP samples (Tables 1-7 and the related text in the results section), whereas only the results presented in Table 1 (demographics), Table 5 (frequency and intensity of use) and Table 8 (IQOS use patterns) are also presented for the IQOS user samples. Both (i) the representative samples of the Japanese General Adult Population (JGAP samples) as well as (ii) the samples of Japanese adult IQOS users registered in Japanese the IQOS owner database (JAIQOS samples) were random samples. Therefore, we believe that the likelihood of selection bias was rather low. Because the present study provides cross-sectional but not longitudinal data of the same participants over time, investigating switching behaviors was not intended for this manuscript. As already stated in our response to comment 2, we amended the discussion (page 22, lines 305-308) and limitation section (page 24, lines 382-384) with regard to the limitations of the cross-sectional design, as well as the limitation section in view of the limited generalizability of the results from the IQOS user (JAIQOS) samples (page 24, lines 389-392). Moreover, in the limitation section we added the fact even though IQOS™ was the first HTP and had the highest use prevalence in Japan, IQOS use behavior may not represent the use behavior of other HTPs available in Japan (page 24, lines 392-394). Reviewer 1 Comment 4. In addition, the authors attempt to generalize the results for IQOS and e-cigarette use in their sample to the rest of the Japanese population by comparing to NHNS and other samples. As currently presented, I did not feel that the conclusions, i.e. Upward exclusive use of IQOS as cigarette use decline, are well supported. The authors do compare some trends, but the comparisons are not rigorous. It would be useful to compare relative changes over time in their sample to relative changes other more representative samples (e.g., NHNS, JASTIS), and provide direct comparisons by age and gender in a table. The authors may then be able to compare whether the trends related to IQOS and cigarette use are the same or different. Given the potential for selection bias, which should be made explicit, these comparisons are important. Authors’ Response 4. We thank Reviewer 1 for raising this point. Regarding the prevalence data of overall tobacco product as well as IQOS and other individual tobacco product use, in the discussion, we compared the study results from the representative JGAP samples with the corresponding data from one of the most comprehensive surveys measuring tobacco use, the representative Japan National Health and Nutrition Survey (Japan NHNS) from the Japanese Ministry of Health, Labour and Welfare. While we indeed present data on exclusive IQOS use, we did not state that with increasing exclusive IQOS use the use of cigarettes declined as Reviewer 1 remarked. Rather, in the manuscript (page 22, lines 302-304) we stated “there was a trend towards a declining prevalence of cigarette smoking concurrent with an increase in smoke-free TNP and total HTP use, especially in case of IQOS use. So, with regard to the decline in overall cigarette smoking prevalence, we are not referring to exclusive IQOS use but to overall smoke-free TNP, total HTP, and IQOS use. Regarding the point that our survey may have suffered from selection bias (see also our response on selection bias to Reviewer 1’s comment 3), we mentioned this aspect in the limitation section (page 24, line 386-389). However, because both (i) the representative samples of the Japanese General Adult Population (JGAP samples, three-stage stratified proportional sampling) as well as (ii) the samples of Japanese adult IQOS users registered in Japanese adult IQOS owner database (JAIQOS samples randomly selected from about 350,000 IQOS users in 2017 and 6 million IQOS users in 2019 registered in the Japanese adult IQOS owner database) were random samples from the respective reference populations, we believe that the likelihood of selection bias was rather low. As opposed to our cross-sectional study that includes adult participants ≥20 years and presents unadjusted data, the Japan Society and New Tobacco Internet Survey (JASTIS) is a longitudinal (cohort) study following both youth and adults aged 15-73 years over time and presents adjusted data. Therefore, given the different study design and age groups included, we cannot directly compare our results from the cross-sectional JGAP and JAIQOS samples with the longitudinal JASTIS study as Reviewer 1 suggested (see also Authors’ Response to Reviewers 2 Minor Comment 2). However, we compared our prevalence data from the representative JGAP samples with the sales data of cigarettes and heated tobacco product (HTP) use (Chart 1 below) as well as with the prevalence data from the representative Japan National Health and Nutrition Survey (Japan NHNS) conducted yearly by the Japan Ministry of Health, Labour and Welfare (Chart 2 below) over time. In 2021, HTP units represented almost 1/3 of the total cigarette and HTP market. The increase in HTP sales was accompanied by a decline in cigarette sales (Chart 1 below). Chart 1 Cummings K. F. et al.(2020) What Is Accounting for the Rapid Decline in Cigarette Sales in Japan? Int J Environ Res Public Health; 17(10): 3570. Doi: 10.3390/ijerph17103570. The sales data for 2020 and 2021 was added to the data published for 2011-2019 by Cummings et al. The prevalence data from the Japan NHNS (Chart 2 below) suggests that the decline in cigarette sales shown in Chart 1 was accompanied by a decrease in smoking prevalence. Until 2017, the Japan NHNS measured only the prevalence of smoking. However, because between 2015 and 2017 HTP sales had already rapidly increased as shown in Chart 1, it can be assumed that between 2015 and 2017 also the HTP use prevalence increased. In 2018 the Japan NHNS was updated to capture the prevalence of both cigarettes and HTPs separately. In 2019, 12% of the adult population were smoking only combustible cigarettes, shown in dark grey, 3.4% were using only HTPs, shown in light blue, 1.1% were using both cigarettes and HTPs, and 0.2% used other or undefined tobacco products (Chart 2 below). Because the Japan NHNS was discontinued in 2020 and 2021 due to the Covid pandemic, there is unfortunately no data for more recent trends. Chart 2. Prevalence data on cigarette and HTP use from the Japan National Health and Nutrition Survey (Japan NHNS) conducted by the Japan Ministry of Health, Labour and Welfare The data presented in Table 4 of our manuscript for cigarette and IQOS use prevalence in the representative GAP samples from 2016-2019 (shown as Chart 3 below; the chart includes also the most recent 2020/2021 GAP data) are similar to the 2016 -2019 data from the Japan NHNS, which shows a decline in cigarette smoking prevalence accompanied with a marked uptake of HTP use as of 2018 when both cigarettes and HTPs were separately measured in the Japan NHNS. Chart 3. Data presented in Table 4 of the manuscript for cigarette and IQOS use prevalence in the representative GAP samples from 2016 -2019 (on the left side of the green dashed line) as well as most recent 2020/2021 prevalence data for cigarette and IQOS use (on the right side of the green dashed line) that are not shown in the manuscript. Given all the information presented above, we believe that our observation of a decline in cigarette smoking prevalence accompanied with an increase in IQOS/HTP use prevalence over the three study years in Japan is supported by independent data."
}
]
}
] | 1
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https://f1000research.com/articles/11-720
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https://f1000research.com/articles/11-1072/v1
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20 Sep 22
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{
"type": "Research Article",
"title": "The circadian clock mediates the response to oxidative stress in a cone photoreceptor‒like (661W) cell line via regulation of glutathione peroxidase activity",
"authors": [
"Kenkichi Baba",
"Ting-Chung Suen",
"Varunika Goyal",
"Adam Stowie",
"Alec Davidson",
"Jason DeBruyne",
"Gianluca Tosini",
"Ting-Chung Suen",
"Varunika Goyal",
"Adam Stowie",
"Alec Davidson",
"Jason DeBruyne",
"Gianluca Tosini"
],
"abstract": "Background: The mammalian retina contains an autonomous circadian clock that controls many physiological functions within this tissue. Our previous studies have indicated that disruption of this circadian clock by removing Bmal1 from the retina affects the visual function, retinal circuitry, and cone photoreceptor viability during aging. In the present study, we employed a mouse-derived cone photoreceptor‒like cell, 661W, to investigate which molecular mechanisms of the circadian clock may modulate cone photoreceptor viability during aging. Methods: Bmal1 knockout (BKO) cells were generated from 661W cells using the CRISPR/Cas9 gene editing tool. Deletion of Bmal1 from 661W was verified by western blot and monitoring Per2-luc bioluminescence circadian rhythms. To investigate the effect of Bmal1 removal on an oxidative stress challenge, cells were treated with hydrogen peroxide (H2O2,1 mM) for two hours and then cell viability was assessed. Cells were also cultured and harvested for gene expression analysis and antioxidant assay. Results: Our data indicated that 661W cells contain a functional circadian clock that mediates the response to an oxidative stress challenge in vitro and that such a response is no longer present in the BKO cell. We also hypothesized that the effect was due to the circadian regulation of the intracellular antioxidant defense mechanism. Our results indicated that in 661W cells, the antioxidant defense mechanism is under circadian control, whereas in BKO cells, there is an overall reduction in this antioxidant defense mechanism, and it is no longer under circadian control. Conclusions: Our work supported the notion that the presence of a functional circadian clock and its ability to modulate the response to an oxidative stress is the underlying mechanism that may protect cones during aging.",
"keywords": [
"Circadian rhythm",
"Bmal1",
"Photoreceptors",
"661W cells",
"Oxidative stress",
"Antioxidant",
"Nrf2",
"GPX"
],
"content": "Introduction\n\nThe presence of a retinal circadian clock in mammals was demonstrated in the 1990s,1,2 and many studies have shown that retinal circadian clocks control many physiological functions within the retinal tissue.3 Additional studies using mice in which clock genes have been deleted have reported that the disruption of retinal circadian clocks has a profound effect on the retina.4–7 In the retina, clock genes are expressed in the photoreceptors and inner nuclear and ganglion cell layers.8–11 In the photoreceptor layer, only the cone photoreceptors seem to express clock genes.9 Consistent with these observations, a series of recent studies using a retina-specific Bmal1 knockout (KO; Chx10Cre; Bmal1fl/fl) mouse have reported that removal of the Bmal1 gene abolished the circadian rhythm of the photic (cone) electroretinogram,4 altered the spectral identity,12 and the viability of the cone photoreceptors during aging.13 Hence, disruption of the circadian clock in the cones affected many biological functions of these cells.14\n\nPhotoreceptors, especially cones, have a high metabolic rate15,16 and contain more mitochondria than rods.17,18 Consequentially, cones produce a high level of reactive oxygen species (ROS). ROS are by-products of mitochondrial aerobic metabolism and an accumulation of ROS during aging is natural and inevitable.19,20 Elevated intracellular levels of ROS cause oxidation and damage to lipids, proteins, nucleotides, and mitochondria.21,22 The daily activity of an organism is closely connected with ROS production, and rhythmic ROS production/cellular oxidation is reported in many organs.23–25 Furthermore, the removal of Bmal1 increases ROS levels in a variety of mammalian organs.26–30\n\nHence, it is possible to speculate that the reduction in cone viability observed in our previous study in mice lacking Bmal114 may have been due to a dysfunction in the circadian regulation of the cells’ antioxidant defenses. Unfortunately, in the mouse retina, cones comprise only 2% to 3% of the total photoreceptors; thus, performing in vivo mechanistic studies of these cells is challenging.\n\nRecent studies have reported that 661W cells, which are a murine cone-like photoreceptor cell line developed by Tan et al.,31 are useful for investigating the fundamental aspects of cone biology in vitro.31,32 Using these cells, several studies have provided important insights into the molecular mechanisms regulating photoreceptor metabolism33–35 and death following exposure to oxidative stress.36,37\n\nThe aim of the present study was first to investigate whether 661W cells contain a functional circadian clock and then to explore whether the cells would be useful for investigating the role of the circadian clock in the modulation of their response to oxidative stress.\n\n\nMethods\n\n661W cells (RRID:CVCL_6240) were grown in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Life Technologies, Carlsbad, CA, USA) supplemented with 5% fetal bovine serum (Gibco) and 1% penicillin/streptomycin at 37°C in a 5% CO2 humidified atmosphere.37 Cells were seeded in 35 mm or 100 mm dishes, 96-well plates (Corning, Inc., Corning, NY, USA), or chamber slides (Lab-Tek, Inc., Grand Rapids, MI, USA) at a concentration of 1 × 104 to 5 × 105 cells in a volume of 0.2 to 5 mL of media and grown to approximately 50% to 90% confluence, depending on the experimental protocol.\n\nPer2-luc, a plasmid that expresses the luciferase gene driven by the Per2 promoter, was used.38 Briefly, 1 μg of Per2-luc and 0.1 μg of pcDNA3 (which expresses the neomycin-resistant gene driven by the cytomegalovirus enhancer-promoter) was transfected by lipofectamine 2000 (Invitrogen, Waltham, MA, USA) into the 661W cells. The cultured 661W cells were then treated with a final concentration of 400 μg/mL geneticin and geneticin-resistant colonies were selected for bioluminescence verification. Cell lines that express luciferase activity in a circadian manner were identified by the bioluminescence emitted from 661W cells. Per2-luc-transfected 661W cells were cultured in DMEM containing 0.1 mM D-luciferase K salt (Molecular Imaging Products Co., Bend, OR, USA), and the bioluminescence emitted from the cells was monitored with either Lumicycle (Actimetrics, Wilmette, IL, USA; see details in Baba et al.39) or a charged-coupled device (CCD) camera (Stanford Photonics, Palo Alto, CA, USA; XR Mega 10Z; see details in Evans et al.40 and Baba et al.39). Briefly, the bioluminescence images of cultured 661W cells were obtained by a Zeiss AxioObserver Z1 microscope (Zeiss, Oberkochen, Germany) with an ×10 Fluar objective lens (Zeiss), Marzhauzer scanning stage with LUDL Mac 5000 controller, and a Stanford Photonics (Palo Alto, CA, USA) XR Mega 10Z cooled intensified CCD camera in a custom-built light-tight chamber maintained at 37°C. Bioluminescence rhythms recorded by Lumicycle were analyzed by Lumicycle analysis software (Actimetrics), and a peak of the Per2-luc rhythm was identified by Origin software (OriginLab Corp., Northampton, MA, USA; see details in Baba et al.41). Briefly, bioluminescence recordings obtained from Lumicycle were detrended by a 24-hour moving average subtraction method and smoothed by a 2-hour moving average. The circadian peak phase was determined as the highest point of the curve picked by Origin software. Per2-luc bioluminescence emitted from 661W cells was captured by a CCD camera every 30 minutes for three days. The intensity of the bioluminescence from consecutive captured images was analyzed with ImageJ software (National Institutes of Health [NIH], Bethesda, MD, USA).\n\nA construct to knock out Bmal1 was purchased from Santa Cruz Biotechnology, Inc. (Dallas, TX, USA; BMAL1 CRISPR/Cas9 KO Plasmid, Santa Cruz sc-419206). The BMAL1 CRISPR/Cas9 KO plasmid is a pool of three different gRNA plasmids with the following sequences: sc-419206 A: Sense: 5′- TAGATAAACTCACCGTGCTA-3′; sc-419206 B: Sense: 5′-CTGCACGTACCCTGAGAATT-3′; sc-419206 C: Sense: 5′-TTACTAGGTACCTTCCATGA-3′. The Per2-luc 661W cells cultured on a 12-well plate were co-transfected with 0.5 μg of the BMAL1 CRISPR/Cas9 KO plasmid and 0.5 μg of the BMAL1-R HDR plasmid (Santa Cruz sc-419206-HDR). The plasmid included a puromycin resistance gene (used for the selection of colonies) and the red fluorescent protein (RFP) to detect the correct insertion of the plasmid in the genome. After selection in a medium containing puromycin (4 μg/mL), only cells with RFP signals were isolated. Then the removal of Bmal1 from the 661W cells was verified by western blotting using the BMAL1 antibody (Cell Signaling Technology, Danvers, MA, USA; cat. no. 14020; RRID:AB_2728705).\n\nThe plasmid pMSCV-Zeo was purchased from Addgene (Watertown, MA, USA; RRID:Addgene_75088). A 1.1-kb EcoRI to EcoRV fragment containing the expression cassette of the bleomycin-resistant gene driven by the PGK promoter was cut from the pMSCV-Zeo and cloned into the corresponding sites of pCMVSport6 to generate pSport6Zeocin. To re-express Bmal1 in the 661W-Bmal1-KO cells, the Bmal1 KO cell line was transfected by lipofectamine 2000 (Invitrogen, Waltham, MA, USA) with 250 ng of pCMVFlagBmal1 and 25 ng of pSport6Zeocin. Zeocin-resistant colonies were isolated and developed into cell lines. Bmal1 expression was verified by western blotting.\n\nCultured 661W cells were collected at different time points and the total RNA was isolated using TRIZOL (Life Technologies). cDNA was synthesized from isolated RNA using a High-Capacity RNA-to-cDNA Kit (Life Technologies). The quantitative polymerase chain reaction (Q-PCR) was performed with the CFX96 Touch Real-Time PCR Detection System (Bio-Rad Laboratories, Hercules, CA, USA) using iQ SYBR Green Supermix (Bio-Rad Laboratories). The primer sequences used to evaluate the gene expression were Per1 forward, 5′-TGAAGCAAGACCGGGAGA-3′ reverse, 5′-CACACACGCCGTCACATCAA -3′; Per2 forward, 5′-GAAAGCTGTCACCACCATAGAA-3′ reverse 5′-AACTCGCACTTCCTTTTCAGG-3′; Bmal1 forward, 5′-AACCTTCCCGCAGCTAACAG-3′ reverse 5′-AGTCCTCTTTGGGCCACCTT-3′; DBP forward 5′-CCTGAGGAACAGAAGGATGA-3′ reverse 5′-ATCTGGTTCTCCTTGAGTCTTCTTG-3′; Nrf2 forward, 5′-CGAGATATACGCAGGAGAGGTAAGA-3′ reverse 5′-GCTCGACAATGTTCTCCAGCTT-3′; 18S ribosomal RNA forward 5′-TTGTTGGTTTTCGGAACTGAGGC-3′ reverse 5′-GGCAAATGCTTTCGCTCTGGTC -3′.\n\nHydrogen peroxide (H2O2, Sigma-Aldrich, St. Louis, MO, USA) was diluted with double-distilled water to 1 M as a working solution, and 2 μl were added to 2 mL of the medium to make the final 1-mM concentration. Liproxstatin-1 (Lip1; Cayman Chemical, Ann Arbor, MI, USA) was dissolved in DMSO (47 mM) and further diluted with PBS to 200 μM. Ten microliters of this solution was added to 2 mL of the medium to make 2 μM of the final concentration.\n\nThe antioxidant capacity and glutathione peroxidase (GPx) activity were determined using commercially available assay kits (Antioxidant Assay Kit, Cayman Chemical cat. no. 709001; Glutathione Peroxidase Assay Kit, Cayman Chemical cat. no. 703102). The 661W and BKO cells were seeded and grown in 100-mm dishes with 5 mL of medium. When the cells reached 80% to 90% confluency, the medium was exchanged. Cells were washed with PBS and harvested using a cell scraper (CELLTREAT Scientific Products, Pepperell, MA, USA) at 26.5 and 38.5 hours after the medium exchange. Cells were then collected in a 1.5-mL tube, and the numbers of cells in each tube were counted using a cell counter (Bio-Rad TC20 Automated Cell Counter). Cells in the tubes were centrifuged (1000 × g for 10 min), and the cell pellet was homogenized in the extraction buffer included in the kits. After centrifuging, the supernatant was collected and the antioxidant capacity or GPx activity was measured according to the manufacturer’s protocol. The microplate reader (Cytation 3; BioTek Instruments, Inc., Winooski, VT, USA) was used to measure the absorbance at 750 and 405 nm for the antioxidant assay and at 340 nm for the GPx assay.\n\nCells were grown to near confluence in 35-mm dishes or 6-well plates (Falcon, Fisher Scientific, Waltham, MA, USA), washed with PBS, treated with trypsin, and transferred to 15-mL conical centrifuge tubes (Falcon) with the addition of 5 mL of medium. After centrifugation (400 x g for 5 min), the cell pellets were resuspended in 5 mL of PBS. Cell pellets obtained after another centrifugation (400 x g for 5 min) were lysed with RIPA buffer (Boston BioProducts, Inc., Milford, MA, USA) and supplemented with a protease inhibitor cocktail (cat. no. 5871S, Cell Signaling Technology). Cell lysates were cleared by centrifugation (17,000 x g for 30 min), and aliquots were mixed with Laemmli buffer, 6X SDS-Sample buffer, (cat. no. BP-11R, Boston Bioproducts, Inc.), heated to 950°C, loaded, and run on a Criterion Midi Protein Gel with the Criterion Vertical Electrophoresis Cell System (Bio-Rad Laboratories). Proteins were transferred from gels onto an Amersham HyBond PVDF membrane (Cytiva Life Sciences, Marlborough, MA, USA) using the Bio-Rad Trans-Blot Turbo Transfer system. Membranes were washed with 1X Tris buffered saline (TBS), diluted from a 20X TBS stock solution (Boston Bioproducts, Inc.), for 5 minutes followed by blocking in 5% non-fat dry milk or bovine serum albumin (BSA) (Boston Bioproducts, Inc.) in TBS. The primary antibody in TBST (0.1% Tween-20 in 1X TBS) was then added to the membrane and placed on a rocking platform at 4°C overnight. The membrane was washed in TBST three times for 10 minutes each time on a rotating platform at room temperature before the secondary antibody in TBST was added. Fluorescence-conjugated antibodies were purchased from Fisher Scientific; they included Invitrogen’s goat-anti-rabbit Alexa Fluor Plus 800 (Thermo Fisher Scientific, Inc.; RRID:AB_2633284) or goat-anti-rabbit Alexa Fluor Plus 680 (Thermo Fisher Scientific, Inc.; RRID:AB_2633283), depending on the experiment. After an 1-hour incubation at room temperature, the membrane was washed in TBST three times for 10 minutes each time, after which imaging was done with the LI-COR Odyssey Fc Imaging system (LI-COR, Lincoln, NB, USA).\n\n661W cells were seeded and cultured in chamber slides (Lab-Tek, Inc.) for immunohistochemical studies. Cells were fixed in paraformaldehyde (PAF) 4% and washed with PBS. Cells were incubated for 45 min in 1% BSA and 0.4% Triton-X100 in PBS to permeabilize the membranes and block unspecific binding. Cells were then incubated overnight at 4°C with primary BMAL1 antibodies (1:1500; cat. no. 14020, Cell Signaling Technology), washed in PBS, and incubated for 2 hours at room temperature in secondary antibodies (anti-rabbit conjugated with Alexa Fluor 488, 1:1000). After washing in PBS, slides were cover-slipped with Vectashield (Vector Laboratories, Newark, CA, USA) and cells were visualized with a fluorescence microscope (Zeiss LSM700).\n\nData were analyzed with a one-way or two-way ANOVA and the Tukey multiple comparison test using SPSS software (IBM; RRID:SCR_016479). A simple paired t-test was performed with the Microsoft Excel (RRID:SCR_016137) data analysis program. The rhythmicity of the oxidative stress response was analyzed by the Nitecap program (https://nitecap.org/: developed by the University of Pennsylvania Perelman School of Medicine).42\n\n\nResults\n\nCultured 661W cells were grown in a culture dish and collected when they were confluent. RNA was isolated from these cells; Per1, Per2, Bmal1, and 18S mRNAs were amplified; and analyzed by electrophoresis. The expression of these genes in the mouse brain, retina, and retinal pigment epithelium (RPE) was also analyzed by electrophoresis to serve as reference points. The results showed that clock genes were expressed in the 661W cells, retina, RPE, and brain (Figure 1A). To examine the circadian oscillation in the 661W cells, the cells were collected 20.5, 26.5, 32.5, and 38.5 hours after the cells were resynchronized by a medium exchange, and the expression levels of Per2, Bmal1, and DBP mRNAs were measured. The Per2 and DBP mRNAs were expressed in a circadian manner (Figure 1B and C, one-way ANOVA, p < 0.05), with peak expression at 20.5 hours. Bmal1 also showed circadian expression (Figure 1D, one-way ANOVA, p < 0.05) with peak expression at 32.5 hours. The bioluminescence emitted from the 661W cells transfected with the Per2-luc reporter also showed a circadian rhythm (Figure 1E). The circadian peak of Per2-luc bioluminescence in the 661W cells occurred 20.47 ± 0.21 hours after the medium exchange, and the average circadian period was 23.18 ± 0.15 hours (mean ± SEM, n = 100). The bioluminescence intensity captured by the CCD camera for three days also showed a circadian rhythm (Figure 1F, peak phase 20.23 hours, period 22.02 hours). A single cell was selected in the area of the CCD image by ImageJ software (RRID:SCR_003070), and a robust Per2-luc circadian rhythm was also observed for a single 661W cell (Figure 1G and H: cell 1 peak: 24.36 hours, period: 20.08 hours; cell 2 peak: 18.43 hours, period 23.90 hours).\n\n(A) Per1, Per2, and Bmal1 mRNA was amplified in mouse brain (1), retina (2), RPE (3), and 661W cells (4). (B to D) Circadian expression of Per2, Bmal1, and DBP mRNA in 661W cells at four different time points (one-way ANOVA, p < 0.05 in all cases, n = 6). (E) Representative Per2-luc bioluminescence circadian rhythm in 661W cells (detrended data) measured by Lumicycle. (F) Per2-luc bioluminescence from 661W cells measured with a CCD camera for 2 days; the bioluminescence rhythm was analyzed. (G to H) A single cell’s Per2-luc bioluminescence was measured with a CCD camera.\n\nSeveral Bmal1 KO (BKO) 661W cell lines were generated using the CRISPR-cas9 gene-editing tool. Western blot analysis showed the successful removal of Bmal1 in cell lines 2, 3, 4, 8 and 9 (Figure 2A). A long-exposure image also confirmed the loss of BMAL1 expression. We selected the cell line with the least signal to be used in our experiments. The deletion of Bmal1 in this line was verified by immunohistochemical studies (Figure 2B). Consistent with these results, we did not observe any rhythmicity in the expression levels of Per2, Bmal1, or DBP mRNA in the BKO cells (one-way ANOVA, p > 0.1 in all cases; Figure 2C to E) or in the Per2-luc bioluminescence (Figure 2F).\n\n(A) Western blot indicating the successful knockout of BMAL1 in multiple cell lines (i.e., lines 2, 3, 4, 8, and 9); others show a truncated Bmal1 (i.e., lines 5, 6, 7, and 10). (B) BMAL1 immunoreactivity was detected in 661W cells (upper panel), but not in a BKO cell line (line 4) (lower panel). (C to D) Loss of rhythmicity in Per2, DBP, and Bmal1 mRNA levels in BKO cells (one-way ANOVA, p > 0.05 in all cases, n = 6). (F) 661W-BKO cells no longer exhibit Per2-luc bioluminescence rhythm (detrended data) as observed in Figure 1E.\n\nThe 661W and BKO cells were cultured and then subjected to an oxidative stress challenge by adding 1 mM of H2O2 to the cultured cells at six-hour intervals starting from the first peak phase of the Per2-luc (Figure 3A) for two consecutive circadian cycles (from 20.5 to 62.5 hours after medium exchange). For the control groups were treated with the same volume of double distilled water (n = 6 to 8 for each time point) and the survival rate was normalized with the control value. The 661W cells showed a clear circadian rhythm in their responses to the oxidative stress challenge (Figure 3B, one-way ANOVA, p < 0.05, Jonckheere-Terpstra-Kendall (JTK) algorithm p < 0.001: period 24.0 hours: amplitude 0.233, n = 7 to 8). The cells were most resistant to the oxidative stress challenge at 26.5 and 50.5 hours (second cycle) and least resistant at 38.5 and 62.5 hours (second cycle). In the BKO cells, the survival rate was greatly reduced (only ~30% survived the H2O2 treatment, two-way ANOVA, p < 0.01 between groups) and no circadian variation was observed (one-way ANOVA, p > 0.05; JTK algorithm p > 0.05, Figure 3B).\n\n(A) Schematic illustration of experimental procedures. Cells were treated with H2O2 at 6-h intervals from the peak phase of the Per2-luc rhythm for two circadian cycles. BKO cells were treated with H2O2 at the same time points as in 661W cells. (B) The survival rate following exposure to H2O2 (1 mM) at different circadian times (from 20.5 to 60.5 h) showed a clear circadian rhythm. The survival rate was highest at 26.5 h and lowest at 38.5 h during the first cycle after medium exchange and at 50.6 h and 60.5 h, respectively, during the second cycle. BKO cells did not show circadian variation in oxidative stress sensitivity and had a lower survival rate compared with 661W cells. (Mean ± SEM, n = 7 to 9, two-way ANOVA followed by Tukey multiple comparison test, †p < 0.05, ‡p < 0.05 compared with 661W cells at 20.5 h, *p < 0.05 compared with same time point for 661W cells).\n\nThe nuclear factor erythroid 2–related factor 2 (Nrf2) is a well-known regulator for antioxidant response elements,43 and the expression of Nrf2 is regulated by the circadian clock via E-box elements.44–46 Hence, we hypothesized that the circadian variation in the sensitivity to oxidative stress was mediated by the circadian regulation of Nrf2. Indeed, Nrf2 mRNA showed a circadian expression in 661W cells (Figure 4A, one-way ANOVA, p < 0.05), whereas in the BKO cells, the expression level of Nrf2 mRNA was arrhythmic and significantly decreased. We measured the antioxidant capacity in 661W and 661W-BKO cells at the time of maximum and minimum cell survival to the oxidative stress challenge (i.e., 26.5 and 38.5 hours). In the 661W cells, the antioxidant capacity at 26.5 hours was fourfold higher than the antioxidant capacity at 38.5 hours (two-way ANOVA followed by the Tukey multiple comparison test, p < 0.05; Figure 4B). The antioxidant capacity of the 661W-BKO cells was significantly reduced (~50%) with respect to what we observed in the 661W cells at 26.5 hours (p < 0.05). We also observed a slight difference in the antioxidant capacity in the BKO cells between 26.5 and 38.5 hours (p < 0.05; Figure 4B). Of the many antioxidants present in the cells, GPx was a possible candidate for the mediation of the circadian response to oxidative stress because GPx is an intracellular antioxidant that enzymatically reduces H2O2 to H2O.47 Thus, we decided to investigate whether GPx activity was also regulated by the circadian clock in the 661W cells. As shown in Figure 4C, the GPx activity was higher at 26.5 hours and lower at 38.5 hours in the 661W cells (two-way ANOVA followed by Tukey multiple comparison test, p < 0.05; Figure 4C). In the BKO cells, the GPx activity was lower at 26.5 hours compared with in the 661W cells (two-way ANOVA followed by Tukey multiple comparison test, p < 0.05), and no difference was observed between the level of GPx activity at 26.5 and 38.5 hours.\n\n(A) Circadian expression of Nrf2 was rhythmic in 661W cells but not in BKO cells (two-way ANOVA, p < 0.05 between groups on the Tukey multiple comparison test, *p < 0.05, one-way ANOVA 661W cells: p < 0.05; BKO cells: p > 0.05, n = 6). (B) Circadian variation in antioxidant capacity was observed in both WT and BKO cells, although antioxidant capacity of BKO cells was lower than of 661W cells at 26.5 h (two-way ANOVA followed by Tukey multiple comparison test, n = 6, **p < 0.01 661W cells vs. BKO cells, †p < 0.05, ‡p < 0.01 26.5 h vs. 38.5 h). (C) Circadian fluctuation of GPx activity was observed in WT 661W cells but not in BKO cells (two-way ANOVA followed by Tukey multiple comparison test, n = 5 to 6, **p < 0.01 WT cells vs. BKO cells, ‡p < 0.01 26.5 h vs. 38.5 h).\n\nFerroptosis is a cell death process that is driven by the accumulation of iron-dependent lipid peroxidation.48 GPx plays an important role in this cell death pathway.49 We hypothesized that ferroptosis mediated the cell death process in 661W and BKO cells after H2O2 exposure. To explore this theory, we investigated whether the ferroptosis inhibitor liproxstatin-1 (Lip1) could prevent cell death from oxidative stress. The 661W and BKO cells were cultured, and pretreated with Lip1 (2 μM) 30 minutes prior to the H2O2 treatment at 26.5 and 38.5 hours. As shown in Figure 5, treatment with Lip1 increased the survival of BKO cells at 26.5 hours (Figure 5A) and almost completely prevented cell death at 38.5 hours (Figure 5B) in both genotypes (two-way ANOVA followed by Tukey multiple comparison test, p < 0.01).\n\n(A) Treatment of Lip1 increased cell viability by approximately 30% in BKO cells at 26.5 h after medium exchange. (B) Lip1 treatment significantly increased cell viability in both cell types from H2O2-induced cell death at 38.5 h after medium exchange (two-way ANOVA followed by Tukey multiple comparison test, n = 6, **p < 0.01 control vs. Lip1).\n\nTo confirm that the effects we observed in the BKO cells were due to the removal of Bmal1, we rescued Bmal1 in the BKO cells by transfecting the Bmal1 construct into the BKO cells. The rescued cell lines were confirmed by western blotting (Figure 6A). Stable BKO-Bmal1–rescued cells were cultured and exposed to an oxidative stress challenge as previously described (Figure 3). Our data indicate that the rescued Bmal1 in the BKO cells significantly increased the cell survival rate (10% – 20%) during the oxidative stress challenge at 20.5, 26.5, and 32.5 hours (two-way ANOVA followed by Tukey multiple comparison test, *p < 0.05; Figure 6B).\n\n(A) Western blot indicating the successful re-expression of BMAL1 in the BKO cells (line #5). (B) Bmal1 rescue restored circadian variation in the sensitivity to oxidative stress in BKO cell (two-way ANOVA followed by Tukey multiple comparison test, n = 6 to 12, *p < 0.05 BKO rescued cell vs. BKO cell).\n\n\nDiscussion\n\nThe effects of circadian dysfunction caused by genetic and environmental manipulations of the retina have garnered considerable interest in recent years. As previously mentioned, experimental evidence indicated that the cone photoreceptors are very susceptible to circadian disruption.4,5,12 However, the lack of a suitable cell model has hampered progress in understanding the molecular mechanism(s) with which the circadian clock may regulate biological functions in these cells. In the present study, we have demonstrated that the cone-like photoreceptor cell line 661W, contains a functional circadian clock; that this circadian clock modulated the response of these cells to an oxidative stress challenge; that the mechanisms by which the circadian clock modulated this response involved the regulation of GPx activity; and that the cell death we observed after H2O2 exposure was due to ferroptosis. We also observed that removal of the clock gene Bmal1 from the cell abolished the circadian response and that the rescue of Bmal1 in the BKO cells increased cell survival after oxidative stress. Thus, we believe that the 661W cell line is a useful new tool for investigating the action of the circadian clock in regulating photoreceptor (cone) biology.\n\nROS are by-products of metabolic processes and are produced according to the metabolic needs of cells.50 In the retina, the high level of ROS production by photoreceptors occurs during the day when the photoreceptors are actively involved in the phototransduction of light signals.51,52 Previous studies suggested that circadian dysfunction increases intracellular ROS level26–30 and that the accumulation of ROS and dysfunction of ROS homeostasis in retinal cells leads to many types of retinal diseases.20 Antioxidants are endogenous products that scavenge excessive ROS. This ROS scavenging system is crucial for cell maintenance and survival.22 Previous studies have shown that the expression patterns of antioxidant enzymes (i.e., GPx, catalase, peroxiredoxin, and superoxide dismutase) are controlled by the circadian clock.53–57 Therefore, a functional circadian clock may provide an important protective function by synchronizing the production of the antioxidant response with the time of maximum ROS production, thus reducing the numbers of ROS in a cell. Our new data supported this notion by demonstrating that in 661W cells, the circadian clock can modulate the response to oxidative stress by regulating the antioxidant capacity (Figures 3 and 4B).\n\nA number of studies have suggested that the involvement of the circadian clock in the regulation of antioxidant elements is mediated through Nrf2.57,58 Indeed, previous investigations have shown that the circadian expression of Nrf2 is under the direct control of the circadian clock via the E-box present on the promoter region of this gene and that Nrf2 shows a similar pattern of expression of Per1 and Per2.12,44 Our results agree with these previous studies, showing that Nrf2 mRNA is rhythmically transcribed with a similar rhythmic pattern of Per2 in 661W cells but not in BKO cells.\n\nOne of the most surprising results obtained in our study regarding the antioxidant capacity of 661-BKO cells in the presence of a circadian rhythm (although at a much lower amplitude than 661W cells) (Figure 4A). A previous study showed that peroxiredoxins, a group of antioxidant proteins, may have a circadian rhythm in redox cycles in red blood cells,56 which have no nucleus and therefore cannot generate a circadian oscillation via the transcriptional translational feedback loops’ clock mechanism.59 Additionally, another recent study has reported that circadian oscillation in the transcriptome and proteome of mammals can be present in the fibroblast and in the mouse liver even when Bmal1 has been removed.60 Although the results reported in these studies are controversial,61,62 our new data may suggest that in some situations, the removal of Bmal1 may not completely abolish circadian oscillations (Figure 4B). However, it is important to notice that although the antioxidant capability has a circadian variation in 661W-BKO cells, the changes did not extend to changes in the GPx antioxidant capability (Figure 4C) and, more importantly, did not translate to cell survivability after an oxidative stress challenge (Figure 3B).\n\nFerroptosis is a newly discovered nonapoptotic cell death cascade that is characteristic of the iron-dependent oxidation of phospholipids.47 Ferroptosis is activated by the dysregulation of the GPx antioxidant defense mechanism, which causes lipid peroxidation and cell death.63 Circadian expression of GPx has been reported in many organs, including the mouse retina,44,57 and accumulating evidence suggests that the dysregulation of GPx causes retinal diseases and blindness.64,65 Our results showed that Lip-1 (inhibiting lipid peroxidation to prevent ferroptosis activation66) prevents cell death from oxidative stress at 38.5 hours in both genotypes, thus suggesting that the cell death that follows H2O2 exposure is probably due to ferroptosis. However, it may be that other cell death pathways (i.e., apoptosis, necroptosis67,68) are involved, since Lip-1 only partially prevented cell death in BKO cells at 26.5 hours.\n\nFinally, it is important to mention that in vivo studies have shown that the magnitude of oxidative stress damage (light-induced photoreceptor damage) is greatly affected by the time of the day. Nocturnal rodents are three to four times more susceptible to light damage at night than during the day.69–71 The circadian dependence of light-induced photoreceptor damage appears to involve changes in the cAMP levels.72 Our new data expands these previous results by suggesting that a change in GPx may be involved in the modulation of the circadian dependence of light-induced photoreceptor damage.\n\n\nConclusion\n\nOur work supports the notion that the presence of a functional circadian clock and its ability to modulate the response to an oxidative stress is the undelaying mechanism that may protect cones during aging.\n\n\nAuthor contributions\n\nKB, T-CS, VG, AS, AD and JD performed experiments and analyzed experimental results. KB and GT planned/designed the studies, provided data/figures, and wrote the manuscript.",
"appendix": "Data availability\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20537982.v1. 73\n\n• qPCR CT values for circadian gene expressions in 661W cells\n\n• Figure 1 clock gene expressions in 661W cells\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20538408.v1. 74\n\n• The peak phases and circadian periods of Per2-luc biouminescence rhythms in 661W cells\n\n• Per2-luc phases and periods in 661W cells\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20538621.v1. 75\n\n• Slide 1: CCD recording from population of 661W cells. Slide 2-4: Single cell recording. Slide 4 may show circadian rhythms of multiple cells since the first peak shows two peaks\n\n• Per2-luc bioluminescence from 661W cells measured with a CCD camera\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20538711.v1. 76\n\n• qPCR CT values for circadian gene expressions in Bmal1 KO cells\n\n• Figure 2 Circadian gene expressions in BKO cells\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20538885.v1. 77\n\n• The cell survival rate following exposure to H2O2 or vehicle control treatment in 661W and BKO cells\n\n• Figure 3 Cell viability from oxidative stress challenge\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20538975.v1. 78\n\n• Circadian variation of cell survival rate was analyzed by Nitecap\n\n• JTK analysis by Nitecap\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20539026.v1. 79\n\n• Data sets for Nrf2 circadian expression in 661W and BKO cells and circadia variation for GPx activity level\n\n• Figure 4 A and C data set Nrf2 expression and GPx activity level in 661W and BKO cells\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20539398.v1. 80\n\n• The spectrometry counts obtained from antioxidant assay in 661W and BKO cells\n\n• Figure 4 B data set Measurement of antioxidant capacity in 661W and BKO cells\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20539485.v1. 81\n\n• The survival rate after Lip1 or vehicle treatment in 661W and BKO cells at two time points\n\n• Figure 5 The survival rate after pretreatment of Lip1 followed by oxidative stress challenge\n\nFigshare: The circadian clock mediates the response to oxidative stress in a cone photoreceptor–like (661W) cell line via regulation of glutathione peroxidase activity, https://doi.org/10.6084/m9.figshare.20539737.v1. 82\n\n• The data set for the survival rate in Bmal1 rescued cells following oxidative stress challenge\n\n• Figure 6 The cell viability in Bmal1 rescued cells following oxidative stress challenge\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 would like to thank Dr. Muayyad Al-Ubaidi (Department of Biomedical Engineering, University of Houston) for kindly donating the 661W cells.\n\n\nReferences\n\nTosini G, Menaker M: Circadian rhythms in cultured mammalian retina. Science. 1996; 272: 419–421. PubMed Abstract | Publisher Full Text\n\nTosini G, Menaker M: The clock in the mouse retina: melatonin synthesis and photoreceptor degeneration. Brain Res. 1998; 789: 221–228. PubMed Abstract | Publisher Full Text\n\nFelder-Schmittbuhl MP, Buhr ED, Dkhissi-Benyahya O, et al.: Ocular clocks: Adapting mechanisms for eye functions and health. Vis. Sci. 2018; 59(12): 4856–4870. Publisher Full Text\n\nStorch KF, Paz C, Signorovitch J, et al.: Intrinsic circadian clock of the mammalian retina: importance for retinal processing of visual information. Cell. 2007; 130: 730–741. PubMed Abstract | Publisher Full Text\n\nBaba K, Ribelayga CP, Michael Iuvone P, et al.: The Retinal Circadian Clock and Photoreceptor Viability. Adv. Exp. Med. Biol. 2018; 1074: 345–350. PubMed Abstract | Publisher Full Text\n\nAit-Hmyed O, Felder-Schmittbuhl MP, et al.: Mice lacking Period 1 and Period 2 circadian clock genes exhibit blue cone photoreceptor defects. Eur. J. Neurosci. 2013; 37: 1048–1060. PubMed Abstract | Publisher Full Text\n\nDeVera C, Dixon J, Chrenek MA, et al.: The Circadian Clock in the Retinal Pigment Epithelium Controls the Diurnal Rhythm of Phagocytic Activity. Int. J. Mol. Sci. 2022; 23(10): 5302. PubMed Abstract | Publisher Full Text\n\nRuan GX, Allen GC, Yamazaki S, et al.: An Autonomous Circadian Clock in the Inner Mouse Retina Regulated by Dopamine and GABA. PLoS Biol. 2008; 6(10): 1–18. Publisher Full Text\n\nLiu X, Zhang Z, Ribelayga CP: Heterogeneous expression of the core circadian clock proteins among neuronal cell types in mouse retina. PLoS One. 2012; 7: e50602. PubMed Abstract | Publisher Full Text\n\nHiragaki S, Baba K, Coulson E, et al.: Melatonin Signaling Modulates Clock Genes Expression in the Mouse Retina. PLoS One. 2014; 9(9): e106819. PubMed Abstract | Publisher Full Text\n\nJaeger C, Sandu C, Malan A, et al.: Circadian organization of the rodent retina involves strongly coupled, layer-specific oscillators. FASEB J. 2015; 29(4): 1493–1504. PubMed Abstract | Publisher Full Text\n\nSawant OB, Horton AM, Zucaro OF, et al.: The Circadian Clock Gene Bmal1 Controls Thyroid Hormone-Mediated Spectral Identity and Cone Photoreceptor Function. Cell Rep. 2017; 21(3): 692–706. PubMed Abstract | Publisher Full Text\n\nBaba K, Piano I, Lyuboslavsky P, et al.: Removal of clock gene Bmal1 from the retina affects retinal development and accelerates cone photoreceptor degeneration during aging. Proc. Natl. Acad. Sci. U. S. A. 2018; 115: 13099–13104. PubMed Abstract | Publisher Full Text\n\nDeVera C, Tosini G: Circadian analysis of the mouse retinal pigment epithelium transcriptome. Exp. Eye Res. 2020; 193: 107988. PubMed Abstract | Publisher Full Text\n\nAmes A 3rd, Li YY, Heher EC, et al.: Energy metabolism of rabbit retina as related to function: high cost of Na+ transport. J. Neurosci. 1992; 12: 840–853. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPunzo C, Xiong W, Cepko CL: Loss of daylight vision in retinal degeneration: are oxidative stress and metabolic dysregulation to blame? J. Biol. Chem. 2012; 287: 1642–1648. Publisher Full Text\n\nHoang QV, Linsenmeier RA, Chung CK, et al.: Photoreceptor inner segments in monkey and human retina: mitochondrial density, optics, and regional variation. Vis. Neurosci. 2002; 19: 395–407. PubMed Abstract | Publisher Full Text\n\nPerkins GA, Ellisman MH, Fox DA: Three-dimensional analysis of mouse rod and cone mitochondrial cristae architecture: bioenergetic and functional implications. Mol. Vis. 2003; 9: 60–73. PubMed Abstract\n\nCampos PB, Paulsen BS, Rehen SK: Accelerating neuronal aging in in vitro model brain disorders: a focus on reactive oxygen species. Front. Aging Neurosci. 2014; 6: 292.\n\nEells JT: Mitochondrial Dysfunction in the Aging Retina. Biology (Basel). 2019; 8(2): 31. Publisher Full Text\n\nGuo C, Sun L, Chen X, et al.: Oxidative stress, mitochondrial damage and neurodegenerative diseases. Neural Regen. Res. 2013; 8(21): 2003–2014. PubMed Abstract | Publisher Full Text\n\nSchieber M, Chandel NS: ROS Function in Redox Signaling and Oxidative Stress. Curr. Biol. 2014; 24(10): R453–R462. PubMed Abstract | Publisher Full Text\n\nDiaz-Munoz M, Hernandez-Munoz R, Suarez J, et al.: Day-night cycle of lipid peroxidation in rat cerebral cortex and their relationship to the glutathione cycle and superoxide dismutase activity. Neuroscience. 1985; 16: 859–863. Publisher Full Text\n\nHardeland R, Coto-Montes A, Poeggeler B: Circadian rhythms, oxidative stress, and antioxidative defense mechanisms. Chronobiol. Int. 2003; 20: 921–962. PubMed Abstract | Publisher Full Text\n\nKondratov RV, Kondratova AA, Gorbacheva VY, et al.: Early aging and age-related pathologies in mice deficient in BMAL1, the core component of the circadian clock. Genes Dev. 2006; 20: 1868–1873. PubMed Abstract | Publisher Full Text\n\nKondratov RV, Vykhovanets O, Kondratova AA, et al.: Antioxidant N-acetyl-L-cysteine ameliorates symptoms of premature aging associated with the deficiency of the circadian protein BMAL1. Aging. 2009; 1: 979–987. PubMed Abstract | Publisher Full Text\n\nAnea CB, Cheng B, Sharma S, et al.: Increased superoxide and endothelial NO synthase uncoupling in blood vessels of Bmal1-knockout mice. Circ. Res. 2012; 111: 1157–1165. PubMed Abstract | Publisher Full Text\n\nAnea CB, Zhang M, Chen F, et al.: Circadian clock control of Nox4 and reactive oxygen species in the vasculature. PLoS One. 2013; 8: e78626. PubMed Abstract | Publisher Full Text\n\nMusiek ES, Lim MM, Yang G, et al.: Circadian clock proteins regulate neuronal redox homeostasis and neurodegeneration. J. Clin. Invest. 2013; 123: 5389–5400. PubMed Abstract | Publisher Full Text\n\nJacobi D, Liu S, Burkewitz K, et al.: Hepatic Bmal1 Regulates Rhythmic Mitochondrial Dynamics and Promotes Metabolic Fitness. Cell Metab. 2015; 22: 709–720. PubMed Abstract | Publisher Full Text\n\nTan E, Ding XQ, Saadi A, et al.: Expression of cone-photoreceptor-specific antigens in a cell line derived from retinal tumors in transgenic mice. Invest. Ophthalmol. Vis. Sci. 2004; 45: 764–768. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAl-Ubaidi MR, Matsumoto H, Kurono S, et al.: Proteomics profiling of the cone photoreceptor cell line, 661W. Adv. Exp. Med. Biol. 2008; 613: 301–311. PubMed Abstract | Publisher Full Text\n\nLayton CJ: Diabetic levels of glucose increase cellular reducing equivalents but reduce survival in three models of 661W photoreceptor-like cell injury. BMC Ophthalmol. 2015; 15: 174. PubMed Abstract | Publisher Full Text\n\nNatoli R, Rutar M, Lu YZ, et al.: The Role of Pyruvate in Protecting 661W Photoreceptor-Like Cells Against Light-Induced Cell Death. Curr. Eye Res. 2016; 41(11): 1473–1481. PubMed Abstract | Publisher Full Text\n\nLin JB, Kubota S, Ban N, et al.: NAMPT-Mediated NAD(+) Biosynthesis Is Essential for Vision in Mice. Cell Rep. 2016; 17: 69–85. PubMed Abstract | Publisher Full Text\n\nChen WJ, Wu C, Xu Z, et al.: Nrf2 protects photoreceptor cells from photo-oxidative stress induced by blue light. Exp. Eye Res. 2017; 154: 151–158. PubMed Abstract | Publisher Full Text\n\nSánchez-Bretaño A, Baba K, Janjua U, et al.: Melatonin partially protects 661W cells from H2O2-induced death by inhibiting Fas/FasL-caspase-3. Mol. Vis. 2017; 23: 844–852. PubMed Abstract\n\nDeBruyne JP, Baggs JE, Sato TK, et al.: Ubiquitin ligase Siah2 regulates RevErbα degradation and the mammalian circadian clock. Proc. Natl. Acad. Sci. U. S. A. 2015; 112(40): 12420–12425. PubMed Abstract | Publisher Full Text\n\nBaba K, Davidson AJ, Tosini G: Melatonin Entrains PER2::LUC Bioluminescence Circadian Rhythm in the Mouse Cornea. Invest. Ophthalmol. Vis. Sci. 2015; 56: 4753–4758. PubMed Abstract | Publisher Full Text\n\nEvans JA, Davidson AJ: Health consequences of circadian disruption in humans and animal models. Prog. Mol. Biol. Transl. Sci. 2013; 119: 283–323. PubMed Abstract | Publisher Full Text\n\nBaba K, Sengupta A, Tosini M, et al.: Circadian regulation of the PERIOD 2::LUCIFERASE bioluminescence rhythm in the mouse retinal pigment epithelium-choroid. Mol. Vis. 2010; 16: 2605–2611. PubMed Abstract\n\nBrooks TG, Mrčela A, Lahens NF, et al.: Nitecap: An Exploratory Circadian Analysis Web Application. J. Biol. Rhythm. 2022; 37(1): 43–52. PubMed Abstract | Publisher Full Text\n\nNguyen T, Nioi P, Pickett CB: The Nrf2-antioxidant response element signaling pathway and its activation by oxidative stress. J. Biol. Chem. 2009; 284(20): 13291–13295. PubMed Abstract | Publisher Full Text\n\nPekovic-Vaughan V, Gibbs J, Yoshitane H, et al.: The circadian clock regulates rhythmic activation of the NRF2/glutathione-mediated antioxidant defense pathway to modulate pulmonary fibrosis. Genes Dev. 2014; 28(6): 548–560. PubMed Abstract | Publisher Full Text\n\nEarly JO, Menon D, Wyse CA, et al.: Circadian clock protein BMAL1 regulates IL-1β in macrophages via NRF2. Proc. Natl. Acad. Sci. U. S. A. 2018; 115(36): E8460–E8468. Publisher Full Text\n\nWible RS, Ramanathan C, Sutter CH, et al.: NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus. elife. 2018; 7: e31656. PubMed Abstract | Publisher Full Text\n\nNg CF, Schafer FQ, Buettner GR, et al.: The rate of cellular hydrogen peroxide removal shows dependency on GSH: Mathematical insight into in vivo H2O2 and GPx concentrations. Free Radic. Res. 2007; 41(11): 1201–1211. PubMed Abstract | Publisher Full Text\n\nDixon SJ, Lemberg KM, Lamprecht MR, et al.: Ferroptosis: an iron-dependent form of nonapoptotic cell death. Cell. 2012; 149(5): 1060–1072. Publisher Full Text\n\nYang WS, Stockwell BR: Ferroptosis: Death by Lipid Peroxidation. Trends Cell Biol. 2016; 26(3): 165–176. Publisher Full Text\n\nSinenko SA, Starkova TY, Kuzmin AA, et al.: Physiological Signaling Functions of Reactive Oxygen Species in Stem Cells: From Flies to Man. Front. Cell Dev. Biol. 2021; 9: 714370. PubMed Abstract | Publisher Full Text\n\nChang JY, Shi L, Ko ML, et al.: Circadian Regulation of Mitochondrial Dynamics in Retinal Photoreceptors. J. Biol. Rhythm. 2018; 33(2): 151–165. PubMed Abstract | Publisher Full Text\n\nGiarmarco MM, Brock DC, Robbings BM, et al.: Daily mitochondrial dynamics in cone photoreceptors. Proc. Natl. Acad. Sci. U. S. A. 2020; 117(46): 28816–28827. PubMed Abstract | Publisher Full Text\n\nReddy AB, Karp NA, Maywood ES, et al.: Circadian orchestration of the hepatic proteome. Curr. Biol. 2006; 16: 1107–1115. Publisher Full Text\n\nFonzo LS, Golini RS, Delgado SM, et al.: Temporal patterns of lipoperoxidation and antioxidant enzymes are modified in the hippocampus of vitamin A-deficient rats. Hippocampus. 2009; 19: 869–880. PubMed Abstract | Publisher Full Text\n\nSani M, Sebaï H, Gadacha W, et al.: Catalase activity and rhythmic patterns in mouse brain, kidney and liver. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 2006; 145: 331–337. PubMed Abstract | Publisher Full Text\n\nO’Neill JS, Reddy AB: Circadian clocks in human red blood cells. Nature. 2011; 469: 498–503. PubMed Abstract | Publisher Full Text\n\nXu YQ, Zhang D, Jin T, et al.: Diurnal variation of hepatic antioxidant gene expression in mice. PLoS One. 2012; 7: e44237. PubMed Abstract | Publisher Full Text\n\nPatel SA, Velingkaar NS, Kondratov RV: Transcriptional control of antioxidant defense by the circadian clock. Antioxid. Redox Signal. 2014; 20(18): 2997–3006. Publisher Full Text\n\nTakahashi JS: Transcriptional architecture of the mammalian circadian clock. Nat. Rev. Genet. 2017; 18(3): 164–179. PubMed Abstract | Publisher Full Text\n\nRay S, Valekunja UK, Stangherlin A, et al.: Circadian rhythms in the absence of the clock gene Bmal1. Science. 2020; 367(6479): 800–806. Publisher Full Text\n\nAbruzzi KC, Gobet C, Naef F, et al.: Comment on “Circadian rhythms in the absence of the clock gene Bmal1”. Science. 2021; 372(6539): eabf0922. Publisher Full Text\n\nNess-Cohn E, Allada R, Braun R: Comment on “Circadian rhythms in the absence of the clock gene Bmal1”. Science. 2021; 372(6539): eabe9230. PubMed Abstract | Publisher Full Text\n\nCao JY, Dixon SJ: Mechanisms of ferroptosis. Cell. Mol. Life Sci. 2016; 73(11-12): 2195–2209. PubMed Abstract | Publisher Full Text\n\nOhira A, Tanito M, Kaidzu S, et al.: Glutathione peroxidase induced in rat retinas to counteract photic injury. Invest. Ophthalmol. Vis. Sci. 2003; 44(3): 1230–1236. PubMed Abstract | Publisher Full Text\n\nLu L, Oveson BC, Jo YJ, et al.: Increased expression of glutathione peroxidase 4 strongly protects retina from oxidative damage. Antioxid. Redox Signal. 2009; 11(4): 715–724. PubMed Abstract | Publisher Full Text\n\nZilka O, Shah R, Li B, et al.: On the Mechanism of Cytoprotection by Ferrostatin-1 and Liproxstatin-1 and the Role of Lipid Peroxidation in Ferroptotic Cell Death. ACS Cent. Sci. 2017; 3(3): 232–243. PubMed Abstract | Publisher Full Text\n\nHanus J, Zhang H, Wang Z, et al.: Induction of necrotic cell death by oxidative stress in retinal pigment epithelial cells. Cell Death Dis. 2013; 4(12): e965. PubMed Abstract | Publisher Full Text\n\nRedza-Dutordoir M, Averill-Bates DA: Activation of apoptosis signalling pathways by reactive oxygen species. Biochim. Biophys. Acta. 2016; 1863(12): 2977–2992. Publisher Full Text\n\nDuncan TE, O’Steen WK: The diurnal susceptibility of rat retinal photoreceptors to light-induced damage. Exp. Eye Res. 1985; 41(4): 497–507. PubMed Abstract | Publisher Full Text\n\nWhite MP, Fisher LJ: Degree of light damage to the retina varies with time of day of bright light exposure. Physiol. Behav. 1987; 39(5): 607–613. Publisher Full Text\n\nOrganisciak DT, Darrow RM, Barsalou L, et al.: Circadian-dependent retinal light damage in rats. Invest. Ophthalmol. Vis. Sci. 2000; 41(12): 3694–3701.\n\nHumphries A, Carter DA: Circadian dependency of nocturnal immediate-early protein induction in rat retina. Biochem. Biophys. Res. Commun. 2004; 320(2): 551–556. PubMed Abstract | Publisher Full Text\n\nBaba K:Figure 1 clock gene expressions in 661W cells. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:Per2-luc phases and periods in 661W cells. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:Per2-luc bioluminescence from 661W cells measured with a CCD camera. figshare. Media. 2022. Publisher Full Text\n\nBaba K:Figure 2 Circadian gene expressions in BKO cells. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:Figure 3 Cell viability from oxidative stress challenge. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:JTK analysis by Nitecap. figshare. Figure. 2022. Publisher Full Text\n\nBaba K:Figure 4 A and C data set Nrf2 expression and GPx activity level in 661W and BKO cells. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:Figure 4 B data set Measurement of antioxidant capacity in 661W and BKO cells. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:Figure 5 The survival rate after pretreatment of Lip1 followed by oxidative stress challenge. figshare. Dataset. 2022. Publisher Full Text\n\nBaba K:Figure 6 The cell viability in Bmal1 rescued cells following oxidative stress challenge. figshare. Dataset. 2022. Publisher Full Text"
}
|
[
{
"id": "151006",
"date": "04 Oct 2022",
"name": "Ethan D. Buhr",
"expertise": [
"Reviewer Expertise retina",
"cornea",
"opsins",
"circadian rhythms"
],
"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\nBaba et al. show that the 661W cell line expresses a functional molecular circadian clock which is lost with the deletion of Bmal1. The circadian oscillation of cellular viability in the face of oxidative chemical stress is lost in Bmal1KO cells, as well as an overall loss in cellular robustness (as nearly all time points have reduced cell survival compared to WT).\nThe authors then show that a rhythm of transcript abundance of the antioxidant gene Nrf2 is reduced in Bmal1KO 661W cells; although, presumably many transcript rhythms are affected by Bmal1 deletion. It is not clear that the Nrf2 rhythm is involved in the antioxidant (Figure 4B), GPx reductions (Figure 4C), or the cell viability of Figure 3. As the authors note, “Of the many antioxidants present in cells,” that Nrf2 and GPx are just two examples of antioxidant-related cellular components. I think Figure 4 works as a figure of three examples of reduced antioxidant-related measures, but it should be clear that these are not being presented as validated causes of the other phenotypes presented like circadian survival rate of Figure 3.\nCan the authors comment on the source of the Bmal1 cDNA that was used in the rescue? The Bmal1 rescue is under the control of the CMV promoter, not a circadian promoter, correct? This would yield a constitutive expression of Bmal1 itself for the rescue. This may not change the results of the Bmal1 rescue, but I think it is worth mentioning.\n\nIn the discussion of the persistence of rhythms after deletion of Bmal1, the authors point to Figure 4B as an example of circadian variation. To be fair, this figure panel shows there is a difference at 2 points in both WT and BMKO cells, but not necessarily a circadian rhythm in antioxidant capacity.\n\nThere are a couple of editing corrections:\na) In the Western blot section of the Methods it says samples were heated to 950degC, instead of 95degC.\nb) In the discussion paragraph on the persistence of rhythms in BmalKO cells, I think the first sentence “in” should be “is”(…the antioxidant capacity of 661-BKO cells is the presence...).\nOverall the paper shows a creative way to assess the rhythms of oxidative stress responses in cone-like cells.\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": "9004",
"date": "21 Nov 2022",
"name": "Kenkichi Baba",
"role": "Author Response",
"response": "Thank you Dr. Buhr for the valuable comments and suggestions. Comment: As the authors note, “Of the many antioxidants present in cells,” that Nrf2 and GPx are just two examples of antioxidant-related cellular components. I think Figure 4 works as a figure of three examples of reduced antioxidant-related measures, but it should be clear that these are not being presented as validated causes of the other phenotypes presented like circadian survival rate of Figure 3. Response: We agree that there are several death pathways triggered by oxidative stress and what we observed in Figure 3 may not exclusively caused by Nrf2 and GPX as we show in Figure 4. However, previous studies have reported that Nrf2 transcription is directly controlled by the circadian clock and Nrf2 is responsible for the control many of the genes mediating antioxidant response and thus we believe that our data suggest a direct involvement of Nrf2 in the response of 661W cells to an oxidative stress challenge. Similarly, we believe that the data show in Figure 4 on GPX activity provides strong evidence that GPX is a key player in the response observed in Figure 3 since this enzyme convert from H2O2 to H2O. We have also measured catalase activity, but unfortunately, catalase activity in 661W cells was found very low. Thus, we believe that the data presented in Figures 4-5 provide compelling evidence about the mechanism that is responsible for the data presented in Figure 3. Comment: Can the authors comment on the source of the Bmal1 cDNA that was used in the rescue? The Bmal1 rescue is under the control of the CMV promoter, not a circadian promoter, correct? This would yield a constitutive expression of Bmal1 itself for the rescue. This may not change the results of the Bmal1 rescue, but I think it is worth mentioning. Response: We have added the reference for the Bmal1 cDNA. Bmal1 expression is under the control of the CMV promoter, therefore we believe it would be expressed steadily in these cells. Comment: In the discussion of the persistence of rhythms after deletion of Bmal1, the authors point to Figure 4B as an example of circadian variation. To be fair, this figure panel shows there is a difference at 2 points in both WT and BMKO cells, but not necessarily a circadian rhythm in antioxidant capacity. Response: We agree with the comment, and we have replaced the term circadian with “a time dependent change” Comment: a) In the Western blot section of the Methods it says samples were heated to 950degC, instead of 95degC. Response: Thank you. We corrected it to 95 C. Comment: b) In the discussion paragraph on the persistence of rhythms in BmalKO cells, I think the first sentence “in” should be “is”(…the antioxidant capacity of 661-BKO cells is the presence...). Response: Thank you for noticing this typo. We have corrected the text as suggested."
}
]
},
{
"id": "151007",
"date": "03 Nov 2022",
"name": "Sujata Rao",
"expertise": [
"Reviewer Expertise Retina",
"circadian rhythms",
"opsins",
"cone photoreceptor."
],
"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 aims to delineate the molecular mechanisms regulated by the circadian clock in the aging cone photoreceptors. This study is a continuation of a previous finding from this group, demonstrating the role of the circadian clock in cone photoreceptor viability during aging. In the current study, the authors have utilized a mouse-derived cone-like cell, 661W, to assess the effects of oxidative stress on these cells. The authors demonstrate that 661W cells contain a functional circadian clock that mediates the response to oxidative stress in vitro. This antioxidant mechanism is abolished when Bmal1 is deleted from these cells. Furthermore, reintroducing Bmal1 restores the circadian response to oxidative stress, providing supporting evidence that Bmal1 mediates the effects. These findings are intriguing and provide additional evidence for the importance of the circadian clock in regulating cellular responses to stress. The data is robust and will be of interest to the vision researchers.\nThere are a few minor points that the authors should clarify\nIn the method section, include how the survival was assessed. Was it the total number of cells or dying cells?\n\nInterestingly, the highest level of Bmal1 transcript is observed at 32.5h. Yet both the maximal oxidative stress-induced survival rate and peak Nrf2 expression occurs at 26.5h when Bmal1 expression is the lowest. Can the authors comment on that?\n\nCould the authors clarify the duration of the H202 and how long after the exposure the cells were harvested for the various assessments?\n\nIn the discussion, it wasn’t clear why the authors state that “removal of Bmal1 may not completely abolish circadian oscillations based on Figure4B”. The data provided is not sufficient to make that conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "9005",
"date": "21 Nov 2022",
"name": "Kenkichi Baba",
"role": "Author Response",
"response": "Thank you Dr. Rao for the Valuable comments and suggestions Comment: In the method section, include how the survival was assessed. Was it the total number of cells or dying cells? Response: Thank you for mentioning. The cell survival rate was calculated from the number of living cells out of total cell counts. We added it in the methods. Comment: Interestingly, the highest level of Bmal1 transcript is observed at 32.5h. Yet both the maximal oxidative stress-induced survival rate and peak Nrf2 expression occurs at 26.5h when Bmal1 expression is the lowest. Can the authors comment on that? Response: Several studies indicate expression level of Nrf2 is regulated via e-box in its promoter and shows similar rhythmic trend as Per1 and Per2 expressions. We believe that the circadian clock directly drives Nrf2 expression and that translates to survival rate against oxidative stress. Comment: Could the authors clarify the duration of the H202 and how long after the exposure the cells were harvested for the various assessments? Response: Thank you for mentioning. For oxidative stress challenge experiment, we treated cells with hydrogen peroxide for two hours and cells were harvested after two hours of treatment for cell counts. We have added details in Methods. Comment: In the discussion, it wasn’t clear why the authors state that “removal of Bmal1 may not completely abolish circadian oscillations based on Figure4B”. The data provided is not sufficient to make that conclusion. Response: Thank you for your comment. We agree that only two-time points data is not sufficient to conclude it as circadian rhythmicity. We rephrased it in the discussion."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1072
|
https://f1000research.com/articles/11-1352/v1
|
21 Nov 22
|
{
"type": "Study Protocol",
"title": "Comparison of the effects of therapeutic exercise with either an educational booklet or vitamin-D3 supplement in the management of chronic low back pain: study protocol for an assessor blinded multicenter randomized clinical trial",
"authors": [
"Muhammad Shahidul Islam",
"K. M. Amran Hossain",
"Md. Sohrab Hossain",
"Rashida Parvin",
"Nadia Afrin Urme",
"Veena Raigangar",
"Iqbal Kabir Jahid",
"Md. Feroz Kabir",
"Md. Ashrafuzzaman Zahid",
"Muhammad Shahidul Islam",
"K. M. Amran Hossain",
"Md. Sohrab Hossain",
"Rashida Parvin",
"Nadia Afrin Urme",
"Veena Raigangar",
"Iqbal Kabir Jahid",
"Md. Feroz Kabir"
],
"abstract": "Background: It is important to know the best intervention approach to replenish serum vitamin D levels along with therapeutic interventions for chronic low back pain (CLBP) patients. From the researcher’s knowledge, no study compared “vitamin D supplement” or “booklet education on sun exposure, nutrition and lifestyle” with therapeutic exercise for CLBP cases. Researchers hypothesize that multidimensional comprehensive management of therapeutic exercise and an education booklet (TEB) on sun exposure, nutrition, and lifestyle might be superior to therapeutic exercise and oral vitamin D supplement (TED) for CLBP patients with vitamin D deficiency. Methods: We planned for an assessor-blinded two-arm multicenter Randomized Clinical Trial (RCT) protocol to compare the efficacy of TEB compared to TED for CLBP patients with vitamin D deficiency at 2 months and 6 months after baseline recruitment in designated centers in Dhaka city. The primary outcome measures will include pain by Brief Pain Inventory (BPI), and serum vitamin D3 level and secondary outcome measures will include disability by Ronald Morris Disability Questionnaire (RMDQ). Discussion: This study will provide evidence for an appropriate prescription for the management of CLBP patients having vitamin D deficiency. Registration: Clinical Trials Registry India (CTRI/2022/11/047074).",
"keywords": [
"Chronic Low Back Pain",
"Therapeutic exercise",
"Vitamin-D3 supplement",
"Booklet"
],
"content": "Introduction\n\nChronic Low back pain (CLBP) is identified as one of the leading contributors to global disease burden.1 It is a commonly prevalent musculoskeletal condition among non-communicable diseases in all countries, ranging from developing to developed countries, and in all age groups from children to the elderly population; affecting almost everyone during their lifespan.2 About 55–80% of people suffer from low back pain (LBP) in their lifetime, and the worldwide yearly cost of managing chronic LBP is estimated to be a trillion dollars.3 The incidence of LBP is linked to several biopsychosocial aspects, including mechanical, traumatic, pathological and degenerative causes; bone health is known to be associated with both degenerative and mechanical types of LBP.4 Approximately 50% of patients seeking treatment for LBP of over 3 months’ duration are found to be additionally suffering from vitamin D and other nutritional deficiencies.5 One study suggests a mean decrease of vitamin D levels may increase overall body pain.6 A systematic review reported that vitamin D has the potential to decrease pain and inflammation by modifying sensory neuron excitability and anti-inflammatory and pro-inflammatory cytokines. Alongside pain remission, vitamin D levels are linked to increases in muscle strength, that contribute to improving function in patients with LBP.7 A strong relationship between LBP and decreased vitamin D level are noted in elderly women, but it is still debated whether low vitamin D can predict severe LBP in the general population.8 The urban population monograph is moving towards a more sedentary lifestyle and extended sitting hours with almost 12 hours spent in sedentary office jobs in Bangladesh, and this is combined with less exposure to sunshine for city dwellers. This has led to increased number of LBP cases with insufficient serum vitamin D levels in Bangladesh; those with a sedentary lifestyle and obesity form the majority of suffers.9\n\nA quasi-experimental study shows that therapeutic exercise and vitamin D supplement can be a promising treatment to battle these LBP cases,10 however the study didn’t elaborate a specific protocol. Other studies suggest that aerobic exercise (low, moderate, high), stretching, balance, motor control exercises, core stability, coordination, muscular strength exercises, and flexibility programs are types of exercises that have significant outcome on LBP. But because of the intricacy of LBP, it is uncertain which of these types of exercises has the best outcome for rehabilitation; this calls for more in depth studies.10,11 Research also recommend the necessity of active rehabilitation, including therapeutic exercise (TE), which is emphasized in evidence-based guidelines for the therapy of chronic low back pain (CLBP), but there is no universal agreement on the most efficient type of exercises.12\n\nVitamin D supplementation can be provided by different approaches including natural approaches, lifestyle education and oral vitamin D supplementation. However, it has been demonstrated that engaging in any type of regular physical exercise increases circulating vitamin D and upregulates the vitamin receptor expression in muscles.13 An educational booklet is an effective intervention approach for health-care professionals to deliver regular education concerning the causes, mechanisms, natural history, and prognosis of LBP, and promote the benefits of physical activity and exercise.14 In previous studies, booklets on lifestyle, exercise and sun exposure14,15 or exercise and vitamin D3 supplementation16 have found to be effective for CLBP. Therapeutic exercise and vitamin D supplements have been found to be effective for the Dhaka city dwellers in Bangladesh,10 and creating an educational booklet can be a great solution to raising awareness of CLBP with vitamin D deficiency.9 Educational booklets on exercise, sun exposure and healthy nutrition have proven to be promising in other studies.14,15 From the researcher’s knowledge, no study comparing the use of “vitamin D supplements” or “booklet education on sun exposure, nutrition and lifestyle” along with therapeutic exercise for CLBP cases has been done.\n\nFor this study researchers proposed a two-tailed hypothesis: use of multidimensional comprehensive management by therapeutic exercise and education booklet on sun exposure, nutrition and lifestyle (TEB) is superior to therapeutic exercise and oral vitamin D supplement (TED), for CLBP patients with vitamin D deficiency considering the following:\n\n1. CLBP patients with vitamin D deficiency in the TEB arm show significant improvement in painful symptoms compared to the TED arm at 2 months and 6 months after baseline recruitment.\n\n2. CLBP patients with vitamin D deficiency in the TEB arm show significant improvement in serum vitamin D levels compared to the TED arm at 2 months and 6 months after baseline recruitment.\n\n3. CLBP patients with vitamin D deficiency in the TEB arm show significant improvement in disability status compared to the TED arm at 2 months and 6 months after baseline recruitment.\n\nThe specific objectives are:\n\n1. To design a protocol of therapeutic exercise, along with an educational booklet on sun exposure, nutrition and lifestyle, and vitamin D supplementation for the CLBP patients with vitamin D deficiency.\n\n2. To evaluate the effectiveness of therapeutic exercise along with education booklet on sun exposure, nutrition and lifestyle, on painful symptoms, serum vitamin D level and disability for CLBP patients with vitamin D deficiency at 2 months and 6 months’ post-test compared to baseline.\n\n3. To explore the effectiveness of therapeutic exercise along with oral vitamin D supplement on painful symptoms, serum vitamin D level and disability for CLBP patients with vitamin D deficiency at 2 months and 6 months post-test compared to baseline.\n\n4. To study the comparative effectiveness of both groups on painful symptoms, serum vitamin D levels and disability for CLBP patients with vitamin D deficiency at 2 months and 6 months’ post-test compared to baseline.\n\n\nMethods\n\nResearchers plan for an assessor blinded two arm multicenter Randomized Clinical Trial (RCT) protocol to compare the efficacy of therapeutic exercise and education booklet on sun exposure, nutrition and lifestyle versus therapeutic exercise and oral vitamin D supplement for CLBP patients with vitamin D deficiency at 2 months and 6 months after baseline recruitment in designated rehabilitation centers in Dhaka city.\n\nFor this potential trial, researchers will follow Standard Protocol Items: Interventional Trials 2013 (SPIRIT) guidelines, to help ensure quality of the interventional trial (Table 1).\n\nAbbreviations: BPI, Brief Pain Inventory; Vit. D3, Serum 25(OH)D; RMDQ, Roland Morris Disability Questionnaire.\n\nTo meet the objectives of the trial and prevent trial contamination, the experimental group interventions will take place at the Centre for the Rehabilitation of the Paralysed (CRP) and control group interventions will take place at SAIC College of Medical Science & Technology. We expect to get cases with similar geographical and baseline criteria of city dwellers having CLBP. Data collection from different sites will increase the generalizability of the study and prevent cross-contamination of data.\n\nEligibility criteria for selecting participants include having (1) CLBP for more than 3 months and central in nature as defined by ICD-10-CM-Code M54.5 criteria, (2) vitamin D deficiency determined by a serum 25(OH) D3 level of less than 20 ng/mL,16 (3) living or working in Dhaka city in any office, industry and corporate setting with a static posture or desk job with at least 6 hours of sitting per day for an average of 22 days per month, (4) age 18 years and above, both genders. Participants that provide informed consent for the study and interventions will be recruited in the study. On the other hand, participants will be excluded if (1) there is presence of any kind of comorbidity that can affect serum vitamin D level like RA, Ankylosing Spondylitis, Osteomalacia, TB spine, etc., and any history of osteoporotic fracture, (2) women more than 50 years or reported post-menopausal women,14 (3) use of calcium, vitamin D3 supplements, resistance training, and high impact weight-bearing activities regularly within the past 6 months, (4) low back pain patients with Dural sign, positive straight leg raise test, or bowel and bladder incontinence and (5) withdrawal of participation during 8 weeks intervention. Participants who are already involved in another study will not be considered for study.\n\nParticipants will receive intervention (Table 2) as per the registered protocol for therapeutic exercise along with advice by booklet, or therapeutic exercise and Vitamin D3 supplement.17\n\n\n\n✓ Avoid long time static sitting and standing. It is recommended that standing work be interspersed with periods of sitting work and vice versa.18\n\n✓ Take naturally vitamin D3 containing foods like milk, cereal, orange juice, yogurt, cereal, mushroom, margarine, hard-boiled eggs, sea fish like tuna, salmon, etc.19\n\n✓ 30-35 minutes of sun exposure between 11 am to 2 pm.15,20\n\n✓ 7–8-hours of sleep per night.21\n\n✓ Avoid stress, smoking and maintain healthy body weight.22\n\n✓ Avoid alcohol consumption.\n\n✓ Do regular physical activity.\n\nBooklet\n\nUsing the created educational booklet, the physician will provide guidelines for CLBP patients with low vitamin D levels to raise awareness regarding appropriate diet and healthy lifestyle, back care and advise to increase nutritional status as well as overall physical function to minimize disability.\n\nTherapeutic exercise\n\nBoth groups will receive therapeutic exercises. Exercises will focus on both back pain and disability minimization of the participants. Each session will last for 25-30 minutes, 4 days per weeks and for 8 weeks. The progression of therapeutic exercise will be as per the registered protocol.17\n\nVitamin D3 supplement\n\nOne group will receive a vitamin-D3 supplement along with therapeutic exercise, which will be provided by a research fund. The patients will be given 40,000 IU vitamin D3 capsule made by a specific pharmaceutical company of Bangladesh per week for 8 weeks.10 A physician will fix the dose, provide a chart of capsule-taking dates and time, a record of this will be kept to avoid any kind of misconduct.\n\nWe expect there will be no major adverse effect for therapeutic exercise and booklet group and that there will be no request of dosage change or worsening of patients’ condition. If any of these occur we will discuss with the patient. If the patient is not willing not to continue, we will stop the intervention, and keep the data for intention to treat analysis. The vitamin D supplement group may experience some adverse effect; we will manage as per the standard measures described in the “safety measures” section. The adherence to these interventions will be monitored through checklist (Extended data 131). We will also monitor adverse effect using a checklist (Extended data 231).\n\nOutcome measurement\n\nPrimary outcome\n\nPain\n\nIn this study, the Brief Pain Inventory (BPI) will be used to measure pain. The BPI is a patient-reported measurement scale that assesses the pain severity, influence of pain on daily function, site of pain, information about pain medication, and quantity of pain relief in the preceding 24 hours.27 This is an 11-point numerical rating scale rated from 0 to 10, where 0 denotes “no pain” and 10 denotes “pain as bad as you can imagine”. A patient is asked to score his/her perceived pain intensity on a scale for the items as worse, least, average in the preceding 24 hours, and worse at right now. BPI has excellent internal consistency for pain severity (Cronbach’s alpha 0.78 to 0.96) and pain interference (Cronbach’s alpha 0.83 to 0.95), and also has good validity and reliability.10\n\nVitamin-D3 level\n\nSerum 25(OH) D will be used to measure the level of Vitamin D3. Tests will be advised by an expert physician, and researchers will collect information from laboratory test reports. Patients will be categorized based on vitamin D levels, such as deficient (less than 20 ng/mL); insufficient (21 to 29 ng/mL); and sufficient (more than 30 to 100 ng/mL).10,20\n\nSecondary outcome\n\nDisability\n\nRoland Morris Disability Questionnaire (RMDQ) will be used to measure disability. RMDQ was developed in order to explain the natural history of back pain. It is a 24-item questionnaire where patients' rated scores might range from “0” (no disability) to “24” (severe disability). For each of the 24 questions that were marked by patients, it counted as a score of 1-point.28 This study will use the Bengali version of RMDQ. It has excellent internal consistency (Cronbach’s alpha = 0.89), test-retest reliability (ICC = 0.95), and validity.29\n\n\nParticipant timeline\n\nAs the sample of the study will be collected by a hospital-based randomization technique, sample size estimations won’t be done. One study supports the idea that a standard calculation for low back pain trials with not less than 152 participants can obtain significant superiority changes with an alpha value.05, 80% power and 95% confidence interval.30\n\nResearchers plan for hospital-based randomization in both study centers from 1st December 2022 to 30th May 2023 by sequential random sampling and eligibility screening. For concealed allocation, a computer based random sequence maintained by independent and blinded person out of the research team will be prepared and protocols will be concealed into envelopes. The treatment providers and the patients will also be blinded as to whether they are in control or experimental group.\n\nWe will follow the Consolidated Standards of Reporting Trials (CONSORT) to maintain the standards of the study procedure (Figure 1). For the initial recruitment the LBP patients attending outdoor clinics of both centers from 1st December 2022 to 30th May 2022 will be primarily screened by the outdoor team and provided participant information sheet (PIS) of the study. The final screening will be performed by the trained primary assessors, one per study setting to check the inclusion and exclusion criteria and provide the subject an ID number, if eligible. The patient will meet the blinded assessor who will then take pretest data in a separate room, and collect a blood sample, before returning the patient to the outdoor pool. From outdoor pool, the patient will have a concealed envelop with another random ID number matched by the initial ID number given and meet the intervention provider (physiotherapist and physician or physiotherapist alone). Patient will receive the intervention provided in the written guideline enclosed in the concealed envelope. After 8 weeks of treatment completion, the patient will be further screened by blinded assessor, and another blood sample will be collected before discharge. After six months, the patient will be invited to the treatment center or visited in their house or workplace for follow up evaluation and blood sample collection. Therapeutic exercise will be provided by a graduate physiotherapist, and medication will be provided by a registered medical practitioner. Patient will pay for the physiotherapy treatment sessions but will not pay for any additional blood tests, medication or booklet.\n\nPatients will be monitored during the intervention session, and the medication chart and home exercise checklist (Extended data 131) will be maintained for recording the interventions. Patient data will be reviewed by a team from a different organization out of the study setting. The completed forms and questionnaire, along with blood report, will be evaluated by the monitoring team. Any kind of change or modifications to the methodology and intervention protocol will be communicated to the Ethics Committees. The research team will have access to the data and interim results and be in charge of making the final decision to change or end the study, hence carrying out interim analysis.\n\nAlthough it is expected that vitamin D3 supplementation and therapeutic exercise will not produce harmful effects on patients, patients should be instructed to inform the physician and physiotherapist if they feel any kind of discomfort (including-gastrointestinal, skin, musculoskeletal problem etc.) after the intervention. Before starting, the physiotherapist and physician will screen patients for any contraindications to intervention. If any serious harmful effects are found, researchers will report this during the final publication. The adverse effects reporting checklist will be provided during intervention (Extended data 231).\n\nData will be analyzed based on its nature. Calculation and data auditing will be done using Microsoft Excel 2016. Data will be analyzed by SPSS version 23, and R-4.2.1 for Windows. Eligibility for parametric analysis will be checked using bell’s curve, skewness, kurtosis, Kolmogorov–Smirnov test and Shapiro–Wilk test. Continuous variables will be represented by using an arithmetic mean and standard deviation. Categorical data will be represented by percentage (%) and frequency. Baseline compatibility will be checked by Pearson correction or chi-square test. For parametric data, the pretest to posttest between group analyses will be conducted through an independent t test and within group analyses through paired sample t tests. For non-parametric data, non-parametric alternative tests like the Wilcoxon Signed Rank test and Mann Whitney U-test will be performed. For the analysis of treatment superiority among three measurements, one-way ANOVA or Friedman’s ANOVA will be used with post-hoc analysis. The level of significance is set as an alpha value <05. We may include intention to treat analysis based on the situation of data collection.\n\nAccording to ethical guidelines, the researchers will abide by the Helsinki declaration. The participants' participation will be entirely voluntary, and they will have the right to withdraw from the trial at any time during the trial. The participants will be assured that participation in or withdrawal from the study will not cause any change to their regular treatment program. Participants will sign the informed consent (Extended data 331). The Institute of Physiotherapy Rehabilitation and Research of the Bangladesh Physiotherapy Association (BPA) has provided ethical permission (BPA-IPRR/IRB/06/16/2060) on 16th June 2022 to proceed with the study (Extended data 431). The trial has been registered with Clinical Trials Registry India (CTRI/2022/11/047074) (Extended data 531). In case of any changes to the protocol, research team will notify to Institutional review board, the trial registry platform and in the later publications. The personal information of the participants will be confidential and stored unanimously in a dataset at the Department of nutrition and food technology at Jashore university of Science & Technology.\n\nThis study has concluded the assignment of health clinics, training of intervention provider, ethical approval and applied for trial registration. We anticipate beginning this trial on 1st December 2022.\n\n\nDiscussion\n\nThere is an increasing concern of LBP and vitamin D deficiency for chronic pain suffers that is leading the working people towards disability and inefficiency to work.5,9 A non-randomized quasi experimental study10 found therapeutic exercise and vitamin D oral supplementation is effective to reduce pain, replenish vitamin D3 level with short term results. Our study will meet the necessity of randomized systematic evaluation of therapeutic exercises and vitamin D supplement compensation in two different approaches, either by sun exposure, nutrition and healthy lifestyle or by taking oral supplements. We will evaluate outcome in both short term (2 months) and long-term effect after 6 months of stopping the intervention. The experimental group is the therapeutic exercise and booklet group because we assume a positive lifestyle and exercise can replace the role of oral medication supplement, as these were derived as a predictor in observational studies.9\n\nThe methodological standard of the proposed trial adheres to the Enhancing the QUAlity and Transparency Of health Research (EQUATOR) guidelines to ensure the rigor of the study. As this is a two tailed hypothesis, we assume any treatment can be superior or both may have similar effect. The similar effect is also a positive finding, because oral vitamin D supplement have some adverse effects if taken for longer durations.12 Moreover, if the study would have four arms including two interventions, a group with only vitamin D supplement and another with therapeutic exercise and a placebo vitamin D supplement, that could ensure true effects. However, researchers had to limit the study considering funding, scope of practice and complicated management issues. As outcome indicators pain and vitamin D3 levels will be used as primary outcomes and disability as secondary outcome, because previous research suggests disability as a consequence.18 BPI measures not only pain severity, but also pain affective interference and pain physical interference,10,27 that is consistent to the effect of intervention.\n\nThe future direction of the study can explain the importance of therapeutic exercise and their role upon the production, absorption, deposition and function of serum vitamin D level for CLBP cases. Evidence shows that exercise improves the metabolic functions of vitamin D and reduces musculoskeletal pain by modifying sensory neuron excitability and anti-inflammatory and pro-inflammatory cytokines,7 thus contributing to the remission of disability. In this study, if education impacts lifestyle changes and has a positive impact, it will lead to further investigation on how the body can self-regulate vitamin D3 level and add to self-remission of CLBP. Also, this study may have a positive outcome on the recurrence of LBP or delaying the episodic pattern of pain in CLBP patients.\n\n\nAuthor contributions\n\nMSI, KMAH, MAZ contributed to Conceptualizing, Planning, Funding Acquisition, Investigation, Administration, Writing (review & editing), and approval. MSH, RP, IKJ, MFK contributed to Investigation, Conceptualizing, Supervision, and review. VR, NAU contributed to Conceptualizing, Writing (review &editing), and approval.",
"appendix": "Data accessibility\n\nNo underlying data are associated with this article.\n\nMendeley Data: Therapeutic Exercise & Vitamin D for CLBP. https://doi.org/10.17632/d4hf2hjjxr.2. 31\n\nThis project contains the following extended data:\n\n- Extended data 1: the medication chart and home exercise checklist\n\n- Extended data 2: the adverse effects reporting checklist\n\n- Extended data 3: Informed consent\n\n- Extended data 4: Institutional Review Board (IRB) permission\n\n- Extended data 5: Clinical Trial Registry\n\n- Extended data 6: SPIRIT Checklist\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nAuthors acknowledges the research assistants of “Amran’s School of thoughts” for their voluntary contribution to conceptualize the study.\n\n\nReferences\n\nFroud R, Patterson S, Eldridge S, et al.: A systematic review and meta-synthesis of the impact of low back pain on people’s lives. BMC Musculoskelet. Disord. 2014; 15(1): 1–4.\n\nHoy D, Bain C, Williams G, et al.: A systematic review of the global prevalence of low back pain. Arthritis Rheum. 2012; 64(6): 2028–2037. Publisher Full Text\n\nPan CC, Simon P, Espinoza Orías AA, et al.: Lumbar facet joint subchondral bone density in low back pain and asymptomatic subjects. Skelet. Radiol. 2020; 49(4): 571–576. PubMed Abstract | Publisher Full Text\n\nBriggs AM, Straker LM, Burnett AF, et al.: Chronic low back pain is associated with reduced vertebral bone mineral measures in community-dwelling adults. BMC Musculoskelet. Disord. 2012; 13(1): 1–10.\n\nCorreia MI, Hegazi RA, Higashiguchi T, et al.: Evidence-based recommendations for addressing malnutrition in health care: an updated strategy from the feedM. E. Global Study Group. J. Am. Med. Dir. Assoc. 2014; 15(8): 544–550. PubMed Abstract | Publisher Full Text\n\nWu Z, Malihi Z, Stewart AW, et al.: The association between vitamin D concentration and pain: a systematic review and meta-analysis. Public Health Nutr. 2018; 21(11): 2022–2037. PubMed Abstract | Publisher Full Text\n\nZadro JR, Shirley D, Ferreira M, et al.: Is Vitamin D Supplementation Effective for Low Back Pain? A Systematic Review and Meta-Analysis. Pain Physician. 2018; 21(2): 121–145.\n\nHao-Wei X, Shu-Bao Z, Yu-Yang Y, et al.: Relationship between vitamin D and nonspecific low back pain may be mediated by inflammatory markers. Pain Physician. 2021; 24(7): 1015.\n\nAli M, Uddin Z: Factors associated with vitamin D deficiency among patients with musculoskeletal disorders seeking physiotherapy intervention: a hospital-based observational study. BMC Musculoskelet. Disord. 2022; 23(1): 1–9.\n\nAli M, Uddin Z, Hossain A: Combined Effect of Vitamin D Supplementation and Physiotherapy on Reducing Pain Among Adult Patients With Musculoskeletal Disorders: A Quasi-Experimental Clinical Trial. Front. Nutr. 2021; 8: 717473. PubMed Abstract | Publisher Full Text\n\nGordon R, Bloxham S: A systematic review of the effects of exercise and physical activity on non-specific chronic low back pain. In Healthcare. 2016; 4(2): 22. PubMed Abstract | Publisher Full Text\n\nPardo GB, Girbés EL, Roussel NA, et al.: Pain neurophysiology education and therapeutic exercise for patients with chronic low back pain: a single-blind randomized controlled trial. Arch. Phys. Med. Rehabil. 2018; 99(2): 338–347. PubMed Abstract | Publisher Full Text\n\nHolick MF: Sunlight and vitamin D for bone health and prevention of autoimmune diseases, cancers, and cardiovascular disease. Am. J. Clin. Nutr. 2004; 80(6): 1678–1688.\n\nSimula AS, Jenkins HJ, Holopainen R, et al.: Transcultural adaption and preliminary evaluation of “understanding low back pain” patient education booklet. BMC Health Serv. Res. 2019; 19(1): 1–1.\n\nAugustine LF, Madhavan KN, Kulkarni B: Optimal duration of sun exposure for adequate cutaneous synthesis of vitamin D in Indian cities: an estimate using satellite-based ultraviolet index data. Biomed. J. Sci. Tech. Res. 2018; 6: 5073–5077.\n\nLakkireddy M, Karra ML, Patnala C, et al.: Efficiency of vitamin D supplementation in patients with mechanical low back ache. J. Clin. Orthop. Trauma. 2019; 10(6): 1101–1110. PubMed Abstract | Publisher Full Text\n\nIslam MS, Zahid MA, Hossain MS, et al.: Effect of Therapeutic Exercise, Educational booklet and Vitamin D3 Supplement for the Management of Chronic Mechanical Low Back Pain Muhammad Shahidul Islam, Dr. Md. Ashrafuzzaman Zahid, Professor Dr. Md. Sohrab Hossain, protocols.io.2022. Publisher Full Text\n\nGallagher KM, Campbell T, Callaghan JP: The influence of a seated break on prolonged standing induced low back pain development. Ergonomics. 2014; 57(4): 555–562. PubMed Abstract | Publisher Full Text\n\nZaman S, Hawlader MD, Biswas A, et al.: High prevalence of vitamin D deficiency among Bangladeshi children: an emerging public health problem. Health. 2017; 09(12): 1680–1688. Publisher Full Text\n\nHarinarayan CV, Holick MF, Prasad UV, et al.: Vitamin D status and sun exposure in India. Dermato-endocrinology. 2013; 5(1): 130–141. Publisher Full Text\n\nGao Q, Kou T, Zhuang B, et al.: The association between vitamin D deficiency and sleep disorders: a systematic review and meta-analysis. Nutrients. 2018; 10(10): 1395. PubMed Abstract | Publisher Full Text\n\nDean E, Söderlund A: What is the role of lifestyle behaviour change associated with non-communicable disease risk in managing musculoskeletal health conditions with special reference to chronic pain? BMC Musculoskelet. Disord. 2015; 16(1): 1–7.\n\nKim D, Cho M, Park Y, et al.: Effect of an exercise program for posture correction on musculoskeletal pain. J. Phys. Ther. Sci. 2015; 27(6): 1791–1794. PubMed Abstract | Publisher Full Text\n\nDunsford A, Kumar S, Clarke S: Integrating evidence into practice: use of McKenzie-based treatment for mechanical low back pain. J. Multidiscip. Healthc. 2011; 4: 393.\n\nFrança FR, Burke TN, Caffaro RR, et al.: Effects of muscular stretching and segmental stabilization on functional disability and pain in patients with chronic low back pain: a randomized, controlled trial. J. Manip. Physiol. Ther. 2012; 35(4): 279–285. PubMed Abstract | Publisher Full Text\n\nYoon JS, Lee JH, Kim JS: The effect of swiss ball stabilization exercise on pain and bone mineral density of patients with chronic low back pain. J. Phys. Ther. Sci. 2013; 25(8): 953–956. Publisher Full Text\n\nFarrar JT, Young JP Jr, LaMoreaux L, et al.: Clinical importance of changes in chronic pain intensity measured on an 11-point numerical pain rating scale. Pain. 2001; 94(2): 149–158. Publisher Full Text\n\nJordan K, Dunn KM, Lewis M, et al.: A minimal clinically important difference was derived for the Roland-Morris Disability Questionnaire for low back pain. J. Clin. Epidemiol. 2006; 59(1): 45–52. PubMed Abstract | Publisher Full Text\n\nIslam SM, Emran M, Baral AB, et al.: Roland Morris disability questionnaire in Bengali for evaluation of patients with low back pain. KYAMC J. 2020; 11(1): 21–25. Publisher Full Text\n\nFroud R, Rajendran D, Patel S, et al.: The power of low back pain trials: a systematic review of power, sample size, and reporting of sample size calculations over time, in trials published between 1980 and 2012. Spine. 2017; 42(11): E680–E686. PubMed Abstract | Publisher Full Text\n\nHossain KMA, Zahid MA, Islam MS: Therapeutic Exercise & Vitamin D for CLBP. Mendeley Data. 2022; V2. Publisher Full Text"
}
|
[
{
"id": "181251",
"date": "28 Jun 2023",
"name": "Giacomo Farì",
"expertise": [
"Reviewer Expertise rehabilitation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis protocol is interesting and in line with the aims of this journal. Some concerns have to be addressed.\nI really appreciate that you provided the clinical trial registration and the IRB approval, but it is still not clear if this study will be a prospective or a retrospective one?\nThen, since you compare three interventions, very different from each other, you should better define the inclusion/exclusion criteria: which Low back pain will you consider? Which diseases will be excluded and which ones no?\nFinally, to improve the rehabilitative lapels of this study, you should explain in the discussion how your results could add new options for chronic low back pain therapy and rehabilitation.\n\nBest regards and good luck\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
},
{
"id": "181246",
"date": "29 Jun 2023",
"name": "Gopal Nambi",
"expertise": [
"Reviewer Expertise Musculoskeletal and sports physiotherapy"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Authors Thanks a lot for the opportunity you have offered me to revise the fascinating manuscript, \"Comparison of the effects of therapeutic exercise...randomized clinical trial\". I thank the authors for their effort in producing this exciting manuscript.\nFrom the editing point of view, I recommend the authors to fully respect the editing requirements imposed by this scientific journal and clearly indicated in the template. More specifically, I mean: the number of words in the abstract and manuscript, the number of keywords and the way to indicate the bibliographic sources.\nAs a significant strength: This proposal is a novelty in the field and adds information to the existing evidence in the literature produced in the field.\nAs a major weakness: The manuscript lacks details and clarity concerning methodological steps that would help improve the understanding of the manuscript.\nKeywords: use MeSH keywords\nAbstract:\nThe background of the study talks only about CLBP.\n\nThe objective of the study is not clear.\n\nMention the study duration and study setting.\n\nMention the character of the study participants.\n\nMention the treatment procedure in short.\n\nMention the outcome measures in short and its duration of measurement.\n\nMention the statistical tests used for the study.\nManuscript\nMention the acronym of abbreviation when it is used for the first time.\n\nPlease recheck the reference number 5.\n\nMention the relation between CLBP and vitamin D deficiency in detail.\n\nMention in detail about Vit D supplement, its role, merits and demerits in CLBP.\n\nHow come this study is differing from the reference study 10?\n\nMention the gaps monitored by the researcher in the previous studies.\n\nMention the study hypothesis.\n\nInclude the clinical significance of this study over clinicians, patients, and researchers after the study hypothesis.\n\nMention who has diagnosed the participants and their qualification and experience.\n\nMention the detail information about randomization, allocation and blinding.\n\nMention in detail about the exercise protocol and the contents involved in booklet.\n\nMention the outcome measures measured in the study and its reliability and validity.\n\nMention the sample size calculation with reference. The information provided is not sufficient.\n\nMention the statistical tests included in the study. The tests mentioned are not suitable.\n\nIs the rationale for, and objectives of, the study clearly described? No\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1352
|
https://f1000research.com/articles/11-1347/v1
|
18 Nov 22
|
{
"type": "Research Article",
"title": "BDNF as a potential predictive biomarker for patients with pediatric cerebral palsy",
"authors": [
"Hanan Hanna",
"Eman R. Youness",
"Hisham A. Aziz Orban",
"Hala T. El-Bassyouni",
"Eman R. Youness",
"Hisham A. Aziz Orban",
"Hala T. El-Bassyouni"
],
"abstract": "Background: Cerebral palsy (CP) is the most common motor disability in children, which is instigated by damage to the developing brain that affects the ability to control the muscles. The main types of CP are spastic CP, dyskinesia CP and mixed CP. The aim of this work was to estimate the concentrations of complete blood count (CBC), erythrocytic sedimentation rate (ESR), C-reactive protein (CRP), brain-derived neurotrophic factor (BDNF), and tumor necrosis factor-α (TNF-α) in children with CP compared to the control group. Methods: A total of 75 Egyptian children were enrolled in this study, 45 had CP and 30 were controls. CBC, ESR, CRP, BDNF, and TNF-α were assessed. Results: The ESR, CRP and TNF-α levels showed statistically significant increases in cases compared with controls. While the neutrophil/lymphocyte ratio and the BDNF levels were significantly lower in CP compared with the controls. When comparing the different groups of CP with each other; there were no significant differences. Regarding the correlation of BDNF and different studied parameters, our study showed a positive correlation between BDNF and TNF levels only within the group with spastic CP. Conclusions: BDNF may be considered as a biomarker or treatment target for CP to avoid further complications as still there is insufficient progress in the prediction, early diagnosis, treatment, and prevention of CP. Furthermore, searching for novel strategies to increase BDNF levels may open a new opportunity for the treatment of CP.",
"keywords": [
"Cerebral palsy",
"BDNF",
"TNF-α",
"ESR",
"CRP"
],
"content": "Introduction\n\nCerebral palsy (CP) is one of the most obvious forms of physical incapacity in childhood; with an estimated worldwide pervasiveness of around 1.5–3 per 1,000.1 CP is a wide umbrella term that covers lesions of the developing brain causing diminished movement and may affect perceptual and even cognitive problems.2 CP is usually confined to a group of disorders affecting posture and movement, causing limitation of activity and non-progressive turbulences, which usually happens during infant or fetal brain development. It was first termed ‘cerebro-spinal disorder’, and soon transitioned to the term cerebral palsy.3 However, in spite of the change in the clinical diagnosis of CP, the definition continued to focus on the brain without stressing the developmental spinal cord dysfunction.4\n\nIn regard to clinical overview, it begins in early childhood and persists throughout the individuals lifetime.2 Children with CP might develop a variety of secondary complications over time that will impact their functional capabilities showing huge variation from one another.5 Complications may include feeding difficulties; pain; fractures; osteoporosis; communication difficulties; drooling; spasticity and contractures; osteopenia; and functional gastrointestinal abnormalities, vomiting, and constipation.6 The associated intellectual impairment in children with CP needs more recognition,7 as intellectual disability is an important and relatively common issue that influences daily activities, the burden of care, and of course quality of life.8\n\nThe etiology of CP is complicated. For more than 100 years, it was speculated that the majority of CP cases were related to infant brain hypoxia in the perinatal period or during labor, which made CP incidence a matter of obstetric and neonatal care quality. CP is a result of heterogeneous risk factors complementary to specific etiology giving a wide variation in associated secondary conditions, functional limitations, severity, clinical features, and evolution of the condition over the lifetime of the person.9 One of the most highlighted risk factors is premature birth, especially before 28 weeks of gestation, which has become one of the most associated risk factors for the development of CP.10 It has long been thought that CP is caused by environmental triggers, recent findings identified rare mutations in single genes that may be the cause of this disorder.11 However, despite all the medical care done in these areas, CP incidence has remained unchanged.12\n\nSurveillance of Cerebral Palsy in Europe (SCPE), aiming to standardize CP classification has suggested a simple classification for patients, dividing them into three chief groups: ataxic, dyskinetic (choreoathetosis & dystonia), spastic (unilateral or bilateral spastic).13 While mixed type is a combination of the aforementioned types. Another classification rendering to data from the Gross Motor Function Classification System (GMFCS): level 1, the patients are able to walk freely; level 2, patients walk with certain (slight) limitations on their own; level 3, patients walk by ancillary apparatus; level 4, patients could move on their own, but within specific limits, she/he could use an electrical wheelchair; level 5, patients are not capable to move on their own in a wheelchair.14\n\nAs for the diagnosis of CP, it is fundamentally based on clinical findings. Early diagnosis is usually based on using standardized neuromotor assessment, findings on magnetic resonance imaging (MRI), and clinical history, moreover, in the greatest clinical settings, CP can only be diagnosed with confidence by the age of 2 years old.15\n\nBrain-derived neurotrophic factor (BDNF) is a member of the neurotrophins (NTs), a family of proteins that support the function of the central nervous system (CNS), and it was recognized in 1982, as a small dimeric protein.16 There are two main types of BDNF present in the human body, pro- and mature BDNF.17 NTs are synthesized mainly in the CNS.18 BDNF plays a crucial part in the development of the nervous system by acting on neuronal development, growth and survival, neurogenesis, cell differentiation, synaptic plasticity and synaptogenesis.19 BDNF is expressed widely in the brain, comprising the hippocampus, cortex, and basal forebrain regions. It crosses the blood-brain barrier in a bi-directional mode and can therefore be detected in the blood.20 Pro-BDNF promotes neuronal cell death whereas mature BDNF stimulates neuronal cell survival and growth.21 Differentiating between the BDNF forms has been well-known as one of the significant factors skewing reliable BDNF measurements, causing contradictory findings.22 Along with the nervous system, BDNF is also found peripherally in the skeletal muscle, lungs smooth muscle cells and heart. The chief reservoir of this protein within the peripheral blood are platelets.23\n\nFurthermore, the maximum concentrations of pro-BDNF are detected perinatally, following which it diminishes with age, while in adulthood it remains detectable at very low levels. These data justify partially that the brains of infants and newborns are more fragile to ischemia owing to lack of sufficient mature BDNF in the CNS and low-frequency neuronal activities.24\n\nWe aimed to assess the circulating concentrations of BDNF, TNF-α, and other blood parameters in children with CP compared with the control group. We then further subdivided CP groups according to clinical neurological affection into spastic, dyskinesia, and mixed groups, comparing the different biomarkers, including the blood level of BDNF, tumor necrosis factor-α (TNF-α), and other parameters with the control group.\n\n\nMethods\n\nThe goal of the study was clarified to the guardians of all participants. Written informed consent was obtained from all the parents of the children before they were enrolled in this study, which was permitted by the Ethical Committee, Faculty of Medicine, Delta University of Science and Technology, Egypt (FM2108007) in July 2021.\n\nA total of 75 Egyptian children were enrolled from October 2021 to March 2022; CP was confirmed by clinical symptoms assessed by a neurological pediatrician. The CP children were enrolled as they were seeking physical therapy and follow up with pediatric clinicians. A total of 45 children with CP and 30 controls were enrolled; and they were matched by age, sex and socioeconomic status. The ages varied from 2 to 7 years old (mean age of controls: 3.9 ± 1.5, mean age of cases: 4.3 ± 1.5). As for control participants, they were selected by pediatric clinicians to be eligible for our study. They were enrolled following physical examination if they were determined to not show any symptoms or signs of active infection or chronic disease.\n\nParticipants were classified into two main groups. Group І comprised the controls, Group II included the participants with CP, which was further divided into three groups, spastic CP (26 patients), dyskinesia CP (12 patients) and mixed CP (seven patients) (Physiopedia).25\n\nExclusion criteria of the CP patients and healthy volunteers included neurological, inflammatory, endocrine, cardiovascular, hepatic, renal or any clinically significant chronic disease and immunocompromised subjects. To all participants the following were done:\n\n1. Detailed history taking: detailed history was taken from all participants including starting of showing any delayed milestones.\n\n2. Complete physical examination: complete physical examination was done for all groups.\n\n3. Anthropometric measurements: namely body weight, height measurements.\n\n4. Biochemical assessments\n\nAssessment of liver function\n\nLiver function enzyme alanine aminotransferase (ALT) was estimated using fully automated chemistry analyzer Cobas-C and Cobas.26\n\nAssessment of C-reactive protein (CRP)\n\nCRP was assessed using a fully automated Nephelometric quantitative technique, which is more specific than Latex. The analyzer includes a dilutor with temperature controlled (37°C) transfer arms; reagent, sample, standards rack stations (with barcode reading); buffer compartment; dilution racks; temperature controlled (37°C) cuvette rotor; cuvette washing device; bar code wand reader; and optical system.27\n\nAssessment of erythrocytic sedimentation rate (ESR)\n\nUsing the Westergren method, which measures the distance (in millimeters) that red blood cells in anticoagulated whole blood fall to the bottom of a standardized, upright, elongated tube due to gravity over one hour, ERS was determined.28\n\nComplete blood count (CBC)\n\nCBC was analyzed using an automated blood cell counter (XE 2100). Haemoglobin; HBG, Neutrophil/lymphocyte ratio (NLR) was evaluated as the absolute neutrophil count divided by the absolute lymphocyte count, while the platelet lymphocyte ratio (PLR) was calculated by platelet count divided by absolute lymphocyte count.29\n\nQuantification of TNF-α\n\nTNF-α levels in serum was measured using a Human TNF alpha ELISA Kit (Abcam Cat# ab181421, RRID:AB_2924775).\n\nQuantification of BDNF\n\nBDNF levels in serum were measured using a Human BDNF ELISA Kit (Abcam Cat# ab212166, RRID:AB_2924770).\n\nBoth ELISA tests were done according to the manufacturer’s instructions. The full protocol can be found at protocols.io.\n\nAssuming that the confidence interval (CI) = 95% and the error = 5%, a cross-sectional study based on the previous situation in literature, was 8% among children (5–15 years old). Knowing that the average incidence of CP is estimated to range between 1.5 and 3.0 per 1,000 live births in Dakahalia, the estimated sample size to achieve 95% confidence and avoid α error, was calculated (Calculator.net).\n\nData were analyzed using IBM SPSS Statistics (RRID:SCR_016479) software package version 20.0 (Armonk, NY: IBM Corp). Checking for normality was performed by the Shapiro-Wilk test. Quantitative data were expressed as a range from minimum to maximum, mean, standard deviation, and median. For normally distributed quantitative variables, Student t-test was used to compare two groups, while one-way ANOVA test was used for comparing the four studied groups and followed by a post hoc test (Tukey) for pairwise comparison. The significance of the obtained results was judged at the 5% level. A Pearson correlation coefficient was performed between BDNF and TNF with different parameters.\n\n\nResults\n\nA total of 75 subjects were involved in our work (Table 1).45 Their age ranged from 2 to 7 years old. A total of 35 patients were male (46.6%), and 40 were female (53.3%). No significant differences between the control group and patients regarding age, sex, weight, and ALT were found (Table 1).\n\n* Statistically significant at p ≤ 0.05. ALT, alanine aminotransferase; CRP, C-reactive protein; TNF, tumor necrosis factor; ESR, erythrocytic sedimentation rate; HBG, hemoglobin; WBCs, white blood cells; BDNF, brain-derived neurotrophic factor.\n\nThe ESR, CBC, hemoglobin, lymphocyte, and NLR showed a statistically significant difference between the control group and cases (Table 2).\n\n* Statistically significant at p ≤ 0.05. CBC, complete blood count.\n\nBDNF levels in the CP group (14.1 ± 2.5 (pg/ml)) were significantly lower (P < 0.001) than those of controls (30.7 ± 4.2 (pg/ml)). When comparing the different groups of CP with each other; there were no significant differences. On the other hand, comparing each subtype of CP with the control group showed a significantly higher value for the control group (P < 0.001) (Tables 3 and 4).\n\n* Statistically significant at p ≤ 0.05. ALT, alanine aminotransferase; CRP, C-reactive protein; TNF, tumor necrosis factor; ESR, erythrocytic sedimentation rate; HBG, hemoglobin; WBCs, white blood cells; BDNF, brain-derived neurotrophic factor.\n\n* Statistically significant at p ≤ 0.05. CBC, complete blood count.\n\nThe TNF level in the CP group (28 ± 3 (pg/ml)) was significantly higher (P < 0.001), than those of the control group (16.4 ± 1.2 (pg/ml)). When comparing the different groups of CP with each other; there was a significant difference between the group with Spastic CP (26 ± 2.8 (pg/ml)) and dyskinesia (32.5 ± 1 (pg/ml)) (P < 0.001). Moreover, when comparing Dyskinesia CP (32.5 ± 1 (pg/ml)) and mixed CP (28 ± 0.8 (pg/ml)) there was a significant difference (P < 0.001), with higher levels found in the Dyskinesia group. On the other hand, comparing spastic CP and dyskinesia CP showed no significant difference (p2 = 0.064) (Tables 3 and 4).\n\nFurthermore, the CRP level was significantly higher in the CP group (10.9 ± 2.60 (mg/l)), than those of the control group (1.7 ± 0.3 (mg/l)) (P < 0.001). While comparing the different groups of CP with each other; there was no significant difference. On the other hand, comparing each subtype of CP with the control; it showed a significantly higher value for the control group (P < 0.001) (Tables 3 and 4).\n\nAlso, the NLR was significantly lower in the CP group (1.1 ± 0.1), than those of the control group (1.6 ± 0.2) (P < 0.001). When comparing the different groups of CP with each other; there was no significant difference. On the other hand, comparing each subtype of CP with the control; it showed a significantly higher value for the control group (P < 0.001) (Tables 2 and 4).\n\nWith regard to the correlation of BDNF with the various studied parameters, our study only showed a positive correlation between BDNF and TNF levels with spastic CP (Table 5), otherwise there were no significant correlations with other parameters (Table 6).\n\n* Statistically significant at p ≤ 0.05. BDNF, brain-derived neurotrophic factor; CRP, C-reactive protein; TNF, tumor necrosis factor.\n\n\nDiscussion\n\nCP is mainly a neuromotor disorder that affects the muscle tone, posture and development of movement.30 Precise CP diagnosis needs either an abnormality on an MRI scan and/or clinical history and motor dysfunction to ensure long-term functional outcomes based on positively modulating neuroplasticity.31\n\nNTs are a family of proteins, which include BDNF, that are actively produced throughout the brain and are implicated in neuronal activity regulation; they also help and stimulate neurogenesis, which is why they are known to play an important role in both the recovery and protective function following neurodegenerative diseases.32\n\nMany researchers have been dedicated to elucidating its role in pathological and physiological conditions. Multiple factors give complexity to the BDNF system, i.e., different receptors with their multiple signaling pathways, the functional isoforms and heterogeneous population of mRNAs, demanding more accurate procedures to make field improvements.33\n\nIn our study, the level of BDNF was significantly lower in the CP group compared with the control group. Hansen et al., stated that the reduced level of BDNF in the CP group was observed in children with severe CP, specifically low intake of n-3 fatty acids, energy, and dietary fibers and low physical activity levels.34 BDNF plays a great role in the development of the nervous system by affecting synaptogenesis, neurogenesis, neuronal development, growth and survival, synaptic plasticity and cell differentiation.19\n\nAL-Ayadhi, suggested in her study a highly possible pathophysiological role played by BDNF in autism, as they also found significantly lower BDNF levels in participants with autism but it was not related to the severity level, this correlation may interpret the pathogenesis of autism and other possible neurological dysfunctions.35\n\nForsgren et al.,36 found a correlation between BDNF and TNF levels in patients with rheumatoid arthritis (RA), they stated that the level of BDNF was lowered significantly with anti-TNF treatment, which was associated with pain relief. Likewise, we found only a positive correlation between BDNF and TNF levels with spastic CP.\n\nOn the other hand, Siang Ng et al., suggested in their study that BDNF is increased in mild cognitive impairment (MCI) cases as a compensatory mechanism in preclinical dementia, supporting the partially inflammatory and neurotrophic hypotheses of cognitive impairment.22 Plasma BDNF appears to be a useful biomarker to differentiate MCI from patients with no cognitive impairment. This supports the suggestion that augmented peripheral BDNF acts as a compensatory mechanism in the preclinical stage of dementia.37\n\nPalasz et al., suggested that NTs has been demonstrated that synaptic plasticity defects associated with insufficient neuronal supply of BDNF and other neurotrophic factors may contribute to neurodegenerative and neuropsychiatric diseases as in Parkinson’s and Alzheimer’s disease.38 Nevertheless, neither efforts to enhance BDNF expression with gene therapy nor direct delivery of exogenous BDNF into the patient’s brain led to any improvements.\n\nYeom et al., stated that a high peripheral BDNF concentration was found in preschool aged children with cognitive and attention intellectual disabilities, suggesting that it may help as a biomarker for any intellectual problems in early life.39\n\nWeinstein et al., found that older adults with higher peripheral BDNF levels had lower chance of developing Alzheimer’s disease.21 Decreased BDNF levels may explain the lack of trophic support, contributing to neuronal degeneration.40\n\nFurthermore, it has been shown that neurodegeneration and psychiatric diseases may be partially affected by low levels of BDNF and other members of the NT family.41 Therefore, a search is needed for new strategies to increase the levels of BDNF as a tool in the treatment and prevention of neurological diseases.38\n\nWu J et al., revealed that children with cerebral palsy have greater levels of TNF-α than controls42; this corresponded to our findings, in addition, they suggested that pharmaceutical therapies to reduce inflammation in infants with cerebral palsy may alleviate symptoms and warrant further investigation. Increased baseline TNF-α levels might be an indicator of more extensive brain damage when correlated with severity.\n\nAlso, it was suggested that the inflammatory response might diminish with age, whereas the cerebral palsy symptoms are not necessarily improved.43 Similarly, Soliman S et al., concluded that TNF-α levels in children with spastic CP are positively correlated with disease severity, showing a significant difference between pretreatment levels of TNF-α, which improved after rehabilitation and correlated with improvement in all outcome measures.44\n\n\nConclusions\n\nBDNF has been shown to have a significant relationship with brain development early in life. However, further studies are needed to assess its value as a biomarker and/or as a treatment to enhance or avoid further complications of CP as still there is insufficient progress in prediction, early diagnosis, treatment, and prevention. Searching for novel strategies to increase BDNF levels may open a new opportunity for the treatment of neurological diseases.",
"appendix": "Data availability\n\nOpen Science Framework: BDNF as Predictor biomarker for Pediatric Cerebral Palsy patients. https://doi.org/10.17605/OSF.IO/5BKAE. 45\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nWe appreciate all patients who participated and contributed samples to the study.\n\n\nReferences\n\nMcCullough N, Parkes J, Kerr C, et al.: The health of children and young people with cerebral palsy: a longitudinal, population-based study. Int. J. Nurs. Stud. 2013; 50(6): 747–756. PubMed Abstract | Publisher Full Text\n\nRosenbaum P, Paneth N, Leviton A, et al.: A report. The definition and classification of cerebral palsy April. Dev. Med. Child Neurol. Suppl. 2007; 109: 8–14. PubMed Abstract\n\nLittle WJ: On the influence of abnormal parturition, difficult labors, premature birth, and asphyxia neonatorum, on the mental and physical condition of the child, especially in relation to deformities. Clin. Orthop. Relat. Res. 1966; 46: 7–22. PubMed Abstract | Publisher Full Text\n\nBrandenburg J, Fogarty M, Sieck G: A Critical Evaluation of Current Concepts in Cerebral Palsy. PHYSIO. 2019; 34: 216–229. PubMed Abstract | Publisher Full Text\n\nNational Institute for Health and Care Excellence (UK): Cerebral palsy in under 25s: assessment and management.Reference Source\n\nKrigger KW M.D.: Cerebral Palsy: An Overview. Am. Fam. Physician. 2006; 73: 1.\n\nYin Foo R, Guppy M, Johnston LM: Intelligence assessments for children with cerebral palsy: a systematic review. Dev. Med. Child Neurol. 2013; 55(10): 911–918. PubMed Abstract | Publisher Full Text\n\nReid SM, Meehan EM, Arnup SJ, et al.: Intellectual disability in cerebral palsy: a population-based retrospective study. Dev. Med. Child Neurol. 2018; 60(7): 687–694. PubMed Abstract | Publisher Full Text\n\nStavsky M, Mor O, Mastrolia SA, et al.: Cerebral palsy trends in epidemiology and recent development in prenatal mechanisms of disease, treatment, and prevention. Front. Pediatr. 2017; 5: 21.\n\nO’Shea TM, Allred EN, Dammann O, et al.: The ELGAN study of the brain and related disorders in extremely low gestational age newborns. Early Hum. Dev. 2009; 85(11): 719–725. PubMed Abstract | Publisher Full Text\n\nJin SC, Lewis SA, Bakhtiari S, et al.: Author Correction: Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nat. Genet. 2020; 53: 1046–1056. Publisher Full Text\n\nReddihough D, Collins KJ: The epidemiology and causes of cerebral palsy. Aust. J. Physiother. 2003; 49(1): 7–12. Publisher Full Text\n\nCans C, Dolk H, Platt MJ, et al.: Recommendations from the SCPE collaborative group for defining and classifying cerebral palsy. Dev. Med. Child Neurol. Suppl. 2007; 109: 35–38. Publisher Full Text\n\nPalisano RJ, Cameron D, Resenbaum PL, et al.: Stability of the gross motor function classification system. Dev. Med. Child Neurol. 2006; 48(6): 424–428. Publisher Full Text\n\nPatel D, Neelakantan M, Karan Pandher K, et al.: Cerebral palsy in children: a clinical overview. Transl Pediatr. 2020; 9: S125–S135. PubMed Abstract | Publisher Full Text\n\nLessmann V, Brigadski T: Mechanisms, locations, and kinetics of synaptic BDNF secretion: an update. Neurosci. Res. 2009; 65: 11–22. PubMed Abstract | Publisher Full Text\n\nYang J, Siao CJ, Nagappan G, et al.: Neuronal release of proBDNF. Nat. Neurosci. 2009; 12: 113–115. PubMed Abstract | Publisher Full Text\n\nConner JM, Lauterborn JC, Yan Q, et al.: Distribution of brain-derived neurotrophic factor (BDNF) protein and mRNA in the normal adult rat CNS: Evidence for anterograde axonal transport. J. Neurosci. 1997; 17: 2295–2313. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLu B, Nagappan G, Lu Y:BDNF and Synaptic Plasticity, Cognitive Function, and Dysfunction. Neurotrophic Factors. Handbook of Experimental Pharmacology. Lewin G, Carter B, editors.Berlin/Heidelberg, Germany;Springer;2014; 223–250. 978-3-642-45105-8.\n\nPan W, Banks WA, Fasold MB, et al.: Transport of brain-derived neurotrophic factor across the blood-brain barrier. Neuropharmacology. 1998; 37: 1553–1561. PubMed Abstract | Publisher Full Text\n\nWeinstein G, Beiser AS, Choi SH, et al.: Serum brain-derived neurotrophic factor and the risk for dementia: the Framingham Heart Study. JAMA Neurol. 2014; 71: 55–61. PubMed Abstract | Publisher Full Text\n\nSiang NT, Coughlan C, Heyn P, et al.: Increased plasma brain-derived neurotrophic factor (BDNF) as a potential biomarker for and compensatory mechanism in mild cognitive impairment: a case-control study AGING.2021; 13(19).\n\nAzoulay D, Urshansky N, Karni A: Low and dysregulated BDNF secretion from immune cells of MS patients is related to reduced neuroprotection. J. Neuroimmunol. 2008; 195: 186–193. PubMed Abstract | Publisher Full Text\n\nAi Chen AI, Xiong L, Tong YU: The neuroprotective roles of BDNF in hypoxic ischemic brain injury. J. Curr. Biomed. Rep. 2013; 1: 167–176. PubMed Abstract | Publisher Full Text\n\nPavone V, Testa G: Orthopedic Management of Children with Cerebral Palsy; Classifications of cerebral palsy. Nova Science Publishers, Inc.;2015; pp. 75–98.\n\nBurtis CA, Ashwood ER, Bruns DE: Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. 5th ed.St Louis:Elsevier Saunders Company;2012.\n\nJones SL: Clinical laboratory Pearls. Lippincott Williams and Wilkins;2001.\n\nFischbach FT RN, BSN, MSN, Dunning MB 111, BS, MS, Ph.D.: A Manual of Laboratory Diagnostic Tests. Edition 7.Lippincott Williams and Wilkins.\n\nChan AS, Rout A: Use of Neutrophil-to-Lymphocyte and Platelet-to-Lymphocyte Ratios in COVID-19. J. Clin. Med. Res. 2020; 12(7): 448–453. PubMed Abstract | Publisher Full Text\n\nGraham HK, Rosenbaum P, Paneth N, et al.: Cerebral palsy. Nat. Rev. Dis. Primers. 2016; 2: 15082. PubMed Abstract | Publisher Full Text\n\nNovak I, Morgan C, Adde L, et al.: Early, accurate diagnosis and early intervention in cerebral palsy: advances in diagnosis and treatment. JAMA Pediatr. 2017; 171: 897–907. PubMed Abstract | Publisher Full Text\n\nHoulton J, Abumaria N, Hinkley SFR, et al.: Therapeutic Potential of Neurotrophins for Repair After Brain Injury: A Helping Hand from Biomaterials. Front. Neurosci. 2019; 13: 790. PubMed Abstract | Publisher Full Text\n\nFoltran RB, Diaz SL: BDNF isoforms, serotonin, and neurogenesis. International Society for Neurochemistry. J. Neurochem. 2016; 138(204): 204–221. Publisher Full Text\n\nHansen S, Lorentzen J, Pedersen L, et al.: Suboptimal Nutrition and Low Physical Activity Are Observed Together with Reduced Plasma Brain-Derived Neurotrophic Factor (BDNF) Concentration in Children with Severe Cerebral Palsy (CP). Nutrients. 2019; 11: 620. PubMed Abstract | Publisher Full Text\n\nAl-Ayadhi L: Serum Levels of Brain-Derived Neurotrophic Factor (BDNF) in Autistic Children in Central Saudi Arabia. The Open Conference Proceedings Journal. 2011; 5: 36–40. Publisher Full Text\n\nForsgren S, Grimsholm TO, Dalén T, et al.: Measurements in the Blood of BDNF for RA Patients and in Response to Anti-TNF Treatment Help Us to Clarify the Magnitude of Centrally Related Pain and to Explain the Relief of This Pain upon Treatment. Int. J. Inflam. 2011; 2011: 1–7. PubMed Abstract | Publisher Full Text\n\nO’Brien JT: The glucocorticoid cascade hypothesis in man: prolonged stress may cause permanent brain damage. B. J. Psych. 1997; 170: 199–201. Publisher Full Text\n\nPalasz E, Wysocka A, Gasiorowska A, et al.: BDNF as a Promising Therapeutic Agent in Parkinson's Disease. Int. J. Mol. Sci. 2020; 21(3): 1170. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChan-Woo Y, Young-Ja P, Sam-Wook C, et al.: Association of peripheral BDNF level with cognition, attention and behavior in preschool children. Child Adolesc. Mental Health. 2016; 10: 10. PubMed Abstract | Publisher Full Text\n\nHock C, Heese K, Hulette C, et al.: Region-specific neurotrophin imbalances in Alzheimer disease: decreased levels of brain-derived neurotrophic factor and increased levels of nerve growth factor in hippocampus and cortical areas. Arch. Neurol. 2000; 57: 846–851. PubMed Abstract | Publisher Full Text\n\nAllen SJ, Watson JJ, Shoemark DK, et al.: GDNF, NGF and BDNF as therapeutic options for neurodegeneration. Pharmacol. Ther. 2013; 138: 155–175. PubMed Abstract | Publisher Full Text\n\nWu J, Li X: Plasma Tumor Necrosis Factor-alpha (TNF-α) Levels Correlate with Disease Severity in Spastic Diplegia, Triplegia, and Quadriplegia in Children with Cerebral Palsy. Med. Sci. Monit. 2015; 21: 3868–3874. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nHimmelmann K, Uvebrant P: The panorama of cerebral palsy in Sweden. XI. Changing patterns in the birth-year period 2003–2006. Acta Paediatr. 2014; 103: 618–624. PubMed Abstract | Publisher Full Text\n\nSoliman S, Labeeb A, Esaily H, et al.: Relation of serum tumor necrosis factor α. level with disease severity in spastic cerebral palsy. Menoufia. Med. J. 2021; 34: 340–46. Publisher Full Text\n\nHanna H: BDNF as Predictor Biomarker for Pediatric Cerebral Palsy Patients. OSF. [Dataset]. 2022. Publisher Full Text"
}
|
[
{
"id": "269379",
"date": "10 May 2024",
"name": "Henrique Gouveia",
"expertise": [
"Reviewer Expertise Nutrition and Neurosciences",
"with emphasis on the alterations caused by experimental Cerebral Palsy and possible nutritional and pharmacological interventions."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general, I suggest having the text proofread by a native speaker, as there are some grammatical errors. Abstract - Given that the abstract needs to present the work in a complete way, I suggest adding some information. In the background, a sentence before the objectives presenting what has been found in the literature about the parameters in the context of CP that were evaluated could better justify the selection of these parameters. In the methods, it would be interesting to add the number of each type of CP among the 45 individuals. - I suggest writing the keywords in full and presenting the acronyms in the abstract, as presented. Introduction - Please check the study by McIntyre et al. (2022) [Ref 1]for more recent data on the prevalence of CP. - The authors presented information on BDNF, but not on the other parameters. It is important to present something about the parameters that were evaluated to justify the evaluation, including data from conditions similar to CP that observed changes in these parameters. Otherwise, the selection of parameters seems to have been random. Methods - The enzyme alanine aminotransferase (ALT) had not been mentioned elsewhere before appearing in the methods, so it would be interesting to standardize the objectives in the methods and introduction. Results - In the description of the results in Table 1, as well as describing in the text the parameters that were not different, I suggest adding the differences found between the groups. - General comment on the table legends: In the legend for table 1, the authors have indicated that “t: Student t-test; χ2: Chi square test”, should they be somewhere in the table? If they don't, just say that the statistical test was used without stating what “t and χ2” mean, as they won't be present in the table. This also applies to “p: p value”, since the table says “p-value”. In other tables, such as 3 and 4, the authors presented “F: F for One way ANOVA test” and “H: H for Kruskal Wallis test”, but there is no F and/or H in the table. In general, I suggest that the authors revise the table legends and leave only the acronyms that were presented in the tables that need to be explained, otherwise just indicate the statistical test performed. - In the description of the results in table 2, the authors reported differences in ESR and hemoglobin, but they were presented in table 1. - In the description of the results in tables 3 and 4, the authors need to review the means and variances used to describe significant differences between the CP and Control groups, since these results were cited in table 1, and not in tables 3 and 4, which in turn present the specific results for each type of CP. - The authors reported in the text that “comparing spastic CP and dyskinesia CP showed no significant difference” with regard to TNF. I believe the authors meant to refer to the comparison between spastic CP and mixed CP. The authors also cited table 4 in this and the previous paragraph (BNDF), but it does not show BDNF or TNF data, but CBC data. - Table 3 also shows other differences that were not mentioned in the text, such as the difference in ESR at p1, and differences in ALT, HBG, and WBCs at p0. This table is different from table 1, which presents the differences only between CP and Control, so the differences need to be presented in the text.\n\n- Table 4 was also cited incorrectly when describing the CRP results. - The description of the results in table 4 needs to be more complete and not just for the NLR, as indicated in table 3. - I suggest that the authors separate the description of tables 5 and 6 to make it clear that 5 is about BDNF and 6 about TNF. Also, why did the authors decide to correlate TNF only with CRP and N/L ratio and not make the same comparisons made with BDNF in table 5? Discussion - I suggest that the authors start the discussion by presenting a summary of the results they found. In addition, the authors focused the discussion only on BDNF and ignored all the other results. Thus, a more complete discussion needs to be done.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1347
|
https://f1000research.com/articles/11-1053/v1
|
15 Sep 22
|
{
"type": "Study Protocol",
"title": "Stage 1 Registered Report: Refinement of tickling protocols to improve positive animal welfare in laboratory rats",
"authors": [
"Vincent Bombail",
"Sarah M. Brown",
"Jessica E. Martin",
"Simone L. Meddle",
"Michael Mendl",
"Emma S.J. Robinson",
"Tayla J. Hammond",
"Birte L. Nielsen",
"Megan R. LaFollette",
"Ignacio Vinuela-Fernandez",
"Emma K.L. Tivey",
"Alistair B. Lawrence",
"Sarah M. Brown",
"Jessica E. Martin",
"Simone L. Meddle",
"Michael Mendl",
"Emma S.J. Robinson",
"Tayla J. Hammond",
"Birte L. Nielsen",
"Megan R. LaFollette",
"Ignacio Vinuela-Fernandez",
"Emma K.L. Tivey"
],
"abstract": "Rat tickling is a heterospecific interaction for experimenters to mimic the interactions of rat play, where they produce 50 kHz ultrasonic vocalisations (USV), symptoms of positive affect; tickling can improve laboratory rat welfare. The standard rat tickling protocol involves gently pinning the rat in a supine position. However, individual response to this protocol varies. This suggests there is a risk that some rats may perceive tickling as only a neutral experience, while others as a positive one, depending on how tickling is performed. Based on our research experiences of the standard tickling protocol we have developed a playful handling (PH) protocol, with reduced emphasis on pinning, intended to mimic more closely the dynamic nature of play. We will test whether our PH protocol gives rise to more uniform increases in positive affect across individuals relative to protocols involving pinning. We will compare the response of juvenile male and female Wistar rats as: Control (hand remains still against the side of the test arena), P0 (PH with no pinning), P1 (PH with one pin), P4 (PH with four pins). P1 and P4 consist of a background of PH, with treatments involving administration of an increasing dosage of pinning per PH session. We hypothesise that rats exposed to handling protocols that maximise playful interactions (where pinning number per session decreases) will show an overall increase in total 50 kHz USV as an indicator of positive affect, with less variability. We will explore whether behavioural and physiological changes associated with alterations in PH experience are less variable. We propose that maximising the numbers of rats experiencing tickling as a positive experience will reduce the variation in response variables affected by tickling and increase the repeatability of research where tickling is applied either as a social enrichment or as a treatment.",
"keywords": [
"rat tickling",
"playful handling",
"protocol",
"positive animal welfare",
"affective neuroscience",
"laboratory animal welfare"
],
"content": "Introduction\n\nDuring 2020 in the UK, 201,600 experimental procedures were carried out on rats, the second most investigated laboratory species (UK Home Office, 2021). Worldwide there has recently been an increasing emphasis on positive welfare, and the introduction of positive experiences to improve animals’ quality of life (Lawrence et al., 2019; Makowska & Weary, 2021). The use of manipulations to enhance positive welfare in laboratory animals has been shown not to be a source of variability (Kentner et al., 2021), and a possible contribution towards improved model validity and data reproducibility (Loss et al., 2021; van de Weerd et al., 2004; Würbel & Garner, 2007). It is therefore likely that ‘happy animals make good science’ (Grimm, 2018; Poole, 1997). For instance, positive welfare might reduce stress caused by aversive procedures (Hinchcliffe et al., 2022). For laboratory rats, a positive handling approach referred to as rat tickling is proposed as an effective and practical approach to positively improve their welfare (https://www.nc3rs.org.uk/rat-tickling; https://na3rsc.org/rodent-handling/). Rat tickling with the human hand was developed to study positive emotions and ultrasonic vocalisations (USVs) in rats by mimicking playful interactions between rats (Panksepp, 1998, Figure 1i). The standard tickling protocol involves initial finger contact with the nape of the neck before flipping the rat and gently pinning it in a supine position whilst making rapid finger movements focusing on the ventral surface as used in human tickling (Cloutier et al., 2018; Figure 1ii).\n\nIllustration of the behaviours seen in rats during: i) social play (Pellis & Pellis, 2013); ii) the Panksepp variation of tickling (Cloutier et al., 2018); and iii) playful handling (Bombail et al., 2019, 2021). Letters indicate rat behaviours that share similar or the same physical characteristics: A) pouncing, B) nape contact, C) pinning, D) chasing, E) boxing and F) flipping. During social play (i) or playful handling (iii), behaviours can occur in any order and do not always occur in each play bout. During tickling, the sequence of behaviour is always B), F) and then C). Drawings by Tayla Hammond.\n\nResearch (see Bombail et al., 2021; LaFollette et al., 2017 for reviews) has shown that when rats are tickled by the human hand, they often produce 50 kHz USVs, which are understood to indicate positive affect in rats (e.g., Barker, 2018, Figure 2i). Other evidence suggests that rats find tickling rewarding as in addition to production of USVs, tickled rats show a reduced latency for approaching the human hand and can be trained to perform operant responses for tickling (Burgdorf & Panksepp, 2001; LaFollette et al., 2017).\n\n(i) Illustration of: (1) frequency modulated 50 kHz USVs, (2) flat 50 kHz USV and (3) 22 kHz USV; the spectrograms are taken from our own recordings and these vocalisations are typically expressed in all rats. Vertical axis represents USV frequency (in kHz) and horizontal scale bar represents 50 ms for USV 1 and 2, and 200 ms for USV 3.\n\n(ii) Relationship between 50 kHz USV production and an affective bias test (redrawn with data available online, and reproduced with permission from Hinchcliffe et al., 2020). Each data point represents, for each of the 16 rats, the 50 kHz USV response to tickling and the substrate preference in the Affective Bias Test, indicative of the degree of emotional valence.\n\n(iii) USVs in playfully handled (PH) rats compared to a control group on the 1st and 5th session of treatment (redrawn with data available online and reproduced with permission from Bombail et al., 2019). By the 5th session, all PH rats showed an increase in USV production in contrast to panel (ii), which used the standard protocol where some rats show little or no increase in USVs.\n\nHowever, individual responses to the standard tickling protocol indicate that there is a risk that some rats may not perceive tickling to be a positive experience. We summarise that evidence below (see also Bombail et al., 2021).\n\nIt is well accepted that rats vary in their response to tickling: The NC3Rs web-site on tickling is clear on this point: “But I hate being tickled; shouldn’t rats hate it too? This is a common concern, and it is true that some rats enjoy it more than others” (https://www.nc3rs.org.uk/tickling-rats-improved-welfare). We initially developed doubts over aspects of the standard tickling protocol (Bombail et al., 2019) with its regular use of pinning due to the individual variation in USVs and behaviour we observed in response to this protocol (e.g., Hinchcliffe et al., 2020; see Figure 2ii). Other work has reported significant levels of individual variation in response to tickling (LaFollette et al., 2017).\n\nIndividual responses to tickling have welfare implications: Rat tickling response is associated with responses indicating affective states ranging from neutral to positive (e.g., Hinchcliffe et al., 2020), and hence tickling may not possibly always be welfare enhancing. We have shown that USVs in response to tickling are correlated with an independent test of affective state (an affective bias test) indicating that rats vary significantly in their affective response to tickling (Hinchcliffe et al., 2020). Figure 2ii taken from Hinchcliffe et al. (2020) shows variation in USVs in response to tickling correlated with the % choice bias for a tickling-associated digging substrate as the validated measure of affective state. Other evidence supporting a relationship between this naturally occurring variation in response to tickling measured as USV production and welfare outcomes, such as affective states, can be found in work from Rygula et al. (2012) and Mällo et al. (2007, 2009).\n\nWe therefore propose that individual variation in response to the standard tickling protocol is a significant issue when promoting the widespread use of tickling as an approach to improving rat welfare. Due to our experiences using the standard tickling protocol we have developed a playful handling (PH) protocol intended to better mimic the dynamic nature of play, giving the rat more choice over how it is tickled (Bombail et al., 2019, Figure 1iii). The PH protocol is described by Bombail et al. (2019) as the handler using one hand to touch, tickle, and play with the rat for 20 second periods interspersed with 20 second pauses. During the active periods, the handler mimicked the rough-and-tumble play seen in adolescent rats, with the hand tickling, chasing and pinning the rat, depending on its response. Our data suggest that the PH protocol resulted in a more uniform increase in USVs across individuals relative to the standard protocol. Figure 2iii adapted from Bombail and colleagues (Bombail et al., 2019) shows USVs in playfully handled rats vs. a control group (who did not play in the day of recording) on the 1st and 5th session of treatment. By the 5th session, all playfully handled rats showed an increase in USV production in contrast to Figure 2ii, which used the standard protocol and where some rats show little or no increase in USVs.\n\nWe conclude that this evidence calls for a scientifically based refinement of tickling to ensure that the positive effects of tickling are maximised and that individual differences in response to tickling are minimised with benefits to rat welfare and the reproducibility of research where tickling is applied as a treatment or more generally as an enrichment. In this report, we define tickling as the standard protocol (e.g., Cloutier et al., 2018) and, although it was initially coined as an equivalent term to tickling (Cloutier et al., 2018), PH as the approach outlined in Bombail et al. (2019).\n\nPH consists in mirroring playful behaviour by allowing for more flexibility between the human handler and the rat and consequently we hypothesise PH will induce a more homogeneous positive affective response. We also hypothesise PH will lead to reduced variability of biological outcomes.\n\nHypothesis 1: (a) We hypothesise that rats exposed to handling protocols that maximise playful interactions (i.e., where pinning number per session decreases) will show an overall increase in total 50 kHz USVs as an indicator of positive affect. (b) We also predict that 50kHz USV measures will be less variable in treatments with less pinning.\n\nHypothesis 2: We hypothesise that the behavioural and physiological changes associated with alterations in PH experience will be less variable when rats are exposed to handling protocols that maximise playful interactions (where pinning number per session decreases). There is no previous data on this question, we cannot generate power calculations and pre-register this hypothesis, this is therefore exploratory work.\n\nThe diagram presented in Figure 3 synthesises the timeline for each three-week long cohort studied. The experimental part of this study will be conducted using eight such cohorts, each made up of 16 animals. The timing of these cohorts will be staggered, so experimental cycles overlap, with 16 animals brought into the facility every week, following successful peer review of this Stage 1 Registered Report submission. A step-by-step protocol is available in Box 1. The experimental work for this study should be completed by 21 December 2022, the data analysis should be completed by 1 July 2023.\n\nPrior to the experiment and from day 1 to day 6 of the first cohort, various optimisation and preparation test recordings will be carried out, this will result in a general level of noise as throughout the experiment (when several cohorts are housed and tested simultaneously)\n\nDay 1. Reception of rats and group formation (morning).\n\n- Temporary mark on tail,\n\n- Weigh each rat,\n\n- Form eight cage pairs based on : (1) sex, (2) provenance (always housed with an individual from a different litter), (3) similar cage weight (monitor total treatment group average as the values must balance by the 8th cohort).\n\nDay 1 to day 6. Rats habituate to facility environment.\n\nDay 7. Habituation to PH testing arena.\n\n- Collect faecal pellets for faecal corticosterone metabolite (FCM) analysis. Weigh rats. Habituation 1: in the morning (start of dark phase), for each of the eight cages, transfer pair into the play arena and leave together for five minutes. Remove any faeces from arena if necessary.\n\n- Habituation 2: in the afternoon, for each of the eight cages, transfer pair into the play arena and leave together for five minutes. Remove any faeces from arena if necessary.\n\nDay 8. Habituation to PH testing arena.\n\n- Preparation of the next cohort (Day 1)\n\n- Habituation 3: in the morning, for each of the 16 individuals, place into the play arena and leave for five minutes. Remove any faeces from arena if necessary.\n\n- Habituation 4: in the afternoon, for each of the 16 individuals, place into the play arena and leave for five minutes. Remove any faeces from arena if necessary.\n\n- Cage bedding is changed.\n\nDay 9 to day 11. Experimental treatment.\n\n- The cage will be moved close to the testing arena five minutes prior to the first of the pair of rats being introduced in the test arena. Both rats will be filmed during this anticipatory phase, to investigate their behaviour.\n\n- From each cage, a rat taken individually into the arena (order of passage pseudo-randomised), recorded for a one min anticipation phase and treated according to the schedule (control, P0, P1 or P4) for 30 seconds. Ultrasonic vocalisation (USV) are recorded. Arena wood shavings stirred between each animals (for odour homogenisation).\n\n- Following this treatment, rats will be gently picked up and returned to the home cage. Their cage mate will then be immediately placed in the arena for testing and the same tickling treatment repeated.\n\n- The home cage is covered with a cardboard screen, behind the plastic curtains protecting other cages from emotional contagion via USV.\n\n- Two hours later, each cages are placed back on the housing rack.\n\nDays 12 and 13 are the weekend, animals are undisturbed except for welfare checks.\n\nDay 14 to day 16. Experimental treatment.\n\n- Morning of Day 14 only: Weigh rats\n\n- Day 15 only: preparation of the next cohort (Day 1)\n\n- The cage will be moved close to the testing arena five minutes prior to the first of the pair of rats being introduced in the test arena. Both rats will be filmed during this anticipatory phase, to investigate their behaviour.\n\n- From each cage, a rat taken individually into the arena (order of passage pseudo-randomised), recorded for a one-minute anticipation phase and treated according to the schedule (control, P0, P1 or P4) for 30 seconds. USV are recorded. Arena wood shavings stirred between each animals (for odour homogenisation).\n\n- Following this treatment, rats will be gently picked up and returned to the home cage. Their cage mate will then be immediately placed in the arena for testing and the same tickling treatment repeated.\n\n- The home cage is covered with a cardboard screen, behind the plastic curtains protecting other cages from emotional contagion via USV.\n\n- Two hours later, each cages are placed back on the housing rack.\n\nDay 17. Collect faecal pellets for FCM analysis. Elevated Plus Maze (EPM) testing late morning (middle of dark phase). Standard EPM protocol, EPM will be cleaned between each animal.\n\nDay 18. Open Field (OF) testing.\n\n- Rats are tested in the OF in the morning, Standard OF protocol, OF will be cleaned between each animal.\n\n- Rat are weighed\n\n- Rats are injected with an overdose of pentobarbital and tissues sampled for molecular studies to investigate physiological impact of experimental treatments. Collect faecal pellets for FCM analysis.\n\n(i) Graphical representation of the experimental protocol. Upon reception, each cohort (n=4 cages, with two males per cage and n=4 cages, with two females per cage) is attributed to cage and treatment, then left to acclimatise for a week. Phase 1 consists of exposure to six sessions (30 seconds daily) of either Control, P0, P1 or P4 treatment (varying in the number of pins administered relative to background playful handling; see Objective 1 above). Finally, the rats are behaviourally tested in Phase 2, using Elevated Plus Maze (EPM) then Open Field (OF), and sacrificed for tissue collection. A step-by-step protocol is outlined in box 1.\n\n(ii) Prediction against which our hypothesis will be tested: we predict P0 and P1 treatments will lead to higher and less variable induction of ultrasonic vocalisation (USV) production, compared to P4.\n\n\nMethods\n\nOur experimental design is a pseudorandomised control trial where every week, each of the eight cages of two male or two female rats will be assigned to one of four treatments (control, P0, P1, P4). Treatment allocation is described below. Within a cage, individuals cannot be considered independent, as they might influence each other in response to the treatment through emotional contagion, we will therefore fit the cage as a random effect for all treatments and both sexes.\n\nAll animal work will be carried out at the Roslin Institute, Edinburgh, U.K., in accordance with the U.K. Animals (Scientific Procedures) Act 1986 and reported in compliance with the ARRIVE guidelines (Bombail, 2022). This work does not involve aversive procedures (and is deemed less harmful and distressful than skilled insertion of a hypodermic needle according to good veterinary practice) and therefore not legally required to have UK Home Office approval. As recommended (Olsson et al., 2022), we collectively discussed welfare and ethical considerations with the Named Animal Care Welfare Officers, veterinarians and scientists involved in the study. Following consideration by the University of Edinburgh’s Animal Welfare and Ethical Review Body (reference NC/W001209/1, 26 July 2022, Establishment number X212DDDBD), it was confirmed the work was subthreshold to regulation under the U.K. Animals (Scientific Procedures) Act 1986, and the committee approved it as detailed in this paper. This study was also approved by the Veterinary Ethical Review Committee of the Royal (Dick) School of Veterinary Studies, University of Edinburgh (reference 92.22, 2 September 2022).\n\nPractical and financial constraints require that we limit this study to a single strain. We will use Wistar Han rats purchased from Charles River Laboratories (CRL, Margate, UK). This outbred strain has been shown to be reliably responsive to tickling and PH (Bombail et al., 2019; Hammond et al., 2019) and is one of the commonly used strains for such experiments (23% of rat tickling studies used Wistar, LaFollette et al., 2017). We will purchase the rats from CRL (16 at a time), aged 3-4 weeks and will complete the research prior to their puberty around 7 weeks of age. LaFollette et al. (2017) found that over 60% of papers on tickling used rats within this time window. We have also recently found evidence of sex differences with female rats producing more USVs than males in response to tickling (Tivey, 2022) and each cohort will consist of equal numbers of males and females.\n\nWe aim to carry out the experiment in eight cohorts of n=8 cages (with two rats per cage) and equal numbers of males and females in each cohort. A total of 128 rats (64 males and 64 females) will be used in this study, in accordance with our power analysis detailed below.\n\nTo the greatest extent possible we will aim for a matching number of males and females coming from the same litter. Depending on availability, the number of litters sampled will be two to four per cohort (we are aiming for two litters per cohort, four males and four females from the same litter). Rat treatment allocation will be spread evenly across all litters to prevent bias due to genetic background and early life experience (i.e., each of the four individuals from each sex will be assigned to each of the four treatments). We have arranged for CRL to only provide animals from experienced parents (sire/dam will have been sired/nursed at least one previous litter). This will reduce variability in pup early life environment caused by differences in parental experience.\n\nOn arrival at the Roslin Institute facility, the rats will be housed in a bespoke behaviour research room with an average room temperature of 22°C and relative humidity of 43%. The rats will be on a 12 h:12 h reverse light cycle (lights off at 06:00), to allow testing of the rats during their dark photoperiod when they are most active and to accommodate the preference of albino rats for lower light intensities (see one of our previous reports (Hammond et al., 2019)). The allocation of rats to cages will be carried out in the following order: sex, litter of origin and body weight. Rats will be weighed and allocated to home cage as pairs of the same sex (but never from the same litter). As much as feasibly possible, we will aim to house together rats of similar weight. Pairs will be assigned to a treatment using a random list generator. We aim to homogenise weights between groups. For each sex, rat weight will be averaged for each treatment, and to avoid potential bias caused by uneven distribution of body weight between treatment groups, adjustments in treatment distribution will be made to balance evenly weights across treatments (e.g., we will assign heavier pairs of animals to treatments that previously contained lighter animals). Rats will be left to acclimatise for up to six days prior to handling.\n\nThe home cages are made of clear plastic with a metal mesh open-top lid (l × d × h: 612 mm × 435 mm × 216 mm), filled with 2 cm-deep woodchip bedding, shredded paper, a 20 cm-long red plastic tunnel, a 10 cm wooden chewstick and a 2 cm diameter wooden ball as enrichment (all as per normal practice in our animal facility). This size cage allows animals to rear and stand on their hind limbs. Rats will have ad libitum access to standard rat chow (current supplier: Teklad Global Rodent Maintenance Diet (14% protein); Envigo, UK) and tap water. The cages will be distributed across four tiers of a standard cage rack. Due to the varying lux levels and other potentially confounding variables, position of the home cages in the rack will be randomised across treatments (as in Hammond et al., 2019). The rats will be checked daily, and nitrile gloves worn when handling the animals. To minimise handling stress, rats will be picked up gently by holding them behind their forelegs and then cupping them with both hands. Cage bedding will be changed once, halfway through the experiment (on the afternoon of day 8), according to the routine protocol (a small volume of soiled litter without faeces will be kept in the cage to maintain a familiar olfactory environment). Body weight will be measured routinely across the study (on days 1, 7, 14, 18).\n\nA unique male experimenter will perform all treatments and behavioural tests. All experiments will be performed in the same room as where the animals are housed, as in previous studies (e.g., Hammond et al., 2019). Using curtains and physical distance, we will prevent emotional contagion phenomena involving USV (i.e., we have confirmed USV cannot be detected by other animals, using our recording equipment). Rats are used to a degree of audible activity in the room throughout the experiment. The play arena, placed behind fabric curtains 6 m away from the home cages, will be a Plexiglas square (60 cm) of depth 25 cm, filled with 3 cm-deep woodchip litter in which Wistar rats have played previously (over 200 sessions by 16 males rats took place by the start of the experiment). We keep the same litter for all experiments and remove the rare faeces produced by the animals (in our experience, exclusively produced during the habituation sessions). Litter is regularly stirred between animals. We use this method to guarantee the litter contains odorants from several rats, thereby standardising, diluting and minimising the impact of individual olfactory cues. This can be replicated in other laboratories by using a mixture off soiled litter and clean litter. Following experimental treatment (described below), cages will be left, loosely covered with carboard screens, for 2 h in an area behind plastic curtains (a switched off Lateral Air Flow cabinet), before being returned to their usual home cage rack position. In the absence of this ‘cool down’ period, in our experience a marked rise in USV production over time can be otherwise be measured in control rats (Lam, 2017).\n\nThe rats will be habituated to handling and the experimental recording arena, to lessen any anxiety or fear due to novelty, as negative affective states inhibit play behaviour (reviewed in Ahloy-Dallaire et al., 2018). For habituation to the treatment arena, rats will be moved in their cage to be beside the treatment arena before being lifted gently into the arena, and left there to explore, first as a pair of cage mates (2 × 5 minutes), on the first day, and then alone (2 × 5 minutes) on the second day.\n\nThe aim of PH is to give all rats a similar amount of hand contact (we approximate 70–80% of human-animal interaction time, e.g., about 24 out of 30 seconds), while being responsive to differences between individuals. The similar amount of physical contact for all individuals is important, since activation of the cortical area in response to touch has been shown to influence USV production (Ishiyama & Brecht, 2016). When not touching the rat, the hand can also approach the animal while the hand is in contact with the wood shavings, to provide sensory cues consistent with a play partner approaching (e.g., about 6 out of 30 seconds).\n\nAnother key component of PH is to be responsive to individual differences, which can range from more playful individuals who will quickly move (accelerate or turn) to face the hand, and display playful behaviour (e.g., joy jumps (Reinhold et al., 2019)) to less playful individuals who move less and more slowly and show little or no play behaviour. An example of PH with a responsive individual is available to watch online here. PH starts with presentation of the back of the experimenter’s hand for a brief sniff and exploration by the rat. The experimenter then starts playing with the rat using a rapid tickling finger motion on the sides, back and front of the rat (alternating region). The experimenter should focus on being playful (unexpected moves, fast change of hand movements, change of pace) rather than simply the physical act of tickling (e.g., Figure 1iii).\n\nPinning consists in approaching the rat during PH as described above. Thumb and middle fingers are then placed behind the front legs, and the animal is gently but swiftly moved onto its back, and upon landing, while the rat is pinned down, it is tickled on the front of its thorax and abdomen involving rapid tickling movements of fingers (e.g., see Cloutier et al., 2018).\n\nIn both PH and standard tickling, movements should reflect that rat play is boisterous (Cloutier et al., 2018) with finger pressure being firm and movements fast.\n\nHypothesis 1: (a) We hypothesise that rats exposed to handling protocols that maximise playful interactions (i.e., where pinning number per session decreases) will show an overall increase in total 50 kHz USVs as an indicator of positive affect. (b) We also predict that 50 kHz USV measures will be less variable in treatments with less pinning.\n\nObjective 1 will be addressed in Phase 1 of the experiment (see Figure 3).\n\nExperimental design: The aim of this objective is to refine the standard tickling protocol based on the rats’ affective response to treatments that vary in PH and number of pins. All rats will be exposed to six sessions of experimental human-animal interaction treatment, over eight days, interrupted by a two-day weekend break. We have chosen a standard session length of 30 seconds that reflects our previous work (Hinchcliffe et al., 2020) and also the practical reality that if tickling is to be used widely in practice it needs to be applied in a time efficient manner (LaFollette et al., 2019). The order of testing of cages, and rats within cage will be pseudo-randomised (a sequence for cage and individuals will be generated from a random list generator). The cage will be moved close to the testing arena five minutes prior to the first of the pair of rats being introduced in the test arena. Both rats will be filmed during this anticipatory phase, to investigate their behaviour.\n\nRats will be removed individually from the home cage, placed into the handling arena and, following an additional one-minute recording of anticipatory play behaviour, the experimental treatments applied:\n\nP0: ‘PH’, where zero pins will be applied; the experimenter using one hand will touch, tickle and chase the rat in a manner that mimics rough and tumble play (Bombail et al., 2019; Figure 1iii).\n\nP1: One pin will be applied at approximately 15 seconds from the start of the tickling session. The rat will be held and flipped into a supine position and the experimenter will gently pin the rat in this position whilst moving their fingers quickly and vigorously but gently on the belly, as is commonly used in human tickling. The pin will last for between 2–4 seconds and the rat will be allowed to right itself at the end of pinning (Cloutier et al., 2018; Figure 1ii). On either side of the pin the experimenter will engage in PH as in P0.\n\nP4: Four pins will be applied from five seconds into the tickling session (four pins being the number delivered during a 15 second pinning session in the standard protocol (Cloutier et al., 2018)); pins will be applied as in P1 and the rat will be allowed to right itself after each pin with a short gap before the next pin. On either side of the pinnings the experimenter will engage in PH as in P0.\n\nControl: We will apply the same control treatment as in our previous work (Bombail et al., 2019; Hammond et al., 2019) where experimenter places their hand against the inside of the arena for the entire session.\n\nFollowing this treatment, rats will be gently picked up and returned to the home cage. Their cage mate will then be immediately placed in the arena for testing and the same tickling treatment repeated.\n\nWe will record the behaviour during the tickling session using a digital HD camcorder. We will record USV using a high-quality microphone designed for recording ultrasonic vocalisations produced by bats (Pettersson M500-384 USB Ultrasound microphone) and Audacity recording software. The microphone will be placed over the centre of the arena, pointing downwards at the arena floor. Total USV per unit of time will be quantified by spectrogram analysis.\n\nMeasures: (i) Vocalisations will be recorded during the handling sessions as in our previous work (Bombail et al., 2019; Hammond et al., 2019) and categorised into 50 kHz USVs and 22 kHz USVs; (ii) We will also record other quantitative behavioural responses to tickling as per our previous work (Hammond et al., 2019).\n\nOur primary response variables for hypotheses 1a and 1b will be:\n\n(a) Total 50 kHz USV: We will analyse 50 kHz USV as indicators of positive affective state (e.g., Barker, 2018; Brudzynski, 2013). We define 50 kHz USV as calls with a peak frequency between 30 and 80 kHz and a short duration between 10–400 ms (based on Brudzynski, (2013) and our own empirical observations). We predict 50 kHz will be significantly increased in P0 and P1 treatments, where pinning is minimised, relative to P4, where play is restricted relative to pinning, and the Control treatment, where there is no play.\n\n(b) Variability of 50 kHz USV production: we will compare individual variability across the different treatments. We predict a greater individual variability in positive affective states in treatments that maximise pinning.\n\nOur secondary response variables will be:\n\n(a) Categorisation of 50 kHz calls: we will analyse sub-types of USV following segregation based on their acoustic properties, according to published criteria (Wright et al., 2010).\n\n(b) Anticipatory solitary play behaviours: We will also analyse anticipatory play behaviour, as this has been shown to be an indicator of positive affect. We will use the ethogram in Table 1, based on observations from our earlier work (Bombail et al., 2019; Champeil-Potokar et al., 2021; Hammond et al., 2019).\n\n(c) Behavioural transitions: we will analyse the number of behavioural transitions (including play) that occur prior to treatment, as indicators of reward anticipation (Anderson et al., 2015).\n\n(d) 22 kHz USV: We will also analyse 22 kHz USVs as indicators of negative affective state (Brudzynski, 2013). We define 22 kHz USV as calls with a frequency between 20–30 kHz, and a long duration between 500–3000 ms (Brudzynski, 2013). We predict overall very low number of events, clustered in treatments that maximise pinning.\n\nAnalyses\n\nData will be analysed in R through General Linear Mixed Models using the lme4 package (Bates et al., 2015), to test our hypothesis that indicators of positive affect are increased in treatments P0, P1 where PH is increased and amount of pinning reduced, relative to P4 and Control (i.e., no play) treatments. Our fixed effects are tickling treatment (Control, P0, P1, P4), sex (male, female) and the tickling*Sex interaction. In addition to testing differences in average USV we will also test whether treatments P0, P1 have reduced the variability of response relative to P4 as we anticipate (using the Levene’s test for equality of variance or equivalent). As individuals from a pair cannot be considered independent, as they might influence each other in response to the treatment, we will fit the cage as a random effect for all treatments and both sexes.\n\nHypothesis: We hypothesise that the behavioural and physiological consequences of tickling will be less variable and more repeatable when rats are exposed to handling protocols that maximise playful interactions and where pinning episode number per session decreases. Due to the paucity of data on the impact PH might have on the variables we will measure, we cannot generate power calculations and pre-register this hypothesis, this is therefore exploratory work.\n\nObjective 2 will be addressed in Phase 2 of the experiment (see Figure 3).\n\nExperimental design: In Phase 2, the day after the final playful or control interaction, rats will undergo behaviour testing with Elevated Plus Maze (EPM) and Open Field (OF) in a balanced design. Following these tests, the rats will be humanely killed by anaesthetic overdose and tissues collected for analysis. Post mortem tissue measures will be critical to assess the impact of our treatments on variability and repeatability of commonly used measures of physiological function. Faecal pellets will be collected on days 17 (morning) and 18 (post cull) for non-invasive corticosterone metabolite analysis, in comparison to pellets collected before treatment starts on day seven.\n\nMeasures: (i) Behavioural measures of response to OF and EPM (Ethovision) will be collected to quantify anxiety behaviour prior to culling; (ii) Physiological measures of stress and inflammation: Faecal samples will be collected on day 18, at the end of Phase 2 (and compared to levels at the start and end of Phase 1) and assayed for corticosterone (Lepschy et al., 2007) using a commercially available corticosterone ELISA (Enzo LifeSciences). Point of cull plasma will be assayed for a set of inflammatory markers including the pro-inflammatory cytokines IL1a, IL1b, IL2, IL6, IFNγ and TNFα and the anti-inflammatory cytokines IL4, IL10, IL13, using a magnetic bead based multiplex ELISA (FIRELEX); our selection of inflammatory markers includes cytokines known to be sensitive in humans to negative and positive affect (Anisman & Merali, 2003; Stellar et al., 2015); (iii) Other tissues such as the brain, pituitary gland, heart, liver, spleen and gut will be collected at culling and flash frozen on dry ice and stored at -80oC for future analyses.\n\nOur primary response variables will be:\n\na) EPM: increased markers of open arm exploration (% time and distance exploring the open arm) reflect reduced anxiety, based on rat aversion of open spaces (Kraeuter et al., 2019).\n\nb) OF: decreased markers of thigmotaxis (% time spent and distance covered close to the peripheral walled area) reflect decreased anxiety, based on rat aversion of open spaces. Markers of activity (rearings, total distance covered, bouts of locomotion) will also be recorded since, although interpretation can be challenging (Denenberg, 1969), they do reflect arousal upon OF arena exploration.\n\nOur secondary response variables will be:\n\na) Physiological and inflammation related variables: we will analyse markers regulated in affective states, and their variability around the treatment mean/median. We expect P0 and P1 to be more effective at inducing anti-inflammatory cytokines and reducing pro-inflammatory cytokines, and faecal corticosterone (Anisman & Merali, 2003; Lepschy et al., 2007; Stellar et al., 2015), in comparison to P4 and control treatments.\n\nb) Body weight: we will keep a record of weight as an indicator of general body condition, we do not expect any treatment-related changes, as per our previous studies (Bombail et al., 2019; Hammond et al., 2019).\n\nAnalyses\n\nUsing the same approach as described for Objective 1, data will be analysed in R using Generalised Linear Mixed Models to ascertain the effects of tickling treatments and sex on behavioural and physiological measures. To test our hypothesis that the biological consequences of tickling will be less variable among rats and more repeatable within rats when rats are tickled using more playful protocols (P1, P0), we will analyse the residual variance from the undertaken models and explore intraclass correlation coefficients of combined random and fixed effects.\n\nA diagram of the experimental procedure is presented in Figure 3i. We also present a graphical representation of our predicted results, which will be tested in our experiments (Figure 3ii).\n\nBrain tissue will be collected for future analysis of neurobiological consequences of the handling treatments. When funding and collaborations can be raised, it is our intention to further explore the biology of positive affective states through analysis of physiological functions that are associated with emotional experiences (e.g., immunology or metabolism). We will also analyse USV production in relation to specific USV types (Wright et al., 2010) using spectrograms from our recordings, with a view to correlating specific USV types to treatments and behaviours.\n\nSpecific aspects of data analysis are described in the descriptions of objectives 1 and 2 above. Prior to analysis, we will visualise and test the data for the assumptions of the cognate statistical approaches (data distribution normality or heteroskedasticity), and when necessary, we will use non-parametric alternatives or data transformation.\n\nPower analysis: Based on our previous data, the most variable response measure is total 50 kHz USVs with data taken from our own and other work (LaFollette et al., 2018; Tivey, 2022) where treatments come closest to matching our proposed treatments. We have used these data to provide us with means per primary fixed effect combinations (i.e., treatment x sex) and pooled standard deviations, with resulting simulations based on the smallest effect size (0.09). Power analysis and sample size estimations were conducted using GLIMMPSE software. The desired power was set at 0.8, the type I error rate at 0.05, the means scale factor was set at 1.0 and the variability scale factor at 1.3 using the Hotelling Lawley Trace test (Hotelling, 1931). Simulations incorporated the non-independence of rats within a cage (cage fitted as a random effect), via a calculated intraclass correlation of 0.17 based on previous data (LaFollette et al., 2018; Tivey, 2022). Additionally, repeated measures over six tickling treatment events/exposures were included in the power analysis. Our fixed effects are treatment (Control, P0, P1, P4), sex (male, female) and the tickling*Sex interaction. Based on simulations detailed above, a sample size of n=16 rats (i.e., n=8 cages) per treatment and sex combinations, or n=64 total experimental units (128 total animals), provides a power of 0.829.\n\nBlinding: We will not be able to blind handlers during the preparatory and experimental phases, as the handlers need to know which handling method they will be using with each rat. We will also not be able to blind collection of quantitative behaviour during tickling sessions, as it will be obvious which handling method is being used in each session. We will blind all other aspects including collection of USVs, analysis of physiological samples, and collation and analysis of behavioural data.\n\nOutlier extraction: We are aware of the high variability in USV response among rats, and are experienced in recording it, and therefore will not exclude rats based on their USV production. For physiological markers we will use data points within the dynamic range of the assay and will be checking replicate quality. In the unlikely event of outlier removal (based on the Grubb’s test (Grubbs, 1969)), this will be explicitly described in the result section.\n\n\nStudy status\n\nWe are currently awaiting publication of this peer-reviewed protocol to start experimental data collection.\n\n\nStudy limitations\n\nWe will assign animals to treatments according to preset criteria to homogenise factors we assume might affect treatment response (sex, litter of origin and social cage environment, body weight). Our pseudo-randomisation procedure will therefore be more deterministic than the computer-run randomisation algorithm; cryptic biases might emerge upon data interpretation. Additionally, the experimenter will be aware of the treatments administered as the rats are handled. He will therefore not be blinded to the treatments. This is limited by the lack of discernible patterns (order of passage pseudo-randomisation).\n\n\nData availability\n\nNo data are associated with this article.\n\nFigshare: ARRIVE guidelines for ‘Stage 1 Registered Report: Refinement of tickling protocols to improve positive animal welfare in laboratory rats’. https://doi.org/10.6084/m9.figshare.20914993 (Bombail, 2022).\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 extremely grateful for conversations with colleagues at the National Centre for Replacement, Refinement and Reduction of Animals in Research, which brought us substantive and substantial enlightenment.\n\n\nReferences\n\nAhloy-Dallaire J, Espinosa J, Mason G: Play and optimal welfare: Does play indicate the presence of positive affective states? Behav. Process. 2018; 156: 3–15. PubMed Abstract | Publisher Full Text\n\nAnderson C, Yngvesson J, Boissy A, et al.: Behavioural expression of positive anticipation for food or opportunity to play in lambs. Behav. Process. 2015; 113: 152–158. Publisher Full Text\n\nAnisman H, Merali Z: Cytokines, stress and depressive illness: Brain-immune interactions. Ann. Med. 2003; 35(1): 2–11. PubMed Abstract | Publisher Full Text\n\nBarker DJ: Ultrasonic Vocalizations as an Index of Positive Emotional State. Handbook of Behavioral Neuroscience. 2018; 25: 253–260. Publisher Full Text\n\nBates D, Mächler M, Bolker BM, et al.: Fitting Linear Mixed-Effects Models Using lme4. J. Stat. Softw. 2015; 67(1): 1–48. Publisher Full Text\n\nBombail V: ARRIVE guidelines for Stage 1 Registered Report_Refinement of tickling protocols to improve positive animal welfare in laboratory rats.pdf. figshare. [Dataset].2022. Publisher Full Text\n\nBombail V, Brown SM, Hammond TJ, et al.: Crying With Laughter: Adapting the Tickling Protocol to Address Individual Differences Among Rats in Their Response to Playful Handling. Front. Vet. Sci. 2021; 8: 623. Publisher Full Text\n\nBombail V, Jerôme N, Lam H, et al.: Odour conditioning of positive affective states: Rats can learn to associate an odour with being tickled. PLoS One. 2019; 14(6): e0212829. PubMed Abstract | Publisher Full Text\n\nBrudzynski SM: Ethotransmission: communication of emotional states through ultrasonic vocalization in rats. Curr. Opin. Neurobiol. 2013; 23(3): 310–317. PubMed Abstract | Publisher Full Text\n\nBurgdorf J, Panksepp J: Tickling induces reward in adolescent rats. Physiol. Behav. 2001; 72(1–2): 167–173. PubMed Abstract | Publisher Full Text\n\nChampeil-Potokar G, Crossouard L, Jérôme N, et al.: Diet Protein Content and Individual Phenotype Affect Food Intake and Protein Appetence in Rats. J. Nutr. 2021; 151(5): 1311–1319. PubMed Abstract | Publisher Full Text\n\nCloutier S, LaFollette MR, Gaskill BN, et al.: Tickling, a Technique for Inducing Positive Affect When Handling Rats. J. Vis. Exp. 2018; 2018(135): 57190. PubMed Abstract | Publisher Full Text\n\nDenenberg VH: Open-field behavior in the rat: what does it mean? Ann. N. Y. Acad. Sci. 1969; 159(3): 852–859. Publisher Full Text\n\nGrimm D: Are happy lab animals better for science? Science. 2018. Publisher Full Text\n\nGrubbs FE: Procedures for Detecting Outlying Observations in Samples. Technometrics. 1969; 11(1): 1–21. Publisher Full Text\n\nHammond T, Bombail V, Nielsen BL, et al.: Relationships between play and responses to tickling in male juvenile rats. Appl. Anim. Behav. Sci. 2019; 221: 104879. Publisher Full Text\n\nHinchcliffe JK, Jackson MG, Robinson ES: The use of ball pits and playpens in laboratory Lister Hooded male rats induces ultrasonic vocalisations indicating a more positive affective state and can reduce the welfare impacts of aversive procedures. Lab. Anim. 2022; 236772211065920. Publisher Full Text\n\nHinchcliffe JK, Mendl M, Robinson ESJ: Rat 50 kHz calls reflect graded tickling-induced positive emotion. Curr. Biol. 2020; 30(18): R1034–R1035. PubMed Abstract | Publisher Full Text\n\nHotelling H: The Generalization of Student’s Ratio.1931; 2(3): 360–378. Publisher Full Text\n\nIshiyama S, Brecht M: Neural correlates of ticklishness in the rat somatosensory cortex. Science (New York, N.Y.). 2016; 354(6313): 757–760. PubMed Abstract | Publisher Full Text\n\nKentner AC, Speno A, Doucette J, et al.: The Contribution of Environmental Enrichment to Phenotypic Variation in Mice and Rats. ENeuro. 2021; 8(2): ENEURO.0539–ENEU20.2021. PubMed Abstract | Publisher Full Text\n\nKraeuter AK, Guest PC, Sarnyai Z: The Elevated Plus Maze Test for Measuring Anxiety-Like Behavior in Rodents. Methods Mol. Biol. 1916. 2019; 69–74. PubMed Abstract | Publisher Full Text\n\nLaFollette MR, Cloutier S, Brady C, et al.: Laboratory animal welfare and human attitudes: A cross-sectional survey on heterospecific play or “rat tickling”. PLoS One. 2019; 14(8): e0220580. PubMed Abstract | Publisher Full Text\n\nLaFollette MR, O’Haire ME, Cloutier S, et al.: Rat tickling: A systematic review of applications, outcomes, and moderators. PLoS One. 2017; 12(4): e0175320. PubMed Abstract | Publisher Full Text\n\nLaFollette MR, O’Haire ME, Cloutier S, et al.: Practical rat tickling: Determining an efficient and effective dosage of heterospecific play. Appl. Anim. Behav. Sci. 2018; 208: 82–91. Publisher Full Text\n\nLam H: Can odour be associated with positive affective states in rats (Rattus norvegicus)? [MSc thesis]. University of Edinburgh.2017.\n\nLawrence AB, Vigors B, Sandøe P: What Is so Positive about Positive Animal Welfare?—A Critical Review of the Literature. Animals: An Open Access Journal from MDPI. 2019; 9(10). PubMed Abstract | Publisher Full Text\n\nLepschy M, Touma C, Hruby R, et al.: Non-invasive measurement of adrenocortical activity in male and female rats. Lab. Anim. 2007; 41(3): 372–387. PubMed Abstract | Publisher Full Text\n\nLoss CM, Melleu FF, Domingues K, et al.: Combining Animal Welfare With Experimental Rigor to Improve Reproducibility in Behavioral Neuroscience. Front. Behav. Neurosci. 2021; 15. PubMed Abstract | Publisher Full Text\n\nMakowska IJ, Weary DM: A Good Life for Laboratory Rodents? ILAR J. 2021; 60(3): 373–388. Publisher Full Text\n\nMällo T, Matrov D, Herm L, et al.: Tickling-induced 50-kHz ultrasonic vocalization is individually stable and predicts behaviour in tests of anxiety and depression in rats. Behav. Brain Res. 2007; 184(1): 57–71. PubMed Abstract | Publisher Full Text\n\nMällo T, Matrov D, Kõiv K, et al.: Effect of chronic stress on behavior and cerebral oxidative metabolism in rats with high or low positive affect. Neuroscience. 2009; 164(3): 963–974. Publisher Full Text\n\nOlsson IAS, Nielsen BL, Camerlink I, et al.: An international perspective on ethics approval in animal behaviour and welfare research. Appl. Anim. Behav. Sci. 2022; 253: 105658. Publisher Full Text\n\nPanksepp J:Affective neuroscience: The foundations of human and animal emotions. Affective neuroscience: The foundations of human and animal emotions. Oxford University Press;1998.\n\nPellis S, Pellis V: The playful brain: venturing to the limits of neuroscience.2013; 257.Reference Source\n\nPoole T: Happy animals make good science. Lab. Anim. 1997; 31(2): 116–124. PubMed Abstract | Publisher Full Text\n\nReinhold AS, Sanguinetti-Scheck JI, Hartmann K, et al.: Behavioral and neural correlates of hide-and-seek in rats. Science (New York, N.Y.). 2019; 365(6458): 1180–1183. PubMed Abstract | Publisher Full Text\n\nRygula R, Pluta H, Popik P: Laughing rats are optimistic. PLoS One. 2012; 7(12): e51959. PubMed Abstract | Publisher Full Text\n\nStellar JE, John-Henderson N, Anderson CL, et al.: Positive affect and markers of inflammation: discrete positive emotions predict lower levels of inflammatory cytokines. Emotion (Washington, D.C.). 2015; 15(2): 129–133. PubMed Abstract | Publisher Full Text\n\nTivey E: Exploring sex differences in the response to tickling in juvenile Wistar rats.2022.Reference Source\n\nUK Home Office: Annual Statistics of Scientific Procedures on Living Animals, Great Britain, 2020 - GOV.UK.2021.Reference Source\n\nvan de Weerd HA , van Loo PLP , Baumans V: Environmental enrichment: Room for reduction? Altern. Lab. Anim. 2004; 32(SUPPL. 2): 69–71. PubMed Abstract | Publisher Full Text\n\nWright JM, Gourdon JC, Clarke PBS: Identification of multiple call categories within the rich repertoire of adult rat 50-kHz ultrasonic vocalizations: Effects of amphetamine and social context. Psychopharmacology. 2010; 211(1): 1–13. PubMed Abstract | Publisher Full Text\n\nWürbel H, Garner JP: NC3Rs #9 Environmental enrichment and systematic randomization Refinement of rodent research through environmental enrichment and systematic randomization Available at. 2007. Authors.Reference Source"
}
|
[
{
"id": "150622",
"date": "12 Oct 2022",
"name": "Timothy M. Errington",
"expertise": [
"Reviewer Expertise I have expertise in replicability",
"reproducibility",
"metascience",
"cellular and biochemical assays (e.g.",
"PCR",
"imaging)",
"and some animal protocols (e.g.",
"tail-vein injections",
"xerograph models). I do not have expertise in rat tickling (or rat handling specifically) nor expertise in behavioural test",
"such as EPM and OF described in this Stage 1 Registered Report."
],
"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 Stage 1 Registered Report outlines the rationale, study design, hypotheses, and analysis strategy for testing whether updated rat tickling protocol (playful handling: PH) leads to a higher and less variable induction of ultrasonic vocalisation (USV) compared to the standard tickling protocol, indictive of an increased positive playful interaction. The authors also describe exploratory experimentation to examine whether the difference in tickling protocols leads to less variation in behavioural and physiological tests\nOverall, this is a well thought out and described protocol. Suggestions below are considerations for the authors to increase transparency of the Stage 1 Registered Report and experimental factors to consider in their design or to include as limitations, or discussion.\nIn Hypotheses section, suggest listing Hypothesis 1 as Confirmatory Hypothesis 1a and Confirmatory Hypothesis 1b (or just making them 1 and 2?). And Hypothesis 2 as Exploratory Hypothesis 1. That way it is even clearer to readers what is confirmatory vs exploratory.\n\nThe authors should include a brief statement of why EMP and OF are the tests they are using.\n\nHow many pins are normally done in the standard tickling procedure? Is P4 equivalent to it? It sounds like there is quite a bit of variation in how the standard tickling procedure is done including number per treatment and number of treatments. On number of treatments, the authors will record and analysis after just 1 treatment (Phase 1) and not also at Phase 2. Since the data are recorded it seems useful to analysis at both points (possibly even incorporating it in the statistical design?)\n\nRelated to point 3, what is the need for a gap between Phase 1 and Phase 2? That is, why not just move from the treatment on days 9-11 into the EPM and OF testing? Is it because the rats should have two treatment sessions spaced apart by 5 days before the behavioural and physiological tests? Either way can the authors elaborate this design decision.\n\nMaybe I missed it, but will the cages assigned to one treatment (e.g., H0) in Phase 1 also be in the same treatment in Phase 2 or will they be randomized?\n\nIt is nice to see the pseudo-randomization. I was going to recommend also introducing the randomization for the order of cages treated (in addition to the order of rats tested in each cage), but it looks like this is part of the design. However, it is only stated once in Objective 1 experimental design. I suggest moving this up earlier in the protocol and possibly repeating it where appropriate, such as when discussing the pseudo-randomization design and rat ordering as it was unclear until this single sentence.\n\nRelated to the need to randomize where possible, especially since the rat handler will not be blind to treatments, I think an unfortunate weakness of this protocol, although I understand why from a practical sense, is the lack of variability of researcher. That is, a single researcher at a single institution with a single rat strain is being used. Three related thoughts on this:\na) The authors might consider discussing the impact of features that are not being accounted for that might impact the outcome (e.g., experience of the handler performing the standard tickling protocol, experience of the handler performing the PH protocol, sex of the researcher (e.g., Sorge et al., 20141).\nb) I am not an expert in this technique, but having a strong proponent of the standard rat tickling protocol could likely provide some quite useful critique – essentially an adversarial collaboration that help with pre-commitment (Brian Nosek and I wrote a piece about it here: https://www.nature.com/articles/d41586-020-02142-6 - and note, I’m not suggesting you cite this, only providing for background with the concept if helpful).\nc) A consideration to keep in mind for the discussion of the outcomes of this (yes, getting ahead for a moment), is one way to address this would be through a ‘many-labs’ style replication of these findings, essentially introducing the variation of researcher, strain, laboratory, etc. Again, this study would need to be completed with results to warrant a ‘many-labs’ approach, but sharing now for future consideration.\n\nAnother potential factor to consider is time of day of the treatment. It is unclear if that is held constant. That is, will the treatment always occur at the same time of day relative to the 12h:12h light cycle of the rats or if it will also be variable across cohorts? I am unsure if this could have an impact on behaviour, but raising as something potentially to track and share at the completion of the study.\n\nFor forming cage pairs for each cohort, while you will always achieve 4 cages of female and 4 cages of male (by design), it seems it might not always be possible to form pairs based on provenance since that will depend on litter size. It is less of a concern if there are rats from many litters, but is there a chance of receiving more than 4 rats of one sex from the same litter during any of the cohorts? It sounds like the authors have already discussed this with the supplier of the rats, but it’s unclear how this is taken into account in the randomization strategy if this issue arises.\n\nIs there any consideration of whether a rat is unable to continue? For example, if a rat forms an infection during the habitation caused by something else, will the authors exclude the rat from the experiment? If any of this is known a priori it would be good to mention, if not, then transparency during report will be sufficient.\n\nI’d recommend adding RRIDs where appropriate (e.g., rat strain).\n\nIt sounds like for the secondary variables of interest (e.g., when coding the anticipatory play behaviour), these will be coded by a researcher from the video recordings and that the researchers will be blinded to the behavioural and physiological tests. This is again great to see, however if the authors could share a little more detail of how they will do this, that would be helpful for transparency.\n\nFor analyses, the authors should include more transparency and more explicitness for confirmatory tests. For example:\na) The p-value threshold (assuming 0.05 based on power analysis) they will consider as significant.\nb)The comparisons they will perform, which is especially important for the primary response variables. So for example, is the test for total 50 kHz USV a contrast of P0 and P1 compared to P4 and Control? Or are the authors suggesting multiple contrasts (e.g., P0 vs P4, P1 vs P4, etc). For example, the legend for Figure 3ii suggests it would be P0 and P1 vs P4 (excluding control).\nc) If relevant, how are multiple tests being corrected for?\nd) What approaches will be used to test data fit the assumptions of the tests (e.g., what specific tests for normality), and same with data transformations (e.g., what are viable options to consider and what is the workflow to consider it sufficient) – this can help make the decision tree the authors will use on whether to use one test vs an alternative more transparent a priori.\ne) And while not necessarily needed now, it would be beneficial to know the authors plan to report effect sizes and uncertainty in their analyses.\n\nHave the authors pre-specified sufficient outcome-neutral tests for ensuring that the results obtained can test the stated hypotheses, including positive controls and quality checks? Yes\n\nAre the 3Rs implications of the work described accurately? Yes\n\nAre a suitable application and appropriate end-users identified? Yes\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": "9022",
"date": "18 Nov 2022",
"name": "Vincent Bombail",
"role": "Author Response",
"response": "We wish to thank this reviewer for their thorough and constructive criticism, and we hope our attempt at addressing their questions has brought more clarity to our manuscript. The Stage 1 Registered Report outlines the rationale, study design, hypotheses, and analysis strategy for testing whether updated rat tickling protocol (playful handling: PH) leads to a higher and less variable induction of ultrasonic vocalisation (USV) compared to the standard tickling protocol, indictive of an increased positive playful interaction. The authors also describe exploratory experimentation to examine whether the difference in tickling protocols leads to less variation in behavioural and physiological tests Overall, this is a well thought out and described protocol. Suggestions below are considerations for the authors to increase transparency of the Stage 1 Registered Report and experimental factors to consider in their design or to include as limitations, or discussion. In Hypotheses section, suggest listing Hypothesis 1 as Confirmatory Hypothesis 1a and Confirmatory Hypothesis 1b (or just making them 1 and 2?). And Hypothesis 2 as Exploratory Hypothesis 1. That way it is even clearer to readers what is confirmatory vs exploratory. This is a good idea and we have updated the text to follow this advice. The authors should include a brief statement of why EMP and OF are the tests they are using. We have added explanatory sentences in the methods section: ‘The EPM and OF tests consist in quantifying exploration behaviour in 2 different structures, that both consist in an area with open spaces (the centre of the OF and the open arms of the EPM) and an area with relatively more enclosed spaces (the periphery of the OF and the closed arms of the EPM). For rats, this ambiguity creates a conflict between the thigmotaxis (preference for proximity to walls) and the motivation to explore open spaces, which is used to assess the emotional response to those novel experiences, and to test for anxiety levels.’ How many pins are normally done in the standard tickling procedure? Is P4 equivalent to it? It sounds like there is quite a bit of variation in how the standard tickling procedure is done including number per treatment and number of treatments. On number of treatments, the authors will record and analysis after just 1 treatment (Phase 1) and not also at Phase 2. Since the data are recorded it seems useful to analysis at both points (possibly even incorporating it in the statistical design?) The protocol from Cloutier et al. (2018) describes there should be 4 to 5 pins per 15 s (2-4s per pin). We also postulated a 30 s treatment would be a practical and effective duration to achieve induction of most individual rat positive affect (based on LaFollette et al., 2018, and our own findings). Our protocol and treatment design synthesise these requirements. Related to point 3, what is the need for a gap between Phase 1 and Phase 2? That is, why not just move from the treatment on days 9-11 into the EPM and OF testing? Is it because the rats should have two treatment sessions spaced apart by 5 days before the behavioural and physiological tests? Either way can the authors elaborate this design decision. There is no gap between Phases 1 and 2, phase 2 starts the next day. To clarify we have added the word ‘next’, in experimental design for objective 2. Maybe I missed it, but will the cages assigned to one treatment (e.g., H0) in Phase 1 also be in the same treatment in Phase 2 or will they be randomized? For phase 2, to investigate the behavioural and physiological correlates of positive experiences, the animals and their treatments will be the same as in phase 1. It is nice to see the pseudo-randomization. I was going to recommend also introducing the randomization for the order of cages treated (in addition to the order of rats tested in each cage), but it looks like this is part of the design. However, it is only stated once in Objective 1 experimental design. I suggest moving this up earlier in the protocol and possibly repeating it where appropriate, such as when discussing the pseudo-randomization design and rat ordering as it was unclear until this single sentence. We have added this to the testing in objective 2: ‘their order of passage will be pseudo-randomised’. Related to the need to randomize where possible, especially since the rat handler will not be blind to treatments, I think an unfortunate weakness of this protocol, although I understand why from a practical sense, is the lack of variability of researcher. That is, a single researcher at a single institution with a single rat strain is being used. Three related thoughts on this: a) The authors might consider discussing the impact of features that are not being accounted for that might impact the outcome (e.g., experience of the handler performing the standard tickling protocol, experience of the handler performing the PH protocol, sex of the researcher (e.g., Sorge et al., 20141). The inclusion of further experimenters in the design could constitute another source of variation, but we agree the involvement of a single experienced male experimenter might constitute a limitation. Over time there will be other sources of variation (e.g. dietary molecules excreted through sweat, fluctuation in mood and playfulness), but the study of human-animal interactions requires such human intervention. We have to start somewhere, and although this will not the ultimate testing of the hypothesis, this will be a first attempt that might next be transposed to other laboratories and rat strains. We have added these points in the study limitations section. b) I am not an expert in this technique, but having a strong proponent of the standard rat tickling protocol could likely provide some quite useful critique – essentially an adversarial collaboration that help with pre-commitment (Brian Nosek and I wrote a piece about it here: https://www.nature.com/articles/d41586-020-02142-6 - and note, I’m not suggesting you cite this, only providing for background with the concept if helpful). Thank you for this interesting read. This protocol, and the study in general, were designed inclusive of different perspectives on tickling, and in collaboration with our co-author Megan LaFollette, who is a proponent of the standard protocol (i.e. the Panksepp protocol with pinning described in Cloutier et al., 2018). c) A consideration to keep in mind for the discussion of the outcomes of this (yes, getting ahead for a moment), is one way to address this would be through a ‘many-labs’ style replication of these findings, essentially introducing the variation of researcher, strain, laboratory, etc. Again, this study would need to be completed with results to warrant a ‘many-labs’ approach, but sharing now for future consideration. This is very interesting. This has been incorporated in the response to point a) above, in the study limitations sections Another potential factor to consider is time of day of the treatment. It is unclear if that is held constant. That is, will the treatment always occur at the same time of day relative to the 12h:12h light cycle of the rats or if it will also be variable across cohorts? I am unsure if this could have an impact on behaviour, but raising as something potentially to track and share at the completion of the study. We have specified time of treatments in the ‘Acclimation, treatment allocation, housing and husbandry section’. For forming cage pairs for each cohort, while you will always achieve 4 cages of female and 4 cages of male (by design), it seems it might not always be possible to form pairs based on provenance since that will depend on litter size. It is less of a concern if there are rats from many litters, but is there a chance of receiving more than 4 rats of one sex from the same litter during any of the cohorts? It sounds like the authors have already discussed this with the supplier of the rats, but it’s unclear how this is taken into account in the randomization strategy if this issue arises. We have discussed this with the supplier (CRL) and we will not receive more than 4 rats of one sex from the same litter. Is there any consideration of whether a rat is unable to continue? For example, if a rat forms an infection during the habitation caused by something else, will the authors exclude the rat from the experiment? If any of this is known a priori it would be good to mention, if not, then transparency during report will be sufficient. We have updated the text to include this information. We will follow local guidelines should rat injury occur. If this were to happen, this information would be described in the methods section, for full transparency about the fate of our experimental rats. I’d recommend adding RRIDs where appropriate (e.g., rat strain). We have added the following information to the materials section: Research Resource Identification, RRID:RGD_2308816 It sounds like for the secondary variables of interest (e.g., when coding the anticipatory play behaviour), these will be coded by a researcher from the video recordings and that the researchers will be blinded to the behavioural and physiological tests. This is again great to see, however if the authors could share a little more detail of how they will do this, that would be helpful for transparency. It will be impossible to deduce the nature of the treatment, since all treatment orders will have been pseudo randomised, and none of the experimenters involved has a good enough memory to remember the treatment group of 64 different cages. For analyses, the authors should include more transparency and more explicitness for confirmatory tests. For example: a) The p-value threshold (assuming 0.05 based on power analysis) they will consider as significant. This has now been specified in the manuscript. b)The comparisons they will perform, which is especially important for the primary response variables. So for example, is the test for total 50 kHz USV a contrast of P0 and P1 compared to P4 and Control? Or are the authors suggesting multiple contrasts (e.g., P0 vs P4, P1 vs P4, etc). For example, the legend for Figure 3ii suggests it would be P0 and P1 vs P4 (excluding control). All treatments will be compared c) If relevant, how are multiple tests being corrected for? We have amended the text accordingly: ‘To account for potential type I errors that may arise from multiple comparisons, we will use Bonferroni correction or equivalent (depending on data distribution)’. d) What approaches will be used to test data fit the assumptions of the tests (e.g., what specific tests for normality), and same with data transformations (e.g., what are viable options to consider and what is the workflow to consider it sufficient) – this can help make the decision tree the authors will use on whether to use one test vs an alternative more transparent a priori. We will use classical tests such as the Bartlett's test for homogeneity of variances and Anderson-Darling test for normality. If necessary, data might be transformed (e.g. square root transformation) e) And while not necessarily needed now, it would be beneficial to know the authors plan to report effect sizes and uncertainty in their analyses. We have added : ‘In the spirit of transparency, we will report effect sizes and uncertainty in our analyses.’"
}
]
},
{
"id": "153996",
"date": "24 Oct 2022",
"name": "Theresa M. Kisko",
"expertise": [
"Reviewer Expertise Social play behaviour in rats",
"Ultrasonic vocalizations",
"Social and affective behaviours and communication."
],
"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: The goal of this protocol is to evaluate the standard “Panksepp” tickling protocol against the authors' own playful handling (PH) protocol and assess which is a more ideal way to ensure the maximum positive experiences for the animals. This is done by varying the amount of pinning and providing a more interactive/reciprocal type of heterospecific play. The authors hypothesise that less pinning and more “playful interactions” will create an overall more positive experience – assessed through primary response variables Total 50-kHz USV and variability of 50-kHz USV across treatments. The second objective is to assess the physiological and behavioural effects of the various pinning and playful handling protocols. The hypothesis is that less pinning and more PH will create less variable behavioural and physiological responses. The authors will assess this through an open field, elevated plus maze and post-mortem tissue measures (pro-inflammatory cytokines) and faecal corticosterone.\nEvaluation: The rationale for refining the tickling protocol is justly described and the authors provide compelling evidence from their previous studies, with descriptions and example figures and graphs, that their playful handling protocol is efficient and that it reduces the variability across individuals. Their methods suggest that more rats are finding the playful handling experience and interaction positive.\nI quite like how the authors have considered the reciprocal nature of playful interactions and incorporated this into their playful handling protocol as the standard tickling does not take this into account enough. For play interactions to remain playful, there needs to be a certain amount of reciprocity and I think the way that the authors can assess the individual rats’ responses to the experimenter hand and interact with the rat in a more dynamic way is an excellent way to ensure that the result is a positive interaction rather than a forced USV release that may not actually be enjoyable. Naturally creating a more fluid emission of 50-kHz USV in contrast to high rates of pinning and a more “coerced” 50-kHz USV emission can provide less confounds in experimental testing and ensure a more positive welfare condition. When Panksepp created and published the standard tickling protocol the field of affective USV research I would argue was still in its infancy. However, over the last two decades, we have learned much more and, therefore, I quite agree that the “older” standardized protocols should be re-evaluated and updated to reflect the knowledge we now know, especially for the benefit of the animals in our care.\nThe experimental methods outlined for objectives 1 and 2 are straightforward and well thought out. I have only a couple of minor queries for them:\nI would question the use of Audacity software in USV analysis though, as in my experience with the USV analysis it is not a common software for assessment. I have never heard of this software being used for USVs. There are some that are more specifically targeted for ultrasonic vocalizations and might possibly provide a more accurate assessment, especially when it comes to the categorization of 50-kHz USV subtypes. There are even several freeware versions that can be used that are user-friendly and intuitive (i.e. Deepsqueek). Have the authors considered comparing one or two files assessed with Audacity to one or two assessed with a specific vocalization software typically used in USV research, i.e. Avisoft or Deepsqueek?\n\nIn terms of the secondary response variable (a) in objective 1, what is the question you are exploring with subtypes? Essentially, I would ask why are you wanting to look at subtypes? Are you looking to see if certain subtypes reflect a more positive interaction? For example, would one expect that with less pinning the rats emit less trills or frequency-modulated subtypes, or just the variability of subtypes emitted during tickling? Are you planning to coordinate the subtype emissions with the behaviour occurring, i.e. while chasing the experimenter's hand, what calls do they primarily emit? This can be quite a complicated assessment and requires accurate synchronization of behaviour and USV times.\n\nHow do you plan to do the categorization? By an independent observer manually categorizing or do you plan to use software that is trained for automated categorizations? There are obviously pros and cons to both, but I think this is an important point to consider when planning categorical USV analysis.\nIn terms of general experimental overview, controls are provided for each instance and the experimental treatments are balanced and pseudorandomized between groups of animals. The collection of tissue and faecal samples to assess physiological responses as well as using standard behavioural assays to further evaluate the effects or consequences of the playful handling protocols provides a nice balance to purely behavioural and vocalization data. This assessment could strengthen results and provide compelling evidence for an effective protocol.\nDiagrams and figures in the protocol are well described and include ample details to allow for sufficient replication studies. All the statistical analyses are well outlined and have been justly described based on the variables and research questions.\nStudy limitations are outlined and clearly have been thought out.\nIn general, I quite like the protocol refinement and I agree that it is justified, and the authors provide compelling reasons and evidence to support their hypothesis. I look forward to the outcome of the experiments.\n\nHave the authors pre-specified sufficient outcome-neutral tests for ensuring that the results obtained can test the stated hypotheses, including positive controls and quality checks? Yes\n\nAre the 3Rs implications of the work described accurately? Yes\n\nAre a suitable application and appropriate end-users identified? Yes\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": "9023",
"date": "18 Nov 2022",
"name": "Vincent Bombail",
"role": "Author Response",
"response": "We wish to thank this reviewer for their encouragements and positive feedback. Some good points are raised, we have addressed the questions below. I would question the use of Audacity software in USV analysis though, as in my experience with the USV analysis it is not a common software for assessment. I have never heard of this software being used for USVs. There are some that are more specifically targeted for ultrasonic vocalizations and might possibly provide a more accurate assessment, especially when it comes to the categorization of 50-kHz USV subtypes. There are even several freeware versions that can be used that are user-friendly and intuitive (i.e. Deepsqueek). Have the authors considered comparing one or two files assessed with Audacity to one or two assessed with a specific vocalization software typically used in USV research, i.e. Avisoft or Deepsqueek? This is a fair point, we have previously used Audacity for visual detection of USV, but we will hopefully gain enough expertise in the use of Deepsqueak, to compare both detection methods. In terms of the secondary response variable (a) in objective 1, what is the question you are exploring with subtypes? Essentially, I would ask why are you wanting to look at subtypes? Are you looking to see if certain subtypes reflect a more positive interaction? For example, would one expect that with less pinning the rats emit less trills or frequency-modulated subtypes, or just the variability of subtypes emitted during tickling? Are you planning to coordinate the subtype emissions with the behaviour occurring, i.e. while chasing the experimenter's hand, what calls do they primarily emit? This can be quite a complicated assessment and requires accurate synchronization of behaviour and USV times[SB1] . We have added a sentence in Data collection/Confirmatory hypothesis, to clarify this use of USV subtypes (‘We will investigate whether certain USV types might be preferably associated with certain treatments’). How do you plan to do the categorization? By an independent observer manually categorizing or do you plan to use software that is trained for automated categorizations[SB2] ? There are obviously pros and cons to both, but I think this is an important point to consider when planning categorical USV analysis. We aim to categorise our USVs according to the previously published description (Wright et al., 2010), as we feel this common referential will contributes toward an improved understanding of rat USV production."
}
]
}
] | 1
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https://f1000research.com/articles/11-1053
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https://f1000research.com/articles/11-1345/v1
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18 Nov 22
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{
"type": "Study Protocol",
"title": "A scoping review protocol on diagnostic and treatment costs of cardiovascular disease management in India",
"authors": [
"Shaik Husna Tasneem",
"Mehnaaz M. Dhanal",
"Merin Renjith",
"Raveesh Subramanian",
"Vijay Shree Dhyani",
"Jisha B. Krishnan",
"Prachi Pundir",
"Andria J.N. Sirur",
"Ambigai Rajendran",
"Shaik Husna Tasneem",
"Mehnaaz M. Dhanal",
"Merin Renjith",
"Raveesh Subramanian",
"Vijay Shree Dhyani",
"Jisha B. Krishnan",
"Prachi Pundir",
"Andria J.N. Sirur"
],
"abstract": "Background: Cardiovascular disease (CVD) is a leading cause of mortality in India. Economic threats due to CVDs have surged, as diagnostic and treatment costs are out-of-pocket expenses. The increasing prevalence of CVDs in India is due to globalization, industrialization, aging, tobacco and alcohol consumption, diet, and sleep patterns. This scoping review provides a summary of the costs incurred in diagnosing and treating CVDs in India. Methods: The JBI updated methodology aligned with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Scoping Reviews (PRISMA-ScR) will guide this scoping review. Searches will be conducted on PubMed, Scopus, Cochrane Library, Embase, Econ Papers, and ProQuest databases. Google Scholar and Shodhganga will be used to search for relevant gray literature. Bibliographic mining will be performed to identify additional relevant studies. The literature published from 2000 onwards will be the primary focus. All direct and indirect costs for the diagnosis and treatment of CVDs across various levels of healthcare settings will be included. A two-stage independent screening, consisting of title and abstract screening, followed by full-text screening, will be conducted to identify eligible articles. Data will be extracted from full-text studies using a customized data extraction form. The results will be compiled and presented in the scoping review performed. Ethics and dissemination: A conference presentation and scientific peer-reviewed journal publication will be the sources for disseminating the review results. This study does not require an ethics review because publicly available sources were used to retrieve data.",
"keywords": [
"cardiovascular disease",
"heart attack",
"hypertension",
"stroke",
"cost analysis",
"cost utility",
"cost effectiveness",
"cost",
"health care cost",
"direct cost",
"indirect cost",
"cost of illness",
"medical cost",
"non-medical cost"
],
"content": "Introduction\n\nNon-communicable diseases (NCDs) are chronic in nature (Chronic diseases fact sheet, GACD), accounting for approximately 70% (41 million) of deaths globally (Noncommunicable diseases, WHO; Noncommunicable diseases Fact sheet, WHO). The global burden of NCDs increased briskly with a proportional rise attributed to cardiovascular diseases (CVDs) (Prabhakaran, Jeemon, and Roy, 2016) and would further increase to 55 million by 2030 if interventions were not opportune (Non-communicable Diseases, National Health Portal Of India). India recorded 63% of NCD fatalities in 2016, of which 27% were attributable to CVDs (Cardiovascular diseases in India, WHO). The World Health Organization (WHO) recommends a country-level target to reduce NCDs by 25% by 2025 and premature deaths by 33% by 2030. This can also prevent additional burden on healthcare costs and assist in attaining sustainable developmental goals (SDGs) (Cobiac and Scarborough, 2017).\n\nThe prevalence of CVDs was estimated to be 271 million worldwide in 1990, and this value doubled to 523 million in 2019. During the same period, the number of CVD-related deaths due to CVD increased from 12.1 million to 18.6 million (Roth et al., 2020).\n\nWHO's action plan aspires to counter the CVD epidemic by encouraging research work, reducing, monitoring and modifying determinants and risk factors and integrating disease prevention programs and controlling local policies under global strategy for the prevention and control of NCDs (2008-2013 Action Plan for the Global Strategy for the Prevention and Control of Noncommunicable Diseases, WHO). Low- and middle-income countries (LMICs) contributes to more than three-quarter of the world’s fatalities due to CVDs, which is attributed to insufficiency in primary healthcare services and the absence of robust universal health coverage (UHC) systems (CVDs Fact sheet, WHO). Out of the three-quarter deaths, around 40% fatalities are considered as premature. There is a need for sufficient data to support the likelihood that genetic, cultural, and environmental variations exist in the causes of CVDs by race and ethnicity. These variations should be considered when developing strategies for CVD prevention and treatment (Anand, Bradshaw, and Prabhakaran, 2020). Prominent unified factors, including economic, political, and cultural globalization, industrialization, and rapid urbanization are significant contributors to the increasing prevalence of CVDs in India. In addition, elevated levels of stress, inadequate physical activity, debilitated food and sleep patterns, heightened alcohol consumption, cigarette and tobacco smoking, and periodic sedentary lifestyles also pose significant risks (Prabhakaran and Yusuf, 2010). Lack of surveillance systems and proper and prompt diagnosis also contribute to the increasing prevalence of CVDs in India (Nag and Ghosh, 2013).\n\nIn 2016, the estimated prevalence of CVDs in India was 54.5 million cases. One in four deaths in India is attributed to CVDs, especially coronary artery disease and stroke, which accounts for greater than 80% of the burden of CVDs in India (Abdul-Aziz et al., 2019). Maximum number of cases are recorded in the Indian states of Kerala, Punjab, Tamil Nadu, Maharashtra, Andhra Pradesh, Himachal Pradesh, West Bengal, and Goa (Prabhakaran et al., 2018). Untimely mortality in India was 23.2 million in 1990, it increased by 59% to 37 million in 2010 because of CVDs (Prabhakaran, Jeemon, and Roy, 2016). Policy makers in India are hopeful that untimely deaths due to CVDs can be reduced by 25% with the implementation of national policies by 2025 (Prabhakaran et al., 2018). The number of deaths and number of hospitalizations due to CVDs in India was estimated at 1.4 million and 6.7 million in 2004 and it is expected to go up to 2.1 million and 10.9 million in 2021, respectively. Most of the hospitalized population belongs to the age group between 25 and 59 years (Srivastava and Mohanty, 2013). The estimated death rate attributed to CVDs in India was 256 per 1,00,000 population in 2019, which is more than double that of Japan, the country with the lowest death rate (77 per 1,00,000 population) (GBD Compare, IHME Viz Hub).\n\nEvery year, approximately 150 million people face financial emergencies owing to healthcare payments. Developing countries have meagre budgets for healthcare and are overly reliant on out-of-pocket health spending when compared to developed countries, which have a tax-funded health system or social health insurance schemes (Ezat Wan Puteh and Almualm, 2017). In 2010, the total cost related to medical care of CVDs was approximately USD 7.5 billion in India (Patel et al., 2020).\n\nThe estimated hospitalization cost for CVDs was INR 94 billion in 2004 and it is expected to project at INR 152 billion by 2021 (Prabhakaran et al., 2018). Prior studies on out-of-pocket expenditure (OOPE) in India have revealed that the hospitalization cost of CVDs could be five times higher in a private setting as opposed to a public one (Prinja et al., 2019). The estimated health care cost of CVDs was INR 8,483 (USD 114) in 2004–2005, which rose to INR 14,380 (USD 194) in 2011–2012 (Patel et al., 2020). Mean OOPE with respect to a specific disease and catastrophic health expenditure with relation to hospitalization in India was around INR 19,210 (the OOPE for heart diseases was approximately INR 40,947 (USD 552) in 2018 (Kastor and Mohanty, 2018). The poor and marginalized sections of the society are the predominant sections affected by OOPE for CVD treatment (Thakur et al., 2011).\n\nTo reduce the total economic burden, the Government of India (GOI) introduced Ayushman Bharat Yojana (ABY), a national health protection mission, in early 2018. This health insurance program is expected to benefit around half a billion poor and vulnerable families (Chowdhury and Mukherjee 2019, Macroscan). GOI is primarily focusing on addressing the increasing damage because of NCDs (Bhargava and Paul, 2020). A total of 150,000 Health and Wellness Centers are proposed to be established across India to give complete primary health-care services that are equivalent to the preeminent causes of huge burden of disease, including CVDs and other NCDs (AYUSHMAN BHARAT Comprehensive Primary Health Care through Health and Wellness Centers Operational Guidelines). Along with that it is expected to transform the grass root structure of primary, secondary, and tertiary health care systems in India (Verma, 2019). By ensuring access to quality health care and financial protection, India is perpetrated in achieving UHC for all by 2030 with ABY as an embryonic stride towards it (The long road to universal health coverage, NITI Aayog). Over the past few decades, CVDs have become a leading cause of mortality, causing a huge social and economic menace. The concept of UHC and insurance is growing constantly, but it is still a long way away to realize its potential, and to achieve this, there needs to be enormous stakeholder collaboration. Although research has been conducted on the costs of CVDs in India, a systematic or scoping review providing a comprehensive summary of the associated costs across various levels and sectors does not exist.\n\nThus, there is a need to synthesize evidence on this subject. To address this, a scoping review of peer-reviewed, non-peer-reviewed, and grey literature articles indicating the cost of CVDs is planned.\n\nThe objective of this review is to summarize the estimated costs associated with CVD care management in India with the available evidence and identify gaps in the literature. This study also aims to report the predominance of out-of-pocket spending and the economic burden of managing CVDs in India. This may aid policymakers in framing appropriate schemes to reduce OOPE and to encourage UHC. This study indirectly projects the potential impacts on inequalities in healthcare and strengthens the knowledge base for UHC in India.\n\n\nMethods\n\nMethods for this scoping review will follow the updated JBI methodology for scoping reviews (The Joanna Briggs Institute Reviewers’ Manual 2015 Methodology for JBI Scoping Reviews) along with Arksey and O'Malley's scoping review methodology (Arksey and O’Malley, 2005) and Levac et al. (Levac, Colquhoun, and O’Brien, 2010) enhanced framework methods. The current protocol follows the Preferred Reporting Items for Systematic review and Meta-Analysis Protocol (PRISMA-P) (Moher et al., 2016) and the future scoping review will follow the PRISMA for Scoping Reviews (PRISMA-ScR) (Tricco et al., 2018). The scoping review will be carried out in five distinct stages:\n\n1. Identification of the research question\n\n2. Identifying relevant studies\n\n3. Selection of eligible studies\n\n4. Data extraction and charting\n\n5. Collating, summarizing, and reporting the results\n\nThe broad question that directs this review is: what are the costs incurred for the diagnosis and treatment of CVDs in India? This review will elucidate relevant concepts by delineating and clarifying them, identifying research gaps, and reporting the most important evidence available to address and inform practice.\n\nInclusion criteria\n\nThe literature published in English language from 2000 onwards will be considered in the scoping review. The population, concept, and context (PCC) frameworks will guide the inclusion and exclusion criteria for this review. Table 1 summarizes the PCC framework that we will use for study selection.\n\nPopulation\n\nStudies that include participants/patients/individuals with borderline or established CVDs of any age in India will be included. As per the types given by WHO, the CVDs include cerebrovascular disease, coronary heart disease (CHD), congenital heart disease, peripheral vascular disease, deep vein thrombosis and pulmonary disease, rheumatic heart disease, their synonyms and commonly used terms will be included for the review (CVDs Fact sheet, WHO).\n\nConcept\n\nThe main concept of this review includes the direct and indirect costs incurred in the management of CVDs in India. This includes direct medical and non-medical costs, along with indirect costs. Direct medical costs include physician visits, emergency room services, and medications, while direct non-medical costs involve food, accommodation, and travel. Indirect costs include the loss of earnings, time, and productivity loss of both patients and their caregivers while seeking medical care (Ibrahim, Pozo-Martin, and Gilbert, 2015). In this review, the direct costs for common diagnostic programs such as blood pressure (BP), fasting lipoprotein profile, body mass index (BMI), blood glucose test, electrocardiogram (ECG), exercise stress test, echocardiogram, nuclear cardiac stress test, abdominal and carotid ultrasound, coronary angiogram, magnetic resonance image (MRI), and coronary computed tomography angiogram (CCTA) will be included (Diagnosing Heart Disease, Patient Education, UCSF Health), (Heart Procedures and Surgeries, American Heart Association), (Common medical tests to diagnose heart conditions, National Heart Foundation of Australia). Common treatment costs such as hospital costs, drug therapy, surgical procedures such as angioplasty, coronary artery bypass surgery (CABG), pacemakers, heart valve surgery, cardiomyoplasty, heart transplant, implantable cardioverter defibrillator, and rehabilitation costs will also be included, and many others will be premeditated and incorporated (Common medical tests to diagnose heart conditions, National Heart Foundation of Australia), (Coronary heart disease, Treatment, NHS), (Heart Procedures and Surgeries, American Heart Association). The diagnostic and treatment programs will be amended subsequently based on the studies. Other related costs will also be included and assessed. OOPE summarizes the cost borne by patients, in addition to the costs covered by a social security scheme or insurance coverage (Burden of out-of-pocket health expenditure, OECD iLibrary, 2009; Lorenzoni et al., 2015).\n\nContext\n\nThis scoping review aims to determine the economic burden of CVDs in India. Therefore, studies on all types of CVDs in India will be considered. This review will consider studies conducted in any clinical setting (e.g., inpatient, outpatient) or healthcare facilities (e.g., hospitals, health centers, nursing homes).\n\nTypes of evidence sources\n\nThe eligible studies include case-control studies, cohort studies, cross-sectional studies, randomized control trials (RCTs), non-RCTs, before-and-after studies, qualitative and quantitative studies, conference papers, and peer and non-peer review studies. Letters to the editor, editorials, commentary perspectives, and reviews will be excluded. Studies on co-occurring diseases and CVDs will also be included. Studies on CVD prevention costs will get excluded, based on the initial scoping process.\n\nSearch strategy\n\nA comprehensive search strategy was developed to retrieve both published and unpublished studies. A primary search of PubMed (RRID:SCR_004846) was performed to identify relevant articles. The keywords used to describe pertinent articles are listed and used to develop a full PubMed search. The search strategy will be customized and modified, consisting of all keywords and index terms using Boolean operators for Scopus (RRID:SCR_022559), Cochrane Library (RRID:SCR_013000), EMBASE (RRID:SCR_001650), EconPapers, and ProQuest (RRID:SCR_006093), followed by the PCC framework described in the JBI methodology for scoping reviews. The key terms will include “cardiovascular disease” “coronary artery disease” OR “heart attack” OR “cardiomyopathy” OR “hypertension” OR “stroke” OR “peripheral artery disease” OR “congenital heart diseases” OR “rheumatic heart disease” AND cost analysis” OR “cost utility” OR “cost effectiveness” AND “cost” OR “health care cost” OR “direct cost” OR “indirect cost” OR “cost of illness” OR “medical cost” OR “non-medical cost”. We will manually search reference lists for additional pertinent studies. Google Scholar (RRID:SCR_008878) and Shodhganga: A reservoir of Indian theses @ INFLIBNET will also be searched to locate grey literature. The authors of the studies will be contacted if any additional information is required. Example search strategy for PubMed is provided in Table 2.\n\nAfter completion of the searches, all identified citations will be collated and transferred to Zotero (RRID:SCR_013784) version 5.0, and duplicates will be removed. In accordance with the eligibility criteria, a two-stage screening process comprising (1) title and abstract screening and (2) full-text screening will be performed. The inclusion and exclusion criteria based on the PCC framework are listed in Table 3. The two stages followed an identical process, where every article will be independently reviewed in teams of two, and the results will be documented in Microsoft Excel (RRID:SCR_016137) spreadsheets. In conclusion, relevant sources will be retrieved. The selected full text will be reviewed in detail based on the eligibility criteria. Further ambiguities regarding the eligibility of an article will be labelled and discussed with a subject expert or a senior reviewer. The reasons for the exclusion of studies will be reported and recorded at the full-text screening stage.\n\nData from these studies will be independently extracted. A custom data extraction form developed by the research team, using Microsoft Excel as an abetting platform, will be used. The data extracted will capture study components such as author names, publication year, publication title, type of CVDs, intervention, target population, population excluded, study setting, study design, sample size, and diagnostic and treatment costs. The data extraction form will be pretested before implementation to ensure that it accurately captures imperative information. The necessary modifications will be made as required during the pilot process. A detailed explanation of all modifications will be provided in the scoping review. The resolution of the differences between the reviewers’ decisions will be discussed with a subject expert or a senior reviewer. Table 4 lists the preliminary data extraction template used in this study.\n\nA PRISMA flow diagram will be used to report the screening process (Moher et al., 2016). The flow diagram displays the decision-making process, as well as the outputs of the searches, elimination of duplicated citations, study selection, complete retrieval, additional bibliography mining, and presentation of the final summary. The results will be presented in graphical, tabular, and detailed descriptive compositions that align with the purpose and scope of this review. Descriptive statistics, such as frequencies and central measures of tendency and plots indicating concepts or aspects of population characteristics, will be used to report the number of studies, type of CVDs, treatment and diagnostic procedures, study type and design, and costs incurred (direct and indirect) either in diagrammatic or tabular arrangements (Peters et al., 2015). Moreover, thematic and narrative approaches will also be incorporated for the analysis of quantitative and qualitative studies. The gaps and limitations in the current literature will be identified and summarized.\n\nCurrently the authors are performing searches on all the electronic databases mentioned.\n\n\nDiscussion\n\nThis scoping review will provide a comprehensive rundown of cost induction for CVD care management in India and raise awareness among patients, clinicians, decision makers, and third-party payers about the economic burden of such chronic diseases. Along with this, one suggestion is to grasp health inequalities and the high priority of UHC for the Indian population.\n\n\n\n1. This is the first scoping evaluation of the costs associated with managing CVDs in India.\n\n2. The current scoping study will employ eight electronic databases and tailored search terms that will be iteratively optimized to obtain as many relevant articles as possible. Grey literature will also be identified and synthesized.\n\n3. An assessment of the quality of the articles included in the scoping review will not be performed because it is beyond the scope of the scoping review.\n\n4. A scoping review was undertaken because the topic has not been extensively reviewed and the scope has a broader agreement.\n\n\nEthics and dissemination\n\nThis study does not require ethical approval because the information and data collected will be obtained from publicly available sources. Regarding dissemination activities, the full review will be presented at a relevant conference and submitted to a peer-reviewed scientific journal for publication to report the outcomes of the scoping review.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nAll the authors have proofread the protocol and given their final approval of the version to be published. Authors would like to acknowledge and extend their gratitude to Dr. Bhumika TV, Assistant Professor and Coordinator, PHESA, PSPH, and MAHE for her support with the development of this protocol.\n\n\nReferences\n\nAbdul-Aziz AA, Desikan P, Prabhakaran D, et al.: Tackling the burden of cardiovascular diseases in India: The essential diagnostics list. Circulation: Cardiovascular Quality and Outcomes.2019; 12(4): e005195.\n\nAnand S, Bradshaw C, Prabhakaran D: Prevention and Management of CVD in LMICs: Why Do Ethnicity, Culture, and Context Matter? BMC Med. 2020; 18(1): 1–5. (June 19, 2021). PubMed Abstract | Publisher Full Text\n\nArksey H, O’Malley L: Scoping Studies: Towards a Methodological Framework. Int. J. Soc. Res. Methodol.: Theory Pract. 2005; 8(1): 19–32. Publisher Full Text\n\nBhargava B, Paul VK: Informing NCD Control Efforts in India on the Eve of Ayushman Bharat. Lancet. 2020. (June 19, 2021). Publisher Full Text\n\nCobiac LJ, Scarborough P: Translating the WHO 25×25 Goals into a UK Context: The PROMISE Modelling Study. BMJ Open. 2017; 7(4): e012805. (June 19, 2021). Publisher Full Text Reference Source\n\nEzat Wan Puteh S, Almualm Y: Catastrophic Health Expenditure among Developing Countries. Health. Syst. Policy Res. 2017; 04(01): 1. (June 19, 2021).Reference SourceReference Source\n\nIbrahim N, Pozo-Martin F, Gilbert C: Direct Non-Medical Costs Double the Total Direct Costs to Patients Undergoing Cataract Surgery in Zamfara State, Northern Nigeria: A Case Series. BMC Health Serv. Res. 2015; 15(1): 1–7. (July 24, 2021).PubMed Abstract | Publisher Full Text\n\nKastor A, Mohanty SK: Disease-Specific out-of-Pocket and Catastrophic Health Expenditure on Hospitalization in India: Do Indian Households Face Distress Health Financing? PLoS One. 2018; 13(5): e0196106. (June 19, 2021). Publisher Full Text PubMed Abstract |\n\nLevac D, Colquhoun H, O’Brien KK. Scoping Studies: Advancing the Methodology. Implement. Sci. 2010; 5(1): 1–9. (June 19, 2021).Reference Source\n\nLorenzoni L, Morgan D, Murakami Y, et al.: Public Expenditure Projections for Health and Long-Term Care for China until 2030. OECD Health Working Papers. 2015; 84: 43.Reference Source\n\nMoher D, et al.: Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) 2015 Statement. Rev. Esp. Nutr. Hum. Diet. 2016; 4(2): 148–160. (October 3, 2022). PubMed Abstract | Publisher Full Text\n\nNag T, Ghosh A: Cardiovascular Disease Risk Factors in Asian Indian Population: A Systematic Review. J. Cardiovasc. Dis. Res. 2013; 4(4): 222–228. (June 19, 2021). PubMed Abstract | Publisher Full Text Reference Source\n\nPatel S, Ram F, Patel SK, et al.: Cardiovascular Diseases and Health Care Expenditure (HCE) of Inpatient and Outpatient: A Study from India Human Development Survey. Clin. Epidemiol. Glob. Health. 2020; 8(3): 671–677. (June 24, 2021). Publisher Full Text Reference Source\n\nPeters MDJ, et al.: Guidance for Conducting Systematic Scoping Reviews. Int. J. Evid. Based Healthc. 2015; 13(3): 141–146. (July 24, 2021). Publisher Full Text Reference Source\n\nPrabhakaran D, et al.: The Changing Patterns of Cardiovascular Diseases and Their Risk Factors in the States of India: The Global Burden of Disease Study 1990–2016. Lancet Glob. Health. 2018; 6(12): e1339–e1351. (June 19, 2021). Publisher Full Text\n\nPrabhakaran D, Jeemon P, Roy A: Cardiovascular Diseases in India: Current Epidemiology and Future Directions. Circulation. 2016; 133(16): 1605–1620. (June 19, 2021). Publisher Full Text Reference Source\n\nPrabhakaran D, Yusuf S: Cardiovascular Disease in India: Lessons Learnt & Challenges Ahead. Indian J. Med. Res. 2010; 132(11): 529–30. (June 24, 2021).Reference Source\n\nPrinja S, et al.: Out-of-Pocket Expenditure and Catastrophic Health Expenditure for Hospitalization Due to Injuries in Public Sector Hospitals in North India. PLoS One. 2019; 14(11): e0224721. (June 19, 2021). PubMed Abstract | Publisher Full Text Reference Source\n\nRoth GA, et al.: Global Burden of Cardiovascular Diseases and Risk Factors, 1990-2019: Update From the GBD 2019 Study. J. Am. Coll. Cardiol. 2020; 76(25): 2982–3021. (June 19, 2021). PubMed Abstract | Publisher Full Text Reference Source\n\nSrivastava A, Mohanty SK. Age and Sex Pattern of Cardiovascular Mortality, Hospitalisation and Associated Cost in India. PLoS One. 2013; 8(5). (June 19, 2021). Publisher Full Text | Free Full Text\n\nThakur JS, et al.: Social and Economic Implications of Noncommunicable Diseases in India. Indian J. Community Med. 2011; 36(SUPPL): 13–S22. (June 19, 2021). PubMed Abstract | Publisher Full Text Reference Source\n\nTricco AC, et al.: PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation. Ann. Intern. Med. 2018; 169(7): 467–473. (October 3, 2022). PubMed Abstract | Publisher Full Text\n\nVerma M: Scope of Management of Noncommunicable Diseases in India through Ayushman Bharat. J. Soc. Health Diabetes. 2019; 7(02): 58–60. (June 19, 2021). Publisher Full Text Reference Source"
}
|
[
{
"id": "199218",
"date": "12 Oct 2023",
"name": "Lauren M. Fletcher",
"expertise": [
"Reviewer Expertise Health Sciences librarian with extensive knowledge and training in evidence synthesis methodology and searching."
],
"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 developed a well-documented and thorough scoping review protocol. The authors aim to document and determine any gaps in the literature on the direct and indirect healthcare costs of cardiovascular disease in India. The scope and aim of this study are well defined and the study design is appropriate for the research proposed.\n\nStudy Identification\nThe authors would benefit from providing a rationale for why a date limit, articles from January 2000 onwards, was used for the review.\n\nThe authors list a number of cardiovascular diseases to be included in the scoping review but did not include heart attacks or stroke within the list of eligible CVDs though they are listed in the search terms. Authors should include the concept of heart attacks/stroke as an included CVD or exclude the concept from the search strategy.\n\nThe authors state indirect healthcare costs as a main concept in addition to direct healthcare costs, but definitions for the types of indirect costs are not stated. The authors should provide information as to the types of indirect healthcare costs that will be considered for inclusion.\n\nThe authors should include MeSH and Emtree controlled vocabulary terms for the searches conducted in PubMed and Embase.\n\nThe authors should consider expanding terminology for direct/indirect healthcare costs. Terminology regarding economic evaluations, expenditure, etc. would be beneficial for expanding the search on direct healthcare costs. Further terminology related to indirect healthcare costs should be considered for the search as well.\n\nThe authors should include what database(s) within the ProQuest platform was searched.\n\nSelection of Eligible Studies\n\nThe authors provide a sound methodology for studying selection.\n\nThe inclusion/exclusion criteria would be aided by the addition of the items suggested in the above points.\n\nData Extraction and Charting\nThe authors provide a detailed methodology for data extraction. Authors would benefit from stating the number of reviewers extracting data and if a reviewer(s) will resolve any data conflicts and/or review the accuracy of extracted data.\n\nThe authors should consider extracting data on any related comorbidities as this could be helpful for future analysis, policy development, etc.\n\nData Analysis and Reporting\n\nThe authors provide a sound proposal for how the anticipated data will be analyzed and reported.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": []
},
{
"id": "212915",
"date": "20 Feb 2024",
"name": "Nilmini Wijemunige",
"expertise": [
"Reviewer Expertise Public health",
"policy policy and health economics with a focus on non-communicable diseases",
"particularly CVD."
],
"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 sets the groundwork for a useful study to quantify costs associated with CVDs. The protocol will benefit with further tightening of definitions, particularly the population, costs and perspectives, and what the term CVD covers.\n\nIntroduction\nDefine CVDs (perhaps when the term is introduced in the first paragraph), as it comes as a bit of a surprise in the methods that the scoping review will also cover CVDs such as rheumatic heart disease, congenital heart disease etc. Is all the data mentioned in the introduction including these conditions as well? 1st sentence: 55 million - specify the country This sentence could be reworded: Low- and middle-income countries (LMICs) contributes to more than three-quarter of the world’s fatalities due to CVDs, which is attributed to insufficiency in primary healthcare services and the absence of robust universal health coverage (UHC) systems. Reason: LMICs account for 84% of the world’s population, but 75% of CVD deaths. The citation makes a slightly different point: that people in LMICs are less likely to benefit from early detection and treatment, and they die at a younger age. This could be linked with the next sentence as well. CVDs was INR 94 billion in 2004 and it is expected to project at INR 152 billion by 2021: it would be useful to give the USD amount in brackets Over the past few decades, CVDs have become a leading cause of mortality, causing a huge social and economic menace. - this sentence is out of place here In the sentence before the objective, it is mentioned that a review is planned of articles “indicating the cost of CVDs”. However the objective says “costs of care management”. “Cost of CVD” could include societal costs as well, so should maintain consistency as to what costs you are focusing on.\n\nMethods\nTable 1 population: make the terms used in the table and text consistent. Suggest using “individuals” instead of participants/patients What does “borderline CVD” mean? Is it risk of CVD? From the search terms, it looks like risk of CVD is not being looked at, and it would be good to mention if you are or are not looking at CVD risk screening costs (primary prevention of CVD), and if not, why not. Table 4: Data extraction would benefit in capturing the perspective of the costs (individual / healthcare / societal costs) - you allude to it with “study perspective”. Please clarify if you are collecting the perspective of the costs as well. Stage 3 - The two stages followed.. should it be “will follow”? Is there a process to ensure harmonization between the teams? Is it the same for title/abstract and full text screening? How many teams are there?\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/11-1345
|
https://f1000research.com/articles/11-1342/v1
|
18 Nov 22
|
{
"type": "Case Report",
"title": "Case Report: Invasive micropapillary ductal breast carcinoma",
"authors": [
"Kakia Anne Faith Namugenyi",
"Kelechi Elizabeth Oladimeji",
"Alungile Mthimba",
"Chris Mzileni",
"Olanrewaju Oladimeji",
"Kelechi Elizabeth Oladimeji",
"Alungile Mthimba",
"Chris Mzileni",
"Olanrewaju Oladimeji"
],
"abstract": "Background: Invasive micropapillary carcinoma (IMPC) of the breast is a rare variant of invasive ductal breast carcinoma (IDC), with most cases characterized by lymph node metastasis and lymphatic vascular invasion. It is a ductal breast cancer subtype with a very high risk of recurrence and therefore requires special attention from breast cancer physicians and radiologists. Case: We present a case of an IMPC that has been followed up for two years since diagnosis and management. Based on clinical breast examination, ultrasound, and mammography, the initial diagnosis was a suspicious mass that required further investigation. Radiological and histological findings informed the diagnosis of a highly suspicious lesion, which turned out to be IMPC. The patient underwent surgery, left mastectomy with nodal dissection. During the 24-month follow-up, ultrasound and mammography revealed no evidence of local recurrence or involvement of the contralateral breast. Conclusions: This case reveals that invasive micropapillary carcinoma is a distinct but poorly recognized variant and subtype of invasive ductal carcinoma.",
"keywords": [
"Invasive micropapillary breast carcinoma",
"clinical breast examination",
"ultrasound",
"mammography",
"diagnosis",
"radiology",
"histology",
"case report"
],
"content": "Introduction\n\nThe histopathological type of breast cancer provides important prognostic information about the natural history and overall outcome of the disease. Of all breast cancer types, invasive micropapillary carcinoma (IMPC) is a rare subtype of invasive ductal carcinoma (IDC) characterized histologically by the formation of micropapillaries within the cystic spaces.1–3 This is due to its distinct presentation, particularly lymphovascular invasion. IMPC was first identified in 1993 and classified separately by the World Health Organization (WHO) in 2003, before being subjected to the general rule for the clinical and pathological registration of breast cancer in 2008.2,3 It accounts for about 2–8% of all breast cancers and is considered to be more aggressive than the other IDC types.1,3 It is also listed as a special histological type in the 2003 and 2012 editions of the WHO classification of breast tumors.4,5 This case report followed the CAse REport (CARE) guidelines as a guiding principle.6,7\n\n\nCase report\n\nA 41-year-old woman black African housewife, presented with a left breast lump for two months. She had no family history of breast cancer and had never had breast surgery.\n\nThe patient was informed and consented to the use of her medical records and clinical images. She understood that she had a rare subtype of cancer and believed that using it as a case study would advance science and improve clinical diagnosis and outcomes for patients with IMPC in the future. Additionally, hospital management gave permission and ethics clearance for this case report was obtained from the Walter Sisulu University Ethic committee (WSU Ethics approval No: 056/2022) on the 14th of June 2022.\n\nDuring clinical breast examination, there was no nipple discharge or associated pain. The left breast mass was clinically palpable with no skin changes or nipple retraction. The mass was firm and fixed to the overlying skin, but it was not attached to the underlying structures. There were palpable mobile lymph nodes in the left axilla.\n\nMammography revealed an oval, spiculated, high-density mass in the upper outer quadrant of the left breast (Figure 1). This was associated with ancillary findings of focal trabecular and Cooper's ligament thickening. There were no associated microcalcifications. Axillary lymphadenopathy was present on the left side.\n\nSpiculated, irregular mass-highly suspicious (white arrows). ACR-BIRADS score 5 (American College of Radiology - Breast Imaging and Data System).\n\nHigh resolution ultrasound (HRUS) showed an oval, not-well circumscribed spiculated, parallel mass which was heterogeneous but predominantly hypoechoic with no posterior features at 2 o’clock (Figure 2). The mass measured 20 × 15 × 21 mm and was in the superficial glandular layer, 4cm from the nipple with moderate vascularity at color Doppler. A second smaller mass was seen next to the larger one which was also hypoechoic and oval shaped with lobulated margins, measuring 8 × 5 × 6 mm. This was thought to be a fibroadenoma or an infiltrated lymph node. Round hypoechoic nodes with eccentric mediastinum and diffusely thickened cortex were seen in the left axillar (Figure 3). The radiological diagnosis was ACR BIRADS category 5 (American College of Radiology- Breast Imaging Reporting and Data System).8,9 As a result, biopsy of the lesion was recommended. Differential diagnoses included invasive ductal carcinomas and lobular carcinomas.\n\nThe patient underwent an incision biopsy at which a 5 × 4 × 2.5 cm irregular, yellow piece of tissue with a 2.5 × 2 × 1.5 cm firm mass was sent to the laboratory for histopathological analysis. On microscopy, sections showed an invasive tumor with a distinctly micropapillary growth pattern –fibrovascular cores lined by epithelial cells located in cystic spaces (Figure 4a and b). The tumor cells showed significant nuclear pleomorphism with lymphovascular invasion and prominent fibrovascular cores with no surrounding fibrous capsule (Figure 4c and d). In addition, there were areas of high-grade ductal carcinoma in situ with a combination of fibro adenomatous change. On immune histochemistry, the tumor stained strongly diffusely positive for estrogen and progesterone receptors and negative for human epidermal growth factor receptor 2 (HER2). The surgical margins were reported to be positive, and the modified Bloom-Richardson grade was reported as III.10 Though the positron emission tomography (PET) scan could have been more informative, unfortunately, this was not available in our center. Hence, distant metastatic work up was done using computed tomography (CT)-abdomen and pelvis at which no suspicious lesions were found. The patient subsequently underwent total right breast mastectomy and axillary lymph node dissection followed by chemotherapy. The patient received cyclophosphamide 600 mg/m2 doxorubicin 60 m2 and 5-Fluoracil 600 mg/m2. All the drugs were given intra venously every 21 days for six cycles. Since the patient’s receptor status was positive for estrogen and progesterone, she is now on tamoxifen 20 mg once a day at night.\n\nHRUS of the mastectomy bed, axillary and supraclavicular lymph nodes, as well as mammography of the right breast, were performed as part of the 12 and 24-month follow-up investigations. The ultrasound and mammography revealed no signs of local recurrence or contra lateral disease.\n\n\nDiscussion\n\nBreast cancer is the most common female malignancy worldwide and is a heterogeneous disease with diverse biological patterns and multiple pathological subtypes.11,12 IMPC is a rare, distinct pathologic intraductal carcinoma subtype known to be aggressive at initial presentation, with a significant propensity for lymph node metastasis and lymphovascular invasion.3 There are two subtypes, mixed (most common) and pure, which is rare.3,11 There is scanty radiological and clinical information on the entity.11,13–15 The unique properties of IMPC make it a breast cancer subtype that breast physicians and imaging professionals should recognize, treat cautiously, and follow up because of its potential for recurrence and poor prognosis.16 Patients with IMPC often present with a painless palpable breast mass,4,11,12,17 which we also observed in the patient in this report. Studies have shown that axillary lymph node involvement is common at presentation.12,16 Some patients may present with axillary lumps before the breast mass is clinically palpable (occult breast cancer).12 Morphologically, the tumor resembles micropapillary tumors of the urinary bladder, colon, lungs, and major salivary glands, where again it shows aggressive behavior with a poor prognosis.2,16\n\nHistopathologically, IMPC is characterized by tubuloalveolar or pseudopapillary structures that lack a fibrovascular core and are surrounded by clear void spaces, as previously mentioned.1–3,18 The micropapillary component in each tumor is variable. However, regardless of the extent of the micropapillary component, tumors with any amount of this particular histological pattern exhibit a more aggressive clinical behavior with a high degree of lymphovascular involvement compared to other types of invasive ductal carcinoma.2,4,17 Immunohistochemical findings in individuals diagnosed with IMPC are more likely to be positive for the expression of estrogen and progesterone hormone receptors than in patients with other types of breast cancer.1–3,17–19 This is consistent with our findings for the patient discussed here.\n\nSo far, there are no typical IMPC imaging identifiers.11 The sonography of the primary lesion shows no typical features. The most common finding in the literature is a poorly circumscribed, homogeneous, hypoechoic mass.4,10,13 One case report was identified reporting a hyperechoic lesion at ultrasound, a feature commonly seen in benign lesions.18 In a study by Jones et al.13 they found that 67% of the patients had sonographically suspicious axillary lymph nodes. Axillary ultrasound is useful in assessing lymph node involvement in patients with IMPC due to the high incidence of lymphovascular invasion by the tumor.2,4,11,13 Adrada et al.4 documented pathologic supra- and infraclavicular nodules in some patients in their study, suggesting that investigation of metastases in IMPC patients should routinely include these sites. Ultrasound can show more lesions in IMPC patients than mammography. Color Doppler may show centripetal increased vascularity, a finding suggestive of malignancy.13\n\nOn mammography, IMPC often presents as an irregular, high-density mass with spiculed or lobulated borders.4,11,13 Mammographic findings in most studies, although with small sample sizes due to the rarity of the tumor, generally suggest a malignant lesion.11,13,17 Microcalcifications were a common feature in most patients with IMPC. The characteristics of the microcalcifications were indeterminate in most studies or rather suggestive of malignancy.11,17 In some patients, the tumor was occult on mammography, as in the study by Adrada et al.4 and Jones et al.13 only architectural distortion was seen on mammography.\n\nJust like mammography and ultrasound, an irregular mass is the most common feature of IMPC on magnetic resonance imaging (MRI). However, MRI is more accurate in determining the anatomical extent of the tumor and more sensitive to the presence of multiple lesions, if present. IMPC demonstrates rapid initial washout kinetics for patients with invasive ductal carcinoma with micropapillary features in the available literature.4,12,16,17 Some cases showed a non-mass-like enhancement characteristic, while lymph node assessment for nodal involvement is more accurate on MRI. IMPC typically shows malignant MRI characteristics and contrasted MRI is able to show the enlargement of the microcapillary bed in breast tumors with a higher sensitivity than mammography or ultrasound.12,17 However, despite the high MRI sensitivity, IMPC cannot be distinguished from other non-micropapillary breast lesions.12,16,17\n\nFollow-up of patients with IMPC requires screening of the remaining breast, but more important is evaluation for recurrences in the mastectomy bed and involvement of the nodes at the different three levels of breast lymphatic drainage. In this regard, HRUS plays a major role in the follow-up of IMPC patients and should be specifically requested by the treating physician. Detection of IMPC by breast imagers and physicians is important as it is believed to have a poorer prognosis than other types of IDC.3,17,18 The major challenges with IMPC is the presentation at an advanced stage usually stage 3 or 4, due to early nodal involvement and lymphovascular invasion.3,16\n\nThe treatment of choice for IMPC is mastectomy plus axillary lymph node removal with adjuvant chemotherapy in cases with tumor size greater than 1 cm and node positive.20 A high proportion of patients with IMPC express hormone receptor positivity estrogen, progesterone and HER2, this makes them beneficiaries of targeted hormone therapy, which improves overall outcome despite the aggressiveness of the disease.16\n\nAs is typical of most case reports, the main limitation is the inability to establish a cause-and-effect relationship. A major strength, however, is the generalizability of these clinical implications, given that the reported case is a rare type of breast cancer with similar clinical features to the few documented breast IMPCs worldwide\n\n\nConclusions\n\nInvasive micropapillary carcinoma is a distinct subtype and a poorly recognized variant of invasive ductal carcinoma. It has significant lymphovascular invasion, extensive lymph node involvement, and a high rate of local recurrence. Malignant imaging features include a high-density irregular mass on mammography, a hypoechoic, non-circumscribed irregular or speculated mass at ultrasound, and an irregular enhancing mass on MRI. Ultrasound is helpful in assessing local and regional recurrences, and MRI is critical in determining the extent and presence of multifocal lesions prior to surgery. If the breast cancer management team recognizes IMPC, it is possible to identify a group of patients with a poor prognosis who may require adjuvant treatment with nodal and post-mastectomy bedside assessment for recurrence at follow-up.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient.",
"appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: CARE checklist for ‘Case Report: Invasive micropapillary ductal breast carcinoma’, https://doi.org/10.6084/m9.figshare.20297112. 7\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe thank Alrika Debeer (NHLS technician) and Dr. Asher Krausey NHLS for the pathology slides.\n\n\nReferences\n\nShen-Li T, Yang Ji-Qiao D, Zheng-Gui TQ-W, et al.: Clinicopathologic study of invasive micropapillary carcinoma of the breast. Oncotarget. 2017; 8(26): 42455–42465.\n\nSiriaunkgul S, Tavassoli FA: Invasive micropapillary carcinoma of the breast. Modern Pathology. 1993; 6(6): 660–662. PubMed Abstract\n\nChen AC, Paulino AC, Schwartz MR, et al.: Population-based comparison of prognostic factors in invasive micropapillary and invasive ductal carcinoma of the breast. British Journal of Cancer. 2014; 111(3): 619–622. PubMed Abstract | Publisher Full Text\n\nAdrada B, Arribas E, Gilcrease M, et al.: Invasive micropapillary carcinoma of the breast: mammographic, sonographic, and MRI features. American Journal of Roentgenology. 2009; 193(1): W58–W63. PubMed Abstract | Publisher Full Text\n\nTavassoli FA, Devilee P: Pathology and genetics. Tumors of the breast and female genital organs WHO classification of tumours. 2003; 6. Publisher Full Text\n\nRiley DS, Barber MS, Kienle GS, et al.: CARE guidelines for case reports: explanation and elaboration document. Journal of Clinical Epidemiology. 2017 Sep 1; 89: 218–235. PubMed Abstract | Publisher Full Text\n\nNamugenyi KAF, Oladimeji KE, Oladimeji O:Checklist for case report on Invasive micropapillary ductal breast carcinoma. figshare. [Dataset]. Journal contribution. 2022. Publisher Full Text\n\nD’Orsi C, Bassett L, Feig S: Breast imaging reporting and data system (BI-RADS). Breast imaging atlas. 2018.\n\nSickles EA, D’Orsi CJ, Bassett LW, et al.: ACR BI-RADS® Atlas, Breast imaging reporting and data system. Reston, VA:American College of Radiology;2013. 39–48.\n\nBloom HJ, Richardson WW: Histological grading and prognosis in breast cancer; a study of 1409 cases of which 359 have been followed for 15 years. British Journal of Cancer. 1957; 11(3): 359–377. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGunhan-Bilgen I, Zekioglu O, Ustun EE, et al.: Invasive micropapillary carcinoma of the breast: clinical, mammographic, and sonographic findings with histopathologic correlation. American Journal of Roentgenology. 2002; 179(4): 927–931. PubMed Abstract | Publisher Full Text\n\nHan CH, Yao WG, He J, et al.: MRI and the pathology of breast invasive micropapillary carcinoma. Oncology Letters. 2020; 20(3): 2811–2819. PubMed Abstract | Publisher Full Text\n\nJones KN, Guimaraes LS, Reynolds CA, et al.: Invasive micropapillary carcinoma of the breast: imaging features with clinical and pathologic correlation. American Journal of Roentgenology. 2013; 200(3): 689–695. PubMed Abstract | Publisher Full Text\n\nTerando AM, Agnese DM, Holmes DR: Treatment and prognosis of rare breast cancers. Annals of Surgical Oncology. 2015; 22(10): 3225–3229. Publisher Full Text\n\nWong S-I, Cheung H, Tse G: Fine needle aspiration cytology of invasive micropapillary carcinoma of the breast. A case report. Acta Cytologica. 2000; 44(6): 1085–1089. PubMed Abstract | Publisher Full Text\n\nHao S, Zhao Y-Y, Peng J-J, et al.: Invasive micropapillary carcinoma of the breast had no difference in prognosis compared with invasive ductal carcinoma: a propensity-matched analysis. Scientific Reports. 2019; 9(1): 1–8. Publisher Full Text\n\nYun SU, Choi BB, Shu KS, et al.: Imaging findings of invasive micropapillary carcinoma of the breast. Journal of Breast Cancer. 2012; 15(1): 57–64. PubMed Abstract | Publisher Full Text\n\nKim M-J, Gong G, Joo HJ, et al.: Immunohistochemical and clinicopathologic characteristics of invasive ductal carcinoma of breast with micropapillary carcinoma component. Archives of Pathology and Laboratory Medicine. 2005; 129(10): 1277–1282. PubMed Abstract | Publisher Full Text\n\nIde Y, Horii R, Osako T, et al.: Clinicopathological significance of invasive micropapillary carcinoma component in invasive breast carcinoma. Pathology International. 2011; 61(12): 731–736. PubMed Abstract | Publisher Full Text\n\nUddin Z, Idrees R, Aftab K, et al.: Invasive Micropapillary Carcinoma of Breast: An Under-recognized Entity. A series of Eight Cases. The Breast Journal. 2012; 18(3): 267–271. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "181143",
"date": "14 Jul 2023",
"name": "Georgios-Ioannis Verras",
"expertise": [
"Reviewer Expertise Breast Surgery",
"Surgical Oncology"
],
"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\nAlthough reports on IMPC are rare and useful for breast clinicians, this report needs a few clarification points before publication.\nBetter describe your decision for the patient to undergo total mastectomy and ALND. Would SLNB suffice? How is the lack of IMPC-specific guidelines impacting our practice?\n\nConsider adding elements to the patient's PMH (estogen use, childbirth etc.)\n\nWas the patient disease-free at 2 years postoperative? Clarify\n\nPlease add more information in the Introduction section regarding the histological peculiarities of the subtype, especially regarding the micropapillary pattern as an imaging finding (see the attached citation)\n\nYou need to discuss more the lymphatic and lumphovascular potential of IMPC. ALND is not always the treatment of choice, and there is currently much debate on that. Please seek and incorporate more literature on trends in surgical management of IMPC such as the ones mentioned below.\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? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1342
|
https://f1000research.com/articles/11-483/v1
|
03 May 22
|
{
"type": "Research Article",
"title": "The effects of beliefs, knowledge, and attitude on herbal medicine use during the COVID-19 pandemic: A cross-sectional survey in Indonesia",
"authors": [
"Heri Kristianto",
"Bayu Anggileo Pramesona",
"Yafi Sabila Rosyad",
"Lili Andriani",
"Tri Antika Rizki Kusuma Putri",
"Yohanes Andy Rias",
"Heri Kristianto",
"Bayu Anggileo Pramesona",
"Yafi Sabila Rosyad",
"Lili Andriani",
"Tri Antika Rizki Kusuma Putri"
],
"abstract": "Background: Herbal medicines are gaining a greater degree of popularity as complementary and alternative medicines during the COVID-19 pandemic. Nonetheless, there is a lack of data concerning the rationale for and factors influencing their use. Methods: A cross-sectional community-based online study involving 1,621 participants was conducted to explore the effects of magical health beliefs, holistic health beliefs, knowledge, and pro- complementary alternative medicine (CAM) attitudes on herbal medicine use in the Indonesian population. Results: Logistic regression findings showed that knowledge about herbal medicines was independently and positively associated with herbal medicine use to a greater extent than herbal medicine non-use (adjusted odds ratio; AOR = 1.20; 95% confidence interval; CI = 1.16 to 1.24). The participants who used herbal medicines had a greater magical health belief score than herbal medicine non-users, with AOR = 1.03 and 95% CI = 1.00 to 1.06. Moreover, holistic health beliefs and pro-CAM attitudes were also found to be independently associated with herbal medicine use. Conclusion: These findings alert nurses to assess the roles of magical health beliefs, holistic health belief, knowledge, and attitudes toward herbal medicine use.",
"keywords": [
"Herbal medicine",
"holistic health belief",
"Indonesia",
"knowledge",
"magical health belief",
"pro-CAM attitude"
],
"content": "Introduction\n\nThe COVID-19 pandemic has caused 5,331,019 deaths worldwide (World Health Organization, 2021) and created widespread anguish, anxiety, and depression among the population (Bueno-Notivol et al., 2021; Nikčević et al., 2021; Yıldırım et al., 2021). This disease has spread throughout Indonesia too, with around 4,260,148 individuals afflicted and 143,986 deaths reported (World Health Organization, 2021). Along with a sense of uncertainty and widespread false information (Apuke & Omar, 2021; Chou et al., 2021), this disease has prompted the population to seek and adopt remedies that promise to be effective at preventing contagion or death and at increasing immunity (Gonzalez et al., 2021; Moscatelli et al., 2021), eventually leading to the use of herbal medicines (Alyami et al., 2020; Shahrajabian et al., 2020).\n\nConsumption of herbal medicines containing specific active substances with antibacterial or antiviral, anti-inflammatory, and immunomodulatory properties is a recent trend in the community. These herbal medicines are believed to have the ability to modify the immune response and thus be effective at preventing or treating COVID-19 (Lee et al., 2019; Nugraha et al., 2020). Herbal medicines remain valuable sources for development of new medication, and their low toxicity makes them attractive prophylactic candidates for treating COVID-19 (Huang et al., 2020). In Indonesia, herbal medicine consumption for the treatment and prevention of illnesses has grown and become more widespread (Rahayu et al., 2020). A national survey revealed an increase of 30.4% to 43.3% in household use of traditional healthcare products from 2013 to 2018 (Kementerian Kesehatan Republik Indonesia, 2018). A few studies have assessed the prevalence and factors related to herbal medicine use in Indonesia (Pengpid & Peltzer, 2018; Rahayu et al., 2020). However, it is arduous to provide precise data on the use of herbal medicines because most recent studies targeted specific groups among the population in specific geographic distributions, thus their results cannot be generalized. Moreover, these reports did not specifically examine herbal medicine use for preventing COVID-19. In light of the current global health crisis, investigating the determinants of the use of herbal medicines is viable for prevention among the community during the COVID-19 pandemic.\n\nKnowledge is a basic component of health practice modifications that measure public understanding of prevention efforts, particularly during a pandemic (Abdulkareem et al., 2020; Muslih et al., 2021). Knowledge may be useful for discovering elements that contribute to the population developing a good attitude toward COVID-19 prevention and implementing healthy practices (Alyami et al., 2020). In the Ethiopian context, the population was familiar with the practice of using herbal medicines but faced challenges related to limited knowledge of herbal medicines (Aina et al., 2020). In Indonesia, with the spike in COVID-19 cases that is currently occurring in 2020, people are turning to herbal medicines to increase their immunity. However, the public health department warns that unproven treatment methods can lead to a false sense of security (Hartanti et al., 2020).\n\nHerbal medicine use itself is most commonly driven by two reported reasons. First, herbal medicines are affordable (Rahayu et al., 2020; Sumarni et al., 2021). Second, uniquely in Indonesia, they resonate more closely with patients’ beliefs, relieve concerns about the adverse effects of pharmaceutical medicines, and satisfy the desire for individualized health care (Rahayu et al., 2020; Sumarni et al., 2021). Magical and holistic health beliefs are related to herbal medicine use (Aarnio & Lindeman, 2004; Bryden et al., 2018). The former increases concurrently with intuitive thinking, represented by affective information processing and the guidance of approach-avoidance behavior (Aarnio & Lindeman, 2004). They are related to approach-avoidance behavior rather than making true-false distinctions about food and nutrition (Aarnio & Lindeman, 2004; Bryden et al., 2018). An instance of a magical health belief is the notion that consuming red beverages increases blood hemoglobin levels (Bryden et al., 2018). In contrast, the latter adheres to the philosophy that the entire individual must be regarded in maintaining health, including the mind, body, and spirit (Bryden et al., 2018). Unfortunately, both magical and holistic health beliefs have yet to be employed in an attempt to explain use of herbal medicines, particularly during the COVID-19 pandemic in Indonesia. Thus, a study of magical and holistic health beliefs in Indonesia should immediately be conducted.\n\nImportantly, as existing literature suggests, attitudes toward complementary alternative medicine (CAM) use have been extensively studied in an attempt to comprehend preferences (Berna et al., 2019; Islahudin et al., 2017). According to a previous study, around 41.1% of respondents with chronic illnesses preferred herbal medicines until these herbal medicines turned ineffective (Berna et al., 2019), which might represent widespread positive pro-CAM attitude. However, additional research is necessary to elucidate the underlying factors that contribute to stronger pro-CAM attitude. Considering that Indonesia is currently suffering from COVID-19 transmission and remains in a continuing battle against this pandemic (Muslih et al., 2021; Rias et al., 2020), the association between knowledge related to herbal medicine use and pro-CAM attitude toward COVID-19 prevention needs to be assessed.\n\nIt is essential that accurate data be accessible to represent community opinions regarding the use of herbal medicine for health care. Therefore, the relationships between magical health beliefs, holistic health beliefs, knowledge, and attitudes toward CAMs on herbal medicine use during the COVID-19 pandemic should be ascertained. It is critical that health professionals, including the nursing community, be aware of the determinants of herbal medicine use, so that this information can be used in planning healthcare services. Therefore, the current study was conducted to investigate the prevalence of herbal medicine use and its determinant factors, such as magical health beliefs, holistic health beliefs, knowledge about herbal medicines, and pro-CAM attitude, in the case of the Indonesian population.\n\n\nMethods\n\nPrimary data was collected as part of this cross-sectional study, with a community-based survey of a representative sample from the western, middle, and eastern regions of Indonesia (Pusat Statistics Indonesia, 2019). Data collection was carried out from July 14 to September 12, 2021. As suggested by previous studies (Muslih et al., 2021; Rias et al., 2020), a web-based recruitment strategy was employed to conduct convenience sampling. An online Google Forms survey was carried out, with a link distributed via the largest and most accessible social media platforms among Indonesians, WhatsApp, Facebook, Instagram, Telegram, and Twitter. This survey relied on the researchers' technological and personal networks. Social media influencers and community leaders also participated in and contributed to the survey (Muslih et al., 2021; Rias et al., 2020). The inclusion criteria used were Indonesian nationals who were aged ≥ 17 to 65 years, able to understand the Indonesian language, in possession of a social media account or internet access, and in agreement to participate in the research as shown by an informed consent form. Meanwhile, the exclusion criteria were those who were suspected of contracting COVID-19, self-isolation, and suffering from a chronic disease as determined by (Kementerian Kesehatan Republik Indonesia, 2020). The total sample size was 1,621.\n\nAll questionnaires, including those on socio-demographic characteristics, knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and complementary and alternative medicine attitude, were translated from English into Indonesian and validated by five experts to ensure the content validation, acceptability, and readability of the questions. Some modifications were made as per the feedback received to enable understanding of the questions. Two professionals from the nursing community independently translated the knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and complementary and alternative medicine attitude from English to Bahasa Indonesia. These translations were then integrated into one and back-translated into English by another English/Bahasa translator professional and a native speaker from Indonesia without prior knowledge of the instrument. The content validity index of items was to confirm the integrity of a construct (Wild et al., 2005). The draft questionnaires were sent to a panel of five experts from the Universitas Andalas, Universitas Muhammadiyah Yogyakarta, and Universitas Muhammadiyah Surabaya, who have worked in fields relating to the subject of this study for over five years, including one specialist in infectious diseases, two experts on nursing community and two nurses with expertise in the complementary therapy field. Our survey was comprised of four major sections.\n\nIn the first section of the online survey, the respondents were given an explanation of the purpose of the survey and were asked for their consent to participate in the survey voluntarily. They were also given an explanation of their right to discontinue participation at any time and the survey’s privacy policy and details that their responses may be published. To proceed to the online survey, they were required to provide informed consent by checking the checkbox “agree” to confirm that they have read all information, including that the survey was set to be completed in a time period of 20 minutes. The second section comprised 11 questions related to socio-demographic characteristics. The third section consisted of one question that assessed the respondents’ herbal medicine use during the COVID-19 pandemic. Finally, the fourth section contained 27 questions across four questionnaires, including questionnaires on knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude. Upon completing the survey, the respondents would receive a thank you note, in which they were encouraged to persuade new Indonesian people from their contact list to take part in the survey. All responses were confidential and provided with informed consent. In ethical terms, this research was approved by the Survey and Behavioral Research Ethics Committee of Institut Ilmu Kesehatan Strada Indonesia (Reference number; 2271/KEPK/II/2021).\n\nThe demographic data collected included age, gender, religion, marital status, education, income, occupation, geographical region, urbanicity, insurance, and perceived risk of COVID-19 infection. Back-translation method was applied to the measuring instruments, i.e., questionnaires on knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitudes, to translate the items from English into the Indonesian language and to ensure linguistic and conceptual equivalence in an item discriminant analysis with a p value of < 0.001. The questionnaires on knowledge of herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude, in addition to the questionnaire on herbal medicine use, used the scales described below (Rias, 2022b).\n\nThe respondents’ knowledge about herbal medicines was assessed using the self-perceived knowledge questionnaire developed by Welz et al., (2019), containing 6 questions. This instrument is a 5-point Likert scale, ranging from 1 (very poor) to 5 (very good). A higher score indicates better self-perceived knowledge (Welz et al., 2019). The Cronbach’s (alpha) α of the instrument was 0.86, and, according to five nursing experts, the content validity value was 0.90 in our study.\n\nMagical health beliefs were assessed with 10 items (Lindeman et al., 2000). A higher score indicates a higher level of magical health beliefs. The response options were “strongly disagree”, “somewhat disagree”, “somewhat agree”, and “strongly agree”, respectively scored 1, 2, 3, and 4. The Indonesian version of the instrument had a Cronbach’s α of 0.87. According to five nursing experts, the content validity value was 0.90 in current study.\n\nHolistic health beliefs were assessed using the holistic health beliefs model developed by Hyland et al., (2003). A higher score indicates a higher level of holistic health beliefs (Hyland et al., 2003). The response options were “strongly disagree”, “somewhat disagree”, “somewhat agree”, and “strongly agree”, respectively scored 1, 2, 3, and 4. In our study, the Indonesian version of the instrument had a Cronbach’s α of 0.09. According to five nursing experts, a content validity value of 0.95.\n\nAssessment of pro-CAM attitude was concerned with the attitude of the participants toward the efficacy and desirability of CAMs (Hyland et al., 2003). The pro-CAM attitude scale included six questions: items 1, 2, 3, and 5 indicated negative questions, and items 4 and 6 indicated positive questions. In this study, the responses to the negative questions were reversed into positive questions. The four possible positive answers were “strongly disagree”, “somewhat disagree”, “somewhat agree”, and “strongly agree”, respectively scored 1, 2, 3, and 4. As a result, the total pro-CAM attitude score ranged from 6 to 24, with higher scores indicating a more pro-CAM attitude. The Indonesian version of the instrument had a Cronbach’s α of 0.78, and, according to five nursing experts, it had a content validity value of 0.95 in present study.\n\nThis was determined by questioning individual respondents about their personal use of herbal treatments to prevent or cure COVID-19-like symptoms. Herbal medicine use was identified using the question: “During the COVID-19 pandemic, have you used any herbal medicine to prevent or cure COVID-19-like symptoms such as sore throat, flu, cough, fever, headache, or fatigue?” (Rias, 2022b).\n\nDescriptive statistics were used to assess sociodemographic characteristics, knowledge of herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude between groups. These variables were evaluated using χ2 statistics or Fisher’s exact test, and the results are presented as percentages (%) and frequencies (n). Continuous variables were evaluated using an independent t-test, and the results are presented as means and standard deviations (SD). The percentage of responses was established by counting the total number of participants per response for the total question. Multicollinearity was determined by calculating the variance inflation factor (VIF) (< 10) (García et al., 2015). This investigation yielded a maximum VIF of 2.56, indicating that multicollinearity effects were minimal. Adjusted beta-coefficients (AOR) with 95% confidence intervals (CIs) were acquired by performing a multiple logistic regression for herbal medicine use related to exposures of interest (knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitudes) after adjusting for potential confounding variables, including personal profile with respect to age, gender, religion, marital status, education, income, occupation, geographical region, urbanicity, insurance, and perceived risk to be infected with COVID-19. SPSS, RRID:SCR_002865 version 25.0 (Chicago, IL) was used for all statistical analyses, and a p-value < 0.05 was considered statistically significant.\n\n\nResults\n\nThe overall sociodemographic characteristics of the participants are summarized in Table 1 (Rias, 2022a). The sample included 1,621 participants, of whom 1,005 (62%) used herbal medicines and 616 (32%) did not use herbal medicines during the COVID-19 pandemic. χ2 values showed that significant differences (p < 0.05) were noted in age, religion, marital status, education, income, occupation, geographical region, insurance, and perceived risk to be infected with COVID-19 between herbal medicine users and herbal medicine non-users. However, no significant differences in gender or urbanicity were revealed between the groups.\n\n* Chi-Square test, with the χ2-value in the bracket behind p-value. p<0.05 indicates statistical significance. IDR, Indonesian Rupiah; HM, Herbal Medicine.\n\nWe reveal the comparisons of knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude between herbal medicine users and herbal medicine non-users during the COVID-19 pandemic in Table 2. We observed that all items of self-perceived knowledge about herbal medicines differed significantly between groups. However, item-4 in holistic health belief and item-5 in pro-CAM attitude did not show any significant differences between groups. Interestingly, all items on the magical health beliefs questionnaire were significantly higher among herbal medicine users (p < 0.01). The mean scores of knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude were significantly higher among the herbal medicine users’ group (p < 0.01).\n\n* independent sample t-test. A p value of <0.05 indicates statistical significance. CAM; Complementary and alternative medicine. Items CAM 1, 2, 3 and 5 was reverse score which indicated that a higher score on the CAM indicate more positive attitudes towards CAM.\n\nAdjusted multiple logistic regression analyses showed that knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude were significantly associated with herbal medicine use (see Table 3). Knowledge about herbal medicines was found to be independently and positively associated with herbal medicine use to a greater degree than with non-use (AOR = 1.20; 95% CI = 1.16 to 1.24) after adjustment for confounding factors. Participants who used herbal medicines had a greater magical health belief score than non-users (AOR = 1.03 and 95% CI = 1.00 to 1.06). Moreover, holistic health beliefs and a pro-CAM attitude were found to be independently associated with herbal medicine use to a greater degree than with herbal medicine non-use during the COVID-19 pandemic after adjustment for confounding factors, including gender, age, religion, marital status, education, income, occupation, geographical region, urbanicity, insurance, and perceived risk of being infected COVID-19.\n\n* A p value <0.05.\n\n** p value <0.001. CAM; Complementary and alternative medicine.\n\n\nDiscussion\n\nIn our study, we undertook a nationwide online survey of the Indonesian population to examine the prevalence of herbal medicine usage and to address its essential factors, including magical health beliefs, holistic health belief, knowledge about herbal medicines, and pro-CAM attitude, during the COVID-19 pandemic.\n\nOur first notable finding addresses the herbal medicine use prevalence rate in the case of the Indonesian population during the COVID-19, which was found to be impressively high at 62% compared to those reported from other countries, including 49% in Vietnam (Nguyen et al., 2021), 30.8% in Turkey (Karataş et al., 2021), 22.1% in Saudi Arabia (Alyami et al., 2020), and 19.3% in Hong Kong (Lam et al., 2021). Why herbal medicine use prevalence estimate was higher in Indonesia than in other countries and why it was increasing were complex topics to discuss. However, one might conclude that cultural and societal contexts as well as individual attitudes and experiences might have a contribution to this high incidence of herbal medicine use (Karataş et al., 2021; Welz et al., 2019). This could also be a result of the unique characteristics of the Indonesian healthcare system (e.g., health insurance and social security policies), traditional beliefs, and powerful herbal medicine advertising efforts (Pengpid & Peltzer, 2018; Rahayu et al., 2020). Throughout the COVID-19 pandemic, considerable emphasis and attention have been given to herbal medicines, with a rising body of evidence indicating that such approaches and preventive measures have been effective at fighting emerging infectious diseases.\n\nAnother finding further of this study demonstrates that knowledge about herbal medicines was positively correlated with herbal medicine use (AOR = 1.20; 95% CI = 1.16 to 1.24). Our finding is consistent with a study from Nigeria, where individuals who had experience using herbal medicines gained high scores of knowledge about herbal medicines (Aina et al., 2020). It was assumed that these herbal medicines could possibly boost immunity and defend the body against COVID-19 infection (Nugraha et al., 2020; Panyod et al., 2020). Herbal medicines were preferable to other complementary and alternative medical treatments due to their abundance and convenience of use (Chaachouay et al., 2021; Nguyen et al., 2021; Panyod et al., 2020). Additionally, these studies suggest that Indonesian people are more receptive and trusting of herbal therapies. Another factor in the use of herbal medications has been consumers' lack of knowledge about possible toxicity. It was indicated that most participants in our survey had a high level of knowledge of herbal therapies with total mean ± SD score was 20.63 ± 3.67. Since the first case of COVID-19 was found in Indonesia in March 2020, information about herbal remedies for COVID-19 protection has been extensively reported; as a result, Indonesians had adequate knowledge (Badan Pengawas Obat dan Makanan Republik Indonesia, 2020; Nugraha et al., 2020). In addition, with the historical and cultural herbal medicine use in Indonesia, it was presumed that a proper understanding of herbal medicines already exists (Badan Pengawas Obat dan Makanan Republik Indonesia, 2020; Nugraha et al., 2020). However, regulations and investigations of visual identification and differentiation of raw medicinal plants as well as safe dosages, safe uses, and side effects as aspects of knowledge of herbal medicines have become increasingly important (Hartanti et al., 2020). Therefore, strengthening knowledge about herbal medicines is critical for improving herbal medicine use in Indonesia during the COVID-19 pandemic.\n\nOur research findings revealed that health beliefs, including holistic and magical health beliefs, were positively associated with the use of herbal medicine related to COVID-19 among the general population in Indonesia. In line with this, a recent research work, in Saudi Arabia, found that the majority of participants consumed herbal medicines during the pandemic era to enhance their immunity and minimize their risk of contracting COVID-19 infection (Alyami et al., 2020). It was also reported in another piece of previous research that there was a common belief that herbal medicines are both safer and of higher quality than prescription medications (Barry, 2018; El Khoury et al., 2016). In order to corroborate previously determined reasons, such as improved health and well-being with a reduction in unpleasant side effects associated with herbal medicines as well as improved holistic health beliefs, more research is required (Rashrash et al., 2017).\n\nMagical health beliefs may aid in determining who is prone to hold such ideas and how magical thinking influences people's health behaviors and willingness or ability to deal with more abstract and intricate scientific knowledge regarding health (Lindeman et al., 2000). This study also suggests, there is a lack of evidence to connect health-related beliefs, such as magical or holistic health belief, to herbal medicine use. However, it is still reasonable to assume that these alternative medical beliefs may contribute to herbal medicine use. Lindeman and colleagues suggested that magical health beliefs, lacking empirical, logical, or scientific basis though they are, have an intuitive appeal due to assumptions about contagion, naturalness, and fundamental knowledge or ontological confusions (Aarnio & Lindeman, 2004). Unlike magical health beliefs, holistic health beliefs are not demonstrably false or representative of cognitive biases or errors. For instance, the holistic health belief that it is critical to balance work and recreation to maintain good health is reasonable (Nijp et al., 2012). Many CAMs promote magical health beliefs and provide non-evidence-based food and health advice that follow magical truths (Bryden et al., 2018). A previous study has showed that magical and holistic health beliefs are associated with CAM attitudes (Bryden et al., 2018). Thus, the influence of generalized alternative health beliefs, such as magical food and health beliefs, and holistic health belief on herbal medicine use should be examined in Indonesia or another country with a high prevalence of herbal medicine use.\n\nUnsurprisingly, Indonesian participants who scored high on pro-CAM attitude toward herbal medicine use were more likely to use herbal medicines (AOR = 1.24; CI 95% = 1.18–1.31). Similarly, a previous study in Vietnam presented a significant association between the attitudes toward herbal medicines and herbal medicine use during the COVID-19 pandemic (Nguyen et al., 2021). Attitude has been identified as the most important predictor of intention to use traditional Chinese medicines, including herbal medicines had significant correlation with attitude followed by previous actions (unstandardized path coefficient (β) = 0.229, p < 0.001), subjective norms (β = 0.190, p > 0.001), and perceived behavioral control (β = 0.190, p > 0.001) (Xia et al., 2021). Prior research’s findings have significant implications for health policymakers interested in promoting the use of traditional medicines, which have helped to combat COVID-19 (Xia et al., 2021). People's positive attitudes toward herbal remedies were major factors in growing herbal medicine use (Al Akeel et al., 2018). In a separate study in Finland, individuals who used or showed favorable attitudes toward CAMs were found less likely to adhere to traditional therapies during the COVID-19 pandemic, but they demonstrated a high level of unwillingness to accept COVID-19 vaccine (Soveri et al., 2021). These findings emphasized the importance of developing trust-building communication strategies for the pros and cons of herbal medicine regulations (Čavojová et al., 2022; Soveri et al., 2021). More generally, based on our findings, we suggest that increasing the positive value of pro-CAM attitude is a potentially effective strategy for improving herbal medicine use by developing proactive policies on safety, quality, and efficacy, as well as rational use.\n\nThere were several limitations to this investigation. First, the findings were built on self-reported data; consequently, respondents might have over- or under-reported their herbal medicine use. Second, as data collection was undertaken online, university-educated and younger individuals may have been overrepresented among the respondents. Another limitation is the lack of participants from the central and eastern regions and persons who did not have insurance, all of whom may be recruited particularly in future studies, as this could affect the generalizability of the findings. However, we used multiple logistic regression analyses to account for a large number of potential confounding variables, thereby minimizing the influence of an unequal distribution.\n\nThe findings of this study provide nurses with information that will help them recognize herbal medicines as one of the most popular complementary and alternative medicines (CAMs) used by the general population to prevent the COVID-19 virus and to comprehend the cultural application of herbal medicines in the future. Additionally, determinant factors such as magical and holistic health beliefs, knowledge, and a pro-CAM attitude toward herbal medicine use may be suggested as primary factors for health care professionals such as nurses or community practice nurses to explore alternative therapies in order to boost immunity and prevent infection of COVID-19. This study contributes to the understanding of the mechanisms of individual herbal medicine use. To begin with, the results indicated that respondents' with a pro-CAM attitude toward herbal medicine use had a considerable impact on their use. Additionally, both magical and holistic health beliefs were a major influence on herbal medicine use. Furthermore, knowledge about herbal medicines was associated with an increased likelihood of using herbal medicines. The present study's key findings have substantial practical implications for healthcare policymakers and professionals, particularly those tasked with developing programs to encourage and regulate herbal medicine use.\n\n\nConclusion\n\nThe present research revealed that knowledge about herbal medicines, magical health beliefs, holistic health beliefs, and pro-CAM attitude were significantly associated with herbal medicine use during the COVID-19 pandemic. Specifically, we concluded that magical and holistic health beliefs were significant predictors of herbal medicine use. Knowledge about herbal medicines, including identified and potential side effects, interaction effect, safe dose, safe use, and raw materials, all played critical roles in predicting herbal medicine use. Finally, policymakers may use our findings to elevate knowledge and attitude as well as health beliefs to encourage the use of herbal medicines in a regulated manner to benefit public health.\n\n\nData availability\n\nFigshare: The Effects of Beliefs, Knowledge, and Attitude on Herbal Medicine Use during the COVID-19 Pandemic, https://doi.org/10.6084/m9.figshare.19559662.v1 (Rias, 2022a).\n\nThis project contains the following underlying data.\n\n- Data_Herbal Use.xlsx\n\nFigshare: Copies of all questionnaires used.pdf, https://doi.org/10.6084/m9.figshare.19618866.v1 (Rias, 2022b).\n\nThis project contains the following extended data.\n\n- Copies of all questionnaires used.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthor contributions\n\nH. Kristianto contributed to Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Visualization, Writing – Original Draft Preparation.\n\nB.A. Pramesona contributed to Conceptualization, Investigation, Methodology, Visualization, Writing – Original Draft Preparation\n\nY.S. Rosyad contributed to Conceptualization, Data Curation, Investigation, Methodology, Writing – Original Draft Preparation\n\nL. Andriani contributed to Conceptualization, Data Curation, Investigation, Methodology, Writing – Original Draft Preparation\n\nT.A.R.K.Putri contributed to Conceptualization, Data Curation, Investigation, Methodology, Writing – Original Draft Preparation\n\nY.A. Rias contributed to Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing",
"appendix": "Acknowledgments\n\nWe would like to thank the Ethics Committee of Institut Ilmu Kesehatan Strada Indonesia, the study participants, and the data collection team members from Institut Ilmu Kesehatan Bahkti Wiyata Kediri and Universitas Brawijaya. We would also like to acknowledge the Universitas Brawijaya for payment of the APC.\n\n\nReferences\n\nAarnio K, Lindeman M: Magical food and health beliefs: a portrait of believers and functions of the beliefs. Appetite. 2004; 43(1): 65–74. PubMed Abstract | Publisher Full Text\n\nAbdulkareem SA, Augustijn E-W, Filatova T, et al.: Risk perception and behavioral change during epidemics: Comparing models of individual and collective learning. PLoS One. 2020; 15(1): e0226483. PubMed Abstract | Publisher Full Text\n\nAina O, Gautam L, Simkhada P, et al.: Prevalence, determinants and knowledge about herbal medicine and non-hospital utilisation in southwest Nigeria: a cross-sectional study. BMJ Open. 2020; 10(9): e040769. PubMed Abstract | Publisher Full Text\n\nAl Akeel MM, Al Ghamdi WM, Al Habib S, et al.: Herbal medicines: Saudi population knowledge, attitude, and practice at a glance. Journal of Family Medicine and Primary Care. 2018; 7(5): 865–875. PubMed Abstract | Publisher Full Text\n\nAlyami HS, Orabi MAA, Aldhabbah FM, et al.: Knowledge about COVID-19 and beliefs about and use of herbal products during the COVID-19 pandemic: A cross-sectional study in Saudi Arabia. Saudi Pharm. J. 2020; 28(11): 1326–1332. PubMed Abstract | Publisher Full Text\n\nApuke OD, Omar B: Fake news and COVID-19: modelling the predictors of fake news sharing among social media users. Telematics Inform. 2021; 56: 101475. PubMed Abstract | Publisher Full Text\n\nBadan Pengawas Obat dan Makanan Republik Indonesia: Pedoman penggunaan herbal dan suplemen kesehatan dalam menghadapi COVID-19 di Indonesia. Badan Pengawas Obat dan Makanan RI. 2020. Reference Source\n\nBarry AR: Patients’ perceptions and use of natural health products. Canadian Pharmacists Journal/Revue Des Pharmaciens Du Canada. 2018; 151(4): 254–262. PubMed Abstract | Publisher Full Text\n\nBerna F, Göritz AS, Mengin A, et al.: Alternative or complementary attitudes toward alternative and complementary medicines. BMC Complement. Altern. Med. 2019; 19(1): 12–83. PubMed Abstract | Publisher Full Text\n\nBryden GM, Browne M, Rockloff M, et al.: Anti-vaccination and pro-CAM attitudes both reflect magical beliefs about health. Vaccine. 2018; 36(9): 1227–1234. PubMed Abstract | Publisher Full Text\n\nBueno-Notivol J, Gracia-García P, Olaya B, et al.: Prevalence of depression during the COVID-19 outbreak: A meta-analysis of community-based studies. Int. J. Clin. Health Psychol. 2021; 21(1): 100196. PubMed Abstract | Publisher Full Text\n\nČavojová V, Šrol J, Ballová Mikušková E: How scientific reasoning correlates with health-related beliefs and behaviors during the COVID-19 pandemic?. J. Health Psychol. 2022; 27(3): 534–547. PubMed Abstract | Publisher Full Text\n\nChaachouay N, Douira A, Zidane L: COVID-19, prevention and treatment with herbal medicine in the herbal markets of Salé Prefecture, North-Western Morocco. Eur. J. Integr. Med. 2021; 42: 101285. PubMed Abstract | Publisher Full Text\n\nChou W-YS, Gaysynsky A, Vanderpool RC: The COVID-19 Misinfodemic: moving beyond fact-checking. Health Educ. Behav. 2021; 48(1): 9–13. PubMed Abstract | Publisher Full Text\n\nEl Khoury G, Ramadan W, Zeeni N: Herbal products and dietary supplements: a cross-sectional survey of use, attitudes, and knowledge among the Lebanese population. J. Community Health. 2016; 41(3): 566–573. PubMed Abstract | Publisher Full Text\n\nGarcía CB, García J, López Martín MM, et al.: Collinearity: revisiting the variance inflation factor in ridge regression. J. Appl. Stat. 2015; 42(3): 648–661. Publisher Full Text\n\nGonzalez KF, Bull MT, Muñoz-Herrera S, et al.: Determinant Factors in Personal Decision-Making to Adopt COVID-19 Prevention Measures in Chile. Int. J. Environ. Res. Public Health. 2021; 18(15): 8131. PubMed Abstract | Publisher Full Text\n\nHartanti D, Dhiani BA, Charisma SL, et al.: The potential roles of jamu for COVID-19: a learn from the traditional Chinese medicine. Pharm. Sci. Res. 2020; 7(4): 12–22. Publisher Full Text\n\nHuang J, Tao G, Liu J, et al.: Current prevention of COVID-19: natural products and herbal medicine. Front. Pharmacol. 2020; 11: 1–18. PubMed Abstract | Publisher Full Text\n\nHyland ME, Lewith GT, Westoby C: Developing a measure of attitudes: the holistic complementary and alternative medicine questionnaire. Complement. Ther. Med. 2003; 11(1): 33–38. PubMed Abstract | Publisher Full Text\n\nIslahudin F, Shahdan IA, Mohamad-Samuri S: Association between belief and attitude toward preference of complementary alternative medicine use. Patient Prefer. Adherence. 2017; 11: 913–918. PubMed Abstract | Publisher Full Text\n\nKarataş Y, Khan Z, Bilen Ç, et al.: Traditional and Complementary Medicine use and beliefs during COVID-19 outbreak: A cross-sectional survey among the general population in Turkey. Adv. Integr. Med. 2021; 8(4): 261–266. PubMed Abstract | Publisher Full Text\n\nKementerian Kesehatan Republik Indonesia: 2018. Hasil utama RISKESDAS 2018. Jakarta Badan Penelitan dan Pengembangan Kesehatan, Kementrian Kesehatan Republik Indonesia.\n\nKementerian Kesehatan Republik Indonesia: Pedoman Pencegahan dan Pengendalian Penyakit Corona Virus (COVID-19). Direktorat Jenderal Pencegahan dan Pengendalian Penyakit (P2P), Kementrian Kesehatan Republik Indonesia. 2020.\n\nLam CS, Koon HK, Chung VC-H, et al.: A public survey of traditional, complementary and integrative medicine use during the COVID-19 outbreak in Hong Kong. PLoS One. 2021; 16(7): e0253890. PubMed Abstract | Publisher Full Text\n\nLee W-Y, Lee C-Y, Kim Y-S, et al.: The methodological trends of traditional herbal medicine employing network pharmacology. Biomolecules. 2019; 9(8): 362–377. PubMed Abstract | Publisher Full Text\n\nLindeman M, Keskivaara P, Roschier M: Assessment of magical beliefs about food and health. J. Health Psychol. 2000; 5(2): 195–209. PubMed Abstract | Publisher Full Text\n\nMoscatelli F, Sessa F, Valenzano A, et al.: COVID-19: Role of nutrition and supplementation. Nutrients. 2021; 13(3): 976–982. PubMed Abstract | Publisher Full Text\n\nMuslih M, Susanti HD, Rias YA, et al.: Knowledge, attitude, and practice of indonesian residents toward covid-19: A cross-sectional survey. Int. J. Environ. Res. Public Health. 2021; 18(9): 4473–4489. PubMed Abstract | Publisher Full Text\n\nNguyen PH, De Tran V, Pham DT, et al.: Use of and attitudes towards herbal medicine during the COVID-19 pandemic: A cross-sectional study in Vietnam. Eur. J. Integr. Med. 2021; 44: 101328–101336. Publisher Full Text\n\nNijp HH, Beckers DGJ, Geurts SAE, et al.: Systematic review on the association between employee worktime control and work-non-work balance, health and well-being, and job-related outcomes. Scand. J. Work Environ. Health. 2012; 38: 299–313. PubMed Abstract | Publisher Full Text\n\nNikčević AV, Marino C, Kolubinski DC, et al.: Modelling the contribution of the Big Five personality traits, health anxiety, and COVID-19 psychological distress to generalised anxiety and depressive symptoms during the COVID-19 pandemic. J. Affect. Disord. 2021; 279: 578–584. PubMed Abstract | Publisher Full Text\n\nNugraha RV, Ridwansyah H, Ghozali M, et al.: Traditional herbal medicine candidates as complementary treatments for COVID-19: a review of their mechanisms, pros and cons. Evid. Based Complement. Alternat. Med. 2020; 2020: 1–12. PubMed Abstract | Publisher Full Text\n\nPanyod S, Ho C-T, Sheen L-Y: Dietary therapy and herbal medicine for COVID-19 prevention: A review and perspective. J. Tradit. Complement. Med. 2020; 10(4): 420–427. PubMed Abstract | Publisher Full Text\n\nPengpid S, Peltzer K: Utilization of traditional and complementary medicine in Indonesia: results of a national survey in 2014–15. Complement. Ther. Clin. Pract. 2018; 33: 156–163. PubMed Abstract | Publisher Full Text\n\nPusat Statistics Indonesia: Statistical yearbook of Indonesia 2020. Indonesia: Badan Pusat Statistics; 2019.\n\nRahayu YYS, Araki T, Rosleine D: Factors affecting the use of herbal medicines in the universal health coverage system in Indonesia. J. Ethnopharmacol. 2020; 260: 112974–112984. PubMed Abstract | Publisher Full Text\n\nRashrash M, Schommer JC, Brown LM: Prevalence and predictors of herbal medicine use among adults in the United States. Journal of Patient Experience. 2017; 4(3): 108–113. PubMed Abstract | Publisher Full Text\n\nRias YA, Rosyad YS, Chipojola R, et al.: Effects of spirituality, knowledge, attitudes, and practices toward anxiety regarding COVID-19 among the general population in Indonesia: a cross-sectional study. J. Clin. Med. 2020; 9(12): 3798–3806. PubMed Abstract | Publisher Full Text\n\nRias YA: Data_Herbal Use.xlsx. figshare. Dataset.2022a. Publisher Full Text\n\nRias YA: Copies of all questionnaires used.pdf. figshare.2022b. Online resource. Publisher Full Text\n\nShahrajabian MH, Sun W, Cheng Q: Traditional herbal medicine for the prevention and treatment of cold and flu in the autumn of 2020, overlapped with COVID-19. Nat. Prod. Commun. 2020; 15(8): 1934578X2095143–1934578X2095110. Publisher Full Text\n\nSoveri A, Karlsson LC, Antfolk J, et al.: Unwillingness to engage in behaviors that protect against COVID-19: the role of conspiracy beliefs, trust, and endorsement of complementary and alternative medicine. BMC Public Health. 2021; 21(1): 684. PubMed Abstract | Publisher Full Text\n\nSumarni W, Sudarmin S, Sumarti SS, et al.: Indigenous knowledge of Indonesian traditional medicines in science teaching and learning using a science–technology–engineering–mathematics (STEM) approach. Cult. Stud. Sci. Educ. 2021: 1–44. Publisher Full Text\n\nWelz AN, Emberger-Klein A, Menrad K: The importance of herbal medicine use in the German health-care system: prevalence, usage pattern, and influencing factors. BMC Health Serv. Res. 2019; 19(1): 911–952. PubMed Abstract | Publisher Full Text\n\nWild D, Grove A, Martin M, et al.: Principles of good practice for the translation and cultural adaptation process for patient-reported outcomes (PRO) measures: Report of the ISPOR task force for translation and cultural adaptation. Value Health. 2005; 8: 94–104. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: WHO Coronavirus (COVID-19) Dashboard. 2021. Retrieved from Reference Source\n\nXia Y, Chang J, Miao H, et al.: Impact of the COVID-19 pandemic on intention to use traditional Chinese medicine: A cross-sectional study based on the theory of planned behavior. J. Integr. Med. 2021; 19(3): 219–225. PubMed Abstract | Publisher Full Text\n\nYıldırım M, Akgül Ö, Geçer E: The effect of COVID-19 anxiety on general health: the role of COVID-19 coping. Int. J. Ment. Heal. Addict. 2021; 20: 1–12. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "142022",
"date": "12 Jul 2022",
"name": "lalu Muhammad Irham",
"expertise": [
"Reviewer Expertise Genomic medicine",
"Pharmacogenomic"
],
"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 summary:\nIn this manuscript, the authors have tried to interlink the effect of beliefs, knowledge, and attitude on herbal medicine use during the COVID-19 pandemic. The manuscript is well written; however, the authors need to explicitly elaborate on a few points\nComments & questions:\n\nIn the abstract part, the term “independently” has an ambiguous meaning. Please consider using more specific terms to avoid misinterpretation of meaning.\n\nThe conclusion of this study does not reflect the title e.g., the role of nurse health care in the herbal medicine used. In the title as well as in the abstract no explanation about the nurse's role but in the conclusion, the authors directly claim that findings alert nurses to assess the role of magical health, etc. please make sure about this.\n\nI don’t find explicitly the finding of attitude toward herbal medicine used in the abstract part, please clarify this.\n\nIn the introduction part. Please mention the full name of COVID-19 as the first mention of the abbreviation.\n\nPlease mention explicitly the accession date of the data of mortality such as the data of COVID-19 mortality “5.331.019”. as well as the data of mortality of Indonesian COVID-19 patients\n“The COVID-19 pandemic has caused 5,331,019 deaths worldwide (World Health Organization, 2021) and created widespread anguish, anxiety, and depression among the population (Bueno-Notivol et al., 2021; Nikcevic et al., 2021; Yıldırım et al., 2021). This disease has spread throughout Indonesia too, with around 4,260,148 individuals afflicted and 143,986 deaths reported (World Health Organization, 2021)”\n\nPlease cite this sentence “Consumption of herbal medicines containing specific active substances with antibacterial or antiviral, anti-inflammatory, and immunomodulatory properties is a recent trend in the community”.\n\n“These herbal medicines are believed to have the ability to modify the immune response and thus be effective at preventing or treating COVID-19 “(Lee et al., 2019; Nugraha et al., 2020). The author should carefully use terms of herbal medicine that can treat COVID-19. So far herbal medicine is just for prevention rather than treating the disease including COVID-19.\n\nI highly recommend to authors to use graphical with good visualization or graphical figure for elaborating the methodology then your readers will more easily understand the methodology that the authors used in the current study.\n\nThe respondents’ knowledge about herbal medicines was assessed using the self-perceived knowledge questionnaire developed by Welz et al., (2019), containing 6 questions.\nReviewer concern here, does the author have permission to use this questionnaire? If you have permission please mention it\n\nThe authors should explain in more detail what type of herbal medicine that authors mean in this study? So, far as I know herbal medicine in Indonesia has several types.\n\n“Another factor in the use of herbal medications has been consumers' lack of knowledge about possible toxicity “. Authors also should explain the negative impact of herbal medicine use. Authors can put this part in the discussion.\n\nFurthermore, knowledge about herbal medicines was associated with an increased likelihood of using herbal medicines.\nReviewer’s concern here about the knowledge? The positive or negative impact of knowledge about herbal medicine? This should be clearly elaborated.\n\nWhat is the role of nurse regarding the herbal medicine use?\n\nAuthors should also explain that the nurses should collaborate with other health care such as pharmacists, medical doctors, etc. to optimize the use of herbal medicine.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8562",
"date": "01 Aug 2022",
"name": "Yohanes Andy Rias",
"role": "Author Response",
"response": "[Version 1; peer review: 1] Response to Reviewer 1 Comments Dear Reviewer #1, Thank you for considering our manuscript and for the valuable suggestions, also the opportunity to resubmit a revised manuscript, which help us to improve the article. We carefully revised the manuscript in accordance with your comments. The revised sections of the manuscript are highlighted with yellow color. Our point-by-point responses to the comments are as follows. We very much hope the revised manuscript is accepted for publication in F1000. Thank you very much for your consideration. Comments & questions: Point 1. In the abstract part, the term “independently” has an ambiguous meaning. Please consider using more specific terms to avoid misinterpretation of meaning. Response 1: Thank you for your comments. We appreciated this reviewer’s comments. Let we clarify and revise this point. We used the term “Independently” When a variable is associated with an outcome after adjusting for multiple other potential prognostic factors (often after regression analysis), the association is independent. Point 2. The conclusion of this study does not reflect the title e.g., the role of nurse health care in the herbal medicine used. In the title as well as in the abstract no explanation about the nurse's role but in the conclusion, the authors directly claim that findings alert nurses to assess the role of magical health, etc. please make sure about this. Response 2: Thank you for your valuable comments. We have already revised the conclusion section that refers to your suggestion (Please see conclusion section in abstract). “The use of herbal medicine during the COVID-19 pandemic was a common practice among Indonesian people. The roles of magical health beliefs, holistic health beliefs, knowledge, and attitudes toward the use of herbal medicine are highlighted by these findings” Point 3. I don’t find explicitly the finding of attitude toward herbal medicine used in the abstract part, please clarify this. Response 3: Thank you for your comments. We appreciated this reviewer’s comments. Let we clarify this point. We already mention the finding of attitude toward herbal medicine used in the abstract section (Please see last sentences in the results section). “Moreover………pro-CAM attitudes were also found to be independently associated with herbal medicine use”. Point 4. In the introduction part. Please mention the full name of COVID-19 as the first mention of the abbreviation. Response 4: Thank you for your comments and suggestion. We add the full name of COVID-19 as the first mention of the abbreviation in the abstract and introduction section (Please see in the abstract line 2 and introduction line 1). Point 5. Please mention explicitly the accession date of the data of mortality such as the data of COVID-19 mortality “5.331.019”. as well as the data of mortality of Indonesian COVID-19 patients “The COVID-19 pandemic has caused 5,331,019 deaths worldwide (World Health Organization, 2021) and created widespread anguish, anxiety, and depression among the population (Bueno-Notivol et al., 2021; Nikcevic et al., 2021; Yıldırım et al., 2021). This disease has spread throughout Indonesia too, with around 4,260,148 individuals afflicted and 143,986 deaths reported (World Health Organization, 2021)” Response 5: Thank you for your comments and suggestion. In this revised manuscript, we add the accession date and new number based on the date of the data on mortality in the world and Indonesia. “The Coronavirus disease 2019 (COVID-19) pandemic has caused 4,621,205 deaths worldwide as of 12 September 2021”. “This disease has spread throughout Indonesia, too, on 12 September 2021, with around 4,167,511 individuals afflicted and 138,889 deaths reported.” Point 6. Please cite this sentence “Consumption of herbal medicines containing specific active substances with antibacterial or antiviral, anti-inflammatory, and immunomodulatory properties is a recent trend in the community”. Response 6: Thank you for your comments and suggestion. We add the references based on the reviewer’s suggestion. “Consumption of herbal medicines containing specific active substances with antibacterial or antiviral, anti-inflammatory, and immunomodulatory properties is a recent trend in the community ( Lee et al., 2019; Nugraha et al., 2020)” Point 7. “These herbal medicines are believed to have the ability to modify the immune response and thus be effective at preventing or treating COVID-19 “(Lee et al., 2019; Nugraha et al., 2020). The author should carefully use terms of herbal medicine that can treat COVID-19. So far herbal medicine is just for prevention rather than treating the disease including COVID-19. Response 7: Thank you for your comments and suggestion. In the revised manuscript, we deleted “treating” based on the reviewer’s suggestion to avoid debate information. Point 8. I highly recommend to authors to use graphical with good visualization or graphical figure for elaborating the methodology then your readers will more easily understand the methodology that the authors used in the current study. Response 8: Thank you for your comments and suggestion. We add the figure of methodology. Point 9. The respondents’ knowledge about herbal medicines was assessed using the self-perceived knowledge questionnaire developed by Welz et al., (2019), containing 6 questions. Reviewer concern here, does the author have permission to use this questionnaire? If you have permission please mention it Response 9: Thank you for your comments. We already permission to use knowledge about herbal medicines questionnaire. Moreover, the questionnaire already publish and added in supplementary information. Welz AN, Emberger-Klein A, Menrad K: The importance of herbal medicine use in the German health-care system: prevalence, usage pattern, and influencing factors. BMC Health Serv. Res. 2019;19(1):911–952. 31823758 10.1186/s12913-019-4739-0 Point 10. The authors should explain in more detail what type of herbal medicine that authors mean in this study? So, far as I know herbal medicine in Indonesia has several types. Response 10: Thank you for your comments. We add information the type of herbal medicine included herbs or herbal product in the herbal medicine use section based on the reviewer’s suggestion. Point 11. “Another factor in the use of herbal medications has been consumers' lack of knowledge about possible toxicity “. Authors also should explain the negative impact of herbal medicine use. Authors can put this part in the discussion. Response 11: Thank you for your suggestions. In this revised manuscript, we add the negative impact of herbal medicine use without depleting the effectiveness of herbal medicine in the discussion section based on the reviewer’s suggestion. “The negative impact of herbal medicine use was associated with lack of information regarding herb toxicity and drug-herb interactions. This is due to the fact that in such instances, the efficacy of such drugs is based solely on the therapeutic effects on the intended pathological condition, with very little information on side effects or toxicity.” Point 12. Furthermore, knowledge about herbal medicines was associated with an increased likelihood of using herbal medicines. Reviewer’s concern here about the knowledge? The positive or negative impact of knowledge about herbal medicine? This should be clearly elaborated. Response 12: Thank you for your suggestions. In this revised manuscript, we add the positive impact of herbal medicine use in the discussion section based on the reviewer’s suggestion. “The beneficial impact of herbal medicine knowledge can enhance the positive attitude toward COVID-19 prevention (Alyami et al., 2020), as well as the awareness of side and interaction effects (Welz et al., 2019). It was assumed that these herbal medicines could possibly boost immunity and defend the body against COVID-19 infection (Nugraha et al., 2020; Panyod et al., 2020)” Point 13. What is the role of nurse regarding the herbal medicine use? Response 13: Thank you for your suggestions. In this revised manuscript, we clarify the role of nurse regarding the herbal medicine use in the discussion section based on the reviewer’s suggestion. “The findings of this study provide nurses with information that will help them recognize herbal medicines as one of the most popular complementary and alternative medicines (CAMs) used by the general population to prevent the COVID-19 virus and to comprehend the cultural application of herbal medicines in the future.” “Additionally, determinant factors such as magical and holistic health beliefs, knowledge, and a pro-CAM attitude toward herbal medicine use may be suggested as primary factors for health care professionals such as nurses or community practice nurses collaborate with other health care such as pharmacists and medical doctors to explore alternative therapies in order to boost immunity and prevent infection of COVID-19.” Point 14. Authors should also explain that the nurses should collaborate with other health care such as pharmacists, medical doctors, etc. to optimize the use of herbal medicine. Response 14: Thank you for your suggestions. In this revised manuscript, we clarify add the new information related the nurses should collaborate with other health care in the discussion section based on the reviewer’s suggestion. “Additionally, determinant factors such as magical and holistic health beliefs, knowledge, and a pro-CAM attitude toward herbal medicine use may be suggested as primary factors for health care professionals such as nurses or community practice nurses collaborate with other health care such as pharmacists and medical doctors to explore alternative therapies in order to boost immunity and prevent infection of COVID-19.”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-483
|
https://f1000research.com/articles/11-429/v1
|
19 Apr 22
|
{
"type": "Research Article",
"title": "Determining staffing needs for improving primary health care service delivery in Kaduna State, Nigeria",
"authors": [
"Agbonkhese I. Oaiya",
"Oluwabambi Tinuoye",
"Layi Olatawura",
"Hadiza Balarabe",
"Hamza Abubakar",
"Oluwabambi Tinuoye",
"Layi Olatawura",
"Hadiza Balarabe",
"Hamza Abubakar"
],
"abstract": "Background: The equitable distribution of a skilled health workforce is critical to health service delivery, and Kaduna state has taken significant steps to revamp the primary health care system to ensure access to health care for its populace. However, some of these investments are yet to yield the desired outcomes due to workforce shortages and inequitable distribution of those available. Methods: A Workload Indicator for Staffing Need study was conducted at the primary health care level in Kaduna state. The study focused on estimating staffing requirements; Nurse/Midwife and Community Health Worker practitioners; Community Health Officer, Community Health Extension Worker and Junior Community Health Extension Worker, in all government prioritized primary health care facilities. Ten focal primary health care facilities in Kaduna North Local Government Area were included in the study. Results: Findings revealed a shortage of Nurses/Midwives and Community Health Workers across the study facilities. For the Nurse/Midwife staffing category, 9/10 PHCs have a Workload Indicator for Staffing Need ratio < 1; indicating that the number of staff in the Nurse/Midwife category is insufficient to cope with the workload. In two of the ten primary health care facilities, there is an excess in the number of CHWs available; a Workload Indicator for Staffing Need ratio > 1 was calculated. Conclusions: The Workload Indicator for Staffing Need study highlights the staffing needs in government prioritized primary health care facilities in Kaduna state. This evidence establishes the basis for the application of an evidence-based approach to determining staffing needs across the primary health care sector in the State, to guide workforce planning strategies and future investments in the health sector. The World Health Organisation Workload Indicator for Staffing Need tool is useful in estimating staffing needs required to cope with workload pressures, particularly in a resources-constrained environment like Kaduna State.",
"keywords": [
"Universal Health Coverage",
"Health Workforce",
"Human Resources for Health",
"Workload Indicators for Staffing Need",
"Nigeria",
"Service Delivery",
"Nurse",
"Midwife",
"Community Health Officer",
"Community Health Extension Worker",
"Junior Community Health Extension Worker."
],
"content": "Introduction\n\nThe equitable distribution of resources, specifically Human Resources for Health (HRH), to meet the needs of the populace is critical for achieving Universal Health Coverage (UHC). However, this critical health system component is plagued with challenges of availability, distribution, skills, and retention. These challenges are prominent in developing countries like Nigeria, where shortages and inequitable distribution of health workforce, poor HRH planning, inadequate recruitment exacerbated by a ban on workforce recruitment, and weak retention strategies, are often encountered.1–4 These frequently result in disparities in health worker densities by geographic location; urban and rural areas, limit access to health care services and inadvertently undermine the quality of care provided all of which are associated with poor health outcomes.\n\nIn the last decade, Nigeria has developed some health system reforms aimed at improving national health indices. One of such reforms is the Primary Health Care (PHC) Minimum Service Package (MSP).5,6 The MSP documents services to be provided by primary health facilities, articulates recommendations on staffing norms and composition, as well as states what services each health worker cadre should provide to meet the health needs of the populace.5,6 The MSP strategy was particularly important because it was birthed in wake of the UHC push in Nigeria and it targets primary healthcare which is the entry point into the health system, where promotive, preventive, and curative services for uncomplicated minor ailments are provided in Nigeria.5–7 The MSP stipulates that at the primary care level, the health workforce should include medical officers, nurses, midwives, community health practitioners, laboratory technicians, pharmacy technicians, health records assistants and environmental health officers.5–7 However, these staffing standards have remained unmet. This may be due to the health workforce crisis that Nigeria is facing as well as the low government spending on health at national and sub-national levels.8 In response to sub-optimal staffing patterns, the Government of Nigeria developed a Task Shifting and Task Sharing (TSTS) policy that allows lower skilled clinical staff to perform high skilled clinical tasks following training.9 However, there are challenges with the implementation and monitoring of this policy.\n\nKaduna is a state in northern Nigeria, with a projected population of 8.98 million people.10 Kaduna is one of the 36 states in Nigeria that have made huge investments in healthcare.11 To attain UHC through community participation, as contained in the national health act, the State adopted and implemented the Ward Health System (WHS) for healthcare.5–7,12 The WHS utilises the electoral wards as the basic operational unit for PHC service delivery. This formed the basis for governments' investment in one PHC facility per ward. There are 255 wards in Kaduna state, and in each ward, the State government prioritized one PHC facility. Since 2015, 255 PHC facilities have benefitted from the government’s investments in establishing and sustaining a multi-level administrative governance structure, improved infrastructure, provision of basic equipment and essential medicines amongst others. However, there have been challenges in meeting the staffing needs for these facilities as stipulated by the MSP because of the State’s limited fiscal space for health spending. As such, the availability of a sufficient, skilled, and equitably distributed workforce to serve the population has remained a challenge.\n\nIn consideration of Kaduna State’s HRH gaps, and an alternative to the staffing norms stipulated in the MSP, there is a need to employ an evidence-based staffing approach that can support the determination of adequate staffing norms in line with existing health system complexities. One of such methods is the Workload Indicators for Staffing Need (WISN) method developed by the World Health Organization (WHO). This study aimed to estimate the staffing requirements for delivery of care at focal primary health facilities by health worker cadre in Kaduna North Local Government Area in Kaduna State, Nigeria employing the WISN methodology.\n\n\nMethods\n\nWritten informed consent was obtained before data collection during the field visit and focus group discussion, and through the Health Research Ethics Committee (HREC) of the Kaduna State Ministry of Health has an approved registration number NHREC/17/03/2018.\n\nThis study employed the WISN methodology to determine staffing needs. WISN is designed by the WHO and supports the evidential determination of the number of health workers by cadre required to cope with the workload in a particular health facility. The WISN methodology considers several relevant components by health worker cadre that includes: (i) services delivered (ii) the time it takes to deliver both clinical and non-clinical services (iii) the total annual work time available to each Health Care Workers (HCW) cadre as well as (iv) retrospective annual service delivery statistics in the health facility.13 Computation of these statistics produces a determined number of HCWs by cadre required in the health facility.\n\nThe WISN study was completed in Kaduna North Local Government Area and included ten (10) primary health facilities. The study population were clinical health workers available and tasked with providing healthcare services to patients at these primary health facilities. These prioritized cadres are Nurse/Midwives and Community Health Workers (CHW), comprising Community Health Officers (CHOs), Community Health Extension Workers (CHEWs) and Junior Community Health Extension Workers (JCHEWS). Reproductive Maternal and Newborn Child Health (RMNCH) services are predominantly provided at the primary care level which makes up most of the health facility visits in the LGA and these services were prioritized for the study.\n\nThree Technical Working Groups (TWGs); Steering Committee, Technical Task Force and Expert Group were inaugurated to conduct the study. These study groups were a subset of the States’ larger HRH TWG, whose objectives include providing advisory and technical support to the state government in workforce policy formulation and technical directions to enable the development of the HRH workforce in the state. The membership composition of the three groups was drawn from relevant Ministries, Departments and Agencies (MDA), health training institutions, Civil Society Organisations (CSO), health facility heads and development partners. These groups were engaged to build local capacity, decide on priority areas of primary healthcare for the state as well as create the utility of study results for workforce planning.\n\nKaduna North Local Government Areas (LGA) was selected for the study for convenience. Consequently, all government prioritized PHC facilities that have been in operation for at least one year before the time of the study were included. Kaduna North LGA is an urban area and one of the most populous areas in the State. The choice of including only government prioritized PHC facilities is hinged on the significant investments made by the State government and donors in these facilities and a resultant increase in service utilization rates.\n\nAfter a review of relevant documents that include the Nigeria Task Shifting and Task Sharing (TSTS) policy, the MSP, Ward Minimum Healthcare Package (WMHCP) and the public service handbook, data collection tools were developed. Service delivery statistics and HRH composition data were extracted manually from secondary sources that include the Nigeria District Health Information System (DHIS2) and KSPHCB Human Resources for Health Information System (HRH-IS) respectively, and tri-angulated during primary data collection. Staff available work time data and activity standards data for both clinical and non-clinical health services were obtained following a focus group discussion with an Expert Group (EG).\n\nClinical health care services within the Reproductive Maternal and New-born Child Health (RMNCH) continuum of care formed the core health services assessed for this study because they are the commonly provided and accessed services within PHC. These services include family planning, antenatal care, post-natal care, immunization, diarrhoea, pneumonia and malaria in children and adults because of their endemicity. Annual RMNCH health service statistics, January to December 2019, were obtained from the national DHIS2. The DHIS2 is the electronic instance of the National Health Management Information System (NHMIS); a paper-based mechanism that aggregates all health care services delivered in a health facility. The annual statistics data collected from the DHIS2 were compared and triangulated with data obtained from the health facility registers during field visits that ran for three weeks between June and July 2021.\n\nFacility workforce data focusing on clinical professional cadre – Nurse/Midwife, CHWs, CHO, CHEW and JCHEW – were obtained from two sources; HRH-IS domiciled in the KSPHCB as well as health facility staff register to facilitate triangulation.\n\nTo obtain information on staff Available Work Time (AWT), the total amount of time available to an HCW by cadre to perform daily tasks in a year considering authorized and unauthorized absences, a multi-step approach was taken. Firstly, a desk review of relevant public service statutory policy, rules, and guidelines; public service handbook, as well as other grey literature was conducted to obtain HCW’s working hours per day, working days per week, and authorized and unauthorized absences allowed within the service. Only resources relevant to public sector workforce administration were included in the desk review. The Staff AWT was subsequently reviewed and approved by the study’s governance structure.\n\nAn Expert Group comprising 17 clinical experts was convened to obtain time spent by HCWs in the study’s cadre of interest on both clinical and non-clinical activities. These experts were purposefully selected and are currently employed in the public service possessing at least 15 years of experience providing health care services at the primary care level. All experts included in the group responded on the time it takes the prioritised health worker cadre to perform these activities to acceptable standards and the mean value of their responses was utilized.\n\nThe data collected were analysed using MS Excel, consistent with the WISN methodology. Activity standards clinical and non-clinical workload components, annual service delivery statistics and AWT for the prioritized cadre for each facility were included. To complete computation, the data collected was defined and analysed as follows:\n\n• Available Working Time: The time a health worker is available in one year to do his or her work, considering authorized and unauthorized absences. AWT in Days is the difference between Possible Working days in a year (PWD) and Non-working days in a year (authorized and unauthorized absences).13–15\n\nWhere in the formula:\n\nAWT is the total staff available working time\n\nA is the number of possible working days in a year\n\nB is the number of days off for public holidays in a year\n\nC is the number of days off for official leave in a year\n\nD is the number of days off due to sick leave in a year\n\nE is the number of days off due to casual leave, study or training leave and maternity leave in a year.\n\n• Activity Standard: The time it takes an HCW of a particular cadre to deliver both clinical and non-clinical services; core, individual and support activities.13\n\n• Standard Workload: The amount of work one HCW can perform in a year within a health service category.13 It is calculated in unit time or rate of work, by dividing AWT by the time taken to conduct the work or multiplying the AWT with the rate of working respectively.\n\n• Core health activities: These are clinical health services. This refers to activities directly related to service delivery performed by all staff of a cadre.\n\n• Support activities: There are non-clinical activities performed by a health worker but not directly related to a patient and usually involve all staff of the same cadre.\n\n• Additional activities: These activities are also not clinically related and are performed by health workers but not directly related to a patient. They usually do not involve all staff of the same cadre.\n\n• Staff requirement for core health activities: This was calculated by taking the aggregate ratio of all annual core health services and standard workload for the identified clinical health services:\n\nCore health activities i = 1,2,3 … n\n\nAWi = Annual statistics for each core clinical health service\n\nSWi = Standard Workload for each core clinical health service\n\n• Staff requirement for support activities: A Category Allowance Standard (CAS) which is the percentage of the working time required to cope with all support activities was estimated and Category Allowance Factor (CAF) was calculated using:\n\nStaff requirement for individual activities: Individual Allowance Standard (IAS) which is the total number of hours per year needed to perform all additional activities undertaken by some HCWs were also calculated. An Individual Allowance Factor (IAF) identifying the staffing requirement to undertake these workloads was estimated using:\n\n• Total staffing requirement was calculated using:\n\nWISN staffing results with fractions were handled as recommended by the WISN guide.13 WISN differences and ratios were also generated. The WISN difference, which is calculated from the variance between the current staffing norm available by cadre and the computed staffing requirements identifies staffing gaps or excesses by cadre. The ratio represents the work pressure experienced by the HCW. A WISN ratio of > 1 indicates the availability of more HCWs than required to meet the facility workload.\n\n\nResults\n\nTwo categories of health care services were included in the study. The clinical health service forms the core health activities, while the non-clinical services comprise both support and additional services. The clinical core health services refer to activities directly related to service delivery performed by all prioritized cadres.13–15 Support activities are part of the non-clinical category, and activities performed by the prioritized cadre are not directly related to patient care and usually involve all staff of the same cadre.13–15 Additional activities are activities performed by these prioritized cadres that are not directly related to patient care and are undertaken by just a staff.13–15\n\nThe workload and activity standards developed and validated by the expert group are presented in Table 1.\n\nA total of 26 health and non-health related services were identified in the state Primary Health Care level; of which 12 are clinical/core health services conducted by both Nurse/Midwife and CHW Practitioners. 14 non-clinical services; 7 support services and 7 individual services were also identified, and the corresponding category and individual allowance standards were also identified.\n\nThe results emanating from the study are based on documented annual workload from the ten (10) primary healthcare facilities in Kaduna North Local Government Area. The WISN results are presented in Table 2.\n\nKaduna North Local Government Area has only 17% of the Nurse/Midwife workforce it requires to provide primary health care services. Overall, the LGA requires about 54 Nurse/Midwives but currently has only 9 leaving a deficit of 45. All but one of the 10 PHCs have WISN ratios less than one (WISN < 1), indicating that the current number of Nurse/Midwife staff available is insufficient to cope with the workload. Primary Health Care Centre Hayin Banki has the lowest WISN ratio of 0.1, while there is no Nurse/Midwife available in Primary Health Centre Unguwar Shanu.\n\nWISN results for CHWs; CHO, CHEW and JCHEW, also indicate a staffing shortage. Results provide an estimated requirement of 121, and an availability of 51 leaving a deficit of 70. CHWs are available in all assessed primary health care centres, with staffing surplus in two PHCs whose WISN ratios are above one (WISN >1); Doka (Zakari Isah) Primary Health Care Centre and Primary Health Care Badarawa. One PHC has the required number of CHWs, while the other seven PHCs have CHW staffing strength that is insufficient to cope with the work pressures.\n\n\nDiscussion\n\nKaduna state has employed several workforce planning strategies that include traditional workforce estimation practices: health service target or disease-focused staffing estimation, health workforce to population ratio and population to facility staff ratio. Although these workforce planning strategies are useful, they are costly to implement and do not incorporate the complexities of the health system that affects health service seeking behaviours and service delivery.14,16–21\n\nThis study applied the WISN methodology, and the literature suggests that this staffing estimating approach is most suitable for guiding the deployment of skilled frontline workers from places with fewer work pressures, to locations with higher work pressures, particularly in a resource-constrained environment.14,22–32 Findings from this study revealed a gap in the number of Nurse/Midwives and CHWs available to provide primary health care services. Our study highlight variability in the availability of skilled HRH in these focal primary health care facilities. Nurses/Midwives are unavailable in all but one primary health facility with WISN ratios less than one, indicating that the current number of staff available is insufficient to cope with the workload. Conversely, CHWs are available in all assessed facilities, with a cumulative 13 staffing excesses in two PHCs; Doka (Zakari Isah) Primary Health Care Centre and Primary Health Care Badarawa, having WISN ratios greater than one; one PHC has the required number of CHWs, while the other seven PHCs have shortages of CHWs. Our findings are consistent with workload studies in Cross River and Rivers states, Nigeria as well as in Burkina Faso,14,15,33 where there were shortages in the Nurse/Midwife cadre of the health workforce.\n\nOur study presents several opportunities for the Kaduna state government. To the best of our knowledge, this study is the first attempt in the application of WISN to estimate staffing requirements in the state. As such, this study provides lessons on how to apply the WISN methodology. More importantly, it outlines the steps taken in establishing the WISN governance structure to drive ownership, knowledge transfer, follow-through on staffing decisions and prevents loss of institutional memory. For example, the study’s steering committee and technical task force were sub-sets of the broader state HRH TWG, which is responsible for guiding the state on sustainable development of HRH within the context of Government development priorities, increasing the availability and equitable distribution of skilled HRH amongst others. This HRH TWG is chaired by the Permanent Secretary and led by State Honourable Commissioner for Health. This study provides an evidence-base to redistribute staff from underutilized health facilities to locations that are experiencing high work pressures. The 13 surpluses CHWs should be redistributed to understaffed health facilities to increase coverage of primary health care services. A WISN scale-up study across the state primary health care structure is recommended to effectively utilize scare HRH towards increasing coverage and improving PHC services.\n\nThe WISN methodology estimates the number of health workers needed to cope with work pressure in the facility. However, there are a few assumptions that the health worker is available and not absent from duties, well-behaved, and that the administered health service is relying on established standards, amongst others. Regardless of having the right numbers in a facility, these workforce productivity and performance inhibiting factors could affect service delivery. A recommendation is for Kaduna state to routinely assess the PHC workforce productivity level to guide incorporating HRH management strategies with planning.\n\nOur study had a few limitations and steps were taken to address them. There are no national or regional activity standards available across the different categories of services; clinical and non-clinical, for the primary health care level. For the study, the Expert Group was tasked with establishing the activity standards, and there were slight variations in the timings provided for the prioritized cadres. To address the marginals variation across the activity standards, an average was taken. Another limitation was with availability and quality of health care data at the facility level. At this level, challenges arose with the storage of paper registers. To address this challenge, we chose to compare and triangulate data with other sources; the national DHIS2. In cases where paper files/registers were unavailable during field trips to the facility due to poor storage facilities, we opted for data with the national DHIS2 data source.\n\n\nConclusion\n\nAs countries strive towards achieving UHC, the need for equitable distribution of frontline health workers has become paramount. Historically, Kaduna state has relied on other ways of determining staffing requirements for health facilities; however, these have been unrealistic, costly, and difficult to implement. Our study applied the WISN methodology to estimate staffing requirements in Kaduna state government prioritized PHC facilities. The study highlights an acute shortage in Nurse/Midwives and CHW practitioners in these prioritized health facilities and provides evidence-based for determining staffing needs.\n\n\nData availability\n\nDue to security restrictions, data cannot be made publicly available. Underlying data for this article are available on government approved health information systems. Annual health service statistics are available on the National Health Management Information System (NHMIS) - http://dhis2nigeria.org.ng, with access only available for users who have login details. Also, health workforce data is also available in the State Human Resources for Health Information System (HRH-IS).\n\nFor readers without access to these platforms, data may be requested by contacting the corresponding author via email (bonkhi@gmail.com) or phone (+2348034118557) and access will be granted to in CSV format.\n\n\nAuthors’ contribution\n\nAIO, OT and HB conceptualized and designed the study, as well as coordinated its implementation. AIO coordinated data collection. AIO and OT analysed the data. AIO and OT drafted the initial manuscript. All authors read, reviewed, and approved the final version of the manuscript.",
"appendix": "Acknowledgements\n\nThe authors acknowledge the support of the Kaduna State Primary Health Care Board. Our profound appreciation also goes to the senior management and staff of the Kaduna State Ministry of Health.\n\n\nReferences\n\nWorld Health Organization: The world health report 2006: working together for health. Ann. Indian Acad. Neurol. 2006; 9: 135–136. Publisher Full Text\n\nAbimbola S, Olanipekun T, Schaaf M, et al.: Where there is no policy: governing the posting and transfer of primary health care workers in Nigeria. Int. J. Health Plann. Manag. 2017; 32: 492–508. PubMed Abstract | Publisher Full Text\n\nAbimbola S, Negin J, Jan S, et al.: Towards people-centred health systems: A multi-level framework for analysing primary health care governance in low-and middle-income countries. Health Policy Plan. 2014; 29: ii29–ii39. PubMed Abstract | Publisher Full Text\n\nBangdiwala SI, Fonn S, Okoye O, et al.: Workforce Resources for Health in Developing Countries. Public Heal. Rev. 2010; 32: 296–318. Publisher Full Text\n\nNational Primary Health Care Development Agency (NPHCDA): Minimum Standards for Primary Health care in Nigeria.2010.\n\nNational Primary Health Care Development Agency (NPHCDA): Ward Health System.2018.\n\nFederal Ministry of Health Nigeria: National Health Policy 2016.2016; 26: 207–12.\n\nFederal Ministry of Health Nigeria: National Health Accounts 2017.2015.\n\nFederal Ministry of Health Nigeria: Task-shifting and task-sharing policy for essential health care services in Nigeria. Federal Ministry of Health Abuja Nigeria; 2014; August; 1–56. [Accessed: 30/12/2016]. Reference Source\n\nNational Bureau of Statistics: Annual Abstract of Statistics.: 869.\n\nKaduna State Bureau of Statistics: 2018 Statistics Year Book.2018.\n\nFederal Government Of Nigeria: National Health Act. Federal Republic of Nigeria Official Gazette; 2014; A139–A172. Reference Source\n\nWorld Health Organization: WISN: Workload Indicators of Staffing Need User’s Manual.2010.\n\nOkoroafor S, Ngobua S, Titus M, et al.: Applying the workload indicators of staffing needs method in determining frontline health workforce staffing for primary level facilities in Rivers state Nigeria. Glob. Heal. Res. Policy. 2019; 4: 35–38. PubMed Abstract | Publisher Full Text\n\nOkoroafor SC, Oaiya AI: Using the workload indicators of staffing need method to determine the staffing requirements for primary healthcare service delivery in Nigeria. J. Glob. Heal. Reports. 2021; 5: e2021091. Publisher Full Text\n\nMcQuide PA, Kolehmainen-Aitken RL, Forster N: Applying the workload indicators of staffing need (WISN) method in Namibia: Challenges and implications for human resources for health policy. Hum. Resour. Health. 2013; 11. PubMed Abstract | Publisher Full Text\n\nHagopian A, Mohanty MK, Das A, et al.: Applying WHO’s workforce indicators of staffing need (WISN) method to calculate the health worker requirements for India’s maternal and child health service guarantees in Orissa State. Health Policy Plan. 2012; 27: 11–18. PubMed Abstract | Publisher Full Text\n\nBurmen B, Owuor N, Mitei P: An assessment of staffing needs at a HIV clinic in a Western Kenya using the WHO workload indicators of staffing need WISN, 2011. Hum. Resour. Heal. 2017; 15: 8–9. PubMed Abstract | Publisher Full Text\n\nHagopian A, Mohanty MK, Das A, et al.: Applying WHO’s “workforce indicators of staffing need” (WISN) method to calculate the health worker requirements for India’s maternal and child health service guarantees in Orissa State. Health Policy Plan. 2012; 27: 11–18. PubMed Abstract | Publisher Full Text\n\nAsamani JA, Dela CC, Reitsma GM: Health service activity standards and standard workloads for primary healthcare in Ghana: A cross-sectional survey of health professionals. Healthcare. 2021; 9: 1–38. Publisher Full Text\n\nLy A, Kouanda S, Ridde V: Nursing and midwife staffing needs in maternity wards in Burkina Faso referral hospitals. Hum. Resour. Health. 2014; 12 Suppl 1: S8. PubMed Abstract | Publisher Full Text\n\nJoarder T, Tune SNBK, Nuruzzaman M, et al.: Assessment of staffing needs for physicians and nurses at Upazila health complexes in Bangladesh using WHO workload indicators of staffing need (WISN) method. BMJ Open. 2020; 10: e035183. PubMed Abstract | Publisher Full Text\n\nJoarder T, Tune SNBK, Nuruzzaman M, et al.: Assessment of staffing needs for physicians and nurses at Upazila health complexes in Bangladesh using WHO workload indicators of staffing need (WISN) method. BMJ Open. 2020; 10: e035183–e035110. Publisher Full Text\n\nNamaganda G, Oketcho V, Maniple E, et al.: Making the transition to workload-based staffing: Using the Workload Indicators of Staffing Need method in Uganda. Hum. Resour. Health. 2015; 13: 89. PubMed Abstract | Publisher Full Text\n\nZodpey S, Negandhi H, Tiwari R: Human Resources for Health in India: Strategic Options for Transforming Health Systems Towards Improving Health Service Delivery and Public Health. J. Health Manag. 2021; 23: 31–46. Publisher Full Text\n\nKakuma R, Minas H, Van Ginneken N, et al.: Human resources for mental health care: Current situation and strategies for action. Lancet. 2011; 378: 1654–1663. PubMed Abstract | Publisher Full Text\n\nTripković K, Šantrić Milićević M, Mandić Miladinović M, et al.: Implementation of the Workload Indicators of Staffing Need (WISN) Method in Determining Staff Requirements in Public Health Laboratories in Serbia. Disaster Med. Public Health Prep. 2020: 1–9. PubMed Abstract | Publisher Full Text\n\nNeuraz A, Guérin C, Payet C, et al.: Patient mortality is associated with staff resources and workload in the icu: A multicenter observational study. Crit. Care Med. 2015; 43: 1587–1594. PubMed Abstract | Publisher Full Text\n\nGriffiths P, Saville C, Ball J, et al.: Nursing workload, nurse staffing methodologies and tools: A systematic scoping review and discussion. Int. J. Nurs. Stud. 2020; 103: 103487. PubMed Abstract | Publisher Full Text\n\nPlate JDJ, Leenen LPH, Houwert M, et al.: Utilisation of Intermediate Care Units: A Systematic Review. Crit. Care Res. Prac. 2017; 2017: 1–10. PubMed Abstract | Publisher Full Text\n\nCometto G, Buchan J, Dussault G: Developing the health workforce for universal health coverage. Bull. World Health Organ. 2020; 98: 109–116. PubMed Abstract | Publisher Full Text\n\nAsamani JA, Ismaila H, Plange A, et al.: The cost of health workforce gaps and inequitable distribution in the Ghana Health Service: an analysis towards evidence-based health workforce planning and management. Hum. Resour. Health. 2021; 19: 15–43. PubMed Abstract | Publisher Full Text\n\nIwelunmor J, Blackstone S, Veira D, et al.: Toward the sustainability of health interventions implemented in sub-Saharan Africa: a systematic review and conceptual framework. Implement. Sci. 2015; 11: 43. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "135713",
"date": "26 Apr 2022",
"name": "Richard F Heller",
"expertise": [
"Reviewer Expertise Public health",
"health services",
"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\nThis paper is a thorough and well written report of a valuable project with important practical results. The findings indicate a gap between the required and provided staffing needs in primary health care in one part of one State in Nigeria.\n\nI have three areas that I feel would improve the understanding of the paper.\nFirst, in the Methods, we learn that the data come from DHIS2 (District Health Information System), an electronic database, triangulated by field visits to health facilities. This is an appropriate method, but the term 'triangulation' does not give us adequate information about what was done. Were field visits made to each of the facilities, how was the data obtained, how was the 'triangulation' actually performed and how were discrepancies resolved?\nSecond, the Methods give us five formulae, which each look fine to me, and relate to Table 2, which is really clear and presents the main results of the study. However, I can't see a description of how the formulae lead to the column headings (N/M and CHW available and calculated) in the Table. Clarifying this would make the paper more understandable.\nFinally, I would have liked to see a discussion of the generalisability of the findings. The choice of Kaduna North LGA (Local Government Areas) is described as purposive, and that is fine, but how representative might this particular LGA be to other settings. Government prioritized health facilities within the LGA were chosen for the study, but how representative might these be to to generality of health facilities.\nI think that it should be quite easy to resolve the issues I have highlighted, which are only matters of presentation rather than questions about the validity of the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "8929",
"date": "04 Nov 2022",
"name": "Agbons Oaiya",
"role": "Author Response",
"response": "Many thanks for your insightful comments. You concerns have been taken care of in the revised manuscript."
}
]
},
{
"id": "135712",
"date": "19 May 2022",
"name": "Pamela A. McQuide",
"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\nThis is an important paper using the evidenced-based approach of the World Health Organization’s (WHO) Workload Indicator of Staffing Need to determine facility level staffing in primary health care (PHC) sites in Kaduna State in Nigeria. The authors have done well in applying this method and results for PHC.\n\nThere are a few considerations for the authors to improve the quality of the paper and a few small mistakes to correct.\nSmall mistakes to correct:\nPage 7 in the table on document on patients 3 minutes but the unit is missing. Is it per patient, per day etc. It would seem that 3 minutes per day to document on patients would not be sufficient.\n\nPage 7, last paragraph states “Nurse/Midwives are unavailable in all but one primary health facility”. I think it should read NM are available in all but one primary health facility.\n\nPage 6 second to last paragraph states Hayin Bank WISN ratio is .10 and in the Table 2, it says .09. It also says Hayin Bank has the lowest WISN ratio, but, Unguwar Sahnu WISN ratio is .0 because they have no Nurse/Midwives. This would be consistent in the abstract which states that 9/10 sties have WISN ratio <1.0 which would include the site with a WISN ratio of 0.0\nRecommendations:\nThe paper did not indicate how the 10 PHC sites were selected. Were they part of the wards discussed in the introduction, randomly selected across Kaduna State or did they represent the different characteristics of sites in Kaduna State or another methodology?\n\nIt would be easier for the reader if the definitions for the types of teams (Steering Committee, Technical Team and Expert Group) are pulled together in the methods section and uses the definitions from WHO. It is fine that they are part of the larger HRH TWG group in this Kaduna State. The definitions in the paper are inconsistent with the WHO definitions in the WISN User Manual (WHO 2010) p. 17. Health service activities are performed by all members of a staff category and regular statistics collected; support activities are performed by all members of a staff category but regular statistics are not collected on them; and additional activities are performed by only a certain members of a staff category and regular statistics are not collected. Some of the support and additional activities can be clinical in nature but no statistics are available for them.\n\nUse of the term triangulated is not used as would be expected. It appears different data were used to fill in for missing data and not to validate the data used with different data sources (e.g. DHIS2 and primary data).\n\nIn the discussion it mentions that two other states in Nigeria had similar WISN results, i.e., Cross River and River State but it did not indicate if the health service activities and standards were comparable for PHC. You also indicated that there were no regional or national standards for PHC but it seems this could lead to adapting standards for the country.\n\nIt might be helpful to put in a small table showing the relationship with health service activities, support activities, and additional activities with the activity standard and the standards workload and allowance factor for the CAF and IAF. It is a little hard to follow in the paper and at times the terms used in the paper are inconsistent. For example, health service activities are sometimes called core activities. If you put all the definitions under methods section, then you can just discuss the results and not have to put in definitions in other parts of the paper. These definitions are important for setting up the study and not in the results section. Use the same terms through-out the paper or it gets confusing.\n\nSince the service statistics are not available, I cannot validate the results given in the paper.\n\nIn the background section you mention previously staffing norms used for budgeting positions. It might be interesting to compare the staffing norms to the actual WISN results to see if they are comparable or if the WISN results could be used to develop new evidenced-based norms that can be used.\n\nIn the Table 2, it gives staff available. Is the staff available consistent with budgeted positions for this facility? You might want to put in a comment in the paper about budgeted positions versus actual positions available.\n\nThank you for using the evidenced based approach using WISN to estimate staffing needs for PHC.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8930",
"date": "17 Nov 2022",
"name": "Agbons Oaiya",
"role": "Author Response",
"response": "Many thanks for your comments. The typos, grammatical errors and other concerns raised have been addressed in the revised submission."
}
]
},
{
"id": "135710",
"date": "20 May 2022",
"name": "Iboro Nelson",
"expertise": [
"Reviewer Expertise Health Systems specifically health financing",
"human resource for health 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\nStrength: The work is a useful contribution to knowledge in the field of human resource for health management. Well-written in simple and understandable English devoid of jargons, the paper frames the problem statement in a lucid manner and situates it contextually. Key concepts such as WISN (Workload Indicators for Staffing Need) and the key steps, DHIS (District Health Information System), Task Shifting and Task Sharing are adequately defined and broken down to the readers’ understanding. The study limitations and mitigation strategies are also clearly discussed.\nWeakness: However, in an attempt to present the evidence-base methodology of WISN approach for health workforce estimation as superior to the other approaches earlier adopted by the State such as disease-focused staffing estimation, and health workforce to population ratio and population to facility staff ratio, the study failed to make recommendations for a major of the study’s findings: the unavailability of Nurses/Midwives in all but one facility in the LGA (Local Government Areas). Besides, some grammatical error gaps which is usually characteristics of such work as this are highlighted for the authors’ consideration.\nGeneral Conclusion: The work has academic merit and is fit for indexing, howbeit a number of minor grammatical errors and changes to the article needs to be addressed and or amended.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8931",
"date": "17 Nov 2022",
"name": "Agbons Oaiya",
"role": "Author Response",
"response": "Many thanks for your comments. The concerns raised have been addressed in the revised submission."
}
]
}
] | 1
|
https://f1000research.com/articles/11-429
|
https://f1000research.com/articles/11-528/v1
|
16 May 22
|
{
"type": "Systematic Review",
"title": "A Review of Wound Healing Mechanisms of Natural Products in Keratinocyte Cells",
"authors": [
"Adryan Fristiohady",
"Rathapon Asasutjarit",
"La Ode Muh Julian Purnama",
"Wirhamsah Al-Ramadan",
"Rathapon Asasutjarit",
"La Ode Muh Julian Purnama",
"Wirhamsah Al-Ramadan"
],
"abstract": "Background: The skin is the largest organ of the human body, around 15% of the body weight consisting of the epidermis, dermis, and subcutaneous. The skin's primary function is to protect our body from external factors that can harm the body by forming a protective barrier that covers the body. This review aims to provide insights related to wound-healing mechanisms of several plants in HaCat cells. Methods: The literature study method used, both from primary and secondary libraries. The library search was conducted using online-based library search instruments from 2009 to 2021, such as NCBI-PubMed and Google Scholar. Results: The wound-healing mechanism includes processes that restore skin integrity through four stages: hemostasis, inflammation, multiplication, and remodeling. Many plants have been studied to have activity in wound-healing by various mechanisms. Conclusions: Therefore, it is essential to research wound-healing mechanisms to find treatments sourced from natural compounds.",
"keywords": [
"Wound-healing",
"Keratinocyte",
"Natural Products"
],
"content": "Introduction\n\nThe skin, including the dermis (deeper layer) and epidermis (surface layer), is the most significant barrier between the external environment and the human body.1,2 Skin protects against environmental factors such as harmful UV rays and pathogens and prevents water loss.3\n\nThe skin’s vital functions are physical, chemical, bacterial, and wound-healing barriers.4 Wound-healing in the skin is one of the mechanisms that maintain homeostasis. In general, the wound-healing process is divided into 4 phases: the coagulation and hemostasis phase, the inflammatory phase, the proliferative phase, and the remodeling phase.5 A wound-healing response begins when the skin layer (epidermis) is injured externally.6 In response to skin damage, epithelialization is referred to as faulty epidermis breakdown.7 Keratinocytes are responsible for discovering the epidermis after injury through epithelialization.8 During new tissue formation, keratinocyte proliferation and migration have essential roles in re-epithelialization and effective wound-healing.9,10\n\nIneffective skin wound-healing is a big problem in the health sector. Several factors, including aging, diabetes, infection, immunodeficiency, and cancer, can lead to unsuccessful wound care and ultimately lead to morbidity and mortality.7 Efficient wound-healing process using traditional medicine, which is based on plant sources.11 Secondary metabolites are highly variable in their structure, so they have great potential for managing and treating drugs.12 Growth rates are a source of many biochemicals that can support skin health and integrity and are widely used in cosmetic formulations.13\n\nIn vitro studies of human skin’s epidermis and dermis have been commonly performed using HaCaT cells.1 HaCaT cells are immortalized human keratinocytes used to study dermatological conditions such as contact dermatitis, psoriasis, or skin cancer due to their high availability and ease of cell culture.5 Therefore, this review article aims to determine the wound-healing mechanism of several plant extracts on HaCaT cells.\n\n\nMethods\n\nThe results are reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.14 Scoping reviews purpose to; establish evidence available, elucidate key ideas, establish how research is done and determine knowledge gaps for a certain topic.\n\nArticles were included based on the following criteria:\n\n1. The studies primarily focus on the molecular mechanism of wound-healing of several compounds and extracts in HaCaT cells\n\n2. The studies using an in vitro approach\n\n3. The studies were published from 8th October 2021 up to 31st March 2022\n\n4. The studies were in English and Indonesian language\n\n5. The study’s full texts were available\n\nArticles were excluded based on the following criteria:\n\n1. The studies were reviews\n\n2. Wound-healing of the skin is a mechanism that maintains homeostasis.\n\n3. In vitro studies\n\n4. The studies were compounds and extracts from plants\n\n5. The studies were on wound-healing mechanisms in HaCaT cells\n\nArticles relevant to the study topic were searched and retrieved electronically from PubMed (https://pubmed.ncbi.nlm.nih.gov/advanced/) and Google Scholar (https://scholar.google.com/) using advanced search builders. The search from the databases was lastly done on 10th December 2021.\n\nAn advanced search in three databases, PubMed and Google Scholar, was searched to identify peer-reviewed articles on wound-healing and wound-healing mechanisms using compounds and extracts against HaCaT cells. Specifically, the search queries consisted of relevant medical subject titles (MeSH) and keywords relevant to the topic. The search terms included:\n\nWound-healing AND HaCaT Cells AND Compounds AND Extracts\n\nThe articles obtained were further vetted using the search strategy and filters outlined in the search strategy section. Assessment of the resulting articles was done independently by all the reviewers. Disagreements between them were resolved through consensus. First, articles from the initial search were obtained. Duplicate references were removed through manual deduplication. The titles and abstracts of the retrieved articles were screened for relevance to the study topic. Full-text reports were examined for compliance with eligibility criteria.\n\nData chatting from the sources of evidence was first assessed independently and then discussed by the team to reach a consensus. The information abstracted was as shown in the table.\n\nThe selection of the review articles based on the molecular mechanisms of action as the primary outcome domain was guided by the following items:\n\n1. Title of study\n\n2. Year of publication – 2009-2021\n\n3. Study objectives – wound-healing mechanism of several compounds and extracts in HaCaT cells\n\n4. Study design – review\n\n5. Results – summary of findings on molecular mechanisms\n\n6. Discussion – detailed explanation of the results and limitations of the review\n\n7. Conflict of interest – Authors declare no conflict of interest\n\nResults from the selected articles were tabulated in the summary of findings. The methodologies and molecular mechanisms of action (interventions) were summarized. It enhanced the comparison of interventions for the different HaCaT cells.\n\n\nResults\n\nSkin is the largest organ of the human body,15 about 15% of the bodyweight consisting of the epidermis, dermis, and subcutaneous (Figure 1). The epidermis is the outermost layer of the skin and maintains a vital barrier against external trauma. The main cellular content of the epidermis is keratinocytes (about 95% of the epidermis), and fibroblasts are the main cellular components of the dermis.6 The epidermis, mainly composed of keratinocytes, is classified into stratum corneum, granular layer, spinous layer, and basal layer, based on the stages of keratinocyte differentiation. Keratinocytes have an essential role in inflammation.16 The skin’s primary function is to protect the body from exogenous factors by forming a protective barrier that covers the body; therefore, any injury or damage to the skin must be repaired immediately to provide continuous protection to our body systems.1\n\nWound-healing is a complex biological mechanism involving cellular interactions between cells, including smooth muscle cells, fibroblasts, endothelial cells, myofibroblasts, keratinocytes, and immune cells.17 Wound-healing processes restore skin integrity through four stages: hemostasis, inflammation, multiplication, and remodeling.18,19\n\n1. Coagulation phase and formation of a platelet scab to cover the wound opening to prevent further blood loss or entry of pathogens,\n\n2. Inflammatory phase, The flow of inflammatory cells to the wound site for protection against pathogens and activates skin cells. During this phase, neutrophils and macrophages are activated by releasing pro-inflammatory cytokines such as IL-1𝛽, IL-6, IL-8, and TNF, and growth factors such as PDGF, TGF-𝛼, TGF-𝛽, IGF-1, and FGF (Figure 2).9\n\n3. Proliferation phase, skin cells multiply rapidly to replace lost cells. Restoring the basal keratinocyte layer in the basement membrane between the epidermis and the dermis begins to proliferate through various signaling molecules during the proliferative stage. When a certain level of repair is reached, the cytoplasmic shape of the keratinocytes is altered to move to the upper layers of the epidermis, differentiate, and transform through different cell layers to reach the final maturation stage. Thus, the proliferation and migration of keratinocytes suture the wound site during wound-healing.9\n\n4. Remodeling Phase. In this phase, fibroblast and a vascular density decrease, old collagen fibers from the initial scar are replaced with matrix, and new collagen fibers are synthesized to form new tissue.9\n\nPlants are the potential for providing wound-healing activities. Many studies reported the activity of plants for wound-healing and its mechanism. Thereby, this study reviews several plants that exhibit wound-healing activity below.\n\nAristolochia bracteolata\n\nAristolochia bracteolata contains aristoctam, aporphines, protobiberberines, flavonoids, alkaloids, tannins, sterols, steroids, and several other compounds used for skin treatments, as well as utilized for its anti-inflammatory properties (Figure 3).20 A. bracteolata extract selectively inhibited cell proliferation at higher concentrations (>100 μg/mL) and lower concentrations (<25 μg/mL). This extract showed linear and dose-dependent cell proliferation. The wound-healing study showed that wound closure was 50,38% ± 1,39 and 69,81% ± 1,89, respectively, at a 25 μg/mL concentration after 24 hours and 48 hours. The extract was tested for anti-inflammatory activity by determining the inhibitory activity on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in 264.7 RAW cells. The results found that A. bracteolata had a strong inhibitory effect on the production of NO and tumor necrosis factor-α/TNF-α. A. bracteolata extract inhibited the expression of the inducible nitric oxide synthase (iNOS) gene by lipopolysaccharide (LPS). A. bracteolata showed decreased pro-inflammatory cytokine mRNA expression concentration-dependent, indicating a mechanism for iNOS inhibition, gene expression analyzed by Real-Time PCR. Type III collagen levels are known to increase during the early stages of healing. During the early stages of wound-healing, type IV collagen is synthesized and replaced by type I collagen in the later stages of wound repair. It is evident from the data that this extract can stimulate collagen production from fibroblast cells, thereby increasing levels of extracellular matrix during tissue repair. The expression and secretion of type I and type IV collagen are also inherent in fibroblasts’ biological function because these proteins are essential components of the extracellular matrix.21\n\nBoerhavia diffusa\n\nThe methanol extract (EM) of the leaves of Boerhavia diffusa significantly increased the viability and migration of human keratinocytes (HaCaT) cells. GC-MS analysis revealed the presence of caffeic acid, ferulic acid, and D-pinitol as the primary bioactive metabolites (Figure 4). The content of secondary metabolites in the extract of punarvana such as phenolics and flavonoids reduces lipid peroxidation, increases collagen fibrils’ survival by increasing collagen fibers’ strength, prevents cell damage, and accelerates DNA synthesis. Phenolics, flavonoids, and terpenoids enhance wound-healing due to their antioxidant and antimicrobial properties. Antioxidants enhance the healing process by reducing the damage caused by free oxygen radicals. D-pinitol, which is an insulinomimetic. Apply topical insulin promotes diabetic wound-healing by regulating wound inflammatory cells and improving cellular function. Bioactive insulin activates the IR/IRS/PI3K/AKT pathway involved in skin wound-healing, leading to tissue regeneration and growth, proliferation, and migration of keratinocytes and fibroblasts. In addition, caffeic and ferulic acids can promote wound-healing mainly due to their potent antioxidant and anti-inflammatory properties.22\n\nAchyrocline satureioides (Lam.)\n\nAchyrocline satureioides (Lam.) extracts are medicinal plants originating from Brazil, Uruguay, Argentina, and Paraguay. This plant contains quercetin, luteolin and 3-O-methylquercetin (Figure 5).23 The results showed a significant increase in the viability of HaCaT cells on ASE-loaded nanoemulsions (NEASE) (up to 5 μg/mL of flavonoids). Preliminary tests showed that NEASE was able to increase cell migration at low flavonoid concentrations. ASE did not induce HaCaT cytotoxicity and tended to increase keratinocyte cell viability compared to controls after 24 h of treatment for all concentrations tested (0.625-10 μg/mL).24\n\nCalophyllum inophyllum Linn.\n\nAnti-inflammatory and wound-healing activities have been reported of calophyllolide (CP) isolated from Calophyllum inophyllum Linn (Figure 6). The results showed that CP did not affect the viability of HaCaT cells in the concentration range. CP reduced fibrosis formation and effectively promoted wound closure in a mouse model without causing weight loss. The molecular mechanisms underlying wound repair reduce MPO activity and increase M2 macrophages. CP prevents a prolonged inflammatory process by downregulating pro-inflammatory cytokines-IL-1β, IL-6, TNF-α, but upregulating anti-inflammatory cytokines, IL-10.25\n\nUlmus parvifolia\n\nThe bark of Ulmus parvifolia contains phenolic compounds and steroid glucosides, used to treat edema. This plant has been isolated containing catechin-7-O-β-D-apiofuranoside (Figure 7).26 The results showed that HaCaT cells grown in the presence of U. parvifolia root bark extract showed a faster and dose-dependent growth rate than untreated cells. Collagen protein remodeling during wound-healing may be affected by proteolytic activity in the extracellular matrix by matrix metalloproteinases (MMPs). MMPs play an essential role in all stages of wound-healing during normal tissue remodeling and morphogenesis by modifying the wound matrix. Understanding the role of MMPs during infection and chronic tissue repair could pave the way in identifying potential targets for chronic wounds. In addition, MMPs also regulate cell-cell and cell-matrix signaling by releasing cytokines and growth factors sequestered in the extracellular matrix (ECM). TGF-β is a family of growth factors that play an essential role in wound-healing by regulating the inflammatory response, keratinocyte proliferation and migration, angiogenesis, collagen synthesis, and ECM remodeling.3\n\nAloe vera\n\nAloe vera extract contains mannose-6-phosphate, increasing wound contraction and collagen synthesis. Isolated polysaccharides from Aloe vera also induce matrix metallopeptidase (MMP)-3 and metallopeptidase inhibitor-2 gene expression during wound repair (Figure 8).27 The gel was tested to be non-cytotoxic against nauplii and compatible with human blood and skin cells. The Aloe vera promotes the attachment and proliferation of HaCaT and HFF1 cells. It also significantly accelerated wound closure through re-epithelialization and wound.28 Aloe vera gel exhibited significant wound-healing properties as indicated by the statistically significant increase in the percentage of wound closure and migration rate for the two highest concentrations used.29\n\nHibiscus syriacus\n\nHibiscus syriacus (HS) contains flavonoids (dihydroquercetin, herbacetin, and kaempferol) (Figure 9). HS ethanol extract accelerated wound-healing activity in epithelial formation and fibronectin production. In addition, HS enhances the expression of genes involved in skin hydration and homeostasis. HS contains compounds that can stimulate the expression of biomarkers relevant to skin regeneration and hydration, thereby counteracting the molecular pathways that cause skin damage and aging. Fibroblasts and keratinocytes are the keys to the wound-healing process in the skin. Treatment of HaCaT cells with 0,002% HS for 24 hours significantly improved the wound-healing response. Wound repair at 0,002 and 0,01% HS increased by 50 and 20%, respectively. Aquaporin 3 (Aqp3) is an integral membrane pore protein expressed more in the basal than in the upper layers of the epidermis. Specifically, the Aqp3 and filaggrin genes were increased by 20 and 58%, respectively. Aqp3 selectively conducts water molecules in and out of cells and prevents the passage of ions and other solutes. Filaggrin is a filament-associated protein that binds to keratin fibers and is responsible for the integrity and waterproofing capacity of the top layer of skin.13\n\nSideroxylon obtusifolium (Roem. & Schult.)\n\nN-Methyl-(2S,4R)-trans-4-Hydroxy-L-Proline (NMP) from the leaves of Sideroxylon obtusifolium (Brazilian medicinal species) has activity as anti-inflammatory and wound-healing management (Figure 10).30 A previous study showed that the methanol fraction of Sideroxylon obtusifolium (MFSO) (50 μg/mL) stimulated HaCaT cells by increasing proliferation and migration rates keratinocytes during wound-healing. MFSO demonstrated stimulation of human keratinocytes (HaCaT) cells and enhanced wound-healing through modulation of inflammation in burns.31\n\nAlternanthera sessilis\n\nAlternanthera sessilis contains 2,4-dihydroxy-2,5-dimethyl-3(2H)-furan-3-one (8,92%), hexadecanoic acid (7,21%), palmitate (5,65%), and L-glutamic acid (5,04 %) (Figure 11). The highest concentration of extract treatment (50 μg/mL) showed a migration rate of 99%. The extract showed a strong positive result of 65%, with a difference of 14% in the migration rate between the two. The extract may act on broad signaling receptors to promote proliferation and migration in HaCat. Higher concentrations are required for epithelial barrier stimulation, while lower doses are sufficient to trigger connective tissue cellular compounds.1\n\nWedelia trilobata L.\n\nGrandiflorenic acid from Wedelia trilobata leaves was assessed for its possible activity on HaCaT keratinocyte proliferation and its effects on in vitro scratch tests, collagen content, TGF-β2 levels, and nitric oxide, TNF- and IL-1β determinations using Raw 264.7 cells. Grandiflorenic acid (2,5 μg/mL) resulted in a 106% percentage of HaCaT keratinocyte viability, induced a migration rate of 100% in the initial in vitro assay, and the collagen content increased to 171,2 μg/mL compared to control (61,1μg/mL) with human fibroblasts. Grandiflorenic acid has potential wound-healing activity due to fibroblast stimulation and inhibition of prolongation of the inflammatory phase of wound-healing, as evidenced by a decrease in inflammatory cytokine levels from Raw 264.7 macrophage cells. Grandiflorenic acid and proteoglycans increased collagen production (Figure 12).12\n\nAegle marmelos L.\n\nThe active compounds isolated from Maja flower (Aegle marmelos L.) are cineol, eugenol, cuminaldehyde, aegelin, 1-hydroxy-5, 7-dimethoxy-2 naphthalene-carboxaldehyde (HDNC), and Luvangetin, which had been purified >98% (Figure 13). Treatment with Maja flowers for 24 hours drastically increases cell motility and expression of keratinocytes in specific cell lines. It enhances protein expression in loricrin, filaggrin, and involucrin (a keratinocyte differentiation marker). Keratinocyte motility is enhanced by the ERK and Akt signaling pathways.32\n\nEriobotryae folium\n\nThe leaves of Eriobotrya japonica contain amygdalin (laetrile and vitamin B1) which have antioxidant activity with an IC50 value of 56,59 μg/mL (Figure 14).33 The ethanolic extract of Eriobotryae folium (EF) increases intracellular and extracellular PGE2 levels in HaCaT cells and inhibits 15-PGDH (ED50: 168,4 μg/mL) with relatively low cytotoxicity (IC50: 250,0 μg/mL). On the other study, EF extract suppressed LPS-induced nitric oxide and PGE2 production by inhibiting inducible nitric oxide synthase and COX-2 expression in lipopolysaccharides that stimulated RAW264 cells decreased MRP4 and PGT expression.34\n\nGlycyrrhiza glabra\n\nGlycyrrhiza glabra (GG) has a positive proliferative effect on keratinocytes. The larger the dose, the higher the rate of proliferation. GG inhibits abnormal cell proliferation and is anticarcinogenic. Although GG has been shown to increase the rate of cell proliferation and migration of keratinocytes and promote wound-healing, the underlying mechanism is unclear. However, GG helps activate proliferation and cytoskeletal rearrangement proteins and promotes wound-healing. The antioxidant effect of some GG constituents, such as glycyrrhizin and glabridin, may also help enhance the wound-healing ability of keratinocytes (Figure 15).35\n\nCalabrian honey\n\nBL1 (multifloral) and BL5 (orange) honey showed the best healing properties among the five kinds of honey tested. Pinocembrin revealed in honey samples BL1 and BL5, is a flavanol with known biological activities, including wound-healing. At high concentrations or after prolonged contact, polyphenols can reduce the production of pro-inflammatory cytokines and interact with metabolism and cell proliferation, thereby healing wounds. Pinocembrin in vitro modulates the production of inflammatory cytokines, such as TNF-, IL-1β, IL-6, and IL-10, by suppressing NF-κB and MAPK activation.36 Pinocembrin and its 7-linolenoyl derivative were found to be innovative wound-healing agents. Immunofluorescence and functional assays showed that GPR120 mediated the activity. Pinocembrin was able to produce wound-healing of HaCaT cells after 6 and 24 h by about +30% compared to untreated. In contrast, the 7-linolenoyl derivative increased HaCaT wound closure by about +40% compared to untreated controls. Activation of GPR120 can impair by increasing levels of TGF-β, which triggers the synthesis of components of the extracellular matrix, thereby contributing to wound-healing induced by keratinocytes. Complex signaling pathways involved in the upregulation of MMPs and the turnover of extracellular matrix components stimulated by attendants can lead to tissue damage or repair processes. In particular, MMP-9 plays an essential role in cell migration and re-epithelialization (Figure 16).37\n\nThymus vulgaris L.\n\nPrevious studies showed that Thyme oleoresin at 25 μg/mL and 50 μg/mL significantly promoted HaCaT cell migration, leading to wound closure. The upper part of the plant is reported to have significant components such as p-cymene, α -terpinene, and thymol (Figure 17). Possible mechanisms in wound-healing are its ability to maintain wound moisture, wound-healing, increase oxygenation by increasing blood supply, increase epithelial cell migration, rapid maturation of collagen and reduce inflammation, increase collagen synthesis, increase the synthesis of hyaluronic acid and dermatan sulfate in wound tissue.38\n\nTrapa japonica\n\nTrapa japonica contains fiber and polyphenols, such as ellagic acid, eugeniin, and gallic acid, which have antioxidant and anti-inflammatory activities (Figure 18). The results showed that the extract of T. japonica decreased the TNF-α, thus significantly decreasing MMP-1 and MMP-9 mRNA expression.39\n\nGracilaria lemaneiformis\n\nGracilaria lemaneiformis contains sulfated galactan, which is anti-inflammatory and antioxidant (Figure 19). The purified Gracilaria lemaneiformis (GLP-2) fraction promoted cell proliferation and migration of HaCat cells through activation of PI3K/aPKC signaling during wound-healing of human keratinocytes. GLP-2 significantly increased wound-healing activity when compared to control cells. The results showed that GLP treatment could increase lamellipodium formation in migrating HaCaT cells. GLP-2 positively regulates Cdc-42, Rac-1, Par-3, and aPKC in HaCaT cells. Cdc42 induces filopodial extension at the cell periphery, which aids in directional cell migration. Par-3 and aPKC are considered proteins that regulate cell polarity involved in the regulation of cell polarization. Increased Akt phosphorylation was considered as an index of activation of the PI3K signaling pathway after cells were injured. In the present study, a significant increase in Akt phosphorylation was observed in GLP-2-treated cells compared to control cells at 12 h during the wound-healing process.40\n\nNerium indicum\n\nNerium indicum (NI) contains oleandrin, flavonoids, and tannins (Figure 20).41 These plants may vary on keratinocyte activity at the wound site at specific doses. Studies have shown that the test materials used, either alone or in combination, positively affect keratinocyte proliferation and migration, an essential factor required for proper wound closure and wound-healing.35\n\nUrtica dioica L.\n\nUrtica dioica L (UD) extract contains saponins, flavonoids, carbohydrates, ketoses, resins, and coumarins (Figure 21). The UD extract increased the proliferation rates of HEK-293 and HaCaT cells by 39% and 30% after 24 h, respectively, compared to control cells. The extract increased the cell population in the G2/M phase by almost 10%. Moreover, the extract caused a twofold increase in the rate of cell migration of both cell lines compared to the control cells. In addition, the extract was found to have moderate anti-inflammatory and antioxidant properties that enhance the overall wound-healing potential.42\n\nCurcuma amarissima\n\nCurcuma amarissima (CA) contains curcumenol, curdione and curzerenone (Figure 22). The results showed that the cell viability test showed that the CA extract increased the viability of HaCaT cells. This increase in cell viability was related to the CA extract’s pharmacological activity in inducing cell proliferation. CA extract rapidly induces ERK1/2 and Akt activation. Consistently, CA extract accelerated cell migration, resulting in rapid healing of the injured human keratinocyte monolayer. In particular, MEK inhibitors (U0126) or PI3K inhibitors (LY294002) blocked CA-induced enhancement of cell monolayer wound-healing. In addition, CA extract induces the expression of Mcl-1, which is an antiapoptotic protein, supporting that the CA extract enhances the survival of human keratinocytes.7\n\nClausena excavata\n\nThe methanol extract of Clausena excavate contains coumarins, flavonoids, and glycosides with various biological properties. These compounds regulate inflammation through inhibition of the MAPK/NF-κB pathway. In addition, it was shown that methanol extract treatment increased TGF-β1 expression, the cytokine increased wound contraction, extracellular matrix deposition, and collagen formation in wound-healing (Figure 23).43\n\nAngelica gigas\n\nAngelica gigas contains Coumarin, decursin, and decursinol angelate (Figure 24). This extract improves wound-healing with HaCaT human keratinocytes. ERK1/2 phosphorylation is essential for cell survival, proliferation, and inhibition of apoptosis. The expression of genes encoding ECM remodeling proteins, inflammatory cytokines, and growth factors is an essential step in human wound-healing. The simultaneous expression of these genes can accelerate this process.44\n\nSalvia haenkei\n\nSalvia haenkei contains rosmarinic acid (Figure 25). Hydroalcoholic extract of S. haenkei effectively increases the wound closure rate in cultured keratinocytes with the almost total invasion of the scrapes after 48 h of treatment. Gene expression analysis showed that S. haenkei regulates the nuclear factor-κB (NF-κB) transcription factor signaling pathway positively. The results showed that the S. haenkei extract does not cause a statistically significant increase in the rate of fibroblast migration. Specifically, this study analyzed the mRNA levels of several genes involved in the early inflammatory phase of skin repairs, such as the transcriptionally active subunit of the transcription factor NF-κB (RelA), the inflammatory cytokine interleukin-6 (IL-6), and tumor necrosis factor-alpha. (TNF-α), inducible nitric oxide synthase (iNOS or NOS2), and the inducible prostaglandin synthesis enzyme cyclooxygenase-2 (COX-2). Tn with S. haenkei increases the IL-6 in fibroblasts and keratinocytes (83.6 and 19.7-fold induction, respectively), whereas TNFα levels only have a mild increasing trend.11\n\nCrassocephalum crepidioides\n\nCrassocephalum crepidioides (Benth.) S. Moore contains β-cubebene, α-farnesene, and α-caryophyllene, which exhibit antioxidant and anti-inflammatory activities (Figure 26). C. crepidioides (CC) extract exhibited anti-inflammatory in vitro assays on the macrophage cell line RAW 246.7. In addition, reduced inflammatory cell density in granulation tissue in 7-day-old wounds, combined with decreased TNF-α and NF-B1 mRNA expression. NF-B1 and TNF-α are essential markers for the degree of inflammation. High levels of TNF-α have been reported to inhibit wound re-epithelialization, myofibroblast formation, and smooth muscle actin (SMA-α). The results showed that CC could improve the wound-healing process through its anti-inflammatory activity. TGF-β1 mRNA was also found to be elevated in granulation tissue. TGF-β1 is involved in many essential effects on the wound-healing process. The activities of TGF-β1 include the induction of fibroblast proliferation, motivating the differentiation of fibroblasts into myofibroblasts, and increasing the synthesis, deposition, and maturation of collagen. The increase in the TGF-β1 gene may explain the increase in fibroblasts and the wound-healing effect.45\n\nWithania somnifera\n\nWithania somnifera contains withaferin A which has anti-inflammatory, antiangiogenic, antimetastatic, and anticancer activities (Figure 27). The results showed that ashwagandha extract (AE) significantly inhibited mRNA expression of inflammatory cytokines, including interleukin IL-8, IL-6, TNF-α, IL-1β, IL-12, and promoted mRNA expression of the anti-inflammatory cytokine TGF-β1 in HaCaT cells. In addition, AE inhibited lipopolysaccharide-induced phosphorylation of p38 and c-Jun N-terminal kinase, as well as NF-κB p65. The results showed that EA was not toxic to HaCaT cells up to a dose of 10 mg/mL. AE inhibits the MAPK/NF-κB pathway. The NF-κB and MAPK signaling pathways are strongly associated with the expression of inflammatory cytokines in HaCaT cells.16\n\nAnemarrhena asphodeloides\n\nMangiferin has been isolated from the plant Anemarrhena asphodeloides (Figure 28). A. asphodeloides (AA) extract promoted inhibiting Th2-type cytokines, pro-inflammatory cytokines, and filaggrin restoration in HaCaT cells. TNF-α/IFN-γ significantly increased mRNA expression of IL-4 in HaCaT keratinocytes. However, pretreatment with AA significantly suppressed the mRNA expression of IL-4. AA pretreatment of TNF-/IFNγ-stimulated HaCaT keratinocytes reduced IL-13 mRNA expression. However, pretreatment with AA significantly suppressed the mRNA expression of IL-6 in a dose-dependent manner. These results suggest that AA has a protective effect on skin keratinocytes by inhibiting the transcription of inflammatory cytokine levels associated with skin barrier dysfunction. TNF-α/IFN-γ co-stimulation decreased filaggrin protein expression and mRNA levels, but pretreatment with AA significantly increased filaggrin protein levels, although mRNA levels increased slightly. The results showed that AA had a filaggrin-recovery effect on TNF-α/IFN-γ-stimulated HaCaT keratinocytes. Treatment with AA increased Keratinocyte HaCaT migration and inhibited the expression of iNOS protein levels. It is possible to assume that AA facilitates wound-healing in the skin barrier through the inhibition of overexpression.46\n\nSasa veitchii\n\nSasa veitchii is a traditional plant that contains lignin, polysaccharides, and chlorophyll (Figure 29). It has many pharmacological activities such as antioxidant, anti-inflammatory, antibacterial and anticancer. HaCaT cells treated with S. veitchii extract for 72 hours showed significantly higher AQP3 expression and mitogen-activated p38 phosphorylated protein kinase (MAPK) than control cells. S. veitchii extract increases AQP3 expression and provides wound-healing and healing effects. The increase in AQP3 expression elicited by the Kumazasa extract may be due to increased transcription via activation of p38 MAPK signaling. It was also found that S. veitchii extract had a proliferative effect on HaCaT cells.47\n\nPeriplaneta americana\n\nPeriplaneta americana contains polyalcohols, amino acids, pyrimidines, uracils, and proteoglycans (Figure 30). P. americana extract showed effects in wound-healing that depend on the Janus-activated kinase/signal transducer pathway and transcriptional activator 3 (JAK/STAT3) and Smad3 activity. Pretreatment with STAT3 inhibitors blocked cell proliferation and migration. This extract promotes the proliferation and migration of immortalized human keratinocyte HaCaT cells. The results showed increased keratinocyte proliferation and migration after treatment (0,3125 mg/mL) for 48 hours. After treatment, JAK/STAT3 signaling expression and Smad3 activation, NF-κB/p65, and β-catenin was significantly upregulated in HaCaT cells and wound tissue after treatment. However, NF-κB and Wnt signaling appear to be minimally activated regardless of the limited expression of NF-κB/P65 and β-catenin upregulation or cell nuclear translocation.48\n\nAngelica tenuissima\n\nAngelica tenuissima root contains decursin and Z-ligustilide (Figure 31). The root extract of A. tenuissima accelerates wound filling under basal conditions in the keratinocytes that make up the epidermal layer. It inhibits the mRNA expression of MMP-1 and elastase. It also increases the collagen content as indicated by the production and secretion of type I procollagen with or without UVB exposure. This extract could be beneficial in suppressing UVB-mediated wrinkling of skin formation and photoaging by increasing PIP levels and decreasing MMP-1 and elastase activity. A. tenuissima can play a role in attenuating the inflammatory response caused by UVB irradiation through upregulation of photo-protective hemeoxygease-1 and suppressing pro-inflammatory cyclooxygenase-2 expression.46\n\nAstragali radix\n\nAstragaloside VI (AS-VI) and cycloastragenol-6-O-beta-D-glucoside (CMG) (Figure 32) enhance skin cell proliferation and migration via activation of the EGFR/ERK signaling pathway, resulting in enhanced wound-healing in vitro. AS-VI actively promotes the proliferation of human keratinocytes (HaCaT) by activating the ERK1/2 pathway rather than the JNK and p38 pathways. This plant shows that astragaloside can activate cellular processes involved in wound-healing. It is mediated, at least in part, by EGFR/ERK1/2, which could be beneficial in wound closure.49\n\nMimosa tenuiflora (Willd)\n\nMimosa tenuiflora bark contains high amounts of saponins and polyphenols such as arabinogalactan (Figure 33). Mimosa tenuiflora (Willd) aqueous extract at concentrations of 10 μg/mL and 100 μg/mL indicated a loss of cell viability and proliferation of dermal fibroblasts. Isolated, ethanol-precipitated compounds (EPC) (10 μg/mL) have shown strong potential to increase viability by stimulating mitochondrial activity and dermal fibroblast proliferation. Stimulation of human keratinocytes was only found at a concentration of 100 μg/mL. EPC did not influence the expression of specific proliferation and differentiation-related genes. Fibroblasts in the connective tissue are the main targets of the arabinogalactan polymer compound from Mimosa tenuiflora. Intense fibroblast stimulation can be noted to initiate wound closure and production of extracellular and filling materials within the wound.50\n\nFitzroya cupressoides\n\nFitzroya cupressoides, commonly called allerce, contain fatty acids, mono and sesquiterpenes, diterpenes, lignans, and phytosterols. Diterpenes and lignans were the most active compounds, with the biomolecules matairesinol, podophyllotoxin, and ferruginol (Figure 34). Allerce extract has a significant effect on wound-healing. The results showed that the extract stimulated cell division in human skin epidermal cells in the context of wound repair. These results also indicated that allerce extract accelerated the healing process after 24 and 48 h of treatment. This effect was promoted principally by stimulating HaCaT cell division in the context of wound repair.51\n\nPlantago australis\n\nThe hydroethanolic extract of Plantago australis contains verbascoside (Figure 35). P. australis extract and verbascoside decreased cell viability at 1000 μg/mL and 100 μg/mL, respectively. The results showed approximately 81,06% wound closure (P. australis extract 25 μg/mL) and 58,7% and 57,77% (Verbascoside 5 and 10 μg/mL). P. australis extract showed a significant reduction in TNF-α. These compounds have wound-healing activity, increase cell migration, and reverse the effects of oxidation in lipopolysaccharide-activated N9 cells. This effect may also be associated with decreased TNF-α, IL-6, IL-12p70, INF-γ, and MCP-1.52\n\n\nConclusion\n\nThe wound-healing mechanism includes processes that restore skin integrity through four stages: hemostasis, inflammation, multiplication, and remodelling. Antioxidant and anti-inflammatory activities play an essential role in wound-healing mechanisms. Many compounds in plants have been studied to have activity in wound-healing by various mechanisms.\n\n\nData availability\n\nFigshare. PRISMA statement checklist. DOI: https://doi.org/10.6084/m9.figshare.19736032.53",
"appendix": "References\n\nMuniandy K, Sivapragasam G, Sean TW, et al.: In Vitro Wound-healing Potential of Stem Extract of Alternanthera sessilis. Evidence-based Complement. Altern. Med. 2018; 2018: 1–13. PubMed Abstract | Publisher Full Text\n\nCao G, Chen B, Zhang X, et al.: Human adipose-derived mesenchymal stem cells-derived exosomal microRNA-19b promotes the healing of skin wounds through modulation of the CCL1/TGF-β signaling axis. Clin. Cosmet. Investig. Dermatol. 2020; 13: 957–971. PubMed Abstract | Publisher Full Text\n\nKang MC, Yumnam S, Park WS, et al.: Ulmus parvifolia accelerates skin wound-healing by regulating the expression of MMPs and TGF-β. J. Clin. Med. 2020; 9(1): 1–11. Publisher Full Text\n\nSorg H, Tilkorn DJ, Hager S, et al.: Skin Wound-healing: An Update on the Current Knowledge and Concepts. Eur. Surg. Res. 2017; 58(1–2): 81–94. PubMed Abstract | Publisher Full Text\n\nGlady A, Vandebroek A, Yasui M: Human keratinocyte-derived extracellular vesicles activate the MAPKinase pathway and promote cell migration and proliferation in vitro. Inflamm. Regen. 2021; 41(1): 4. PubMed Abstract | Publisher Full Text\n\nAslantürk ÖS, Aşkın Çelik T, Sönmez YM: Investigation of Antioxidant and in vitro Wound-healing Activity of Fulvic Acid. J. Inst. Sci. Technol. 2019; 9(3): 1316–1326. Publisher Full Text\n\nNimlamool W, Saranyapin P, Jirapak R, et al.: Curcuma amarissima extract activates growth and survival signal transduction networks to stimulate proliferation of human keratinocyte. Biology (Basel). 2021; 10(4). PubMed Abstract | Publisher Full Text\n\nBucekova M, Martin S, Ivana V, et al.: Bee-derived antibacterial peptide, defensin-1, promotes wound re-epithelialisation in vitro and in vivo. Sci. Rep. 2017; 7(1): 7313–7340. PubMed Abstract | Publisher Full Text\n\nKim D, Ku B, Choi EM: Se-methylselenocysteine stimulates migration and antioxidant response in HaCaT keratinocytes: Implications for wound-healing. J. Trace Elem. Med. Biol. 2020; 58: 126426. PubMed Abstract | Publisher Full Text\n\nRitto D, Supita T, Sawana S, et al.: Astaxanthin induces migration in human skin keratinocytes via Rac1 activation and RhoA inhibition. Nutr. Res. Pract. 2017; 11(4): 275–280. PubMed Abstract | Publisher Full Text\n\nScrima M, Carmela M, Filomena M, et al.: Evaluation of wound-healing activity of salvia haenkei hydroalcoholic aerial part extract on in vitro and in vivo experimental models. Clin. Cosmet. Investig. Dermatol. 2020; Volume 13: 627–637. PubMed Abstract | Publisher Full Text\n\nBalekar N, Nakpheng T, Srichana T: Wound-healing potential of grandiflorenic acid isolated from Wedelia trilobata (L.) leaves. Songklanakarin J. Sci. Technol. 2013; 35(5): 537–546.\n\nDi Martino O, Tito A, De Lucia A, et al.: Hibiscus syriacus Extract from an Established Cell Culture Stimulates Skin Wound-healing. Biomed. Res. Int. 2017; 2017: 1–9. PubMed Abstract | Publisher Full Text\n\nPage MJ, Joanne ME, Patrick BM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews Systematic reviews and Meta-Analyses.2021. Publisher Full Text\n\nZhu M, Yunpeng C, Qianwen S, et al.: Mesenchymal stromal cells pretreated with pro-inflammatory cytokines promote skin wound-healing through VEGFC-mediated angiogenesis. Stem Cells Transl. Med. 2020; 9(10): 1218–1232. PubMed Abstract | Publisher Full Text\n\nSikandan A, Shinomiya T, Nagahara Y: Ashwagandha root extract exerts anti-inflammatory effects in HaCaT cells by inhibiting the MAPK/NF-κB pathways and by regulating cytokines. Int. J. Mol. Med. 2018; 42(1): 425–434. PubMed Abstract | Publisher Full Text\n\nMuthukumar T, Anbarasu K, Prakash D, et al.: Effect of growth factors and pro-inflammatory cytokines by the collagen biocomposite dressing material containing Macrotyloma uniflorum plant extract-In vivo wound-healing. Colloids Surfaces B Biointerfaces. 2014; 121: 178–188. PubMed Abstract | Publisher Full Text\n\nBan E, Seonghee J, Mijung P, et al.: Accelerated wound-healing in diabetic mice by miRNA-497 and its anti-inflammatory activity. Biomed. Pharmacother. 2020; 121(August 2019): 109613. PubMed Abstract | Publisher Full Text\n\nSu L, Lanqing F, Xiaodong L, et al.: Loss of CAR promotes migration and proliferation of HaCaT cells, and accelerates wound-healing in rats via Src-p38 MAPK pathway. Sci. Rep. 2016; 6(December 2015): 1–13. PubMed Abstract | Publisher Full Text\n\nNandhini DU, Nandhini U, Rajasekar M, et al.: A review on worm killer: Aristolochia bracteolata. J. Pharmacogn. Phytochem. 2017; 6(2): 06–09. Reference Source\n\nGirija DM, Kalachaveedu M, Subbarayan R, et al.: Aristolochia bracteolata enhances wound-healing in vitro through anti-inflammatory and proliferative effect on human dermal fibroblasts and keratinocytes. Pharm. J. 2017; 9(6): s129–s136. Publisher Full Text\n\nJuneja K, Mishra R, Chauhan S, et al.: Metabolite profiling and wound-healing activity of Boerhavia diffusa leaf extracts using in vitro and in vivo models. J. Tradit. Complement. Med. 2020; 10(1): 52–59. PubMed Abstract | Publisher Full Text\n\nPetrovick GF, Petrovick PR, Bassani VL: Achyrocline satureioides (Lam.) DC., Asteraceae: Development of granules from spray dried powder. Brazilian J. Pharmacogn. 2010; 20(5): 796–803. Publisher Full Text\n\nBalestrin LA, Tainá K, Silveira FFN, et al.: Achyrocline satureioides (Lam.) dc (asteraceae) extract-loaded nanoemulsions as a promising topical wound-healing delivery system: in vitro assessments in human keratinocytes (hacat) and het-cam irritant potential. Pharmaceutics. 2021; 13(8) PubMed Abstract | Publisher Full Text\n\nNguyen VL, Tri TC, Quan NBC, et al.: Anti-inflammatory and wound-healing activities of calophyllolide isolated from Calophyllum inophyllum Linn. PLoS One. 2017; 12(10): 1–16. PubMed Abstract | Publisher Full Text\n\nIrfan M, Woo KH, Ha LD, et al.: Ulmus parvifolia Modulates Platelet Functions and Inhibits Thrombus Formation by Regulating Integrin αIIbβ3 and cAMP Signaling. Front. Pharmacol. 2020; 11(May): 1–11. PubMed Abstract | Publisher Full Text\n\nAnanda H, Ade Z: REVIEW: AKTIVITAS TANAMAN LIDAH BUAYA (Aloe vera Linn) SEBAGAI PENYEMBUH LUKA. Farmaka. 2014; 15(2): 82–89.\n\nRahman MS, Rashedul I, Masud RM, et al.: Characterization of burn wound-healing gel prepared from human amniotic membrane and Aloe vera extract. BMC Complement. Altern. Med. 2019; 19(1): 1–15. PubMed Abstract | Publisher Full Text\n\nMorné F, Clarissa W, Sias H, et al.: Wound-healing Effects of Aloe muth-muth: in vitro Investigations Using Immortalized Human Keratinocytes (HaCaT). Biology (Basel). 2020; 9: 1–10. Publisher Full Text\n\nde Aquino PEA, TFG de Silva , Almeida SF, et al.: The Wound-healing Property of N-Methyl-(2S,4R)-trans-4-Hydroxy-L-Proline from Sideroxylon obtusifolium is Related to its Anti-Inflammatory and Antioxidant Actions. J. Evidence-Based Integr. Med. 2019; 24: 2515690X1986516. PubMed Abstract | Publisher Full Text\n\nde Souza TdFG , Magalhães PT, Soares MF, et al.: Human keratinocyte (HaCaT) stimulation and healing effect of the methanol fraction from the decoction from leaf from Sideroxylon obtusifolium (Roem. & Schult.) T.D. Penn on experimental burn wound model. bioRxiv. 2020. Publisher Full Text\n\nAzmi L, Sébastien H, Adeline KO, et al.: In vitro wound-healing activity of 1-hydroxy-5,7-dimethoxy-2-naphthalene-carboxaldehyde (HDNC) and other isolates of Aegle marmelos L.: Enhances keratinocytes motility via Wnt/β-catenin and RAS-ERK pathways. Saudi Pharm. J. 2019; 27(4): 532–539. PubMed Abstract | Publisher Full Text\n\nMarianne RS, Septiani R, Yuliana Y: Aktivitas Antioksidan Ekstrak Etanol Daun Biwa (Eriobotrya japonica (Thunb.) Lindl.) Terhadap DPPH (1,1-diphenyl-2-picrylhydrazyl). Talent. Conf. Ser. Trop. Med. 2018; 1(3): 086–089. Publisher Full Text\n\nIm DY, Lee KI: Prostaglandin E 2 Up-regulation and Wound-healing Effect of the Ethanol Extract of Eriobotryae Folium in Human Keratinocyte. Korean J. Med. Crop Sci. 2014; 22(6): 457–462. Publisher Full Text\n\nKotian SR, Bhat KMR, Padma D, et al.: Influence of traditional medicines on the activity of keratinocytes in wound-healing: An in-vitro study. Anat. Cell Biol. 2019; 52(3): 324–332. PubMed Abstract | Publisher Full Text\n\nGoverna P, Carullo G, Biagi M, et al.: Evaluation of the in vitro wound-healing activity of calabrian honeys. Antioxidants. 2019; 8(2): 1–16. PubMed Abstract | Publisher Full Text\n\nMazzotta S, Paolo G, Vittoria B, et al.: Pinocembrin and its linolenoyl ester derivative induce wound-healing activity in HaCaT cell line potentially involving a GPR120/FFA4 mediated pathway. Bioorg. Chem. 2020; 108(October): 2021. PubMed Abstract | Publisher Full Text\n\nAnitha ROY, Subeeksha VS, Lakshmi T: The wound-healing property of thyme oleoresin from thymus vulgaris l. On hacat keratinocytes. Asian J. Pharm. Clin. Res. 2018; 11(9): 169–171. Publisher Full Text\n\nJang JD, Minkyung K, He NG, et al.: Antiaging Activity of Peptide Identified from Fermented Trapa Japonica Fruit Extract in Human Dermal Fibroblasts. Evidence-based Complement. Altern. Med. 2020; 2020: 1–8. PubMed Abstract | Publisher Full Text\n\nVeeraperumal S, Mai QH, Shan ZS, et al.: Polysaccharides from Gracilaria lemaneiformis promote the HaCaT keratinocytes wound-healing by polarised and directional cell migration. Carbohydr. Polym. 2020; 241(March): 116310. PubMed Abstract | Publisher Full Text\n\nChetwani K, Agnihotri RK, Chaturvedi P: Aqueous, Acetone and Ethanolic extract of Nerium indicum L. as potential antibacterial agent against Pseudomonosa aeruginosa. Int. J. Appl. Environ. Sci. 2017; 12(9): 1721–1732.\n\nKasouni AI, Chatzimitakos TG, Stalikas CD, et al.: The Unexplored Wound-healing Activity of Urtica dioica L. Extract: An in vitro and in vivo Study.2021; pp. 1–20.\n\nAalbaayit SFA, Abba Y, Rasedee A, et al.: Effect of Clausena excavata Burm. F. (Rrutaceae) leaf extract on wound-healing and antioxidant activity in rats. Drug Des. Devel. Ther. 2015; 9: 3507–3518. PubMed Abstract | Publisher Full Text\n\nHan J, Wook J, Anh HN, et al.: Decursin and decursinol angelate improve wound-healing by upregulating transcription of genes encoding extracellular matrix remodeling proteins, inflammatory cytokines, and growth factors in human keratinocytes. Biochem. Biophys. Res. Commun. 2018; 499(4): 979–984. PubMed Abstract | Publisher Full Text\n\nCan NM, Thao DTP, Gil G: Wound-healing Activity of Crassocephalum crepidioides (Benth.) S. Moore. Leaf Hydroethanolic Extract. Oxidative Med. Cell. Longev. 2020; 2020: 1–10. PubMed Abstract | Publisher Full Text\n\nPark YA, Ryul LS, Woo LJ, et al.: Suppressive effect of fermented Angelica tenuissima root extract against photoaging: Possible involvement of hemeoxygenase-1. J. Microbiol. Biotechnol. 2018; 28(8): 1391–1400. PubMed Abstract | Publisher Full Text\n\nIkarashi N, Miho K, Izumi F, et al.: Wound-healing and skin-moisturizing effects of sasa veitchii extract. Healthcare. 2021; 9(6): 1–12. PubMed Abstract | Publisher Full Text\n\nSong Q, Xie Y, Gou Q, et al.: JAK/STAT3 and Smad3 activities are required for thewound-healing properties of Periplaneta americana extracts. Int. J. Mol. Med. 2017; 40(2): 465–473. PubMed Abstract | Publisher Full Text\n\nLee SY, Liang CW, Xiang LZ, et al.: Astragaloside VI and cycloastragenol-6-O-beta-D-glucoside promote wound-healing in vitro and in vivo. Phytomedicine. 2018; 38(December 2016): 183–191. PubMed Abstract | Publisher Full Text\n\nZippel J, Deters A, Hensel A: Arabinogalactans from Mimosa tenuiflora (Willd.) Poiret bark as active principles for wound-healing properties: Specific enhancement of dermal fibroblast activity and minor influence on HaCaT keratinocytes. J. Ethnopharmacol. 2009; 124(3): 391–396. PubMed Abstract | Publisher Full Text\n\nCarvajal F, Duran C, Aquea F: Effect of alerce (Fitzroya cupressoides) cell culture extract on wound-healing repair in a human keratinocyte cell line. J. Cosmet. Dermatol. 2020; 19(5): 1254–1259. PubMed Abstract | Publisher Full Text\n\nde Moura Sperotto ND , Luiza S, Moisés VR, et al.: Wound-healing and anti-inflammatory activities induced by a Plantago australis hydroethanolic extract standardized in verbascoside. J. Ethnopharmacol. 2018; 225(April): 178–188. PubMed Abstract | Publisher Full Text\n\nFristiohady A: PRISMA_2020_checklist (1).docx. figshare. Dataset. 2022. Publisher Full Text"
}
|
[
{
"id": "139306",
"date": "20 Jun 2022",
"name": "Kok-Yong Chin",
"expertise": [
"Reviewer Expertise Natural products",
"bone and joint metabolism"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe abstract is not informative. The background should cover the rationale of using plant material in facilitating wound healing. The results should cover the common pathways of different plants in promoting wound healing.\n\nIntroduction: the anatomy of the skin and the process of wound healing should be presented here, not in the results.\n\nMethods: PRISMA flow chart on article identification. The rationales for limiting years of publication to 2009-2021 were not presented. Other details like article management were not disclosed. This makes the search not replicable.\n\nResults: There is no effort in the synthesis of search results.\n\nThere is no discussion, no schematic diagram to sum up the mechanisms of plant-derived substances involved in facilitating wound healing.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No",
"responses": []
},
{
"id": "141489",
"date": "19 Jul 2022",
"name": "David Leavesley",
"expertise": [
"Reviewer Expertise Cutaneous wound healing and tissue repair",
"human epithelial cell physiology",
"extracellular interface."
],
"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 document claims to be a systematic review of human keratinocyte wound healing in response to exogenously applied products derived from natural materials; specifically, products manufactured from plants. Traditional and Complementary Medicine (T&CM) practices based on natural products provide essential health care for more than half of the world population (WHO). However, 17.5% (1 in 6) of WHO Member States include T&CM in their national essential medicines list. This review discusses including T&CM in the clinical management of cutaneous wound healing.\nIntroduction\nI recommend that the authors expand their summary “Skin protects against environmental factors such as harmful UV rays and pathogens and prevents water loss”, to include less widely-recognised functions of skin. For example, skin is integral to our immune, nervous and endocrine systems, providing sensory functions (touch, vibration, temperature, electromagnetic energy, pain), thermoregulation, excretion (sweat), storage (water, blood, fats, glycans, xenobiotics), recognition and detection of pathogens, chemicals, toxins, and synthesizes many critical enzymes, antimicrobials, and biological response modifiers (e.g. hormones, cytokines, adipokines, chemokines, neuropeptides). (See Exp Dermatol. 2002; 11(2): 159–187)1\nIt is not clear to me why “wound-healing” might be considered a “barrier” [Introduction]. Perhaps it is because wound-healing restores skin barrier functions?\nI am also at a loss to comprehend why “epithelialization is referred to as faulty epidermis breakdown” [Introduction]. Epithelialisation is the process that demarcates initial responses to injury, that collectively attempt to reestablish barrier function and cutaneous homeostasis, from subsequent physiological events, that collectively attempt to restore skin structure and secondary functions.\nNot all “traditional medicine” (T&CM), “is based on plant sources”. [Introduction] This statement is misleading.\nIt is not made clear that referred to “Secondary metabolites” are molecular species derived from processing compounds present in T&CM. [Introduction]\nI fail to comprehend how “Growth rates” represent “a source of many biochemicals” (sic)? A rate describes something the changes over time. Is the author referring to biochemical products that change over time as a cause, or an effect, of wound healing processes?\nHaCaT cells are epithelial. HaCaT cells are not capable of modelling mesenchymal cells, the cell type that constitute the human dermis. The statement is inaccurate. Importantly, HaCaT cells have been characterised as a premalignant phenotype (Am J Pathol. 2001; 159(4): 1567–1579)2. It is not clear how cells having this genotype / phenotype recapitulate normal human skin?\nI disagree that “high availability and ease of cell culture” are robust, relevant criteria, to select HaCaT as suitable to model human skin in vitro.\n\nEligibility Criteria\nI am confused. How can inclusion criteria specify “2. The studies using an in vitro approach”; yet exclusion criteria specify “3. In vitro studies”.\nSearch Strategy\nSearch strategy is claimed to be “advanced search in three databases, PubMed and Google Scholar…” using MeSH terms and Boolian operators: “Wound-healing AND HaCaT Cells AND Compounds AND Extracts”.\nFYI, “Please identify the third database?\nSearches of the database using the Boolian operator “AND” will severely limit results to strings that only include all three terms. Strings that did not include the words “Cells”, or “Compounds”, or “Extracts” would not be found. As Compounds” is not a recognised MeSH Term (www.nlm.nih.gov/mesh/meshhome), not data should be expected to be returned from the search, as described in this manuscript. Please revise using the accurate search strategy. In my opinion, this strategy (i.e. using Boolian operators), introduces bias into the search results. For example, works that instead used “tissue repair”, “skin repair”, “skin healing’, “traditional Chinese medicine”, “indigenous medicine”, “wound care”, “herbal medicine”, “wound treatment”, “supplement”, “botanical”, “mixture”, “formulation”, “preparation”, would not be returned.\nWhat was the rationale for inclusion criteria: “3. studies were published from 8th October 2021 up to 31st March 2022”, but subsequently limiting selected publications to “2. Year of publication – 2009-2021”?\nWhat effect did selecting articles using “3. Study objectives – wound-healing mechanism of several compounds and extracts in HaCaT cells”, have on studies reporting results acquire from analysis of single ‘compounds and extracts’?\nSynthesis of Results\nWhat is the origin of “different HaCaT cells”?\nResults\nThe opening paragraph reporting Results, is a repeat of discussion previously reported in the Introduction.\nFigure 1 reports the gross anatomy of human skin. It identifies the “Subcutaneous layer” (sic); however, no mention of the subcutaneous layer is present in the text.\nWound-healing\nThe data cited in support of “Wound-healing processes restore skin integrity through four stages: hemostasis, inflammation, multiplication, and remodeling” (sic) are inappropriate. Please replace with original references, for example Singer & Clark. N Engl J Med. 1999. 341(10):738-463.\nThe descriptor “multiplication” phase is ambiguous. The four phases of mammalian cutaneous wound-healing are usually described with adjectives. Thus, more commonly these are: hemostasis, inflammation, proliferation, and remodeling.\nAfter identifying the four phases of wound-healing, the nomenclature is immediately changed to “Coagulation phase”, “Inflammatory phase”, “Proliferation phase” and “Remodeling phase”.\nWhat are “IL-1?, IL-6, IL-8, and TNF, and growth factors such as PDGF, TGF-?, TGF-?, IGF-1, and FGF”? These abbreviations have not previously been described.\nThe statement “Restoring the basal keratinocyte layer in the basement membrane between the epidermis and the dermis begins to proliferate through various signaling molecules during the proliferative stage” (sic) does not make sense. How does the “basement membrane… begin to proliferate”? What is “a certain level of repair”?\nHow does “the cytoplasmic shape of the keratinocytes… alter(ed) to move to the upper layers of the epidermis”? This statement is misleading; the shape of keratinocytes does not facilitate cell motility. Cell motility, also called cell migration, is a dynamic process involving intracellular second messenger molecules, cytoskeleton (actin microfilaments, tubulin microtubules, keratin intermediate filaments, and a large population of accessory molecules that include adhesive glycoproteins, crosslinking proteins, signalling molecules, ATPases, GTPases.\nThere is no evidence that keratinocytes “transform” as they migrate apically during squamous differentiation. The term “transform” has a specific meaning in human biology; it is unrelated to differentiation.\nThe metaphorical concept that “the proliferation and migration of keratinocytes suture the wound site during wound-healing”, is not widely supported. While this concept might be appropriate to describe cutaneous wound-healing in rodents and mammals, where healing occurs primarily by contraction, it does not describe cutaneous wound-healing as it occurs in humans. In humans, cutaneous wound-healing is mediated primarily by reepithelialisation; only a minor contribution is from contraction. There is nothing akin to sutures in cutaneous wound-healing in humans.\nFigure 2 is inaccurate and misleading. 1. Pathogens are located in the dermis, beneath an intact basement membrane. 2. Mast cells are illustrated, but not described in the text.\nI recommend that Figures 3 – 35 be combined and presented as a single figure, or possibly as a table.\n“Plants are the potential…l” is grammatically incorrect. It should read ‘Plants have the potential…’\nIt would be helpful for the reader to be informed what is the basis for selecting the plant species, subjects of subsequent discussion.\nThe statement “wound closure was 50,38%±1,39 and 69,81%±1,89, respectively” is meaningless without also reporting closure measures from untreated, control wounds evaluated in the same “wound-healing study” (sic). The wound-healing study is not identified. Please identify “The wound-healing study” (sic)!\nThe rationale for assaying “anti-inflammatory activity by determining the inhibitory activity on lipopolysaccharide (LPS)-induced nitric oxide (NO) production in 264.7 RAW cells” (sic) escapes me. 264.7 RAW cells are a murine macrophage cell lines created by transformation with Abelson leukemia virus. LPS, also known as endotoxin, is a component of cell wall from Gram-negative bacteria. 264.7 RAW cells are very sensitive to LPS, and respond when recognised by the receptor TLR4, by generating ROS and NOS, part of macrophage’ antimicrobial pathways. It is not clear whether “The wound-healing study” evaluated wounds infected with Gram-negative bacteria, or uninfected wounds.\nHow do the “results found… (a strong inhibitory effect)? This is poor grammar.\nHow does “A. bracteolate showed decreased pro-inflammatory cytokine mRNA expression concentration-dependent, indicating a mechanism for iNOS inhibition, gene expression analyzed by Real-Time PCR” (sic)? The absence of methodology assures this statement cannot be tested and verified by others.\nThe discussion of collagen gene expression and synthesis under “Aristolochia bracteolate” has no relevance. No evidence is reported, nor is any evidence cited.\nWhat is the evidence “The methanol extract (EM) of the leaves of Boerhavia diffusa significantly increased the viability and migration of human keratinocytes (HaCaT) cells”?\nWhat is the evidence “…caffeic acid, ferulic acid, and D-pinitol (are) the primary bioactive metabolites”?\nWhat is the evidence “…secondary metabolites in the extract of punarvana such as phenolics and flavonoids reduces lipid peroxidation, increases collagen fibrils’ survival by increasing collagen fibers’ strength, prevents cell damage, and accelerates DNA synthesis” (sic)?\nWhat is the evidence “Phenolics, flavonoids, and terpenoids enhance wound-healing due to their antioxidant and antimicrobial properties”?\nWhat is the evidence “Apply topical insulin promotes diabetic wound-healing by regulating wound inflammatory cells and improving cellular function” (sic)?\nWhat is the evidence “The results showed a significant increase in the viability of HaCaT cells on ASE-loaded nanoemulsions” (sic)?\nWhat is the evidence “ASE did not induce HaCaT cytotoxicity and tended to increase keratinocyte cell viability”? (What is ASE?)\nWhat is the evidence “Anti-inflammatory and wound-healing activities have been reported of calophyllolide (CP) isolated from Calophyllum inophyllum Linn”?\nWhat is the evidence “results showed that CP did not affect the viability of HaCaT cells in the concentration range” (sic)?\nWhat is the evidence “CP reduced fibrosis formation and effectively promoted wound closure in a mouse model without causing weight loss”?\nWhat is the evidence “results showed that HaCaT cells grown in the presence of U. parvifolia root bark extract showed a faster and dose-dependent growth rate than untreated cells” (sic)?\nWhat is the evidence “…polysaccharides from Aloe vera also induce matrix metallopeptidase (MMP)-3 and metallopeptidase inhibitor-2 gene expression during wound repair”?\nWhat is the evidence “The gel was tested to be non-cytotoxic against nauplii and compatible with human blood and skin cells” (sic)?\nWhat is the evidence “Aloe vera promotes the attachment and proliferation of HaCaT and HFF1 cells”?\nWhat is the evidence “HS ethanol extract accelerated wound-healing activity in epithelial formation and fibronectin production”?\nWhat is the evidence “HS enhances the expression of genes involved in skin hydration and homeostasis”? What are the “genes involved in skin hydration and homeostasis”?\nWhat is the evidence “NMP from the leaves of Sideroxylon obtusifolium (Brazilian medicinal species) has activity as anti-inflammatory and wound-healing management”?\nWhat is the evidence “The extract showed a strong positive result of 65%, with a difference of 14% in the migration rate between the two” (sic)?\nWhat is the evidence “Grandiflorenic acid (2,5 μg/mL) resulted in a 106% percentage of HaCaT keratinocyte viability, induced a migration rate of 100% in the initial in vitro assay” (sic)?\nWhat is the evidence “Treatment with Maja flowers for 24 hours drastically increases cell motility and expression of keratinocytes in specific cell lines” (sic)?\nWhat is the evidence “ethanolic extract of Eriobotryae folium (EF) increases intracellular and extracellular PGE2 levels in HaCaT cells and inhibits 15-PGDH…”?\nWhat is the evidence “GG inhibits abnormal cell proliferation and is anticarcinogenic”?\nWhat are the “Previous studies (that) showed that Thyme oleoresin at 25 μg/mL and 50 μg/mL significantly promoted HaCaT cell migration, leading to wound closure”?\nWhat is the evidence “The purified Gracilaria lemaneiformis (GLP-2) fraction promoted cell proliferation and migration of HaCat cells through activation of PI3K/aPKC signaling during wound-healing of human keratinocytes”?\nWhat is the evidence “UD extract increased the proliferation rates of HEK-293 and HaCaT cells by 39% and 30%”?\nWhere are the “results (that) showed that the cell viability test showed that the CA extract increased the viability of HaCaT cells”?\nWhat is the evidence “methanol extract of Clausena excavate contains coumarins, flavonoids, and glycosides with various biological properties”? What are these “various biological properties”?\nWhat is the evidence Angelica gigas “extract improves wound-healing with HaCaT human keratinocytes”?\nWhat is the evidence “reduced inflammatory cell density in granulation tissue in 7-day-old wounds, combined with decreased TNF-α and NF-B1 mRNA expression” (sic)?\nWhere are the “results (that) showed that ashwagandha extract (AE) significantly inhibited mRNA expression of inflammatory cytokines”?\nWhat is the evidence “A. asphodeloides (AA) extract promoted inhibiting Th2-type cytokines, pro-inflammatory cytokines, and filaggrin restoration in HaCaT cells” (sic)?\nThe sentence “It is possible to assume that AA facilitates wound-healing in the skin barrier through the inhibition of overexpression” (sic) is incomplete.\nWhat is the evidence “S. veitchii extract increases AQP3 expression and provides wound-healing and healing effects” (sic)?\nWhat is the evidence “root extract of A. tenuissima accelerates wound filling under basal conditions in the keratinocytes” (sic)?\nWhat is the evidence “This plant shows that astragaloside can activate cellular processes involved in wound-healing”?\nWhat is the evidence “Mimosa tenuiflora (Willd) aqueous extract… indicated a loss of cell viability and proliferation of dermal fibroblasts” (sic)?\nWhat is the evidence “Allerce extract has a significant effect on wound-healing”?\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No",
"responses": []
},
{
"id": "141492",
"date": "01 Aug 2022",
"name": "Sisir Nandi",
"expertise": [
"Reviewer Expertise Drug Design and development research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors have carried out a critical review on the Wound Healing Mechanisms utilizing Natural Products. This is very significant and the article can be accepted after major revision.\nThe sentence \"In general, the wound-healing process is divided into 4 phases: the coagulation and hemostasis phase, the inflammatory phase, the proliferative phase, and the remodeling phase.\" should be revised. See for example:\n\n\"It also involves phagocytosis, chemotaxis, neocollagenesis, collagen degradation, and collagen remodeling. The epithelization process initiates production of new glycosaminoglycans and proteoglycans are a few more important processes of healing of a wound.\"\nRoy et al., Current Drug Discovery Technologies, 2020, 17, 534-541, DOI: 10.2174/1570163817666200123122532\n\nNatural sourced chitosan is a very good composition for the formulation of wound healing. See, for example:\n\"Chitosan is a maring sponge natural linear polysachharide that has been greatly used in the formulations like nanoparticles, hydrogels, implants, films, fibers, etc for the wound healing.\"\n\nH. Roy, A. Gummadi, Sisir Nandi (2021) Potential Biomedical Applications of Marine Sponge-Derived Chitosan: Current Breakthroughs in Drug Delivery for Wound Care. In: Kumar P., Kothari V. (eds) Wound Healing Research. Springer, Singapore. https://doi.org/10.1007/978-981-16-2677-7_16\n\nThe introduction section should contain Alopathy generic medicine name commonly used for the wound healing.\n\nAuthors should add a Table before results. Table should summarise the Sl. number, plant name, extracts, active component isolated if any and citation.\n\nThe authors have not been sincere in organizing and checking the manuscript. There are a lot of mistakes, English grammar as well as sentence structure.\n\nSome natural formulations should be given in the results section.\n\nConclusion section should be re framed.\n\nInclude sketches, flow diagrams, table for applications describing mechanism of wound healing action that would be more informative to the readers\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "8834",
"date": "07 Oct 2022",
"name": "David Leavesley",
"role": "Reviewer Response",
"response": "The authors should not be required to cite their reviewers work. I am confident alternative literature is available to substantiate the authors statements."
}
]
}
] | 1
|
https://f1000research.com/articles/11-528
|
https://f1000research.com/articles/10-280/v1
|
09 Apr 21
|
{
"type": "Systematic Review",
"title": "SARS-CoV-2 and the role of close contact in transmission: a systematic review",
"authors": [
"Igho J. Onakpoya",
"Carl J. Heneghan",
"Elizabeth A. Spencer",
"Jon Brassey",
"Annette Plüddemann",
"David H. Evans",
"John M. Conly",
"Tom Jefferson",
"Carl J. Heneghan",
"Elizabeth A. Spencer",
"Jon Brassey",
"Annette Plüddemann",
"David H. Evans",
"John M. Conly",
"Tom Jefferson"
],
"abstract": "Background: SARS-CoV-2 transmission has been reported to be associated with close contact with infected individuals. However, the mechanistic pathway for transmission in close contact settings is unclear. Our objective was to identify, appraise and summarise the evidence from studies assessing the role of close contact in SARS-CoV-2 transmission. Methods: This review is part of an Open Evidence Review on Transmission Dynamics of SARS-CoV-2. We conduct ongoing searches using WHO Covid-19 Database, LitCovid, medRxiv, PubMed and Google Scholar; assess study quality based on the QUADAS-2 criteria and report important findings on an ongoing basis. Results: We included 181 studies: 171 primary studies and 10 systematic reviews. The settings for primary studies were predominantly in home/quarantine facilities (31.6%) and acute care hospitals (15.2%). The overall reporting quality of the studies was low to moderate. There was significant heterogeneity in design and methodology. The frequency of attack rates (PCR testing) was 3.5-75%; attack rates were highest in prison and wedding venues, and in households. The frequency of secondary attack rates was 0.3-100% with rates highest in home/quarantine settings. Three studies showed no transmission if index cases had recurrent infection. Viral culture was performed in three studies of which two found viable virus; culture results were negative where index cases had recurrent infections. Ten studies performed genomic sequencing with phylogenetic analysis – the completeness of genomic similarity ranged from 81-100%. Findings from systematic reviews showed that children were significantly less likely to transmit SARS-CoV-2 and household contact was associated with a significantly increased risk of infection. Conclusions: The evidence from published studies demonstrates that SARS-CoV-2 can be transmitted via close contact settings. The risk of transmission is greater in household contacts. There was wide variation in methodology. Standardized guidelines for reporting transmission in close contact settings should be developed to improve the quality reporting.",
"keywords": [
"Close contact",
"transmission",
"COVID-19",
"systematic review"
],
"content": "Introduction\n\nThe SARS-CoV-2 (COVID-19) pandemic is a major public health concern. Based on WHO data, there have been over 120 million confirmed cases and over two and a half million deaths globally as of 20th March 20211. Many national governments have implemented prevention and control measures and vaccines are now being approved and administered; the overall global spread of the virus now appears to be slowing. Current evidence from epidemiologic and virologic studies suggest SARS-CoV-2 is primarily transmitted via respiratory droplets and direct and indirect contact2,3. However, controversy still exists about how the virus is transmitted and the relative frequency of the modes of transmission and if these modes may be altered in specific settings4,5.\n\nAlthough close contact is thought to be associated with transmission of SARS-CoV-2, there is uncertainty about the thresholds of proximity for “close contact” and the factors that may influence the transmission in a “close contact”. Furthermore, there is lack of clarity about how research should be conducted in the setting of transmission with close contact which may include transmission via any one of or the combination of respiratory droplets, direct contact, or indirect contact.\n\nSeveral studies investigating the role of close contact in SARS-CoV-2 transmission have been published but the pathways and thresholds for transmission are not well established. The objective of this review was to identify, appraise and summarize the evidence from primary studies and systematic reviews investigating the role of close contact in the transmission of SARS-CoV-2. Terminology for this article can be found in Box 1.\n\n\n\nClose contact: Someone who was within 6 feet of an infected person for a cumulative total of 15 minutes or more over a 24-hour period starting from 2 days before illness onset (or, for asymptomatic patients, 2 days prior to test specimen collection) until the time the patient is isolated1; The World Health Organization (WHO) additionally includes direct physical contact with a probable or confirmed case, direct care for a patient with probable or confirmed COVID-19 disease without using proper PPE, and other situations as indicated by local risk assessments.\n\nAttack rate: The proportion of those who become ill after a specified exposure2.\n\nSecondary attack rate: The probability that infection occurs among susceptible persons within a reasonable incubation period following known contact with an infectious person or an infectious source3.\n\nCycle threshold: The number of cycles required for the fluorescent signal to cross the threshold. Ct levels are inversely proportional to the amount of target nucleic acid in the sample4.\n\n1https://www.cdc.gov/coronavirus/2019-ncov/global-covid-19/operational-considerations-contact-tracing.html#:~:text=Close contact is defined by, time the patient is isolated\n\n2https://www.who.int/foodsafety/publications/foodborne_disease/Annex_7.pdf\n\n3Halloran ME. Secondary Attack Rate. In: Peter A, Theodore C, editors. Encyclopedia of Biostatistics. New York: John Wiley & Sons Ltd; 2005\n\n4https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7521909/\n\n\nMethods\n\nWe are undertaking an open evidence review examining the factors and circumstances that impact on the transmission of SARS-CoV-2, based on our published protocol last updated on the 1 December 2020 (Version 3: 1 December 2020, Extended data: Appendix 16). This review aims to identify, appraise, and summarize the evidence (from peer-reviewed studies or studies awaiting peer review) examining the role of close contact in the transmission of SARS-CoV-2 and the factors that influence transmissibility. We are conducting an ongoing search in WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 for keywords and associated synonyms. For this review, we also conducted searches on PubMed. The searches for this update were conducted up to 20th December 2020 (Extended data: Appendix 26). We did not impose any language restrictions.\n\nWe included studies of any design that investigated transmission associated with close contact but excluded predictive or modelling studies. We reviewed the results for relevance and for articles that appeared particularly relevant, we undertook forward citation matching to identify relevant results. We assessed the risk of bias of included primary studies using five domains from the QUADAS-2 criteria7; we adapted this tool because the included studies were not primarily designed as diagnostic accuracy studies. We did not perform formal assessments of the quality of included systematic reviews but summarized their findings, including quality of their included studies as reported by the authors. We extracted the following information from included studies: study design characteristics including the definition used of “close contact”, population, main methods, and associated outcomes including the number of swab samples taken with frequency and timing of samples, and cycle thresholds and samples concentrations. We also extracted information on viral cultures including the methods used. One reviewer (IJO) assessed the risk of bias from primary studies, and these were independently verified by a second reviewer (EAS). One reviewer (IJO) extracted data from the included primary studies, and these were independently checked by a second reviewer (CJH). One reviewer (CJH) extracted data from the included systematic reviews, and these were independently checked by a second reviewer (IJO). Disagreements in the data extraction or bias assessments were resolved by consensus. We presented the results in tabular format, and bar charts used to present the frequency of positive tests. We reported results of specific subgroups of studies where relevant. Because of substantial heterogeneity across the included studies, we considered meta-analyses inappropriate.\n\n\nResults\n\nWe identified 1202 non-duplicate citations of which 229 were considered eligible (Figure 1). We excluded 48 full-text studies for various reasons (see Extended data: Appendix 36 for the list of excluded studies and reasons for exclusion). Finally, we included 181 studies: 171 primary studies and 10 systematic reviews (see Extended data: Appendix 4 for references to included studies). The main characteristics of the included primary studies and systematic reviews are shown in Table 1 and Table 2, respectively.\n\nNone of the included primary studies reported a published protocol except one (Helsingen 2020). The risk of bias of the included primary studies is shown in Table 5. Only 61 studies (35.7%) adequately reported the methods used, and 97 (56.7%) adequately described the sources of sample collection. Only six studies (3.5%) adequately reported methods used to address biases. The overall quality of the studies was judged as low to moderate (see the risk of bias graph in Figure 2).\n\nWe included 10 systematic reviews investigating the role of close contact in SARS-CoV-2 transmission (Table 2). The studies included in the reviews were primarily observational. In one review (Chen 2020), there was a higher risk of infection in close contacts and healthcare workers without PPE compared to the general population. A second review (Chu 2020) found a significant association between proximity of exposure (distance <1m), absence of barriers (not using face covering or eye protection) and the risk of infection. The authors of three reviews (Li 2020, Ludvigsson 2020, Zhu 2020) concluded that children were unlikely to be the main conduit for transmission of SARS-CoV-2, and results of one review (Koh 2020) showed that adults with close contact exposure were significantly more likely to be infected compared with children (14 studies, RR: 1.71 (95% CI: 1.35, 2.17)). In one review (Xu 2020), the attack rates were significantly less in students compared with staff (p<0.01). One review (Fung 2020) reported household SARs ranging from 3.9% to 36.4%, but also highlighted the lack of SARS-CoV-2 research in Africa, South Asia, and Latin America. One review (Madewell 2020) found that SARs were higher in households from symptomatic index cases than asymptomatic index cases, and one review (Yanes-Lane 2020) concluded that the proportion of asymptomatic infection was high (20–75%). In two reviews (Koh 2020, Yanes-Lane 2020), studies judged to be of low quality were excluded from their meta-analyses. In one review (Chen 2020), the overall quality was reported as low, while 80% of included studies were reported as moderate or high quality in another two (Fung 2020, Madewell 2020). Another review (Chu 2020) reported the overall risk of bias as low-to-moderate, and one (Xu 2020) rated the overall quality as low. Three reviews did not assess study quality (see Table 2).\n\nWe found 171 primary studies (Table 1). In general, the studies did not report any hypothesis but assessed epidemiological or mechanistic evidence for transmission associated with close contact settings. Ninety-three studies (54.4%) were conducted in Asia, 43 (25.1%) in Europe, 27 (15.8%) in North America, five (2.9%) in South America and three (1.8%) in Australasia. The study settings included home/quarantine facilities (n=54), hospital (n=26), social/religious gatherings (n=13), public transport (n=7) care homes (n=4), and educational settings (n=8). Thirteen studies used two settings (home plus one other setting). In 25 studies (15.2%), the settings were multiple (3 or more different settings). Two studies were conducted in professional sports settings: one Super League Rugby (Jones 2020) and one football team (Schumacher 2020)\n\nAll the included studies were observational in design except one RCT (Helsingen 2020): 24 studies were described as cohort, nine were case series and 12 cross-sectional. One study used a before and after study design. The number of close contact participants included ranged from 4 to 8437. Three studies (Chen 2020a, Hong 2020, Yang 2020) examined transmission dynamics in close contacts of index or primary cases with recurrent SARS-CoV-2 infections.\n\nEighty-two studies (46.8%) reported definitions of close contacts (Table 3). There was a variation in the definitions across the studies. Seventeen studies (9.9%) defined close contact as exposure to the index or primary case within two metres for at least 15 minutes while four defined it as being within 2m for at least 10 minutes. In 24 studies, there was no specified distance reported - close contact definitions included unprotected exposure, living in the same household or bedroom, sharing a meal, or having repeated and prolonged contact. In five studies of airline passengers, close contact was defined as all passengers on the flight (Chen 2020), seated within two rows of the index case (Draper 2020, Pavli 2020, Speake 2020), or being within 2m for at least 15 minutes (Khanh 2020). Eighty-seven studies (50.9%) did not define close contact and the definition was unclear in four studies. Twenty-nine studies (17%) defined other types of contacts including primary contact, secondary contact, high-risk contact, household contact, social contact, and work contact (see Table 3).\n\nEighteen studies (10.5%) reported data on the contact duration between close contacts and the index or primary cases (Table 3). The average contact duration ranged from 30 minutes to 8 days across 16 studies that investigated transmission rates using RT-PCR. In two studies that examined transmission using serology (Agergaard 2020, Hong 2020), the durations of contact were two weeks and 258 person-days, respectively. The mean contact duration was either unclear or not reported in 148 studies (90.2%).\n\nA total of 110 studies (64.3%) used RT-PCR as a test method for confirming SARS-CoV-2 positivity, while eight studies (4.8%) exclusively investigated transmission using serology. In 24 studies (14%), both PCR and serology were used to investigate close contact in SARS-CoV-2 transmission. Thirty-one studies (18.1%) did not report the test method used. For PCR, the timing of sample collection varied from within 24 hours to 14 days after exposure to the index or primary case; for serology, this ranged from 2–10 weeks post-exposure. In total, 71 studies (41.5%) reported the timing of sample collection. The timing of sample collection was either not reported or unclear in 100 studies (58.5%).\n\nTwenty-two studies (12.9%) reported Ct values for determining PCR test positivity: ≤40 (eight studies), <37 (five studies), ≤35 (three studies), <38 (two studies), one each for <25, ≤30, <32 and <36 (or 39). Only eight studies reported the Ct values for close contacts in their results – these ranged from 16.03 to 38.\n\nThirty-two studies reported conducting serological tests to assess transmission of SARS-CoV-2 (Table 4). There was variation in the description of the tests. Fifteen studies determined the antibody responses to SARS-CoV-2 spike proteins using Immunoglobulin G (IgG) and IgM while 11 used only IgG. In 17 studies, the threshold for serological positivity was not reported. Three studies (Kuwelker 2020, Ng 2020, Yang 2020) performed neutralisation assays to confirm positive serologic samples. In one study (Torres 2020), study participants self-administered the serological tests.\n\nThree studies (Ladhani 2020a, Speake 2020, Yang 2020) performed viral culture, while 10 studies (Böhmer 2020, Firestone 2020, Jiang 2020, Ladhani 2020a, Lucey 2020, Pung 2020, Sikkema 2020, Speake 2020, Taylor 2020, Wang 2020) performed genome sequencing (GS) plus phylogenetic analysis.\n\nTwenty-three studies reported data on attack rates using RT-PCR (Table 6). The settings included healthcare (n=3), household (n=8), public transport (n=2), educational settings (n=3). In one study of 84 children in daycare centres during the first few weeks of the pandemic (Desmet 2020), the AR was 0%; similar results were reported in another study of hospital healthcare workers (Basso 2020). The frequency of ARs in the remaining 21 studies ranged from 3.5 to 75% (Figure 3a). The ARs were highest in weddings (69%), prison (69.5%) and households (75%). Attack rates appeared lower in healthcare settings; two healthcare settings with higher ARs (Ladhani 2020, Ladhani 2020a) included nursing home residents – the definition of SARS-CoV-2 infection in both studies did not include the full constellation of respiratory and non-respiratory symptoms. In sports settings, the AR during matches was between 4.2% and 4.7%.\n\nTwenty-nine studies reported data on ARs using serology (Table 6). The settings included educational (n=4), households (n=4) and healthcare (n=3). In eight studies, the frequency of attack was 0%. The frequency of attacks in the remaining 21 studies ranged from 0.7% to 75% (Figure 3b). The frequency of attacks was highest in households but lower in educational settings - especially daycare centres.\n\nOverall, 126 studies (73.7%) reported data on secondary ARs (Table 6). The studies reported the rates based on RT-PCR tests, except for one study (Angulo-Bazán 2020) that used serology. In 16 of these studies, the SAR was 0%. The secondary ARs in the remaining 110 studies ranged from 0.3 to 100% (see Figure 4). The highest frequencies of secondary ARs (75–100%) occurred in household or quarantine settings; similar findings were observed when studies with higher reporting quality were examined (57–75%). In the three studies of index or primary cases with recurrent infections, there was no positive case amongst the 1518 close contacts across the studies.\n\nForty-six studies (26.9%) reported results on the risk of infection (Table 7). One study of airline passengers (Khanh 2020) showed that seating proximity was significantly associated with the risk of contracting SARS-CoV-2 (RR 7.3, 95% CI 1.2–46.2); a second study (Speake 2020) reported that not sitting by the window was associated with a significantly increased risk of infection (RR 5.2; 95% CI 1.6–16.4; p<0.007)). The results of five studies (Chen 2020b, Doung-ngern 2020, Hobbs 2020, Wang 2020b, Wu 2020) showed that use of face covering during close contact with infected cases was associated with significantly lower risks of infection compared with no face covering; findings from one of these studies (Doung-ngern 2020) showed that wearing masks all the time during contact was not significantly different from wearing masks sometimes. The result of one study (Rosenberg 2020) showed that the incidence of infection significantly increased with age (p<0.0001), while those from another study (Poletti 2020) showed that being 70 years or older was associated with a significantly increased risk of SARS-CoV-2-related death (p<0.001), while another study (Zhang 2020a) reported that elderly close contacts (≥60 years) had a higher SAR compared with younger age groups. Findings from five studies (Bi 2020, Hu 2020a, Islam 2020, Luo 2020a, Wu 2020, Zhang 2020a) showed that household contact settings had significantly higher risks of infection compared with other types of contact settings, e.g., social, healthcare, workplace and public transport. One study (Lewis 2020) showed that the risk of infection was significantly increased amongst household contacts who were immunocompromised (OR 15.9, 95% CI 2.4–106.9). Finally, three studies (Bi 2020a, Wu 2020, Zhang 2020a) showed that the more frequent contacts with an index case was significantly associated with an increased risk of infection.\n\nThree studies (Ladhani 2020a, Speake 2020, Yang 2020) performed viral culture (Table 8). All studies utilised Vero E6 cells for viral culture. In Ladhani 2020a (a study of elderly nursing home residents), positive samples with a Ct of <35 were incubated on Vero E6 cells and confirmed by cytopathic effect (CPE) up to 14 days post-inoculation. Positive culture results were obtained for symptomatic, post-symptomatic, pre-symptomatic and asymptomatic cases (21 residents and 12 staff); higher Ct values was significantly associated with decreasing ability to recover the virus (p<0.001). Among residents the virus was isolated 12 days before symptom onset and up to 13 days after and in staff up to 6 days before and 7 days after symptom onset. In Speake 2020, specimens were inoculated in Vero-E6 cells and inspected for CPE daily for up to 10 days with identity confirmed using “in-house” PCRs. The primary cases had boarded the flight from a cruise ship and had SARS-CoV-2 with the strain A2-Ruby Princess (A2-RP). Nine of 17 (53%) of PCR-positive samples grew SARS-CoV-2 in culture. Eight secondary cases who were in the same flight cabin with the infected travellers from the cruise ship all had viruses of the A2-RP strain (3 by full and 1 by partial sequence) (Table 8). In the third study of index patients with recurrent infection swab specimens were also inoculated on Vero cells, and monitored for CPE daily for 10 days (Yang 2020). All four viral cultures were negative (0%).\n\nTen studies (Böhmer 2020, Firestone 2020, Jiang 2020, Ladhani 2020a, Lucey 2020, Pung 2020, Sikkema 2020, Speake 2020, Taylor 2020, Wang 2020) performed GS and phylogenetic analysis (Table 9). The studies were primarily conducted in outbreak clusters and methods used for performing these investigations were essentially similar across the studies. The completeness of genomic similarity ranged from 81–100% across six studies (Firestone 2020, Jiang 2020, Lucey 2020, Sikkema 2020, Speake 2020, Wang 2020). Transmission from one case to a contact was demonstrated by nonsynonymous nucleotide polymorphism in SARS-CoV-2 from these two cases onwards, but not in any cases detected prior to this instance (Böhmer 2020). In one study of skilled nursing home facilities (Taylor 2020), samples from 75 residents and five healthcare staff shared genetically related strains. In another study of care homes (Ladhani 2020a), reported nine separate introductions of SARS-CoV-2 into care homes by healthcare staff. In one study which used multiple settings (Pung 2020), the viral genomic sequences for four cases in one cluster shared identical sequences over the full genome length and shared a common base difference relative to the earlier sequences (see Table 8).\n\n\nDiscussion\n\nWe identified 171 primary studies assessing the role of close contact in transmission of SARS-CoV-2. The evidence from these observational studies suggest that the risk of transmission is significantly increased through close contact with an infected case - the greater the frequency of contact, the greater the risk. Household contact setting is significantly more likely to result in transmission of SARS-CoV-2 compared to other types of contact settings. This risk of transmission appears to decrease with use of face masks and in cases where the index or primary cases are in the paediatric age group. The risk of close contact transmission is significantly increased in the elderly. Enclosed environments and social gatherings appear to increase the likelihood of close contact transmission. Close contact with persons having recurrent infection with SARS-CoV-2 is unlikely to result in transmission of the virus. There is wide heterogeneity in study designs and methods and the overall quality of evidence from published primary studies is sub-optimal. The results of systematic reviews also suggest that household contact setting increases the risk of transmission and being elderly is also associated with increased risks of transmission and mortality.\n\nThe positive results of viral cultures observed in two studies support the results of PCR and serologic tests showing that close contact setting was associated with transmission of SARS-CoV-2. The failure to successfully isolate the virus in the third study supports the view that individuals who are re-infected are unlikely to transmit the virus in close contact settings. The positive findings from all 10 studies that performed GS and phylogenetic analysis with identical strains supports the hypothesis that close contact setting is associated with SARS-CoV-2 transmission through respiratory droplets or direct contact. The failure of the majority of studies to report Ct values casts doubts on the strengths of any reported associations because of the likelihood of false positives, as is the lack of (and variation in) reporting of the timelines for sample collections. The variations observed in the definitions of close contacts also cast further doubts on the validity of overall results.\n\nThe results of our review are consistent with several guidelines suggesting that close contact with index cases can result in transmission of SARS-CoV-28–10. Our findings are also consistent with those of a systematic review which concluded that face masks are effective for preventing transmission of respiratory viruses11. The results of our review also support those of a previous review which showed that the elderly are at increased risk of infection and mortality with coronavirus12. However, our review contains a greater number of studies compared to each of the included individual reviews and shows evidence demonstrating positive culture of virus as well as genomic evidence of close contact transmission. This differs from the findings from our reviews of fomite, orofecal and airborne transmission that failed to show evidence of either positive culture or genomic sequences demonstrating SARS-CoV-2 transmission13–15.\n\nTo our knowledge, this is the most comprehensive review to date investigating the role of close contact in the transmission of SARS-CoV-2. We extensively searched the literature for eligible studies, accounted for the quality of included studies and have reported outcomes (viral culture and GS) that were previously unreported in previous reviews. However, we recognize some limitations. We may not have identified all relevant studies examining the role of close contact in transmission - this is especially true for unpublished studies. We included results from non-peer reviewed studies which may affect the reliability of the review results. However, such studies could potentially be of research benefit because of the ongoing pandemic; in addition, we performed forward citation search of relevant studies.\n\nFuture studies should endeavour to include Ct values (or preferably convert the Ct values to number of genome copies using standard curves) when reporting research results and should describe the timing and methods of sample collection. Details surrounding the proximity, timing, and activities within the context of close contact need to be described. In studies of elderly subjects, more detailed description of baseline demographics should be reported. Further studies showing virus isolation in close contact settings should be conducted to strengthen the current evidence base; this could include performing serial cultures. Similarly, more research examining genomic sequences and phylogenetic trees in suspected close contact transmissions should be conducted - this should also extend to research examining other modes of transmission. The variation in methods and thresholds of the serological tests add to the confusion about diagnostic accuracy of testing; indeed, some authors have questioned the value of serological tests for diagnosing SARS-CoV-216. To overcome the challenge of interpreting antibody responses, guidelines for better reporting of serological tests and results should be developed; this has previously been emphasized by other authors. Internationally recognized research dictionary of terms defining and describing close contact settings should be developed. Standardized guidelines for reporting research results should be a priority. Local, national, and international health organisations should promote good hygiene measures including advising against close contact with SARS-CoV-2 infected individuals; use of medical masks should be encouraged in circumstances where close contact with infected cases is likely. Activities in enclosed settings should be discouraged and social distancing in close contact settings should be encouraged.\n\n\nConclusion\n\nThe evidence from published observational studies and systematic reviews indicate that SARS-CoV-2 can be transmitted via close contact settings. Household contact and increased frequency of contact with infected cases significantly increase the risk of transmission. The quality of evidence from published studies is low-to moderate. Variations in study designs and methodology restrict the comparability of findings across studies. Standardized guidelines for the reporting of future research should be developed.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: Extended data: SARS-CoV-2 and the Role of Close Contact in Transmission: A Systematic Review, https://doi.org/10.6084/m9.figshare.14312630.v16.\n\nThis project contains the following extended data:\n\nUpdated Protocol\n\nSearch Strategy\n\nList of Excluded Studies\n\nReferences to Included Studies\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThis work was commissioned and paid for by the World Health Organization (WHO). Copyright on the original work on which this article is based belongs to WHO. The authors have been given permission to publish this article. The author(s) alone is/are responsible for the views expressed in the publication. They do not necessarily represent views, decisions, or policies of the World Health Organization.\n\n\nReferences\n\nWorld Health Organization: WHO Coronavirus Disease (COVID-19) Dashboard. [Last Accessed 20/03/2021]. Reference Source\n\nWorld Health Organization: Modes of transmission of virus causing COVID-19: implications for IPC precaution recommendations. [Accessed 16/01/2021]. Reference Source\n\nWorld Health Organization: Coronavirus disease 2019 (COVID-19) Situation Report – 73. [Accessed 28 February 2021]. Reference Source\n\nTanne JH: Covid-19: CDC publishes then withdraws information on aerosol transmission. BMJ. 2020; 370: m3739. PubMed Abstract | Publisher Full Text\n\nTang JW: SARS-CoV-2 and aerosols-Arguing over the evidence. J Virol Methods. 2021; 289: 114033. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOnakpoya I, Heneghan C, Spencer E, et al.: Extended data: SARS-CoV-2 and the Role of Close Contact in Transmission: A Systematic Review. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14312630.v1\n\nWhiting PF, Rutjes AWS, Westwood ME, et al.: QUADAS-2: a revised tool for the quality assessment of diagnostic accuracy studies. Ann Intern Med. 2011; 155(8): 529–36. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Q&A: How is COVID-19 transmitted? [Accessed 06/04/2021]. Reference Source\n\nCenter for Disease Control and Prevention: COVID-19 Overview and Infection Prevention and Control Priorities in non-US Healthcare Settings. Updated Feb. 26, 2021. Reference Source\n\nPublic Health England: Guidance 12. COVID-19 infection prevention and control guidance: glossary of terms.Updated 21 January 2021. Reference Source\n\nLiang M, Gao L, Cheng C, et al.: Efficacy of face mask in preventing respiratory virus transmission: A systematic review and meta-analysis. Travel Med Infect Dis. 2020; 36: 101751. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPark JE, Jung S, Kim A, et al.: MERS transmission and risk factors: a systematic review. BMC Public Health. 2018; 18(1): 574. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOnakpoya IJ, Heneghan CJ, Spencer EA, et al.: SARS-CoV-2 and the role of fomite transmission: a systematic review [version 1; peer review: awaiting peer review]. F1000Res. 2021; 10: 233. Publisher Full Text\n\nHeneghan CJ, Spencer EA, Brassey J, et al.: SARS-CoV-2 and the role of orofecal transmission: a systematic review [version 1; peer review: awaiting peer review]. F1000Res. 2021; 10: 231. Publisher Full Text\n\nHeneghan C, Spencer EA, Brassey J, et al.: SARS-CoV-2 and the role of airborne transmission: a systematic review [version 1; peer review: awaiting peer review]. F1000Res. 2021; 10: 232. Publisher Full Text\n\nBastos ML, Tavaziva G, Abidi SK, et al.: Diagnostic accuracy of serological tests for covid-19: systematic review and meta-analysis. BMJ. 2020; 370: m2516. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "121151",
"date": "07 Mar 2022",
"name": "Kevin Escandón",
"expertise": [
"Reviewer Expertise Infectious diseases epidemiology",
"virology",
"public health."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comments We commend the authors for attempting to conduct a systematic review on one of the most controversial topics related to the COVID-19 pandemic: SARS-CoV-2 transmission. This is an important effort that required much dedication and careful analysis. Unfortunately, we think this manuscript falls short of scientific quality and utility due to major methodologic and conceptual flaws.\nFirst, this systematic review in its current version fails to provide an accurate and updated picture of the existing evidence. We reviewed this manuscript in February 2022, two years into the pandemic, and while SARS-CoV-2 transmission remains a topic of great relevance, the picture regarding the modes of transmission is much clearer now than one year ago due to numerous epidemiologic and lab-based studies. Given this evidence, the WHO and the general scientific community agree that SARS-CoV-2 can be transmitted via droplet, short-range aerosol, long-range aerosol, and less frequently via fomites. This systematic review should be updated to reflect the most recent evidence.\n\nSecond, and most importantly, there are methodological flaws, conceptual concerns, and unsupported conclusions, as detailed below. Systematic reviews are designed to summarize evidence on specific questions or focused problems with pre-defined criteria to bring understanding and clarity through insightful analyses (even if no meta-analyses are conducted) of existing evidence. Close contact is not only poorly defined in most articles, but is actually addressed in less than a half of the articles included. Importantly, close contact is not a transmission mechanism itself, rather a feature of transmission mechanism(s). The authors erroneously conclude that studies that identified identical strains in close contacts using genome sequencing and phylogenetic analysis support transmission via respiratory droplets. The authors do not acknowledge that short-range aerosol transmission is also a possible (and a likely one) explanation.\nNote that given the absence of line numbers, we are not providing numbered comments.\nIntroduction\nThe introduction should be updated as statistics are over one year old (March 2021).\n\nThe authors mention that the “spread of the virus appears to be slowing”. This statement is not necessarily true considering the recent, recurring, and constantly evolving waves of infection attributed to increasingly transmissible variants of SARS-CoV-2. Furthermore, no citation is provided for this statement.\n\n\"Current evidence from epidemiologic and virologic studies suggest SARS-CoV-2 is primarily transmitted via respiratory droplets and direct and indirect contact\". This sentence is not properly supported by current data; the authors rather cited two WHO 2021 resources. The authors must acknowledge airborne transmission – a route of transmission accepted by both WHO and CDC. Note that respiratory transmission of inhalable particles is the dominant mode of transmission, especially short-range. Indirect droplet / contact / fomite transmission is estimated to be minor.\nRecommended references: Zhang & Duchaine 20201 and Leung 20212.\n\nThe aim of this study is to assess the evidence from primary studies and existing systematic reviews investigating the role of close contact on SARS-CoV-2 transmission. This is aligned with the manuscript title (\"SARS-CoV-2 and the role of close contact in transmission...\"), the introduction, the methods, and figure and table titles. However, one major challenge is that the \"close contact\" framework is neither clearly defined in the literature nor is it often standardized in methods of primary studies. Authors address several aspects of transmission, from settings to distance, populations, testing/lab methods (PCR, serology, viral culture, GS and phylogenetic analysis), attack rates, risk of infection, etc. We agree that all of these are variables that influence or describe transmission. But close contact is only defined in 46.8% of included studies which causes concern over the use of consistently applied inclusion criteria. This systematic review seems to evaluate different aims and ends providing general descriptions of different subtopics related to transmission, not only to close contact. It is not appropriate for this study on the role of close contact to make such inference on the interaction between an infector and an infectee if not explicitly stated in the primary study.\nTerminology\nThe authors seem to be using the CDC criteria but this is not clarified in the box definition and the citation link seems to be inadequate.\n\nIt should be \"2 days prior to positive test\" instead of \"2 days prior to test specimen collection\".\n\nSome of the references are textbooks or web resources not easy to navigate or links are not active. Authors are encouraged to use the most relevant scientific articles on COVID-19 wherever possible.\n\nSynonyms often used to close contact are close/short range and close proximity. The latter could be more beneficial since the word “contact” is often understood as physical and conspicuous encounters.\n\nWhile it's understandable that definitions are needed to assess evidence, it is equally important to mention their limitations from the outset. For example, close contact is arbitrary for purposes of contact tracing—we know that the definition results in missing cases of exposure and infection at longer ranges.\nMethods\nThe inclusion of articles identified via preprint servers is justifiable if the search criteria include very recent dates in an attempt to capture the most recent research. However, this systematic review only includes articles up to December 20th 2020 – if the authors choose to use this date or a recent one, articles on preprint servers should not be included.\n\nThe search strategy is not reproducible and more detail is required. For example, a detailed search strategy for the WHO COVID-19 database, LitCovid, medRxiv, and Google Scholar are not included in the Appendix 2. Nor is it clear exactly which keywords were used in the PubMed search, for example, were other terms used to capture the concept of duration and proximity of exposure?\n\nIt is not clear if authors defined “close contact” for inclusion in their systematic review.\n\nAdditional detail is required to explain how the QUADAS-2 tool was adapted for this study and if or how it was validated for this purpose. https://figshare.com/articles/figure/Extended_data_SARS-CoV-2_and_the_Role_of_Close_Contact_in_Transmission_A_Systematic_Review/14312630/1?file=27243050\n\nThe QUADAS-2 tool was designed for studies primarily designed as diagnostic accuracy studies and its use is likely to fall short to assess the quality of studies for this systematic review.\nAnalyses of primary studies\nAlthough authors have included extended data containing the protocol and references to included and excluded studies, this remains outdated (March 2021). Several features are discussed and while some of them could suggest close contact transmission, there is quite a bit of heterogeneity in how these studies of transmission inform the role of close contact.\n\nWhile we agree that close-contact transmission is a dominant feature of SARS-CoV-2 transmission through the inhalation of respiratory particles, this systematic review does not help advance the aim mentioned - understanding the role of close contact. The authors could revise this work so it separately addresses features of transmission using standardized or limited definitions for each one. Attribution of such analyses to close contact (i.e., its potential role) should result from the interpretation of such findings altogether rather than from \"direct assessment of the impact of close contact in transmission\" since most studies do not define or measure close contact systematically.\nAnalyses of reviews\nThe authors included 10 systematic reviews allegedly investigating close-contact SARS-CoV-2 transmission. Some concerns make questionable the inclusion of such heterogeneous publications for an analysis that at best describes these almost individually without advancing the understanding of the role of close contact in SARS-CoV-2 transmission, which is the ultimate purpose of the authors' systematic review. It is expected that studies included in such publications are primarily observational, since randomized designs are complex and it remains unclear how research should ideally address gaps in our understanding of transmission. Findings of some of the included reviews (Li, Ludvigsson, Zhu) are not described with regard to close contact, but only to population groups; others are only mentioned with regard to asymptomatic infection or attack rates. We find this analysis in general unhelpful.\n\nThe authors analyze features different from close contact in the sections following \"Primary studies\". All these analyses are related to primary studies, so this should be reorganized for clarity. Again, there is a detailed description of studies that do not address close contact, e.g., \"The result of one study (Rosenberg 2020) showed that the incidence of infection significantly increased with age (p<0.0001), while those from another study (Poletti 2020) showed that being 70 years or older was associated with a significantly increased risk of SARS-CoV-2-related death (p<0.001),\"\nDiscussion\nAuthors should be careful in interpreting what their systematic review found, for instance that many studies report household transmission suggests that transmission occurs in indoor environments with higher exposure. Exposure results from concentration and time of contact with infectious respiratory particles. It, therefore, depends on a mix of frequency of contacts, range of contact, and infectiousness of index cases. But household transmission may perfectly encompass risk of infection beyond 3 m, 6 m, or any other definition of close contact. We do expect that the risk of infection is greatest with the longest contact, though, but the definition of a close contact remains nebulous and the associated risk could vary depending on the environmental conditions that favor transmission. Because the purpose of this systematic review is to address transmission, the authors must discuss at least generally the interplay of these factors. SARS-CoV-2 transmission is a complex phenomenon that depends on the interaction between viral properties (infectious dose and infectivity correlates), the host and their features (breathing rate, respiratory tract morphology, target tissues, receptor distribution, host barriers, immune responses), and the environment (temperature, humidity, salinity, pH, the medium or materials of the contaminated objects or surfaces, ventilation/airflow, ultraviolet radiation). Authors also should acknowledge that existing evidence suggests that transmission in close-contact settings is likely to be dominated by short-range respiratory inhalation of infectious virions.\n\nThe authors superficially mention the role of face masks in decreasing the risk of transmission from the pediatric population. This is a dangerous misinterpretation of evidence of two things that should be analyzed separately, i.e., 1) the efficacy of respiratory protection and 2) the risk of transmissibility from different populations. Certainly, this review was not designed to assess either of these aspects as a research question. As for respiratory protection, not all masks (or respirators) are expected to provide the same degree of protection. And if not correctly/consistently worn, they may not reduce risk. As for the usually overclaimed risk of children to transmit SARS-CoV-2, many potential confounders easily make this group appear highly contagious but it is unlikely this is due to intrinsic features of that population. Therefore, claims about it should be carefully framed to avoid stigmatization or unfair focalization and perceived efficacy of preventive strategies.\n\nDiscussion unrelated to close contact is seen, e.g., \"being elderly is also associated with increased risks of transmission and mortality\".\n\n\"The positive results of viral cultures observed in two studies support the results of PCR and serologic tests showing that close contact setting was associated with transmission of SARS-CoV-2\".\nWe are unsure how this manuscript supports this conclusion. Similarly, this conclusion is not supported by the data \"The positive findings from all 10 studies that performed GS and phylogenetic analysis with identical strains supports the hypothesis that close contact setting is associated with SARS-CoV-2 transmission through respiratory droplets or direct contact.\"\n\nWe agree with the authors on the high heterogeneity of existing studies and that \"The variations observed in the definitions of close contacts also cast further doubts on the validity of overall results.\"\n\n\"The results of our review are consistent with several guidelines suggesting that close contact with index cases can result in transmission of SARS-CoV-2\"\nThe authors acknowledge that the evidence for close contact transmission is only low-to-moderate quality, thus, it is a stretch to say that close contact is consistently demonstrated as a risk factor. Guidelines have been evolving throughout the pandemic and while close contact may be associated with increased risk of transmission, this study could provide much stronger evidence if transmission properties were assessed in a clearly defined, systematic, and reproducible way.\n\n\"Our findings are also consistent with those of a systematic review which concluded that face masks are effective for preventing transmission of respiratory viruses.\"\nIt is unclear how this systematic review regarding the role of close contract on transmission events contributes to the discussion regarding the role of face masks – more description is needed to make this link explicit. Furthermore, the efficacy of face masks is a complex topic and confounded by a number of factors.\n\nNecessary updates\nSeveral of the preprints included in the systematic review and/or cited in the manuscript have been published; given that this manuscript is outdated and an update is needed, authors should take that opportunity to update preprints that have been published and make sure their findings remain unchanged and adjust accordingly. Some of the preprints now published are:\nHelsingen 20203 Paireau 20204 Kuwelker 20205 Lyngse 20206 Jones 20207 Chen 20208 Fontanet 20209 Armann 202010 Charlotte 202011 Angulo-Bazan 202012\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? No",
"responses": [
{
"c_id": "8442",
"date": "06 Jul 2022",
"name": "IGHO ONAKPOYA",
"role": "Author Response",
"response": "Peer reviewers, comment: We commend the authors for attempting to conduct a systematic review on one of the most controversial topics related to the COVID-19 pandemic: SARS-CoV-2 transmission. This is an important effort that required much dedication and careful analysis. Unfortunately, we think this manuscript falls short of scientific quality and utility due to major methodologic and conceptual flaws. Authors' response: We thank the reviewers for their positive comments and constructive criticisms. We have extensively revised the manuscript to address their concerns. Peer reviewers' comment: First, this systematic review in its current version fails to provide an accurate and updated picture of the existing evidence. We reviewed this manuscript in February 2022, two years into the pandemic, and while SARS-CoV-2 transmission remains a topic of great relevance, the picture regarding the modes of transmission is much clearer now than one year ago due to numerous epidemiologic and lab-based studies. Given this evidence, the WHO and the general scientific community agree that SARS-CoV-2 can be transmitted via droplet, short-range aerosol, long-range aerosol, and less frequently via fomites. This systematic review should be updated to reflect the most recent evidence. Authors' response: The review was submitted in March last year at the start of the pandemic; however, it took a long time before undergoing peer review. We have now updated the review to reflect the most recent evidence focused on the transmission associated with close contact. We updated our searches up till 30/04/2022. Peer reviewers' comment: Second, and most importantly, there are methodological flaws, conceptual concerns, and unsupported conclusions, as detailed below. Systematic reviews are designed to summarize evidence on specific questions or focused problems with pre-defined criteria to bring understanding and clarity through insightful analyses (even if no meta-analyses are conducted) of existing evidence. Close contact is not only poorly defined in most articles, but is actually addressed in less than a half of the articles included. Importantly, close contact is not a transmission mechanism itself, rather a feature of transmission mechanism(s). The authors erroneously conclude that studies that identified identical strains in close contacts using genome sequencing and phylogenetic analysis support transmission via respiratory droplets. The authors do not acknowledge that short-range aerosol transmission is also a possible (and a likely one) explanation. Authors' response: We used the term “close contact settings” for our review, and we acknowledge variations in the definitions of close contact across the studies included in our review (see Table 3). We do not make any claims that close contact is a transmission mechanism but is associated with transmission from any of a number of mechanisms. We have added (with reference) that short-range aerosol transmission is a possible explanation for the identified identical strains in close contacts. Peer reviewers' comment: Note that given the absence of line numbers, we are not providing numbered comments. Authors' response: OK Introduction Peer reviewers' comment: The introduction should be updated as statistics are over one year old (March 2021). The authors mention that the “spread of the virus appears to be slowing”. This statement is not necessarily true considering the recent, recurring, and constantly evolving waves of infection attributed to increasingly transmissible variants of SARS-CoV-2. Furthermore, no citation is provided for this statement. Authors' response: We have updated the searches to April 2022. We have provided a citation to show that the infection rate is decreasing (https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19/latestinsights), and have also noted that the virus continues to evolve. Peer reviewers' comment: \"Current evidence from epidemiologic and virologic studies suggest SARS-CoV-2 is primarily transmitted via respiratory droplets and direct and indirect contact\". This sentence is not properly supported by current data; the authors rather cited two WHO 2021 resources. The authors must acknowledge airborne transmission – a route of transmission accepted by both WHO and CDC. Note that respiratory transmission of inhalable particles is the dominant mode of transmission, especially short-range. Indirect droplet / contact / fomite transmission is estimated to be minor. Recommended references: Zhang & Duchaine 20201 and Leung 20212. Authors' response: We wish to thank the reviewer for this comment. We have updated the information and referenced the CDC and the WHO. The CDC statement suggests that exposure with infection occurs in 3 principal ways including inhalation of fine respiratory droplets, deposition of respiratory droplets and particles on exposed mucous membranes, splashes and sprays ‘and touching mucous membranes with hands soiled by virus contained in respiratory fluids” (Scientific Brief: SARS-CoV-2 Transmission | CDC). They openly acknowledge the relative contributions of the modes of transmission outlined are unquantified and difficult to establish. We have revised the statement to state that the virus is primarily transmitted through exposure to infectious respiratory fluids such as fine aerosols, respiratory droplets, and added a further reference (https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/sars-cov-2-transmission.html). The WHO states “available evidence continues to suggest that SARS-CoV-2 can spread from an infected person’s mouth or nose in small liquid particles when the person coughs, sneezes, sings, breathes or talks, by inhalation or inoculation through the mouth, nose or eyes. These liquid particles are different sizes, ranging from larger ‘respiratory droplets’ to smaller ‘aerosols.\" Current evidence suggests that the virus spreads mainly between people who are in close contact with each other, typically within 1 metre, They also indicate that “the virus can also spread to others through aerosols at longer (beyond the typical 1 metre distance) distances. The risk of long-distance aerosol transmission is higher in poorly ventilated and/or crowded indoor settings” and further discuss transmission through fomites but acknowledge data is limited. Similar to the CDC they indicate the many challenges in working out the presence and transmission of infectious viruses. Rather than state the respiratory transmission of inhalable particles is the dominant mode of transmission we would prefer a more cautious scientifically based response and acknowledge the gap in knowledge in this area. Infection prevention and control during health care when coronavirus disease (COVID-19) is suspected or confirmed (who.int) Peer reviewers' comment: The aim of this study is to assess the evidence from primary studies and existing systematic reviews investigating the role of close contact on SARS-CoV-2 transmission. This is aligned with the manuscript title (\"SARS-CoV-2 and the role of close contact in transmission...\"), the introduction, the methods, and figure and table titles. However, one major challenge is that the \"close contact\" framework is neither clearly defined in the literature nor is it often standardized in methods of primary studies. Authors address several aspects of transmission, from settings to distance, populations, testing/lab methods (PCR, serology, viral culture, GS and phylogenetic analysis), attack rates, risk of infection, etc. We agree that all of these are variables that influence or describe transmission. But close contact is only defined in 46.8% of included studies which causes concern over the use of consistently applied inclusion criteria. This systematic review seems to evaluate different aims and ends providing general descriptions of different subtopics related to transmission, not only to close contact. It is not appropriate for this study on the role of close contact to make such inference on the interaction between an infector and an infectee if not explicitly stated in the primary study. Authors' response: We thank the reviewer for this comment to which we have thought a great deal. We can respond by stating that although only 46.8% (now 39.1%) defined close contact, the authors in the other included studies reported within their studies that they were investigating close contact. We acknowledge that not all studies provided precise definitions and that is a limitation. We set out to summarize the evidence from published studies that assess the association with close contact transmission in COVID-19. As stated earlier, we have used the term “close contact settings” for our review. Terminology Peer reviewers' comment: The authors seem to be using the CDC criteria but this is not clarified in the box definition and the citation link seems to be inadequate. Authors' response: Thanks. We have revised the definition. Peer reviewers' comment: It should be \"2 days prior to positive test\" instead of \"2 days prior to test specimen collection\" Authors' response: Thanks. We have revised the text accordingly. Peer reviewers' comment: Some of the references are textbooks or web resources not easy to navigate or links are not active. Authors are encouraged to use the most relevant scientific articles on COVID-19 wherever possible Authors' response: We have used the updated citations for the relevant articles. Peer reviewers' comment: Synonyms often used to close contact are close/short range and close proximity. The latter could be more beneficial since the word “contact” is often understood as physical and conspicuous encounters. Authors' response: We have broadly used “close contact setting” to allow us to capture the range of studies assessing transmission characteristics of SARS-CoV-2. We appreciate the reviewers’ suggestions of close proximity/range. However, these may be more useful for more focused review questions as they also have their limitations, e.g., direct contact would not be covered by these; however, direct contact has been described as a subset of close contact in some studies. Peer reviewers' comment: While it's understandable that definitions are needed to assess evidence, it is equally important to mention their limitations from the outset. For example, close contact is arbitrary for purposes of contact tracing—we know that the definition results in missing cases of exposure and infection at longer ranges. Authors' response: Thank you for this suggestion. We have noted this in the limitations section. Peer reviewers' comment: The inclusion of articles identified via preprint servers is justifiable if the search criteria include very recent dates in an attempt to capture the most recent research. However, this systematic review only includes articles up to December 20th 2020 – if the authors choose to use this date or a recent one, articles on preprint servers should not be included. Authors' response: We have updated the searches and used the most up-to-date citations for the included studies. Peer reviewers' comment: The search strategy is not reproducible and more detail is required. For example, a detailed search strategy for the WHO COVID-19 database, LitCovid, medRxiv, and Google Scholar are not included in the Appendix 2. Nor is it clear exactly which keywords were used in the PubMed search, for example, were other terms used to capture the concept of duration and proximity of exposure? Authors' response: Thank you. We have included the full search strategy. Peer reviewers' comment: It is not clear if authors defined “close contact” for inclusion in their systematic review. Authors' response: We used the CDC and WHO definitions (see Box 1). Peer reviewers' comment: Additional detail is required to explain how the QUADAS-2 tool was adapted for this study and if or how it was validated for this purpose. https://figshare.com/articles/figure/Extended_data_SARS-CoV-2_and_the_Role_of_Close_Contact_in_Transmission_A_Systematic_Review/14312630/1?file=27243050 Authors' response: We did not use all the domains in QUADAS-2 and have clarified this in the manuscript methods section. We did not validate the checklist, and have noted this in our limitations. Peer reviewers' comment: The QUADAS-2 tool was designed for studies primarily designed as diagnostic accuracy studies and its use is likely to fall short to assess the quality of studies for this systematic review. Authors' response: QUADAS-2 is used to assess reporting quality in diagnostic reviews. See https://www.bristol.ac.uk/media-library/sites/quadas/migrated/documents/quadas2reportv4.pdf. As noted in our methods, we adapted the checklist for the review. Analyses of primary studies Peer reviewers' comment: Although authors have included extended data containing the protocol and references to included and excluded studies, this remains outdated (March 2021). Several features are discussed and while some of them could suggest close contact transmission, there is quite a bit of heterogeneity in how these studies of transmission inform the role of close contact. Authors' response: We have updated the searches and included the most up-to-date citations. Peer reviewers' comment: While we agree that close-contact transmission is a dominant feature of SARS-CoV-2 transmission through the inhalation of respiratory particles, this systematic review does not help advance the aim mentioned - understanding the role of close contact. The authors could revise this work so it separately addresses features of transmission using standardized or limited definitions for each one. Attribution of such analyses to close contact (i.e., its potential role) should result from the interpretation of such findings altogether rather than from \"direct assessment of the impact of close contact in transmission\" since most studies do not define or measure close contact systematically. Authors' response: We included a table showing how the included studies defined close contact. Our objective was to identify, appraise and summarise the evidence from studies investigating transmission in close contact settings. It is equally possible that with close contact there may be transmission via large respiratory droplets and direct physical contact as well as the possibility of short-range fine aerosol and in all fairness, it should be stated as such and not that inhalation is the dominant route as this reviewer contends. It is best to be consistent with all possibilities as suggested by the CDC and WHO and many other publications. Analyses of reviews Peer reviewers' comment: The authors included 10 systematic reviews allegedly investigating close-contact SARS-CoV-2 transmission. Some concerns make questionable the inclusion of such heterogeneous publications for an analysis that at best describes these almost individually without advancing the understanding of the role of close contact in SARS-CoV-2 transmission, which is the ultimate purpose of the authors' systematic review. It is expected that studies included in such publications are primarily observational, since randomized designs are complex and it remains unclear how research should ideally address gaps in our understanding of transmission. Findings of some of the included reviews (Li, Ludvigsson, Zhu) are not described with regard to close contact, but only to population groups; others are only mentioned with regard to asymptomatic infection or attack rates. We find this analysis in general unhelpful. Authors' response: Thanks for this comment. The included systematic reviews are considered appropriate since they do fit the definition of close contact based on our original protocol - this relates to structural and population settings. We can discuss the limitations of these reviews and the included studies. Li, Ludvigsson and Zhu fit the definitions. See https://www.ecdc.europa.eu/en/covid-19/surveillance/surveillance-definitions. Some of the findings from the reviews are helpful. Indeed at least 2 reviews included only studies with high reporting quality. Peer reviewers' comment: The authors analyze features different from close contact in the sections following \"Primary studies\". All these analyses are related to primary studies, so this should be reorganized for clarity. Again, there is a detailed description of studies that do not address close contact, e.g., \"The result of one study (Rosenberg 2020) showed that the incidence of infection significantly increased with age (p<0.0001), while those from another study (Poletti 2020) showed that being 70 years or older was associated with a significantly increased risk of SARS-CoV-2-related death (p<0.001),\" Authors' response: Thank you for pointing this out and we have revised the section on primary studies. We have enumerated the definitions of close contacts in the included studies in Table 3 and reported that several studies did not report a definition). Several studies showed that being elderly was significantly associated with increased risk of infection. Rosenberg 2020 included household contacts. We have revised the statement. Discussion Peer reviewers' comment: Authors should be careful in interpreting what their systematic review found, for instance that many studies report household transmission suggests that transmission occurs in indoor environments with higher exposure. Exposure results from concentration and time of contact with infectious respiratory particles. It, therefore, depends on a mix of frequency of contacts, range of contact, and infectiousness of index cases. But household transmission may perfectly encompass risk of infection beyond 3 m, 6 m, or any other definition of close contact. We do expect that the risk of infection is greatest with the longest contact, though, but the definition of a close contact remains nebulous and the associated risk could vary depending on the environmental conditions that favor transmission. Because the purpose of this systematic review is to address transmission, the authors must discuss at least generally the interplay of these factors. SARS-CoV-2 transmission is a complex phenomenon that depends on the interaction between viral properties (infectious dose and infectivity correlates), the host and their features (breathing rate, respiratory tract morphology, target tissues, receptor distribution, host barriers, immune responses), and the environment (temperature, humidity, salinity, pH, the medium or materials of the contaminated objects or surfaces, ventilation/airflow, ultraviolet radiation). Authors also should acknowledge that existing evidence suggests that transmission in close-contact settings is likely to be dominated by short-range respiratory inhalation of infectious virions. Authors' response: Thank you. We have enumerated the complex range of factors at play and the epidemiologic associations in relation to close contact transmission (with references) and have acknowledged the various potential modes of transmission. We agree that transmission is a complex phenomenon and indeed is poorly understood. Musing about issues surrounding the biology of virus particles is beyond the scope of our review which focuses on epidemiologic associations. Peer reviewers' comment: The authors superficially mention the role of face masks in decreasing the risk of transmission from the pediatric population. This is a dangerous misinterpretation of evidence of two things that should be analyzed separately, i.e., 1) the efficacy of respiratory protection and 2) the risk of transmissibility from different populations. Certainly, this review was not designed to assess either of these aspects as a research question. As for respiratory protection, not all masks (or respirators) are expected to provide the same degree of protection. And if not correctly/consistently worn, they may not reduce risk. As for the usually overclaimed risk of children to transmit SARS-CoV-2, many potential confounders easily make this group appear highly contagious but it is unlikely this is due to intrinsic features of that population. Therefore, claims about it should be carefully framed to avoid stigmatization or unfair focalization and perceived efficacy of preventive strategies. Authors' response: We do not believe we are being superficial but rather trying to stay true to the findings. Our statements regarding the effectiveness of face masks are based on the findings from the included studies and we need to stay focused on the findings and avoid making speculative statements. We have added a caveat that there is uncertainty about the extent to which the different types of masks influence the risk of transmission. Peer reviewers' comment: Discussion unrelated to close contact is seen, e.g., \"being elderly is also associated with increased risks of transmission and mortality\". Authors' response: Thank you for pointing this out. We have removed the statement. Peer reviewers' comment: The positive results of viral cultures observed in two studies support the results of PCR and serologic tests showing that close contact setting was associated with transmission of SARS-CoV-2\". We are unsure how this manuscript supports this conclusion. Similarly, this conclusion is not supported by the data \"The positive findings from all 10 studies that performed GS and phylogenetic analysis with identical strains supports the hypothesis that close contact setting is associated with SARS-CoV-2 transmission through respiratory droplets or direct contact.\" Authors' response: We have revised the statement to indicate that transmission can occur in close contact settings. Peer reviewers' comment: We agree with the authors on the high heterogeneity of existing studies and that \"The variations observed in the definitions of close contacts also cast further doubts on the validity of overall results.\" Authors' response: Thank you. Peer reviewers' comment: \"The results of our review are consistent with several guidelines suggesting that close contact with index cases can result in transmission of SARS-CoV-2\" The authors acknowledge that the evidence for close contact transmission is only low-to-moderate quality, thus, it is a stretch to say that close contact is consistently demonstrated as a risk factor. Guidelines have been evolving throughout the pandemic and while close contact may be associated with increased risk of transmission, this study could provide much stronger evidence if transmission properties were assessed in a clearly defined, systematic, and reproducible way. Authors' response: Thank you for this comment. We have revised the sentence to discuss the “association” with transmission as opposed to \"can result in transmission”. We have added a caveat to note that guidelines keep evolving based on emerging evidence. Peer reviewers' comment: \"Our findings are also consistent with those of a systematic review which concluded that face masks are effective for preventing transmission of respiratory viruses.\" It is unclear how this systematic review regarding the role of close contract on transmission events contributes to the discussion regarding the role of face masks – more description is needed to make this link explicit. Furthermore, the efficacy of face masks is a complex topic and confounded by a number of factors. Authors' response: We have revised the statements. We have deleted the texts relating to mortality in the elderly. Peer reviewers' comment: Necessary updates Several of the preprints included in the systematic review and/or cited in the manuscript have been published; given that this manuscript is outdated and an update is needed, authors should take that opportunity to update preprints that have been published and make sure their findings remain unchanged and adjust accordingly. Some of the preprints now published are: Helsingen 20203 Paireau 20204 Kuwelker 20205 Lyngse 20206 Jones 20207 Chen 20208 Fontanet 20209 Armann 202010 Charlotte 202011 Angulo-Bazan 202012 Authors' response: Thank you. We have now updated the citations for the references."
}
]
},
{
"id": "123867",
"date": "05 Apr 2022",
"name": "Richard Wamai",
"expertise": [
"Reviewer Expertise Global 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\nI have read this manuscript with keen interest and over several weeks during which COVID-19 has continued to evolve with new studies coming out and policy changes across countries I have been traveling in (Kenya and US). This manuscript deals with the question of availability of evidence for role of close contact in COVID-19 transmission. This question seems obvious now given 2+ years of generalized policy around the world for physical or social distancing. A lay observation would be to say that there is unequivocal evidence that close proximity has a role in the transmission of COVID (after all we have been told to distance). The authors of the present manuscript deal with the question of availability of scientific evidence for this generalized policy.\nClearly, a lot (if not all) of the NPIs (non-pharmaceutical interventions) have been implemented without evidence whether they work (Halperin DT, Hearst N, Hodgins S, et al. (2021)1 - I am a co-author in this study. The current manuscript shows just how murky the state of evidence of these NPIs is. Consider the state of evidence of mask-wearing; just the Bangladeshi study is the only RCT we have, and the evidence that masks work from this trial is not that great (Abaluck J, Kwong LH, Styczynski A, et al., 20222)\nIn my view, assessment of the merits of this manuscript should center on two things. The first is whether the authors have identified all the evidence available as published in scientific literature. The second is whether the authors make good-faith representation of the studies they have reviewed. I say “good-faith” because there are questions raised by the existing reviews and comments of this manuscript. Additionally, “good-faith” means to me that the authors have not omitted results from the studies. On these two accounts I write my recommendation. A systematic/scoping review is a unique type of study because authors should be presenting in good faith the information from the studies reviewed.\n1. Have the authors examined all of the available evidence (=published studies) on the question?\nThe authors both say they have and have documented and included the method of their search for the literature reviewed (Appendix 2). The only problem I see with this is that studies reviewed were only those published as of December 20, 2020. That was the first full year of the pandemic. Publications from 2021 are not included. One would presume that it is more likely that more studies on the effect of distancing could have been conducted in 2021. Those studies are not included in this manuscript, and that is a shortcoming. One – and at the minimum necessary – revision that could be made is to add the timeframe of the review in the Title of the manuscript. In my view, it is not necessary for the authors to begin including the studies from 2021 as that would require a full new search and a re-write of large potions of the manuscript.\n2. Have the authors presented truthfully and good-faith the evidence from the studies?\nThis is the central question for this manuscript, and it appears more so the case given the extensive comments by the readers. In my view, all of the criticism is not warranted. Criticism is due where the authors have not presented results from the studies reviewed truthfully and in good-faith. Criticism is also due where gaps in evidence is not acknowledged or are pertaining. I do not think the readers present counter evidence, i.e., show that the authors have summarized results from a specific study or set of studies erroneously. In the same vein I am not convinced that readers demonstrate that the authors have misinterpreted results from the studies they have reviewed; such misinterpretation would be strong grounds for Not Approving this manuscript or calling for its revisions, of course. If the readers are presenting evidence to counter the evidence from the studies presented by the authors from other studies that is acceptable. But that should also be weighed against my point 1 above. For instance, could the initial search have missed such studies raised by the readers?\nAlso, I would not engage in some of the debates presented. For instance, I do not think the manuscript should be criticized because “these authors may lack key expertise in their team”. I have read through the contributors’ listed expertise. I do not think any special expertise above and beyond what the author team has is needed to conduct a systematic review or truthfully and in good-faith summarize the evidence from the reviewed studies. In addition, I do not think that simply because persons in the author team are members of a decision-making body like the WHO that disqualifies them from objectivity or removes their training in science and scholarship. On the contrary, I think there is great value when decision-makers also participate in science. The obvious problem, of course, is where there are conflicts of interests, or where such persons are compromised. However, we have to take the consideration that in a multi-authored manuscript not one of the authors influences the entire narrative of the manuscript or results presented. Persons whose employment or affiliation positions may – or may be perceived to – compromise any perspectives presented in a manuscript they have co-authored should of course declare the conflicts of interests. Declaration of conflicts of interests is a standard protocol required in journal standards.\nHaving said the above, I have a few other observations or questions of my own.\nQ1: On table 5, many studies are of no assessed quality, i.e., miss the quality measures specified in this table. What if studies missing all (or even just 2) of these measures are excluded in the analysis? So, if only those applicable as judged in Fig 2 are included.\nQ2: On page 46, “Risk of Infection”. Is not ‘risk of infection’ similar to AR (attack rate) in the sense that AR reports risk of infection? In this section too (with Fig 3a) we would expect AR and SAR results to indicate risk of infection. Where, correspondingly, ARs and SARs are higher than risk of infection is high. Thus, risk of infection analysis do not present different results. Is this not how this should be understood?\nQ3: “Implications for Research”, page 58. The text, \"Local, national, and international health organisations should promote good hygiene measures including advising against close contact with SARS-CoV-2 infected individuals; use of medical masks should be encouraged in circumstances where close contact with infected cases is likely. Activities in enclosed settings should be discouraged and social distancing in close contact settings should be encouraged.\" - To me, and objectively assessing the timing of the pandemic where we are today (April 1st 2022), this text is mostly ‘water under the bridge’ and should thus be updated – if this manuscript is to be indexed. See discussions, e.g., in Halperin DT, Hearst N, Hodgins S, et al. (2021)1.\nAdditionally, I am not convinced the authors have presented compelling evidence here to warrant prompting such measures this text I highlight here include. The authors should strictly adhere to the evidence of their manuscript; it is wrong for the authors to echo the chorus of songs we have heard about these NPIs when there is no or limited evidence they work. Thirdly, as a further reason to exclude this concluding text, in this manuscript there is no discussion about hygiene. Evidence presented does not show close contact be avoided whatever the case. For instance, relevant studies reviewed show no transmission from (index) persons with previous repeated infection. Given this and the fact that by now many (if not most) people will have been infected (i.e., generalized spread) even multiple times (e.g., CDC. Nov. 16, 2021. Estimated COVID-19 Burden, https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/burden.html), should we still be advocating for quarantine and masking? We argue for adherence to evidence (Halperin DT, Hearst N, Hodgins S, et al., 20211.\nFinally, there will be a few grammatical errors that should be checked.\nI am grateful for the opportunity to read this manuscript and share my observations which I hope will help guide the authors in determining merit worthiness for indexing as well as contribute to continued discussions.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "8443",
"date": "06 Jul 2022",
"name": "IGHO ONAKPOYA",
"role": "Author Response",
"response": "Peer reviewer's comment: I have read this manuscript with keen interest and over several weeks during which COVID-19 has continued to evolve with new studies coming out and policy changes across countries I have been traveling in (Kenya and US). This manuscript deals with the question of availability of evidence for role of close contact in COVID-19 transmission. This question seems obvious now given 2+ years of generalized policy around the world for physical or social distancing. A lay observation would be to say that there is unequivocal evidence that close proximity has a role in the transmission of COVID (after all we have been told to distance). The authors of the present manuscript deal with the question of availability of scientific evidence for this generalized policy. Authors' response: Thank you. Peer reviewer's comment: Clearly, a lot (if not all) of the NPIs (non-pharmaceutical interventions) have been implemented without evidence whether they work (Halperin DT, Hearst N, Hodgins S, et al. (2021)1 - I am a co-author in this study. The current manuscript shows just how murky the state of evidence of these NPIs is. Consider the state of evidence of mask-wearing; just the Bangladeshi study is the only RCT we have, and the evidence that masks work from this trial is not that great (Abaluck J, Kwong LH, Styczynski A, et al., 20222) Authors' response: Thank you for this observation. As at the time we conducted the initial review, the evidence base was poor. Peer reviewer's comment: In my view, assessment of the merits of this manuscript should center on two things. The first is whether the authors have identified all the evidence available as published in scientific literature. The second is whether the authors make good-faith representation of the studies they have reviewed. I say “good-faith” because there are questions raised by the existing reviews and comments of this manuscript. Additionally, “good-faith” means to me that the authors have not omitted results from the studies. On these two accounts I write my recommendation. A systematic/scoping review is a unique type of study because authors should be presenting in good faith the information from the studies reviewed. Authors' response: Thank you for focusing your peer review on the evidence as presented in the manuscript. Peer reviewer's comment: 1. Have the authors examined all of the available evidence (=published studies) on the question? The authors both say they have and have documented and included the method of their search for the literature reviewed (Appendix 2). The only problem I see with this is that studies reviewed were only those published as of December 20, 2020. That was the first full year of the pandemic. Publications from 2021 are not included. One would presume that it is more likely that more studies on the effect of distancing could have been conducted in 2021. Those studies are not included in this manuscript, and that is a shortcoming. One – and at the minimum necessary – revision that could be made is to add the timeframe of the review in the Title of the manuscript. In my view, it is not necessary for the authors to begin including the studies from 2021 as that would require a full new search and a re-write of large potions of the manuscript. Authors' response: We have updated the electronic searches up till 30/04/2022 because of the comments from reviewer #1 and re-written several aspects of the manuscript to reflect this update. Peer reviewer's comment: 2. Have the authors presented truthfully and good-faith the evidence from the studies? This is the central question for this manuscript, and it appears more so the case given the extensive comments by the readers. In my view, all of the criticism is not warranted. Criticism is due where the authors have not presented results from the studies reviewed truthfully and in good-faith. Criticism is also due where gaps in evidence is not acknowledged or are pertaining. I do not think the readers present counter evidence, i.e., show that the authors have summarized results from a specific study or set of studies erroneously. In the same vein I am not convinced that readers demonstrate that the authors have misinterpreted results from the studies they have reviewed; such misinterpretation would be strong grounds for Not Approving this manuscript or calling for its revisions, of course. If the readers are presenting evidence to counter the evidence from the studies presented by the authors from other studies that is acceptable. But that should also be weighed against my point 1 above. For instance, could the initial search have missed such studies raised by the readers? Authors' response: We thank the reviewer for making this point. We agree with you that the criticisms were not justified. We searched, identified, and analyzed the available evidence at that time point. Peer reviewer's comment: Also, I would not engage in some of the debates presented. For instance, I do not think the manuscript should be criticized because “these authors may lack key expertise in their team”. I have read through the contributors’ listed expertise. I do not think any special expertise above and beyond what the author team has is needed to conduct a systematic review or truthfully and in good-faith summarize the evidence from the reviewed studies. In addition, I do not think that simply because persons in the author team are members of a decision-making body like the WHO that disqualifies them from objectivity or removes their training in science and scholarship. On the contrary, I think there is great value when decision-makers also participate in science. The obvious problem, of course, is where there are conflicts of interests, or where such persons are compromised. However, we have to take the consideration that in a multi-authored manuscript not one of the authors influences the entire narrative of the manuscript or results presented. Persons whose employment or affiliation positions may – or may be perceived to – compromise any perspectives presented in a manuscript they have co-authored should of course declare the conflicts of interests. Declaration of conflicts of interests is a standard protocol required in journal standards. Authors' response: Again, we agree with the reviewer. We have enough expertise in our team and have co-authored hundreds of systematic reviews. Peer reviewer's comment: Having said the above, I have a few other observations or questions of my own. Authors' response: Thank you. We have responded to each observation. Peer reviewer's comment: Q1: On table 5, many studies are of no assessed quality, i.e., miss the quality measures specified in this table. What if studies missing all (or even just 2) of these measures are excluded in the analysis? So, if only those applicable as judged in Fig 2 are included. Authors' response: If we removed studies missing all or even 2 domains, we think the overall quality would still be low to moderate. Only 9 studies adequately dealt with bias. Peer reviewer's comment: Q2: On page 46, “Risk of Infection”. Is not ‘risk of infection’ similar to AR (attack rate) in the sense that AR reports risk of infection? In this section too (with Fig 3a) we would expect AR and SAR results to indicate risk of infection. Where, correspondingly, ARs and SARs are higher than risk of infection is high. Thus, risk of infection analysis do not present different results. Is this not how this should be understood? Authors' response: The AR is a crude measure of the rate of infection in a group. The risk of infection compares the rate of attacks between or across groups, based on other variables, e.g., seating proximity. (See Box 1). Peer reviewer's comment: Q3: “Implications for Research”, page 58. The text, \"Local, national, and international health organisations should promote good hygiene measures including advising against close contact with SARS-CoV-2 infected individuals; use of medical masks should be encouraged in circumstances where close contact with infected cases is likely. Activities in enclosed settings should be discouraged and social distancing in close contact settings should be encouraged.\" - To me, and objectively assessing the timing of the pandemic where we are today (April 1st 2022), this text is mostly ‘water under the bridge’ and should thus be updated – if this manuscript is to be indexed. See discussions, e.g., in Halperin DT, Hearst N, Hodgins S, et al. (2021)1. Authors' response: We understand the point the reviewer makes. These statements were based on our understanding at that time. We have revised this section with the updated evidence. We have included the suggested reference. Peer reviewer's comment: Additionally, I am not convinced the authors have presented compelling evidence here to warrant prompting such measures this text I highlight here include. The authors should strictly adhere to the evidence of their manuscript; it is wrong for the authors to echo the chorus of songs we have heard about these NPIs when there is no or limited evidence they work. Thirdly, as a further reason to exclude this concluding text, in this manuscript there is no discussion about hygiene. Evidence presented does not show close contact be avoided whatever the case. For instance, relevant studies reviewed show no transmission from (index) persons with previous repeated infection. Given this and the fact that by now many (if not most) people will have been infected (i.e., generalized spread) even multiple times (e.g., CDC. Nov. 16, 2021. Estimated COVID-19 Burden, https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/burden.html), should we still be advocating for quarantine and masking? We argue for adherence to evidence (Halperin DT, Hearst N, Hodgins S, et al., 20211. Authors' response: Thank you for raising this issue and we agree that we should stay focused on the evidence found in our review. We have accordingly revised the text as above. Peer reviewer's comment: Finally, there will be a few grammatical errors that should be checked. Authors' response: Thanks. We have re-checked the manuscript for grammatical errors. Peer reviewer's comment: I am grateful for the opportunity to read this manuscript and share my observations which I hope will help guide the authors in determining merit worthiness for indexing as well as contribute to continued discussions. Authors' response: Thank you for your helpful feedback which we believe has helped to improve the quality of the manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/10-280
|
https://f1000research.com/articles/11-705/v1
|
27 Jun 22
|
{
"type": "Research Article",
"title": "Saudi Arabian students in postgraduate dental programs: Investigating factors associated with burnout",
"authors": [
"Amal Asiri"
],
"abstract": "Background: Burnout related to emotional and physical study or work demands affects an individual’s performance and wellbeing. This study focused on Saudi Arabian dental residents studying in the United States and the United Kingdom who are faced with many challenges in the pursuit of a higher education degree. Methods: A survey including demographic and Maslach Burnout inventory (MBI) questions was distributed to assess this population’s level of burnout. The MBI has been widely used in the literature to assess three components of burnout: emotional exhaustion (EE), depersonalization (DEP), and (diminished) personal accomplishment (PA). Potential predictors of burnout level, tested for statistical significance, included: (1) country (US vs UK), (2) hours of work, (3) sponsorship status, (4) marital status (5) gender, and (6) prior work experience. Results: The number of participants from the UK was 29 and from the US was 64 (n=93). The total number of participants who completed the survey was 87. Using multiple regression analyses, those found to predict EE included hours of work, sponsorship status, and gender. Only gender was found to predict PA. None of the variables were predictive of DEP. Moreover, after controlling for the demographic variables, the country where studying did not help account for the level of burnout. Conclusion: In the literature, burnout was found to be prevalent among dental postgraduate students. This study suggests that Saudi Arabian dental residents experience high burnout due to emotional exhaustion when compared to other medical professionals. Moreover, Female residents are more likely to report experiencing burnout than their male counterparts. Limitations of the study, implications for practice and suggestions for further research are offered in the discussion.",
"keywords": [
"Burnout",
"health care providers",
"postgraduate residents",
"emotional exhaustion",
"depersonalization",
"personal accomplishment",
"Maslach burnout inventory",
"dentistry."
],
"content": "Introduction\n\nDental students experience high levels of stress due to the nature of their studies and profession. In the US, a dental student typically spends three to four years in dental school following a three-four year bachelor’s degree in a related major. In Saudi Arabia, dental school is a five-year commitment preceded by one preparatory year and ending with one year of internship in public clinics. After passing licensure exams and graduation, some graduates choose to pursue higher education. They compete for acceptance in a variety of postgraduate dental specialty programs where they continue their studies for a few more years. Table 1 illustrates different dental program timelines according to program location. The dental curriculum demands intense memorizing of detailed information across an array of disciplines. Requirements include dental laboratory duties, managing of a variety of routine and unpredictable clinical situations, and multiple written, clinical, and licensing examinations throughout dental school years. Numerous studies have indicated that the rigorous training requisites, as well as the span of competencies across clinical, theoretical, and interpersonal requirements, increase rates of stress and burnout in postgraduate dental students.1–5 Furthermore, there has been an increase in the number of international dental students in postgraduate programs, in which international students can experience additional stressors relating to socio-cultural adjustment, self-efficacy, educational gaps, and other challenges.6,7\n\nStress is a broad term that can be defined in several ways, though it generally pertains to an individual being overburdened or pressured by the requirements of a given environment, to the point where wellbeing is compromised.1,3 Burnout was defined as “a psychological syndrome emerging as a prolonged response to chronic interpersonal stressors on the job”.8,p.103 Persistent exposure to stress can lead to burnout, which involves work or school-related exhaustion and disengagement.4 Studies have found that in addition to the workload itself, dental students experience fatigue, chronic sleep deprivation, an increased likelihood of being on-call, as well as stressors relating to debt accrued from the high costs of education and unsteady financial standing.9\n\nStudies have shown that stress perceived by dental students increases, on average, as students’ progress in dental school, with seniors reporting higher stress and burnout compared to first and second year dental students.3 A study by Harrison et al.,10 employed a sample of 334 students at a US dental school ranging from first to fourth year enrollment. Participants were assessed with the Perceived Wellness survey, the Mental Health inventory, and the Medical Outcomes Study Social Support survey. The results indicated that first-year students reported less social support, and that Asian and Hispanic students indicated less happiness and mental wellbeing compared to the other ethnic subgroups. Notably, whether students were international was not factored in this study. The researchers suggested the need for more wellbeing support in dental programs to address varying student needs.10 As dental students are increasingly enrolling in clinical and non-clinical specialty post-graduate programs, either soon after graduation or elsewise during their career, added stressors can hinder wellbeing.6\n\nWhile stress and burnout related to the study and practice of dentistry in the predoctoral level has been widely studied, the literature is relatively sparse when it comes to stress in post-graduate dental students and residents. Furthermore, literature that specifically assesses international students in postgraduate dental programs is lacking. The average length of a post graduate program is two-three years depending on sought credentials and specialty. Program requirements vary in different countries, and coping mechanisms also vary across different cultures. Divaris et al.,11 assessed 99 students in a postgraduate dental program in Greece, including clinical, non-clinical, and PhD students. The Graduate Dental Environmental Stress questionnaire was administered to measure stress, and the Maslach Burnout Inventory (MBI) measured burnout, specifically on the scales of personal accomplishment, emotional exhaustion, and depersonalization. On all three scales of the MBI survey, there was a positive correlation of perceived stress and burnout where most of the sample (44%) were deemed burnout cases on the emotional exhaustion scale, followed by personal accomplishment (38%) and depersonalization (13%). Furthermore, perceived stress was prominent among clinical students compared to non-clinical and PhD programs.11 Similarly, when assessing stress and burnout in Swiss dental residents applying the same instruments, it was found that insufficient leisure time, as well as curriculum and research requirements, were among the top stressors.4 The specific requirements in a dental program have considerable effects on students’ capacity to take on the workload, cope with stress, and reduce risks of burnout.\n\nTo compare stress and burnout in undergraduate and postgraduate dental students, a study by Mandava et al.,12 assessed 285 students across five regions in India. The questionnaire to measure stress was formulated by the International Stress Management Association including the Maslach Burnout Inventory. With a response rate of 71%, 142 participant responses were included in the analysis. Results indicated no statistical significance correlating stress and burnout in undergraduate students; however, there was a significant correlation between stress and burnout among postgraduate orthodontic students. Emotional exhaustion and depersonalization were positively correlated with perceived stress measured by the International Stress Management Association questionnaire, as also supported by Divaris et al.,11 using the Graduate Dental Environment Stress (GDES). However, personal achievement was negatively correlated with burnout.12\n\nStudies addressing stress and burnout in the Saudi dental residents population are especially lacking or limited to dental residents in the same specialty or within one institution. A study by Al-Sowygh13 assessed perceived stress among 425 undergraduate dental students at a Saudi Arabian dental program with the Dental Environmental Stress questionnaire and found that clinical requirements correlated with the highest stress levels, particularly among fourth and fifth-year students. Notably, ‘social stressors’ and ‘performance pressure’ were heightened among married students compared to single students.13 However, a study by Al-Shayea14 assessed perceived anxiety, depression, and stress among postgraduate orthodontic students across three institutions in Saudi Arabia. The researchers found that married students, and students over the age of 30, indicated lower levels of anxiety, though stress was persistent across all categories and institutions. This study employed the Depression Anxiety Stress Scale to a sample of 79 students, of which 51.9% indicated moderate stress levels.14 This indicates the general pervasiveness of stress in postgraduate programs, contrary to more varied results when assessing undergraduate dental students. Saudi Arabian dental residents studying abroad potentially undergo added stress due to relocating to a new country and culture and moving away from family and home for a prolonged period of time. The aim of this study is to assess burnout and stress levels in Saudi Arabian dental residents enrolled in dental specialty postgraduate programs in the United Kingdom and the United States. Furthermore, this assessment will provide data for comparison between the MBI means of dental residents and medical professionals. This analysis was conducted to shed some light on possible contributory factors that residents might want to take into consideration when planning to study abroad.\n\nThis research will address the following research questions: 1) What level of burnout, on average, do Saudi Arabian students enrolled in postgraduate programs report as measured by the emotional exhaustion (EE), depersonalization (DP), and (diminished) personal accomplishment (PA) subscales of the Maslach Burnout Inventory (MBI)?; 2) What proportion of variation in levels of burnout among Saudi Arabian students enrolled in postgraduate programs is accounted for by the set of predictors which includes: country where studying, hours of work, being sponsored or not, marital status, and prior work experience?; and, 3) Which of the following predictors accounts for unique variation in levels of burnout among these students? The predictors are (1) country (US vs UK), (2) hours of work, (3) sponsorship status, (4) marital status (5) gender, and (6) prior work experience. These questions will be assessed with a quantitative comparative research design assessing Saudi students enrolled in postgraduate dental programs in the UK and the US using the Maslach Burnout Inventory - Human Services Survey for Medical Personnel (MBI-HSS MP),15 which is a variation of the MBI tool adapted for medical personnel to measure burnout by addressing three scales: 1) feelings of emotional exhaustion due to work duties, 2) depersonalization measuring lack of sympathy and impersonal attitudes toward patients, and 3) personal accomplishment measuring feelings about success and achievement related to the profession.\n\nProgram designs have a significant impact on stress and burnout in postgraduate dental students, and studies indicate that more individualized support for students is needed to reduce stress and burnout.1 Different approaches have been applied in an effort to reduce risks of stress and burnout. Ahmed et al.,1 compared a case-based curriculum and a subject-based curriculum for fifth and sixth-year dental and medical students at Kuwait University and found the case-based format correlated with higher stress levels. Some of the leading sources of stress were related to inconsistent feedback from varying instructors, challenges in effective communication with instructors, and workload amount.1 Factors relating to inconsistent feedback, communication challenges are likely to be heightened for international students, in addition to gaps in knowledge and standards in US programs compared to the home country.6 The American Dental Education Association specifies guidelines for robust learning environments for diverse students, as well as measures to address linguistic and cultural backgrounds.16 However, it is unclear what measures are generally applied to address stress in postgraduate programs. To the researchers’ knowledge, there has yet to be a study comparing the stress and burnout among a specific international population in postgraduate dental programs in the United States and the United Kingdom. The study was designed to inform Saudi students about possible predictors of burnout when planning on studying abroad and can also guide US and UK. postgraduate programs in regard to addressing stress and burnout considerations for international students.\n\nThe terms used in this article pertain to the psychological experiences of burnout and stress. The author also clarifies in this section the elaborate educational requirements for a dental student in the locations of interest of this study. This clarification highlights the educational journey of postgraduate dental residents leading to their enrollment in residency programs in the US or UK. The educational timeline for the US and Saudi Arabia were acquired based on the author’s experience of studying in both countries. The UK dental educational timeline was acquired from the General Dental Council (GDC), the licensing body for dentists practicing in the UK.17\n\nBurnout: According to Maslach and Leiter,8 burnout is a psychological syndrome emerging as a prolonged response to chronic interpersonal stressors on the job. The three key dimensions of this response are an overwhelming exhaustion, feelings of cynicism and detachment from the job, and a sense of ineffectiveness and lack of accomplishment.\n\nStress: According to Baum,18 stress is an uncomfortable emotional experience accompanied by predictable biochemical, physiological, and behavioral changes.\n\nUndergraduate dental student: Undergraduate students enrolled in a dental school.\n\nPostgraduate dental student: Students who graduated from a dental school awarding a dental degree, who successfully passed licensure exams and are enrolled in a higher education specialty program. These students are referred to as ‘residents’ when the type of postgraduate program they are enrolled in requires a clinical residency.\n\nClinical postgraduate dental specialty programs: Those programs with a heavy focus on the clinical procedures of a certain branch in dentistry. The postgraduate students enrolled in this type of program are referred to as ‘residents’. These programs typically require residents to diagnose and treat a vast number of patients throughout the duration of the program. They award graduates degrees in the clinical specialties of dentistry, e.g., orthodontics, endodontics, periodontics, etc.\n\nNon-clinical postgraduate dental specialty programs: Those programs with less focus on direct patient-doctor interactions. They vary in nature and requirements according to the field of study. These programs award degrees in the nonclinical specialties of dentistry, e.g., public health and community dentistry, oral biology and biomaterials etc. This term also potentially includes non-clinical degrees in clinical specialties, e.g., Doctor of Philosophy degrees (PhD) in endodontics.\n\nTimeline of dental studies in Saudi Arabia: Undergraduate dental student, intern, licensure exam, dentist, postgraduate dental student.\n\nTimeline of dental studies in the United States: Pre-dental student, dental student, licensure exams, dentist, postgraduate dental student.\n\nTimeline of dental studies in the United Kingdom: Undergraduate dental student, foundation dental training, registration for licensure procedure, dentist, postgraduate dental student.\n\nNote: For the sake of simplifying, the term ‘undergraduate dental student’ is used in this study to include all dental students pre-graduation from dental school regardless of location.\n\n\nMethods\n\nThis study has been performed in accordance with the Declaration of Helsinki regulations and guidelines. Participation in the study was voluntary and confidential through anonymous, non-identifying survey design. Written informed consent was obtained from all study participants. Approval from the institutional review board (IRB) was obtained on 2/27/2019 with protocol #19-53.\n\nDirect communication with the Saudi Arabian Cultural Mission was conducted to identify programs with Saudi Arabian dental residents enrollment. Communication with Saudi Arabian dental residents enrolled in these programs was then initiated by the study representatives in the US and the UK directly whether face-to-face, e-mail, or social media accounts. The target population is Saudi Arabian dental residents enrolled in UK-based and US-based post graduate programs in the following clinical specialties: endodontics, fixed and removable prosthodontics, oral and oromaxillofacial surgery, orthodontics, oral medicine, operative and restorative dentistry, advanced education in general dentistry, oral radiology, and pediatric dentistry and periodontics. These specialties were selected due to their clinical nature with repeated resident-patient interactions. The programs award graduates either a certificate of advanced graduate study (CAGS) or a Master of Science degree (MS, MSc) upon completion. All programs require residents to be proficient in the English language as indicated by their Test of English as a Foreign Language (TOEFL) or International English Language Testing System (IELTS) scores. Non-clinical programs with lowered or no direct patient contact were excluded due to the nature of the study requiring repetitive direct contact with patients to report the burnout experience.\n\nThe sampling method used is the non-probability quota sampling technique. Although ideal, a stratified random sample from the population is not feasible. Based on a power analysis using the software G*Power, it was determined that to detect a small-medium effect (f2 = .09), a sample size of 158 is needed (α = 0.05, power = .80, # of predictors = 6). Given the main focus of this study being the comparison between residents in two countries (i.e., UK and US), the minimum number of participants desired was 79 participants for each country. The G*Power software can be freely downloaded from http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/. As it turned out, the sample size obtained was just 87 cases with complete data (from both countries combined) and given the R2 values obtained (which were translated into f2 values of .23, .02, and .08), the power was .91, .12, and .43 for the regression models predicting EE, DEP, and PA, respectively. This limitation to statistical conclusion validity will be noted in the discussion.\n\nTo address the research questions, the criterion variables are emotional exhaustion (EE), depersonalization (DP), and professional accomplishment (PA); the control variables are hours of work per week, marital status, gender, prior work experience, and sponsorship status; and the predictor variable is country.\n\nThe survey starts with an informed consent page followed by the first part of the survey. This first part was created by the author and includes demographic questions regarding program location, age, gender, marital status and family living arrangements. Other questions address specialty program type and length, resident position/year, hours of work per week, sponsorship status and work experience prior to joining the program.\n\nTo assess perceived stress and burnout, the second part of the survey includes the English version of the Maslach Burnout Inventory Human Services Survey for Medical Personnel MBI-HSS (MP). It was distributed to participants via a web link. According to Maslach et al.,19 sufficient levels of stability estimates and internal-consistency reliability estimates (Cronbach’s alpha) are reported for the three MBI-HS scores from a broad sample of workers in professions related to human-services. Cronbach’s alphas were .90, .79, and .71 for emotional exhaustion, depersonalization, and personal accomplishment, respectively. Multiple studies were cited in which test-retest coefficients for the three scale scores were reported for a variety of samples; for example, over a few weeks (.82, .60; and .80, respectively); three months (.75, .64, and .62, respectively); and up to one year (.60, .54, and .57, respectively).\n\nThe MBI section is the second part of the survey,15 which contains 22 items to assess burnout on the three identified scales: emotional exhaustion, depersonalization and professional accomplishment. Participants will be asked to rank item responses on a seven-point Likert scale where 0 means ‘never’, 1: ‘a few times a year or less’, 2: ‘once a month or less’, 3: ‘a few times a month’, 4: ‘once a week’, 5: ‘a few times a week’, and 6: ‘every day’. The survey was not piloted prior to this study.\n\nContact was made via e-mail with informal representatives of the Saudi Arabian dental residents in the US and the UK, given their spread out locations from the author, located in Western US and the Northeastern US while the third was in the UK. Moreover, their network connections with Saudi Arabian dental residents who are enrolled in a variety of dental programs in both countries.\n\nThe two representatives handed out paper recruitment flyers to residents within both of their schools and sent out emails with the flyers attached to acquaintance residents in other schools. These flyers invited potential participants to provide the representatives with their email addresses for the online survey link to be sent out to. The flyers included assurance statements about the anonymous and voluntary nature of the survey. Once residents responded to the flyer in person or by email by providing their preferred email address, the email addresses were added to a list of recipients on the survey website, SurveyMonkey, and the survey link was forwarded to the list through the website itself. The website used to administer the survey is an online survey tool (SurveyMonkey.com, Palo Alto, CA, US) allowing for anonymous responses and voluntary participation. Once they received the link via email, clicking on it takes the respondent to the consent form page first. Reading and signing the consent by clicking on the appropriate button was mandatory to view the survey questions. Otherwise, the link automatically redirected responders to exit the survey. The anticipated response was 80%. However, due to low participation rate, contact with prominent social media figures in the Saudi dental field on Twitter was initiated. These influencers have many followers who are mostly dental field professionals and students. A web link was distributed in a Twitter post by two social media figures in an attempt to reach out to as many potential respondents as possible. This helped improve response rate significantly. The surveys were available online for a period of three months. Data collection started towards the end of February 2019 and continued until early May 2019. To improve response rate, an incentive of $5 Starbucks™ e-gift cards were to be offered to 20 participants who were going to be chosen randomly. Participants were given the choice to sign up for these gift cards after filling out the survey where they were asked to provide any e-mail address to send the e-gift card randomly to it. A physical randomization technique was going to be used where participants who provide e-mail addresses were going to be written on pieces of papers, mixed in a bowl and chosen 20 randomly. However, only three participants signed up for the gift cards, which were sent to the provided e-mail addresses without the need for randomization since the number of gift card interested participants was below 20. Subsequently, data was downloaded to a Microsoft Excel (2019) spreadsheet and the statistical package for the social sciences (SPSS) software (IBM SPSS Statistics for Windows, version 23 (IBM Corp., Armonk, N.Y., USA) which can be found at (https://www.ibm.com/sa-en/analytics/spss-statistics-software) was used to run the appropriate statistical analyses.\n\nThe data for this research is available in the Harvard Dataverse repository.20 In order to evaluate the research questions, an α level of 0.05 was employed. Descriptive statistics along with t-tests and multiple regression analysis was used. A table of descriptive statistics and zero order correlations for all variables is provided as shown in Table 2.\n\n* SACM = Saudi Arabian Cultural Mission.\n\n** Correlation is significant at the 0.05 level (2-tailed).\n\n*** Correlation is significant at the 0.01 level (2-tailed).\n\nThe first research question (RQ) involves descriptive statistics including means, medians, and standard deviations which are reported for the three scales of the MBI and compared to existing norms for medical professionals21 using a series of three one-sample t-tests for the three subscales. To address the second RQ, a simultaneous multiple regression analysis was performed for each of the three MBI subscales utilizing the five control variables and the key predictor (country) in the model. The R2 was used to gauge the proportion of variation in levels of burnout that the set of variables explains with similar analyses for the other subscales. To address the third RQ, three sequential multiple regression analyses were performed predicting the scores of each subscale separately. In Block 1, the five control variables were entered. In Block 2, the key predictor (country) was entered. The change in R2 (ΔR2) and its level of significance was used to answer the research question. The results for both RQ2 and RQ3 are summarized as shown in Tables 4, 5, and 6.\n\nReliability was evaluated using Cronbach’s alpha for the three MBI-HSS (MP) scales yielding coefficients of 0.819 for EE, 0.642 for DEP, and 0.708 for PA. That the reliability for DEP was below .70 suggests a potential threat to statistical conclusion validity for analyses involving depersonalization, a limitation to be noted in the discussion, as well.\n\n\nResults\n\nThe purpose of the study was to assess the burnout experienced by Saudi Arabian dental residents studying abroad through the means of the MBI survey tool by assessing the three dimensions of burnout; emotional exhaustion (EE), depersonalization (DP), and personal achievement (PA).\n\nThe assessment results are compared to other medical professionals results in RQ one. In RQ two and three, subscale scores from each of the three dimensions of the MBI are examined via multiple regression analyses to determine which predictors account for unique variation in the indicators of burnout.\n\nA total of 93 residents responded to the survey. The number of complete responses was 87. Over two-thirds (68.8%) of respondents were studying in the United States while about one- third (31.2%) of the respondents were studying in the United Kingdom. Male respondents comprised 58.1% of the sample while 41.9% were female. More respondents were married (64.5%) than single (35.5%). Prior work experience, specialty and hours of work per week demographics are shown in Table 3. Most respondents had a few years of prior work experience before beginning their postgraduate programs abroad. Respondents from a wide range of specialties participated in the survey, where Fixed and Removable Prosthodontics residents were the most numerous at 21.5% while Oral Medicine residents were the fewest (2.2%). Most of the sample reported being dual sponsored by the Saudi Cultural Mission and an employer. Over a quarter of the sample reported a high number of work hours per week where they were required to work 51 hours per week in program related activities and requirements.\n\n* SACM = Saudi Arabian Cultural Mission.\n\nTo address the first research question, as to the level of burnout, one-sample t-test analyses were performed, employing an alpha level of.05 to compare the means of Saudi dental residents to that of the medical profession for the three MBI scales. The means of the medical professionals (2.466, 1.424, and 4.566 for EE, DP, and PA, respectively) were obtained from the MBI manual.19 There is evidence to suggest a statistically significant difference between the means of Saudi Arabian dental residents (M = 2.73, SD = 1.20) and the medical professionals population means in EE (p = .043). Specifically, we are 95% confident that the dental residents are at least .009 and at most.52 points higher in emotional exhaustion. However, there was insufficient evidence to suggest a statistically significant difference in DP (p = .860) and PA (p = .510), based on the dental residents’ sample statistics (M = 1.45, SD = 1.16) and (M = 4.41, SD = .96) respectively as shown in Table 2.\n\nMultiple regression analyses were conducted to address research questions two and three regarding the proportion of variation accounted for by the set of six predictors and which predictors account for unique variation in the levels of burnout. Tables 4, 5 and 6 summarize the results of analyses for the three subscales, respectively.\n\nEmotional exhaustion\n\nIn Table 4, the multiple regression model for EE with all six predictors was statistically significant and explained 18.8% of the variation, F(6, 80) = 3.087, p = .009, R2 = .188. Whereas the set of five variables in the first block accounted for 16.8% of the variance, knowing the country in which the student was a dental resident explained an additional 2.0% of the variance in EE. This increase, however, was not statistically significant, F(1, 80) = 1.954, p = .166. Three of the predictors accounted for unique variation in levels of EE. The unstandardized regression coefficient for hours worked per week, b = .229, t (80) = 2.993, p = .004, indicates that for each additional unit increase of the predictor (10 hours increments), EE scores increased by .229 points, controlling for other predictors. Of more interest was the coefficient associated with Sponsorship, b = .712, t (80) = 2.491, p = .015, where being sponsored is associated with an increase of .712 points on the EE scale while controlling for other predictors.\n\nOnce other variables are taken into account, gender was a statistically significant predictor for the EE scale as well. On average, the EE scores of females (coded 1) were .550 points higher than males (coded 0), b = .550, t (80) = 2.091, p = 040. Those studying in the US (coded 1) had lower EE scores, on average, than those studying in the UK (coded 0), but the difference was not statistically significant, b = -.383, p = .166.\n\nDepersonalization\n\nIn Table 5, the multiple regression model for depersonalization (DEP), the set of six predictors was statistically significant but explained just 2.2% of the variation, F(6, 80) = .297, p = .937, R2 = .022. Whereas the set of five variables in the first block accounted for 2.1% of the variance, knowing the country in which the student was a dental resident explained less than 1% more of the variance in DEP. This increase was not statistically significant, F(1, 80) = 0.039, p = .844. None of the predictors accounted for unique variation in levels of DEP. Those studying in the US (coded 1) had higher DEP scores, on average, than those studying in the UK (coded 0), but the difference was not statistically significant, b = .057, p = .844.\n\nPersonal accomplishment\n\nIn Table 6, the multiple regression model for personal accomplishment (PA) with all six predictors was not statistically significant and explained 7.8% of the variation, F(6, 80) = 1.128, p = .354, R2 = .078. Whereas the set of five variables in the first block accounted for 7.0% of the variance, knowing the country in which the student was a dental resident explained less than 1% of the variance in PA. This increase, then, was not statistically significant, F(1, 80) = .686, p = .410. Gender was the only predictor that accounted for unique variation in levels of PA. On average, the PA scores of females (coded 1) were.490 points lower than males (coded 0), b = -.490, t (80) = -2.181, p = .032. Those studying in the US (coded 1) had lower PA scores, on average, than those studying in the UK (coded 0), but the difference was not statistically significant, b = -.193, p = .410.\n\n\nDiscussion\n\nThe findings of this study aligned with those of previous research in terms of burnout prevalence in dental postgraduate students. Mandava et al.,12 and Divaris et al.,11 reported a similar positive correlation between stress and burnout by employing different methodologies. However, some results suggested new information when compared with previous research findings. Mandava et al.,12 found no significant differences between males and females in reporting burnout.\n\nMultiple studies suggested higher burnout on the three MBI scales in physicians22 and health care staff.23 The sample mean for the EE MBI scale was significantly different from the medical professionals population mean provided by the MBI manual. The sample means were significantly higher in EE compared to the medical professional means. This suggests that Saudi Arabian dental residents experience high burnout due to emotional exhaustion when compared to other medical professionals. The DP and PA scales means were not found to be significantly different between the two.\n\nIn the multiple regression analysis, the EE model was found to vary significantly according to hours of work per week, sponsorship status, and gender. This suggests that increased workload contributes to higher burnout. Interestingly, dual income residents from a sponsor job and the SACM experienced more emotional exhaustion than their SACM-only single income or self-sponsored counterparts. This could be explained by the added pressure from employers on residents to meet multiple requirements and achievements before returning to the workforce. Moreover, it is suggested that females experienced more emotional exhaustion and less sense of personal achievement than their male counterparts. This aligns with a study by Minamizono et al.,24 suggesting that female nurses in Japan reported higher stress and subsequent intention to leave careers due to assigned gender roles and socio-cultural pressures. Balancing work and family life could potentially contribute to added pressures on females in health care. Interestingly, marital status and prior work experience did not explain any variance or difference in the analyses. This differs from findings by Al-Shayea14 where married students were found to report less stress and burnout compared to their single counterparts.\n\nStatistical assumptions include those underlying the use of multiple regression analysis such as: normality, linearity, homoscedasticity, and independence of the error terms. A methodological limitation of self-reporting assumes complete transparency in responding to the survey. However, the effect of this assumption is assumed to have been minimized by the anonymous and voluntary nature of this study. Moreover, responses from residents in different dental specialty programs limit the equal distribution of subjects across the specialty type category. This study is also limited by the concurrent political circumstances of the program countries and Saudi Arabia. It’s also important to note that generalizability or external validity is limited to the characteristics of the participants. Furthermore, some dental specialties were not included in this study due to the nature of these programs being only indirectly interactive with patients, e.g., oral histology and oral pathology.\n\nReliability testing of the MBI scales revealed sufficient internal consistency for EE and PA but not for DEP. This can be related to the number of items in the scale. DEP has five items only while EE and PA have nine and eight items respectively. This limitation has likely affected the multiple regression results pertaining to DEP where none of the individual predictors was statistically significant. This could also be explained by another limitation this study faced where the number of complete responses were insufficient to detect subtle effects. Increasing the incentive promised to participants or contacting residency program directors requesting recruitment of their residents in a formal way where they set aside time for residents to complete the survey during working hours could have increased the response rate. However, due to time and financial constraints and the researcher’s limited social network in dental schools in the US and the UK, these methods were not feasible. There was a difficulty in reaching out to all residents due to variation in physical location between different countries, schools and specialties. This results in limited statistical power to the analysis and poses a threat to statistical conclusion validity.\n\nMore investigation is needed to evaluate the differences in reported burnout in the excluded specialties and across various program types, e.g., fellowship and PhD programs, to broaden our understanding of this phenomenon and inform future residents who are opting to pursue postgraduate studies. Although this is a comparative study, it is imperative to adopt a longitudinal study design to allow for causal inferences in understanding how burnout progresses over time in health care professionals and the effect it could have on patient care and medical errors. Cultural and social norms affecting female professionals should be explored to ensure better awareness in this critically affected subgroup, in particular. Moreover, qualitative study designs utilizing open ended questions could be used to elicit, for example, participants’ experience as a resident, including their feelings related to burnout and the expectations they perceive their sponsors to have for them during their programs.\n\n\nConclusion\n\nBurnout is a serious problem facing healthcare professionals. International students are at an even higher risk potentially due to change in social and professional environment, cultural differences and financial limitations. The following presents some suggestions for problems facing healthcare professionals.\n\nFor dental residents, it is recommended to find ways to reduce stress and sequentially burnout by time management measures, relaxation and leisure activities. Residents need to be aware of the symptoms of burnout and educate themselves about the signs and how to combat them as early as possible. They should not be afraid to seek help or guidance from their supervisors or program directors.\n\nResidency programs can improve residents’ experiences by providing seminars to educate residents about burnout and plan regular leisurely activities with possible credits towards their degrees to entice residents into participation. Female residents were found to experience higher burnout in this study sample. This was supported by results of another study as well.24 Therefore, females should be considered a critical group to be further encouraged to de-stress and express their perception of personal achievements with faculty or counselors as a part of their official programs. A required psychology course can be offered as a part of the dental residency program to allow dental residents to explore a variety of psychological issues that could affect their careers, their patients and patient care. Another recommendation for dental programs would be to provide online counseling for health care specialties students. This option provides convenience for these students who often have rotations in multiple locations (e.g. clinics, hospitals and campuses) so that they can access psychological care online anywhere.\n\nThe Saudi Arabian sponsors investment in the medical and dental health care professionals can benefit from providing these individuals with a good experience during their studies abroad. Alleviating burnout in residents can be achieved by simplifying the necessary procedures and paperwork required to maintain sponsorship. Saudi Arabian academic advisors can play an integral role in providing mental health support to those in need of it. These measures should enhance their academic experience and subsequently their professional performance once they return to practice in Saudi Arabia. It can also help in retaining health care professionals and their relationships with co-workers and staff to enhance the health care services they provide to the Saudi Arabian patient population.\n\nBurnout is a multifactorial issue facing healthcare specialty students. It can be reduced through the efforts of all the stakeholders involved in the students’ education process. It is imperative to further explore this phenomenon and employ a multitude of ways to overcome this issue to aim for better mental health care and psychological stability for health care professionals leading to elevated performance and optimum experiences for patients seeking their services and expertise.\n\n\nData availability\n\nHarvard Dataverse: Asiri, Amal, 2022, “Saudi Arabian Students in Postgraduate Dental Programs: Investigating Factors Associated with Burnout”, https://doi.org/10.7910/DVN/NTBYPX.20\n\nThis project contains the following underlying data:\n\n• Excel Data File with Legend. (Anonymized survey responses for demographic and MBI sections)\n\n• SPSS Data File. (survey responses tabulations)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nHarvard Dataverse: Asiri, Amal, 2022, “Saudi Arabian Students in Postgraduate Dental Programs: Investigating Factors Associated with Burnout”, https://doi.org/10.7910/DVN/NTBYPX.20\n\nThis project contains the following extended data:\n\n• Demographic part of the survey (blank English copy of the demographic section of the survey).\n\n• Participants Recruitment Flyer.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe author would like to thank Dr. Shatha Zahran and Dr. Abrar Demyati for help with distributing the survey.\n\n\nReferences\n\nAhmad FA, Karimi AA, Alboloushi NA, et al.: Stress level of dental and medical students: comparison of effects of a subject-based curriculum versus a case-based integrated curriculum. J. Dent. Educ. 2017 May; 81(5): 534–544. PubMed Abstract | Publisher Full Text\n\nAndre A, Pierre GC, McAndrew M: Quality of life among dental students: a survey study. J. Dent. Educ. 2017 Oct; 81(10): 1164–1170. Publisher Full Text\n\nElani HW, Allison PJ, Kumar RA, et al.: A systematic review of stress in dental students. J. Dent. Educ. 2014 Feb; 78(2): 226–242. PubMed Abstract | Publisher Full Text\n\nDivaris K, Lai CS, Polychronopoulou A, et al.: Stress and burnout among Swiss dental residents. Schweiz. Monatsschr. Zahnmed. 2012; 122(7-8): 610–615. PubMed Abstract\n\nMurphy RJ, Gray SA, Sterling G, et al.: A comparative study of professional student stress. J. Dent. Educ. 2009 Mar; 73(3): 328–337. Publisher Full Text\n\nAssael L: Current status of postdoctoral and graduate programs in dentistry. J. Dent. Educ. 2017 Aug; 81(8): eS41–eS49. PubMed Abstract | Publisher Full Text\n\nYusoff Y: INTERNATIONAL STUDENTS’ ADJUSTMENT IN HIGHER EDUCATION: RELATION BETWEEN SOCIAL SUPPORT, SELF - EFFICACY, AND SOCIO - CULTURAL ADJUSTMENT. Aust. J. Bus. Manag. Res. 2011; 01(01): 01–15. Publisher Full Text\n\nMaslach C, Leiter MP: Understanding the burnout experience: recent research and its implications for psychiatry. World Psychiatry. 2016 Jun; 15(2): 103–111. PubMed Abstract | Publisher Full Text\n\nVinson LA, Nies JQ, Jones JE, et al.: Stress and the pediatric dental resident: Contributing factors and coping mechanisms. J. Educ. Ethics Dent. 2016 Jul 1; 6(2): 61. Publisher Full Text\n\nHarrison PL, Shaddox LM, Garvan CW, et al.: Wellness among dental students: an institutional study. J. Dent. Educ. 2016 Sep; 80(9): 1119–1125. Publisher Full Text\n\nDivaris K, Polychronopoulou A, Taoufik K, et al.: Stress and burnout in postgraduate dental education. Eur. J. Dent. Educ. 2012 Feb; 16(1): 35–42. PubMed Abstract | Publisher Full Text\n\nMandava P, SankarSingaraju G, Ganugapanta VR, et al.: Comparison of stress, burnout and its association among postgraduate orthodontic and undergraduate students in India. Indian J. Dent. Sci. 2018 Apr 1; 10(2): 66. Publisher Full Text\n\nAl-Sowygh ZH: Academic distress, perceived stress and coping strategies among dental students in Saudi Arabia. Saudi Dent. J. 2013 Jul 1; 25(3): 97–105. PubMed Abstract | Publisher Full Text\n\nAl-Shayea EI: PERCEIVED DEPRESSION, ANXIETY AND STRESS AMONG SAUDI POSTGRADUATE ORTHODONTIC STUDENTS: A MULTI-INSTITUTIONAL SURVEY. Pak. Oral Dent. J. 2014 Jun 1; 34(2).\n\nMaslach C, Jackson S: The Maslach Burnout Inventory–Human Services Survey for Medical Personnel (MBI-HSS (MP).2018.Reference Source\n\nADEA: Policy. American Dental Education Association;2018.\n\nHow to join the Register: General Dental Council.[cited 2022Apr14].Reference Source\n\nBaum A: Stress, intrusive imagery, and chronic distress. Health Psychol. 1990; 9(6): 653–675. PubMed Abstract | Publisher Full Text\n\nMaslach C, Jackson SE, Leiter MP, et al.: Maslach burnout inventory manual. Menlo Park. CA:Mind Garden Inc;2016.\n\nAsiri A: Saudi Arabian Students in Postgraduate Dental Programs: Investigating Factors Associated with Burnout.2022. Harvard Dataverse, V3, UNF:6:ts4d/9djA9J7WTYjscdS1g== [fileUNF]. Publisher Full Text\n\nMaslach C, Jackson S, Leiter MP: Maslach Burnout Inventory. third edition. Palo Alto.\n\nSoler JK, Yaman H, Esteva M, et al.: Burnout in European family doctors: the EGPRN study. Fam. Pract. 2008 Aug 1; 25(4): 245–265. PubMed Abstract | Publisher Full Text\n\nPiko BF: Burnout, role conflict, job satisfaction and psychosocial health among Hungarian health care staff: A questionnaire survey. Int. J. Nurs. Stud. 2006 Mar 1; 43(3): 311–318. PubMed Abstract | Publisher Full Text\n\nMinamizono S, Nomura K, Inoue Y, et al.: Gender division of labor, burnout, and intention to leave work among young female nurses in Japan: a cross-sectional study. Int. J. Environ. Res. Public Health. 2019 Jan; 16(12): 2201. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "153979",
"date": "02 Nov 2022",
"name": "S Kimberly Haslam",
"expertise": [
"Reviewer Expertise Burnout in dental hygiene professionals and oral health students (dental hygiene and dentistry)"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nUsually depersonalization is abbreviated DP not DEP.\nIntroduction: Remove memorization to understanding or another verb. I hope dental students do not just memorize the material.\nPersistent exposure to stress can lead to burnout, which involves work or school-related exhaustion and disengagement.4- should include reduced personal accomplishment. A better reference would be one of the Maslach articles.\n\nUnless it is necessary, the information from other studies is a bit long. Do not have to state response rate, how many people were enrolled in the study etc. Instead just the main findings.\n\nDefinition of Terms Should use the definition for the MBI-HSS MP (which included medical personal). Also include definitions for EE, DP and PP - If possible I would suggest a glossary at the end of the paper with definitions. Defining Burnout, EE, DP and PA in the introduction would be preferable.\n\nPost-graduate students should have the disciplines listed so it does not need to be repeated in the methods\n\nMethods:\nDid not state the methodology used: Cross sectional study perhaps?\nInstrumentation\nMultiple studies were cited in which test-retest coefficients for the three scale scores - this was not cited?\nProcedure\n\nWhat happened to the list of emails after they were uploaded on Survey Monkey? Drawing the emails from a hat, does that break confidentiality?\nData Analysis\nThe Table should be in the results - not 100% sure why you did a zero order correlation on this section as it is just demographics.\nResults:\nI thought your participants were dental residents, you include medical professional population. Where did you get these results from? If you did not survey the medical population then this section should be in the discussion.\n\nI looked but could not find a description for Block 1 & Block 2\nDiscussion:\nMaslach studies the 3 domains of burnout, in their research they do not give a total burnout score. Please be aware the EE is not burnout - it is one of the domains of burnout. Some researchers do calculate a burnout score \"An alternative approach considers individuals to have burnout if they have a high EE score plus either a high DP score or a low PA score (PA score less than 33)\"\n\nTherefore, I would make it clear in this sentence that you are talking about EE: \"dental residents experience high burnout due to emotional exhaustion when compared to other medical professionals.\" Should read High levels of EE (not burnout) when compared...\nThis is throughout the discussion, please be specific to the domains.\n\nLimitations\n\nI have always been taught not to use contractions in professional papers 'It's\"\nThere are limitations to survey based research - such as recall bias.\n\nConclusion\n\nThe first paragraph is not a conclusion from your study. Could state something about the prevalence of burnout in the dental residents instead. A conclusion should not contain new information. It is a recap of the main points. The conclusion in the abstract is more applicable to the topic. Here you are introducing ways to reduce stress, which is great, but it should be in the discussion not the conclusion.\nAlso there was not a research question on this topic. All this is based on previous research, yet there is limited citations. I would suggest rewriting the conclusion.\n\nCitations # 15 this is a link to an individual report on the Maslach survey. .\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": []
}
] | 1
|
https://f1000research.com/articles/11-705
|
https://f1000research.com/articles/11-1333/v1
|
16 Nov 22
|
{
"type": "Research Article",
"title": "A Robust image watermarking for copyright protection using Multiresolution Walsh-Hadamard transform and Schur using Differential evolution",
"authors": [
"Swaraja K",
"Meenakshi K",
"Ushakumari Ch",
"Kishore D",
"Swaraja K",
"Ushakumari Ch",
"Kishore D"
],
"abstract": "\\textit{Background} The proposed watermarking framework is based on the multi-resolution Walsh-Hadamard Transform (MR-WHT) along with Schur factorization. For embedding, the cover image is converted into a frequency domain using MR-WHT before Schur factorization is applied. \\textit{Methods} The upper triangle's highest stable eigenvalues in the Schur factorization are employed as reliable embedding locations for the watermark. The singular values of these coefficients are updated with the singular values of the watermark, and the matrix array generated by the biggest eigenvalues is further factorised by singular value decomposition using multiple scaling factors and Differential evolution (DE). Later, an inverse SVD, inverse Schur, and inverse multiresolution Walsh-Hadamard transform is executed to obtain a watermarked image. \\textit{Results} The simulation results show that the proposed method is imperceptible and robust against existing watermarking algorithms used in the literature.",
"keywords": [
"MR-WHT",
"Singular Value Decomposition",
"Schur factorization",
"PSNR",
"SSIM",
"NCC",
"Transparancy",
"Robustness"
],
"content": "Introduction\n\nThe enormous progress in digital technology and the advancement in processor speed, combined with internet access, augmented the ease with which multimedia content including audio, images, and videos were reproduced and duplicated. As a result, owners of associated metadata must contend with the challenge of safeguarding their digital property against copyright violations and other forms of exploitation. As a result, owners of multimedia content must overcome the challenge of preventing copyright infringement and other types of exploitation of their digital content. Digital watermarking provided an effective method of preventing fraudulent and illegal replication of digital media. However, better and more advanced watermarking techniques are required as the use of multimedia documents grows at an exponential rate. Thus, digital watermarking has evolved into a multidisciplinary research field involving communications theory, signal processing, and multimedia coding.\n\nDigital watermarking1 is a technique for concealing information that is embedded in a multimedia object. The object could be any type of multimedia, such as an invisible signal embedded directly in digital media. Spatial and spectral domain methods are the two most commonly used methods for digital watermarking. The first type of algorithm embeds a watermark by modifying image pixels. The second category, for example the Discrete Cosine Transform, embed watermarks in spectrum coefficients (DCT)2–5 and other different transforms.6–18 Techniques in the spectrum domain are considered to be superior compared with those of the spatial domain. In the least perpetually significant coefficients of a transform of an image in the spectral domain, one can insert a watermark. The watermark can be spread across various transform coefficient bands. This will increase the watermarks’ transparency and prevent watermarked image visual degradation. Additionally, the watermark is distributed unevenly, making it extremely challenging for the hacker to remove it.\n\nOne issue with current watermarking techniques is that they struggle with the optimization of imperceptibility and robustness because it has been discovered that these two parameters are incompatible. As a result, many techniques to optimize transparency and robustness19–22 are used in the literature. Genetic-algorithms (GA),23–27 Differential-evolution,28–30 Particle-swarm optimization (PSO),31–34 and fuzzy-logic35,36 are currently used in literature for optimizing the transparency and robustness. A GA was used to find optimum thresholds for quantizing wavelet coefficients.32 Oguz FindiK et al.33 used PSO for watermarking color images. Shieh et al.37 identified a fitness function depending on factors related to robustness and imperceptibility. After DCT transformation, the transformed image is segmented into 8 × 8 and four bands are randomly selected for watermark embedding and given to a fitness function. Following GA, the four robust bands with the highest fitness are used for embedding the watermark. Their performance metrics are found to be improved. Another use of GA is demonstrated by aslantas et al.,9 who used GA to investigate the best watermarking strategy based on SVD. To embed the watermark, multiple scaling factors were applied to the singular values of the original image. Additionally, a GA was used in an embedded method based on the quantization index modulation (QIM) technique.38\n\nMuch research has been focused on achieving HVS image characteristics and it has been demonstrated that the DHT has a poor threshold difference for noise processing at low compression quality.39 These facts may aid DHT-based schemes in achieving simultaneous optimum performance, as well as achieving optimal robustness against low quality compression while also having a higher embedding capacity, resulting in better performance than DCT or wavelet-based schemes. As a result, we believe that using Walsh-Hadamard characteristics to design optimal data hiding schemes with a high degree of robustness and imperceptibility is a worthwhile endeavor.\n\n\nPreliminaries\n\nUsing a hybridized multiresolution fast Walsh-Hadamard transform and Schur transform with differential evolution, a reliable hybrid watermarking is developed in this paper.\n\nOf all the orthogonal transforms that are currently in use, it has the lowest computational complexity. Functionally identical kernels serve as the foundation for the Walsh-Hadamard transform. The kernel of forward Walsh-Hadamard transform is found by:\n\nThe inverse kernel of WHT is given by:\n\nThe Walsh-Hadamard transform40 is a square array with orthogonal rows and columns of ones with plus and minus signs. The transform is computed quickly using the successive doubling method and has the advantage of having almost identical forward and inverse kernels and less computational complexity. The algorithm exhibits resilience to compression at low quality levels. Compared to other popular transforms, Walsh-Hadamard is more resilient to image manipulation because the multivalued kernels make it such that the values of the pixels in the block alter by various amounts.41 Therefore, real-time hardware implementation is better suited for it.\n\nIf a square matrix A has all linearly independent eigenvectors, then an invertible matrix P exists with the property that P−1AP = Λ, where Λ is a diagonal matrix. However, not all square matrices can be diagonalized. QR factorization or Schur factorization can help to address this weakness. Schur asserts that any invertible matrix can be expressed as the multiplication of the upper triangle matrix (T) with the unitary matrix (U).\n\nFor some unitary matrix U and upper triangular matrix T. In matrix T, the diagonal entries of T are the eigenvalues of A.\n\nSVD is a mathematical tool that is frequently used in image watermarking, compression, and retrieval. Every real matrix A, according to this theory, can be broken down into a multiplication of 3 matrices, W, D, F where WWT = I, FFT = I and the largest singular values are contained in the diagonal matrix, S. Zero is the singular value of the matrix above rank r.\n\nIn SVD, singular values stand in for the layer’s luminance and singular vectors for the image’s geometry. The largest singular values of the SVD have the greatest energy preservation and resistance to small perturbations, making them immune to the majority of signal processing as well as image compression operations.42\n\nA generation is the term used to describe the population in each iteration of the evolution, which typically begins with a population of randomly chosen individuals. Every member of the population has their fitness assessed once every generation; in most optimization algorithms, the fitness is the value of the objective function. The current population is stochastically selected for the fittest individuals, and each individual’s genome is altered (through crossover and possibly through random mutation) to create a new generation. The following algorithm iteration uses the new generation of candidate solutions. The central concept of DE is a method for generating trial parameter vectors. A vector with weighted difference within two members of the population is accumulated to a third member by DE to create new parameter vectors. If the newly produced vector has a relatively low objective function when compared to the population of predefined member, it will be replaced in the next generation by the vector to which it was compared. The aforementioned generation process can, but does not have to, include the comparison vector. Furthermore, to maintain the record of the growth made during the minimization procedure, the parameter vector xbest, G, which is best is calculated for each generation G, is measured. Consider the watermarking system with real valued properties\n\nThe watermarking system has constraints in the form of:\n\nSystem optimization implies varying the D-dimensional parameter vector.\n\nAccording to scheme DE1 of Ref. 43 for all vectors Xi, G for j = 0,1,2, …, N − 1, a trial vector (v) is produced in accordance to:\n\n\nProposed watermarking algorithm\n\nMost emerging watermarking methods employ a single transformation function that must be fine-tuned. Moreover, multiple scaling components are recommended in the literature for fine adjusting because singular values reveal different tolerances to different scaling factors. So multiple scaling factors are proposed in the literature.9 The proposed algorithm contains three steps: a watermark concealing algorithm, a watermark extraction algorithm, and a computation of multiple scaling factor.\n\nThis subsection describes the proposed watermarking algorithm based on the hybridized multiresolution fast Walsh-Hadamard transform and Schur transform using DE as shown in Figure 1.\n\n\n\n1. The cover image A is subjected to a FWHT2 transform.\n\nThe significant coefficients of WHT2 lie in the mid and upper bands of frequency of the translated image. Therefore, the watermark is implanted in the mid and high frequency zones of the image.\n\n2. Apply MR-WHT2 to B, given in Equations 10–13. Multiresolution is applied by row followed by column modification. Row-wise modification results from Equations 10–13:\n\nColumn-wise modification results:\n\n3. The multiresolution Walsh-Hadamard transform decomposes image into LL, LH, HL and HH bands.\n\n4. Extract the HH band for watermark embedding.\n\n5. Suppose that the cover image size is R × S. The size of HH band after the MR-WHT2 transform is R × S, where P and Q are M2 and N2. The HH band is segmented into 8 × 8 blocks and the number of R × S is 0 to m-1 and 0 to n-1, where m and n are R8 and S8.\n\n6. Apply Schur factorization to each 8 × 8 block of HH band. Schur factorization decomposes images into unitary matrix (U) and upper traingular matrix (T).\n\n7. Employ HEBS (high eigenvalue block selection) to obtain the largest eigenvalue of each each 8 × 8 block and its size is the same as the watermark and denotes it array (C). Apply SVD to array B and w, as given in Equation 14.\n\n8. Amended singular values are obtained from wc and ww given in the equation below:\n\n9. Apply the inverse SVD.\n\n10. Replace the coefficients in Bnew with high eigenvalue blocks in the T matrix of Schur factorization. The modified upper traingular matrix is denoted by Tnew.\n\n11. Apply the inverse Schur transform.\n\n12. Merge all 8 × 8 blocks to form Hnew.\n\n13. Remap all bands LL,LH, HL and HHnew to form Q.\n\n14. Apply the inverse multiresolution to the Q obtained from the column and row transformation. Undo column-wise modification results.\n\n15. Undo row-wise modification.\n\n16. Perform inverse FWHT2D to obtain the watermarked image D.\n\nThe proposed watermarking framework is based on non-blind watermarking, which requires an original image for extraction. The host and the watermarked image are subjected to FWHT2D followed by forward multiresolution to obtain LL, LH, HL, and HH bands, as well as LLW, LHW, HLW, and HHW bands, respectively.\n\n1. Apply Schur factorization to HH and HHW bands.\n\n2. Compute the HEBS in upper triangular matrix of Schur factorization to form a matrix array of M and MW, respectively.\n\n3. Apply forward SVD to M and MW to obtain singular values.\n\n4. Obtain singular values of the watermark from wwa and wc by using Equation 22.\n\n5. Obtain the inverse SVD to extract the watermark.\n\nThe proposed work utilizes the DE to search for multiple scaling factors (msfs) in order to strengthen the robustness of the proposed scheme. The logo embedded size is 32 × 32. Therefore, the size of msf’s is 32. If the input population size is 100, then 100 strings of 32 variables is stochastically generated, out of which each 32 string represents a possible solution. The fitness function is computed with the structural similarity (S.S.I.M) among A and D and cross correlation is computed between the original and the extracted watermark.\n\nThe strings that provided the higher fitness values after all strings in a generation have been examined are chosen for the upcoming generation. Then, using genetic operators crossover and mutation operators from these strings, the population of the upcoming generation is produced. The aforementioned procedures are repeated until a predetermined stopping criterion, such as the maximum generation number, is met.\n\n\nSimulation results and discussion\n\nThe proposed algorithm implements on benchmark images airplane, Zelda, Lena, and Baboon, each 512 × 512 in size. The watermark used is a java cup. The algorithm is implemented on Matlab-2013 (RRID:SCR 001622), 4GB RAM, duo core processor. The transparency of the image which is watermarked is judged by peak signal to noise ratio and is given by:\n\nHere, MSE is the mean square within the original and reconstructed image given in Equation 27.\n\nwhere, X and Y stand for the gray values of the host and watermarked image; Imax is the maximum intensity of the 8 bit image i.e. 255, and M and N are the height and width of the image. The PSNR values of the watermarked image is compared to algorithms developed by Refs. 44–46, with the proposed algorithm as shown in Figure 3. The high PSNR of the proposed algorithm reveals that the proposed watermarking scheme offers high imperceptibility. As shown in Figure 2, the distortion introduced by watermark is negligible and there is no distinction seen between the host and watermarked images of Zelda, Lena and Baboon.\n\nThe high peak signal to noise ratio and N.C.C close to 1 signifies that the proposed method is highly imperceptible, as well as robust to attacks.\n\nThe settings of the parameter of DE are, F = 0.5, Cr = 0.5, NP = 32, population = 10, maximum number of generations = 200. This section describes the performance of the projected watermarking framework for the various experiments. The Watermarked image is altered when various attacks are considered.\n\nThe robustness of proposed framework is contrasted with other methods based on normalized cross correlation. The normalized cross correlation (N.C.C) lies between 0 to 1. If the N.C.C is nearer to 1, the more similar the extorted watermark will be to the embedded one. The proposed algorithm is compared with a pure SVD, simple genetic algorithm, SVD based on a micro genetic algorithm, multiresolution Walsh-Hadamard tranform, and proposed algorithm multiresolution Walsh-Hadamard transform and Schur transform with DE.\n\nThe different attacks utilized in the framework of watermarking are:\n\n1. Average filtering: The image which is watermarked is subjected to a low pass mask of 3 × 3 neighborhood. Averaging removes sharp variations in the image such as edges and noise. The extorted watermark is 100% identical to the inserted watermark.\n\n2. Rotation is the important attack during image watermarking. The size of the image typically increases when it is rotated. Therefore, some of the useful information is lost in order to return to its original form. The extracted watermark is 94.48% identical to the inserted watermark.\n\n3. Symmetric cropping: the watermarked image is cropped on both sides. The extracted watermark is 95.55% identical to the original watermark.\n\n4. Histogram equalization: histogram equalization is used to adjust the contrast of the image. The extracted watermark is 99.99% identical to the inserted watermark.\n\n5. Gaussian noise: the marked image is subjected to Gaussian noise, having a zero mean with a normalized variance of 0.01. The extracted watermark is 99.50% identical to the original watermark.\n\n6. JPEG compression: the watermarked image is compressed to a specified ratio of compression of 60%. The extracted watermark is 99.65% identical to the original watermark.\n\n7. A significant attack on image watermarking is scaling. High frequency components are eliminated. Thus, important information could be lost. The image is reduced in size to one-fourth of its original size and placed back in its original location before the extraction process in the proposed watermarking. The proposed watermarking is 99.99% identical to the original watermark. The original watermark and the extracted watermark from the above attacks is shown in Figure 4.\n\nThe proposed algorithm is compared with existing optimization algorithms like pure SVD, SVD+GA, SVD+SGA, SVD+μ GA, DCT+DE. The N.C.C values are compared in Table 1.\n\n\nAuthor contributions\n\nK. Meenakshi, K. Swaraja: Conception and design of study. Ch. Ushakumari, K. Swaraja: Acquisition, analysis and/or interpretation of data. D. Kishore, K. Meenakshi: Drafting the manuscript and revising.\n\n\nData availability\n\nFigshare:[copyright protection using Multiresolution Walsh Hadamard transform] DOI: 10.6084/m9.figshare.20408937\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nMaity SP, Delpha C: Optimization in digital watermarking techniques. Advanced Techniques in Multimedia Watermarking: Image, Video and Audio Application. USA:IGI Global Pub.;2010; 369–406.\n\nLiu J-C, Chen S-Y: Fast two-layer image watermarking without referring to the original image and watermark. Image Vis. Comput. 2001; 19(14): 1083–1097. Publisher Full Text\n\nBriassouli A, Strintzis MG: Locally optimum nonlinearities for dct watermark detection. Image Processing, IEEE Transactions on. 2004; 13(12): 1604–1617. PubMed Abstract | Publisher Full Text\n\nLin SD, Shie S-C, Guo JY: Improving the robustness of dct-based image watermarking against jpeg compression. Comput. Stand. Interfaces. 2010; 32(1): 54–60. Publisher Full Text\n\nPatra JC, Phua JE, Bornand C: A novel dct domain crt-based watermarking scheme for image authentication surviving jpeg compression. Digit. Signal Process. 2010; 20(6): 1597–1611. Publisher Full Text\n\nLiu R, Tan T: An svd-based watermarking scheme for protecting rightful ownership. Multimedia, IEEE Transactions on. 2002; 4(1): 121–128. Publisher Full Text\n\nShieh J-M, Lou D-C, Chang M-C: A semi-blind digital watermarking scheme based on singular value decomposition. Comput. Stand. Interfaces. 2006; 28(4): 428–440. Publisher Full Text\n\nAslantas V: A singular-value decomposition-based image watermarking using genetic algorithm. AEU - Int. J. Electron. Commun. 2008; 62(5): 386–394. Publisher Full Text\n\nAslantas V: An optimal robust digital image watermarking based on svd using differential evolution algorithm. Opt. Commun. 2009; 282(5): 769–777. Publisher Full Text\n\nRuanaidh JJKÓ, Dowling WJ, Boland FM: Watermarking digital images for copyright protection. IEE Proceedings-Vision, Image and Signal Processing. 1996; 143(4): 250–256. Publisher Full Text\n\nZheng D, Zhao J, El Saddik A: Rst-invariant digital image watermarking based on log-polar mapping and phase correlation. Circuits and Systems for Video Technology, IEEE Transactions on. 2003; 13(8): 753–765. Publisher Full Text\n\nLiu Y, Zhao J: A new video watermarking algorithm based on 1d dft and radon transform. Signal Process. 2010; 90(2): 626–639. Publisher Full Text\n\nChen W-Y, Chen C-H: A robust watermarking scheme using phase shift keying with the combination of amplitude boost and low amplitude block selection. Pattern Recogn. 2005; 38(4): 587–598. Publisher Full Text\n\nGanic E, Eskicioglu AM: Robust embedding of visual watermarks using discrete wavelet transform and singular value decomposition. J. Electron. Imaging. 2005; 14(4): 043004–043004. Publisher Full Text\n\nFalkowski BJ, Lim L-S: Image watermarking using hadamard transforms. Electron. Lett. 2000; 36(3): 211–213. Publisher Full Text\n\nFalkowski BJ, Rahardja S:Walsh-like functions and their relations. Vision, Image and Signal Processing, IEE Proceedings. IET;1996; 143. : 279–284.\n\nFalkowski BJ: Properties and ways of calculation of multi-polarity generalized walsh transforms. Circuits and Systems II: Analog and Digital Signal Processing. IEEE Transactions on. 1994; 41(6): 380–391. Publisher Full Text\n\nKutter M, Voloshynovskiy SV, Herrigel A:Watermark copy attack. Electronic Imaging. International Society for Optics and Photonics;2000; pp. 371–380.\n\nShen H, Zhu Y, Zhou X, et al.:Bacterial foraging optimization algorithm with particle swarm optimization strategy for global numerical optimization. Proceedings of the first ACM/SIGEVO Summit on Genetic and Evolutionary Computation. ACM;2009; pp. 497–504.\n\nHanmandlu M, Verma OP, Kumar NK, et al.: A novel optimal fuzzy system for color image enhancement using bacterial foraging. Instrumentation and Measurement, IEEE Transactions on. 2009; 58(8): 2867–2879. Publisher Full Text\n\nBakwad KM, Pattnaik SS, Sohi BS, et al.: Multimodal function optimization using synchronous bacterial foraging optimization technique. IETE J. Res. (Medknow Publications & Media Pvt. Ltd.). 2010; 56(2): 80. Publisher Full Text\n\nAgarwal C, Mishra A, Sharma A: Gray-scale image watermarking using ga-bpn hybrid network. J. Vis. Commun. Image Represent. 2013; 24(7): 1135–1146. Publisher Full Text\n\nWang C, Ni J, Huang J: An informed watermarking scheme using hidden markov model in the wavelet domain. Information Forensics and Security, IEEE Transactions on. 2012; 7(3): 853–867. Publisher Full Text\n\nShih FY, Yi-Ta W: Enhancement of image watermark retrieval based on genetic algorithms. J. Vis. Commun. Image Represent. 2005; 16(2): 115–133. Publisher Full Text\n\nShih FY, Yi-Ta W: Robust watermarking and compression for medical images based on genetic algorithms. Inf. Sci. 2005; 175(3): 200–216. Publisher Full Text\n\nYazd I: Digital image watermarking based on parameters amelioration of parametric slant-hadamard transform using genetic algorithm.2012.\n\nVahedi E, Zoroofi RA, Shiva M: Toward a new wavelet-based watermarking approach for color images using bio-inspired optimization principles. Digit. Signal Process. 2012; 22(1): 153–162. Publisher Full Text\n\nAli M, Ahn CW, Siarry P: Differential evolution algorithm for the selection of optimal scaling factors in image watermarking. Eng. Appl. Artif. Intell. 2014; 31: 15–26. Publisher Full Text\n\nAslantas V, Kurban R: Fusion of multi-focus images using differential evolution algorithm. Expert Syst. Appl. 2010; 37(12): 8861–8870. Publisher Full Text\n\nLei B, Tan E-L, Chen S, et al.: Reversible watermarking scheme for medical image based on differential evolution. Expert Syst. Appl. 2014; 41(7): 3178–3188. Publisher Full Text\n\nTao H, Zain JM, Ahmed MM, et al.: A wavelet-based particle swarm optimization algorithm for digital image watermarking. Integr. Comput. Aided Eng. 2012; 19(1): 81–91. Publisher Full Text\n\nWang Y-R, Lin W-H, Yang L: An intelligent watermarking method based on particle swarm optimization. Expert Syst. Appl. 2011; 38(7): 8024–8029. Publisher Full Text\n\nFındık O, Babaoğlu İ, Ülker E: A color image watermarking scheme based on hybrid classification method: Particle swarm optimization and k-nearest neighbor algorithm. Opt. Commun. 2010; 283(24): 4916–4922. Publisher Full Text\n\nNaheed T, Usman I, Khan TM, et al.: Intelligent reversible watermarking technique in medical images using ga and pso. Optik-International Journal for Light and Electron Optics. 2014; 125(11): 2515–2525. Publisher Full Text\n\nSanti P: Maity and Seba Maity. Multistage spread spectrum watermark detection technique using fuzzy logic. Signal Processing Letters, IEEE. 2009; 16(4): 245–248. Publisher Full Text\n\nHsieh M-S: Perceptual copyright protection using multiresolution wavelet-based watermarking and fuzzy logic. arXiv preprint arXiv:1007.5136. 2010.\n\nShieh C-S, Huang H-C, Wang F-H, et al.: Genetic watermarking based on transform-domain techniques. Pattern Recogn. 2004; 37(3): 555–565. Publisher Full Text\n\nKumsawat P, Attakitmongcol K, Srikaew A: A new approach for optimization in image watermarking by using genetic algorithms. Signal Processing, IEEE Transactions on. 2005; 53(12): 4707–4719. Publisher Full Text\n\nRamkumar M, Akansu AN: Capacity estimates for data hiding in compressed images. Image Processing, IEEE Transactions on. 2001; 10(8): 1252–1263. PubMed Abstract | Publisher Full Text\n\nPratt W, Kane J, Andrews HC: Hadamard transform image coding. Proc. IEEE. 1969; 57(1): 58–68. Publisher Full Text\n\nGonzalez RC, Richard E: Woods, digital image processing. Prentice Hall Press;2002.0-201-18075-8.\n\nRun R-S, Horng S-J, Lai J-L, et al.: An improved svd-based watermarking technique for copyright protection. Expert Syst. Appl. 2012; 39(1): 673–689. Publisher Full Text\n\nStorn R, Price K: Differential evolution–a simple and efficient heuristic for global optimization over continuous spaces. J. Glob. Optim. 1997; 11(4): 341–359. Publisher Full Text\n\nVeeraswamy K, Srinivaskumar S, Chatterji BN: Designing quantization table for hadamard transform based on human visual system for image compression. ICGST-GVIP Journal. 2007; 7(3): 31–38.\n\nBhatnagar G, Raman B: Robust watermarking in multiresolution walsh-hadamard transform. Advance Computing Conference, 2009. IACC 2009. IEEE International. IEEE;2009; pp. 894–899.\n\nSanthi V, Arulmozhivarman P: Hadamard transform based adaptive visible/invisible watermarking scheme for digital images. Inf. Secur. Tech. Rep. 2013; 5: 202. Publisher Full Text"
}
|
[
{
"id": "202814",
"date": "17 Oct 2023",
"name": "Ledya Novamizanti",
"expertise": [
"Reviewer Expertise Image Processing",
"watermarking"
],
"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 work presents a robust image watermarking for copyright protection using Multiresolution Walsh-Hadamard transform and Schur transform using differential evolution. The paper is not clear, not innovative enough and insufficient experiments. Besides, some problems are listed as follows:\nThe problem definition of this work is not clear. In introduction or in related work section, the drawbacks of each conventional technique should be described clearly. The authors should emphasize the difference with other methods to clarify the position of this work further.\n\nDon’t use acronym without explanation. e.g. DHT, etc. All acronyms must be defined before use.\n\nThe language needs improvement, and there are confusions in formulae and character descriptions. For instance, on the page 5, it's unclear whether \" FWHT2\", \"WHT2\" and the term \" FWHT2D\" in page 7 refer to the same element. Furthermore, many variable are not specified.\n\nDuplicate formulas in Eq. (1) and (2).\n\nDistinguish mathematical expression from programming code. Don’t use “:” in equations. For instance, see Eq. (10), (11), (12), 13), etc.\n\nComparative literature is too scarce and older.\n\nThe experimental section is not convincing. With only four test images, the sample size is inadequate. Although the paper claims to propose a robust watermarking algorithm, it fails to demonstrate the robustness in the experimental comparison.\n\nThe statement \"it has been demonstrated that the DHT has a poor threshold difference for noise processing at low compression quality\" should be supported by specific references or citations to studies that have demonstrated this. Adding such evidence would enhance the credibility of this claim.\n\nWhile the introduction suggests that using Walsh-Hadamard characteristics is a \"worthwhile endeavor,\" it would be beneficial to explicitly state the research gap or problem the study aims to address. This would provide clarity on the study's objectives and what it seeks to contribute to the existing literature.\n\nIt would be helpful to explicitly state the research hypothesis or objectives in the introduction. This would provide a clear sense of what the study aims to investigate or demonstrate.\n\nThe sentence \"These facts may aid DHT-based schemes in achieving simultaneous optimum performance...\" could be rephrased for greater clarity.\n\nProvide an illustration related to MR-WHT.\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?\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": "214541",
"date": "06 Nov 2023",
"name": "Ankit Rajpal",
"expertise": [
"Reviewer Expertise Image and Video Watermarking",
"Explainable AI",
"and Medical Image 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\nUsing the multi-resolution Walsh-Hadamard transform (MR-WHT) and Schur factorization, the authors came up with a framework for watermarking. The paper has the following shortcomings:\nThe motivation and objective of the proposed work are not clear.\n\nThe related research work is not recent. Moreover, a comparison with state-of-the-art methods is not provided.\n\nThe block diagram and the algorithmic steps for both watermark embedding and extraction lack coherence. For example, there is no mention of differential evolution in the algorithm.\n\nEqs. (1) and (2) have the same RHS.\n\nThe standard images used for the experimentation are limited.\n\nThe discussion section highlighting the strengths and limitations of the proposed work may be included.\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? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "192201",
"date": "06 Nov 2023",
"name": "Amine Khaldi",
"expertise": [
"Reviewer Expertise Watermarking"
],
"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 presentation is not clear. What is the objective of the conducted research? What is the novelty related scientific literature?\n\nIt seems to me that the authors have conducted some experiments on a dataset without really proposing a \"system\"\n\nThe paper is not well organized and lack of numerous descriptions that makes it hard to read and understand. Several key points of the literature, strongly related to this paper has been forgotten.\n\nPlease, clearly explain how your solution advances existing approaches,\n\nRedraw the graphs with high resolution (at least 300 dpi)\n\nThere is a need to strengthen the Abstract. The author should improve the abstract to include the following in its body: a brief background, brief description of methods and results, and finally conclusions.\n\nAdd detailed related work section. Discuss the motivation and limitations of previous works\n\nEvery time a method/formula is used for something, it needs to be justified by either (a) prior work showing the superiority of this method, or (b) by your experiments showing its advantage over prior work methods - comparison is needed, or (c) formal proof of optimality. Please consider more prior works.\n\nThe descriptions given in this proposed scheme are not sufficient that this manuscript only adopted a variety of existing methods to complete the experiment where there are no strong hypothesis and methodical theoretical arguments. Therefore, the reviewer considers that this paper needs more works\n\nMore experiments, especially comparative experiments, should be involved to verify the performances of the proposed algorithm.\n\nThe author should justify and discuss in more details the obtained results\n\nThere was no discussion for the full paper and future works. I suggest the authors expand the discussion of the whole work in the last section, then point out the shortcomings of the work, and finally discuss possible future work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1333
|
https://f1000research.com/articles/10-1165/v1
|
17 Nov 21
|
{
"type": "Research Article",
"title": "Pattern changes of cutaneous dermatoses among Iraqi women preceding and during the COVID-19 pandemic",
"authors": [
"Galawish A. Abdullah"
],
"abstract": "Background: We compared the pattern of cutaneous dermatoses among Iraqi females of all ages between 4 months preceding the coronavirus disease 2019 (COVID-19) pandemic, and the same months 1 year later within the COVID-19 pandemic. Methods: This was a cross-sectional study, that targeted all female patients attending an outpatient clinic for dermatology and venereology in Al-Kindy teaching hospital, Baghdad between October 2019 to the end of January 2020, and the same 4-month duration 1 year later (October 2020 to the end of January 2021) after the COVID-19 peak period had passed and there was no or partial curfew to exclude seasonal impact. Results: A total of 2657 female-patients of all ages were enrolled in this study with 1314 females during the 4 months pre COVID-19, and 1343 females during the pandemic. The mean age of patients presented before the pandemic was 27.2±16.6 years, while the mean age of patients during the pandemic was 28.1±15.6 years with no statistically significant difference in mean ages (P >0.05). Hair loss in general with telogen effluvium specifically increased significantly. Cutaneous contagious viral infections were reduced significantly and specifically of these molluscum contagiosum and condylomata accuminata. Other forms of infections including bacterial and parasitic were also reduced while dermatophytosis was increased but not to a significant level. Acne vulgaris, rosacea, lichen planus, urticaria, pityriasis rosea, seborrheic dermatitis, and vitiligo were increased, but psoriasis, alopecia areata, other types of dermatitis, and melasma were reduced but none to a significant level. Conclusions: The COVID-19 pandemic resulted in changes in the pattern of diseases presented to an out-patient clinic for dermatology and venereology. This could be either related to COVID-19 infection or stress associated with the pandemic, because of curfew, or wearing facemasks which may cause a decrease or increase in certain diseases.",
"keywords": [
"COVID-19",
"cutaneous dermatosis",
"female"
],
"content": "Introduction\n\nThe first reported case of coronavirus disease 2019 (COVID-19) was in Wuhan, China in December 2019 and after that it spread globally.1 Till 16 September 2021 the total confirmed cases all over the world reached 226,236,577 and the total deaths 4,654,548, while in Iraq it reached 1,963,264 and the mortality 21,631 according to the World Health Organization (WHO) reports.2\n\nThe Republic of Iraq officially reported the first confirmed case of COVID-19 on February 24, 2020 in Al-Najaf government and after that it started to increase in all cities of Iraq, and many measurements including total and partial curfew on week-ends had been taken in order to limit spread of infection.3 The pattern of diseases including dermatological diseases started changing during the era of COVID-19 pandemic and a lot had been changed since then.4\n\nThe aim of this study was to investigate the changes in the profile of dermatological diseases among Iraqi females of all ages before and during the COVID-19 pandemic.\n\n\nMethods\n\nThe study was approved by scientific committee (Research Ethics Committee) of Al-Kindy college of medicine, university of Baghdad. All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards (Code: 2019/C081). All patients attending the Al-Kindy teaching hospital in Baghdad are routinely informed that their data could be used for medical research, and their personal information would not be disclosed. In cases below the age of 18 years, the patients care giver would be responsible for giving the approval. If patients do not consent, their data is not shared.\n\nThis study involved a cross-sectional survey carried out in the out-patient clinic for dermatology and venereology in Al-Kindy teaching hospital, Baghdad. The data was collected from the medical records of all enrolled female patients who attended the out-patient clinic for 8 months, 4 of them before the first COVID-19 case was diagnosed in Iraq (from October 2019 to the end of January 2020), and the other four months 1 year later (from October 2020 to the end of January 2021) to exclude seasonal impact.\n\nThe data were collected retrospectively from all female patients attending the dermatology out-patient’s clinic during the study period. Inclusion criteria included female patients of any age who were examined by the same dermatologist and had been given a definitive diagnosis. Exclusion criteria was if a definitive diagnosis had not been recorded.\n\nThe study variables included patients’ age and the definite dermatological diagnosis for each patient.\n\nDiagnosis was made by clinical examination. Some cases required specific investigation in the form of dermoscopic and wood-light examination, scraping test, routine histopathological examination and immunohistochemistry for selected cases to confirm diagnosis.\n\nThis study mainly faced two types of bias: selection bias and information bias. Some degree of selection bias was evident because the cases enrolled were examined by the same dermatologist, which was done to ensure that the steps of examination and diagnosis was offered to all patients had similar quality, the other cause of selection bias that this was a single center study. Information bias was limited because the data entry was double checked and that any case without a clear and definite diagnosis was excluded from the study.\n\nThe collected data were analyzed by Statistical Package for the Social Sciences (SPSS), version 22. The descriptive analysis focused on frequencies, and percentages, and percent change. While the Chi-square (goodness of fit) test was used to find the associations between variables and significance of percent change. A P-value ≤ 0.05 was considered statistically significant.\n\n\nResults\n\nA total of 2657 female patients were enrolled in this study with 1314 before the COVID-19 pandemic, and 1343 1-year into the pandemic.13 The mean age of patients during the period before COVID-19 was 27.2 ± 16.6 years, while the mean age of patients during the pandemic was 28.1 ± 15.6 years. There was no significant difference between the mean age of the patients before and during the COVID-19 pandemic (P-value > 0.05).\n\nTable 1 shows that hair loss in general was significantly increased during COVID-19 pandemic. Viral infections in general reduced significantly, while diseases like lichen planus, pityriasis rosea, urticaria, rosacea, vitiligo, acne vulgaris, cutaneous fungal infections, and cutaneous leishmaniasis all increased. On the other hand, bacterial and parasitic infections, psoriasis, pruritis, melasma, and dermatitis were decreased but not to a significant level. Uncommon dermatosis included cases with pemphigus vulgaris, bullous pemphigoid, dermatitis herpetiformis, erythema multiforme, and pityriasis rubra pilaris.\n\n* The Chi-square statistic is significant at the P-value < 0.05 level.\n\nCutaneous viral infections in general reduced significantly during COVID era, specially molluscum contagiosum and condylomata accuminata, while herpes zoster increased but it was not significant (Table 2).\n\n* The Chi-square statistic is significant at the P-value < 0.05 level.\n\nThere was a reduction in the percentage of the most common forms of cutaneous bacterial infections after the peak of the COVID-19 pandemic, but it was not statistically significant (Table 3). Dermatophytosis increased while cutaneous candidiasis decreased but neither were statistically significant (Table 4).\n\n* Cutaneous tuberculosis, bacillary angiomatosis, and acute paronychia.\n\nParasitic infections including scabies and pediculosis decreased during COVID-19 pandemic but also not statistically significant (Table 5).\n\nHair loss in general and telogen effluvium specifically increased significantly from the pre COVID-19 period. Cases of female baldness, trichotillomania, and acquired hair shaft anomaly had increased, and cases of alopecia areata and traction alopecia had decreased, however, these changes were not statistically significant (Table 6).\n\n* The Chi-square statistic is significant at the P-value < 0.05 level.\n\nSeborrheic dermatitis and to little extent contact dermatitis increased, while all other types of dermatitis were reduced, and all are not statistically significant (Table 7).\n\n** Pityriasis alba, juvenile plantar dermatitis, and dyshydrotic dermatitis.\n\n\nDiscussion\n\nThere are many cutaneous manifestations that appeared to be associated with COVID-19 infection.5,6 To the best of our knowledge, this is the only study investigating the pattern of dermatologic diseases among Iraqi women who presented to an outpatient dermatological clinic in the 4 months before COVID-19 outbreak and compared to the same 4 months one year later that were not in the partial or complete curfew. In this study we choose only female patients of all ages because we believe that females are more aware of their skin and hair than males in our society.\n\nKutlu and Metin 2020 from Turkey compared 2 months (April and May 2019) to the same months in 2020 which were at the beginning of the era of COVID-19. They found that wart, molluscum contagiosum, and dermatophytosis were significantly decreased while scabies increased over this time period.4 In our study all types of cutaneous infections and infestations which are contagious like viral, bacterial, and parasitic had decreased but not to a significant level except for molluscum contagiosum and condylomata accuminata which may have been due to closure and curfew, decreasing of extra-marital sexual activity, and decreased families visiting each other. Although herpes zoster is considered to be viral infection, it was probably increased as it results from reactivation of a latent virus and not a new infection.\n\nDermatophytosis in our study had increased 1 year after the start of the pandemic but not to a significant level mostly because many families bought pets to their children during a period of ban, and these were the source of most dermatophytosis in our cases.\n\nThe same previous Turkish study found that telogen effluvium and Alopecia areata increased significantly,4 while in our study hair loss in general with telogen effluvium specifically was increased significantly because of fever due to COVID-19 infection which is considered an important cause of telogen effluvium.7 Alopecia areata cases may have decreased because it is a chronic disease and asymptomatic so patients may have postponed visiting a dermatologic clinic to avoid COVID-19 infection.\n\nLichen planus, pityriasis rosea, and urticaria were increased during COVID-19 era but not to a significant level; the reason may be because pityriasis rosea and urticaria have been reported in many studies to be associated with COVID-19 infection as a direct or indirect cause,5,8 but lichen planus was not, and because these diseases are itchy and their cutaneous lesions are usually generalized, patients may have worried about their illness and if it is related to COVID-19 infection or not. Psoriasis and melasma are usually chronic diseases, sometimes asymptomatic, so some patients might have postponed attending to dermatology clinic, which may explain the reduction in frequency of these disease during the COVID-19 pandemic; however, Kutlu and Metin reported that psoriasis frequency increased significantly during the COVID-19 pandemic.4\n\nAcne vulgaris and rosacea had increased during the pandemic but also not to a significant level. This increase may have been due to wearing a face mask to reduce the risk of contamination; Han C in 2020 reported an increased flare of acne caused by long time mask wearing during the pandemic, and they attributed that to long- time mask wearing which could increase the flare of acne due to higher temperature and humidity on the surface of facial skin caused by expired air and the perspiration,9 this could also explain the increase in rosacea.\n\nAll types of dermatitis decreased except seborrheic dermatitis but not to a significant level. This may be due to the fact that most acne patients have some sort of seborrheic dermatitis, so because acne was increasing, seborrheic dermatitis increased too. Singh M and Abtahi B during COVID-19 (March through April 2020) found that there was an increase of irritant contact dermatitis among the general population likely due to overuse of antiseptic agents and frequent hand and face washing.10–12\n\nThere are some limitations to our study. These are that this research was a single center study and data was only measured over a short period (October to January) which cannot cover all dermatological diseases that could increase or decrease in a certain season.\n\n\nConclusions\n\nThe COVID-19 pandemic resulted in changes in the diseases presented to an out-patient clinic for dermatology and venereology. This could be either related to infection with COVID-19 or stress associated with the pandemic or because of closure and wearing mask.\n\n\nData availability\n\nFigshare: Data_Dr_Galawish.xlsx. https://doi.org/10.6084/m9.figshare.16640476.v1.13\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nMy great thanks to Dr. Moshtaq Alrubayee who assisted in doing statistics of this study and to Dr. Amman Talib (consultant dermatologist) who assisted me in language editing.\n\n\nReferences\n\nWorld Health Organization: Listings of WHO’s response to COVID-19 Online. World Health Organization; 2020 [updated 29 June; cited 2021 10 Aug]. Publisher Full Text Reference Source\n\nWorld Health Organization: WHO Coronavirus (COVID-19) Dashboard. World Health Organization; 2021 [cited 2021 10 Aug]. Reference Source\n\nNovel Coronavirus (COVID-19): Update from Iraq’s Ministry of Health: Government of Iraq: 2020 [updated 25 Feb 2020; cited 2021 10 Aug]. Reference Source\n\nKutlu Ö, Metin A: Relative changes in the pattern of diseases presenting in dermatology outpatient clinic in the era of the COVID-19 pandemic. Dermatol. Ther. 2020; 33(6): e14096. PubMed Abstract | Publisher Full Text\n\nGenovese G, Moltrasio C, Berti E, et al.: Skin manifestations associated with COVID-19: current knowledge and future perspectives. Dermatology. 2021; 237: 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGalván Casas C, Catala A, Carretero Hernández G, et al.: Classification of the cutaneous manifestations of COVID-19: a rapid prospective nationwide consensus study in Spain with 375 cases. Br. J. Dermatol. 2020; 183(1): 71–77. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOlds H, Liu J, Luk K, et al.: Telogen effluvium associated with COVID-19 infection. Dermatol. Ther. 2021; 34(2): e14761. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEhsani AH, Nasimi M, Bigdelo Z: Pityriasis rosea as a cutaneous manifestation of COVID-19 infection. J. Eur. Acad. Dermatol. Venereol. 2020; 34: e436–e437. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHan C, Shi J, Chen Y, et al.: Increased flare of acne caused by long-time mask wearing during COVID-19 pandemic among general population. Dermatol. Ther. 2020; 33: e13704. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlsaidan MS, Abuyassin AH, Alsaeed ZH, et al.: The Prevalence and Determinants of Hand and Face Dermatitis during COVID-19 Pandemic: A Population-Based Survey. Dermatol. Res. Pract. 2020; 2020: 1–8. Publisher Full Text\n\nAbtahi-Naeini B: Frequent handwashing amidst the COVID-19 outbreak: prevention of hand irritant contact dermatitis and other considerations. Health Science Reports. 2020; 3(2): e163. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSingh M, Pawar M, Bothra A, et al.: Overzealous hand hygiene during the COVID 19 pandemic causing an increased incidence of hand eczema among general population. J. Am. Acad. Dermatol. 2020; 83(1): e37–e41. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbdullah G: Data_Dr_Galawish.xlsx. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "123154",
"date": "14 Feb 2022",
"name": "Dursun Turkmen",
"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\nThe publication is well thought out and well prepared. The COVID-19 pandemic has probably changed the profiles of patients applying to dermatology outpatient clinics all over the world. In the early stages of the pandemic, the applications of patients to outpatient clinics decreased significantly under strict quarantine conditions. Patients avoided applying to hospitals unless there were important reasons. Also, people experienced great anxiety. Due to this concern, our diseases, which are especially affected by psychological conditions, may have increased.\nThe article is well written. I think it would be appropriate for publication if the authors broadened the discussion a bit by also using the following articles:\nTuran C, Metin N, Utlu Z, Öner Ü, Kotan ÖS. Change of the diagnostic distribution in applicants to dermatology after COVID-19 pandemic: What it whispers to us?.1\n\nTurkmen D, Altunisik N, Sener S, Colak C. Evaluation of the effects of COVID-19 pandemic on hair diseases through a web-based questionnaire.2\n\nTurkmen D, Altunisik N, Mantar I, Durmaz I, Sener S, Colak C. Comparison of patients' diagnoses in a dermatology outpatient clinic during the COVID-19 pandemic period and pre-pandemic period. 3\nDue to the COVID-19 pandemic, countries have taken various measures. The measures taken and the working conditions of hospitals vary from country to country. To better understand the findings obtained by the authors in their study, we may have the opportunity to make more reliable interpretations in our country, especially when compared to our own studies on the same subject. I am curious about the comments of the authors about the reasons for the differences. At the same time, I think that the article will be more interesting and more understandable with the evaluations to be made.\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": "7984",
"date": "10 May 2022",
"name": "Galawish Ahmed",
"role": "Author Response",
"response": "Dear Doctor, Thank you for reviewing my article, and we appreciate your opinion, I think that only Turkmen et al (2021) is directly related to my article, and I am going to add their results and discuss them in my article. Best regards"
}
]
}
] | 1
|
https://f1000research.com/articles/10-1165
|
https://f1000research.com/articles/11-1328/v1
|
16 Nov 22
|
{
"type": "Research Article",
"title": "Tumour cell suppression by spiroleucettadine through dual regulation of cell cycle and apoptosis",
"authors": [
"Ben Watts",
"Maddie Berry",
"Abigail Bland",
"Michael Badart",
"Bill Hawkins",
"John Ashton",
"Ben Watts",
"Maddie Berry",
"Abigail Bland",
"Michael Badart",
"Bill Hawkins"
],
"abstract": "Background: Spiroleucettadine is an alkaloid originally derived from the yellow Leucetta sea sponge. Spiroleucettadine has previously been shown to inhibit the growth of various cancer cell lines and has a high anti-proliferative activity against a non-small cell lung cancer cell line (H522). The mediators of these anti-proliferative effects have not been determined. Therefore, in this study we measured changes in cell death and cell proliferation and their immediate protein mediators in response to spiroleucettadine, toward the aim of ultimately determining target(s) for spiroleucettadine in cancer cells and a more precise description of its mechanism of action. Methods: We used flow cytometry to investigate changes in the cell cycle apoptosis and Western blot to investigate associated protein changes following exposure of H522 cells to varying concentrations of spiroleucettadine. Results: We found evidence for cell cycle arrest at G2/M and associated increases in cyclin B1 expression and CDK1 phosphorylation, as well as an increase in apoptosis alongside marked increase in Bim expression, consistent with activation of the intrinsic apoptotic pathway Conclusions: Any targets for spiroleucettadine that may be proposed are constrained to those with mechanisms of actions that lead to G2/M arrest, induction of the intrinsic apoptotic pathway, and changes in the expression of associated proteins.",
"keywords": [
"apoptosis",
"cancer",
"cell cycle",
"cyclins",
"H522 cells",
"lung adenocarcinoma",
"spiroleucettadine"
],
"content": "Introduction\n\nLung cancer is divided broadly into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). NSCLC accounts for 80–85% of lung cancer deaths (Navada, Lai et al., 2006, Lemjabbar-Alaoui, Hassan et al., 2015) and is one of the leading causes of death worldwide (Pao and Girard, 2011, Ettinger, Akerley et al., 2013). NSCLC can be further divided into squamous cell lung cancer (~25-30% of lung cancers), adenocarcinomas (~40% of lung cancers) or large cell anaplastic carcinomas (~10% of lung cancers) (Lemjabbar-Alaoui, Hassan et al., 2015). Adenocarcinomas arise from alveolar cells situated in the smaller airway epithelium (Travis, Brambilla et al., 2015). Approximately 30-60% of lung adenocarcinomas arise through the development of mutations in epidermal growth factor receptor (EGFR), Kirsten rat sarcoma viral oncogene homolog (KRAS) and anaplastic lymphoma kinase receptor (ALK) genes (Herbst, Heymach et al., 2008, Bronte, Rizzo et al., 2010, Pao and Girard, 2011) with a small percentage containing other targetable oncogenic drivers (Liu, Du et al., 2020). Of the large percentage of lung adenocarcinoma patients with no targetable mutations, only approximately 20% will show even a temporary and partial response to existing chemotherapies, although a prolonged survival can still occasionally occur (Nishio, Nakamura et al., 1999).\n\nAlthough there has been considerable progress in the treatment of NSCLC in targeted drug treatment and immunotherapy, there has been relatively little progress in the development of new chemotherapies, particularly in comparison to other cancers (Lemjabbar-Alaoui, Hassan et al., 2015). As a minority of NSCLCs have a molecular profile suitable for treatment with targeted or immunotherapies, this means that there remains an unmet need for more chemotherapies for NSCLC.\n\n(-)- Spiroleucettadine is an alkaloid first isolated by Ralifo and Crews (2004) from the yellow Leucetta sea sponge. Following the synthesis of spiroleucettadine by Lamb, Aberle et al. (2017), spiroleucettadine was tested for anti-cancer effects against the NCI-60 cell lines (Badart, Barnes et al., 2020). Spiroleucettadine inhibited the growth of multiple cancer types including leukaemia, melanoma, non-small cell lung, colon, renal and ovarian cancers with varying growth inhibition. Of particular interest, spiroleucettadine had the highest anti-proliferative activity against the NSCLC cell line H522 with an EC50 of 0.37 μM (Badart, Barnes et al., 2020).\n\nThe mechanism of action for these anti-proliferative effects has not been determined. In this study we investigated the changes in cell death and cell proliferation in response to spiroleucettadine, as well as changes in mediators of apoptosis and the cell cycle to characterise the late mediators of cancer cell growth suppression by spiroleucettadine, toward the aim of ultimately determining specific cellular target(s) leading to these effects.\n\n\nMethods\n\nWe performed our initial experiments on three human lung adenocarcinoma cell lines, each with distinct oncogenic drivers: H522 (p53 mutated – gifted from Eccles Lab, University of Otago, NZ); A549 (KRAS mutated – gifted from Giles Lab, University of Otago, NZ); and H3122 (ALK mutated – gifted from Engelman Lab, Harvard Massachusetts General Hospital Cancer Center, US). As H522 cells showed the greatest cytotoxic response to spiroleucettadine we performed our later experiments investigating mechanisms of action only on these cells.\n\n(-)-Spiroleucettadine was prepared using the procedures described by Badart et al. (2020). Purity was ascertained using high performance liquid chromatography (HPLC) and found to be >98% pure and > 96% enatiomenic excess (ee). HPLC conditions included: Diacel CHIRALPAK IC-3 chiral column, Shimadzu ELSD-LT II detector, eluting with acetonitrile.\n\nColourless semi-solid\n\n[α]20D = -23.0 (c = 1.23, CHCl3)\n\n1H NMR (500 MHz, MeOH-d4) δ: 7.45 (d, J = 8.6 Hz, 2H), 6.99 (dd, J = 10.5, 2.2 Hz, 1H), 6.88 (d, J = 8.5 Hz, 2H), 6.01 (app. d, J = 10.8 Hz, 1H), 5.93 (dd, J = 10.1, 2.3 Hz, 1H), 5.92 (dd, J = 10.1, 2.3 Hz, 1H), 3.80 (s, 3H), 3.21 and 3.17 (abq, J = 14.5 Hz, 2H), 2.79 (s, 3H), 2.40 (s, 3H), 2.22 and 2.07 (abq, J = 13.2 Hz, 2H).\n\n13C NMR (125 MHz, MeOH-d4) δ: 186.9, 161.2, 160.2, 152.5, 151.5, 134.2, 129.0, 128.4, 127.4, 114.2, 104.0, 84.0, 78.6, 55.7, 49.0, 38.6, 29.0, 26.2.\n\nνmax (ATR-IR) cm-1 3293, 3057, 2928, 2853, 2837, 2809, 1699, 1669, 1629, 1610, 1511, 1437, 1393, 1329, 1300, 1246, 1177, 1158, 1031, 1013, 733, 500, 585.\n\nHRMS-ESI: calcd. for C20H23N3NaO4 [M + Na+]: 392.1581; found 392.1592.\n\nH522 and H3122 cells were maintained in Roswell Park Memorial Institute (RPMI)1640 medium supplemented with 1% streptomycin/penicillin and 5% foetal bovine serum (FBS) (Life Technologies, NZ Ltd), while A549 cells were maintained in RPMI1640 supplemented with 1% streptomycin/penicillin and 2% FBS. All cell lines were incubated at 37°C, 5% CO2, 95% humidified air. Cells were passaged at approximately 80-90% confluency. Phosphate buffered saline (PBS) (Sigma-Aldrich, US) was used to wash cells before trypsinisation using TrypLE (ThermoFisher, NZ) to detach cells from the flasks. Cells were then centrifuged for three minutes at 1200 rpm in fresh media. Supernatant was removed, and cells were resuspended in fresh media for transfer into new tissue culture flasks.\n\nH522 cells were harvested at approximately 80-90% confluency; cells were PBS-washed before trypsinisation using TrypLE to detach cells from flasks. Cells were then centrifuged for three minutes at 1200 rpm in fresh media, the supernatant removed, and cells resuspended in fresh media for plating. H522 cells were seeded into 96-well plates at a density of 10×103 cells/well and incubated for 24 hours to allow cells to adhere to the plate. Cells were then treated with increasing concentrations of spiroleucettadine (0, 0.01, 0.05, 0.1, 0.2, 0.3, 0.5, 0.75, 1, 5, 10, 50 μM) and further incubated for 72 hours, 96 or 144 hours. Following this, cells were fixed with 10% trichloroacetic acid (TCA, Sigma-Aldrich, NZ) for 30 minutes at 4°C. TCA was rinsed off using distilled water and the plate was dried. Sulforhodamine B (SRB, Sigma-Aldrich, NZ) (0.4%) in acetic acid (1%, Merck, US) was added to wells to stain for cellular protein for 10 minutes at room temperature. SRB was then aspirated, and wells were washed with 1% acetic acid and the plate was dried. Tris/HCl (10 mM, Sigma-Aldrich, NZ) was then added to solubilise the SRB dye. Absorbance of wells was read using the Benchmark Plus microplate spectrophotometer at 510 nm. Absorbance values were then used to calculate approximate cell number from a constructed standard curve of absorbance versus cell number.\n\nH522, H3122 and A549 cells were harvested at approximately 80-90% confluency. PBS was used to wash cells before trypsinisation using TrypLE to detach cells from plastic vessels. Cells were then centrifuged for three minutes at 1200 rpm in fresh media. The supernatant was removed, and cells were resuspended in fresh media for plating. H522, H3122 and A549 cells were counted using a haemocytometer, seeded into 96-well plates at a density of 10×103, 7×103 and 4×103 cells/well, respectively, and incubated for 24 hours in order for the cells to adhere to the wells. Cells were then treated with the vehicle control (dimethyl sulfoxide, DMSO, Sigma-Aldrich, US) or increasing concentrations of spiroleucettadine (0, 0.01, 0.05, 0.1, 0.2, 0.3, 0.5, 0.75, 1, 5, 10, 50 μM for H522 cells or 0, 0.01, 0.05, 0.1, 0.2, 0.5, 1, 2, 3, 5, 10, 50, 100 μM for A549 and H3122 cells) and further incubated for 72 hours. The same procedure was conducted for the SRB stain as stated in the “Time course cell number assay” section. The concentration of each drug required to reduce cell viability by 50% (EC50) was determined from three-parameter Hill equations fit to data using nonlinear regression using GraphPad Prism 8 software, from three independent experiments, performed in triplicate. EC50 values are expressed as mean ± SD.\n\nCell cycle analysis was carried out using flow cytometry. H522 cells were harvested at approximately 80-90% confluency and cells were washed with PBS before trypsinisation using TrypLE to detach cells from flasks before being centrifuged for three minutes at 1200 rpm in fresh media. After the supernatant was removed, cells were resuspended in fresh media for plating at a density of 3×105 cells/well in six-well plates. Plates were then incubated for 24 hours to allow for cell adherence. Cells were then treated with either vehicle control (0.1% DMSO) or spiroleucettadine concentrations standardised to the cell viability EC50 (0.5×, 1.0× and 2.0× EC50) for 24 hours.\n\nMedium was then removed, and cells were washed with PBS before trypsinisation using TrypLE for approximately five minutes. Fresh media was then added, and the cells were collected in falcon tubes. Cells were then centrifuged at 2000 rpm for four minutes. Supernatant was then discarded, and the pellet was resuspended in cold PBS. Centrifugation was repeated once before fixing the cells using cold 70% ethanol dropwise while gently mixing with a vortex. Tubes were stored at 4°C until analysis was carried out. On the day of flow cytometry analysis, cells were centrifuged at 1500 rpm for 10 minutes at 4°C, supernatant was discarded, and pellet resuspended in cold PBS. Centrifugation was carried out as described above and cells were resuspended in FxCycle PI/RNase solution (Life Technologies, US). The cell suspension was then placed in test tubes and incubated in the dark at room temperature for 30 minutes. Cell cycle assay was then carried out using a BD FACSCanto II flow cytometer (BDBiosciences, US). Data from three independent experiments were analysed using FlowJo analysis software.\n\nThe mode of cell death following exposure to spiroleucettadine was determined for H522 cells using propidium iodide (PI, Waltham, Massachusetts, US) and annexin V-APC (BD Biosciences, San Jose, California, US) staining by flow cytometry. The cells were harvested at approximately 80-90% confluency and PBS was used to wash cells before trypsinisation using TrypLE. Cells were then centrifuged for three minutes at 1200 rpm in fresh media. The supernatant was removed, and cells were resuspended in fresh media for plating. Plates were incubated for 24 hours to allow for cell adherence. Cells were then treated with either vehicle control (0.1% DMSO) or various concentrations of spiroleucettadine (0.5×, 1.0× and 2.0×EC50) for 24 hours.\n\nMedia was collected and cells were washed with warm PBS before trypsinisation using TrypLE for approximately five minutes. Fresh media was then added and collected in falcon tubes. Cells were then centrifuged at 2000 rpm for four minutes at 4°C. The supernatant was then discarded, and the pellet was resuspended in cold PBS. Centrifugation, resuspension, and centrifugation (as previously described) was carried out once more. The supernatant was discarded, and the cell pellet was resuspended in annexin V binding buffer (0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 1.4 M NaCl, 25 mM CaCl2, pH 7.4, Sigma-Aldrich, US) and transferred to a Falcon 5 mL FACS tube. Annexin V-APC was added to each tube and mixed gently prior to the 15-minute incubation in the dark at room temperature. Following this incubation, annexin V binding buffer and PI (50 μg/mL) was added to each tube and kept in the dark until analysis.\n\nSamples were analysed on BD FACSCanto II flow cytometer. Data obtained was analysed using FlowJo analysis software (BD Biosciences). Three biological independent experiments were performed.\n\nPrimary antibodies against CDK2 (RRID:AB_22761290), CDK4 (RRID:AB_20783990), cyclin B1 (RRID: AB_491024), cyclin D1 (RRID: AB_2259616), Bax (RRID: AB_2716251), Bcl-2 (RRID:AB_2064177), Bim (RRID: AB_10692515), and cleaved caspase 3 (RRID: AB_2341188) were purchased from Cell Signalling Technology (Danvers, Massachusetts, USA). Antibodies against β-tubulin (RRID: AB_477577) and CDK1 (RRID: AB_258879) were purchased from Sigma-Aldrich (USA). Antibodies against pCDK1 (RRID: AB_2533722) and pCDK4 (RRID: AB_2809179) were purchased from Invitrogen (Waltham, Massachusetts, USA). Horseradish peroxidase (HRP) conjugated goat anti-mouse and HRP conjugated goat anti-rabbit secondary antibodies were purchased from Merck Millipore (Burlington, Massachusetts, USA).\n\nCell lysate preparation\n\nH522 cells were seeded in petri dishes at a density of 1×106 cells/dish and incubated in 5% CO2, 95% humidified air, 37°C for 24 hours. H522 cells were treated with vehicle (0.05% DMSO) or spiroleucettadine (0.5 ×, 1.0 × and 2.0 × EC50) for 24 hours. On the following day, cells were washed with ice-cold PBS and lysed with lysis buffer (50 mM Tris base (pH-7.5), 150 mM NaCl, 1 mM ethylenediaminetetraacetic acid EDTA (Merck (Kenilworth, New Jersey, USA), 1 mM sodium orthovanadate, 2.5 mM sodium pyrophosphate, 10 mM sodium fluoride (Sigma-Aldrich, US) and complete protease inhibitor cocktail (Sigma-Aldrich, US)). Cell lysates were collected by scraping and sonicated three times for 7 s each followed by centrifugation at 10,000 rpm for 8 min at 4°C. The supernatant was transferred to a new Eppendorf tube before protein concentration was determined. The protein concentration of cell lysates was determined by bicinchoninic acid (BCA) assay as described in Smith et al., (1985). Briefly, bovine serum albumin (BSA, Sigma-Aldrich, NZ) protein standard (0.5 mg/mL) was used to obtain the standard curve. BCA solution (50:1) was prepared freshly by adding 50 volumes of BCA protein assay reagent A (Merck (Kenilworth, US) and 1 volume of 4% copper sulphate pentahydrate (CuSO4.5H2O) (Sigma-Aldrich, US) solution. BCA solution was added to each well (containing either the standards or samples) and incubated in the dark at 37°C for 30 minutes. Absorbance was measured at 562 nm using Bio-Rad Benchmark Plus microplate reader. A standard curve was used to determine the protein concentration of samples and each sample was normalised to obtain 200 μg/μL of protein. Laemmli sample buffer (62.5 mM Tris HCl, 1% (w/v) SDS, 10% glycerol, 0.005% bromophenol blue, 355 mM β-mercaptoethanol, Sigma-Aldrich, US) (pH 6.8)) was added to each sample and denatured by boiling at 95°C for 5 min. The samples were frozen at -20°C until required.\n\nGel electrophoresis and antibody labelling\n\nSodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to separate proteins based on their molecular weight (Blake, Johnston et al., 1984). Different percentages of resolving gels ranging from 10% to 15% (30% acrylamide/bisacrylamide (29:1) (Bio-Rad, US) solution, lower Tris buffer (1.5 M tris/HCl pH8.8, 0.4% SDS), 50% glycerol, 10% APS, dH2O, N,N,N,N-tetramethyethylene diamine TEMED, Sigma-Aldrich, US) and a stacking gel (30% acrylamide/bisacrylamide (29:1) solution, upper Tris buffer (0.5 M tris/HCl pH6.8, 0.4% SDS), 10% of APS, dH2O, TEMED) were made depending upon the type of proteins of interest. Samples were defrosted and 20 μL of protein was loaded in each well of gels. Precision Plus Protein kaleidoscope (a molecular weight protein marker) was loaded in each gel to identify the respective proteins based on their molecular weight. Gels were run in a Bio-Rad Mini-Protean III apparatus at 80 V in SDS-running buffer (25 mM Tris base, pH 8.3, 0.192 M glycine, 0.1% SDS) for approximately for 15 min until the protein get migrated to the end of stacking gel. Then, the voltage was increased to 120 V until the protein reached to the bottom of resolving gel.\n\nThe proteins were transferred to a methanol activated polyvinylidene fluoride (PVDF, Sigma-Aldrich, US) membrane in transfer buffer (25 mM Tris-base, pH 8.3, 0.192 M glycine, 0.1% sodium dodecyl sulphate (SDS, Sigma-Aldrich, US) and 20% methanol) using a Bio-Rad wet transfer system at 100 V for 90 minutes. After the completion of the transfer, membranes were placed in 2% BSA blocking solution and placed on a shaker for one hour at room temperature. This was followed by incubation with respective primary antibody (diluted in 2% or 5% BSA) overnight at 4°C. The dilution of primary antibody used was as follows: CDK1 (1:1000), CDK2 (1:1000), CDK4 (1:1000), CDK6 (1:1000), pCDK1 (1:1000), pCDK4 (1:1000), cyclin B1 (1:1000), cyclin D1 (1:1000), cleaved caspase-3 (1:1000), Bcl-2 (1:1000), Bim (1:1000), Bax (1:1000), β-tubulin (1: 2000). After this, membranes were washed in TBST (0.05% Tween 20 (VWR International, Radnor, US), 0.025 mM Tris base, 0.1 M NaCl, pH 7.4) six times (5 min each) and incubated with HRP conjugated goat anti-mouse or goat anti-rabbit secondary antibodies (1:3000 in 5% non-fat milk in TBS) for 1 h at room temperature. Following incubation, membranes were washed with TBST six times (5 min each). Protein bands were visualised using SuperSignal West Pico Chemiluminescent Substrate and CL-XPosure film (Thermo Fisher Scientific, Waltham, Massachusetts, US). The developing process consisted of exposure to developer fluid, followed by a distilled water wash, then washed in fixer fluid Carestream Health (Rochester, New York, US) and lastly washed again in distilled water.\n\nDensitometric analysis\n\nThe images were scanned using Bio-Rad GS-710 densitometer and densities of each band were quantified using Quantity One software (Bio-Rad). The densities of the respective proteins were normalised to β-tubulin. Three independent experiments were performed. Data is presented as mean ± SEM. Statistical significance was determined using one-way ANOVA with Bonferroni post hoc test using Prism 9 (GraphPad Software, US).\n\nCell viability was normalised to control and analysed by nonlinear regression using GraphPad Prism 9 software. Drug concentrations were log-transformed using the X = log(X) function. Nonlinear regression analysis was carried out using the log (inhibitor) versus response – four parameter variable slope function. Time course cell viability assays were plotted as cell number versus spiroleucettadine concentration and analysed with nonlinear regression using GraphPad Prism 9 software. This provided EC50 values in different cell lines and at different drug exposure lengths. Comparison of mean spiroleucettadine EC50 values in different cell lines was done using an extra sum of squares F test. Identical statistical analysis was used to compare spiroleucettadine EC50 values following differing cell exposure times to spiroleucettadine. Data is presented as mean ± SD, where p < 0.05 was the minimum requirement for statistically significant difference. Experiments were carried out in triplicate using three biological replicates.\n\nCell cycle and apoptosis data was gathered using FlowJo 10 software. Comparison between treatments was carried out using GraphPad Prism 9 software. To determine whether different concentrations of spiroleucettadine caused changes to cell numbers in each stage of the cell cycle, or to determine whether cells were viable or apoptotic, data was analysed using two-way ANOVA coupled with post hoc Bonferroni tests. Data is presented as mean ± SEM, where p < 0.05 was the minimum requirement for statistically significant difference. Experiments were carried out in triplicate using three biological replicates.\n\nStatistical analysis of Western blot data was carried out by calculating the relative expression of the protein of interest in comparison to the β-tubulin loading control. To assess whether various concentrations of spiroleucettadine caused changes in protein expression, one-way ANOVA were used coupled with post hoc Bonferroni tests. Data are presented as mean ± SEM where p < 0.05 was the minimum requirement for statistically significant difference. Experiments were carried out using three biological replicates.\n\n\nResults\n\nWe first confirmed the sensitivity of human adenocarcinoma cell lines (H522, A549, and H1322) using the SRB assay to determine cell viability at various concentrations of spiroleucettadine. The EC50 concentration of spiroleucettadine with respect to cell viability was 0.72 ± 0.09 μM in H522 cells, the lowest of the three cell lines tested (Table 1).\n\nData are expressed as mean plus or minus standard deviation and p values were calculated from 1-factor ANOVA with cell type as the independent variable.\n\nTo test whether the EC50 for H522 cells sensitivity to spiroleucettadine varies with the amount of time the cells are exposed to spiroleucettadine we measured H522 cell number across a range of spiroleucettadine concentrations when spiroleucettadine was applied to cells for three, four or six days (this controls for the changing numbers of cells in the control wells, to which drug treated cells are normalised in the method used for Figure 1A). This showed that duration of drug exposure had no significant effect on cell number (Figure 1B) confirming the relative sensitivity of H522 cells to spiroleucettadine compared to A549 and H3122 cells (Table 1B). We therefore used H522 cells and spiroleucettadine concentrations calculated from 0.72 μM (the 3-day EC50 for cell viability) in the experiments described below. Furthermore, from the high degree of cell growth suppression at three days following exposure to this drug concentration, we inferred that significant cell cycle, apoptosis, and protein expression changes, would be detectable after 24 hours (when cellular processes have been activated, but cell number are sufficient for measurements to be robust).\n\n(A) Effect of a range of concentrations of spiroleucettadine on the viability of H522 (circles), H3122 (triangles), and A549 cells (squares). Data points are displayed as mean ± SD (n = 3 biological replicates). (B) Effect of duration of exposure to various concentrations of spiroleucettadine on H522. Cell number was counted after 3, 4 or 6 days exposure to spiroleucettadine. Data are displayed as mean ± SEM (n = 3 biological replicates).\n\nTo characterise the mode of cell growth suppression by spiroleucettadine more precisely, we assayed its effects first on the cell cycle and then on cell cycle mediators. No significant changes in cell number were detected in the sub G1, G0/G1, S and G2/M phases following 24-hour treatment with spiroleucettadine at 0.72 μM (1×EC50) or 0.36 μM (0.5×EC50) (Figure 2A). However, 1.44 μM (2×EC50) resulted in a significant decrease (~15%) in cells in the G0/G1 phase (p < 0.001) and a significant increase (~35%) in cells in the G2/M phase (p < 0.0001) (Figure 2A) suggesting that spiroleucettadine increases the number of cells in G2/M arrest.\n\n(A) Effect of spiroleucettadine on cell cycle arrest in H522 cells following 24 hours exposure to vehicle control (DMSO 0.1%) or 0.5 × cell viability assay EC50 (0.36 mM), 1 × EC50 (0.72 mM) and 2 × EC50 (1.44 mM) of spiroleucettadine. Bar denotes; Sub G1, G0/G1, S, G2/M. (B) Representative flow cytometry cell cycle histogram. Differently shaded histograms denote different treatments (from front to back: control; 0.36 mM; 0.72 mM; 1.44 mM). Data analysed with two-way-ANOVA followed by Bonferroni post-hoc tests and are presented as mean ± SEM (n = 3 biological replicates). * p < 0.05 of cells in G0/G1 phase compared with control; Δ p < 0.05 of cells in G2/M phase versus all control.\n\nWe did not detect any statistically significant changes in protein expression using Western blotting for CDK1, CDK4 or the phosphorylation of CDK4 (pCDK4) after 24-hour treatment with spiroleucettadine at concentrations up to 1.4 μM (2 × EC50) (p > 0.05) (Figure 3A, C-E). A significant increase (~50% and ~95%, respectively) in the expression of pCDK1, was, however, observed following treatment with 0.72 μM and 1.44 μM spiroleucettadine for 24 hours (p < 0.01) (Figure 3B).\n\nTreatment conventions are as above. for 24 hours. Representative Western blots and densitometry (n = 3 biological replicates) are shown for: (A) CDK1; (B) pCDK1; (C) CDK4; (D) pCDK4. Data are expressed as mean ± SEM determined and analysed by one-way-ANOVA with Bonferroni post-hoc tests (n = 3 biological replicates). * p < 0.05.\n\nWhen we assayed for changes in expression of cyclin B1 and cyclin D1 in H522 cells following 24-hour exposure to spiroleucettadine using Western blotting, we found a significant increase in cyclin B1 expression in response to both 0.72 μM and 1.44 μM spiroleucettadine for 24 hours (p < 0.05) (~45% higher than that of the control treatment group) (Figure 4A). Cyclin D1 expression was significantly reduced (p < 0.05) by all concentrations of spiroleucettadine tested: ~35% for 0.36 μM (0.5 × cell viability EC50); ~38% for 0.72 μM (EC50); and ~60% for 1.42 μM (2 × EC50) (Figure 4B).\n\nTreatment and densitometry conventions are as above. Representative Western blots and densitometry (n = 3 biological replicates) are shown for: (A) cyclin B1; (B) cyclin D1.\n\nTo characterise the induction of apoptosis in H522 cells by spiroleucettadine we used annexin V and propidium iodide staining with flow cytometry. A significant increase in the percentage of cells in the early apoptotic stage was observed following 1.42 μM (2 × cell viability EC50) treatment when compared control (p < 0.05) (Figure 5). The increase, while statistically significant, was relatively small with ~0.5% cells in the early apoptotic phase in the control treatment group compared to ~2.3% in spiroleucettadine-treated cells. In addition, 1.42 μM spiroleucettadine over 24 hours produced a significant (p < 0.001) increase in the percentage of cells in the late apoptotic phase in comparison to all lower concentration treatments tested (Figure 5). The percentage of cells in the late apoptotic phase ranged from ~2-3% in the control cells to ~11% in treated cells (Figure 5).\n\nTo characterise the drivers of apoptosis induced by spiroleucettadine more precisely we assayed changes in protein expression of apoptosis mediators Bax, Bcl-2, Bim, and cleaved caspase 3 in H522 cells. After 24 hours of treatment, the expression of neither Bax nor Bcl-2 was significantly changed by any concentrations of spiroleucettadine tested (p > 0.05, Figure 6). The expression of Bim was substantially and significantly increased following treatment by both 0.72 μM and 1.44 μM spiroleucettadine over 24 hours (~83% and ~150%, respectively, p < 0.01) (Figure 6). Cleaved caspase 3 expression was substantially and significantly increased (~385%) following treatment with 1.44 μM spiroleucettadine over 24 hours (p < 0.0001) (Figure 6).\n\n* p < 0.01, ** p < 0.0001 versus control. Treatment and densitometry conventions are otherwise as above. Representative Western blots and densitometry (n = 3 biological replicates) are shown for: (A) Bax; (B) Bcl-2; (C) Bim; (D) cleaved caspase 3.\n\n\nDiscussion\n\nThe identification of new anticancer agents for non-oncogene dominant NSCLC has been challenging. Although considerable progress has been made in the treatment for EGFR, ALK, and PDL-1 positive subtypes, NSCLC is generally resistant to chemotherapy. Building on recent work showing potential anti-cancer properties of spiroleucettadine (Badart, Barnes et al., 2020), we first identified a cell line (H522) with particular sensitivity to the compound and then characterised the mode and mediators of cell growth suppression.\n\nWe found that in lung adenocarcinoma H522 cells, spiroleucettadine at 1.44 μM decreases the number cells in the G0/G1 phase of the cell cycle and increased the proportion of cells in the G2/M phase over 24 hours, suggesting a G2/M arrest. Consistent with this, we found a strong increase in the phosphorylation of CDK1 and expression of cyclin B1 and cyclin D1 over the same period, both mediators of cell cycle transition from G2/M. Cyclin D1 expression – a mediator of the G0/G1 transition expression – was significantly reduced. Apoptosis was also induced by spiroleucettadine, evidenced by both flow cytometry and increased expression of cleaved caspase 3. Expression of Bim, a mediator of the intrinsic apoptosis pathway, was profoundly induced by spiroleucettadine. The picture that emerges from these results is a familiar one from induction of apoptosis by cell cycle arrest and activation of mitotic checkpoints by cytotoxic chemotherapies.\n\nWe hypothesised that by analogy with other natural product derivatives, namely taxanes, vincra alkaloids, and in particular eribulin, the mechanism of action of spiroleucettadine might also be disrupting microtubules in mitotic spindle formation, which would be consistent with the results discussed above, namely G2/M arrest, as cells in the G2 phase are preparing for mitotic division in the M phase including mitotic spindle formation (Schmidt, Rohe et al., 2017). However, although this hypothesis deserves more extensive investigation, we did not find any evidence of this using immunocytochemistry for α-tubulin, which has previously been shown for microtubule disrupters (Florian and Mitchison, 2016).\n\nOur experiments did not show any evidence of an induction of cell cycle arrest at G1 which aligns with the absence of p53 in H522 cells; cells without p53 cannot be arrested in G1 (Murray, 1994). This raises the question of why H522 cells were more sensitive to cell growth suppression than other cells tested. It may be that H522 cells lack a tumour suppressor, p53, but not a positive driver of cell growth, such as ALK, EGFR, or KRAS as for the other cell lines tested. This may make H522 cells more sensitive to drugs that disrupt the cell cycle than the other cell lines. However, loss of tumour suppression mediators is generally associated with resistance anticancer therapeutics, not sensitivity (Song and Xu, 2007, Goldstein, Marcel et al., 2011).\n\nThe increase of phosphorylation of CDK1 by spiroleucettadine may offer another avenue for further investigations into mechanism of action. Phosphorylation of WEE1 and Myt1 kinases on tyrosine 15 (Tyr15) lead to the phosphorylation of CDK1. Also, CDK-activating kinases (CAKs) phosphorylate CDK1 at threonine 161 (T161) (Atherton-Fessler, Parker et al., 1993, Pavletich 1999). In addition, the induction of Bim – a Bcl-2 homology 3 (BH3) only pro-apoptotic – implies activation of the intrinsic apoptosis pathway (Youle and Strasser, 2008, Tzifi, Economopoulou et al., 2012, Warren, Wong-Brown et al., 2019).\n\n\nConclusions\n\nSpiroleucettadine has sub-micromolar suppression of H522 cancer cell growth, through G2/M arrest and induction of the intrinsic apoptosis pathway. This is associated with the phosphorylation of CDK1 and the expression of Bim, respectively. Proposed targets for spiroleucettadine are thereby constrained to those with mechanisms of actions that lead to these cellular and biochemical changes.",
"appendix": "Data availability\n\nZenodo: Sprioleucettadine Ashton, https://doi.org/10.5281/zenodo.7117555 (Ashton et al., 2022).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAshton J, Watts B, Bland A, et al.: Sprioleucettadine Ashton.2022. Publisher Full Text\n\nAtherton-Fessler S, Parker LL, Geahlen RL, et al.: Mechanisms of p34cdc2 regulation. Molecular and Cellular Biology. 1993; 13(3): 1675–1685. PubMed Abstract\n\nBadart M, Barnes EM, Cording AP, et al.: Synthesis and biological evaluation of (-) and (+)-spiroleucettadine and analogues. ChemMedChem. 2020.\n\nBlake M, Johnston K, Russell-Jones G, et al.: A rapid, sensitive method for detection of alkaline phosphatase-conjugated anti-antibody on Western blots. Analytical Biochemistry. 1984; 136(1): 175–179. PubMed Abstract | Publisher Full Text\n\nBronte G, Rizzo S, La Paglia L, et al.: Driver mutations and differential sensitivity to targeted therapies: a new approach to the treatment of lung adenocarcinoma. Cancer Treatment Reviews. 2010; 36: S21–S29. Publisher Full Text\n\nEttinger DS, Akerley W, Borghaei H, et al.: Non-small cell lung cancer, version 2.2013. Journal of the National Comprehensive Cancer Network. 2013; 11(6): 645–653; quiz 653. PubMed Abstract | Publisher Full Text\n\nFlorian S, Mitchison TJ: Anti-microtubule drugs. The Mitotic Spindle. 2016;403–421. Publisher Full Text\n\nGoldstein I, Marcel V, Olivier M, et al.: Understanding wild-type and mutant p53 activities in human cancer: new landmarks on the way to targeted therapies. Cancer Gene Therapy. 2011; 18(1): 2–11. PubMed Abstract | Publisher Full Text\n\nHerbst R, Heymach J, Lippman S: Lung Cancer. New England Journal of Medicine. 2008; 359(13): 1367–1380. Publisher Full Text\n\nLamb RA, Aberle NS, Lucas NT, et al.: Total Synthesis of (−)-Spiroleucettadine. Angewandte Chemie International Edition. 2017; 56(46): 14663–14666. PubMed Abstract | Publisher Full Text\n\nLemjabbar-Alaoui H, Hassan OU, Yang Y-W, et al.: Lung cancer: Biology and treatment options. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer. 2015; 1856(2): 189–210. PubMed Abstract | Publisher Full Text\n\nLiu W-J, Du Y, Wen R, et al.: Drug resistance to targeted therapeutic strategies in non-small cell lung cancer. Pharmacology & Therapeutics. 2020; 206: 107438. Publisher Full Text\n\nMurray A: Cell cycle checkpoints. Current Opinion in Cell Biology. 1994; 6(6): 872–876. Publisher Full Text\n\nNavada S, Lai P, Schwartz A, et al.: Temporal trends in small cell lung cancer: analysis of the national Surveillance, Epidemiology, and End-Results (SEER) database. Journal of Clinical Oncology. 2006; 24(18_suppl): 7082–7082. Publisher Full Text\n\nNishio K, Nakamura T, Koh Y, et al.: Drug resistance in lung cancer. Current Opinion in Oncology. 1999; 11(2): 109. Publisher Full Text\n\nPao W, Girard N: New driver mutations in non-small-cell lung cancer. The Lancet Oncology. 2011; 12(2): 175–180. Publisher Full Text\n\nPavletich NP: Mechanisms of cyclin-dependent kinase regulation: structures of Cdks, their cyclin activators, and Cip and INK4 inhibitors. Journal of Molecular Biology. 1999; 287(5): 821–828. PubMed Abstract | Publisher Full Text\n\nRalifo P, Crews P: A new structural theme in the imidazole-containing alkaloids from a calcareous Leucetta sponge. The Journal of Organic Chemistry. 2004; 69(26): 9025–9029. PubMed Abstract | Publisher Full Text\n\nSchmidt M, Rohe A, Platzer C, et al.: Regulation of G2/M transition by inhibition of WEE1 and PKMYT1 kinases. Molecules. 2017; 22(12): 2045. PubMed Abstract | Publisher Full Text\n\nSong H, Xu Y: Gain of function of p53 cancer mutants in disrupting critical DNA damage response pathways. Cell Cycle. 2007; 6(13): 1570–1573. PubMed Abstract | Publisher Full Text\n\nTravis WD, Brambilla E, Nicholson AG, et al.: The 2015 World Health Organization classification of lung tumors: impact of genetic, clinical and radiologic advances since the 2004 classification. Journal of Thoracic Oncology. 2015; 10(9): 1243–1260. Publisher Full Text\n\nTzifi F, Economopoulou C, Gourgiotis D, et al.: The role of BCL2 family of apoptosis regulator proteins in acute and chronic leukemias. Advances in Hematology. 2012; 2012: 1–15. PubMed Abstract | Publisher Full Text\n\nWarren CF, Wong-Brown MW, Bowden NA: BCL-2 family isoforms in apoptosis and cancer. Cell Death & Disease. 2019; 10(3): 1–12. Publisher Full Text\n\nYoule RJ, Strasser A: The BCL-2 protein family: opposing activities that mediate cell death. Nature Reviews Molecular Cell Biology. 2008; 9(1): 47–59. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "231785",
"date": "31 Jan 2024",
"name": "Brad Sutherland",
"expertise": [
"Reviewer Expertise Cell biology",
"pharmacology",
"cell culture 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\nThis manuscript by Watts et al. presents an investigation into the mechanisms of tumour cell suppression by the alkaloid spiroleucettadine. While it has been previously shown by the authors that spiroleucettadine has anti-proliferative effects against H522 cells, the mechanisms have not been determined. The authors present some nice data showing anti-proliferative activity with varying potency of spiroleucettadine across three non-small cell lung cancer lines, and explore changes in cell cycle pathways and apoptotic proteins indicating mechanisms by which spiroleucettadine can induce cell cycle arrest and induce apoptosis. Overall, this is a solid paper highlighting novel mechanisms of action of an alkaloid that has anti-proliferative properties for non-small cell lung cancer. I have only a few comments below.\nSpecific comments:\nIt is interesting that spiroleucettadine has different potencies on different tumour cell lines. But according to figure 1A, there appears to be greater efficacy (lower viability at higher concentrations) with cell lines that have lower potency. A discussion around the differences between cell lines and how spiroleucettadine acts on these should be included. The phosphorylated CDK1 result highlights an increase with spiroleucettadine. While these results were relative to beta-tubulin levels, it is also customary to determine how phosphorylated protein changes relative to the same total protein. So phosphorylated CDK1 should be analysed relative to total CDK1 levels to show that the level of CDK1 does not influence this (which it shouldn’t as Fig 3A shows no change in CDK1 expression with spiroleucettadine). There is inconsistency with regards to the apoptosis assay as to how long spiroleucettadine was exposed to the cells for. In the methods and results text it says 24h, in figure 5A legend its says 24 or 48h, in figure 5B-E legend it says 48 hours. If it is 24h, then flow cytometry plots from 24h not 48h exposure should be shown in figure 5.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1328
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https://f1000research.com/articles/10-844/v1
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23 Aug 21
|
{
"type": "Research Article",
"title": "Environmental Uncertainty as a Moderator of Entrepreneurship Orientation and Innovation Capability during the Pandemic: A Case of Written Batik SMEs in Yogyakarta",
"authors": [
"Humam Santosa Utomo",
"Susanta Susanta",
"Susanta Susanta"
],
"abstract": "Background: Written batik is one of Indonesia's cultural heritages that must be preserved. During the Covid-19 pandemic, written batik producers in Indonesia experienced increasing challenges due to the uncertainty of the business environment. Innovation is a solution to the problems faced by SMEs during a pandemic to survive. This study aims to examine the effect of entrepreneurship orientation on innovation capability. This study also examines the role of moderating environmental uncertainty in strengthening the effect of entrepreneurship orientation on innovation capability. Methods: The research was conducted at the centre of small and medium-sized batik companies Giriloyo, Bantul, Yogyakarta, Indonesia. Respondents of this study were 130 small and medium companies selected by random sampling. The questionnaire is used as a primary data collection tool. WarpPLS has been used to analyze the effect between variables in this study. Results: Entrepreneurial orientation is an important aspect in improving the innovation capabilities of SMEs. Environmental uncertainty during the COVID-19 pandemic has strengthened the effect of entrepreneurial orientation on innovation capabilities. Conclusions: The findings of this study indicate that entrepreneurial orientation has a significant effect on innovation capabilities. Environmental uncertainty significantly strengthens the effect of entrepreneurship orientation on innovation capability.",
"keywords": [
"entrepreneurship orientation",
"innovation capability",
"environmental uncertainty",
"written batik"
],
"content": "Introduction\n\nWritten batik is one of the traditional products developed by SMEs (Small and medium-sized enterprises) in Yogyakarta, Indonesia. Indonesian batik was officially recognized by UNESCO on October 2, 2009 as an Intangible Cultural Heritage (ICH) at the UNESCO meeting in Abu Dhabi. Indonesian batik consists of written batik, printed batik, and combination batik. Written batik has a higher level of uniqueness than printed batik, so it requires a longer processing time. Giriloyo is an area where people make written batik their main livelihood. The Batik center in Giriloyo maintains and develops written batik.\n\nDuring the Covid-19 pandemic, most SMEs experienced the problem of decreasing sales due to a reduced number of buyers. Limitations on social interaction and travel has caused a decrease in tourists visiting Yogyakarta so that the demand for batik products has decreased dramatically. Environmental uncertainty increases from time to time so it is a big challenge for SMEs. The strength of SMEs in sustaining business varies during a pandemic. Entrepreneurial orientation helps businesses survive by creating innovations that are relevant to a pandemic situation. Product innovation is needed during times of crisis to serve changing market demands. SMEs can also develop marketing innovations through online media.\n\nResearch examining the effect of entrepreneurial orientation on innovation has received much attention from previous researchers1–3. Environmental uncertainty has also been examined in regard to innovation and company performance4,5. However, studies on environmental uncertainty as a moderating variable that strengthens or weakens the effect of entrepreneurship orientation on innovation during the crisis are still minimal. A company's external environment is predicted to influence the use of company resources in creating innovation. Specifically, this study aims to examine the moderating effect of environmental uncertainty on the effect of entrepreneurial orientation on innovation capability. The formulation of the research problem is as follows:\n\nRQ1: Does entrepreneurship orientation have an effect on innovation capability?\n\nRQ2: Does environmental uncertainty moderate the effect of entrepreneurship orientation on innovation capability?\n\nResource-Based View (RBV) focuses on the concept of company attributes that are difficult to imitate as a source of superior performance and competitive advantage6,7. Thus, innovation is one of the keys to organizational success to develop and survive. The use of organizational resources is directed at achieving a sustainable competitive advantage to achieve the expected performance. According to Conner8, firm performance variance depends on input ownership and the unique ability to utilize resources. The company's unique resources are difficult for competitors to imitate because they result from extended learning, a supportive cultural climate, and are not easy to buy. This study focuses on entrepreneurial orientation, which is one of the characteristics of a company as a company resource. A solid entrepreneurial orientation encourages the creation of innovations to increase company competitiveness.\n\nEntrepreneurship is the ability to think creatively and act innovatively as a basis, resource, and process to face lifestyle challenges9. Zahra & Shaker define entrepreneurship as innovation and strategic renewal10. Shane suggests that entrepreneurial processes stem from perceptions about the availability of opportunities or situations in which resources are transformed into profitable businesses11. Entrepreneurial orientation is the view of an entrepreneur which is then implemented in managing a business through creative activities, the courage to take advantage of opportunities while taking risks, and not giving up on difficult situations. Therefore entrepreneurship orientation has a positive effect on the creation of innovative products and company performance.\n\nThe rapidly changing business environment is a challenge for entrepreneurs. Changes in the business environment create uncertainty. Miller revealed that environmental uncertainty refers to the perception of the uncertainty of environmental variables that impact organizational performance12. Changes in markets, technology, and the regulatory environment are all factors that cause environmental uncertainty13,14. Market uncertainty refers to market uncertainty, changes in market structure, and the level of competition within an industry13. Regulatory uncertainty refers to the uncertainty of the actions of regulatory agencies that create and enforce regulations and policies14. SMEs can have difficulty understanding the environment and this places SMEs in challenging situations related to strategic decision making15,16. The lack of information held by SMEs further hinders SMEs in making comprehensive decisions17 which can lead to severe errors in decision making15,16,18. SMEs continue to align strategies to change the changing environment that is currently full of uncertainty19.\n\nInnovation has been generally recognized as a critical factor for company success in terms of sales growth, profit, and competitiveness20,21. Innovation capability is conceptualized into two types, namely innovation as a process and innovation as a result22. This study emphasizes the importance of innovation as a process. Hult et al. describe innovation as new processes, products, and ideas from the organization23. Thornhill defines innovation as a process that begins with an idea, namely the development of findings and the introduction of new products, processes and new services in the market24. Each company has different abilities in creating innovation. The ability to innovate describes how much strength the company has in creating creative ideas and innovations. The capability for innovation shows how much the company is able to develop new products according to market demand25. Innovation capability in the context of this research is the ability of SMEs to develop new processes, new products, or new services according to market demand during the crisis due to the Covid-19 pandemic.\n\nEntrepreneurial orientation directs the behaviour of SMEs to create innovations. Entrepreneurship-minded SMEs dare to create new products needed by the market to improve market performance marked by opening new markets and increasing sales. Lee & Hsieh found that entrepreneurship has a significant influence on innovation and performance26. The findings of Lin et al. on textile companies in Taiwan also show that entrepreneurial intensity affects innovation capabilities27. Thus, the following hypothesis can be formulated:\n\nH1: Entrepreneurship orientation has a significant effect on innovation capability.\n\nHigh environmental uncertainty causes difficulties for SMEs in determining marketing strategies so that the innovations that are set may not be following rapidly changing market demands19. The acceleration of SMEs in implementing innovation strategies is not proportional to the rapid changes in the market caused by uncertain regulations. This of course also has an impact on the marketing performance of SMEs. However, an unyielding attitude, the courage to take risks, and the courage to take advantage of every opportunity will actually trigger an entrepreneurial spirit to create new innovations during crisis times. Absorption power is stronger in external environments that are in high dynamism compared to environments with low dynamism2. Thus, environmental uncertainty is predicted to strengthen the effect of entrepreneurship orientation on innovation capability during the pandemic. Thus, the following hypothesis can be formulated:\n\nH2: Environmental uncertainty significantly strengthens the effect of orientation on innovation capability.\n\n\nMethods\n\nThis type of research is explanatory research, namely research conducted to investigate the relationship between variables. This study aims to investigate and explain the causal relationship between variables by testing hypotheses as well as providing explanations. The variables of this research consist of entrepreneurship orientation and innovation capability as an independent variable and dependent variables. The effect of these two variables is moderated by environmental uncertainties. A quantitative approach was used in analyzing this research28. The entrepreneurship orientation variable refers to Sulistyo & Siyamtinah9 and Shane11. Variable innovation capability is based on Thornhill24. Environmental uncertainty variables refer to Bstieler13 and Engau et al.14. The research was conducted in Bantul district, Yogyakarta Special Region province, Indonesia.\n\nThe population of this study were all batik SMEs in the Giriloyo batik centre, as many as 520 Batik SMEs. Written approval from the Chairperson of the Giriloyo Written Batik Group was obtained in accordance with document 8/VIII/2020. The research sample of 130 respondents was randomly selected using the Excel application. Sample size refers to the suggestion of Hair et al.29 that the sample size is at least 100 respondents if the model contains five or fewer constructs. All respondents filled out the questionnaire completely. The data collection tool is a questionnaire with a Likert scale ranging from strongly disagree to strongly agree30. Testing the validity and reliability of the instrument involved 30 respondents. The questionnaire was distributed in August 2020 offline by visiting respondents one by one to fill out the questionnaire and received approval from the Chairperson of the Batik Giriloyo SME group. Data processing used WarpPLS 6.031 to test the effect between variables in the structural model. Equivalent functions can be caried out on the open-source software R (R Project for Statistical Computing, RRID:SCR_001905).\n\n\nResults\n\nTable 1 shows the coefficient of all items ≥ 0.3 so it can be stated that the instrument produces valid data (Sekaran, 2011). The Cronbach coefficient ≥ 0.6 indicates the instrument used is reliable (Malhotra, 2010).\n\nTable 2 shows that the majority of respondents were male (76.15%), most of the entrepreneurs are 26–45 years old (53.06%). Most of the companies were > 10 years old (45.39%) and most of the respondents were married (84.62%).\n\nMeasurement of model fit and quality indices refers to the WarpPLS analysis tool31,32. The measurement results show the following. Average Path Coefficient (APC) was 0.328, p < 0.001; average R-squared (ARS) was 0.258, p < 0.001; average adjusted R-square (AARS) was 0.248, p < 0.001; average block VIF (AVIF) was 1.022, acceptable if ≤ 5; average full collinearity VIF (AFVIF) was 1.901, acceptable if ≤ 5; Tenenhaus GoF (GoF) was 0.316, acceptable if ≥ 0.25; Sympson’s Paradox Ratio (SPR) was 1,000, acceptable if ≥ 0.7; Statistical Suppression Ratio (SSR) was 1,000, acceptable if ≥ 0.7; Nonlinear Bivariate Causality Direction Ratio (NLBCDR) was 1.000, acceptable if ≥ 0.7. These results indicate that the model is supported by good data and has quality indicators that meet the requirements in the WarpPLS.\n\nHypothesis 1 states that entrepreneurship orientation influences innovation capability. The results (Table 3) show that p-value is <0.000, so hypothesis 1 is accepted. Positive coefficients indicate that entrepreneurship orientation has a significant positive effect on innovation capability.\n\n* significant at the 0.01 level\n\nHypothesis 2 states that environmental uncertainty significantly strengthens the effect of entrepreneurship orientation on innovation capability. The results (Table 3) show that the p-value is <0.000, so hypothesis 2 is accepted. Positive coefficients indicate that environmental uncertainty strengthens the effect of entrepreneurship orientation on innovation capability.\n\n\nDiscussion\n\nThe results of this study reveal two essential things in creating innovation and contributing to the field of entrepreneurship (see Figure 1). First, entrepreneurship orientation has a significant effect on innovation capability. The results of this study reinforce the argument of RBV6,7. According to RBV, competitive advantage and superior performance are the result of company attributes that are difficult to imitate by competing companies. One of the attributes or resources the company has is an entrepreneurship orientation. Entrepreneurship orientation enhances the company's innovation capabilities. These results are consistent with Lee & Hsieh who found that entrepreneurship directly affects innovation and performance26. These results support the research of Lin et al.27 on textile companies in Taiwan which concluded that high entrepreneurial intensity affects innovation ability and encourages sustainable innovation. Martínez et al. have also found that entrepreneurial orientation has a significant positive effect on company innovation1. Entrepreneurial orientation possessed by entrepreneurs includes market orientation, creative thinking, utilizing company resources effectively, and the courage to take advantage of every opportunity, the courage to take risks, and never give up on difficult situations. Entrepreneurial orientation encourages proactive behaviour so that creativity and company innovation emerge.\n\nSecond, environmental uncertainty significantly strengthens the effect of entrepreneurial orientation on innovation capability. This finding shows that high environmental uncertainty is responded to positively by entrepreneurs who have a solid entrepreneurial orientation to create innovation. Uncertainty is considered a challenge that increases the entrepreneurial spirit to survive through product and service innovation. During the Covid-19 pandemic, written batik-producing SMEs in Yogyakarta experienced a very drastic decline in sales due to declining tourism. SMEs cannot sell their products at batik outlets so their turnover has dropped dramatically. Meanwhile, the government also makes regulations on social distancing so that direct contact between consumers and producers is minimized. Environmental uncertainty is a challenge for SMEs to protect their companies from bankruptcy. This environmental uncertainty does not reduce the entrepreneurial spirit, but instead increases the entrepreneurial spirit to create innovation.\n\nIn line with the findings of Zhai et al.,2 the absorption capacity of SMEs is stronger in an external environment that has high dynamics compared to an environment with low dynamics. Efforts made by SMEs are creating product innovation and service innovation. SMEs not only add new product lines that consumers need during a pandemic, but also add online sales services through information and communication technology. SMEs adapt by utilizing online marketing techniques to serve consumers so that the marketing reach is broader and more flexible.\n\nThese findings provide a theoretical contribution. Environmental uncertainty does not always have a negative connotation, but instead triggers the ability to increase innovation. Environmental uncertainty strengthens the influence of entrepreneurship orientation on innovation ability. This finding is important and unique in the literature.\n\nThe results of this study have managerial implications for entrepreneurs and the government in fostering SMEs. Strengthening the entrepreneurial aspect must be emphasized on batik entrepreneurs because in an unstable condition, SMEs can still seize opportunities by creating innovations. Environmental uncertainty has actually spurred the spirit of SMEs to create new ideas in serving consumers. The government needs to increase its role in fostering SMEs, especially in conditions of uncertainty so that SMEs can immediately adapt to a rapidly changing environment.\n\n\nConclusions\n\nThis study found that innovation capability was determined by entrepreneurship orientation. The views and attitudes of entrepreneurs encourage the creation of new innovations in the form of innovative products and new services. Environmental uncertainty actually strengthens the role of entrepreneurship orientation in creating innovation. Entrepreneurs learn and adapt to the rapidly changing business environment. These findings contribute to the management of SMEs during times of crisis. Based on a business orientation, environmental uncertainty actually increases innovation capabilities.\n\nThis study has limitations. First, this study was conducted during the Covid-19 pandemic and did not compare to regular times, meaning longitudinal studies are needed. Second, this study does not classify the level of environmental uncertainty so that the relationship between uncertainty level and innovation is unknown. Third, this paper discusses innovation and does not yet discuss SME performance. Various innovations carried out by SMEs have not certainly had positive implications for the performance of SMEs. Likewise, entrepreneurship orientation and environmental uncertainty may have different effects on SME performance. Therefore, further research is needed to obtain more comprehensive research results.\n\n\nData availability\n\nFigshare: a dataset of research results in written batik Giriloyo, Indonesia. https://doi.org/10.6084/m9.figshare.14563521.v132\n\nThis project contains the following underlying data.\n\n• Data130 resp.cvc (questionnaire results)\n\n• KUESIONER.pdf (Blank research questionnaire).\n\n• RESULTS OF DATA PROCESSING.pdf (results of statistical analysis)\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\nEthical Consideration\n\nThis study was approved by the ethics commission for the human respondent at the Research and Community Service Institutions (LPPM) Universitas Pembangunan Nasional Veteran Yogyakarta (number: Sket/23/UN62.21/KL 00/VII/2020).\n\n\nParticipant consent\n\nWritten informed consent for participation and for publication of their data was obtained from all participants. Written approval from the Chairperson of the Giriloyo Written Batik Group was obtained in accordance with document 8/VIII/2020.",
"appendix": "Acknowledgements\n\nThe author is grateful to Universitas Pembangunan Nasional Veteran Yogyakarta for supporting this research. The authors acknowledge Santi Putri for helping this research, and Tika Amalia Sholihah who collected the samples.\n\n\nReferences\n\nEduardo J, Martínez V, Maldonado Guzmán G, et al.: The impact of entrepreneurial orientation on the innovation of SME´s in Mexico. Int J Arts Commer. 2015. Reference Source\n\nZhai YM, Sun WQ, Tsai SB, et al.: An empirical study on entrepreneurial orientation, absorptive capacity, and SMEs’ innovation performance: A sustainable perspective. Sustain. 2018; 10(2): 314. Publisher Full Text\n\nMusawa MS, Ahmad K: Entrepreneurial Orientation and Innovation Performance: The Moderating Role of Competitive Environment. J Glob Econ. 2019; 7(1): 2–7. Reference Source\n\nKraus S, Rigtering JPC, Hughes M, et al.: Entrepreneurial orientation and the business performance of SMEs: A quantitative study from the Netherlands. Rev Manag Sci. 2012; 6: 161–182. Publisher Full Text\n\nHerani R, Andersen O: Does environmental uncertainty affect entrepreneurs’ orientation and performance? empirical evidence from Indonesian SMEs. Gadjah Mada Int J Bus. 2012; 14(1). Publisher Full Text\n\nBarney J: Firm Resources and Sustained Competitive Advantage. J Manage. 1991; 17(1): 99–120. Publisher Full Text\n\nPrahalad CK, Hamel GP, Mehrotra LCS: COMPETING FOR THE FUTURE. Int J Res Found Hosp Healthc Adm. 2014. Publisher Full Text\n\nConner KR: A Historical Comparison of Resource-Based Theory and Five Schools of Thought Within Industrial Organization Economics: Do We Have a New Theory of the Firm? J Manage. 1991; 17(1): 121–154. Publisher Full Text\n\nSulistyo H, Siyamtinah: Innovation capability of SMEs through entrepreneurship, marketing capability, relational capital and empowerment. Asia Pacific Manag Rev. 2016; 21(4): 196–203. Publisher Full Text\n\nZahra SA: Predictors and financial outcomes of corporate entrepreneurship: An exploratory study. J Bus Ventur. 1991; 6(4): 259–285. Publisher Full Text\n\nShane S: A General Theory of Entrepreneurship: The Individual-Opportunity Nexus. 2003. Publisher Full Text\n\nMiller KD: Industry and Country Effects on Managers’ Perceptions of Environmental Uncertainties. J Int Bus Stud. 1993; 24: 693–714. Publisher Full Text\n\nBstieler L: The moderating effect of environmental uncertainty on new product development and time efficiency. J Prod Innov Manage. 2005; 22(3): 267–284. Publisher Full Text\n\nEngau C, Hoffmann VH: Effects of regulatory uncertainty on corporate strategy-an analysis of firms’ responses to uncertainty about post-Kyoto policy. Environ Sci Policy. 2009; 12(7): 766–777. Publisher Full Text\n\nJohnson AM, Lederer AL: The effect of communication frequency and channel richness on the convergence between chief executive and chief information officers. J Manag Inf Syst. 2005; 22(2): 277–252. Publisher Full Text\n\nXu H, Koronios A: Understanding information quality in e-Business. J Comput Inf Syst. 2005; 45(2): 73–82. Reference Source\n\nFredrickson JW, Mitchell TR: Strategic Decision Processes: Comprehensiveness and Performance in an Industry with an Unstable Environment. Acad Manag J. 1984; 27(2): 399–423. Reference Source\n\nJohnston M, Gilmore A, Carson D: Dealing with environmental uncertainty: The value of scenario planning for small to medium-sized entreprises (SMEs). Eur J Mark. 2008; 42(11/12): 1170–1178. Publisher Full Text\n\nPadukkage A, Hooper V, Toland J: Implications of environmental uncertainty for business-IT alignment: A comparative study of SMEs and large organizations. In: ACIS 2015 Proceedings - 26th Australasian Conference on Information Systems. 2015; 115. Reference Source\n\nBattor M, Battor M: The impact of customer relationship management capability on innovation and performance advantages: testing a mediated model. J Mark Manag. 2010; 26(9–10): 842–857. Publisher Full Text\n\nSivadas E, Dwyer FR: An examination of organizational factors influencing new product success in internal and alliance-based processes. J Mark. 2000; 64(1): 31–49. Publisher Full Text\n\nSaunila M: Innovation capability in SMEs: A systematic review of the literature. J Innov Knowl. 2020; 5(4): 260–265. Publisher Full Text\n\nHult GTM, Hurley RF, Knight GA: Innovativeness: Its antecedents and impact on business performance. Ind Mark Manag. 2004; 33(5): 429–438. Publisher Full Text\n\nThornhill S: Knowledge, innovation and firm performance in high- and low-technology regimes. J Bus Ventur. 2006; 21(5): 687–703. Publisher Full Text\n\nAdler P, Shenbar A: Adapting your technological base: the organizational challenge. Sloan Manage Rev. 1990. Reference Source\n\nLee JS, Hsieh CJ: A Research In Relating Entrepreneurship, Marketing Capability, Innovative Capability And Sustained Competitive Advantage. J Bus Econ Res. 2010. Reference Source\n\nLin SF, Miao2 Q, Nie K: A case study on entrepreneurship for sustained innovation. AFRICAN J Bus Manag. 2012; 6(2): 493–500. Publisher Full Text\n\nKerlinger FN: Asas-asas Penelitian Behavioral. Yogyakarta UGM Press xiii. 2010.\n\nHair JF, Anderson RE, Tatham RL, et al.: Multivariate Data Analysis, Multivariate Data Analysis. 2018.\n\nUtomo HS, Susanta S: Giriloyo Written Batik Research Questionnaire. 2021. Publisher Full Text\n\nKock N: WarpPLS 5.0 User Manual. 2015; 45. Reference Source\n\nUtomo HS, Susanta S: a dataset of research results in written batik Giriloyo, Indonesia. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14563521.v1"
}
|
[
{
"id": "92922",
"date": "07 Sep 2021",
"name": "Reni Shinta Dewi",
"expertise": [
"Reviewer Expertise Knowledge Management",
"RBV",
"HRM",
"Strategic 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\nBackground:\nAll industries are affected by The Covid-19 Pandemic, but why only written batik is reviewed. Give the evidence support. The urgency of this research has not been explored.\n\nConceptual Model:\nThe model is not clearly especially the explanation for the path of Environmental Uncertainty as a moderator variable.\n\nMethod of Research:\nThe population is 520, but your sample is 130. Can you clarify how you got it. And How do you make sure your sample complies with random requirement. You should be defines the entrepreneurial orientation with clearly, because one of your dimension is market orientation. You should explain how to building the capability that direct connect with market orientation.\n\nDiscussion and Conclusion:\nIn your article said that: According to RBV, competitive advantage and superior performance are the result of company attributes that are difficult for competing companies to imitate. One of the attributes or resources owned by the company is an entrepreneurial orientation.\n\nProve the theoretical and empirical support of the statement.\n\nWhat your advise for the future research?\n\nWhat the managerial implication for the SME?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "150655",
"date": "21 Sep 2022",
"name": "Andreas Walmsley",
"expertise": [
"Reviewer Expertise Entrepreneurship",
"Entrepreneurship Education",
"SMEs",
"Career 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\nA timely study that adds to the literature seeking to understand and explain the relationship between environmental change and levels of innovation. The relationship between Entrepreneurial Orientation and Innovation Capability is explored and then Environmental Uncertainty is added as a moderator. The authors recognise some limitations of the study in the conclusion and yet there is sufficient originality and novelty here to merit publication. I think other researchers will be able to draw on these findings in testing some of the hypothesised relationship and also developing more complex models. That said, it is in part the simplicity of the model that is being tested that is one of the paper’s strengths.\nI have only one recommendation and that is that the authors are consistent in the use of either the term ‘entrepreneurial orientation’ or ‘entrepreneurship orientation’. Similarly, the author changes between innovation capability and innovation ability. I would recommend being consistent here too.\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/10-844
|
https://f1000research.com/articles/10-1270/v1
|
10 Dec 21
|
{
"type": "Research Article",
"title": "Antenatal care visits performance among unmarried women in Indonesia: Does unintended pregnancy matter? A cross-sectional study",
"authors": [
"Ratna Dwi Wulandari",
"Agung Dwi Laksono",
"Nikmatur Rohmah",
"Agung Dwi Laksono",
"Nikmatur Rohmah"
],
"abstract": "Background: Unmarried women who experience unintended pregnancy tend to hide their pregnancy and not attend pregnancy care services. The study analyzed the effect of unintended pregnancy on antenatal care (ANC) visits among unmarried women in Indonesia. Methods: The study employed secondary data from the Indonesian Demographic and Health Survey (IDHS) 2017. This cross-sectional study involved unmarried women aged 15-49 years old who gave birth in the last five years. The 2017 IDHS used stratification and multistage random sampling, and the task obtained 508 respondents as samples. The variables analyzed included ANC visits, unintended pregnancy, residence, age, marital status, education, employment, wealth, and health insurance ownership. The study used the binary logistic regression test at the final stage. Results: The results show that unmarried women who had an unintended pregnancy were 0.588 times more likely than those who did not have an unintended pregnancy to have ANC visits ≥ four times (AOR 0.588; 95% CI 0.587-0.588). The analysis indicates that unmarried women who have an unintended pregnancy in Indonesia are less likely to complete ANC visits. Apart from unintended pregnancy, the study found seven other independent variables as significant determinants of ANC visit performance: type of residence, age group, marital status, education level, employment status, wealth status, and health insurance ownership. Conclusion: The study concluded that unmarried women who experienced an unintended pregnancy in Indonesia were less likely to complete ANC visits.",
"keywords": [
"Unintended pregnancy",
"antenatal care",
"maternal health",
"unmarried women",
"public health"
],
"content": "Introduction\n\nDuring 2015-2019, there were at least 121.0 million unintended pregnancies each year.1 Unintended pregnancy is untimely, unplanned, unwanted at conception, or pregnancy which occurs earlier than desired.2 The definition of unintended pregnancies has complex considerations. The condition influenced the terms by how they (a person or the partner) feel about the pregnancy itself, or generally, their reproductive plans. Unintended pregnancy occurs when a woman wishes to become pregnant at a future date but not at the time she became pregnant, or pregnancy occurs when the woman does not want to become pregnant at the time or at any time in the future.3 Unintended pregnancy can result from not using contraception or using contraception inadequately during sex. Despite having no desire to become pregnant, women with low perceived susceptibility were more likely not to have used contraception at the previous sex.4\n\nUnintended pregnancy has the risk of causing various disorders to women and their babies. Women who experience unintended pregnancy are at risk of experiencing decreased physical function, general health, vitality, and social function. The mental health of women who experienced an unintended pregnancy was 9.19 times more likely to decline than women with a desired pregnancy. Women with unintended pregnancies are at risk of developing poor mental health in the future, depression, and parenting stress.5–7 Besides, other threats that can occur are increased body weight during inadequate pregnancy, the increased risk of giving birth by Sectio Caesarea, the duration of breastfeeding is shorter, and children born from unintended pregnancy at the age of under five have a low developmental score.8,9 Various conditions that arise from unintended pregnancy can threaten a woman's health during pregnancy and childbirth and affect the infant's birth development.\n\nThe government should take measures to reduce unintended pregnancy. However, the reality is that unintended pregnancy in Indonesia is still relatively high. For example, the proportion of unintended pregnancy among women of childbearing age in Indonesia was 15.4% in 201210 and increased to 16.3% in 2020.11\n\nMost unintended pregnancies occur in women with the intention of not wanting any more children.11 Women with high parity and experiencing pregnancy complications are more likely to experience unintended pregnancy.12 Meanwhile, the majority of unintended pregnancies in Indonesia occurred in married women. As many as 3.26% of unintended pregnancies occurred in women who were never married or had no partners (widows).12 Moreover, a study conducted by Rohmah et al. reported that pregnancy among teenagers in Indonesia was 5.7% in women who were not married or had no partners.13 Although the proportion of unintended pregnancies among unmarried women in Indonesia is small, the problems they cause are more complex than those of married women.\n\nPregnancy in unmarried women is much more likely to happen accidentally and have adverse effects.14 In a qualitative study in the Nagari Sungayang community, one of Indonesia's western regions, an unmarried woman's pregnancy is considered an act that religion prohibits. The situation contradicts the traditional values and culture of the local community.15 On the other hand, in Indonesia, where most of the population is Muslim; they believe that a child born due to pregnancy outside or before a legal marriage is considered a child born out of adultery.16 Therefore pregnancy for an unmarried woman is regarded as a disgrace. Some people try to cover up this disgrace by getting married even though their age is not sufficient. As a result, underage marriages occur, causing depression, anxiety, fear, and stress.17\n\nThe main burden of unintended pregnancy for single or divorced/widowed women is physical changes during pregnancy. The added responsibility is gaining a negative status from society. The unfavorable position of this society is even more dominant for unmarried women. Some of the burdens of unmarried mothers due to pregnancy outside of marriage include the financial responsibility of child care, conflict, no support from family, negative labels from others, and past regrets.18 Women who are unable to bear the burden of unintended pregnancy often decide to have an abortion. During 2010-2014, 59% of unintended pregnancies in developed countries and 55% of unintended pregnancies in developing countries ended with abortion.19 During 2015-2019 the proportion of unintended pregnancies that ended with abortion increased.1 Thus, women bear a double burden, and if they were making inappropriate decisions about unintended pregnancy, it would create more complex problems. These problems include medical complications due to unhealthy abortion, post-traumatic stress, the legal burden of an abortion, socioeconomic issues, childbirth in adolescence, and more susceptibility to divorce if women carried out marriage after pregnancy.19\n\nUnintended pregnancy in unmarried women is one of the most difficult challenges faced by the health system. A previous study reported the case of an unmarried woman who became pregnant twice out of wedlock and had not received antenatal care (ANC) services, either in the public or private health sector. We should note that unmarried women who experience unintended pregnancy tend to hide their pregnancies and not carry out pregnancy care.10 Unmarried women are less innovative in finding information related to pregnancy.14 Considering the huge impact caused by unintended pregnancy on unmarried women, it is necessary to evaluate the implementation of ANC. This evaluation aims to ensure that unmarried women receive adequate services during pregnancy and obtain good delivery outcomes. Based on the background narration, the study aims to analyze the effect of unintended pregnancy on ANC visits performance among unmarried women in Indonesia.\n\n\nMethods\n\nThe research used secondary data from the Indonesian Demographic and Health Survey in 2017 (the 2017 IDHS). The 2017 IDHS is part of the Demographic and Health Survey (DHS) series conducted by the Inner City Fund (ICF). The ICF designed the 2017 IDHS sampling design to be able to present national and provincial estimates.\n\nImplementation of the 2017 IDHS used four types of questionnaires: households, women of childbearing age, married men, and young men. This study specifically took a sub-sample of women of childbearing age, with criteria aged 15-49 years. The survey used the household questionnaire to record all household members and guests who stayed the night before the interview in the selected households. The primary purpose of this household questionnaire is to determine respondents who are eligible to be interviewed individually (eligible respondents). Data collection carried out on women of childbearing age refers to the 2015 DHS phase 7 questionnaire, which accommodates several of the latest issues according to international comparability. The survey conducted data collection between 24 July - 30 September 2017.\n\nThe 2017 IDHS determined samples through stratification and multistage random sampling. The survey collected 50,730 eligible women in the final stage and successfully interviewed 49,627 women (97.8%).\n\nIn this study, the 2017 IDHS was chosen as the analysis material because it can estimate national representation. The data used in this study are from the 'IDIR71FL_Individual Recode' dataset of the Indonesia 2017 Standard DHS. The analytical research units were unmarried women aged 15-49 years who gave birth in the last five years (IDIR71FL_Individual Recode dataset).\n\nSome respondents do not represent the desired population in the study. To avoid bias, the study defines a target population with a sample of only unmarried women of childbearing age who have given birth in the last five years. In this study, the researcher carried out the sampling step by selecting based on two criteria: marital status (never in a union, or widowed, or divorced, or no longer living together/separated) and giving birth in the last five years. In the final, the study described 508 women as the sample.\n\nThe study employed ANC visits as an outcome variable. The Ministry of Health of the Republic of Indonesia recommends that the ANC be performed at least four times during pregnancy, i.e. one time in the first trimester, one time in the second trimester, and two times in the third trimester.20 Therefore, the operational description of ANC utilization used in this study was the respondent's awareness of ANC use during pregnancy. The ANC used consists of two parameters, namely < four visits and ≥ four visits.21\n\nThe research used unintended pregnancy as an exposure variable. The study defines unintended pregnancy as an unwanted pregnancy or mistimed pregnancy. Women endured an unwanted pregnancy when they did not want to be pregnant or have any children. However, a mistimed pregnancy occurred at this time when a woman did not want to be pregnant, but later.22 The unintended pregnancy consists of two categories: no and yes.\n\nApart from unintended pregnancy, other independent variables, as control variables, were analyzed: residence type, age group, marital status, education level, employment status, wealth status, and health insurance ownership. The residence type consists of urban and rural. The age group consists of seven categories: 15-19 years, 20-24 years, 25-29 years, 30-34 years, 35-39 years, 40-44 years, and 45-49 years. Marital status consists of two classifications: never in a union and divorced/widowed. Meanwhile, education level consists of four categories: no formal education, primary, secondary, and higher. Employment status consists of two types: unemployed and employed. Finally, the health insurance ownership consists of the uninsured and insured.\n\nThe IDHS measured wealth status based on the wealth quintile of each family. Households were scored based on the number and types of existing items, such as televisions, bicycles, cars, and housing characteristics, such as drinking water sources, sanitation facilities, and primary flooring materials. The study calculated scores of these variables using the principal component analysis. National wealth quintiles were arranged based on household scores for each person in the household and then divided by the distribution into the same five categories, of which accounted for 20% of the population, namely quintile 1 (poorest), quintile 2 (poorer), quintile 3 (middle), quintile 4 (richer), and quintile 5 (richest).23\n\nThe researcher used the Chi-Square test to see the relationship between ANC visit performance and other variables in the initial stage. Then, the researcher employed binary logistic regression to determine the predictors and see their odds ratios in the final step. The analysis carried out all the statistical processes using the IBM SPSS Statistic 21 software.\n\nMoreover, the researchers created a distribution map of the percentage of unintended pregnancy among unmarried women by the province in Indonesia. The study issued a shapefile of administrative boundary polygons by the Indonesian Bureau of Statistics for the task.\n\nThe 2017 Indonesia DHS follows the Standard DHS survey protocol under The Demographic and Health Surveys (DHS) Program (DHS-7) approved by The Institutional Review Board of Inner City Fund (ICF) International, which was previously reviewed and approved by the ORC Macro IRB in 2002. DHS surveys that follow the standard are categorized under the approval of the DHS-7 Program, and the approval document is attached. The Institutional Review Board of ICF International complied with the United States Department of Health and Human Services requirements for the Protection of Human Subjects (45 CFR 46).\n\nThe IDHS removed from the dataset the names of the respondents. Besides, for their participation in this report, the respondents have given written approval. The IDHS obtained informed consent from all subjects. For participants under 18 years, the survey received informed consent from a parent or legal guardian. On https://dhsprogram.com, the authors have obtained permission to use ICF International's 2017 IDHS dataset.\n\n\nResults\n\nThis study presents the distribution map of the percentage of unintended pregnancy among unmarried women by the province in Indonesia in Figure 1. The figure shows a trend towards a higher distribution of unintended pregnancy rates in Indonesia's central region.\n\nTable 1 shows the descriptive statistics of unmarried women in Indonesia. Table 1 shows that unmarried women in both ANC visit categories controlled those who did not experience an unintended pregnancy.\n\n*** p < 0.001.\n\nBased on the type of residence, unmarried women living in rural areas drove both ANC visits categories. Meanwhile, unmarried women in the 20-24 age group dominated the ANC visits category < four times based on the age group. Moreover, unmarried women aged 25-29 populated the ANC category for ≥ four visits.\n\nTable 1 shows that the marital status of unmarried women with the divorced/widowed category occupied the two types of ANC visits. However, according to education level and employment status, unmarried women with secondary education and employment dominate the two categories of ANC visits.\n\nBased on wealth status, the most deficient unmarried women occupied both categories of ANC visits. However, according to health insurance ownership, uninsured unmarried women dominate the ANC visits < four times. Meanwhile, in various ANC visits ≥ four times, the two types of health insurance ownership have an equal frequency.\n\nTable 2 shows the results of binary logistic regression of ANC visit performance among unmarried women in Indonesia. This final stage analysis uses “ANC visits < four times” as a reference.\n\n*** p < 0.001; AOR: adjusted odds ratio; CI: confidence interval.\n\nTable 2 shows that unmarried women who experienced an unintended pregnancy were 0.588 times less likely than those who did not experience an unintended pregnancy to have ANC visits ≥ four times (AOR 0.588; 95% CI 0.587-0.588). Thus, this analysis indicates that unmarried women who have an unintended pregnancy in Indonesia are less likely to complete ANC visits.\n\nApart from unintended pregnancy, the study found all the independent variables as a significant determinant of ANC visit performance. Based on the type of residence, unmarried women living in rural areas are 1.406 times more likely than unmarried women living in urban areas to make ANC visits ≥ four times (AOR 1.406; 95% CI 1.405-1.407). These results indicate that living in rural areas is a protective factor for unmarried women to complete ANC visits.\n\nTable 2 also indicates that the age group is a determinant of the ANC visits performance. For example, unmarried women in the 20-24 age group were 1.276 times more likely than unmarried women in the 15-19 age group to have ANC visits ≥ four times (AOR 1.276; 95% CI 1.274-1.277). Meanwhile, unmarried women in the 35-39 age group were 2.414 times more likely than unmarried women in the 15-19 age group to have ANC visits ≥ four times (AOR 2.414; 95% CI 2.411-2.417). Moreover, unmarried women in the 45-49 age group are 35.009 times more likely than unmarried women in the 15-19 age group to have ANC visits ≥ four times (AOR 35.009; 95% CI 34.849-35.170).\n\nAccording to marital status, unmarried women never in union are 1.513 times more likely than unmarried women who are divorced/widowed to have ANC visits ≥ four times (AOR 1.513; 95% CI 1.511-1.516). Thus, unmarried women who have experienced marriage in Indonesia are less likely to have complete ANC visits.\n\nThe analysis also found that women in all education levels were more likely than those with no education to make ≥ four ANC visits. Unmarried women with primary education were 4.404 times more likely than unmarried women to have ANC visits ≥ four times (AOR 4.404; 95% CI 4.396-4.412). Unmarried women with secondary education are 4.875 times more likely to make ANC visits ≥ four times (AOR 4.875; 95% CI 4.867-4.883). Besides, unmarried women with higher education are 2.504 times more likely than unmarried women to make ANC visits ≥ four times (AOR 2.504; 95% CI 2.499-2.509).\n\nBased on employment status, employed unmarried women have a probability of 1.305 times than unemployed unmarried women to make ANC visits ≥ four times (AOR 1.305; 95% CI 1.304-1.306). This information shows that employment is a protective factor for unmarried women in Indonesia to complete ANC visits.\n\nThe binary logistic regression results found that all wealth status categories were more likely than the poorest to complete ANC visits. Unmarried women with the more deficient category's wealth status are 2.073 times more likely than the most deficient unmarried women to make ANC visits ≥ four times (AOR 2.073; 95% CI 2.072-2.075). Unmarried women with a wealth status in the middle category are 3.010 more likely to make ANC visits ≥ four times (AOR 3.010; 95% CI 3.008-3.013). Unmarried women with wealth status in the more affluent category were 2.313 times more likely than the poorest unmarried women to make ANC visits ≥ four times (AOR 2.313; 95% CI 2.311-2.315). Moreover, the richest unmarried women have 3,950 times the probability of making ANC visits ≥ four times than the most deficient unmarried women (AOR 3.950; 95% CI 3.946-3.955).\n\nFinally, according to health insurance ownership, insured unmarried women have a probability of 1.219 times more likely than uninsured unmarried women to make ANC visits ≥ four times (AOR 1.219; 95% CI 1.218-1.220). This analysis indicates that insured is a protective factor for unmarried women in Indonesia to complete ANC visits.\n\n\nDiscussion\n\nThe analysis found that unmarried women who had an unintended pregnancy in Indonesia were less likely to complete ANC visits. Less than optimal prenatal care in women with an unintended pregnancy is common in many countries on various continents, such as Africa, Asia, the USA, and Europe.24 Several previous studies in the USA, Iran, Kenya, and Ethiopia also revealed a strong association between pregnancy unwantedness and the frequency and timing of ANC visits.25–29\n\nMany factors can explain the finding, including socio-cultural and psychological factors. Marriage in Indonesia symbolizes a religious, social order while experiencing pregnancy in an unmarried woman will carry social stigma.30,31 The health value of people who share extramarital incubation, which the community sees as a disgrace, is considered less important than social values. By conducting ANC visits, the surrounding community will be aware of extramarital pregnancies, a massive social threat. The women even felt stigma until the fetus in the womb grew into a child and had a severe psychological impact.31\n\nSocial stigma and psychological burden for unmarried women who experience pregnancy do not only occur in Indonesia. In many communities in some developing countries, unmarried woman pregnancies tend to be associated with poverty and low education.32 For example, a study in Sri Lanka found that women who became pregnant outside of wedlock realized that they had violated social norms, so they tended to blame themselves; some even attempted suicide.33\n\nThis study indicates that living in rural areas is a protective factor for unmarried women to complete ANC visits. The situation means that unmarried women living in rural areas have better ANC visits than unmarried women in cities. Rural regions in Indonesia are characterized by high community awareness and togetherness compared to urban areas. Social relations in rural communities are heightened and tend to last longer,34 thus building a good interaction pattern who cares about each other in the neighborhood. Bullying and negative social sanctions are not common in rural areas due to the politeness culture, which is still firmly attached.35 Thus, we felt this condition reduces the psychological burden of a woman who experiences an unwanted pregnancy.\n\nContrary to rural areas, urban areas have more modern culture, and politeness in the interaction pattern is lower. As a result, there is a fear among women who experience unwanted pregnancies of receiving bullies from their environment.36,37 This phenomenon makes women with unintended pregnancies in urban areas reluctant to have regular pregnancy checks.\n\nThe study also found age group as a determinant of the ANC visits performance. Although previous research has found variations in knowledge about pregnancy health, the older the mother is during pregnancy, more aware they are of their health risk.38,39 The situation influences the decision-making of pregnant women whether to use ANC according to standards or not. The study results can explain why the ANC of four visits is significant in the 45-49 year age group. The results align with a lesson in Thailand that found that pregnant women over 35 years old had the highest score in promoting completed ANC visits.40\n\nSeveral other studies widely revealed the low utilization of ANC in the age group of 15-19 years old.41,42 The incidence of unwanted pregnancy at an early age is generally experienced by those who are still students. The younger the gestational age, the higher the social burden borne by the family. Adolescents who experience unintended pregnancies tend to be in a terrible condition, feel sad, depressed, and not receive support from their parents.43 The situation is their barrier to utilizing ANC according to standards.\n\nUnmarried women who have experienced marriage in Indonesia are less likely to have complete ANC visits. The status of widowed or divorced in several regions in Indonesia is stigmatized, especially for those who became divorced.30 This stigmatization will undoubtedly worsen for widows or divorced women who experience pregnancy because the “naughty woman” label will be attached.31 The socio-psychological burden faced by widows or divorced women who experience unwanted pregnancies is much heavier than the other women's. The situation was what became an obstacle for the widow or divorced women to carry out ANC checks regularly. Many previous studies have found that widows or divorced women are more likely to experience unsafe sex because doing it without contraception.12\n\nMeanwhile, the study results found that all education levels led a better chance of making ANC visits ≥ four times than no education. These results indicate that the higher a person's education, the higher her understanding of pregnancy risk.44,45 Even though pregnant women still feel the social burden, higher education can better control the situation. Educated pregnant women can choose healthier behavior due to sufficient background knowledge.46 Several other studies have shown a direct influence between education and health behavior in pregnant women.46,47 Finally, several previous studies often found education a strong determinant of better health sector performance.48–51\n\nOn the other side, the results of the analysis indicate that the employment is a protective factor for unmarried women in Indonesia to complete ANC visits. Society saw working women as more independent women. Some jobs also require specific educational levels. Thus, working women generally have a more educated social environment than women who do not work.52 There is a growing trend of women joining the workforce, and more and more women are working in the formal sector. The condition is in line with the increasing education level of women.53 The higher a person's education level, the more modern their mindset tends to be, accepting changes more efficiently, and being more resilient. Previous research has shown that working women's self-image is higher than that of unemployed women.54 Women with a better self-image can better control their behavior, including being more independent in making decisions about their health. These conditions make employment a protective factor for unmarried women who experience unintended pregnancies.\n\nMoreover, results of the binary logistic regression test found that women in all the above poorest wealth status categories are more likely than the poorest to complete ANC visits. This study's products align with previous research that found that wealth significantly affects the fair use of antenatal care.55 Previous studies have also confirmed inequality in receiving health services between the rich and the poor.56\n\nFinally, the analysis found that insurance ownership is a protective factor for unmarried women in Indonesia to complete ANC visits. However, spending to pay for health services remains a consideration in utilizing health services. Health insurance participants no longer need to think about paying for the health services they receive. Meanwhile, people who do not have health insurance still have to pay a fee every time they attend health services. The condition is a barrier to health services for people who do not have insurance.57 Even though Indonesia's primary health services can be obtained free of charge for ANC services, not all people access the Puskesmas (public health centers).58 In Indonesia, many people use private practicing midwives to receive ANC services, namely 40.5%, because private practicing midwives are more affordable.59 Of course, people who do not have health insurance have to pay a fee to receive ANC services from private midwives. It becomes natural if people do not have insurance, the ANC utilization rate is lower than those with insurance.\n\nThe author performed the analysis using a secondary dataset from the 2017 IDHS to analyze the phenomenon superficially because it was unable to capture the reasons behind each finding. Several previous studies could not capture the complexity of the problem of unmarried women's in Indonesian culture.60–62 As a result, we require more qualitative research to capture the reason for each phenomenon.\n\n\nConclusions\n\nBased on the analysis results, the study concluded that women who experienced an unintended pregnancy in Indonesia had a lower probability of having complete ANC visits. Apart from unintended pregnancy, the study also found seven independent variables to determine ANC visit performance. The seven variables are residence, age group, marital status, education level, employment, wealth status, and health insurance ownership.\n\n\nData availability\n\nData used in this study are from the IDIR71FL_Individual Recode dataset of the Indonesia 2017 Standard DHS, available from the Demographic and Health Survey (DHS) website https://dhsprogram.com. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.",
"appendix": "Acknowledgments\n\nThe author would like to thank ICF International, which has agreed to allow the author to analyze the 2017 IDHS dataset in this article.\n\n\nReferences\n\nBearak J, Popinchalk A, Ganatra B, et al.: Unintended pregnancy and abortion by income, region, and the legal status of abortion: estimates from a comprehensive model for 1990–2019. Lancet Glob Health. 2020; 8(9): e1152–e1161. PubMed Abstract | Publisher Full Text\n\nCDC: Unintended Pregnancy. Reprod Health. 2019; 1.\n\nGuttmacher: Unintended Pregnancy in the United States. Guttmacher Institute; 2019; 1.\n\nBritton LE, Judge-Golden CP, Wolgemuth TE, et al.: Associations Between Perceived Susceptibility to Pregnancy and Contraceptive Use in a National Sample of Women Veterans. Perspect Sex Reprod Health. 2019; 51(4): 211–218. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAli A: Relationship between unwanted pregnancy and health-related quality of life in pregnant women. J Coll Physicians Surg Pak. 2016; 26(6): 507–512. PubMed Abstract | Publisher Full Text\n\nHerd P, Higgins J, Sicinski K, et al.: The implications of unintended pregnancies for mental health in later life. Am J Public Health. 2016; 106(3): 421–429. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBahk J, Yun SC, Kim Y-m, et al.: Impact of unintended pregnancy on maternal mental health: A causal analysis using follow up data of the Panel Study on Korean Children (PSKC). BMC Pregnancy Childbirth. 2015; 15(1): 1–12. Publisher Full Text\n\nOmani-Samani R, Ranjbaran M, Mohammadi M, et al.: Impact of Unintended Pregnancy on Maternal and Neonatal Outcomes. J Obstet Gynecol India. 2018; 69(May): 136–141. Publisher Full Text\n\nFoster MA, Hofmeister MG, Kupronis BA, et al.: Increase in Hepatitis A Virus Infections — United States, 2013–2018. Morb Mortal Wkly Rep. 2019; 68: 413–415. Publisher Full Text\n\nDini LI, Riono P, Sulistiyowati N: The Effect of Unwanted Pregnancy Status on Maternal Behavior During Pregnancy and After Birth in Indonesia (Pengaruh Status Kehamilan Tidak Diinginkan Terhadap Perilaku Ibu Selama Kehamilan Dan Setelah Kelahiran Di Indonesia). J Kesehat Reproduksi. 2016; 7(2): 119–133.\n\nSupriyatna DFST, Wilopo SA: The fertility intentions of women of childbearing age and unwanted pregnancies in Indonesia: analysis of 2020 Performance Monitoring and Accountability data (Intensi fertilitas wanita usia subur dan kehamilan tidak diinginkan di Indonesia: analisis data). Ber Kedokt Masy. 2020; 34(5): 185–193.\n\nSaptarini I, Suparmi S: Determinants of Unwanted Pregnancy in Indonesia (Determinan Kehamilan Tidak Diinginkan Di Indonesia). J Kesehat Reproduksi. 2016; 7(1) Publisher Full Text\n\nRohmah N, Yusuf A, Hargono R, et al.: Determinants of teenage pregnancy in Indonesia. Indian J Forensic Med Toxicol. 2020; 14(3): 2080–2085.\n\nRahmadi I, Ocviyanti D: Unintended pregnancy in unmarried women in Indonesia. In: Obstetric and Gynecology Case Report.2020; p. 21–7.\n\nFauziah R, Erianjoni E: Community Response to Pregnant Women Before Marriage in Nagari Sungayang, Sungayang District, Tanah Datar Regency (Respon Masyarakat Pada Perempuan Yang Hamil Sebelum Menikah Di Nagari Sungayang Kecamatan Sungayang Kabupaten Tanah Datar). J Perspekt J Kaji Sosiol dan Pendidik. 2019; 2(3): 302–309.\n\nUlfah M: Out of wedlock Pregnant Woman: Child Status (Wanita Hamil Di Luar Nikah: Status Anak). J Pembaharuan Huk. 2015; II(3): 329–334.\n\nAsman A: Underage Marriage Due to Pregnancy Outside of Marriage and Psychological Impacts on Children in Makrampai Village, West Kalimantan (Pernikahan di Bawah Umur Akibat Hamil di Luar Nikah dan Dampak Psikologis Pada Anak di Desa Makrampai Kalimantan Barat). Al-Istinbath J Huk Islam. 2019; 4(1): 79. Publisher Full Text\n\nYulianingsih AD, Masykur AM, Psikologi F, et al.: The Experience of Adolescents as Single Mother: Phenomenology Study of Girls Who Experiencing Married By Accident (Pengalaman Remaja Sebagai Single Mother: Studi Fenomenologi Pada Remaja Perempuan Yang Mengalami Married By Accident). J Empati. 2019; 8(1): 200–211.\n\nBearak J, Popinchalk A, Alkema L, et al.: Global, regional, and subregional trends in unintended pregnancy and its outcomes from 1990 to 2014: estimates from a Bayesian hierarchical model. Lancet Glob Health. 2018; 6(4): e380–e389. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNational Population and Family Planning Board, Statistics Indonesia, Ministry of Health, The DHS Program: The 2017 Indonesia Demographic and Health Survey. Jakarta: 2018. Reference Source\n\nLaksono AD, Rukmini R, Wulandari RD: Regional disparities in antenatal care utilization in Indonesia. PLoS One. 2020; 15(2): e0224006. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRizvi F, Williams J, Hoban E: Factors Influencing Unintended Pregnancies amongst Adolescent Girls and Young Women in Cambodia. Int J Environ Res Public Health. 2019; 16(20): Article number 4006. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWulandari RD, Qomarrudin MB, Supriyanto S, et al.: Socioeconomic Disparities in Hospital Utilization among Elderly People in Indonesia. Indian J Public Heal Res Dev. 2019; 10(11): 1800–1804.\n\nHajizadeh M, Nghiem S: Does unwanted pregnancy lead to adverse health and healthcare utilization for mother and child? Evidence from low- and middle-income countries. Int J Public Heal. 2020; 65: 457–468. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlene M, Yismaw L, Berelie Y, et al.: Prevalence and determinants of unintended pregnancy in Ethiopia: A systematic review and meta-analysis of observational studies. PLoS One. 2020; 15(4): Article number e0231012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbame DE, Abera M, Tesfay A, et al.: Relationship between unintended pregnancy and antenatal care use during pregnancy in Hadiya Zone, Southern Ethiopia. J Reprod Infertil. 2019; 20(1): 42–51. PubMed Abstract | Free Full Text\n\nOchako R, Gichuhi W: Pregnancy wantedness, frequency andtiming of antenatal care visit among women of childbearing age in Kenya. Reprod Health. 2016; 13(51): 51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSayehmiri K, Ebtekar F, Zarei M, et al.: Prevalence of unwanted pregnancy among Iranian women: An updated meta-analysis. BMC Pregnancy Childbirth. 2019; 19(1): Article number 491. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRice WS, Turan B, Stringer KL, et al.: Norms and stigma regarding pregnancy decisions during an unintended pregnancy: Development and predictors of scales among young women in the U.S. South. PLoS One. 2017; 12(3): Article number e0174210. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAustralian Goverment: Refugee Review Tribunal: Country Advice Indonesia.2010; p. 1. Reference Source\n\nPurbanova R, Demartoto A, Murti B: Social Development of Children Under-Five as the Impact of Extramarital Pregnancy. J Matern Child Health. 2017; 2(3): 214–222.\n\nAfrose T, Chattopadhyay A, Habib N, et al.: Adolescent pregnancy, a social stigma. MOJ Anat Physiol. 2015; 1(5): 116–120. Publisher Full Text\n\nJordal M, Wijewardena K, Olsson P: Unmarried women's ways of facing single motherhood in Sri Lanka - a qualitative interview study. BMC Womens Health. 2013; 13(1): Article number 5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHerdiana D: The Impact of Housing Development on The Social Change of Villagers (Case of Jayamekar Village, Bandung Barat District). J Pembang Wil dan Kota. 2018; 14(4): 265–280. Publisher Full Text\n\nPermatasari L: Difference in High and Low Bullying Behavior in Adolescent in the City and in the Village. Sanata Dharma University; 2016. Reference Source\n\nJamaludin AN: Urban Sociology Understanding Urban Society and Its Problems (Sosiologi Perkotaan Memahami Masyarakat Kota dan Problematikanya). Bandung: CV Pustaka Setia.2015; 55 p. Reference Source\n\nWulandari RD, Laksono AD, Rohmah N: Urban-rural disparities of antenatal care in South East Asia: a case study in the Philippines and Indonesia. BMC Public Health. 2021; 21: Article number 1221. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRajbanshi S, Norhayati MN, Hazlina NHN: High-risk pregnancies and their association with severe maternal morbidity in Nepal: A prospective cohort study. PLoS One. 2020; 15(12): Article number e0244072. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWulandari RD, Laksono AD, Nantabah ZK: Effect of Marital Status on Completeness of Antenatal Care Visits among Childbearing Age Women in Rural Indonesia. Medico-Legal Updat. 2020; 20(4): 1432–1437.\n\nThaewpia S, Howland L, Clark M, et al.: Relationships among Health Promoting Behaviors and Maternal and Infant Birth Outcomes in Older Pregnant Thais. Pac Rim Int J Nurs Res. 2013; 17(1): 28–38. Reference Source\n\nMekonnen T, Dune T, Perz J: Maternal health service utilisation of adolescent women in sub-Saharan Africa: A systematic scoping review. BMC Pregnancy Childbirth. 2019; 19(1): Article number 366. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAtuhaire S, Mugisha J: Determinants of antenatal care visits and their impact on the choice of birthplace among mothers in Uganda: a systematic review. Obs Gynecol Int J. 2020; 11(1): 77–81. Publisher Full Text\n\nAziato L, Hindin M, Maya E, et al.: Adolecents' Responses to an Unintended Pregnancy in Ghana: a Qualitative Study. J Pediatr Adolesc Gynecol. 2016; 29(6): 653–658. PubMed Abstract | Publisher Full Text\n\nOechsle A, Wensing M, Ullrich C, et al.: Health knowledge of lifestyle-related risks during pregnancy: A cross-sectional study of pregnant women in germany. Int J Environ Res Public Health. 2020; 17(22): Article number 8626. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWulandari RD, Laksono AD: Education as predictor of the knowledge of pregnancy danger signs in Rural Indonesia. Int J Innov Creat Chang. 2020; 13(1): 1037–1051.\n\nFathnezhad Kazemi A, Hajian S, Ebrahimi-Mameghani M, et al.: The perspectives of pregnant women on health-promoting behaviors: An integrative systematic review. Int J Women's Heal Reprod Sci. 2018; 6(2): 97–105.\n\nKazemi AF, Hajian S, Ebrahimi-Mameghani M, et al.: A review of various aspects of health promotion behavior during pregnancy: Review article. Tehran Univ Med J. 2019; 76(10): 647–653.\n\nIpa M, Widawati M, Laksono AD, et al.: Variation of preventive practices and its association with malaria infection in eastern Indonesia: Findings from community-based survey. PLoS One. 2020; 15(5): e0232909. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaksono AD, Wulandari RD, Kusrini I, et al.: The effects of mother's education on achieving exclusive breastfeeding in Indonesia. BMC Public Health. 2021; 21(1): 14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMegatsari H, Laksono AD, Ibad M, et al.: The community psychosocial burden during the COVID-19 pandemic in Indonesia. Heliyon. 2020; 6(10): Article number e05136. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSeran AA, Antaria MD, Haksama S, et al.: Disparities of the use of hormonal and non-hormonal contraceptive drugs in urban and rural areas in Indonesia and the world. Syst Rev Pharm. 2020; 11(9): 66–73.\n\nMeriko C, Hadiwirawan O: The Psychological Well-being of Women with Multiple Roles (Kesejahteraan Psikologis Perempuan Yang Berperan Ganda). J Psikol Unsyiah. 2019; 2(1): 68–99. Publisher Full Text\n\nInternational Labour Organization: Women at Work: Trends 2016. Geneva: 2016.\n\nWadhawan K: A Comparative Study of Self-Esteem of Working and Non-Working Women in Relation to their Psychological Well-Being. Int J Appl Res. 2016; 2(6): 531–532.\n\nWulandari RD, Putri NK, Laksono AD: Socioeconomic Disparities in Antenatal Care Utilisation in Urban Indonesia. Int J Innov Creat Chang. 2020; 14(2): 498–514.\n\nMakar M, Worple E, Dove J, et al.: Disparities in care: Impact of socioeconomic factors on pancreatic surgery: Exploring the national cancer database. Am Surg. 2019; 85(4): 327–334. PubMed Abstract | Publisher Full Text\n\nJohar M, Soewondo P, Pujisubekti R, et al.: Inequality in access to health care, health insurance and the role of supply factors. Soc Sci Med. 2018; 213: 134–145. PubMed Abstract | Publisher Full Text\n\nLaksono AD, Wulandari RD: Determinant of the Puskesmas Utilization in Madura Island. Indian J Public Heal Res Dev. 2019; 10(11): 576–581.\n\nNurjasmi E: The situation of midwifery services during the Covid-19 pandemic and entering the new-normal era (Situasi pelayanan kebidanan pada masa pandemi Covid-19 dan memasuki era new-normal). Jakarta, Indonesia: Indonesian Midwives Association; 2020; 1–32. Reference Source\n\nWidyastari DA: Revisiting the New Indonesia's Marriage Act 2019: will it be effective to prevent adolescent marriage?. INSIGHTS Public Heal J. 2019; 1(1). Publisher Full Text\n\nPanjaitan AA: Model of Prevention of Adolescent Unwanted Pregnancy in Indonesia: Review Article. Int J Res Law, Econ Soc Sci. 2019; 1(2): 60–73. Publisher Full Text\n\nLaksono AD, Soedirham O, Saptandari P, et al.: Study of family size among tenggerese in Indonesia. Int J Innov Creat Chang. 2020; 13(4): 964–978."
}
|
[
{
"id": "148531",
"date": "28 Oct 2022",
"name": "Manoja Das",
"expertise": [
"Reviewer Expertise Child health and maternal health",
"health systems",
"implementation research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present the status of ANC in women with unintended pregnancies in Indonesia and the associated risk factors. The manuscript may be improved with attention to some of the following components.\n\n1. Abstract\n\n1.1. Results - The statement \"The results show that unmarried women who had an unintended pregnancy were 0.588 times more likely than those who did not have an unintended pregnancy to have ANC visits ≥ four times (AOR 0.588; 95% CI 0.587-0.588).\"\nIt is better to say that these women had lower complete ANC contacts (not more likely, as mentioned).\n\n1.2. The statement \"Apart from unintended pregnancy, the study found seven other independent variables as significant determinants of ANC visit performance: type of residence, age group, marital status, education level, employment status, wealth status, and health insurance ownership.\"\nIt may be useful to report the specific findings for these variable with significant inference.\n\nAny report on the outcome of these unintended pregnancies?\n\n2. Methods\n2.1. Variables - Please clarify if the unintended pregnancy was captured as a specific variable in the IDHS survey or a derived variable. If derived, please indicate how was it derived.\n\n3. Results\n3.1. Please indicate the total sample collected under IDHS 2017, the number of total pregnancies and outcomes, and the number of unintended deliveries.\n\n3.2. If there are any findings on the type of delivery care received by them and places of delivery and infant outcomes, it would be useful.\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?\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": "8960",
"date": "14 Nov 2022",
"name": "Ratna Dwi Wulandari",
"role": "Author Response",
"response": "The authors present the status of ANC in women with unintended pregnancies in Indonesia and the associated risk factors. The manuscript may be improved with attention to some of the following components. 1. Abstract 1.1. Results - The statement \"The results show that unmarried women who had an unintended pregnancy were 0.588 times more likely than those who did not have an unintended pregnancy to have ANC visits ≥ four times (AOR 0.588; 95% CI 0.587-0.588).\" It is better to say that these women had lower complete ANC contacts (not more likely, as mentioned). Response: The author revised the sentence, \"The results show that unmarried women who had an unintended pregnancy were 0.588 times less likely than those who did not have an unintended pregnancy to have ANC visits ≥ four times (AOR 0.588; 95% CI 0.587-0.588).\" 1.2. The statement \"Apart from unintended pregnancy, the study found seven other independent variables as significant determinants of ANC visit performance: type of residence, age group, marital status, education level, employment status, wealth status, and health insurance ownership.\" It may be useful to report the specific findings for these variable with significant inference. Any report on the outcome of these unintended pregnancies? Response: The author deletes the statement, and focuses only on the purpose of the study, to analyze the effect of unintended pregnancy on ANC visits among unmarried women in Indonesia. 2. Methods 2.1. Variables - Please clarify if the unintended pregnancy was captured as a specific variable in the IDHS survey or a derived variable. If derived, please indicate how was it derived. Response: The author captured unintended pregnancy as a specific variable in the 2017 IDHS (IDIR71FL dataset: v367) 3. Results 3.1. Please indicate the total sample collected under IDHS 2017, the number of total pregnancies and outcomes, and the number of unintended deliveries. Response: total sample: 49,627; unmarried women: 15,160; unmarried women who births in the last five years: 508; Unintended: 129"
}
]
}
] | 1
|
https://f1000research.com/articles/10-1270
|
https://f1000research.com/articles/11-616/v1
|
06 Jun 22
|
{
"type": "Case Report",
"title": "Case Report: Takotsubo cardiomyopathy in a postoperative patient without cardiological disease",
"authors": [
"Luis Coaguila-Cusicanqui",
"Vanessa Castillo-Atoche",
"Roberto Montalvo-Suyon",
"Yuriko Cavero-Reyes",
"Virgilio E. Failoc-Rojas",
"Luis Coaguila-Cusicanqui",
"Vanessa Castillo-Atoche",
"Roberto Montalvo-Suyon",
"Yuriko Cavero-Reyes"
],
"abstract": "Background: Takotsubo cardiomyopathy (TC) is characterized by a clinical presentation that mimics acute coronary syndrome but is reversible. Alterations of Takotsubo in patients without previous heart disease remain a challenge for diagnosis. Case report: We present a case of an 80-year-old patient from Peru. The patient underwent surgery, with the diagnosis of Chilaiditi’s syndrome. One day after surgery, she presented with dyspnea, tachycardia, and electrocardiographic changes. The diagnosis of Takotsubo syndrome with cardiogenic shock and renal failure on hemodialysis was made. She was hospitalized in the Intensive Care Unit and was managed with vasopressors and nitroglycerin. There was no cardiac lesion in the cineangiogram or occlusion of arteries. The patient was extubated and received daily dialysis until discharge. Conclusions: Takotsubo is an emotional, non-cardiac, or post-traumatic stressful event that triggers myocardial injury with segmental anomalous, the possible etiology of which is the release of an endothelial neurotransmitter caused by stress. Emergency physicians should be aware of this as even patients without previous cardiac pathologies when exposed to stressors (such as surgeries) develop emergency symptomatology similar to myocardial infarction. Thus, emergency physicians should identify any cardiac abnormalities after a stressor, as well as be prepared for the diagnosis of TC.",
"keywords": [
"Takotsubo cardiomyopathy",
"electrocardiography",
"Peru"
],
"content": "Introduction\n\nTakotsubo cardiomyopathy (TC), also known as stress cardiomyopathy, apical-ballooning syndrome or broken heart syndrome, is characterized by a clinical presentation that mimics acute coronary syndrome (ACS).1 The estimated prevalence of TC is between 2% and 3% in patients with suspected ACS, but it can be higher reaching up to 10% in women.1,2\n\nTC presents a transient regional systolic dysfunction of the left ventricle that is extended beyond the coronary artery supplying area and seems to follow the anatomic cardiac sympathetic innervation.2,3 This mimics an ACS (myocardial infarction with ST-segment elevation) or unstable angina.4\n\nThe most frequent symptoms are chest pain, dyspnea, or syncope (75.9%, 46.9%, and 7.7%, respectively) according to the International Takotsubo Registry.5 There are still uncertainties concerning its pathophysiology, diagnosis, and treatment.6\n\nThis case report is about an elderly woman who was admitted to hospital for surgery, but in the post-operative phase, she presented with a complication similar to ACS, which was later diagnosed as TC. Here, we report the clinical symptoms and how the patient’s condition was improved.\n\n\nCase report\n\nWe present a case of an unemployed 80-year-old female patient from Cajamarca, Peru with a history of arterial hypertension and Type 2 diabetes mellitus for the last 10 years by which she has followed irregular treatment. She was admitted for an emergency to a hospital in Lambayeque, in the North West of Peru. On admission, the patient complained of stabbing abdominal pain in the right hemiabdomen, nausea, and constant vomiting after suffering a fall from approximately one meter. Once in the emergency department, she was evaluated by the surgery service that made the diagnosis of closed abdominal trauma and Chilaiditi’s syndrome and she was taken to the operating room to undergo surgery. A day after admission for surgery, she was taken to the recovery room. There, she started presenting with moderate dyspnea and tachycardia. After performing a Holter electrocardiogram (ECG), sinus rhythm, paroxysmal atrial fibrillation, and infrequent ventricular extrasystoles without abnormalities in the ST-segment were found. Echocardiography was also carried out, which revealed that the patient presented 75% preserved left ventricular ejection fraction (LVEF) with preserved motility, no hypertrophy or dilation of cavities, and Type 1 diastolic dysfunction. During the first five days after admission for an emergency, the patient continued presenting dyspnea, which was aggravating until it became severe with added oliguria. This was a diagnostic challenge because the description on the ECG suggested ACS or some other cardiac pathology (which had previously been ruled out). Seven days after admission for emergency and three days after surgery, she was admitted to the Intensive Care Unit (ICU) with a thrombolysis in myocardial infarction (TIMI) risk score of nine (probability of mortality of 35.9% over 30 days). In the ICU, the patient started with severe respiratory insufficiency, marked hypotension, and anuria, requiring intubation and ventilation support, hemodynamic support with vasopressor therapy (norepinephrine by continuous intravenous infusion at a dose of 0.12 and 004 μg/kg/min each day), and dialysis support.\n\nThe day after she was admitted to the ICU (post-operative day four), the patient presented with atrial fibrillation with high ventricular response; then, amiodarone infusion was administered reverting the dysrhythmia. At the moment of the dysrhythmia, serial ECG was performed in which marked negative T-waves in II, III, and augmented vector foot (aVF) leads, and all precordial leads were observed (Figure 1). Neither ST-segment disorder nor pathologic Q-waves were present. For this reason, the cardiology department performed echocardiography for the second time (post-operative day eight) where 44% LVEF systolic dysfunction, dilated left ventricle, mild mitral insufficiency, and severe aortic insufficiency with marked apical dyskinesia and contraction of basal segments were evidenced. In the cineangiogram, neither lesions nor occlusion were found in the trunk of the left coronary artery, anterior descending artery, circumflex artery or right coronary artery (Figure 2).\n\nSuspecting of ACS, anti-ischemic therapy was begun with digoxin 0.125 mg per day and cardiac enzymes were required, which resulted in troponin T elevation (0.35 ng/ml) and troponin I (0.55 ng/ml). Considering these results, coronarography was performed where no coronary lesions with natriuretic peptide (pro B-type natriuretic peptide (ProBNP)) 35,000 pg/ml (normal values: 0-222 pg/ml) were evidenced.\n\nThe diagnosis of Takotsubo syndrome with cardiogenic shock and renal failure on hemodialysis was made. An added septic process was ruled out with cultures and procalcitonin, which were negative. To complete the diagnostic study, abdominal transmission electron microscopy (TEM) and renal echography were conducted, ruling out a neoplastic process, pheochromocytoma or any other spreading process.\n\nA total of 10 days after admission to the ICU (post-operative day 13), the patient ceased presenting shock; so, vasopressor infusion was discontinued (norepinephrine by continuous intravenous infusion at a dose of 0.12 and 004 μg/kg/min, which she received for two days). It should be noted that dobutamine by continuous intravenous infusion was also administered, but only for 24 hours (a dose of 5 μg/kg/min); then it was discontinued because the patient started presenting hypotension and tachyarrhythmia.\n\nA total of 13 days after admission to the ICU (post-operative day 16), continuous intravenous infusion of nitroglycerin was given at a dose of 20–40 mcg/min, which was administered for 24 hours and control echocardiography was performed during the infusion of nitroglycerin, which showed that the patient was not presenting with systolic dysfunction (LVEF: 65%), motility was preserved with Type 1 diastolic dysfunction, with mild aortic and mitral insufficiency, and no apical dyskinesia. On echocardiographic findings, up to the date of reversion of the clinical picture of marked systolic dysfunction, negative T-waves persisted without evidence of ST-disorder or pathological Q-waves.\n\nInfusion of nitroglycerin was discontinued by evidence of clinical improvement. Therefore, the patient continued treatment with atorvastatin (sublingual, 40 mg/day), enoxaparin (subcutaneous injection, 40 mg/day), digoxin (intravenous, 0.125 mg/day), and daily dialysis support.\n\nThe patient was removed from mechanical ventilation, being extubated 15 days after hospitalization in the ICU (post-operative day 18). She continued with non-invasive ventilator assistance for a further three days. Then, she was continued with low flow oxygen therapy with FIO2 0.30 via nasal cannula. After that, the patient was discharged from the Internal Medicine service with daily dialysis support because of persistent anuria. Before discharge, pheochromocytoma, intracranial involvement, previous ischemic heart disease and severe organic valvular heart disease could be excluded. The patient progressed favorably until discharge.\n\nAt three months of follow-up, the patient did not present any hospital readmission, preserved systolic function (LVEF: 62%) and no other cardiac abnormalities, however, the patient eventually reported precordial pain without becoming disabling.\n\n\nDiscussion\n\nTC implies a diagnostic challenge because the initial clinical picture may be difficult to differentiate from ACS. TC is not uncommon but there are not many reports in Peru, perhaps due to the lack of adequate clinical suspicion.\n\nIt has been observed that TC affects women (85–90%) aged between 65 and 70 years old more often than men,5,6 which is similar to what was observed in the present clinical case. This could be explained by the fact that estrogens regulate the myocardial sympathetic tone and vascularization in women of reproductive age. This sympatholytic effect of estrogens is lost after menopause, leading to an effect in the abnormality of the contraction of the left ventricle of TC.7 Other causes have been related to the higher frequency of emotional or physical stress.1 We should also consider that TC can also appear in young women, children, and newborns.3\n\nThe diagnosis was mainly made by addressing one of the four criteria of Mayo Clinic for the diagnosis of TC: 1) mid and apical dyskinesia of the left ventricular segments with regional wall motion abnormalities; 2) absence of obstructive coronary artery disease; 3) appearance of new ECG abnormalities (T-wave inversion); and 4) absence of pheochromocytoma or myocarditis.8 That is why the diagnostic suspicion and the search for the disease allowed us to rule out other possible causes of cardiomyopathy and ACS. It is recommended to consider this differential diagnosis in patients with ACS.\n\nThe etiology of Takotsubo is still uncertain but may be associated with catecholamine elevations during times of emotional or physical stress, and we believe that a post-surgical catecholamine overload and a brain-heart connection hypothesis may have caused the Takotsubo syndrome in this case report, without the need for prior cardiac pathology.9,10\n\nElevated troponin and natriuretic peptide (proBNP) levels were found in this case. These laboratory findings are frequent in patients with TC reported in international registries,5 which is why it is considered as a diagnostic criterion.\n\nThe patient reported with TC was treated with norepinephrine and dobutamine at standard doses; however, thinking of a cardiogenic problem, may induce additional catecholaminergic stress, so TC may be precipitated by exposure to these two drugs.6,7 The pathogenic role of catecholamines is explained because high levels of catecholamines have been observed in patients with TC as well as an inflection of the left ventricle.11 Catecholamines can produce induced microvascular spasm or cardiac toxicity.6\n\nCardiac complications are common in TC. Despite the absence of lesions in cineangiogram, complications like acute cardiac insufficiency (12–45%), atrial fibrillation (7–17%), cardiogenic shock (17–30%), and dysrhythmia (5–15%)5,8,12 have been reported. Patients with TC have a high risk of developing atrial fibrillation, ranging from 7.75–17.57%.11,13 In this case report, atrial fibrillation, ventricular extrasystoles, dysrhythmia, ST-segment abnormalities, and aorta and mitral insufficiency are registered. It is important to discuss that atrial fibrillation does not increase in-hospital mortality, but it can lead to higher levels of comorbidities such as ventricular dysrhythmias, longer hospital stays, and the development of cardiac arrest.11,14\n\nThe prognosis is generally favorable because in-hospital mortality ranges from 1–8%.2 In this case, the patient was discharged from the hospital with clinical improvement. It has been observed that mortality rates of TC are higher in male patients than in female ones (8.4% vs. 3.6%, respectively; p<0.001).14\n\nThis case explains that stress cardiomyopathy has in-hospital mortality of up to 5%. Most deaths occur among patients that develop unstable manifestations, including cardiac arrest or cardiogenic shock. The recovery of the left ventricular contraction is gradual, generally from 1 to 2 weeks although it can be fast (within 48 hours) or late (up to 6 weeks).\n\nOne important problem to solve is the need to determine the risk factors and the pathophysiological mechanisms in this disease, as well as the physiology of the patient already recovered from TC to determine, with certainty, the specific care these patients require in the long term. It is also important to conduct more research on cardiac and endocrine functions to find out why this disease mostly affects women. Higher methodological quality studies should be carried out to determine the best therapeutic option for these patients.\n\nIt is proposed that when faced with an unexpected and severe stress response, the autonomic nervous system synthesizes sympathetic neuronal exits and adrenomedullary hormones. The epinephrine released from the adrenal medulla and the norepinephrine from the cardiac and extracardiac sympathetic nerves reach the adrenoceptors in the blood vessels and the heart.1 In this case report our patient did not have previous cardiac complications, so this support would be based on the release of catecholamines due to stress that has an expression in the cardiac receptors.\n\nThe frequency of TC in patients with ACS is often underestimated since there is not yet full knowledge of this disease, so it is recommended that physicians also consider the differential diagnosis in a patient admitted to hospital with ACS and evaluate the electrocardiogram and early invasive coronary angiography.\n\n\nConclusions\n\nTC is a relatively benign and reversible disease, but as it is reported in this study, to reach the diagnosis and indicate appropriate treatment is highly complex. It is frequent in women and can occur as a complication of pathology or stress. Takotsubo is an emotional, non-cardiac, or post-traumatic stressful event that triggers myocardial injury with segmental anomalous, the possible etiology of which is an endothelial neurotransmitter caused by stress.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.",
"appendix": "References\n\nKurowski V, Kaiser A, von Hof K , et al.: Apical and midventricular transient left ventricular dysfunction syndrome (tako-tsubo cardiomyopathy): frequency, mechanisms, and prognosis. Chest. 2007; 132(3): 809–816. PubMed Abstract | Publisher Full Text\n\nHassan S, Tornvall P: Epidemiology, pathogenesis, and management of takotsubo syndrome. Clin. Auton. Res. 2018; 28(1): 53–65. PubMed Abstract | Publisher Full Text\n\nKato K, Lyon AR, Ghadri JR, et al.: Takotsubo syndrome: aetiology, presentation and treatment. Heart. 2017; 103(18): 1461–1469. PubMed Abstract | Publisher Full Text\n\nWedekind H, Moller K, Scholz KH: Tako-tsubo cardiomyopathy. Incidence in patients with acute coronary syndrome. Herz. 2006; 31(4): 339–346. Publisher Full Text\n\nTemplin C, Ghadri JR, Diekmann J, et al.: Clinical Features and Outcomes of Takotsubo (Stress) Cardiomyopathy. N. Engl. J. Med. 2015; 373(10): 929–938. PubMed Abstract | Publisher Full Text\n\nSharkey SW, Windenburg DC, Lesser JR, et al.: Natural history and expansive clinical profile of stress (tako-tsubo) cardiomyopathy. J. Am. Coll. Cardiol. 2010; 55(4): 333–341. PubMed Abstract | Publisher Full Text\n\nAbraham J, Mudd JO, Kapur NK, et al.: Stress cardiomyopathy after intravenous administration of catecholamines and beta-receptor agonists. J. Am. Coll. Cardiol. 2009; 53(15): 1320–1325. Publisher Full Text\n\nSheppard MN: Takotsubo Syndrome - Stress-induced Heart Failure Syndrome. Eur. Cardiol. 2015; 10(2): 83–88. PubMed Abstract | Publisher Full Text\n\nWang X, Pei J, Hu X: The Brain-Heart Connection in Takotsubo Syndrome: The Central Nervous System, Sympathetic Nervous System, and Catecholamine Overload. Cardiol. Res. Pract. 2020; 2020: 4150291.\n\nEzad S, McGee M, Boyle AJ: Takotsubo Syndrome Associated with ST Elevation Myocardial Infarction. Case Rep. Cardiol. 2019; 2019: 1010243.\n\nYassin AS, Subahi A, Adegbala O, et al.: Clinical impact of atrial fibrillation on short-term outcomes and in-hospital mortality in patients with Takotsubo Syndrome: A propensity-matched national study. Cardiovasc. Revasc. Med. 2019; 21: 522–526. Publisher Full Text\n\nLyon AR, Bossone E, Schneider B, et al.: Current state of knowledge on Takotsubo syndrome: a Position Statement from the Taskforce on Takotsubo Syndrome of the Heart Failure Association of the European Society of Cardiology. Eur. J. Heart Fail. 2016; 18(1): 8–27. PubMed Abstract | Publisher Full Text\n\nEspinoza-Alva D, Pampa-Quenta DO, Rodriguez-Olivares RR, et al.: Clinical features and complications of Takotsubo syndrome in a peruvian social security referral center. Rev. Peru. Med. Exp. Salud Publica. 2019; 36(2): 255–259. PubMed Abstract | Publisher Full Text\n\nBrinjikji W, El-Sayed AM, Salka S: In-hospital mortality among patients with takotsubo cardiomyopathy: a study of the National Inpatient Sample 2008 to 2009. Am. Heart J. 2012; 164(2): 215–221. Publisher Full Text"
}
|
[
{
"id": "141232",
"date": "05 Jul 2022",
"name": "Carlos Culquichicon",
"expertise": [
"Reviewer Expertise Epidemiological methods"
],
"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 case report presented a patient attending the emergency room due to an initial abdominal trauma. Days after the surgery, she developed Takotsubo syndrome as a complication but reversed in the discharge.\n- Provide summarized details about the \"electrocardiographic changes\" in the abstract section.\n- \"The diagnosis of Takotsubo syndrome with cardiogenic shock and renal failure on hemodialysis was made\". It is unclear whether the Takotsubo diagnosis was made during or before hemodialysis.\n- In the 3rd paragraph of the discussion section, the authors mention that some other cardiomyopathies were ruled out. It might be good to know which diseases were ruled out and the rationale.\n- It would be great if an English-native clinical expert checks the accuracy of medical terminology.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "8973",
"date": "02 Nov 2022",
"name": "Virgilio E Failoc-Rojas",
"role": "Author Response",
"response": "Response to Reviewer 1 - Provide summarized details about the \"electrocardiographic changes\" in the abstract section. Response: Thank you. We have added the suggested information. - \"The diagnosis of Takotsubo syndrome with cardiogenic shock and renal failure on hemodialysis was made\". It is unclear whether the Takotsubo diagnosis was made during or before hemodialysis. Response: Thank you. We have revised the sentence for clarity. - In the 3rd paragraph of the discussion section, the authors mention that some other cardiomyopathies were ruled out. It might be good to know which diseases were ruled out and the rationale. Response: Thank you. We have added the requested diseases and the rationale. - It would be great if an English-native clinical expert checks the accuracy of medical terminology. Response: Thank you. The medical terminology was revised as suggested."
}
]
},
{
"id": "144264",
"date": "18 Jul 2022",
"name": "John D. Horowitz",
"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\nThis is a case report of a patient whose takotsubo syndrome (TTS: note the name) was diagnosed after an intra-abdominal operation on an elderly woman. There is a great deal wrong with the report, and I will try to cover some of it:-\nIt is not mentioned what were the findings at laparotomy. Was there, in fact, any intra-abdominal pathology?? If so, this is secondary TTS: if not, it is likely that the abdominal pain reflected the onset of TTS of primary type.\n\nThe clinical details are deficient. It is not mentioned specifically, but I presume that the patient was seriously hypotensive. This occurs mainly because in the acute stages of TTS, there is inappropriate vasodilatation and extravasation of fluid from the vasculature to the interstitium. This was not mentioned. The patient was treated with pressor agents, despite the fact that TTS is caused by an aberrant response to released catecholamines, and by infused nitroglycerine, despite the fact that there is already increased tissue sensitivity to nitric oxide, together with a propensity towards nitrosative stress. The correct consideration would have been fluid administration as primary care: this would have averted renal functional deterioration.\n\nTTS is neither a cardiomyopathy nor a transient disorder. It is inflammatory within the myocardium, transiting to energetic impairment, and eventually variable fibrosis. This was entirely omitted. The long-term prognosis is none too good either, partially because of an association with cancer. None of this was stated.\n\nNT-proBNP is not a natriuretic peptide: it is actually inert.35,000 represents the upper limit of most commercial assays: I suspect that the notation should be > 35,000.\n\nThe case is particularly relevant because it should have stimulated discussion on the nature of peri-operative myocardial injury in general: as the authors should know, this area remains controversial and tainted by (admitted) data falsification. There is increasing evidence that many of these cases are TTS rather than infarction. None of this was mentioned.\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? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No",
"responses": [
{
"c_id": "8974",
"date": "02 Nov 2022",
"name": "Virgilio E Failoc-Rojas",
"role": "Author Response",
"response": "Response to Reviewer 2 It is not mentioned what were the findings at laparotomy. Was there, in fact, any intra-abdominal pathology?? If so, this is secondary TTS: if not, it is likely that the abdominal pain reflected the onset of TTS of primary type. Response: Thank you. Findings on laparotomy were provided. As suggested by the report, TS was assumed to have appeared after surgery. The clinical details are deficient. It is not mentioned specifically, but I presume that the patient was seriously hypotensive. This occurs mainly because in the acute stages of TTS, there is inappropriate vasodilatation and extravasation of fluid from the vasculature to the interstitium. This was not mentioned. The patient was treated with pressor agents, despite the fact that TTS is caused by an aberrant response to released catecholamines, and by infused nitroglycerine, despite the fact that there is already increased tissue sensitivity to nitric oxide, together with a propensity towards nitrosative stress. The correct consideration would have been fluid administration as primary care: this would have averted renal functional deterioration. Response: Thank you for your comment. Hypotension was mentioned in the last sentence of the first paragraph in Case Report section. We agree on the suggested management of TS, we have noted this in the Discussion. TTS is neither a cardiomyopathy nor a transient disorder. It is inflammatory within the myocardium, transiting to energetic impairment, and eventually variable fibrosis. This was entirely omitted. The long-term prognosis is none too good either, partially because of an association with cancer. None of this was stated. Response: Thank you. As far as we know, the etiology and pathophysiology of TS remains poorly understood to date, reason for which there is still no consensus on the terminology to date https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7612566/. However, we have followed the recent publications and decided to revise the term for Takotsubo syndrome. Also, we have revised the information on the prognosis as suggested. NT-proBNP is not a natriuretic peptide: it is actually inert.35,000 represents the upper limit of most commercial assays: I suspect that the notation should be > 35,000. Response: Thank you. We have revised the notation. The case is particularly relevant because it should have stimulated discussion on the nature of peri-operative myocardial injury in general: as the authors should know, this area remains controversial and tainted by (admitted) data falsification. There is increasing evidence that many of these cases are TTS rather than infarction. None of this was mentioned. Response: Thank you. We have dedicated this comment in a part of the discussion on diagnosis."
}
]
},
{
"id": "144262",
"date": "25 Jul 2022",
"name": "Takeshi Nishimura",
"expertise": [
"Reviewer Expertise Emergency medicine",
"Trauma",
"Intensive care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis report \"Case Report: Takotsubo cardiomyopathy in a postoperative patient without cardiological disease\" is well written, and this reviewer understands what the authors tried to review with their unique case.\nPoints of review:\nDescribe the findings of the laparotomy. Chilaiditi's syndrome does not require a surgical treatment.\n\nAdd the information of cardiac enzyme (CK-MB).\n\nNitroglycerine is not appropriate to treat TC. Show the reason why authors applied this treatment.\n\nDiscussion is incoherent, each paragraph should include the topics authors would like to emphasize. The mixing of short and long paragraphs makes following the right discussion points difficult.\n\nAuthors just addressed the knowledge which is already known in previous reports. Readers would like to know academic aspects from this case. To improve the quality of this case report, this reviewer recommends authors to reconsider the concept of this case.\nAlso, I recommend the manuscript be proofread.\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? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "8975",
"date": "02 Nov 2022",
"name": "Virgilio E Failoc-Rojas",
"role": "Author Response",
"response": "Response to Reviewer 3 Describe the findings of the laparotomy. Chilaiditi's syndrome does not require a surgical treatment. Response: Thank you. We have described the findings of laparotomy. Indeed, Chilaiditi's syndrome generally has conservative management. However, the main diagnosis was closed abdominal trauma, which did require immediate surgery. Add the information of cardiac enzyme (CK-MB). Response: Thank you. We have added the information of cardiac enzyme. Nitroglycerine is not appropriate to treat TC. Show the reason why authors applied this treatment. Response: Thank you. We have provided the reason why nitroglycerine was used. Discussion: each paragraph should include the topics authors would like to emphasize. The mixing of short and long paragraphs makes following the right discussion points difficult. Response: Thank you for your feedback. This section was revised accordingly. Authors just addressed the knowledge which is already known in previous reports. Readers would like to know academic aspects from this case. To improve the quality of this case report, this reviewer recommends authors to reconsider the concept of this case. Response: Thank you. We have provided more information on academic aspects from the case. The message of this case was reevaluated, and it was reinforced in the conclusion. Also, I recommend the manuscript be proofread. Response: Thank you. The manuscript was proofread as suggested."
}
]
}
] | 1
|
https://f1000research.com/articles/11-616
|
https://f1000research.com/articles/11-458/v1
|
25 Apr 22
|
{
"type": "Software Tool Article",
"title": "Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App",
"authors": [
"Pritam Saha",
"Özgun Babur",
"Chris Sander",
"Augustin Luna",
"Chris Sander"
],
"abstract": "Introduction: CausalPath compares experimentally measured changes in molecular profiles against curated biological pathways and infers causality between changes in measured features from profiling experiments (e.g., RNA-seq or proteomics from total or phospho-protein levels). Methods: We developed the CausalPath Cytoscape App, an app (i.e., plugin) for visualizing results from the CausalPath method within the Cytoscape Java-based desktop network analysis and visualization platform. Use Cases: Users are given instruction that represents use cases in multiple cancer research areas through the visualization of CausalPath analysis results generated from data by the Clinical Proteomic Tumor Analysis Consortium. Discussion: The CausalPath Cytoscape App visualizes the set of known interactions that are supported by molecular profiling data via the CausalPath method. This integration of CausalPath and Cytoscape benefits users interested in performing secondary analyses (e.g., module detection) on the sub-networks that result from CausalPath analysis by utilizing the many analytical features available in the Cytoscape software ecosystem.",
"keywords": [
"proteomics",
"network analysis",
"Cytoscape app",
"Cytoscape",
"mechanistic hypotheses",
"curated signaling"
],
"content": "Introduction\n\nCausalPath is a recently developed software tool that allows users to map proteomic and other molecular profiles to pathway information from the Pathway Commons database (RRID: SCR_001749) and other resources.1–4 CausalPath focuses on providing users a means to assess causality among correlated measurements. CausalPath can generate a network model of molecular signal flow that is consistent with both the profiling data and the published literature (Figure 1A). Results in the generated network model are linked to Pathway Commons, an integrative database of molecular interactions, and literature connections, therein.3,5\n\nA: CausalPath maps data from experiments and curated literature resources to provide users with mechanistic hypotheses of experimental observations. B: CausalPath results for luminal (luminal A and luminal B) samples compared to basal-like samples; samples were profiled via proteomic mass spectrometry. The right-hand panel shows differential abundance measures for the ESR1 along with measured phosphorylation sites (e.g., ESR1 S294). Note: ESR1 appears yellow because Cytoscape uses yellow for network selections; unselected ESR1 would appear red, in this example, because ESR1 has an increased abundance in luminal versus basal breast cancer. C: Snippets of the SIF and .format input files are shown.\n\nSeveral tools currently support the visualization of CausalPath, including causalpath.org, Newt, and ChiBE.2,6,7 A comparison of unique features of these tools with respect to usage with CausalPath has been previously discussed in one of our recent publications.1 The CausalPath Cytoscape app provides a tool for importing, visualization, and utilizing CausalPath results from within Cytoscape, thereby facilitating user access to additional analyses not found in the aforementioned CausalPath tools.8 Cytoscape is a widely used extensible bioinformatics environment for the analysis and visualization of biological networks with nearly 10 million downloads since 2014.8 By providing users with a Cytoscape-based interface for the visualization of CausalPath results, users have access to the Cytoscape ecosystem of functionality. Briefly, this allows CausalPath users to have access to Cytoscape features such as network layouts and sharing of CausalPath results through to Network Data Exchange (NDEx).9 Additionally, various secondary analyses are available for users to run including, for example, gene set analysis through tools (e.g., through NDEx Integrated Query), module detection, and various network propagation methods.8\n\n\nMethods\n\nThe work is implemented in the Java 16 programming language using the Cytoscape software platform. Multiple Cytoscape application programming interfaces (APIs) have been used to call the different functionalities. The CausalPath Cytoscape App13 is described in the three following sections:\n\nThe user interface consists of two panels (as seen in Figure 1):\n\n1 Input Panel: A panel component that appears on the left that is built using Cytoscape swing-application-api where users select files from their local file storage. The Java Swing library is used to choose the appropriate file and the Cytoscape io-api to read the network file. The panel contains a progress bar to show the progress and a help button that uses Cytoscape service-api to redirect to the CausalPath project website.\n\n2 Information Panel: A panel component appearing on the right where a node or edge-specific information is shown when a user selects a node or edge.\n\nData from the network and format files is stored using multiple data structures (e.g., HashMaps with different class types and Arrays). A network view is created using Cytoscape view-model-API for the network and different styles for each node and edge are configured using Cytoscape presentation-api. Finally, we used the Cytoscape work-api to show the network. By default, the app lays out the network using a force-directed layout.\n\nCausalPath visualizations include annotations on nodes (i.e., small circles attached to nodes). These annotations provide information on post-translational modifications (i.e., phosphorylations) as well as information on non-proteomic data (e.g., gene expression data and copy number information). To provide these annotations, we have made use of the Cytoscape enhancedGraphics plugin and the vizmap-api to map the sites to each node and we have used the “Label” chart type. Annotations are placed on the border of nodes when they are present in the input data (e.g., the example in Figure 1). This app uses the Cytoscape vizmap-api to map the sites to each node and we have used the “Label” charts style from the enhanced Graphics plugin to design the site annotations for each node. The visual notation of CausalPath uses a notation outlined previously1,2 with one exception. Instead of using border colors to indicate the activatory or inhibitory nature of the site, we used the text color of the letter within the annotation circle. This change was done to Cytoscape as this was the representation available with vizmap-api labels chart.\n\nThe CausalPath Cytoscape App requires two input files to visualize CausalPath result networks:\n\n• Network file (with a .sif extension): The network data contains multiple rows where each row consists of tab-separated values where the first value refers to the source node, the second value refers to the edge type, and the third one refers to the target node.\n\n• Format File (with a .format extension): The.format file also has multiple rows where each row consists of space and pipe-separated values. Each row can contain one of the multiple possible categories of information. The categories include: 1) styling for a node (e.g. color, border color, border width), 2) styling information for each site-related annotation linked to a particular node, or 3) “tooltip” information that will appear in the right-hand information panel, such as specific measured node values. More details can be found on this GitHub repository.\n\nThe minimum system requirements for use of the CausalPath Cytoscape app include: Hardware: CPU: 1 GHz CPU, Memory: 512MB, Monitor: 1024×768 resolution; Software: Java 11.\n\nHere, we provide installation and usage instructions for the CausalPath Cytoscape app for visualizing existing CausalPath results. Users that desire to additionally run a CausalPath analysis must do so separately. We have recently published a detailed protocol for how users can do this locally on their computers (1). Additionally, the protocol provides guidance on available options for conducting a CausalPath analysis. A collection of results from previous work is available on Zenodo and will be used here as input files for the CausalPath Cytoscape app.2\n\nTo install the CausalPath Cytoscape app users must first install Cytoscape.8 Next, users must install the enhanceGraphics app from the “Apps -> App Manager …” menu of Cytoscape. After this, users can then install the CausalPath Cytoscape app App Manager menu.\n\nOnce installed users can visualize the results using the CausalPath Cytoscape app and run any additional analyses available from Cytoscape. The steps to visualize CausalPath results in Cytoscape are as follows. First, with Cytoscape open, users enable the CausalPath by clicking the App menu and then CausalPath. Next, from the Cytoscape Control Panel menu that appears, users will load both their SIF network and .format file. Lastly, users need to click the “Submit” button to visualize the network.\n\n\nUse case\n\nFigure 1 (partial view of the network) is a visualization of the results generated by CausalPath for a dataset taken from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) (RRID:SCR_017135) breast cancer study that collected proteomic and phosphoproteomic profiles for 105 of the original The Cancer Genome Atlas (TCGA) (RRID:SCR_003193) breast cancer samples with mass spectrometry; see data availability section for information on the input files used in this section.10 Specifically, Figure 1 shows luminal (luminal A and luminal B) samples compared to basal-like samples. Briefly, these results highlight overexpression of the ESR1 gene and genes directly downstream of ESR1 in luminal samples as compared to basal-like samples; a key characteristic of basal-like breast cancer is that it is hormone-receptor negative (estrogen-receptor and progesterone-receptor negative).11\n\nThe causative.sif and causative.format input files (Figure 1C) from the LumAB-vs-Basal folder are loaded by using the clicking app “SIF File” and “Format File” buttons of the Input Panel shown in Figure 1B; the full path to these two input files within the Zenodo12 archive is CausalPath-data/CPTAC-BRCA/subtypes/LumAB-vs-Basal; see data availability section for information on the Zenodo archive and the data formats section for a description of the contents of .sif and .format files. After clicking the “Submit” button users will see the resulting output visualization as shown in Figure 1B. For node or edge-specific information, the user should select that node or edge. The information regarding that node or edge will be shown in the side panel as shown in Figure 1. Users can also visualize multiple networks at the same time by repeating the instructions to load networks in the “Installation and usage” section. Additionally, we note for readers that the Zenodo archive provided in the data availability section12 provides pre-computed results for many of the cancer types (e.g., ovarian, bladder, renal, thyroid, pancreatic, colon, etc.) for which there is TCGA proteomics data. These CausalPath results for each of these cancer types can be visualized in the same manner as described above.\n\n\nDiscussion\n\nThe CausalPath Cytoscape app is a software tool for visualizing network models with consistency with both the profiling data and the published literature. Use of CausalPath aids researchers who seek to understand the results of their experimental data and who would otherwise manually explore scientific literature to assess concordance with existing findings. By providing this tool as a Cytoscape app, we simplify the installation and use of CausalPath with existing analysis pipelines that combine other analyses available through Cytoscape that, for example, include a gene set and network modularity analyses.\n\n\nData availability\n\nThe source data used in Figure 1 comes from a previous study using CausalPath results for LuminalAB-vs-Basal-like breast cancer comparison.2 The CausalPath input data and analysis results are publicly available on Zenodo (https://doi.org/10.5281/zenodo.4477801).12\n\n\nSoftware availability\n\nThe CausalPath Cytoscape app is available from the Cytoscape App Store: https://apps.cytoscape.org/apps/causalpathcytoscapeapp. The app is compatible with versions of Cytoscape 3.7 and above.\n\nSource code available at: https://github.com/cannin/causalpath_cytoscape_app\n\nArchived source code at the time of publication: https://doi.org/10.5281/zenodo.608165913\n\nLicense: Apache License 2.0 license.",
"appendix": "Acknowledgements\n\nWe thank Scooter Morris and Alexander Pico for their valuable feedback regarding Cytoscape during the development of the project. Additionally, we would like to thank the coordinators of the Google Summer of Code program.\n\n\nReferences\n\nLuna A, Siper MC, Korkut A, et al.: Analyzing causal relationships in proteomic profiles using CausalPath. STAR Protoc. 2021 Dec 17; 2(4): 100955. PubMed Abstract | Publisher Full Text\n\nBabur Ö, Luna A, Korkut A, et al.: Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns (N Y). 2021 Jun 11; 2(6): 100257. PubMed Abstract | Publisher Full Text\n\nRodchenkov I, Babur O, Luna A, et al.: Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 2020 Jan 8; 48(D1): D489–D497. PubMed Abstract | Publisher Full Text\n\nBarsi S, Szalai B: Modeling in systems biology: Causal understanding before prediction?. Patterns (N Y). 2021 Jun 11; 2(6): 100280. PubMed Abstract | Publisher Full Text\n\nCerami EG, Gross BE, Demir E, et al.: Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan; 39(Database issue): D685–D690. PubMed Abstract | Publisher Full Text\n\nBalci H, Siper MC, Saleh N, et al.: Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinformatics. 2021 Jun 16; 37(10): 1475–1477. PubMed Abstract | Publisher Full Text\n\nBabur O, Dogrusoz U, Demir E, et al.: ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinformatics. 2010 Feb 1; 26(3): 429–431. PubMed Abstract | Publisher Full Text\n\nShannon P, Markiel A, Ozier O, et al.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov; 13(11): 2498–2504. PubMed Abstract | Publisher Full Text\n\nPillich RT, Chen J, Rynkov V, et al.: NDEx: A Community Resource for Sharing and Publishing of Biological Networks. Methods Mol. Biol. 2017; 1558: 271–301. PubMed Abstract | Publisher Full Text\n\nMertins P, Mani DR, Ruggles KV, et al.: Proteogenomics connects somatic mutations to signalling in breast cancer. Nature. 2016 Jun 2; 534(7605): 55–62. PubMed Abstract | Publisher Full Text\n\nBadve S, Dabbs DJ, Schnitt SJ, et al.: Basal-like and triple-negative breast cancers: a critical review with an emphasis on the implications for pathologists and oncologists. Mod. Pathol. 2011 Feb; 24(2): 157–167. PubMed Abstract | Publisher Full Text\n\nBabur Ö, Luna A, Korkut A, et al.: CausalPath Analysis Inputs and Outputs. Zenodo. 2021. Publisher Full Text\n\nPritam, Özgun, Chris, et al.: CausalPath Cytoscape App Source Code (1.0.2). Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "135821",
"date": "10 May 2022",
"name": "Ruth Isserlin",
"expertise": [
"Reviewer Expertise Bioinformatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe publication “Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App” by Saha et al describes a new Cytoscape app developed for users of the Causalpath program to visualize their results in the Cytoscape ecosystem. This enables users of the Causalpath to have access to all the features present in Cytoscape when analyzing their results. On the initial read of the paper I had difficulty understanding the purpose and workings of the app. Only after reading both of the papers describing causalpath method and the detailed protocol did I begin to understand the current application note. I feel like this paper could benefit from either an expansion of the introduction and background section or a advisory to read both the previous papers prior to reading this paper.\n\nMethods - User Interface: There are a lot of links in the user interface to the different methods and code. There is no link to the causalpath.org website. I think it would be beneficial to have a link to the site where they can generate the data needed to run in the app. If you are concerned with the number of links listed in the app maybe having the title Causal Path be a direct link to the website as possible suggestion.\n\nIn the methods section it would be useful to make a separate section called 'data' with a link to the data download on zenodo and a brief description of the analysis done to create the files contained in it. Additionally, a recommendation of which files to use to try out the app. There is mention of the zenodo download but I think it would be beneficial to have it in its own section, right at the start of the methods section so readers can easily grab the file and try out the app.\n\n“To install the CausalPath Cytoscape app users must first install Cytoscape.8 Next, users must install the enhanceGraphics app from the “Apps -> App Manager …” menu of Cytoscape. After this, users can then install the CausalPath Cytoscape app App Manager menu.” - maybe have a causalpath app collection available as well that installs both the required apps so there is no need to install the two different apps.\n\nFeature - remembering the previous directory would be very helpful especially when using the dataset supplied on zenodo that consists of many different analyses embedded in a complicated file structure.\n\nBug - the requirement to unselect the network in network panel in order to create a new causalpath network should be fixed.\nThere is a specific example in the paper to get the figure that is shown in the paper but when you use any of the other data the networks are not coloured or even laid out using any of the cytoscape layouts. Why is this? Is all of that done manually by the user as opposed to being automated in the app? It seems that I can get coloured networks only when I choose files from the subtypes directory.\n\nMinor issues: \"The CausalPath Cytoscape app provides a tool for importing, visualization, and utilizing CausalPath results from within” - mixture of tenses. Would be better as - “The CausalPath Cytoscape app provides a tool for importing, visualizing, and utilizing CausalPath results from within”.\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": [
{
"c_id": "8740",
"date": "07 Sep 2022",
"name": "Augustin Luna",
"role": "Author Response",
"response": "We thank the reviewer for their time. Our detailed responses are below and we have submitted a new manuscript version. The publication “Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App” by Saha et al describes a new Cytoscape app developed for users of the Causalpath program to visualize their results in the Cytoscape ecosystem. This enables users of the Causalpath to have access to all the features present in Cytoscape when analyzing their results. On the initial read of the paper I had difficulty understanding the purpose and workings of the app. Only after reading both of the papers describing causalpath method and the detailed protocol did I begin to understand the current application note. I feel like this paper could benefit from either an expansion of the introduction and background section or a advisory to read both the previous papers prior to reading this paper. Methods - User Interface: There are a lot of links in the user interface to the different methods and code. There is no link to the causalpath.org website. I think it would be beneficial to have a link to the site where they can generate the data needed to run in the app. If you are concerned with the number of links listed in the app maybe having the title Causal Path be a direct link to the website as possible suggestion. Response: We have added the link under the title to the CausalPath website. In the methods section it would be useful to make a separate section called 'data' with a link to the data download on zenodo and a brief description of the analysis done to create the files contained in it. Additionally, a recommendation of which files to use to try out the app. There is mention of the zenodo download but I think it would be beneficial to have it in its own section, right at the start of the methods section so readers can easily grab the file and try out the app. Response: We have edited the Methods section based on the comments. We now have a “Data and usage” section to better communicate with and instruct users. We use the phrasing \"strongly advised\": \"Users are strongly advised to read the two previous CausalPath publications\" to address this feedback and another comment by the reviewer to put an advisory notice for users. We have reordered the Methods to such so that this “Data” section is seen earlier by readers and follow the reviewers suggestion to advise users to download the archive of past results. “To install the CausalPath Cytoscape app users must first install Cytoscape.8 Next, users must install the enhanceGraphics app from the “Apps -> App Manager …” menu of Cytoscape. After this, users can then install the CausalPath Cytoscape app App Manager menu.” - maybe have a causalpath app collection available as well that installs both the required apps so there is no need to install the two different apps. Response: We are grateful to the reviewer for highlighting this thing. As it is the structure of Cytoscape to download the enhanceGraphics app separately because it is the library that is provided by Cytoscape to provide advanced style algorithms. Additionally, we will continue to gauge interest by other users for alternative installation methods. Feature - remembering the previous directory would be very helpful especially when using the dataset supplied on zenodo that consists of many different analyses embedded in a complicated file structure. Response: We appreciate the reviewer for mentioning this issue. We have added this feature to our app to remember the last browsed directory such that users can track the previously opened files. Bug - the requirement to unselect the network in network panel in order to create a new causalpath network should be fixed. Response: We appreciate the reviewer for finding this bug in the app. We have fixed the issue in our next version. Now, the user can create as many networks without any hindrance. There is a specific example in the paper to get the figure that is shown in the paper but when you use any of the other data the networks are not coloured or even laid out using any of the cytoscape layouts. Why is this? Is all of that done manually by the user as opposed to being automated in the app? It seems that I can get coloured networks only when I choose files from the subtypes directory. Response: In Figure 1D, we have included images of two additional networks from the collection available in the Zenodo archive; the causative .sif and .format files were loaded. This should help illustrate for users that not all networks will have all (or necessarily even many nodes) colored. This is entirely dependent on the CausalPath analysis conducted and its results. Minor issues: \"The CausalPath Cytoscape app provides a tool for importing, visualization, and utilizing CausalPath results from within” - mixture of tenses. Would be better as - “The CausalPath Cytoscape app provides a tool for importing, visualizing, and utilizing CausalPath results from within” Response: We have edited the text."
}
]
}
] | 1
|
https://f1000research.com/articles/11-458
|
https://f1000research.com/articles/11-7/v1
|
05 Jan 22
|
{
"type": "Research Article",
"title": "Low power, less occupying area, and improved speed of a 4-bit router/rerouter circuit for low-density parity-check (LDPC) decoders",
"authors": [
"Chinnaiyan Senthilpari",
"Rosalind Deena",
"Lee Lini",
"Rosalind Deena",
"Lee Lini"
],
"abstract": "Background: Low-density parity-check (LDPC) codes are more error-resistant than other forward error-correcting codes. Existing circuits give high power dissipation, less speed, and more occupying area. This work aimed to propose a better design and performance circuit, even in the presence of noise in the channel. Methods: In this research, the design of the multiplexer and demultiplexer were achieved using pass transistor logic. The target parameters were low power dissipation, improved throughput, and more negligible delay with a minimum area. One of the essential connecting circuits in a decoShder architecture is a multiplexer (MUX) and a demultiplexer (DEMUX) circuit. The design of the MUX and DEMUX contributes significantly to the performance of the decoder. The aim of this paper was the design of a 4 × 1 MUX to route the data bits received from the bit update blocks to the parallel adder circuits and a 1 × 4 DEMUX to receive the input bits from the parallel adder and distribute the output to the bit update blocks in a layered architecture LDPC decoder. The design uses pass transistor logic and achieves the reduction of the number of transistors used. The proposed circuit was designed using the Mentor Graphics CAD tool for 180 nm technology. Results: The parameters of power dissipation, area, and delay were considered crucial parameters for a low power decoder. The circuits were simulated using computer-aided design (CAD) tools, and the results depicted a significantly low power dissipation of 7.06 nW and 5.16 nW for the multiplexer and demultiplexer, respectively. The delay was found to be 100.5 ns (MUX) and 80 ns (DEMUX). Conclusion: This decoder’s potential use may be in low-power communication circuits such as handheld devices and Internet of Things (IoT) circuits.",
"keywords": [
"LDPC decoder",
"multiplexer",
"demultiplexer",
"pass transistor logic"
],
"content": "Introduction\n\nLow-density parity-check (LDPC) codes are considered more error resistant when compared to other forward error-correcting codes. These error-based circuits have been proved by their performance in the presence of noise in the channel.1 Hence, LDPC decoders have been used more actively for communication applications. Different approaches may be used in the design of an LDPC decoder. One such structure is the layered approach, consisting of a layered design, memory unit, computational block, full adders, parity check unit, bit update unit, and router/reverse router circuits.2 The decoding process begins with data being received into the decoder through the bit update block. The bit update block receives data, arranges them into their vectors according to the system requirements, and stores them. These data are routed to the parallel adder through the routing circuit and the data bus. The parallel adder now computes the memory block stored in the previous iteration and the new vector. The output of the computation is checked for errors using the parity checker.3 The result goes through another computation process to generate the original vector stored in the bit update unit for the next iteration. Also, new values after the parity check are stored in the memory block.\n\nRouters form an integral part of this architecture, sending data bits through the routers’ different layers. Routers are multiplexer or demultiplexer circuits used to select appropriate data to be sent or to distribute the received data bits to other units. Multiplexers (MUX) and Demultiplexers (DEMUX) form the basic units of data paths. They are used in applications like processor buses in CPUs, network switches, and digital signal processing stages, involving resource sharing and graphic controllers. In large-scale systems, multiplexers aid in the reduction of integrated circuits used in some designs. In this research, the design of the multiplexer and demultiplexer is achieved using pass transistor logic.4 According to existing authors of the multiplexer, demultiplexer, and LDPC encoder circuits, a higher number of transistors leads the critical path and results in higher power dissipation.5\n\nThe proposed method reduced the number of transistors in the design and the regular arrangement of transistors, thereby reducing the critical path. The target was low power dissipation, improved throughput, and smaller delay with a minimum area. Low power design is essential when this circuit is used along with many other components for communication purposes. Pass Transistor Logic (PTL) has the advantage of reducing the number of transistors by eliminating redundant transistors. Here the transistors act as switches to pass different logic levels between nodes of a circuit. This paper’s main objective was to design and develop routers and bit update blocks for the LDPC decoder. The proper design of the router, rerouted, and LDPC circuit reduces the critical path, power dissipation, and speed increases. This paper reviews the related work in designing multiplexers and demultiplexers and describes the design methodology used in the proposed circuits. The results obtained from the simulation are analyzed, and conclusions are then made regarding the proposed circuits.\n\nUnlike the main building blocks such as the adders and parity checkers, routers form a crucial support system to the decoder. The routers’ function, mainly comprised of multiplexers and demultiplexers, helps arrange data bits according to the system configuration and passes the information through appropriate layers. Binary signals control multiplexers.2 The analogue MUX/DEMUX was designed using ternary inverters to control the circuits, and CMOS transmission gates were used.6–8 The design improved and proved to be excellent for ternary inverters. With the idea of switching activities suggested by Anitha and Javachitra,9 adiabatic logic reduces the power by offering back the stored energy to the supply and this was used for the 16:1 multiplexer and 1:16 demultiplexer. The results indicated that they had less power dissipation than conventional CMOS circuits. An 11 Gb/s CMOS demultiplexer using redundant multi-valued logic (RMVL) was proposed by Ahn and Kim (2006).10 The circuit received serial binary data, which was converted to parallel redundant multi-valued data. The converted data are reconverted to parallel binary data. This makes it possible to achieve higher operating speeds than that of conventional binary logic. The implemented DEMUX consisted of eight integrators and was designed with a 0.35 μm standard CMOS process. The DEMUX achieved the maximum data rate of 11 Gb/s and the average power consumption of 69.43 mW. This circuit was expected to operate faster than 11Gb/s in the high operating frequency’s deep-submicron process. A demultiplexer has been designed with 36 transistors using 90 nm CMOS technology.7 Auto-generation technique and semi-custom layout design were integrated. There was an improvement in power consumption and area due to the semi-customized demultiplexer layout.\n\n\nMethods\n\nThe router circuit in a decoder is a bank of MUX and DEMUX that forward the appropriate estimate terms from memory to the corresponding bit update circuit. The proposed MUX, DEMUX, bit update circuit, and proposed LDPC circuits logic simulations are executed mainly to validate the circuit’s functionality. The designed circuit had the required logic behaviour. In the layout, the memory cell’s charging and discharging were validated by the aspect ratio factor and expressed with current scaling methods. The proposed circuits were validated by reliable, optimum data of the designed parameters. Modern communication systems demand high reliability and optimum data rate, which makes the standards for future communication technology move towards methods of error correction that enable high throughput decoding with optimum performance based on the Shannon capacity.\n\nThe multiplexer is a combinational logic circuit that selects an appropriate analogue (or) digital signal from several input signals and forwards it to a single output line.11 A multiplexer has several input lines and a single output line. The selection of the appropriate input is based on unique control lines called select lines. Figure 1 depicts a basic multiplexer with four inputs I0, I1, I2, I3, and a single output line (Z). Multiplexers can be designed for a 2n number of inputs. In this design, we used a 4 × 1 MUX because it is simpler to cascade these circuits for many inputs, and the decoder was also for 4-bit data. There are two select lines, S0, S1 which are the control lines of the circuit. The MUX is 4 × 1, representing four inputs and one output. An additional set of input lines control each input line’s selection according to these control input’s binary conditions, which indicated ‘HIGH’ (1) or ‘LOW’ (0). Multiplexers have an even number of 2n data input lines and some control inputs that match the number of data inputs. The truth table for the 4 × 1 MUX is shown in Table 1.\n\nThe output Z is obtained from the Boolean expansion.\n\nThe equation (1) was expanded using associative and commutative laws to obtain an appropriate and optimized circuit equation for implementing the multiplexer.11 Any single input line is selected instantly depending on the combination of select lines input to be connected to the output Z. For example, if the select lines combination S1S0 is a logic ‘0’ a logic ‘1’ (01), then input line I1 would be connected to the output Z, referring to Table 1. Adding more control address lines (n) allowed the multiplexer to control more inputs to switch 2n inputs. Still, each control line configuration will connect only one input to the output. In our proposed circuit, optimization of the circuit is done using pass transistor logic to design the multiplexer.\n\nA 4 × 1 MUX was designed as shown in Figure 1, and the input to the multiplexer in this circuit was from a bit update block (BUB), part of the LDPC decoder structure. The inputs were from the 4-bit update units used in the decoder circuit designed for this research. The multiplexer aimed to receive the updated data bits from the bit update unit and rearrange the vectors according to the circuit’s requirements.12 The multiplexer circuit was designed using pass transistor logic. The MUX comprised NMOS and PMOS circuits for the inverters and only NMOS circuits for the remaining circuit. The inverter complemented the select input signals S0(SA) and S1(SB). The multiplexer was configured to have series-connected switches so that, based on the input combination of S0 and S1, one of the inputs was selected to pass the input to the output. The multiplexer passed a signal when the controlling voltage was logic low.\n\nThe circuit used NMOS because electron mobility is better than hole mobility, and hence the performance will be better. The inputs I0, I1, I2, and I3 fed from the 4-bit update circuits had the bit update unit’s computation values. The selection of the input that was given to the router was based on the select inputs S1 and S0. Inputs I0, I1, I2, and I3 were chosen to connect to the output line Z. Assuming the select inputs had an input combination of S0 = 0 and S1 = 1. The S0 input was fed to an inverter circuit formed by the pass transistors, which passed the value ‘0’ to the circuit, and the S1 with a logic ‘1’ was given to the other inverter circuit. The NMOS controlled the ground and the output in one inverter circuit, while PMOS connected the input supply VDD and the output.13 The transistors then did what they are best designed for, that is the NMOS allowed a logic ‘0’, and the PMOS allowed a logic ‘1’. It acted like a 2 × 1 MUX, where the inputs are logic 0 and logic 1. The input variable acted as the control signal and determined which input should be sent to the output. Hence, a combination of both inverters at the input would help select the signal sent to the output. This would be either I0, I1, I2, or I3. In our example, I2 was fed to the output Z = I2.\n\nMultiplexer design can be enlarged to have many more inputs by using the basic multiplexer circuits. A 16 × 1 MUX can be designed using 2 × 1, 4 × 1, and 8 × 1 MUX. As per basic MUX circuit design, 4 × 1 multiplexers are used so 16 inputs are available. Inputs I0 to I3 (for bits zero to three) are for the first multiplexer (to PMOS), I4 to I7 (for bits four to seven) to the second, and so on where the last multiplexer has inputs I12 to I15 (for bits 12 to 15). Every multiplexer’s select inputs are combined in parallel into two main selection lines that connect all four multiplexers.14,15 The output from each multiplexer is now fed as four inputs to another 4 × 1 multiplexer. The output from this multiplexer becomes the main output of the circuit.\n\nA demultiplexer is a combinational circuit that routes a single input line to multiple digital output lines. The demultiplexer of 2n outputs has ‘n’ select lines to select which output lines need to be connected to the input.13,14 In simple terms, it is a data distributor. The demultiplexer is a 1 × 4 unit, implying a single input line Y and four output lines, D0, D1, D2, and D3. There are two select lines, S0 and S1. The select lines help to decide to which output line the input line Y should be connected. The select lines are controlled by the binary combination of 0 and 1. The select lines S0 and S1 can take on 00, 01, 10, and 11. These are the four possible combinations for two input signals and hence four possible output lines. The combination and connection of input Y to the output lines D0, D1, D2, and D3, follow the truth table given in Table 2. The data input to be connected to the particular output line is obtained from the equation,\n\nThe Boolean expression in equation (2) is obtained from the truth table in Table 2, which can be implemented using basic logic gates or CMOS logic. Adding more address line inputs, it is possible to switch more outputs giving 1-to-2n data line outputs.16 The proposed demultiplexer was also a 1 × 4 demultiplexer constructed using pass transistor logic, as shown in Figure 2. In the figure, two inverter circuits form the input point for the DEMUX. The inverters were constructed with opposite polarity Metal Oxide Semiconductor Field Effect Transistors (MOSFETs) with their gates connected to form the input voltage Vin shown as SA and SB. The drain terminals of both MOSFETs were connected to form a typical output.17 These MOSFETS were connected in such a way (complementary) that only one MOSFET conducts when the input has a low or high input voltage due to the complementary connection.\n\nThe Gate-Source voltage VGS is equal to Vin, that is:\n\nWhere VDD is the supply voltage, the input voltage can have values from 0 to VDD. When SA = Vin = VDD, the PMOS transistor gets cut off while the NMOS conducts and current flows to the ground terminal, and the output voltage is ‘0’. The ‘0’ volts are now applied to one of the inputs of transistor T5, which is in series with T6.\n\nIf input SB had an input value of ‘0’ volts, the NMOS transistor inverter was cut off while PMOS conducted to give a path to the power supply and the output now had a value VDD. The second input to transistor T5 was ‘0’. The transistor had inputs 0, 1 and gave an output ‘0’, indicating that the line DA had been selected to distribute the input from the parity check circuit of the layered decoder circuit. Hence, the other lines DB, DC, and DD were selected to feed that input for other input combinations to SA and SB. The input fed at line D (Y in the truth table) was distributed to any four outputs represented by D0, D1, D2, and D3. The distribution was based on the select inputs S0 (SA) and S1(SB). In Figure 2, the select lines are connected to two inverters at the first stage of the DEMUX. Each inverter created the terms given in equation (2). The inverter drove the value of S0, and if it was a ‘0’, then the output could be a ‘1’, similar to the S1 input. The following transistors drove the input to the outputs based on the bit pattern of S1S0.\n\nThe bit update circuit is an integral part of many circuits, where temporary storage and stored data updates are required periodically. These circuits have memories that will store some predetermined subset of codeword bits, though only one at a time. The circuit uses basic logic gates: the EXOR gate, a latch, and a multiplexer and inverter. It is like a loop operation, where input data bits received are fed into the multiplexer, and it is compared with the previously stored data from the latch. The EXOR gate will help identify new data and is given to the MUX, where the select inputs will ensure the new data is stored in the latch. This recently stored data is then sent to the next section of a large application circuit.\n\nIn the proposed circuit, the data input was from the DEMUX circuit, transmitting data bits received. The bit update circuit ensured that new data received was always updated and stored and then distributed through the reverse router to the parallel adder blocks in the decoder through the data bus. The bit update circuit usually works in tandem with two memories, one as an accumulator for a new data set and the other supplies the last iteration’s data.18 These two memories act in an alternating manner. A multiplexer worked like a cross switch to facilitate their alternating operation.\n\nThe proposed bit update circuit was designed using the pass transistor logic to reduce the number of transistors. The delay needed to be reduced in the circuit, and hence the technology used was adequate. The circuit shown in Figure 3 comprises a 2 × 1 multiplexer circuit with a latch. The latch acted as the temporary storage or memory for the data bits. The data bit stored in the latch was given to an EXOR gate connected to an AND gate delay circuit. This was to create a delay so that the bits reached the multiplexer within the clock pulse. The EXOR input was also fed to MUX as one of the select inputs.\n\nA proposed decoder architecture is described in this section, which follows the layers of component decoding. The top-level architecture is shown in Figure 4. One type of decoding technique is the layers of components decoding. It generally includes layer-by-layer processing rows of a parity check matrix.16 Each layer is processed sequentially, and the processing of each layer depends on data processed in an immediate previous layer. Decoders using the layered technique are designed to have an inbuilt latency for processing the data between layers. By way of explanation, say if a layer in the parity check matrix needs to be processed, data processed by a previous layer need to be received initially. But it may be that these data are unavailable yet because they are still processed in the previous layer or the data bus and have yet to reach their destination. Latency such as this has an impact on the performance of the decoder. Some problems like this need to be addressed in layered decoding methods. In the proposed circuit, improvements were made to a layered component decoding approach. The method proposed used a plurality of parallel computation blocks coupled to the memory, multiple parity check blocks connected to the computation blocks, and multiple bit update blocks connected to the parity check block. Each bit update block had a memory. The received codeword split in this system, and at least one column/row was grouped and processed.\n\nA low-density parity-check code suitable for efficient hardware implementation was designed with a belief propagation decoder circuit. Codes were arranged according to a sample H matrix whose rows and columns represented the parity check matrix. The decoder circuit had a parity check value that estimated memory, which could be arranged in groups and was logically connected to different data lengths and depths. A parallel adder generated approximate values that were fed to the parity check circuit. The new bitstream generated new values of estimates. These values generated were then stored back in the memory and fed to the bit update circuit. The bit update circuit then updated the new value for the subsequent input data received. Here, layered components decoding was performed by applying the decoding algorithm to each successive layer. Since no particular algorithm was developed, we used a standard to show how the improved decoder works. Applying a decoding algorithm for a particular layer included the use of calculations done in previous layers. The decoding was done using parallelized decoding hardware, and hence its performance may be better than the conventional approach.\n\nThe memory block was a local RAM for storing the estimates that were derived within the iteration. These estimates were stored in the memory to save the chip area. The storage memory had one output coupled to one input of the parallel adder. This was connected to the negative input of the parallel adder to provide a subtrahend for subtraction that took place in the parallel adder. The output of the parallel adder was applied to the parity check update circuitry. This block performed the updating of estimates obtained from memory for each of the parity check nodes. The output of the parity check circuit was applied back to the memory to store updated values. It was also applied to the router circuit to update the input nodes’ Log-Likelihood Ratio (LLR). The router circuitry collected multiplexers and demultiplexers that forward the appropriate estimate terms from memory to the corresponding bit update circuit. The bit update circuits were accumulators through which the current values of LLR of the input nodes were maintained from one iteration to the next iteration.\n\nThe LDPC code was within a parity check matrix H of m × j values and showed a value, H. c = 0 when multiplied by the vector c, considering the Galois field, where c was the transmitted word vector. The Galois field is a finite field that contains a finite number of elements. For each row m of the parity check matrix H, the parity check could be done as H1c1+H2c2+ … Hjcj = 0 over the Galois field. Hence, a parity check equation, the EXOR function of ‘c’, could be written considering the rows of the H matrix having a ‘1’ in their columns.\n\nReferring to Figure 4, soft data received was routed into the decoder system through the data bus. The received data was first routed into the bit update block. Here the data was initialized into its components of a vector. Let us assume the vector for the received data as ‘L’. We defined a set where all the bit columns for a row ‘m’ and the bits in the H matrix have a one in row ‘m’. This makes the checksum for a row over a finite field. The LDPC decoder helps detect errors in the received data when checked for every row in the matrix. When data is received, the values may not be precisely binary values of 1 or 0 but some fractional value and represented by several bits. Hence a probability of whether the bits are 1 or 0 can be represented using the LLR given by:\n\nwhere rj is the input bit value.\n\nAs every input bit arrives, the estimated value is written based on the LLR. Initially, an estimate was assumed for the LLR based on the type of channel being used.\n\nA vector ‘Rmj’ was stored in the SRAM. These were estimates stored in the SRAM after every iteration or cycle of the decoding process and the updated value in the next iteration. The memory stores a few corresponding rows of values of Rmj, representing vector R values for m rows and j columns from a parity check matrix. For every row, the vector L was written as for the checksum:\n\nThe vector was then stored in the BUB. The data were fed into the reverse router block by data buses, where the data was rearranged as required by the system from the BUB. The values of the vector L were given as input to the parallel adder (PA). The other input to the parallel adder came from the memory with the values of the data stored in the form of the components of vector R. The parallel adder performed the operation approximations and subtraction of vector R from L. The results of this subtraction operation in the form of output ‘sum’ were given as input to the parity check circuit and the second set of parallel adders (PA2). A checksum, a sequence of numbers and letters used to detect errors introduced during data transmission, was carried out in the parity check block. The results of this operation were then fed to the second set of parallel adder blocks and the memory block for storage. In the PA2, the computation of the earlier subtraction (R) results and the checksum were added to regenerate the vector L. The new values of L were now sent to the router block to be rearranged into components of vector L. These values were given to the BUB to be stored for the next iteration.\n\n\nResults and discussion\n\nThe DEMUX and MUX circuits developed here were tested as part of the decoder circuit. The results obtained after simulations at different voltage values and using 180 nm technology are highlighted below, with improvements obtained.\n\nThe 1 × 4 demultiplexers for the LDPC decoder were constructed to have one input D and four outputs D0, D1, D2, and D3. The demultiplexer had two select inputs S0 and S1. The select inputs formed the decision-maker to connect the input to a selected output. The selection was based on the four possible combinations of the select input, namely, S0 = 0 and S1 = 1, S0 = 0 and S1 = 1, S0 = 1 and S1 = 0, and finally, S0 = 1 and S1 = 1, representing the binary form 00, 01, 10, and 11. The proposed demultiplexer was simulated to check its characteristics using the Mentor graphics PADS VX.2.7 x86, a CAD tool for 180 nm technology (Open-access software that can perform an equivalent function is DSCH version 2.7for schematic design and MICROWIND version 2.0 for layout analysis).\n\nThe string of data bits was given as input D with the select inputs S0, S1 varied for the four possible combinations. The output satisfied the truth table of the demultiplexer of Table 2. It should also be noted that the voltage rises and falls in Figures 5(a) to 5(c), which are not exactly zero or one. There was a distortion of the signal, but it showed a considerable voltage level to be read as 0 or 1. The voltage variation of 1V, 1.3V, and 1.5V did not significantly affect the output waveforms with only a slight variation in the peak voltage values.\n\nThe waveforms shown in Figures 5(a) to 5(c) represent the distribution of bits received from the adder circuit (refer to Figure 4). The data’s choice is based on S0 (SA) and S1 (SB). The waveforms of D0, D1, D2, and D3 also show the effect of the gates’ switching characteristics, and the peak voltage drops, which is slightly due to the capacitive effect at the input nodes. As the output voltage increases in time, the biasing voltages decrease. A decreasing value of the gate-source voltage reduces the charge density and reduces the output voltage, which does not reach VDD.\n\nThe output voltage was seen to have a delay in reaching the final voltage. This was due to the parasitic capacitance, the gate channel capacitance between the gate-source and gate-drain terminals. Any switching action in the device leads to the formation of parasitic capacitance. A sudden change of voltage from zero to a high value creates a capacitive effect which can be realized as an RC circuit. Resistance is created, and the device consumes more power to drive the circuit, which depicts a delay in the device’s output voltage. It creates a delay when it drives zero loads. The parasitic delay grows linearly with the number of inputs. This effect was seen in the waveforms for the demultiplexer, which displayed a slow increasing ramp voltage. According to simulation result, the demultiplexer area is 10.5 × 25.555 μm2.\n\nThe reverse router had a multiplexer to transmit data bits from the bit update circuit to the parallel adder through the data bus. The characteristic of the multiplexer was to choose a particular input to be connected to the output. The selection of the input was based on the two select signals. In Figure 3, the schematic of the multiplexer is shown. The multiplexer had four inputs IA, IB, IC, and ID, and a single output Z. The select inputs were SA and SB. Hence the multiplexer was a 4 × 1 MUX. Since there are only two select lines, the possible input lines were four, and the possible combination was SBSA = 00, SBSA = 01, SBSA = 10, and SBSA = 11. In line with the truth table in Table 1, if SB = 0 and SA = 0, the line selected would be IA since the combination 00 is for I0(IA) line. The schematic in Figure 3 is simulated using the test bench. The 180 nm technology was used for the simulation and voltage values of 1 V, 1.3 V, 1.5 V, and 2.5 V. The output observed satisfied the truth table, Table 1. Here the threshold voltage loss restricts the output voltage to the range [0V, VDD – VTn].\n\nThe proposed multiplexer circuit was simulated for voltage versus time using 180 nm for input voltages of 1 V, 1.3 V, and 1.5 V, and the output waveforms are shown in Figures 6(a) to 6(c), respectively. Figures 6(a) to 6(c) show the output voltage of the selected input to be given to the output. Even though the output waveform represented the correct selected input, it delayed reaching the maximum voltage. For some inputs, it did not reach the minimum zero value. It was the delay caused by the inverter, and the threshold voltage loss restricted the maximum voltage. Charging the output for a logic one voltage was very slow compared to the transition to a logic 0. The parasitic capacitance increased the charging time from low to high since it was diverted from the output node. The charging of the output capacitance was time-dependent and began as linear as (t/2τn) and then levelled out.\n\nSince Vout(t) increases in time, the device bias voltages VGS – VDD – Vout (t) = VDS decreases with time. A decreasing value of VGS reduces the channel charge density, while smaller VDS shows a reduction of the drain-source electric field. This indicates that it is difficult to pass a logic 1 voltage through the n-channel transistor. The spikes seen in the output were caused due to the capacitive coupling of the input to the output by the gate-drain capacitance. As the input suddenly increased from 0 V to VDD, the capacitance did not have enough time to drop its voltage instantly. Hence, it would have retained some amount of charge and is seen as spikes of voltage. The proposed multiplexer circuit area is 9.9 × 32.155 μm2.\n\nThe multiplexer and demultiplexer circuits were simulated using the SilTerra CEDEC pyxis project of the Mentor graphics CAD tool PADS VX.2.7 x86. The simulation environment was an input voltage value of 1 V, 1.3 V, and 1.5 V for 180 nm technology, tabulated in Table 3. The results showed a low power dissipation in nanowatts. This is because of pass transistor logic, which reduced the number of transistors used and is reflected in the results. A reduced number of transistors (12, 14) led to lower power dissipation and reduced layout area. The delay is only 80 ns and 130 ns for DEMUX and MUX, respectively.\n\nTable 4 shows a comparison of the proposed circuit with various published research. It can be seen that the proposed circuit performs better. In terms of power dissipation, the proposed multiplexer circuit has a power dissipation of 7.067 nW, whereas Bousseaud and Negra7 had a value of 5 mW. The approach used by Bousseaud and Negra7 used a transmission gate, while pass transistor logic is used in the proposed circuit. Pass Transistor Logic (PTL) does provide an advantage in the design of circuits with the elimination of redundant transistors. When the number of transistors was reduced, it had a lower power dissipation as each transistor occupied some area and dissipated power. For the DEMUX circuit, the power dissipation produced by Saseendran and Mehra6 had a value of 142 uW, and for the proposed circuit, it was 5.14 nW. The input voltage also tended to be at a lower value of 1.5 V. There was a huge difference in the number of transistors used in the design.\n\nThe bit update circuit received new data and then arranged them into its vectors and routes them to the multiplexer as input to the parallel adder. In each iteration of the decoder circuit, the bit update circuit restored new data values after rewriting the data received from the router circuit with data from the transmitter received through the data bus. The bit update circuit was simulated for voltage versus time using 180 nm for input voltages of 1 V, 1.3 V 1.5 V, and 2.5 V, and the output waveforms are shown in the Figures 7(a) to 7(d), respectively.\n\nFigures 7(a) to 7(d) depict the output obtained for the bit update circuit. The arrival of the clock signal at the input nodes caused clock skew due to the capacitive coupling effect. At the output of 1.5V, it can be observed that the waveform has glitches. Glitches are temporary changes in the value of the output. They were caused due to the skew in the input signals to the gate of the transistor. Glitches can be reduced by gate sizing and path balancing techniques. Propagation of glitches can be reduced by using a smaller number of inverters, which tend to amplify and propagate glitches. At a higher voltage of 2.5 V, the output showed a smooth and expected waveform. The area of the bit update circuit is 46.42 × 14.62 μm2.\n\nThe whole LDPC circuit was designed according to Figure 4. The components added to the test bench would be the VDD, the ground terminal (GND), DC, and pulse. The DC was the input voltage of 1 V, 1.3 V, and 1.5 V. We needed to set the delay (1ns), initial value (0 V), period (50 ns), the pulse value and the rise time and fall time, and the width of the pulse. The bit pattern to be run through the decoder was also specified. The proposed decoder circuits were simulated for voltage vs. time effect on the output voltage for different input voltages, as shown in Figures 8(a) to 8(c). The input voltages used were 1 V, 1.3 V, and 1.5 V at 180 nm technology.\n\nThe carry inputs to the second set of parallel adders are also shown as check 0 to check 3. The output was measured at various points of the circuit, that is, the output of the memory unit (Vo1), the output of the adder (Vo2), the output of the parity check (Vo3), the output of the router (Vo4), and the final at the reverse router (VoF). It was observed that at the initial points of the check, the output voltage did not suffer from any loss of signal. As the circuit became larger, all effects of power loss come into play due to the different circuits. At the final output (VoF), glitches were observed at regular intervals. This happened to off-pass transistors where the source and drain were initially high and then pulled low. The output of the router circuit shows the waveform reached the peak voltage but did not reach the zero line. This represents the presence of some minimum voltage that did not allow the voltage to reach zero. Practically, the drain current of a CMOS transistor does not reach zero once the voltage of the gate terminal goes below the threshold voltage.\n\nThese values are the most updated: the parity check unit block (PUCB) and the values used for the next iteration.23 The flow of data into the circuit with the input of received data at the bit update circuit was tested with bits of data given using the rows from a standard H matrix. Every stage of the movement of the bits through each layer, namely bit update, reverse router through the data bus to parallel adder one and from the adder to the parity check block, a second set of the parallel adders, and the stored data in the memory has been simulated and outputs observed.\n\nThe results of individual layers and the entire decoder are tabulated in Table 5. Various input voltages were given to observe the effect on the decoder. The decoder circuit designed achieved low power dissipation and a reasonable delay improvement.\n\nIn Table 6, the obtained results for the LDPC decoder are compared and analyzed with other published work.\n\nThe proposed circuit performed better in power dissipation than work done by Lee et al.21 The power dissipated by the proposed circuit is in nanowatts, while all references are in milliwatts (19, 21). This may be because the proposed circuit was designed using pass transistor logic, which reduced the number of transistors. CMOS circuits dissipate power during switching times.\n\nHence, reducing the switching activity reduced the power dissipation. Other studies19–21 achieved 7.92 Gbps, 3.9 Gbps and 1956.5 Mbps for 90 nm, 65 nm, and 90 nm technology, respectively. The proposed circuit simulated for 180 nm obtained the throughput 12.184 Mbps, 12.496 Mbps, and 12.496 Mbps for input voltages of 1V, 1.3V, and 1.5V. The throughput didn’t give a better value because the circuit was designed to function well at lower voltages, which is a trade-off with low supply voltage, lower power dissipation, and smaller area with throughput. We used 1V, 1.3V, and 1.5V, and performance at 1.5V was much better in power dissipation and throughput. At lower voltages, the noise margin becomes critical. The area of the proposed circuit is in nanometres squared, which is also reduced compared to Bhargava et al.21 (Table 6).\n\n\nConclusion\n\nThe proposed router circuit, which includes the multiplexer and demultiplexer circuits was designed using pass transistor logic. The proposed circuit gave better power dissipation and throughput performance compared with existing circuits due to the reduced critical path. The circuits were simulated using the Mentor Graphics CAD tool for the design and layout. The results obtained show a significant improvement in power dissipation, area, and delay. For the multiplexer, the improvement in power was 99%, but there was a difference in the technology used. The number of transistors used in the proposed circuit was also significantly reduced, which was the intention of this work. The delay obtained was 80 ns, and the area of 10.5 × 25.55 μm2 for the demultiplexer and 9.9 × 32.15 μm2 was considered small. The designed circuit silicon area utilization ensured reduced delay and power dissipation, making the router circuitry seemingly fitting for use in the decoder circuit. The multiplexer and demultiplexer circuits can be used in an LDPC decoder, which uses the layered approach. The multiplexer received input from the bit update block based on the state of the select inputs. The select inputs chose which data bits needed to be routed to the parallel adder block for the next iteration.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
"appendix": "Acknowledgements\n\nWe would like to thank the anonymous referees for their valuable suggestions. We thank our beloved Multimedia University for supporting this work.\n\n\nReferences\n\nHassan AES, Dessouky M, Elazm AA, et al.: Evaluation of Complexity Versus Performance for Turbo Code and LDPC Under Different Code Rates. The Fourth International Conference on Advances in Satellite and Space Communications. Egypt: 2012; 98–102.\n\nJahangir MZ, Mounika J: Design and simulation of an innovative CMOS ternary 3to1multiplexer and the design of ternary half adder using ternary 3 to 1 multiplexer. Microelectron. J. 2019; 90: 82–87. Publisher Full Text\n\nUeng Y-L, Yang B-J, Chung-Jay Yang C-J, et al.: An efficient Multi-standard LDPC decoder design using Hardware-friendly Shuffled Decoding. IEEE Transactions on Circuits and Systems-1. 2013; 60(3): 743–756. Publisher Full Text\n\nZhao Z, Yang K, Zheng H, et al.: Design, Simulation, and Implementation of a CMOS analog decoder (480,240) for Low-Density Parity-Check Codes. IEEE Access Journal. 2017; 5: 17381–17391. Publisher Full Text\n\nKhan SA: Digital Design of Signal Processing Systems-A Practical Approach. Wiley publications; 2011. Publisher Full Text\n\nSaseendran TK, Mehra R: Area and Power Efficient CMOS De-multiplexer Layout on 90nm Technology. International Journal of Scientific Research Engineering & Technology (IJSRET). 2015; 102–105. 2278–0882 EATHD-2015 Conference Proceeding.\n\nBousseaud P, Negra R: Low power high-speed 10 Gb/s 4∶1 multiplexer for sliding-IF digital-centric transmitter in 65nm CMOS. German Microwave Conference (GeMiC), Bochum,. 2016; pp. 349–352. Publisher Full Text\n\nPandey V, Akashe S: Design Techniques for Self-Voltage Controllable Circuit on 2:1 multiplexer using 45nm Technology. Int. J. Comput. Appl. 2014; 89: 11–18. Publisher Full Text\n\nAnitha K, Jayachitra R: Design, and Analysis of CMOS and Adiabatic logic using 1:16 Multiplexer and 16:1 Demultiplexer. International Journal of Advanced Research in Electrical, Electronics and Instrumentation Engineering. 2015; 4(12): 8–17.\n\nAhn SH, Kim JB: Design of an 11Gb/s CMOS Demultiplexer Using Redundant Multi-Valued Logic. 8th International Conference on Solid-State and Integrated Circuit Technology Proceedings, Shanghai, China. 1580–1582.\n\nKapilachander T, Shanavas HI, Venkataraman V: Technical Study on low power VLSI methods. International Journal Information Engineering and Electronic Business. 2012; 4: 60–70. Publisher Full Text\n\nKavitha S, Hashim FH, Md. Mamun IR, et al.: Design of a low-power and high throughput error detection and correction circuit using the 4t ex-or method. Journal of Engineering Science and Technology (JESTEC). 2017; 12(8): 2010–2027.\n\nMcKay DJC, Neal RM: Near Shannon Limit performance of low-density parity-check codes. Electron. Lett. 1996; 32: 1645. Publisher Full Text\n\nPant D, Pandey A, Mehra R: CMOS Design of 2:1 Multiplexer Using Complementary Pass Transistor Logic. National Conference ADVICE-12, NITTTR, Chandigarh. 2012; pp 1–7.\n\nPari SC: Low Power Arithmetic Circuit Design for Multimedia Applications. Sharma M, Gautam R, Khan M, editors. Design and Modeling of Low Power VLSI Systems. Hershey, PA: IGI Global; 2016; (pp. 252–282). Publisher Full Text\n\nSelvam RDK, Senthilpari C, Lini L: Design of a 16-bit adder for decoder application circuit. J. Eng. Sci. Technol. (JESTEC). 2019; 249–260.\n\nSelvam RDK, Senthilpari C, Lini L: Improved Speed Low Power Low Voltage SRAM Design for LDPC Application circuits. Journal of Engineering Science and Technology (JESTEC). 2018; 822–837.\n\nKavitha S, Hashim FH, Kamal N: A New Approach of an Error Detecting and Correcting Circuit by Arithmetic Logic Blocks. Int. J. Electron. Telecommun. 2018; 65(2): 313–318.\n\nSipos E, Festila L, Oltean G: Towards reconfigurable circuits based on ternary controlled analog multiplexers/demultiplexers. Proceedings of the 12th International Conference KES Part III Heidelberg, Berlin. 2008; 351–359.\n\nSenthilpari C, Velrajkumar P, Diwakar JSF: Design A Low Power and High Throughput Error Detection and Data Correction Architecture by Razor II Method. PalArch's J. Archaeol. Egypt/ Egyptol. 2020; 17(9): 4393–4410.\n\nLee X-R, Chen C-L, Chang H-C, et al.: A 7.92 Gb/s 437.2 mW Stochastic LDPC Decoder Chip for IEEE 802.15.3c Applications. IEEE Trans. Circuits Syst. 2015; 62(2): 507–516. Publisher Full Text\n\nBhargava L, Bose R, Balakrishnan M: Novel hardware implementation of LLR-based non-binary LDPC decoders. 2013 National Conference on Communications (NCC), 2013. 2017; pp 1–5. Publisher Full Text\n\nIsmail M, Ahmed I, Coon J: Low Power Decoding of LDPC Codes. International Scholarly ResearchNotices. 2013; 2013: 1–12. Publisher Full Text"
}
|
[
{
"id": "121437",
"date": "17 Feb 2022",
"name": "Suthendran Kannan",
"expertise": [
"Reviewer Expertise Wireless Communication"
],
"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 have gone through this manuscript titled “Low power, less occupying area, and improved speed of a 4-bit router/re-router circuit for low-density parity-check (LDPC) decoders’’ which is well written and formatted. Even though some points are against its quality as listed below:\nAbstract is well written; according to the title, this manuscript occupies less area, which has to be illustrate in the result section of the abstract The introduction is excellent, but if the author adds a text about sections it is well and good Is it necessary to keep tables 1 and 2? If not, remove it Why not give an equation number for the below text equation “Gate-Source voltage VGS is equal to Vin, that is:” Page number 4? Figure 5 (a)- 5(c); the output waveform got a skew problem, how to get it and explain in the relevant page? The results and explanations are good, and sufficient materials included.\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "142900",
"date": "19 Jul 2022",
"name": "Hamed Farbeh",
"expertise": [
"Reviewer Expertise Reliability",
"Fault tolerance",
"Internet-of-Things",
"Memory technology",
"Hardware accelerators."
],
"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 proposes an efficient circuit for parity check decoder to reduce power consumption, delay, and area of the circuit. The authors tried to optimize the (de)mux circuitry for passing the data bits through the circuit. The evaluation on 180nm technology node show considerable improvement in targeted parameters. The manuscript is fluent and the contributions are clear. My major concerns are as follows:\nThe evaluations are performed on outdated 180nm feature size. As we are on less than 5nm technology, how scalable and valid are the observations and improvements of this work? What about the compatibility of the proposal to very smaller technology nodes? A discussion in these directions is necessary. The authors reported the absolute value of some parameters, but it does not make any sense when not compared to the state-of-the-art or a reference value. It is recommended to report the comparative values (maybe the percentage of improvements can help). By “EXOR” gate, are the authors referring to well-known “XOR” gate? Table 4 is strange to me. The authors reported their evaluation on the proposed circuit and the competitors, but they are not evaluated based on the same technology node. When comparing several designs for a circuit, their efficiency is comparable only when evaluated in the same scenario. To my understanding, the authors just used the report of each paper in the table for other schemes and did not implement them in their own experimental platform. If so, the results cannot be technically sound. I strongly recommend the authors to evaluate all schemes in the same evaluation platform. The literature review is weak and needs to be more comprehensive. In minimum, the state-of-the-art (DE)MUXs in Table 4 should be discussed. This helps to better highlight the distinction between this work and the existing ones.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-7
|
https://f1000research.com/articles/11-1295/v1
|
11 Nov 22
|
{
"type": "Research Article",
"title": "Development of phase change materials for low-temperature thermal energy storage application",
"authors": [
"Kamal Nayan",
"Abhishek Anand",
"Amritanshu Shukla",
"Dharam Buddhi",
"Atul Sharma",
"Kamal Nayan",
"Abhishek Anand",
"Amritanshu Shukla",
"Dharam Buddhi"
],
"abstract": "Background: Energy storage is very critical for reducing the mismatch between demand and supply thus offering better management capabilities. It reduces the peak energy demand and increases efficiency, security, and reliability. There is unavailability of low-cost phase change materials (PCMs) in the lower temperature range. Methods: This study discusses the creation of eutectic from capric acid and paraffin wax. A series of blending of capric acid/paraffin wax (CA/PW) were prepared, having variable weight-composition. The thermophysical properties were obtained using differential scanning calorimetry, Further, thermal cycle testing was done to understand the thermal stability and reliability of the prepared eutectics. Results: The area underneath the peak is used to calculate the latent heat of fusion, and the tangent of the steepest slope at the peak of the crest is used to calculate the melting temperature (Tm). Differential scanning calorimetry results showed the developed eutectic had an appropriate melting temperature and adequate latent heat of fusion of 29.86 °C - 30.60 °C and 154.15–198.62 kJ/kg respectively, and can be used for various thermal energy storage applications in buildings, solar absorption chillers, surgical dress/clinical bed, and photovoltaic systems. Conclusions: The accelerated thermal cycle of the same confirmed its thermal stability up to 500 heating and cooling cycles. It was discovered that variable heating and cooling speeds had no significant influence on the melting temperature and latent heat of fusion of PW/CA eutectics. Further, the economic study revealed that the created PCM is inexpensive and readily available in the Indian market.",
"keywords": [
"Phase change materials",
"Capric acid",
"Paraffin",
"DSC"
],
"content": "Introduction\n\nWhen energy output is insufficient to meet demand, efficient use of existing energy is critical.1 Thermal energy may be stored in three ways, namely: thermochemical energy storage, sensible heat storage, and latent heat storage (LHS). Thermal energy is absorbed or released in a thermochemical heat storage method by using a completely reversible chemical mechanism to break and mend molecular bonds. In sensible heat storage, thermal energy is stored by heating a solid or liquid to the appropirate temperature. The LHS method relies on the absorption or release of heat during the solid-liquid transition, or liquid-gas transition, as a storage medium. Phase change materials (PCMs) are a type of LHS material that can store and release a significant amount of energy per unit mass.2 This energy transfer happens whenever there is a transition from solid to liquid or liquid to solid. This whole process is isothermal. Among all the listed methods, the LHS is the most appealing, and it is capable of compensating for the energy mismatch between the production and consumption of heat.3,4 There are different kinds of PCMs (organic, inorganic, eutectic) that can melt or solidify at a range of temperatures, and they can be used for a range of applications depending on the temperature. PCMs, find their application in energy-efficient buildings, industrial waste heat recovery, central air-conditioning systems, solar thermal energy storage, temperature-adapted greenhouses, and thermoregulating fibers.3,4\n\nAmong the PCMs investigated, fatty acids, paraffin wax (PW), and their mixtures have drawn a lot of attention. The reasons being that fatty acids have high latent heat of fusion (LHF), exhibit consistent melting, and freezing characteristics, as well as freezing without supercooling, low vapor pressure, non-toxic, minimal volume change during solid-liquid/liquid-solid transitions, self-nucleating characteristics, good chemical and thermal stability over an extended duration of usage, and easy availability.3,5 Animal and plant-derived fatty acids have the extra benefit of providing a constant supply, notwithstanding fuel shortages. Apart from that, fatty acids are abundant due to their bio-origin and are recyclable, eco-friendly due to lower carbon emissions, and essential for long-term growth.6 The major challenge of employing fatty acids as PCM is their pungent stench, corrosive nature, and notably their rapid sublimation rate.7 On the other hand, the advantage of using PW is that it is non-corrosive, safe, reliable, chemically stable, inert below 500 °C, has low vapor pressure in the melt form, minimal volume change during solid-liquid, and liquid-solid transition, and is less expensive as compared to other PCMs.3,8 PW has certain undesirable characteristics, such as being mildly flammable and incompatible with plastic containers.3,8 In his research, Kahwaji et al. looked at the thermophysical properties, thermal stability, and chemical compatibility of paraffin PCMs. PW48, PW52, and PW58 have melting temperature (Tm) values of 48.2 1.5 °C, 51.8 1.5 °C, and 57.7 1.5 °C, respectively. For the same, the LHF were 156 16 kJ/kg, 171 17 kJ/kg, and 197 20 kJ/kg, respectively. The thermal stability of paraffin PCMs was reported to be over 3000 thermal cycles with no notable change in Tm and LHF.9 In their solar chimney, Fadaei et al. employed PW as the PCM. The Tm and LHF of the paraffin utilized were recorded to be 44-46 °C and 189 kJ/kg, respectively. And it was discovered that using PW as PCM improved the solar chimney's thermal efficiency.10 Omara et al. studied the thermal performance of a solar water heating system combined with PCM that used a flat plate as a heat source in their study. The system's total energy and exergy were determined to be 85 and 76 %, respectively, and the recorded Tm of paraffin PCM was found to be 56 °C.11 Agarwal and Sarviya12 measured the Tm of commercial and LHF paraffin samples as 41-55 °C and 176 kJ/kg, respectively. Commercial PW was determined to be suitable for sun dryer applications based on the findings of the trial. Mahdi et al.13 conducted an experimental study on latent heat thermal helical coil thermal energy storage for melting and solidification phases. PW (type P56-58) was chosen for the job. PW was been determined to have Tm and LHF of 48.3-62 °C and 114.5 kJ/kg, respectively. The results demonstrated that coiled tube latent heat energy storage may be effectively utilized in solar thermal applications. To minimize the absolute drying time of crops in typical sun dryers, Vijayrakesh et al. used PW with Tm equal to 53.7 °C and LHF equal to 190 kJ/kg as PCM-packed floor.14 Bhagyalakshmi et al. developed a binary eutectic mixture of palmitic acid (60%) and PW (40%). The recorded Tm, solidification temperature, latent heat during charging, and latent heat during discharging were 52.6–59.8 °C, 40.9–47.1 °C, 214.7 kJ/kg, and 194.6 kJ/kg respectively.15\n\nThermal energy storage (TES) systems still confront some serious challenges including the stability and reliability of PCM/construction material composites. The PCM must remain useful for an extended length of time in the thermal system. Another major concern is that after repeated cycles of heating and cooling, long-term use of PCM leads to leakage from the building material. Another issue is the thermal stress caused by PCMs and corrosion, which leads to the downfall of the building material.5,16,17 In addition, PCMs for low-temperature applications are scarce. A lot of studies have been carried out during the last few decades, particularly in this direction, however, there is still a need for commercial PCM especially working between 30-60 °C, and should be widely accessible and reasonably priced in the local market.\n\nA eutectic mixture is a mixture of multiple solids that melts or solidifies at a single temperature lower than the constituents' melting points. Generally, the melting point is sharp, and it has a somewhat larger storage density than the parent materials. The authors in their study chose capric acid (CA) and PW because of their high LHF, appropriate heat transfer properties throughout the phase change transition, easy availability, and low cost of the material. Aside from that, there is a scarcity of PCMs operating in the temperature range of 25-32 °C for construction and solar applications, and those that are available are considerably more expensive than other PCMs. The study's overall purpose is to create low-cost PCMs for TES applications. Binary mixes based on 98.5 % purity CA and laboratory grade (LR-grade) PW with varying weight ratios (10/90, 20/80, 30/70, 40/60, 50/50, 60/40, 70/30, 80/20,90/10, 92/08, 94/06, 96/04, and 98/02) were created for this purpose. The differential scanning calorimetry (DSC) method was used to assess their thermal properties. The developed PCM in the present study is cheap to buy (see Table 2) and readily accessible in India and abroad and can be employed for thermal energy applications.\n\n\nMethods\n\nThe CA (purity 98.5%) and LR grade PW were procured from the Avra Synthesis Pvt. Ltd., Hyderabad, India, and SD fine-CHEM Ltd., Mumbai, India respectively, and the same was utilized without any purification for the preparation of mixtures. To determine the composition of the eutectic mixture, a sequence of binary combinations of CA and PW with different weight proportions were produced (10/90, 20/80, 30/70, 40/60, 50/50, 60/40, 70/30, 80/20,90/10, 92/08, 94/06, 96/04, and 98/02) from their liquid mixtures at constant temperature (70 °C), using magnetic stirrer with a hot plate. Thirteen such units (100g each) were made employing a mixture of CA and PW. These mixtures were initially in liquid form and then kept at room temperature for about an hour for gentle cooling and solidification. Throughout the experiment, an extremely precise and dependable semi-analytical digital balance with an accuracy of about ±0.0001 g was used to complete all weights measurements. The key thermal characteristics required to establish any material as a PCM for TES systems are LHF, Tm, and Tf. The Tm, LHF, of CA, PW, and their eutectic mixes were determined using the DSC method. In DSC, a sample and a reference material is heated in separate aluminum pans at a constant rate of temperature rise. Differences in temperature between the two are proportional to the difference in heat flow between them, and the DSC curve serves as the record. PerkinElmer DSC 4000 equipment was used to test the thermal behavior of all produced eutectics. The prepared samples were investigated between 15 °C and 80 °C at a 2 °C min-1 heating rate. Throughout the experiment, nitrogen was used as a purge gas, and the constant flow rate was maintained at 20 ml min−1. The largest deviation in enthalpy and temperature measurements was ±2% and ±0.1°C respectively. Thermal properties such as Tm, LHF, Tf, and LHC of CA, and PW procured from Avra Synthesis Pvt. Ltd. and SD fine-CHEM Ltd. respectively were measured by DSC with 2 °C scanning heating/cooling rate at 0th cycle and information provided from the manufacturer is listed in Table 1.\n\na Measured through differential scanning calorimetry (DSC) with 2°C scanning heating/cooling rate at zeroth cycle.\n\nb One US$ = 76.3065 INR (15 December 15, 2021, 14:10:00 UTC, https://www.google.com/finance/quote/USD-INR).\n\n\nResults and discussion\n\nThe CA’s DSC curve has a single, sharp peak that represents the solid-to-liquid transition (Figure 1). The PW’s DSC curve (Figure 2) contains two peaks: the first, which is not as sharp and significant suggests a solid-solid transition, and the second, which is sharp and significant, shows a solid-liquid transformation.12 Figures 1 and 2 show the melting curve of CA and PW respectively, measured using DSC with a 2 °C scanning heating and the cooling rate at 0th cycle.\n\nThe onset melting point, peak melting point, and LHF of the prepared samples are listed in Table 2. Based on the result, it is clear that the melting point of mixes increases with decreasing the mass ratio of PW until it reaches 8%, and then it decreases at 6% and a further decrease in mass percentage again increases the melting point. In the case of LHF, it was discovered that raising the mass percentage of CA in the mixture causes LHF to rise. LHF of developed mixtures grew until the CA amount reached 94%, after which it began to decline. Figure 3 shows the DSC melting thermograph of a binary eutectic mixture of CA and PW (PWCA-0694). Most of the developed mixes have sufficient LHF value, and based on their melting point range (26.14 °C-30.60 °C), they can be used for TES applications in solar absorption chillers, buildings, surgical dress, clinical beds, and photovoltaic systems.5,16,17\n\na Measured through Differential scanning calorimetry. PWCA, paraffin wax capric acid.\n\nTo check the effect of different heating and cooling rates on Tm, different heating and cooling rates were used for the 400th thermal cycle of the CA/PW eutectic mixture to examine the influence of scan rate on Tm and LHF. The Figure 4 displays the CA/PW eutectic mixture (94/06 wt.%) DSC curve for the 400th heating and cooling cycle at 1 °C min-1, 2 °C min-1, and 5 °C min-1 scan rates. To investigate whether the heating/cooling pace has any influence on Tm, CA/PW, eutectic mixture (94/06 wt.%) in a cyclic manner was scanned at different heating rates (1, 2, and 5 °C min-1) under a constant flow of nitrogen at a flow rate of 20 ml min-1. During solid-liquid transition different scan rates produced different heat flow magnitudes. The DSC curve of the CA/PW eutectic mixture (94/06 wt.%) for various heating and cooling rates exhibited a smaller peak for low scan rate and a bigger peak for high scan rate Figure 4. The onset melting point did not change much with different scan rates because the leading edge slope remained constant. Based on the findings, it is reasonable to say that the onset melting point is independent of heating and cooling rates. Figure 4 shows, with increasing scan rate, the peak melting point shifts towards higher temperature. LHF for different scan rates can be approximated by peak area divided by scan rate.18 From the Table 3, it can be seen that for different scan rates LHF is nearly the same. And the table depicts Tm and LHF of PWCA-0694 for the 400th heating/cooling cycle for different scanning rates. Based on the findings, for the 400th heating/cooling cycle, there is not much difference in Tm and LHF at different scan rates, indicating the thermal behavior of samples to be similar at different heating and cooling rates.\n\na Measured through differential scanning calorimetry.\n\nThe Tm and LHF of a binary eutectic mixture (PWCA-0694) were measured after every 100th heat cycle, for a total of 500 cycles. The Figure 5 shows the DSC curves for the 0th- 500th thermal cycle at the succession of 100 thermal cycles of eutectic PCM. The maximum deviation in Tm and LHF was found to be +0.36 °C and -39.65 kJ/kg respectively as shown in Figure 6. The negative and positive values of Tm and LHF are solely relative to the 0th cycle, where positive represents an increase in value and negative represents a decrease in value relative to the 0th cycle. The Tm and LHF variation of the developed eutectic mixture is within acceptable limits. The developed mixture was thermally stable up to 500 cycles.\n\nThe PCMs developed by the authors' group are fairly less expensive in contrast to materials already in use in the market for alike applications (see Table 2). Whether, as per the information received from the local vendors, the cost of our CA is 20.96 $/kg and PW is 14.44 $/kg in the Indian market. The cost of the developed eutectic mixture is 15.09 – 20.82 $/kg, which may be further reduced by 30% to 40% if mass production is done.\n\n\nConclusions\n\nThe PCM development for TES applications is presented in this paper, which is based on binary mixes of CA and PW with various weightratios. The DSC technique was used to analyze the thermal characteristics of these binary blends, which revealed that a few of the developed materials had suitable phase change temperatures and high LHF. The most promising mass percentages of PW contained in CA were determined to be 02–10 wt.%, with reduced Tm of 29.86 °C - 30.42 °C and LHF 154.15–198.62 kJ/kg. From DSC analysis, it was found that the Tm of mixes raises with decreasing the mass percentage of PW until it reaches 8%, and then it decreases to 6% and a further decrease in mass percentage again increases the melting point. In the case of LHF, it was discovered that raising the mass percentage of CA in the combination causes LHF to rise. LHF of developed mixtures grew until the CA percentage reached 94%, after which it began to decline. The developed mixes were found to be suitable for TES applications in buildings, solar absorption chillers, surgical dress/clinical beds, and photovoltaic systems. Because of congruent mixing, desired melting range, and high LHF, PWCA0694 (CA 94 wt.% and PW 06 wt.%) was found to be the most promising mixture of all. From DSC analysis, its melting point was found to be 30.16 °C and LHF to be 198.62 kJ/kg and can be used for application in buildings and photovoltaic systems. Per the findings, different heating and cooling pace have virtually negligible influence on PWCA0694's Tm and LHF. It was also found that with increasing scan rate, the peak melting point shifts towards higher temperature. DSC analysis of 400th thermal cycles with varied scan rates revealed almost identical results, demonstrating that the thermal characteristics of the sample were constant except for the peak melting point, which rose with increasing heating rate. Accelerated thermal cycling test confirmed the structural and thermal stability of our developed PCM up to 500 thermal cycles. From the investigation, it was also found that the maximum percentage difference in Tm and LHF of PWCA0694 was +0.36°C and -39.65 kJ/kg respectively, which were within an acceptable range. The cost of our developed eutectic is cheap and are easily available in Indian or abroad market. If mass production is done then it can further reduce by 30-40%.",
"appendix": "Data availability\n\nFigshare: DSC data, https://doi.org/10.6084/m9.figshare.21424239.v2. 19\n\nFigshare: Cost analysis data, https://doi.org/10.6084/m9.figshare.21424491.v1. 20\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\nJacobson MZ, Delucchi MA: Providing all global energy with wind, water, and solar power, Part I: Technologies, energy resources, quantities and areas of infrastructure, and materials. Energy Policy. 2011; 39: 1154–1169. Publisher Full Text\n\nTian Y, Zhao CY: A review of solar collectors and thermal energy storage in solar thermal applications. Appl. Energy. 2013; 104: 538–553. Publisher Full Text\n\nSharma A, Tyagi VV, Chen CR, et al.: Review on thermal energy storage with phase change materials and applications. Renew. Sust. Energ. Rev. 2009; 13: 318–345. Publisher Full Text\n\nZhou D, Zhao CY, Tian Y: Review on thermal energy storage with phase change materials (PCMs) in building applications. Appl. Energy. 2012; 92: 593–605. Publisher Full Text\n\nSharma A, Shukla A, Chen CR, et al.: Development of phase change materials for building applications. Energ. Buildings. 2013; 64: 403–407. Publisher Full Text\n\nOkogeri O, Stathopoulos VN: What about greener phase change materials? A review on biobased phase change materials for thermal energy storage applications. Int. J. Thermofluids. 2021; 10: 100081. Publisher Full Text\n\nRozanna D, Chuah TG, Salmiah A, et al.: Fatty Acids as Phase Change Materials (PCMs) for Thermal Energy Storage: A Review. Int. J. Green Energy. 2005; 1: 495–513. Publisher Full Text\n\nReza Vakhshouri A: Paraffin as Phase Change Material, Paraffin - an Overview.2020. Publisher Full Text\n\nKahwaji S, Johnson MB, Kheirabadi AC, et al.: A comprehensive study of properties of paraffin phase change materials for solar thermal energy storage and thermal management applications. Energy. 2018; 162: 1169–1182. Publisher Full Text\n\nFadaei N, Kasaeian A, Akbarzadeh A, et al.: Experimental investigation of solar chimney with phase change material (PCM). Renew. Energy. 2018; 123: 26–35. Publisher Full Text\n\nOmara AAM, Abuelnuor AAA, Dafaallah MAA, et al.: Energy and Exergy analysis of solar water heating system integrated with phase change material (PCM). 2018 Int. Conf. Comput. Control. Electr. Electron. Eng. ICCCEEE. 2018; (2018): 1–5. Publisher Full Text\n\nAgarwal A, Sarviya RM: Characterization of Commercial Grade Paraffin wax as Latent Heat Storage material for Solar dryers. Mater. Today Proc. 2017; 4: 779–789. Publisher Full Text\n\nMahdi MS, Mahood HB, Khadom AA, et al.: Experimental investigation of the thermal performance of a helical coil latent heat thermal energy storage for solar energy applications. Therm. Sci. Eng. Prog. 2019; 10: 287–298. Publisher Full Text\n\nVijayrakesh K, Muthuvel S, Gopinath GR, et al.: Experimental investigation of the performance of paraffin wax-packed floor on a solar dryer. J. Energy Storage. 2021; 43: 103163. Publisher Full Text\n\nBhagyalakshmi P, Rajan K, Senthil Kumar KR: A comparative study of spherical and cylindrical shells thermal energy storage systems using paraffin wax-palmitic acid and their eutectic mixture. Int. J. Ambient Energy. 2021; 43: 4153–4162. Publisher Full Text\n\nSharma A, Shukla A, Chen CR, et al.: Development of phase change materials (PCMs) for low temperature energy storage applications. Sustain. Energy Technol. Assessments. 2014; 7: 17–21. Publisher Full Text\n\nAnand A, Shukla A, Kumar A, et al.: Development and characterization of ternary mixture series of medium- and long-chain saturated fatty acids for energy applications. Energy Storage. 2020; 2: 1–10. Publisher Full Text\n\nWang G, Harrison IR: Polymer melting: heating rate effects on DSC melting peaks. Thermochim. Acta. 1994; 231: 203–213. Publisher Full Text\n\nNayan K, Anand A, Shukla A, et al.:DSC data. figshare. [Dataset].2022. Publisher Full Text\n\nNayan K, Anand A, Shukla A, et al.:Cost analysis.xlsx. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "347775",
"date": "18 Dec 2024",
"name": "Veerakumar Chinnasamy",
"expertise": [
"Reviewer Expertise Thermal Energy Storage and Phase Change 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\nThis article presented research on preparing a binary eutectic PCM using CA and PW. The phase change properties and thermal cycling stability were investigated. The following comments need to be addressed: The eutectic point of the CA/PW mixture has to be estimated theoretically and compared with the experimental results. What is the rationale behind the shift in peak melting point at the different heating rates? Why the onset melting point is not affected by the heating rate? In conclusion, it is mentioned that \"The most promising mass percentages of PW contained in CA were determined to be 02–10 wt.%\". This is confusing and it should be 10wt%, not 02-10wt%. What is the meaning of 'congruent mixing' mentioned in the conclusion? Generally, at the eutectic point, a concurrent phase change occurs.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1295
|
https://f1000research.com/articles/11-1281/v1
|
09 Nov 22
|
{
"type": "Research Article",
"title": "PD-L1 expression as predictor of immunotherapy eligibility in penile squamous cell carcinoma patients",
"authors": [
"Muhammad Haritsyah Warli",
"Fauriski Febrian Prapiska",
"Ginanda Putra Siregar",
"Bungaran Sihombing",
"Syah Mirsya Warli",
"Muhammad Haritsyah Warli",
"Fauriski Febrian Prapiska",
"Ginanda Putra Siregar",
"Bungaran Sihombing"
],
"abstract": "Background: Penile cancer is a rare malignancy and potentially lethal disease with an incidence of 0,6-2,1 per 100.000. Squamous cell carcinoma (SqCC) is the most commonly found penile malignancy. PD-L1 is a tumor marker that co-stimulates the receptor PD-1 to suppress T-cell-mediated antitumor immunity. Methods: This study is a retrospective cohort study with a total sampling method. The slides taken from the biopsies of seventy-six male patients from Haji Adam Malik Hospital diagnosed with penile squamous cell carcinoma who have already undergone penile biopsy were re-examined for this study, and PD-L1 levels were measured accordingly. Statistical methods were used to assess the association between PD-L1 levels and with SqCC stage. Results: A total of 76 male patients are the subjects of this study. PD-L1 positivity is identified in 25 patients with +1 intensity in 10 patients (13,2%), +2 in 7 patients (9,2) and +3 intensity in 8 patients (10,5%). There are 36 patients (47,4%) diagnosed with stage T3 SqCC, 35 patients (46,1%) with stage N2 SqCC, and 10 patients (13,2%) with stage M1 SqCC. There is significant correlation between PD-L1 expression and metastasis (p=0,022). However, there is no significant correlation between PD-L1 expression and stage N tumor (p=0,167). Conclusions: PD-L1 highly expressed in advanced stage penile SqCC (32.9%), which is associated with the high-risk clinicopathologic features and poor clinical outcomes. These findings showed a potential usage of immunotherapy in advanced penile SqCC treatment.",
"keywords": [
"immunotherapy",
"penile cancer",
"PD-L1",
"squamous cell carcinoma"
],
"content": "Introduction\n\nPenile cancer is a rare malignancy due to its low incidence rate. The age-standardized incidence rate is 0.84 cases per 100.000 person-years (by the world standard population).1 In Western countries, penile cancer is a potentially lethal disease with incidence of 0.6-2.1 per 100.000.2,3 Squamous cell carcinoma (SqCC) is a lethal disease which accounts for the most common penile malignancies.2,4\n\nLocal excision or laser therapy is the primary treatment for patients with low stage tumor. One of the most important prognostic factors is the involvement of regional lymph node which decreases survival from >90% to ~50% when metastases of lymph nodes are present.3 Patients with metastases such as lymph node metastases have worse prognosis compared to patients with carcinoma in situ, which are associated with substantial mortality and morbidity.5,6\n\nTumor cells use immunosuppressive mechanisms to avoid antitumor immune response, thus it is now considered one of the cancer hallmarks.7 One of the tumor hallmarks is PD-L1 which co-stimulate the receptor PD-1 to down-regulate the T-cell-mediated antitumor immunity.8,9 PD-L1 expression can also be aberrant in different malignancies.10–14 This characteristic of PD-L1 also provides new immunotherapy treatments for some solid tumors.15 For example, it is also possible to augment tumor cell killing by inhibiting PD-1/PD-L1 interaction.16,17\n\nMembranous PD-L1 has been investigated in different malignancies including breast cancer, melanoma, head and neck cancer, and non-small-cell lung cancer.17–19 However, only a limited number of studies have investigated the expression of PD-L1 in penile squamous cell carcinoma.21\n\nA number of studies have reported that positive expression of PD-L1 is associated with poor clinic-pathological features and worse outcome in other organs malignancies, such as bladder cancer.19 Based on these findings, PD-L1 expression may be a predictive biomarker to predict treatment response and oncological outcome in other malignancies, such as penile squamous cell carcinoma.\n\nIn this study, we investigated the correlation between PD-L1 expression and poor prognosis. We examined the correlation between PD-L1 expression and survival of penile SqCC and analyzed the adjusted hazard ratios (HR) of the patients with PD-L1 expression compared to anatomical stage of the tumor.\n\n\nMethods\n\nThe design of this study is retrospective cohort with total sampling method. Fifty male patients from Haji Adam Malik Hospital diagnosed with penile squamous cell carcinoma who have already undergone penile biopsy and/or penectomy in year 2014 – 2019 are the subjects of this study.\n\nThe slides taken from the biopsies were re-examined for the purposes of this study. We also took data about the overall survival and the status of their survival. We were tracing the subjects for 36 months and taking notes of their conditions at that time to obtain the data needed for survival analysis. The data31 obtained are listed in a table consisting of age, tumor stage, PD-L1 intensities, overall survival, and the status of the patients (dead or alive).\n\nImmunochemistry staining method done in this study was HE stain. Reagent used to stain PD-L1 in this IHC staining was MD21R clone (Medaysis CA), ready to use (rabbit PD-L1 antibody). The positive control in this staining is placenta tissue. PD-L1 antibody is diluted with ratio 1 uL PD-L1: 100 uL IHC diluent and then mixed for 5 minutes.\n\nPretreatment was done with EDTA pH8.0, 15 minutes using a Pressure Cooker, or 30 – 60 minutes using a water bath at 95o – 99oC. Deparaffination and rehydration were done by using Bond Dewax Solution for 3 times, alcohol for 3 times, and Bond Wash Solution for 3 times. We retrieved the antigen by using Bond Epitope Retrieval Solution I for 4 times. We mixed the solution with PD-L1 (Medaysis) primary antibody for 1 hour. The detection was done by using post primary procedure for 8 minutes, Bond Wash Solution for two times, and polymer for eight minutes. We used DAB mixture for staining and hematoxylin for counterstaining.\n\nPD-LI expression was assessed on cytoplasm and/or tumor cell membranes and TILs. The positive control used was the placenta. PD-LI expression is considered positive if it has a score of +2 or +3 and is considered negative if it has a score of +1 and 0. Semi-quantitative assessment by using the H-score. PD-LI expression was graded as low (0-150) or high (151-300).\n\nPD-LI staining was performed on 500 tumor cells and 100 TILs. Semi-quantitative assessment refers to research by Chovanec et al. who used histoscore (H-score). The percentage of stained cells was assessed on a scale of 0-100%. Intensity measurement then given a score of 0-3 (0 = none; 1 = weak; 2 = moderate; and 3 = strong).\n\nThe dominant staining intensity rated in 10 large fields view with 400× magnification (3+ indicate strongly stained, 2+ indicate moderately stained, 1+ indicate weakly stained, and 0 indicate unstained). Percentage of stained tumor cells A = percentage of tumor cells intensity in 3+ {3 × (%Cells 3+)}, B = percentage of tumor cells intensity in 2+ {2 × (%Cells 2+)}, C = percentage of tumor cells intensity in 1+ {1 × (%Cells 1+)}. Total Histo-score values calculated by A+B+C\n\nTotal value obtained ranges from 0 to 300, thus PD-L1 expression is categorized into “1” for negative (0 – 99) and “2” for positive (100 – 300).\n\nThe protocol of the sample processing in this study is available from Protocols.io DOI: http://doi.org/10.17504/protocols.io.bp2l69b4klqe/v1.\n\nWe analyzed the subjects and made a table describing the characteristics of the subjects. Association between expression of PD-L1 and poor prognosis tumor was examined using Fisher’s exact test. Poor prognosis tumor parameters examined in this study are the N tumor staging for lymph nodes infiltration and M tumor staging for metastasis. All statistical analyses were completed using SPSS version 20, and statistical significance was defined as P<0.05\n\nThis study has been given permission from the Health Research Ethics Committee (KEPK) of the Universitas Sumatera Utara (USU; No. 381/KEPK/USU/2012, dated April 22, 2022). Informed consent from participants was waived by the Ethics Committee as the samples were taken from the previously collected biopsies slides.\n\n\nResults\n\nTotal of 76 male patients are the subjects of this study. The median age of diagnosis was 50.4 years. Patient characteristics including age, stage T tumor, stage N tumor, metastasis, and PD-L1 intensity are summarized in Table 1.\n\nThe tumor stage T is classified as T1, T2, T3, and T4. Most patients are diagnosed with SqCC stage T3 (47.4%). Lymph node infiltrating tumor is stated as stage N. There are 35 patients (46.1%) diagnosed with stage N2 SqCC. Metastasis was found in 10 patients (13.2%). Anatomic stage shows the tumor progression described by the combination of stage T, N, and M. Anatomic stage 0 – 2 accounts for stage T0-3 with N0 and M0. Anatomic stage 3 – 4 accounts for stage T1 – 4, stage N1 – 3, and stage M0 – 1.\n\nPD-L1 positivity is identified in 25 patients with +1 intensity in 10 patients (13.2%), +2 in 7 patients (9.2) and +3 intensity in 8 patients (10.5%). Poor prognosis parameters we examined in this study are stage N and stage M tumor. Stage N tumor indicates if the tumor has already infiltrated lymph nodes and its severity is classified as N0, N1, N2, and N3. Stage M is classified as M0 and M1. M0 indicates no metastasis and M1 indicates metastasis.\n\nIn this study, we examined the correlation between PD-L1 expression and poor prognosis by using Fischer’s exact tests. We found out that there is significant correlation between PD-L1 expression and metastasis (P=0.022). However, there is no significant correlation between PD=L1 expression and stage N tumor (P=0.167). The correlation between PD-L1 expression and poor prognosis is summarized in Table 2.\n\n\nDiscussion\n\nIt has been demonstrated that PD-1/PD-L1 plays an important role in anti-tumor immune response evasion.8 PD-L1 can be detected on tumor cells, which contribute to inhibit local immune response. Other studies have also demonstrated the correlation between PD-L1 expression and clinical outcome.13,22\n\nOur study revealed low presentation of tumor PD-L1 expression (19.7%) compared to other studies on penile SqCC (range 40 – 62%). Discrepancies in these findings may be due to smaller sample size in our study compared with other studies. This also might be caused by the low prevalence of penile cancer in Asian men in general, compared to other races.23 Larger study is needed to compare PD-L1 expression between races and its relation to metastasis and survival rate in each group.\n\nIn our study we found out that there is a significant correlation between PD-L1 expression and stage M tumor (P=0.022). This result show similarities with the study conducted by Udager et al., which reported that there is strong correlation between PD-L1 expression and metastases.21\n\nIn addition, Udager et al. (2016) reported that there is also significant correlation between PD-L1 in tumor cells and positive lymph node status.21 However, in our study, we examined that there is no significant correlation between PD-L1 expression and stage N tumors.\n\nPD-L1 expression in tumor cells is used as a predictive biomarker in lung cancer.24–26 Unfortunately, no clinical data about the response to checkpoint inhibitors in the penile SqCC setting. However, the squamous histology of penile SqCC resembles that of lung SqCC. Based on these data, we can assume that PD-L1 expression in tumor cell might be a predictive biomarker in penile SqCC.27 Evidently, as a predictive biomarker for response to therapy, PD-L1 expression is organ dependent. While PD-L1 expression associated with response to anti-PDL1 agents in bladder cancer patients, no correlation found between PD-L1 expression and response to anti PDL-1 agent in lung cancer.28\n\nThere are several compounds that should be considered to give anti-PD-L1 immunotherapy. Each compound is associated with a specific aspect diagnostic PD-L1 IHC assay. These assays use different antibodies and have unique cut-offs for determining PD-L1 positive expression. Different antibodies used in diagnostic method will determine the positive expression of PD-L1 differently.21\n\nFurther study should be done to investigate the necessity of giving immunotherapy to patients with PD-L1 positive penile SqCC. Several studies reported that clinical trials using the anti-PD-1 nivolumab have demonstrated clinical response which is independent of PD-L1 expression.29,30 On the other hand, Su et al. reported that patient their studies responded well to immunotherapy. They suggested that immunotherapy could be a great option for the treatment of metastatic penile SqCC. Nowadays, there are also ongoing trials by using various monoclonal antibodies, such as atezolizumab, pembrolizumab, and avelumab to investigate immunotherapeutic effects in PD-L1 positive penile SqCC.30 Based on these findings, we suggest further study about immunotherapy due to the PD-L1 positive expression in penile SqCC.\n\nThe major strength of this study is the integration of PD-L1 expression with pre-existing data. Our study is focused in examining the correlation between PD-L1 expression and poor prognosis linked to survival. The major weakness of this study is low presentation of tumor PD-L1 expression (19.7%) compared to other studies on penile SqCC (range 40 – 62%) due to small size samples. Several slides used in this study also have decreased in quality due to long period research.\n\n\nConclusion\n\nPD-L1 positively expressed by several cases of penile SqCC in our cohort Indonesian patient subjects is associated with poor clinical outcome. We found out the significant correlation between PD-L1 expression and metastases. In our study, we also examined that PD-L1 expression correlates strongly with survival, makes it may benefit from immunotherapy.",
"appendix": "Data availability\n\nFigshare: Data of PD-L1 in Penile Squamous Carcinoma.xlsx, https://doi.org/10.6084/m9.figshare.21378411.v1. 31\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nMontes Cardona CE, García-Perdomo HA: Incidence of penile cancer worldwide: systematic review and meta-analysis. Rev. Panam. Salud Publica. 2017; 41: 1–10. Publisher Full Text\n\nBarnholtz-Sloan JS, Maldonado JL, Pow-sang J, et al.: Incidence trends in primary malignant penile cancer. Urol. Oncol. 2007; 25: 361–367. PubMed Abstract | Publisher Full Text\n\nMoses KA, Winer A, Sfakianos JP, et al.: Contemporary management of penile cancer: greater than 15 year MSKCC experience. Can. J. Urol. 2014; 21: 7201–7206. PubMed Abstract\n\nDiorio GJ, Leone AR, Spiess PE: Management of penile cancer. Urology. 2016; 96: 15–21. Publisher Full Text\n\nMaddineni SB, Lau MM, Sangar VK: Identifying the needs of penile cancer sufferers: a systematic review of the quality of life, psychosexual and psychosocial literature in penile cancer. BMC Urol. 2009; 9: 8. PubMed Abstract | Publisher Full Text\n\nHakenberg OW, Comperat EM, Minhas S, et al.: EAU guidelines on penile cancer: 2014 update. Eur. Urol. 2015(67): 142–50.\n\nHanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell. 2011; 144: 646–674.\n\nDong H, Strome SE, Salomao DR, et al.: Tumor-associated B7-H1 promotes T-cell apoptosis: a potential mechanism of immune evasion. Nat. Med. 2002; 8: 793–800. PubMed Abstract | Publisher Full Text\n\nLatchman YE, Liang SC, Wu Y, et al.: PD-L1-deficient mice show that PD-L1 on T cells, antigen-presenting cells, and host tissues negatively regulates T cells. Proc. Natl. Acad. Sci. U. S. A. 2004; 101: 10691–10696. PubMed Abstract | Publisher Full Text\n\nKatsuya Y, Fujita Y, Horinouchi H, et al.: Immunohistochemical status of PD-L1 in thymoma and thymic carcinoma. Lung Cancer. 2015; 88: 154–159. PubMed Abstract | Publisher Full Text\n\nNomi T, Sho M, Akahori T, et al.: Clinical significance and therapeutic potential of the programmed death-1 ligand/programmed death-1 pathway in human pancreatic cancer. Clin. Cancer Res. 2007; 13: 2151–2157. PubMed Abstract | Publisher Full Text\n\nGadiot J, Hooijkaas AI, Kaiser AD, et al.: Overall survival and PD-L1 expression in metastasized malignant melanoma. Cancer. 2011; 117: 2192–2201. Publisher Full Text\n\nBellmunt J, Mullane SA, Werner L, et al.: Association of PD-L1 expression on tumor-infiltrating mononuclear cells and overall survival in patients with urothelial carcinoma. Ann. Oncol. 2015; 26: 812–817. Publisher Full Text\n\nQin T, Zeng YD, Qin G, et al.: High PD-L1 expression was associated with poor prognosis in 870 Chinese patients with breast cancer. Oncotarget. 2015; 6: 33972–33981. PubMed Abstract | Publisher Full Text\n\nBordon Y: Immunotherapy: checkpoint parley. Nat. Rev. Cancer. 2015; 15: 3. Publisher Full Text\n\nIwai Y, Ishida M, Tanaka Y, et al.: Involvement of PD-L1 on tumor cells in the escape from host immune system and tumor immunotherapy by PD-L1 blockade. Proc. Natl. Acad. Sci. USA. 2002; 99: 12293–12297. PubMed Abstract | Publisher Full Text\n\nCurran MA, Montalvo W, Yagita H, et al.: PD-1 and CTLA-4 combination blockade expands infiltrating T cells and reduces regulatory T and myeloid cells within B16 melanoma tumors. Proc. Natl. Acad. Sci. USA. 2010; 107: 4275–4280. PubMed Abstract | Publisher Full Text\n\nKim HR, Ha SJ, Hong MH, et al.: PD-L1 expression on immune cells, but not on tumor cells, is a favorable prognostic factor for head and neck cancer patients. Sci. Rep. 2016; 6: 36956. PubMed Abstract | Publisher Full Text\n\nHuang Y, Zhang SD, McCrudden C, et al.: The prognostic significance of PD-L1 in bladder cancer. Oncol. Rep. 2015; 33: 3075–3084. Publisher Full Text\n\nThompson RH, Kuntz SM, Leibovich BC, et al.: Tumor B7-H1 is associated with poor prognosis in renal cell carcinoma patients with long-term follow-up. Cancer Res. 2006; 66: 3381–3385. PubMed Abstract | Publisher Full Text\n\nUdager AM, Liu TY, Skala SL, et al.: Frequent PD-L1 expression in primary and metastatic penile squamous cell carcinoma: potential opportunities for immunotherapeutic approaches. Ann. Oncol. 2016; 27: 1706–1712. PubMed Abstract | Publisher Full Text\n\nGoodman MT, Hernandez BY, Shvetsov YB: Demographic and Pathologic Differences in the Incidence of Invasive Penile Cancer in the United States, 1995-2003. Cancer Epidemiol. 2007; 16(9): 1833–1839. Publisher Full Text\n\nLipson EJ, Vincent JG, Loyo M, et al.: PD-L1 Expression in the Merkel Cell Carcinoma Microenvironment: Association with Inflammation, Merkel Cell Polyomavirus, and Overall Survival. Cancer Immunol. Res. 2013; 1: 54–63. PubMed Abstract | Publisher Full Text\n\nReck M, Rodriguez-Abreu D, Robinson AG, et al.: Pembrolizumab versus chemotherapy for PD-L1-positive non-small-cell lung cancer. N. Engl. J. Med. 2016; 375: 1823–1833. Publisher Full Text\n\nPowles T, Duran I, van der Heijden MS , et al.: Atezolizumab versus chemotherapy in patients with platinum-treated locally advanced or metastatic urothelial carcinoma (IMvigor211): a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2018; 391: 748–757. PubMed Abstract | Publisher Full Text\n\nMcDermott DF, Sosman JA, Sznol M, et al.: Atezolizumab, an antiprogrammed death-ligand 1 antibody, in metastatic renal cell carcinoma: long-term safety, clinical activity, and immune correlates from a phase Ia study. J. Clin. Oncol. 2016; 34: 833–842. PubMed Abstract | Publisher Full Text\n\nDavidson S, et al.: PD-L1 Expression in men with penile cancer and its association with clinical outcomes. Eur. Urol. Oncol. 2019; 2: 214–221. Publisher Full Text\n\nCocks M, Taheri D, Ball MW, et al.: Immune-Checkpoint Status in Penile Squamous Cell Carcinoma: A North American Cohort. Hum. Pathol. 2017; 59: 55–61. PubMed Abstract | Publisher Full Text\n\nBrahmer J, Reckamp KL, Baas P, et al.: Nivolumab versus docetaxel in advanced squamous-cell non-small-cell lung cancer. N. Engl. J. Med. 2015; 373: 123–135. Publisher Full Text\n\nMotzer RJ, Escudier B, McDermott DF, et al.: Nivolumab versus everolimus in advanced renal-cell carcinoma. N. Engl. J. Med. 2015; 373: 1803–1813. PubMed Abstract | Publisher Full Text\n\nWarli MH, Prapiska FF, Siregar GP, et al.:PD-L1 expression as predictor of immunotherapy eligibility in penile squamous cell carcinoma patients.xlsx. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "235146",
"date": "19 Jan 2024",
"name": "Thomas S. Gerald",
"expertise": [
"Reviewer Expertise Urologic oncology",
"biomarkers"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, the authors analyze PD-L1 expression as a biomarker for nodal and distant disease and report that there is an association between expression and distant metastases but not regional disease.\n\nThere are significant omissions in the baseline patient and tumor characteristics, pathologic variables from the specimen, clinical staging information, additional therapies received by the patients, and controlling for additional variables in the statistical analysis.\n\nA more comprehensive description of baseline patient demographics and tumor characteristics must be reported. Are the nodal and metastatic staging characteristics reported based on imaging and/or exam (clinical) or from inguinal node dissection (pathologic)? Was TNM staging assigned at the time of specimen retrieval, and if not, when, and did patients undergo additional regional or systemic therapy?\n\nI am not familiar with the PD-L1 IHC utilized in this study. Most analyses use a Dako or Ventana based assay, which is what FDA guidelines are based on for recommendations for systemic therapy. Therefore, I have doubts regarding the applicability of this assay used.\n\nThe statistical analysis utilized as univariate Fisher's exact test, which is unlikely a strong enough evaluation. Sensitivity, specificity, PPV, NPV should be reported and multivariate analysis including other clinical anhd pathology variables should be performed.\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? 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": "235150",
"date": "09 Feb 2024",
"name": "Jan Hrudka",
"expertise": [
"Reviewer Expertise pathology",
"immunohistochemistry",
"molecular pathology"
],
"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\nWarli and colleagues present a conclusive and understandable written retrospective study focused on the clinical importance of PD-L1 expression in penile squamous cell carcinoma. The authors document a significant association of membranous PD-L1 positivity with advanced disease stage, i.e. presence of lymph nodal and/or distant metastasis.Several methodological issues need to be fixed, several confusing formulations need to be amended and discussion needs to be broadened on several questions.\nIn the introduction, the authors state: “...patients with metastases … have worse prognosis compared to patients with carcinoma in situ” This is confusing as the term carcinoma in situ refers to a non-invasive carcinoma. “CIS” should be replaced with i.e. “localized tumors”. In the methods section, the sentence “PD-L1 staining was performed on 500 tumor cells and 100 TILs” is highly confusing. Did the authors mean “was evaluated”? There is an unusually high proportion of patients in the T3 stage (47%). How do the authors explain such a high proportion of advanced tumors in their cohort? Is there any selection bias? The authors use a histoscore semiquantitative method to evaluate PD-L1 positivity. Why did they not use standard tumor proportion score (TPS) or combined proportion score (CPS)? Please mention in the discussion these scoring systems and explain in the discussion why histoscore was used. I significantly miss any photographs of both histology and PD-L1 immunohistochemistry. The authors state in the result section, in the discussion and in the conclusion that they prove that PD-L1 is linked to “poor prognosis”. This is obviously an overstatement. The authors solely prove that PD-L1 is linked to the advanced stage of penile cancer. To assess prognosis, a survival analysis (Kaplan Meier, Cox regression…) based on the patient´s follow up needs to be calculated. Please, either amend the formulation, or provide a survival analysis. Recently, a study analyzing a large cohort of penile cancer patients focusing on PD-L1 expression and its associations with p16 status, tumor mutational burden (TMB), tumor infiltrating lymphocytes (TILs) and survival was published [1] - please, see and cite. Aforementioned study showed an association of PD-L1 positivity with HPV (p16) negativity, high TMB and high TILs. Warli et al. state there is a small proportion of PD-L1+ cancers in their cohort. The authors should provide a rationale for this and broaden the discussion in this way. Could it be given to the relatively high proportion of HPV-associated cancers in their cohort (Indonesian population)? Could a previous circumcision play a protective role in case of HPV-negative cancer which correlates with poor hygiene? Knowledge of HPV (or p16) status in this cohort would be of great interest. What was the proportion of HPV/p16+ cases? Was there any link to stage and PD-L1? The authors should add a p16 analysis and broaden their results and discussion. More papers linked to the topic, which should be read and eventually cited: [2], [3], [4], [5]\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? 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": []
},
{
"id": "235143",
"date": "27 Feb 2024",
"name": "Dr.Sourav Kumar Mishra",
"expertise": [
"Reviewer Expertise Medical oncologist with focus on Genitourinary oncology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is appropriate in its design and conclusions. The authors need to revise the grammars and English language used in summarizing their study. Then only will it become appropriate to convey what this study intends to convey.Overall this study adds to the growing literature on the application of immunotherapy in penile 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?\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/11-1281
|
https://f1000research.com/articles/11-767/v1
|
11 Jul 22
|
{
"type": "Research Article",
"title": "Dental education during the pandemic – cross-sectional lecturer-side evaluation for the use of digital teaching concepts",
"authors": [
"Ephraim Nold",
"Vivienne Demeter",
"Kurt-Jürgen Erdelt",
"Daniel Edelhoff",
"Anja Liebermann",
"Ephraim Nold",
"Vivienne Demeter",
"Kurt-Jürgen Erdelt",
"Daniel Edelhoff"
],
"abstract": "Background: The COVID-19 pandemic resulted in significant restrictions on dental teaching. The aim of this investigation was to evaluate the attitudes of faculty members towards digital teaching formats and the effort creating digital lectures. We hypothesized that on the lecturer side there is no difference between the various digital teaching concepts in terms of workload and effort and that there is no increase in workload and effort when switching to digital teaching concepts. Methods: All German dental faculties were invited to the online survey by an anonymous voluntary questionnaire from January to April 2021. The questionnaire consisted of 27 questions that could be answered with a visual analog scale, free text answers, or with fixed answer options. Data was analyzed using the Kolmogorov-Smirnov test and an exploratory data analysis (α=0.05). Results: Before the pandemic, 24.8% of the participating lecturers were using digital teaching and 64.4% had no previous experience. After the outbreak of the pandemic 100% of the dental teaching was initially held online. More than 80% of the lecturers stated that they offer online lectures (86.1%), online seminars (81.2%), and/or online bedside teaching (33.7%). 88.1% see face-to-face teaching as the preferred teaching format. The lecturers also see the greatest opportunities for interaction in the area of analog teaching and significantly worse in synchronous and asynchronous digital teaching. In the course of the pandemic, respondents' attitudes towards online teaching improved in the median of 24.0 to a median of 50.0. Conclusions: Faculty members have positively changed their attitudes towards online teaching formats over the course of the pandemic. Although they see the greatest learning success in conventional face-to-face teaching formats and the creation of digital lectures is associated with a higher effort, they want more online lessons in the future.",
"keywords": [
"pandemic",
"digital teaching concept",
"lecturer-side evaluation",
"questionnaire",
"lecture"
],
"content": "Introduction\n\nThe use of digital media in university teaching, also called e-learning, has been a popular form of teaching and learning for more than 20 years and has experienced a significant boom since the 2000s.1 In particular, students appreciate the flexible online access to the digital teaching tools as well as the individual adaptability regarding different learning speeds.2 Investigations show, however, that face-to-face teaching, especially personal feedback from the faculty, cannot be completely replaced.2–5\n\nThe COVID-19 pandemic with its worldwide restrictions in the field of dental education and the need to discontinue face-to-face teaching in many places showed6 that the implementation of digital learning as well as teaching support in dental training still has deficiencies.7 However, the call for digital teaching concepts, especially web-based offers, became louder.8\n\nThe effectiveness of digital teaching concepts has already been proven by numerous authors.9–11 Particularly in the area of blended learning, an effectiveness that was not lower than in the case of face-to-face teaching was reported.3 The acceptance of distance learning by students has also been examined in numerous investigations and positive results were reported almost without exception.10,12–17\n\nAlthough the use of digital teaching concepts was extensively described by the students, investigations that examined the topic on the part of the lecturers can hardly be found.18 In addition to the effectiveness of the teaching method mentioned and the acceptance by the students, the question of the creation effort for digital teaching units, the acceptance on the lecturer’s side and their ability to use digital media is a decisive factor for the increased use of digital teaching concepts within the dental curriculum.\n\nAlthough Schlenz et al.,18 reported in an investigation about the acceptance of online teaching of a high level of acceptance by both students and lecturers, but there is little to be found in the literature on the question of creation effort for online teaching concepts. Zitzmann et al., also assumed in their systematic review of the use of digital teaching concepts in dental education that, despite the considerable effort involved in creating digital courses, a long-term relief of the teaching effort can be expected,2 and August et al.,19 proposed that lecturers to work together across universities due to the high time required to create digital content in order to minimize the overall effort, whereas a quantification of the creation effort was not mentioned.\n\nThe technological progress of the past 10 years has created countless new options in the field of teaching and enabled to practice digital teaching in different ways.20 Concerning asynchronous teaching formats, the outstanding strength is that they can be consumed flexibly in time and place and thus made available to a theoretically unlimited audience over a longer period of time.21,22 Synchronous formats offer, also without being tied to a specific location, the advantage of direct communication between lecturer and student.\n\nTherefore, the aim of this cross-sectional investigation is to analyze the lecturer-sided acceptance and teaching effort during and after the switch to digital teaching during the pandemic as well as to examine the differences between the various digital teaching concepts as survey-based research. In addition, an insight into the nationwide implementation of dental online teaching is given.\n\nThe hypothesis states that on the lecturer side 1. there is no difference between the various digital teaching concepts in terms of workload and effort, and 2. there is no increase in workload and effort when switching to digital teaching concepts.\n\n\nMethods\n\nA declaration of no objection was approved by the ethics committee of the Medical School (Project KB 20/036). Written informed consent was obtained from participants prior to inclusion in the study.\n\nAll dental schools, like all other universities were forced to replace their conventional lectures in the auditorium during the pandemic period, by different digital teaching concepts. These digital concepts were performed for lectures, seminars, and bedside teaching, whereby the exact use of the various online concepts can now be assumed to be known. Most digital teaching concepts used were:\n\n1. asynchronous (e.g., prerecorded PowerPoint presentations with audio explanations),\n\n2. synchronous using livestreams, and\n\n3. synchronous using conference systems (e.g., Zoom, Big Blue Button, Jitsi as examples).\n\nThis cross-sectional study was a survey-based research by an online questionnaire among dental lecturers from different dental schools at German university hospitals, including various departments responsible for dental teaching.\n\nAll German dental schools were invited for the online survey by sending a link for an anonymous online questionnaire by e-mail. The link was sent directly to the heads of the departments of prosthodontics in all German universities and they forwarded the link to their employees within the department. There were no specific exclusion or inclusion criteria. Participants had to be lecturers at dental schools. The questionnaire time frame for recruitment was from January to April 2021.\n\nThe questionnaire was generated using an online survey platform (Questionstar, Hannover, Germany) and consisted of 27 questions (Questions: Q) in the German language. A total of seven questions could be answered using a visual analog scale (VAS), three free text answers, and 17 with fixed-answer options (Table 1).32 The VAS answers were marked by the students with a scroll bar on a line, which reflected the range from 0% to 100% (Figure 1). The questions with fixed-answer options were marked just with a click. Some questions were specifically asked in case the different teaching formats were held. Therefore, it was possible that some questions were not answered by the lecturers if the respective teaching format was not held. Before the questionnaire was sent out, it was validated internally by five highly experienced staff members of the Department of Prosthodontics in Munich. All of these staff members and researchers included are active as lecturers at the University of Munich and have more than five years of experience. The questionnaire was discussed in the research group and checked by the study directors to establish content validity. After validation, a short cut was created from Q7 to Q10-12, 17-19, whereas Q20, 22 and Q6 was swapped with Q7. The data was collected from the platform Questionstar (Questionstar, Hannover, Germany) and made available as an Excel file. Data analysis was performed with the help of a research engineer with a high level of statistic expertise.\n\nThe questionnaires were examined with the statistical program SPSS 26 (IBM, New York, NY, USA) with a significance level of p=0.05. Normality of data distribution was analyzed using the Kolmogorov-Smirnov test and an exploratory data analysis. The median values of the questions and the range of deviation of the interquartile range (IQR) were used due to non-parametric analysis. In addition, the Friedmann and Wilcoxon test was performed to compare the results and respective answers.\n\n\nResults\n\nA total of 101 lecturers (46 women, 55 men) participated in the survey with a drop-out of 17 lecturers with incomplete questionnaires (drop-out rate: 14%). All results (100%) showed a deviation from the normal distribution and were consequently evaluated non-parametrically.\n\nFigure 2 shows the distribution of the lecturers at the different universities. A total of 13.9% were under 30 years of age, 35.6% between 30 and 40 years of age, 16.8% between 41 and 50 years of age, 15.8% between 51 and 60 years of age, and 17.8% over 60 years of age.\n\nAmong the participating faculty, 3% reported their position within the university as visiting lecturer, 37.6% as research associate, 55.4% as functional/senior physician/chief senior physician or director, and 4.0% with no information.\n\nRegarding the percentage of teaching in the total activity, 13.9% of the lecturers indicated a percentage value of less than 25%, 51.5% indicated a percentage value between 25 and 50%, 28.7% indicated a value of 51 to 75%, and 5.9% of the lecturers even indicated a teaching percentage of more than 75%.\n\nWhen asked about years of previous teaching experience, 11.9% lecturers reported having less than two years of teaching experience. 18.8% of lecturers indicated teaching experience between two and five years, 17.8% between six and 10 years, and 51.5% with over half of lecturers indicated teaching experience of over 10 years.\n\nAmong lecturers, online lectures were presented from the university’s own office by 67.3%, from teaching spaces such as lecture halls or conference rooms by 15.8%, from home office by 13.9%, and 3.0% gave no response. Overall, 86.1% of all lecturers held online lectures, 81.2% online seminars, and 33.7% online bedside teaching since the pandemic initially forced to teach 100% online. Among these, 24.8% of the lecturers reported that they had held online events prior to the pandemic and 25.7% had attended training events on online teaching. 36.6% of the participating lecturers had also dealt with online teaching in self-study before the pandemic. However, 64.4% of the lecturers stated that they had no experience with online teaching prior to pandemic.\n\n62.4% of the lecturers stated that the university had given them the online teaching format. In contrast, 37.6% of the lecturers were able to determine the online teaching format themselves. 88.1% of the lecturers prefer to work with the conventional teaching format, i.e., face-to-face teaching, and 11.9% with online teaching. The desired teaching format, depending on the age group is shown in Figure 3.\n\nFor online lecture, 78.8% of the lecturers selected the Zoom/WebEx/Jitsi/BigBlueButton format, 64.7% the lecture with audio, e.g., with PowerPoint, and 12.9% a live broadcast for the conventional lecture. For the online seminar, 87.7% of the lecturers reported using the Zoom/WebEx/Jitsi/BigBlueButton format, 9.9% a live broadcast of the seminar, and 44.4% the set to audio seminar e.g., with PowerPoint. For online bedside teaching, 87.7% reported using the Zoom/WebEx/Jitsi/BigBlueButton format, 3.2% a live broadcast of the bedside teaching, and 25.8% the bedside teaching set to audio, e.g., with PowerPoint. In addition, the results on the individual instructional formats showed no correlation between gender and the age group queried.\n\nWhen asked about problems encountered with the internet and the teaching format, 34.7% of the lecturers stated that they had never had problems with the Internet connection, with the general median being 8.0 (IQR: 35.0). In addition, 37% reported never having had problems using the teaching format, with the median here being 7.5 (IQR: 24.0).\n\nTable 2 shows the separate results comparing the analog and digital teaching formats as well as the conversion of the teaching formats before and during the pandemic.\n\nSuperscript letters indicate significant differences between answer possibilities.\n\nFigures 4 and 5 represent the amount of online teaching prior and the desire after the pandemic. In addition, Figure 6 shows the respective results divided by gender.\n\n81.2% of the lecturers are of the opinion that online teaching should in principle be more strongly integrated in dental education in the future; for 18.8%, on the other hand, online teaching should not be more implemented.\n\n\nDiscussion\n\nThe COVID-19 pandemic led to major changes worldwide, especially in social coexistence, as well as work and education. Especially in the field of medical and dental training, which due to their patient-centeredness are related to a high level of physical proximity, fast, alternative solutions had to be sought. An essential way to create infection-preventing distance was the introduction or expansion of digital teaching concepts. Almost all lecturers had to address this often new task.23\n\nThe explosive nature of the topic and the concern of almost all lecturers at German universities caused the high number of participants in the present investigation. Although the survey was not based on personalized links or traceable participation, but on voluntary participation, with 101 participating lecturers, a relatively large field of participants could be registered compared to other lecturer surveys.18,24\n\nThe gender and age structure of the present study showed no significant differences between male and female participant numbers between certain age groups. In contrast, the results showed differences in the professional status of the participants. With over 50% of the participants (median 55.4%) the group of the senior physicians, senior physicians; senior consultants or directors are the most frequently represented group. This is not surprising in view of the fact that people in this position often have the predominant teaching performance and teaching responsibility and thus have the highest thematic interest in participating. As a result, most of the study participants were able to state that they had teaching experience of more than 10 years (51.5%).\n\nWith 51.5%, more than half of the respondents recorded a share of 25% and 50% in teaching, referred to their entire professional activity. 94.1% of those questioned also stated that more than 25% of their work was done outside of teaching. Clinical dental work beyond of teaching usually does not take place at home. Therefore, many lecturers are tied to one specific location. So at least 94.1% cannot fully exploit the advantages of digital teaching concepts.21 This restriction could be assumed to be the cause of the fact that only 13.9% of the respondents stated that they teach from home, while 83.1% of the study participants locate their teaching activities in the university (67.3% from the university’s own office and 15.8% from classrooms such as lecture halls or conference rooms). In this regard other authors report similar results. Schlenz et al.,18 identified share of 60.0% of the lecturers who gave lectures from the university’s own office, while 2.9% used specially equipped conference rooms.\n\nEbner et al.,25 described a worldwide hype of digital teaching at universities, triggered by the pandemic. How much this trend has changed in the field of dental teaching was shown by the question of experience with online teaching. Although the acceptance, the usefulness and the effectiveness of digital learning formats have been described for decades,10,12,14–17,26–28 only 24.8% of respondents said that they had offered digital teaching prior to pandemic. In addition, 64.4% of the participating lecturers had no previous experience. These results were in line with previous investigations.18 After the outbreak of the pandemic, more than 80% of the lecturers said they were doing online lectures (86.1%), online seminars (81.2%), and/or online bedside teaching (33.7%), which represented a sharp increase.\n\nThis rapid development in the implementation of digital content in the dental curriculum also harbors certain dangers. In spring 2020, COVID-19 caused considerable restrictions in dental teaching.23 The rapid changes in university teaching that became necessary as a result hit the universities and lecturers suddenly. As the present study shows, only 25.7% of the respondents were able to state that they had taken part in corresponding advanced training events on digital teaching by the time the pandemic broke out, and 36.6% of the respondents had dealt with the topic at least in self-study.\n\nIt can be assumed that, not least because of the lack of experience with digital teaching concepts until then, the selection of the teaching format was specified by the university for 62.4% of the participants. Against the background of countless digital possibilities in the field of teaching,20 this appears to be a sensible measure to create clear university structures. In addition, the license agreements represented a certain university restriction and focus on individual suppliers. Since a large number of students must be able to attend synchronous lectures, seminars, and bedside teaching in digital formats, licenses are often unavoidable.\n\nAlthough authors who examined the acceptance of digital teaching concepts on the part of students reported very high acceptance values, combined with the demand for more online teaching,2 this development was not clearly reflected on the part of the lecturers.\n\nWith 88.1% of the respondents, the vast majority indicated that classroom teaching was the preferred form of teaching, despite having had experience with digital teaching in the meantime. The reasons for this were certainly multilayered. For many lecturers, one reason could be the sudden need for digital offers combined with a lack of previous experience. This situation possibly led to excessive demands, at least temporarily. It should not be forgotten that digital teaching concepts also has disadvantages that are often described, such as eye fatigue from working on the screen and thus a decrease in receptivity or a lack of motivation.4,29 Another decisive disadvantage of digital teaching concepts is the reduced interaction both between students and between students and lecturers.30 The selection of the teaching format suggests that this point is not insignificant on the lecturer side. Although formats in which discussed slides are used and which can be called up repeatedly, if necessary, with slight modifications, can be ‘recycled’ again and again, the preferred teaching formats, regardless of the type of course, were the “live” formats such as Zoom, WebEx, Jitsi, or BigBlueButton. These formats allow far more direct communication.\n\nAt the same time, the participants also evaluated the learning success of analog teaching as the greatest. On a scale from 0-100, the participants gave the analog lessons a median value of 82.0 for learning success, while digital, synchronous formats were rated significantly worse with a median value of 61.0. The participants rated the digital asynchronous teaching significantly worse.\n\nThe participants evaluated the differences in the interaction options with similar clarity, but even more clearly. Corresponding to the assessment of the learning success, the respondents see the greatest opportunities for interaction in the area of analog teaching (median 100.0). The opportunities for interaction with synchronous digital teaching (median 61.0) are seen as significantly worse. In asynchronous digital teaching, the lecturers see almost no opportunity for interaction (median 0.0).\n\nAlthough a majority of the lecturers still prefer to use analog teaching and consider this to be more productive, the attitude towards online teaching has changed positively. While the respondents rated their attitudes towards online teaching on a scale of 0-100 with a median of 24.0, this improved during the pandemic to a median value of 50.0.\n\nAt the same time, however, in the relatively short period of the pandemic, the lecturers neither had the perceived knowledge of digital teaching concepts (before median 60.0 after 77.0) nor the perceived competence in the implementation of digital content (before median 68.0, After 69.0) significantly improved.\n\nSurprisingly, the surveyed lecturers did not perceive any difference in the workload of their teaching activity between the workload before and during the pandemic. Although there was a tendency to describe additional effort before the pandemic, it was not statistically significant. When asked about the effort required to create individual teaching formats, a mixed picture emerges. While a significant additional effort is seen in the creation of lectures with digital formats (analog median 50.0, digital median 73.0), there is no significant difference between the creation of digital and analog formats when creating seminars and bedside teaching. This result could possibly be explained with the workflow of the various creation modes. While bedside teaching and seminars focus on working out certain issues in small groups, the lecturer takes the active part in lectures, while the students usually only receive the information.31 The second one is therefore better suited to be reproduced multiple times in asynchronous form. However, due to the storage of audio files, this requires more creation effort than digital lectures. The seminars or bedside-teaching, which are mostly offered as synchronous formats, differ little in terms of creation effort from their analog form.\n\nWhen presenting the teaching units, on the other hand, the respondents see a significant additional effort both in the area of the lectures and in the area of the seminars. Only with bedside teaching a significant additional effort is seen in the analog form of learning.\n\nWhen updating existing teaching units, however, this difference was small, so that no significant difference could be analyzed either in lectures (analog median 63.0, digital median 64.0) or in seminars (analog median 64.0, digital median 58.0).\n\nBasically, the results clearly show how university dental teaching has changed since the pandemic. As already described in previous studies, the surveyed lecturers would like to continue online teaching after the pandemic.18 While the respondents in this study estimated the median proportion of their online teaching before the pandemic to be 4.8% (SD ± 11.44), they hope for a proportion of 40% (SD ± 25.8) in the future. The results suggest that female lecturers in particular are in favor of implementing more online teaching (male 30 %, female 50%).\n\nDue to its high proportion of crucial practical skills, dental training is not suitable for being fully taught in distance learning. However, the results show that there is a high level of willingness on the part of the lecturers to continue to design at least the theoretical part of the training digitally. At the same time, the participating lecturers point out the weaknesses of digital teaching in the area of interaction, which should be reduced as much as possible by choosing the appropriate format.\n\nThe present study had some limitations, on the one hand, in the composition of the field of participants and, on the other hand, in the circumstances in which the switch to digital teaching took place.\n\nSince participation in this study was voluntary, a field of participants that was unevenly large between the various universities emerged. In order to take this fact into account, the present results must be viewed taking into account the weighting shown in Figure 2. Voluntary participation also means that only the more motivated employees pre-selectively declared themselves study participants. As we had no information about how many employees of the other universities received the questionnaire and how many did not participate, it was not possible to determine a drop-out rate.\n\nAnother limitation is the current situation under which the switch to digital teaching offers was mostly not voluntary. Here it would be advisable to collect the results again in further studies with a suitable interval. This would allow a realistic assessment of the attitudes towards digital teaching concepts on the part of the lecturers.\n\nIn summary, it can be stated that although the study participants offer significantly more digital teaching in times of the pandemic and have significantly positively changed their attitude towards online teaching, the learning success of analog teaching is rated highest. In the case of lectures in particular, the participating lecturers see a considerable amount of additional work involved in creating digital files. In general, the teachers at German universities are positive about the increased use of digital teaching and hope to be able to offer a far higher proportion of the teaching units digitally in the future.\n\n\nConclusion\n\nWithin the limitations of the present cross-sectional survey-based investigation, the following conclusions could be drawn:\n\n1. Faculty members positively changed their attitude towards online teaching formats during the COVID-19 pandemic.\n\n2. Lecturers rated the learning success with analog face-to-face teaching formats the highest.\n\n3. Lecturers evaluated an additional effort in creating digital lectures.\n\n4. More online teaching would be preferred by lecturers in the future.\n\n\nData availability\n\nOpen Science Framework. Dental education during the pandemic – cross-sectional lecturer-side evaluation for the use of digital teaching concepts. https://doi.org/10.17605/OSF.IO/QD9KT.32\n\nThe project contains the following underlying data:\n\n• Excel_File_b.xlsx. (raw underlying data of anonymized questionnaire responses).\n\n• Excel_File_b.csv (raw underlying data of anonymized questionnaire responses).\n\nThe project contains the following extended data:\n\n• Questionnaire unvalidated. (Original unvalidated questionnaire in English).\n\n• Questionnaire unvalidated German. (Original unvalidated questionnaire in German).\n\n• Questionnaire Final validated (Final validated English questionnaire used in this study).\n\n• Questionnaire Final validated German (Final validated German questionnaire used in this study).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgments\n\nThe authors would like to thank all participating lecturers at the various German dental schools for their support and participation in the survey.\n\n\nReferences\n\nHubackova S: History and Perspectives of Elearning. Procedia Soc Behav Sci. 2015; 191: 1187–1190. Publisher Full Text\n\nZitzmann NU, Matthisson L, Ohla H, et al.: Digital Undergraduate Education in Dentistry: A Systematic Review. Int J Environ Res Public Health. 2020; 17(9): 3269. PubMed Abstract | Publisher Full Text\n\nBains M, Reynolds PA, McDonald F, et al.: Effectiveness and Acceptability of Face-to-Face, Blended and E-learning: A Randomised Trial of Orthodontic Undergraduates. Eur J Dent Educ. 2011; 15(2): 110–117. PubMed Abstract | Publisher Full Text\n\nJeganathan S, Fleming PS: Blended Learning as an Adjunct to Tutor-led Seminars in Undergraduate Orthodontics: A Randomised Controlled Trial. Br Dent J. 2020; 228(5): 371–375. PubMed Abstract | Publisher Full Text\n\nMehta S, Clarke F, Fleming PS: An Assessment of Student Experiences and Learning Based on a Novel Undergraduate E-learning Resource. Br Dent J. 2016; 221(3): 131–136. PubMed Abstract | Publisher Full Text\n\nIyer P, Aziz K, Ojcius DM: Impact of COVID-19 on Dental Education in the United States. J Dent Educ. 2020; 84(6): 718–722. Publisher Full Text\n\nBarabari P, Moharamzadeh K: Novel Coronavirus (COVID-19) and Dentistry - A Comprehensive Review of Literature. Dent J (Basel). 2020;21; 8(2): 53. PubMed Abstract | Publisher Full Text\n\nMeng L, Hua F, Bian Z: Coronavirus Disease 2019 (COVID-19): Emerging and Future Challenges for Dental and Oral Medicine. J Dent Res. 2020; 99(5): 481–487. PubMed Abstract | Publisher Full Text\n\nRosenberg H, Grad HA, Matear DW: The Effectiveness of ComputerAided, Self-Instructional Programs in Dental Education: A Systematic Review of the Literature. J Dent Educ. 2003; 67(5): 524–532. PubMed Abstract | Publisher Full Text\n\nReissmann DR, Sierwald I, Berger F, et al.: A Model of Blended Learning in a Preclinical Course in Prosthetic Dentistry. J Dent Educ. 2015; 79(2): 157–165. PubMed Abstract | Publisher Full Text\n\nFouad AF, Burleson JA: Effectiveness of an Endodontic Diagnosis Computer Simulation Program. J Dent Educ. 1997; 61(3): 289–295. PubMed Abstract | Publisher Full Text\n\nKomolpis R, Johnson RA: Web-Based Orthodontic Instruction and Assessment. J Dent Educ. 2002; 66(5): 650–658. PubMed Abstract | Publisher Full Text\n\nSchultze-Mosgau S, Zielinski T, Lochner J: Web-Based, Virtual Course Units as a Didactic Concept for Medical Teaching. Med Teach. 2004; 26(4): 336–342. PubMed Abstract | Publisher Full Text\n\nReynolds PA, Harper J, Dunne S, et al.: Portable Digital Assistants (PDAs) in Dentistry: Part II--Pilot Study of PDA Use in the Dental Clinic. Br Dent J. 2007; 202(8): 477–483. PubMed Abstract | Publisher Full Text\n\nMitov G, Dillschneider T, Abed MR, et al.: Introducing and Evaluating MorphoDent, a Web-Based Learning Program in Dental Morphology. J Dent Educ. 2010; 74(10): 1133–1139. PubMed Abstract | Publisher Full Text\n\nVuchkova J, Maybury T, Farah CS: Digital Interactive Learning of Oral Radiographic Anatomy. Eur J Dent Educ. 2012; 16(1): e79–e87. PubMed Abstract | Publisher Full Text\n\nMahrous A, Schneider GB, Holloway JA, et al.: Enhancing Student Learning in Removable Partial Denture Design by Using Virtual Three-Dimensional Models Versus Traditional Two-Dimensional Drawings: A Comparative Study. J Prosthodont. 2019; 28(8): 927–933. PubMed Abstract | Publisher Full Text\n\nSchlenz MA, Schmidt A, Wöstmann B, et al.: Students’ and Lecturers’ Perspective on the Implementation of Online Learning in Dental Education due to SARS-CoV-2 (COVID-19): A Cross-Sectional Study. BMC Med Educ. 2020; 20(1): 354. PubMed Abstract | Publisher Full Text\n\nAugust JN, Boyd LD, Giblin-Scanlon L: Bridging the Theory-Practice Gap with Dental Hygiene Instrumentation Videos. J Dent Educ. 2018; 82(9): 961–967. PubMed Abstract | Publisher Full Text\n\nGoodacre CJ: Digital Learning Resources for Prosthodontic Education: The Perspectives of a Long-Term Dental Educator Regarding 4 Key Factors. J Prosthodont. 2018; 27(9): 791–797. PubMed Abstract | Publisher Full Text\n\nTowers A, Field J, Stokes C, et al.: A Scoping Review of the Use and Application of Virtual Reality in Pre-Clinical Dental Education. Br Dent J. 2019; 226(5): 358–366. PubMed Abstract | Publisher Full Text\n\nReichert J, Praml G, Fischer M, et al.: NetWoRM: National and International Network for E-Learning in. Occup Med. 2004; 44: 378–379. PubMed Abstract\n\nQuinn B, Field J, Gorter R, et al.: COVID-19: The Immediate Response of European Academic Dental Institutions and Future Implications for Dental Education. Eur J Dent Educ. 2020; 24(4): 811–814. PubMed Abstract | Publisher Full Text\n\nShah R, Cunningham SJ: Implementation of the Virtual Learning Environment Into a UK Orthodontic Training Programme: The Postgraduate and Lecturer Perspective. Eur J Dent Educ. 2009; 13(4): 223–232. PubMed Abstract | Publisher Full Text\n\nEbner M, Schön S, Braun C, et al.: COVID-19 Epidemic as E-Learning Boost? Chronological Development and Effects at an Austrian University against the Background of the Concept of “E-Learning Readiness”. Future Internet. 2020; 12: 94. Publisher Full Text\n\nCurnier F: Teaching Dentistry by Means of Virtual Reality--the Geneva Project. Int J Comput Dent. 2010; 13(3): 251–263. PubMed Abstract\n\nLuz PB, Stringhini CH, Otto BR, et al.: Performance of Undergraduate Dental Students on ICDAS Clinical Caries Detection After Different Learning Strategies. Eur J Dent Educ. 2015; 19(4): 235–241. PubMed Abstract | Publisher Full Text\n\nAlves LS, de Oliveira RS , Nora ÂD, et al.: Dental Students’ Performance in Detecting in vitro Occlusal Carious Lesions Using ICDAS with E-Learning and Digital Learning Strategies. J Dent Educ. 2018; 82(10): 1077–1083. PubMed Abstract | Publisher Full Text\n\nKubicek H, Breiter A, Fischer A, Wiedwal C: Organizational Embedding of E-learning at German Universities. Germany:Institute for information management Bremen GmbH;2004. [German]\n\nEuler D, Seufert S: Change Management in Higher Education: Implementation of E-Learning as a Sustainable Innovation. Zeitschrift für Hochschuldidaktik. 2005, 03/2005; 3–15. [German]\n\nUniversity Rectors’ Conference: Recommendations for Ensuring the Quality of Study and Teaching in Bachelor and Master Courses. HRK Hochschulrektorenkonferenz die Stimme der Hochschulen. 2005. [German]\n\nNold: Dental education during the pandemic – cross-sectional lecturer-side evaluation for the use of digital teaching concepts.2022, June 22. Publisher Full Text"
}
|
[
{
"id": "143883",
"date": "26 Jul 2022",
"name": "Maximiliane Amelie Schlenz",
"expertise": [
"Reviewer Expertise digital dentistry",
"intraoral scanners",
"restorative dentistry",
"clinical dentistry",
"dental education",
"dental materials",
"implant prosthetic",
"removable and fixed prothodontics",
"gerodontology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review the manuscript “Dental education during the pandemic – cross-sectional lecturer-side evaluation for the use of digital teaching concepts”. The general approach to investigating the lecturers' perception towards digital teaching across all German Dental Schools is of high interest, not only limited to the topic of teaching during the COVID-19 pandemic, but rather for new digital teaching opportunities related to the new medical licensure act for dentistry in Germany. Furthermore, this study provides valuable information for lecturers around the world that like to implement or improve digital teaching in dental education. I have to emphasize the elaborate Discussion section and clear subsumption of the results to the available literature.\n\nAnswers to F1000 questions according to guidelines for reviewing:\nThe study design is appropriate and the work have an academic merit.\n\nThe work is clearly and accurately presented and the relevant current literature is cited.\n\nThe materials and methods section contains sufficient details to replica the study by others.\n\nAs far as I can see, the source data underlying the results are available.\n\nThe statistical analysis is appropriate and well interpreted.\n\nThe conclusions drawn are adequately supported by the results of the study.\n\nFrom my point of view, the manuscript is general acceptable for publication. However, I suggest to address the following small points:\nPlease, revise the manuscript regarding a consistent wording (e.g. analog or conventional, classroom teaching or event). Otherwise, the readers might get confused.\n\nI suggest to revise the title: “Dental education during the COVID-19 pandemic – cross-sectional lecturer-side evaluation for the application of digital teaching concepts”.\n\nPlease, extend the null hypothesis regarding the aspects “handling/attitude” (Questions 10-21C) towards digital teaching. These valuable aspects are not addressed in the null hypothesis yet, because only workload and effort are considered.\n\nI suggest to add a paragraph describing the established German face-to-face teaching concept to the introduction section, because in other countries digital concepts might be already implemented before COVID-19 pandemic.\n\nAdd the investigated aspects “handling/attitude” (Questions 10-21C) to the Introduction section and highlight more the key aspect of your questionnaire survey not investigating just one single dental school, but rather including all locations in Germany.\n\nPlease, add the period that you asked the lecturers for. I guess you were interested in the period March 2020 to January 2021?\n\nFor better clearance, add the measured data (0 to 100) to the scroll bar in Figure 1. Otherwise, it is a little bit difficult to interpret data of Table 2. In addition, I suggest explaining the analysis of the scroll bar in the legend of Table 2 and design the column “Answer possibility” clearer.\n\nPlease, increase the font of Figure 2-6.\n\nI suggest to approve the manuscript with reservations.\nGood luck and keep well!\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": "8922",
"date": "24 Oct 2022",
"name": "Anja Liebermann",
"role": "Author Response",
"response": "Dear Mr Gamal, Dear Ms Schlenz, Thank you for taking the time to edit our article. We tried to consider your comments to the best of our knowledge. We changed the title of the manuscript, as suggested by Mr. Gamal and Ms. Schlenz, and incorporated the references described by Mr. Gamal in the Introduction chapter. Unfortunately, we could not find any comparable studies in dentistry that examine the change in teaching from the lecturer's perspective during the pandemic. We will pursue the literature on this topic and supplement the article if necessary. In the Introduction chapter, we took up Mr. Gamal's suggestion and reorganized the last paragraph. Furthermore, we have included the date of the ethical statement in the text and added in the study design that the universities in question are all located in Germany. In the discussion, we described in more detail the limitations of this study. The mentioned formatting in Table 2 presented us with challenges. While the criticism for the PDF format is valid, in the online version of the article the results are aligned with choices in the same line. We provided Table 2 with appropriate values (Low:0, high:100). The same applies to the font size of the illustrations mentioned by Ms. Schlenz. Again, the criticism only applies to the PDF version of the article, but not to the online version. Appropriate formatting of f1000reaserch may help here. We have gratefully complied with the notification of the uniform formulations. We also briefly described the established German presence concept and expanded the hypotheses to include this aspect. Also we added the requested period to the article. In order to enable better interpretability of the data, we have provided the scroll bar with the appropriate values (0 to 100). We hope to have taken up your suggestions in the desired way and remain with kind regards."
}
]
},
{
"id": "151553",
"date": "27 Sep 2022",
"name": "Mohammed Gamal",
"expertise": [
"Reviewer Expertise pharmaceutical chemistry",
"green chemistry",
"instrumental analysis",
"medical survey research",
"clinical sciences"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is very interesting. It is very well written in a very clear language. It worth publication after minor revisions.\n1. Title should be modified to be dental education in Germany to reflect the geographical location for the study.\n2. The following article should be cited1,2,3,4\n3. Comparisons of dental education studies from lecturers points of view from different developed countries e.g. UK, USA, during pandemic should be stated and illustrated in discussions.\n4. Introduction should be ended with the main aim of the research paper. Therefore, I recommend reorganization of the last paragraph in introduction to be above aim statements “The hypothesis states that on the lecturer side 1. There is no difference between the various digital teaching concepts in terms of workload and effort, and 2. There is no increase in workload and effort when switching to digital teaching concepts.”\n5. Date of ethical statement should be provided.\n6. In study design [All dental schools, like all other universities] add in Germany.\n7. In table 2 , results should be aligned with choices i.e. in the same level on the same line.\n8. Future research plans and study limitations should be 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? 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": "8923",
"date": "24 Oct 2022",
"name": "Anja Liebermann",
"role": "Author Response",
"response": "Dear Mr Gamal, Dear Ms Schlenz, Thank you for taking the time to edit our article. We tried to consider your comments to the best of our knowledge. We changed the title of the manuscript, as suggested by Mr. Gamal and Ms. Schlenz, and incorporated the references described by Mr. Gamal in the Introduction chapter. Unfortunately, we could not find any comparable studies in dentistry that examine the change in teaching from the lecturer's perspective during the pandemic. We will pursue the literature on this topic and supplement the article if necessary. In the Introduction chapter, we took up Mr. Gamal's suggestion and reorganized the last paragraph. Furthermore, we have included the date of the ethical statement in the text and added in the study design that the universities in question are all located in Germany. In the discussion, we described in more detail the limitations of this study. The mentioned formatting in Table 2 presented us with challenges. While the criticism for the PDF format is valid, in the online version of the article the results are aligned with choices in the same line. We provided Table 2 with appropriate values (Low:0, high:100)..The same applies to the font size of the illustrations mentioned by Ms. Schlenz. Again, the criticism only applies to the PDF version of the article, but not to the online version. Appropriate formatting of f1000reaserch may help here. We have gratefully complied with the notification of the uniform formulations. We also briefly described the established German presence concept and expanded the hypotheses to include this aspect. Also, we added the requested period to the article. In order to enable better interpretability of the data, we have provided the scroll bar with the appropriate values (0 to 100). We hope to have taken up your suggestions in the desired way and remain with kind regards."
}
]
},
{
"id": "151554",
"date": "11 Oct 2022",
"name": "Jens Christoph Türp",
"expertise": [
"Reviewer Expertise Evidence-based dentistry",
"orofacial pain",
"temporomandibular disorders",
"occlusion"
],
"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 by the five authors addresses a timely topic: teaching in times of the Covid 19 epidemic. Specifically, they examined how digital teaching in dentistry (here: prosthodontics) has changed as a result of the pandemic ‒ and how faculty have responded to the unexpected challenges. I will share my impressions, comments, and suggestions below. Before doing so, I would like to emphasize that I agree with all the suggestions made by the reviewer Maximiliane Amelie Schlenz (University of Giessen). Therefore, I will not address the manuscript-related points mentioned by her in my review.\nIn the following, I will present my points in chronological order according to the sequence of the individual parts of the manuscript.\nABSTRACT (1) Background: the authors should better visually emphasize the two aims of their study by labeling them \"(a)\" and \"(b)\": \"The aim of this investigation was to evaluate (a) the attitudes of [...] and (b) the effort creating digital lectures.\" (2) Results: The precise numbers (24.8%, 64.4%, 86.1%, 81.2%, 33.7%, etc.) given to one decimal place suggest a mathematical accuracy, which in reality ‒ not least because of the methodology (see later) ‒ is rather due to chance. It would therefore be more advantageous to paraphrase the calculated values linguistically instead, e.g., by writing \"a quarter\", \"far more than half\", \"the vast majority\", \"about a third\", etc. (3) Results: In contrast to the German language, sentences in English must not begin with Arabic numerals (\"88.1% see face-to-face teaching\"). Instead, in such cases, the numbers are written out. In this specific case, however (see point 2 above), a paraphrase like \"Four out of five lecturers see ...\" would be the better linguistic choice. (4) Results: Results are presented by the authors only for the first objective, but none for the second aim (effort/workload). (5) Results: The first two sentences of the results provide information for which no aim was provided in \"Background\". Therefore, one could add another ‒ first ‒ aim there: \"[...] was to evaluate the changes in the percentage of digital teaching.\" (6) Conclusions: they are relatively trivial. The results provide possibilities for a more attractive conclusion.\nINTRODUCTION (1) 2nd paragraph, end of the first sentence: \"still has deficiencies\". The reader would certainly like to know which deficiencies are involved. (2) 3rd paragraph, second sentence: \"blended learning\". A brief explanation of what is meant by this term would be helpful since it cannot be assumed that all readers of the article are familiar with it. (3) 4th paragraph, first sentence: (a) \"described by the students\". Which students are meant and to what does this statement refer? (b) \"Investigations\" can no more be \"found\" than studies can be read. Investigations/studies are planned, funded, conducted, and completed, but never found or read. What is \"found\" are articles in a literature search, and what is \"read\" are articles about a study. (4) Paragraphs 4 and 5: Both begin with \"Although\". This can easily be improved.\nMETHODS (1) 2nd paragraph (Study design): This paragraph belongs in the introduction. (2) 3rd paragraph (Participant recruitment): \"All German dental schools\". The reader would certainly like to know how many dental schools there are in Germany. (3) 3rd paragraph (Participant recruitment): Of great importance is an indication of whether there was a maximum number of study participants per site ‒ and if not, why not. If you look at Figure 2, you can see why this question is important (possibility of bias in the results). The authors should also mention whether external lecturers, i.e., lecturers not permanently employed at the dental clinic (e.g., lecturers working in private practice [external senior physicians/dentists; Privatdozenten; adjunct professors]) were also allowed to participate in the study. (4) 4th paragraph (Questionnaire development): The explanations are partly incomprehensible, especially the third last sentence (\"After validation, a short cut was created from ...\"). More detailed explanations are required here. The aim of a good methodology section should always be to enable the reader, at least theoretically, to repeat the study without asking the authors. For this purpose, the authors must disclose from the beginning everything that is necessary to understand the applied methodology. (5) 5th paragraph (Data analysis): \"The questionnaires were examined with ...\". By whom were they examined/evaluated? (6) Figure 1: The scale should have two anchor points labeled \"0\" and \"100\".\nRESULTS (1) Fig. 2: It is clear from this figure that the results obtained in this study are very unlikely to be representative of dental prosthodontic teaching in Germany, but rather a biased sample. Of the 30 (?) dental universities in Germany, only 18 are represented in this study. These 18 are weighted differently. Not unexpectedly, study participants from the University of Munich make up the majority with about one-fifth of the total number. Interestingly, no one from the University of Cologne, where one of the authors is from, participated. This bias does not devalue the study, but it does diminish its general validity. This drawback should be highlighted more in the discussion than the authors do in a brief section toward the end of the discussion. (2) In the text, as already mentioned above in the \"Abstract\" section, pseudo-exact numerical values should be avoided in favor of rounding or linguistic descriptions. What on earth are \"34.7% of the lecturers\" in view of 84 participants (\"101 lecturers\" minus \"17 lecturers with incomplete questionnaires\"; see Results, 1st par.)? (3) Paragraph 8: \"lecture with audio, e.g., with PowerPoint\". PowerPoint is primarily visual, not audio. (4) Paragraph 9: What exactly do the \"general medians\" indicate? What do they refer to? How do the numerical values come about? (5) Table 2: The given values of the medians and IQR should be at the level of the respective answer options a), b) and c).\nDISCUSSION (1) A good discussion always starts with the highlight of the study results (\"Where is the meat?\"), but not with general statements like \"The COVID-19 pandemic led to major changes worldwide, ...\" - everyone knows that. (2) The discussion is unnecessarily long. The probability that an article will be read increases if it is kept short. (3) What has been pointed out before also applies to the discussion: Avoid giving exact numbers from the study. (4) The authors compare the two teaching formats analogue (lecture hall; seminar room) versus digital (computer). Possibly, however, another aspect plays a role: the lecturer. After all, until the beginning of the pandemic, holding online lectures was never an issue for her/him. Now she/he is forced to speak into a microphone in an unfamiliar environment (her/his office, her/his home) and an unfamiliar format, sitting in front of his computer. You could say: instead of a familiar theatre performance, she/he is suddenly forced to deliver a radio play, a format completely unfamiliar to her/him. This change is not easy for every lecturer. Consequently, some lecturers deliver a presentation that is below the standards they have been used to in the lecture hall; in addition, they have to deal with technical problems, speak in a monotone voice, etc. In such cases, however, the differences in the evaluations concern less the teaching format, but rather the performance of the lecturer. This aspect should be examined more closely in the discussion. (5) Paragraph 14: \"bedside-teaching\". Do the authors mean \"chairside teaching\"? (6) Paragraphs 15 and 16: Both start with \"When\".\nCONCLUSION (1) What does the following sentence mean: \"Lecturers evaluated an additional effort in creating digital lectures\"?\nREFERENCES (1) Ref. 29 and 30: The titles of the papers are given in English. However, the articles have been published in German. The corresponding original German titles are: 29: Organizational Embedding of E-Learning at German Universities. Institute for Information Management Bremen 30: Change Management in Higher Education: The Sustainable Implementation of e-Learning Innovations. A disregard of the original title and replacement of the same by an own translation (which in the case of reference 30 is inaccurate, since it should read: Change Management in University Teaching: The Sustainable Implementation of e-Learning Innovations) is not permitted without a corresponding note. (2) The following literature should be included1,2,3\nGENERAL REMARKS (1) The text needs linguistic (English) improvement. (2) Sentences in scientific English are shorter than in German. Therefore, two shorter sentences are better than one long one.\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": []
}
] | 1
|
https://f1000research.com/articles/11-767
|
https://f1000research.com/articles/11-1276/v1
|
08 Nov 22
|
{
"type": "Research Article",
"title": "Granite classification using machine learning and edge computing",
"authors": [
"Madhavi Karanam",
"Krishna Chythanya Nagaraju",
"Gotham Sai P",
"SaiKiran Manasa S",
"Pranay Krishna G",
"Madhavi Karanam",
"Gotham Sai P",
"SaiKiran Manasa S",
"Pranay Krishna G"
],
"abstract": "Background: The outlook and the aura of any place are highly dependent on how a place is decorated and what materials are used in designing it. Granite is such a kind of rock which is vastly used for this purpose. Granite flooring and counters have a major influence on the interior d ́ecor which is essential to set the mood and ambience of a house. A system is needed to help the end users differentiate between granites, which enhance the grandeur of their house and also check the frauds of different color granite being sent by the merchant as compared to what was selected by the end user. Several models have been developed for this cause using CNN and other image processing techniques. However, a solution for this purpose must be precise and computationally efficient. Methods: For this purpose,researchers in this work developed a machine learning based granite classifier using Edge Computing and a website to help users in choosing which granite would go well with their d ́ecor is also built. The developed system consists of a color sensor [TCS3200] integrated with an ESP8266 board. The data pertaining to RGB contrasts of different rocks is acquired by using the color sensor from a dealership.This data is used to train a Machine Learning algorithm to classify the rock into different granite types from a granite dealer and yield the category prediction. Results: The proposed system yields a result of 94% accuracy when classified using Random Forest Algorithm. Conclusion: Thus, this system provides an upper hand for the end users in differentiating between different types of granites.",
"keywords": [
"Granite",
"Machine Leaning",
"Edge Computing",
"Random Forest",
"SVM",
"TCS3200",
"ESP8266"
],
"content": "Introduction\n\nGranite is a coarse-grained igneous rock. It is formed when magma is compressed due to the pressure underground. It is one of the most common rocks found on earth crust and constitutes a multimillion dollar granite industry. Granite owing to its beauty and composition, it is used in a wide range of applications which encompass house decor, flooring, counter tops etc. This flexibility of granite has instigated many people to cheat with the quality and type of granite. With the advancing technologies, like machine learning and Internet of Things (IOT) the verification and analysis of such samples has become an easy task. These technologies have made it possible to go about any particular task in an efficient and remote manner with pinpoint precision. This has led some researchers to explore the field and produce some workable solutions, models which recognize the type of granite using Convolutional Neural Network (CNN) on images of granite. These models classify the granites based on image patterns of different types of granite.1\n\nModels which use Computer Vision to classify rocks using the colors and textures of granites obtained from images. This model considers the color of granite and it’s texture as the distinguishing factor.2 Models were developed which apply Machine Learning on data gathered using a spectrophotometer. These models gather data from a spectrophotometer and then apply Machine Learning to differentiate between granite types.3\n\nThe solutions currently developed all rely on heavy computing techniques and are not portable. A solution which can be executed from anywhere at any time needs to be developed to better cater the needs of end users. To meet the demands of end users and make the system more portable and efficient, a model with Machine Learning and Edge Computing is experimented in this work. The increasing standards of living and per capita income have also inspired people to try different styles and experience various luxuries, primarily the looks of their houses. This sudden inflow of income and need for granite has instigated some merchants to fraud the end users by charging for a higher quality rock and issuing a lower quality rock. With these frauds on the incline, the financial situations are on a decline. It’s high time that we develop a method to verify the quality of the rock and terminate the frauds. The end users also often seek suggestions to choose from the plethora of granites that are available in the market. It is important now more than ever to devise a solution to corroborate the granite received in order to prevent the fraud efficiently and effectively without compromise on the portability. The integration of ML and Edge Computing is an effective way to do the required task much more easily.\n\nThis project utilizes the color variations of granites to classify them into various categories by collecting the color values from separate points on the rock and applying Machine Learning on them. The major objective of this work is to verify the rock delivered based on color.\n\n\nPrevious work\n\nThe homogeneity of pieces of granites being used based on color is very important for the aesthetic of place where granites are being used. In general humans carry out the classification process based on quality and look using human experience and exposure along with a bit of creativity. This opens doors for artificial intelligence based works to be carried out in this field in selection of a specific color granite.\n\nReference 1 work follows convolution neural network usage for granite classification. The researchers used transfer learning on MNSIT networks and CIFAR networks on a dataset of 1000 RGB images. Using Nearest Neighbor classifier with CIFAR they claim to achieve an accuracy of above 85% in classifying granites.\n\nIn the work2 an expert system was developed based on computer vision concepts to classify granites. The authors claim that Support Vector Machine out performs than other methods they tried in classifying granites based on color and texture. The classification of granites using automatic artificial intelligence based systems would provide benefits of creating a repeatable procedure which is not possible in manual general process followed for decades in market. This further add to substantial upgrading in quality assessment procedures for companies. Also, lessening of losses owing to cancellation of order at customer site besides easy warehouse management can be achieved. The work was carried out using lot of 48 granites of twelve classes on total which were subdivided in to 64 samples per class and images were captured using a standard procedure in lab but finally the cropped image of “544×544 pixels” was used in experimentation. They used methods based on co occurance matrix, Gobor features, chromatic features and Local Binary Patterns. The work made use of multiple classifiers including “Support Vector classifier”, “Linear Classifier” “Naïve Bayes’”, “Nearest Neighbor” etc.\n\nIn some works sum and differences of histograms along with LVQ neural networks is used to classify granites.4 In the letter published by Ref. 5 the researchers claim to use “wavelet analysis” to classify the granites. Discrete wavelet transformation is used to generate sequences of signals in their work. The researchers made use of 30 image database having three classes of granites. The work claims to obtain 90% accuracy using LVQ neural networks.\n\nWith the work6 the researchers have proposed an “electro-mechanical system” that robotically categorizes marbles while on conveyor belt itself based on a “hierarchical clustering approach”. They made use of Programmable Logic Controller along with an auxiliary micro controller to bind between PLC and Matlab. Clustering based classification was implemented along with hierarchical classification based on cascaded features of color, texture and spectral. 83.6% accuracy as recorded in their work for correct classification of marbles. Reference 7 work makes use of transfer learning on AlexNet and VGGNet to develop a Convolution Neural Network based granite tiles classification using a dataset of 2000 RGB images classified into 25 classes. Out of experiments they observed that fine tuning VGGNet they could record an accuracy of almost 99.3%.\n\nThe authors of Ref. 8 have implemented there own CNN architecture and good bring out an accuracy of around 96.1% in marble quality classification. The authors of Ref. 9 have done extensive experimentation by examining fifteen varieties of convolution neural networks to sort dolomitic stone tiles. They observed that “DenseNet201” model could yield an accuracy of 83.24% while trained on a 489 digital image data set of granites classified into 3 classes.\n\n\nMethods\n\nThe Model developed takes the color values of granite as input and then feeds it to a machine learning algorithm. The sensor relays data to a nodemcu, which analyses it and deploys a machine learning model to verify the granite being sampled and classifies it into a specific class of rock.\n\nMachine learning is a part of Artificial Intelligence (AI) that trains a computing machine to learn from data and improve. The term machine learning depicts an automated process of pattern recognition and feature detection in any data. Machine learning also increased the comforts of living, personal assistants are now available which cater to a person’s personal needs and desires. Machine learning can be categorised as Supervised machine learning, Unsupervised machine learning, Semisupervised learning as shown in Figure 1 below.\n\nMachine learning models require a large amount of data to be trained on for efficient prediction and increased accuracy. The data can be obtained from a variety of methods including real time data collection as done in this work. This data can be processed in a lot of ways such as normalization, removing data or filling the missing data with mean, median or mode and other ways. After processing the data, the Machine learning models are ready to be trained. The authors opted for classification model of ML to be implemented for this work as objective is to classify granites based on color. There are several Algorithms which analyze the data and predict/classify the output. Each of them works on a different principle and the ML model. Training is the part where the machine learns the data and analyses it. The Output and the efficiency majorly depend on this part. The data is trained to provide a specific output depending on the input provided. Evaluation of a model refers to the part where the model’s efficiency is tested. In this work Accuracy and Confusion matrix are considered to evaluate trained model. The overall machine learning process discussed can be depicted in figure as shown in Figure 2.\n\nEdge computing refers to a distributed computing paradigm, in which the data is stored and computations are executed closer to the actual site in order to improve response time and carry the functions of any process faster. It’s more of a topology. The purpose of Edge computing is to move the entire computation of any process away from data centers and closer to the edge of the network in order to reduce the stress and load on the data center for efficient and quicker responses. It exploits the functions and specifications of smart objects like smart phones, controller boards etc., which have built-in memory to perform tasks and provide services instantaneously rather than accessing the data centers and retrieving information for every task.\n\nDataset used is collected from a granite dealership with the consent of pertaining dealers in real time. This collected data is then used to train the developed IoT based machine learning model using edge computing. The Features of the dataset include RGB values of different types of granites and the last column giving the color of granite. The sample of data set collected is shown in Figure 3 below.\n\nThe sensors were taken to a dealership and the RGB values pertaining to the different classes of granites are recorded. This data is then stored in a csv file for easier training of ML models.\n\nThe ESP8266 and color sensor were integrated to build the experimental setup for the purpose of recording the RGB values of granites and for the collection of dataset. A dealer was contacted to get the permission for recording the values of granites and after taking necessary precautions and permission. The values of red granite, black granite and white granite were collected and tabulated as shown in Figure 3 below. The data was collected by one of the authors of this work as can be found in image of Figure 4 below. The dataset acquired accommodates 90 rows with 12 columns of rgb values describing 3 classes. A program was written in Arduino IDE to collect the sensor readings. The sensor gives “rgb” values at each point by adjusting the s0 and s1 pins. These RGB values are stored in an array. The seuence diagram of idea carried out can be seen in the figure below. The overall system architecture of the idea implemented can be seen as in Figure 5 below. This work is implemented using Arduino IDE for edge computing, python language to perform machine learning and HTML, CSS to develop the web application. With the help of special libraries, machine learning is carried out on the Arduino platform. The Arduino (IDE) software makes the uploading of code to the NodeMCU much easier and quicker. Python Language is used to implement the machine learning modules using Scikit Learn library which is then transferred to Arduino.\n\nThe Dataset built already is given to train machine learning models to learn. After the data is trained and models learnt the process, various algorithms are evaluated and compared to select the one with highest accuracy for classification i.e. Random forest. The Implementation of this project is done in 3 steps: 1. Data collection: collection of data from the granite dealership; 2. Model Selection: various ML algorithms were observed and a model is fixed; 3. Deployment: The model is deployed into a nodemcu for real time usage.\n\nVarious machine learning algorithms are used to classify any particular data and each one of them is dependent on a specific mathematical concept. These concepts are then applied to find a most suitable correlation with the given data or a function that best fits the data being analyzed. The algorithms that are compared for better output in this work are: Random Forests Algorithm10; Support Vector Machine Algorithm11; K-Nearest Neighbors (KNN) Algorithm.12 The algorithms are implemented in python and then converted to C for it to be executed in NodeMCU. NodeMCU is an open-source firmware, used for IoT applications on open source boards. Lua scripting language is used to implement the firmware on Espressif SDK for Esp8266. Esp8266 image is shown in figure below. A Wi-fi soc from espressif systems is available on the board. A dual in-line package provided by the prototyping hardware integrates a USB controller with an MCU and antenna laden board. UART, DAC and ADC interfaces are supported by the board and can be accessed through a specific set of pins among the 21 pins available on the board.\n\nThe deployment is done using python IDLE and Arduino IDE. Micromlgen is an open source library developed to bring machine learning to microcontrollers. It essentially converts a ML code into an optimized c code for the microcontrollers to execute it. This acts as an alternative to the Tensorflow package which is computationally complex and cannot be used on boards with smaller capacities and memories. Micromlgen supports some of the basic machine learning algorithms like SVM, Random Forests, Decision trees, Gaussian Naive Bayes, XGBoost among others. The obtained output code in C is then written in a header file which is to be included in the arduino sketch. Thus, ML is implemented in the NodeMCU effectively. The sensor is then connected to the NodeMCU and the model is loaded onto the board. The physical model gets ready and can be used to classify granites in real time.\n\nTCS3200 color sensor contains a TAOS TCS3200 RGB sensor chip and 4 white LEDs. The image of TCS3200 color sensor is shown in the image in figure given below. The chip forms the most important module of the sensor, which is basically a color light-to-frequency converter. The sensor is arduino compatible, which makes it very useful and easy to handle. The corresponding frequency of various colors is given as output by sensing the presence of Red, Green and Blue colors. This module can be used in a variety of applications such as granite classification, color matching tests, color sorting robots, etc. The setup built for Edge Computing using ESP8266 and TCS3200 for carrying out the idea can be seen in the image of Figure 6 below.\n\nThe Figure 7 above shows the sample results found during experimentation.\n\n\nConclusion\n\nIn this work the model built helps the users in choosing a granite that enhances the grandeur of their house and also reduces losses for return orders at merchant end. The model aims to help the end users in ascertaining the quality and type of granite they received. Improvising the age- old techniques of image classification, this model does the task with edge computing for increased efficiency and effectiveness. The researchers tested the dataset using several machine learning algorithms which have produced satisfactory results. Random Forest classifier gave 94% accuracy, SVM exhibited 78% accuracy and KNN could only achieve 75% accuracy. The values have been shown tabular form in Table 1 above. Random Forest algorithm yielded the best results. The accuracy can be improved by collecting larger data.\n\n\nAuthor contributions\n\nMrs. K. Madhavi was chief mentor for the work and supervised the whole research taken up with time to time inputs. She took care of reviewing the article and methodology.\n\nMr. Krishna Chythanya conceptualised the idea and assisted in Implementing the research with proper evaluations time to time and also writing the article.\n\nMr. P. Gowtham Sai was instrumental in collecting data as well as implementing the code.\n\nMr. S. Saikiran Manasa was contributing in algorithm implementation and evaluation.\n\nMr. G. Pranay Krishna was playing role during documentation and review.\n\n\nData availability\n\nFigshare. datasetG raniteClassi f ication.csv. DOI: 10.6084/m9.figshare.20301006.\n\nThis project contains the following underlying data:\n\n‐ The data set has around 90 rows each consisting of 12 coloumns that stands of RGB values of Granite. Each of RGB is represented by 4 values respectively in a row. These values are recorded using TCS3200 color sensor on granite peices. The values were recorded by visiting couple of near by granite dealer shops in Hyderabad, Telangana, India. The last column denotes the color of granite and thisacts as a target variable in case of machine learning algorithms to predict the color of granite.\n\n\nSource code\n\nZenodo. GRANITE CLASSIFICATION USING MACHINE LEARNING AND EDGE COMPUTING. DOI: 10.5281/zenodo.6835324.\n\n‐ The RAR file consists of three folders. Each folder has got code for each of the three machine learning algorithms implemented for Granite Classification using Edge Computing. The code has folders by name KNN, SVM and Random Forest.",
"appendix": "References\n\nFerreira A, Giraldi G: Convolutional neural network approaches to granite tiles classification. Expert Syst. Appl. 2017; 84: 1–11. Publisher Full Text\n\nBianconi F, González E, Fernández A, et al.: Automatic classification of granite tiles through colour and texture features. Expert Syst. Appl. 2012; 39(12): 11212–11218. Publisher Full Text\n\nAraújo M, Martínez J, Ordóñez C, et al.: Identification of granite varieties from colour spectrum data. Sensors. 2010; 10(9): 8572–8584. PubMed Abstract | Publisher Full Text\n\nTomás-Balibrea L-M, et al.:Automatic classification system of marble slabs in production line according to texture and color using artificial neural networks. International Conference on Computer Analysis of Images and Patterns. Springer;1999; pp. 167–174.\n\nLuis-Delgado JD, Martinez-Alajarin J, Tomas-Balibrea LM: Classification of marble surfaces using wavelets. Electron. Lett. 2003; 39(9): 714. Publisher Full Text\n\nAlper Selver M, Akay O, Alim F, et al.: An automated industrial conveyor belt system using image processing and hierarchical clustering for classifying marble slabs. Robot. Comput. Integr. Manuf. 2011; 27(1): 164–176. Publisher Full Text\n\nAther M, Khan B, Wang Z, et al.: Automatic recognition and classification of granite tiles using convolutional neural networks (cnn). Proceedings of the 2019 3rd International Conference on Advances in Artificial Intelligence. 2019; pages 193–197.\n\nKaraali I, Eminağaoğlu M: A convolutional neural network model for marble quality classification. SN Appl. Sci. 2020; 2(10): 1–6. Publisher Full Text\n\nOuzounis AG, Sidiropoulos GK, Papakostas GA, et al.: Interpretable deep learning for marble tiles sorting. DeLTA. 2021; 101–108.\n\nHo TK:Random decision forests. Proceedings of 3rd international conference on document analysis and recognition. Vol. 1. .IEEE;1995; pp. 278–282.\n\nMeyer D, Wien FT: Support vector machines. R News. 2001; 1(3): 23–26.\n\nPeterson LE: K-nearest neighbor. Scholarpedia. 2009; 4(2): 1883. Publisher Full Text"
}
|
[
{
"id": "157142",
"date": "16 Dec 2022",
"name": "Ratan Lal",
"expertise": [
"Reviewer Expertise Formal Verification",
"Cyber-Physical Systems",
"Robotics",
"Machine Learning",
"Internet of Things"
],
"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 consider the problem of identifying the quality of Granite rock to help people and avoid fraud in Granite rocks. The broad approach is the following. First, a set of RGB colors for real images is collected through the color sensors. Then, the data has been used to train different machine learning models, such as Random Forest, Support Vector Machine, and K Nearest Neighbor. Upon training the model, the best among the selected models has been considered to deploy on NodeMCU, which is an open-source firmware used for IoT applications on open-source boards. The model is trained through Scikit Learn Library in python, and then it is converted into C using Micromlgen in order to deploy the ML model on the NodeMCU. Finally, the Random Forest model has 94% accuracy, and it is deployed on the NodeMCU.\nPros:\nThe idea of identifying the quality of Granite rock using IoT devices is interesting.\n\nThe paper is written well.\n\nMajor Comments:\nI recommend the authors use the term “prediction” in place of “verification” as the machine learning model does not always give an accurate result.\n\nIt would be good if the authors could report the confusion matrix for the Random Forest model.\n\nI recommend the authors remove methods:, results: heading and conclusion: paragraph from the abstract.\nMinor comments:\nOn page 6, seuence -> sequence\n\nOn page 7, python IDLE -> python IDE\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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "225152",
"date": "27 Nov 2023",
"name": "Blessing Olamide Taiwo",
"expertise": [
"Reviewer Expertise Engineering application of 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\nFirstly, I want to thank the authors for putting this great work together and for their efforts.\nThe manuscript presents the development of machine learning based granite classifier using Edge Computing and a website to help users in choosing which granite would go well with their decor is also built. The authors considered color sensor [TCS3200] integrated with an ESP8266 board in the work.\nI have the following comments and recommendation to improve the current state of the work.\n1. Grammar and Presentation:\nThe work needs some rephrasing and corrections to improve the grammar and presentation. (Pg 4 last paragraph and other areas).\n2. Literature Review:\nThe author provides some literature about previous work, but i recommend they include recent works relating to optimization algorithms, ensemble learning classifiers to provide more ground to users about the methodology used in this work.\n3. Model Result validation and Data description:\nI recommend that the author should provide the data in Table form and also provide the testing input dataset along with Figure 7.\nThe use of ROC as part of the result assessment should be included in the result section.\n\"ROC curve is a graphical representation of the performance of a binary classifier system as its discrimination threshold is varied. It is created by plotting the true positive rate (TPR) against the false positive rate (FPR) at various threshold settings.\"\nAuthors should provide the chart for both FPR and TPR for both training data only for testing data to enhance the result interpretation.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "225149",
"date": "27 Nov 2023",
"name": "Zhi Yu",
"expertise": [
"Reviewer Expertise Mining Engineering",
"Application of machine learning technique"
],
"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. The abstract requires revision, with the removal of specific terms such as background, methods, and results.\n2. Clarify the term \"d’ecor?\" in the abstract.\n3. Provide an introduction to the development of the machine learning model.\n4. Introduce the data preprocessing steps and specify the ratio of training to testing datasets.\n5. Include a comparative analysis of model performance.\n6. Add sections on limitations and future scope.\n7. In the introduction, highlight the limitations of prior studies and underscore the significance of this paper.\n8. Enhance the quality of the figures presented in the paper.\n9. Reorganize the content of the article for better flow.\n10. Clarify the content of Figure 7, specifically the phrase \"Lest me guess you?\"\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?\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": []
}
] | 1
|
https://f1000research.com/articles/11-1276
|
https://f1000research.com/articles/11-1275/v1
|
08 Nov 22
|
{
"type": "Review",
"title": "Intraoral repair of fractured ceramics: a literature review",
"authors": [
"Firas K. Alqarawi",
"Abdulkareem A. Alhumaidan",
"Abdulrahman Aldakhili",
"Abdullah Alfayez",
"Tahani Abushowmi",
"Anwar Alramadan",
"Fawaz Alzoubi",
"Abdulkareem A. Alhumaidan",
"Abdulrahman Aldakhili",
"Abdullah Alfayez",
"Tahani Abushowmi",
"Anwar Alramadan",
"Fawaz Alzoubi"
],
"abstract": "Background: Fracture or chipping of veneering ceramic resulting in aesthetic and functional issues is a frequent technical complication encountered with fixed dental prostheses. Treatment options include extraoral or intraoral repair of the ceramic restoration; the latter being minimally invasive and cost-effective. We reviewed the various intraoral repair techniques for ceramic fractures and their efficiency in the last decade. Methods: A literature search was carried out between 2017 and 2022 using the PubMed database with keywords: intraoral, repair, ceramics, porcelain, and ‘porcelain fused to metal’. Screening of abstracts and full texts was carried out to determine the final list of eligible studies. Results: Twenty-one eligible studies were included in the review which consisted of 17 in vitro studies, three case reports, and one prospective clinical study. Researchers and dentists preferred repairing cracked veneered zirconia-based restorations intraorally if the restoration is in acceptable condition. However, successful intraoral repair of veneering fractures relies on the bond between the previous restoration and the new repair material, the right adhesive resin, and adequate surface conditioning. The review indicated that the best technique to fix chipping in a complex made of zirconia core and veneering ceramic is to treat the veneering ceramic with hydrofluoric acid before covering the core ceramic with silica. Conclusion: Intraoral repair is an efficient and economic procedure without the need for repeated sessions. However, the success and longevity of the restoration rely on the technical skills of the clinicians and adherence to prescribed protocols.",
"keywords": [
"Intraoral",
"restoration",
"ceramics",
"fixed partial dentures",
"zirconia",
"porcelain chipping",
"veneering."
],
"content": "1. Introduction\n\nModern cosmetic dentistry places a strong emphasis on aesthetics, and thus finds a wide usage of ceramic and porcelain in teeth restoration to achieve the most natural-looking aesthetics. However, the accelerated usage of dental porcelains is accompanied by the risk of fractures (Hammond et al. 2009). Owing to its brittle nature, porcelain veneering, when exposed to masticatory forces, clenching, and moisture causes cracks or chipping (Rosentritt, Steiger et al. 2009). Studies have shown that the most frequent technical issue associated with dental restorations were ceramic fractures, which were followed by porcelain chipping and loss of retention (Vagropoulou, Klifopoulou et al. 2018). According to a systemic literature review, chipping of the veneering ceramic is one of the most frequent technical complications occurring at a rate of 12.7% following a three-year observation period (Pjetursson, Sailer et al. 2015). Consequently, patients with ceramic fractures might have aesthetic and functional issues that need an immediate fix. Direct repairs have been suggested in such conditions where the broken prosthesis displays good adaptation and acceptable aesthetics (Mesquita, Al-Haj Husain et al. 2021).\n\nIn bilayered dental prostheses, such as metal-ceramic fixed dental prostheses (FDP), fractures in veneering ceramic may be treated either by replacing the existing restoration or by repairing it intraorally. Removal of FDP can be challenging as it can lead to deformation of the metal and iatrogenic fracture of the sound tooth tissues that can seriously compromise the longevity of the tooth. Additionally, replacing FDPs is typically a difficult and expensive process that adds significantly to chairside time, which is not always well received by the patient (Özcan and Volpato 2017). Furthermore, it is associated with the risk of harming the tooth that serves as the abutment (Kocaağaoğlu, Manav et al. 2017).\n\nOn the other hand, intra-oral ceramic restoration repair is minimally invasive and most cost-effective making it an ideal choice (Aslam, Hassan et al. 2018). Furthermore, intraoral repair has recently been suggested as a potential therapy alternative if the indications and treatment techniques are suitable (Agingu, Zhang et al. 2018). Repairing the ceramic restoration intraorally is a temporary but effective solution. The easiest way is to polish the surface and prevent future failures. If the repair cannot be done by polishing, the missing part is replaced with composite resin, or the chipped part is cemented using resin cement. A new veneer layer is prepared and bonded to the existing restoration (Kimmich and Stappert 2013).\n\nIntraoral repair is a simpler technique to treat veneer ceramic fractures than total replacement or extraoral repair methods (Polat, Tokar et al. 2021). Veneering porcelain flaws that expose the restoration's core material create a special challenge for intraoral repair. Particularly with metal frameworks, it can be challenging for the dentist to match the colour of the framework with veneer without compromising the aesthetic outcome. To achieve functional success, the dentist must effectively bond the veneering porcelain to the core material (Kimmich and Stappert 2013). However, selecting the best system that would deliver a trustworthy result is often difficult for clinicians. Hence, this article reviews studies that have investigated intraoral repair techniques for ceramic fractures and their efficiency in the last five years.\n\n\n2. Methods\n\nThe literature search was conducted using the PubMed database for studies that investigated intraoral repair techniques for ceramic fractures. All studies published in English from January 2017 through August 2022 were considered for review. The search strategy was derived from appropriate keywords representing the concepts: “intraoral repair”, “ceramics”, “porcelain”, “porcelain fused to metal”, and “efficacy”. The primary outcome of the review included the efficacy of the intraoral repair technique used. Articles were excluded if published in a language other than English, not published in the last five years, or if full text is unavailable.\n\nAfter applying the criteria, study selection was undertaken by first screening the abstract and title followed by the full-text versions of relevant studies to determine the final list of eligible studies. Data were extracted from the studies following the completion of full-text screening. All data were summarized. No statistical analysis was performed.\n\n\n3. Results\n\nThe literature search from PubMed retrieved 21 eligible studies that were included in this review to understand the intraoral repair techniques used for treating ceramic fractures. The findings of the included studies have been summarized in Table 1.\n\nThe current literature review included 17 in vitro studies, three case reports, and one prospective clinical study. Various ceramic types were included in these studies such as glass-based ceramics with three subclasses: predominantly glass (feldspathic glass), moderately filled glass (leucite), and highly filled glass (leucite disilicate based); glass-infiltrated ceramics (In-Ceram groups); and non-glass-based ceramics: polycrystalline ceramics (alumina, zirconia). Likewise, various surface treatments such as polished surface, air abraded, or ground using a special silicon carbide bur (SiC Grinding Bur), yttrium-aluminum-garnet laser (Neodymium, Erbium, Chromium, Scandium, Gallium, CO2 laser) treatment were employed across the studies to improve the to increase the surface roughness and bond strength. The repair systems included in the articles were Clearfil Repair, Clearfil Majesty Esthetic, Clearfil Photoposterior, Clearfil porcelain repair system, Shofu (P and R) repair system, Estelite Sigma Quick composite repair system, Cimara, and Cimara Zircon Repair System and BISCO Intraoral repair kit.\n\nThe results of the studies included in this review are broadly divided into surface treatment methods and intraoral repair techniques employed in the studies.\n\nMost of the included studies have emphasized different surface treatment methods. An in vitro study from Iran compared the effectiveness of new ceramic surface treatments (laser and universal adhesive) with the traditional method for improving the bond strength of composite resin to ceramic during repairs. The group consisting of hydrofluoric (HF) acid, silane, and conventional adhesives had the highest shear bond strength (SBS) (mean: 12.0481 MPa) compared to the traditional adhesive and laser technology group (mean: 2.5766 MPa). HF acid surface treatment produced significantly greater SBS than laser (P < 0.001) (Benli, Kilic et al. 2022, Kiomarsi, Jarrah et al. 2022). Holler et al. compared two distinct surface pretreatment techniques to repair a lithium-disilicate glass-ceramic (LDS) to see how they would react to simulated intraoral circumstances (increased temperature and humidity). Significantly less tensile bond strength (TBS) was produced by higher temperatures and humidity. Self-etching glass-ceramic primer (MEP), however, was a good option for intraoral ceramic repair since it was less susceptible to environmental factors than grit blasting (GBL). The results indicated that a rubber dam should be used during the clinical intraoral repair of lithium-disilicate glass ceramics, especially when utilising GBL (Höller, Belli et al. 2022).\n\nSantos et al. evaluated the bond strength of universal adhesive systems in comparison to a zirconia primer; and the bonding effectiveness of these materials onto different zirconia surface treatments. Grit-blasted zirconia promoted interlocking of universal adhesive systems to zirconia and had higher bond strength than polished ones (Dos Santos, de Lima et al. 2019).\n\nBenli et al. assessed the effect of two different lasers in combination with HF etching on the surface roughness of zirconia-reinforced lithium silicate (ZLS) ceramics and their SBS to composite resin. The mean SBS values for the HF etching group were highest for neodymium-doped yttrium aluminum garnet (Nd: YAG) laser (17.1 ± 1.65 MPa) and Nd: YAG laser + HF gel group (16.65 ± 1.11 MPa) making them the therapy of choice for the intraoral repair of fractured ceramics (Benli, Kilic et al. 2022). Likewise, Hakimaneh et al. found heat treatment of silane with erbium-doped yttrium aluminum garnet (Er: YAG) and CO2 lasers to be effective as HF etching for treating fractured porcelain. However, this treatment failed to improve the micro SBS between feldspathic porcelain and composite resin (Hakimaneh, Shayegh et al. 2020). Tokar et al. found that erbium, chromium: yttrium scandium gallium garnet (Er, Cr: YSGG) laser surface treatments with different pulses can be safely recommended in the treatment of fractured zirconia ceramics and can strengthen the SBS between zirconia and composite resin. Shorter pulse laser irradiation performed better compared to longer pulse rates in terms of mean SBS (Tokar, Polat et al. 2019).\n\nSattabanasuk et al. assessed the efficacy of resin adhesion to glass-ceramic surfaces that had previously undergone various treatments and found that silane solution could be used to achieve mechanical and/or chemical retention. The study found that regardless of the tested adhesive, the resin-ceramic bond depended upon both mechanical and chemical retention. The authors suggested that adding a silane monomer to the adhesive formulation may not be the best way to achieve silanization and hence recommend regularly applying a silane solution to a glass-ceramic surface to ensure resin adherence (Sattabanasuk, Charnchairerk et al. 2017).\n\nPolat et al. compared the effectiveness of Er, Cr: YSGG laser with short and long pulse durations to different surface roughening techniques for repairing zirconia ceramics with various surface configurations and found there were no discernible variations among sandblasting and Er, Cr: YSGG laser treatments (Polat, Tokar et al. 2021). Tatar and Ural investigated surface treatments for chipping to reduce the problems related to bonding between hybrid materials and composites and found that the most effective method was air abrasion with silica-coated aluminum oxide (Tatar and Ural 2018). A similar study by Libecki et al. where the aim was to check the efficacy of different surface treatment options (air abraded, polished surface, or ground using a special silicon carbide bur), reported that the TBS is high when the ceramic is conditioned with air abrasion or roughened with silicon carbide bur (Libecki, Elsayed et al. 2017). Ozdemir and Yanikoglu assessed the SBS of nano-hybrid and nano-ceramic composite resins to feldspathic porcelain (Vita and Ivoclar) and found the latter to possess lower SBS compared with the former (Ozdemir and Yanikoglu 2017). A study by Chen et al. evaluated if silane contamination of dentin impacts the binding strength of the tissue and found that there were no adverse effects on SBS due to contamination of dentin with silane before etching (Chen, Hammond et al. 2017).\n\nVarious intraoral techniques employed in the studies included in the review are listed below. Passia et al. evaluated the long-term outcome of posterior all-ceramic FDPs made from veneered zirconia ceramic with either a fixed-to-fixed (FF) or a cantilever design (CA). The cumulative 13-year survival rate was 43.2% (FF) (CI: 22.8–66.2%) and 52.5% (CA) (CI: 32.5–71.8); and success rate was 29.5% (FF) (CI:12.1–55.9%) and 22.5% (CA) (CI: 7.9–49.3%) respectively. The survival rates were comparable and failure rates were high, irrespective of the design (Passia, Chaar et al. 2019). An in vitro study analyzed the long-term performance of fabrication techniques on anterior teeth and found that the pressed groups (923.7 N) exhibited significantly higher fracture resistance and crown strength than the milled groups (797.5 N), (p = 0.0002) (Gerogianni, Lien et al. 2019). In a study by Sanal and Kilinc, SBS and color stability of four ceramic veneers (VITAVM 9, VITA VM 13, VITA VMK 95, and IPS e.max Ceram) treated with different repair systems (Vertise Flow, Fusio Liquid Dentin, Constic, and BISCO intraoral repair kit + Filtek Supreme) was examined. The findings of the study indicated that Constic self-adhesive composite resin had the lowest color stability value, but that there was no discernible difference between it and the other repair methods (Sanal and Kilinc 2020).\n\nA study by Meirelles et al., reported five-year survival of intraoral repair of cracked porcelain veneered zirconia framework restoration with composite resin reconstruction, suggesting that it could be a suitable alternative therapy (Meirelles, da Rocha et al. 2020). Gul and Uygun evaluated the micro-TBS of the nanocomposite resin to three CAD/CAM blocks utilizing various intraoral repair procedures. In comparison to the other repair methods examined, the Cimara System, Clearfil Repair, and Porcelain Repair systems significantly improved (p<0.05) the binding strength of nanohybrid resin composite to all CAD/CAM blocks (Gul and Altınok-Uygun 2020). A case report by Mesquita et al. reported that proper execution of the direct veneering strategies yields fast and effective solutions to fracture or chipping of the veneering ceramic, without the need to replace the prosthesis. The durability of the repair relies on the quality of the interface created and the clinician's hold on the adhesive procedures (Mesquita, Al-Haj Husain et al. 2021).\n\nYadav et al. reported that the ClearfilTM repair method had higher SBS (29.16 Mpa) than Primer and Cera resin bond repair material for cohesive fractures, whereas the latter had higher SBS (27.23 Mpa) for adhesive fractures compared to ClearfilTM repair method in metal-ceramic restorations (Yadav, Dabas et al. 2019). The retrospective analysis conducted by Gabelotto et al. discussed the clinical phases of an intraoral composite resin repair and a fractographic examination of the failure reasons for the chipping of the veneering ceramic of an anterior single crown. Fractographic analysis revealed that failure was a result of crack development during function, most likely brought on by an occlusal interference, and thereby improved the knowledge of the origin of failure to avoid failures in the future (Garbelotto, Fukushima et al. 2019).\n\n\nDiscussion\n\nThe current review aimed to summarize the available literature on the effectiveness of intraoral repair techniques for ceramic fractures. Twenty-one relevant studies published in English between 2016 and 2022 which discussed various surface treatments and intraoral repair systems were included in the review.\n\nIt is a common observation in a dental practice that despite having a high success rate, chipping or fracture of the veneering ceramic is the main cause of clinical failure for veneered zirconia-based restorations (Pjetursson, Sailer et al. 2015). Given the complexities of veneered zirconia-based restorations, clinicians and researchers have explored a variety of intraoral repair techniques to treat the chipping and protect the intact structures. Under appropriate conditions, intraoral repair acts as a potential therapy option. Dental professionals now have a great deal of interest in the scientific basis, therapeutic methods, and clinical effectiveness of the intraoral repair of cracked veneered zirconia-based restorations. Reviewing the intraoral repair of veneered zirconia-based restorations would improve practitioners' understanding of the advised procedures when zirconia repair is required (Agingu, Zhang et al. 2018).\n\nUnderstanding the complexities of porcelain fractures is the first step. Porcelain fractures can be static, cohesive, or adhesive. The material used for framework fabrication determines the repair procedure (Aslam, Hassan et al. 2018). Regardless of their high 5-year survival rate of 90.4% (95% CI: 84.8–94.0%), porcelain-veneered zirconia FDPs can eventually crack and get chipped off. This is fundamentally due to the loss of adhesion between zirconia and veneering ceramics (Pjetursson, Sailer et al. 2015). A variety of factors can cause the fracture of veneered porcelain on metal-ceramic crowns, which include lack of sufficient porcelain framework support, intra-ceramic flaws, or para-functional occlusion (Haselton, Diaz-Arnold et al. 2001). Porcelain fracture can manifest clinically with no metal substrate exposure, modest metal substrate exposure, or significant metal exposure. Although fabricating a new crown seems desirable, it is not always possible. In such cases, the option of intraoral restoration is deemed of immense importance (Haselton, Diaz-Arnold et al. 2001).\n\nBefore the build-up of the veneer layer, a succession of thermal sintering cycles and accompanying cooling processes are used to prepare crowns and FPDs. The matching of thermal expansion between the porcelain and the underlying framework, whether metal or ceramic, is crucial to avoid breaking following the firing. Delamination of the porcelain can occur when the coefficient of thermal expansion (CTE) of the framework is significantly higher than that of the porcelain (Swain 2009). Other researchers believe that there should be a similarity in the CTE of both veneering porcelain and substructure to eliminate any stresses in the layered porcelain (Aboushelib, Kleverlaan et al. 2006, Swain 2009). Fracture is a potential risk for veneered ceramics with such residual stress. A tensile stress zone can form below and at the edge of the contact surface of the veneer layer resulting from the combination of compressive residual stress and local stress brought on by mastication (Taskonak, Mecholsky et al. 2005). Several elements influence the development of thermally induced residual stress and contribute to porcelain chipping which includes the veneer's overall thickness, cooling rate, and shape. Guazzato et al. (2010) found that rapid cooling and increased porcelain veneer thickness increase the risk of crack occurrence (Guazzato, Walton et al. 2010). Zirconia may also crack due to the volume expansion (3–4%) occurring during the thermal tempering at high temperatures, which is done to facilitate tetragonal to monoclinic transition (Piconi and Maccauro 1999).\n\nMeeting the requirements for repairing a failed restoration is the next essential step. The establishment of a permanent bond between the previous restoration and the new repair material is the key to a successful repair. Therefore, choosing the right adhesive resin and restorative substance, as well as adequate surface conditioning of the substrate, is important. To increase bond strength, the surface is roughened using a variety of surface preparation processes (Duzyol, Sagsoz et al. 2016). Acid etching using hydrofluoric acid (HF) is an optimal approach for roughening feldspar ceramic surfaces for resin composite bonding. In comparison with HF treatment alone, the introduction of a silane coupling agent after HF results in stronger resistant bonds. Further, newer surface modifications, such as surface abrading airborne particles, have been developed with advancements in adhesive technology. The initial step in this approach is air abrasion using aluminum oxide particles. Increased resin composite-porcelain bond strengths are reportedly achieved by sandblasting the porcelain's surface with aluminum oxide particles (35–250 μm) (Duzyol, Sagsoz et al. 2016). After air abrasion, chemical adhesion can be generated using specialized primers that interact with a material's surface. To chemically bind the inorganic filler particles to the resin matrix, the most commonly used primer is a silane coupling agent, which is also employed in the construction of composites (Loomans and Özcan 2016).\n\nThe wettability of the composite to be utilized as a repair material is increased by applying intermediate adhesive resin to the silanized surface. It is often recommended, but not required, to mix identical composite materials when doing composite-composite repairs due to the variable effects of different substrate materials (Baur and Ilie 2013). Usage of adhesive resin, silanization, and HF acid etching, adhesion to glassy matrix ceramics has been thoroughly established. Optimal surface conditioning of indirect composite restorations can be achieved by using airborne particle abrasion followed by an adhesive resin with a silane coupling agent (Loomans and Özcan 2016).\n\nIn the current review, HF etching in combination with laser treatment or silane and traditional adhesive was found to strengthen the link between porcelain and composite resin (Hakimaneh, Shayegh et al. 2020, Benli, Kilic et al. 2022, Kiomarsi, Jarrah et al. 2022). However, durable TBS was observed when surface treatment with air abrasion or roughening the zirconia surface with a silicon carbide bur was offered for the repair of zirconia ceramic after chipping of its veneers (Libecki, Elsayed et al. 2017).\n\n\nConclusion\n\nWith the limitations of this narrative review, we can conclude that intraoral repair of ceramic fractures offers esthetics and comfort to patients when a restoration cannot be removed or changed. The current review indicated that the best technique to fix chipping in a complex made of zirconia core and veneering ceramic is to treat the veneering ceramic with HF before covering the zirconia core ceramic with silica. Both ceramic substrates must then be covered with adhesive resin and silane. The intraoral repair utilizing resin-based composite materials has significant advantages since it retains most of the restoration, prevents needless loss of healthy tooth structure, and is a quick and simple, reasonably priced procedure with no need for repeated sessions. The skills of the clinicians in using these tools and techniques as well as adherence to prescribed procedures and protocols are crucial to the effectiveness of these treatments.",
"appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAboushelib MN, Kleverlaan CJ, Feilzer AJ: Microtensile bond strength of different components of core veneered all-ceramic restorations. Part II: Zirconia veneering ceramics. Dent. Mater. 2006; 22(9): 857–863. Publisher Full Text\n\nAgingu C, Zhang C-Y, Jiang N-W, et al.: Intraoral repair of chipped or fractured veneered zirconia crowns and fixed dental prosthesis: clinical guidelines based on literature review. J. Adhes. Sci. Technol. 2018; 32: 1–13.\n\nAslam A, Hassan S, Nayyer M, et al.: Intra-oral Repair Protocols for Fractured Metal-Ceramic Restorations - Literature Review. South African dental journal. Suid Afrikaanse tandarts tydskrif. 2018; 73.\n\nBaur V, Ilie N: Repair of dental resin-based composites. Clin. Oral Investig. 2013; 17(2): 601–608. PubMed Abstract | Publisher Full Text\n\nBenli M, Kilic EHH, Gumus BE, et al.: Effects of Various Laser Treatments on Surface Characterization and Repair Bond Strength of Zirconia-Reinforced Lithium Silicate Ceramics. Int. J. Prosthodont. 2022; PubMed Abstract | Publisher Full Text\n\nChen L, Hammond BD, Alex G, et al.: Effect of silane contamination on dentin bond strength. J. Prosthet. Dent. 2017; 117(3): 438–443. PubMed Abstract | Publisher Full Text\n\nDos Santos RA, de Lima EA , Mendonça LS, et al.: Can universal adhesive systems bond to zirconia? J. Esthet. Restor. Dent. 2019; 31(6): 589–594. PubMed Abstract | Publisher Full Text\n\nDuzyol M, Sagsoz O, Polat Sagsoz N, et al.: The Effect of Surface Treatments on the Bond Strength Between CAD/CAM Blocks and Composite Resin. J. Prosthodont. 2016; 25(6): 466–471. PubMed Abstract | Publisher Full Text\n\nGarbelotto LGD, Fukushima KA, Ozcan M, et al.: Chipping of veneering ceramic on a lithium disilicate anterior single crown: Description of repair method and a fractographic failure analysis. J. Esthet. Restor. Dent. 2019; 31(4): 299–303. PubMed Abstract | Publisher Full Text\n\nGerogianni P, Lien W, Bompolaki D, et al.: Fracture Resistance of Pressed and Milled Lithium Disilicate Anterior Complete Coverage Restorations Following Endodontic Access Preparation. J. Prosthodont. 2019; 28(2): 163–170. PubMed Abstract | Publisher Full Text\n\nGuazzato M, Walton TR, Franklin W, et al.: Influence of thickness and cooling rate on development of spontaneous cracks in porcelain/zirconia structures. Aust. Dent. J. 2010; 55(3): 306–310. PubMed Abstract | Publisher Full Text\n\nGul P, Altınok-Uygun L: Repair bond strength of resin composite to three aged CAD/CAM blocks using different repair systems. J Adv Prosthodont. 2020; 12(3): 131–139. Publisher Full Text\n\nHakimaneh SMR, Shayegh SS, Ghavami-Lahiji M, et al.: Effect of Silane Heat Treatment by Laser on the Bond Strength of a Repair Composite to Feldspathic Porcelain. J. Prosthodont. 2020; 29(1): 49–55. PubMed Abstract | Publisher Full Text\n\nHammond B, Swift EJ, Brackett W: INTRAORAL REPAIR OF FRACTURED CERAMIC RESTORATIONS. J. Esthet. Restor. Dent. 2009; 21: 275–284. PubMed Abstract | Publisher Full Text\n\nHaselton DR, Diaz-Arnold AM, Dunne JT Jr: Shear bond strengths of 2 intraoral porcelain repair systems to porcelain or metal substrates. J. Prosthet. Dent. 2001; 86(5): 526–531. Publisher Full Text\n\nHöller B, Belli R, Petschelt A, et al.: Influence of Simulated Oral Conditions on Different Pretreatment Methods for the Repair of Glass-Ceramic Restorations. J. Adhes. Dent. 2022; 24(1): 57–66.\n\nKimmich M, Stappert CF: Intraoral treatment of veneering porcelain chipping of fixed dental restorations: a review and clinical application. J. Am. Dent. Assoc. 2013; 144(1): 31–44. PubMed Abstract | Publisher Full Text\n\nKiomarsi N, Jarrah A, Chiniforoush N, et al.: Effect of surface treatment with laser on repair bond strength of composite resin to ceramic. Dent Res J (Isfahan). 2022; 19: 30. PubMed Abstract\n\nKocaağaoğlu H, Manav T, Albayrak H: In Vitro Comparison of the Bond Strength between Ceramic Repair Systems and Ceramic Materials and Evaluation of the Wettability. J. Prosthodont. 2017; 26(3): 238–243. PubMed Abstract | Publisher Full Text\n\nLibecki W, Elsayed A, Lehmann F, et al.: Efficacy of Different Surface Treatments for Intraoral Repair of Veneered Zirconia Frameworks. J. Adhes. Dent. 2017; 19(4): 323–329. PubMed Abstract | Publisher Full Text\n\nLoomans B, Özcan M: Intraoral Repair of Direct and Indirect Restorations: Procedures and Guidelines. Oper. Dent. 2016; 41(S7): S68–s78. PubMed Abstract | Publisher Full Text\n\nMeirelles PD, da Rocha LS , Pecho OE, et al.: Intraoral repair of a chipped porcelain-zirconia restoration. J. Esthet. Restor. Dent. 2020; 32(5): 444–450. PubMed Abstract | Publisher Full Text\n\nMesquita AMM, Al-Haj Husain N, Molinero-Mourelle P, et al.: An Intraoral Repair Method for Chipping Fracture of a Multi-unit Fixed Zirconia Reconstruction: A Direct Dental Technique. Eur. J. Dent. 2021; 15(1): 174–178. PubMed Abstract | Publisher Full Text\n\nÖzcan M, Volpato CAM: Intra-oral repair technique for ceramic fracture using direct resin composite.2017.\n\nOzdemir H, Yanikoglu ND: The Bond Strength of Nanohybrid and Nanoceramic Composites to Feldspathic Porcelain. Contemp. Clin. Dent. 2017; 8(4): 558–564. PubMed Abstract | Publisher Full Text\n\nPassia N, Chaar MS, Kern M: Outcome of posterior fixed dental prostheses made from veneered zirconia over an observation period of up to 13 years. J. Dent. 2019; 86: 126–129. PubMed Abstract | Publisher Full Text\n\nPiconi C, Maccauro G: Zirconia as a ceramic biomaterial. Biomaterials. 1999; 20(1): 1–25. Publisher Full Text\n\nPjetursson BE, Sailer I, Makarov NA, et al.: All-ceramic or metal-ceramic tooth-supported fixed dental prostheses (FDPs)? A systematic review of the survival and complication rates. Part II: Multiple-unit FDPs. Dent. Mater. 2015; 31(6): 624–639. PubMed Abstract | Publisher Full Text\n\nPolat S, Tokar E, Asar NV, et al.: Evaluation of Efficacy of Various Surface Conditioning Methods on the Repair Bond Strength of Composite to Different Fracture Types of Zirconia Ceramics. Scanning. 2021; 2021: 5537761.\n\nRosentritt M, Steiger D, Behr M, et al.: Influence of substructure design and spacer settings on the in vitro performance of molar zirconia crowns. J. Dent. 2009; 37(12): 978–983. Publisher Full Text\n\nSanal FA, Kilinc H: Evaluating Ceramic Repair Materials in Terms of Bond Strength and Color Stability. Int. J. Prosthodont. 2020; 33(5): 536–545. PubMed Abstract | Publisher Full Text\n\nSattabanasuk V, Charnchairerk P, Punsukumtana L, et al.: Effects of mechanical and chemical surface treatments on the resin-glass ceramic adhesion properties. J. Investig. Clin. Dent. 2017; 8(3): e12220. PubMed Abstract | Publisher Full Text\n\nSwain MV: Unstable cracking (chipping) of veneering porcelain on all-ceramic dental crowns and fixed partial dentures. Acta Biomater. 2009; 5(5): 1668–1677. PubMed Abstract | Publisher Full Text\n\nTaskonak B, Mecholsky JJ Jr, Anusavice KJ: Residual stresses in bilayer dental ceramics. Biomaterials. 2005; 26(16): 3235–3241. PubMed Abstract | Publisher Full Text\n\nTatar N, Ural C: Repair Success of Two Innovative Hybrid Materials as a Function of Different Surface Treatments. Int. J. Prosthodont. 2018; 31(3): 267–270. PubMed Abstract | Publisher Full Text\n\nTokar E, Polat S, Ozturk C: Repair bond strength of composite to Er,Cr:YSGG laser irradiated zirconia and porcelain surfaces. Biom. J. 2019; 42(3): 193–199. Publisher Full Text\n\nVagropoulou GI, Klifopoulou GL, Vlahou SG, et al.: Complications and survival rates of inlays and onlays vs complete coverage restorations: A systematic review and analysis of studies. J. Oral Rehabil. 2018; 45(11): 903–920. PubMed Abstract | Publisher Full Text\n\nYadav JS, Dabas N, Bhargava A, et al.: Comparing two intraoral porcelain repair systems for shear bond strength in repaired cohesive and adhesive fractures, for porcelain-fused-to-metal restorations: An in vitro study. J. Indian Prosthodont Soc. 2019; 19(4): 362–368. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "155374",
"date": "28 Nov 2022",
"name": "Lomaya Ghanem",
"expertise": [
"Reviewer Expertise Fixed Prosthdodontics",
"ceramics",
"pressing",
"bonding",
"CADCAM."
],
"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\nIntraoral repair of fractured veneering ceramic is a very relevant, economic and conservative clinical approach. The review herein clearly exhibits the fracture types, their conforming repair protocol in relevance to the restoration core material (metal or ceramic), highlighting procedures and materials used. The herein review is supported with literature consistent with current research. Language, context, and drawn conclusions: clear\nIt furnishes a practical source for research, and provides an accessible overview and understanding of the topic, as well as recommendations for management of intraoral repair using the existing practices.\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": "344687",
"date": "03 Dec 2024",
"name": "Philipp-Cornelius Pott",
"expertise": [
"Reviewer Expertise dentistry",
"adhesive dentistry",
"adhesion to ceramic materials and metals",
"prosthodontics",
"all-ceramics"
],
"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 have addressed a clinically highly relevant topic. The summarized literature is well suited to provide an overview of modern strategies for the repair of ceramic fractures. Particularly noteworthy is the fact that the authors consider not only various repair techniques but also various ceramics in a differentiated way. This nicely highlights the fact that not every repair strategy can be applied equally to all materials or material combinations. I also particularly like the fact that the authors address possible causes of damage to restorations at the beginning of the discussion. In the methodology section, chapter 2.1, it is stated that studies published between January 2017 and August 2022 have been included. However, a different time period (2016 to 2022) is given in the first chapter of the discussion. This is probably just a typo, which should be easy to correct. Nevertheless, a fairly extensive presentation of intraoral ceramic repair has already been made here, but unfortunately I miss two important aspects that should be added to the discussion: 1. Age of the restoration to be repaired. Unfortunately, silicate ceramics absorb moisture over time. This moisture absorption cannot be reversed intraorally. Accordingly, this reduces the prognosis for a secure, stable bond. In zirconium dioxide ceramics, so-called low-temperature degradation occurs over time under the conditions prevailing intraorally (Borchers et al Ref 1; Kohorst et al. Ref 2). This also reduces the long-term prognosis of a restoration that may need to be repaired. 2. Surface pretreatment with plasma. The application of cold argon plasma to ceramic surfaces, for example, increases hydrophilicity and thus improves wettability with adhesives, thereby increasing the long-term stability of the ceramic-composite bonds (Pott et al. ref 3). Corresponding application devices are also available for dentistry.\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": "344693",
"date": "02 Jan 2025",
"name": "Rafael Delgado-Ruiz",
"expertise": [
"Reviewer Expertise Prosthodontics",
"CAD-CAM",
"Digital technologies",
"Optical Scanners",
"Dental Implants",
"Thermography"
],
"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 conducted a review of techniques for the intraoral repair of fractured dental ceramics, addressing a relevant and clinically significant topic for the journal's audience. Fractured ceramics represent a common complication in dental practice, often requiring effective clinical intervention and repair.\nThe authors performed a non-structured search on PubMed for articles published in English between 2017 and 2022 related to intraoral ceramic repair, identifying 21 articles. Of these, 17 were in-vitro studies, 3 were case reports, and 1 was a prospective clinical study. However, the clinical data is limited, as the case reports and the prospective study together account for only 50 patients. Given this lack of robust clinical evidence, the conclusions of the manuscript should be interpreted with caution.\n\nIn addition, the second part of the conclusions \"The intraoral repair utilizing resin-based composite materials has significant advantages since it retains most of the restoration, prevents needless loss of healthy tooth structure, and is a quick and simple, reasonably priced procedure with no need for repeated sessions. The skills of the clinicians in using these tools and techniques as well as adherence to prescribed procedures and protocols are crucial to the effectiveness of these treatments.\" although logical, is not supported by the articles included in this review.\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? Partly",
"responses": []
},
{
"id": "344694",
"date": "07 Jan 2025",
"name": "Punit Fulzele",
"expertise": [
"Reviewer Expertise CADCAM",
"Digital technologies",
"Dentistry."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis review addresses the intraoral repair of fractured dental ceramics, a common and clinically significant issue in dental practice. The authors conducted a non-structured PubMed search for articles published in English between 2017 and 2022, identifying 21 relevant studies. This review considers various techniques and ceramic types to provide a comprehensive overview of modern repair strategies for ceramic fractures and current repair protocols for different fracture types and core materials. It is a valuable resource for research and clinical practice due to its practical relevance and accessibility. Although the clinical studies were limited to 50 patients, the conclusions must be interpreted cautiously. There is an inconsistency in the reported timeframe for the included studies. Two critical aspects have not been discussed: the age of the restoration and the impact it has on the repair prognosis-surface pretreatment with plasma for improved bond stability. The review's conclusions, while logical, are not fully supported by the included articles. There is, however, a well-structured summary of existing practices and recommendations for managing intraoral ceramic repairs. Despite some limitations, it offers dental professionals a valuable resource for understanding and implementing current repair strategies. Additional clinical data and the additional aspects mentioned could be included in future reviews to give a more comprehensive topic analysis.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1275
|
https://f1000research.com/articles/11-760/v1
|
07 Jul 22
|
{
"type": "Research Article",
"title": "Peruvian children toothbrushing during the COVID-19 pandemic",
"authors": [
"María Claudia Garcés-Elías",
"Jorge A. Beltrán",
"César Eduardo Del Castillo-López",
"Andrés A. Agudelo-Suárez",
"Roberto A. León-Manco",
"Jorge A. Beltrán",
"César Eduardo Del Castillo-López",
"Andrés A. Agudelo-Suárez",
"Roberto A. León-Manco"
],
"abstract": "Background: Toothbrushing is a convenient, inexpensive, widespread and culturally accepted method, resulting in an ideal public health outcome. This study aimed to determine the impact of the COVID-19 pandemic on toothbrushing in Peruvian children. Methods: This was a cross-sectional study conducted using a database of children aged 0 to 11 years, with a final sample of 39,124 participants, 15,974 in 2019 (62.03%) and 7088 in 2020 (55.54%). General toothbrushing, daily toothbrushing and minimum frequency of two times a day were dependent variables; the year was considered as the independent variable. In addition, other covariates such as geographical landscape, area of residence, place of residence, altitude, wealth index, health insurance cover, sex and age. Descriptive, bivariate and multivariate statistical analyses were applied. Results: General toothbrushing was 96.19% (n=51 013), daily toothbrushing was 87.47% (n=42 246) and minimum toothbrushing two times a day was 84.53% (n=33 957). In multivariate form, the year presented a negative association with daily toothbrushing (RPa: 0.97; CI95%: 0.96-0.98; p<0.001) and minimum toothbrushing two times a day (RPa: 0.97; CI95%: 0.95-0.98; p<0.001), adjusted for the previously associated co-variables.\nConclusions: The year 2020 of the COVID-19 pandemic negatively impacted daily toothbrushing and minimum twice-daily toothbrushing of Peruvian children.",
"keywords": [
"COVID-19",
"Toothbrushing",
"Oral Health",
"Oral Hygiene",
"Peru"
],
"content": "Introduction\n\nThe World Health Organization (WHO) states that diseases of the oral cavity are associated with certain risk factors, including inadequate oral hygiene, which is a practice mediated by the social and commercial determinants of health, and which vary depending on each population.1 It is also established that this healthy habit should be adopted before the first year of life, which would strengthen its continuity over time; it is also recommended that this practice should be done at least twice a day together with the use of fluoride toothpaste, which is an effective measure for the prevention of early childhood caries. It is important to mention that toothbrushing is a convenient, economical, widespread and culturally accepted method, making it an ideal measure for public health.2,3\n\nOn the other hand, the COVID-19 pandemic has caused substantial changes in governments and their populations, which were established to control the spread of the virus and its possible harmful effects on the health of individuals, in addition to avoiding the collapse of health systems.4 Consequently, many of these drastic measures, such as social immobilization, quarantines and cessation of economic activities, had adverse effects on the health and welfare of communities, especially in vulnerable population groups, such as children and adolescents, in whom sociodemographic factors such as age and economic status, in addition to their state of health and special needs, have mediated the magnitude of the impact that the health emergency has had on their daily lives.5 Likewise, these changes in lifestyles could have had repercussions on the exercise of habits that would influence the oral health of children, such as an adequate sleep routine, an increase in the frequency of consumption of foods and beverages with high sugar content and a reduction in the frequency of tooth brushing.6\n\nIn Peru, previous reports have documented low adherence to the practice of toothbrushing, especially in individuals under five years of age belonging to families with low income and whose parents had the lowest level of education. In addition, it has been observed that the practice of this habit has been increasing in recent years, despite the fact that, in sectors such as the highlands of the country, there are still differences in its practice.7,8 However, there are few studies that expose this problem, highlighting the need for its analysis, especially in scenarios as complex as the one that occurred due to the COVID-19 pandemic. In this sense, the purpose of the present investigation was to determine the impact of the COVID-19 pandemic on tooth brushing in Peruvian children.\n\n\nMethods\n\nA cross-sectional study was carried out using the databases obtained from the Demographic and Family Health Survey (ENDES) for the years 2019 and 2020, developed by the National Institute of Statistics and Informatics of Peru (INEI); the survey was applied only once per year, through home interviews. The ENDES has a stratified two-stage cluster sample design representative at the national and regional levels, as well as according to rural and urban areas. It also includes information on general toothbrushing, daily toothbrushing and toothbrushing at least twice a day in children from 0 to 11 years of age. In relation to the periods to be evaluated, the year 2019 considered a sample size of 36760 households; while for 2020, the sample size consisted of 37390 households. The primary databases contained a total of 167560 participants for 2019, and for 2020 a total of 177414; however, for this analysis only the records of those who answered the question on general toothbrushing, daily toothbrushing and toothbrushing at least twice a day were considered, establishing a final sample of 56816 subjects, 38203 for 2019 (67.24%) and 18613 for 2020 (32.76%).9\n\nOn the other hand, general toothbrushing, daily toothbrushing and toothbrushing at least twice a day were considered as dependent variables, while the year was taken as an independent variable, classified as 2019 and 2020, highlighting that the latter included the period of the COVID-19 pandemic in Peru. Additionally, other covariates were considered within the study, such as the geographical landscape, classified into Metropolitan Lima (capital of the country), rest of the coast, highlands and jungle; area of residence, classified into urban and rural; place of residence organized into capital, city, town and countryside; altitude defined as less than 2,500 meters above mean sea level (MAMSL) and from 2,500 MAMSL and more; in addition, a Wealth Index, a variable defined by the willingness of each household to use and consume goods and services. Then, through the method used in the Demographic and Health Survey Program of the United States, a score was assigned to each household, as well as to each of its inhabitants, which served to categorize each dwelling, following a hierarchy that goes from quintile one to quintile five (from the poorest to the richest).10,11 Likewise, the holding of health insurance was considered, considering that within Peru there are simultaneously public and private insurance institutions. The public sector includes: Integrative Health Insurance (SIS), Peruvian Social Security (EsSalud), Armed Forces Health Insurance and Police Forces Health Insurance; while in the public or private sector, Health Care Provider Companies (EPS) offer additional coverage to that provided by social security and its essential plan.12 On the other hand, the covariables sex and age, classified as 0 to 5 years and 6 to 11 years were also considered. Similarly, these have been analyzed in previously published research.7,8\n\nThe databases were extracted from the INEI's official website, through multiple sources of information, and then unified into a single matrix to be analyzed in STATA v. 17 software. This was done using the complex sample module, since it is a national survey with possible representative estimates.\n\nThe statistical analysis began with a descriptive analysis for each of the variables to obtain their absolute and relative frequencies. Subsequently, we continued with a bivariate analysis using a Chi-square test that allowed us to find associations between the variables studied. Next, for multivariate analysis, tests such as Poisson regression were run to obtain crude prevalence ratios (PR) and adjusted prevalence ratios (aPR). It is worth mentioning the svy command was used to determine representative estimates, because the survey design was included in the data analysis, where the sampling patterns were differentiated in the stratum, primary sampling unit and weights. For this research, a confidence level of 95% and a value of p<0.05 was used as an indicator of statistical significance in all tests.\n\nFor the development of this study, the researchers used freely available information provided by the INEI which, since it is a secondary analysis of anonymous information, does not require ethical approval.\n\n\nResults\n\nGeneral toothbrushing was 96.19% (n=51 013), daily toothbrushing was 87.47% (n=42 246) and minimum toothbrushing two times a day was 84.53% (n=33 957); the sample was mainly associated to metropolitan Lima with 34.20% (n=10 125), 77.53% (n=50 037) from urban areas, 34.20% (n=101 125) from the capital and 78.79% (n=52 378) residing at less than 2 500 MAMSL. According to the Wealth Index, 22.06% (n=19 244) were mainly poor participants, while 75.38% (n=228 594) had health insurance. A total of 74.51% (n=138 395) were male and 62.74% (n=25 194) were between six and 11 years of age (Table 1).\n\nIn a bivariate manner, general toothbrushing was associated with geographical landscape, area of residence, place of residence, altitude and age (p<0.05); daily toothbrushing was associated with year, geographical landscape, area of residence, place of residence, altitude, Wealth Index and age (p<0.05); and minimum toothbrushing two times a day was associated with year, geographical landscape, area of residence, place of residence, altitude, Wealth Index, health insurance cover, sex and age (p<0.05) (Table 2). In multivariate form, the year presented a negative association with daily toothbrushing (RPa: 0.97; 95%CI: 0.96-0.98; p<0.001) and minimum toothbrushing two times a day (RPa: 0.97; 95%CI: 0.95-0.98; p<0.001) adjusted for the previously associated co-variables (Table 3).\n\n* Chi-square test.\n\n\nDiscussion\n\nToothbrushing stands out as one of the main protective strategies for oral health, especially when it is done with fluoride toothpaste; therefore, it is essential to guarantee the practice of this habit in population groups with a higher risk of dental caries, such as children. In this regard, there are factors associated with the frequency of this practice, such as the frequency of brushing by parents and caregivers, as well as having received help from others; in addition, barriers have been reported such as lack of time to carry it out and little cooperation from the child. This shows that healthy behaviors such as tooth brushing in children, are linked to the parents' own practices and family support during its realization.13,14\n\nAmong the findings of this research, it was observed that the year of the COVID-19 pandemic outbreak negatively impacted daily toothbrushing and its practice frequency of at least twice a day. Coincidentally, some studies evaluated whether the changes caused by the COVID-19 pandemic would have affected oral health habits, finding a reduction in the frequency of toothbrushing. Gotler et al. reported that approximately a quarter of the subjects studied reduced the frequency of this practice both during the day and at night; they also observed that this phenomenon was reported mainly in older children.6 Additionally, in another study applied to parents in the same context, the proportion of children whose oral health had worsened was remarkable, despite their brushing practices. Furthermore, they highlighted that, in order to maintain adequate oral hygiene, there are mediating factors such as the degree of awareness, socioeconomic level, access to health services, among others.15\n\nLikewise, another study in Brazil evaluated whether the modification of sleeping habits would influence the oral hygiene of children during the period of confinement, observing that the emergence of changes in the family routine of parents or caregivers would be relevant in the oral hygiene of the child, especially in the younger pediatric population, who depend on adults to perform tooth brushing.16 On the other hand, Folayan et al. reported that in the COVID-19 pandemic, one tenth of the adult individuals evaluated reported having reduced the regularity with which they brushed their teeth; likewise, the interruption of this healthy habit would be linked to the development of disorders such as anxiety and decreased psychological well-being.17 From the aforementioned, it can be derived that the modification of such an important daily routine due to such complex scenarios as a health emergency would influence the deterioration of oral hygiene maintenance.\n\nRegarding general brushing, this research determined that there is an association between this type of practice and the geographical characteristics surrounding the children, such as geographical landscape, area, place of residence and altitude. In 2017, Hernández-Vásquez et al. concluded that a considerable fraction of Peruvian children under 12 years of age did not practice toothbrushing, especially those settled in the highlands and urban sectors of Peru; likewise the absence of this habit was observed with greater predominance in those wiofth five years of age or younger.7 A study applied in the United Arab Emirates showed that children whose day-care centers were located in rural areas had a greater experience of caries and a higher amount of visible plaque compared to other geographical areas; in addition, the same publication established infrequent tooth brushing as a factor associated with the high prevalence of dental caries in that community,18 which could explain the health conditions of these children.\n\nIn addition, it is noted that age is also associated with general toothbrushing, in line with previous studies such as that of Sun et al. in China, where it was found that slightly less than half of the participating children brushed their teeth less than once a day, showing the great risk to which children in China under five years of age are exposed; there was also a marked relationship between the age of initiation of toothbrushing and the experience of childhood caries.19 However, as an indicator, general toothbrushing is generic, due to it only evaluating the performance or not of this practice, without considering its regularity.\n\nOn the other hand, in addition to the characteristics previously mentioned, the Wealth Index also presents statistical differences when evaluating daily toothbrushing; it was observed that the greater the purchasing power, the greater the frequency of this type of brushing. A study in Brazil showed that, for the most part, the frequency of brushing in children was twice a day; however, those who brushed only once during this period predominantly belonged to families with a low socioeconomic level. Furthermore, the researchers ratified the fact that compliance with this preventive habit depended on the commitment and collaboration of parents or caregivers.20 In addition, Chen et al. reported an evident positive gradient between the frequency of child toothbrushing and the educational levels of the parents, observing that the children of parents with a higher level of education had a higher propensity to brush twice a day or more,21 implying the relationship between a higher level of education and economic stability.\n\nToothbrushing at least twice a day together with toothpaste with fluoride levels equal to or higher than 1000 parts per million, turns out to be an adequate preventive practice as established in the Peruvian regulations, through the Clinical Practice Guidelines for the prevention, diagnosis and treatment of dental caries in girls and boys, in force since 2017.22 Within this research, it was mentioned that exercising this habit twice a day presents association with all the variables analyzed, such as geographical landscape, area and place of residence, altitude, Wealth Index, health insurance cover, sex and age. In this regard, a previous study using the ENDES determined that between 2013 and 2018 in Peru, there was a progressive trend of adequate brushing frequency, defined as the exercise of tooth brushing from twice a day to more. However, in the rural communities of the country, the percentage of children who exercise this practice is significantly lower, which can also be observed in the Sierra region.8\n\nLikewise, Soltani et al. documented that by 2014, toothbrushing frequency in Iranian children aged four to six years was low; in addition, it was associated with socioeconomic and demographic factors, and access to health services,23 a similar result to those presented in this study. In this sense, it was noted that the evaluation of the habit of brushing two or more times presents a greater number of associated factors, and it is observed that the better the living conditions, the higher the frequency of tooth brushing. In this sense, it is understood that national surveys provide essential information on the performance of hygiene practices necessary for oral health care; however, there are indicators that show greater precision and degree of compliance with the expected result, such as the one that evaluates the performance of the practice as established by the health authority, and not only analyzes without considering the continuity and precision of the preventive habit.\n\nCertain limitations were generated by the study, where the nature of the design should be considered: being a cross-sectional study, does not allow establishing causal relationships to the phenomenon studied. In addition, since the information was obtained from secondary sources, inaccuracies in the results are a possibility, due to possible errors at the time of collection, as well as the emergence of recall bias, due to self-reporting by the participants. Despite the above, the ENDES continues to be an important source of information on the oral health situation with national representativeness.\n\nIt is important to consider toothbrushing as a fundamental hygiene habit for the prevention of diseases of the oral cavity, so the establishment and maintenance of this habit should begin as early as possible, in order to promote optimal conditions of health and quality of life that are sustainable over time. Despite this, in Peru there have been conditions and social characteristics that have established differences in the practice of this preventive habit. However, as a result of the COVID-19 pandemic and its consequent provisions, the oral hygiene practices of Peruvian children under 11 years of age were affected, especially in those facing conditions of greater vulnerability, which already existed prior to the health emergency, but which during this complex situation have worsened and extended to a greater part of the population. It is necessary to address this problem from a multidisciplinary perspective, involving the participation of health professionals, parents, teachers and other stakeholders. Furthermore, the political decision-makers must ensure compliance with their programs and interventions in oral health and monitor the results achieved, paying special attention to indicators based on scientific evidence, which will reveal with certainty whether the oral health of Peruvian children is at risk.\n\nIn this sense, the year 2020 of the COVID-19 pandemic negatively impacted daily toothbrushing and minimum twice daily toothbrushing of Peruvian children; the associated factors being geographical landscape, area of residence, place of residence, altitude, health insurance coverage, Wealth Index, sex and age.\n\n\nData availability\n\nThe data analyzed are freely accessible and provided by the National Institute of Statistics and Informatics of Perú, for 2019 (https://www.datosabiertos.gob.pe/dataset/encuesta-nacional-demograf%C3%ADa-y-salud-familiar-endes-2019-instituto-nacional-de-estad%C3%ADstica-4/) and 2020 (https://www.datosabiertos.gob.pe/dataset/encuesta-demográfica-y-de-salud-familiar-endes-2020-instituto-nacional-de-estad%C3%ADstica-e-2).",
"appendix": "Acknowledgements\n\nWe would like to thank the Facultad de Estomatología de la Universidad Peruana Cayetano Heredia (UPCH) for covering the publication charges.\n\n\nReferences\n\nWorld Health Organization: Oral Health.2022. Accessed February 19, 2022.Reference Source\n\nMejàre IA, Klingberg G, Mowafi FK, et al.: A systematic map of systematic reviews in pediatric dentistry--what do we really know?. PLoS One. 2015; 10(2): e0117537. PubMed Abstract | Publisher Full Text\n\nBoustedt K, Dahlgren J, Twetman S, et al.: Tooth brushing habits and prevalence of early childhood caries: a prospective cohort study. Eur. Arch. Paediatr. Dent. 2020; 21(1): 155–159. PubMed Abstract | Publisher Full Text\n\nBenke C, Autenrieth LK, Asselmann E, et al.: Lockdown, quarantine measures, and social distancing: Associations with depression, anxiety and distress at the beginning of the COVID-19 pandemic among adults from Germany. Psychiatry Res. 2020; 293: 113462. PubMed Abstract | Publisher Full Text\n\nSingh S, Roy D, Sinha K, et al.: Impact of COVID-19 and lockdown on mental health of children and adolescents: A narrative review with recommendations. Psychiatry Res. 2020; 293: 113429. PubMed Abstract | Publisher Full Text\n\nGotler M, Oren L, Spierer S, et al.: The impact of COVID-19 lockdown on maintenance of children's dental health: A questionnaire-based survey. J. Am. Dent. Assoc. 2022; 153(5): 440–449. PubMed Abstract | Publisher Full Text\n\nHernández-Vásquez A, Azañedo D: Cepillado dental y niveles de fluororor en pastas dentales usadas por niños peruanos menores de 12 años [Tooth brushing and fluoride levels in toothpaste used by peruvian children under 12 years old]. Rev. Peru. Med. Exp. Salud Publica. 2019; 36(4): 646–652. Publisher Full Text\n\nSolis G, Pesaressi E, Mormontoy W: Tendencia y factores asociados a la frecuencia de cepillado dental en menores de doce años, Perú 2013-2018 [Trend and factors associated with the frequency of tooth brushing in children under twelve years old, Peru 2013-2018]. Rev. Peru. Med. Exp. Salud Publica. 2019; 36(4): 562–572. Publisher Full Text\n\nNational Institute of Statistics and Informatics: Demographic and Family Health Survey.2021. Accessed February 20, 2022.Reference Source\n\nUnited States Agency for International Development: The Demographic and Health Surveys Program. Wealth index.2016. Accessed March 02, 2022.Reference Source\n\nNational Institute of Statistics and Informatics: Demographic and Family Health Survey.2013. Accessed March 13, 2022.Reference Source\n\nGovernment of Peru. Health Insurance of Peru:2022. Accessed March 23, 2022.Reference Source\n\nMartin M, Rosales G, Sandoval A, et al.: What really happens in the home: a comparison of parent-reported and observed tooth brushing behaviors for young children. BMC Oral Health. 2019; 19(1): 35. Publisher Full Text\n\nMartin M, Pugach O, Avenetti D, et al.: Oral Health Behaviors in Very Young Children in Low-Income Urban Areas in Chicago, Illinois, 2018-2019. Prev. Chronic Dis. 2020; 17: E152. Publisher Full Text\n\nGoswami M, Grewal M, Garg A: Attitude and practices of parents toward their children's oral health care during COVID-19 pandemic. J. Indian Soc. Pedod. Prev. Dent. 2021; 39(1): 22–28. PubMed Abstract | Publisher Full Text\n\nBaptista AS, Prado IM, Perazzo MF, et al.: Can children's oral hygiene and sleep routines be compromised during the COVID-19 pandemic?. Int. J. Paediatr. Dent. 2021; 31(1): 12–19. PubMed Abstract | Publisher Full Text\n\nFolayan MO, Ibigbami OI, Oloniniyi IO, et al.: Associations between psychological wellbeing, depression, general anxiety, perceived social support, tooth brushing frequency and oral ulcers among adults resident in Nigeria during the first wave of the COVID-19 pandemic. BMC Oral Health. 2021; 21(1): 520. PubMed Abstract | Publisher Full Text\n\nElamin A, Garemo M, Gardner A: Dental caries and their association with socioeconomic characteristics, oral hygiene practices and eating habits among preschool children in Abu Dhabi, United Arab Emirates - the NOPLAS project. BMC Oral Health. 2018; 18(1): 104. PubMed Abstract | Publisher Full Text\n\nSun X, Bernabé E, Liu X, et al.: Early life factors and dental caries in 5-year-old children in China. J. Dent. 2017; 64: 73–79. PubMed Abstract | Publisher Full Text\n\nLima CV, Pierote JJ, de Santana Neta HA , et al.: Caries, Toothbrushing Habits, and Fluoride Intake From Toothpaste by Brazilian Children According to Socioeconomic Status. Pediatr. Dent. 2016; 38(4): 305–310. PubMed Abstract\n\nChen L, Hong J, Xiong D, et al.: Are parents' education levels associated with either their oral health knowledge or their children's oral health behaviors? A survey of 8446 families in Wuhan. BMC Oral Health. 2020; 20(1): 203. PubMed Abstract | Publisher Full Text\n\nMinistry of Health: Ministerial Resolution No. 422-2017/MINSA. Guía Técnica: Guía de Práctica Clínica para la Prevención, Diagnóstico y Tratamiento de la Caries Dental en Niñas y Niños (Technical Guide: Clinical Practice Guide for the Prevention, Diagnosis and Treatment of Dental Caries in Children).2017. Accessed April 21, 2022.Reference Source\n\nSoltani R, Eslami AA, Akhlaghi N, et al.: Toothbrushing frequency among 4-6-year-old Iranian children and associated maternal attitude and sociobehavioral factors. Dent. Res. J. (Isfahan). 2017; 14(1): 50–56. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "145020",
"date": "22 Aug 2022",
"name": "Iris Lucia Espinoza Santander",
"expertise": [
"Reviewer Expertise Oral Pathology and Inequalities in Oral 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\nThis is a study with the aim to determine the impact of the COVID-19 pandemic on toothbrushing (general toothbrushing, daily toothbrushing and toothbrushing at least twice a day) in Peruvian children from 0 to 11 years of age. The study was carried out using the databases obtained from the Demographic and Family Health Survey (ENDES) for the years 2019 and 2020, developed by the National Institute of Statistics and Informatics of Peru (INEI).The article is generally well written and structured. However, in my opinion the paper has some shortcomings regarding text structure and minor inconsistencies. Below I have provided remarks:\nMethods The author should explain what is the mean of the variable “general tooth brush”. The authors should write in methods the questions (dependent variables) used in the surveys 2019 and 2020. Were the same questions used in both years? This should be explicitly mentioned. Additionally, the authors should mention the reference categories in General toothbrushing, Daily toothbrushing and Toothbrushing at least twice a day (table 3).\nDiscussion The text of the discussion seems a bit long and it does not contain the most appropriate order. I suggest considering a reorder the discussion1. The first paragraph of the discussion should briefly reiterate what the study did and what it showed, statement of principal findings. The second paragraph should address the Strengths and weaknesses of the study. The paragraphs which follow should then discuss how the findings support or refute the current literature. The final paragraph should tie it all together – so what? Where next? What are the implications for practice? Unanswered questions and future 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? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8987",
"date": "07 Nov 2022",
"name": "MARIA CLAUDIA GARCES ELIAS",
"role": "Author Response",
"response": "Dear reviewer, we appreciate your comments, suggestions and corrections. We will respond to them below: 1.Explain what is the meaning of the variable “general tooth brush”, write in methods the questions (dependent variables) used in the surveys 2019 and 2020 and mention if they are the same questions used in both years, mention the reference categories in dependent variables. We accepted what was suggested and the modifications were made in the indicated sections (materials and methods and Table 3). 2. Reorder the discussion, the first paragraph of the discussion should briefly reiterate what the study did and what it showed. The second paragraph should address the strengths and weaknesses of the study. The paragraphs which follow should then discuss how the findings support or refute the current literature. The final paragraph should tie it all together – so what? Where next? What are the implications for practice? Unanswered questions and future research. Suggestions were accepted and the order of the discussion was modified as recommended by the reviewer. The first and second paragraphs were modified as indicated and the penultimate paragraph, where the final idea is rounded off and recommendations are made, was maintained."
}
]
},
{
"id": "150600",
"date": "31 Oct 2022",
"name": "Gino Montenegro Martínez",
"expertise": [
"Reviewer Expertise 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\nIntroduction\n\nThe pandemic for covid-19 has relevant implications for population health; one of them relates to oral health. This article addresses a pertinent topic for dentistry; it is well-written and articulates the research problem very well.\n\nIt is necessary to introduce other characteristics related to toothbrushing practices in children, supported by literature, to be part of the discussion of the results. In the last phrase of the introduction section, the authors write, “there are few studies that expose this problem,” but there are no references to those studies.\n\nMethods\nThe design is according to the objective of the study. The authors explain the process followed to get the results. It is recommended to define the reference category for statistical procedures.\n\nResults\nIt is well-written; the description of the tables is accurate and highlights relevant results for the study.\n\nDiscussion\n\nThe discussion section shows other factors related to toothbrushing practice unavailable in this study because of source information. In this sense, it is essential to consider this limitation in the study conclusions.\n\nThe discussion section should be oriented to explicate this study's results more than comparing them.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8988",
"date": "07 Nov 2022",
"name": "MARIA CLAUDIA GARCES ELIAS",
"role": "Author Response",
"response": "Dear reviewer, we appreciate your suggestions, recommendations and corrections. These were answered below: 1. Introduction: In the last phrase of the introduction section, the authors write, “there are few studies that expose this problem,” but there are no references to those studies. Accepted and the change was made. 2. Methods: It is recommended to define the reference category for statistical procedures. Accepted and the change was made. 3. Discussion: The discussion section shows other factors related to toothbrushing practice unavailable in this study because of source information. In this sense, it is essential to consider this limitation in the study conclusions. Accepted and included within the study limitations. 4. The discussion section should be oriented to explicate this study's results more than comparing them. It is accepted and in the main findings paragraph information is added and an explanation of the findings is written."
}
]
}
] | 1
|
https://f1000research.com/articles/11-760
|
https://f1000research.com/articles/11-1270/v1
|
08 Nov 22
|
{
"type": "Genome Note",
"title": "Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri",
"authors": [
"Osamu Nishimura",
"Kazuaki Yamaguchi",
"Yuichiro Hara",
"Kaori Tatsumi",
"Jeramiah J Smith",
"Mitsutaka Kadota",
"Shigehiro Kuraku",
"Osamu Nishimura",
"Kazuaki Yamaguchi",
"Yuichiro Hara",
"Kaori Tatsumi",
"Jeramiah J Smith",
"Mitsutaka Kadota"
],
"abstract": "The hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and they are one of only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming to reconstruct a high-coverage protein-coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of the gene models promise a high utility in various comparative analyses including phylogenomics and phylome exploration.",
"keywords": [
"hagfish",
"cyclostome",
"whole genome assembly",
"gene prediction"
],
"content": "Introduction\n\nExtant jawless fishes (cyclostomes) are divided into two groups, hagfishes (Myxiniformes) and lampreys (Petromyzontiformes).1 They have been studied from various viewpoints mainly because they occupy an irreplaceable phylogenetic position among the extant vertebrates, having diverged from all other vertebrates during the early Cambrian period. Even after massive efforts of whole genome sequencing for invertebrate deuterostomes,2,3 genome-wide sequence information for species in this irreplaceable taxon was limited until the genome analyses for two lamprey species, the sea lamprey Petromyzon marinus and the Arctic lamprey Lethenteron camtschaticum, which were published in 2013.4,5\n\nIn parallel, biological studies involving individual genes have been conducted for both lampreys and hagfishes. Developmental biologists, in particular, have largely relied on lampreys whose embryonic materials are accessible through artificial fertilization,6 whereas studies on hagfishes have been limited to non-embryonic materials, with a few notable exceptions.7–9 This type of molecular biological study is expected to be more thoroughly performed if a comprehensive catalogue of genes is available. For lampreys, derivation of a reliable comprehensive gene catalogue was long hindered by the peculiar nature of protein-coding sequences, which are characterized by high GC-content, codon usage bias, and biased amino acid compositions.5,10,11 To reinforce existing resources for lampreys, we previously performed a dedicated gene prediction for L. camtschaticum12 and provided a gene catalogue with comparable or superior completeness to other equivalent resources.4,13\n\nAs of July 2022, no whole genome sequence information is available for hagfishes except for the one at Ensembl13 that remains unpublished, a fact that hinders the comprehensive characterization of gene repertoires and their expression patterns. Currently, some efforts for genome sequencing and analysis are ongoing that aim to resolve large-scale evolutionary and epigenomic signatures,9 inspired partly by the relevance of hagfish to understanding patterns of whole genome duplications14–19 and chromosome elimination.20–22 In contrast to those efforts, which are necessarily targeting reconstruction of the genome at chromosome scale, in this study we aimed at providing a data set covering as many full-length protein-coding genes as possible, to enable gene-level analysis on molecular function and evolution of hagfishes, an indispensable component of the vertebrate diversity.\n\n\nMethods\n\nA 48cm-long adult male individual of Eptatretus burgeri caught at the Misaki Marine Station in June 2013 was used for the study. After anesthetization in 1% tricaine and decapitation, the testis was sampled from which genomic DNA was extracted with the conventional phenol/chloroform extraction method,23 and the genome sequencing was performed as outlined in Figure 1. The study was conducted with all efforts to ameliorate any suffering of animals, in accordance with the institutional guideline Regulations for the Animal Experiments by the Institutional Animal Care and Use Committee (IACUC) of the RIKEN Kobe Branch. The extracted genomic DNA was sheared using an S220 Focused-ultrasonicator (Covaris), which allowed us to retrieve DNA fragments of variable length distributions. Table 1 includes detailed information on amounts of starting DNA as well as conditions for shearing. The sheared DNA was subjected to paired-end library preparation using the KAPA LTP Library Preparation Kit (KAPA Biosystems). The optimal number of PCR cycles for library amplification was determined by quantitative PCR based on SYBR Green, using the KAPA Real-Time Library Amplification Kit (KAPA Biosystems) with Illumina library compatible primers (5′-AATGATACGGCGACCACCGA-3′ and 5′-CAAGCAGAAGACGGCATACGA-3′), and an aliquot of adaptor-ligated DNA,24 at 98°C for 45 sec followed by 25 cycles of amplification at 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds, in ABI 7900HT Real Time PCR system (Thermo Fisher Scientific). The optimal Ct value was determined in SDS 2.4 software (Thermo Fisher Scientific) as cycles that reaches FS1 (Fluorescent Standard 1) but does not exceed FS2 (Fluorescent Standard 2). Libraries were further size selected using Agencourt AMPure XP (Beckman Coulter). Mate-pair libraries were prepared using the Nextera Mate Pair Sample Prep Kit (Illumina), employing our customized iMate protocol.25 Detailed information of the paired-end and mate-pair libraries are described in Table 1. Libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems) and sequenced on HiSeq 1500 (Illumina) operated by HiSeq Control Software v2.0.12.0 using HiSeq SR Rapid Cluster Kit v2 (Illumina) and HiSeq Rapid SBS Kit v2 (Illumina), or on HiSeq X (Illumina) operated by HiSeq Control Software v3.3.76, or on MiSeq operated by MiSeq Control Software v2.3.0.3 using the MiSeq Reagent Kit v3 (600 Cycles) (Illumina). Read lengths were 127 or 251 nt on HiSeq 1500, 151 nt on HiSeq X, and 251 nt on MiSeq. Base calling and generation of fastq files were performed with RTA v1.17.21.3 (Illumina, RRID:SCR_014332) and bcl2fastq v1.8.4 (Illumina, RRID:SCR_015058) for the sequencing data of HiSeq 1500 and MiSeq, or by RTA v2.7.6 and bcl2fastq v2.15.0 for the sequencing data of HiSeq X. Illumina adaptor sequences and low-quality bases were removed from the paired-end sequencing reads by Trim Galore v0.3.3 (RRID:SCR_011847) with the ‘--stringency 2 --quality 30 --length 25 --paired --retain_unpaired’ options. Mate-pair reads were processed to identify the junction adaptor by NextClip v1.126 (RRID:SCR_005465) with the default parameters.\n\nSamples, raw data, and products are indicated with green letters, while computational steps are labelled in black. See Methods for the details including the choice of the programs used in individual computational steps.\n\nTotal RNAs were extracted from the liver tissue and the blood of the above-mentioned adult individual with Trizol reagent (Thermo Fisher Scientific) following the manufacturer’s instruction. The RNA was treated with DNase I to digest genomic DNA. Quality control was performed with Bioanalyzer 2100 (Agilent Technologies), which yielded the RIN values of 8.7 and 9.1 for the respective tissues. Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).27 The amount of total RNA used for library preparation and the number of PCR cycles applied for library amplification are described in Table 1 and Figure 2. Removal of Illumina adaptor sequences and low-quality bases was performed with Trim Galore v0.3.3 as outlined above. Alignment of the RNA-seq reads to the genome assembly was performed by HISAT2 v2.2.128 (RRID:SCR_015530) with the options ‘-k 3 -p 20 --pen-noncansplice 1000000’.\n\na, Shotgun DNA libraries analyzed by Bioanalyzer High Sensitivity DNA Kit (Agilent). b, Mate-pair libraries analyzed by Bioanalyzer High Sensitivity DNA Kit. c, RNA-seq libraries analyzed by TapeStation High Sensitivity D1000 ScreenTape Assay Kit (Agilent).\n\nDe novo genome assembly and scaffolding of Illumina short reads processed as described above were performed by the program PLATANUS v1.2.429 (RRID:SCR_015531) with its default parameters. The assembly employed paired-end reads and single reads whose pairs had been removed for quality filtering, and the scaffolding employed paired-end and mate-pair reads. The gap closure employed all of the single, paired-end, and mate-pair reads after processing. The obtained sequences were further scaffolded with paired-end RNA-seq reads with the program P_RNA_Scaffolder30 (commit 7941e0f on May 30, 2019, at GitHub) with the options ‘-s yes -b yes -p 0.90 -t 20 -e 100000 -n 100’, followed by another gap closure run with PLATANUS ‘gap_closure’ using the same set of reads used in the above-mentioned gap closure run. The resultant genomic sequences were further screened for the species’ own mitochondrial DNA fragments, contaminating organismal sequences, PhiX sequences loaded as a control in the Illumina sequencing system, and sequences shorter than 500 bp, as performed previously.31\n\nTo obtain species-specific repeat libraries, RepeatModeler v1.0.832 (RRID:SCR_015027) was executed with its default parameters. Repeat element detection in the genome sequence was performed by RepeatMasker v4.0.533 (RRID:SCR_012954), which employs the National Center for Biotechnology Information (NCBI) RMBlast v2.2.2734 (RRID:SCR_022710), using the custom repeat library obtained above by RepeatModeler. Genomic regions detected as repeats were soft-masked by RepeatMasker with the ‘-nolow -xsmall’ options.\n\nConstruction of gene models was performed by employing the gene prediction pipeline BRAKER v2.1.435 (RRID:SCR_018964) with the options ‘--min_contig=500 --prg=gth --softmasking --UTR=off’ (Figure 1). This computation employed RNA-seq read alignments in BAM files onto the genome assembly and a set of peptide sequences prepared as follows. The set of peptide sequences used as homolog hints included the predicted proteins of the Arctic lamprey (34,362 sequences, previously designated as GRAS-LJ12), which were aligned to the soft-masked genome assembly.\n\n\nResults\n\nOur technical procedure employing the genome assembly program PLATANUS29 that previously produced genome assemblies for multiple shark species with modest investment36 yielded genome sequences consisting of 4,519,897 scaffolds (Assembly 1 in Figure 1) with an N50 length of 238 Kbp (length cutoff=500 bp). To improve the continuity of fragmentary sequences that were derived from transcribed regions but were separated from exons, the sequences in Assembly 1 were further scaffolded with paired-end RNA-seq reads, which resulted in 4,505,643 sequences (Assembly 2) with an N50 length of 264 Kbp (length cutoff=500 bp). These sequences were filtered for the length of >500 bp, processed again for gap closure with the program PLATANUS, and scanned for contaminants of microbes and artificial oligos used for sequencing. Through this procedure, we have obtained 114,941 sequences with the minimum and maximum lengths of 500 bp and 2.064 Mbp, respectively, marking the N50 scaffolding length of 293 Kbp (Assembly 3).\n\nUsing the resultant genome sequences (Assembly 3), genome-wide prediction of protein-coding sequences were performed with the program pipeline BRAKER.35 After preliminary runs with variable parameters and input data sets, we conducted a prediction run with transcript evidence and peptide hints, which resulted in a set of 46,295 genes, with the maximum length of the putative peptides of 19,580 amino acids. These sequences have systematic identifiers Eptbu0000001–Eptbu0046295 with suffixes ‘.t1’–‘.t6’ depending on the multiplicity of predicted peptide variants derived from alternative splicing. These sequences are available under https://figshare.com/projects/eburgeri-genome/77052.37–41\n\nTo confirm the coverage of the genome assembly, paired-end RNA-seq reads were aligned to the genome sequence (Assembly 3) with splicing-aware read mapping program HISAT2 as described in the Methods section. This computation resulted in mapping of the reads to the nuclear and the mitochondrial genome sequences of E. burgeri at high proportion, at 91.64% and 5.17% respectively.\n\nIt has been previously shown that completeness scores of cyclostome genomes tend to be underestimated, when their rapid-evolving nature and phylogenetic position is not taken into consideration.27 In this study, completeness of the genome assemblies was assessed with CEGMA v2.542 (RRID:SCR_015055) and BUSCO v2.0.143 (RRID:SCR_015008). For both CEGMA and BUSCO, we employed not only the reference gene sets provided with these pipelines but also the core vertebrate genes (CVG) that was developed specifically for vertebrates from isolated lineages such as elasmobranchs and cyclostomes.27 The completeness assessments executed using CEGMA and CVG on the gVolante webserver44,45 returned percentages of single-copy orthologs detected as ‘complete’ of 65%, and ‘complete or partial/fragmented’ of 91%. Use of BUSCO v2.0.143 with CVG resulted in the detection of 'complete' single-copy orthologs of 83.7%, and ‘complete or partial/fragmented’ single-copy orthologs of 93.6% (Table 2). The difference of the completeness scores between the assessments of the genome assembly and the gene models might be explained by decreased sensitivity of detecting divergent multi-exon genes in the genome. Altogether, the resultant set of gene models is expected to encompass more than 90% of the protein-coding genes in the E. burgeri genome.\n\na The construction of this gene model was performed without predicting alternative splice variants, and the number of peptides is thus not included in the relevant cell.\n\nb The completeness was scored by the use of the pipeline BUSCO v2 with the one-to-one ortholog set CVG (see Methods).\n\nThis data set is oriented towards gene-level analysis including phylogenomic analysis and phylome exploration aiming at studying gene family evolution, rather than the analysis of complete genome structure. Importantly, the total length of the genome sequences obtained in this study amounts only to approximately 1.7 Gbp which is smaller by more than 1 Gbp than the genome size estimate based on flow cytometry of nuclear DNA content21 (2.91 Gbp). For investigating the structural evolution of the whole genome, such as chromosome elimination or large-scale synteny conservation, it may be advisable to wait for other resources to be released without embargo.\n\nThe obtained gene models sometimes include multiple transcripts and their deduced amino acid sequences per gene, because of predicted alternative splice variants. For use in phylogenomics and ortholog clustering, a set of amino acid sequences without splice variants (doi: 10.6084/m9.figshare.11971932)37 has also been made available. These sequence data are available for BLAST searches on the Squalomix project site (https://transcriptome.riken.jp/squalomix/).",
"appendix": "Data availability\n\nFigshare: Underlying data for ‘Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri’ (https://figshare.com/projects/eburgeri-genome/77052).\n\nThis project contains the following underlying data:\n\n• Data file 1: gene coding nucleotide sequences, Eburgeri_v1.gene.fna.gz (https://doi.org/10.6084/m9.figshare.11967795.v2) 37\n\n• Data file 2: genes' peptide sequences, Eburgeri_v1.gene.faa.gz (https://doi.org/10.6084/m9.figshare.11968119.v2) 38\n\n• Data file 3: genes' peptide sequences without alternative splicing variants, Eburgeri_v1.gene-noisoform.faa.gz (https://doi.org/10.6084/m9.figshare.11971932.v2) 39\n\n• Data file 4: Inshore hagfish genome assembly, Eburgeri_v1.genome.fna.gz (https://doi.org/10.6084/m9.figshare.11967789.v3) 40\n\n• Data file 5: gene model, Eburgeri_v1.gene-model.gff3.gz (https://doi.org/10.6084/m9.figshare.11967474.v2) 41\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\nNCBI Protein: Whole genome shotgun sequencing project [Eptatretus burgeri (Inshore hagfish)]. Accession number BROF01000000, https://identifiers.org/ncbiprotein:BROF01000000\n\nDDBJ SRA Submission: Sequence data [Eptatretus burgeri (Inshore hagfish)]. Accession number DRA010216, https://ddbj.nig.ac.jp/resource/sra-submission/DRA010216\n\n\nAcknowledgements\n\nWe thank Masumi Nozaki for assistance in sampling. The authors acknowledge Kazu Tanimoto, Kaori Tanaka, and Chiharu Tanegashima at Laboratory for Phyloinformatics in RIKEN Center for Biosystems Dynamics Research (BDR) for technical assistance.\n\n\nReferences\n\nKuraku S, Ota KG, Kuratani S: Timetree of life. Kumar S, Hedges B, editors.2009.\n\nDehal P, et al.: The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002; 298: 2157–2167. PubMed Abstract | Publisher Full Text\n\nPutnam NH, et al.: The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008; 453: 1064–1071. PubMed Abstract | Publisher Full Text\n\nMehta TK, et al.: Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proc. Natl. Acad. Sci. U. S. A. 2013; 110: 16044–16049. PubMed Abstract | Publisher Full Text\n\nSmith JJ, et al.: Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat. Genet. 2013; 45: 415–421. 421e411-412. PubMed Abstract | Publisher Full Text\n\nNikitina N, Bronner-Fraser M, Sauka-Spengler T: The sea lamprey Petromyzon marinus: a model for evolutionary and developmental biology. Cold Spring Harb. Protoc. 2009; 2009: pdb emo113. PubMed Abstract | Publisher Full Text\n\nOisi Y, Ota KG, Kuraku S, et al.: Craniofacial development of hagfishes and the evolution of vertebrates. Nature. 2013; 493: 175–180. PubMed Abstract | Publisher Full Text\n\nOta KG, Kuraku S, Kuratani S: Hagfish embryology with reference to the evolution of the neural crest. Nature. 2007; 446: 672–675. PubMed Abstract | Publisher Full Text\n\nPascual-Anaya J, et al.: Hagfish and lamprey Hox genes reveal conservation of temporal colinearity in vertebrates. Nat. Ecol. Evol. 2018; 2: 859–866. PubMed Abstract | Publisher Full Text\n\nManousaki T, et al.: Jawless Fishes of the World. Orlov AM, Beamish RJ, editors.Cambridge Scholars Publishing;2016; Vol. 1. : pp. 2–16.\n\nQiu H, Hildebrand F, Kuraku S, et al.: Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case. BMC Genomics. 2011; 12: 325. Publisher Full Text\n\nKadota M, et al.: CTCF binding landscape in jawless fish with reference to Hox cluster evolution. Sci. Rep. 2017; 7: 4957. PubMed Abstract | Publisher Full Text\n\nYates AD, et al.: Ensembl 2020. Nucleic Acids Res. 2020; 48: D682–D688. PubMed Abstract | Publisher Full Text\n\nKuraku S: Insights into cyclostome phylogenomics: pre-2R or post-2R. Zool. Sci. 2008; 25: 960–968. PubMed Abstract | Publisher Full Text\n\nSacerdot C, Louis A, Bon C, et al.: Chromosome evolution at the origin of the ancestral vertebrate genome. Genome Biol. 2018; 19: 166. PubMed Abstract | Publisher Full Text\n\nEscriva H, Manzon L, Youson J, et al.: Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution. Mol. Biol. Evol. 2002; 19: 1440–1450. PubMed Abstract | Publisher Full Text\n\nSimakov O, et al.: Deeply conserved synteny resolves early events in vertebrate evolution. Nat. Ecol. Evol. 2020; 4: 820–830. PubMed Abstract | Publisher Full Text\n\nSmith JJ, Keinath MC: The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. Genome Res. 2015; 25: 1081–1090. PubMed Abstract | Publisher Full Text\n\nSmith JJ, et al.: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat. Genet. 2018; 50: 270–277. PubMed Abstract | Publisher Full Text\n\nKojima NF, et al.: Whole chromosome elimination and chromosome terminus elimination both contribute to somatic differentiation in Taiwanese hagfish Paramyxine sheni. Chromosom. Res. 2010; 18: 383–400. PubMed Abstract | Publisher Full Text\n\nNakai Y, et al.: Chromosome elimination in three Baltic, south Pacific and north-east Pacific hagfish species. Chromosom. Res. 1995; 3: 321–330. PubMed Abstract | Publisher Full Text\n\nNakai Y, Kubota S, Kohno S: Chromatin diminution and chromosome elimination in four Japanese hagfish species. Cytogenet. Cell Genet. 1991; 56: 196–198. PubMed Abstract | Publisher Full Text\n\nKuraku S, Qiu H, Meyer A: Horizontal transfers of Tc1 elements between teleost fishes and their vertebrate parasites, lampreys. Genome Biol. Evol. 2012; 4: 929–936. PubMed Abstract | Publisher Full Text\n\nTanegashima C, et al.: Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei. Sci Data. 2018; 5: 180200. Publisher Full Text\n\nTatsumi K, Nishimura O, Itomi K, et al.: Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing. Biotechniques. 2015; 58: 253–257. Publisher Full Text\n\nLeggett RM, Clavijo BJ, Clissold L, et al.: NextClip: an analysis and read preparation tool for Nextera long mate pair libraries. Bioinformatics. 2014; 30: 566–568. PubMed Abstract | Publisher Full Text\n\nHara Y, et al.: Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation. BMC Genomics. 2015; 16: 977. PubMed Abstract | Publisher Full Text\n\nKim D, Paggi JM, Park C, et al.: Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 2019; 37: 907–915. PubMed Abstract | Publisher Full Text\n\nKajitani R, et al.: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res. 2014; 24: 1384–1395. Publisher Full Text\n\nZhu BH, et al.: P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads. BMC Genomics. 2018; 19: 175. PubMed Abstract | Publisher Full Text\n\nHara Y, et al.: Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes. BMC Biol. 2018; 16: 40. PubMed Abstract | Publisher Full Text\n\nSmit AFA, Hubley R: RepeatModeler Open-1.0. (2008-2010).Reference Source\n\nSmit AFA, Hubley R, Green P: RepeatMasker Open-4.0. (2013-2015).Reference Source\n\nAltschul SF, et al.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25: 3389–3402. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoff KJ, Lomsadze A, Borodovsky M, et al.: Whole-Genome Annotation with BRAKER. Methods Mol. Biol. 2019; 1962: 65–95. Publisher Full Text\n\nHara Y, et al.: Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates. Nat. Ecol. Evol. 2018; 2: 1761–1771. PubMed Abstract | Publisher Full Text\n\nRIKEN Kobe PL:Inshore hagfish gene coding nucleotide sequence. figshare. Dataset.2022. Publisher Full Text\n\nRIKEN Kobe PL:Inshore hagfish genes' peptide sequences. figshare. Dataset.2022. Publisher Full Text\n\nRIKEN Kobe PL:Inshore hagfish genes' peptide sequences without alternative splicing variants. figshare. Dataset.2022. Publisher Full Text\n\nRIKEN Kobe PL:Inshore hagfish genome assembly. figshare. Dataset.2022. Publisher Full Text\n\nRIKEN Kobe PL:Inshore hagfish gene model. figshare. Dataset.2022. Publisher Full Text\n\nParra G, Bradnam K, Ning Z, et al.: Assessing the gene space in draft genomes. Nucleic Acids Res. 2009; 37: 289–297. PubMed Abstract | Publisher Full Text\n\nSimao FA, Waterhouse RM, Ioannidis P, et al.: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31: 3210–3212. PubMed Abstract | Publisher Full Text\n\nNishimura O, Hara Y, Kuraku S: Evaluating genome assemblies and gene models using gVolante. Methods Mol. Biol. 1962; 1962: 2019. PubMed Abstract | Publisher Full Text\n\nNishimura O, Hara Y, Kuraku S: gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics. 2017; 33: 3635–3637. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "155282",
"date": "30 Nov 2022",
"name": "Vincent Laudet",
"expertise": [
"Reviewer Expertise Eco-Evo-Devo"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this manuscript the authors present a genome of a hagfish (Eptatretus burgeri) determined from testis DNA. This is completed by transcriptome data from two tissues. The importance of hagfish for vertebrate evolution is obvious and this sequence is of course a very useful resource for the community. However I found the paper a bit disappointing for three main reasons:\nIn lamprey there is a fascinating phenomenon called “programmed genome rearrangement” in which we see the loss of ca 10-15% of the DNA in somatic cells during early development, producing a somatic genome that is different from the germline genome. This process is known to exist in hagfish. However, the author does not mention this in the introduction whereas of course this explains why they choose to sequence testis DNA. This should be added of course. No analysis of this phenomenon is done. For example, one could wonder what is the extent of this genome completeness when compared to other cyclostome genomes available.\n\nI wonder why the authors have only determind transcriptomes of two tissues, the liver and the blood. I think brain and testis (especially because of the programmed genome rearrangement present in lamprey) would have been also particularly interesting.\n\nI found the Busco value for single copy gene (83%) quite low, indicating that many genes are only partial. But even the value for partial genes (93.6%) is relatively low. Given the importance of hagfish in vertebrate genome evolution I wonder why the authors have not put more efforts in reaching better levels. This is particularly vexing given the programmed genome rearrangement phenomenon discussed above.\nMinor point\nMaterial and Methods. The sentence “The study was conducted with all efforts to ameliorate any suffering of animals, in accordance with the institutional guideline Regulations for the Animal Experiments by the Institutional Animal Care and Use Committee (IACUC) of the RIKEN Kobe Branch.” is bizarre. I think it would be better to replace “ameliorate” by “avoid”.\n\nAre the rationale for sequencing the genome and the species significance clearly described? No\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": "155853",
"date": "22 Dec 2022",
"name": "Daniel Ocampo Daza",
"expertise": [
"Reviewer Expertise Vertebrate evolution",
"comparative genomics",
"gene family evolution"
],
"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 provided an important resource for the bioinformatic study of phylogenomics and gene family evolution representing an under-studied yet crucial branch of vertebrate evolution, the agnathans. I look forward to start using this resource in my own research. The way the authors have shared all their data openly on the figshare platform is ideal.\nIn my estimation, the procedures undertaken to isolate, sequence, assemble and evaluate this genome-wide protein coding gene set from the inshore hagfish Eptatretus burgeri constitute the current standard practices, even the state of the art. To accompany the genomic sequencing with concurrent transcriptomic sequencing for the identification of transcripts is excellent. Of course, the identification of transcripts from more tissues is always desirable, but the tissues selected here (blood and liver) are appropriate and I doubt that the inclusion of more tissues would have raised the completeness statistics achieved in the study in a major way.\nThe study is only limited by avoiding a full-scale whole-genome sequencing project with the associated whole-genome analyses, however considering the substantial known challenges for such a project in an agnathan species, some of which the authors mention in this manuscript, it is understandable and acceptable that the publication of a coding gene set is a worthwhile goal in and of itself. Like I mentioned above, it will be a valuable resource.\nI have only the following minor comments pertaining to the text of the manuscript itself or some general points on vertebrate evolution. I have used the pagination of the provided PDF as a guide to where in the manuscript I direct my comments.\nThe authors have used \"testis\", singular, consistently throughout the manuscript rather than the plural \"testes\". Perhaps it is worth shortly mentioning that hagfishes only have one testis? This could be done simply on page 3 by writing \"the single testis was sampled...\" The word \"sampled\" also suggests that only part of the testis was used. Was the whole organ used for DNA extraction?\nIn the abstract the authors write that hagfishes \"arose from agnathan (...) lineages\". This is a confusing statement. Hagfishes in themselves are an extant agnathan lineage that arose from an ancestral, extinct agnathan lineage. Perhaps this statement can be rewritten more clearly.\nThe word choice \"irreplaceable\"\nin the first paragraph on page 3 is strange and I don't think it applies. The authors have similarly used \"indispensable\" further down in the text, at the end of the 3rd paragraph on page 3. I suggest using \"a scientifically valuable phylogenetic position among extant vertebrates\" (remove \"the\" before \"extant\") in the first instance and perhaps \"an important and under-studied component of vertebrate diversity\" (remove \"the\" before \"vertebrate diversity\").\nIt is an overstatement to write that agnathans diverged from the vertebrate stem during the early Cambrian. What is this based on? The best fossil evidence indicates that agnathans were present in the late Silurian, at the earliest, and were abundant in the Ordovician. Haikouichthys, an early Cambrian vertebrate is sometimes called an agnathan, but it is not at all clear that it belongs to the stem agnathan lineage that gave rise to lampreys and hagfishes. It is likely more closely related to the stem craniate lineage. Is the overstatement based on molecular time-estimations? These often overshoot time estimations in the far past, whereby it is important to also consider the fossil evidence.\nIn paragraph 2 on page 3, I suggest writing \"the peculiar nature of their protein-coding sequences\".\nRegarding the first sentence on paragraph 3, page 3: I don't think this conveys the situation accurately. I suggest something like this instead: \"As of July 2022, there is only one whole genome resource for hagfishes, a genome assembly from Eptatretus burgeri with corresponding gene models available in Ensembl. A description and analysis of this whole genome sequence has not yet been published.\" This \"unpublished\" genome has also been a valuable resource, especially because it also allows for the study of conserved synteny, so it should not be downplayed. I also don't entirely agree that because a description and analysis has not yet been published, this \"hinders the comprehensive characterization of gene repertoires and their expression patterns.\" There are predicted gene models/annotations available in the Ensembl database. The gene set presented in this manuscript obviously provide better evidence for protein-coding gene sequence, but the Ensembl genome assembly and gene models are not entirely useless. The authors should present the advantages of their approach and the resulting gene set without understating the usefulness of the previously available genome assembly.\nIn line 3 of paragraph 3 on page 3 I suggest: \"Currently, some efforts to sequence and analyse hagfish genomes are ongoing...\" The original phrasing does not mention hagfishes specifically.\nHow was the species of the sampled hagfish determined? The manuscript only describes that it was caught at the Misaki Marine Station in 2013. Do other hagfish species inhabit the location where the sampled hagfish was caught? The brown hagfish Eptatretus atami, for example, also occurs in the sea around Japan. Was the location or habitat where it was caught used to determine the species, or were physical/anatomical characteristics used? Or indeed both?\nIn line 3 of the 4th paragraph on page 3, i suggest \"and genome sequencing was performed...\" removing \"the\" before \"genome sequencing\".\nIn the last line of the 1st paragraph on page 6, \"as performed previously\" seems to suggest something previously described in the present manuscript, not a previously published study. Please make this clearer.\nThe first sentence on paragraph 4 of page 6 (\"Our technical procedure...\" ) is very long and difficult to follow. Please break this up and clarify. I the same sentence, what does \"with modest investment\" mean?\nIn the next to last line of paragraph 4 on page 6 I suggest \"we obtained\" rather than \"we have obtained\".\nIn the second line of paragraph 7 on page 6 I suggest \"In this study, the completeness...\"\nIn line 5 of the same paragraph I suggest \"that were developed specifically for vertebrates...\"\nIn line 8 of the same paragraph I suggest \"The use of BUSCO...\"\nIn line 3 of the 2nd paragraph on page 7 I suggest \"which is more than 1 Gbp smaller\" rather than \"which is smaller by more than 1 Gbp\".\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
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https://f1000research.com/articles/11-1270
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https://f1000research.com/articles/11-1070/v1
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20 Sep 22
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{
"type": "Research Article",
"title": "Incorporating reading strategies for EFL undergraduate learners in Saudi Arabia: A think-aloud study",
"authors": [
"Arif Ahmed Mohammed Hassan Al-Ahdal",
"Yasamiyan Alolaywi",
"Yasamiyan Alolaywi"
],
"abstract": "Background: In language learning, reading is a skill that enables interaction with a text in whatever field of knowledge the learner is pursuing. Readers tend to use strategies such as comprehension, interpretation and conception of decoding written language and texts to enhance their reading capacity. This research explores the reading strategies applied by Saudi English as a Foreign Language (EFL) learners and compares the reading abilities of male and female EFL students. Methods: The study interviewed three EFL students about the reading strategies they applied while reading passages and texts. Then an International English Language Testing System (IELTS) reading test was handed over to 26 randomly selected students. Results: The study found that the reading strategies used by the students interviewed involved skimming, scanning, guessing the meaning from context, identifying the mean idea, and summarizing the body of the text in question. Moreover, the study revealed that both male and female students scored low in the IELTS tests that the researchers conducted. The average mean score they reached was 7.15 out of 20. However, even in the low scoring ratio, female students (M=7.69) outperformed male students (M= 6.62) and the difference between them remained significant, P=.000. Conclusions: The study recommends that the language instructors help EFL learners in developing their reading strategies and applying them every time they read any text.",
"keywords": [
"EFL Learners",
"Reading Strategies",
"Hearing Abilities",
"Language Instructors"
],
"content": "Introduction\n\nWhile talking and hearing abilities are gained from infancy or through time, reading is actually a learned skill that can be strengthened. Since reading involves intellectual functions like encoding additional knowledge, using cognitive skills, engaging a layout for current understanding; it is different from literacy. The skills used in literacy, on the other hand, invite various strategies and metacognitive and cognitive approaches that define learners’ awareness of which method works best for them and then selecting them. Substantial research and triarchic theory of intelligence by Sternberg points out that students with high achievement rates seem to be more metacognitive than students with lower achievement rates (Sternberg, 1985). Although simply having that metacognitive skill is not enough; factors such as motivation, persistence, focus and self-reliance play an important role for a successful path to learning.\n\nLanguage researchers have shown a keen interest in the ‘think-aloud’ (expressing the thoughts as they occur) technique as a reading strategy. The technique provides ample data for further research into cognitive processes and this study used the same technique with the undergraduate EFL learners in the classrooms of Saudi Universities. Despite the studies that have been conducted previously, there are limited studies that identify the reading levels of the Saudi EFL learners and their IELTS performance levels. Also, there has been no investigation of the reading strategies used by EFL learners and how they impact them across gender divides. This paper attempts to explain how the undergraduate male and female participants approach the reading strategies. It also denotes how a ‘think-aloud’ approach can be viewed through a qualitative as well as quantitative lens where the participants are more like quasi-researchers who voice the words in their heads while trying to complete the assigned tasks.\n\n\nLiterature review\n\nReading strategies have been discussed widely in previous research (Li, 2020). Reading strategies play a major role in helping students to understand texts (Suraprajit, 2019; Al-Ahdal, 2020). However, tertiary level students were found to have decisive problems in reading academic texts because of their use of ineffective reading techniques (Al-Mekhlafi, 2018). Kuhn (2000) defines metacognition as what enhances metacognitive awareness of what one thinks and how one recognizes and maintains strategic control while applying these strategies to process new information. Some of these strategies have been used over a period of time by the students to help them in comprehension. It has been suggested that ‘think-aloud’ (expressing the thoughts as they occur) is a particularly effective strategy for readers who struggle while reading an unfamiliar text (Olshavsky, 1997).\n\nThe studies of reading strategies spread over many dimensions (Al-Mekhlafi, 2018; Bagci & Unveren, 2020; Deliany & Cahyono, 2020; Deliany & Cahyono, 2020; Suraprajit, 2019; Wahyono, 2019; Al-Ahdal & Al-Awaid, 2014). Wahyono (2019) explored the correlations between reading strategies and reading comprehension while Deliany and Cahyono (2020) investigated EFL students’ use of metacognitive reading strategies. Similarly, Suraprajit (2019) detected the use of bottom-up and top-down reading strategies in reading academic business language. Al-Mekhlafi (2018) also investigated the EFL learners’ frequent use of reading strategies. Reading approaches, as according to Fandiño et al., (2019), may be divided into three categories: global schemes, dilemma (e.g., rereading), and supporting reading skills (e.g., taking notes).\n\nMuch research has been undertaken in the journals on various elements of strategy usage and metacognitive strategies in reading (Dąbrowska, 2018; Li & Clariana, 2019; Zhang et al., 2019; Guo et al., 2018) by emphasizing the significance of instructional tactics in literature classrooms (Ferrara et al., 2020). Ample research concentrating on the effects of instructional techniques on students’ reading skills show that activities have a favorable impact on the EFL learners (Altiok et al., 2019; Jin et al., 2020). Biological sex and competency variations on techniques usage have also been identified in related studies (e.g., Dąbrowska, 2018; Guo et al., 2018; Li & Clariana, 2019; Jansen et al., 2019). Variability between good readers and those who have difficulty, according to Dąbrowska (2018), are influential determinants in the adoption of effective learning strategies. Furthermore, Jansen et al. (2019) performed a survey in a scenario where a lack of competence in the goal of linguistic knowledge (English) was asserted, and the investigator found that competency was indeed a determinant in adopting techniques for learning. Likewise, research conducted by Guo et al., (2018) studied how Chinese EFL students observe self-regulatory strategies in reading. Results showed that fluency was a predictor among the EFL students who incorporated several methods in their reading approach. Garner’s (1990) theory of settings proposes that strategies need to be changed according to the context. The classroom instructions do not always support the strategy used and the learners fall back on their old routine practices instead of adapting to the new methods.\n\nThink-aloud methods as reading techniques\n\nThe think-aloud strategy for reading has been adapted by several researchers (Bai, 2018; Camilo et al., 2020; Follmer & Sperling, 2018; Huang, 2019; Lan, 2020; Li & Clariana, 2019; Reiber-Kuijpers et al., 2021; Wei, 2020). They employed think-aloud procedures in their studies for the process of recognizing metacognitive strategies. Li and Clariana (2019) conducted think-aloud research with 26 students of various levels of proficiency and they found that proficiency was beneficial in the application of several techniques. Along the same lines, Reiber-Kuijpers et al. (2021) employed think-aloud techniques to compare the strategies that both the successful readers and the less advanced readers used while reading and found that successful readers used many more tactics. Similarly, utilizing think-aloud protocols, Lee et al. (2019) determined several learning techniques in the outcomes of a study including 80 learners. The study revealed that developing literacy strategy and teaching reading skills should be tackled in a comparable research area. Tinzmann et al. (1990) ascertain that even training students to the thinking aloud habit keeps the classroom interactions robust. Ozek and Civelek (2006) consider the think-aloud strategy as an effective assessment tool to explore students’ reading strengths and weaknesses as it gives an insight to the reader’s mind which is otherwise unobservable (Block, 1986). Gunning (1996) asserts that think-aloud can be used to comprehend features such as seeking information using prior knowledge, visualizing texts, observing and solving word or comprehension related problems. The role of reflection and guidance from the teacher cannot be ruled out, if the teacher needs the reading strategy to work and for that they need to provide an environment where the student can think while they are reading (Chamot and O’Malley, 1994, p.11 cited by Lavadenz, 2003; Farr & Conner, 2004).\n\nReading strategies have been the focus of many previous studies (Al-Mekhlafi, 2018; Bagci & Unveren, 2020; Deliany & Cahyono, 2020; Deliany & Cahyono, 2020; Suraprajit, 2019; Wahyono, 2019; Al-Ahdal & Almarshedi). For example, Deliany and Cahyono (2020) studied EFL students’ implementation of metacognitive reading tactics and reported that most students had high metacognitive reading strategies. Also, the study found that there was no significant difference between the male learners and the female learners in the use of reading techniques. Furthermore, Suraprajit (2019) examined the use of bottom-up and top-down reading strategies in academic business language in a study that used a questionnaire to collect data from Thai students. The study reported that the top-down strategy was the most commonly used method of instruction. It focused on activities that constructed meaning by utilizing background knowledge, making predictions and searching the reading material to assert or discard the predictions that were made. In contrast, the bottom-up strategy focuses on the text which is read and analyzed from start to finish. Students did want to use their time reading aloud, identifying tenses or dividing the sentences into small elements. This was the least preferred method of instruction.\n\nMoreover, Al-Mekhlafi (2018) investigated strategies commonly used by the EFL learners. The study found that students used different reading strategies extensively and there was no significant difference between the levels of students in the use of reading strategies. Similarly, Nazurty et al., (2019) studied how frequently the Indonesian student teachers use reading strategies. The study investigated the use of reading strategies at pre-reading level, reading level and post-reading level. The findings showed that cognitive reading strategies were used by EFL students in all three different phases of reading. Furthermore, the study reported the tendency of female students to use cognitive strategies while male students used metacognitive strategies. Additionally, Wahyono (2019) explored students’ perceptions on reading strategies and their scores in reading comprehension in studies that indicate the correlation between reading strategies and comprehension of students. Findings of the study showed that the four cognitive pre-reading strategies including preview, prediction, prior knowledge, and purpose were used by all the students. In addition to those, many students used cognitive reading strategies such as rehearsal, developing new language, summarization, guessing meaning from context, and employing imagery for memorization. Furthermore, the study reported a correlation between reading strategies and reading comprehensions with a coefficient of 0.61. Think-Aloud Protocols (TAPs) provide valuable information about how learners solve problems, what obstacles they face, how and in what contexts they use these strategies in their learning tasks (Someren et al., 1994).\n\nUsing the Think-aloud-protocol pattern, this study aims to answer the following questions:\n\n1. What reading strategies do EFL students employ when answering reading questions?\n\n2. Are there any significant differences in the level of reading ability between the male students and the female students?\n\n\nMethods\n\nA mixed-method research approach was utilized in the study as data were analyzed both quantitatively and qualitatively. A reading test was used to assess students’ ability and applicability of the reading strategies. This is quantitatively assessed. Furthermore, the qualitative data were collected by interviewing three students during the reading session. The data collected through the two instruments were mixed in answering the research questions to triangulate and validate the findings. This study employed a think-aloud protocol design to gather verbal data on cognitive and metacognitive reading strategies used by undergraduate students enrolled in the EFL department in Qassim University for the academic year (1443AH). This is an explanatory design relying on the verbal protocols of the participants. Data analysis aimed to explore both cognitive and metacognitive reading strategy types that the participants used while engaged in a reading task.\n\nThe study sample consisted of 26 EFL students selected from the Department of English and Translation, College of Sciences and Arts, Methnab, Qassim University that were divided equally by gender (13 males and 13 females). All the students were native speakers of Arabic majoring in English. The ages of the participants ranged from 20 to 22 years. These students were randomly assigned to the study from a group of students who were enrolled in a Reading and Vocabulary Building Course. The selection of participants was based on the criteria of using the odd numbers from the list of students. Afterwards, three students (two males, and one female) were purposefully selected based on their proficiency levels to participate in the reading thinking-aloud task and to answer the interview questions. Table 1 below shows some demographic data about the study sample:\n\nInstruments\n\nReading test\n\nA reading test was administered to the participating EFL students to measure their reading abilities and to engage them in think-aloud sessions. The reading was selected from an already valid and reliable IELTS reading test taken from (Hayes & Read, 2004) and can be found under Extended data (a copy of the interview questions can be found under Extended data (Al-Ahdal Arif, ‘Incorporating reading strategies’, 2022). IELTS testing is an international standardized testing of English language proficiency for non-native English language speakers with an established worldwide credibility to assess language fluency. The test consists of a reading passage from a general topic and a set of twenty questions where each question is worth one point (Appendix A). The questions have different formats involving multiple-choice questions, matching, and summarizing the text.\n\nInterviews\n\nThe three purposefully selected students underwent a semi-structured interview session in order to explore their perceptions and prior knowledge of reading strategies. The interviews were a part of the think-aloud sessions which were conducted with an effort to gain more in-depth information about the respondents’ reading habits. The interview questions were adapted from Ghavamin, et al. (2013) (a copy of the interview questions can be found under Extended data (Al-Ahdal Arif, ‘Incorporating reading strategies’, 2022). The interview focused on the learning and reading strategies that the learners used while reading a text and the steps they take to improve upon their reading abilities.\n\nThink-aloud sessions\n\nProcedure\n\nInitially, twenty-six undergraduate students majoring in English were assigned to the current study (13 males and 13 females). The students were required to complete a reading comprehension test during a Reading and Vocabulary Building class in one hour. Afterwards, three participants were purposefully selected to take part in a think-aloud session to verbalize all the thoughts and processes going on in their minds while they were taking the test. As stated above, the interview questions were adapted from Ghavamin, et al. (2013). This means that the questions were already valid and reliable in the original study. Furthermore, the researchers administrated them on two students who were excluded from the study. The students reported the clarity and understandability of the interview questions. The researchers recruited them based on their previous verbal consent to participate in the study.\n\nEvery week, the instructor explained to the students a new reading strategy (e.g., scanning, skimming, previewing, guessing the unknown word, etc.) Students in each think-aloud session were required to apply the studied reading strategies to the target reading texts. They were also asked to report what they had comprehended from the text aloud. This procedure continued for the whole semester and at the end of the semester, the impact of the think-aloud strategy was assessed through a reading test. Students also reported their knowledge about the strategies they mastered and applied through an interview.\n\nThe think-aloud protocols were then recorded using a mobile phone and their responses transcribed by the researchers after. The interview was held in the English Department with three students. It took 15 minutes for each student to answer the five interview questions. As stated earlier, the interview was held in English, and when there was a language barrier, Arabic was used. Furthermore, the answers were transcribed, cleaned and themed. They appear in the results section along with the students’ number, i.e. (student 1-3). Then, the data were decoded and classified into categories based on the reading strategies adopted by these sampled students. The types of reading strategies adopted by the EFL learners while performing the reading task were identified and examined. The researchers also analyzed the extent to which gender differences played a role in learners’ comprehension and utilization of the reading strategies learned over a course of time.\n\nEthics statement\n\nEthical approval was obtained from the Scientific and Ethical Committee of Qassim University on (29/3/2022). Informed verbal consent was obtained from participants for the use and publication of their data.\n\nData analysis\n\nData for this research were gathered during the second semester of the academic year 2021-2022. Data were analyzed both quantitatively and qualitatively. The raw scores obtained from the reading tests were coded and calculated using statistical tool SPSS or Statistical Package for the Social Sciences, (Version 26) used for complex statistical data analysis. Descriptive statistics were reported involving minimum and maximum scores, frequencies, mean scores along with the standard deviation. Moreover, data gathered from the semi-structured interviews during the think-aloud sessions were analyzed qualitatively. This was done manually by applying the following steps: The students’ answers were anonymously presented using the word ‘Student’ to maintain the privacy of those participants. As soon as the data were transcribed, they were cleaned; a close examination of the students’ transcripts was required to identify appropriate themes and classifications. Each student’s responses were divided into five parts to answer the five interview questions. In this study, the analysis was conducted at sentence level. This means that every student’s interview was semi-open so, they were transcribed into short sentences focusing on the reading strategies they used (see the quotations of students 1 to 3 below). Wherever appropriate, quotes from the students’ responses were also used to support the themes identified in the tests.\n\n\nResults\n\nResearch Question 1. What reading strategies do ESL students employ when answering reading questions? This question is answered through analyzing the students’ responses at the interview stage of the study. Students used various reading strategies depending on the types of reading questions they answered. They reported using the following reading strategies: reading for overall understanding, scanning and guessing the meaning, identifying the part of speech of certain vocabulary, and summarizing. The full results can be found under Underlying data (Al-Ahdal Arif, ‘Incorporating reading strategies’, 2022). Their answers were: “In the beginning, I read mainly to get the gist of the text. For further reading, I scan the text and try to guess the meaning from the body of the text. It helps me identify the part of speech being used in the text and I’m able to guess the meaning from the context of the passage. Using this information, I summarize the main idea that emerged from the text,” (Student 1). Similar strategies were also reported by the previous student: “I use all three types of strategies: skimming, scanning and guessing the meaning of the text from the context of the passage,” (Student 2). Furthermore, the same focus was mentioned by another student: “I use guessing contextual meaning from the text drawing inferences, identifying part of speech and comprehending what the writer intends to say,” (Student 3).\n\nRQ2. Are there any significant differences in the level of reading ability among male and female students? The second research question will be answered using the students’ responses to the IELTS test. According to Table 2, the average mean score of the students was 7.15 and the standard deviation was 3.173. Male students’ mean score in the reading test was (M=6.62) with a standard deviation of (Std=2.663) whereas the mean score of female students was (M=7.69) and standard deviation of (Std=3.683) in the reading test. Female students outperformed male students in the reading competence and the difference in their scores was significant. The P value is.000 which is less than.05. We found there was a significant difference in reading ability between the male and female students in the study. Female students used reading strategies more effectively than their male counterparts during the reading tasks. They applied reading strategies, i.e., skimming, scanning, guessing the meaning of unfamiliar words using the context, etc. more frequently and effectively.\n\n\nDiscussion\n\nThe present research intends to investigate the reading strategies used by EFL students in order to get insight into their cognitive abilities. The study reported that students used various reading strategies depending on the reading questions. Some of the strategies were: reading to get an understanding of the main point of the text, skimming, scanning, guessing the meaning from the context, identifying the central idea and summarizing it. Students’ use of such reading strategies enabled them to comprehend various types of texts which developed their cognitive abilities used for language learning and acquisition. Many studies found that EFL learners used reading strategies to comprehend the academic reading texts as well. The study proved that the students employed cognitive and meta cognitive reading techniques while reading and that they preferred a top-down approach to a bottom-up approach. Michael Yeldham (2004) cites Vandergrift in his study of top-down and bottom-up approach who agrees that strategy instruction needs to be predominantly top-down, because then the learners become more aware using the information they already have to fill gaps in their understanding (Vandergrift, 2004).\n\nThe students used reading strategies extensively and their level of learning didn’t factor highly into using these strategies. While the study of the Indonesian student teacher reading programs showed that the EFL learners used different learning strategies during pre-reading and post-reading periods, their reading abilities improved with the wide variety of learning strategies used over a period of time. The study by Hoang Nguyen and Daniel R. Terry (2017) of Vietnamese EFL learners and staff found that the English learning success was attributed to multiple elements and not any single factor therefore the use of strategies and teachers’ flexibility in adapting the strategy to the needs of their students go hand in hand.\n\nThe students did not fare so well in the IELTS reading test with a mean score of 7.15 out of 20. Male students scored (6.62) lower than female students (7.69) and the difference between them is significant. In this, the finding differed from Deliany and Cahyono (2020), who reported that there was no difference between male and female EFL students using metacognitive reading strategies. This finding may co-relate the findings of Nazurty et al. (2019) who reported that while the female students used more cognitive strategies, the male students used metacognitive strategies. In a study to train the students’ metacognitive skills based on gender differences, Nunaki, Damopolii, Kandowangko, and Nusantri (2019) developed a 4-D research model to test both male and female students of a senior high school in Indonesia. The study supports the findings that there are no differences in the metacognitive skills used by the male or female students in inquiry-based learning.\n\n\nConclusions\n\nThe global scheme, rereading and supporting reading skills methods serve a variety of functions, but they all stem from complicated cognitive processes. In this research, scanning techniques, questionnaire/interviewing and testing of the participants were used. These studies used think-aloud protocols to assess EFL’s students’ metacognition and usage of worldwide reading skills while taking into account regularly used approaches in developing language studies. The study also suggests that students need to be trained to develop their metacognitive skills and that strategies alone do not result in successful outcomes. With the combined efforts of language instructors, curriculum design experts and motivated students, a successful implementation of strategies and effective learning can take place. As a result, the impact of instructional strategies could be demonstrated in aiding the reading abilities of the students. The study seeks to assess how EFL students approach and utilize think-aloud protocols in light of the relevant research and earlier investigations. Think-aloud is both a method of inquiry and a flexible mode of goal-oriented instruction. The success of its implementation depends on how well it can be used in classroom teaching. Some well-rehearsed exchanges between the teacher and the students are required to judge the competence levels of their EFL learners. Thus, incorporated into instructional approaches in schools in Saudi Arabia, think-aloud can lead to a constructive and engaging classroom environment that facilitates textual comprehension as well as social interaction.\n\n\n\n1. EFL instructors need to give a combination of prompts that are relatable and culturally familiar.\n\n2. Instructors need to refrain from giving any feedback during the reading process even if students mispronounce or misread certain words. Only when the student has read their piece should the researchers interfere.\n\n3. The instructors can introduce simple warm-up exercises before they begin using the think aloud technique to make the task easier for the learners.\n\n4. Switching back and forth from the native language to the foreign language might complicate the learning process and confuse the EFL learners so the instructor needs to ensure that only the target language is used in the process.\n\n5. Non-verbal cues such as body language and gestures and paralinguistic features such as tone of the voice and rhythm of the speech along with verbal expressions play an important role in learning a foreign language and instructors need to take note of that and include it in their data collection.\n\n6. Pairing up students can be an interesting feature of further studies where one student reads and the other one listens and takes notes and vice versa.\n\n7. Instructors are advised to extend the activities to other features of language learning such as short story building, storytelling and poetry reading activities in groups.\n\n8. Instructors need to provide a follow-up to their study so that the students recognize their efforts and work on their limitations.\n\n9. Instructors’ consistent use of learning strategies for academic purposes will motivate language learners to follow suit.\n\n10. Instructors can model the activity by ‘role-playing’ or practicing the strategy with the learners before they incorporate it into their lesson plans.\n\n11. Further research exploring the gender differences based on age, grade-level and competency level can provide new insight on the success of cognitive-led studies.\n\n\n\n1. The study did not investigate the metacognitive reading techniques that can be further used in similar studies.\n\n2. If prompts are too complicated and require interpretation, they can be counter-productive to the learning intended for the participant.\n\n3. While the participant is trying to read by thinking aloud, questions should not be asked during the process as it may break their rhythm of thought process.\n\n4. Time restrictions may shorten the scope of the activity planned.\n\n5. Verbalization alone may not be an effective approach.\n\n6. Breaking into native language patterns might impede the progress made during the learning activity.\n\n\nData availability\n\nFigshare: Incorporating reading strategies for EFL undergraduate learners in Saudi Arabia: A think-aloud study. https://doi.org/10.6084/m9.figshare.20401917.v1. (Al-Ahdal Arif, ‘Incorporating reading strategies’, 2022)\n\nThis project contains the following underlying data:\n\n- Raw Scores.xlsx\n\n- Results.docx\n\n- Transcriptions of the students Responses.docx\n\n- Students’ paper.pdf\n\n- Dataset.sav\n\nThis project contains the following extended data:\n\n- Interview Questions.docx\n\n- Reading Test.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAl-Ahdal AAMH: EBook interaction logs as a tool in predicting learner performance in reading. Asiatic: IIUM. J. Engl. Lang. Lit. 2020; 14(1): 174–188.Reference Source\n\nAl-Ahdal A, Alolaywi Y: Incorporating reading strategies for EFL undergraduate learners in Saudi Arabia: A think-aloud study. figshare. [Dataset]. Journal Contribution. 2022. Publisher Full Text\n\nAl-Ahdal AAMH, Almarshedi RM: Metalinguistic awareness and academic achievement: Finding correlations among high-achieving EFL learners. J. Lang. Linguist. Stud. 2022; 18(Special Issue 1): 472–483.\n\nAl-Ahdal AAMH, Al-Awaid SAA: Reflective teaching and language teacher education programmes: A milestone in Yemen and Saudi Arabia. J. Lang. Teach. Res. 2014; 5(4): 759–768. Publisher Full Text\n\nAl-Mekhlafi AM: EFL Learners’ Metacognitive Awareness of Reading Strategies. Int. J. Instr. 2018; 11(2): 297–308. Publisher Full Text\n\nAltıok S, Başer Z, Yükseltürk E: Enhancing metacognitive awareness of undergraduates through using an e-educational video environment. Comput. Educ. 2019; 139: 129–145. Publisher Full Text\n\nBagci H, Unveren D: Investigation of the Relationship between Metacognitive Awareness of Reading Strategies and Self-Efficacy Perception in Reading Comprehension in Mother-Tongue: Sample of 8th Graders. International Journal of Educational Methodology. 2020; 6(1): 83–98.\n\nBai B: Understanding primary school students’ use of self-regulated writing strategies through think-aloud protocols. System. 2018; 78: 15–26. Publisher Full Text\n\nBlock E: The comprehension strategies of second language readers. TESOL Q. 1986; 20: 463–494. Publisher Full Text\n\nBoulware-Gooden R, Carreker S, Thornhill A, Joshi RM:2007.\n\nBrown JD, Rogers TS:Introspection research: verbal protocols. Doing second language research. New York:Oxford University Press;2004; (pp. 53–78).\n\nCamilo C, Garrido MV, Calheiros MM: The social information processing model in child physical abuse and neglect: A meta-analytic review. Child Abuse Negl. 2020; 108: 104666. PubMed Abstract | Publisher Full Text\n\nChamot AU, O'malley JM: The CALLA handbook: Implementing the cognitive academic language learning approach. Reading, MA: Addison-Wesley Publishing Company;1994.\n\nDąbrowska E: Experience, aptitude and individual differences in native language ultimate attainment. Cognition. 2018; 178: 222–235. PubMed Abstract | Publisher Full Text\n\nDeliany Z, Cahyono BY: Metacognitive reading strategies awareness and metacognitive reading strategies use of EFL university students across gender. Stud. Engl. Lang. Educ. 2020; 7(2): 421–437. Publisher Full Text\n\nEricsson KA, Simon HA: Protocol analysis: Verbal reports as data. (Rev. ed.).Cambridge, MA:MIT Press;1993.\n\nFandiño FGE, Muñoz LD, Velandia AJS: Motivation and E-Learning English as a foreign language: A qualitative study. Heliyon. 2019; 5(9): e02394. PubMed Abstract | Publisher Full Text\n\nFarr R, Conner J: Using think-alouds to improve reading comprehension. Repéré à : http://www.readingrockets.org/article/102.2004.\n\nFerrara AM, Panlilio CC: The role of metacognition in explaining the relationship between early adversity and reading comprehension. Child Youth Serv. Rev. 2020; 112: 104884. Publisher Full Text\n\nFollmer DJ, Sperling RA: Interactions between reader and text: Contributions of cognitive processes, strategy use, and text cohesion to comprehension of expository science text. Learn. Individ. Differ. 2018; 67: 177–187. Publisher Full Text\n\nGarner R: When children and adults do not use learning strategies: Toward a theory of settings. Rev. Educ. Res. 1990; 60(4): 517–529. Publisher Full Text\n\nGhavamin M, Ketabi S, Tavakoli M: L2 reading strategies used by Iranian EFL learners: A think-aloud study. Read. Psychol. 2013; 34(4): 355–378. Publisher Full Text\n\nGunning TG: Creating reading instruction for all children.Allyn and Bacon, Order Processing, PO Box 11071, Des Moines, IA 50336-1071;1996.\n\nGuo Y, Xu J, Liu X: English language learners’ use of self-regulatory strategies for foreign language anxiety in China. System. 2018; 76: 49–61. Publisher Full Text\n\nHayes B, Read J:IELTS Test Preparation in New Zealand: Preparing Students for the IELTS Academic Module.Cheng L, Watanabe Y, editors. Washback in Language Testing. Resource Contexts and Methods. New Jersey:Lawrence Erlbaum;2004; (pp 97–111).\n\nHuang TC: Do different learning styles make a difference when it comes to creativity? An empirical study. Comput. Hum. Behav. 2019; 100: 252–257. Publisher Full Text\n\nJansen RS, Van Leeuwen A, Janssen J, et al.: Self-regulated learning partially mediates the effect of self-regulated learning interventions on achievement in higher education: A meta-analysis. Educ. Res. Rev. 2019; 28: 100292. Publisher Full Text\n\nJin T, Liu X, Lei J: Developing an effective three-stage teaching method for collaborative academic reading: evidence from Chinese first-year college students. J. Engl. Acad. Purp. 2020; 45: 100853. Publisher Full Text\n\nKuhn D: Theory of mind, metacognition and reasoning: A lifespan perspective.2000.\n\nLan YJ: Immersion into virtual reality for language learning. Psychol. Learn. Motiv. 2020; 72: 1–26. Publisher Full Text\n\nLavadenz M: Think aloud protocols: Teaching reading processes to young bilingual students.Eric. Digest.2003; 3(14). https://digitalcommons.lmu.edu/education_fac\n\nLavi R, Tal M, Dori YJ: Perceptions of STEM alumni and students on developing 21st century skills through methods of teaching and learning. Stud. Educ. Eval. 2021; 70: 101002. Publisher Full Text\n\nLee J, Knowles Z, Whitehead AE: Exploring the use of think aloud within Women’s artistic gymnastics judging education. Psychol. Sport Exerc. 2019; 40: 135–142. Publisher Full Text\n\nLi J: Development and validation of second language online reading strategies inventory. Comput. Educ. 2020; 145: 103733. Publisher Full Text\n\nLi P, Clariana RB: Reading comprehension in L1 and L2: An integrative approach. J. Neurolinguistics. 2019; 50: 94–105. Publisher Full Text\n\nPressley M, Wharton-McDonald R, Mistretta-Hampston J, et al.: Literacy Instruction in 10 Fourth-Grade Classrooms in Upstate New York. Sci. Stud. Read. 1998; 2(2): 159–194. Publisher Full Text\n\nNazurty R, Priyanto N, AnggiaPratiwi S, et al.: Learning Strategies in Reading: The Case of Indonesian Language Education Student Teachers. Univ. J. Educ. Res. 2019; 7(11): 2536–2543. Publisher Full Text\n\nNguyen H, Terry RD: English Learning Strategies among EFL Learners: A Narrative Approach.2017.\n\nNunaki J, Damopolli I, Kandowangko N, et al.: The effectiveness of inquiry-based learning to train the students' metacognitive skills based on gender differences.2019. http://repository.unipa.ac.id:8080/xmlui/bitstream/handle/123456789/346/artikel.pdf?sequence=1&isAllowed=y\n\nOlshavsky JE: Reading as a problem-solving: An investigation of strategies. Read. Res. Q. 1997; 12: 654–674. Publisher Full Text\n\nOzek Y, Civelek M: A Study on the use of cognitive reading strategies by ELT students. Asian EFL J. 2006 August; 14.Reference Source\n\nReiber-Kuijpers M, Kral M, Meijer P: Digital reading in a second or foreign language: A systematic literature review. Comput. Educ. 2021; 163: 104115. Publisher Full Text\n\nTinzmann MB, Jones BF, Fennimore TF, et al.: New learning and thinking curricula require collaboration. In What is the collaborative classroom ? NCREL;1990.\n\nVan Someren M, Barnard YF, Sandberg J: The think aloud method: a practical approach to modelling cognitive .London:Academic Press;1994.\n\nSternberg RJ: Implicit theories of intelligence, creativity and wisdom. J. Pers. Soc. Psychol. 1985; 49(3): 607–627. Publisher Full Text\n\nSuraprajit P: Bottom-up vs top-down model: The perception of reading strategies among Thai university students. J. Lang. Teach. Res. 2019; 10(3): 454–460. Publisher Full Text\n\nVandergrift L: 1. Listening to learn or learning to listen? Annu. Rev. Appl. Linguist. 2004; 24: 3–25. Publisher Full Text\n\nWahyono E: Correlation between Students’ Cognitive Reading Strategies and Reading Comprehension. JurnalStudi Guru Dan Pembelajaran. 2019; 2(3): 256–263. Publisher Full Text\n\nWei X: Assessing the metacognitive awareness relevant to L1-to-L2 rhetorical transfer in L2 writing: The cases of Chinese EFL writers across proficiency levels. Assess. Writ. 2020; 44: 100452. Publisher Full Text\n\nYilmaz FGK, Yilmaz R: Impact of pedagogic agent-mediated metacognitive support towards increasing task and group awareness in CSCL. Comput. Educ. 2019; 134: 1–14. Publisher Full Text\n\nZhang LJ, Thomas N, Qin TL: Language learning strategy research in System: Looking back and looking forward. System. 2019; 84: 87–92. Publisher Full Text"
}
|
[
{
"id": "150900",
"date": "26 Sep 2022",
"name": "Asmara Shafqat",
"expertise": [
"Reviewer Expertise Academic reading and writing",
"Corpus linguistics",
"Pragmatics",
"Discourse",
"Corpus Driven Teaching Methods",
"Learning styles of the learners and teachers. EAP and ESP and all ELT issues."
],
"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, \" Incorporating reading strategies for EFL undergraduate learners in Saudi Arabia: A think-aloud study\" is a wonderful work in Saudi Arabia context. The researcher tried to put all the convincing ideas in a systematic organization of the research pattern, however, the article requires proofreading. There are issues of subject verb agreement at some places.\nBesides this, writing results should be according to the APA or other standardized writing style suggested by the journal's guidelines, for instance, mentioning P- value should be formally written and other values in the results.\nThere is a suggestion about the number of the participants taken for the interview. It has been mentioned that there were two male interviewees and 1 female interviewee. There should be equal representation of the gender as it was done for the reading test and overall population of the study.\nThere were 13 males and 13 females, therefore, at least there should be 2 female interviewees like there were 2 males for interview.\nAnother noticeable thing is, there was nothing mentioned in the method which inferential statistical measure or researcher applied and on what parameters that statistical test was chosen to test the second research question.\nWith the minor amendments, this manuscript can be accepted for indexing.\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? Yes",
"responses": []
},
{
"id": "150898",
"date": "27 Sep 2022",
"name": "Ahdi Hassan",
"expertise": [
"Reviewer Expertise Applied Linguistics",
"corpus linguistics",
"English language"
],
"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\nIncorporating reading strategies for EFL undergraduate learners in Saudi Arabia: A think-aloud study: Review Report\nThe paper is well written and organized. It lays down the reading strategies as applied by Saudi EFL students along with the \"think aloud\" variable. The abstract gives a clear and concise summary of the paper through the essential elements such as, importance, aims, methods, results and conclusion. It is suggested that the Keywords may be arranged alphabetically with addition of the term \"think aloud\".\n\nThe introduction is well-composed, and adequately introduces the topic with a demonstration of the shortcomings of previous research. However, the researchers may add some ‘think aloud’ studies.\n\nThe literature review is adequately wide and deep with many up-to-date and main resources. Authors are advised to work more about the sections \"reading strategies\" and it may be subdivided into reading comprehension, think aloud, etc. or the authors should identify the correlation between such elements.\n\nIn the research questions, authors are recommended to add the adjective \"Saudi\" to identify the EFL learners involved.\n\nThe methods section is organized with discussion on the research design, population, selection of the participants, etc. The study identifies how the participants were chosen, the ethical consideration and the procedures followed as well as the instrument. Generally, the method used here can be replicated and reapplied.\n\nResults were clearly presented and organized according to the two research questions. The discussion section interprets and compares the findings with previous research findings. However, there are minor mistakes in the use of in-text citations. Authors are advised to edit them, for example, \"The study by Hoang Nguyen and Daniel R. Terry (2017); Nunaki, Damopolii, Kandowangko, and Nusantri (2019)\".\n\nThe study ends with a pertinent conclusion and some recommendations, implementations and limitations. Suggestions for further research are also set.\n\nThe references are up-to-date and written according to the journal outline.\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": "150896",
"date": "27 Sep 2022",
"name": "Gilbert C. Magulod jr",
"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 paper can contribute to the EFL undergraduate learners in Saudi Arabia. The study is a mixed methods research which is commendable. However, the following should be considered to revise the paper:\n\nIn the introduction, there is a need for the author to present the problem in the global issue down to the local issue.\n\nIn the abstract, the qualitative finding should be emphasized. it should also reflect a separate discussion of the qualitative component. What themes have been developed?\n\nThe author should provide another statement of the problem focusing on the qualitative component?\n\nFor the quantitative component, present the normality of data to justify the use of inferential statistics.\n\nThe paper can be a contributory to enhance reading strategies of EFL learners.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1070
|
https://f1000research.com/articles/11-813/v1
|
22 Jul 22
|
{
"type": "Research Article",
"title": "Professional qualifications of medical affairs pharmaceutical physicians and other internal stakeholders in the pharmaceutical industry",
"authors": [
"Ravi Jandhyala"
],
"abstract": "Background: Medical affairs pharmaceutical physicians (MAPPs) have unique value to pharmaceutical companies due to their accountability for activities that benefit regulators, payors, prescribers and patients. This study assessed whether MAPPs’ specialist training and education in pharmaceutical medicine could account for this level of value by determining whether there was significant variation in education and training between MAPPs and other internal stakeholders of pharmaceutical companies. Methods: A systematic search of LinkedIn profiles from the 10 pharmaceutical companies by revenue was conducted between June and October 2021. Job title and type and year of undergraduate and postgraduate qualifications were extracted. A one-sided Mann-Whitney test assessed for differences in the total number of qualifications between MAPPs and other internal stakeholders involved in medical affairs using MAPPs as the reference group. Other internal stakeholders included medical affairs pharmacists (MAPharm), other medical affairs professionals (MAOth), and market access (MAcc), commercial (COmm) and sales professionals. Sub-group analysis determined differences in undergraduate and postgraduate education. Results: In total, 524 profiles were included. Compared to all other internal stakeholders, MAPPs had a significantly higher number of undergraduate (p < 0.001) and postgraduate (MAPharm, p = 0.003; MAOth, p = 0.004; MAcc, COmm and Sales, p < 0.001) qualifications. Additionally, MAPPs had a significantly longer time to industry than other internal stakeholders apart from MAPharm. Of those with clinical qualifications, MAPPs were almost twice as likely to have business qualifications. Conclusions: Of all internal stakeholders, MAPPs had the highest number of qualifications and the best match between expertise and the contextual demands of decision-makers in the pharmaceutical industry. Pharmaceutical companies in the UK can use these findings to clarify role boundaries and decision-making power based on the nature and level of expertise of each internal stakeholder.",
"keywords": [
"Medical affairs",
"pharmaceutical physicians",
"degree qualifications",
"decision-making"
],
"content": "Introduction\n\nThe pharmaceutical industry is a unique context due to the need to balance both commercial and patient interests. The idea that organisational survival is predicated on commercial success is a well-established business principle within and beyond the pharmaceutical industry; however, the nature and importance of pharmaceutical medicine expertise is less well-recognised,1 which may have problematic implications for interprofessional collaboration2 and patient-centricity.3 The International Federation of Associations of Pharmaceutical Physicians and Pharmaceutical Medicine and other leading experts4,5 have advocated for the role of medical affairs pharmaceutical physicians (MAPPs) and defined its competencies, activities and importance to drug development, adoption and post-adoption and launch processes.6,7 MAPPs aim to identify gaps between practice and evidence-based guidelines,8–13 improve patient outcomes and decrease healthcare costs.14–16 Additionally, MAPPs optimise medicine adoption by facilitating engagements between pharmaceutical companies and regulators, payors and prescribers17 and may hold greater weight with prescribers than those in non-medically qualified roles.18\n\nCollaboration between stakeholders in the pharmaceutical industry17,19 is necessary for optimal medicine prescribing and to improve patients’ health,20 so engagement with regulators, payors and prescribers is vital to pharmaceutical company success. The value of medical affairs pharmaceutical physicians (MAPPs) to pharmaceutical companies has been established as distinct from that of other internal stakeholders due to their unique accountability for activities that benefit all external stakeholders (regulators, payors, prescribers, and patients).21 However, the reasons why they are able to make such a unique contribution have not been characterised. Medical affairs pharmaceutical physicians (MAPPs) have education and training in competencies that cover the entire scope of medical affairs practice and medicine adoption,21–25 while other stakeholders may have more general educational backgrounds supporting competencies that cover a smaller number of specialist domains (Table 1).26–29 Therefore, it was hypothesised that variation in educational background may account for MAPPs’ unique value to pharmaceutical companies.\n\nThe aim of this study was to determine whether significant variation in qualifications existed between MAPPs and internal stakeholders in the pharmaceutical industry, which could explain their unique value to pharmaceutical companies.\n\n\nMethods\n\nA systematic search and comparative quantitative analysis of social media data was conducted prospectively according to a predefined protocol. No specific guidelines were consulted. LinkedIn was searched between June and October 2021 for profiles of professionals in the pharmaceutical industry, including MAPPs, medical affairs pharmacists (MAPharms), other medical affairs professionals (MAOths) and market access (MAcc), commercial (COmm) and sales professionals (for search strings, see Table 2). As with all self-report data, consideration was given to the likely correctness and completeness of information provided on LinkedIn profiles. In the absence of data suggesting potential skew, we assumed that self-reported data quality would fall within a normal distribution, with the majority within acceptable limits and comparable to other self-report data. Additionally, a study assessing the criterion validity of LinkedIn profile elements suggested that it can be used as an accurate source of data on professionals’ qualifications.30 LinkedIn has also been reported as more accurate than other forms of biodata, such as resumes,31 possibly due to the group regulation of individual behaviour according to expectations of adherence to social norms, such as honesty.32\n\nTo be included, profiles needed to belong to a professional who was employed at one of the 10 largest pharmaceutical companies by revenue at the time of study, in particular Pfizer, GlaxoSmithKline, Merck & Co., Bayer Pharmaceuticals, Roche, Abbvie, Johnson & Johnson, Sanofi, Gilead Sciences and Novartis. It was assumed that these pharmaceutical companies would have sufficient organisational similarity as to ensure a broad likeness of job descriptions, person specifications and educational requirements for employment within the study sample. The sample of profiles was limited to those whose qualifications were recognised by UK employers to ensure a baseline level of comparability. Data on their undergraduate and postgraduate education (type of degree and year of qualification), date of entry into the pharmaceutical industry, relative age, and research experience were extracted by two research analysts and reviewed by an experienced systematic reviewer to provide outcome data, using MS Excel, comprising the number of degrees and years to first employment in the pharmaceutical industry.\n\nThe research hypothesis was tested using a one-sided Mann-Whitney test to assess whether the total number of degrees varied significantly between MAPPs and the other internal stakeholders, using MAPPs as the reference group. Sub-group analysis was performed to determine differences in the level of education (undergraduate and postgraduate) of MAPPs versus other internal stakeholders. The analysis was extended to determine the number of years taken by professionals to gain entry into the pharmaceutical industry, which was taken as a measure of how well the industry recognised their expertise. This was calculated by subtracting the year in which a professional graduated from their first degree/qualification from the year in which professionals took their first job at a pharmaceutical company. If obtained values were negative, then they were statistically adjusted by replacing the year at graduation with the year of entry to ensure that all values were above zero. All statistical analyses were performed using R v4.1.1, and p-values < 0.05 were considered statistically significant.\n\n\nResults\n\nThe search yielded 9299 profiles with 1209 unique profiles meeting inclusion criteria for review. Of these, 685 were excluded due to missing educational data, unavailability of profiles, professionals not being in primary employment at a pharmaceutical company and professionals being employed in non-medical affairs functions, such as clinical development, regulatory affairs and so on. In total, 524 profiles were included across MAPPs (88), MAPharm (66), MAOth (86), MAcc (97), COmm (94) and sales (93). GlaxoSmithKline was the most represented employer, followed by Abbvie and Roche, with fewest participants being employed by Bayer Pharmaceuticals (Figure 1).\n\nAs shown in Table 3, most qualifications were in the area of science and scientific research (BSc, n = 261; MSc, n = 150; PhD, n = 80), followed by pharmacy (BPharm, n = 40; MPharm, n = 58; PharmD, n = 9), medicine (MBBS/MBChB/BMBCh, n = 68; MD, n = 34) and business (MBA, n = 60). Business and either science, medical or pharmacy qualifications were found in all study groups, but of those with clinical qualifications, MAPPs were almost twice as likely to have business qualifications in the form of MBAs. Of all groups, professionals in the MAoth group were about twice as likely as MAPPs and MPharms and three times as likely as MAcc professionals to have scientific research expertise. Sales and COmm professionals had the least amount of clinical and research expertise, although the COmm group had one of the highest frequencies of business qualifications.\n\nOf all internal stakeholders, MAPPs had the highest median number of degree qualifications, followed by MAPharms, MAOth and MAcc. Commercial and sales had the lowest. MAPPs had a significantly higher number of total degrees than all other stakeholders (Table 4, Figure 2a). Subgroup analysis showed that MAPPs had significantly more undergraduate and postgraduate degrees than all other internal stakeholders, but the difference between MAPPs and MAPharm and MAOth was at a lower significance level (Table 4, Figure 2b). It took MAPPs significantly longer after their first degree to enter the pharmaceutical industry than all other internal stakeholders, but the difference from MAPharm was at a lower significance level (Figure 3).\n\n* p < 0.001.\n\n** p ≤ 0.005.\n\n\nDiscussion\n\nHistorical tensions between commercial and scientific interests in the pharmaceutical industry have created interprofessional working conditions that may have a negative impact on patient and organisational outcomes. Matching human capital with contextual demands for expertise and ensuring that decision-making is carried out by appropriately qualified employees may improve outcomes in domains where both clinical and business factors must be taken into account, such as the pharmaceutical industry. To achieve this, it is first necessary to understand the human capital contributed by each internal stakeholder employed by pharmaceutical companies. This study assessed the expertise of internal stakeholders in the pharmaceutical industry and showed that while MAPPs had significantly more total, undergraduate and postgraduate degree qualifications than all other internal stakeholders, non-MAPP stakeholder groups tended to be characterised by specific types of expertise. Of those with clinical expertise, MAPPs were twice as likely to have business expertise in the form of MBAs, making their training most likely to result in competencies that cover all domains necessary for pharmaceutical company success.\n\nMAPPs had significantly more total, undergraduate and postgraduate degree qualifications than all other internal stakeholders although the latter was at a higher significance level for MAcc, COmm and Sales professionals than for MAPharm and MAOth. There is little previous research comparing the number of qualifications of those in the pharmaceutical industry. However, the results were largely in line with previous findings suggesting that of those with an education in healthcare, physicians were by far most likely to seek out postgraduate study.33 The proportion of physicians with management training in this study (13.6%) also reflected earlier findings.34 The qualifications of physicians have not often been compared to those in non-clinical roles, except in the context of hospital leadership. About twice as many professionals in this study had undergraduate degrees and twice as many had master’s or PhD degrees as those in a previous study in a hospital context.35 This may reflect the comparatively greater need for specialist knowledge in the pharmaceutical industry.\n\nAdditionally, MAPPs took significantly longer than all other internal stakeholders apart from MAPharm to enter the pharmaceutical industry after the completion of their first degree. The obvious explanation for this is that MAPPs took longer because they spent more years in education and training. For this to be true, it would be expected that the pattern of differences in qualifications of internal stakeholders compared to MAPPs would reflect the pattern of differences in time to industry. However, all but MAOth and MAPharm had significantly fewer degree qualifications than MAPPs at a significance level of p < 0.001, whereas all but MAPharm had significantly less time to industry than MAPPs at a significance level of p < 0.001. The variation could be explained by the higher number of postgraduate diplomas and certificates completed by MAPPs and MAPharms, assuming they were full time courses. As specialist training in pharmaceutical medicine is in the format of postgraduate diplomas and certificates, the data suggests that while MAOth may accrue a higher number of years of experience in the pharmaceutical industry earlier in their careers, MAPPs may be spending this time developing domain-specific expertise applicable to the pharmaceutical industry in specialist training.\n\nA certain number of years of experience is a common entry requirement for job roles in pharmaceutical companies, especially those in leadership, which reflects the assumption that time spent working within a specific industry allows for the development of domain-specific skills and knowledge. This is in line with human capital theory, which suggests that number of years of experience is a measure of expertise.36 However, evidence suggests that it is not just the number of years of experience that matters but what those years are spent doing. For example, job tenure alone was unrelated to four domains of work performance36 and clinical skills,37,38 with talent alone37 and training alone38 explaining variation in expertise in clinical contexts. Clinical expertise only seems to be related to years of experience when there is access to the necessary learning experiences.39 Thus, there is a need to assess what constitutes valuable learning experiences within medical affairs practice to understand how expertise can best be developed through both experience and training. Additionally, the pharmaceutical industry may consider developing postgraduate on-the-job training programs to attract MAPPs and facilitate the match between training, expertise and role demands.\n\nDespite differences in time to industry, the difference in postgraduate degree qualifications between MAPPs and MPharm/MOth was at a lower significance level than that of other internal stakeholders, which suggested that MAPharm and MOth also held meaningful specialist expertise. In this study, MOth professionals were about twice as likely to have research expertise than MAPPs and MAPharms. This is to be expected, as entry requirements for medical leads, medical science liaisons and medical information specialists often include a PhD qualification. Of the three groups, MAPPs were about twice as likely to have business expertise at postgraduate level. Therefore, they were the most likely to have expertise that covers the domains necessary for pharmaceutical company success, followed by MAPharms. Additionally, physicians trained in both medicine and management may be better leaders,34,40 which supports the value of this type of dual expertise to the pharmaceutical industry.\n\nThe study did not collect data on the subject of internal stakeholders’ PhD qualifications, but it may be interesting to do so in further research to determine the value of these qualifications to role competencies as well as organisational and patient outcomes given the need for a scientific-medical approach in the pharmaceutical industry.41 While COmm and sales had fewest qualifications over the least number of domains, the skills most important for success for these groups may be measured differently, for example, as psychosocial skills,42 rather than as academic and clinical certifications. This may reflect the different nature of their expertise and role competencies. Additionally, training for some roles, such as medical information specialists and medical science liaisons may be appropriately matched to their specific role scope. In any case, it may be helpful to clarify and define role boundaries and organisational decision-making power within pharmaceutical companies to reflect the specific types of expertise of each internal stakeholder.\n\nIt is estimated that about 50% of the study population were likely to have profiles on Linkedin,43,44 so the sample could not be said to be fully representative. Despite this, our findings are sufficient to fulfil the aim of the study to evidence MAPP expertise in the context of expertise in the pharmaceutical industry. Further research using a wider range of recruitment strategies that examines in more detail the comparative qualitative aspects of pharmaceutical professionals’ education may be useful, especially with regards to scope and match to medical affairs competencies and impact on patient, research and organisational outcomes. Although many profiles, especially those of professionals in older age groups, were excluded on the basis of missing data, this limitation is likely to have affected all professional groups similarly, mitigating its impact on findings. However, there has been a general trend towards younger professionals having a greater number of degrees in recent years,45 so the total number of degrees in all groups may be overestimated given the potential skew towards lower ages in this sample. While self-reported education and experience on Linkedin is generally more accurate than other forms of self-report in this context,46 it is possible that profiles were not up-to-date, and the attainment of a degree qualification does not necessarily denote quality scholarship or the amount of time spent studying.\n\n\nConclusions\n\nOf all internal stakeholders, MAPPs had the highest number of qualifications and the longest time to industry as well as the best match between expertise and the contextual demands of decision-makers in the pharmaceutical industry. Pharmaceutical companies can use these findings to clarify role boundaries and decision-making power based on the nature and level of expertise of each internal stakeholder. These findings have provided some explanation for MAPPs’ unique value by suggesting that their educational background is a significant factor distinguishing them from other internal stakeholders. Further study is needed to understand how this education and training may develop expertise that accounts for their unique value, that is, how competencies developed during education and training may be relevant to their work with all external stakeholders. Understanding what constitutes useful learning experiences for developing expertise in medical affairs may be beneficial and could facilitate the development of specialised on-the-job training programs to ensure a match between training, expertise and role demands.\n\n\nEthical approval\n\nThis study was exempt from requiring ethical approval under the King’s College of London research ethics guidelines, as no human participants were recruited and unidentifiable human data were collected for this study.\n\n\nData availability\n\nThe underlying data to this research 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. Any queries about the methodology should be directed to the corresponding author.\n\n\nAuthor contributions\n\nRJ conducted the study and developed and approved the manuscript. The author affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted, and any discrepancies from the study as planned (and, if relevant, registered) have been explained.",
"appendix": "Acknowledgements\n\nThe author wishes to thank Medialis staff for their support in running the study, analysing the data and writing the manuscript.\n\n\nReferences\n\nMorris T, Brostoff JM, Stonier PD, et al.: Evolution of Ethical Principles in the Practice of Pharmaceutical Medicine From a UK Perspective. Front. Pharmacol. 2020; 10: 1525. PubMed Abstract | Publisher Full Text\n\nLiberati EG, Gorli M, Scaratti G: Invisible walls within multidisciplinary teams: Disciplinary boundaries and their effects on integrated care. Soc. Sci. Med. 2016; 150: 31–39. PubMed Abstract | Publisher Full Text\n\nBelrhiti Z, Van Belle S, Criel B: How medical dominance and interprofessional conflicts undermine patient-centred care in hospitals: historical analysis and multiple embedded case study in Morocco. BMJ Glob. Health. 2021; 6(7): e006140. PubMed Abstract | Publisher Full Text\n\nSetia S, et al.: Evolving role of pharmaceutical physicians in medical evidence and education. Adv. Med. Educ. Pract. 2018; 9: 777–790. PubMed Abstract | Publisher Full Text\n\nU.S. Food & Drug Administration: The Drug Development Process.2018 [cited 2021 25-03].\n\nBritish Medical Association: The pharmaceutical physician.2013 [cited 2021 25-03].\n\nKhosla S, et al.: Real world evidence (RWE)–a disruptive innovation or the quiet evolution of medical evidence generation? F1000Res. 2018; 7(111): 1–14.\n\nGrol R: Successes and failures in the implementation of evidence-based guidelines for clinical practice. Med. Care. 2001; 39(8 Suppl 2): II–54. Publisher Full Text\n\nCochrane LJ, Olson CA, Murray S, et al.: Gaps between knowing and doing: understanding and assessing the barriers to optimal health care. J. Contin. Educ. Heal. Prof. 2007; 27(2): 94–102. PubMed Abstract | Publisher Full Text\n\nBuchan H: Gaps between best evidence and practice: causes for concern. Med. J. Aust. 2004; 180(6 Suppl): 48. Publisher Full Text\n\nSetia S, Subramaniam K, Tay JC, et al.: Hypertension and blood pressure variability management practices among physicians in Sin-gapore. Vasc. Health Risk Manag. 2017; 13: 275–285. PubMed Abstract | Publisher Full Text\n\nSetia S, Subramaniam K, Teo BW, et al.: Ambulatory and home blood pressure monitoring: gaps between clinical guidelines and clinical practice in Singapore. Int. J. Gen. Med. 2017; 10: 189–197. PubMed Abstract | Publisher Full Text\n\nSetia S, Fung SS, Waters DD: Doctors’ knowledge, attitudes, and compliance with 2013 ACC/AHA guidelines for prevention of ath-erosclerotic cardiovascular disease in Singapore. Vasc. Health Risk Manag. 2015; 11: 303–310. PubMed Abstract | Publisher Full Text\n\nSaslow D, Solomon D, Lawson HW, et al.: American Cancer Society, American Society for Colposcopy and Cervical Pathology, and American Society for Clinical Pathology screening guidelines for the prevention and early detection of cervical cancer. CA Cancer J. Clin. 2012; 62(3): 147–172. PubMed Abstract | Publisher Full Text\n\nKomajda M, Lapuerta P, Hermans N, et al.: Adherence to guidelines is a predictor of outcome in chronic heart failure: the MAHLER survey. Eur. Heart J. 2005; 26(16): 1653–1659. PubMed Abstract | Publisher Full Text\n\nMccullough ML, Patel AV, Kushi LH, et al.: Following cancer prevention guidelines reduces risk of cancer, cardiovascular disease, and all-cause mortality. Cancer Epidemiol. Biomark. Prev. 2011; 20(6): 1089–1097. PubMed Abstract | Publisher Full Text\n\nGreen BN, Johnson CD: Interprofessional collaboration in research, education, and clinical practice: working together for a better future. J. Chiropr. Educ. 2015; 29(1): 1–10. PubMed Abstract | Publisher Full Text\n\nJandhyala R: Influence of Pharmaceutical Company Engagement Activities on the Decision to Prescribe: A Pilot Survey of UK Rare Disease Medicine Prescribers. Pharmaceut. Med. 2020; 34(2): 127–134. PubMed Abstract | Publisher Full Text\n\nSweiti H, et al.: Physicians in the pharmaceutical industry: their roles, motivations, and perspectives. Drug Discov. Today. 2019; 24(9): 1865–1870. PubMed Abstract | Publisher Full Text\n\nJackson SHD, Mangoni AA, Batty GM: Optimization of drug prescribing. Bri. J. Clin. Pharmacol. 2004; 57(3): 231–236.\n\nJandhyala R: Development and Validation of the Medical Affairs Pharmaceutical Physician Value (MAPPval) Instrument. Pharm. Med. January 7, 2022. Publisher Full Text\n\nSilva H, Stonier P, Buhler F, et al.: Core competencies for pharmaceutical physicians and drug development scientists. Front. Pharmacol. 2013; 4. Accessed February 9, 2022. PubMed Abstract | Publisher Full Text\n\nJandhyala R: Development of a Definition for Medical Affairs Using the Jandhyala Method for Observing Consensus Opinion Among Medical Affairs Pharmaceutical Physicians. Front. Pharmacol. 2022; 13. Accessed February 23, 2022. PubMed Abstract | Publisher Full Text\n\nJandhyala R: A medicine adoption model for assessing the expected effects of additional real-world evidence (RWE) at product launch. Curr. Med. Res. Opin. 2021; 37(9): 1645–1655. PubMed Abstract | Publisher Full Text\n\nImamura K, Criscuolo D, Jurczynska A, et al.: International Perception of Competence, Education, and Training Needs Among Biomedical Professionals Involved in Medicines Development. Front. Pharmacol. 2019; 10: 188. PubMed Abstract | Publisher Full Text\n\nGonzalez J, Bryant S, Hogan M, et al.: Comparison of Postdoctoral Pharmacy Training Programs: Drug Information Residencies and Medical Information Fellowships. Ther. Innov. Regul. Sci. 2019; 53(4): 446–454. PubMed Abstract | Publisher Full Text\n\nNguyen C: The role of a pharmacist as a medical information specialist in the pharmaceutical industry. Curr. Pharm. Teach. Learn. 2020; 12(2): 127–131. PubMed Abstract | Publisher Full Text\n\nTheron P, Britland M, Holder D, et al.: Promoting Best Practices for Medical Science Liaisons Position Statement from the APPA, IFAPP, MAPS and MSLS. Ther. Innov. Regul. Sci. 2021; 55(6): 1139–1144. PubMed Abstract | Publisher Full Text\n\nMedical Science Liaison Society: Medical Science Liaison Guidelines.2018. Accessed January 13, 2022.Reference Source\n\nCubrich M, King RT, Mracek D, et al.: Examining the criterion-related validity evidence of LinkedIn profile elements in an applied sample. Comput. Hum. Behav. 2021; 38. Publisher Full Text\n\nGuillory J, Hancock JT: The Effect of Linkedin on Deception in Resumes. Cyberpsychol. Behav. Soc. Netw. 2012; 15(3): 135–140. PubMed Abstract | Publisher Full Text\n\nAguado D, Andrés JC, García-Izquierdo AL, et al.: LinkedIn “big four”: Job performance validation in the ICT sector. J. Work Organ. Psychol. 2019; 35: 53–64. Publisher Full Text\n\nSethi A, Schofield S, McAleer S, et al.: The influence of postgraduate qualifications on educational identity formation of healthcare professionals. Adv. Health Sci. Educ. 2018; 23(3): 567–585. PubMed Abstract | Publisher Full Text\n\nXirasagar S, Samuels ME, Curtin TF: Management training of physician executives, their leadership style, and care management performance: an empirical study. Am. J. Manag. Care. 2006; 12(2): 101–108. PubMed Abstract\n\nChen KC, Hsieh FC, Hsiao YJ: Hospital Board of Directors’ Composition and Financial Performance: Empirical Evidence from Taiwan. Inquiry. 2021; 58: 004695802110248. PubMed Abstract | Publisher Full Text\n\nNg TWH, Feldman DC: Does longer job tenure help or hinder job performance? J. Vocat. Behav. 2013; 83(3): 305–314. Publisher Full Text\n\nLiu Z, Zhang Z, Kunkel D, et al.: Is Experience in Hemodialysis Cannulation Related to Expertise? A Metrics-based Investigation for Skills Assessment. Ann. Biomed. Eng. 2021; 49(7): 1688–1700. PubMed Abstract | Publisher Full Text\n\nGreen W, Shahzad MW, Wood S, et al.: Improving junior doctor medicine prescribing and patient safety: An intervention using personalised, structured, video-enhanced feedback and deliberate practice. Br. J. Clin. Pharmacol. 2020; 86(11): 2234–2246. PubMed Abstract | Publisher Full Text\n\nCarrigan AJ, Magnussen J, Georgiou A, et al.: Differentiating Experience From Cue Utilization in Radiological Assessments. Hum. Factors. 2021; 63(4): 635–646. PubMed Abstract | Publisher Full Text\n\nXirasagar S, Samuels ME, Stoskopf CH: Physician leadership styles and effectiveness: an empirical study. Med. Care Res. Rev. 2005; 62(6): 720–740. PubMed Abstract | Publisher Full Text\n\nSilva H, Kerpel-Fronius S, Stonier PD, et al.: Grand Challenges in Pharmaceutical Medicine: Competencies and Ethics in Medicines Development. Frontiers Media SA;2021. Publisher Full Text\n\nKakeesh DF, Al-Weshah GA, Dababneh RB: Leveraging market share through selling skills: the mediating role of adaptive selling behaviour. Int. J. Bus. Perform. Manag. 2021; 22(4): 363–379. Publisher Full Text\n\nWoitowich NC, Arora VM, Pendergrast T, et al.: Gender Differences in Physician Use of Social Media for Professional Advancement. JAMA Netw. Open. 2021; 4(5): e219834. PubMed Abstract | Publisher Full Text\n\nAuxier B, Anderson M: Social media use in 2021. Pew Research Center;2021.\n\nPeter TL, Mandler.: The Crisis of the Meritocracy: Britain’s Transition to Mass Education since the Second World War. Oxford:Oxford University Press;2020.\n\nGuillory J, Hancock JT: The Effect of Linkedin on Deception in Resumes. Cyberpsychol. Behav. Soc. Netw. 2012; 15(3): 135–140. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "148656",
"date": "12 Sep 2022",
"name": "Jonathan Day",
"expertise": [
"Reviewer Expertise Clinical Development Physician working in Rare Disease Drug development (Skeletal Dysplasia",
"Gene Therapy",
"Bleeding Disorders",
"Thrombosis and Inflammation). Original background in cardiovascular 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\nThe author analyzed professional qualifications (using a well-known professional social media platform) across different types of employees (Medical Affairs Physicians, Market Access, Commercial, Sales) at pharmaceutical companies across the UK and reports on the significant variation in the number and type of qualifications as well as time taken in education prior to joining the pharmaceutical industry. Those working in Medical Affairs positions tended to have spent more time in education and therefore had a larger number of undergraduate and postgraduate qualifications, including business qualifications (MBA). The author concludes that those with greater levels of education, more qualifications and more relevant experience might be better placed to make decisions that impact clinical as well as business factors across the pharmaceutical industry.\n\nSuggestions:\nFigure 1 is not very high resolution (at least in the PDF I have access to) and is therefore difficult to interpret easily. A higher resolution Figure or one with larger font size would be helpful.\nThe Discussion does address some of the limitations of this study. The link between qualifications and business impact is somewhat subjective and could do with some statements to this effect. For instance, Medical Affairs professionals might spend more time in education prior to joining the Industry but those who join other functions (such as commercial and sales) will arguably develop other highly relevant skills and experience through their work experience. These competencies would not be captured in the current analysis. Different entry level qualifications at the time of starting a job in the Industry will also likely inform on an employee’s seniority level (and thus decision maker influence) within the organization. Additionally, beyond seniority and qualifications many other competencies will inform on an individual’s degree of influence and success as a decision maker. Attainment of these attributes is not a unique challenge in the pharmaceutical industry and something likely relevant to all sectors.\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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8948",
"date": "07 Nov 2022",
"name": "Ravi Jandhyala",
"role": "Author Response",
"response": "Firstly, we would like to take this time to thank the reviewer for their efforts and positive review. A detailed response to the reviewer comments is provided below. Comment: Figure 1 is not very high resolution (at least in the PDF I have access to) and is therefore difficult to interpret easily. A higher resolution Figure or one with larger font size would be helpful. Answer: Thank you for bringing this to our attention. We have revised the image and submitted a higher resolution and more detailed copy alongside this revised manuscript. Comment: Medical Affairs professionals might spend more time in education prior to joining the Industry but those who join other functions (such as commercial and sales) will arguably develop other highly relevant skills and experience through their work experience. These competencies would not be captured in the current analysis. Different entry level qualifications at the time of starting a job in the Industry will also likely inform on an employee’s seniority level (and thus decision maker influence) within the organization. Additionally, beyond seniority and qualifications many other competencies will inform on an individual’s degree of influence and success as a decision maker. Attainment of these attributes is not a unique challenge in the pharmaceutical industry and something likely relevant to all sectors. Answer: Thank you for the excellent suggestion. We have revised the discussion to address the concerns raised and have included further insights into the qualification and experience attained by MAPPs."
}
]
},
{
"id": "145143",
"date": "26 Oct 2022",
"name": "Domenico Criscuolo",
"expertise": [
"Reviewer Expertise I have 47 years’ experience in drug development",
"with a special focus on Medical Affairs"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nVery interesting paper, underlining the importance of high level qualifications for physicians working in the Medical Affairs department of the pharmaceutical industry.\nThe author made a careful search via LinkedIn of profiles of professionals in the pharmaceutical industry, and finally selected 524 profiles with full educational details.\nThe analysis of these data demonstrate that physicians are the professional group with higher postgraduate education, and this finding is relevant for the role Medical Affairs physicians must cover.\nThe manuscript is well written, has a few tables and several references and does not need any revision.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8942",
"date": "26 Oct 2022",
"name": "Ravi Jandhyala",
"role": "Author Response",
"response": "Dear Domenico Criscuolo, Thank you for the outstanding and positive review of this manuscript. Best wishes, Ravi"
}
]
}
] | 1
|
https://f1000research.com/articles/11-813
|
https://f1000research.com/articles/11-790/v1
|
13 Jul 22
|
{
"type": "Research Article",
"title": "Effects of concomitant benzodiazepines and antidepressants long-term use on perspective-taking",
"authors": [
"Ana R. Gonçalves",
"Márcia Soares",
"Helena Garcez",
"Carina Fernandes",
"Mariana R. Pereira",
"Celeste Silveira",
"João Marques-Teixeira",
"Fernando Barbosa",
"Márcia Soares",
"Helena Garcez",
"Carina Fernandes",
"Mariana R. Pereira",
"Celeste Silveira",
"João Marques-Teixeira",
"Fernando Barbosa"
],
"abstract": "Background: Benzodiazepines and antidepressants are known to alter responses to empathic pain when used alone, however the effects of their combined use on empathy are unknown. In order to examine the effects of concomitant benzodiazepines and antidepressants long-term use on perspective-taking, we analyzed behavioral and neural changes on perspective-taking ability using event-related potentials. Methods: To this purpose, 13 long-term concomitant benzodiazepines and antidepressants users and 13 healthy controls performed a task designed to assess affective perspective-taking with simultaneous EEG recording. Results: The behavioral results revealed similar performance between groups. The neural results showed no significant differences between groups for the N170 and late positive potential (LPP) components. These results seem to suggest that long-term use of benzodiazepines and antidepressants together does not affect perspective-taking abilities nor the processing of related information. Conclusions: The concomitant benzodiazepines and antidepressants long-term use seem to preserve the perspective-taking ability of social cognition.",
"keywords": [
"Empathy",
"ERP",
"performance",
"psychotropic medication",
"social cognition"
],
"content": "Introduction\n\nEmpathy is involved in several aspects of social cognition. It has been proposed to notably contribute to prosocial behavior1,2 and to regulate aggression.3 Empathy is defined as the ability to experience and understand the feelings of another person, while also understanding the origin of the feelings, that is, whose belong to whom.4 Previous research based on psychometric data has defined different facets of empathy: empathic concern, personal distress, perspective-taking and fantasy.5,6\n\nPerspective-taking enables us to make inferences, understand and foresee other’s mental and emotional states – an ability known as Theory of Mind7 as well as to have empathic ability. The ability to take the perspective of another person is known as emotional perspective-taking and is determinant for the success of social interactions.8\n\nThe use of benzodiazepines has been reported to facilitate aggressive9 and violent behavior,10,11 leading to suspicion of their inhibitory effects on empathic responses. Bearing this in mind, Nilsonne and colleagues12 investigated the effects of oxazepam on emotional mimicry and empathic responding. Using an experiment on empathy for pain, the authors found that oxazepam did not inhibit empathic responses to others’ pain.12 Benzodiazepines are often added to antidepressants in initial depression treatment but previous research showed that the simultaneous use is long term.13 Nonetheless, a previous study suggested that antidepressant treatment reduces behavioral and neural responses to pain empathy14 and may have a cumulative effect to that caused by the use of benzodiazepines.\n\nTo our knowledge, these are the only studies examining the effects of benzodiazepines and antidepressants, when used alone, on empathy. Furthermore, there is no information on the neural temporal dynamics of empathy processes under the use of such medication. The current study examines the effects of concomitant benzodiazepines and antidepressants long-term use on perspective-taking using event-related potentials (ERPs). To this purpose, we used a task previously adapted by our group15 in which scenarios presenting two persons engaged in social interactions, depicting emotional and neutral scenes, are shown to participants. In each scenario, one person has the face masked. In the next display, a target facial expression of emotion (FEE) is presented and participants are asked to judge whether this FEE is congruent or not with the emotion expected to be portrayed by the masked person. Thus, in each scenario, participants must infer the affective mental state of the masked intervener. Then, to an accurate decision, participants also have to compare the inferred emotion to the emotion presented in the target FEE, and decide wether they were congruent or incongruent. Using this experimental manipulation, we will be able to investigate perspective-taking abilities through the behavioral performance and, with simultaneous EEG recording, to assess how these abilities modulate two ERP components - the N170 and the late positive potential (LPP). These components are known to be typically influenced by the affective and evaluative congruency.\n\nThe N170 is a negative deflection usually peaking at ~170 ms post-stimulus in occipito-temporal sites. This component seems to reflect the earliest stage of facial structure encoding16 and is sensitive to the emotional content of a face.17,18 Concerning the influence of context, higher N170 amplitudes are usually recorded in congruent trials when pictures are used as contextual stimuli.19–22\n\nThe LPP is a positive deflection usually peaking at 300-700 ms after the stimulus onset in centro-parietal sites.23 This component represents facilitated attention to emotional stimuli and has larger amplitudes after emotionally arousing pictures in comparison to neutral ones.24 In the present study, the congruency between a prime and a target is manipulated, and previous studies using a similar experimental manipulation, reported that LPP indexes the processing of affective or evaluative congruency, and exhibits larger amplitudes to incongruent targets compared to congruent ones.24 Furthermore, cognitive appraisal and motivated attention,25 as well as morally good actions26 and helping scenes27 also modulate the LPP component.\n\nThe research on this field is essential considering that benzodiazepines and antidepressants are the most prescribed drugs in the world28,29 despite their unwanted effects (e.g., psychomotor, and cognitive impairments; see Ref. 30). Benzodiazepines act at the limbic system, including at the thalamic and hypothalamic levels of the central nervous system31 through GABAA receptors.32 Antidepressants were shown to increase the activation of dorsolateral, dorsomedial and ventrolateral prefrontal cortices and to decrease the activation of the amygdala, hippocampus, parahippocampal region, ventral anterior cingulate cortex, orbitofrontal cortex, and insula.33 Since some of these structures are involved in perspective-taking processes,34 we may expect impaired performance of long-term concomitant benzodiazepines and antidepressants users on our perspective-taking task. Regarding electrophysiological results, as we expected a decreased perspective-taking ability in the group of long-term concomitant benzodiazepines and antidepressants users, we anticipated that N170 and LPP modulations would be absent in this group. Additionally, neurocognitive measures were collected to explore whether performance on the perspective-taking task is related to cognitive performance.\n\n\nMethods\n\nA total of 60 participants were recruited from the community and local University to two groups: a long-term concomitant benzodiazepines and antidepressants users group (experimental) and a control group, matched on age and years of formal education. The experimental group consisted of subjects who had a minimum period of concomitant benzodiazepines and antidepressants use of one year. We excluded participants with scores inferior to 22 (cutoff for mild cognitive impairment35) in the Montreal Cognitive Assessment (MoCA36; n = 1), as well as participants who reported uncorrected visual impairments (n = 1), history of brain injury and neurological diagnosis (n = 2). Participants reporting use of psychotropic medication besides benzodiazepines and antidepressants (n = 4), and psychiatric diagnosis aside from anxiety and depression (except severe conditions rendering study participation impossible) were also excluded from the experimental group. We also excluded participants from the control group if they reported use of psychotropic medication (n = 13) and psychiatric diagnosis (n = 4). Additionally, 9 participants dropped out the study at the end of the neuropsychological assessment. Thus, the final sample was composed of 13 experimental subjects (all female; Mage = 44.1, SD = 10.0; Myears of education = 15.9, SD = 2.4) and 13 control subjects (12 female; Mage = 46.5, SD = 10.9; Myears of education = 16.9, SD = 4.9). They each gave written, informed consent and received EUR 20 (gift card). The study was approved by the local Ethics Committee.\n\nSelf-report measures\n\nAnxiety and depression traits were measured by the Hospital Anxiety and Depression Scale (HADS37; Portuguese version by Pais-Ribeiro et al.38), and psychopathological symptomatology by the Brief Symptom Inventory (BSI39; Portuguese version by Canavarro40).\n\nNeuropsychological measures\n\nExecutive functioning was assessed using the Trail Making Test (TMT41; normative data by Cavaco et al.42), and the INECO Frontal Screening (IFS43; Portuguese version by Moreira et al.44). Semantic fluency and phonemic fluency tests were used to assess non-motor processing speed, language production and executive functions (see Ref. 45; Portuguese versions by Cavaco et al.46). Short-term memory was assessed by the Corsi Block-Tapping Task (CBTT47).\n\nEmotional perspective-taking task\n\nThis task was adapted from a previous fMRI study that assessed perspective-taking8 as described in our prior work15 examining perspective-taking ability during an ERP experiment. Succinctly, the protocol used by Derntl et al.8 was adapted according to experimental designs of previous studies addressing contextual congruency.19–23,48,49 Contextual congruency implies the matching between a target facial expression of emotion (FEE) and the emotion portrayed by a masked face in a previous scenario.15 Thus, participants had to recall perspective-taking abilities to accurately judge the contextual congruency: they had to see the scenario and examine it from another’s perspective, and then judge whether a FEE shown next was congruent or not with the emotion expected to be portrayed by the masked person.\n\nTo this purpose, participants viewed 360 pictures representing scenes of two persons engaged in social interactions. Each scenario presented one of the actors’ faces masked, and participants were instructed to infer the respective emotional expression. The scenarios depicted emotional (anger, fear, disgust, sadness, happiness) and neutral scenes and all actors were adult Caucasians. After the scenario display, a target FEE was presented, and participants were asked to judge it as congruent or incongruent with the inferred FEE of the masked person. Next, an unlimited duration screen with the response options was presented until key press. During this screen, participants used two response buttons held in the right and left hand. Participants were asked to respond only during this response screen, to prevent overlap of preparatory response potentials with the ERP components of interest. The structure of each trial is depicted in Figure 1.\n\nAs the original set of stimuli,8 ten scenarios for each emotional condition were included, with six repetitions for each one. For congruent conditions, the FEE was randomly selected from all alternative actors with the congruent emotion; the incongruent conditions included FEE selected from all the incongruent alternatives. This results in 30 congruent trials and 30 incongruent trials for each emotional condition. The FEE was selected from the NimStim Face Stimulus Set,50 picking the five most accurately identified facial expressions for each emotional category (see Ref. 50) which led to 30 female and 30 male facial stimuli. Participants viewed the images on a 17-in. screen from a distance of 115 cm, with 6.67° × 8.55° visual angle, and a refresh rate of 60 Hz. E-Prime 2.0 (Psychology Software Tools, Inc., Sharpsburg, PA, USA) was used to control the experiment and collect responses. After a block of six practice trials, participants completed two experimental blocks of 180 trials each, with a pause between them.\n\nAll participants were tested individually in two experimental sessions to avoid fatigue effects. In the first session, a semi-structured interview and the MoCA were conducted to assess inclusion criteria. The remaining neuropsychological tests and self-report measures were then administered in a random order between participants. Participants meeting the inclusion criteria were invited to participate on a second session, in which the emotional perspective-taking task was performed simultaneously to EEG recording. This second session was part of a larger research protocol, demanding all experimental tasks to be performed in random order. After the placement of the EEG cap, participants read the instructions and completed a practice block.\n\nThe eletroencephalographic (EEG) data were recorded on the acquisition software V4.5.2 (2008, Electrical Geodesics Inc., Eugene, OR, USA – EGI) using a 128-electrode Hydrocel Geodesic Sensor Net, connected to a Net Amps 300 amplifier (EGI). Impedances were kept below 50 kOhm for all electrodes since this is a high-input impedance system. Data were recorded with a sampling rate of 500 Hz, filtered with a notch filter of 50 Hz and the electrodes were referenced to the vertex (Cz).\n\nThe EEG raw data were pre-processed in the EEGLAB version 13,51 a MATLAB toolbox (2017, The Math-works Inc., Natick, MA, USA). Continuous EEG signal was downsampled to 250 Hz, bandpass filtered (0.2−30 Hz), and submitted to an Independent Components Analysis (ICA) decomposition. Eyeblinks, saccades, and cardiac activity artifacts were corrected, by subtracting the corresponding Independent Component activity from the data, followed by visual inspection to ensure the correction did not alter the signals outside the time windows of the artifacts. Channels with artifacts were interpolated (up to a maximum of 10% of the sensors) using the spherical spline interpolation method.52 The EEG signal was re-referenced to the average of all electrodes. EEG records were segmented into epochs (-200 to 800 ms) time-locked to the onset of the target FEE and visually inspected for manual artifact rejection. Trials in which participants gave incorrect responses were also excluded. All epochs were baseline corrected (200 ms pre-stimulus) and averaged by congruency (congruent, incongruent) and emotion (anger, fear, disgust, sadness, happiness, neutral).\n\nAccording to previous studies, and visual inspection of ERP grand-average and topographical maps, three time windows and three regions of interest (ROIs)2 were chosen for statistical analysis. The higher amplitude of the N170 component is exhibited bilaterally at occipitotemporal regions, precisely at P7/P8 and PO7/PO8, being more marked at the inferior locations as P9/P10 and PO9/P10 (Rossion and Jacques 2008). A negative maximum over these regions was recorded in our topographical maps, leading us to set a ROI containing these and a cluster of surrounding electrodes, to increase the signal-to-noise ratio.53,54 Accordingly, the peak amplitudes for the N170 were extracted in the [140, 240] ms time window after FEE onset, at right (electrodes 83, 84, 89, 90 [PO8], 91, 95 [P10], 96 [P8]) and left (70, 66, 69, 65 [PO7], 64 [P9], 58 [P7], 59) ROIs. Regarding the LPP component, other studies reported that its higher amplitude occurs over centro-parietal sites such as CPz and Pz.23 Our topographical maps are in accordance with this result, so we extracted the mean LPP amplitudes at the centro-parietal ROI (54, 55 [CPz], 61, 62 [Pz], 78, 79). The time window of this component was divided into an early (LPPe; 300–500 ms after FEE onset) and a late component (LPPl; 500–700 ms after FEE onset) given its temporally broad distribution (e.g., Ref. 48).\n\nStudent’s t-tests were used to analyze group differences in neuropsychological performance and self-report measures. Whenever necessary, non-parametric tests were performed. Perspective-taking results were obtained from accuracy rates (percentage of correct responses in relation to the total number of trials) calculated by participant and condition. The effects of emotion, congruency, and group on perspective-taking results were analyzed in a mixed ANOVA. The group (experimental, control) was used as between-participants factor, whereas emotion (anger, fear, disgust, sadness, happiness, neutral) and congruency (congruent, incongruent) were used as within-participants factors. The same analysis was performed for reaction times.\n\nThe electrophysiological data were analyzed by mixed factors ANOVAs with group as between-participants factor, and emotion and congruency as within-participant factors. For N170, the hemisphere (left, right) was also used as within-participant factor.\n\nTo test the influence of cognitive abilities in behavioral performance and ERPs modulation, a Linear Regression Model was computed for each group. Scores of cognitive tests (raw scores) in which differences between groups were detected were entered as main predictors of behavioral measures and N170, and LPPs modulation (independent models). For N170, LPPe and LPPl modulation, the model was applied to each electrode or electrode cluster examined in the ERP data analysis.\n\nThe threshold for statistical significance was set at α = .05, and the p-values reported for t-tests are from one-tailed tests. Statistical analysis was performed using SPSS 24 (IBM Corp., Armonk, NY, USA). Violations of sphericity in ANOVA were corrected via the Greenhouse-Geisser method.\n\n\nResults\n\nNeuropsychological data analysis revealed no differences between groups in IFS, CBTT, TMT, PF, nor SF (all p > .313). However, significant group differences were observed on depression, t(24) = -3.735, p < .002, anxiety, t(24) = -3.156, p = .004, and psychopathological symptomatology, t(24) = -4.450, p < .001. Experimental subjects had higher scores in these self-report measures (see Table 1).\n\nAccuracy rates and reaction times are shown in Table 2. These were examined using mixed factors ANOVAs. The results showed that experimental and control subjects were equally accurate in their responses, F(1, 24) = 0.68, p = .417. However, a main effect of emotion, F(5, 120) = 28.2, p < .001, η2p = 0.541, ε = 1.000, revealed accuracy rates significantly higher following scenarios portraying happiness (all p < .001), sadness (all p < .033), and neutral scenes (all p < .027), without significant differences between the latter (p > .998). Scenarios portraying anger, disgust, and fear elicited similar accuracy rates (all p > .988). We also found a significant emotion x group interaction, F(5, 120) = 3.32, p = .008, η2p = .121, along with a significant emotion x congruency interaction, F(5, 120) = 9.31, p < .001, η2p = .280. No other significant interactions emerged (all F < 0.78, p > .387).\n\nRegarding reaction times, no significant differences were found between the groups F(1, 24) = 2.22, p = .149. Also, no main effects were found for emotion, F(5, 120) = 1.21, p = .309, or congruency, F(1, 24) = 0.91 p = .350, factors. The analysis also showed that none of the interactions – emotion x group, congruency x group, emotion x congruency, and emotion x congruency x group – was statistically significant for reaction times (all p > .150).\n\nThe Linear Regression analysis was significant for accuracy rates of scenarios portraying happiness in control subjects F(5, 7) = 10.9, p = .002. Anxiety (Adj R2 = .712, β = - .42, p = .035) and psychopathological symptomatology (Adj R2 = .712, β = - .53, p = .008) were main predictors of accuracy rates for happiness scenarios. For participants from the experimental group, the model was not significant (all p > .234).\n\nPeak amplitudes for N170 component are presented in Table 3 and mean amplitude for LPPs components are presented in Table 4.\n\nThe repeated measures ANOVA revealed no significant differences on the N170 amplitude between groups, F(1, 22) = 0.33, p = .571. A main effect of emotion emerged, F(5, 110) = 2.60, p = .029, η2p = .106, ε = .782, but the main effects of congruency and hemisphere were not significant (all F < 1.96). Pairwise comparisons revealed that faces portraying sadness elicited higher N170 amplitudes than faces portraying anger (p = .050) and neutral faces (p = .012). Additionally, the analysis showed that none of the interactions was statistically significant (all p > .150).\n\nFor the LPPe component, no significant differences were found on the mean amplitude between groups, F(1, 22) = 0.22, p = .647. A main effect of emotion was not found on the LPPe mean amplitude, F(5, 110) = 1.15, p = .338, but the main effect of congruency was significant F(1, 22) = 18.5, p < .001, η2p = .457, ε = .984. Additionally, a significant emotion x congruency interaction emerged, F(5, 110) = 4.32, p = .004, η2p = .164. Pairwise comparisons revealed that congruent conditions elicited higher LPPe amplitudes than incongruent conditions (p < .001) (Figure 2). No other significant interactions emerged (all F < 0.95, p > .435).\n\nSolid lines (blue) = congruent condition, broken lines (red) = incongruent condition.\n\nRegarding the LPPl, the pattern of results found was similar to the LPPe: no significant differences were found on the mean amplitude between groups, F(1, 22) = 1.80, p = .194; the main effect of emotion was not significant, F(5, 110) = 1.59, p = .168, but a main effect of congruency emerged, F(1, 22) = 12.5, p = .002, η2p = .363, ε = .923. The analysis also revealed a significant emotion x congruency interaction, F(5, 110) = 2.81, p = .038, η2p = .113. Pairwise comparisons revealed that congruent conditions elicited higher LPPe amplitudes than incongruent conditions (p = .002) (Figure 2). No other significant interactions emerged (all F < 1.92, p > .096).\n\nThe Linear Regression model was neither significant for N170 (all p > .089) nor LPPe (all p > .056) components in both groups. The model was significant for LPPl amplitudes in control subjects, F(5, 6) = 5.36, p = .026. Anxiety was a marginally main predictor of LPPl amplitudes for congruent conditions (Adj R2 = .543, β = -.504, p = .054). For experimental subjects, the model was not significant (all p > .680).\n\n\nDiscussion\n\nIn the present study, concomitant benzodiazepines and antidepressants users and control subjects were presented with scenarios presenting two persons (one person with the face masked) engaged in social interactions, depicting emotional and neutral scenes, and asked to judge whether a FEE shown next was congruent or not with the emotion expected to be portrayed by the masked person.\n\nOur results did not reveal group differences in perspective-taking ability, contrary to what we expected. Nonetheless, these results are consistent with the neural responses, revealing no differences in the processing of perspective-taking information as we will discuss later. The only studies12,14 examining the effects of benzodiazepines and antidepressants on empathy did it for each class of drug isolated, using an experiment on empathy for pain. One study examined the effect of one single administration of oxazepam on empathy for pain and showed that empathic responses to other’s pain were not inhibited.12 Another study examined the effect of a three months antidepressant therapy on the responses to an empathy for pain task, in patients with major depressive disorder.14 The results suggested that antidepressant treatment reduces behavioral and neural responses to pain empathy.14 Bearing im mind that the ability of identifying FEE is required in the present task, we should mention the results of a previous meta-analysis by our group.55 The meta-analysis examining how benzodiazepines administration affects the identification of FEE showed that participants receiving benzodiazepines were less accurate at identifying FEE of anger compared with those receiving placebo.55 The identification of the remaining facial expressions (disgust, sadness, fear, surprise, and happiness) appears to be unaffected by benzodiazepines administration. However, these studies are methodologically far from our study which makes any comparison of the results impossible.\n\nA main effect of emotion emerged consistent with the results of a previous study conducted by our group15: greater accuracies were reported for scenarios portraying happiness, sadness, and neutral scenes. Similar to the identification of happy faces,56–58 happiness scenarios seem to be recognized more accurately than any other scenarios.\n\nThe current sample of concomitant benzodiazepines and antidepressants users scored higher in self-report measures of anxiety, depression, and psychopathological symptomatology. Anxiety and psychopathological symptomatology predicted accuracy rates for happiness scenarios in control subjects. This result was unexpected since it was not found in our previous study.15\n\nRegarding electrophysiological data, we did not find significant differences between groups in the N170 component, but a main effect of emotion emerged similar to the pattern found in behavioral data. Furthermore, previous studies found a N170 modulated by emotion59,60 providing evidence that early face processing can reflect processing of the emotional expression. In accordance with our previous study,15 this component was not modulated by the congruency between the emotional contexts and the target’s FEE. As noted by the authors,15 this was unexpected since previous studies using pictures as contexts reported a systematically higher N170 in congruent trials.19–22 However, a congruency modulation in N170 was previously not found in studies using verbal instead of visual stimuli.48,49\n\nConsistent with our previous work,15 the results obtained in the LPPs were similar in the early and late time-windows, revealing higher amplitudes in congruent than in incongruent trials. This pattern is opposite to the one reported by previous studies using context-target congruency tasks, i.e., larger LPPs after incongruent FEE.48,61 However, while higher LPP amplitudes elicited by incongruent trials were reported in tasks requiring an evaluative congruity between primes and facial23,62 or verbal targets,63 our task required attending the scenes, inferring the mental state of the masked interveners, and deciding if the FEE displayed after the scene matched the one previously inferred. The recognition of the masked person’s emotion in the stimuli displayed by the target FEE may explain the increased amplitudes to congruent stimuli since the LPP is also modulated by the explicit recognition of stimuli, exhibiting larger amplitudes in response to recognized stimuli vs. new.64,65\n\nNoteworthy, there are several factors related to the combined use of psychotropic medication that may influence the perspective-taking ability, namely the type of antidepressants (tricyclic antidepressants (TCAs), selective serotonin reuptake inhibitors (SSRIs), serotonin-noradrenaline reuptake inhibitors, noradrenergic and specific serotonergic antidepressants, monoamine oxidase inhibitors, and other antidepressants) and benzodiazepines (short-acting or long-acting), the dose of each drug, and the percentage of days of concomitant drug use. However, we were not able to test these variables as potential moderators of any concomitant drug use effects observed, due to the small sample of the present study. The literature in the present field is still very limited and multi-center studies pursuing the influence that long-term use of benzodiazepines and antidepressants may have on social cognition, including perspective-taking ability, are needed.\n\nContrary to our hypothesis, the modulation of N170 and LPPs components was present in the group of concomitant benzodiazepines and antidepressants users. Overall, the results seem to indicate that long-term use of these psychotropic substances together do not affect perspective taking abilities and neither the processing of related information. Although the evidences of deficits in several general cognitive abilities in long-term benzodiazepine users,31,66 the combined use of benzodiazepines and antidepressants on long-term seem to preserve at least the perspective-taking ability of social cognition. Nevertheless, the lack of previous studies with a similar sample, makes any interpretation difficult to support. We hope, however, to have brought important evidence to light, which may help future research on social cognition under the influence of benzodiazepines and antidepressants.\n\n\nData availability\n\nDANS: Psychotropic long-term use and perspective taking: behavioral and neural dataset, https://doi.org/10.17026/dans-xjs-kje4.\n\nThis project contains the following underlying data:\n\n- Accuracy.xlsx\n\n- LPPe_Congruent.xlsx\n\n- LPPe_Incongruant.xlsx\n\n- LPPI_Congruent.xlsx\n\n- LPPI_Incongruent.xlsx\n\n- N170_Congruent.xlsx\n\n- N170_Incongruent.xlsx\n\n- Reaction_times.xlsx\n\n- Sociodemographic_neuropsychological.xlsx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nSinger T, Seymour B, O’Doherty JP, et al.: Empathic neural responses are modulated by the perceived fairness of others. Nature. 2006; 439: 466–469. PubMed Abstract | Publisher Full Text\n\nHein G, Lamm C, Brodbeck C, et al.: Skin conductance response to the pain of others predicts later costly helping. PLoS One. 2011; 6: e22759. PubMed Abstract | Publisher Full Text\n\nEisenberg N: Age changes in prosocial responding and moral reasoning in adolescence and early adulthood. J. Res. Adolesc. 2005; 153(3): 235–260.\n\nSprecher S, Fehr B: Compassionate love for close others and humanity. J. Soc. Pers. Relat. 2005; 22(5): 629–651. Publisher Full Text\n\nDavis M: A multidimensional approach to individual differences in empathy. JSAS Catalog. Select. Doc. Psychol. 1980; 10: 85.\n\nDavis M: Measuring individual differences in empathy: evidence for a multidimensional approach. J. Pers. Soc. Psychol. 1983; 44: 113–126. Publisher Full Text\n\nDecety J, Jackson PL: The functional architecture of human empathy. Behav. Cogn. Neurosci. Rev. 2004; 3(2): 71–100. PubMed Abstract | Publisher Full Text\n\nDerntl B, Finkelmeyer A, Toygar TK, et al.: Generalized deficit in all core components of empathy in schizophrenia. Schizophr. Res. 2009; 108(1): 197–206. PubMed Abstract | Publisher Full Text\n\nHall R, Zisook S: Paradoxical reactions to benzodiazepines. Brit. J. Clin. Pharmacol. 1981; 11: 99S–104S. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDåderman AM, Lidberg L: Flunitrazepam (Rohypnol) abuse in combination with alcohol causes premeditated, grievous violence in male juvenile offenders. J. Am. Acad. Psychiatry Law. 1999; 27: 83–99. PubMed Abstract\n\nDåderman AM, Fredriksson B, Kristiansson M, et al.: Violent behavior, impulsive decision-making, and anterograde amnesia while intoxicated with flunitrazepam and alcohol or other drugs: a case study in forensic psychiatric patients. J. Am. Acad. Psychiatry Law Online. 2002; 30: 238–251.\n\nNilsonne G, Tamm S, Golkar A, et al.: Effects of 25mg oxazepam on emotional mimicry and empathy for pain: a randomized controlled experiment. R. Soc. Open Sci. 2017; 4: 160607. PubMed Abstract | Publisher Full Text\n\nvan Dijk KN , de Vries CS , ter Huurne K , et al.: Concomitant prescribing of benzodiazepines during antidepressant therapy in the elderly. J. Clin. Epidemic. 2002; 55(10): 1049–1053. PubMed Abstract | Publisher Full Text\n\nRütgen M, Pletti C, Tik M, et al.: Antidepressant treatment, not depression, leads to reductions in behavioral and neural responses to pain empathy. Transl. Psychiatry. 2019; 9: 164. PubMed Abstract | Publisher Full Text\n\nFernandes C, Gonçalves AR, Pasion R, et al.: Age-related decline in emotional perspective-taking: Its effect on the late positive potential. Cogn. Affect. Behav. Neurosci. 2019; 19: 109–122. PubMed Abstract | Publisher Full Text\n\nBentin S, Allison T, Puce A, et al.: Electrophysiological studies of face perception in humans. J. Cogn. Neurosci. 1996; 8(6): 551–565. PubMed Abstract | Publisher Full Text\n\nHinojosa JA, Mercado F, Carretié L: N170 sensitivity to facial expression: A meta-analysis. Neurosci. Biobehav. Rev. 2015; 55: 498–509. PubMed Abstract | Publisher Full Text\n\nAlmeida PR, Ferreira-Santos F, Chaves PL, et al.: Perceived arousal of facial expressions of emotion modulates the N170, regardless of emotional category: Time domain and time-frequency dynamics. Int. J. Psychophysiol. 2016; 99: 48–56. PubMed Abstract | Publisher Full Text\n\nRighart R, de Gelder B : Context influences early perceptual analysis of faces: an electrophysiological study. Cereb. Cortex. 2006; 16(9): 1249–1257. PubMed Abstract | Publisher Full Text\n\nRighart R, de Gelder B : Rapid influence of emotional scenes on encoding of facial expressions: an ERP study. Soc. Cogn. Affect. Neurosci. 2008; 3(3): 270–278. PubMed Abstract | Publisher Full Text\n\nRighart R, de Gelder B : Recognition of facial expressions is influenced by emotional scene gist. Cogn. Affect. Behav. Neurosci. 2008; 8(3): 264–272. PubMed Abstract | Publisher Full Text\n\nHietanen JK, Astikainen P: N170 response to facial expressions is modulated by the affective congruency between the emotional expression and preceding affective picture. Biol. Psychol. 2013; 92(2): 114–124. PubMed Abstract | Publisher Full Text\n\nHerring DR, Taylor JH, White KR, et al.: Electrophysiological responses to evaluative priming: the LPP is sensitive to incongruity. Emotion. 2011; 11(4): 794–806. PubMed Abstract | Publisher Full Text\n\nFoti D, Hajcak G: Deconstructing reappraisal: Descriptions preceding arousing pictures modulate the subsequent neural response. J. Cogn. Neurosci. 2008; 20(6): 977–988. PubMed Abstract | Publisher Full Text\n\nWeinberg A, Hajcak G: Beyond good and evil: The time-course of neural activity elicited by specific picture content. Emotion. 2010; 10(6): 767–782. PubMed Abstract | Publisher Full Text\n\nYoder KJ, Decety J: Spatiotemporal neural dynamics of moral judgment: a high-density ERP study. Neuropsychologia. 2014; 60: 39–45. PubMed Abstract | Publisher Full Text\n\nCowell JM, Decety J: Precursors to morality in development as a complex interplay between neural, socioenvironmental, and behavioral facets. Proc. Natl. Acad. Sci. USA. 2015; 112(41): 12657–12662. PubMed Abstract | Publisher Full Text\n\nAshton H: The diagnosis and management of benzodiazepine dependence. Curr. Opin. Psychiatry. 2005; 18: 249–255. Publisher Full Text\n\nBorda MG, Jaramillo-Jimenez A, Oesterhus R, et al.: Benzodiazepines and antidepressants: Effects on cognitive and functional decline in Alzheimer's disease and Lewy body dementia. Int. J. Geriatr. Psychiatry. 2021; 36(6): 917–925. PubMed Abstract | Publisher Full Text\n\nLader MH: Limitations on the use of benzodiazepines in anxiety and insomnia: are they justified? Eur. Neuropsychopharmacol. 1999; 9: S399–S405. PubMed Abstract | Publisher Full Text\n\nBarker MJ, Greenwood KM, Jackson M, et al.: Cognitive effects of long-term benzodiazepine use: a meta-analysis. CNS Drugs. 2004a; 18: 37–48. Publisher Full Text\n\nBraestrup C, Squires RF: Brain specific benzodiazepine receptors. Br. J. Psychiatry. 1978; 133: 249–260. Publisher Full Text\n\nDelaveau P, Jabourian M, Lemogne C, et al.: Brain effects of antidepressants in major depression: a meta-analysis of emotional processing studies. J. Affect. Disord. 2011; 130(1-2): 66–74. PubMed Abstract | Publisher Full Text\n\nDavid N, Aumann C, Santos NS, et al.: Differential involvement of the posterior temporal cortex in mentalizing but not perspective taking. Soc. Cogn. Affect. Neurosci. 2008; 3(3): 279–289. PubMed Abstract | Publisher Full Text\n\nFreitas S, Simões M, Santana I: Montreal Cognitive Assessment (MoCA): Pontos de corte no Défice Cognitivo Ligeiro, Doença de Alzheimer. Demência Frontotemporal e Demência Vascular. Sinapse. 2014; 1: 18–30.\n\nNasreddine ZS, Phillips NA, Bédirian V, et al.: The Montreal Cognitive Assessment, MoCA: a brief screening tool for mild cognitive impairment. J. Am. Geriatr. Soc. 2005; 53: 695–699. Publisher Full Text\n\nSnaith RP, Zigmond AP: The hospital anxiety and depression scale manual. Windsor:NFER-Nelson;1994.\n\nPais-Ribeiro J, Silva I, Ferreira T, et al.: Validation study of a Portuguese version of the Hospital Anxiety and Depression Scale. Psychol. Health Med. 2007; 12: 225–237. PubMed Abstract | Publisher Full Text\n\nDerogatis LR: BSI: Brief Symptom Inventory. 3rd ed.Minneapolis:National Computers Systems;1997.\n\nCanavarro MC;Inventário de sintomas psicopatológicos - BSI.Simões MR, Gonçalves M, Almeida LS, editors. Testes e provas psicológicas em Portugal. Braga:SHO/APPORT; 1999; vol. II: p. 87–109.\n\nArmitage SG: An analysis of certain psychological tests used for the evaluation of brain injury. Psychol. Monogr. 1946; 60: i–48. Publisher Full Text\n\nCavaco S, Gonçalves A, Pinto C, et al.: Trail Making Test: regression-based norms for the Portuguese population. Arch. Clin. Neuropsychol. 2013; 28: 189–198. PubMed Abstract | Publisher Full Text\n\nTorralva T, Roca M, Gleichgerrcht E, et al.: INECO Frontal Screening (IFS): a brief, sensitive, and specific tool to assess executive functions in dementia. J. Int. Neuropsychol. Soc. 2009; 15: 777–786. PubMed Abstract | Publisher Full Text\n\nMoreira HS, Lima CF, Vicente SG: Examining Executive Dysfunction with the Institute of Cognitive Neurology (INECO) Frontal Screening (IFS): normative values from a healthy sample and clinical utility in Alzheimer’s disease. J. Alzheimers Dis. 2014; 42: 261–273. PubMed Abstract | Publisher Full Text\n\nStrauss E, Sherman EM, Spreen O: A compendium of neuropsychological tests: administration, norms, and commentary. 3rd ed.New York:Oxford University Press;2006.\n\nCavaco S, Gonçalves A, Pinto C, et al.: Semantic fluency and phonemic fluency: regression-based norms for the Portuguese population. Arch. Clin. Neuropsychol. 2013b; 28: 262–271. PubMed Abstract | Publisher Full Text\n\nWechsler D: WMS - III. Escala de memória de Wechsler. Lisboa:CEGOCTEA;2008.\n\nDiéguez-Risco T, Aguado L, Albert J, et al.: Judging emotional congruency: Explicit attention to situational context modulates processing of facial expressions of emotion. Biol. Psychol. 2015; 112: 27–38. Publisher Full Text\n\nDozolme D, Brunet-Gouet E, Passerieux C, et al.: Neuroelectric correlates of pragmatic emotional incongruence processing: empathy matters. PLoS One. 2015; 10(6): e0129770. PubMed Abstract | Publisher Full Text\n\nTottenham N, Tanaka JW, Leon AC, et al.: The NimStim set of facial expressions: judgments from untrained research participants. Psychiatry Res. 2009; 168(3): 242–249. PubMed Abstract | Publisher Full Text\n\nDelorme A, Makeig S: An open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. J. Neurosci. Methods. 2004; 134(1): 9–21. PubMed Abstract | Publisher Full Text\n\nPerrin F, Pernier J, Bertrand O, et al.: Spherical splines for scalp potential and current density mapping. Electroencephalogr. Clin. Neurophysiol. 1989; 72(2): 184–187. PubMed Abstract | Publisher Full Text\n\nMusial PG, Baker SN, Gerstein GL, et al.: Signal-to-noise ratio improvement in multiple electrode recording. J. Neurosci. Methods. 2002; 115(1): 29–43. PubMed Abstract | Publisher Full Text\n\nZeman PM, Till BC, Livingston NJ, et al.: Independent component analysis and clustering improve signal-to-noise ratio for statistical analysis of event-related potentials. Clin. Neurophysiol. 2007; 118(12): 2591–2604. Publisher Full Text\n\nGarcez H, Fernandes C, Barbosa F, et al.: Effects of benzodiazepines administration on identification of facial expressions of emotion: a meta-analysis. Psychopharmacology. 2020; 237(1): 1–9. PubMed Abstract | Publisher Full Text\n\nKirita T, Endo M: Happy face advantage in recognizing facial expressions. Acta Psychol. 1995; 89: 149–163. Publisher Full Text\n\nWells LJ, Gillespie SM, Rotshtein P: Identification of emotional facial expressions: effects of expression, intensity, and sex on eye gaze. PLoS One. 2016; 11: 1–20. Publisher Full Text\n\nGonçalves AR, Fernandes C, Pasion R, et al.: Emotion identification and aging: Behavioral and neural age-related changes. Clin. Neurophysiol. 2018; 129(5): 1020–1029. PubMed Abstract | Publisher Full Text\n\nEger E, Jedynak A, Iwaki T, et al.: Rapid extraction of emotional expression: evidence from evoked potential fields during brief presentation of face stimuli. Neuropsychologia. 2003; 41(7): 808–817. PubMed Abstract | Publisher Full Text\n\nKrombholz A, Schaefer F, Boucsein W: Modification of N170 by different emotional expression of schematic faces. Biol. Psychol. 2007; 76(3): 156–162. PubMed Abstract | Publisher Full Text\n\nDiéguez-Risco T, Aguado L, Albert J, et al.: Faces in context:modulation of expression processing by situational information. Soc. Neurosci. 2013; 8(6): 601–620. PubMed Abstract | Publisher Full Text\n\nWerheid K, Alpay G, Jentzsch I, et al.: Priming emotional facial expressions as evidenced by event-related brain potentials. Int. J. Psychophysiol. 2005; 55(2): 209–219. PubMed Abstract | Publisher Full Text\n\nZhang Q, Li X, Gold BT, et al.: Neural correlates of cross-domain affective priming. Brain Res. 2010; 1329: 142–151. PubMed Abstract | Publisher Full Text\n\nMünte TF, Urbach TP, Duzel E, Kutas M:Event-related brain potentials in the study of human cognition and neuropsychology.Boller GJ, Rizzolatti G, editors. Handbook of Neuropsychology. 2nd ed.Netherlands:Elsevier Science Publishers;2000; Vol. 1: p 1–97.\n\nDanker JF, Hwang GM, Gauthier L, et al.: Characterizing the ERP Old–New effect in a short-term memory task. Psychophysiology. 2008; 45: 784–93. PubMed Abstract | Publisher Full Text\n\nBarker MJ, Greenwood KM, Jackson M, et al.: Persistence of cognitive effects after withdrawal from long-term benzodiazepine use: a meta-analysis. Arch. Clin. Neuropsychol. 2004b; 19: 437–454. Publisher Full Text"
}
|
[
{
"id": "146668",
"date": "30 Aug 2022",
"name": "Helena Hartmann",
"expertise": [
"Reviewer Expertise Empathy",
"perspective taking / theory of mind",
"neuroimaging (fMRI)",
"placebo analgesia"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI am an expert on empathy (specifically in the domain of pain) and Theory of Mind, but don’t have any experience with EEG.\nSummary In general, the main question of the present manuscript was to investigate whether the combined use of benzodiazepines and antidepressants affect perspective taking. In a between-subjects design, the authors compared users of both medication with controls on the behavioral and neural level (using event-related potentials) in a perspective-taking task. The groups did not differ in their task performance nor in their neural activity. The authors conclude that taking benzodiazepines and antidepressants together does not affect perspective-taking abilities.\nStrengths The research question is interesting and relevant, given that concomitant use of multiple medications is common and investigating this increases ecological validity (as compared to investigating effects of single medications alone). The manuscript is well structured and easy to follow. The methods are appropriately detailed, and allow for replication of the study. Results are clearly described and relevant statistics are reported. I appreciate that the authors openly shared their data. I also really like the last paragraph of the discussion, as it appropriately highlights limitations and caveats of the work.\nI have significant reservations, as outlined below, which include many comments that need to be addressed, before I can recommend the article to be of sufficient quality. My comments are structured into major and minor, and as they appear in the text. I hope the authors find my suggestions helpful to improve the manuscript.\nMajor The authors start their abstract and introduction talking about empathy and the different parts of empathy, however, the study investigated only a part of empathy, i.e., perspective taking. It might be misleading to speak of empathy generally, as researchers often also include the more emotional, affect sharing component under this term, as well as concern/sympathy. For example, the first sentence of the abstract talks about results regarding empathic pain, which relates more to affect sharing and not to perspective taking. The abstract and introduction should clearly state what exact concepts are being investigated here and introduce them adequately to avoid misunderstandings. For example, the authors could make a case that affective empathy has been researched a lot in regard to medication interactions, while this is less the case for cognitive empathy?\nWhy were the scores of the cognitive tests included in a single analysis left raw and not standardized (in order to better compare the beta values between the measures)?\nThe authors mention that “Scores of cognitive tests (raw scores) in which differences between groups were detected were entered as main predictors of behavioral measures and N170, and LPPs modulation (independent models).” However, this violates the assumption of independence of covariate and treatment effect (see Field et al., 2012, p. 465-466, who states: “when treatment groups differ on the covariate, putting the covariate into the analysis will not ‘control for’ or ‘balance out’ (…) differences (Lord, 1967, 1969)”).1,2,3 According to his argument, only covariates where the groups do not differ on can be used as covariates.\nFurthermore, why were the regressions run separately for the two groups and how do the authors explain effects in the control but not the experimental group?\nWhy do the authors not follow up on the significant emotion x group interaction in the accuracy ANOVA? If I am not mistaken, this interaction hints at a group effect specific to some emotions and independent of congruency? It might be interesting to follow up on, even if the authors did not have specific hypotheses on this effect.\nAs the authors report null findings regarding effects of concomitant use of benzodiazepines and antidepressants on perspective taking, I urge them to redo their analyses using a Bayesian framework (e.g. in JASP, https://jasp-stats.org/, which is similarly straightforward as SPSS). This would give the reader an indication of the relative evidence for the null compared to alternative hypothesis, especially also considering the rather low sample size. This would make the authors’ conclusion that “the combined use of benzodiazepines and antidepressants on long-term seem to preserve at least the perspective-taking ability of social cognition” much stronger.\nIt sounds to me like the ROIs for the ERP analysis were not chosen independently, but based on the data that they collected (e.g. Button, 2019), but then also affirmed with previous literature. Could the authors comment on this?4\nResults, Behavioral Results: How do the authors explain that the LPPe/LPPl were higher for congruent vs. incongruent conditions, when previous studies found the opposite (as stated in the introduction)? Also, I am a bit confused by those results as the authors also found an interaction between emotion and congruency in both LPPe and LPPl. In that case, the main effect of congruency should not be interpreted and plotted in Fig. 2, but instead the interaction? I think there is a typo in the paragraph about the LPPI as the authors still talk about LPPe there in the second to last sentence.\nWhy was reaction time also analyzed? Is this measure also related to perspective taking? What hypotheses did the authors have here?\nOne important point for me is whether the task actually measured perspective taking. From what I understood, you measured accuracy rates (and reaction times), so not how good participants were necessarily in finding out the emotion of the masked person, but how good they were in matching the emotion they thought fitted with an emotion they see in a picture afterwards. This to me sounds more like emotion identification. I would appreciate a discussion of the limitations of this task in the discussion.\nDiscussion: Why is the meta analysis mentioned at all if it is \"methodologically far\" from the present study? Does it help to interpret the findings of this study in any way?\nIn general, the few significant results that the study finds are not discussed at all in light of current literature but just mentioned as being \"unexpected\". A more throrough discussion of what these results could mean is warranted.\nMinor Introduction, Paragraph 2: The last part of the first sentence (starting with “Perspective-taking enables us…”) reads a bit grammatically wrong – please recheck (maybe another “– “ after “Theory of Mind”?\nIntroduction, Paragraph 2: Please revise the sentence “The ability to take the perspective of another person is known as emotional perspective-taking and is determinant for the success of social interactions”. This is not necessarily true, because taking the perspective of another person is also a cognitive process and does not need to be emotional. Maybe the authors mean “The ability to understand the emotions of another person is …”?\nIntroduction, Paragraph 3: How was the oxazepam study on emotional mimicry? In the sentence later the authors specify that that study measured empathy for pain, which is typically \"affect sharing\". Please revise so this becomes a bit clearer.\nIntroduction, Paragraph 3: I would appreciate some statistics/numbers on the concomitant use of benzodiazepines and antidepressants compared to single use of either, so that the context for and necessity of the study is set better.\nIntroduction, Paragraph 7: Are the “neurocognitive” measures the same as the “neuropsychological” measures mentioned in the methods?\nJust an idea: The authors could also make a case in the introduction that investigating the concomitant use of the medications is ecologically more valid as this better reflects real medication use, as opposed to taking a single medication? (if there is evidence for that)?\nDo the authors think that gender of the people in the video might have had an influence on the results? Were the stimuli for congruent and incongruent conditions balanced in terms of gender?\nMethods, Participants: How many people in the experimental group were excluded based on having \"psychiatric diagnosis aside from anxiety and depression\"?\nMethods, Procedures: “… were invited to participate IN a second session….”\nMethods, Statistical analysis, Paragraph 2: “…were analyzed by a mixed ANOVA… with group as A between-subjects factor…”\nResults: Please add the test statistics to Table 1. It might also be nice to report all full ANOVA results in the Supplement.\nResults, Behavioral Results: “…were examined using A mixed factor ANOVA”\nDiscussion, Paragraph 2: “Bearing IN mind…”\nDiscussion, Paragraph 8: “…substances together neither affect … nor the processing of related information.”\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": [
{
"c_id": "8893",
"date": "07 Nov 2022",
"name": "Ana Gonçalves",
"role": "Author Response",
"response": "I have significant reservations, as outlined below, which include many comments that need to be addressed, before I can recommend the article to be of sufficient quality. My comments are structured into major and minor, and as they appear in the text. I hope the authors find my suggestions helpful to improve the manuscript. R: We thank Helena Hartmann for the careful review of our manuscript and the important points raised below. We will comment on each point, tracking the corresponding changes that were made in the manuscript. Major The authors start their abstract and introduction talking about empathy and the different parts of empathy, however, the study investigated only a part of empathy, i.e., perspective taking. It might be misleading to speak of empathy generally, as researchers often also include the more emotional, affect sharing component under this term, as well as concern/sympathy. For example, the first sentence of the abstract talks about results regarding empathic pain, which relates more to affect sharing and not to perspective taking. The abstract and introduction should clearly state what exact concepts are being investigated here and introduce them adequately to avoid misunderstandings. For example, the authors could make a case that affective empathy has been researched a lot in regard to medication interactions, while this is less the case for cognitive empathy? R: We appreciate your suggestion. We added the following information to the abstract and introduction sections: (abstract) \"(…) the perspective-taking facet of (…)\"; (introduction, paragraph 4) \"Thus, the effects of medication interactions used for long periods on the perspective-taking facet of empathy are still unknown.\" In our opinion, the concept of perspective-taking is adequately introduced in the first paragraphs. Why were the scores of the cognitive tests included in a single analysis left raw and not standardized (in order to better compare the beta values between the measures)? R: In most situations, to test the difference between performance on two tasks, it is necessary to standardize the scores. However, when a subject’s performance is compared with that of controls on the same task, under two different experimental conditions, the standardization is unnecessary, Crawford and Garthwaite (2005). Crawford, J. R., & Garthwaite, P. H. (2005). Testing for Suspected Impairments and Dissociations in Single-Case Studies in Neuropsychology: Evaluation of Alternatives Using Monte Carlo Simulations and Revised Tests for Dissociations. Neuropsychology, 19(3), 318–331. https://doi.org/10.1037/0894-4105.19.3.318 The authors mention that “Scores of cognitive tests (raw scores) in which differences between groups were detected were entered as main predictors of behavioral measures and N170, and LPPs modulation (independent models).” However, this violates the assumption of independence of covariate and treatment effect (see Field et al., 2012, p. 465-466, who states: “when treatment groups differ on the covariate, putting the covariate into the analysis will not ‘control for’ or ‘balance out’ (…) differences (Lord, 1967, 1969)”).1,2,3 According to his argument, only covariates where the groups do not differ on can be used as covariates. R: This is a good point. We wanted to examine the association between neuropsychological functioning and behavioral/ERP components, regardless of the direction of the influence of the effects. The choice of multiple linear regression was only to allow entering multiple neuropsychological measures and to control for their covariance in a practical manner (an alternative would be to use partial correlations, but it is a less common form of analyzing data in this field and are mathematically equivalent to the regression models employed). Note that this was not the main analysis of the study, and was intended to verify if the differences that we detected in neuropsychological functioning could account for the behavioral/ERP results in the experimental group. We know that it is a bad idea to adjust for covariates when we suspect these covariates could have been affected by the treatment, however we were less cautious here because the analyses were run separately for the experimental and control group. Furthermore, why were the regressions run separately for the two groups and how do the authors explain effects in the control but not the experimental group? R: The regression was first computed only for the experimental group since it was our group of interest. To further explore and clarify the results, the analysis was extended to the control group. This information was added to the methods section (statistical analysis, paragraph 3). Regarding the effects in the control group but not the experimental, it is now addressed in the discussion: \"Furthermore, a meta-analysis examining the boundary conditions of threat-related attentional biases in anxiety showed that a significant bias also occurred with stimuli outside awareness. Additionally, the bias is present in different types of anxious populations, including nonclinical individuals, and is not observed in non anxious individuals. This attentional bias in anxious individuals may account for higher accuracy rates when identifying emotional situations. However, our results showed accuracy rates predicted by anxiety and psychopathological symptomatology only in control subjects and regarding happiness scenarios. Here we should consider that ceiling effects could have account for these results. In fact, ceiling effects have been known to hinder solid interpretations of the results, especially for facial expressions of happiness.\" Why do the authors not follow up on the significant emotion x group interaction in the accuracy ANOVA? If I am not mistaken, this interaction hints at a group effect specific to some emotions and independent of congruency? It might be interesting to follow up on, even if the authors did not have specific hypotheses on this effect. R: Although we found a significant emotion x group interaction, none of the post-hoc comparisons achieved significance (all p >.066). This information was added to the results section. As the authors report null findings regarding effects of concomitant use of benzodiazepines and antidepressants on perspective taking, I urge them to redo their analyses using a Bayesian framework (e.g. in JASP, https://jasp-stats.org/, which is similarly straightforward as SPSS). This would give the reader an indication of the relative evidence for the null compared to alternative hypothesis, especially also considering the rather low sample size. This would make the authors’ conclusion that “the combined use of benzodiazepines and antidepressants on long-term seem to preserve at least the perspective-taking ability of social cognition” much stronger. R: We appreciate your suggestion for an alternative analysis which we will consider in future work. A Bayesian framework could provide additional information, but the choice of the present analysis allowed us to compare the performance between groups as we intended. We have now emphasized the limitation of having a low sample size in the discussion. The present form is (discussion, last paragraph): \"However, we should bear in mind that the small sample of the study is a limitation when drawing conclusions. Additionally, the lack of previous studies with a similar sample, makes any interpretation difficult to support. Further research within this field conducted with a larger sample is necessary to strengthen the present finding. We hope, however, to have brought important evidence to light, which may help future research on social cognition under the influence of benzodiazepines and antidepressants.\" It sounds to me like the ROIs for the ERP analysis were not chosen independently, but based on the data that they collected (e.g. Button, 2019), but then also affirmed with previous literature. Could the authors comment on this?4 R: The ROIs for the ERP analysis were chosen based on visual inspection of ERP grand-average and topographical maps of our EEG records. These results were in accordance with previous studies and led us to set the specified ROIs. This is a common procedure in this field. Results, Behavioral Results: How do the authors explain that the LPPe/LPPl were higher for congruent vs. incongruent conditions, when previous studies found the opposite (as stated in the introduction)? Also, I am a bit confused by those results as the authors also found an interaction between emotion and congruency in both LPPe and LPPl. In that case, the main effect of congruency should not be interpreted and plotted in Fig. 2, but instead the interaction? I think there is a typo in the paragraph about the LPPI as the authors still talk about LPPe there in the second to last sentence. R: Previous studies that reported higher LPP amplitudes elicited by incongruent trials used tasks requiring an evaluative congruity between primes and facial or verbal targets, whereas our task required attending the scenes, inferring the mental state of the masked interveners, and deciding if the FEE displayed after the scene matched the one previously inferred. The recognition of the masked person’s emotion in the stimuli displayed by the target FEE in our task may explain the increased amplitudes to congruent stimuli since the LPP is also modulated by the explicit recognition of stimuli, exhibiting larger amplitudes in response to recognized stimuli vs. new (discussion, paragraph 6). In our opinion, such plots representing the emotion x congruency interaction will be hard to interpret given the large amount of information represented. There was a typo in the paragraph about LPPl. LPPe was changed to LPPl: \"Pairwise comparisons revealed that congruent conditions elicited higher LPPl amplitudes than incongruent conditions (p = .002) (Fig. 2).\" Why was reaction time also analyzed? Is this measure also related to perspective taking? What hypotheses did the authors have here? R: We appreciate this comment. Previous studies (Abramowitz et al., 2014; Smith et al., 2014) found that schizophrenia outpatients showed poorer performance and took significantly longer to complete an emotional perspective-taking task than healthy controls. In our study, we analyzed reaction times because we expected worst performance of the experimental group on the perspective-taking task and longer reaction times could be observed. We added this information to introduction (last paragraph): \"Furthermore, considering that it was previously found that subjects from a clinical sample took longer to complete an emotional perspective-taking task, besides showing poorer performance than healthy controls35,36, we analyzed reaction times to clarify if they were affected in our study.\" A.C. Abramowitz, E.J. Ginger, J.K. Gollan, M.J. Smith. Empathy, depressive symptoms, and social functioning among individuals with schizophrenia. Psychiatry Res., 216 (2014), pp. 325-332 M.J. Smith, W.P. Horan, D.J. Cobra, T.M. Karpouzian, J.M. Fox, J.L. Reilly, et al. Performance-based empathy mediates the influence of working memory on social competence in schizophrenia. Schizophr. Bull., 40 (2014), pp. 824-834 One important point for me is whether the task actually measured perspective taking. From what I understood, you measured accuracy rates (and reaction times), so not how good participants were necessarily in finding out the emotion of the masked person, but how good they were in matching the emotion they thought fitted with an emotion they see in a picture afterwards. This to me sounds more like emotion identification. I would appreciate a discussion of the limitations of this task in the discussion. R: This is an interesting issue. The current experimental design was based on previous studies assessing contextual congruency (Diéguez-Risco, Aguado, Albert, & Hinojosa, 2013), defined here as the matching between a target emotion portrayed in a facial expression and the emotion portrayed by the previous scenario. However, distinct from previous studies, an accurate decision in our task requires an accurate inference of the emotional state of the masked intervener. We instructed participants to attend the scenes, infer the mental state of the masked interveners, and decide if the FEE displayed after the scene matched the one previously inferred. Thus, with this experimental manipulation, we investigated perspective-taking abilities through the behavioral performance (see introduction, paragraph 4; methods, emotional perspective-taking task, paragraph 1; discussion, paragraph 6). Discussion: Why is the meta analysis mentioned at all if it is \"methodologically far\" from the present study? Does it help to interpret the findings of this study in any way? R: The meta-analysis assessed the effects of benzodiazepines administration on the ability of identifying facial expressions of emotion (FEE), an ability required in the task of the present study. The meta-analytic results could help to interpret any effects observed of the concomitant use of benzodiazepines and antidepressants on the perspective-taking ability. In general, the few significant results that the study finds are not discussed at all in light of current literature but just mentioned as being \"unexpected\". A more throrough discussion of what these results could mean is warranted. R: We appreciate this comment that will considerably improve the work. This issue is now addressed in the discussion: \"Furthermore, a meta-analysis examining the boundary conditions of threat-related attentional biases in anxiety showed that a significant bias also occurred with stimuli outside awareness. Additionally, the bias is present in different types of anxious populations, including nonclinical individuals, and is not observed in non anxious individuals. This attentional bias in anxious individuals may account for higher accuracy rates when identifying emotional situations. However, our results showed accuracy rates predicted by anxiety and psychopathological symptomatology only in control subjects and regarding happiness scenarios. Here we should consider that ceiling effects could have account for these results. In fact, ceiling effects have been known to hinder solid interpretations of the results, especially for facial expressions of happiness.\" Minor Introduction, Paragraph 2: The last part of the first sentence (starting with “Perspective-taking enables us…”) reads a bit grammatically wrong – please recheck (maybe another “– “ after “Theory of Mind”? R: We added another “-” to the text. Introduction, Paragraph 2: Please revise the sentence “The ability to take the perspective of another person is known as emotional perspective-taking and is determinant for the success of social interactions”. This is not necessarily true, because taking the perspective of another person is also a cognitive process and does not need to be emotional. Maybe the authors mean “The ability to understand the emotions of another person is …”? R: This is an interesting issue. We followed the definition of emotional perspective-taking of Derntl and colleagues (2009) but we agree that taking the perspective of another person is also a cognitive process. The present form of the above-mentioned sentence is: \"The ability to correctly infer the emotional states of another person is known as emotional perspective-taking and is determinant for the success of social interactions.\" Introduction, Paragraph 3: How was the oxazepam study on emotional mimicry? In the sentence later the authors specify that that study measured empathy for pain, which is typically \"affect sharing\". Please revise so this becomes a bit clearer. R: The study of Nilsonne and colleagues investigated the effects of oxazepam on emotional mimicry and empathic responding using two experiments. The empathy experiment investigated the effects of oxazepam by pain stimulating the participant and a confederate. The emotional mimicry experiment was deleted from the sentence to make it clearer (introduction, paragraph 3): \"(…) investigated the effects of oxazepam on empathic responding.\" Introduction, Paragraph 3: I would appreciate some statistics/numbers on the concomitant use of benzodiazepines and antidepressants compared to single use of either, so that the context for and necessity of the study is set better. R: The main goal of the present study was based on the real and current context of benzodiazepines (BZDs) being often additionally administered to antidepressants (ADs), to manage anxiety or insomnia in patients with depression, since ADs have minimal therapeutic effects during the initial weeks of administration. The decision to investigate the combined use of these drugs is due to knowledge of the current context from clinical practice of some team members. The numbers for this practice of combined prescription in the USA are reported in Bushnell et al. (2017): \"one in 10 patients who initiated ADs concomitantly initiated BZDs in the USA. However, BZDs are sometimes continued for longer periods than intended in real-world clinical practice, possibly owing to their dependency—one study found that approximately 12% of patients who received concomitant BZD and AD therapy (AD+BZD) continued long-term BZD use.\" In our opinion, the context and necessity of the study is now better set out although we did not mention statistics/numbers (introduction, last paragraph): \"It is common to prescribe benzodiazepines and antidepressants simultaneously in initial depression treatment, however it has been previously reported that the simultaneous use extends beyond the initial period and becomes long term.\" Bushnell G, Sturmer T, Gaynes B, Pate V, Miller M. Simultaneous antidepressant and benzodiazepine new use and subsequent long-term benzodiazepine use in adults with depression, United States, 2001-2014. JAMA Psychiatry. 2017;74(7):747–55. Introduction, Paragraph 7: Are the “neurocognitive” measures the same as the “neuropsychological” measures mentioned in the methods? R: The neurocognitive measures are the same neuropsychological measures listed in the methods section. Just an idea: The authors could also make a case in the introduction that investigating the concomitant use of the medications is ecologically more valid as this better reflects real medication use, as opposed to taking a single medication? (if there is evidence for that)? R: We appreciate this comment. We added information in line with your suggestion (introduction, last paragraph): \"It is common to prescribe benzodiazepines and antidepressants simultaneously in initial depression treatment, however it has been previously reported that the simultaneous use extends beyond the initial period and becomes long term.\" Do the authors think that gender of the people in the video might have had an influence on the results? Were the stimuli for congruent and incongruent conditions balanced in terms of gender? R: This is a good point. The FEE was selected from the NimStim Face Stimulus Set, picking the five most accurately identified facial expressions for each emotional category which led to 30 female and 30 male facial stimuli. These stimuli were balanced in terms of gender for congruent and incongruent conditions (15 female and 15 male for both conditions). In our opinion, it is unlikely that the gender of actors in the stimuli might have influenced the results, since the stimuli were balanced for both conditions and the set was the same for the two groups (only the order of stimuli presentation changed between participants in a random way). Methods, Participants: How many people in the experimental group were excluded based on having \"psychiatric diagnosis aside from anxiety and depression”? R: Two participants were excluded based on that criteria but I considered them in the number of participants excluded by taking psychotropic medication besides benzodiazepines and antidepressants. This was changed accordingly in the text. Methods, Procedures: “… were invited to participate IN a second session….” R: It was a typo and was corrected to \"…in a second session…\". Methods, Statistical analysis, Paragraph 2: “…were analyzed by a mixed ANOVA… with group as A between-subjects factor…” R: \"a\" was deleted. Results: Please add the test statistics to Table 1. It might also be nice to report all full ANOVA results in the Supplement. R: The tests statistics were added to Table 1. Results, Behavioral Results: “…were examined using A mixed factor ANOVA” R: \"a\" was added before \"mixed factors ANOVA\". Discussion, Paragraph 2: “Bearing IN mind…” R: It was a typo and was corrected to \"…in mind…\". Discussion, Paragraph 8: “…substances together neither affect … nor the processing of related information.” R: The sentence was changed to \"…substances together neither affect … nor the processing of related information.\""
},
{
"c_id": "9014",
"date": "14 Nov 2022",
"name": "Helena Hartmann",
"role": "Reviewer Response",
"response": "I want to thank the authors for their replies to all of my comments and for a successful revision. All of my comments were addressed and I have no further questions :)"
}
]
}
] | 1
|
https://f1000research.com/articles/11-790
|
https://f1000research.com/articles/11-1178/v1
|
17 Oct 22
|
{
"type": "Clinical Practice Article",
"title": "Effectiveness, survival and safety of guselkumab attending to basal characteristics in moderate-to-severe psoriatic patients: a cohort study",
"authors": [
"Ricardo Ruiz-Villaverde",
"Lourdes Rodriguez-Fernandez-Freire",
"Jose C. Armario-Hita",
"Amalia Pérez-Gil",
"Fiorella Vasquez Chinchay",
"Manuel Galán-Gutiérrez",
"Lourdes Rodriguez-Fernandez-Freire",
"Jose C. Armario-Hita",
"Amalia Pérez-Gil",
"Fiorella Vasquez Chinchay",
"Manuel Galán-Gutiérrez"
],
"abstract": "Background: Psoriasis is a chronic inflammatory disease which can impact quality of life. In the past decade multiple biologic treatments have been released with encouraging results. Guselkumab is a monoclonal antibody targeting IL-23p19. Multiple randomized clinical trials have demonstrated its efficacy in psoriasis, but response differences among patient subpopulations have not been extensively reported. Furthermore, patients in real life are often non-eligible for clinical trials and their responses may differ from pivotal studies. Methods: This is a retrospective, observational study of real clinical practice of patients receiving guselkumab treatment in Spain. Patients treated with guselkumab were included between February 2019 to December 2021. This study evaluates the potential differential effect of baseline demographic and disease characteristics on therapeutic responses to guselkumab. We measured effectiveness and survival by the psoriasis area and severity index, the dermatology life quality index as well as Kaplan meier curves, respectively. Categorical and quantitative variables are reported with frequencies, and with mean and standard deviation, respectively. Differences between groups in psoriasis area and severity index and dermatology life quality index, were calculated using a mixed-effects analysis. Survival was calculated using Kaplan meier curves and log-rank tests. Results: A total of 87 patients were included. In this study, our objective was to evaluate the effectiveness, safety and survival of guselkumab attending to demographic characteristics. No differences in psoriasis area and severity index or dermatology life quality index baseline values or therapeutic responses were noted at 52 weeks of follow-up among all the subgroups analysed (age, sex, psoriasis duration, body mass index, and comorbidities). A difference in drug survival was only seen between gender groups. Conclusions: Our research has demonstrated the consistency of guselkumab effectiveness across patient subgroups. No baseline features affected the effectiveness or drug survival of guselkumab, except for lower drug survival in female patients.",
"keywords": [
"Guselkumab",
"Psoriasis",
"Effectiveness",
"Survival",
"Safety",
"Demographic characteristics"
],
"content": "Introduction\n\nPsoriasis (PSO) is a chronic inflammatory disease characterized by skin lesions that can be painful, disabling, disfiguring, and thereby negatively impact the patients’ quality of life.1 It impacts the general quality of life (usually measured by the dermatology life quality index (DLQI)) and the pruritus that may cause (visual analog scale (VAS) pruritus) and influences the psychological sphere, work productivity as well as personal and family relationships.2 PSO affects between 1.5-3% of the general population in Europe, with a similar prevalence in men and women.1–3\n\nTreatment of moderate to severe PSO has radically changed in the past decade; patients have benefited from translational research leading to development of multiple biologic agents such as anti-interleukin (IL)-173,4 and anti-IL23p19.5,6 Our current understanding of the pathophysiology of PSO has been driven by a cytokine disbalance with predominant involvement of the interleukin (IL)-23/Th-17 axis, as well as keratinocyte hyperproliferation and immune activation.1–3\n\nIL-23 produced by dendritic cells and keratinocytes in PSO plaques promotes the differentiation, expansion and maintenance of Th17 as well as the production of the corresponding cytokines such as IL-17A, IL-17F, TNFα and IL-22.7 The role of IL-23 as “master regulator” of inflammation in PSO has justified the development of selective IL-23p19 inhibitors and confirmed by their therapeutic success.2–4\n\nGuselkumab (GUS) is a fully human anti-IL-23 immunoglobulin-G1-lambda monoclonal antibody, that binds the p19 subunit of interleukin 23.5 It has been currently approved by the United States Food and Drug Administration (FDA) and the European Medicines Agency (EMA) for the treatment of adult patients with moderate-to-severe PSO who are candidates for systemic therapy.2 The EMA has also approved the use of GUS for treatment of active psoriatic arthritis in adult patients who have had an inadequate response or who have been intolerant to a prior disease-modifying antirheumatic drug therapy.2,6 Three phase-III, randomized, double-blind, placebo-controlled clinical trials have proved the efficacy and safety of GUS in PSO treatment.7–9 VOYAGE 1 and VOYAGE 2 randomized clinical trials compared GUS to adalimumab showing its superiority at 16 weeks and increasing and maintaining these results over time.7,8 The NAVIGATE trial, a phase-III, multicenter, randomised, double-blind trial that compared the efficacy of the switching from UST to GUS in patients presenting an inadequate response (IGA≥2) after 16 weeks open-label treatment with the anti-IL12/23.8 Furthermore, GUS treatment has been compared to other biologics, such as secukinumab, proving the superiority of the anti-IL23p19.3\n\nThe response of various subpopulations of patients — defined by baseline demographic features including weight, PSO disease characteristics and previous PSO treatments — has been assessed using pooled data from the VOYAGE 1 and VOYAGE 2 trials.10,11 GUS was superior to placebo at week 16 and superior to adalimumab at week 24 in all subpopulations except in the Black or African American population, which included few patients.10,11 There is scarce evidence on the behaviour of GUS in different profile of patients. Patients in real life are often non-eligible for clinical trials, and their response, as regards efficacy and safety, may differ from those in pivotal studies. Thus, findings in clinical trials may not be extrapolatable to real life practice.9\n\nAccordingly, we have performed a retrospective, longitudinal, observational study of real clinical practice of patients receiving treatment with GUS 100 mg subcutaneously every eight weeks in six tertiary hospitals in Spain in order to evaluate the potential differential effect of baseline demographic and disease characteristics on therapeutic response to this biologic agent.\n\n\nMethods\n\nThis is a retrospective, observational study of real clinical practice of patients receiving GUS treatment in Spain. It included patients from six different dermatological centers in Spain who started treatment with guselkumab between February 2019 to December 2020. The information of the patients was collected retrospectively from clinical records. The inclusion criteria were patients with moderate-to-severe psoriasis on guselkumab treatment for their psoriasis. Patients with other inflammatory diseases were excluded from the study. We use PASI and DLQI as variables to measure the effectiveness of GUS between subgroup of patients. Survival was measured by Kaplan-meier curves and safety by the reporting of adverse events. As a limitation of the study, we did not applied any method to avoid bias. Categorical and quantitative variables are reported with frequencies (%), and with mean and standard deviation (SD), respectively. Differences between groups in PASI and DLQI, were calculated using a mixed-effects analysis. Survival was calculated using Kaplan meier curves and log-rank tests.\n\nA total of 87 patients with moderate-to-severe plaque PSO treated with GUS were included in this retrospective observational study. This cross-sectional analysis includes information of patients who started treatment with GUS between February 2019 to December 2020. A total of six tertiary hospitals in Andalusia (Spain) participated in this study: Hospital Universitario San Cecilio, (Granada, Spain), Hospital Universitario Virgen del Rocio, (Sevilla, Spain); Hospital Universitario Puerto Real, (Puerto Real, Cádiz, Spain); Hospital Universitario Virgen de Valme, (Sevilla, Spain); Hospital Quirón Salud Sagrado Corazón (Sevilla, Spain), Hospital Universitario Reina Sofia (Córdoba, Spain). Information from patients was collected retrospectively from clinical records. This study has been approved by Ethics Committee of Hospital Universitario San Cecilio (DER-HUSC-2020-004). Before inclusion into the study, patients gave their written informed consent.\n\nThe inclusion criteria used for this study were: 1) adult moderate-to-severe plaque PSO patients; 2) PSO diagnosis from over 1 year ago; 3) patients on GUS treatment 100 mg subcutaneous (at week 0 and 4, followed by a maintenance dose every 8 weeks; other posology were also included). The exclusion criteria were: 1) presence of other inflammatory diseases such as rheumatoid arthritis, Crohn disease, ulcerative colitis and/or ankylosing spondylitis. Missing data at different timepoints was due in part to COVID19 situation, where some patients refused to attend to the hospital for medical follow-up.\n\nClinical efficacy was evaluated using the absolute PASI10 score at baseline and weeks 4, 12, 24, 36, and 52 (Figure 1). The impact of PSO during treatment was also assessed by the dermatology life quality index (DLQI)11 at baseline and weeks 4, 12, 24, 36, and 52 (Figure 2).\n\nEvolution of absolute PASI score in A) female vs male; B) ranges of age; C) year of psoriasis evolution; D) ranges of body mass index and E) patients with or without comorbidities. Mixed-effects analysis, *, p<0.05. PASI, psoriasis area and severity index.\n\nEvolution of DLQI score in A) female vs male; B) ranges of age; C) year of psoriasis evolution; D) ranges of body mass index and E) patients with or without comorbidities. Mixed-effects analysis, *, p<0.05. DLQI, dermatology life quality index.\n\nSeveral subgroups of patients were established to understand and compare the effectiveness, survival and safety of GUS in different profiles of patients found in real world evidence (RWE): 1) gender (female vs male); 2) ranges of age (≥25-<45, ≥45-<65, ≥65-<85); 3) years of PSO evolution (0-10, 11-20, 21-30, 31-40); 4) ranges of BMI (normal weight, overweight, obese) and 5) presence or absence of comorbidities.\n\nTreatment survival was evaluated through Kaplan-Meyer survival curves according to the variables corresponding to baseline demographic characteristics, if any. Survival was evaluated up to week 93. For drug survival analysis, treatment discontinuations due to any cause were the event of interest. Primary failure was considered failure to reach PASI 90 or PASI>3 after applying the biologics and secondary failure is defined as failure to maintain PASI 90 or PASI>3 after 12 weeks of treatment.\n\nSafety was also evaluated attending to treatment-emerging adverse events (AEs), serious AEs and discontinuations due to AEs and/or lack of efficacy (primary or secondary failure). No laboratory tests were performed.\n\nCategorical and quantitative variables are reported with frequencies (%), and with mean and standard deviation (SD), respectively. Differences between groups in PASI and DLQI, were calculated using a mixed-effects analysis. Survival was calculated using Kaplan meier curves and log-rank tests. A p<0.05 was considered statistically significant. Data were analysed using GraphPad Prism version 8.0.0 for Windows (GraphPad Software, RRID: SCR_002798, San Diego, California USA,\n\n\nResults\n\nA total of 87 patients were included.34 Their demographic data, comorbidities, and baseline characteristics of disease at the start of GUS are summarized in Table 1. The population was composed of 60.9% male, with a mean age and PSO evolution of 49.9 (14.6) and 20.4 (9.5) years, respectively. On average their BMI was 29.22 (5.8) and they presented with multiple comorbidities such as: psoriatic arthritis (PSA, 13.8%), diabetes (20.7%), arterial hypertension (AHT, 23.0%), dyslipidaemia (28.7%), depression (13.8%) and fat liver (8.0%). Their clinical characteristic scores were PASI 14.6 (7.2), BSA 22.3 (16.6), VAS pruritus 6.0 (2.2) and DLQI 15.8 (5.4). Of note, eighty-two patients included had been previously under biologic treatments.\n\nMultiple subgroup analyses were performed to detect which variables could modify the response to GUS: gender, age, PSO duration, BMI, or presence of other comorbidities.\n\nGender\n\nThis analysis included a total of n=34 female and n=53 male (Figure 1A). At baseline female and male presented with a PASI score of 14.23 (5.93) and 14.9 (8.00), respectively (Supplementary Table 1). After 12 weeks of treatment the values decreased to 1.43 (1.93) and 1.99 (2.42) for women and men. Also, at 52 weeks, PASI values remain low (female 0.36 (0.73) vs male 1.07 (1.23)) (Supplementary Table 1).\n\nDLQI values at baseline were 17.00 (3.51) for female and 15.09 (5.79) for male (Figure 2A). After 12 weeks, DLQI decreased markedly to 1.85 (2.67) and 1.88 (3.15) for women and men, respectively (Supplementary Table 2). DLQI values also remain low after one year of treatment\n\nAfter 52 weeks of follow-up, no gender-related differences in PASI and DLQI scores were found (Figures 1, 2).\n\nRanges of age\n\nAnother analysis was made by age subgroups where 85 participants were included (Figure 1B). A group including patients under 25 years was not included in the analysis, due to small sample size (n=2). At baseline the PASI value for the groups ≥25-<45, ≥45-<65, ≥65-<85 was 14.18 (5.79), 13.72 (7.13) and 17.32 (8.90), respectively. After 12 weeks of treatment the value corresponding to this ranges of age ≥25-<45, ≥45-<65, ≥65-<85 was 1.70 (1.79), 1.15 (1.32) and 3.04 (3.80) respectively; and after 52 weeks these values remained low at 0.58 (0.96), 1.15 (1.25) and 1.05 (1.42) respectively (Supplementary Table 1).\n\nThe DLQI value presented with a similar trend showing at baseline values of 15.54 (5.18), 15.76 (5.04) and 16.45 (7.15) (Figure 2B). After 12 weeks of treatment, all the groups presented a DLQI score lower than 1.7 and after 52 weeks of treatments the DLQI values were 1.1 (1.59), 2.5 (3.38) and 0.5 (0.71) for the ranges of age ≥25-<45, ≥45-<65, ≥65-<85, respectively (Supplementary Table 2).\n\nAt 52 weeks of follow-up, neither PASI nor DLQI differences were noted among the subgroups mentioned at the timepoints evaluated.\n\nYears of PSO evolution\n\nAn analysis based on the number of years of PSO evolution was also performed, including 16, 34, 27 and 10 patients in the following groups, respectively: 0-10, 11-20, 21-30, 31-40 (Figures 1C, 2C). PASI values at base line were 12.68 (4.19), 16.23 (8.76), 12.67 (5.3), 17.69 (8.34) for the following groups, respectively, 0-10, 11-20, 21-30, 31-40. After 12 weeks, all values remained under a score of 2.2 and at 52-weeks of treatment PASI values were 0.77 (0.59), 0.23 (0.83), 1.75 (1.26) and 0.5 (0.71) for the 0-10, 11-20, 21-30, 31-40 ranges of age, respectively (Figure 1C) (Supplementary Table 1).\n\nThe DLQI values, presented a similar trend as PASI’s (Figure 2C). For the 0-10, 11-20, 21-30, 31-40 groups, baseline data were 14.00 (2.66), 15.93 (6.06), 16.35 (6.32), 16.00 (4.38) and subsequently, 52-weeks data were 0.50 (0.55), 1.36 (1.96), 3.17 (3.97) and 0.00 (0.00) respectively (Supplementary Table 2).\n\nNo differences on PASI and DLQI scores at 52 weeks were found on both analyses, except for worse PASI score at 52 weeks of follow-up in the subgroup of patients with PSO of 21-30 years’ evolution (Figure 1C, p=0.0163 between group 11-20 and 21-30).\n\nRanges of BMI\n\nThe analysis by BMI categories (Figures 1D, 2D), included 14, 28 and 41 patients in the BMI ranges normal-weight (18.5– 24.9), overweight (25–29.9) and obese (≥30), respectively (Figure 1D). A total of 4 patients with a BMI <18.5, were excluded from the analysis due to the small sample size. At baseline, the overweight group presented the highest PASI score (*p=0.0187; overweight vs obese patients). After 12 weeks of treatment, the PASI values decreased to 1.17 (1.29), 2.33 (3.24) and 1.73 (1.75) for the normal weight, overweight and obese, respectively (Supplementary Table 1). No differences between groups were observed at this point. The data from the 3 groups presented a trend towards a decrease until week 52, were the PASI values were 0.44 (0.61) for normal-weight, 0.49 (0.90) for overweight and 1.48 (1.33) for obese patients. The DLQI values at baseline, presented a similar score for the 3 groups: normal-weight 16.14 (4.91), overweight 16.1 (6.19) and obese 15.3 (5.25) (Figure 2). After the induction phase (12 weeks) DLQI values remain low and were maintained until 52 weeks of treatment: 1.75 (2.22) for normal-weight, 2.00 (2.16) for overweight and 2.38 (3.66) for obese patients (Supplementary Table 2).\n\nNo differences in PASI and DLQI were noted among the subgroups after 52 weeks of follow-up.\n\nPresence or absence of comorbidities\n\nFinally, subgroup analyses were also made according to the presence of baseline comorbidities including psoriatic arthritis (PSA), diabetes, dyslipidaemia, arterial hypertension, fatty liver disease, and depression (Figures 1E, 2E). A total of 28 without comorbidities and 59 patients with comorbidities, were included in this study.\n\nPatients with or without comorbidities presented a baseline PASI score of 14.29 (7.36) and 15.38 (7.02), respectively. After 12-weeks of treatment their PASI remained under 1.79 points and at the end of the study their values still decreased to 0.98 (1.19) and 0.58 (1.03), for patients with and without comorbidities, respectively (Supplementary Table 1).\n\nOn the other hand, the DLQI score at baseline was very similar between both groups (with comorbidities: 15.67 (5.23); without comorbidities: 15.92 (5.93)). At the end of the study these values decreased to 2.13 (2.87) and 0.38 (0.74), for patients with and without comorbidities, respectively (Supplementary Table 2).\n\nThere were no differences in PASI nor DLQI values for patients with and without comorbidities along the 52-weeks of study.\n\nDrug survival was evaluated in every subgroup of patients up to week 93 of treatment, to study which variables could be associated with a greater or poorer treatment maintenance.\n\nAfter 52 weeks of follow-up, no serious adverse events were detected. Only one adverse event (headache) and three discontinuations were notified (one primary failure and two secondary failures). No infections were reported.\n\nGender\n\nIn this analysis, mean follow-up time was 46.2 (25.2) for female and 49.8 (22.2) for male. At 93 weeks of treatments the survival proportions were 84.4% for women and 100% for men. The log-rank test showed a statistically significant difference among both curves (Figure 3A; p=0.0097). Four treatment discontinuations were reported, all in the female group: headache, primary failure, and two secondary failures.\n\nA) Gender; B) Ranges of age; C) Years of psoriasis evolution; D) Ranges of body mass index; E) Presence or absence of comorbidities. Log-rank (Mantel Cox) test; *, p<0.01; **, p<0.001. W/O Comorb., without comorbidities; With Comorb., with comorbidities.\n\nRanges of age\n\nThe following ranges of age, ≥25-<45, ≥45-<65, ≥65-<85, presented a mean follow up of 52.4 (21.8), 44.7 (24.9) and 44.6 (21.4) weeks, respectively. At 93 weeks of treatment, survival proportions were 93.2% (group ≥25-<45), 94.4% (group ≥45-<65) and 91.7% (group ≥65-<85) (Figure 3B). There was no difference in drug survival between groups (Figure 3B; non-significant (ns), p=0.7349). There were two discontinuations in the ≥25-<45 group (headache, secondary failure), one in the ≥45-<65 group (secondary failure) and one in the ≥65-<85 group (primary failure).\n\nYears of PSO evolution\n\nThe analysis of the four subgroups of patients attending to ranges of PSO evolution showed a mean follow-up of (weeks): 53.4 (15.3) (range 0-10 years), 49.7 (23.1) (range 11-20 years), 46.6 (26.4) (range 21-30 years) and 47.8 (25.6) (range 31-40 years). Maximum follow up for all groups were 88 weeks. At this point, the survival proportions were: 90.9% (range 0-10 years), 96% (range 11-20 years), 95.5% (range 21-30 years) and 85.7 (range 31-40 years). There was no difference in drug survival between groups (Figure 3C; ns, p=0.7321) and discontinuations were observed in all groups: two secondary failure (range 0-10 and 11-20 years), one headache (range 21-30 years) and one primary failure (range 31-40 years).\n\nRanges of BMI\n\nMean follow-up time for normal weight, overweight and obese patients was 46.6 (20.1), 49.6 (28.5) and 50.5 (17.7), respectively. The maximum common follow-up was 76 weeks, at this timepoint where the survival proportions were: 82.5% (normal weight), 90,9% (overweight) and 100% (obese). There was no difference in drug survival between groups (Figure 3D; ns, p=0.1554). There were two discontinuations in the overweight group (headache, secondary failure) and another two in the overweight group (primary and secondary failure).\n\nPresence or absence of comorbidities\n\nMean follow-up for patients with and without comorbidities was 50.6 (23.1) and 44.2 (23.6), respectively. After 88 weeks of treatment (maximum follow-up point between both groups) the survival proportions were 98,1% and 85,1% for patients with and without comorbidities, respectively. There was a trend towards a statistical significance difference between both groups (Figure 3E; ns, p=0.0534). A total of four discontinuations were reported: one in the group with comorbidities (primary failure) and three in the group without comorbidities (headache, two secondary failures).\n\nSome limitations of this study are its nature of retrospective study and the presence of unbalanced groups and subsequently the absence of adjustment in clinical and demographic basal characteristics between them. Some groups presented a limited sample size. Also, safety evaluation was suboptimal in comparison to clinical trials, due to the clinical practice setting of the study (no local inflammatory reactions have been described at the injection site, nor upper respiratory tract infections).\n\n\nDiscussion\n\nAlmost five years after the approval of GUS for moderate-to-severe PSO in patients candidates for systemic therapy, long term responses to GUS in open label extensions of RCTs and clinical practice series regarding have been published.12–14\n\nIn 2018, Gordon and colleagues published a pooled analysis of phase III VOYAGE 1 and 2 where they evaluated the efficacy of GUS vs placebo and adalimumab attending to demographic and baseline clinical characteristics.4 They analysed a total of 1829 patients in which they evaluated the percentage of patients achieving investigator's global assessment (IGA) 01/1 and IGA 0 in the study. Their conclusions were that GUS was superior to placebo at week 16 and to adalimumab at 24 weeks of treatment among different subgroups of patients (baseline demographics, disease characteristics and previous PSO treatments). Also, GUS superiority to adalimumab, evaluated by the proportion of patients achieving IGA 0/1, presented a similar response between male and female (83.9% vs 83.5%), baseline ranges of age (<45, ≥45-<65, ≥65: 87.0% vs 80.1% vs 80.5%, respectively), PSO duration (years) (<15 vs ≥15; 83.7% vs 83.8%), previous systemic and biologic treatments among others. Specifically for obese patients, GUS presented better performance than the anti-TNFα.12 To our knowledge, no DLQI comparisons have been performed with GUS in subgroups of patients. Our data indicate that demographic data do not contribute any impact on DLQI outcomes over time.\n\nWhen evaluating RWE studies, indirect comparison is complicated as data is plotted in different formats and diverse clinical parameter are used to determine PSO improvement. Even though, our data, that evaluated the effectiveness of GUS through absolute PASI, presented similar overall results. The effectiveness of GUS seems not to be impacted by gender, age, PSO duration, BMI nor by presence or absence of comorbidities over time. However, it is worth highlighting than older patients (≥65-<85) and those with longer story of PSO tended to present poorer responses than their counterparts. Also, it has to me mentioned that the lack of significant differences could be influenced at this point by a small sample size.\n\nBMI data analysis in previous reports has yielded contradictory results; in some studies a worse response has been observed in obese patients,15–34 whereas in others, no differences in response have been found among BMI subgroups.11,23 Snast et al. observed a PASI90 response at week 24 in 23% of obese patients, versus 56% in non-obese participants, but statistical significance was not reached (p=0.07).25 Galluzzo et al. did not find obesity to be associated with poorer response.23 In our study, we also observed no response differences were detected among BMI subgroups attending to absolute PASI or DLQI scores. According to another study, patients with comorbidities have poorer responses23; PASI100 response rate was 100% for patients without comorbidities, in contrast to 46.2% in participants with comorbidities.23 Our study detected no response differences among comorbidities and without comorbidities subgroups.\n\nIn general, our study showed that drug survival did not differ among subgroups defined by age, BMI, year of PSO evolution and comorbidities but was better in men vs women [Log-rank (Mantel Cox) test, p=0.0097] (Figure 3A). According to Iznardo et al,25 worse drug survival was seen in patients with psoriatic arthritis; however, we didn’t evaluate this comorbidity independently.\n\n\nConclusions\n\nOur research included a total of 87 patients treated with GUS under real world conditions. Our main goal was to evaluate the consistency of GUS efficacy across patient subgroups. Ultimately, no baseline features affected the efficacy of GUS, including sex, age, PSO duration, BMI or comorbidities. Drug survival was only affected by the gender of the patient, with worse outcomes for females (survival proportions at 93 weeks: 84.4% and 100% for women and men (p=0.0097), respectively). Our results indicated that GUS is a very versatile biologic alternative, effective, secure with a good persistence performance, for the treatment of different profile of patients found in a real practice setting. Our results are consistent with those of previous studies that demonstrated the effectiveness of GUS in non-RCT conditions.\n\n\nData availability\n\nFigshare: Effectiveness, survival and safety of guselkumab attending to basal characteristics in moderate-to-severe psoriatic patients: a cohort study. https://doi.org/10.6084/m9.figshare.20981053.v1.34\n\nThis project contains the following underlying data.\n\n- Data file 1. Demographics.csv\n\n- Data file 2. Baseline data.csv\n\n- Data file 3. Data at 12 weeks of treatment.csv\n\n- Data file 4. Data at 24 weeks of treatment.csv\n\n- Data file 5. Data at 36 weeks of treatment.csv\n\n- Data file 6. Data at 52 weeks of treatment.csv\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\nAuthors contributions\n\nConceptualization: RRV, LRFF, JCAH, APP, FVC, MGG.\n\nResources: RRV, LRFF, MGG, APG, JCAH.\n\nWriting – Original Draft Preparation: RRV.\n\nWriting – Review & Editing: RRV, LRFF, JCAH, APP, FVC, MGG.",
"appendix": "Acknowledgements\n\nThe writing of this article was supported by a medical writer.\n\n\nReferences\n\nRuiz-Villaverde R, Rodriguez-Fernandez-Freire L, Armario-Hita JC, et al.: Super responders to guselkumab treatment in moderate-to-severe psoriasis: a real clinical practice pilot series. Int. J. Dermatol. 2021; 61: 1029–1033. PubMed Abstract | Publisher Full Text\n\nMeneguin S, Aparecida De Godoy N, Fernandes Pollo C, et al.: Quality of life of patients living with psoriasis: a qualitative study.[cited 2022 May 31]. Publisher Full Text\n\nLangley RG, Elewski BE, Lebwohl M, et al.: Secukinumab in Plaque Psoriasis — Results of Two Phase 3 Trials. N. Engl. J. Med. 2014; 371(4): 326–338. PubMed Abstract | Publisher Full Text\n\nGordon KB, Blauvelt A, Papp KA, et al.: Phase 3 Trials of Ixekizumab in Moderate-to-Severe Plaque Psoriasis. N. Engl. J. Med. 2016; 375(4): 345–356. Publisher Full Text\n\nBlauvelt A, Papp KA, Griffiths CEM, et al.: Efficacy and safety of guselkumab, an anti-interleukin-23 monoclonal antibody, compared with adalimumab for the continuous treatment of patients with moderate to severe psoriasis: Results from the phase III, double-blinded, placebo- and active comparator–controlled VOYAGE 1 trial. J. Am. Acad. Dermatol. 2017; 76(3): 405–417. PubMed Abstract | Publisher Full Text\n\nGordon KB, Strober B, Lebwohl M, et al.: Efficacy and safety of risankizumab in moderate-to-severe plaque psoriasis (UltIMMa-1 and UltIMMa-2): results from two double-blind, randomised, placebo-controlled and ustekinumab-controlled phase 3 trials. Lancet. 2018; 392(10148): 650–661. PubMed Abstract | Publisher Full Text\n\nBlauvelt A: T-Helper 17 Cells in Psoriatic Plaques and Additional Genetic Links between IL-23 and Psoriasis. J. Investig. Dermatol. 2008; 128(5): 1064–1067. PubMed Abstract | Publisher Full Text\n\nLangley RG, Tsai TF, Flavin S, et al.: Efficacy and safety of guselkumab in patients with psoriasis who have an inadequate response to ustekinumab: results of the randomized, double-blind, phase III NAVIGATE trial. Br. J. Dermatol. 2018; 178(1): 114–123. PubMed Abstract | Publisher Full Text\n\nRuiz-Villaverde R, Rodriguez-Fernandez-Freire L, Armario-Hita JC, et al.: Guselkumab: Mid-term effectiveness, drug survival, and safety in real clinical practice. Dermatol. Ther. 2021; 34(2). Publisher Full Text\n\nChalmers RJG: Assessing Psoriasis Severity and Outcomes for Clinical Trials and Routine Clinical Practice. Dermatol. Clin. 2015; 33(1): 57–71. PubMed Abstract | Publisher Full Text\n\nFinlay AY, Khan GK: Dermatology Life Quality Index (DLQI)-a Simple Practical Measure for Routine Clinical Use.1994; Vol 19.\n\nGordon KB, Blauvelt A, Foley P, et al.: Efficacy of guselkumab in subpopulations of patients with moderate-to-severe plaque psoriasis: a pooled analysis of the phase III VOYAGE 1 and VOYAGE 2 studies Funding sources. British Journal of Dermatology Linked Comment: Feldman Br. J. Dermatol. 2018; 178: 132–139. Publisher Full Text\n\nWorld Health Organization: Global report on psoriasis.2016 [cited 2022 May 31].Reference Source\n\nReich K, Armstrong AW, Langley RG, et al.: Guselkumab versus secukinumab for the treatment of moderate-to-severe psoriasis (ECLIPSE): results from a phase 3, randomised controlled trial. Lancet. 2019 Sep 7; 394(10201): 831–839. PubMed Abstract | Publisher Full Text\n\nCarrascosa J-M, Jacobs I, Petersel D, et al.: Biosimilar Drugs for Psoriasis: Principles, Present, and Near Future. Dermatol. Ther. (Heidelb). 2018 Jun; 8(2): 173–194. PubMed Abstract | Publisher Full Text\n\nLópez-Sánchez C, Puig L: Guselkumab in the treatment of moderate-to-severe plaque psoriasis. Immunotherapy. 2020 Apr; 12(6): 355–371. Publisher Full Text\n\nArmstrong AW, Read C: Pathophysiology, Clinical Presentation, and Treatment of Psoriasis: A Review. JAMA. 2020 May 19; 323(19): 1945–1960. PubMed Abstract | Publisher Full Text\n\nBen Abdallah H, Johansen C, Iversen L: Key Signaling Pathways in Psoriasis: Recent Insights from Antipsoriatic Therapeutics. Psoriasis (Auckl). 2021; 11: 83–97. PubMed Abstract | Publisher Full Text\n\nTremfya|European Medicines Agency.Reference Source\n\nBoehncke W-H, Brembilla NC, Nissen MJ: Guselkumab: the First Selective IL-23 Inhibitor for Active Psoriatic Arthritis in Adults. Expert. Rev. Clin. Immunol. 2021 Jan; 17(1): 5–13. PubMed Abstract | Publisher Full Text\n\nReich K, Armstrong AW, Foley P, et al.: Efficacy and safety of guselkumab, an anti-interleukin-23 monoclonal antibody, compared with adalimumab for the treatment of patients with moderate to severe psoriasis with randomized withdrawal and retreatment: Results from the phase III, double-blind, placebo- and active comparator-controlled VOYAGE 2 trial. J. Am. Acad. Dermatol. 2017 Mar; 76(3): 418–431. PubMed Abstract | Publisher Full Text\n\nGriffiths CEM, Papp KA, Kimball AB, et al.: Long-Term Efficacy of Guselkumab for the Treatment of Moderate-to-Severe Psoriasis: Results from the Phase 3 VOYAGE 1 Trial Through Two Years. J. Drugs Dermatol. 2018 Aug 1; 17(8): 826–832. PubMed Abstract\n\nGriffiths CEM, Papp KA, Song M, et al.: Continuous treatment with guselkumab maintains clinical responses through 4 years in patients with moderate-to-severe psoriasis: results from VOYAGE 1. J. Dermatolog. Treat. 2020 Jul 13; 33: 848–856. Publisher Full Text\n\nReich K, Griffiths CEM, Gordon KB, et al.: Maintenance of clinical response and consistent safety profile with up to 3 years of continuous treatment with guselkumab: Results from the VOYAGE 1 and VOYAGE 2 trials. J. Am. Acad. Dermatol. 2020 Apr; 82(4): 936–945. PubMed Abstract | Publisher Full Text\n\nBenhadou F, Ghislain PD, Guiot F, et al.: Real-life effectiveness and short-term (16-week) tolerance of guselkumab for psoriasis: a Belgian retrospective multicentre study. J. Eur. Acad. Dermatol. Venereol. 2020 Dec; 34(12): e837–e839. PubMed Abstract | Publisher Full Text\n\nFougerousse A-C, Ghislain P-D, Reguiai Z, et al.: Effectiveness and short-term (16-week) tolerance of guselkumab for psoriasis under real-life conditions: a retrospective multicenter study. J. Eur. Acad. Dermatol. Venereol. 2020 Oct; 34(10): e644–e646. PubMed Abstract | Publisher Full Text\n\nLee EB, Reynolds KA, Pithadia DJ, et al.: Drug survival of guselkumab for psoriasis in a real-world setting: a single-center retrospective chart review. J. Dermatolog. Treat. 2020 Jun; 31(4): 342–343. PubMed Abstract | Publisher Full Text\n\nMegna M, Fabbrocini G, Cinelli E, et al.: Guselkumab in moderate to severe psoriasis in routine clinical care: an Italian 44-week real-life experience. J. Dermatolog. Treat. 2020 Aug 4; 33: 1074–1078. Publisher Full Text\n\nBonifati C, Morrone A, Cristaudo A, et al.: Effectiveness of anti-interleukin 23 biologic drugs in psoriasis patients who failed anti-interleukin 17 regimens. A real-life experience. Dermatol. Ther. 2021 Jan; 34(1): e14584. PubMed Abstract | Publisher Full Text\n\nMaliyar K, O’Toole A, Gooderham MJ: Long-Term Single Center Experience in Treating Plaque Psoriasis With Guselkumab. J. Cutan. Med. Surg. 2020 Dec; 24(6): 588–595. PubMed Abstract | Publisher Full Text\n\nRuggiero A, Fabbrocini G, Cinelli E, et al.: Efficacy and safety of guselkumab in psoriasis patients who failed ustekinumab and/or anti- interleukin -17 treatment: A real-life 52-week retrospective study. Dermatol. Ther. 2020 Dec; 34. Publisher Full Text\n\nGalluzzo M, Tofani L, Lombardo P, et al.: Use of Guselkumab for the Treatment of Moderate-to-Severe Plaque Psoriasis: A 1 Year Real-Life Study. J. Clin. Med. 2020 Jul 9; 9(7). PubMed Abstract | Publisher Full Text\n\nSnast I, Sherman S, Holzman R, et al.: Real-life experience of guselkumab in patients with psoriasis. Dermatol. Ther. 2020 Nov; 33(6): e13964. PubMed Abstract | Publisher Full Text\n\nRuiz-Villaverde R, Fernández-Freire LR, Armario-Hita JC, et al.: Effectiveness, survival and safety of guselkumab attending to basal characteristics in moderate-to-severe psoriatic patients: a cohort study. figshare. Dataset.2022. Publisher Full Text"
}
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[
{
"id": "153465",
"date": "01 Nov 2022",
"name": "Pedro Mendes-Bastos",
"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\nI consider this study to be of high value in order to gain greater insight into guselkumab’s behaviour as a psoriasis treatment in the real world setting. It brings valuable information and the conclusions are soundly based on the results; however, minor revisions are needed. These revisions are listed below.\n\"It impacts the general quality of life (usually measured by the dermatology life quality index (DLQI)) and the pruritus that may cause (visual analog scale (VAS) pruritus) and influences the psychological sphere, work productivity as well as personal and family relationships.” - This sentence needs rewriting because it is not clear.\n\n\"anti-interleukin (IL)-173,4 and anti-IL23p19.” - Antagonists at the end?\n\n\"Our current understanding of the pathophysiology of PSO...\" - It’s better to replace \"has been driven” by “is characterized by a cytokine disbalance with predominant involvement of the interleukin (IL)-23/Th-17 axis, as well as keratinocyte hyperproliferation and immune activation”.\n\n\"and was confirmed by their therapeutic success\". The “was” is missing.\n\nCorrect the sentence, according to this suggestion: \"Furthermore, GUS treatment has been compared to other biologics, such as secukinumab, and the CLEAR head-to-head trial proved the superiority of this anti-IL23p19 antagonist.\"\n\nThe sentence: \"GUS was superior to placebo at week 16 and superior to adalimumab at week 24 in all subpopulations except in the Black or African American population, which included few patients” is not clear. ADA was superior to GUS in the Black or African American population? This is not clear. Please rewrite the sentence.\n\n\"Kaplan-Meyer\" needs uniformization across the manuscript as it is spelled differently. Please uniformize.\n\nPlease correct: \"As a limitation of the study, we did not applied any method to avoid bias.” - \"we did not apply\" would be the grammatically correct form.\n\nIn the methods section, you need to define what “moderate-to-severe psoriasis” meant when recruiting. Was it just a question of PASI>10? Was it PASI>10 or DLQI>10? Was it other criteria? Please provide a sentence to clarify.\n\nPrimary failure was considered a failure to reach PASI 90 or PASI>3 after applying the biologics and secondary failure is defined as failure to maintain PASI 90 or PASI>3 after 12 weeks of treatment. - This sentence is confusing and needs clarification. What was the timeline for primary failure evaluation? PASI<3, right? Please rewrite the sentence.\n\n\"Safety was also evaluated attending to treatment-emerging adverse events (AEs), serious AEs and discontinuations due to AEs and/or lack of efficacy (primary or secondary failure).“ \"attending\" —> change to \"according\", please. I don’t understand how safety is assessed through a lack of efficacy.\n\n\"No laboratory tests were performed” - Not at all, or the performed laboratory tests were not considered for analysis in this study? Please clarify.\n\n\"fat liver\" —> Please change to \"fatty liver disease\".\n\n\"Their clinical characteristic scores were PASI 14.6 (7.2), BSA 22.3 (16.6), VAS pruritus 6.0 (2.2) and DLQI 15.8 (5.4)” - Do you mean their mean characteristics scores? Please add “mean”.\n\n\"DLQI values at baseline were 17.00 (3.51) for female and 15.09 (5.79) for male (Figure 2A). After 12 weeks, DLQI decreased markedly to 1.85 (2.67) and 1.88 (3.15) for women and men, respectively (Supplementary Table 2). DLQI values also remain low after one year of treatment” - It looks as if the last sentence is missing the mean information for DLQI at 52 weeks. Could you include it?\n\n\"At baseline the PASI value for the groups ≥25-<45, ≥45-<65, ≥65-<85 was 14.18 (5.79), 13.72 (7.13) and 17.32 (8.90), respectively.“ - Do you mean their means scores? Please add “mean”.\n\n\"After 12 weeks of treatment the value corresponding to this ranges of age ≥25-<45, ≥45-<65, ≥65-<85 was 1.70 (1.79), 1.15 (1.32) and 3.04 (3.80) respectively; and after 52 weeks these values remained low at 0.58 (0.96), 1.15 (1.25) and 1.05 (1.42) respectively (Supplementary Table 1). - Do you mean their means scores? Please add “mean”.\n\n\"The DLQI value presented with a similar trend showing at baseline values of 15.54 (5.18), 15.76 (5.04) and 16.45 (7.15) (Figure 2B). After 12 weeks of treatment, all the groups presented a DLQI score lower than 1.7 and after 52 weeks of treatments the DLQI values were 1.1 (1.59), 2.5 (3.38) and 0.5 (0.71) for the ranges of age ≥25-<45, ≥45-<65, ≥65-<85, respectively (Supplementary Table 2).”- Do you mean their means scores? Please add “mean”.\n\n\"PASI values at base line were 12.68 (4.19), 16.23 (8.76), 12.67 (5.3), 17.69 (8.34) for the following groups, respectively, 0-10, 11-20, 21-30, 31-40. After 12 weeks, all values remained under a score of 2.2 and at 52-weeks of treatment PASI values were 0.77 (0.59), 0.23 (0.83), 1.75 (1.26) and 0.5 (0.71) for the 0-10, 11-20, 21-30, 31-40 ranges of age, respectively (Figure 1C) (Supplementary Table 1).” - Do you mean their means scores? Please add “mean”.\n\n\"The DLQI values, presented a similar trend as PASI’s“ —> remove the ’s, please.\n\n\"After 12 weeks of treatment, the PASI values decreased to 1.17 (1.29), 2.33 (3.24) and 1.73 (1.75) for the normal weight, overweight and obese, respectively (Supplementary Table 1).\" - Do you mean their means scores? Please add “mean”.\n\n\"The data from the 3 groups presented a trend towards a decrease until week 52, were the PASI values were 0.44 (0.61) for normal-weight, 0.49 (0.90) for overweight and 1.48 (1.33) for obese patients. The DLQI values at baseline, presented a similar score for the 3 groups: normal-weight 16.14 (4.91), overweight 16.1 (6.19) and obese 15.3 (5.25) (Figure 2). After the induction phase (12 weeks) DLQI values remain low and were maintained until 52 weeks of treatment: 1.75 (2.22) for normal-weight, 2.00 (2.16) for overweight and 2.38 (3.66) for obese patients (Supplementary Table 2).” - Do you mean their means scores? Please add “mean”.\n\"were the PASI values were 0.44 “ —> This part is not clear. Please correct the language.\n\n\"A total of 28 without comorbidities and 59 patients with comorbidities, were included in this study.” - Remove the comma.\n\n\"Patients with or without comorbidities presented a baseline PASI score of 14.29 (7.36) and 15.38 (7.02), respectively. After 12-weeks of treatment their PASI remained under 1.79 points and at the end of the study their values still decreased to 0.98 (1.19) and 0.58 (1.03), for patients with and without comorbidities, respectively (Supplementary Table 1).\" - Do you mean their means scores? Please add “mean”.\n\n\"Drug survival was evaluated in every subgroup of patients up to week 93 of treatment, to study which variables could be associated with a greater or poorer treatment maintenance.” - Remove the comma.\n\n\"In this analysis, mean follow-up time was 46.2 (25.2) for female and 49.8 (22.2) for male.“ - Do you mean weeks? Please add “weeks”.\n\n\"Almost five years after the approval of GUS for moderate-to-severe PSO in patients candidates for systemic therapy, long term responses to GUS in open label extensions of RCTs and clinical practice series regarding have been published.” - Please remove “regarding”.\n\n\"Even though, our data, that evaluated the effectiveness of GUS through absolute PASI, presented similar overall results.” - Please correct the language. I suggest: “Despite of that, by evaluating the effectiveness of GUS through absolute PASI, our data presented similar overall results”.\n\n\"Our results indicated that GUS is a very versatile biologic alternative, effective, secure with a good persistence performance, for the treatment of different profile of patients found in a real practice setting.“ - This sentence needs language correction. I suggest: \"Our results indicate that GUS is a very versatile biologic drug for the treatment of different profiles of patients found in a real practice setting, showing effectiveness, safety, and a favorable persistence performance.”\n\n\"Acknowledgments: The writing of this article was supported by a medical writer.\" - Could you provide the name of the medical writer or the company for which he/she works? It would be more transparent.\nI would appreciate if all the corrections are sent to me separately or highlighted in the text for easier revision. Thank you.\n\nIs the background of the cases’ history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the conclusion balanced and justified on the basis of the findings? Yes",
"responses": [
{
"c_id": "8972",
"date": "07 Nov 2022",
"name": "Ricardo Ruiz Villaverde",
"role": "Author Response",
"response": "Response to reviewer: To Dr. Mendes Bastos, I consider this study to be of high value in order to gain greater insight into guselkumab’s behaviour as a psoriasis treatment in the real world setting. It brings valuable information and the conclusions are soundly based on the results; however, minor revisions are needed. These revisions are listed below. AUTHOR REPLY: Thank you very much for the exhaustive review you have carried out on our manuscript which will allow us to improve its quality. \"It impacts the general quality of life (usually measured by the dermatology life quality index (DLQI)) and the pruritus that may cause (visual analog scale (VAS) pruritus) and influences the psychological sphere, work productivity as well as personal and family relationships.” - This sentence needs rewriting because it is not clear. AUTHOR REPLY: It has been rephrasing according to the reviewer's suggestion. \"anti-interleukin (IL)-173,4 and anti-IL23p19.” - Antagonists at the end? AUTHOR REPLY: Selective blockers. \"Our current understanding of the pathophysiology of PSO...\" - It’s better to replace \"has been driven” by “is characterized by a cytokine disbalance with predominant involvement of the interleukin (IL)-23/Th-17 axis, as well as keratinocyte hyperproliferation and immune activation”. AUTHOR REPLY: It has been rephrasing according to the reviewer's suggestion. \"and was confirmed by their therapeutic success\". The “was” is missing. AUTHOR REPLY. It has been added. Correct the sentence, according to this suggestion: \"Furthermore, GUS treatment has been compared to other biologics, such as secukinumab, and the CLEAR head-to-head trial proved the superiority of this anti-IL23p19 antagonist.\" AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. The sentence: \"GUS was superior to placebo at week 16 and superior to adalimumab at week 24 in all subpopulations except in the Black or African American population, which included few patients” is not clear. ADA was superior to GUS in the Black or African American population? This is not clear. Please rewrite the sentence. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Kaplan-Meyer\" needs uniformization across the manuscript as it is spelled differently. Please uniformize. AUTHOR REPLY: It has been reviewed. We totally agreed with the reviewer. Please correct: \"As a limitation of the study, we did not applied any method to avoid bias.” - \"we did not apply\" would be the grammatically correct form. AUTHOR REPLY: It has been reviewed. We totally agreed with the reviewer. In the methods section, you need to define what “moderate-to-severe psoriasis” meant when recruiting. Was it just a question of PASI>10? Was it PASI>10 or DLQI>10? Was it other criteria? Please provide a sentence to clarify. AUTHOR REPLY: It has been reviewed and all the criteria have been added. Primary failure was considered a failure to reach PASI 90 or PASI>3 after applying the biologics and secondary failure is defined as failure to maintain PASI 90 or PASI>3 after 12 weeks of treatment. - This sentence is confusing and needs clarification. What was the timeline for primary failure evaluation? PASI<3, right? Please rewrite the sentence. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Safety was also evaluated attending to treatment-emerging adverse events (AEs), serious AEs and discontinuations due to AEs and/or lack of efficacy (primary or secondary failure).“ \"attending\" —> change to \"according\", please. I don’t understand how safety is assessed through a lack of efficacy. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion \"No laboratory tests were performed” - Not at all, or the performed laboratory tests were not considered for analysis in this study? Please clarify. AUTHOR REPLY: It has been reviewed and clarified. \"fat liver\" —> Please change to \"fatty liver disease\". AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Their clinical characteristic scores were PASI 14.6 (7.2), BSA 22.3 (16.6), VAS pruritus 6.0 (2.2) and DLQI 15.8 (5.4)” - Do you mean their mean characteristics scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"DLQI values at baseline were 17.00 (3.51) for female and 15.09 (5.79) for male (Figure 2A). After 12 weeks, DLQI decreased markedly to 1.85 (2.67) and 1.88 (3.15) for women and men, respectively (Supplementary Table 2). DLQI values also remain low after one year of treatment” - It looks as if the last sentence is missing the mean information for DLQI at 52 weeks. Could you include it? AUTHOR REPLY: The values have been added. \"At baseline the PASI value for the groups ≥25-<45, ≥45-<65, ≥65-<85 was 14.18 (5.79), 13.72 (7.13) and 17.32 (8.90), respectively.“ - Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"After 12 weeks of treatment the value corresponding to this ranges of age ≥25-<45, ≥45-<65, ≥65-<85 was 1.70 (1.79), 1.15 (1.32) and 3.04 (3.80) respectively; and after 52 weeks these values remained low at 0.58 (0.96), 1.15 (1.25) and 1.05 (1.42) respectively (Supplementary Table 1). - Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"The DLQI value presented with a similar trend showing at baseline values of 15.54 (5.18), 15.76 (5.04) and 16.45 (7.15) (Figure 2B). After 12 weeks of treatment, all the groups presented a DLQI score lower than 1.7 and after 52 weeks of treatments the DLQI values were 1.1 (1.59), 2.5 (3.38) and 0.5 (0.71) for the ranges of age ≥25-<45, ≥45-<65, ≥65-<85, respectively (Supplementary Table 2).”- Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"PASI values at base line were 12.68 (4.19), 16.23 (8.76), 12.67 (5.3), 17.69 (8.34) for the following groups, respectively, 0-10, 11-20, 21-30, 31-40. After 12 weeks, all values remained under a score of 2.2 and at 52-weeks of treatment PASI values were 0.77 (0.59), 0.23 (0.83), 1.75 (1.26) and 0.5 (0.71) for the 0-10, 11-20, 21-30, 31-40 ranges of age, respectively (Figure 1C) (Supplementary Table 1).” - Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"The DLQI values, presented a similar trend as PASI’s“ —> remove the ’s, please. AUTHOR REPLY: It has been removed. \"After 12 weeks of treatment, the PASI values decreased to 1.17 (1.29), 2.33 (3.24) and 1.73 (1.75) for the normal weight, overweight and obese, respectively (Supplementary Table 1).\" - Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"The data from the 3 groups presented a trend towards a decrease until week 52, were the PASI values were 0.44 (0.61) for normal-weight, 0.49 (0.90) for overweight and 1.48 (1.33) for obese patients. The DLQI values at baseline, presented a similar score for the 3 groups: normal-weight 16.14 (4.91), overweight 16.1 (6.19) and obese 15.3 (5.25) (Figure 2). After the induction phase (12 weeks) DLQI values remain low and were maintained until 52 weeks of treatment: 1.75 (2.22) for normal-weight, 2.00 (2.16) for overweight and 2.38 (3.66) for obese patients (Supplementary Table 2).” - Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"were the PASI values were 0.44 “ —> This part is not clear. Please correct the language. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"A total of 28 without comorbidities and 59 patients with comorbidities, were included in this study.” - Remove the comma. AUTHOR REPLY: It has been removed. \"Patients with or without comorbidities presented a baseline PASI score of 14.29 (7.36) and 15.38 (7.02), respectively. After 12-weeks of treatment their PASI remained under 1.79 points and at the end of the study their values still decreased to 0.98 (1.19) and 0.58 (1.03), for patients with and without comorbidities, respectively (Supplementary Table 1).\" - Do you mean their means scores? Please add “mean”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Drug survival was evaluated in every subgroup of patients up to week 93 of treatment, to study which variables could be associated with a greater or poorer treatment maintenance.” - Remove the comma. AUTHOR REPLY: It has been removed. \"In this analysis, mean follow-up time was 46.2 (25.2) for female and 49.8 (22.2) for male.“ - Do you mean weeks? Please add “weeks”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Almost five years after the approval of GUS for moderate-to-severe PSO in patients candidates for systemic therapy, long term responses to GUS in open label extensions of RCTs and clinical practice series regarding have been published.” - Please remove “regarding”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Even though, our data, that evaluated the effectiveness of GUS through absolute PASI, presented similar overall results.” - Please correct the language. I suggest: “Despite of that, by evaluating the effectiveness of GUS through absolute PASI, our data presented similar overall results”. AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Our results indicated that GUS is a very versatile biologic alternative, effective, secure with a good persistence performance, for the treatment of different profile of patients found in a real practice setting.“ - This sentence needs language correction. I suggest: \"Our results indicate that GUS is a very versatile biologic drug for the treatment of different profiles of patients found in a real practice setting, showing effectiveness, safety, and a favorable persistence performance.” AUTHOR REPLY: It has been rephrased according to the reviewer's suggestion. \"Acknowledgments: The writing of this article was supported by a medical writer.\" - Could you provide the name of the medical writer or the company for which he/she works? It would be more transparent. AUTHOR REPLY: It has been added."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1178
|
https://f1000research.com/articles/10-1044/v1
|
15 Oct 21
|
{
"type": "Research Article",
"title": "Changes in mammography screening in Ontario and Alberta following national guideline dissemination: an interrupted time series analysis",
"authors": [
"Christine Fahim",
"Natasha Wiebe",
"Rosane Nisenbaum",
"Jemila S. Hamid",
"Joycelyne E. Ewusie",
"Marcello Tonelli",
"Paula Brauer",
"Elizabeth Shaw",
"Neil Bell",
"Dawn Stacey",
"Nathalie M. Holmes",
"Sharon E. Straus",
"Natasha Wiebe",
"Rosane Nisenbaum",
"Jemila S. Hamid",
"Joycelyne E. Ewusie",
"Marcello Tonelli",
"Paula Brauer",
"Elizabeth Shaw",
"Neil Bell",
"Dawn Stacey",
"Nathalie M. Holmes",
"Sharon E. Straus"
],
"abstract": "Background: In November 2011, the Canadian Task Force on Preventive Health Care released guidelines for screening women at average breast cancer risk. Weak recommendations (framed using GRADE methodology) were made for screening women aged 50 to 74 years every two to three years, and for not screening women aged 40 to 49 years.\nMethods: We conducted an interrupted time series analysis using administrative data to examine bilateral mammography use before and after a national guideline dissemination strategy targeting primary care physicians. Women aged 40 to 74 years living in Ontario or Alberta from 30th November 2008 to 30th November 2014 were included. Strata included age, region of residence, neighbourhood income quintile, immigration status, and education level.\nResults: In both provinces, mammography use rates were lower in the post-intervention period (527 vs. 556 and 428 vs. 465/1000 participant-months - the monthly screening rate/1000 - in Ontario and Alberta, respectively). In Ontario, mammography trends decreased following guideline release to align with recommendations for women aged 40 to 74 (decrease of 2.21/1000 women, SE 0.26/1000, p<0.0001). In Alberta, mammography trends decreased for women aged 40 to 49 years (3/1000 women, SE 0.32, p<0.001) and 50 to 69 (2.9/1000 women, SE 0.79, p<0.001), but did not change for women aged 70 to 74 (0.7/1000 women, SE 1.23, p=0.553). In both provinces, trends in mammography use rates were sustained for up to three years after guideline release.\nConclusions: The guideline dissemination strategy appeared to increase uptake of guideline-concordant screening practice in women aged 40 to 49 years in Ontario and Alberta and for women aged 50 to 74 years in Ontario. Further work is required to understand these findings and whether shared decision making about mammography between women and providers increased among women considering mammography.",
"keywords": [
"Breast Cancer",
"Mammography",
"Screening",
"Preventive Health Care",
"Knowledge Translation"
],
"content": "Abbreviations\n\nAKDN: Alberta Kidney Disease Network\n\nCCI: Canadian Classification of Health Intervention procedure codes\n\nCMAJ: Canadian Medical Association Journal\n\nICES: Institute for Clinical Evaluative Sciences\n\nITS: Interrupted Time Series\n\nOBSP: Ontario Breast Screening Program\n\nOCR: Ontario Cancer Registry\n\nOHIP: Ontario Health Insurance Program\n\nRPDB: Registered Persons Database\n\nTask Force: Canadian Task Force on Preventive Health Care\n\n\nIntroduction\n\nThe Canadian Task Force on Preventive Health Care (Task Force) was reconstituted in 2009 to develop and disseminate evidence-based clinical practice guidelines to support preventive practices in primary care. Breast cancer screening was the first topic selected for guideline development because the U.S. Preventive Services Task Force1 had produced recommendations in 2009 favouring screening for women aged 40 years and older, yet questions about costs and benefits remained given the lower rate of breast cancer at younger ages and the potential risk of harms.2\n\nBreast cancer is the most common cancer in Canadian women with one in eight women receiving a diagnosis over her lifetime and one in thirty-three dying from the disease. In 2020, there were an estimated 27,400 new cases and 5,100 deaths from breast cancer, which is 13% of all cancer deaths in women in Canada. Mammography can identify asymptomatic breast cancer, but there are harms associated with screening, including overdiagnosis.3 Several provinces and countries have implemented breast cancer screening programs with established targets; for instance, Alberta Health Services identified a target of screening 70% of eligible women aged 50 to 74 years every two years, which is consistent with the Canadian target of screening 70% of eligible women every 30 months.\n\nIn 2011, the Task Force aimed to provide a recent review of evidence to inform breast cancer screening practices. In keeping with the use of Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology, the Task Force reviewed available evidence using a systematic review to develop screening guidelines for women at average risk of breast cancer (see Box 1 for recommendations).4 The Task Force developed weak recommendations based on moderate to low quality evidence. In keeping with GRADE methods, weak recommendations are those for which the benefits probably outweigh the harms, or the harms probably outweigh the benefits, but uncertainty exists.4,5 The guidelines also highlighted the need for clinicians to help patients make a decision that is consistent with the patient’s informed values and preferences.4 This guideline was an update to the 2001 guideline published by the Task Force which recommended screening with mammography every one to two years for women aged 50 to 69.6,7\n\nRecommendations follow the Grading of Recommendations Assessment, Development and Evaluation (GRADE) nomenclature\n\n• For women aged 40–49 years we recommend not routinely screening with mammography. (Weak recommendation; moderate quality evidence)\n\n• For women aged 50–69 years we recommend routinely screening with mammography every two to three years. (Weak recommendation; moderate quality evidence)\n\n• For women aged 70–74 years we recommend routinely screening with mammography every two to three years. (Weak recommendation; low quality evidence)\n\nThe Task Force developed a tailored guideline dissemination strategy in partnership with stakeholder groups, including primary care physicians and women in the target age groups. We evaluated the impact of this dissemination strategy by investigating mammography use in Ontario and Alberta before and after the strategy was implemented.\n\nThe objective of this study was to determine, using an interrupted time series, the impact of the 2011 Task Force breast cancer screening guidelines on rates of mammography screening by age group in Ontario and Alberta. We hypothesized that there would be a significant change in mammography screening rates over time to align with the Task Force breast cancer recommendations, and that effects would be sustained for up to three years post-guideline release.\n\n\nMethods\n\nWe performed an interrupted time series (ITS) analysis to examine mammography use in Ontario and Alberta 36 months before (30th November 2008 to 30th November 2011) and after (1st December 2011 to 30th November 2014) the breast cancer screening guidelines were released in Canada in November 2011.\n\nThis study was approved by the Unity Health Toronto Research Ethics Board (REB# 12-220). Participant consent was waived by the REB, given all data analyses were conducted by ICES and Alberta Health Services using aggregate, non-identifiable data.\n\nWe included women aged 40 to 74 years who lived in Ontario or Alberta between November 2008 and November 2014. In Ontario, the Registered Persons Database (RPDB) and the Ontario Cancer Registry (OCR) were used to identify eligible participants. The databases were accessed and linked by ICES scientists8,9 and not by members of the study team. The OCR database is considered the most comprehensive cancer registry in the province; the Institute for Clinical Evaluative Sciences (ICES) has access to data from January 1964 to present. Via a validated administrative algorithm, we identified eligible participants in Ontario; we used International Classification of Diseases for Oncology (ICD-O-3) C50 topography codes to identify women with a diagnosis of breast cancer. The algorithm is a sequence of programming codes in SAS software to assemble the cohort of people who were alive (i.e. no death date or death date was after the index date), were eligible for health care (i.e. date of end of eligibility was after the index date), and had an Ontario postal code at the index date. There is no available link to the SAS codes. Women with a history of breast cancer and/or a bilateral mastectomy before each period were excluded from the analysis. Bilateral mastectomy was identified using the Canadian Classification of Health Intervention (CCI) procedure codes. In Alberta, the Alberta Kidney Disease Network (AKDN) database (incorporating data from Alberta Health), which includes >99% of adult Albertans, was used to identify participants.10 MT had access to de-identified data in the AKDN database; specifically, no health care numbers or names were available. For Alberta data, a validated administrative algorithm was used to identify and exclude women with a history of breast cancer using ICD-9 174 and ICD-10 C50 codes and 1 hospitalization or 2 claims in 2 years.11,12 Procedure codes from claims data (CCP codes 97.12A, 97.12B, and 97.22A) were used to exclude women with previous bilateral mastectomies (extended data).\n\nThe intervention was the Task Force’s guideline dissemination strategy, which included theory- and evidence-based printed and online education materials and a mass media campaign.13–18 The content of the education materials was based on the guideline recommendations, discussions with stakeholders about barriers to implementing the recommendations, and barriers to guideline implementation. The mass media campaign focused on key messages for the target audiences as identified from discussions with the Task Force and its stakeholders. The detailed approach to developing and testing the education materials is available online. The guidelines were published in the Canadian Medical Association Journal (CMAJ) on 21st November 2011 accompanied by a mass media launch.4 The print CMAJ (including the guidelines) was mailed to over 60,000 primary care and specialty physicians nationally. The printed education materials provided in this mailing included a one-page decision algorithm for patients and clinicians, and a one-page ‘Frequently Asked Questions’ document for patients and clinicians. These education materials were also available on the Task Force’s website along with a patient decision aid infographic explaining the risks and benefits of mammograms, a video and script that role modelled shared decision making (the process for patients and physicians to collectively make a decision regarding treatment), a presentation on the methods used to create the guidelines, and the systematic review used to inform guideline development.19\n\nData were cleaned to ensure that participants were adult and female. The Ontario and Alberta datasets were analysed separately and were not linked. NW conducted and oversaw the analysis of the Alberta data and RN oversaw the analysis of the Ontario data. Use of bilateral mammogram was the primary outcome, identified from the Ontario Health Insurance Program (OHIP, fee code in ‘X185’ and ‘X178’) and Ontario Breast Screening Program (OBSP) databases in Ontario and the AKDN claims data (CCP codes X27C, X27D, X27E)10 in Alberta. For both Ontario and Alberta data, a mammogram was considered a duplicate if repeated within seven days and was then removed from the data; the date of the first mammogram within each time period was used for analysis. Additional variables collected included age group, setting (rural versus non-rural), income quintile, immigrant status, visible minority status1, and education status. Urban area was defined as having a population of at least 1,000 and a density of 400 or more people per square kilometre. Income quintile was used as a proxy for the women’s socioeconomic status and was based on their postal code (neighbourhood) using Statistics Canada census data. Immigrant status and visible minority status were defined as the percentage of immigrants and visible minorities in the postal code, respectively. Education was specified as the proportion of women with a bachelor’s degree as the highest level of educational attainment. Details on immigrant, minority, and education status were not available for Alberta participants.\n\nData were summarized descriptively using mammography counts and rates per 1000 participant-months. Data from each province were aggregated monthly to calculate rates (number of monthly screening tests/1000 participant-months) and ITS was performed using segmented regression. The model was defined as:\n\nwhere Ratet is the rate of breast cancer screening at each month t (t = 1 to 72 months) and et is the random error at time t. β0 is the intercept or pre-intervention baseline level of the rate; β1 is the slope of the rate until the intervention is introduced (slope prior to the intervention); β2 is the change in rate level that occurs in the period immediately following the introduction of intervention; and β3 is the change in rate trend (i.e. difference between post-intervention and pre-intervention slopes). We used this approach to test the significance of β2 (an immediate intervention effect) and β3 (significant intervention effect over time to determine sustained impact).21\n\nSubgroup analyses were performed for age categories. In Ontario, subgroup analyses were also separately performed by rural or urban setting, neighbourhood income quintile (mean income per person equivalent in an area obtained from census data), education categories (population in a neighbourhood with a bachelor’s degree), immigration categories (population in a neighbourhood of immigrant status), and minority categories (created as a % of visible minority in a total population by postal code). The cut off values for categories were determined using distributions of the 1st and 3rd quartiles (interquartile range) of the neighbourhood distributions at pre- and post-intervention periods.\n\nFor Ontario data, regression parameters were estimated by maximum likelihood using SAS Enterprise Guide, version 7.15 software procedure AUTOREG (SAS Institute Inc., Cary, NC, USA), which adjusts for autocorrelation.22,23 For Alberta data, analysis was conducted using Stata MP 15.1 software command ‘itsa’; however, the same models and parameters were used.24 Canadian mammography screening is recommended every 24 to 36 months25; final models included autogressive terms for only up to 12 lags, selected by backward elimination. The Durbin-Watson statistic was calculated to test autocorrelation terms. All statistical tests were two-sided and statistical significance was defined as a p-value less than 0.05.\n\n\nResults\n\nDescriptive\n\nA total of 2,935,241 women were included before guideline dissemination and 3,098,205 women were included after dissemination; the cohorts had similar demographic characteristics (Table 1). Overall, the number of women who had a mammogram decreased in the post-intervention period compared to pre-intervention (527 versus 556 per 1000 participant-months, respectively). Similar trends were observed in women aged 40 to 49 and 50 to 69 years. The proportion of women aged 70 to 74 years who underwent a mammogram was slightly higher in the post-intervention period (Table 1). Both at pre- and post-guideline release, women in higher income quintiles (compared to lower quintiles) and women in rural areas (compared to urban areas) had higher screening mammography use.\n\nITS results\n\nAmong women aged 40 to 49 years, monthly screening mammography rates increased before the guideline release (slope 0.06/1000, SE 0.01/1000, p < 0.0001). Immediately following the guideline release, there was a significant rate decrease of 2.21 per 1000 women (SE 0.26/1000, p < 0.0001) who received a mammogram. This rate was sustained; however, the slope was not, meaning the rate of women who received a mammogram did not continue to decrease further during this period (Table 2, Figure 1).\n\nAmong women aged 50 to 69 years, monthly screening mammography rates decreased before the guideline release (Table 2). Immediately following the guideline release, there was a significant increase of 3.82 per 1000 women who received a mammogram. This rate was sustained; however, the slope was not.\n\nAmong women aged 70 to 74 years, monthly screening mammography rates decreased before the guideline release (Table 2). Immediately following the guideline release, there was a significant increase of 7.50 per 1000 women who received a mammogram. This rate was sustained three years following the intervention.\n\nAmong all women, rates of mammography screening were significantly declining pre-guideline release; following the release, a significant decrease in mammography use was observed in all income quintiles and across all education levels. There were no significant changes to the slopes in the three years following the guideline release. Similar trends (significantly decreasing slope, increase in mammography use, no significant difference in slope three years after guideline release) were observed across neighbourhoods with a low, moderate, or high percentage of women who were immigrants or identified as a visible minority and among women in urban and rural areas (Table 2).\n\nDescriptive\n\nA total of 788,131 women were included pre-intervention and 861,014 women were included post-intervention; demographic details are provided in Table 1. Overall, mammography use decreased post-intervention compared to pre-intervention (428 versus 465 per 1000 participant-months, respectively).\n\nThese trends were observed in women aged 40 to 74 years. In both the pre- and post-intervention periods, women in higher income quintiles had increased rates of mammography use compared to women in low income quintiles (Table 1). In Alberta, women residing in urban areas had higher rates of mammography use pre- and post-intervention as compared to women residing in rural areas.\n\nITS results\n\nAmong women aged 40 to 49 years, monthly screening mammography rates in Alberta were slightly decreasing before guideline release. Immediately following guideline release, there was a significant rate decrease of 3 per 1000 women who received a mammogram. This rate was sustained; however, the rate of women who received a mammogram did not decrease further during this period (post- minus pre-intervention slope difference 0.0015/1000, SE 0.02/1000, p = 0.933).\n\nAmong women aged 50 to 69 years, monthly screening mammography rates were stable. Immediately following the guideline release, there was a significant decrease of 2.9 per 1000 women who received a mammogram; this rate was sustained for the remainder of the study period (Figure 2, Table 3).\n\nAmong women aged 70 to 74 years, monthly screening mammography rates were stable before the guideline release. Immediately following the guideline release, there were no significant changes in the rate of women aged 70 to 74 who received a mammogram.\n\nAll strata (by age, income quintile, rural/urban region) experienced significant drops in mammography rates at intervention, with the exception of women 70 to 74 years. Prior to the intervention, most slopes were stable pre- and post-intervention with the exception of women 40 to 49 years (rate decreased immediately post-intervention) and women in high income quintiles, who demonstrated a slight decrease in mammography use prior to guideline release (Income Q5, see Table 3). Trends were stable three years following guideline release, with the exception of women living in rural areas, for whom mammography rates continued to decrease over time.\n\n\nDiscussion\n\nIn comparing rates of mammography screening following guideline dissemination, we observed trend differences in the two provinces. Overall, Alberta women underwent less mammography screening both pre- and post-guideline dissemination compared to Ontario women. In both provinces, fewer women underwent mammography in the 36 months after guideline dissemination compared to the same period before guidelines were released. In Ontario, mammography rates among women aged 40 to 49 years decreased immediately following guideline release and increased for women aged 50 to 74, in keeping with the guideline recommendations. In Alberta, mammography use decreased for women aged 40 to 69 and did not significantly change among women aged 70 to 74. In Ontario, mammography use decreased overall following guideline release across all income quintiles and education levels and among women living in both urban and rural areas. Similarly, in Alberta, mammography decreased among women in all income quintiles and decreased for women living in both urban and rural areas; the rate of mammography use continued to decrease among women living in rural areas in Alberta.\n\nIn both Ontario and Alberta, mammography among women aged 40 to 49 years immediately decreased following guideline release. This decrease may correlate with the difference in screening recommendations in the 2011 guideline compared to the previous 2001 Task Force guideline, which suggested that upon reaching the age of 40, women should consider the benefits and risks of screening to determine whether to begin routine mammography between 40 and 49 or whether to delay until age 50.7 Similarly, rates of mammography among women aged 50 to 59 in Alberta may have decreased following the recommendation for extending screening intervals to 2 to 3 versus 1 to 2 years.25,26\n\nOur results are similar to findings reported in the United States (U.S.), where an overall decline in mammography for women aged 40 to 49 years was observed post-dissemination of the 2009 U.S. Preventive Services Task Force guidelines.27–29 For women aged 50 to 69 years, U.S. studies showed a decline in mammography following release of their national guidelines, which were similar to the Task Force recommendations.27–29 Given the Canadian Task Force’s weak (or ‘conditional’) recommendation to screen women aged 50 to 69 and advice to engage in shared decision making about screening, fewer women may have decided not to undergo screening.4\n\nHigher income levels were associated with more screening. These results are similar to those from other studies of breast cancer screening conducted in the U.S.30–34 and Canada.35 In Ontario, women living in rural areas had higher mammogram screening rates compared to women living in urban areas; this may indicate the effect of organized screening programs in rural communities. Additional studies further examining trends in Canadian breast cancer screening, particularly following the most recent 2018 release of the Task Force's breast cancer guideline update, may provide further insights into these trends.\n\nThere are several limitations to this study. Firstly, individual level data (such as exact age, education status, ethnicity) were not available; rather, these data were available as categories, and education and immigration status were only available at a neighbourhood level. Consequently, we were not able to investigate the impact of patient level factors on screening activities. Secondly, there may have been other interventions targeting breast cancer screening in Ontario and Alberta during the study periods. In Ontario, for instance, Cancer Care Ontario launched a campaign to increase screening for breast, cervical, and prostate cancer in November 2012. This media campaign encouraged people to send cards to friends and family to undergo cancer screening. However, the Task Force engaged provincial partners on the guidelines and we were not able to identify any large-scale strategies that may have overlapped with dissemination. An additional confounder may be that pay-per-performance models (meaning practitioners receive compensation based on their activities, such as screening, and not a standard salary) were introduced in Ontario at this time; however, the models don’t definitively explain the trends observed in this study, as the literature is not conclusive on the impact of these models on rates of breast cancer screening.36,37 In addition, we were not able to assess the use of shared decision making, which was recommended in the guideline, as these data are not captured in administrative databases. Finally, these data were not created to answer the specific research question, which is a limitation of all population-level administrative database studies.\n\nIn summary, the decline in mammography for women aged 40 to 49 years was in alignment with guideline recommendations. Future strategies should focus on optimizing implementation of the recommendations for women aged 50 to 74 years. This requires understanding barriers to behavioural changes at the clinician and patient level and investigating the use of shared decision making.\n\n\nData availability\n\nThe datasets generated and analysed during the current study are not publicly available. They could potentially be made available with assistance from the corresponding author, if for the purpose of further research. Obtaining Ontario data which are owned by the Ontario Ministry of Health and Long-Term Care would require providing a research protocol and consultation with ICES, who will also request a budget be submitted for data access and analysis. Researchers could alternatively request to obtain a similar dataset for Alberta or Ontario data.\n\nOpen Science Framework: Changes in mammography screening in Ontario and Alberta following national guideline dissemination: an interrupted time series analysis. http://doi.org/10.17605/OSF.IO/5H2T8.38\n\nThis project contains the following extended data:\n\n- Supplementary File 1: Sustaining Change_OntarioandAlbertaPopulationData\n\n- Supplementary File 2: Supplementary File 2_Sustaining Change_OntarionandAlbertaCodes\n\nData are available under the terms of the CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.\n\n\nDisclaimer\n\nThis study is based in part by data provided by Alberta Health and Alberta Health Services. The interpretation and conclusions contained herein are those of the researchers and do not represent the views of the Government of Alberta or Alberta Health Services. Neither the Government of Alberta nor Alberta Health Services express any opinion in relation to this study.",
"appendix": "Acknowledgements\n\nThe authors thank Fatiah De Matas for her assistance with the figures. SES is funded by a Tier 1 Canada Research Chair; MT is funded by the David Freeze chair in Health Services Research; DS is funded by a University of Ottawa Research Chair.\n\n\nReferences\n\nNelson HD, Tyne K, Naik A, et al.: Screening for breast cancer: an update for the US Preventive Services Task Force. Ann. Intern. Med. 2009; 151: 727–37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNelson HD, Pappas M, Cantor A, et al.: Harms of breast cancer screening: systematic review to update the 2009 US Prevetive Services Task Force Recommendation. Ann. Intern. Med. 2016; 164: 256–67. PubMed Abstract | Publisher Full Text\n\nWoloshin S, Schwartz LM: The benefits and harms of mammography screening: understanding the trade-offs. JAMA. 2010; 303(2): 164–5. PubMed Abstract | Publisher Full Text\n\nThe Canadian Task Force on Preventive Health Care: Recommendations on screening for breast cancer in average-risk women aged 40-74 years. CMAJ. 2011; 183: 1991–2001. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuyatt GH, Oxman AD, Vist GE, et al.: GRADE: an emerging consensus on rating quality of evidence and strength of recommendations. BMJ. 2008; 336(7650): 924–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStrumpf EC, Chai Z, Kadiyala S: Adherence to cancer screening guidelines across Canadian provinces: an observational study. BMC Cancer. 2010; 10: 304. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRingash J, ; the Canadian Task Force on Preventive Health Care: Preventive health care, 2001 update: screening mammography among women aged 40-49 years at average risk of breast cancer. CMAJ. 2001; 164(4) 469–76. PubMed Abstract | Free Full Text\n\nICES Data & Privacy: Data Dictionary.Reference Source\n\nSchull MJ, Azimaee M, Marra M, et al.: ICES: Data, Discovery, Better Health. Int J Popul Data Sci. 2020; 4(2): 1135. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHemmelgarn BR, Clement F, Manns BJ, et al.: Overview of the Alberta kidney disease network. BMC Nephrol. 2009; 10(1): 30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTonelli M, Wiebe N, Fortin M, et al.: Methods for identifying 30 chronic conditions: application to administrative data. BMC Med. Inform. Decis. Mak. 2015; 15(1): 31. Publisher Full Text\n\nPenberthy L, McClish D, Pugh A, et al.: Using hospital discharge files to enhance cancer surveillance. Am. J. Epidemiol. 2003; 158(1): 27–34. PubMed Abstract | Publisher Full Text\n\nMichie S, Johnston M, Abraham C, et al.: Making psychological theory useful for implementing evidence based practice: a consensus approach. Qual. Saf. Health Care. 2005; 14(1): 26–33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMichie S, Johnston M, Francis J, et al.: From theory to intervention: mapping theoretically derived behavioural determinants to behaviour change techniques. Appl. Psychol. 2008; 57(4): 660–80. Publisher Full Text\n\nCabana MD, Rand CS, Powe NR, et al.: Why don't physicians follow clinical practice guidelines?: A framework for improvement. JAMA. .1999; 282(15): 1458–65. PubMed Abstract | Publisher Full Text\n\nGrimshaw J, Thomas R, MacLennan G, et al.: Effectiveness and efficiency of guideline dissemination and implementation strategies. Health Technol. Assess. 2004; 8. PubMed Abstract | Publisher Full Text\n\nGrilli R, Ramsay C, Minozzi S: Mass media interventions: effects on health services utilisation. Cochrane Libr. 2002. Publisher Full Text\n\nFarmer AP, Légaré F, Turcot L, et al.: Printed educational materials: effects on professional practice and health care outcomes. Cochrane Database Syst. Rev. 2008; 3(3). Publisher Full Text\n\nCanadian Task Force on Preventive Health Care: Breast Cancer Update (2011).Reference Source\n\nStatistics Canada: 2006 Census of Population – Visible minority groups (15).Reference Source\n\nHuitema BE, McKean JW: Design specifications issues in time-series intervention models. Educ. Psychol. Meas. 2000; 60(1): 38–58. Publisher Full Text\n\nSAS Institute Inc: SAS Enterprise Guide version 7.15.Cary, NC, USA.\n\nPenfold RB, Zhang F: Use of interrupted time series analysis in evaluating health care quality improvements. Acad. Pediatr. 2013; 13(6 Suppl): S38–44. Publisher Full Text\n\nStataCorp MP 15.1: Stata Statistical Software: Release 15. College Station, TX:StataCorp LLC.;2017.\n\nCanadian Task Force on the Periodic Health Examination: Canadian Guide to Clinical Preventive Health Care. Ottawa:Health Canada;1994.\n\nU.S Preventive Services Task Force Guide to Clinical Preventive Services: An Assessment of the Effectiveness of 169 Interventions. Baltimore, Maryland:Williams and Wilkins;1989.\n\nRutten LJF, Ebbert JO, Jacobson DJ, et al.: Changes in US preventive services task force recommendations: effect on mammography screening in Olmsted County, MN 2004–2013. Prev. Med. 2014; 69: 235–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWharam JF, Landon B, Zhang F, et al.: Mammography rates 3 years after the 2009 US Preventive Services Task Force guidelines changes. J. Clin. Oncol. 2015; 33(9): 1067–74. PubMed Abstract | Publisher Full Text\n\nLee JY, Malak SF, Klimberg VS, et al.: Change in Mammography Use Following the Revised Guidelines from the US Preventive Services Task Force. Breast J. 2017; 23(2): 164–8. PubMed Abstract | Publisher Full Text\n\nSprague BL, Bolton KC, Mace JL, et al.: Registry-based study of trends in breast cancer screening mammography before and after the 2009 US Preventive Services Task Force recommendations. Radiology. 2014; 270(2): 354–61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCummings DM, Whetstone LM, Earp JA, et al.: Disparities in mammography screening in rural areas: analysis of county differences in North Carolina. J. Rural. Health. 2002; 18(1): 77–83. PubMed Abstract | Publisher Full Text\n\nHarris DM, Miller JE, Davis DM: Racial differences in breast cancer screening, knowledge and compliance. J. Natl. Med. Assoc. 2003; 95(8): 693–701. PubMed Abstract | Free Full Text\n\nDavis TC, Arnold C, Berkel HJ, et al.: Knowledge and attitude on screening mammography among low-literate, low-income women. Cancer. 1996; 78(9): 1912–20. PubMed Abstract | Publisher Full Text\n\nEheman CR, Benard VB, Blackman D, et al.: Breast cancer screening among low-income or uninsured women: results from the National Breast and Cervical Cancer Early Detection Pogram, July 1995 to March 2002 (United States). Cancer Causes Control. 2006; 17(1): 29–38. PubMed Abstract | Publisher Full Text\n\nVahabi M, Lofters A, Kumar M, et al.: Breast cancer screening disparities among immigrant women by world region of origin: a population-based study in Ontario, Canada. Cancer Med. 2016; 5(7): 1670–86. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKiran T, Wilton AS, Moineddin R, et al.: Effect of payment incentives on cancer screening in Ontario primary care. Ann. Fam. Med. 2014; 12(4): 317–23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nScott A, Sivey P, Ouakrim DA, et al.: The effect of financial incentives on the quality of health care provided by primary care physicians. Cochrane Database Syst. Rev. 2011; 7(9): CD008451. Publisher Full Text\n\nFahim C, Wiebe N, Nisenbaum R, et al.: Changes in mammography screening in Ontario and Alberta following national guideline dissemination: an interrupted time series analysis. OSF. 2021. Publisher Full Text\n\n\nFootnotes\n\n1 ‘Visible minority’ is a term used in the ICES database. 20"
}
|
[
{
"id": "148600",
"date": "20 Sep 2022",
"name": "Sisse Helle Njor",
"expertise": [
"Reviewer Expertise Evaluation of cancer screening"
],
"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\nPage 4, 'Setting and participants' line 2: What information did you receive from the Cancer Registry?\nPage 4, 'Setting and participants' last 2 lines: For readers that do not know the system it would be nice to know what '1 hospitalization or 2 claims in 2 years' means.\nPage 4, 'Outcomes' line 7: '…. was considered a duplicate if repeated within seven days…' Does this mean that two mammograms are included if they are more than 7 days apart. If yes, the authors should discuss how this has affected their results\nPage 5, 'Statistical analysis', line 1: How is participant-month defined and calculated?\nPage 5, 'Descriptive', line 2: It would be nice to have proportions in table 1, so that it is easy to see that the cohorts had similar demographic characteristics.\nPage 10, 'ITS results': It is surprising that the decrease for 40-49y is almost similar in Alberta and Ontarios as the decrease seem to be quite larger in Alberta, when you look at figure 1 and 2.\nPage 12, 'Discussion', last 2 lines: Please explain why we then also see a decrease in Ontario among those aged 50-69y. At the moment there is only an explanation for Alberta. A minor thing: Shouldn't 50 to 59 …. be 50 to 69?\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": "8979",
"date": "07 Nov 2022",
"name": "Christine Fahim",
"role": "Author Response",
"response": "Response to Reviewer 1 Page 4, 'Setting and participants' line 2: What information did you receive from the Cancer Registry? Thank you for this question. The Ontario Cancer Registry (OCR) was used to exclude women from the analysis – specifically those with a history of breast cancer prior to the start of the study period. We used dxcode = 174.x, where x is any digit. Women with mastectomy at any time prior to the start of the period were also excluded. Page 4, 'Setting and participants' last 2 lines: For readers that do not know the system it would be nice to know what '1 hospitalization or 2 claims in 2 years' means. Thank you. This refers to our exclusion of women with hospitalization of breast cancer or malignant neoplasm of the breast; we have specified this in the manuscript. Page 4, 'Outcomes' line 7: '…. was considered a duplicate if repeated within seven days…' Does this mean that two mammograms are included if they are more than 7 days apart. If yes, the authors should discuss how this has affected their results. Thank you for this comment. We did not explore the number of mammograms per woman; rather, whether a woman received a mammogram, or not, within the study period. Page 5, 'Statistical analysis', line 1: How is participant-month defined and calculated? Thank you for flagging this. Our interrupted time series was calculated as the number of monthly screening tests divided by the total number of women at risk at the beginning of the month. We have clarified this in the methods and have removed use of the term ‘participant month’ to avoid confusion. Page 5, 'Descriptive', line 2: It would be nice to have proportions in table 1, so that it is easy to see that the cohorts had similar demographic characteristics. Thank you, in addition to the totals, we provide the rates per 1000 women to allow for comparisons across the pre/post guideline groups. Page 10, 'ITS results': It is surprising that the decrease for 40-49y is almost similar in Alberta and Ontario as the decrease seem to be quite larger in Alberta, when you look at figure 1 and 2. Thank you for this comment. In Ontario, screening for women 40-49years was increasing before the guideline release and decreased by 2.21/ 1000 women immediately following release. In Alberta, mammography screening was slightly decreasing pre guideline release. Following the release there was a decrease of 3/1000 women. Page 12, 'Discussion', last 2 lines: Please explain why we then also see a decrease in Ontario among those aged 50-69y. At the moment there is only an explanation for Alberta. A minor thing: Shouldn't 50 to 59 …. be 50 to 69? Thank you for this comment. We did not observe a decrease in Ontario for those 50-69. Rather, we observed an increase of 3.8/1000 women who underwent mammography screening. With respect to Alberta, mammography decreased for women aged 40-49 and for women aged 50-69, but increased slightly for women aged 70-74 (please see Table 3). We therefore indicate that “in Alberta, mammography use decreased for women aged 40-69”."
}
]
},
{
"id": "148598",
"date": "20 Sep 2022",
"name": "Jacqueline M. Hirth",
"expertise": [
"Reviewer Expertise Population health",
"primary and secondary cancer prevention",
"women's 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 manuscript described the change in mammography screening, as a rate of screenings per 1000 participant months, in Ontario and Alberta, Canada, before and after a national change in guideline on mammography. While the topic is important in assessing the impact of guidelines on practice, there are some issues the authors may want to consider addressing to strengthen their manuscript.\nGeneral\nIn the abstract and body of the paper, the new guidelines are described as “weak recommendations.” This description gives the impression that the authors may feel that the guidelines are inappropriate. Therefore, we suggest that this wording be amended to, “recommendations based on weak evidence.” This would help an international audience get a clearer picture of what is meant by the authors.\n\nThe purpose of the paper is not well-developed. There is mention of a dissemination strategy, which is discussed in the methods, but does not seem to be tested for or mentioned in the conclusion. If there was no comparison for differences in dissemination strategies, then it appears that the manuscript evaluates the effect of the guideline change on mammography rates, but not dissemination strategy of the guidelines. We recommend changing the second to last paragraph in the introduction to reflect that dissemination strategy was not assessed and the methods section to reflect that it was the change in guidelines that was assessed rather than the dissemination strategy.\nAbstract\nAmend description of “weak recommendations” to “recommendations based on weak evidence.”\n\nRecommend removing information about dissemination strategy in line with recommendations above.\n\nRecommend clarifying that “trends in mammography use rates” be changed to “declining trends in mammography use rates” in last sentence of results in abstract. Consider removing standard errors to stay within word limit.\n\nRecommend changing conclusion to indicate that it was the guideline that changed uptake, rather than the dissemination strategy.\n\nThe conclusion does not match the results in the abstract. The results indicate a decrease in mammography trends, but the conclusion indicates that there was an increased uptake in guideline-concordant screening practice. As this was not actually assessed (would require individual level data) the conclusion would be more accurate if discussed along the lines of, “decreasing trends in mammography rates among 40-49 year old women indicated that this group may be receiving fewer screenings, possibly in response to the new guidelines.”\nIntroduction\nThe dissemination strategy was not elaborated on in the introduction. Since this study did not test the dissemination strategy, it is recommended that the description of the strategy be moved from Methods section to the Introduction section.\n\nChange “weak recommendations” to “recommendations based on weak evidence.”\nMethods\nWe recommend reorganization of the methods section.\nBegin with the setting and participants with integration of the dates of data collection in the current first sentence, followed by the ethics statement then Outcomes and statistical analysis.\n\nWe recommend that the description of the dissemination strategy be shortened and included in the Introduction section.\n\nWe recommend that the statistical analyses used (ITS) be moved to the statistical analyses section. The method used for this study looked like a retrospective population surveillance study.\n\nProvide a justification for using interrupted times series analyses in the statistical analyses section.\n\nResults\nWere the women included in the study cohorts? This was mentioned in sentence 1 of Results section. With shifting ages across the timeline, it seems they could be described as the “study population,” as women would shift into different age groups across the times assessed.\n\nRecommend using p-value designation of <0.001 in last column of tables where currently 0.0000 is listed, as these are more accepted statistical notations in the literature.\n\nIn the Alberta results section, Alberta was mentioned in the text as well as subheading. Would be more clear if the Ontario section was written in similar fashion. At first I thought that the total population estimates were for the entire study, not just Ontario.\nDiscussion\nIt appears new results are added in first paragraph. We saw no evidence of direct comparisons of mammography rates between Alberta and Ontario in the results section. Recommended to amend statistical analyses section and results section accordingly. The first paragraph of the Discussion section could then be the final paragraph of the Results section.\n\nLast sentence in 3rd paragraph not clear. If fewer women decided not to undergo screening, wouldn’t the trend have been positive after guideline implementation?\n\nConsider subheadings for Limitations and Conclusion sections.\n\nThe Conclusion section in the Discussion appears to differ from the conclusion in the Abstract.\n\nGiven the importance placed on shared decision-making in the conclusion, more context could be given in the Introduction and/or Discussion section(s).\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? Partly",
"responses": [
{
"c_id": "8980",
"date": "07 Nov 2022",
"name": "Christine Fahim",
"role": "Author Response",
"response": "Response to Reviewer 2 This manuscript described the change in mammography screening, as a rate of screenings per 1000 participant months, in Ontario and Alberta, Canada, before and after a national change in guideline on mammography. While the topic is important in assessing the impact of guidelines on practice, there are some issues the authors may want to consider addressing to strengthen their manuscript. General 1. In the abstract and body of the paper, the new guidelines are described as “weak recommendations.” This description gives the impression that the authors may feel that the guidelines are inappropriate. Therefore, we suggest that this wording be amended to, “recommendations based on weak evidence.” This would help an international audience get a clearer picture of what is meant by the authors. Thank you for this comment. Our language is consistent with that of GRADE methodology (https://bestpractice.bmj.com/info/toolkit/learn-ebm/what-is-grade/; PMCID: PMC4364259) that provides a tool for rating the quality of evidence for clinical guidelines. GRADE recommendations can be ‘strong’ or ‘weak’ depending on the strength of the evidence. According to the GRADE definition, “weak recommendations imply that there is likely to be an important variation in the decision that informed persons are likely to make.. a weak recommendation indicates that engaging in a shared decision making process is essential, while a strong recommendation suggests that it is not usually necessary to present both options” (Siemieniuk and Guyatt, BMJ). Because the Canadian Task Force used GRADE methodology to develop their guideline and recommendations, we believe it is important to refer to the terms that the guideline developers used. However, we appreciate the author’s guidance that ‘weak recommendations’ may be unclear and we have ensured details around GRADE methodology have been included in the introduction. 2. The purpose of the paper is not well-developed. There is mention of a dissemination strategy, which is discussed in the methods, but does not seem to be tested for or mentioned in the conclusion. If there was no comparison for differences in dissemination strategies, then it appears that the manuscript evaluates the effect of the guideline change on mammography rates, but not dissemination strategy of the guidelines. We recommend changing the second to last paragraph in the introduction to reflect that dissemination strategy was not assessed and the methods section to reflect that it was the change in guidelines that was assessed rather than the dissemination strategy. Thank you for this important point. The dissemination strategy was passive and was disseminated via avenues considered ‘routine’ for primary care practitioners (including via a leading Canadian medical journal, at conferences, etc.) The aim was to determine mammography trends following release of the guideline and the dissemination strategy, rather than test the dissemination strategy in a controlled study design. We recognize that the findings may not be causally linked to the dissemination strategy, and we have amended our introduction to clarify the purpose and outline potential confounders in our limitations section. We have also clarified the study objective in the introduction. Abstract 1. Amend description of “weak recommendations” to “recommendations based on weak evidence.” In order to remain consistent with GRADE language, we have revised this sentence to “weak recommendations based on GRADE terminology (i.e., the benefits and risks are closely balanced and/or uncertain). 2. Recommend removing information about dissemination strategy in line with recommendations above. Thank you, we have removed “dissemination strategy targeting primary care physicians” from the abstract and the sentence in the abstract now reads “We conducted an interrupted time series analysis using administrative data to examine bilateral mammography use before and after release of a national breast cancer screening guideline”. 3. Recommend clarifying that “trends in mammography use rates” be changed to “declining trends in mammography use rates” in last sentence of results in abstract. Consider removing standard errors to stay within word limit. Thank you for this comment. The trends did not decline in all cases. While we saw a decrease in screening for all women in Ontario, and for women aged 40-69 in Alberta, we did not see a decrease among women aged 70-74 in Alberta. 4. Recommend changing conclusion to indicate that it was the guideline that changed uptake, rather than the dissemination strategy. Thank you, we have revised the concluding sentence. 5. The conclusion does not match the results in the abstract. The results indicate a decrease in mammography trends, but the conclusion indicates that there was an increased uptake in guideline-concordant screening practice. As this was not actually assessed (would require individual level data) the conclusion would be more accurate if discussed along the lines of, “decreasing trends in mammography rates among 40-49 year old women indicated that this group may be receiving fewer screenings, possibly in response to the new guidelines.” Thank you for this comment. We have revised the wording as suggested by the reviewer. Introduction 1. The dissemination strategy was not elaborated on in the introduction. Since this study did not test the dissemination strategy, it is recommended that the description of the strategy be moved from Methods section to the Introduction section. Thank you; our goal was to evaluate the impact of guideline release, which was disseminated using a national strategy. We thus have kept the description of the strategy in the methods section. We recognize there are limitations to drawing conclusions of impact of the strategy, which we have outlined in the limitations. 2. Change “weak recommendations” to “recommendations based on weak evidence.” Please see comments above regarding consistency with GRADE language. Methods We recommend reorganization of the methods section. 1. Begin with the setting and participants with integration of the dates of data collection in the current first sentence, followed by the ethics statement then Outcomes and statistical analysis. Thank you for this suggestion. We have reorganized the methods section accordingly. 2. We recommend that the description of the dissemination strategy be shortened and included in the Introduction section. Thank you, please see above comment for our rationale. 3. We recommend that the statistical analyses used (ITS) be moved to the statistical analyses section. The method used for this study looked like a retrospective population surveillance study. Thank you, we have provided details on the ITS in the statistical analysis section. 4. Provide a justification for using interrupted times series analyses in the statistical analyses section. Thank you, this has been provided. Results 1. Were the women included in the study cohorts? This was mentioned in sentence 1 of Results section. With shifting ages across the timeline, it seems they could be described as the “study population,” as women would shift into different age groups across the times assessed. Thank you for this comment. We have revised “cohorts” to “study populations”. 2. Recommend using p-value designation of <0.001 in last column of tables where currently 0.0000 is listed, as these are more accepted statistical notations in the literature. Thank you for this suggestion, we have updated the tables accordingly. 3. In the Alberta results section, Alberta was mentioned in the text as well as subheading. Would be more clear if the Ontario section was written in similar fashion. At first I thought that the total population estimates were for the entire study, not just Ontario. Thank you for this suggestion, we have added “in Ontario” to provide clarity for this section. Discussion 1. It appears new results are added in first paragraph. We saw no evidence of direct comparisons of mammography rates between Alberta and Ontario in the results section. Recommended to amend statistical analyses section and results section accordingly. The first paragraph of the Discussion section could then be the final paragraph of the Results section. Thank you. We have moved the first paragraph of the discussion to the results. 2. Last sentence in 3rd paragraph not clear. If fewer women decided not to undergo screening, wouldn’t the trend have been positive after guideline implementation? We observed a decrease in screening rates for all women, except for those aged 70-74 in Alberta. 3. Consider subheadings for Limitations and Conclusion sections. Thank you for this suggestion. We have added subheadings for Limitations and Conclusions. 4. The Conclusion section in the Discussion appears to differ from the conclusion in the Abstract. Thank you; we have revised our wording to ensure consistency and clarity. 5. Given the importance placed on shared decision-making in the conclusion, more context could be given in the Introduction and/or Discussion section(s). Thank you; we have added included wording on shared decision making in the introduction, and have also described the concept in the ‘intervention’ section of the methods."
}
]
}
] | 1
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https://f1000research.com/articles/10-1044
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https://f1000research.com/articles/11-1266/v1
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07 Nov 22
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{
"type": "Research Article",
"title": "Indonesia mixed contraception method skewness background 1997-2012: A mixed method study",
"authors": [
"Dyah Utari"
],
"abstract": "Background: Indonesia's decentralization policy adopted in 1999 had implications for the programs of national ministries and agencies, including the family planning program. Since 1999, there has been a \"relaxation in family planning program effort\" since many districts have a low commitment to family planning. The trend of contraceptive mix in Indonesia leading to hormonal methods, especially injections, has occurred since 2007. This study aimed to describe the mixed conditions of contraception in Indonesia from 1997 to 2012 and explore the link between the availability of facilities and infrastructure with this plan. Methods: The quantitative research used was a cross-sectional design using secondary data from the Indonesian Demographic and Health Survey (IDHS), and In-depth interviews were employed as the qualitative approach in this study. It was found based on the results of the quantitative analysis that the trend of contraceptive mix tilted to the injection method. Results: The qualitative study results indicate that the contraceptive mix is affected by infrastructure as the main factor. Conclusion: In conclusion, there is a close relationship between the decentralization policy and the condition of the contraceptive mix. Thus, it is recommended that the central and local governments re-prioritize family planning programs and assure the availability of supporting facilities and infrastructure.",
"keywords": [
"contraceptive mix",
"family planning programs",
"decentralization"
],
"content": "Introduction\n\nThe global population is currently around 7.7 billion people, with an average increase of 2.2 percent per year.1 The total fertility rate in the world will be 2.406 in 2020.2 Within this range, Indonesia ranked 102 with a Total Fertility Rate (TFR) of 2.6 in 2012.3 The population growth rate Laju Pertumbuhan Penduduk (LPP) for the 2000-2010 period was 1.49%, which was an increase compared to the 1990-2000 period, which was 1.45%.4\n\nIncreasing fertility will reduce economic growth5; according to the theory of Malthus (1798), the high fertility rate results in poverty due to limited natural resource carrying capacity.6 A study conducted in China in 2007 by Li and Zhang revealed that economic growth negatively correlates with fertility and population growth.7\n\nDecreased fertility creates demographic dividends by increasing the ratio of the labor force to total dependency.8 The most important factor affecting fertility decline is contraceptives.9 Meeting contraceptive needs can change the future and lives of millions of women in poor and developing countries.10 Smaller families will improve family welfare.11\n\nA factor that can sustain a sustainable decline in fertility is strengthening family planning services by expanding the choice of methods offered to the community. This result is in line with research conducted by Magadi and Curtis. Preferences, needs, and beliefs regarding contraception vary widely in society. Magadi and Curtis' study concluded that family planning programs must be able to accommodate the varying needs of contraceptive users.12\n\n50% or more of contraceptive users in a country use mixed contraceptive methods. Shifting the contraceptive mix is very important for the government, donor countries (aid providers), and researchers who study contraceptive dynamics.13 The proportion of the contraceptive mix defined by the reproductive health community has no optimal or ideal term, and the ideal distribution can be seen generally from a woman's optimal reproductive time.14\n\nSkewed contraceptive method mix and unequal access are still a problem in poor and developing countries.13,15,16 A study in 2006 showed that 34 of the 96 countries studied had a mixed type of contraception that deviated (skewed).17 A similar study by Bertrand et al. in 2014 indicated that 33 of the 109 countries had a skewed method mix.13 A high concentration of one or more specific types of contraception is a sign that the available methods in the community are not evenly distributed.17\n\nSince 2007, Indonesia has already had mixed views towards hormonal methods, particularly injections.3 This skewness, however, is thought to be the result of several factors, including lack of knowledge among acceptors about the method used, provider preferences for specific methods because the incentives received by providers for using the injection method are too high, and support and promotion for the use of vasectomy and implants. Moreover, tubectomy lacks15 and limited access, make acceptors choose only available and affordable methods.\n\nThe implications of decentralization in health services include service delivery, health financing, and workforce. Decentralization is associated with more positive primary health services women receive.18 The goverment has the most crucial role in the success of the family planning program through the use of contraceptives.19\n\nIn Indonesia, the problem that developed after establishing the decentralization policy was the decline in the institutional capacity of the family planning program, this happened because the commitment of each region was different depending on political conditions and leadership. Political commitment, policy, and investment in the health system can increase access to family planning.10 An exploratory study conducted by Budisuari and Rachmawati in 2011 in East Java, Bali, and Central Kalimantan concluded that these policy differences resulted in the absence of a clear vertical path as to who was responsible for causing a lack of coordination in terms of the provision of tools there was an incompatibility between the needs and the tools provided by the central government.20 A study conducted in West Kalimantan concluded that the obstacles to implementing family planning programs were caused by a decrease in the number of Penyuluh Lapangan Keluarga Berencana/Family Planning Educator (PLKB) and the ability of local government budgets to provide contraceptives.21\n\nThis study aims to:\n\n1. Obtain an overview of trends in the contraceptive mix in Indonesia in 1997, 2003, 2007, and 2012;\n\n2. Analyze the variables that most influence the selection of contraceptives;\n\n3. Analyze the implications of decentralization policies on the contraceptive mix in Indonesia.\n\nIt is hoped that the results can provide policy input to related stakeholders.\n\n\nMethods\n\nThis study used a combination approach including quantitative methods and qualitative methods. The quantitative research used was a cross-sectional design using secondary data from the Indonesian Demographic and Health Survey (IDHS). The data used were the 1997 IDHS, 2003 IDHS, 2007 IDHS, and 2012 IDHS to see the contraceptive mix trend. The qualitative element of the research used in-depth interviews which were conducted in December 2017 with six informants from each of the selected provinces.\n\nThe research was carried out in two stages:\n\n1. The first stage examined the trend of the contraceptive mix in 1997 (before decentralization), 2003, and 2007 (when decentralization was implemented), and 2012 (representing current conditions). The data used in this stage was data on the percentage distribution of the use of various contraceptive methods, collected from the Indonesian Demographic and Health Survey (IDHS) in 1997, 2003, 2007 and 2012. The data was then processed to determine the occurrence of skewed contraceptive mix by looking at the distribution. If there is one method that has a distribution of more than 50%, it can be concluded that there was a downward trend in the contraceptive mix in that year.\n\n2. The second stage examined the implications of the decentralization policy on the contraceptive mix. This stage was carried out through in-depth interviews with informants\n\nQuantitative phase\n\nThe sample of this study were all women who met the inclusion criteria in 1997, 2003, 2007, and 2012 IDHS data. The inclusion criteria for the study were as follows:\n\n1. Age 15-49 years\n\n2. Married and or been married before\n\n3. Using modern contraceptives\n\nMeanwhile, the exclusion criteria were incomplete data. The number of samples obtained after selecting the inclusion criteria for the survey was 18,186 respondents.\n\nThis study was a further analysis of the Demographic and Health Survey (IDHS) data. The data used were the 1997 IDHS, 2003 IDHS, 2007 IDHS, and 2012 IDHS data.\n\nThe sample in the 1997 IDHS is a replication of the 1994 IDHS sample. The sample is stratified by province and type of urban and rural areas. The first stage of sample selection was Area Enumeration. Samples were selected systematically using proportional probability according to the size of the population. The second step involved selecting approximately 70 families with clear boundaries and only one segment was selected with a proportional probability measure. The third step was to select 25 families for each segment using systematic sampling.\n\nThe sample frame used in the 2007 IDHS was differentiated according to the stages of selecting the sampling unit, namely the sample frame for selecting the census block and the sample frame for selecting households. In the selection of census blocks, the sample frame used was the list of selected 2007 SAKERNAS (Survei Angkatan Kerja Nasional/National Labor Force Survey) census blocks. For household selection, the sample frame used was the list of households resulting from the 2007 SAKERNAS listing.\n\nThe sample size of census blocks and households for all selected provinces has been determined to be 1,694 census blocks and 42,350 households. From all the household samples, it is hoped that 33,880 female respondents who have been married aged 15-49 years can be obtained.\n\nThe 2012 IDHS was implemented in all 33 provinces in Indonesia and spread over 1,840 census blocks covering urban and rural areas. With a census block sample of this size, a total sample of 46,000 households was obtained for this survey. From all the household samples, i55,200 female respondents of childbearing age aged 15-49 years can be obtained.\n\nFrom the IDHS survey sample, the research sample was then selected according to the inclusion criteria as described in the population sample section.\n\nFor the data analysis, we used univariate analysis on the variables of contraceptive use to see contraceptive method mix trends from 1997 to 2012 in each province. Multinomial logistic regression analysis was used to analyze the determinants of the selection of contraception and the most influencing variables. The dependent variable used was the contraceptive method. The independent variables included age, parity, knowledge, side effects, the desired number of children, economic level, sources of family planning information, access, types of area, costs, facilities, and information. This study does not require validity and reliability tests because it uses Demographic and Health Survey data.\n\nQualitative phase\n\nIn-depth interviews were employed as the qualitative approach in this study to see the policy process from the perspective of the policyholder so that the Indonesian family planning policy process could be better understood.\n\nThe selection of informants in this study focused on the representation of the problems studied. In-depth interviews were conducted with informants who met the basic criteria of Neuman as follows:\n\n1. The informant is familiar with the problem and is in position to witness the events;\n\n2. The individual is currently involved in the field;\n\n3. The person can make time for interview22\n\nThe informants involved were policymakers, namely representatives of the provincial Badan Kependudukan dan Keluarga Berencana Nasional/The National Family Planning Coordinating Agency (BKKBN). They were selected according to the mapping of the contraceptive mix in each province.\n\nThe provinces selected were the most balanced contraceptive mix, the most skewed contraceptive mix, and the provinces with special conditions. From the results of the contraceptive mix trend in the previous stage, representatives of the three criteria above were selected for in-depth interviews as follows:\n\na. Bali Province and Yogyakarta Province represent groups with a relatively balanced contraceptive mix;\n\nb. The provinces of West Nusa Tenggara, East Nusa Tenggara, and Papua Province represent groups with skewed contraceptive mixtures;\n\nc. West Java Province represents a group with special conditions, namely provinces with good family planning programs, but the contraceptive mix is skewed.\n\nThe informants were contacted during the 2018 BKKBN national work meeting.\n\nThe research location was Jakarta. In-depth interviews were held on 2-3 February 2018 during the 2018 BKKBN national work meeting. In-depth interviews were divided into six sessions with one informant in each session. The duration of interviews ranged from one to two hours per session.\n\nThe interviewer conducted an in-depth interview that used a semi-structured interview guide. A copy of the interview guide used can be found under Extended data.23 The interviewer could develop questions to explore more in-depth information from the informant but focused on the set research objectives. The equipment used for the interview were:\n\n• Voice recorder;\n\n• Stationery for taking notes;\n\n• Interview guide\n\nThe interview guide included several points: Organizational structure, Legacy policies Policy socialization, Policy implementation, Situation analysis and evaluation, and Infrastructure\n\nThe qualitative data processing began with transcribing the voice recordings, then cleaning the voice recording data with the results of transcripts and data notes to check accuracy.\n\nThe stages of data analysis were as follows:\n\n1. Sorting transcript data into numerical matrices based on themes and characteristics that have been adapted to the research objectives\n\n2. Data management and security, verification of data, and anonymization\n\n3. Data triangulation was carried out by re-checking the relevant stakeholders. This triangulation process was carried out in March 2017 using the expert judgment method. The selected experts are experts from the central BKKBN\n\n4. Theme analysis is the process of coding information that produces a complex and complete list of themes or indicators, groupings related to themes and a combination of several themes of this research. The theme analysis consists of three lines, namely data reduction, data presentation and conclusion drawing.\n\nEthical statement\n\nWe obtained ethical approval for this study from University of Indonesia Faculty of Public Health Research Ethical Clearance Commission on 03-08-2017 (456/UN2.F10/PPM.00.02/2017).\n\nWritten informed consent was sought from the participants for their involvement in this study and the publication of their data. Only one participant consented to the sharing of their data. Participants were informed of their right to withdraw and that they could refuse to answer any questions. Participants were given information related to in-depth interview procedures, documentation, data confidentiality, and the risks and benefits involved in the research.\n\n\nResults\n\nThe contraceptive mix is described as a frequency distribution with a proportion measure. The contraceptive mix criteria are skewed if there is a contraceptive method whose proportion exceeds 50%.\n\nThe results of the dynamics of the contraceptive mix in 1997, 2003, 2007, and 2012 are shown for each of the five or four provinces as follows (the full dataset can be found under Underlying data23):\n\nIn Figure 1 it can be seen that the proportion of the use of injectable contraceptive methods in each province has increased every year.\n\nIn Figure 2 it can be seen that the proportion of IUD use in each province has decreased in contrast to the use of injectable contraceptives.\n\nJust as most provinces experienced skewed, the national figure also skewed to the injection method as shown in Figure 3:\n\nThe following are the results of the multinomial logistic regression analysis used to see the variables that have the most influence on selecting contraceptive methods. The relative risk ratio (RRR) was used to interpret the results of the tendency value, which serves to find a comparison between the probability of an event to the probability of it not occurring.\n\nFrom the three groupings related to the trend of the contraceptive mix in each province, the informants then took part in in-depth interviews:\n\na. Province of Bali and Province of Yogyakarta represent group I\n\nb. Provinces of West Nusa Tenggara, East Nusa Tenggara, and Papua Provinces represent group II\n\nc. West Java province is grouped separately because it has a good family planning program but with a skewed contraceptive mix.\n\nThe focus of the in-depth interviews was to obtain information on conditions prior to decentralization and the current condition of the Human Resources, Institutional, Funding, and Infrastructure variables. Decentralization policies that were explored through in-depth interviews were used as a barrier. The results of the interviews found which components of the decentralization policy supported the selection of the right contraceptive method and which components hindered the selection of the right contraceptive method.\n\nThe Human Resources variable of this study was focused on field officers, namely PLKB. Aspects that are observed from human resources are adequacy, government efforts to meet human resource needs, competency improvement programs, payroll systems, and problems that arise with the decentralization policy. Institutional variables include organizational structure, district/city commitments, and current conditions and problems that arise with the decentralization policy. Budget variables include budget sources, allocations, adequacy, accountability and transparency, and problems that arise with the decentralization policy. The infrastructure variables include infrastructure, provision of contraceptives, and distribution of contraceptives.\n\n\nDiscussion\n\nThe contraceptive mix refers to the percentage of women who use contraception based on their chosen technique.13,22 The calculation of the research contraceptive mix used the proportion of each method in each province in the four survey periods. The slope of the proportion of various contraceptives is that 50% or more of contraceptive users in a country use a similar contraceptive method.14\n\nThe contraceptive mix in 1997 showed that three provinces deviate towards use of contraceptives, namely South Kalimantan Province and Central Kalimantan Province. Mixed methods skewedness leads to the pill contraceptive method with 65.01% for South Kalimantan Province and 60.17% for Central Kalimantan Province. The province that skewed towards the injection contraceptive method was East Nusa Tenggara (54.72%). The national contraceptive mix rate has not been skewed.\n\nThe decentralization of the family planning program is regulated in Government Regulation Number 38 of 2007 concerning the Sharing of Government Affairs between the Government, Provincial Government, and Regency/City Government. This regulation explains that the family planning program and 31 other functions, including government affairs, are shared between levels and government affairs. In 2007, 21 Provinces experienced a trend toward the injection method. National figures have skewed towards the injection method. This shift is problematic if caused by policy, lack of access to various methods, or provider bias.17\n\nTwenty-one provinces were skewed in the contraceptive mix toward the injection method in 2021. The national figure has skewed towards the injection method (54.89%). These results are consistent with research in 2006 by Sullivan from 96 countries studied, 34 of which have a skewed contraceptive mix type.17 The trend toward the injection method confirmed that this type of contraception has increased the most.24 A high concentration of one or more specific types of contraception is a sign that the availability of the method in society is uneven.25\n\nThe contraceptive mix is an essential indicator of the achievement of the family planning program. With the commitment of the Indonesian government to Family Planning 2020, 120 million women use modern contraception. Plans made to achieve this commitment include the enforcement of family planning service regulations through the National Health Insurance referring to the Universal Health Coverage scheme, increasing the contraceptive mix, availability, quality, and supply chain management of contraception, encouraging the involvement of the younger generation, implementation of an integrated approach through the Family Planning village.26\n\nThe deviation proportion of the contraception mix is the result of several factors, including acceptors' lack of knowledge about the method used, providers' preference for specific methods because the incentives for using injection methods are high, and support and promotion for the use of vasectomy, implants, and much less tubectomy.15 The shift towards injection methods and the reduction in use of other methods, especially the IUD, had an unexpected impact because the injection failure rate was relatively high.27 The IUD is the most effective method after tubectomy and vasectomy (Stephen Searle, 2014). An increase in the use of IUDs can be achieved by counseling on the use of contraception through to Ante Natal Care (ANC).28\n\nThe everyday use of the IUD is partly due to people's assumption that the IUD can cause infertility. The research results state that the IUD is safe for women who have never given birth.29 The IUD does not affect the return of fertility.28,30 The return of fertility after IUD removal ranges from 3-to 4 months31,32 to 12 months,29,33 and 18 months.29 The IUD does not affect fertility after discharge.34\n\nBased on the age of the respondents, it can be seen that respondents aged 20-35 years (compared to those aged <20 and >35 years) have the highest tendency of 5.8 times to select the injection method compared to selecting the MOP/MOW method. Respondents with parity category 0-2 times (compared to those who have given birth >2 times) are 6.2 times more likely to use the condom method than the MOP/MOW method.\n\nThere is a lower tendency (compared to higher education levels) at the secondary education level to select the IUD method than the MOP/MOW method. Respondents with secondary education did not show a statistical relationship with the selection of condom method. Respondents with low education have a lower tendency (compared to higher education levels) to select the IUD and condom methods.\n\nIn general, the poor, middle, affluent, and richest economic statuses have a lower tendency (compared to the poorest economic status) to select all methods (pills, injections, IUDs, implants, and condoms) compared to selecting the MOP/MOW method. Based on knowledge about family planning, respondents with less knowledge (compared to those who have good knowledge) tend to select the injection method 2.2 times more than the MOP/MOW method.\n\nIn general, respondents who have experienced side effects of contraception, choose to have less than two children, and obtain family planning information sources from non-health workers have a lower tendency to select a variety of contraceptive methods such as pills, injections, IUDs, implants, and condoms, compared to the MOP/MOW method.\n\nExternal factors influence the selection of a particular contraceptive method in the form of exposure to information that increases the individual's knowledge of determining the selection of the right contraceptive. The information exposure can come from field officers (PLKB) and health workers who contact respondents.\n\nThere is no statistical relationship between the intensity of field officers' visits and the selection of family planning methods. Statistically, the variable that has the most vital relationship with the selection of contraception is the variable cost, with a significance of 0.001 and an OR of 9.001. These results can be caused by field officers' insufficient numbers and incompetence.\n\nIn connection with the decentralization policy, each region needs adequate infrastructure to support the family planning program. The availability of contraceptives and infrastructure can be an impetus for an individual to decide on a suitable contraceptive method. The decentralization policy has had a positive impact in some areas and a negative impact in some other areas. Skewness is due to the inadequacy of existing method alternatives and provider bias.35 This study confirms the availability of contraceptives and the role of providers in influencing the contraceptive methods used by the community. Reasonable access is accompanied by a better balance of contraceptive mix.36\n\nContraceptive method mix is the proportion of contraceptive usage. The contraceptive method mix is influenced by selecting contraception at the individual level. There are many reasons why a person selects contraception. This study resulted in the variables of respondent's age, parity, education, side effects of contraception, number of children, and sources of information having a significant relationship with the selection of contraceptive method (p-value of 0.05). These results affirm research that the selection of contraceptives can be influenced by age, the number of living children, education, religion, desire to have children, visits by health care providers, and husband's views on contraceptives.37\n\nThe results of a study on the number of children variable follow several previous studies. Analysis of Indonesia Family Life Survey(IFLS) data in 1997-2000 in Indonesia states that women most widely utilize contraception with 1-2 children.38 In addition, women with more children tend to want to use contraception more than those who have fewer children.37-40 The desired child's gender preference influences the number of children owned in some countries.\n\nThe results of the analysis on the side effect evaluation variables have a relationship with the selection of family planning methods. A study in Japan regarding the evaluation of the use of oral contraceptives states that a person's experience with a contraceptive and abortion influences the selection of contraception that will be used later41 and experience related to the selected contraceptive method and attitude factors.42\n\nThe variable of education level has a relationship with the selection of contraceptives (p-value 0.001-0.02). The knowledge variable has a significant relationship with the selection of contraceptive pill, injection, implant, and condom method compared to the MOW/MOP contraceptive method (p-value 0.001). The knowledge variable is not significantly related to the selection of the IUD contraceptive method compared to the MOW/MOP contraceptive method (p-value 0.90).\n\nThe higher the education level, the more likely women are to use contraception.37,41,43 if someone has a higher education, they are likely to have more knowledge regarding contraception.44 In addition to education, factors that influence knowledge of contraception are exposure to information from mass media, social media, socialization from providers, and information obtained informally from other individuals. Government policies and campaigns to increase public knowledge regarding quality and quantity are needed to promote gender equality further.45\n\nIncreasing public knowledge about family planning should be initiated as early as possible. An effective way is to include reproductive health education and the introduction of contraceptives in school curriculum. The age of menarche and the high rate of unwanted pregnancies in adolescents make the curriculum on reproductive health important. The optimal time to provide reproductive health education is when children begin to understand sexual activity and can have sex physiologically.46 Formal reproductive health education and the introduction of contraceptives do not increase children's early sex activity and can reduce unwanted pregnancies in adolescence.47\n\nThe results of the analysis of the age variable are related to the selection of contraception. In Indonesia, the results of the IFLS analysis in 1997-2000 show that the majority of contraceptive users are under 40 years old.48 Women aged 30-34 years used contraception more than other age groups. Meanwhile, research in Mongolia concluded that the increasing age of women increases the desire to use contraception.49 Things to consider in the selection of a contraceptive method among the 40 years+ age group include irregular menstrual frequency, sexual problems, and possible signs of menopause, all of which respond to hormonal contraception.50\n\nThe results of the parity analysis are related to the selection of contraception. Parity is the number of times a woman has given birth, whether live or stillborn. A woman's age affects her choice of contraception and how many children she wants to have.51 Research in Japan related to age, parity, and abortion concluded that parity at a young age influences the selection of contraception, and contraception after abortion reduces the risk of repeated abortions.52\n\nThe study results show that the distance variable (p-value 0.000) has a relationship with the selection of contraceptive methods. The type of area (p-value 0.000) and facilities (p-value 0.000) have a significant relationship with the choice of contraceptive method of the respondents. These results are in line with research by Khalil et al. in Afghanistan, which states that most women who do not use contraceptives are illiterate and live in rural areas.53 The use of contraceptives in Pakistan tends to decrease among women who live in rural areas, are less educated, and are poor.54\n\nIn Indonesia, a study conducted by Rahayu et al. (2009) showed that there were more users of modern contraceptives in urban areas than in rural areas.37 Similar results to Kiswanto's (2015) study stated that in 1997 users of contraceptives lived in urban areas. In 2007, users in rural areas increased, but the percentage of users in urban areas remained higher.38 Achana et al. (2015), who conducted a spatial analysis of contraceptive users in Ghana, concluded that most contraceptive users live in urban areas.55 Women who live in urban areas and have a high level of education are more likely to use modern contraception.37,41,50,53,56\n\nThe variable cost is significantly related to the selection of the pill contraceptive method (p-value 0.000), the injection contraceptive method (p-value 0.000), the IUD contraceptive method (p-value 0.04), and the condom contraceptive method (p-value 0.000). There is no significant relationship between the implant contraceptive method (p-value of 0.009). People in rural areas may select the pill and injection method because of their low cost.37\n\nThe type of facility influences the choice of contraception (p-value 0.001). People obtain contraceptive services in two types: public and private services. The quality of the two services influences the perception of selecting contraception. A study in Tanzania comparing public services and private services stated that public services offered more modern contraceptive services and had more guiding protocols than private services.57\n\nThe results of the provider variable research are not related to the selection of contraception. These results do not follow some previous studies. Research by Ugaz et al. in 2016 stated that the leading cause of stagnation in the number of users of long-term contraceptives is the lack of knowledge of providers causing the information provided to clients to be less accurate. Thus, the perception of long-term contraceptive users, especially IUDs and implants, becomes negative.58 Results of the study that are not following previous research are possible because this study only focuses on field officers (PLKB). Meanwhile, the proportion of respondents who received visits from field officers was small.\n\nVarious things influence the selection of contraception. The results of the quantitative analysis of this study resulted in the variable that most influenced the selection of contraception method. It was the variable cost—other variables much influence the selection of the method. Several studies have stated that the provider variable has a significant effect.\n\nHealth workers have duties at the end of the family planning program because they deal directly with acceptors/families.59 An evaluation study with a multilevel analysis in China regarding sterilization methods concluded that family planning officers increased sterilization participation rates, especially in women with high parity.60 A study conducted in Bangladesh in 2004 showed that family planning officers have a significant role in the success of contraceptive use, especially the contraceptive pill.61 The influence of the provider is enormous on the selection of contraceptive methods.62 A literature review related to the role of providers in increasing IUD use described that many providers had a low or uneven level of knowledge about IUDs and limited training.62\n\nThe results of the qualitative analysis showed that the family planning program facilities and infrastructure received support from a special allocation fund which was realized for supporting facilities and infrastructure such as motorbikes and cars. In 2016, DAK can be used for non-physical facilities like family planning, operational facilities, and infrastructures such as service cars, mobile phones, motorbikes, and uniforms. In other words, it is beneficial to meet the needs of facilities and infrastructure. These facilities are used for outreach operations and family planning village operations. Decentralization improves infrastructure facilities and equipment in primary and secondary health care institutions and expands the scope of health services.63 Decentralization also improves the distribution of public services, people receive easier access to contraceptives, health services, and health information.18,26–28,61,64,65\n\nThe provinces of East Nusa Tenggara and Papua stated that the facilities and infrastructure from the BKKBN were sufficient prior to decentralization. After decentralization, due to a lack of local commitment to the family planning program, vehicles and buildings were used/transferred by other agencies. However, facilities and infrastructure are less supportive for remote areas. Therefore, decentralization has successfully led to disparities in the distribution of health services between rich and poor regions.66\n\nDecentralization increases equitable access to contraceptives at all levels of society. This condition occurs in several provinces, such as East Nusa Tenggara. The informant from the province of East Nusa Tenggara said “Support for other facilities, vehicles, and contraceptives, is powerful. If we compare the e-infrastructure at that time to the Regional Government, the BKKBN is seen as a luxurious institution if we want. However, when did the reforms take place in what year?\" (Informant from East Nusa Tenggara Province). Some remote areas require more operational tools than other regions due to the terrain and topography of the area, and there are still many tribes in the interior, and it is tough to reach services. In line with a study in Spain regarding consumer satisfaction, it is stated that decentralization does not increase consumer satisfaction with the health services provided.67\n\nThe distribution of contraceptives from the central government to the network of six provinces is considered sufficient. There are no difficulties found with contraception distribution in Yogyakarta, Bali, West Java, and West Nusa Tenggara, both urban and suburban regions. There are contraceptive transport cars that distribute contraceptives to the network level. If the stock of contraception is empty and there is no one from the center, it can apply for transfer of contraception from another province. If the cross-subsidy cannot be fulfilled, the center will intervene to meet ends. A study in Nepal in 2010 stated that decentralization is positively related to service access, utilities, and improving the quality of services provided to the community.62,68,69\n\nThe distribution of contraceptives from the center uses an e-catalog ordered according to the needs of each region. For Papua Province, the distribution of contraceptives was carried out by the central government. Procurement of contraceptives by the central government cannot be done in large quantities at once because the community's needs are minimal. If there is a request from the district/city, then the distribution of contraception will be made. For the Province of Bali, it is stated that stock calculations from the center often do not meet the needs. For example, the calculated proportion of women of childbearing age have the greatest need for intra uterine devices (IUD). However, the available contraceptives are pills and injections.\n\nUntil 2017, the procurement of contraceptives by the central government through the BKKBN was carried out based on the BPJS (Social Security Administrator for Health) Law. The procurement of medical devices in 2018 is under the province's authority. In this case, more vigilance is needed because procurement requires auctions prone to fraud.\n\nDecentralization has great potential and can be optimal if district/city leaders understand the importance of family planning programs. In general, the main objective of decentralization to bring services closer to the community is not believed to have been achieved. This is because Family Planning programmes are mostly financed by the province, and contraception is still fully borne by the central government. The informant from Bali province said that “… yes now, in 2018, the procurement of contraceptives is returned to the regions, if in the past it was in the regions, now it is being reversed again. So before, we have procured at the center for several years, because following the laws including the BPJS Law that contraceptives are 100% by BKKBN, provided by BKKBN…” (Informant from Bali Province).\n\nProvision of contraceptives is performed by calculating the number of acceptors, community demand, type of contraception (recurring or not), and planning targets for new participants. The calculation results are then recalculated with the remaining contraceptives from the previous year both in regional warehouses, district warehouses, and on the network. Minimum stock production is two years and three years for Bali Province. Due to the nature of the cooperation with the BPJS, practical midwives are included in the network and must deliver contraceptives to health facilities and networks that have partnered with the BPJS. Contraceptives for low-income families must be covered and free regardless of the type of contraception used. These results confirm the theory that decentralization increases budget allocation for the poor.70\n\nThe limitations of this study were: 1) Qualitative research is carried out at the provincial BKKBN representative level. For a more in-depth study, research should be carried out at the district/city level; 2. Analysis at the individual level uses data from one survey, namely IDHS 2012, to represent current conditions. With the implementation of the 2017 IDHS, it is hoped that further research will be carried out to reflect actual conditions better.\n\n\nConclusions\n\nGenerally, decentralization has different outcomes in different regions; some areas face negative consequences, according to a study done in 22 countries using panel data that indicated decentralization is not linearly correlated to equal distribution of health services.71 Decentralization in Southeast Asia is considered not achieving the expected goal of bringing services closer to society.72 The studies in Gana and Guatemala resulted in fewer (centralized) options associated with better performance for two main functions (inventory control and information systems). In contrast, more choice (decentralization) was associated with better performance in budgeting and planning.73\n\nContraception is closely related to a person's reproductive rights, part of human rights. Thus, the government must fulfill the rights of every citizen as stated in the 1945 Constitution, which mandates guarantees of human rights. The right to health is also stated in national instruments in article 28H paragraph (1) and Article 34 paragraph (3) amendments to the 1945 Constitution, Article 9 of Law no. 39 of 1999 concerning Human Rights, and article 12 of Law no. 11 of 2005 concerning Ratification of the Covenant on Economic, Social and Cultural Rights. The provisions in the 1945 Constitution above are further regulated in Law no. 36 of 2009 concerning health. Thus, the government must provide the family planning program's infrastructure.\n\nSuggestions that can be conveyed based on the research findings include:\n\n1. More attention should be given to remote areas in terms of distribution of contraceptives, provision of infrastructure, and availability of human resources\n\n2. The policy direction should include aspects of quality and guarantee of availability\n\n3. Making areas with poor family planning programs (can refer to indicators of the contraceptive mix and program coverage) a top priority\n\n4. Formulating substance guidelines related to family planning programs so that district/city leaders understand the essence of choosing the right contraceptive method so that the program implemented can be on target\n\n5. Incorporate reproductive health education into the primary and junior secondary school curriculum.",
"appendix": "Data availability\n\nData used in this study are from the Demographic and Health Survey (DHS). Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.\n\nIDHS 1997: https://dhsprogram.com/data/dataset/Indonesia_Standard-DHS_1997.cfm?flag=0\n\nIDHS 2003: https://dhsprogram.com/data/dataset/Indonesia_Standard-DHS_2003.cfm?flag=0\n\nIDHS 2007: https://dhsprogram.com/data/dataset/Indonesia_Standard-DHS_2007.cfm?flag=0\n\nIDHS 2012: https://dhsprogram.com/data/dataset/Indonesia_Standard-DHS_2012.cfm?flag=0\n\nDue to ethical restrictions, the interview transcripts from the informants from Bali, Yogyakarta, West Nusa Tenggara, East Nusa Tenggara, and West Java are available upon request from the corresponding author at dyahutari@upnvj.ac.id.\n\nFigshare: Indonesia mixed contraception Method skewness 1997-2012. https://doi.org/10.6084/m9.figshare.20405907. 23\n\nThis project contains the following underlying data:\n\n- CURRENT CONTRACEPTIVE METHOD 1997 UNTIL 2012.xlsx\n\n- MIX METHODE COMPARISON FROM IDHS 1997_2012.xls\n\n- WEIGHTED IDHS DATA FROM 1997 UNTIL 2012.sav\n\n- Fix_Transkrip Papua.pdf (interview transcript from Papua Province participant)\n\nThis project contains the following extended data:\n\n‐ DEPTH INTERVIEW GUIDANCE.doc\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 author would like to thank you to Dr. Tris Eryando, MA and Prof. dr. Purnawan Junadi, MPH., Ph. D and also Universitas Pembangunan Nasional Jakarta.\n\n\nReferences\n\nPopulation|United Nations:(accessed Apr. 22, 2022).Reference Source\n\nFertility rate, total (births per woman)|Data:(accessed Apr. 22, 2022).Reference Source\n\nBadan Pusat Statistik, Badan Koordinasi Keluarga Berencanan Nasional, Departemen Kesehatan, and Macro International: Survei Demografi dan Kesehatan Indonesia 2012. Sdki. 2013; 16.\n\nBadan Pusat Statistik, Badan Koordinasi Keluarga Berencanan Nasional, Departemen Kesehatan, and Macro International: Survei Demografi dan Kesehatan Indonesia 2012. Sdki. 2013; 115: 570–578. Publisher Full Text\n\nBarro RJ: Determinants of Economic Growth in a Panel of Countries. Ann. Econ. Financ. 2003; 274: 231–274.\n\nMalthus TR: An essay on the principle of population, as it affects the future improvement of society. Contemp. Sociol. 1798; 6(3): 340. Publisher Full Text\n\nLi H, Zhang J: Do high birth rates hamper economic growth? Rev. Econ. Stat. 2007; 89(February): 110–117. Publisher Full Text\n\nRoss J: Understanding the Demographic Dividend. POLICY Proj. 2004; (September): 1–8.\n\nPallikadavath S, Rajan SI, Wilson C: Low Fertility in Developing Countries: Causes and Implications. J. Biosoc. Sci. 2017; 49(S1): S1–S3. Publisher Full Text\n\nCarr B, Gates MF, Mitchell A, et al.: Giving women the power to plan their families. Lancet. 2012; 380(9837): 80–82. PubMed Abstract | Publisher Full Text\n\nSujarwoto S: Small Family Norms and Family Well-Being in Indonesia, 2006–2014. J. Biosoc. Sci. 2017; 49(S1): S96–S115. PubMed Abstract | Publisher Full Text\n\nMagadi MA, Curtis SL: Trends and Determinants of Contraceptive Method Choice in Kenya.1995. Publisher Full Text\n\nBertrand JT, Sullivan TM, Knowles EA, et al.: Contraceptive method skew and shifts in method mix in low- and middle-income countries. Int. Perspect. Sex. Reprod. Health. 2014; 40(3): 144–153. PubMed Abstract | Publisher Full Text\n\nRoss J, Keesbury J, Hardee K: Trends in the contraceptive method mix in low- and middle-income countries: analysis using a new "average deviation" measure. Glob. Heal. Sci. Pract. 2015; 3(1): 34–55. PubMed Abstract | Publisher Full Text\n\nHull TH, Mosley H: Revitalization of family planning in Indonesia. no. February 2009.\n\nBarot S: Sexual and Reproductive Health and Rights Are Key to Global Development: The Case for Ramping Up Investment. Guttmacher Policy Rev. 2015; 18(1): 1–7. Reference Source\n\nSullivan TM, Bertrand JT, Rice J, et al.: Skewed contraceptive method mix: why it happens, why it matters. J. Biosoc. Sci. 2006; 38(4): 501–521. PubMed Abstract | Publisher Full Text\n\nZarychta A: Making social services work better for the poor: Evidence from a natural experiment with health sector decentralization in Honduras. World Dev. Sep. 2020; 133: 104996. Publisher Full Text\n\nSchwandt HM, et al.: ‘Family planning in Rwanda is not seen as population control, but rather as a way to empower the people’: examining Rwanda’s success in family planning from the perspective of public and private stakeholders. Contracept. Reprod. Med. Nov. 2018; 3(1): 1–7. Publisher Full Text\n\nBudisuari M, Rachmawati T: Analisis Pengembangan Kebijakan Keluarga Berencana Di Jawa Timur, Bali Dan Kalimantan Tengah. Bul. Penelit. Sist. 2011. Reference Source\n\nPurwaningsih SS: The Decentralization of the Family Planning Program: Challenges and Issues, the West Kalimantan Province Case (Bahasa Indonesia). J. Kependud. Indones. 2012; VII(2): 109–125.\n\nNeuman W: Social Research Methods: Qualitative and Quantitative Approaches. 2000; vol. 30. Publisher Full Text\n\nUtari D:Indonesia mixed contraception Method skewness 1997-2012. figshare. Dataset.2022. Publisher Full Text\n\nSutherland EG, Otterness C, Janowitz B: What happens to contraceptive use after the introduction of injectables in 13 countries. Int. Perspect. Sex. Reprod. Health. 2011; 37(4): 202–208. PubMed Abstract | Publisher Full Text\n\nSeiber EE, Bertrand JT, Sullivan TM, et al.: Changes in Contraceptive Method Mix in Developing Countries Changes in Contraceptive Method Mix In Developing Countries.2017; vol. 33(no. 3): pp. 117–123.\n\nP. D. United Nation: Department of Economic and Social Affairs. Trends in contraceptive use Worldwide 2015. 2015. Publisher Full Text\n\nHatcher RA, Rinehart W, Blackburn R, et al.: The essentials of contraceptive technology. 2003; (no. March).\n\nStephen Searle E: The intrauterine device and the intrauterine system. Best Pract. Res. Clin. Obstet. Gynaecol. 2014; 28(6): 807–824. Publisher Full Text\n\nLohr PA, Lyus R, Prager S: Use of intrauterine devices in nulliparous women. Contraception. 2017; 95(6): 529–537. Publisher Full Text\n\nAnwar M, Widayanto S, Maruo T, et al.: Return of Fertility after the Removal of Intrauterine Devices: A Comparison of Inert and Copper Bearing Devices. Asia Ocenia Obs. Gynaecol. 1993; 19(I): 77–83. Publisher Full Text\n\nBelhadj H, et al.: Recovery of Fertility After Use of The Levonogestrel 20mcg/d or Copper T 380 Ag Intrauterine Device.1986; vol. 34(no. 3): pp. 261–267.\n\nZhu H, et al.: Fertility in older women following removal of long-term intrauterine devices in the wake of a natural disaster. Contraception. 2013; 87(4): 416–420. PubMed Abstract | Publisher Full Text\n\nAmran Y, et al.: Perceptions of Contraception and Patterns of Switching Contraceptive Methods Among Family-planning Acceptors in West Nusa Tenggara, Indonesia. J. Prev. Med. Public Health. Jul. 2019; 52(4): 258–264. PubMed Abstract | Publisher Full Text\n\nWilson JC: A prospective New Zealand study of fertility after removal of copper intrauterine contraceptive devices for conception and because of complications: A four-year study. Am. J. Obstet. Gynecol. 1989; 160(2): 391–396. Publisher Full Text\n\nSeiber EE, Bertrand JT, Sullivan TM: Changes in contraceptive method mix in developing countries. Int. Fam. Plan. Perspect. 2007; 33(3): 117–123. PubMed Abstract | Publisher Full Text\n\nRoss J, Hardee K, Mumford E, et al.: Contraceptive Method Choice in Developing Countries. Int. Fam. Plan. Perspect. 2001; 24(1): 15–40. Publisher Full Text\n\nRahayu R, Utomo I, Mcdonald P: Contraceptive Use Pattern among Married Women in Indonesia. Soc. Res. (New. York). 2009. Publisher Full Text\n\nKiswanto E: THE DYNAMICS OF THE USE OF CONTRACEPTIVES IN EVER-MARRIED WOMEN IN INDONESIA: DATA ANALYSIS IFLS 1997, 2000 AND 2007.2015; vol. 23, pp. 17–37.\n\nAl-balushi MS, Ahmed MS, Islam MM: Determinants of contraceptive use in oman.2015; vol. 50(no. 1): pp. 51–64.\n\nPalamulen: Socio-economic and demographic factors affecting contraceptive use in Malawi. Afr. J. Reprod. Health. 2013; 17(3): 91–104.Reference Source\n\nNakamura S: Determinants of contraceptive choice among Japanese women: ten years after the pill approval. Rev. Econ. Househ. 2013; 14(3): 553–575. Publisher Full Text\n\nFrost JJ, Darroch JE: Linked references are available on JSTOR for this article: Factors Associated with Contraceptive Choice and Inconsistent Method Use, United States, 2004.2016; vol. 40(no. 2): pp. 94–104. Publisher Full Text\n\nDeRose LF, Ezeh AC: Decision-Making Patterns and Contraceptive Use: Evidence from Uganda. Popul. Res. Policy Rev. 2010; 29(3): 423–439. Publisher Full Text\n\nUnderstanding women’s contraceptive decision-making dynamics in nepal.2006.\n\nHull TH: Demographic Perspectives on the Future of the. J. Popul. Res. 2003; 20(1): 51–66. Publisher Full Text\n\nKirby D: The impact of sex education on the sexual behaviour of young people. United Nations. Dep. Econ. Soc. Aff. 2011; 1–19.\n\nKohler PK, Manhart LE, Lafferty WE: Abstinence-Only and Comprehensive Sex Education and the Initiation of Sexual Activity and Teen Pregnancy. J. Adolesc. Health. 2008; 42(4): 344–351. PubMed Abstract | Publisher Full Text\n\nKiswanto E, Si M, Alfana MAF: Penyusunan Proyeksi Penduduk Indonesia.\n\nGeretulya A, Falkingham J, Brown J: Determinants of Current Contraceptive Use and Method Choice in Mongolia. J. Biosoc. Sci. 2007; 39(06): 801–817. PubMed Abstract | Publisher Full Text\n\nBaird DT, et al.: Female contraception over 40. Hum. Reprod. Update. 2009; 15(6): 599–612. Publisher Full Text\n\nLindh I, Andersson Ellström A, Blohm F, et al.: A longitudinal study of contraception and pregnancies in the same women followed for a quarter of a century. Hum. Reprod. 2010; 25(6): 1415–1422. PubMed Abstract | Publisher Full Text\n\nHeikinheimo O, Gissler M, Suhonen S: Age, parity, history of abortion and contraceptive choices affect the risk of repeat abortion. Contraception. 2008; 78(2): 149–154. PubMed Abstract | Publisher Full Text\n\nKhalil B, Sarfraz M, Khan R: Socio-Economic and Demographic Determinants of Contraceptive Uptake in Pakistan. Pakistan J. Med. Res. Pak J Med Res. 2015; 54(2): 40–45.\n\nCarton TW, Agha S: Changes in contraceptive use and method mix in Pakistan: 1990-91 to 2006-07. Health Policy Plan. 2012; 27(2): 166–174. PubMed Abstract | Publisher Full Text\n\nAchana FS, et al.: Spatial and socio-demographic determinants of contraceptive use in the Upper East region of Ghana. Reprod. Health. 2015; 12(1): 29. PubMed Abstract | Publisher Full Text\n\nDasgupta ANZ, Zaba B, Crampin AC: Contraceptive dynamics in rural northern Malawi: A prospective longitudinal study. Int. Perspect. Sex. Reprod. Health. 2015; 41(3): 145–154. PubMed Abstract | Publisher Full Text\n\nKakoko DC, Ketting E, Kamazima SR, et al.: Provision of family planning services in Tanzania: a comparative analysis of public and private facilities. Afr. J. Reprod. Health. 2012; 16(4): 140–148. PubMed Abstract\n\nUgaz J, Banke K, Rahaim S, et al.: Private providers’ knowledge, attitudes and misconceptions related to long-acting and permanent contraceptive methods: a case study in Bangladesh. Contraception. 2016; 94(5): 505–511. PubMed Abstract | Publisher Full Text\n\nShafiqullah H, Morita A, Nakamura K: The family planning conundrum in Afghanistan.2016; pp. 1–7. Publisher Full Text\n\nBrown JJ, Bohua L, Padmadas SS: A multilevel analysis of the effects of a reproductive health programme that encouraged informed choice of contraceptive method rather than use of officially preferred methods, China 2003-2005. Popul. Stud. (NY). 2010; 64(2): 105–115. PubMed Abstract | Publisher Full Text\n\nSaha UR, Khan M a, Begum M, et al.: Determinants of pill failure in rural Bangladesh. J. Biosoc. Sci. 2004; 36: 39–50. PubMed Abstract | Publisher Full Text\n\nDaniele MAS, Cleland J, Benova L, et al.: Provider and lay perspectives on intra-uterine contraception: A global review. Reprod. Health. 2017; 14(1): 1–12. PubMed Abstract | Publisher Full Text\n\nRajesh K, Thomas MB: Decentralization and Interventions in the Health Sector. J. Health Manag. 2012; 14(4): 417–433. Publisher Full Text\n\nAndersson K, Batar I, Rybo G: Return to fertility after removal of a levonorgestrel-releasing intrauterine device and Nova-T. Contraception. 1992; 46(6): 575–584. PubMed Abstract | Publisher Full Text\n\nIssa A a, Amr MF: Fertility after removal of the intrauterine Contraceptive Devices. Curr. Ther. Res. 1998; 59(4): 257–261. Publisher Full Text Reference Source\n\nGonzález-Block M, Leyva R, Ata OZ, et al.: Health Services Decentralisation in Mexico: Formulation, Implementation and Results of Policy. Health Policy Plan. 1989; 4(4): 301–315. Publisher Full Text\n\nAnton JI, De Bustillo RM, Macias EF, et al.: Effects of health care decentralization in Spain from a citizens’ perspective. Eur. J. Health Econ. 2014; 15(4): 411–431. Publisher Full Text\n\nFP2020 Country Actions for Acceleration: Indonesia Actions for Acceleration 2017-2018.2017.\n\nRegmi K, Naidoo J, Pilkington PA, et al.: Decentralization and district health services in Nepal: Understanding the views of service users and service providers. J. Public Health (Bangkok). 2010; 32(3): 406–417. PubMed Abstract | Publisher Full Text\n\nFaguet JP: Does decentralization increase government responsiveness to local needs? Evidence from Bolivia. J. Public Econ. 2004; 88(3–4): 867–893. Publisher Full Text\n\nKang Y, Cho W, Jung K: Does decentralization matter in health outcomes? evidence from 22 oecd unbalanced panel data for 1995–2005. Int. Rev. Public Adm. 2012; 17(1): 1–32. Publisher Full Text\n\nMalesky EJ, Hutchinson FE: Why Has Decentralization Not Delivered on Its Promises in Southeast Asia? J. Southeast Asian Econ. 2016; 33(2): 125–138. Publisher Full Text\n\nBossert T, Chitah MB, Bowser D: Decentralization in Zambia: Resource allocation and district performance. Health Policy Plan. 2003; 18(4): 357–369. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "170870",
"date": "22 May 2023",
"name": "Yuli Amran",
"expertise": [
"Reviewer Expertise Health biostatistics",
"Family Planning (behavior on contraceptive use)"
],
"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. Is the work clearly and accurately presented and does it cite the current literature? --> Partly\nThe article does not cite the current literature (Most of the literature used was more than 5 years old when this article was first published).\n\nAbstract section; I think is less relevant than the problems presented with the research objectives. The author observed that during 1997-2012 the use of contraceptive mixes that were not by the optimal time for women's reproduction was one of the effects of decentralization. Even though the decentralization of the family planning program officially started with Presidential Decree No. I03 of 2001, then it was updated to become Presidential Decree No. 30 of 2003, that in early 2004, various family planning programs became the authority of the local government. Meaning that decentralization was not the main reason for irregularities in the selection of contraceptives in 1997 and 2003.\n\nI cannot properly understand the urgency of the results of this research. In my opinion, women who are young (<35 years), and want children or increase the number of children, have no problem using injectable contraception or pills. However, if a woman wants to space or limit pregnancies, using both types of contraception may not be effective because the behavior of most contraceptive users in Indonesia lacks discipline while using both contraceptives requires high discipline so as not to experience failure. Instead of the authors only describing contraceptive use by region, I suggest the authors to study contraceptive options in the age group >= 35 years and have had more than two children if the data is available. Maybe the results can describe the problem in choosing the type of contraception and what causes it?\n2. I don't see a comprehensive interpretation of the results of multivariate analysis (multinomial regression analysis). I suggest the author make a clear interpretation so that the reader understands well the research results presented in Table 1.\n3. It is not clear whether the qualitative research describes the situation in 1997, 2003, 2007 or 2012?\n4. In my opinion the conclusions made do not answer the research objectives. It is best if the points of exposure to the conclusions are made relevant to the research objectives.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/11-1266
|
https://f1000research.com/articles/11-1264/v1
|
07 Nov 22
|
{
"type": "Review",
"title": "Performance Characteristics and Efficiency Enhancement Techniques of Solar PV System: A review",
"authors": [
"Prashant Kumar Shalwar",
"Bhupendra Gupta",
"Jyoti Bhalavi",
"Anand Bisen",
"Prashant Kumar Shalwar",
"Jyoti Bhalavi",
"Anand Bisen"
],
"abstract": "In constant degradation of conventional sources and shifting fuel costs, has prompted research into alternate power generating options in recent years. A substantial study has been conducted in the literature to properly harvest power from green energy resources. This publication aims to provide a quick assessment of various PV Performance Characteristics on different factors (such as varying irradiation, temperature, parallel & series connection, tilt angle, shading, environment impact, and different type of PV modules), to bring all of the research activities in this field under one tent. This work resulted that the efficiency and performance of the PV system are greatly affected by module temperature, irradiation, shadow, and tilt angle. Hence, each of the characteristics of the solar PV module has been examined critically with reasons, remedies, and techniques applied. Finally, a concise review with enumerated data has been presented which lightened the pathway for new researchers working in Solar Photovoltaics.",
"keywords": [
"Solar Photovoltaic (SPV)",
"PV module",
"Performance characteristics",
"Tilt angle",
"Shading effect",
"Solar Irradiation",
"Panel temperature",
"Panel efficiency",
"Solar emulator"
],
"content": "Acronyms\n\nANSYS: Analysis of Systems Software\n\na-Si: H single: Hydrogenated amorphous Silicon with single-junction\n\nBIPV: building-integrated photovoltaics\n\nBL: Bridge linked\n\nCdTe: Cadmium Telluride\n\nCIGS: Copper indium gallium selenide\n\nCIS: Copper Indium Selenide\n\nDHI: Diffused Horizontal Irradiation\n\nDSSC: Dye-sensitized solar cell\n\nEFG-Si: Edge-defined Film-fed Silicon\n\nFEM: Finite element method\n\nFF: Fill Factor\n\nFPV: Flexible photovoltaic\n\nGaAs: Gallium arsenide\n\nGHI: Global Horizontal Irradiation\n\nHIT: Heterojunction Intrinsic Thin layer\n\nIsc: Short Circuit Current\n\nMATLAB: Matrix laboratory\n\nMBB: Multi bus bar\n\nm-Si: Monocrystalline silicon\n\nPERC: Passivated Emitter and Rear Cell\n\nPm: Maximum Power\n\nPR: Performance ratio\n\np-Si: Polycrystalline silicon\n\nPV: Photovoltaic\n\nSILO-ED: Silicide on Oxide-based Electrostatically Doped\n\nSPV: Solar photovoltaic\n\nSTC: Standard test condition\n\nTiO2: Titanium dioxide\n\nTCT: Total cross tied\n\nVIBGYOR: Violet, Indigo, Blue, Green, Yellow, Orange, Red\n\nVoc: Open Circuit Voltage\n\n\nIntroduction\n\nAs energy demands are increasing day by day, and expected to reach over 200% by 2040-50 as compared to 2020.1 Therefore, the effectiveness and perfection of photovoltaic (PV) panels have now become a universal issue, particularly in developing countries like India.2 Electricity energy generation is shifting towards renewables like solar energy internationally.3 The global dependence on electricity is growing, as environmental issues grow extra focus is being paid to solar energy.3 Solar irradiance can generate heat, cause a change in chemical progressions, or create power. The total solar light received onto the earth's surface exceeds the world’s present energy consumption needs.4 Thus the amount of solar energy received can meet human energy needs if properly utilized. In India, almost 62% of the total area receives a yearly average direct solar radiation of 5 kWh/m2/day.5\n\nThe solar PV cell works on the basic principle of photo electricity. The light photons of a specific wavelength 400-700 nm (visible light, near to infrared) are converted into electricity as direct current. In 1954, the first solar PV cell made up of silicon semiconductor material produced electricity when focused under solar light at Bell Laboratory.6 Under present harsh environmental conditions, solar electric power is the only eco-friendly and sustainable source of electricity generation for the future.7 In the commercial market, presently three basic types of solar PV modules are available: Monocrystalline, Polycrystalline, and Thin-film solar cells.7 Current research and progress has developed two more technology types; Passivated Emitter and Rear Cell (PERC) solar cells8 and half-cut solar PV cells.9 The performance of monocrystalline silicon solar cells has shown remarkable improvement in the past years, these designs originally showed only 15% efficiency in the 50s and then increased to 17% in the 70s and up to 28% presently.10 PERC solar cell technology/architecture has the best potential to produce high-efficiency solar cells at a competitive price.11 This technology enables solar cell manufacturers to achieve high efficiencies as compared to standard solar cells. 1% absolute gain in efficiency is possible with PERC solar cell architecture as it enables improved light capture near the rear surface and gets most of the electrons out of the solar cell. This technology optimized the (i) light capture near the rear surface of the structure and (ii) optimize electron emission/capture. 24.7% efficiency has been recorded with PERC architecture solar cells.11\n\nThis paper gives a brief review of the present status of solar PV systems, performance characteristics and efficiency enhancement, reasons, remedies, and technological aspects.\n\n\nTypes of solar PV cells and their efficiencies\n\nBasically, solar cells can be classified according to the 1st, 2nd, and 3rd generations. 1st generation cells include; polycrystalline and single crystalline solar cells. Under 2nd generation; thin film solar PV cells are included. Solar PV of 3rd generation comprises; polymer or organic solar cell (carbon-based organic compound’s thin layer), perovskite film (500 to 1000 nm, efficiency up to 25.2%) solar cell, multi-junction solar cell, transparent (absorb sunlight) and semi-transparent (absorb ultraviolet light) solar cell, concentrated (curved mirror/lenses) solar cell, DSSC (dye-sensitized solar cell) or light absorbing dye solar cells, nano thick materials based solar cell (absorb both sunlight and interior light).12 Table 1 gives a screenshot comparison of efficiencies for different types of solar cells.\n\n\nLiterature review (performance parameters of different Solar PV installations)\n\nPerformance parameters and module efficiencies for different Solar PV installations at different locations have been briefly covered. How photovoltaics modules can be used in elevated performance, and how to explore their efficiency under various applications/situations, are discussed in this section:\n\nAhmad Fudholi et al. (2014) explored the determination of electrical and thermal performance at different radiation using a photovoltaic thermal water collector. Radiation level considered was 500 to 800 W/m2 while mass flow rates range from 0.011 kg/s to 0.041 kg/s. The maximum performance was found at 800 W/m2 while the flow rate was 0.041 kg/s. They recorded 68.4% absorber efficiency and 13.8% PV efficiency.20\n\nJayanth K.G. & Venkatesh B (2017) in their work, comparisons between climate conditions were taken with a south-facing tilt and north-facing tilt, and the temperature was also monitored and the effect measured during performance analysis. Under partial shading conditions, at 15-degree tilt angle, current and voltage recorded was 0.14 A and 16 V (on South facing) and 0.1 A and 12 V (on North facing). Under without shading conditions, at 15-degree tilt angle, current and voltage recorded was 0.3A and 17 V (on South facing) and 0.26 A, 15 V (on North-facing).21\n\nPratish Rawat (2017) observed that solar PV panel is greatly responsive toward solar insolation as it is white light and composed of seven colors. In the study, wavelength is studied to examine the performance of the PV module and found each of these colors produced different efficiency, violet 7.52%, blue 6.89%, green 8.62%, yellow 8.54%, orange 7.91%, and red 9.73%. They concluded that best filter color is between yellow and red (wavelength between 600 nm to 700 nm) for best voltage produced in the range of 0.3137V to 0.2804V respectively.22\n\nShahab Ahmad et al. (2021) focused on the issue of electrical performance degradation of on-field PV modules. This experimental work concluded that factors responsible for performance degradation are; environmental conditions where panels located, quality of material used to manufacture PV cells, processing techniques used, amongst other factors. Solder bond cracking and encapsulate charring are major reasons behind degradation of electrical parameters for solar cells. Short circuit current (Isc) decreases and hence efficiency.23\n\nYong Sheng Khoo et al. (2014) explored 3 different PV system models used to determine the effect of orientation and panel tilt angle in Singapore. They measured GHI (Global Horizontal Irradiation) and DHI (Diffused Horizontal Irradiation) hourly. For horizontal irradiance measurement the sensor position was 60° NE while for vertical irradiance measurement sensor facing North, South, East, and West. Different panel tilt angles tested were 10°, 20°, 30°, 40°. The solar panel tilted 10° facing east reported maximum power.24\n\nGeorge Cristian Lazaroiu et al. (2015) evaluated the proficiency of a fixed photovoltaic and another equipped with sun tracker in the analytical approach. The inclusion of a sun tracker resulted in a significant increase in the energy generated by 12–21%. It does so because in the morning and evening the sun tracker system helps to increase the performance.25\n\nNallapaneni Manoj Kumar et al. (2017) emphasize the techno-economic analysis of the anticipated crystalline-based solar PV plant. It has free position mounting also called an open frame/rake structure. As a result, this study concluded that 12 hectares is adequate for a 20 MW solar plant to meet the complete electrical necessities. When compared against the universal norm which was 1MW per 2 hectares, it clearly reduces the space required.26\n\nZoltán Nagy et al. (2016) explored the building integration photovoltaics (BIPV) opportunities of flexible thin film PV (FPV) solar cells. Partial shading conditions and curved PV system were been analysed and tested. They suggested that with a flat and horizontal shape modules its efficiency is 12.5 to 13%. On the other hand, when the same modules are curved, it resulted in only a 6% efficiency.27\n\nAhsan, et al. (2016) created a study considering the economic analysis of an off-grid PV system of 1KW capacity setup at 28.5616° N, 77.2802° E, and located in India 293 m above sea level. It gives a rate of return of 1.714% on investment on the assumption of cost of energy at Rs. 0.9724/kWh and life of the product at 25 years. The study is restricted to a moderate home in a rural area. This system produced solar energy of approximately 3100 kWh per year. Out of which, 2933 kWh per year is delivered to the user, while approximately 170 kWh of energy is unexploited, owing to battery full condition or short demand.28\n\nElias M. Salilih et al. (2019) explored a model which considered constant load conditions at 2, 4, and 6 Ω under the performance of a distinctive PV module or panel. The region was tropical Jigjiga Eastern Ethiopia, (9.35° N, 42.8° E). By a detailed numerical algorithm, the electrical properties of the given module have been determined. It is found that the load of 4 Ω resulted in the maximum daily energy output, it is also concluded that all weather conditions do not result in the same load conditions being favourable.29\n\nChong Li (2018) in their study used seven different types of PV systems in the same region, at the coordinates of 32.0438° N and 118.7785° E, approximately 68 m above sea level, measurements based on ambient temperature and monthly average solar irradiation were taken. This is a performance-focused analysis of the module, this study tested different PV constructions and found different efficiency: polycrystalline silicon (p-Si) at 6%, cadmium telluride (CdTe) thin-film at 6.3%, monocrystalline silicon (m-Si) at approximately 9.3%, Copper Indium Selenide (CIS) thin film 7.8%, Edge-defined Film-fed Silicon (EFG-Si) 8.0%, Heterojunction Intrinsic Thin layer (HIT) 15.7%, and Hydrogenated amorphous Silicon with single-junction (a-Si: H single-PV) 3.15%. They concluded that HIT is the most optimum architecture, and p-Si and CdTe as the appropriate choices for the area considered.30\n\nCuce et al. (2013) explored the effects of two major environmental conditions; solar intensity (200 to 1000 W/m2) and panel temperature (15–60°C). As the temperature of the cell rises, the voltage level drops dramatically. As the light intensity level fluctuated, the shunt resistance of photovoltaic modules stayed nearly constant. With the increase in cell heat, a linear drop in the resistor has been seen. As a result, shunt resistance is very sensitive to temperature coefficient (Tc) and both series resistance and shunt resistance linearly decreases with increasing Tc. High illumination intensity (W/m2) was unaffected by the disparities of intensity in light.31\n\nRamaprabha & Mathur (2012) analyzed the power production by the SPVA (solar photovoltaic array) under different shading conditions (75%, 20%, and no shading). They also tested designs in a different arrangement such as parallel, series, series-parallel (SP) and total cross-tied (TCT), bridge-linked (BL) as-well-as honeycomb (HC) configurations. For the above analysis, a generalized M-code was developed using Matrix laboratory (MATLAB). Research has resulted in conclusions that to get the highest probable power output under partially shading situations, it is compulsory to attach a bypass diode in anti-parallel with a module of cells. The best configuration found in TCT arrangement for maximum power output, however, HC was also near to TCT.32\n\nKamal sign at al. (2021) experimentally investigated the performance of poly crystalline silicon based conventional PV panel using water circulation for cooling. Cupper tubes (6.35 mm diameter) have been attached behind the panel using single cupper absorbing plate to circulate water as cooling fluid. With water flow rate of 0.0166 kg/sec, 15.23% temperature reduction was achieved and nearly 6% increment in electrical efficiency reported.33\n\nKazem & Chaichan (2016) investigated the output power loss due to dust deposition on PV modules in Oman. They considered different-sized dust particles collected from six locations in Oman. The majority (64%) of the dust particles had sizes ranging from 3 to 62 μm. The amount of dust deposited on solar panels differed from one place to the next. The low surface weight concentration of dust (1 g/m2) did not result in any substantial energy yield loss. However, after being exposed to the outdoors for more than 3 months, the results indicate that the PV module's output drops by up to 35–40%, suggesting that cleaning should be done every 3 months.34\n\nHussain et al. (2017) experimentally studied the effect of duct on solar PV panels. They concluded that up to 60% power loss reported with different size and weight of dust particles. With rise husk deposited on panels, 3.88 W power loss concluded.35\n\nVeeramanikandan et al. (2022) experimentally investigated the effect of temperature on the performance of solar PV panel at Coimbatore, Tamilnadu, India. They analyzed transient temperature distribution in panels using Ansys software. They concluded that temperature is the most critical parameter that significantly impacts on panel efficiency.36\n\nA comprehensive review of SPVS installed at various locations with a variety of efficiency at different process parameters is given in Table 2. Some important information drawn from the Table 2 are; (i) process parameters affecting the SPVS efficiency include panel surface temperature, shading of solar cells, irradiance, tilt of panel, series-parallel/total cross tied combinations, solar cell materials, dust deposition, fabrication techniques used by the different manufacturers, etc. (ii) research work is going on worldwide to improve the SPVS efficiency considering economics and Installation/space requirements. (iii) Practically 12-20% efficiencies reported by different researchers for different SPVS installations worldwide with different types of solar cells and design architecture.\n\n\n\n• Efficiency 12.168 % for temperature 66.98°C.\n\n• Efficiency 13.05% for temperature 54°C.\n\n• Mesh size 0.5 m.\n\n\n\n• DA (Daylight autonomy) and UDI (Daylight illuminance) prove to be more reliable in the study.\n\n• Subsequently, a proper combination between daylight, electric light, and shading influence should be also carefully analyzed,\n\n• It reveals a great energy saving as well as user comfort improvement.\n\n\n\n• In the vicinity of Arequipa and Tacna, the annual performance ratio (PR) is 0.83 for an sc-Si while for mc-Si in Lima 0.70 to 0.77.\n\n• Direct Current Annual PR 0.97 for a-Si/sc-Si.\n\n\n\n• In the conclusion, when exposure is 130kWh/m2 the thin-film modules were 50% in a performance degraded.\n\n• CIS module degraded by more than 20%.\n\n\n\n• The monthly average Direct Solar Irradiance for a year is 968 W/m2.\n\n• Diffuse solar irradiance 88.22W/m2.\n\n• Reflected solar irradiance 4.70 W/m2.\n\n• The beam radiation 91%, diffuse radiation 8%, and reflected radiation 0.4% found.\n\n\n\n• The efficiency as a function of the irradiance can be calculated with a fair degree of accuracy from the STC I-V curve.\n\n• Low irradiance losses however are determined with low accuracy.\n\n\n\n• The losses, by a particular state of the incident sunlight, are about 7–8% as compared to experimental 14–15%.\n\n• The losses caused by low irradiation are 3%.\n\n• Due to the polarization of the open skylight, it was 1-2%.\n\n• Caused by the reflection of incident 3%.\n\n• Due to spectral effects, it was approx. 1%.\n\n• Due to the temperature of the module loss at 7%.\n\n\n\n• IRR was found to be 5.4 to 8.6% and it may be increased by 0.7-0.9%.\n\n• Module efficiency (ηm; STC) 15.54 %\n\n• Optimal tilt angles 28-29°\n\n• Electricity production is more than fixed-tilt. And offers 3.21-3.71%,\n\n• Seasonal tilt amendment offers 3.65-4.25%\n\n• Monthly tilt amendment (S4) offers 4.5-5.3%.\n\n\n\n• Open-circuit voltage of 0.4% per 1°C increases temperature while using a 5W PV panel.\n\n• 0.6% decrease in maximum power output, for incremental one-degree panel temperature.\n\n• Each 1°C increase in surface temperature fills factor decreases by 0.32%.\n\n• VOC, Maximum Power Pm, and FF are 12.16%, 18.18%, and 9.60% respectively for panel temperatures 35°C to 65°C.\n\n\n\n• The power output is 13 to 68% compared to TCT and\n\n• 19 to 140% compared to SP.\n\n\n\n• mc-Si PV system\n\n• a-Si PV system.\n\n\n\n• The PR of the mc-Si ranges from approx. 57 to 93.\n\n• For a-Si, PR ranges from approx. 53.7 to 87.6.\n\n• The high capture losses occurred in a-Si as related to mc-Si.\n\n\n\n• Output power losses were found to be 31.4% for 30° fixed panel while 23.1% for 45° tilt.\n\n• The output power losses were 8.5% when two axis tracking system is adopted.\n\n\nConclusion\n\nThis review discussed the most important operating parameters like solar irradiation, PV panel temperature, tilting angle effect, parallel and series combination effect of diode, shading, environment impact, different types of solar panels, PV materials, and different light wavelengths and their effect on the efficiency of the solar PV system. Also, socio-economic, techno-economic, and recent improvements in SPV technologies have been discussed. Significant conclusions are:\n\nSolar irradiation is always advantageous for higher efficiencies however, simultaneously it increases the temperature of the solar panel which adversely affects it. In India, the value of solar irradiation ranges from 100 W/m2 to 900 W/m2 (per season). Solar panels are designed to work in cool environment near to 25°C. Hence, in India appropriate cooling technologies are advantageous to optimize the power output.\n\nSolar panel temperature between 15°C to 35°C is advantageous. Panels are designed to perform at peak efficiency between this ranges. The optimum temperature considered is 25°C (77°F). Each degree increase of panel temperature would cause efficiency drop by 0.5%.\n\nThe tilt angle of solar panels ideally is 15° added to the latitude during winter and subtracting 15° from latitude during summer in the northern hemisphere (like in India) and panel facing south, while it reverses in the southern hemisphere. This is the optimum condition for maximum solar irradiation. For the city of Jabalpur, Madhya Pradesh, India optimum tilt angle is (23.18 plus 15°) 38.18°.\n\nShading of solar panels adversely affects the efficiency of PV modules. Shading just one solar cell in the module can lead to zero power output. 1% shading can reduce 50-70% of power output. The use of a bypass diode in proper string and blocking diodes is the best way to prevent failure of solar panels and discharging battery. Module-level power electronics are also beneficial to reduce shading losses.\n\nSolar PV cell manufacturer is another important criterion to be considered when selecting system configuration and electrical components matching. Manufacturing and architecture processes reasonably direct affect the performance and efficiency of the PV modules, panels as well as the overall system. Manufacturing factors affecting efficiency include; cell design, silicon type, cell layout and configuration, and solar panel size. Presently, companies (like LonGi, Canadian Solar, Trina Solar, SunPower, LG, Panasonic, REC Solar, CSUN, and Solaria) manufacture/assemble solar panels with 20-23% panel efficiency and supplying commercially in the market.",
"appendix": "Data availability\n\nNo data are associated with this study.\n\n\nReferences\n\nRaina G, Sinha S: Outlook on the Indian scenario of solar energy strategies: Policies and challenges. Energ. Strat. Rev. 2019; 24: 331–341. Publisher Full Text\n\nBehura AK, Kumar A, Rajak DK, et al.: Towards better performances for a novel rooftop solar PV system. Sol. Energy. 2021; 216: 518–529. Publisher Full Text\n\nGul M, Kotak Y, Muneer T: Review on recent trend of solar photovoltaic technology. Energy Explor. Exploit. 2016; 34(4): 485–526. Publisher Full Text\n\nShaikh MRS, Waghmare SB, Labade SS, et al.: A Review Paper on Electricity Generation from Solar Energy. Int. J. Res. Appl. Sci. Eng. Technol. 2017; V: 1884–1889. Publisher Full Text\n\nSingh R, Banerjee R: Estimation of rooftop solar photovoltaic potential of a city. Sol. Energy. 2015; 115: 589–602. Publisher Full Text\n\nMughal S, Sood YR, Jarial RK: A Review on Solar Photovoltaic Technology and Future Trends. International Journal of Scientific Research in Computer Science, Engineering and Information Technology. 2018; 4: 227–235.\n\nNayan MF, Ullah SMS, Saif SN: Comparative Analysis of PV Module Efficiency for Different Types of Silicon Materials Considering the Effects of Environmental Parameters. 3rd International Conference on Electrical Engineering and Information Communication Technology (ICEEICT).2016. Publisher Full Text\n\nWöhrle N, Fellmeth T, Greulich J, et al.: Understanding the rear-side layout of p-doped bifacial PERC solar cells with simulation driven experiments. Energy Procedia. 2017; 124: 225–234. Publisher Full Text\n\nHanifi H, Schneider J, Bagdahn J: Reduced shading effect on half-cell modules – measurement and simulation. 31st European Photovoltaic Solar Energy Conference and Exhibition.2015; 2529–2533.\n\nTyagi VV, Rahim NAA, Rahim NA, et al.: Progress in solar PV technology: Research and achievement. Renew. Sust. Energ. Rev. 2013; 20: 443–461. Publisher Full Text\n\nKashyap S, Pandey R, Madan J, et al.: Design and simulations of 24.7% efficient silicide on oxide-based electrostatically doped (SILO-ED) carrier selective contact PERC solar cell. Micro and Nanostructures. 2022; 165: 207200. Publisher Full Text\n\nDhilipan J, Vijayalakshmi N, Shanmugam DB, et al.: Performance and efficiency of different types of solar cell material – A review. Mater. Today: Proc. 66: 1295–1302. article in press. Publisher Full Text\n\nHe X, JihuaiWu YT, Xie Y, et al.: TiO2 single crystalline nanorod compact layer for high-performance CH3NH3PbI3 perovskite solar cells with an efficiency exceeding 17%. J. Power Sources. 2016; 332: 366–371. Publisher Full Text\n\nZhang C, Chen L, Zhu Y, et al.: Fabrication of 20.19% Efficient Single- Crystalline Silicon Solar Cell with Inverted Pyramid Microstructure. Nanoscale Res. Lett. 2018; 13: 991. 1-8. PubMed Abstract | Publisher Full Text\n\nZhao J: Recent advances of high-efficiency single crystalline silicon solar cells in processing technologies and substrate materials. Sol. Energy Mater. Sol. Cells. 2004; 82: 53–64. Publisher Full Text\n\nHutchby JA, Timmons ML, Venkatasubramanian R, et al.: High-efficiency tandem solar cells on single- and poly-crystalline substrates. Sol. Energy Mater. Sol. Cells. 1994; 35: 9–24. Publisher Full Text\n\nKashyap S, Madan J, Pandey R, et al.: 22.8% efficient ion implanted PERC solar cell with a roadmap to achieve 23.5% efficiency: A process and device simulation study. Opt. Mater. 2022; 128(112399): 112399. Publisher Full Text\n\nJoshi A, Khan A, Afra SP: Comparison of half cut solar cells with standard solar cells. Advances in Science and Engineering Technology International Conferences (ASET) Proceedings. 2019; pp. 1–3. Publisher Full Text\n\nHanifi H, Dassler D, Schneider J, et al.: Optimized tab width in half-cell modules. Energy Procedia. 2016; 92: 52–59. Publisher Full Text\n\nFudholi A, Sopian K, Yazdi MH, et al.: Performance analysis of photovoltaic thermal (PVT) water collectors. Energy Convers. Manag. 2014; 78: 641–651. Publisher Full Text\n\nJayanth KG, Venkatesh B: Performance Analysis of Solar Module with Climatic Data. International Journal of Advanced Research in Electrical, Electronics and Instrumentation Engineering. 2017; 6(5): 3468–3476. Publisher Full Text\n\nRawat P: Performance Analysis of 300W Solar Photovoltaic Module under Varying Wavelength of Solar Radiation. Int. J. Res. Appl. Sci. Eng. Technol. 2017; V: 2478–2482. Publisher Full Text\n\nAhmad S, Zafar FU, Noman M: Electrical performance degradation analysis of field exposed silicon-based PV modules. Journal of Mechanics of Continua and Mathematical Sciences. 2021; 16(5): 27–35. Publisher Full Text\n\nKhoo YS, André Nobre RM, Yang D, et al.: Optimal Orientation and Tilt Angle for Maximizing in-Plane Solar Irradiation for PV Applications in Singapore. IEEE J. Photovolt. 2014; 4: 647–653. Publisher Full Text\n\nLazaroiu GC, Longo M, Roscia M, et al.: Comparative analysis of fixed and sun tracking low power PV systems considering energy consumption. Energy Convers. Manag. 2015; 92: 143–148. Publisher Full Text\n\nKumar NM, Sudhakar K, Samykano M: Techno-economic analysis of 1 MWp grid connected solar PV plant in Malaysia. Int. J. Ambient. Energy. 2019; 40(4): 434–443. Publisher Full Text\n\nHofer J, Nagy Z, Schlueter A: Electrical design and layout optimization of flexible thin-film photovoltaic modules. 32nd European Photovoltaic Solar Energy Conference and Exhibition. 2016. Publisher Full Text\n\nAhsan S, Javed K, Rana AS, et al.: Design and cost analysis of 1 kWphotovoltaic system based on actualperformance in Indian scenario. Perspect. Sci. 2016; 8: 642–644. Publisher Full Text\n\nSalilih EM, Birhane YT: Modeling and Analysis of Photo-Voltaic Solar Panel under Constant Electric Load. Hindawi J. Renew. Energy. 2019; 2019: 1–10. Publisher Full Text\n\nLi C: Comparative Performance Analysis of Grid-Connected PV Power Systems with Different PV Technologies in the Hot Summer and Cold Winter Zone. Hindawi Int. J. Photoenergy. 2018; 2018: 1–9. Publisher Full Text\n\nCuce E, Cuce PM, Bali T: An experimental analysis of illumination intensity and temperature dependency of photovoltaic cell parameters. Appl. Energy. 2013; 111: 374–382. Publisher Full Text\n\nRamaprabha R, Mathur BL: A Comprehensive Review and Analysis of Solar Photovoltaic Array Configurations under Partial Shaded Conditions. Int. J. Photoenergy. 2012; 2012: 1–16. Publisher Full Text\n\nSingh K, Singh S, Deep Chand K, et al.: Experimental performance study of photovoltaic solar panel with and without water circulation. Mater. Today: Proc. 2021; 46: 6822–6827. Publisher Full Text\n\nKazem HA, Chaichan MT: Experimental analysis of the effect of dust’s physical properties on photovoltaic modules in Northern Oman. Sol. Energy. 2016; 139: 68–80. Publisher Full Text\n\nHussain A, Batra A, Pachauri R: An experimental study on effect of dust on power loss in solar photovoltaic module. Renewables: Wind, Water, and Solar. 2017; 4(9): 1–13. Publisher Full Text\n\nVeeramanikandan M, Arjunan TV, Gunasekar N, et al.: Design optimization and experimental evaluation of novel photovoltaic modules in comparison with a conventional photovoltaic module. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects. 2022; 44: 8627–8643. Publisher Full Text\n\nLaha SK, Sadhu PK, Ganguly A, et al.: A comparative study on thermal performance of a 3-D model based solar photovoltaic panel through finite element analysis. Ain. Shams Eng. J. 2022; 13: 101533. Publisher Full Text\n\nBellia L, Marino C, Minichiello F, et al.: An overview on solar shading systems for buildings. Energy Procedia. 2014; 62: 309–317. Publisher Full Text\n\nRomero-Fiances I, Muñoz-Cerón E, Espinoza-Paredes R, et al.: Analysis of the Performance of Various PV Module Technologies in Peru. Energies. 2019; 12(186): 1–19. Publisher Full Text\n\nMeyer EL, Ernest van Dyk E: Assessing the Reliability and Degradation of Photovoltaic Module Performance Parameters. IEEE Trans. Reliab. 2004; 53: 83–92. Publisher Full Text\n\nDaut I, Irwanto M, Irwan YM, et al.: Clear Sky Global Solar Irradiance on Tilt Angles of Photovoltaic Module in Perlis, Northern Malaysia. International Conference on Electrical, Control and Computer Engineering Pahang, Malaysia. 2011; pp. 445–450. Publisher Full Text\n\nEikelboom JA, Reinders AHME: Determination of the irradiation dependent efficiency of multi crystalline Si PV modules on basis of IV curve fitting and its influence on the annual performance.1997.\n\nParretta A, Sarno A, Vicari LRM: Effects of solar irradiation conditions on the outdoor performance of photovoltaic modules. Opt. Commun. 1998; 153: 153–163. Publisher Full Text\n\nÖmer Gönül A, Duman C, Barutçu B, et al.: Techno-economic analysis of PV systems with manually adjustable tilt mechanisms. Engineering Science and Technology, an International Journal. 2022; 35: 101116. Publisher Full Text\n\nKumar TA, Murthy CSN, Mangalpady A: Performance analysis of PV panel under varying surface temperature. MATEC Web of Conferences. 2018; 144: 04004. Publisher Full Text\n\nBelhaouas N, Ait Cheikh M-S, Agathoklis P, et al.: PV array power output maximization under partial shading using new shifted PV array arrangements. Appl. Energy. 2017; 187: 326–337. Publisher Full Text\n\nTripathi B, Yadav P, Rathod S, et al.: Performance analysis and comparison of two silicon material based photovoltaic technologies under actual climatic conditions in Western India. Energy Convers. Manag. 2014; 80: 97–102. Publisher Full Text\n\nDarwish ZA, Kazem HA, Sopian K, et al.: Impact of Some Environmental Variables with Dust on Solar Photovoltaic (PV) Performance: Review and Research Status. Int. J. Energy and Environment. 2013; 7: 152–159."
}
|
[
{
"id": "155201",
"date": "06 Dec 2022",
"name": "Ramalingam Senthil",
"expertise": [
"Reviewer Expertise Solar Energy",
"Energy Storage"
],
"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\nEditorial Note from F1000Research – 22/06/2023: This report has been updated to include a conflict of interest statement which was not declared at the time of publishing of this report.\nThe performance characteristics and efficiency enhancement techniques are reviewed here. But the state-of-the-art of review is missing. An overview of the present techniques and the significance of the present review over the existing review articles need to be stated. The following comments need to be addressed by the authors.\nMajor:\nState the research gap and novelty of the presented review.\n\nInclude recent references to strengthen the introduction section and motivation of the present review. A few recent references are given here1,2,3,4,5.\n\nState the importance of the present review.\n\nProvide critical analysis of the status of the parametric optimization of solar PV. Prioritize the parameters influencing the solar PV output power.\n\nAdd the authors' own discussion and recommendations on performance enhancement technologies.\n\nThe conclusion section is too long. Provide significant conclusions. The remaining points can be provided in a “Discussion” section.\nMinor:\nDo not give abbreviations for one-time or two times appearing phrases. Define the abbreviation at its first appearance and then use the abbreviation. Several abbreviations are there unnecessarily.\n\nThe tables are lengthy. Make it give the data crisply.\n\nAdd further scope for solar PV research in this context.\n\nImprove English and grammar.\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
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https://f1000research.com/articles/11-1264
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https://f1000research.com/articles/11-1263/v1
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07 Nov 22
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{
"type": "Research Article",
"title": "Effect of Moringa oleifera leaf extract on salivary gland damage in Sjögren's syndrome mice model",
"authors": [
"Agus Joko Susanto",
"Bambang Purwanto",
"Ambar Mudigdo",
"Brian Wasita",
"Bambang Purwanto",
"Ambar Mudigdo",
"Brian Wasita"
],
"abstract": "Background Sjögren's syndrome is a chronic autoimmune disease characterized by lymphocytic infiltration and inflammation of the exocrine glands, especially the lacrimal and salivary glands. Moringa oleifera (MO) leaves are rich in polyphenols and flavonoids which have antioxidant activity which is also shown when extracted with ethanol. This study aimed to probe the effect of Moringa oleifera leaf extract on malondialdehyde (MDA), interleukin-17 (IL-17), matrix metalloproteinase-9 (MMP-9), and caspase-3 levels and salivary gland damage in Sjögren's syndrome mice model. Methods Thirty-two samples were divided into four treatment groups: 200 mg/kg BW MO-ethanol leaf extracts with 1.23 mg/kg BW dexamethasone group (T2), 1.23 mg/kg BW dexamethasone alone group (T1), normal control group/C- (without induction of Ro antigen (SSA) and extract of MO-ethanol), and negative group/C+ (with induction of Ro antigen (SSA) on day 42). MDA, IL-17, MMP-9, and caspase-3 levels and salivary gland epithelium damage (histopathological changes) were measured 14 days post-Ro antigen (SSA) induction. The method used to measure MDA level was Thiobarbituric Acid Reactive Substance (TBARS) while IL-7 and MMP-9 were ELISA. Some of the salivary gland was used for histological preparations using the paraffin method withoud Harris Hematoxylin–Eosin (HE) staining. Then for the examination of caspase-3, we used the standard procedure of immunohistochemically staining. The salivary gland epithelium damage examination used the HE staining of histological preparation.\nResults There were significant differences in MDA, IL-17, MMP-9, and caspase-3 levels in the group given a 200 mg/kg BW dose of MO-ethanol leaf extract compared to the control group. The administration of the extract also significantly reduced the degree of necrosis of the salivary gland epithelium. Conclusions Moringa oleifera leaf extract reduced MDA, IL-17, MMP9, and caspase-3 levels and salivary epithelial damage.",
"keywords": [
"Moringa oleifera leaf extract",
"Sjögren's syndrome",
"Salivary gland",
"Apoptosis"
],
"content": "Introduction\n\nSjögren’s syndrome (SS) is a systemic, complex, and multifactorial autoimmune disease. The triggering events of autoimmune disease and the pathophysiology of SS are unknown, but it is thought that both genetic and environmental factors play an important role (Igoe and Scofield 2013). The incidence of SS ranges between 0.01% and 0.72% globally (Brito-Zerón et al. 2016). Women are more likely to have SS compared with men, with a percentage value of 9:1 and a mean age of 56 years (Stefanski et al. 2017). The prevalence of SS is also found to be higher in the elderly population (Haugen et al. 2008). SS predominantly appears in women around or after menopause, although it can develop at any age (Brito-Zerón et al. 2009; Haugen et al. 2008). In Indonesia, there are no epidemiological data related to SS cases; only systemic lupus erythematosus and rheumatoid arthritis (RA), thus SS does not have adequate data.\n\nOxidative stress occurs in many autoimmune diseases, along with the excess production of reactive oxygen species (ROS) and reactive nitrogen species, which are related to the inflammatory process. The sources of such reactive species include nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) oxidases (NOXs), the mitochondrial electron transport chain, nitric oxide (NO) synthases, and other enzymes (Smallwood et al. 2018). Various cluster of differentiation/CD4+ T cell subsets emerge to contribute to primary Sjögren’s syndrome (pSS) pathogenesis, including the T helper (Th) 1, follicular T helper, and T helper 17 (Th17) cells. T helper 17 cells play a role in mucosal barrier physiology and pathogen-associated inflammatory responses. T helper 17 cells producing interleukin 17 (IL-17) are also found in salivary gland lesions and are high in peripheral blood (Verstappen et al. 2018). Interleukin 17 promotes the production of metalloproteinase matrix 9 (MMP-9) and harms the mice's corneal barrier (Chauhan et al. 2009; de Paiva et al. 2009). In SS patients there is an increase in MMP-9 gene expression and plasma levels (Hulkkonen et al. 2004). MMP-9 is an important inflammatory mediator involved in SS immunopathogenesis (Pflugfelder SC 2014). B lymphocyte cells also play an important role in the pathogenesis of SS by several mechanisms, namely, as cytokine producers, antigen-presenting cells, and autoantibody secretors (Nocturne and Mariette 2018). Autoantibodies that are characteristic of pSS include anti-Ro/Sjögren's syndrome antigen type A (anti-Ro/SSA) antibodies, which can be detected in 70–100% of patients with SS, and anti-La Sjögren syndrome type B antigen (anti-La/SSB), which has detection rates ranging from 40 to 90% (Wenzel et al. 2001). Anti-La antibodies are not always positive, however, the combination of the two is more likely to lead to SS than anti-Ro antibodies alone (Scofield et al. 2018). Anti-Ro antibodies are a more specific diagnostic marker and are included on Sjogren's syndrome criteria when compared with anti-La (Shiboski et al. 2017).\n\nSjogren's syndrome primarily affects the salivary and tear glands. In the ACR/EULAR classification criteria for the diagnosis of primary Sjogren's syndrome, the presence of focal lymphocytic sialadenitis in the labial salivary glands and a focal score ≥ 1 foci/4 mm has the highest score, which is 3. The diagnosis of Sjogren's syndrome is established if the total score is ≥4.\n\nCurrently, there is no effective drug for the management of the etiology of SS (Shen et al. 2019; Vivino et al. 2019). Therapeutic approaches are limited to topical and systemic to treat sicca and systemic symptoms, with the aim of improving quality of life (Carsons et al. 2017; Shih et al. 2017). Although diagnostic criteria and guidelines for the management of SS have been developed, gaps remain with respect to effective specific therapies and their impact on patients (Romão et al. 2018). The imbalance of cytokines and their pathological effects is one aspect that can be a target for therapy (Sambataro et al. 2017).\n\nMoringa oleifera (MO) is reported to have anti-inflammatory, antimicrobial, antioxidant, anticancer, cardiovascular, hepatoprotective, anti-ulcer, diuretic, antiurolithiasis, and anthelmintic functions (Farooq et al. 2012). M. oleifera leaf extract, ripe or still soft, exhibits strong antioxidant activity against free radicals, prevents oxidative damage to key biomolecules, and provides significant protection against oxidative damage. Furthermore, various animal safety studies involving M. oleifera leaf extracts have shown a high level of safety (Mahmood et al. 2010; Stohs and Hartman 2015). The ethyl acetate fraction of M. oleifera extract in in vitro studies contained high levels of phenols and antioxidant activity. This fraction can inhibit the production of cytokines by macrophages in vitro triggered by cigarette smoke extracts, such as tumor necrosis factor (TNF), interleukin-6 (IL-6), and interleukin-8 (IL-8). In addition, it inhibits the expression of RelA, which is a gene involved in the NF-κB (activated B-cell kappa-light-chain-enhancing nuclear factor) p65 inflammatory signaling pathway (Kooltheat et al. 2014).\n\nAs aforementioned, M. oleifera leaves have antioxidant activity, so there is a need for research to assess whether there is any effect of M. oleifera (Kelor) leaf extract on salivary gland damage and the levels of IL-17, MMP-9, malondialdehyde (MDA), epithelial necrosis, and caspase-3 levels in primary SS model rats.\n\n\nMethods\n\nAn experimental laboratory technique with a post-test only control group design was performed. The sampling method used in this study was purposive sampling. Male mice, BALB/c strain, aged 8–10 weeks, body weight (BW) 26–27.5 g, no physical disability, and normal activity were the inclusion criteria. Mice that died during the treatment period was the exclusion criteria. Sample size was determined by Federer's formula [(n − 1) (t − 1) > 15], so the obtained minimum samples number was six mice for each group. Two mice were added to each group to anticipate mice death, so that the final sample size was 32.\n\nThirty-two samples were divided into four treatment groups: 200 mg/kg BW MO-ethanol leaf extracts with 1.23 mg/kg BW dexamethasone group (T2), 1.23 mg/kg BW dexamethasone alone group (T1), normal control group/C- (without induction of Ro antigen (SSA) and extract of MO-ethanol), and negative group/C+ (with induction of Ro antigen (SSA) on day 42). The treatment in the form of dexamethasone and MO-ethanol leaf extracts given for 14 days. MDA, IL-17, MMP-9, and caspase-3 levels and salivary gland epithelium damage (histopathological changes) were observed 14 days post-Ro antigen (SSA) induction. The method used to measure MDA level was Thiobarbituric Acid Reactive Substance (TBARS) while IL-7 and MMP-9 were ELISA. Some of the salivary gland was used for histological preparations using the paraffin method without Harris hematoxylin–eosin (HE) staining for the examination of caspase-3 with the standard procedure of immunohistochemical staining. The salivary gland epithelium damage examination used the HE staining of histological preparation.\n\nHistopathological preparations were observed and scored according to the following categories:\n\nScore 0: No necrosis\n\nScore 1: Mild necrosis\n\nScore 2: Moderate necrosis\n\nScore 3: Severe necrosis.\n\nInterventions of BALB/c mice, histopathological preparations for epithelial necrosis, and histopathological reading of epithelial necrosis were conducted at the Experimental Animal Care Center (PAU UGM, Yogyakarta), Histology and Cell Biology Laboratory (Faculty of Medicine, UGM, Yogyakarta), and Anatomical Pathology and Histology Laboratory (Faculty of Medicine, UNS Surakarta), respectively. The authors were unaware of the allocation group so that all the mice were handled, monitored and treated in the same way while conducting the experiment.\n\nThis mice model was conducted for 42 days. BALB/c mice were immunized with a short peptide of 60-kD Ro antigen (SSA) that triggered an immune response and formed anti-Ro antibodies. There was a decrease in mouse salivary flow and T lymphocyte infiltration (both CD4+ and CD8+ T cells), in immunized mice similar to SS in humans (Scofield et al. 2018). BALB/c mice have a similar response to the nucleotide-binding and oligomerization domain/NOD-like receptor gene, C3H/HeJ. The C3H/HeJ gene has implications for the pathogenesis of SS (Kim et al. 2017; Sellers 2017). The average BW of BALB/c mice at 8, 9, and 10 weeks old was 26.2±1.4, 27.0±1.4, and 27.4±1.4 g, respectively. Mice were reared on a diet containing 6% fat according to the LabDiet® 5K52 feed formulation.\n\nMice were kept in four cages made of plastic tubs covered with wire at the top. The conditions during acclimatization and treatment were controlled in a fixed environmental range, namely in a room that had 12 hours of light and 12 hours of darkness with a room temperature ranging from 23-26°C with the aim that the test animals could adapt according to the animal's biological time and the conditions to be occupied during the experiment. Temperature, water supply, the number of mice in the cage, and the change of husks were all done the same for all groups of mice. Adaptation to mice with care in cages with a size of 28 × 30 × 12 cm so that they can move freely and not be stressed.\n\nAt the end of the study, euthanasia and removal of salivary glands were performed. We made 3 mm horizontal incision on the skin placed 1 mm below the ear lobe to expose the glands underneath. After identifying the parotid gland, we used the curved forceps to pull the gland out, used a scalpel to separate the gland from the surrounding tissue. The tissue was then put into a container containing 10% neutral buffer formalin. The sample was then made preparations with Harris Hematoxylin Eosin staining.\n\nThe leaf extracts were washed with tap water and dried at 24°C for a day and subsequently in an oven for two consecutive days at 45°C. The extracts was then ground using a mechanical blender and stored in a vacuum container. M. oleifera leaves were completely crushed using 90% ethanol (ethanol: distilled water, 9:1) and then put into a shaking aspirator bottle for 3 days at 24°C. The residue was filtered using Whatman filter paper No. 1, and the filtrate was condensed using a rotary evaporator at 40°C. The condensed residue softened and became dark green in color, and was then freeze-dried. The freeze-dried extracts were weighed, and stored in closed containers, before being properly labeled and stored at −20°C. Administration of M. oleifera leaf extract in ethanol at 200 mg/kg BW for 14 days showed anti-inflammatory activity (Both et al. 2017; Karthivashan et al. 2016).\n\nThe normality test used was the Shapiro–Wilk test. Numerical data were subsequently analyzed using ANOVA, then processed using the Tukey HSD (Honest Significant Difference) post hoc test for normally distributed and homogeneous data and the Games–Howell post hoc test for non-homogeneous data. The Kruskal-Wallis test was conducted on an abnormal distribution and continued with Mann-Whitney post hoc test. Independent t-tests were performed to compare the treatment group with other groups. The statistical analysis used was SPSS 22 for windows and a p value<0.05 was considered statistically significant.\n\n\nResults\n\nDifferences in MDA levels based on groups can be seen in Table 1. The C(−) control group had the lowest MDA level (1.55±0.2 mg/ml), whereas the C(+) group had the highest MDA level (10±0.5 mg/ml). Based on a one-way ANOVA, there was a significant difference in MDA levels with C(−) as reference (p< 0.05). Levene’s test value was p=0.03, and the Games–Howell post hoc test was conducted (Table 2).\n\n** =Statistically significant at the 1% level (p<0.001).\n\n** =Statistically significant at the 1% level (p<0.001).\n\nThe difference in MDA levels with the T2 group as a reference compared to other groups is shown in Table 3. It exhibits the significant difference in MDA levels of the T2 treatment group post-Ro (SSA) antigen induction when compared to the C(−), C(+), and T1 groups (p<0.001). This was the most striking difference between the T2 and the C(+) cluster with p<0.001 (95% CI 6.58–7.47). It is clear that the T2 group was more effective in reducing MDA levels post-Ro (SSA) antigen induction than the other groups.\n\n** =Statistically significant at the 1% level (p<0.001).\n\nDifferences in IL-17 levels based on groups can be seen in Table 4. Based on a one-way ANOVA, there was a significant difference in IL-17 levels with C(−) as reference (p<0.05). Levene’s test value was p=0.92. The Tukey HSD post hoc test was subsequently conducted (Table 5).\n\n** =Statistically significant at the 1% level (p<0.001).\n\n** =Statistically significant at the 1% level (p<0.001).\n\nTable 5 shows that IL-17 levels post-Ro (SSA) antigen induction in the C(+), T1, and T2 groups were significantly different from the C(−) control group with p<0.001. This showed effective treatment in reducing IL-17 levels. Differences in IL-17 levels between the T2 group and the other groups is shown in Table 6. The table demonstrates that there is a significant difference in IL-17 levels of the T2 treatment group post-Ro (SSA) antigen induction when compared with the C(−), C(+), and T1 groups with p<0.001. The most significant difference was between the T2 and C(+) groups with p<0.001 (95% CI 37.44–44.74). It can be concluded that the T2 group was more effective in reducing IL-17 levels post-Ro (SSA) antigen induction than the other groups.\n\n** =Statistically significant at the 1% level (p<0.001).\n\nDifferences in MMP-9 levels based on groups can be seen in Table 7. According to a one-way ANOVA, there was a significant difference in MMP-9 levels with C(−) as reference (p<0.05) and Levene's test value p=0.28, and then the Tukey HSD post hoc test was conducted (Table 8). Table 8 shows that MMP-9 levels post-Ro (SSA) antigen induction in the C(+), T1, and T2 groups were significantly different from the C(−) control group with p<0.001. This showed effective treatment in reducing MMP-9 levels. Differences in MMP-9 levels between the T2 group and the other groups are revealed in Table 9.\n\n** =Statistically significant at the 1% level (p<0.001).\n\n** =Statistically significant at the 1% level (p<0.001).\n\n** =Statistically significant at the 1% level (p<0.001).\n\nTable 9 displays that there are significant differences in MMP-9 levels of the T2 treatment group post-Ro (SSA) antigen induction when compared to the C(−), C(+), and T1 groups with p<0.001. The most significant difference was between the T2 and C(+) groups with p<0.001 (95% CI 18.55–20.70). It can be seen that the T2 group was more effective in reducing MMP-9 levels post-Ro (SSA) antigen induction than the C(−), C(+), and T1 groups.\n\nDifferences in caspase-3 levels based on groups can be seen in Table 10. Based on a one-way ANOVA, there was a significant difference in caspase-3 levels with C(−) as reference (p<0.05) and Levene's test value p=0.01. The Games–Howell post hoc test was subsequently conducted (Table 11).\n\n** =Statistically significant at the 1% level (p<0.001).\n\n** =Statistically significant at the 1% level (p<0.001).\n\nTable 11 shows that caspase-3 levels post-Ro (SSA) antigen induction in the C(+), T1, and T2 groups were significantly different from the C(−) control group with p<0.001. This showed effective treatment in reducing caspase-3 levels. Differences in caspase-3 levels between the T2 group and the other groups is shown in Table 12. Table 12 shows that there are significant differences in caspase-3 levels of the T2 treatment group post-Ro (SSA) antigen induction when compared to the C(−), C(+), and T1 groups with p<0.001. The most significant difference was between the T2 and C(+) groups with p<0.001 (95% CI 4.43–4.69). It can be concluded that the T2 group had more effective results in reducing caspase-3 levels post-Ro (SSA) antigen induction than the other groups.\n\n** =Statistically significant at the 1% level (p<0.001).\n\nA total of 11 mice were induced by Ro (SSA) antigen, and their salivary glands were collected. These samples were prepared with Harris hematoxylin and eosin staining and evaluated using a scoring system, which can be seen in Figure 1. Differences in salivary gland epithelial necrosis based on groups can be seen in Table 13. Table 13 shows that there is a significant difference in salivary gland epithelial necrosis scores between various groups with p<0.001, and then a Mann–Whitney post hoc test was conducted (Table 14).\n\n(A, B, C, and D) Magnification at 100× and (E, F, G, and H) 400×. Arrows indicate lymphocytic infiltration.\n\n** =Statistically significant at the 1% level (p<0.001).\n\n* =Statistically significant at the 5% level (p<0.05).\n\n** =Statistically significant at the 1% level (p<0.001).\n\nTable 14 shows that dexamethasone administration, with or without MO-ethanol extract, was more effective in preventing damage, upon histopathological examination, to salivary gland epithelial necrosis 14 days post-induction of Ro antigen (SSA). There was also a significant difference after being given MO-ethanol extract at a dose of 200 mg/kg BW in reducing the degree of salivary gland epithelial necrosis.\n\n\nDiscussion\n\nThe pathogenesis of SS involves autoantigen presentation, B and T cells, and autoantibody-mediated mechanisms of tissue injury (anti-SSA/Ro and anti-SSA/La antibodies). This mechanism causes cell fragmentation. TNF-α triggers endothelial cell adhesion molecules such as E-selectin that in turn trigger polymorphonuclear (PMN) cell arrest, which also involves IL-17 (microcirculation) and initiation of inflammatory responses (MMP-9 secretion, lysozyme, and caspase-3 pathways). PMN cells, especially neutrophils, trigger the activation of MMP-9 that degrades collagen leading to basement membrane damage. Neutrophils also secrete lysozyme enzymes that can affect mitochondrial oxygenation and the GMP cycle, triggering epithelial necrosis. The inflammatory process makes cells swell, so that the cell membrane ruptures, which leads to epithelial necrosis. Caspase-3 activation, which acts as an executor, promotes DNA fragmentation and ends with cell death through apoptosis. Basement membrane damage, epithelial necrosis, and epithelial cell apoptosis result in destruction to the salivary and lacrimal glands. Macrophages and lymphocytes are the main source of IL-6, especially in the inflammatory process. Together with IL-1 and TNF-α, IL-6 is able to activate T cells, induce an acute inflammatory response, and increase C-reactive protein (CRP) synthesis by hepatocytes. CRP is one of the inflammatory mediators that lowers nitric oxide synthase levels in the endothelium, which encompass endothelial dysfunction. NFκB has activity in initiating the inflammatory process and increasing proinflammatory cytokines (TNF-α), adhesion molecules, and NADPH transcriptions. Angiotensin II increases ROS production through NOX stimulation via a type 1 receptor (AT1R/Angiotensin II type 1 receptor). Angiotensin II and TNF-α have activity to stimulate NFκB activation in ROS-dependent pathways, which can further increase the production of cytokines and other proinflammatory chemokines. The formation of more ROS than antioxidants causes oxidative stress. MDA is used as a reference for the emergence of indicators of oxidative stress (Both et al. 2017; Brito-Zerón et al. 2009; Nakamura et al. 2018; Pflugfelder SC 2014; Verstappen et al. 2018).\n\nM. oleifera leaves exhibit antioxidant activity due to their high polyphenol content. They exhibit strong antioxidant activity against free radicals, thus prevent oxidative damage to major biomolecules and provide protection against oxidative damage. M. oleifera leaf extract is a prospective indicator of oxidative stress according to decreasing serum MDA levels. This would prevent the apoptotic process that is characterized by a decrease in caspase-3 levels in serum, and epithelial necrosis followed by a decrease in serum MMP-9 and IL-17 levels so that lacrimal and salivary gland damage can be minimized (Charoensin 2014; Verma et al. 2009).\n\nThis study showed that administration of 200 mg/kg BW of MO-ethanol leaf extract in SS model mice could significantly reduce MDA levels compared to the negative control group. This is in accordance with Nadimin’s study (2016), which aimed to determine the effect of M. oleifera extract on MDA levels during pregnancy in Makassar, Indonesia. This study was divided into two denominations: the intervention and the control. It was found that MDA levels in the control group were greater than those in the intervention cluster (p=0.033) (Nadimin 2016). The powder form of MO leaves could also reduce MDA levels in pregnant women, with p=0.028 (Misrawati and Marliah 2018). Several other studies have also shown that administration of MO-ethanol extract can reduce MDA levels in various diseases (Albrahim and Binobead 2018; Almufazar 2018; Wulandari et al. 2017).\n\nThis study showed that administration of MO-ethanol leaf extract significantly reduced IL-17 levels. The effect of MO-ethanol leaf extract, which can reduce IL-17 levels, was also useful in cases of inflammation due to ultraviolet-B/UV-B exposure (El Shanawany et al. 2019). The study by Ma et al. (2018) on psoriasis-induced mice showed a decrease in IL-17 levels (p<0.05) when given MO seed extract. A previous study showed that M. oleifera significantly reduced serum levels of IgG/Immunoglobulin G, IL-2, and IL-17 in sheep coinfected with Fasciola gigantica and Clostridium novyi (Engsuwan et al. 2021). Several studies addressing other cytokines including TNF-α, IL-6, IL-8, IL-1β, IL-10, NO, and PGE2 (prostaglandin E2) have been conducted. Kooltheat et al. (2014) found that MO can abolish the production of monocyte-derived macrophage factors, such as TNF-α, IL-6, and IL-8 (Xiao et al. 2020). Wardhani (2020) found that M. oleifera has a hepatoprotective effect by inhibiting TNF-α, IL-1β, IL-6, and IL-10. M. oleifera also inhibits fatty liver disease by inhibiting lipogenesis via the NF-κB pathway as characterized by decreased LDL-R/low-density lipoprotein receptor, SRB1c, DGAT2/diacylglycerol o-acyltransferase 2, and PPARγ/peroxisome proliferator activator γ and increased insulin sensitivity (Wardhani 2020).\n\nXie et al. (2021) evaluated the inhibitory effect induced by the alkaloids contained in M. oleifera on the proliferative and migratory phases in in vivo or in vitro methods on human prostate cell cancer (PC3). This study shows that M. oleifera will inhibit proliferation and induce cell apoptosis which causes cell cycle arrest. Furthermore, M. oleifera suppresses the migration of prostate cancer cells and inhibits the expression of MMP-9 (Xie et al. 2020). The study of Xie et al. (2020) also showed that western blotting results of Moringa oleifera alkaloids extract treatment at 200 g/ml inhibited the expression of MMP-2 (p<0.05) and MMP-9 cell migration-associated proteins compared to the control. Both studies were in accordance with the recent study, especially regarding the MO-ethanol leaf extract effect that can reduce MMP-9 levels compared to the control group.\n\nSeveral studies, which analyzed the anti-inflammatory effect of MO leaf extract on caspase-3 levels, have been conducted. The study of Mousa et al. (2019), which aimed to determine the anti-inflammatory effect of MO leaves on thioacetamide intoxicated rats, showed that MO-ethanol leaf extract is able to downregulate caspase-3. The study by Bahr and Farouk (2016), which aimed to determine the hepatoprotective effect of MO leaf extract on experimental animals combined with lornoxicam, obtained significant results in reducing caspase-3 levels (p<0.05). Rijal et al. (2016) observed changes in caspase-3 expression (apoptosis) in PCG (primary congenital glaucoma) trabecular cell cultures treated with Moringa oleifera leaf extract. This study showed a significant change in caspase-3 expression (apoptosis) after administration of methanol extract of Moringa oleifera leaves at doses of 20, 30, and 40 g/ml in primary congenital glaucoma trabecular meshwork cell cultures (Wulandari et al. 2019). In accordance with these studies, this research showed that MO-ethanol leaf extract could significantly reduce caspase-3 levels.\n\nIn this study, it was shown that administration of MO-ethanol leaf extract significantly reduced salivary gland epithelial necrosis scores in the treatment group compared to the control group. It occurred due to the anti-inflammatory mechanism of MO-ethanol. The study conducted by Fatmawati et al. (2019), which observed histopathological features of the pancreas in diabetic rats induced by streptozotocin, showed changes in Langerhans insula repair compared to the hyperglycemic control group and also restored weight loss to normal. The study conducted by Kamaliani et al. (2018) found that the administration of M. oleifera ethanol extract (200 mg/kg BW) in diabetic Wistar rat kidneys causes fatty degeneration compared to the control group. They explained that a dose of 200 mg/kg BW was an optimal dose without causing necrosis. Ijioma et al. (2018) also investigated several doses of MO-ethanol leaf extract (200, 400, and 800 mg/kg BW) in the stomach of aspirin-induced rats, which showed epithelial surface protection, characterized by more mucus granules and better results than those of Cimetidine in which patches of intact superficial cells were observed.\n\nThis study had several strengths. Firstly, the study proved that MDA, IL-17, MMP-9, and caspase-3 levels and salivary gland epithelium decreased significantly when given MO-ethanol extract compared to those given only Ro (SSA) antigen and dexamethasone. MO-ethanol extract could be a complementary therapy. Secondly, the study was expected to form the basis for further research. Thirdly, the research will hopefully become a protocol in human clinical trials and could inspire future researchers to conduct research using human samples.\n\nHowever, the study also had several limitations. Firstly, many other dependent variables such as markers of salivary gland damage (IFN-γ/interferon gamma, IL-6, BAFF/B-cell-activating factor, TGF-β/Transforming Growth Factor-β, LAMP3/Lysosome-associated membrane glycoprotein 3) were not observed. Secondly, the study did not observe any variation in dose of MO-ethanol leaf extract. Further research can be conducted with MO-ethanol leaf extract dose variations to determine minimum and maximum doses that can be given as supportive therapy in SS. Finally, the study method used IHC (immunohistochemistry) and ELISA (enzyme-linked immunosorbent assay) techniques; other techniques such as immunofluorescence could be performed in further research.\n\n\nConclusion\n\nAdministration of 200 mg/kg BW MO-ethanol extract 14 days post-induction by Ro (SSA) antigen significantly reduced MDA, IL-17, MMP-9, and caspase-3 levels and salivary epithelium damage (histopathological changes). MO-ethanol at a dose of 200 mg/kg BW can inhibit the apoptosis process of SS.\n\n\nEthical approval\n\nThe experiments were approved by the ethical guidelines by Dr. Moewardi Hospital Ethical Committee (approved number: 178/II/HREC/2022).\n\n\nAuthor contributions\n\nConceptualization, Agus Susanto; Data curation, Agus Susanto, Ambar Mudigdo and Brian Wasita; Formal analysis, Agus Susanto; Funding acquisition, Agus Susanto; Investigation, Agus Susanto and Brian Wasita; Methodology, Agus Susanto; Project administration, Agus Susanto and Brian Wasita; Resources, Agus Susanto and Brian Wasita; Software, Agus Susanto; Supervision, Bambang Purwanto and Ambar Mudigdo; Validation, Ambar Mudigdo and Brian Wasita; Visualization, Brian Wasita; Writing – original draft, Agus Susanto; Writing – review & editing, Agus Susanto and Bambang Purwanto.",
"appendix": "Data availability statement\n\nData repository name: [Raw Data Agus Joko Susanto.xlsx]. https://10.6084/m9.figshare.21388788.org/ (Nadimin 2016).\n\nThe project contains the following underlying data:\n\n- [Raw data Agus Joko Susanto] (raw data).\n\nData repository name: ARRIVE checklist for ‘[ARRIVE Guidelines-Author Checklist -.pdf]’. https://10.6084/m9.figshare.21388866.org/ (Albrahim and Binobead 2018).\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 Fatna Andika Wati and Dyah Rohmania Agustiana for their indispensable assistance in manuscript preparation.\n\n\nReferences\n\nAlbrahim T, Binobead MA: Roles of Moringa oleifera Leaf Extract in Improving the Impact of High Dietary Intake of Monosodium Glutamate-Induced Liver Toxicity, Oxidative Stress, Genotoxicity, DNA Damage, and PCNA Alterations in Male Rats. Oxidative Med. Cell. Longev. 2018; 2018: 1–11. PubMed Abstract | Publisher Full Text\n\nAlmuzafar HM: Effect of Moringa oleifera leaves extract on the oxidative stress and gastric mucosal ulcer induced by indomethacin in rats. Afr. J. Biotechnol. 2018; 17(3): 51–56.\n\nBahr HI, Farouk SM: Comparative Ameliorative Effect of Basil Oil and Moringa oleifera on Lornoxicam- Mediated Histological and Biochemical Alterations in Albino Rat Liver. J. Veterinar. Sci. Technol. 2016; 7(2): 1–11.\n\nBoth T, Dalm VA, van Hagen PM , et al.: Reviewing primary Sjögren's syndrome: beyond the dryness - From pathophysiology to diagnosis and treatment. Int. J. Med. Sci. 2017; 14(3): 191–200. PubMed Abstract | Publisher Full Text\n\nBrito-Zerón P, Baldini C, Bootsma H, et al.: Sjögren syndrome. Nat. Rev. Dis. Primers. 2016; 2(16047). Publisher Full Text\n\nBrito-Zerón P, Soria N, Muñoz S, et al.: Prevalence and clinical relevance of autoimmune neutropenia in patients with primary Sjögren's syndrome. Semin. Arthritis Rheum. 2009; 38(5): 389–395. PubMed Abstract | Publisher Full Text\n\nCarsons SE, Vivino FB, Parke A, et al.: Treatment Guidelines for Rheumatologic Manifestations of Sjögren's Syndrome: Use of Biologic Agents, Management of Fatigue, and Inflammatory Musculoskeletal Pain. Arthritis Care Res. (Hoboken). 2017; 69(4): 517–527. PubMed Abstract | Publisher Full Text\n\nCharoensin S: Antioxidant and anticancer activities of Moringa oleifera leaves. J. Med. Plant Res. 2014; 8(7): 318–325.\n\nChauhan SK, El Annan J, Ecoiffier T, et al.: Autoimmunity in dry eye is due to resistance of Th17 to Treg suppression. J. Immunol. 2009; 182(3): 1247–1252. PubMed Abstract | Publisher Full Text\n\nDe Paiva CS, Chotikavanich S, Pangelinan SB, et al.: IL-17 disrupts corneal barrier following desiccating stress. Mucosal Immunol. 2009; 2(3): 243–253. PubMed Abstract | Publisher Full Text\n\nEl Shanawany EE, Fouad EA, Keshta HG, et al.: Immunomodulatory effects of Moringa oleifera leaves aqueous extract in sheep naturally co-infected with Fasciola gigantica and Clostridium novyi. J. Parasit. Dis. 2019; 43(4): 583–591. PubMed Abstract | Publisher Full Text\n\nEngsuwan J, Waranuch N, Limpeanchob N, et al.: Anti-inflammatory effect of Moringa oleifera Lam. leaf extract on UVB-irradiated human keratinocytes. Songklanakarin. J. Sci. Technol. 2021; 43(3): 774–780.\n\nFarooq F, Rai M, Tiwari A, et al.: Medicinal properties of Moringa oleifera: An overview of promising healer. J. Med. Plant Res. 2012; 6(27): 4368–4374.\n\nFatmawati A, Bachri MS, Nurani LH: Combination Effects of Moringa oleifera Leaf Ethanol Extractand Andrographis paniculata Herb on Blood Glucose Levels and Pancreas Histopathology of Diabetic Rats Induced by Streptozotocin. Trad. Med. 2019; 24(2): 85–90. Publisher Full Text\n\nHaugen AJ, Peen E, Hultén B, et al.: Estimation of the prevalence of primary Sjögren's syndrome in two age-different community-based populations using two sets of classification criteria: the Hordaland Health Study. Scand. J. Rheumatol. 2008; 37(1): 30–34. PubMed Abstract | Publisher Full Text\n\nHulkkonen J, Pertovaara M, Antonen J, et al.: Matrix metalloproteinase 9 (MMP-9) gene polymorphism and MMP-9 plasma levels in primary Sjogren’s syndrome. Rheumatology. 2004; 43(12): 1476–1479. PubMed Abstract | Publisher Full Text\n\nIgoe A, Scofield RH: Autoimmunity and infection in Sjögren's syndrome. Curr. Opin. Rheumatol. 2013; 25(4): 480–487. PubMed Abstract | Publisher Full Text\n\nIjioma SN, Nwaogazi EN, Nwankwo AA, et al.: Histological exhibition of the gastroprotective effect of Moringa oleifera leaf extract. Comp. Clin. Pathol. 2018; 27(2): 327–332. PubMed Abstract | Publisher Full Text\n\nKamaliani BR, Setiasih NLE, Winaya IBO: Gambaran Histopatologi Ginjal Tikus Wistar Diabetes Melitus Eksperimental yang Diberikan Ekstrak Etanol Daun Kelor. Buletin Veteriner Udayana. 2018; 11(1): 71–77.\n\nKarthivashan G, Kura AU, Arulselvan P, et al.: The modulatory effect of Moringa oleifera leaf extract on endogenous antioxidant systems and inflammatory markers in an acetaminophen-induced nephrotoxic mice model. PeerJ. 2016; 4: e2127–e2118. Publisher Full Text\n\nKim SK, Choe JY, Lee GH: Enhanced expression of NLRP3 inflammasome-related inflammation in peripheral blood mononuclear cells in Sjögren's syndrome. Clin. Chim. Acta. 2017; 474: 147–154. PubMed Abstract | Publisher Full Text\n\nKooltheat N, Sranujit RP, Chumark P, et al.: An ethyl acetate fraction of Moringa oleifera Lam. Inhibits human macrophage cytokine production induced by cigarette smoke. Nutrients 2014. 2014; 6(2): 697–710. Publisher Full Text\n\nMahmood KT, Mugal T, Haq IU: Moringa oleifera: a natural gift-A review. Int. J. Pharm. Sci. Res. 2010; 2(11): 775–781.\n\nMisrawati, Marliah: Pengaruh Pemberian Tepung Daun Kelor Pada Ibu Hamil Terhadap Kadar Malondialdehid (MDA). Jurnal Ilmiah Kesehatan Sandi Husada. 2018; 10(1): 48–54. Publisher Full Text\n\nMousa AA, El-Gansh H, Eldaim M, et al.: Protective effect of Moringa oleifera leaves ethanolic extract against thioacetamide-induced hepatotoxicity in rats via modulation of cellular antioxidant, apoptotic and inflammatory markers. Environ. Sci. Pollut. Res. Int. 2019; 26(31): 32488–32504. Publisher Full Text\n\nNadimin: The Influence Provision of Moringa Leaf Exctracy (Moringa Oliefera) against the Level of Mda (Malondialdehyde) in Pregnant Women. IJSBAR. 2016; 27(3): 48–56.\n\nNakamura H, Horai Y, Shimizu T, et al.: Modulation of Apoptosis by Cytotoxic Mediators and Cell-Survival Molecules in Sjögren's Syndrome. Int. J. Mol. Sci. 2018; 19(8): 1–19.\n\nNocturne G, Mariette X: B cells in the pathogenesis of primary Sjögren syndrome. Nat. Rev. Rheumatol. 2018; 14(3): 133–145. Publisher Full Text\n\nPflugfelder SC: What causes dryness in Sjögren's syndrome patients and how can it be targeted?. Expert. Rev. Clin. Immunol. 2014; 10(4): 425–427. PubMed Abstract | Publisher Full Text\n\nRomão VC, Talarico R, Scirè CA, et al.: Sjögren's syndrome: state of the art on clinical practice guidelines. RMD Open. 2018; 4: 1–8. Publisher Full Text\n\nSambataro D, Sambataro G, Dal Bosco Y, et al.: Present and future of biologic drugs in primary Sjögren's syndrome. Expert. Opin. Biol. Ther. 2017; 17(1): 63–75. PubMed Abstract | Publisher Full Text\n\nScofield RH, Fayyaz A, Kurien BT, et al.: Prognostic value of Sjögren's syndrome autoantibodies. J Lab Precis Med. 2018; 3: 1–11. Publisher Full Text\n\nSellers RS: Translating Mouse Models. Toxicol. Pathol. 2017; 45(1): 134–145. Publisher Full Text\n\nShen L, He J, Kramer JM, et al.: Sjögren's Syndrome: Animal Models, Etiology, Pathogenesis, Clinical Subtypes, and Diagnosis. J. Immunol. Res. 2019; 2019: 1–3. Publisher Full Text\n\nShiboski CH, Shiboski SC, Seror R, et al.: International Sjögren's Syndrome Criteria Working Group. 2016 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Primary Sjögren's Syndrome: A Consensus and Data-Driven Methodology Involving Three International Patient Cohorts. Arthritis Rheumatol. 2017; 69(1): 35–45. Publisher Full Text\n\nShih KC, Lun CN, Jhanji V, et al.: Systematic review of randomized controlled trials in the treatment of dry eye disease in Sjogren syndrome. J. Inflamm. (Lond). 2017; 14(26): 1–11. Publisher Full Text\n\nSmallwood MJ, Nissim A, Knight AR, et al.: Oxidative stress in autoimmune rheumatic diseases. Free Radic. Biol. Med. 2018; 125: 3–14. Publisher Full Text\n\nSreelatha S, Padma PR: Antioxidant activity and total phenolic content of Moringa oleifera leaves in two stages of maturity. Plant Foods Hum. Nutr. 2009; 64(4): 303–311. PubMed Abstract | Publisher Full Text\n\nStefanski AL, Tomiak C, Pleyer U, et al.: The Diagnosis and Treatment of Sjögren's Syndrome. Dtsch. Arztebl. Int. 2017; 114(20): 354–361. PubMed Abstract | Publisher Full Text\n\nStohs SJ, Hartman MJ: Review of the Safety and Efficacy of Moringa oleifera. Phytother. Res. 2015; 29(6): 796–804. PubMed Abstract | Publisher Full Text\n\nVerma AR, Vijayakumar M, Mathela CS, et al.: In vitro and in vivo antioxidant properties of different fractions of Moringa oleifera leaves. Food Chem. Toxicol. 2009; 47(9): 2196–2201. PubMed Abstract | Publisher Full Text\n\nVerstappen GM, Corneth O, Bootsma H, et al.: Th17 cells in primary Sjögren's syndrome: Pathogenicity and plasticity. J. Autoimmun. 2018; 87: 16–25. PubMed Abstract | Publisher Full Text\n\nVivino FB, Bunya VY, Massaro-Giordano G, et al.: Sjogren's syndrome: An update on disease pathogenesis, clinical manifestations and treatment. Clin. Immunol. 2019; 203: 81–121. PubMed Abstract | Publisher Full Text\n\nWardhani TM: Pemanfaatan Tanaman Kelor (Moringa oleifera, Lam.) sebagai Sumber Terapi Preventif dan Kuratif pada Pasien Perlemakan Hati dengan Sindrom Metabolik. SCRIPTA SCORE Scientific Medical Journal. 2020; 1(2): 1–11.\n\nWenzel J, Gerdsen R, Uerlich M, et al.: Antibodies targeting extractable nuclear antigens: historical development and current knowledge. Br. J. Dermatol. 2001; 145(6): 859–867. PubMed Abstract | Publisher Full Text\n\nWulandari LP, Santoso B, Purwanto B: Kadar Malondialdehid tikus model Sindroma Ovarium Polikistik dengan daun kelor (Moringa oleifera). Jurnal Biosains Pascasarjana. 2017; 19: 224–236. Publisher Full Text\n\nWulandari LR, Umiati S, Sujuti H: Protective effect of methanol extract of Kelor (Moringa oleifera) leaves on Glutathione Peroxidase (GPx) levels in trabecular meshwork cell culture of primary congenital glaucoma patients. Eurasia J. Biosci. 2019; 13: 839–844.\n\nXiao X, Wang J, Meng C, et al.: Moringa oleifera Lam and its Therapeutic Effects in Immune Disorders. Front. Pharmacol. 2020; 11: 1–9. Publisher Full Text\n\nXie J, Luo F, Shi CY, et al.: Moringa oleifera Alkaloids Inhibited PC3 Cells Growth and Migration Through the COX-2 Mediated Wnt/β-Catenin Signaling Pathway. Front. Pharmacol. 2020; 11: 1–12. Publisher Full Text\n\nXie J, Peng L, Yang M, et al.: Alkaloid Extract of Moringa oleifera Lam. Exerts Antitumor Activity in Human Non-Small-Cell Lung Cancer via Modulation of the JAK2/STAT3 Signaling Pathway. Evid. Based Complement. Alternat. Med. 2021; 2021: 1–12."
}
|
[
{
"id": "312785",
"date": "19 Aug 2024",
"name": "Yogendra Nayak",
"expertise": [
"Reviewer Expertise Pharmacology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript can be accepted, but before indexing, some points need to be addressed.\n1. Under the extraction and standardization process, temperature is kept very low. In such a condition, it is necessary to have a Rorary Evaporator with a Vacuum.\n2. The instruments used sources can be added, for Rotary evaporator, Freez dryer etc\n3. Methods require references cited, especially for Federer's formula, Scorings etc.\n4. Why Harris Hematoxylin is used? generally, people go for Periodic Acid-Schiff (PAS) Stains or Immunohistochemical Stains, such as anti-CD3, anti-CD20, and anti-IgG.\n5. In clinical/human conditions, focal lymphocytic sialadenitis, Acinar atrophy or Ductal dilations are seen; these observations in preclinical models can do this research into a translational potential for screening in human trials.\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": []
}
] | 1
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https://f1000research.com/articles/11-1263
|
https://f1000research.com/articles/11-654/v1
|
14 Jun 22
|
{
"type": "Case Report",
"title": "Case Report: Severe gastrointestinal bleeding revealing metastatic multifocal gastrointestinal angiosarcoma",
"authors": [
"Khaoula Chabbouh",
"Radhouane Zarg El Ayoun",
"Amel Khsiba",
"Cyrine Makni",
"Slim Zribi",
"Salwa Nechi",
"Emna Chelby",
"Lamine Hamzaoui",
"Radhouane Zarg El Ayoun",
"Amel Khsiba",
"Cyrine Makni",
"Slim Zribi",
"Salwa Nechi",
"Emna Chelby",
"Lamine Hamzaoui"
],
"abstract": "Background: Angiosarcoma is a rare soft-tissue sarcoma that can arise in any soft-tissue structure or viscera. Only individual case reports and small series of gastrointestinal angiosarcoma have been reported in the literature. In this paper, we report the first African case of small intestine epithelioid angiosarcoma. Case report: Here, we present the case of a 66-year-old man who presented with melena and anemia. Physical examination showed the presence of two subcutaneous masses on the right and left flanks. Esophagogastroduodenoscopy, duodenoscopy and jejunoscopy revealed multiple purpuric and hemorrhagic nodules and masses, some of which were bleeding. Pathological study of the ampullary formation and of a subcutaneous nodule concluded to the diagnosis of epithelioid angiosarcoma. Blood transfusions and interventional endoscopy by argan plasma coagulation were required due to a continued drop in hemoglobin. A drop in hemoglobin persisted and the patient died within 10 days. Conclusions: Angiosarcoma has a very poor prognosis due to delayed prognosis and insufficient therapeutic management. Interventional endoscopy to control bleeding can be considered in localized forms. Chemotherapy may help to prolong survival in metastatic and disseminated angiosarcoma. Further studies should be conducted to improve the prognosis.",
"keywords": [
"Angiosarcoma",
"gastrointestinal tract",
"gastrointestinal bleeding",
"cutaneous metastasis",
"case report"
],
"content": "Introduction\n\nAngiosarcoma is a malignant tumor that has morphological and immunohistochemical characteristics that resemble those of endothelial cells. It is a rare soft tissue sarcoma. It mainly occurs in the skin, breast, heart and liver but it can also be found in any soft tissue structure or viscus.1 It rarely involves the gastrointestinal (GI)2 tract and only individual case reports and small series have been reported in the literature.2 It can be both primary, seated in the GI tract, or secondary to the direct extension of a retroperitoneal tumor. A metastatic origin is just as possible.3 There are few cases where synchronous intestinal and subcutaneous angiosarcoma have been reported.4,5 The diagnosis of GI angiosarcoma is often delayed as it usually presents with non-specific signs such as GI bleeding and anemia. The diagnosis is based on pathological study and immunohistochemistry. The prognosis of angiosarcoma is generally poor due to delayed diagnosis and insufficient therapeutic management.1\n\nIn this paper, we report the first African case of small intestine epithelioid angiosarcoma revealed by melena and low hemoglobin level, which also presented with a similar neoplasm arising from multifocal subcutaneous tissues.\n\n\nCase report\n\nA 66-year-old Tunisian man, a retired taxi driver, with a medical history of hypertension and who stopped treatment two weeks before, presented in February 2020 with a one-month history of chest pain, dyspnea, melena and fatigue.\n\nHe was first admitted in the visceral and digestive surgery department of Mohamed Taher Maamouri Hospital.\n\nOn admission, physical examination of the patient showed pale skin. His blood pressure was 130/90 mmHg and his pulse 88 bpm. We also noted the presence of two subcutaneous masses on the right and left flanks measuring 3 cm in diameter. Hemoglobin level was 5.7 g/dL. Mean corpuscular volume level was 88 fL. The white blood cells count was 8,100 per μL and platelet count was 229,000 platelets per μL of blood. Plasma creatinine level was 213 μmol/L (Normal value <90 μmol/L).\n\nEsophagogastroduodenoscopy and duodenoscopy revealed multiple purpuric and hemorrhagic nodules of the ampullary region, the duodenal bulb and the duodenum, with a size ranging from 5 mm to 10 mm in diameter (Figure 1). A subsequent jejunoscopy showed multiple other erythematous and purpuric nodules and masses, some of which were bleeding. A colonoscopy was performed with no exceptional features noted.\n\nPathological study of the biopsies of the ampullary formation concluded in the presence of a mixed tumor with solid and vascular architecture in the form of anastomosed slits infiltrating the chorion and sparing the submucosa. The cells bordering the vascular slits had an abundance of eosinophilic cytoplasm, vesicular nuclei, and prominent nucleoli. Immunohistochemical analysis revealed a tumor positivity for vimentin and erythroblast transformation specific related gene (ERG) (Figure 2). The tumor was negative to other markers both vascular (CD31 and CD34) and non-vascular (AE1AE3, CD45, MelanA, HMB45, Dog-1, CD138, PS100, actin, desmin and HHV8). TFE3 was not expressed. Therefore, the pathological study concluded to the diagnosis of epithelioid angiosarcoma.\n\n(A) Vascular slits. (B) Epithelioid cells. (C) Nuclear expression of erythroblast transformation specific related gene. (D) Negative for epithelial marker (AE1AE3).\n\nBiopsy of a subcutaneous nodule and pathological study confirmed a cutaneous and muscular tumoral lesion characteristic for epithelioid angiosarcoma (Figure 2).\n\nA computed tomography (CT) scan, performed as part of the extension assessment, showed the presence of a left apical sub-pleural nodule of 3 mm diameter, subcutaneous nodules on the right and left flanks and on the right posterior chest wall measuring 28 * 22 mm, 36 * 18 mm and 18 * 9 mm, respectively. They were associated to masses with heterogeneous contrast enhancement of the right gluteus maximus and left gluteus medius muscles (Figure 3).\n\nThe patient was transfused with a unit of red blood cells daily during a week due to a continued drop in hemoglobin. One week after his hospitalization, he underwent interventional endoscopy to control active bleeding by argan plasma coagulation. A drop in hemoglobin persisted and the patient died within 10 days.\n\n\nDiscussion\n\nAngiosarcomas are a subtype of soft-tissue sarcoma with vascular or lymphatic differentiation. They are rare, representing 1–2% of soft tissue sarcomas.1 Angiosarcomas can develop at any age but are more common in patients during their sixth decade.1,6 Although they are usually found in skin and subcutaneous tissues, they can arise in any soft-tissue structure or viscera due the ubiquity of blood vessels and lymphatics.1 Thus, internal organs may be affected such as the liver, spleen, heart and uncommonly the GI tract.7 Within the GI tract, the small intestine is the most frequent location.2 Still, it is hard to distinguish between primary and metastatic angiosarcoma.4 A retrospective study of 66 cases of angiosarcoma of the small intestine showed that angiosarcoma of cutaneous or aortic origin often metastasized to the small intestine.8 In our case, it was difficult to ascertain whether small intestinal angiosarcoma was primary or metastatic spread from cutaneous and muscular masses as angiosarcoma was multifocal at outset.\n\nThe predisposing factors of small intestine angiosarcoma are still unclear. Studies have shown that a history of exposure to radiation, environmental toxins or foreign bodies as well as certain familial syndromes such as neurofibromatosis may be predisposing factors.1 Our patient did not have any of these predisposing factors.\n\nClinical presentation of small intestine angiosarcoma consists of non-specific symptoms. It includes mainly abdominal pain, anemia, GI bleeding, fatigue, weight loss and occasionally abdominal obstruction and perforation. Therefore, delayed diagnosis often occurs after substantial searches for a source of bleeding using endoscopy, enteroscopy or capsule endoscopy. On endoscopy, GI lesions may appear as a nodule, hemorrhagic mass, purpuric nodules, or submucosal mass.9 The extent of angiosarcoma can be assessed by CT, magnetic resonance imaging, or positron emission tomography scans.9 The definitive diagnosis is confirmed by pathological and immunohistochemical examinations.\n\nAngiosarcoma is histologically classified into three subtypes: a) spindle-shaped endothelial cells; b) epithelioid with large, round or polygonal cells; c) pleomorphic cells.10 It is difficult to distinguish such tumors from poorly differentiated carcinoma, lymphoma or malignant melanoma. Hence, immunohistochemical study is essential to establish a definitive diagnosis of angiosarcoma, by showing the expression of vascular markers such as CD31, CD34, factor VIII, vimentin, endothelin-1, vascular endothelial growth factor receptor, ERG and ulex europaeus agglutinin-1.1 In our case, the tumor was only positive for vimentin and ERG. ERG appears as an important marker to consider in the diagnosis of undifferentiated tumors of the digestive tract.\n\nThe prognosis of angiosarcoma is very poor with a survival ranging from 10 days11 to 33 months.3 Our patient died 10 days after diagnosis despite interventional endoscopy by argan plasma coagulation to control active bleeding. Surgical resection is considered the treatment of choice for small intestine angiosarcoma.12 However, microscopically margin-negative resection is almost impossible in disseminated angiosarcomas. Adjuvant treatment with chemotherapy could prolong survival in metastatic angiosarcoma.13 In our case, the patient died before any chemotherapy could be considered.\n\n\nConclusions\n\nThis is the first African case of small intestine associated with synchronous subcutaneous angiosarcoma. Its non-specific clinical signs can lead to delayed diagnosis and worsen the prognosis. In such poorly differentiated and confusing tumor, ERG appears as an important marker to consider in the antibody panel of pathological diagnosis. Interventional endoscopy to control bleeding can be considered in localized forms, but no evidence has been reported in the literature discussed. In our case, it was of little help. The prognosis remains poor due to delayed diagnosis and insufficient therapeutic management although chemotherapy may help to prolong survival in metastatic and disseminated angiosarcoma. Further studies should be conducted to improve the prognosis.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from a relative of the patient.",
"appendix": "References\n\nYoung RJ, Brown NJ, Reed MW, et al.: Angiosarcoma. Lancet Oncol. 2010; 11(10): 983–991. Publisher Full Text\n\nSchizas D, Mastoraki A, Giannakodimos I, et al.: Primary Angiosarcoma of the Gastrointestinal Tract: A Systematic Review of the Literature. J. Investig. Surg. 2020; 35: 400–408. Publisher Full Text\n\nAllison KH, Yoder BJ, Bronner MP, et al.: Angiosarcoma involving the gastrointestinal tract: a series of primary and metastatic cases. Am. J. Surg. Pathol. 2004; 28(3): 298–307. PubMed Abstract | Publisher Full Text\n\nSadhu S, Pattari S, Shaikh F, et al.: Colonic metastasis from subcutaneous angiosarcoma: A diagnostic dilemma. Indian J. Surg. 2010; 72(Suppl 1): 328–330. PubMed Abstract | Publisher Full Text\n\nFujii Y, Koibuchi-Yamaoka H, Taniguchi N, et al.: Metastasis from a primary angiosarcoma of the scalp to the colon: sonographic and CT findings. J. Clin. Ultrasound 2008; 36(2): 110–112. PubMed Abstract | Publisher Full Text\n\nWatanabe K, Hoshi N, Suzuki T, et al.: Epithelioid angiosarcoma of the intestinal tract with endothelin-1-like immunoreactivity. Virchows Arch. A Pathol. Anat. Histopathol. 1993; 423(4): 309–314. PubMed Abstract | Publisher Full Text\n\nChami TN, Ratner LE, Henneberry J, et al.: Angiosarcoma of the small intestine: a case report and literature review. Am. J. Gastroenterol. 1994; 89(5): 797–800. PubMed Abstract\n\nLi R, Ouyang ZY, Xiao JB, et al.: Clinical Characteristics and Prognostic Factors of Small Intestine Angiosarcoma: a Retrospective Clinical Analysis of 66 Cases. Cell. Physiol. Biochem. 2017; 44(2): 817–827. PubMed Abstract | Publisher Full Text\n\nSaad A, Cappell MS, Amin M: Endoscopic findings with GI angiosarcoma correspond with the propensity of these vascular tumors to cause GI bleeding: two case reports and review of the literature. Dig. Dis. Sci. 2013; 58(6): 1797–1801. PubMed Abstract | Publisher Full Text\n\nHuntington JT, Jones C, Liebner DA, et al.: Angiosarcoma: A rare malignancy with protean clinical presentations. J. Surg. Oncol. 2015; 111(8): 941–950. PubMed Abstract | Publisher Full Text\n\nChen JL, Mok KT, Tseng HH, et al.: Duodenal angiosarcoma: an unusual cause of severe gastrointestinal bleeding. J. Chin. Med. Assoc. 2007; 70(8): 352–355. Publisher Full Text\n\nNi Q, Shang D, Peng H, et al.: Primary angiosarcoma of the small intestine with metastasis to the liver: a case report and review of the literature. World J. Surg. Oncol. 2013; 11: 242. PubMed Abstract | Publisher Full Text\n\nKrikelis D, Judson I: Role of chemotherapy in the management of soft tissue sarcomas. Expert. Rev. Anticancer. Ther. 2010; 10(2): 249–260. Publisher Full Text"
}
|
[
{
"id": "140873",
"date": "02 Aug 2022",
"name": "Meriam Sabbah",
"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\nThis is an interesting rare case of gastrointestinal angiosarcoma revealed by bleeding. The report is well written and complete with the clinical, endoscopic, histologic, morphological findings and evolution of the patient. However, to improve the quality of the article, I think authors should remove some figures (especially endoscopic and CT scan figures); some grammatical errors should be corrected (esp. argon instead of argan) and the evolution of the patient should also be detailed (How did the patient die? Was surgical treatment performed?).\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": [
{
"c_id": "8870",
"date": "07 Nov 2022",
"name": "Khaoula Chabbouh",
"role": "Author Response",
"response": "The new version is not very different from the first one. I just corrected some spelling mistakes and removed the CT-scan figure as it was not of very good quality. For the endoscopy figure, I think it is good to keep it to know the endoscopic aspect of this rare pathology."
}
]
}
] | 1
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https://f1000research.com/articles/11-654
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https://f1000research.com/articles/11-1262/v1
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07 Nov 22
|
{
"type": "Policy Brief",
"title": "Military health and performance optimization: a circadian strategy in response to governmental policies",
"authors": [
"Allison Brager",
"Ashlee McKeon",
"Dale W. Russell",
"Rachel R. Markwald",
"Ashlee McKeon",
"Dale W. Russell",
"Rachel R. Markwald"
],
"abstract": "In 2017, USS Fitzgerald and USS John S. McCain, both guided-missile destroyers, experienced underway collisions that resulted in the deaths of 17 Sailors and degradation of national defense as two warships were removed from the frontline. This incident garnered Congress’ attention leading to numerous fatigue management policies and working groups instituted at various levels across the Department of Defense. One policy of the Department of the Navy (3120.2A; Dec 11, 2020) specifically addressed risk mitigation factors for maritime operations occurring in the overnight and early morning hours around the circadian nadir or trough in alertness and vigilance. Despite these circadian challenges that come with mission demands of military service, there are many opportunities as outlined in the Department of Navy policy to reduce and/or eliminate the performance-related risks associated with circadian misalignment. In regard to actionable systems and processes aligned with these policies, the first step is to perform a risk assessment to identify circadian-related problems that could arise in response to conducting the military training exercise or operation. The second step is to integrate a means to monitor 24-hour physiology, mitigate performance risk through fatigue countermeasures, and/or re-align the circadian timing system of military personnel to enhance sleep, manage fatigue, and optimize performance. Most importantly, the approach is not a one size fits all. Each military operation will require unique adaption (re-alignment) to the environment and each military operation may require a unique countermeasure(s).",
"keywords": [
"caffeine",
"light",
"national security",
"sleep",
"sleep deprivation",
"shift work"
],
"content": "Disclaimer\n\nI (AB, AM, DR) am a military service member or employee of the U.S. Government. This work was prepared as part of my official duties. Title 17, U.S.C. §105 provides that copyright protection under this title is not available for any work of the U.S. Government. Title 17, U.S.C. §101 defines a U.S. Government work as work prepared by a military service member or employee of the U.S. Government as part of that person’s official duties. The opinions or assertions contained herein are the private views of the author, and are not to be construed as official, or as reflecting true views of the Department of the Army, the Department of the Navy, or the Department of Defense.\n\nIn the US, the Department of Defense (DoD) employees millions of personnel to support national security efforts, which often entail physically and cognitively demanding works that leads to acute and chronic physiological strain and emotional distress. Throughout the War on Terrorism (2005–2019), the incidence rates of obstructive sleep apnea (OSA) and insomnia increased from 11 to 333 and 6 to 272 (per 10,000) in active-duty service members (ADSM), respectively (Moore et al., 2021). This increased incidence rate has led to the development of a military-specific sleep questionnaire aimed to assess factors precipitating sleep disturbances in military personnel for use in medical treatment facilities (Mysliwiec et al., 2021). Ultimately, increased incidence rates of sleep disturbances and sleep disorders threaten our national security interests and mission accomplishment. Insufficient and non-restorative sleep directly compromise military performance, impacting most if not all aspects of physical training, cognitive performance (including decision-making and risk assessment), and interpersonal communication (reviewed in Good et al., 2020).\n\nIn addition to the inability to achieve sufficient and restorative sleep, fatigue-related mishaps/near misses are also common. Although the majority receive little public attention, two major mishaps garnered both Congress’ and the public’s attention. In 2017, USS Fitzgerald and USS John S. McCain, both guided-missile destroyers, experienced underway collisions that resulted in the deaths of seventeen Sailors and degradation of national defense as two warships were removed from the frontline. These collisions occurred in the overnight and early morning hours around the circadian nadir or trough in alertness and vigilance. Subsequent separate investigations by the National Transportation Safety Board and the Government Accountability Office (GAO, 2021) found that Surface Force (SURFOR) Sailors are not obtaining adequate sleep and that fatigue played a role in these incidents. Indeed, a large follow-up study found that SURFOR Sailors were only obtaining an average of ~5.5 hours of sleep per day (Russell et al., 2021). The GAO’s investigation recommended that SURFOR take action to identify, monitor, and address the factors contributing to sleep loss and fatigue (GAO, 2021). As a result, the SURFOR has embarked on research efforts to better monitor and manage fatigue to include understanding the extent to which operational factors impact sleep quantity and quality across the 24-hour day.\n\nAs a result of these safety-related incidents, numerous fatigue management policies and working groups have been instituted at various levels throughout the Department of Defense has developed to include the recent CNSF policy (Department of the Navy, 2020) which the authors of this paper have supported. U.S. Congressionally appropriated research and development initiatives now center on fatigue management and target military operations occurring during the circadian nadir (Mantua et al., 2020; Brown et al., 2020; Hernández et al., 2018; Harrison et al., 2022; Chabal et al., 2022). In some cases, commanders of military units have implemented circadian-centered fatigue management policies. For example, the U.S. Army’s fleet of commercial truck drivers have restricted “twilight” driving (between sunset and sunrise) after the National Highway Traffic Safety Administration determined that accidents involving commercial trucks are highest around the circadian nadir (Brager, 2022).\n\nThe common U.S. military modus operandi is winning our nation’s wars at night, which means that high-risk night operations against enemy forces are a priority over daytime operations; for instance, the capture of Osama bin Laden by Navy SEALS in Abbottabad, Pakistan in 2011 during the circadian nadir highlights the value of this modus operandi from the vantage point of senior military leaders. Elite, special operations units such as the U.S. Army Rangers are assessed, selected, and trained to fight at night. As a result, Army Rangers are a target population for circadian studies focused on military operations (Mantua et al., 2020; Ritland et al., 2021). As part of winning our nation’s wars through night operations, readiness continues to be the “#1 priority” endorsed by the Joint Chiefs of Staff. What this means for the military components is that a soldier, sailor, marine, airman, and guardian (Space Force) must be able to switch from daytime to nighttime operations performed at an extremely high operational tempo regarding physical and cognitive load at a moment’s notice. A secondary feature of readiness is that there is limited time allotted for sufficient recovery from military operations. Thus, how do military personnel perform and recover optimally given operational constraints?\n\nMilitary operations to include night operations (2200 – 0800) and continuous/sustained operations (> 24 h to weeks/months) present unique cases of acute and chronic circadian misalignment and/or disruption. For example, the U.S. Navy maintains a forward deployed global presence that requires staffing of round the clock operations for months at a time. Sailors operate on shift work schedules that require sleeping and working at all times of the day and night in order to maintain the ship as combat ready. This chronic circadian disruption that results from nightwork and shift rotations likely contributes to the sleep deficiency widely reported by Sailors (Russell et al., 2021). While a US Navy ship or submarine is an example of an austere environment, there are many additional examples of austere environments across the US military where personnel must endure sudden changes in altitude, time zones, and climate that as a result, have multitudinous impacts on sleep quantity and quality (Mantua et al., 2019). In some studies such as at the Belgrano II Argentine Antarctic station, longitudinal assessments of circadian biomarkers of core body temperature, sleep architecture, and neurocognitive performance have been assessed (Folgueira et al., 2019). These ecological studies are important for our field because the Antarctic station revealed that the human circadian timing system can in fact adapt to extreme changes in latitude (constant darkness/constant light) and climate largely by adopting multi-phasic sleep schedules that do not impact measures of cognition. As such, there are three major themes of circadian disruption in military personnel:\n\ni. Night operations\n\nii. Continuous/sustained operations\n\niii. Extreme environments (constant darkness/constant light)\n\nThe U.S. defense strategy is broadly defined by “ends, ways, and means” (Miller et al., 2017). Ends are objectives (goals), ways are tactics for accomplishing ends, and means are resources provided for the ways. From the perspective of monitoring and mitigating circadian misalignment and/or fatigue experienced while operating near or at the circadian nadir, a circadian-centered military strategy can be defined as:\n\ni. Ends (Objective) - Adjust and recover quickly from circadian challenges.\n\nii. Ways (Tactic) – Identify a tactic that meets all or most of the following parameters for monitoring and/or mitigating circadian disruption:\n\na. The tactic has primary application for mass (unit-level) with secondary potential for inter-individual optimization.\n\nb. The tactic is robust and has shown proof of concept in controlled laboratory and field-based studies.\n\nc. The tactic can be seamlessly and effortlessly measured using emerging sensor technologies or single time point collections (e.g., blood, saliva, and sweat).\n\nd. The tactic has a known impact on end-point military performance in that the mission can continue with appropriate application of a countermeasure such as blue-enriched light pulsing, tactical napping, sleep banking, or psychostimulant administration.\n\niii. Means (Resources) – An evidence-based resource that is holistic/non-pharmacological (napping), technological (blue-enriched light protocol), and pharmacologic (caffeine/hypnotic) in nature.\n\nTable 1 outlines examples of ends, ways, and means with examples (below) based on supporting studies. First, recent advancements in wearable technologies provide cardiorespiratory biomarkers of circadian phase. These biomarkers include temporal distributions in heart rate, respiratory rate, and skin temperature. In fact, biometrics from one commercial off-the-shelf (COTS) wearable (Oura Ring) was interfaced with dim-light melatonin onset (DLMO) data in in Navy personnel to determine overall impact of transitioning from daytime to nighttime aviation operations on circadian phase (McDonough, 2022). Second, recent evidence shows that inter-individual variability in circadian phase is predictive of PVT (psychomotor vigilance test) performance in response to sleep deprivation (Sletten et al., 2015; Bermudez et al., 2016). The PVT is the most ecological valid measure of neurocognition and has successfully been used to measure longitudinal changes in circadian phase in one of the most austere places in the world: Belgrano II Argentine research station (Folgueira et al., 2019). Third, recent technological development of non-invasive sensors to measure small metabolites predictive of circadian phase are emerging (Bhide et al., 2021). Although several small metabolites have been screened and identified to be predictive of circadian phase and metabolic status (reviewed in Chen et al., 2014), the highest yield candidates for military use and application include cortisol and lactate as both are strongly predictive of anabolic versus catabolic processes (Cadegiani et al., 2019) and are circadian-driven (Guan and Lazar, 2021).\n\nThe type of measure and subsequent countermeasure adopted will vary with type of military operation.\n\n\n\n• Dim-Light Melatonin Onset (DLMO)\n\n• Cardiorespiratory Output via Wearables\n\n\n\n• Use DLMO which is moderately feasible to collect during nighttime training operations, develop a photic phase-response curve via blue-enriched light exposure\n\n• Monitor 24 h peaks and troughs in heart rate, respiratory rate, and skin temperature prior to mission execution in order to best time time-point stimulant supplementation (i.e., caffeine dosing)\n\n\n\n• Attention/Vigilance via Psychomotor Vigilance Test\n\n• Cardiorespiratory Output via Wearables\n\n\n\n• Cardiorespiratory, activity and sleep output via Wearable devices\n\n• Small metabolites in sweat\n\n\n\n• Monitor 24 h peaks and troughs in physiological measures during sustained operations to develop photic (liand non-photic (via 5-HT supplementation) phase response curves aligned with “peak” performance zones.\n\n• Monitor and manage indicators of circadian disruption such as sleep patterns in order to develop mitigation strategies such as adjustments to the watchbill organization, and use of napping strategies.\n\nDespite an increasing understanding that circadian misalignment has acute and chronic negative consequences to health and performance, security and defense strategies will not likely change. The following assumptions must be considered when developing and deploying circadian-centered ends, ways, and means into real-time military operations:\n\na. We will fight at night.\n\nb. We will engage in continuous and sustained operations\n\nc. We will operate in austere and extreme environments\n\nd. We will continue to recruit for, assess for, select for, and train for these circadian challenges.\n\nThe bottom line is that fatigue is inevitable. It is a matter of balancing and calculating risks of operational performance/safety versus providing opportunities for rest/recovery outside circadian nadirs. The military routinely uses risk assessment matrices to inform decision-making. The matrices (adapted from ATP 5-19; Figure 1) measure risk through (i) frequency of occurrence; and (ii) consequences of failure. Circadian-centered strategies from Table 1 can be integrated along this matrix to mitigate risk. Ideally, the intent is to reduce risk to acceptable levels (green: performance optimization, control for performance compromises (amber) through countermeasures, and avoid catastrophe (red or blue) at all costs. Thus, it is through a circadian-centered strategy that the entire military system of health and performance can be optimized and enhanced.\n\nCircadian-centered strategies outlined in Table 1 can be integrated to reduce, control, and avoid severe and catastrophic risk in military health and performance. This figure has been adapted from Department of the Army ATP 5-19 with permission from the Department of the Army.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "References\n\nBermudez E, et al.: Prediction of Vigilant Attention and Cognitive Performance using Self-Reported Alertness, Circadian Phase, Hours Since Awakening, and Accumulated Sleep Loss. PLoS One. 2016; 11: e0151770. PubMed Abstract | Publisher Full Text\n\nBhide A, et al.: Next-Generation Continuous Metabolite Sensing toward Emerging Sensor Needs. ACS Omega. 2021; 6(9): 6031–6040. PubMed Abstract | Publisher Full Text\n\nBrager A: Commanding Fatigue Management in the United States Army's Fleet of Commercial Truck Drivers. Sleep Health. 2022; 8(7): 261–262. PubMed Abstract | Publisher Full Text\n\nBrown S, et al.: Blue Light Exposure Effects on Sleep Attributes in a 72-Hour Military Exercise. Proceedings of the Human Factors and Ergonomics Society Annual Meeting.2020; 64(1).\n\nCadegiani F, et al.: Inter-correlations among Clinical, Metabolic, and Biochemical Parameters and their Predictive Value in Healthy and Overtrained Male Athletes: the EROS-CORRELATIONS Study. Front Endocrinol. 2019; 10. PubMed Abstract | Publisher Full Text\n\nChabal S, et al.: Dissertation: Personal Light Treatment Devices as a Viable Countermeasure for Submariner Fatigue.NAVAL SUBMARINE MEDICAL RESEARCH LAB GROTON CTNAVAL HEALTH RESEARCH CENTER SAN DIEGO CALEIDOS HOLDINGS INC SAN DIEGO CA.2022.\n\nChen L, et al.: PPARs Integrate the Mammalian Clock and Energy Metabolism. PPAR Res. 2014; 2014: 1–6. PubMed Abstract | Publisher Full Text\n\nDepartment of the Army: Army Techniques Publication 5-19 Risk Management Headquarters.November 2021.\n\nDepartment of the Navy: COMNAVSURFPAC/COMNAVSURFLANT INSTRUCTION 3120.2A. COMPREHENSIVE CREW ENDURANCE MANAGEMENT POLICY.Dec 11 2020.\n\nFang B, et al.: Using GRO-Seq to Measure Circadian Transcription and Discover Circadian Enhancers. Circadian Clocks. 2021. PubMed Abstract | Publisher Full Text\n\nFolgueira A, et al.: Sleep, Napping and Alertness during an Overwintering Mission at Belgrano II Argentine Antarctic station. Sci Rep. 2019; 9(1): 10875. PubMed Abstract | Publisher Full Text\n\nGood C, et al.: Sleep in the United States Military. Neuropsychopharmacology. 2020; 45: 176–191. PubMed Abstract | Publisher Full Text\n\nGuan D, Lazar MA: Interconnections between circadian clocks and metabolism. J Clin Investig. 2021 Aug 2; 131(15): e148278. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarrison E, et al.: The Development, Implementation, and Feasibility of a Circadian, Light, and Sleep Skills Program for Shipboard Military Personnel (CLASS-SM). Int J Environ Res Public Health. 2022; 19(5). PubMed Abstract | Publisher Full Text\n\nHernández L, et al.: Morning Cortisol is Associated with Stress and Sleep in Elite Military Men: A Brief Report. Mil Med. 2018; 183(9): e255–e259. PubMed Abstract | Publisher Full Text\n\nMantua J, et al.: A Review of Environmental Barriers to Obtaining Adequate Sleep in the Military Operational Context. Mil Med. 2019; 184(7-8): e259–e266. PubMed Abstract | Publisher Full Text\n\nMantua J, et al.: Sleep Loss during Military Training Reduces Testosterone in U.S. Army Rangers: A Two-Study Series. Int J Sports Exerc Med. 2020; 6: 6. Publisher Full Text\n\nMcDonough M: Dissertation: Aviation Shiftwork: Safely Transitioning from Day to Night Flights. NAVAL POSTGRADUATE SCHOOL MONTERREY CA.2022.\n\nMiller G, et al.: On Strategy as Ends, Ways, and Means. The US Army War College Quarterly Parameters. 2017; 47. Publisher Full Text\n\nMoore B, et al.: Incidence of Insomnia and Obstructive Sleep Apnea in Active Duty United States Military Service Members. Sleep. 2021; 44(7). PubMed Abstract | Publisher Full Text\n\nMysliwiec V, et al.: The Military Service Sleep Assessment: an instrument to assess factors precipitating sleep disturbances in U.S. military personnel. J Clin Sleep Med. 2021; 17(7): 1401–1409. PubMed Abstract | Publisher Full Text\n\nRitland B, et al.: Association between Self-Reported Sleep Quality and Musculoskeletal Injury in Male Army Rangers. Mil Med. 2021. PubMed Abstract | Publisher Full Text\n\nRussell D, et al.: Self-reported Sleep and Sleep Deficiency: Results from a Large Initiative of Sailors Attached to US Navy Warships. J Sleep Res. 2021; 30(6): e13397. PubMed Abstract | Publisher Full Text\n\nSletten T, et al.: Inter-individual Differences in Neurobehavioural Impairment following Sleep Restriction are Associated with Circadian Rhythm Phase. PloS One. 2015; 10: e0128273. PubMed Abstract | Publisher Full Text\n\nUS Government Accountability Office: GAO-21-366 Highlights, NAVY READINESS: Additional Efforts Are Needed to Manage Fatigue, Reduce Crewing Shortfalls, and Implement Training.2021."
}
|
[
{
"id": "188038",
"date": "10 Aug 2023",
"name": "Wessel M.A. van Leeuwen",
"expertise": [
"Reviewer Expertise Sleep",
"sleepiness",
"fatigue",
"shift work",
"circadian rhythms",
"working hours",
"performance."
],
"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 strategy as to how to deal with reduced performance as a consequence of circadian misalignment. Examples of such misalignments are presented and respective countermeasures given.\nThe contextual overview is rather limited and slightly inadequate as well. Sustained wakefulness for more than 24 hours, for instance, is not just a circadian misalignment issue, but also a homeostatic sleep pressure problem. Moreover, these two interact in a rather devastating way, making performance possibilities during the circadian trough after sustained wakefulness almost zero. These factors, i.e. the homeostatic sleep pressure and its interaction with circadian homeostasis would need to be taken up and discussed in far greater detail.\nRegarding the countermeasures being discussed and proposed, a greater and more thorough discussion as to how effective they actually are would be needed. Especially, the focus on caffeine intake has strong disadvantages that need to be taken up (e.g. half life of caffeine, individual differences in caffeine sensitivity, etc.). Even blue (enriched) light exposure can have far going negative consequences when used excessively during the circadian nadir.\n\nA point pretty much ignored by the authors is that circadian rhythms differ between individuals, and that they may arguably differ that much that the need to perform during ones own circadian nadir could potentially be removed by using individual rhythm data as well as strategically placed sleep episodes.\nA famous quote by the Dutch cyclist Joop Zoetemelk is \"the Tour de France is won in bed\". The same lesson could be taken into account by the US military: wars are won in bed. This indicates the, not just anecdotal, evidence that sleep is of vital importance and in fact the only real countermeasure against reduced performance as a consequence of sustained or misaligned operations. The authors put too much focus on caffeine consumption without discussion the obvious disadvantages of this doubtful countermeasure.\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? Partly\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly",
"responses": []
},
{
"id": "188035",
"date": "14 Aug 2023",
"name": "Emily A Schmied",
"expertise": [
"Reviewer Expertise Military mental health",
"military sleep health promotion interventions",
"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\nThrough a combination of scientific research, historical examples, and military doctrine, the authors introduce the importance of circadian health to the success and safety of military operations. The paper presents strategies for monitoring and managing circadian misalignment and/or fatigue that may be implemented in a variety of operational settings and scenarios. Given that the purpose of the paper is to inform policy and procedure, the paper would be strengthened by expanded discussion of the feasibility of implementing the proposed tools and strategies in various settings, as well as a demonstration of the application of the risk assessment matrix in the context of policy making.\nIn terms of the writing quality, it is relatively easy to follow, though a few typos should be resolved (e.g., there is a typo in the sentence on page 3 starting with, “As a result”).\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? Partly\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly",
"responses": []
},
{
"id": "188044",
"date": "18 Aug 2023",
"name": "Anna Sjörs Dahlman",
"expertise": [
"Reviewer Expertise Sleep and fatigue issues in various occupational groups. Driver/operator impairments and performance. Occupational 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 policy brief presents a strategy for how to assess and mitigate circadian misalignment and fatigue in military operations. The strategy involves risk assessment to identify circadian-related problems, physiological monitoring, fatigue countermeasures, and circadian re-alignment techniques to enhance sleep, mitigate fatigue and optimize performance. Given the unique challenges faced in military operations, e.g., 24-h operation, night work, and austere environments, mitigating fatigue and sustaining readiness is important.\nThe message in the policy brief is relatively clear but some details regarding the implementation need clarification and the recommendation to perform 24h monitoring should be justified. The feasibility of implementing the countermeasures should also be discussed. The problem description could benefit from including information about inter-individual differences in the sensitivity to circadian misalignment and fatigue. A few sections should be clarified or further explained to make it more accessible to the target population.\nComments:\nThe aim of the policy brief itself could be described more in detail. The authors describe that there is work ongoing with fatigue management policies at various levels of the DoD. Why is this policy brief then needed? A clarification of what is currently not being implemented would strengthen the message.\n\nScope of the problem paragraph 3: The first part of the paragraph (first sentence) is hard to follow. Please re-phrase to clarify.\n\nScope of the problem paragraph 3: Circadian-centered fatigue management policies are mentioned. To make the text more accessible, please explain what this means or give an example.\n\nIt is somewhat unclear if the suggestion is to perform the strategy in all regular operations or if the suggestion is to perform it in field trials that can inform policy making. Do you mean that all military operations should perform first a risk assessment and then do 24-h physiology measurement on all crewmembers and apply various fatigue countermeasures? Or should this be performed in field-based studies (of representative types of operations) to ensure that the tactic is robust and can be applied generally? This could be described further.\n\nIf understood correctly, the suggestion is to continuously measure circadian misalignment on all crewmembers in regular operation. Is it realistic to perform 24h physiology monitoring reliably in all military operations? Given that physiological monitoring is usually quite intrusive, time consuming to analyze, and face practical challenges in the operational environment, it should be justified more clearly why such physiological monitoring is important.\n\nThe authors mention that commercial off-the-shelf wearables for physiological monitoring have been used in previous studies. It is, however, not mentioned whether the devices provided reliable measurements in operational environments. Having reliable sensor technologies is crucial if measurements are done in regular poerations. There are several aspects of military operations that could interfere with measurements. Wearables are not always convenient or safe to use in austere environments and for instance physically demanding work tasks can interfere with circadian rhythms of hormones like cortisol. There are also potential privacy issues (depending on who will have access to the data) that are not mentioned.\n\nTable 1, last row, column 3: The description of the countermeasure involving photic and non-photic stimuli to phase-shift might be difficult for non-experts to understand. Could it be simplified or explained differently?\n\nOne important aspect that is not mentioned in the policy brief is personnel management and the importance of having sufficient crewmembers to enable rest and recovery between shifts. It is not clear if this is out of the scope of the policy brief, but it could certainly affect fatigue and cause performance degradation over time.\nMinor comments\nSpell and grammar check carefully to correct minor typos, e.g. remove one ‘in’ on page 4, last paragraph ‘DLMO data in in Navy personnel’.\n\nSpell out acronyms and abbreviations the first time, e.g. CNSF policy.\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? Partly\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly",
"responses": []
},
{
"id": "191481",
"date": "22 Aug 2023",
"name": "Brieann Satterfield",
"expertise": [
"Reviewer Expertise Sleep",
"sleep loss",
"fatigue",
"individual differences",
"neurobehavioral performance",
"shift work"
],
"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 policy brief outlines processes/strategies to monitor and mitigate performance-related impairments associated with circadian misalignment in military operations. The authors propose a circadian-centered strategy that includes measurement of various physiological parameters (e.g., circadian phase via DLMO; vigilant attention performance via PVT; cardiorespiratory parameters via wearables) and associated countermeasures to combat circadian misalignment induced fatigue.\nThe current policy brief gives a clear overview of circadian misalignment being the underlying problem to achieving restorative sleep, yet largely ignores a primary role of the homeostatic sleep drive alone and in interaction with the circadian rhythm to drive overall performance. The interaction of these processes, particularly in sustained/continuous operations greater than 24 hours, can have catastrophic consequences on mission success if not accurately accounted for. The brief could therefore be strengthened by introducing the role of the homeostatic process, the importance of obtaining sufficient sleep duration, and the homeostatic process’ interaction with the circadian system.\n\nAdditionally, it would be beneficial if the proposed tools and mitigation strategies were discussed in the context of feasibility of implementation, data management, and for various operational settings, as not all tools/strategies offer a “one size fits all” solution and caveats should be presented.\nInter-individual differences have been well-established in regards to both human circadian rhythmicity, sleep physiology, and neurobehavioral performance. Such individual differences could therefore impact how the proposed strategies are implemented. These should be discussed briefly.\nThe policy brief reads well and is easy to follow. It may be useful to introduce some larger sleep/circadian related concepts in more detail (e.g., what is circadian misalignment, circadian process, homeostatic process, etc.).\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? Partly\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1262
|
https://f1000research.com/articles/11-85/v1
|
24 Jan 22
|
{
"type": "Method Article",
"title": "Estimating the sample size of sham-controlled randomized controlled trials using existing evidence",
"authors": [
"George C.M. Siontis",
"Adriani Nikolakopoulou",
"Romy Sweda",
"Dimitris Mavridis",
"Georgia Salanti",
"Adriani Nikolakopoulou",
"Romy Sweda",
"Dimitris Mavridis",
"Georgia Salanti"
],
"abstract": "Background: In randomized controlled trials (RCTs), the power is often ‘reverse engineered’ based on the number of participants that can realistically be achieved. An attractive alternative is planning a new trial conditional on the available evidence; a design of particular interest in RCTs that use a sham control arm (sham-RCTs). Methods: We explore the design of sham-RCTs, the role of sequential meta-analysis and conditional planning in a systematic review of renal sympathetic denervation for patients with arterial hypertension. The main efficacy endpoint was mean change in 24-hour systolic blood pressure. We performed sequential meta-analysis to identify the time point where the null hypothesis would be rejected in a prospective scenario. Evidence-based conditional sample size calculations were performed based on fixed-effect meta-analysis. Results: In total, six sham-RCTs (981 participants) were identified. The first RCT was considerably larger (535 participants) than those subsequently published (median sample size of 80). All trial sample sizes were calculated assuming an unrealistically large intervention effect which resulted in low power when each study is considered as a stand-alone experiment. Sequential meta-analysis provided firm evidence against the null hypothesis with the synthesis of the first four trials (755 patients, cumulative mean difference -2.75 (95%CI -4.93 to -0.58) favoring the active intervention)). Conditional planning resulted in much larger sample sizes compared to those in the original trials, due to overoptimistic expected effects made by the investigators in individual trials, and potentially a time-effect association. Conclusions: Sequential meta-analysis of sham-RCTs can reach conclusive findings earlier and hence avoid exposing patients to sham-related risks. Conditional planning of new sham-RCTs poses important challenges as many surgical/minimally invasive procedures improve over time, the intervention effect is expected to increase in new studies and this violates the underlying assumptions. Unless this is accounted for, conditional planning will not improve the design of sham-RCTs.",
"keywords": [
"meta-analysis",
"sequential methods",
"power calculation",
"renal sympathetic denervation"
],
"content": "Introduction\n\nA central decision when designing a randomized-control trial (RCT) is the number of patients that should be enrolled. RCTs including too few participants have been characterized as having limited clinical value and being unethical.1 However, conducting adequately powered trials often presents practical difficulties and investigators sometimes end up performing ‘reverse engineering’ in their sample size calculations.2 Instead of defining the treatment effect that is expected in the particular setting, which along with other parameters will result in the sample size needed, the ‘expected’ treatment effect is derived by the available-based usually on practical and economic considerations-sample size. This practice may result to unrealistically large treatment effects to justify the small number of participants to be enrolled.\n\nDesigning a new trial using the existing evidence in the form of meta-analysis has several advantages.2–5 Meta-analysis provides more powerful and precise effect estimates over individual trials which is an important advantage when the necessary means for conducting a large trial of adequate power are not available. Conditional planning of a new trial means that the calculations for the required sample size are not based on the power of the trial as stand-alone experiment but on the power of the resulting meta-analysis of the available evidence. The concept of conditional planning builds upon and combines ideas of meta-analysis and living systematic reviews,6,7 which are continuously updated as new data become available over time, and evidence-based sample size calculations2,3,5 which base the determination of sample size on the existing available evidence.8 This typically leads to smaller required sample sizes compared to that obtained using the conventional approach.9\n\nConditional planning of new trials should ideally be placed in a collaborative framework, where investigators of trials on the same topic work together to determine the similarities and differences of their studies and the prospective nature of the meta-analysis. The approach has been recently promoted as a promising route towards expediting drug licensing and inform reimbursement.10\n\nMinimizing the required sample size is particularly important in specific settings where achieving a large sample size in a trial is challenging. This includes interventions for rare diseases, expensive or very cumbersome interventions, early-phase trials in drug development or when the control intervention poses important health risks and raises ethical concerns. RCTs with sham-controlled interventions (sham-RCTs) feature many of these characteristics and are typically small and underpowered.11–13 This makes the use of conditional planning promising in this context. However, the method makes a series of assumptions. Among others it is assumed that the true underlying effect size (which we assume is unbiasedly estimated by the summary effect) should not change over time. This is rather unlikely to happen in sham-RCTs as the learning curve applies to most surgical/minimally invasive interventions and studies of their efficacy show larger effects over time. Hence, the conditional power approach is both promising and challenging to be applied in this context.\n\nIn this paper, we aim to illustrate some of the challenges encountered when sham-RCTs are designed using the conventional approach to calculate the sample size and explore any potential advantages of using existing evidence both in drawing inferences about the differences between the interventions (active versus sham intervention) and when planning a new future study. We included RCTs comparing renal sympathetic denervation to a sham intervention for the control of arterial hypertension in patients with resistant hypertension with or without the combination of different antihypertensive medications. To this aim, we attempt to replicate the sample size calculations as described in individual trials, perform standard and sequential meta-analysis and calculate the sample size that would have been required conditional on the existing evidence in each step of the evidence synthesis.\n\n\nMethods\n\nWe performed a systematic literature search (last search in December 2019) limited to English-language articles published in Medline and the Cochrane Central Register of Controlled Trials (CENTRAL) using the terms “randomized (randomised) controlled trial”, “sham”, “renal denervation”, “arterial hypertension”, as subject headings and text words, was conducted by one investigator. The detailed search algorithms can be found as Extended data.43 The reference lists of original studies, review papers, and relevant meta-analyses of the interventions of interest initially identified by the electronic searches were also reviewed in an attempt to identify additional eligible trials. For each eligible sham-RCT, we also retrieved any publicly available study protocol, in which details related to the study design were provided. We excluded trials which were terminated preterm. No further limitations were applied.\n\nThe full text reports of relevant trials and their protocols were retrieved, and data on study design, patient and intervention characteristics, the outcome of interest, time to follow-up, and the exact description of the active intervention were extracted. Information about sample size calculations were independently extracted by two investigators in separate using prespecified data extraction forms. Any discrepancies were resolved by consensus after consulting a third investigator.\n\nWe extracted from each study the following information about sample size calculations: type I error, type II error or power, assumptions in the control group (standard deviation), the superiority margin (when relevant) for the primary efficacy endpoint, the anticipated treatment effect (mean difference), the recruitment period, randomization ratio, the calculated sample size and the achieved sample size for each arm. Details related to power calculations were retrieved from the main document, supplementary material, and previously published protocols of the trials. The outcome of interest was mean change in 24-hour ambulatory systolic blood pressure (SBP).\n\nWe first attempted to replicate the sample size calculations described in individual trials. We hypothesized that the tests were two-sided and the type I error at 5% and power 80% unless different assumptions were stated. All other parameters for the power calculations were adopted as reported in the original articles. Sample size recalculations were performed by using the power command in Stata 15.14 We also calculated the relative difference between the achieved and initially calculated sample size as (achieved sample size - calculated sample size)/achieved sample size.\n\nWe performed standard and sequential pairwise meta-analysis for mean differences (MD).15,16 As heterogeneity was low in this setting, we performed fixed effect meta-analyses. The available sham-RCTs were included in the sequential (cumulative) meta-analysis following the chronological order of publication and drawn boundaries calculated using an adaptation of the continuous alpha-spending function.16,17 Crossing a boundary indicates strong evidence against the null hypothesis of equal means between active and sham procedures. We recorded the timepoint when one of the boundaries is crossed; this is the time point that the addition of a published study to the meta-analysis rejects the null hypothesis. We called this timepoint ‘final’ indicating that beyond this timepoint no further research is needed. We calculated the ‘unnecessary’ sample size as the total sample size of studies published after the final timepoint. All analyses were performed in R (version 4.0.2; R-Project for Statistical Computing) using the package meta and self-programmed routines.18\n\nWe examine the scenario where the identified studies were a-priori planned and aimed to test the null hypothesis that the mean SBP is the same between active invasive and sham intervention. We calculate the conditional power of meta-analysis to estimate the required sample size in several steps of the analysis. In the sample size calculations, the difference in SBP in the new trial is assumed to be sufficiently similar to the ones observed and included in the meta-analysis. We assume absence of time-effect interaction between effect modifiers and time (i.e. the effect size is the same between early and later studies). We consider the sequential order of the trials until the final timepoint. We start with the first published trial, and we calculate the sample size needed for a second trial which, when added to the first trial their synthesis will lead into a rejection of the null hypothesis using the conditional power method.2 Then, we synthesize the data from the first two published trials and we estimate the sample size needed in a third trial using again the conditional power; the difference in SBP in the new trial is assumed to be sufficiently similar the one estimated from the meta-analysis of the first two trials. We continue until the final timepoint. We compare the estimated sample size and the anticipated effect size from the conditional planning approach to those presented in the original papers. Analyses have been performed in Stata 15 using 1,000 simulations. Box 1 summarizes the key aspects in sample size calculations based on the conditional power of a meta-analysis.\n\n\n\n\nResults\n\nIn the Online Figure (see Extended data43) we summarize details of the study selection process. Overall, six sham-RCTs (with a total of 981 patients)19–27 comparing renal sympathetic denervation (n=585 patients) to a sham-intervention (n=396 patients) were deemed eligible (Table 1). Random allocation was 1:1 in 5 trials21–27 and 2:1 in one19,20 of the trials giving more weight to patients randomized to the active intervention. Two of the trials23–25 were not prospectively powered; this is because they were designed as small-scale proof-of-concept trials to minimize exposure of patients to an interventional procedure with not previously documented efficacy (based on the findings of SYMPLICITY HTN-3 trial19,20). 24-hour ambulatory SBP and daytime ambulatory SBP were the primary endpoints in 4 and 2 trials, respectively. The majority of the trials (5 out of 6) were single-blinded, but outcome assessment was performed in blinded manner in all trials (Table 1). Follow-up period for reported results ranged from 2 up to 6 months. While the sample size in the first trial20 was relatively large (535 participants), the sample sizes of subsequent individual trials ranged from 69 to 146 with a median of 80 participants.\n\n* The trial was also powered for this efficacy endpoint.\n\n** Not prospectively powered. Proof-of-concept trials. There were no powered endpoints in the trials.\n\nThree sham-RCTs were designed to show superiority of renal denervation over sham intervention, two were not prospectively powered, and in one trial the authors do not specify their perspective (Table 2, Box 2). We were able to replicate the sample size calculations in 3 of the trials21,22,27 and in 2 of the studies no power analyses were performed.24,25 In one study19,20 the power calculation was made for both the safety and subsequently for the efficacy primary outcome based on historical data and we were not able to replicate these (Table 2, Box 2, Online Table 1 in the Extended data43).\n\n* Assumed difference (mean and standard deviation) between the two groups of interventions for the respective primary efficacy outcome in each trial.\n\n** Calculated based at each stage on the previous meta-analysis for mean difference, standard deviation of the one considered by the investigators in individual trials and assumed 80% power.\n\n*** Calculated based at each stage on the previous meta-analysis for mean difference, standard deviation of 10 (the minimum observed in any arm) and assumed 80% power.\n\n**** We were not able to recalculate the sample size calculations of the specific trial even after contacting the principal investigator of the trial.\n\n\n\nThe achieved sample size was in all cases larger than that calculated and the relative difference was between 11% to 19% (Table 2). The anticipated mean differences used in sample size calculations by the study authors were larger than those which were actually observed in the trials, or in the trials published before (Figure 1). Consequently, each study could not detect any important differences between the active and sham interventions. This can be attributed to the over-optimistic effect considered in the sample size calculations to be able to conform with the available sample of patients for recruitment (‘reverse engineered’ sample size calculation).\n\nTwo of the trials (SPYRAL HTN-OFF MED and SPYRAL HTN-ON MED) were designed as proof-of-concept trials. Therefore, they were not prospectively powered and assumed effects are not provided.\n\nAbbreviation: SBP, systolic blood pressure.\n\nThe standard meta-analysis forest plot illustrates the individual results of each trial and its contribution (weight) to the summary effect (Figure 2 panel A); the cumulative meta-analysis plot shows how the evidence evolved over time (Figure 2 panel B). Data used are available in Online Table 2 (see underlying data43). The estimated heterogeneity variance was zero. If a meta-analysis was conducted immediately after the publication of the fourth study (when 755 patients had been randomized in total), the summary mean difference favoring the active intervention would have been found to be -2.76 (95%CI -4.93 to -0.59). Even after accounting for the sequential nature of the data accumulation, the addition of the fourth study would provide evidence against the null hypothesis (Figure 3). The final time point is therefore the time of publication of the fourth study (in 2017). The total sample size randomized thereafter (in the fifth and sixth trials) could be considered redundant (226 study participants in total, of which 114 randomized to sham).\n\nAbbreviation: RCT, randomized controlled trial.\n\nThe sample size of each future study calculated based on conditional power of meta-analysis is presented in Table 2. The summary effect of the meta-analysis after each study was included was much smaller than the anticipated effect used by the authors in their sample size calculations (Figure 2). Consequently, sample size calculations using the meta-analysis mean difference results to substantially larger calculated sample size compared to that calculated by the trialists (Table 2).\n\nThe large sample sizes calculated with conditional power compared to that calculated by the trials is explained by the fact that the trialists chose unrealistically large anticipated mean differences. If studies had been planned prospectively, the third study would have needed 260 participants per arm and the synthesis of the first three studies would have been enough to reject the null hypothesis. The total sample size from the three trials would have been 1126 (the achieved sample size from the first two trials and the estimated using conditional power from the third trial), while the total achieved sample size in the published studies is 981. Τhis means that the sample size with conditional planning under this scenario is larger than the total observed in the studies (Figures 1 and 2, Table 2).\n\n\nDiscussion\n\nCritical review of the available evidence in terms of systematic reviews and meta-analyses of RCTs can provide an in-depth summary of available evidence on a specific topic and contribute in the planning of future research agenda in two ways: by identifying gaps in knowledge on which efforts should be focused, and by contributing to the conditional planning of a future trial based on the relevant existing evidence.9,28–30 For the latter, both, pairwise and network meta-analyses, have been proposed as appropriate tools.3–5,31 Here, in a retrospectively designed scenario of the particular setting of sham-RCTs, we demonstrated how sequential meta-analysis and conditional planning of a future trial can provide an alternative strategy to the practice of conducting many small, underpowered RCTs with unrealistically large assumed expected treatment differences. Through sequential meta-analysis of sham-controlled trials, investigators can achieve conclusive findings earlier than individual small-scale trials and hence avoid exposing patients to sham-related risks. However, as we illustrated in our example, conditional planning of a future sham-RCT poses important challenges, since invasive procedures may improve over time and the intervention effect is expected to increase in new studies which violates the underlying assumptions.\n\nSystematic reviews of sham-RCTs constitute an ideal setting for considering existing evidence when planning new studies as it is even more imperative to prevent exposure of patients to risks related to the sham intervention. The dataset of trials we used, which has been previously extensively synthesized in meta-analyses,13 was no exception to the practice of setting large expected differences. The exaggerated power calculations were also reflected by the fact that the achieved sample size was always larger than the calculated. Moreover, individual trials in the early phase resulted in conflicting findings compared to subsequent trials, although statistical heterogeneity was estimated at zero.32 Differences among the trials were attributed to variability in sample sizes, study design (i.e. proof-of-concept trials), blinding of outcomes assessors, patient characteristics, modification of procedural technique and ablation catheters over time, physicians’ experience, medical treatment protocols, and outcome adjudication methods which may yield differences not only among the trials but even in the same trial.13,32 Nevetheless, the resulted sample sizes based on conditional planning were much larger than those used in individual trials. This can be also attributed to the overoptimistic expected effect sizes in individual trials and to a small trend of increase in the intervention effect over time, possibly because of a learning curve effect in performing the specific procedure.\n\nClinical research is characterized by sequential flow. New studies are built on the knowledge of the previous ones by using either prior information in making the decision to conduct a new trial or meta-analysis of existing evidence to design the subsequent trial. Even though both approaches have been established under different conditions, concerns have been raised regarding potential sources of biases due to the sequential design, particularly when a clinically relevant effect is ignored in sample size calculations.33 In this scenario, appropriate specification of clinically relevant effects is an important aspect in planning future trials to avoid unrealistic expectations. Along these lines, previous evaluations have shown the appropriateness of conditional planning under different scenarios of inconclusive meta-analysis (confidence interval of the summary effect includes effect sizes with different implications).3\n\nConditional planning in a frequentist or Bayesian framework can be applied for planning future research agenda.4,5,34–37 Nowadays, clinical trials are becoming costly and time consuming; whereas consideration of such approaches in planning future trials can potentially overcome obvious challenges (i.e. lower recruitment rates than expected or limited funding sources), better prioritize research agenda and subsequently mitigate the growing problem of wasteful research efforts in the biomedical field.9,30,38,39 It is of obvious importance to better design the required future single study or studies, in order to maximize their efficiency and potentially provide the information needed to make informed decisions in clinical effectiveness research. It could be that a small-scale study is needed to confirm previous findings or alternatively new studies may be deemed unnecessary in a scenario where the existing evidence suggests a small effect size which is unlikely to subsequently change. However, particular attention should be paid on the required assumptions of the method before embarking on applying conditional planning of new trials (Box 1).\n\nOur evaluation has several limitations. First, we chose an example of relatively limited number of available trials with small sample sizes and special design (sham-RCTs with two of them serving as proof-of-concept studies). Even though our example can be representative of the size of the available sham-RCTs in any medical field, the small number of studies might have resulted in clinical heterogeneity not manifesting in the data as statistical heterogeneity. In a real application, imputing a value for heterogeneity, informed for example by empirical predictive distributions,40,41 and performing random-effects would be a reasonable model choice. Second, sequential methods have inherited limitations since they have been mainly built on the principal of statistical significance and do not differentiate between clinically relevant and non-relevant effects. Along these lines, the Cochrane Handbook authors underline the methodological limitations that arise from sequential methods.42 Third, the applied method of conditional planning is based on aggregated findings of completed trials. However, investigators may need to adapt a trial’s design (i.e. sample size re-calculations) after its launch. These interim findings could potentially provide important insights for the planning of future trials, but available statistical approaches cannot safely consider this information. Finally, we applied a retrospective analysis while aiming to illustrate the process in a hypothetical prospective framework. In an actual application, the process should be planned and undertaken prospectively by a collaborative panel including clinicians, decision makers, methodologists and patient representatives.\n\n\nConclusions\n\nSequential meta-analysis of sham-controlled trials can help answering the research question earlier and avoid unnecessarily exposing patients to sham-related risks. However, conditional planning of new sham-RCTs poses important challenges. As many surgical/minimally invasive procedures improve over time, the intervention effect is expected to increase in new studies and this violates the underlying assumptions. Unless this is accounted for, conditional planning will not improve the design of sham-RCTs.\n\n\nData availability\n\nZenodo: Estimating the sample size of sham-controlled randomized controlled trials using existing evidence. https://doi.org/10.5281/zenodo.5865523.43\n\nThis project contains the following underlying data:\n\n- Online Table 2: Mean changes in each group of intervention and the difference between the groups for the efficacy outcome of 24-hour ambulatory systolic blood pressure as given in individual trials\n\nZenodo: Estimating the sample size of sham-controlled randomized controlled trials using existing evidence. https://doi.org/10.5281/zenodo.5865523.43\n\nThis project contains the following extended data:\n\n- Online Box 1: Medline and CENTRAL search algorithm\n\n- Online Figure: Study selection flowchart.\n\n- Online Table 1: Sample-size recalculations in individual sham RCTs in Stata.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Rerefences\n\nOtte WM, Tijdink JK, Weerheim PL, et al.: Adequate statistical power in clinical trials is associated with the combination of a male first author and a female last author. elife. 2018; 7. PubMed Abstract | Publisher Full Text\n\nSutton AJ, Cooper NJ, Jones DR, et al.: Evidence-based sample size calculations based upon updated meta-analysis. Stat. Med. 2007; 26: 2479–2500. PubMed Abstract | Publisher Full Text\n\nRoloff V, Higgins JPT, Sutton AJ: Planning future studies based on the conditional power of a meta-analysis. Stat. Med. 2013; 32: 11–24. PubMed Abstract | Publisher Full Text\n\nNikolakopoulou A, Mavridis D, Salanti G: Using conditional power of network meta-analysis (NMA) to inform the design of future clinical trials. Biom. J. 2014; 56: 973–990. PubMed Abstract | Publisher Full Text\n\nSalanti G, Nikolakopoulou A, Sutton AJ, et al.: Planning a future randomized clinical trial based on a network of relevant past trials. Trials. 2018; 19: 365. PubMed Abstract | Publisher Full Text\n\nElliott JH, Turner T, Clavisi O, et al.: Living Systematic Reviews: An Emerging Opportunity to Narrow the Evidence-Practice Gap. PLoS Med. 2014; 11. Publisher Full Text\n\nCréquit P, Trinquart L, Yavchitz A, et al.: Wasted research when systematic reviews fail to provide a complete and up-to-date evidence synthesis: The example of lung cancer. BMC Med. 2016; 14: 8. PubMed Abstract | Publisher Full Text\n\nSalanti G, Nikolakopoulou A: Actively Living Network Meta-Analysis. Accessed 31 May 2021. Reference Source\n\nChalmers I, Bracken MB, Djulbegovic B, et al.: How to increase value and reduce waste when research priorities are set. Lancet. 2014; 383: 156–165. PubMed Abstract | Publisher Full Text\n\nNaci H, Salcher-Konrad M, Kesselheim AS, et al.: Generating comparative evidence on new drugs and devices before approval. Lancet. 2020; 395: 986–997. PubMed Abstract | Publisher Full Text\n\nMiller FG, Kaptchuk TJ: Sham procedures and the ethics of clinical trials. J. R. Soc. Med. 2004; 97: 576–578. PubMed Abstract | Publisher Full Text\n\nGalpern WR, Corrigan-Curay J, Lang AE, et al.: Sham neurosurgical procedures in clinical trials for neurodegenerative diseases: Scientific and ethical considerations. Lancet Neurol. 2012; 11: 643–650. Publisher Full Text\n\nSardar P, Bhatt DL, Kirtane AJ, et al.: Sham-Controlled Randomized Trials of Catheter-Based Renal Denervation in Patients With Hypertension. J. Am. Coll. Cardiol. 2019; 73: 1633–1642. PubMed Abstract | Publisher Full Text\n\nStataCorp.: Stata Statistical Software: Release 15. College Station, TX: StataCorp LLC; 2017.\n\nHiggins JPT, Whitehead A, Simmonds M: Sequential methods for random-effects meta-analysis. Stat. Med. 2011; 30: 903–921. PubMed Abstract | Publisher Full Text\n\nNikolakopoulou A, Mavridis D, Egger M, et al.: Continuously updated network meta-analysis and statistical monitoring for timely decision-making. Stat. Methods Med. Res. 2018; 27: 1312–1330. PubMed Abstract | Publisher Full Text\n\nDemets DL, Lan KKG: Interim analysis: The alpha spending function approach. Stat. Med. 1994; 13: 1341–1352. PubMed Abstract | Publisher Full Text\n\nBalduzzi S, Rücker G, Schwarzer G: How to perform a meta-analysis with R: A practical tutorial. Evid. Based Ment. Health. 2019; 22: 153–160. PubMed Abstract | Publisher Full Text\n\nKandzari DE, Bhatt DL, Sobotka PA, et al.: Catheter-based renal denervation for resistant hypertension: Rationale and design of the SYMPLICITY HTN-3 trial. Clin. Cardiol. 2012; 35: 528–535. PubMed Abstract | Publisher Full Text\n\nBhatt DL, Kandzari DE, O’Neill WW, et al.: A Controlled Trial of Renal Denervation for Resistant Hypertension. N. Engl. J. Med. 2014; 370: 1393–1401. Publisher Full Text\n\nDesch S, Okon T, Heinemann D, et al.: Randomized Sham-Controlled Trial of Renal Sympathetic Denervation in Mild Resistant Hypertension. Hypertension. 2015; 65: 1202–1208. PubMed Abstract | Publisher Full Text\n\nMathiassen ON, Vase H, Bech JN, et al.: Renal denervation in treatment-resistant essential hypertension. A randomized, SHAM-controlled, double-blinded 24-h blood pressure-based trial. J. Hypertens. 2016; 34: 1639–1647. PubMed Abstract | Publisher Full Text\n\nKandzari DE, Kario K, Mahfoud F, et al.: The SPYRAL HTN Global Clinical Trial Program: Rationale and design for studies of renal denervation in the absence (SPYRAL HTN OFF-MED) and presence (SPYRAL HTN ON-MED) of antihypertensive medications. Am. Heart J. 2016; 171: 82–91. Publisher Full Text\n\nTownsend RR, Mahfoud F, Kandzari DE, et al.: Catheter-based renal denervation in patients with uncontrolled hypertension in the absence of antihypertensive medications (SPYRAL HTN-OFF MED): a randomised, sham-controlled, proof-of-concept trial. Lancet. 2017; 390: 2160–2170. Publisher Full Text\n\nKandzari DE, Böhm M, Mahfoud F, et al.: Effect of renal denervation on blood pressure in the presence of antihypertensive drugs: 6-month efficacy and safety results from the SPYRAL HTN-ON MED proof-of-concept randomised trial. Lancet. 2018; 391: 2346–2355. PubMed Abstract | Publisher Full Text\n\nAzizi M, Schmieder RE, Mahfoud F, et al.: Endovascular ultrasound renal denervation to treat hypertension (RADIANCE-HTN SOLO): a multicentre, international, single-blind, randomised, sham-controlled trial. Lancet. 2018; 391: 2335–2345. PubMed Abstract | Publisher Full Text\n\nAzizi M, Schmieder RE, Mahfoud F, et al.: Six-Month Results of Treatment-Blinded Medication Titration for Hypertension Control After Randomization to Endovascular Ultrasound Renal Denervation or a Sham Procedure in the RADIANCE-HTN SOLO Trial. Circulation. 2019; 139: 2542–2553. PubMed Abstract | Publisher Full Text\n\nFerreira ML, Herbert RD, Crowther MJ, et al.: When is a further clinical trial justified?. BMJ (Online). 2012; 345. Publisher Full Text\n\nGoudie AC, Sutton AJ, Jones DR, et al.: Empirical assessment suggests that existing evidence could be used more fully in designing randomized controlled trials. J. Clin. Epidemiol. 2010; 63: 983–991. PubMed Abstract | Publisher Full Text\n\nIoannidis JPA, Greenland S, Hlatky MA, et al.: Increasing value and reducing waste in research design, conduct, and analysis. Lancet. 2014; 383: 166–175. PubMed Abstract | Publisher Full Text\n\nJones HE, Ades AE, Sutton AJ, et al.: Use of a random effects meta-analysis in the design and analysis of a new clinical trial. Stat. Med. 2018; 37: 4665–4679. PubMed Abstract | Publisher Full Text\n\nPocock SJ, Bakris G, Bhatt DL, et al.: Regression to the Mean in SYMPLICITY HTN-3: Implications for Design and Reporting of Future Trials. J. Am. Coll. Cardiol. 2016; 68: 2016–2025. PubMed Abstract | Publisher Full Text\n\nKulinskaya E, Huggins R, Dogo SH: Sequential biases in accumulating evidence. Res. Synth. Methods. 2016; 7: 294–305. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShohoudi A, Stephens DA, Khairy P: Bayesian adaptive trials for rare cardiovascular conditions. Futur. Cardiol. 2018; 14: 143–150. PubMed Abstract | Publisher Full Text\n\nWason JMS, Trippa L: A comparison of Bayesian adaptive randomization and multi-stage designs for multi-arm clinical trials. Stat. Med. 2014; 33: 2206–2221. PubMed Abstract | Publisher Full Text\n\nBittl JA, He Y: Bayesian Analysis: A Practical Approach to Interpret Clinical Trials and Create Clinical Practice Guidelines. Circ. Cardiovasc. Qual. Outcomes. 2017; 10. PubMed Abstract | Publisher Full Text\n\nBerry DA: Introduction to Bayesian methods III: Use and interpretation of Bayesian tools in design and analysis. Clin. Trials. 2005; 2: 295–300. PubMed Abstract | Publisher Full Text\n\nMacleod MR, Michie S, Roberts I, et al.: Biomedical research: Increasing value, reducing waste. Lancet. 2014; 383: 101–104. Publisher Full Text\n\nSiontis GCM, Sweda R, Windecker S: Cardiovascular clinical trials in the era of a pandemic. J. Am. Heart Assoc. 2020; 9: e018288. PubMed Abstract | Publisher Full Text\n\nTurner RM, Davey J, Clarke MJ, et al.: Predicting the extent of heterogeneity in meta-analysis, using empirical data from the Cochrane Database of Systematic Reviews. Int. J. Epidemiol. 2012; 41: 818–827. PubMed Abstract | Publisher Full Text\n\nRhodes KM, Turner RM, Higgins JPT: Predictive distributions were developed for the extent of heterogeneity in meta-analyses of continuous outcome data. J. Clin. Epidemiol. 2015; 68: 52–60. PubMed Abstract | Publisher Full Text\n\nHiggins JPT, Thomas J, Chandler J, et al.: Cochrane Handbook for Systematic Reviews of Interventions. 2nd ed.Chichester (UK): John Wiley & Sons; 2019. Publisher Full Text\n\nSiontis G, Nikolakopoulou A, Sweda R, et al.: Estimating the sample size of sham-controlled randomized controlled trials using existing evidence.2022. Publisher Full Text"
}
|
[
{
"id": "129149",
"date": "11 Apr 2022",
"name": "Thomas Karagiannis",
"expertise": [
"Reviewer Expertise Evidence synthesis",
"Systematic reviews",
"Diabetes Mellitus"
],
"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 do not have any particular comments on the methodological aspects of the paper as it appears to be methodologically sound.\nIn my opinion, the most important limitation of this methodological study is that the conditional sample size calculation method, as presented by the authors, is based on the principle of statistical significance (i.e. the treatment effect as produced by a meta-analysis of available trials) and not on the rationale/principle of what value is considered clinically relevant (i.e. a conventional approach in which the anticipated treatment effect of an intervention is based on the minimal clinically important difference). I believe that the authors should emphasize this issue in their discussion; I do realize that they make mention to this limitation in the discussion (Limitations section), but I think it should be further elaborated in the context of clinical/practical implications. For example, one might wonder whether an alternative approach combining elements of both the conventional and the conditional approaches might be more reasonable when designing a new trial, i.e. use the minimal clinically important difference in sample calculation and adjust the planned sample size based on previous similar trials in the sense that the cumulative sample of all available trials (be means of a meta-analysis) would be adequately powered to collectively assess the minimal clinically important effect estimate.\nRegardless, I believe that it is noteworthy that this paper highlights various shortcomings/limitations of individual trials when it comes to sample size calculation, such as the use of “reverse engineering” (calculation is based on practical or unspecified considerations resulting in unrealistically large assumed treatment effects which in turn lead to inadequate sample size). I was also interested to see that, based on table 2, the replicated/recalculated sample size (975+488) in SYMPLICITY HTN-3 trial was much larger the sample size originally calculated in the actual trial (316+158), which implicates that sample size calculation in individual studies can still be flawed even when a minimal clinically important difference (not reverse engineering) is used.\nFinally, I noticed in Box 2 that SYMPLICITY HTN-2 trial is mentioned. I am wondering why this trial was not included in the pool of studies.\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": "8977",
"date": "07 Nov 2022",
"name": "Georgios Siontis",
"role": "Author Response",
"response": "We were pleased to receive the comments of the Reviewer. We are grateful for the very insightful comments that helped us to improve our work further. In the revised version of our manuscript we have addressed all of the suggestions/comments made by the reviewer. In more detail: Reviewer 1: I do not have any particular comments on the methodological aspects of the paper as it appears to be methodologically sound. Reply: Thank you for your feedback. In my opinion, the most important limitation of this methodological study is that the conditional sample size calculation method, as presented by the authors, is based on the principle of statistical significance (i.e. the treatment effect as produced by a meta-analysis of available trials) and not on the rationale/principle of what value is considered clinically relevant (i.e. a conventional approach in which the anticipated treatment effect of an intervention is based on the minimal clinically important difference). I believe that the authors should emphasize this issue in their discussion; I do realize that they make mention to this limitation in the discussion (Limitations section), but I think it should be further elaborated in the context of clinical/practical implications. For example, one might wonder whether an alternative approach combining elements of both the conventional and the conditional approaches might be more reasonable when designing a new trial, i.e. use the minimal clinically important difference in sample calculation and adjust the planned sample size based on previous similar trials in the sense that the cumulative sample of all available trials (be means of a meta-analysis) would be adequately powered to collectively assess the minimal clinically important effect estimate. Reply: We thank the reviewer for this thought-provoking comment. We certainly agree that methodological developments, along with interpretation of findings in clinical applications, should move away from the principle of statistical significance. We argue, however, that conventional sample size calculations are also based on statistical significance, despite making use of a minimal clinically important difference. What is measured (in conventional sample size calculations) is the expected sample size to detect the minimal clinically important difference as statistically significant. Thus, conditional power used in this paper in fact makes the two approaches comparable. Alternative evidence-based sample size calculation approaches include planning new studies based on a desired precision of the updated meta-analysis effect. We write in the Discussion: “Along these line, previous evaluations have shown the appropriateness of conditional planning under different scenarios of inconclusive meta-analysis (confidence interval of the summary effect includes effect sizes with different implications) [3].” And we also added: “Further development and establishment of evidence-base sample size calculation approaches that would move away from the principles of statistical significance would be an important step forward in the field.”. Regardless, I believe that it is noteworthy that this paper highlights various shortcomings/limitations of individual trials when it comes to sample size calculation, such as the use of “reverse engineering” (calculation is based on practical or unspecified considerations resulting in unrealistically large assumed treatment effects which in turn lead to inadequate sample size). I was also interested to see that, based on table 2, the replicated/recalculated sample size (975+488) in SYMPLICITY HTN-3 trial was much larger the sample size originally calculated in the actual trial (316+158), which implicates that sample size calculation in individual studies can still be flawed even when a minimal clinically important difference (not reverse engineering) is used. Reply: We thank the reviewer for this concrete comment. Finally, I noticed in Box 2 that SYMPLICITY HTN-2 trial is mentioned. I am wondering why this trial was not included in the pool of studies. Reply: Thank you for pointing this. Indeed, SYMPLICITY HTN-2 trial was not included in the current analysis because the control arm was “standard of care” and not a sham intervention."
}
]
},
{
"id": "150812",
"date": "17 Oct 2022",
"name": "Waldemar Siemens",
"expertise": [
"Reviewer Expertise Meta-research",
"meta-analysis",
"living systematic review"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present an empirical example comparing renal sympathetic denervation to sham intervention and provide data and calculations on power, cumulative meta-analysis, and sequential meta-analysis aiming to present the idea of conditional power. Many important points are well addressed and methodological aspects are well connected to the clinical relevance of the methods. I have some major and minor questions and encourage the authors to comment to improve the manuscript.\nMajor comments:\nLimitations: “performing random-effects would be a reasonable model choice” - Why have you worked with the FE model then?\nIf conditional power would say that only a “small trial” is needed: Would this be a problem regarding the sampling error? Should trials have a minimum size to avoid sampling error? As the trial gets smaller, the problem of chance increases, or? Could you comment on that and reflect you approach (conditional power)?\nThis is an empirical example. Could a reasonable simulation study add value? If yes, how could it look like?\n\nMinor comments:\nAbstract:\nYou could add more numeric results in the results of you abstract if appropriate.\n\nBackground:\n“This typically leads to smaller required sample sizes compared to that obtained using the conventional approach.” - I wonder if a disadvantage of this approach is that the sampling error increases with a small sample size in a trial. Could you comment on that?\n“Among others it is assumed that the true underlying effect size (which we assume is unbiasedly estimated by the summary effect) should not change over time. This is rather unlikely to happen in sham-RCTs as the learning curve applies to most surgical/minimally invasive interventions and studies of their efficacy show larger effects over time. Hence, the conditional power approach is both promising and challenging to be applied in this context.” - Does the fixed-effect (FE) model makes sense in this context? Clinical trials vary in their PICO by nature, which makes it hard to assume the FE model.\n“As heterogeneity was low in this setting, we performed fixed effect meta-analyses.” - Shouldn’t that be a choice based on the homogeneity of the trials according to the PICO scheme?\n\nBox 1:\n“The variability of the true treatment effect across trials should be low. Otherwise, even the planning of huge trials will not result in the anticipated conditional power.” - This again puts the FE model into question, or? Should the conditional power calculations be based the random-effects model?\nResults:\n\nTable 1 / meta-analysis: Is it appropriate to pool “24-hour ambulatory SBP” with “Daytime ambulatory SBP”?\n\nLink for “Online Table 2”: Only “Table 2” is a link and leads to Table 2 in the manuscript, not to Online Table 2. Please check all link in the manuscript.\n“heterogeneity variance” (p. 5) - Do you mean the between-study variance Tau^2? Please be more precise.\n\n“The total sample size randomized thereafter (in the fifth and sixth trials) could be considered redundant (226 study participants in total, of which 114 randomized to sham).” - I think this should be one key message of the paper exactly with this wording, i.e., how many patients would not receive sham. It adds weight for a clinically meaningful understanding of the methods presented.\n\n“The large sample sizes calculated with conditional power compared to that calculated by the trials is explained by the fact that the trialists chose unrealistically large anticipated mean differences.” - Sometimes you already interpret your results in the discussion section. Please move the explaining sentences rather to the discussion.\n\n“Figure 3. Hypothetical prospectively planned sequential fixed effect meta-analysis framework (type I error=5%, power=90%).” - I suggest adding more sentences for explaining Figure 3. Not everyone is familiar with sequential meta-analysis so it might be important to help readers understand the idea of it.\n\nDiscussion:\nFeasibility of large trials when trial authors would consider conditional power.\n\nStop when rejecting the null hypothesis is defined as the “final time point”, correct? How does this fit to clinical relevance of results? One could argue to stop if a threshold of irrelevance is not anymore included by the 95% CI for example.\n\nHave prediction intervals a role in cumulative meta-analysis and sequential meta-analysis to describe heterogeneity?\nIs the R code available? You may add it to zenodo.\n\n“Unless this is accounted for, conditional planning will not improve the design of sham-RCTs.” - Could you explicitly say what you mean by “this” to avoid misunderstandings in the conclusion? Somehow I find it hard to follow, maybe also because you word your statement with a negation. Please consider rewriting it.\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? Partly\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "8978",
"date": "07 Nov 2022",
"name": "Georgios Siontis",
"role": "Author Response",
"response": "We were pleased to receive the comments of the Reviewer. We are grateful for the very insightful comments that helped us to improve our work further. In the revised version of our manuscript we have addressed all of the suggestions/comments made by the Reviewer. In more detail: Reviewer 2: The authors present an empirical example comparing renal sympathetic denervation to sham intervention and provide data and calculations on power, cumulative meta-analysis, and sequential meta-analysis aiming to present the idea of conditional power. Many important points are well addressed and methodological aspects are well connected to the clinical relevance of the methods. I have some major and minor questions and encourage the authors to comment to improve the manuscript. Reply: Thank you for your feedback. Major comments: Limitations: “performing random-effects would be a reasonable model choice” - Why have you worked with the FE model then? Reply: We thank the reviewer for this comment. In fact, our intention was to employ a random-effects meta-analysis model. As the between-study variance (r2) estimation was 0, this was equivalent to fixed-effect. We realize that this was not clearly stated, and we thus now have rephrased to clarify our approach. In particular, we write in the ‘Standard and sequential meta-analysis’ section: “We intended to perform random-effects meta-analysis, but as between-study variance (r2) was estimated at 0 in this setting, our calculations are identical to those from a fixed effect meta-analysis.”. We did not change the term “fixed-effect” in the abstract and the figure legends. An alternative strategy would be to inform heterogeneity from empirical distributions (our references 40 and 41). However, such an approach would be appropriate in a prospective application of sequential meta-analysis and conditional planning, rather than a retrospective application, like the one presented in this paper. This is because in a prospective application, estimation of heterogeneity in the first stages of the reviews would be suboptimal. Moreover, imputing a value for heterogeneity would make results from “conventional” and “evidence-based” sample size calculations non-comparable. We already wrote in the Discussion: “In a real application, imputing a value for heterogeneity, informed for example by empirical predictive distributions [40, 41], and performing random-effects would be a reasonable model choice”. And we now added: “Such an approach would be less reasonable in a retrospective application of the methods and would mitigate the comparability between conventional and evidence-based sample size calculations.” If conditional power would say that only a “small trial” is needed: Would this be a problem regarding the sampling error? Should trials have a minimum size to avoid sampling error? As the trial gets smaller, the problem of chance increases, or? Could you comment on that and reflect you approach (conditional power)? Reply: This is a topic that would benefit from further investigation. On one hand, a small trial should be a desirable outcome of the conditional planning method, on the other hand it would indeed be associated with greater within-study variation. Although this potentially large within-study variation is in theory incorporated in the conditional planning method (saying for example that an addition of such a study would render conclusive the updated meta-analysis effect, which is our goal), it would probably question the requirement of such individual study to be a standalone experiment. We added in the Discussion: “However, conditional planning might in theory result to recommendations of very small trials, which would be associated with great within-study variance and not be standalone experiments. Setting a minimum sample size for a future trial designed using conditional planning would be a potential remedy for such a situation.”. This is an empirical example. Could a reasonable simulation study add value? If yes, how could it look like? Reply: We thank the reviewer for this interesting comment. We do believe that a simulation study could contribute on the evaluation of the robustness of the method, and this could be a follow-up project. In such a simulation study, one should construct scenarios reflecting various assumptions being and not being met. We added under “Limitations”: “A comprehensive simulation study would be a more appropriate tool to investigate the performance and robustness of the method under a variety of settings.” Minor comments: Abstract: You could add more numeric results in the results of you abstract if appropriate. Reply: We have added in the Abstract: “Conditional planning resulted in much larger sample sizes compared to those in the original trials (relative increase between achieved and calculated sample size ranged between 11-19%), …”. Background: “This typically leads to smaller required sample sizes compared to that obtained using the conventional approach.” - I wonder if a disadvantage of this approach is that the sampling error increases with a small sample size in a trial. Could you comment on that? Reply: Please see our response on your second comment from ‘Major comments’. “Among others it is assumed that the true underlying effect size (which we assume is unbiasedly estimated by the summary effect) should not change over time. This is rather unlikely to happen in sham-RCTs as the learning curve applies to most surgical/minimally invasive interventions and studies of their efficacy show larger effects over time. Hence, the conditional power approach is both promising and challenging to be applied in this context.” - Does the fixed-effect (FE) model makes sense in this context? Clinical trials vary in their PICO by nature, which makes it hard to assume the FE model. Reply: Please see our response on your first comment from ‘Major comments’. Our intention was to perform a random-effects meta-analysis, but heterogeneity being 0 ended up to a fixed-effect model. “As heterogeneity was low in this setting, we performed fixed effect meta-analyses.” - Shouldn’t that be a choice based on the homogeneity of the trials according to the PICO scheme? Reply: We have now rephrased this sentence to: “We intended to perform random-effects meta-analysis, but as between-study variance (r2) was estimated at 0 in this setting, our calculations are identical to those from a fixed effect meta-analysis.” Box 1: “The variability of the true treatment effect across trials should be low. Otherwise, even the planning of huge trials will not result in the anticipated conditional power.” - This again puts the FE model into question, or? Should the conditional power calculations be based the random-effects model? Reply: Please see our response on your first comment from ‘Major comments’. Furthermore, we acknowledge that heterogeneity might be estimated to be zero due to large within-study variation. We write in the ‘Limitations’ section: “Even though our example can be representative of the size of the available sham-RCTs in any medical field, the small number of studies might have resulted in clinical heterogeneity not manifesting in the data as statistical heterogeneity.”. Results: Table 1 / meta-analysis: Is it appropriate to pool “24-hour ambulatory SBP” with “Daytime ambulatory SBP”? Reply: Thank you for mentioning this. Yes, both measurements are highly consistent in changes of similar magnitude for the patient populations recruited in the individual trials. Link for “Online Table 2”: Only “Table 2” is a link and leads to Table 2 in the manuscript, not to Online Table 2. Please check all link in the manuscript. Reply: Done. “heterogeneity variance” (p. 5) - Do you mean the between-study variance Tau^2? Please be more precise. Reply: The text has been revised as follows: “The estimated between-study variance (r2) was zero.”. “The total sample size randomized thereafter (in the fifth and sixth trials) could be considered redundant (226 study participants in total, of which 114 randomized to sham).” - I think this should be one key message of the paper exactly with this wording, i.e., how many patients would not receive sham. It adds weight for a clinically meaningful understanding of the methods presented. Reply: Thank you for this comment. We now mention in Abstract: “Sequential meta-analysis provided firm evidence against the null hypothesis with the synthesis of the first four trials (755 patients, cumulative mean difference -2.75 (95%CI -4.93 to -0.58) favoring the active intervention)), with the fifth and sixth trial to be considered redundant (226 study participants in total, of which 114 randomized to sham).” “The large sample sizes calculated with conditional power compared to that calculated by the trials is explained by the fact that the trialists chose unrealistically large anticipated mean differences.” - Sometimes you already interpret your results in the discussion section. Please move the explaining sentences rather to the discussion. Reply: The above-mentioned sentence has been moved to the Discussion as suggested. “Figure 3. Hypothetical prospectively planned sequential fixed effect meta-analysis framework (type I error=5%, power=90%).” - I suggest adding more sentences for explaining Figure 3. Not everyone is familiar with sequential meta-analysis so it might be important to help readers understand the idea of it. Reply: Thank you for pointing this issue. We now mention in Methods: “Meta-analyses of medical interventions may result in false positive or false negative results, due to low statistical power when the required number of randomised participants or trials has not been reached. Under this scenario, trial sequential analysis of a meta-analysis may amend these problems by handling a meta-analysis of several RCTs in an analogous manner to interim analysis of a single RCT.” Discussion: Feasibility of large trials when trial authors would consider conditional power. Reply: We are not sure what the reviewer means with this comment. Is it related to the previous comment about the large within-study variation if small trials are recommended by conditional planning approach? If yes, we refer to our response (and amendments in the paper) on this comment. Stop when rejecting the null hypothesis is defined as the “final time point”, correct? How does this fit to clinical relevance of results? One could argue to stop if a threshold of irrelevance is not anymore included by the 95% CI for example. Reply: A limitation of sequential methods lies on them being based on the principles of statistical significance. We write in the ‘Limitations’: “Second, sequential methods have inherited limitations since they have been mainly built on the principal of statistical significance and do not differentiate between clinically relevant and non-relevant effects. Along these lines, the Cochrane Handbook authors underline the methodological limitations that arise from sequential methods [42].» We could indeed extend the methodology to account for clinically relevant results, but such an approach would require further development and evaluation of its feasibility. Have prediction intervals a role in cumulative meta-analysis and sequential meta-analysis to describe heterogeneity? Reply: Yes, prediction intervals fall naturally within the principles of cumulative meta-analysis, although they have not been used in this way. We refer to the Appendix A2 (a short paragraph) of our methodological paper: Nikolakopoulou A, Mavridis D, Egger M, Salanti G. Continuously updated network meta-analysis and statistical monitoring for timely decision-making. Statistical Methods in Medical Research. 2016 Jan. We do not think that a discussion of the topic would fit in the current paper but please advise if this was the intention of your comment. Is the R code available? You may add it to zenodo. Reply: Yes. The R code is available upon request. “Unless this is accounted for, conditional planning will not improve the design of sham-RCTs.” - Could you explicitly say what you mean by “this” to avoid misunderstandings in the conclusion? Somehow I find it hard to follow, maybe also because you word your statement with a negation. Please consider rewriting it. Reply: Thank you for your comment. In our conclusive statement, “this” corresponds to the expected increase of the intervention effect in new studies. We have rephrased the conclusive statement as follows: “Unless this expected change is accounted for, conditional planning will not improve the design of sham-RCTs.”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-85
|
https://f1000research.com/articles/11-924/v1
|
11 Aug 22
|
{
"type": "Systematic Review",
"title": "The contradictory effects of coffee intake on periodontal health: a systematic review",
"authors": [
"Taufan Bramantoro",
"Amalia Ayu Zulfiana",
"Muhammad Subhan Amir",
"Wahyuning Ratih Irmalia",
"Nor Azlida Mohd Nor",
"Alexander Patera Nugraha",
"Agung Krismariono",
"Amalia Ayu Zulfiana",
"Muhammad Subhan Amir",
"Wahyuning Ratih Irmalia",
"Nor Azlida Mohd Nor",
"Alexander Patera Nugraha",
"Agung Krismariono"
],
"abstract": "Background: Drinking coffee is known to have both positive and negative aftermath on periodontal health. The current study is aiming to systematically review the impact of coffee consumption on periodontal health status. Methods: An article search was carried out in two electronic databases (PUBMED and Web of Sciences). The assessment of the included articles were conducted using Joanna Briggs Institute (JBI) critical appraisal tool. Data were analyzed qualitatively. Result: A total of 10 articles were included in this study. Most (5) of the studies discovered a negative correlation between coffee intake and periodontal health, while 4 other studies found the protective effect of daily coffee consumption against alveolar bone loss. Last, only one study found that coffee intake did not relate with periodontitis. Conclusion: The effect of coffee consumption on periodontal health was fragmented since coffee has complex components that may give either beneficial effects or negative impact on periodontal health.",
"keywords": [
"bone loss",
"caffeine",
"coffee",
"periodontal health",
"periodontitis",
"tooth loss"
],
"content": "Introduction\n\nCoffee has been considered as one of the most consumed beverages among adults worldwide.1 Reported by International Coffee Organization, the world consumption of coffee increased by 1% from 2017 to 2021, with the highest increase found in Africa and the largest consumption reported in Europe. The similar trend also happened on the coffee production by the coffee-exporting-countries, showing an increase of 6.3% in a year since 2019.2\n\nThere are several reasons for people decided consuming coffee or not. For coffee drinkers, one of the leading motives reported are due to its health benefits, taste and pleasure.3 In terms of health, a systematic review reported drinking coffee is associated with the lower risk of diabetes.4 Other protective effects of coffee intake had been reported in epidemiological studies; giving therapeutic effect for cardiovascular diseases, Alzheimer’s disease, gastritis, and other chronic diseases.5 Meanwhile, some other people may still avoid drinking coffee due to their belief for its adverse effects, such as anxiety and insomnia.3,6 Thus, aside from giving several health benefits, daily coffee intake in adequate dose might also had some negative impacts.3\n\nThe contradictory effects of daily coffee intake are also found in oral health fields. Many studies reported the protective effects of coffee consumption on periodontal health, while others discovered its drawbacks. The antioxidant and anti-inflammatory effects of caffeine contained in coffee might lead to beneficial results for periodontal diseases. In contrary, a study indicated that the daily coffee consumption may delay the bone repair after tooth extraction.7 Thus, we are aiming to systematically review the impact of coffee consumption on periodontal health status.\n\n\nMethod\n\nWe used two electronic databases (PubMed and Web of Science) as our tools to search the potential literatures. The literature search through databases was performed on 6 April 2022 until 14 April 2022. We constructed the keywords for each database. For PubMed, we used the following keywords; ((((((coffee [MeSH]) OR (caffeine [MeSH])) OR (“coffee intake”)) OR (“coffee consumption”)) OR (“caffeine intake”)) OR (“caffeine consumption”)) AND ((((mouth [MeSH]) OR (tooth [MeSH])) OR (((“oral health” [MeSH]) OR (“periodontal health”)) OR (“periodontal index” [MeSH]))) OR (((“tooth loss”[MeSH]) OR (periodontitis [MeSH])) OR (periodontal disease [MeSH]))). Meanwhile for Web of Science, the keywords were (((((ALL=(coffee)) OR ALL=(“coffee intake”)) OR ALL=(“coffee consumption”)) OR ALL=(“caffeine intake”)) OR ALL=(“caffeine consumption”)) OR ALL=(caffeine) AND (((((((ALL=(mouth)) OR ALL=(tooth)) OR ALL=(“oral health”)) OR ALL=(“periodontal index”)) OR ALL=(“periodontal health”)) OR ALL=(“periodontal disease”)) OR ALL=(periodontitis)) OR ALL=(“tooth loss”). During the literature search, no time limit was set.\n\nAll types of experimental and observational studies in English language were included. No duplicate studies and no treatment or clinical trial studies included. Study subjects include adults without any gender and age restrictions, and any other objects of in vivo and in vitro studies. Study factor or exposure included in the studies were coffee or caffeine intake in a daily basis, any other interventions using caffeine or coffee. Outcome of studies included were oral health status, periodontal health status, periodontal diseases, tooth loss and any other assessment of periodontal conditions.\n\nThe aforementioned keywords gave a total number of 895 articles, consisting of 243 and 652 articles from PubMed and Web of Science respectively. We excluded one literature as it was a book chapter. After excluding duplicates and languages, we had 829 potential articles to be reviewed. After conducting title and abstract reading, we had remaining 47 studies. Two researchers reviewed the full text of those studies and finally selected ten of them which met the inclusion criteria. Critical appraisal had been done by two reviewers separately using JBI Critical Appraisal tools. The flow diagram of the selection of study is shown in Figure 1.\n\n\nResults\n\nThe included studies in this review were originally from Asia, America, Europe, and Africa. Out of ten studies, three were from Korea, two were from Japan, another two were from America, and the remaining three were from each of Brazil, Germany, and Egypt. The year of publication ranged from 1999 to 2022. Half of the included studies used cross-sectional study design, three studies were randomized controlled trial, one study used cohort study design, and another one used quasi-experimental study design. This review including studies with various subject, six studies observing the effect of coffee intake on human,8–13 three studies exploring the cellular changes using rats as the subject,14–16 and one in vitro study observing the coffee effect using UMR106-01 rat osteoblast-like cells.17 The summary of the included study were tabulated based on the results, whether coffee intake have positive (Table 1) or negative effect (Table 2) on periodontal health.\n\nHuman studies\n\nAmong six studies, two studies used data from national survey, and choosing the eligible participants based on some criteria. One study used data from dental longitudinal studies, one study used data from Genome and Epidemiology Study, one used general population, and one other study selected chronic periodontitis patients who had received initial treatment as the participants of the study. All of the human studies used questionnaire to assess the dose of daily coffee consumption (all six studies),8–13 one study also used Cornell Medical Index (CMI) to gain coffee consumption in addition to questionnaire.9 Two studies admitted that validity and reliability test of the questionnaire were not performed sufficiently, therefore, further research is required.11,12\n\nThe assessment of periodontal health was mostly performed using various reliable ways, however, one study only ask whether the participants ever diagnosed with periodontitis without further clinical examination.11 The clinical oral examination performed to assess periodontal health including scoring method according to American Association of Periodontology by probing pocket depth and clinical attachment level,12 using Community Periodontal Index (CPI),8,10 radiographic examination to measure alveolar bone loss, measurement of probing depth,9,13 bleeding on probing,9,13 gingival recession,13 and examining supragingival calculus,9,13 and plaque index score.13 Aside from periodontal health, caries measurement using DMFT index was also performed.13\n\nIn terms of bias, some studies also observed several confounding factors, such as Body Mass Index (BMI)9,11,13 and other nutritional intake,11 smoking and alcohol habit,9,11–13 medical history such as diabetes,8,9,12,13 cholesterol level8 and coronary heart diseases,12,13 blood sample analysis,8 and other socio-demographic factors.10,12\n\nAnimal studies\n\nThe animal studies were performed with various designs. One study induced periodontitis on rats by means of ligature placement, then made comparisons between groups with and without caffeine ingestion (Bezerra et al). The two other studies observed the effect of giving green coffee bean extract (Abbas) and powdered coffee (Kobayashi) on periodontal health of the rats. Histological examinations were performed to assess the effect, by observing bone structure and volume (Abbas, bezerra, kobayashi), RANKL expression (bezerra), measuring serum oxidative stress and antioxidant capacity, 8-OHdG and Nrf2 positive cells, and gene expression analysis (Kobayashi).\n\nIn vitro study\n\nThe only one in vitro study was observing any possible interaction between Prostaglandin E2 (PGE2) and caffeine using UMR106-01 rat osteoblast-like cells.\n\n\nDiscussion\n\nThe favorable effects of coffee intake on periodontal health\n\nThe minority of the included studies managed to reveal the benefits of coffee intake on periodontal health. Studies found that coffee intake might be beneficial against periodontal disease.9,10 Another study on patient with periodontitis during maintenance phase of therapy also showed those who drank more than one cup of coffee in a day had lower prevalence of severe periodontitis. However, no such significant difference found on the prevalence of moderate periodontitis.12 An in vivo study using revealed that consuming coffee had a protective effect against periodontal diseases. The result showed a lower ratio of 8-OHdG-positive cells in the group with the highest dose of coffee intake, compared to those in the control and other treatment group with lower dose of coffee. The study also identified that coffee intake improve the antioxidant activity in periodontal tissue by upregulating Nrf2 signaling pathway.16 However, Hong et al (2021) revealed that there is no significant association between coffee intakes and periodontitis as the adjusted ratio were not statistically significant.11\n\nThe drawbacks of coffee consumption on periodontal health\n\nFive studies found out that consuming coffee might also have negative impacts on periodontal tissue, especially the alveolar bone. An animal study comparing the effect of consuming two different dietary supplement (green coffee extract/GC and Agiolax®/Ag) on alveolar bone loss. Both supplements showing deleterious effect towards periodontal health, however, GC groups showed greater alveolar bone loss compared to Ag groups.14 Another study on periodontitis-induced rats by placing a cotton ligature also showing that caffeine ingestion causing larger area of bone loss, even though without ligature placement, caffeine alone was unable to induce alveolar bone loss.15 The only in-vitro study in this review investigated the interaction between caffeine and prostaglandin E2 (PGE2) on rats’ osteoblast-like cells. It showed significant inhibition of cell proliferation when both caffeine and PGE2 were incubated together and the inhibition were stronger as the dose higher.17 Lastly, two human studies also indicated the destructive effect of coffee on periodontal tissue.8,13\n\nInterestingly, the current review covers several study designs and settings, taking humans, animals, and culture medium as their objects of study. However, some studies did not state the possible confounding factors and ways to deal with it.8–10\n\nPeriodontitis is an inflammatory disease that mainly caused by microorganisms that present as the destruction of teeth supporting tissue. Periodontitis is also associated with the presence of reactive oxygen species (ROS) as a result of hyperactivity of peripheral blood neutrophils. Its hyperactivity may occur as a reaction of host-immune reaction to the inflammation of periodontitis. Not only neutrophils, the infection of bacteria producing ROS might also be contributed to the oxidative stress in periodontitis, leading to the progression of alveolar bone loss.\n\nCoffee is considered as one of the most antioxidant-rich beverages as it has various components that were found to have antioxidant and anti-inflammatory properties; caffeine, chlorogenic acid, and caffeic acid. Due to the presence of such effects, there might be protective impacts of coffee in periodontal diseases.8,10 A study suggest that phenolic content in coffee have strong antioxidant properties, thus might reduce oxidative stress due to bacterial activity. In addition, the recent replacement of cream with skimmed milk powder in the coffee mix is thought to be helpful in preventing osteoporosis, thus can also be protective against periodontal bone loss.10,18 Milk belongs to dairy products, with calcium and casein content that is helpful in bone and tooth mineral preservation.18 Other explanation of the coffee protective effect against alveolar bone loss is also presented by Ng et al. It was stated that caffeine has immunomodulatory actions by inhibiting cyclic adenosine monophosphatase (cAMP)-phospodiesterase, thus increasing the concentration of intracellular cAMP.9 Another supporting result was also presented by Machida et al that observed the effect of consuming coffee during the maintenance phase of periodontal therapy.12 Besides, chlorogenic acid contents in coffee also known to act as antimicrobial agent by reducing the protease activity of Porphyromonas gingivalis. Those are bacteria that commonly found in plaque biofilm that plays role in the periodontal disease progression.11,19\n\nA cellular molecular observation also found that chlorogenic acid contained in coffee can significantly decrease malondialdehyde, which is the result of lipid peroxidation degradation, and increase catalase, superoxide dismutase, and glutathione. Thus, reducing oxidative stress. However, the study was focus on the anti-aging effect of coffee intake toward oxidative stress on periodontal tissues, without considering the normal flora. Thus, the effect on periodontal disease might be slightly different.16\n\nThe similar findings have been shown through gene expression analysis. Some genes that were having a role in the antioxidant effect were highly expressed in the highest percentage of coffee group; glutamate cysteine ligase modifier subunit, ferritin, and hypoxanthine phosphoribosyltransferase 1 genes.20 Glutamate cysteine ligase (modifier subunit) has a role to maintain the synthesis of glutathione, one of the largest intracellular antioxidants. Meanwhile, ferritin has a protective role against iron-dependent oxidative stress. The cellular defense against oxidative stress may occur through the activation of Nrf2 signaling pathways which controls the genes that involved in the elimination of reactive oxidants by increasing the cellular antioxidant capacity.21 This notion is consistent with the study result showing the more frequent of Nrf2 nuclear translocation in the highest percentage of coffee group.20 It is indicated that the continuous intake of coffee lead to some increase in the antioxidant capacity of the periodontal tissue, decreasing age-related oxidative stress in the tissues. The systemic increase of antioxidant activities may contribute to a decrease in oxidative damage at the local level.22 Hence, the systemic approaches including dietary habits may also provide promising benefits in the treatment of periodontal diseases.12\n\nIn contrast, many studies reported the detrimental effects of coffee intake on periodontal disease.8,13–15,17 Hypotheses explaining the association might focus on the caffeine as the major content in coffee.8,14 Caffeine is reported to affect calcium metabolism and evoking bone mineral density. Thus, long-term caffeine intake denotes one of the risk factors in the advancement of periodontitis pathology. Another study revealed that caffeine may increase bone loss and alter bone healing following tooth extraction.8 There are several pharmacological and cellular activities of caffeine on bone metabolism related to osteoblast proliferation and calcium metabolism.8,14,15 Caffeine is known to be able to inhibit the osteoblast-like cells proliferation, also have negative impacts towards the viability of osteoblast, leading to the increase of apoptosis rate of the cells.15 The negative impacts towards these cells are due to the caffeine ability to disrupt the mitochondria of osteoblast and osteocyte in vivo.17 Caffeine can also increase the expression of the receptor activator of NF-κB ligand (RANKL), as the result of low calcium levels in blood. The low level of calcium will be responded by the increase secretion of parathyroid hormone, and stimulate the osteoclast to increase calcium blood levels through expressing RANKL.14 Alveolar bone loss in periodontitis is mediated by tumor necrosis factor (TNF)-α, interleukin (IL)-6, RANKL, and prostaglandin E2 (PGE2) as the response to a pathogens. A combination of PGE2 and caffeine in blood strongly inhibit osteoblast proliferation.15,17 This might be the reason behind the absence of coffee consumption effect toward healthy periodontal tissue. The contradictory effects of coffee consumption might be caused by several factors. First of all, the roast degree can alter the amount of chlorogenic acid content in the coffee, thus might also affect its anti-oxidant, anti-bacterial and anti-inflammatory activity.19 Secondly, the caffeine content in each coffee consumed may vary, and the last possible causes is the additives content in coffee (milk, sugar, cream) consumed might also contribute to different effects of coffee.23 In addition, the effects of coffee on health work in a dose-dependent manner. The high dose of caffeine administered daily in an in vivo study that causes bone destruction was equivalent to 1,360mg/70kg0.75 in humans.15 This dosage was equivalent to 16 cups of coffee per day. Meanwhile, the suggested daily intake of coffee that is considered to be safe is around four-five cups per day.\n\n\nConclusion\n\nThe effect of coffee consumption on periodontal health was fragmented since coffee has complex components that may give either beneficial effects or negative impact on periodontal health. Drinking coffee in routine and in a proper dosage may give benefits on periodontal health, but it also potentially has detrimental effects if excessive dosage consumed.\n\nAs we did limit the language to be English only, many studies written in non-English were not covered in this review which may lead to language bias. The various designs used in the selected studies gave a wide range of results and it is not feasible to quantitatively summarize the selected studies. Besides, the measurement of periodontal health as the study outcome is various, giving a challenge to meaningfully compare among one and another. Moreover, the majority of studies were a cross-sectional study which cannot answer the causality of the findings. In future studies, it will be necessary to observe the potential antioxidant effects on periodontal tissue by measuring the antioxidant marker on gingival crevicular fluid (GCF) sample.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nFigshare: PRISMA_2020_checklist. The contradictory effects of coffee intake on periodontal health- a systematic review. DOI: https://doi.org/10.6084/m9.figshare.20412261.v1.24\n\nFigshare: PRISMA Flowchart. DOI: https://doi.org/10.6084/m9.figshare.20412252.25\n\nFigshare: Table - The contradictory effects of coffee intake on periodontal health- a systematic review. DOI: https://doi.org/10.6084/m9.figshare.20412270.v1.26\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nÖzen AE, del Mar Bibiloni M , Pons A, et al.: Fluid intake from beverages across age groups: a systematic review. J. Hum. Nutr. Diet. Off. J. Br. Diet. Assoc. 2015; 28: 417–442. PubMed Abstract | Publisher Full Text\n\nInternational Coffee Organization - What’s New. http\n\nSamoggia A, Riedel B: Consumers’ Perceptions of Coffee Health Benefits and Motives for Coffee Consumption and Purchasing. Nutr. 2019; 11: 653.\n\nHuxley R, et al.: Coffee, decaffeinated coffee, and tea consumption in relation to incident type 2 diabetes mellitus: a systematic review with meta-analysis. Arch. Intern. Med. 2009; 169: 2053–2063.\n\nBidel S, Tuomilehto J: The Emerging Health Benefits of Coffee with an Emphasis on Type 2 Diabetes and Cardiovascular Disease. Eur. Endocrinol. 2013; 9: 99.\n\nSousa AG, Machado LMM, da Silva EF , et al.: Personal characteristics of coffee consumers and non-consumers, reasons and preferences for foods eaten with coffee among adults from the Federal District, Brazil. Food Sci. Technol. 2016; 36: 432–438. Publisher Full Text\n\nMacedo RM, Brentegani LG, de Lacerda SA : Effects of coffee intake and intraperitoneal caffeine on bone repair process – A histologic and histometric study. Braz. Dent. J. 2015; 26: 175–180. PubMed Abstract | Publisher Full Text\n\nHan K, Hwang E, Park JB: Association between consumption of coffee and the prevalence of periodontitis: The 2008-2010 Korea National Health and Nutrition Examination Survey. PLoS One. 2016; 11: 1–11.\n\nNg N, Kaye EK, Garcia RI: Coffee Consumption and Periodontal Disease in Males. J. Periodontol. 2014; 85: 1042–1049. PubMed Abstract | Publisher Full Text\n\nKim YR, Nam SH: Comparison of periodontal status according to the additives of coffee: Evidence from Korean national health and nutrition examination survey (2013–2015). Int. J. Environ. Res. Public Health. 2019; 16. Publisher Full Text\n\nHong SJ, Kwon B, Yang BE, et al.: Evaluation of the Relationship between Drink Intake and Periodontitis Using KoGES Data. Biomed. Res. Int. 2021; 2021: 1–8. PubMed Abstract | Publisher Full Text\n\nMachida T, et al.: Severe periodontitis is inversely associated with coffee consumption in the maintenance phase of periodontal treatment. Nutrients. 2014; 6: 4476–4490. PubMed Abstract | Publisher Full Text\n\nStruppek J, et al.: The association between coffee consumption and periodontitis: a cross-sectional study of a northern German population. Clin. Oral Investig. 2022; 26: 2421–2427. PubMed Abstract | Publisher Full Text\n\nAbbass MMS, El-Baz DAH: The effect of daily intake of green coffee bean extract as compared to Agiolax® on the alveolar bone of albino rats. Dent. Med. Probl. 2018; 55: 125–131. PubMed Abstract | Publisher Full Text\n\nBezerra JP, da Silva LRF , de Alvarenga Lemos VA , et al.: Administration of High Doses of Caffeine Increases Alveolar Bone Loss in Ligature-Induced Periodontitis in Rats. J. Periodontol. 2008; 79: 2356–2360. PubMed Abstract | Publisher Full Text\n\nKobayashi T, et al.: Effects of coffee intake on oxidative stress during aging-related alterations in periodontal tissue. In Vivo. 2020; 34: 615–622. PubMed Abstract | Publisher Full Text\n\nKamagata-Kiyoura Y, et al.: Combined Effects of Caffeine and Prostaglandin E 2 on the Proliferation of Osteoblast-Like Cells (UMR106-01). J. Periodontol. 1999; 70: 283–288. PubMed Abstract | Publisher Full Text\n\nZupo R, et al.: Beverages Consumption and Oral Health in the Aging Population: A Systematic Review.2021; 8.\n\nTsou S, Hu S, Yang J, et al.: Nutrients Potential Oral Health Care Agent from Coffee against Virulence Factor of Periodontitis.2019; 1–12.\n\nKobayashi T, et al.: Effects of Coffee Intake on Oxidative Stress During Aging-related Alterations in Periodontal Tissue. Vivo Athens Greece. 2020; 34: 615–622.\n\nNguyen T, Nioi P, Pickett CB: The Nrf2-Antioxidant Response Element Signaling Pathway and Its Activation by Oxidative Stress. J. Biol. Chem. 2009; 284: 13291–13295. PubMed Abstract | Publisher Full Text\n\nTamaki N, Tomofuji T, Yamamoto T: Relationship Between Periodontal Condition and Plasma Reactive Oxygen Metabolites in Patients in the Maintenance Phase of Periodontal Treatment.2008. Publisher Full Text\n\nSong I, Han K, Ryu J, et al.: Coffee Intake as a Risk Indicator for Tooth Loss in Korean Adults. Sci. Rep. 2018; 8: 2392–2397. PubMed Abstract | Publisher Full Text\n\nBramantoro T: PRISMA_2020_checklist The contradictory effects of coffee intake on periodontal health- a systematic review. figshare. Dataset.2022. Publisher Full Text\n\nBramantoro T: PRISMA Flowchart. figshare. Figure.2022. Publisher Full Text\n\nBramantoro T: Table - The contradictory effects of coffee intake on periodontal health- a systematic review. figshare. Dataset.2022. Publisher Full Text"
}
|
[
{
"id": "152682",
"date": "11 Oct 2022",
"name": "Ananto Ali Alhasyimi",
"expertise": [
"Reviewer Expertise Orthodontics",
"Biomechanics",
"Local material"
],
"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 of this study have investigated the systematic review of coffee consumption impact on periodontal health status. The authors of the study came to the conclusion, based on the findings of the research, that the effect of coffee consumption on periodontal health was fragmented due to the complex components that coffee contains, each of which has the potential to either give positive effects or have a negative impact on periodontal health. The findings have a number of intriguing implications, and the authors deserve praise for carrying out this research.\nNonetheless, the authors need to resolve some minor difficulties such as the following:\nGeneral The manuscript's content is relevant to the journal's scope and presents novel findings. The study results are significant enough to be worth reading about and have a high impact on Dentistry field The title explains clearly what the manuscript is about and draws attention to the significance of the research findings. Introduction was well-written, indicate a gap, raise a research question. The author(s) carefully explain the goal of the study and announce the current research, emphasizing what is new and why it matters while also providing up-to-date references.\nMethods Reviewers should take care to minimize potential for bias and weed out unimportant or poorly conducted studies. The authors have followed the procedures for conducting a good systematic review, which include things like coming up with a good clinical question to answer, creating a protocol (with inclusion and exclusion criteria), conducting a thorough and extensive literature search, and screening the abstracts of the studies found in the search, before moving on to reading the selected full texts (PRISMA).\nResults Clear, accurate, and well-presented results that are in line with the methodologies used are presented. Discussion and conclusion. The Author(s) logically explained the findings and compared the findings with current findings in the research field. The implications of the findings for future research and potential applications were clearly mentioned. Strengths, limitations, and recommendations were also mentioned detailly. Author(s) writes the conclusion: “The effect of coffee consumption on periodontal health was fragmented since coffee has complex components that may give either beneficial effects or negative impact on periodontal health. Drinking coffee in routine and in a proper dosage may give benefits on periodontal health, but it also potentially has detrimental effects if excessive dosage consumed.” Maybe you can add the optimum dose and a safe/proper dose coffee consumption daily.\nReferences Needs improvement. Some of abbreviations journal were not write properly. Ref no 2 is not accurate. Ref 18 & 18 has not mentioned the name of journal.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "8896",
"date": "13 Oct 2022",
"name": "Taufan Bramantoro",
"role": "Author Response",
"response": "Thank you for the valuable advices. The new version has been uploaded."
}
]
},
{
"id": "150488",
"date": "19 Oct 2022",
"name": "Mohammed Aljunaid",
"expertise": [
"Reviewer Expertise Oral",
"Dental Medicine and Periodontology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you very much for giving me the opportunity to review this article, I have completed my evaluation and after reading this Systematic Review carefully I am of the opinion that this manuscript should be considered for indexing.\nThe idea is very well-conceived and presented clearly, objectives are well organized, and results are completely justifying the hypothesis.\nIn general, this manuscript provides sound information and a good contribution in the field dentistry, the study has investigated the systematic review of coffee consumption's impact on periodontal health status.\nAbstract: The abstract seems highly well. Methods, results, and conclusions are correlated to the study and are understandable.\nIntroduction: The literature was clearly stated for publication, but the authors should improve the aim of study.\nMethods: Methods are comprehensive, and I do believe they cover the idea.\nResults: The results could cover the objectives.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "8927",
"date": "24 Oct 2022",
"name": "Taufan Bramantoro",
"role": "Author Response",
"response": "Thank you very much for the advice. We have rewritten our aim to be more specific. Thank you."
}
]
}
] | 1
|
https://f1000research.com/articles/11-924
|
https://f1000research.com/articles/11-1261/v1
|
07 Nov 22
|
{
"type": "Research Article",
"title": "Risk factors and housing effect on malaria infection: A case-control study",
"authors": [
"Noor Alis Setiyadi",
"Ira Handayani",
"Sayono Sayono",
"Tepanata Pumpaibool",
"Irfanul Chakim",
"Noor Alis Setiyadi",
"Ira Handayani",
"Sayono Sayono",
"Tepanata Pumpaibool"
],
"abstract": "Background: This study aims to demonstrate the different risk factors between low and high endemicity area and housing effect on malaria infection. Methods: This study is a case-control study with a ratio of 1:2 comparing low (Jambi) and high (Sumba) endemicity areas. Initial screening of malaria was done to assign cases and controls following inclusion criteria. The selected cases and controls were then assessed with a structured questionnaire in relation to risk factors of malaria infection. Additionally, to discover the impact of house type on malaria infection, a total of 72 houses was observed in a series of six weeks (between 28 June and 12 August 2018) human landing catch (HLC) observations that includes three types of houses; malaria, non-malaria, and permanent dwellings. The HLC was done indoors and outdoors for each house type each night. A weekly screening was taken to monitor the malaria infection rate of each house type. Results: Jambi and Sumba shared several similar individual and environmental risk factors. However, agricultural activity or visiting forestry areas is a protective factor for malaria infection in Jambi but is a risk factor in Sumba. The general linear mixed univariate model result indicates the difference in risk factor variables between Jambi and Sumba. The entomological survey found that only malaria houses significantly differed in the number of means collected mosquitoes compared with the other type of houses. Weekly screening found that the incidence rate of malaria houses is highest among others. Conclusion: The risk factors are inevitably crucial for malaria prevention strategy. Risk factor management needs to consider the location where the endemicity level may differ for each risk factor, and housing improvement is not a proper strategy before controlling other environmental factors.",
"keywords": [
"Risk factors",
"different endemicity areas",
"housing effect",
"case-control",
"malaria."
],
"content": "Introduction\n\nMalaria is a disease that is not solely transmitted by itself, instead, it requires a specific vector to successfully inject itself to the host body. Theoretically, this is based on a causal concept of epidemiology that the occurrence of a diseases depends on three primary factors: (i) the host, (ii) the agent, and (iii) the environmental factors. Studies in the Amhara region, the northwestern part of Ethiopia, suggested an insight into critical factors comprising malaria risk. In general, three factors have been recognized to be the key factors deriving malaria risk: climate variables, entomological parameters, and human population dynamics. The impact of climate variables is inevitably accounted for as a potential circumstance in malaria transmission, as it known to be an enhancement factor of malaria transmissibility due to increasing vector capacity by providing potential sources of breeding places, increasing mosquito longevity, and feeding rates.1–11 It is plausible that the interconnection of co-factors such as environmental constraints affecting the entomological and parasitological constituents enhance the transmissibility of malaria. However, a broad range of influences could drive the transmission pattern of malaria from either humans or the vector.10,12 Therefore, instead of controlling the impact of climate change, upgrading public health interventions and socioeconomic conditions might better affect malaria.13\n\nBesides climate change, whose alterations on various aspects have been well documented, another essential variable driving malaria transmissions are the entomological parameter and human population dynamics. Biological and behavioral variations of mosquito species, such as vector-habitat relationships; factors affecting vector population abundance; host-seeking behavior; and the emergence of vector resistance to insecticides, have been known to affect the transmission pattern of malaria.7,14–16 Endophilic mosquitoes tend to feed and rest indoors, thus poorly constructed dwellings and close proximity with vector breeding sites along with human’s behavior attracting mosquitoes such as unprotected sleep and placing their livestock in the house intensify the chance of mosquito contact.17 However, there is an observed behavioral change in the feeding habits of mosquitoes from endophilic to exophilic and its feeding time from late evenings to early evenings.18,19 It is also possible that vector control intervention could change the natural behavior of mosquitoes from endophilic to exophilic which is caused by avoiding control strategies such as insecticide exposure which are usually utilized inside human dwellings.18,20,21 On the other hand, the human population dynamic also becomes a potential source of malaria transmission by increasing the likelihood of spreading the disease mainly through import cases. The imported cases can either be from recent migration or short-term travel.22,23 A study report from Ethiopia in the 1980s found that a large population movement affects high transmission rates of malaria.24 This large movement of the human population might have a close relationship with agricultural work,25 and these immigrant workers are more likely to live in non-permanent houses, which are vulnerable to mosquito bites, and occasionally sleep outside, as well as having inadequate information about malaria risk.22,26 A difference in practical agricultural activities as suitable habitats of vector mosquitoes may be the predisposing factor of malaria transmission.20 Additionally, an untraceable small number of mobile sub-population groups might delay the malaria elimination strategy due to its higher risk of infection or might even re-introduce malaria in previously eliminated areas.22\n\nMoreover, besides evidence from Ethiopia, plenty of studies have associated several other risk factors influencing malaria transmission, mostly published in recent years.27–38 In the late’90s, it was known that the older the patient, the less the incidence of malaria as well as less knowledge of malaria prevention. Several other associated factors were included such as exposure to forests and receiving previous antimalarial treatment.27,39 Bed nets could not be a very effective protective measure in a setting such as the environment in which this study was done; environmental intervention may be better applied.27 In pregnant women, the associated factors of malaria infection are lack of education, and non-possession of insecticide-treated nets (ITNs) followed by a decrease of parasite density as age increased.28 Children under the age of five years were also particularly at risk of being infected by malaria parasites, especially in sub-Saharan Africa.29 The associated risks of this particular at-risk population are mostly sociodemographic related factors such as the main floor and main wall material of the house and availability of electricity. However, indoor residual spraying (IRS) significantly reduced a child’s risk of malaria, with additional information that older children have a higher risk of malaria, notwithstanding that their risk decreases with increases in cluster altitude and their caregiver’s education level.30 Another study showed an exciting method to discover the associated factors of malaria infection. Pinchoff et al.,31 used a case-control approach based on positively detected incidence by a rapid diagnostic test (RDT) with a sophisticated statistical method. They found that, in multivariate model generalized by generalized estimating equations (GEE), the odds of being RDT positive are highest in five-17 years old (8.83 odds compared to 18 years old (or more)) and do not vary between seasons. Additionally, there is an interaction between age and report of symptoms, with an almost 50% increased odds of reporting symptoms with decreasing age category. Instead of using a case-control approach, Elijah Chirebvu et al.,32 uses a more convenient method over which the history of malaria infection is an independent variable and found that the correlated factors of malaria are household income, late outdoor activities, time spent outdoors, travel outside of the study area, non-possession of ITNs, hut/house structure, and homestead location from bodies of water. In addition, the proximity of a health facility and low vegetation cover are advantageous protective factors.\n\nAnother interesting study by Kazembe et al.,33 used a spatial regression analysis to estimate risk factors. These findings based on regression estimation found that the children who visited rural areas have six times the risk of being infected by malaria parasites, as with previous findings the higher the age of the children, the more the likelihood of being infected notwithstanding that the risk reduces as individuals gain a higher sociodemographic status. Proximity to a garden, river, or standing water are not associated but act as a cofactor of increased risk. Furthermore, this study showed that a spatial cluster of households of the infected patients affects the risk of transmission which may be explained by the variability of the environmental factors. A group of researchers,34 using a secondary database on a nation-wide scale with a regression model, found that wealth status is the first socio-economic factor which mostly contributed to the difference of malaria risk among African children. They did not find any demographic factor among the associated variables. On the other hand, sex of child and river or water body proximity are not associated with the risk of being infected with malaria. The country of resident and temperature could be a cofactor in the analysis with supplementary information of negative associations between population density and malaria incidence. One thing that should be noted, is that the study completed a comparison study of differing malaria risk and found there are several differences in associated variables between low and high-risk countries.34\n\nIn Indonesia, such risk factors have not been extensively discovered. Several studies were attempting to determine the associated factors of malaria. Based on active and passive surveillance assessing three common species of malaria in Aceh, a study35 found that the related factors are male (AOR 12.5), adult (OR 14.05), visiting the forest within the previous month regardless of the reason (OR 5.6), and working place located in the forest with overnight stays (OR 7.9). In Papua a study36 adopting the Bayesian hierarchical logistic model found that rural Papuans, as well as those who live in poor, densely forested, lowland districts, are at higher risk of being infected of malaria with the additional information of nine areas on the island having higher-than-expected malaria risks. Environmental factors such as the distance of the resident to forest areas, altitude, and rainfall are also associated with malaria. These environmental factors were also found to be strongly varied spatially in different regions.37 Additionally, a case-control study in the Purworejo district has found that not sleeping under a bed net and not closing doors and windows from 6 p.m. to 5 a.m. are associated with higher risks of malaria.38 With that limited information on malaria risk factors and the fact that there are such varying associated variables, the current study has an objective to uncover the risk factors with a broad categorical variable including individual and environmental factors. To strengthen the differences between low and high-countries as well as spatial effect of malaria, this study also included a comparison of risk factors between different endemicity areas. Additionally, to prove the risk of the sociodemographic factor, a series of entomological observations that include house type materials and condition was also included.\n\n\nMethods\n\nThe local community and house owners gave permission for conducting this research in their surroundings and properties. This study was approved by the ethics commission of Hasanuddin university, Indonesia with ethical approval number: 663/H4.8.4.5.31/PP36-KOMETIK/2016. Written informed consent was obtained from all participants and mosquito collectors.\n\nThe design of the current study was case-control with a 1:2 ratio. There were four stages in this study; field malaria sampling, assessment of malaria risk factors, entomological survey, and mosquito species identification and plasmodium detection. Field malaria sampling was done for the purpose of assigning cases and controls in accordance with researchers’ criteria. The assigned cases and controls were then examined using a structured questionnaire to assess the associated malaria risk factors. A series of entomological surveys was then conducted in order to understand the effect of house type on malaria infection. There were three types of houses included in this study, namely; malaria houses (it was a non-permanent house where malaria was present at least once in the duration of one year back from the point this research started); non-malaria houses (it was a non-permanent house where malaria was absent in the duration of one year back from the start of this research); and permanent houses (it was a well-constructed house where all parts of the house closed properly). A series of human landing catch (HLC) observations were performed on these three types of houses every day for three weeks. Additionally, weekly screening on these three types of houses was carried out to monitor malaria incidence in each house type. Finally, the collected mosquito and blood samples were transferred to the laboratory for species identification and plasmodium detection.\n\nParticipant recruitment\n\nField malaria screening was done using tympanic temperature, rapid diagnostic test (RDT) and microscopic slide examination. People who tested positive for malaria by RDT, microscopic examination, or a combination of the two were identified, and those who met the eligibility criteria were designated as cases. Those who did not meet the eligibility criteria as cases were assigned as controls.\n\nEligibility criteria\n\nSince we used a total sample, all positively detected malaria people were included in this study unless they refused or were unwilling to complete all the study protocols. In the case of children, the guardians were asked for their willingness and ability to participate in this study.\n\nMethods of selection\n\nThe selection of controls was by criteria of an absence of malaria infection for at least a one-year period. To avoid geographical bias in controls that may lead to different vectorial capacities, the controls were selected based on their closest location by distance to the selected cases.\n\nField malaria sampling was conducted in two localities from the western and eastern part of Indonesia, namely Jambi province and Sumba Island as part of Nusa Tenggara province. The sampling activity was from 1st February until 31st October 2018. According to the national data of the Ministry of Health of Indonesia in 2016, Jambi province has an annual parasite index of 0.14 per 1,000 inhabitants, and Nusa Tenggara province has 5.41 per 1,000 inhabitants.40\n\nMalaria screening was initially undertaken based on tympanic temperature. The screening was performed daily from 1 February 2018-31 May 2018 in Jambi, and from 1 June 2018-31 October 2018 in Sumba. Following the STROBE reporting guidelines, this study investigates the relationship between exposures and a health outcome. The exposure in this study was set as the risk factors, which were divided into two risk factor categories; individual and environmental exposures. A person who had a tympanic temperature of more than 37.5 was selected to be tested for the possibility of malaria infection. A finger prick for both microscopic slide and filter paper was taken after tympanic temperature screening. The slide was examined by two independent microscopists. Following up on the results of microscopic examination, positively detected malaria patients were treated with dihydroartemisinin+piperaquine tablets based on body weight and age as recommended by the Ministry of Health, Republic of Indonesia.41 All patients in our study sites were closely monitored to observe the medical condition of the patients due to malaria and potential re-infection.\n\nRisk factors of malaria were examined by structured questionnaire comprised of both individual and environmental variables.80 The structured questionnaire was developed and created by the researcher. The questionnaire that has been created was then tested for content validity by two independent reviewers. Initially, an unpublished systematic review has been done to discover all possible risk factors associated with malaria. The risk factors were then categorized as two observational points; ‘individual’ and ‘environmental’. The ‘Individual’ section in the questionnaire is comprised of demographic and behavioral variables such as level of education, possession of mosquito nets, and spending nights in the forest. The ‘environmental’ section in the questionnaire consists of observable environmental risk factors such as the absence of gauze and closed ceilings in the house, the existence of shrubs, and the existence of livestock near the house. A day after malaria infection had been confirmed in each respondent, the researchers visited the respondent’s house to assess malaria risk factors using the structured questionnaire. The ‘individual’ section was obtained by interviewing the respondent using the questionnaire. The questionnaire was originally made in the Indonesian language, and thus the interview process with participants used the Indonesian language. All participants were able to complete the interview process. The researchers only assisted in filling out the form based on the answers provided by the participants. As soon as the interview was over, the researchers then assessed the possible risk factors in and around the house following the questionnaire. There are 12 environmental and 15 individual variables examined in the current study. The environmental factors are as follows: without gauze or barrier on ventilation, the existence of shrubs, no predator fish in the stagnant water, the presence of livestock inside household, the presence of any livestock nearby house, household wall material, the presence of puddle/stagnant water, the presence of rice field, house floor construction is not permanent, the presence of a ceiling of the house, hanging clothes inside the house, and the presence of a pool of water. On the other hand, the individual factors are: night activity outdoor, possession of bed nets, using mosquito repellant, using any kind of insecticide/pesticide, education level, previous antimalarial drug consumption, salary less than one million-rupiah, type of occupation, contact with malaria patient, high mobility, sex, age, visited a forest from previous month for any reason, working place is in the forest and requiring overnight stay.\n\nThe entomological survey of the current study was done for the purpose of observing the possible difference of mosquito bites between malaria, non-malaria, and permanent houses. A malaria house is defined as any non-permanent house that had a malaria infection at least once in the one-year period before the research started. A non-malaria house is defined as a non-permanent house that had no malaria infection in the one-year period before the research started. A permanent house is defined as any permanent house, properly closed, near malaria and non-malaria houses. A village with the highest incidence rate among our study sites was chosen to be the location of the entomological survey. According to the above-mentioned definition of three types of houses, the researchers then assigned the houses that match the definition. The data used for house selection was from routine screening by the local health office. A purposive sampling was performed to pick up malaria houses. The criteria used for this purposive sampling is the location with the highest malaria incidence and density. Non-malaria houses were selected by the nearest location to the malaria house to avoid distance bias. Due to limited number of permanent houses in study sites, purposive sampling was done and the nearest permanent houses to malaria house were selected. Malaria and non-malaria houses were the same house type, as non-permanent or not well-constructed houses. Because of the observational measurement of malaria cases, this entomological survey will support the finding of the malaria risk factors in which is often correlated with human dwellings. This survey was initially started by a week of pre-observational human landing catch (HLC) and then followed up by up to three weeks of a comparative observational HLC survey between the three types of houses. Pre-observational HLC was done to objectively select the location with the appropriate number of Anopheles species. To avoid disparity of mosquito species and abundance and indeed biases, the distance of the three kinds of houses has been set up not to exceed two km. The result of the initial screening was used to differentiate between malaria, non-malaria, and permanent dwellings. Non-malaria and permanent houses were defined as houses with an absence of malaria infection for at least one year prior to the screening. Additionally, to confirm the presence or absence of malaria infections, weekly screening was conducted throughout the study. If a malaria infection was detected in non-malaria and/or permanent houses, then the house will be excluded completely and a new household will be selected and included in the study. After initial screening, the selected houses were numbered and picked randomly for weekly HLC. In detail, a weekly schedule was made by shuffling the house number each day. Each day had four houses to be enrolled in. At the end of each week, a new shuffle was made with the same strategy repeatedly until the end of the research period. There were two houses per house types per day (two for malaria, two for non-malaria, and two for permanent houses). Two houses per group were necessary because it required human bait inside and outside the house to encompass both endophilic and exophilic mosquitoes. There were 12 houses in total per house types (six days of collection per week). However, with three repetitions (three weeks), the total sample was 36 houses per house types. Shuffling and repetition were done to avoid a disproportionate number of mosquitoes per house.\n\nMosquito species from the HLC survey were detected by an entomologist from Eijkman institute for Molecular Biology, Jakarta, under dissecting microscopy following a previously published species identification key.42 To confirm the species from an entomologist, randomly chosen samples were subjected to molecular examination using Internal transcribed spacer 2 (ITS2) primers. Afterward, to detect the presence of Plasmodium in the mosquito saliva, a mitochondrial based primer was used according to previous publication. For this molecular examination, we used MytaqTM HS Red Mix. The PCR mix contains purified DNA samples (1 μl per sample), double distilled water (10.7 μl), primers (0.4 μl) and MytaqTM HS Red Mix (12.5 μl). The PCR condition is as follows: 95° one minute of initial denaturation, 95° 15 seconds of denaturation, 54° (ITS2) and 48° (mitochondrial DNA for Plasmodium) of annealing, 72° 10 seconds of extension, 72° 15 minutes of final extension, and 4° for holding. The amplified product of PCR was then visualized in Biorad Gel documentation XR imaging system. The successful amplified product was then purified using ExoSAP-IT cleanup reagent to remove primers and dNTPs. The PCR reaction was run with Big-Dye terminator RR Mix and purified to remove dye-ddNTPs. Eventually, the samples were sent to the Biochem sequencing facility. After samples were successfully sequenced, the results were delivered and analyzed.\n\nChi-square X2 and logistic regression were used to determine the relationship of each variable with malaria bivariate and multivariate, respectively. Additionally, a general linear mixed analysis was carried out to discover the potential difference in terms of risk factors variable between Jambi and Sumba by summing all associated variables into a total variable with conditioning the number of cases and controls (prospective cases from Sumba and all cases from Jambi). IBM SPSS v20.0 (Chicago, SPSS Inc.) was used to run the statistical analysis both bivariate and multivariate. Logistic regression was done for univariate analysis to find the strongly associated independent variables with the risk of malaria infection. level of significance of p < 0.05 was determined for the association threshold. In order to find a different in associated variables, GLM (generalized linear model) analysis was applied. The GLM analysis was set to equate starting from the number of cases and control and the only associated variables that the sites share in the same manner. Kruskal-Wallis was used to determine the difference in each house type of HLC survey. For the visualization of the data, we used Graph Pad Prism 7. For molecular data, the result of Sanger sequencing was then sent to the National Center for Biotechnology Information (NCBI) website to blast with the genomic data bank.\n\nFollowing the STROBE reporting guidelines for case control study, several potential sources of bias have been identified and addressed. First, to avoid an uneven distribution of risk factors between cases and controls, we have added a comparison of 1:2 between cases and controls. Second, the questionnaire was carefully arranged and validated to avoid low reliability and validity. Third, in order to minimize the imbalanced number of vectors in the HLC site, we set up the HLC site so as not to exceed 2 km. Fourth, to prevent bias in HLC houses, a malaria weekly screening was conducted, and if the screened house was malaria positive, it was then excluded and replaced. Fifth, to prevent bias in HLC houses, a strict randomization protocol was undertaken.\n\n\nResults\n\nThis research had a study duration of four months in Jambi, the western part of Indonesia, and another four months in Sumba Island, the eastern part of Indonesia, from February to October 2019. The total of 157 cases of both locations were successfully collected during the field sampling time.80 The proportion of case and control was following a 1:2 ratio. Therefore, out of 158 cases, there were 328 controls with a percentage of 32.3% and 67.7%, respectively. The basic demography of each location is presented in Table 1. The proportion of sex between Jambi and Sumba have a slightly similar pattern of male and female. The age strata from the two sites are identical at six-24 years. However, Sumba has more cases in children (0-5 years).\n\nSeveral individual factors from both Sumba and Jambi have been associated with malaria incidence (Tables 2 and 3). In Jambi, night activity outdoor (OR = 0.32; CI: 013-0.79), history of visiting forest areas in the previous month (OR = 0.35; CI: 0.15-0.84), and working place is located inside the forest (OR = 0.17; CI: 0.07-0.43) were protective factors against malaria infection. The individual risk factor for malaria infection in Jambi were not having a bed-net for sleeping (OR = 2.09; CI: 1.04-4.18), low level of education (OR = 1.01; CI: 0.29-3.45), occupation (P value = 0.000), and contact with malaria-infected patient (OR =. 3.37; CI: 1.62-7.01). The observed environmental factors that are associated with malaria in Jambi are the existence of shrubs around house areas (OR = 28.00; CI: 6.45-121.59), the existence of puddles or stagnant water around the house area (OR = 2.49; C I: 1.05-5.98), the presence of livestock nearby the house area (OR = 6.36; CI: 2.94-13.79), and the proximity of houses to forestry areas (OR = 10.84; CI: 3.97-29.58). There were eight associated individual variables with malaria from Sumba. The risk factors of malaria in Sumba are not having a bed net for sleeping (OR = 2.55; CI: 1.52-4.29), low level of education (OR = 6.09; CI: 2.12-17.47), never consumed antimalarial drug (OR = 4.16; CI: 2.09-8.28), if they ever had contact with malaria person (OR = 17.33; CI: 8.04-37.32), frequent traveling outside of the residential area (OR = 5.22; CI: 2.32-11.74), if they ever visited the forest in a previous month (OR = 1.96; CI: 1.03-3.73), and requiring an overnight stay in the forest (OR = 2.88; CI: 1.22-6.81). Additionally environmental risk factors associated with malaria are existence of shrubs surrounding house (OR = 20.99; CI: 8.24-53.46), existence of puddles or stagnant water surrounding the house area (OR = 39.98; CI: 13.86-115.32), existence of livestock inside house (OR = 3.24; CI: 1.70-6.18), existence of livestock nearby house (OR = 9.44; CI: 2.87-31.07), non-permanent house wall (OR = 5.22; CI: 1.81-15.06), non-permanent floor construction (OR = 20.79; CI: 2.81-153.79), house is in a close proximity to rice fields (OR = 14.69; CI: 0.75-286.96), and not having a ceiling of the house (OR = 19.72; CI: 1.18-330.29). Since Jambi and Sumba have different endemicity level, the generalized linear model (GLM) was applied to discover if any difference in risk factor variables from both sites. Due to any difference in the number of cases of both locations, only prospective cases from Sumba were included in the analysis. Prospective cases are those who enumerated within five to seven days after being confirmed by a rapid diagnostic test or the result from two independent microscopists or combination of both. The result of GLM indicates that there is a difference in risk factor variable from both Jambi and Sumba (P value = 0.002) (Table 4).\n\nIn order to discover the effect of house type with malaria infection, a series of entomological observations were carried out as described in the methods section. A total of 2,435 Anopheles mosquitoes were successfully collected from both sites. Out of the total collected Anopheles, 2.9% (71) is from Jambi, and the rest 97.1% (2,364) is from Sumba. Jambi was dominated with Anopheles balabacensis (79%), followed by other species; An. Maculatus (18%), An. barbirostris (1.41%) and An. sinensis (1.41%). Two species accounted to 40% and 58% of the total mosquitors catched in Sumba, An. aconitus and An. Sundaicus, respectively. The other species found were An. maculatus (1.06%), An. subpictus (0.17%), An. barbirostris and An. vagus (0.084%) and An. farauti and An. leucosphyrus (0.04%). No plasmodium was detected either from salivary nor abdominal part of the mosquitoes over 250 randomly selected mosquitoes from both Jambi and Sumba.\n\nThere is a significant difference between the total number of mosquitoes collected from Jambi and Sumba (P value ≤ 0.0001) (Figure 1). As explained in the methods section, this entomological observation characterized the houses into three types: malaria houses, non-malaria houses, and permanent houses. There is no significant difference in each house types from Jambi (P value = 0.1856). Although malaria houses from Jambi have the highest mean collected mosquitoes (0.64) than the other house types, permanent house types (0.34) have a higher mean of collected mosquitoes than the non-malaria house (0.29) (Figure 2). On the contrary, there is a significant difference between malaria-houses vs non-malaria houses (P value = 0.0143) and permanent houses (P value = 0.0351) in Sumba as presented in Figure 3. However, no difference was observed between non-malaria houses and permanent houses (P-value ≥ 0.9999). Additionally, if both sites are combined (Figure 4), only malaria-houses and non-malaria houses have a significant difference in the number of collected mosquitoes (P value = 0.0301). Permanent house type is slightly higher in the mean number of collected mosquitoes compared to non-malaria houses (5.6 and 5.032, respectively).\n\n(P value ≤ 0.0001).\n\n(P value = 0.1856).\n\nMalaria-houses vs non-malaria houses (P value = 0.0143) and permanent houses (P value = 0.0351).\n\nMalaria vs non-malaria houses (P value = 0.0301).\n\nDuring the entomological observation, weekly malaria screening was conducted to ensure the presence or absence of malaria in each house types as well as to discover the incidence rate of each house types. Malaria has detected only one in the first week from Jambi. Otherwise, 10 cases were detected during three weeks of observation from Sumba (Table 5). If the number of cases is transformed into an incidence rate per collection method per year, then malaria houses from Jambi have 1.4 incidence rate per year and null for other types of houses. However, considering the difference in the endemicity level in Sumba, malaria houses have 8.7 incidence rate per year while non-malaria and permanent dwellings have the same rate of 2.9. Additionally, based on the calculated odds ratio, the odds of malaria houses compared to other house type is 3.77 (CI: 0.76-18.81) while non-malaria versus permanent houses have the odds of 1 (CI: 0.14-7.30).\n\n\nDiscussion\n\nBased on the Indonesian basic health profile, Jambi was categorized to have low cumulative incidence, while Sumba as part of Nusa Tenggara province has high cumulative incidence.40 By transforming the total number of collected cases in each location, Jambi and Sumba, then both sites have a high cumulative incidence of malaria (5.4 and 15.7, respectively). There is a discrepancy of classifying endemicity level between national data and the collected data from the current study. This phenomenon partly can be explained by the different denominators of the data, as national data considers a total number of populations in a provincial level rather than each sub-district level. Considering the fact that malaria varies greatly between sub-district and district and is not uniformly distributed, this may be the case.43,44\n\nOne of the interesting findings of the current study is the different patterns for the source of infection between Jambi and Sumba. Night activity outdoor, history of visiting forest areas from the previous month, and working place is located inside the forest are protective factors in Jambi, while the history of visiting forest areas and requiring an overnight stay inside a forest are risk factors in Sumba. This finding suggests that most of the case from Jambi was infected in the residential areas and forest areas were the source of malaria infection from Sumba. This finding underline that visiting forest areas are not always a risk for malaria infection as previous research has found.32,35,36,39 The phenomenon may be explained by the relationship of human and mosquito infection over which may be caused by uneven distribution of mosquito bites across the human population. For example, a study showed that in several areas a core group of the human population receive a substantial proportion of mosquito bites.45 Additionally, another finding indicates that a group with more individuals experiences a lower rate of mosquito bites.46\n\nJambi and Sumba share the same individual risk factors, namely no possession of bed net for sleeping, low education level, and if they ever contacted a malaria infected patient. It is common that bed nets and low education levels are a risk factor for malaria as previously discovered.28,32,38 The effective impact of bed nets has been extensively described in previous studies.47,48 Although defining the coverage of the bed net use is problematic.49,50 The effect of education on malaria infection has also been found from the previous study.28 Studies have demonstrated that the poor performance of children at school is a risk of malaria, and if knowledge of prevention is adequately elevated it will lower the incidence of malaria.51,52 While other researchers found that the performance of education may be temporary and not prolonged.53 Additionally, most of the cases had contact with the other cases being compared to control suggesting that they may have an infection during the interaction process. Considering the proximity of the distance of houses as neighboring, cases may also sleep in the same house or be involved in a late conversation or another way of interaction in which mosquitoes could bite them simultaneously.\n\nThere are several differences in individual risk factors between Jambi and Sumba. Occupation is statistically significant to be the risk factor of malaria in Jambi. This finding is in line with the previous discussion where most of the controls are a farmer that require them to go to the forestry areas. Most of the cases have an occupation that needs them to reside in the housing area such as a midwife, workshop worker, or odd jobs. On the other hand, in Sumba, having never consumed antimalarial drugs and traveling outside the residential area are the risk factors of malaria infection. Considering the effectiveness of the current antimalarial drugs, the higher number of antimalarial drug consumption in cases is since the majority of the cases may have re-infection that requires them to be prescribed with frequent antimalarial drug. It was described that re-infection is a common situation in a high transmission area.54 The risk of traveling outside residential areas with malaria infection is in line with a previous study.32 The participant of the current study may have traveled in neighboring villages in which infection rate are high. There are several studies that have demonstrated the risk of traveling into a high infection rate area.55,56 A reporting system need to be established to identify import cases from neighboring villages or areas.57,58\n\nThere are several same environmental factors between Jambi and Sumba, i.e., the existence of shrubs and puddles/stagnant water surrounding the household area and the presence of livestock near the house area. Studies have found that bushes are a risk factor in a densely forested area and can encourage mosquitoes to breed.31,59,60 Since case and control resided in a densely forested, basic biological attributes of the vector may play a role. It was shown that shrubs promote the malaria transmission capacity by providing an abundant source of sugar for the male mosquito while lack of sugar source contributes to lower insemination rate to females.61,62 Moreover, as observed in An. gambiae, Anopheles mosquitoes are distributed among dense growths of brush.63,64 They may rest in the shrub prior to get ready to bite. The existence of puddles/stagnant water was found to be a potential breeding place where Anopheles mosquito could oviposit.65–68 Although, evidence has suggested that no or low Anopheles larvae density is found when water is identified as turbid as puddles, drains, or swamps.69 As previously described, the existence of livestock nearby the house area increases the chance of mosquito contact.17 It was previously found that the presence of livestock at the household level can significantly alter the local species composition, feeding and resting behavior of malaria vector.70 However, the net impact of livestock-associated variation in malaria vector ecology on malaria exposure risk was unknown.70 In addition, the pattern of host attraction and biting behavior of Anopheles mosquito in Indonesia has not been yet extensively studied and only limited to one locality.71 Anopheles mosquito can be attracted to livestock even with the primary vector of malaria, because of their biting preference as zoo-anthropophilic species.72 Furthermore, placing livestock inside the house is also significantly correlated with malaria in Sumba, suggesting a different cultural behavior of tethering livestock inside. Our study demonstrates the importance of controlling malaria using livestock-based intervention or using any zoo-prophylactic agent as described elsewhere.73,74\n\nHouse construction has been associated with malaria in Sumba such as non-permanent house walls, non-permanent floor construction, and not having a ceiling of the house. Such factors are in line with the previous report regarding the associated demographic factor of malaria infection underlying the importance of human dwelling construction.17,29 However, this finding may not be the case since there is a difference with entomological finding as discussed below. Additionally, the proximity of the house to forest areas and rice fields are the risk factor for malaria in Jambi and Sumba, respectively. As discussed previously, housing location in proximity to lower vegetation cover is the protective factor for malaria.32 Jambi and Sumba have different agricultural activity. Most of the people from Jambi work on rubber and palm plantations that require a large area of land, a single person could only handle five-10 hectares. On the contrary, Sumbanese people are mostly working on cashew or rice which requires a relatively limited space of land. Agricultural activities have been shown to be a predisposing factor for malaria in which suitable habitat of the vector may take place.20,25 It was previously described that rice field agro-ecosystems contributed significant vector populations.75,76 However, with the same densely forested areas, the source of infection is different between the two sites as noted in the above discussion.\n\nPrevious studies have found differences in associated variables between low and high-risk countries.34 As well as environmental factors, these are also varied across spatially different regions.37 In order to strengthen this fact, in the current study, we selected a different annual parasite index area for comparison. Based on GLM, there is a significant difference in the risk factor between Jambi and Sumba. The GLM analysis was set to equate starting from the number of case and control and the only associated variables that the sites share the same manner. It suggests that the frequency of risk factor variables between Jambi and Sumba is in a different state following its differing annual parasite index (API). Additionally, considering the fact of the different number of associated individual and environmental variables between Jambi and Sumba suggests that a high API area like Sumba has more diverse risk factors than low API area.\n\nFinding from the current study and the other indicates that housing construction is associated with malaria infection.77 Others recommended that improved housing is a promising intervention for malaria.78,79 However, our entomological observation found that housing construction does not necessarily lead to decreased risk of Anopheles bites. Only malaria houses were found to be significantly different with non-malaria or permanent and non-malaria houses. Permanent house types had a higher mean number of collected Anopheles mosquito than non-malaria house regardless of the sites. This finding is also supported by malaria infection rate of the house types that malaria house type is higher than the two types of houses while non-malaria and permanent houses share the same number of infection rate. This phenomenon can be best explained by the existence of risk factors other than only housing types such as the presence of livestock, shrubs, puddles/stagnant water, or housing localities. As long as the other environmental risk factors are not controlled then the housing improvement program may not be effective as stated in the previous findings.78,79\n\nDespite the findings given from this study, there are some limitations that need to be addressed in the future. The number of samples is not equal between the two locations where Jambi is substantially low. Due to an extremely low number of cases, a convenience sampling technique was performed, thus leaving inadequate analysis for Jambi. It is also necessary for future research to increase the number of samples of houses for mosquito density in each house type. Finally, to find the best association model, future research needs to consider matching analysis when performing a case-control study for malaria risk factors.\n\n\nConclusion\n\nIn the current study and the others have demonstrated that risk factors play a notable role in the malaria infection. In summary, there is information on our findings for malaria control strategies1; visiting forested areas is not always a risk factor for malaria as a source of infection may differ between location,2 livestock-based intervention or using any zoo-prophylactic agent is inevitably effective to avoid mosquito attraction regardless of the area,3 improving dwelling strategy may not be successful before controlling other environmental factors, and4 risk factors are site-dependent suggesting that applying risk factor management need to consider the endemicity status of an area.\n\n\nData availability\n\nZenodo: Risk factors and housing effect on malaria infection: A case-control study. https://doi.org/10.5281/zenodo.6960903.80\n\nThe project contains the following underlying data:\n\n• Jambi gabungan.pzfx (It contains data on the number of mosquitoes collected per house type in Jambi)\n\n• Jambi vs sumba T-test.pzfx (it contains on total number of mosquitoes collected regardless of the house type in both Jambi and Sumba)\n\n• Sumba gabungan.pzfx (It contains data on the number of mosquitoes collected per house type in Sumba)\n\n• Sumba-jambi gabungan 2.pzfx (it contains combined data on the number of mosquitoes collected per house type in Jambi and Sumba)\n\nZenodo: Risk factors and housing effect on malaria infection: A case-control study. https://doi.org/10.5281/zenodo.7040054.80\n\nThe project contains the following underlying data:\n\n• Supplementary questionnaire.docx (English questionnaire used in this research).\n\n• Supplementary questionnaire.docx (Indonesian (originial) version of the questionnaire used in this research).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: STROBE checklist for ‘Risk factors and housing effect on malaria infection: A case-control study’. https://doi.org/10.5281/zenodo.7040054.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nLindsay S, Martens W: Malaria in the African highlands: past, present and future. Bull. World Health Organ. 1998; 76(1): 33–45. PubMed Abstract\n\nAbeku TA, De Vlas SJ, Borsboom G, et al.: Forecasting malaria incidence from historical morbidity patterns in epidemic-prone areas of Ethiopia: a simple seasonal adjustment method performs best. Tropical Med. Int. Health. 2002; 7(10): 851–857. PubMed Abstract | Publisher Full Text\n\nTeklehaimanot HD, Lipsitch M, Teklehaimanot A, et al.: Weather-based prediction of Plasmodium falciparum malaria in epidemic-prone regions of Ethiopia I. Patterns of lagged weather effects reflect biological mechanisms. Malar. J. 2004; 3(1): 41. PubMed Abstract | Publisher Full Text\n\nZhou G, Minakawa N, Githeko AK, et al.: Association between climate variability and malaria epidemics in the East African highlands. Proc. Natl. Acad. Sci. U. S. A. 2004; 101(8): 2375–2380. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPaaijmans KP, Read AF, Thomas MB: Understanding the link between malaria risk and climate. Proc. Natl. Acad. Sci. 2009; 106(33): 13844–13849. PubMed Abstract | Publisher Full Text\n\nJima D, Getachew A, Bilak H, et al.: Ethiopia Malaria Indicator Survey Working Group: Malaria indicator survey 2007, Ethiopia: coverage and use of major malaria prevention and control interventions. Malar. J. 2010; 9(58). PubMed Abstract | Publisher Full Text\n\nMabaso M, Ndlovu N: Critical review of research literature on climate-driven malaria epidemics in sub-Saharan Africa. Public Health. 2012; 126(11): 909–919. PubMed Abstract | Publisher Full Text\n\nMidekisa A, Senay G, Henebry GM, et al.: Remote sensing-based time series models for malaria early warning in the highlands of Ethiopia. Malar. J. 2012; 11(1): 165. PubMed Abstract | Publisher Full Text\n\nBeck-Johnson LM, Nelson WA, Paaijmans KP, et al.: The effect of temperature on Anopheles mosquito population dynamics and the potential for malaria transmission. PLoS One. 2013; 8(11): e79276. PubMed Abstract | Publisher Full Text\n\nSiraj A, Santos-Vega M, Bouma M, et al.: Altitudinal changes in malaria incidence in highlands of Ethiopia and Colombia. Science. 2014; 343(6175): 1154–1158. PubMed Abstract | Publisher Full Text\n\nMidekisa A, Beyene B, Mihretie A, et al.: Seasonal associations of climatic drivers and malaria in the highlands of Ethiopia. Parasit. Vectors. 2015; 8(1): 339. PubMed Abstract | Publisher Full Text\n\nChaves LF, Koenraadt CJ: Climate change and highland malaria: fresh air for a hot debate. Q. Rev. Biol. 2010; 85(1): 27–55. PubMed Abstract | Publisher Full Text\n\nGething PW, Smith DL, Patil AP, et al.: Climate change and the global malaria recession. Nature. 2010; 465(7296): 342–345. PubMed Abstract | Publisher Full Text\n\nGatton ML, Chitnis N, Churcher T, et al.: The importance of mosquito behavioural adaptations to malaria control in Africa. Evolution. 2013; 67(4): 1218–1230. PubMed Abstract | Publisher Full Text\n\nNurhayani N, Sari DN, Bestari RS, et al.: UJI EFEKTIVITAS EKSTRAK ETANOL DAUN TEMBAKAU (Nicotiana tabacum L.) TERHADAP MORTALITAS LARVA Anopheles aconitus. Biomedika. 2021; 13(1): 68–75.\n\nKandita RT, Aisyah R, Putri WB: Uji Efektivitas Ekstrak Buah Leunca (Solanum Nigrum L.) Sebagai Insektisida Terhadap Nyamuk Aedes Aegypti Dan Anopheles Aconitus. Biomedika. 2015; 7(2). Publisher Full Text\n\nAnimut A, Balkew M, Lindtjørn B: Impact of housing condition on indoor-biting and indoor-resting Anopheles arabiensis density in a highland area, central Ethiopia. Malar. J. 2013; 12(1): 393. PubMed Abstract | Publisher Full Text\n\nKibret S, Lautze J, McCartney M, et al.: Malaria and large dams in sub-Saharan Africa: future impacts in a changing climate. Malar. J. 2016; 15(1): 448. PubMed Abstract | Publisher Full Text\n\nMassebo F, Balkew M, Gebre-Michael T, et al.: Blood meal origins and insecticide susceptibility of Anopheles arabiensis from Chano in South-West Ethiopia. Parasit. Vectors. 2013; 6(1): 44. PubMed Abstract | Publisher Full Text\n\nKibret S, Alemu Y, Boelee E, et al.: The impact of a small-scale irrigation scheme on malaria transmission in Ziway area, Central Ethiopia. Tropical Med. Int. Health. 2010; 15(1): 41–50. PubMed Abstract | Publisher Full Text\n\nYohannes M, Haile M, Ghebreyesus TA, et al.: Can source reduction of mosquito larval habitat reduce malaria transmission in Tigray, Ethiopia? Tropical Med. Int. Health. 2005; 10(12): 1274–1285. PubMed Abstract | Publisher Full Text\n\nYukich JO, Taylor C, Eisele TP, et al.: Travel history and malaria infection risk in a low-transmission setting in Ethiopia: a case control study. Malar. J. 2013; 12(1): 33. PubMed Abstract | Publisher Full Text\n\nAlemu K, Worku A, Berhane Y, et al.: Spatiotemporal clusters of malaria cases at village level, northwest Ethiopia. Malar. J. 2014; 13(1): 223. PubMed Abstract | Publisher Full Text\n\nNega A, Meskal F: Population migration and malaria transmission in Ethiopia.1991.\n\nDeressa W, Ali A, Berhane Y: Review of the interplay between population dynamics and malaria transmission in Ethiopia. Ethiop. J. Health Dev. 2006; 20(3). Publisher Full Text\n\nSchicker RS, Hiruy N, Melak B, et al.: A venue-based survey of malaria, anemia and mobility patterns among migrant farm workers in Amhara Region, Ethiopia. PLoS One. 2015; 10(11): e0143829. PubMed Abstract | Publisher Full Text\n\nMendez F, Carrasquilla G, Muñoz A: Risk factors associated with malaria infection in an urban setting. Trans. R. Soc. Trop. Med. Hyg. 2000; 94(4): 367–371. PubMed Abstract | Publisher Full Text\n\nFana SA, Bunza MDA, Anka SA, et al.: Prevalence and risk factors associated with malaria infection among pregnant women in a semi-urban community of north-western Nigeria. Infect. Dis. Poverty. 2015; 4(1): 24. PubMed Abstract | Publisher Full Text\n\nWHO: World Malaria Report 2016. In.; 2016.\n\nRoberts D, Matthews G: Risk factors of malaria in children under the age of five years old in Uganda. Malar. J. 2016; 15(1): 246. PubMed Abstract | Publisher Full Text\n\nPinchoff J, Chaponda M, Shields TM, et al.: Individual and household level risk factors associated with malaria in Nchelenge District, a region with perennial transmission: a serial cross-sectional study from 2012 to 2015. PLoS One. 2016; 11(6): e0156717. PubMed Abstract | Publisher Full Text\n\nChirebvu E, Chimbari MJ, Ngwenya BN: Assessment of risk factors associated with malaria transmission in Tubu village, northern Botswana. Malar. Res. Treat. 2014; 2014: 1–10. PubMed Abstract | Publisher Full Text\n\nKazembe LN, Mathanga DP: Estimating risk factors of urban malaria in Blantyre, Malawi: A spatial regression analysis. Asian Pac. J. Trop. Biomed. 2016; 6(5): 376–381. Publisher Full Text\n\nMfueni Bikundi E, Coppieters Y: Importance of risk factors associated with malaria for Sub-Saharan African children. Int. J. Environ. Health Res. 2017; 27(5): 394–408. PubMed Abstract | Publisher Full Text\n\nHerdiana H, Cotter C, Coutrier FN, et al.: Malaria risk factor assessment using active and passive surveillance data from Aceh Besar, Indonesia, a low endemic, malaria elimination setting with Plasmodium knowlesi, Plasmodium vivax, and Plasmodium falciparum. Malar. J. 2016; 15(1): 468. PubMed Abstract | Publisher Full Text\n\nHanandita W, Tampubolon G: Geography and social distribution of malaria in Indonesian Papua: a cross-sectional study. Int. J. Health Geogr. 2016; 15(1): 13. PubMed Abstract | Publisher Full Text\n\nHasyim H, Nursafingi A, Haque U, et al.: Spatial modelling of malaria cases associated with environmental factors in South Sumatra, Indonesia. Malar. J. 2018; 17(1): 87. PubMed Abstract | Publisher Full Text\n\nCahyaningrum P, Sulistyawati S: Malaria Risk Factors in Kaligesing, Purworejo District, Central Java Province, Indonesia: A Case-control Study. J. Prev. Med. Public Health. 2018; 51(3): 148–153. PubMed Abstract | Publisher Full Text\n\nEkawati LL, Johnson KC, Jacobson JO, et al.: Defining malaria risks among forest workers in Aceh, Indonesia: a formative assessment. Malar. J. 2020; 19(1): 1–14.\n\nRI K:Profil kesehatan Indonesia tahun 2016. Profil kesehatan Indonesia. Ministry of health of Indonesia; 2017; 186–190.\n\nKemenkes R: Buku Saku Penatalaksanaan Kasus Malaria. Direktorat P2PTVZ Kementerian Kesehatan, Republik Indonesia, Jakarta. 2017.\n\nPanthusiri P: Illustrated keys to the mosquitoes of Thailand IV. Anopheles. Southeast Asian J. Trop. Med. Public Health. 2006; 37(2).\n\nHaque U, Sunahara T, Hashizume M, et al.: Malaria prevalence, risk factors and spatial distribution in a hilly forest area of Bangladesh. PLoS One. 2011; 6(4): e18908. PubMed Abstract | Publisher Full Text\n\nWangdi K, Singhasivanon P, Silawan T, et al.: Development of temporal modelling for forecasting and prediction of malaria infections using time-series and ARIMAX analyses: a case study in endemic districts of Bhutan. Malar. J. 2010; 9: 251. PubMed Abstract | Publisher Full Text\n\nChurcher TS, Trape JF, Cohuet A: Human-to-mosquito transmission efficiency increases as malaria is controlled. Nat. Commun. 2015; 6: 6054. PubMed Abstract | Publisher Full Text\n\nCummins B, Cortez R, Foppa IM, et al.: A spatial model of mosquito host-seeking behavior. PLoS Comput. Biol. 2012; 8(5): e1002500. PubMed Abstract | Publisher Full Text\n\nOtoto EN, Mbugi JP, Wanjala CL, et al.: Surveillance of malaria vector population density and biting behaviour in western Kenya. Malar. J. 2015; 14: 244. PubMed Abstract | Publisher Full Text\n\nMukhtar AYA, Munyakazi JB, Ouifki R, et al.: Modelling the effect of bednet coverage on malaria transmission in South Sudan. PLoS One. 2018; 13(6): e0198280. PubMed Abstract | Publisher Full Text\n\nAgusto FB, Del Valle SY, Blayneh KW, et al.: The impact of bed-net use on malaria prevalence. J. Theor. Biol. 2013; 320: 58–65. Publisher Full Text\n\nMutuku FM, King CH, Mungai P, et al.: Impact of insecticide-treated bed nets on malaria transmission indices on the south coast of Kenya. Malar. J. 2011; 10: 356. PubMed Abstract | Publisher Full Text\n\nVitor-Silva S, Reyes-Lecca RC, Pinheiro TR, et al.: Malaria is associated with poor school performance in an endemic area of the Brazilian Amazon. Malar. J. 2009; 8: 230. PubMed Abstract | Publisher Full Text\n\nAmoran OE: Impact of health education intervention on malaria prevention practices among nursing mothers in rural communities in Nigeria. Niger. Med. J. 2013; 54(2): 115–122. PubMed Abstract | Publisher Full Text\n\nVorasan N, Pan-Ngum W, Jittamala P, et al.: Long-term impact of childhood malaria infection on school performance among school children in a malaria endemic area along the Thai-Myanmar border. Malar. J. 2015; 14: 401. PubMed Abstract | Publisher Full Text\n\nSagara I, Sangare D, Dolo G, et al.: A high malaria reinfection rate in children and young adults living under a low entomological inoculation rate in a periurban area of Bamako, Mali. Am. J. Trop. Med. Hyg. 2002; 66(3): 310–313. Publisher Full Text\n\nSiri JG, Wilson ML, Murray S, et al.: Significance of travel to rural areas as a risk factor for malarial anemia in an urban setting. Am J Trop Med Hyg. 2010; 82(3): 391–397. Publisher Full Text\n\nMendez F, Carrasquilla G, Munoz A: Risk factors associated with malaria infection in an urban setting. Trans. R. Soc. Trop. Med. Hyg. 2000; 94(4): 367–371. PubMed Abstract | Publisher Full Text\n\nSetiyadi NA, Loahasiriwong W, Murti B, et al.: TB Treatment and Multidrug-Resistant of Tuberculosis (MDR-TB) in Central Java of Indonesia: A Case-Control Study. Indian J. Public Health Res. Dev. 2019; 10(11): 1965. Publisher Full Text\n\nSetyowati M, Setiyadi NA, Suharyo S, et al.: Development of Health Information System in TB Control Decision Support: Territoriality-Based Approach.2020.\n\nBarros FS, Honorio NA: Deforestation and Malaria on the Amazon Frontier: Larval Clustering of Anopheles darlingi (Diptera: Culicidae) Determines Focal Distribution of Malaria. Am. J. Trop. Med. Hyg. 2015; 93(5): 939–953. PubMed Abstract | Publisher Full Text\n\nVittor AY, Pan W, Gilman RH, et al.: Linking deforestation to malaria in the Amazon: characterization of the breeding habitat of the principal malaria vector, Anopheles darlingi. Am. J. Trop. Med. Hyg. 2009; 81(1): 5–12. PubMed Abstract\n\nMuller GC, Junnila A, Traore MM, et al.: The invasive shrub Prosopis juliflora enhances the malaria parasite transmission capacity of Anopheles mosquitoes: a habitat manipulation experiment. Malar. J. 2017; 16(1): 237. PubMed Abstract | Publisher Full Text\n\nBeier JC, Killeen GF, Githure JI: Short report: entomologic inoculation rates and Plasmodium falciparum malaria prevalence in Africa. Am. J. Trop. Med. Hyg. 1999; 61(1): 109–113. Publisher Full Text\n\nClarke JL, Pradhan GD, Joshi GP, et al.: Assessment of the grain store as an unbaited outdoor shelter for mosquitoes of the Anopheles gambiae complex and Anopheles funestus (Diptera: Culicidae) at Kisumu, Kenya. J. Med. Entomol. 1980; 17(1): 100–102. Publisher Full Text\n\nSmith A, et al.: Observations on the man-biting habits of some mosquitoes in the South Pare area of Tanganyika. East Afr. Med. J. 1961; 38(5): 246–255.\n\nMattah PA, Futagbi G, Amekudzi LK, et al.: Diversity in breeding sites and distribution of Anopheles mosquitoes in selected urban areas of southern Ghana. Parasit. Vectors. 2017; 10(1): 25. PubMed Abstract | Publisher Full Text\n\nCoetzee M, Fontenille D: Advances in the study of Anopheles funestus, a major vector of malaria in Africa. Insect Biochem. Mol. Biol. 2004; 34(7): 599–605. PubMed Abstract | Publisher Full Text\n\nHargreaves K, Koekemoer LL, Brooke BD, et al.: Anopheles funestus resistant to pyrethroid insecticides in South Africa. Med. Vet. Entomol. 2000; 14(2): 181–189. Publisher Full Text\n\nKibret S, Wilson GG, Ryder D, et al.: Can water-level management reduce malaria mosquito abundance around large dams in sub-Saharan Africa? PLoS One. 2018; 13(4): e0196064. PubMed Abstract | Publisher Full Text\n\nSattler MA, Mtasiwa D, Kiama M, et al.: Habitat characterization and spatial distribution of Anopheles sp. mosquito larvae in Dar es Salaam (Tanzania) during an extended dry period. Malar. J. 2005; 4(4): 4. PubMed Abstract | Publisher Full Text\n\nMayagaya VS, Nkwengulila G, Lyimo IN, et al.: The impact of livestock on the abundance, resting behaviour and sporozoite rate of malaria vectors in southern Tanzania. Malar. J. 2015; 14: 17. PubMed Abstract | Publisher Full Text\n\nSt Laurent B, Burton TA, Zubaidah S, et al.: Host attraction and biting behaviour of Anopheles mosquitoes in South Halmahera, Indonesia. Malar. J. 2017; 16(1): 310. PubMed Abstract | Publisher Full Text\n\nSt Laurent B, Oy K, Miller B, et al.: Cow-baited tents are highly effective in sampling diverse Anopheles malaria vectors in Cambodia. Malar. J. 2016; 15(1): 440. PubMed Abstract | Publisher Full Text\n\nFranco AO, Gomes MG, Rowland M, et al.: Controlling malaria using livestock-based interventions: a one health approach. PLoS One. 2014; 9(7): e101699. PubMed Abstract | Publisher Full Text\n\nKirnowordoyo S: Supalin: Zooprophylaxis as a useful tool for control of A. aconitus transmitted malaria in Central Java, Indonesia. J. Commun. Dis. 1986; 18(2): 90–94. PubMed Abstract\n\nSingh N, Singh OP, Soan V: Mosquito breeding in rice fields and its role in malaria transmission in Mandla district, M.P. Indian J. Malariol. 1989; 26(4): 191–198. PubMed Abstract\n\nRobert V, Le Goff G, Ariey F, et al.: A possible alternative method for collecting mosquito larvae in rice fields. Malar. J. 2002; 1: 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSharma RK, Singh MP, Saha KB, et al.: Socio-economic & household risk factors of malaria in tribal areas of Madhya Pradesh, central India. Indian J. Med. Res. 2015; 141(5): 567–575. PubMed Abstract\n\nTusting LS, Bottomley C, Gibson H, et al.: Housing Improvements and Malaria Risk in Sub-Saharan Africa: A Multi-Country Analysis of Survey Data. PLoS Med. 2017; 14(2): e1002234. PubMed Abstract | Publisher Full Text\n\nMorakinyo OM, Balogun FM, Fagbamigbe AF: Housing type and risk of malaria among under-five children in Nigeria: evidence from the malaria indicator survey. Malar. J. 2018; 17(1): 311. PubMed Abstract | Publisher Full Text\n\nChakim I: Risk factors and housing effect on malaria infection: A case-control study.2022. Publisher Full Text"
}
|
[
{
"id": "191011",
"date": "29 Nov 2023",
"name": "Simone Ladeia-Andrade",
"expertise": [
"Reviewer Expertise Tropical diseases",
"malaria",
"epidemiology",
"clinical trials"
],
"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\nThe study is valuable for being original with field strategies to demonstrate individual and environmental factors that may favor malaria transmission in regions of Indonesia. Its methodological design, analysis and data interpretation, however, could be clearer.\nThe authors identify the study as being of the “Case-Control” type and compare two areas with different degrees of endemicity for malaria. However, some questions get confused. Case-Control are retrospective studies starting from the outcome and considering the previous time from exposure. Thus, like Cohort studies, Case-Controls are of causal analysis, that is, they inform about risk factors. In this study, however, this definition did not seem very clear. Some questions:\n- There is the possibility of variation in the intensity of malaria transmission throughout the year and an assessment of the incidence over four months in each location would not represent this reality.\n- The evaluation of study sites at different times of the year removes the comparability between areas in a case-control study.\n- It did not seem clear what was considered case and control. At a given moment, they were indicated as being the areas under comparison (Case=high endemic area; Control=low endemic area), however, in other moments, \"Case\" seemed to be groups of individuals with malaria (one year ago or in the active search done in the study) and \"Control\" those without malaria within each area or independent of the area. In addition, house types become comparative analysis groups. With all this, the reader misses the progress of the study design and its conclusions.\nI would like to suggest that the authors reassess whether this is really a Case-Control study that evaluates risk factors (causality) or if it would not be a Cross-sectional study with a control area, which evaluates “associated factors” with malaria. Then structure the methodology and data presentation according to this conclusion.\nSPECIFIC CONSIDERATIONS\nABSTRACT:\n- I suggest that the abstract be improved, according to modifications to be made in the text - study design and methodology, results and conclusion.\n- The country where the study is carried out is not informed in the Abstract.\n- Among the results presented in the Abstract, the authors inform that “agricultural activity or visiting.\n- \"forestry areas is a protective factor for malaria infection in Jambi”. Is this interpretation correct or is it just the reverse of it being a risk factor in Sumba? Was there enough sampling in Jambi for this type of conclusion?\n- The conclusion presented in the Abstract is generic and does not specify causalities or associations.\nINTRODUCTION\n- PAGE 3 - 1st PARAGRAPH – “Malaria is a disease that is not solely transmitted by itself, instead, it requires a specific vector to successfully INJECT ITSELF to the host body” - INJECT ITSELF? I suggest changing the sentence.\n- PAGE 3 - 3rd PARAGRAPH – “In pregnant women, the associated factors of malaria infection are lack of education, and non-possession of insecticide-treated nets (ITNs) followed by a DECREASE OF PARASITE DENSITY AS AGE INCREASED”. In fact, there is a decrease in parasite density as age increases, but is this a risk factor for pregnant women? Is this interpretation correct?\n- The introduction needs wording corrections. There are sentences that are not very well structured and difficult to understand. The information is also random and could be organized in a way that better directs the importance of the study carried out.\n- It would be important to inform in the Introduction which are the main vector species and how they behave in Indonesia. This information would help to support the discussion of the results.\nSTUDY DESIGN\n- It would be important to present the characteristics of the study areas, life habits and activities of their populations.\n- The text “There were four stages in this study; field malaria sampling, assessment of malaria risk factors, entomological survey, and mosquito species identification and Plasmodium detection” – This information does not make the study design clear.\n- Regarding the text - “Field malaria sampling was done for the purpose of assigning cases and controls in accordance with researchers’ criteria” – Who are the cases and controls?\n- Regarding the text - “A series of entomological surveys was then conducted in order to understand the effect of house type on malaria infection” – Where? In the most endemic area (case) and in the least endemic area (control)? How did you do it and what was the sampling?\n- Regarding the text: “There were three types of houses included in this study, namely; malaria houses (it was a non-permanent house where malaria was present at least once in the duration of one year back from the point this research started); non-malaria houses (it was a non-permanent house where malaria was absent in the duration of one year back from the start of this research); and permanent houses (it was a well-constructed house where all parts of the house closed properly)” – It is not possible to understand this division into these three types of houses, as it mixes a selection based on the presence or absence of malaria, with a selection based on the level of closure of the walls. It doesn't seem like a meaningful comparison. More clearly, the definition of “permanent residences” as one of the 3 types of houses does not seem clear, since the other two types are defined by having or not having malaria. “Permant houses” are houses that may or may not have cases of malaria? I suggest clarifying the meaning and importance in the analysis of this definition.\n- It was informed that the type of house would be one of the investigated risk factors. This investigation was done by looking at 72 homes over 6 weeks, but it was not clear how many homes were evaluated in each comparison area. If it is a Case-Control study, the boxes should be Cases VERSUS Controls. This drawing is not clear.\n- If you are comparing 2 areas with different endemicities, were the types of houses “malaria”, “non-malaria” and “permanent residences” selected in both areas?\n- Regarding the text - “weekly screening on these three types of houses was carried out to monitor malaria incidence in each house type” – What did this screening consist of? Was it the collection of blood samples from all residents? What was the sampling? It is important to explain better.\nPARTICIPANT SELECTION - PARTICIPANT RECRUITMENT\n- What and how was the sampling of participants done?\n- “People who tested positive for malaria by RDT, microscopic examination, or a combination of the two were identified, and those who met the eligibility criteria were designated as cases.” – Does it mean that \"Case\" would be the positive individual regardless of the area? Does the study compare areas or people? What about the cases that occurred in the previous year. It's confusing. It is important to make it more clear.\nELIGIBILITY CRITERIA\n- Regarding the sentence - \"Since we used a total sample, all positively detected malaria people were included in this study” – Being negative at the time of the research does not mean that it could not be positive at another time. Thus, this criterion is adequate for the study proposal?\nMETHODS OF SELECTION\n- “The selection of controls was by criteria of an absence of malaria infection for at least a one-year period”. – Does this mean that “Cases” would be individuals with malaria at the time of the study or who had malaria in the last year?\nFIELD MALARIA SAMPLING\n- The screening was performed from 1 February 2018 - 31 May 2018 in Jambi, and from 1 June 2018 - 31 October 2018 in Sumba. As malaria transmission can be seasonal, couldn´t these different data collection periods influence the results?\n- Sampling was not clear. If the authors proposed to compare areas with different endemicities, was there not a representative sampling of each area under comparison? On the other hand, if the authors intended to compare individuals with malaria versus individuals without malaria regardless of the area, the selection of the sample based on the tympanic temperature does not guarantee that those without fever at the moment do not have malaria or that they will not have malaria later, mainly in the most endemic area. Finally, it is necessary to better clarify the sampling carried out according to the study design.\n- The temperature unit needs to be informed (oC).\nASSESSMENT OF MALARIA RISK FACTORS\n- Why is contact with malaria patient a risk factor? It would be necessary to specify which type of contact.\nENTOMOLOGICAL SURVEY\n- The authors performed a pre-observational HLC in order to select the location with the appropriate number of Anopheles species. This selection would make sense to describe species variety and vector behavior. In a comparison of areas it does not make sense as it would bias the results. I suggest that the objective of the entomological survey be better clarified.\n- In weekly screening, if a malaria infection was detected in non-malaria and/or permanent houses, these houses were excluded – Is this not biased?\nSOURCE OF BIAS\n- The biases are not very clear.\nRESULTS\n- In the 2nd line, the authors inform that there were 157 cases of both locations, then they say that there were 158 cases and in the table, the sum of Sumba and Jambi is 157 cases. Is the value 158 wrong?\n- It would be good to clarify that the percentages of 32.3% and 67.7% are the frequency of cases and controls among the participants, regardless of the study area.\n- Table 1 presents the basic demography of the study areas, however, it would be important to compare statistical analyzes between them for each variable. I would suggest a column for Sumba, a column for Jambi and a p-value of the comparison between the two (as in table 2 and 3), to show that the areas are comparable, except for endemicity.\n- The authors mention that outdoor night activity, history of visiting forest areas in the previous month, and working place is located inside the forest were PROTECTIVE FACTORS against malaria infection in Jambi. Is this interpretation correct? Could it be that these variables are NOT factors associated with malaria transmission in Jambi, but in Sumba?\n- The authors inform that the individual risk factor for malaria infection in Jambi were:\n\n. not having a bed-net for sleeping (OR = 2.09; CI: 1.04-4.18) – It is important to be careful when interpreting these data, as the CI is very close to 1.\n\n. low level of education (OR = 1.01; CI: 0.29-3.45) – Be careful when interpreting these data, as this CI is not significant\n\n. occupation (P value = 0.000) – what was the OR and CI?\n\n. contact with malaria-infected patient (OR = 3.37; CI: 1.62-7.01) – What was the type and time of contact?\n- I think Table 4 is expendable.\n- Page 10, 1st paragraph – The result of the mosquito species captured was presented between the areas, but in the methodology it was not clear whether the captures occurred in both areas. It would be important to inform more clearly.\n- Figures 1 presents very little data, which can only be in the text.\n- Figure 2 – The Y axis is described as number of mosquitoes. Would it be the absolute number of mosquitoes? This was not clear because they are not integers. Furthermore, statistical analysis is not possible with such small n. Perhaps only the data in Figure 3 or Figure 4 make sense.\n- Maybe Figures 2 and 3 can be in the same figure (A and B).\n- Incidence rate is calculated in longitudinal studies and the design of this study was not clear. Furthermore, the periods of the year in which the data were collected were different for each area, which made them incomparable in terms of the incidence of malaria.\nDISCUSSION\n- The authors discuss the discrepancy of classifying endemicity level between national data and the collected data from the current study, but the study does not show the representativeness that the sample taken has of the total population or of each area, nor was the methodology designed to present this information.\n- The authors argue that “night activity outdoors, history of visiting forest areas from the previous month, and working place is located inside the forest are protective factors in Jambi” – is this interpretation correct? Are they protective factors or just not risk factors?\n- Could different behavior of mosquito species be a cause of the different outbreaks of infection in Jami and Sumba?\n- The authors discuss the outcome of bed nets as a risk factor, but it is not clear how their use was evaluated in each area.\n- “In Sumba, having never consumed antimalarial drugs was a risk factor to malaria infection” – This sounds strange. This result is initially discussed citing the effectiveness of the current antimalarial drugs, which would indicate a question about drug resistance. Next, the authors consider earlier treated re-infections. However, none of these possibilities means “risk factor” for a new infection. I suggest that the authors review the interpretation of the results more carefully.\n- In the discussion, the authors cite characteristics of the study areas, such as agricultural activities, which were not informed before in the text. I suggest you better describe the areas in the Methodology.\n- There are very confusing or unclear paragraphs, such as the 3rd paragraph on page 15.\n- A multivariate analysis would be required to assess the individual contribution of each variable to the risk of malaria in each study site.\nCONCLUSION\nThe authors cite “risk factors”, when they must specify which factors they are referring to.\nGENERAL STRUCTURE OF THE TEXT\nI suggest that the entire text be revised. There are spelling problems, verb tenses (sometimes the authors use the present, sometimes the past, sometimes the future), sentence structure, excessive repetition (for example, the definition of types of houses appears several times in the text), lack of unit of measurement of temperature (oC), etc.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1261
|
https://f1000research.com/articles/11-1256/v1
|
04 Nov 22
|
{
"type": "Review",
"title": "Machine learning algorithms: their applications in plant omics and agronomic traits’ improvement",
"authors": [
"Itunuoluwa Isewon",
"Oluwabukola Apata",
"Fesobi Oluwamuyiwa",
"Olufemi Aromolaran",
"Jelili Oyelade",
"Oluwabukola Apata",
"Fesobi Oluwamuyiwa",
"Olufemi Aromolaran",
"Jelili Oyelade"
],
"abstract": "Agronomic traits of plants especially those of economic or aesthetic importance are threatened by climatic and environmental factors such as climate change, biotic, and abiotic stresses. These threats are now being mitigated through the analyses of omics data like genomics, transcriptomics, proteomics, metabolomics, and phenomics. The emergence of high-throughput omics technology has led to an avalanche of plant omics data. Plant research demands novel analytical paradigms to extract and harness large plant omics data for plant improvement effectively and efficiently. Machine learning algorithms are well-suited analytical and computational approaches for the integrative analysis of large unstructured, heterogeneous datasets. This study presents an overview of omics approaches to improve plant agronomic traits and crucial curated plant genomic data sources. Furthermore, we summarize machine learning algorithms and software tools/programming packages used in plant omics research. Lastly, we discuss advancements in machine learning algorithms' applications in improving agronomic traits of economically important plants. Extensive application of machine learning would advance plant omics studies. These advancements would consequently help agricultural scientists improve economically important plants’ quality, yield, and tolerance against abiotic and biotic stresses and other plant health-threatening issues.",
"keywords": [
"Agronomic traits",
"machine learning",
"multi-omics",
"plant improvement"
],
"content": "1. Introduction\n\nThe global agricultural system is threatened by ecological events such as climate change and other environmental stresses.1,2 These events affect the yield, stability, and quality of production of economically important plants, i.e., medicinal plants, fruit crops, food crops, cereal or grain crops, legume seed crops or pulses, etc.1,3 These challenges are addressed by omics approaches via numerous unconventional improvement methodologies.4,5 Omics approaches involve analysis of the constituents of genome sequence and other macromolecules generated from encoded genomic information. The utilization of omics-derived knowledge and technologies in plant improvement strategies is limited and difficult. Other drawbacks of omics technologies include a lack of data integration and effective phenotype-genotype correlation strategies. As a result, promoting the integration of computational biology and plant genomics to assist plant development is critical.6,7 This paper gives an overview of omics methodologies for improving plant agronomic traits as well as essential curated plant genomic data sources. We discuss the bioinformatics software, tools, and packages that are utilized in omics-based plant improvement research. We also dissect how machine learning algorithms has been used to improve agronomic features of commercially significant plants, their major contributions and future outlook in plant omics and agronomics.\n\nGenome sequencing was made possible with the advent of sequencing technologies.8,9 Complete sequencing of a plant genome was first demonstrated for a model plant named Arabidopsis (Arabidopsis thaliana)10,11 and afterward for rice (Oryza sativa). Subsequently, the whole genome of over 250 species in the plant kingdom have been sequenced: bryophytes, pteridophytes, gymnosperms, and angiosperms12,13 (Figure 1). Angiosperms account for 95% of the sequenced species, most of which are economically important plants or their wild relatives (Figure 2). Food crops like rice, wheat, beans, oat, maize, and soybean are among the sequenced plants, as are ornamental plants like orchid and hibiscus, industrial plants like oilseed, hemp, and spice/herbs like garlic, ginger, turmeric, moringa, artemisia, and neem, which are known for their high therapeutic value.\n\nMost sequenced plants are angiosperms and are subdivided into three groups. Most of the sequenced angiosperms fall under rosids and asterids clades. Other sequenced angiosperms clades are grouped here as other dicots.\n\n94% of sequenced plants are angiosperms consisting of both monocots and dicots. Percentage of other plants are 1%, 2%, 3% for Pteridophytes, Bryophytes, and Gymnosperms, respectively.\n\nThere have been a variety of databases created to access plant genome datasets.14,11 The model plant A. thaliana genome database launched in 2001 was the premier plant genome database.10,15 Subsequently, many databases and resources have been developed for plant genomes. The earliest genome databases were essentially archives of genome sequence data. These databases have expanded into genome portals/hubs that combine different genomic data and web servers that offer online genomics analysis. The availability of annotated plant genome data has led to many discoveries, including genome organization and gene function.16 These discoveries elucidate the complexity, evolution, and dynamics of plant genomes, contributing to a deeper understanding of plant biology.6,17 Available genomic information includes cis-elements, gene expression data, protein interactome, transcriptional and post-transcriptional data. These genome databases exist as single species and comprehensive databases as shown in Table 1.\n\nPlant studies involving the analysis of biological macromolecules are collectively termed plant omics. Omics is a broad field of study encompassing subfields like genomics, transcriptomics, proteomics, metabolomics, phenomics, glycomics, lipidomic, etc. Plant genomics involves studying the compositions, organizations, functions, and structures of genetic materials (DNA/RNA) and molecular genetic networks of interactions in the plant genome.17,18 While genome structure and organization are studied in structural genomics,13,19 functional genomics investigates the functions, interaction, and regulation of gene and gene products.5,20\n\nPlant functional genomics is a goldmine in agronomic traits improvement. It incorporates other omics approaches like transcriptomics, proteomics, metabolomics, phenomics, etc.16,21 (Figure 3). Other aspects of genomics are epigenomics, mutagenomics, and pangenomics.22 Epigenetic changes, such as histone modifications, small RNA and DNA methylations occurring at the genomic phase, are dissected within epigenomics. Mutagenomics is used to explore mutation events mediating modified genotype and phenotype in mutant species. Pangenomics studies the whole set of genomic sequences present in the entire population of a species. It also explores dispensable genomes that are individual specific or partially shared. Mutagenomics and pangenomics are new omics techniques in crop sciences.22,23\n\nRepresentation of major omics approaches in plant molecular studies and the methods utilized in conventional analysis of plant omics datasets.\n\nPlant transcriptomics involves investigating the control of plant metabolite production processes at the RNA level. Transcript-level gene expression control regulates the whole plant's development and growth.24 Plant proteomics explores the structural and functional features of proteins in a living organism. It encompasses studies on plants’ typical morphological and physiological properties.16,22 The role of proteins in controlling the plant metabolic processes is also studied in plant proteomics, especially in medicinal plants.25\n\nPlant metabolomics involves profiling primary and secondary metabolites in plants.26 Metabolic data are useful when developing metabolic correlation networks. These networks can aid comparative analysis of cellular compartments such as carbon and nitrogen transport and partitioning in plants.27 In addition, the molecular and cellular regulation of different enzymatic processes can also be investigated.25 Plant phenomics involves the systematic study of phenotypes such as plant composition, growth, and production analysis. This study can be conducted both in controlled environments and in the field. Field phenomics involves the measurement of phenotypes that exist under both cultivated and natural conditions. Studies in controlled environments involve glasshouses, growth chambers, and other systems where growth conditions can be manipulated.28 These multi-omics approaches have emerged successful for plant research, including agronomic traits improvement over the last few decades. Agronomic traits are desirable plants’ genetic or phenotypic features, i.e., quality traits, disease resistance, pest resistance, insecticide tolerance, temperature, drought, and other adverse environmental factors tolerance traits. Quality traits encompass morphological features like plant height, seed weight; physiological features like chlorophyll content and photosynthetic rate29; economic features like improved crop yield, processing, and storage; pharmaceutical and industrial features like the elimination of toxins and allergen, increased nutritional or dietary value and increased medicinal values.30 Recent research suggests that when multi-omics technologies are integrated, they can be better harnessed to improve genetic development, crop breeding science, plant stress resistance, and other agronomic traits.22,23\n\n\n2. Major areas of application of omics technologies for agronomic traits improvement\n\nGenomics-assisted pre-breeding is a genetic manipulation strategy to improve agronomic traits of interest in plants at the DNA level.31 Genomics-assisted pre-breeding approaches positively contribute to the efficiency of diseases and climate-resilient crop development.32–34 Crop breeding across the globe has relied on a series of phenotypic selection and crossing before the genomic era to generate superior crop genotypes.35 Genome sequence availability has paved the way for identifying all genes and genetic variants associated with agronomics traits.36,37 Besides, it has made it possible to assess genotype level changes incurred during breeding processes.38 Plant breeders have utilized genomics and bioinformatics in gene-level resolution of agronomic variation using quantitative trait loci (QTL) mapping39–41 and genome-wide association studies (GWAS).42,43 For instance, studies have recently been conducted to develop multiple stress-adaptable rice species that are disease and climate resilient using genomics-assisted breeding techniques such as quantitative trait locus (QTL), gene/markers-phenotype association and phenotype selection.44–46 Pea breeding projects used genetic marker-trait associations to boost valued yield and market-preferred agronomic traits.47,48 Miedaner et al.43 used high-density genotype arrays and comprehensive phenotyping of the same species population across diverse conditions, locations, and seasons in genomic selection and population mapping to speed the breeding of disease resistance traits in maize, small-grain cereals, and wheat. Hu et al.39 harnessed genomic selection (GS) and genome-wide genetic variants to prevent reiterated phenotyping in breeding cycles. These studies indicate new breeding techniques such as speed breeding and genomic selection to boost genetic and trait improvements. However, the lack of robust phenotypic data limits the efficient utilization of available genomic information and technologies in genomics-assisted breeding.\n\nVariation in gene content among individuals within the same species is caused by genetic variation ranging from single-nucleotide polymorphisms to substantial structural variants (SVs). Due to human and natural selection acts, this variation offers the raw material on which evolution occurs.49,50 Deviation in agricultural plants’ phenotypic and genetic characteristics is referred to as crop diversity.36 The understanding of crop diversity is enhanced by plant genomics at both species and gene levels.51 According to recent research, a single reference genome is insufficient to capture a species' entire genetic diversity landscape. Pan-genome analysis provides a platform for evaluating a species' genetic diversity by looking at its whole genomic repertoire. Pan-genomic studies have shed new light on the landscape of diversity and improvement of major crops such as Brachypodium distachyon,52 Brassica Spp.,53–55 maize,56 rice,57,58 soybean,59 wheat60 etc. Evolution in plant diversity is correlated with and relatively predictable by heterogenous biotic and abiotic environmental stress induced by global climate change. These stresses, in turn, affect crop yield and crop-growing seasons.61 A study on natural plant populations shows that the organization and evolution of plant populations’ diversity at all genomic regions is nonrandom at the molecular and organismal level.62,63 Therefore, plants can evolve under climatic gradients resulting in clinal adaptation. Hence, the breeding of climate resilience crops can be facilitated by understanding the genomic basis of clinal adaption in crop species.64\n\nBiotic stresses are instigated by living organisms such as insects, parasitic plant nematodes, diseases, or weeds in production agriculture.65 Genomics approaches to biotic stress include ribonucleic acid interference (RNAi) silencing and transgenesis. RNA interference (RNAi) silencing is employed against viruses and some fungi, while transgenesis has been exploited to develop resistance against some fungi, for example, Fusarium head blight.66 Genome-wide identification and expression analysis in legume crops also revealed the role of small RNA biogenesis mediators in biotic stress response regulation.42\n\nAbiotic stresses, such as low or high temperatures, heavy metals, insufficient or excessive water, high salinity, ultraviolet radiation, are hostile to developing plants, resulting in significant wane in crop yield worldwide.67 According to Kumar et al.,28 knowledge of plants' response to abiotic stresses can be enhanced by integrating information generated from metabolomics and proteomics with genomics data. Sustenance of yield in crops threatened by abiotic stresses is a significant challenge in breeding resilient crop varieties.68 A study on Brassica oleracea shows that heat stress transcription factors are integral to signal transduction pathways functioning in response to environmental stresses and are suggested to contribute significantly to various stress responses.62 Heat stress transcription factors genes were identified in the in silico analysis of B. oleracea. The identified genes may be exploited in developing crop varieties resilient to global climate change.1,62\n\nPopulation genomics is employed to study adaptation and speciation. Population genomics datasets are used in GWAS to detect the genes responsible for adaptive phenotypic variations of large plant population samples.35,69 For instance, Bamba et al. identified specific adaptation loci in a GWA study and unveiled the molecular basis of genetic trade-offs. It also showed that ecological fitness could be predicted by polygenic effects of several loci associated with local climate.35 Medicinal plants’ diversity is of exceptional interest because of their ethnomedicine role. GWAS studies on adaptive genotypic and phenotypic variation provide a framework to assess the diversity of medicinal plant application across different cultures and infer modifications in plant use over time.70,71 Other genomic approaches such as genomic selection, nested association mapping, genetic diversity, and allele mining have been integrated into crop improvement programs to address the genetic issues associated with maize productivity and nutritional contents.72\n\nPlant omics studies have greatly helped our understanding and interpretation of plant responses to ecological influences and their contribution to key developmental processes important for crop yield and food quality. However, there are still some problems, such as a lack of data integration and robust techniques for phenotype-genotype correlation. Also, the use of omics-derived knowledge and tools in plant improvement strategies is limited and difficult. As a result, there is a pressing need to promote the integration of computational biology and plant genomics to benefit plant improvement.6,7\n\n\n3. Applications of machine learning in plant omics and agronomics\n\nMachine learning (ML) is a computer science field that utilizes algorithms to learn and capture the characteristics of target patterns of complex datasets.73 Machine learning algorithms are generally classified into the following categories; supervised, semi-supervised, unsupervised, reinforcement, and deep learning.74 A supervised ML algorithm is trained using a labeled dataset. It learns to respond more accurately based on these training sets by comparing its output with the given input.67,73 Semi-supervised algorithms provide a tool that harnesses the potential of both supervised and unsupervised learning. These algorithms are ideally adapted for model building and can be used for classification, regression, and prediction.75 Unsupervised learning is all about identifying unexplained existing patterns from the data to generate pattern rules. Unsupervised learning is a learning approach focused on statistics and thus applied to the issue of discovering a hidden structure in unlabeled data.7,74,76\n\nReinforcement learning is considered an intermediate form of learning as the algorithm is only provided with an answer that tells whether the output is correct or not.75 Deep learning is built on artificial neural networks (ANN). The algorithms extract higher-level features from the raw input using multiple layers of neural networks. Learning of the algorithm can be unsupervised, semi-supervised, or supervised.73 Machine learning approaches provide unique techniques for integrating and analyzing omics data, allowing for the improvement of crops and other economically important plants. Some machine learning algorithms have been used to developed tools specifically for plant omics analysis. Table 2 highlights the existing machine learning tools for plant omics analysis. Machine learning algorithms have a broad range of applications in plant genomics. These algorithms play vital roles in genome assembly, iterative gene regulatory network inference, and the identification of true SNPs in polyploid plants.77\n\nPrecision breeding is a genetic engineering technique that involves reproducing organisms of the same species together to preserve desirable characteristics and create a stronger hybrid.84 Traditional statistical methods mainly used in plant breeding strategies are ineffective in plant data analysis because of the non-deterministic and nonlinear nature of plant features attributed to environment, genotype, and interaction.85 Machine learning has enabled effective plant phenotyping and data mining for patterns such as genotype and trait correlation.39 It has also been successful in genomic selection. Genomic selection is a critical method used in selecting plant species with genetic gains of interest in plant breeding. Applying different ML algorithms in building GS models has produced robust and accurate prediction.86,87 Multilayer neural networks (NNs) have been used in genetic value prediction in plant breeding. NN models are efficient in predicting genetic value, regardless of the population size, heritability, or coefficient of variation. Thus, the ANN is promising for genetic value prediction in unbiased experiments.88 Multilayer NNs have been utilized to select bean genotypes with highly stable phenotypes using 13 genotypes of common beans between 2002 and 2006. The integration of this model in plant breeding has enabled precise genetic value prediction and selection.89\n\nAlso, deep learning generated a robust prediction accuracy in grain yield compared to the conventional linear statistical methods used in traditional plant breeding when analyzing multiple traits with mixed ordinal, continuous, and binary phenotype data. Univariate and multivariate deep learning models' predictive performance was assessed using the Durum wheat (Triticum turgidum var. durum Desf.) dataset. Deep learning model performance shows that it has a promising potential to be a successful model for accurate genomic prediction in plant breeding.90 The flexibility of machine learning algorithms makes them a viable alternative to traditional parametric methods for predicting categorical and continuous responses in genomic selection.91\n\nAn ensemble of RF and SVM was implemented to improve genotype-phenotype classification using manually derived root trait datasets. The combined model accurately identified the most distinguishing root traits and corresponding cultivar differentiation. The model's performance demonstrates the potential of ML approaches in unbiased cultivars classification and trait selection.92\n\nAdditionally, predictive models have aided the integration of additive and dominance effects in GWAS and have enhanced the prediction of complex agronomic traits in polyploid plant species. For instance, a study revealed the feasibility of genome-wide prediction of potato agronomic traits despite being an autotetraploid food crop. It also shows that GWA prediction is viable in selecting breeding values in elite germplasm with substantial non-additive genetic variance.93\n\nPlant phenomics is a systematic study of plant phenotypes.28 In recent years, plant field phenotyping has gotten a lot of attention with the possibility of crop fields' high-throughput analysis.94 The application of machine learning methods and the various technological developments for image analysis have improved quantitative crop traits assessment.92,94,95 For instance, CNN-based detection and analysis of wheat spikes using wheat field trials images captured over one planting season achieved an average accuracy of 88 to 94% across diverse groups of test images. CNN's high-performance accuracy shows that it is a robust model for genome-based selection and prediction in plant breeding.96 Also, the RF algorithm was used in plant image segmentation involving the acquisition and processing of several plant images samples.97 The predictions made by the model enabled the discovery of various parameters relevant to plant growth.94\n\nML learning has been exploited in identifying favorable agronomic traits, including abiotic and biotic stress resistance. ML algorithms are integrated into conventional statistical methodologies to optimize the accuracy of plants stresses prediction and detection.96 For instance, 25,000 soybean leaflets images exposed to varied diseases and nutritional perturbation were used to develop a convolutional neural network (CNN), which can infer the image features of the disease types and dietary deficiencies at high resolution. The prediction accuracy of the ML framework was very close to that of human expert diagnosis. Other plants’ induced stresses can also be identified, classified, and quantified using the model. The model can also be adapted to identify, classify, and quantify the induced stresses in other plants.95\n\nRandom forest has been used to predict metabolite and transcript markers in drought tolerance prediction using experimental drought-stressed plant field trial datasets. The low error rate recorded in the model shows that the model could be considered as an alternative model for accurate prediction and identification of molecular markers.98 RF was used to identify suitable features combination for phenotypic traits prediction using data derived from various agro-management treatment experiments. This approach achieved optimal prediction accuracy and improved plant breeding strategies by enabling maximal allocation of stress management resources.99 Sanz-Carbonell and colleagues used deep sequencing and computational approaches such as PCA and Clustering analysis to infer the biotic and abiotic stress responses regulatory network mediated by miRNA. 24 miRNAs were used in this study, all of which are known to alter expression significantly under stressful conditions. The prediction generated inference that target genes of miRNAs down-regulated under stress conditions contribute to plant response to stress, whereas miRNAs that are up-regulated control genes associated with growth and development.67 Soybean fields were screened for tolerance to soybean iron chlorosis deficiency (abiotic stress in soybean) using linear discriminant analysis (LDA) and SVM. The phenotypic data obtained from soybean fields were used in model training and predicting soybeans' iron chlorosis deficiency stress. The ML application has helped evaluate the severity of real-time stress in the soybean sector.95\n\nPlant diseases and pests pose a significant threat to agriculture. Early identification of plant diseases and pests would aid in developing effective treatment strategies while economic losses are mitigated.100 Diverse ML approaches for precise disease recognition and prediction have been implemented in plant populations.101,102 Neural networks (NNs) have achieved impressive results in plant disease prediction using image classification. A deep convolutional network was implemented in leaf image classification model for disease recognition. The developed model showed a high predictive performance in distinguishing plant leaves from their surroundings and recognized 13 plant diseases types on healthy leaves.103 In another approach, a heterogeneous ensemble of deep-learning-based neural network models was used in detecting tomato plants diseases and pests using images collected on-site by imaging devices of varying resolutions. The ensemble model successfully handled image complexity in the plant's surrounding area and recognized nine different diseases and pests.100,104 Therefore, deep CNNs are promising in automatic classification and detection of diseases traits from leaf images. In addition, CNN has shown optimal performance when implemented in plant–pathogen interaction, pest, and disease recognition in some studies. These studies include prediction of pests and diseases occurrence in cotton105; rice plant diseases and pests recognition106; rice blast disease prediction107,108; image-based potato tuber disease detection109 and so on. The CNN model is a high-performing method for detecting plant diseases, and it can be implemented and optimized for practical applications.\n\nSVM has also been used for weather-based rice blast prediction and has proven suitable for plant disease forecasting with incredible predictive accuracy. A world-first SVM-based web server for rice blast prediction was developed. Plant scientists and farmers have benefited from this tool, especially in their decision-making.110 In the pixel-wise quantification and identification of powdery mildew diseased barley tissue, SVM classification was used to establish hypersensitive response spots using multispectral imaging of diseased barley plants. SVM application enabled precise automatic identification of barley interaction with powdery mildew.111\n\nRecently, a data-driven ML approach named ApoplastP was proposed. RF classifier is the base algorithm for ApoplastP and has shown high performance in predicting protein localization in plant apoplast. At first, differences in the constituents of apoplastic and intracellular plant proteins were unknown. However, the advent of ApoplastP enabled the exploration of differences in the composition of plant proteins. The plant apoplast is integral to plant–pathogen interactions, transport, and intercellular signaling. Hence, integrating and optimizing machine learning algorithms in apoplastic localization prediction will aid functional studies and help predict whether an effector will localize to the apoplast or enter the plant cells.112\n\nAlso, RF has been implemented to build an inter-species protein–protein interaction (PPI) prediction model using Arabidopsis–pathogen PPI data acquired both experimentally and from PPI public databases-UniProt. A critical assessment of the model performance showed that random forest integration with linear statistical methods using sequence information and network attributes as model features resulted in substantial and robust improvement in performance.24\n\nIn addition, RF classification has been used to exploit protein biomarkers' potential in precision breeding using biomarkers generated assays of 104 potatoes (Solanum tuberosum) peptides. These peptides were selected using diagonal linear discriminant analysis, bagging, principal component analysis (PCA), and SVM and then classified with RF classifiers. The ML algorithms' application helped identify Phytophthora infestans resistance in leaves, tubers and its effect on plant yield using potato leaf secretome data.109 Early disease detection enables farmers to use timely and targeted crop protection strategies. With the use of ML, researchers have improved the accuracy of object detection and recognition systems dramatically.\n\nML applications in plant genomics and agronomics have majorly contributed to efficient breeding of crops with desirable agronomic traits, plant phenotyping, genetic trait prediction, and precise disease prediction such as in rice, soybeans, maize, beans, etc.72,95,106,110 However, several limitations still exist. Firstly, the black-box nature of some sophisticated ML algorithms inhibits interpretation. The plant research community is more interested and fascinated with the biological implications of the prediction than the accuracy of the predictive model. Hence, there is a need for further processing and careful interpretation of the predictive model output using conforming biological knowledge. Additionally, the dimensionality of omics datasets poses challenges such as multicollinearity, overfitting, and sparsity which are difficult to avoid. Though contemporary machine learning methods and the huge sample size can partially alleviate these problems, the model’s accuracy can be significantly enhanced by using different fine-tuning, augmentation, and optimization techniques.107 Data integration from various sources is necessary for GS-assisted breeding and other trait improvement approaches.113 Simultaneous analysis of multiple omics datasets can advance our understanding of complex biological phenomena.78,79 Another challenge is the limited and inconsistent information on plant-pathogen interaction phenotypic information. The ML models used in plant disease recognition can be extended by enriching the plant disease database with plant-pathogen interaction phenotype data. Developing more robust classification algorithms with an expanded number of diseases classes will improve plant disease recognition and forecasting.103,105,108,106 Finally, a comprehensive plant database must be constructed to facilitate comparative studies and promote research collaborations on critical plant science problems.\n\n\n4. Conclusion\n\nMachine learning has shown tremendous promise in studying enormous high-dimensional data sets, although it is still limited in plant molecular studies application. An in-depth understanding of ML models will stimulate ML implementation for plant biological data analysis. As sequenced plant genome data continues to accumulate, ML will accelerate all plant genomic research fields, including identifying genes associated with biotic and abiotic stress resistance and other genes with significant functions, understanding gene regulation mechanisms, exploring plant genome genetic framework, and estimating breeding values. These advancements would help agricultural researchers improve the quality and yield of crops with stronger tolerance to abiotic and biotic stress and other plant health-threatening issues.\n\n\nData availably statement\n\nOSF: Extended data for “Machine learning algorithms: their applications in plant omics and agronomic traits’ improvement”, https://doi.org/10.17605/OSF.IO/TE6GC.14\n\nFiles included:\n\nSupplementary Table 1. Published sequenced plant genomes. Hundreds of plant genomes have been sequenced and published since 2000. The statistics for each genome are taken from the publication, despite several model plants having significant updates to genome assemblies and gene counts. NA, data not available in publication; Mb, megabases; kb, kilobases.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nMousavi-Derazmahalleh M, Bayer PE, Hane JK, et al.: Adapting legume crops to climate change using genomic approaches. Plant Cell Environ. 2019; 42: 6–19. PubMed Abstract | Publisher Full Text\n\nUnited Nations Convention to Combat Desertification (UNCCD).: Sustainable Development Knowledge Platform:n.d. (accessed August 24, 2020).Reference Source\n\nZhang Q, Xu M, Xia X, et al.: Crop genetics research in Asia: improving food security and nutrition. Theor. Appl. Genet. 2020; 133: 1339–1344. PubMed Abstract | Publisher Full Text\n\nAnalysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000; 408: 796–815. Publisher Full Text\n\nMichael TP, VanBuren R: Progress, challenges and the future of crop genomes. Curr. Opin. Plant Biol. 2015; 24: 71–81. Publisher Full Text\n\nBorevitz JO, Ecker JR: PLANT GENOMICS: The Third Wave. Annu. Rev. Genom. Hum. Genet. 2004; 5: 443–477. PubMed Abstract | Publisher Full Text\n\nAbadi S, Yan WX, Amar D, et al.: A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Comput. Biol. 2017; 13: e1005807. PubMed Abstract | Publisher Full Text\n\nMarri PR, Ye L, Jia Y, et al.:Advances in Sequencing and Resequencing in Crop Plants.Varshney RK, Pandey MK, Chitikineni A, editors. Plant Genetics and Molecular Biology. Cham:Springer International Publishing;2018; pp. 11–35. PubMed Abstract | Publisher Full Text\n\nAkhtar MS, Alaraidh IA, Hakeem KR:Experimental Approaches for Genome Sequencing.Hakeem KR, Shaik NA, Banaganapalli B, et al., editors. Essentials of Bioinformatics, Volume III: In Silico Life Sciences: Agriculture. Cham:Springer International Publishing;2019; pp. 159–165. Publisher Full Text\n\nHuala E, Dickerman AW, Garcia-Hernandez M, et al.: The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 2001; 29: 102–105. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu S, Li G, Yang J, et al.: Aquatic Plant Genomics: Advances, Applications, and Prospects. Int. J. Genomics. 2017; 2017: 1–9. PubMed Abstract | Publisher Full Text\n\nPryer KM, Schneider H, Zimmer EA, et al.: Ann Banks, Deciding among green plants for whole genome studies. Trends Plant Sci. 2002; 7: 550–554. PubMed Abstract | Publisher Full Text\n\nCooper L, Jaiswal P:The Plant Ontology: A Tool for Plant Genomics.Edwards D, editor. Plant Bioinformatics. New York, NY:Springer New York;2016; pp. 89–114. Publisher Full Text\n\nIsewon IM, Apata OR, Oluwamuyiwa FA, et al.: Machine Learning Algorithms: Their Applications in Plant Omics and Agronomic Traits Improvement.2022. Publisher Full Text\n\nChen F, Dong W, Zhang J, et al.: The Sequenced Angiosperm Genomes and Genome Databases. Front. Plant Sci. 2018; 9. PubMed Abstract | Publisher Full Text\n\nRai A, Yamazaki M, Saito K: A new era in plant functional genomics. Curr. Opin. Syst. Biol. 2019; 15: 58–67. Publisher Full Text\n\nAbdurakhmonov IY:Genomics Era for Plants and Crop Species – Advances Made and Needed Tasks Ahead.Abdurakhmonov IY, editor. Plant Genomics. InTech;2016. Publisher Full Text\n\nShrivastava P, Kumar R: Soil salinity: A serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J. Biol. Sci. 2015; 22: 123–131. PubMed Abstract | Publisher Full Text\n\nTerryn N, Rouzé P, Montagu MV: Plant genomics. FEBS Lett. 1999; 452: 3–6. Publisher Full Text\n\nExposito-Alonso M, Drost H-G, Burbano HA, et al.: The Earth BioGenome project: opportunities and challenges for plant genomics and conservation. Plant J. 2020; 102: 222–229. PubMed Abstract | Publisher Full Text\n\nHoltorf H, Guitton M-C, Reski R: Plant functional genomics. Naturwissenschaften. 2002; 89: 235–249. Publisher Full Text\n\nYang Y, Saand MA, Huang L, et al.: Applications of Multi-Omics Technologies for Crop Improvement. Front. Plant Sci. 2021; 12: 1846. PubMed Abstract | Publisher Full Text\n\nMuthamilarasan M, Singh NK, Prasad M: Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective. Adv. Genet. 2019; 103: 1–38. PubMed Abstract | Publisher Full Text\n\nYang S, Li H, He H, et al.: Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods. Brief. Bioinformatics. 2019; 20: 274–287. PubMed Abstract | Publisher Full Text\n\nBabar MM, Zaidi N-SS, Pothineni VR, et al.:Application of Bioinformatics and System Biology in Medicinal Plant Studies.Hakeem KR, Malik A, Vardar-Sukan F, et al., editors. Plant Bioinformatics: Decoding the Phyta. Cham:Springer International Publishing;2017; pp. 375–393. Publisher Full Text\n\nWolfender J-L, Rudaz S, Hae Choi Y, et al.: Plant Metabolomics: From Holistic Data to Relevant Biomarkers. Curr. Med. Chem. 2013; 20: 1056–1090. PubMed Abstract | Publisher Full Text\n\nKempinski C, Jiang Z, Bell S, et al.:Metabolic Engineering of Higher Plants and Algae for Isoprenoid Production.Schrader J, Bohlmann J, editors. Biotechnology of Isoprenoids. Cham:Springer International Publishing;2015; pp. 161–199. PubMed Abstract | Publisher Full Text\n\nKumar J, Pratap A, Kumar S:Plant Phenomics: An Overview.Kumar J, Pratap A, Kumar S, editors. Phenomics in Crop Plants: Trends. Springer India, New Delhi:Options and Limitations;2015; pp. 1–10. Publisher Full Text\n\nTshikunde NM, Mashilo J, Shimelis H, et al.: Agronomic and Physiological Traits, and Associated Quantitative Trait Loci (QTL) Affecting Yield Response in Wheat (Triticum aestivum L.): A Review. Front. Plant Sci. 2019; 10. PubMed Abstract | Publisher Full Text\n\nFan G, Liu X, Sun S, et al.: The Chromosome Level Genome and Genome-wide Association Study for the Agronomic Traits of Panax Notoginseng. IScience. 2020; 23: 101538. PubMed Abstract | Publisher Full Text\n\nVarshney RK, Bohra A, Yu J, et al.: Designing Future Crops: Genomics-Assisted Breeding Comes of Age. Trends Plant Sci. 2021; 26: 631–649. PubMed Abstract | Publisher Full Text\n\nVarshney RK, Singh VK, Kumar A, et al.: Can genomics deliver climate-change ready crops? Curr. Opin. Plant Biol. 2018; 45: 205–211. PubMed Abstract | Publisher Full Text\n\nThudi M, Palakurthi R, Schnable JC, et al.: Genomic resources in plant breeding for sustainable agriculture. J. Plant Physiol. 2021; 257: 153351. PubMed Abstract | Publisher Full Text\n\nZenda T, Liu S, Dong A, et al.: Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel, Switzerland). 2021; 11. PubMed Abstract | Publisher Full Text\n\nBamba M, Kawaguchi YW, Tsuchimatsu T: Plant adaptation and speciation studied by population genomic approaches. Develop. Growth Differ. 2019; 61: 12–24. PubMed Abstract | Publisher Full Text\n\nGedil M, Menkir A: An Integrated Molecular and Conventional Breeding Scheme for Enhancing Genetic Gain in Maize in Africa. Front. Plant Sci. 2019; 10: 1430. PubMed Abstract | Publisher Full Text\n\nJha UC, Sharma KD, Nayyar H, et al.: Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes. Int. J. Mol. Sci. 2022; 23: 2217. PubMed Abstract | Publisher Full Text\n\nKole C, Muthamilarasan M, Henry R, et al.: Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Front. Plant Sci. 2015; 6. Publisher Full Text\n\nHu H, Scheben A, Edwards D: Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline. Agriculture. 2018; 8: 75. Publisher Full Text\n\nSingh RK, Prasad A, Muthamilarasan M, et al.: Breeding and biotechnological interventions for trait improvement: status and prospects. Planta. 2020; 252: 54. PubMed Abstract | Publisher Full Text\n\nJia B, Conner RL, Penner WC, et al.: Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). Int. J. Mol. Sci. 2022; 23: 7639. PubMed Abstract | Publisher Full Text\n\nGarg V, Agarwal G, Pazhamala LT, et al.: Genome-Wide Identification, Characterization, and Expression Analysis of Small RNA Biogenesis Purveyors Reveal Their Role in Regulation of Biotic Stress Responses in Three Legume Crops. Front. Plant Sci. 2017; 8. PubMed Abstract | Publisher Full Text\n\nBarreto FZ, Rosa JRBF, Balsalobre TWA, et al.: A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.). PLoS One. 2019; 14: e0219843. PubMed Abstract | Publisher Full Text\n\nSandhu N, Yadav S, Catolos M, et al.: Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding. Front. Plant Sci. 2021; 12. PubMed Abstract | Publisher Full Text\n\nHe Z, Xin Y, Wang C, et al.: Genomics-Assisted Improvement of Super High-Yield Hybrid Rice Variety “Super 1000” for Resistance to Bacterial Blight and Blast Diseases. Front. Plant Sci. 2022; 13: 881244. PubMed Abstract | Publisher Full Text\n\nSandhu N, Singh J, Singh G, et al.: Development and validation of a novel core set of KASP markers for the traits improving grain yield and adaptability of rice under direct-seeded cultivation conditions. Genomics. 2022; 114: 110269. PubMed Abstract | Publisher Full Text\n\nBohra A, Saxena KB, Varshney RK, et al.: Genomics-assisted breeding for pigeonpea improvement. Theor. Appl. Genet. 2020; 133: 1721–1737. PubMed Abstract | Publisher Full Text\n\nMohanty JK, Jha UC, Dixit GP, et al.: Harnessing the hidden allelic diversity of wild Cicer to accelerate genomics-assisted chickpea crop improvement. Mol. Biol. Rep. 2022; 49: 5697–5715. Publisher Full Text\n\nMiedaner T, Boeven ALG-C, Gaikpa DS, et al.: Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize. Int. J. Mol. Sci. 2020; 21: E9717. PubMed Abstract | Publisher Full Text\n\nTao Y, Zhao X, Mace E, et al.: Exploring and Exploiting Pan-genomics for Crop Improvement. Mol. Plant. 2019; 12: 156–169. PubMed Abstract | Publisher Full Text\n\nMuthamilarasan M, Theriappan P, Prasad M: Recent advances in crop genomics for ensuring food security. Curr. Sci. 2013; 105: 155–158.\n\nGordon SP, Contreras-Moreira B, Woods DP, et al.: Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nat. Commun. 2017; 8: 2184. PubMed Abstract | Publisher Full Text\n\nLin K, Zhang N, Severing EI, et al.: Beyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage. BMC Genomics. 2014; 15: 250. PubMed Abstract | Publisher Full Text\n\nGolicz AA, Bayer PE, Barker GC, et al.: The pangenome of an agronomically important crop plant Brassica oleracea. Nat. Commun. 2016; 7: 13390. PubMed Abstract | Publisher Full Text\n\nHurgobin B, Golicz AA, Bayer PE, et al.: Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus. Plant Biotechnol. J. 2018; 16: 1265–1274. PubMed Abstract | Publisher Full Text\n\nHirsch CN, Foerster JM, Johnson JM, et al.: Insights into the Maize Pan-Genome and Pan-Transcriptome. Plant Cell. 2014; 26: 121–135. PubMed Abstract | Publisher Full Text\n\nWang W, Mauleon R, Hu Z, et al.: Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018; 557: 43–49. PubMed Abstract | Publisher Full Text\n\nZhao Q, Feng Q, Lu H, et al.: Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat. Genet. 2018; 50: 278–284. PubMed Abstract | Publisher Full Text\n\nLi Y, Zhou G, Ma J, et al.: De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. Nat. Biotechnol. 2014; 32: 1045–1052. PubMed Abstract | Publisher Full Text\n\nMontenegro JD, Golicz AA, Bayer PE, et al.: The pangenome of hexaploid bread wheat. Plant J. 2017; 90: 1007–1013. PubMed Abstract | Publisher Full Text\n\nNeeta L, Golicz A, Singh M, et al.: Genome-wide analysis of the Hsf gene family in Brassica oleracea and a comparative analysis of the Hsf gene family in B. oleracea, B. rapa and B. napus. Funct. Integr. Genomics. 2019; 19: 515–531. PubMed Abstract | Publisher Full Text\n\nNdjiondjop MN, Alachiotis N, Pavlidis P, et al.: Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. Theor. Appl. Genet. 2019; 132: 1145–1158. PubMed Abstract | Publisher Full Text\n\nNevo E: Ecological genomics of natural plant populations: the Israeli perspective. Methods Mol. Biol. 2009; 513: 321–344. PubMed Abstract | Publisher Full Text\n\nOlatoye MO, Hu Z, Maina F, et al.: Genomic Signatures of Adaptation to a Precipitation Gradient in Nigerian Sorghum. G3 (Bethesda). 2018; 8: 3269–3281. PubMed Abstract | Publisher Full Text\n\nJuliana P, Poland J, Huerta-Espino J, et al.: Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics. Nat. Genet. 2019; 51: 1530–1539. PubMed Abstract | Publisher Full Text\n\nRicroch AE:What Will Be the Benefits of Biotech Wheat for European Agriculture?Bhalla PL, Singh MB, editors. Wheat Biotechnology: Methods and Protocols. New York, NY:Springer;2017; pp. 25–35. Publisher Full Text\n\nSanz-Carbonell A, Marques MC, Bustamante A, et al.: Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon. BMC Plant Biol. 2019; 19: 78. PubMed Abstract | Publisher Full Text\n\nMochida K, Shinozaki K: Genomics and Bioinformatics Resources for Crop Improvement. Plant Cell Physiol. 2010; 51: 497–523. PubMed Abstract | Publisher Full Text\n\nKatuuramu DN, Branham SE, Levi A, et al.: Genome-Wide Association Analysis of Resistance to Pseudoperonospora cubensis in Citron Watermelon. Plant Dis. 2022; 106: 1952–1958. PubMed Abstract | Publisher Full Text\n\nTeixidor-Toneu I, Jordan FM, Hawkins JA: Comparative phylogenetic methods and the cultural evolution of medicinal plant use. Nat Plants. 2018; 4: 754–761. Publisher Full Text\n\nGuidini R, Jahani M, Huang K, et al.: Genome Wide Association Mapping in Sunflower (Helianthus annuus L.) reveals Common Loci and Putative Candidate Genes for resistance to Diaporthe gulyae and D. helianthi causing Phomopsis Stem Canker. Plant Dis. 2022. Publisher Full Text\n\nChakradhar T, Hindu V, Reddy PS: Genomic-based-breeding tools for tropical maize improvement. Genetica. 2017; 145: 525–539. PubMed Abstract | Publisher Full Text\n\nSun S, Wang C, Ding H, et al.: Machine learning and its applications in plant molecular studies. Brief. Funct. Genomics. 2020; 19: 40–48. Publisher Full Text\n\nAlzubi J, Nayyar A, Kumar A: Machine Learning from Theory to Algorithms: An Overview. J. Phys. Conf. Ser. 2018; 1142: 012012. Publisher Full Text\n\nCarbonell JG, Michalski RS, Mitchell TM:1 - AN OVERVIEW OF MACHINE LEARNING.Michalski RS, Carbonell JG, Mitchell TM, editors. Machine Learning. San Francisco (CA):Morgan Kaufmann;1983; pp. 3–23. Publisher Full Text\n\nMatukumalli LK, Grefenstette JJ, Hyten DL, et al.: Application of machine learning in SNP discovery. BMC Bioinformatics. 2006; 7: 4. PubMed Abstract | Publisher Full Text\n\nEsposito S, Carputo D, Cardi T, et al.: Applications and Trends of Machine Learning in Genomics and Phenomics for Next-Generation Breeding. Plants. 2020; 9: 34. PubMed Abstract | Publisher Full Text\n\nZhang N, Rao RSP, Salvato F, et al.: MU-LOC: A Machine-Learning Method for Predicting Mitochondrially Localized Proteins in Plants. Front. Plant Sci. 2018; 9. PubMed Abstract | Publisher Full Text\n\nKushwaha SK, Chauhan P, Hedlund K, et al.: NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction. Bioinformatics. 2016; 32: 1223–1225. PubMed Abstract | Publisher Full Text\n\nCarvalho TFM, Silva JCF, Calil IP, et al.: Rama: a machine learning approach for ribosomal protein prediction in plants. Sci. Rep. 2017; 7: 16273. PubMed Abstract | Publisher Full Text\n\nPal T, Jaiswal V, Chauhan R: DRPPP: A machine learning based tool for prediction of disease resistance proteins in plants. Comput. Biol. Med. 2016; 78: 42–48. PubMed Abstract | Publisher Full Text\n\nSilva JC, Carvalho T, Fontes E, et al.: Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae. BMC Bioinformatics. 2017; 18: 431. PubMed Abstract | Publisher Full Text\n\nMa C, Xin M, Feldmann KA, et al.: Machine Learning-Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis. Plant Cell. 2014; 26: 520–537. PubMed Abstract | Publisher Full Text\n\nvan Dijk ADJ , Kootstra G, Kruijer W, et al.: Machine learning in plant science and plant breeding. IScience. 2021; 24: 101890. PubMed Abstract | Publisher Full Text\n\nNiazian M, Niedbała G: Machine Learning for Plant Breeding and Biotechnology. Agriculture. 2020; 10: 436. Publisher Full Text\n\nGuzzetta G, Jurman G, Furlanello C: A machine learning pipeline for quantitative phenotype prediction from genotype data. BMC Bioinformatics. 2010; 11: S3. PubMed Abstract | Publisher Full Text\n\nCrossa J, Pérez-Rodríguez P, Cuevas J, et al.: Genomic Selection in Plant Breeding: Methods, Models, and Perspectives. Trends Plant Sci. 2017; 22: 961–975. PubMed Abstract | Publisher Full Text\n\nPeixoto LA, Bhering LL, Cruz CD: Artificial neural networks reveal efficiency in genetic value prediction. Genet. Mol. Res. 2015; 14: 6796–6807. PubMed Abstract | Publisher Full Text\n\nCorrêa AM, Teodoro PE, Gonçalves MC, et al.: Artificial intelligence in the selection of common bean genotypes with high phenotypic stability. Genet. Mol. Res. 2016; 15. Publisher Full Text\n\nMontesinos-López OA, Montesinos-López A, Tuberosa R, et al.: Multi-Trait, Multi-Environment Genomic Prediction of Durum Wheat With Genomic Best Linear Unbiased Predictor and Deep Learning Methods. Front. Plant Sci. 2019; 10. Publisher Full Text\n\nGonzález-Camacho JM, Ornella L, Pérez-Rodríguez P, et al.: Applications of Machine Learning Methods to Genomic Selection in Breeding Wheat for Rust Resistance. Plant Genome. 2018; 11: 170104. PubMed Abstract | Publisher Full Text\n\nZhao BG, Rewald B: Phenotyping: Using Machine Learning for Improved Pairwise Genotype Classification Based on Root Traits. Front. Plant Sci. 2016; 7. Publisher Full Text\n\nEndelman JB, Carley CAS, Bethke PC, et al.: Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato. Genetics. 2018; 209: 77–87. PubMed Abstract | Publisher Full Text\n\nSelvaraj MG, Valderrama M, Guzman D, et al.: Machine learning for high-throughput field phenotyping and image processing provides insight into the association of above and below-ground traits in cassava (Manihot esculenta Crantz). Plant Methods. 2020; 16: 87. PubMed Abstract | Publisher Full Text\n\nDobbels AA, Lorenz AJ: Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system. Plant Methods. 2019; 15: 97. PubMed Abstract | Publisher Full Text\n\nHasan MM, Chopin JP, Laga H, et al.: Detection and analysis of wheat spikes using Convolutional Neural Networks. Plant Methods. 2018; 14: 100. PubMed Abstract | Publisher Full Text\n\nde Carvalho RRB , Marmolejo Cortes DF, Sousa MBE, et al.: Image-based phenotyping of cassava roots for diversity studies and carotenoids prediction. PLoS One. 2022; 17: e0263326. PubMed Abstract | Publisher Full Text\n\nSprenger H, Erban A, Seddig S, et al.: Metabolite and transcript markers for the prediction of potato drought tolerance. Plant Biotechnol. J. 2018; 16: 939–950. PubMed Abstract | Publisher Full Text\n\nParmley KA, Higgins RH, Ganapathysubramanian B, et al.: Machine Learning Approach for Prescriptive Plant Breeding. Sci. Rep. 2019; 9: 17132. PubMed Abstract | Publisher Full Text\n\nFuentes A, Yoon S, Kim SC, et al.: A Robust Deep-Learning-Based Detector for Real-Time Tomato Plant Diseases and Pests Recognition. Sensors (Basel). 2017; 17. PubMed Abstract | Publisher Full Text\n\nDanilevicz MF, Gill M, Anderson R, et al.: Plant Genotype to Phenotype Prediction Using Machine Learning. Front. Genet. 2022; 13: 822173. PubMed Abstract | Publisher Full Text\n\nSimón D, Borsani O, Filippi CV: RFPDR: a random forest approach for plant disease resistance protein prediction. PeerJ. 2022; 10: e11683. PubMed Abstract | Publisher Full Text\n\nSladojevic S, Arsenovic M, Anderla A, et al.: Deep Neural Networks Based Recognition of Plant Diseases by Leaf Image Classification. Comput. Intell. Neurosci. 2016; 2016: 1–11. PubMed Abstract | Publisher Full Text\n\nWang Q, Qi F, Sun M, et al.: Identification of Tomato Disease Types and Detection of Infected Areas Based on Deep Convolutional Neural Networks and Object Detection Techniques. Comput. Intell. Neurosci. 2019; 2019: 9142715–9142753. PubMed Abstract | Publisher Full Text\n\nXiao Q, Li W, Kai Y, et al.: Occurrence prediction of pests and diseases in cotton on the basis of weather factors by long short term memory network. BMC Bioinformatics. 2019; 20: 688. PubMed Abstract | Publisher Full Text\n\nLi D, Wang R, Xie C, et al.: A Recognition Method for Rice Plant Diseases and Pests Video Detection Based on Deep Convolutional Neural Network. Sensors (Basel). 2020; 20. PubMed Abstract | Publisher Full Text\n\nLiang W-J, Zhang H, Zhang G-F, et al.: Rice Blast Disease Recognition Using a Deep Convolutional Neural Network. Sci. Rep. 2019; 9: 2869. PubMed Abstract | Publisher Full Text\n\nNettleton DF, Katsantonis D, Kalaitzidis A, et al.: Predicting rice blast disease: machine learning versus process-based models. BMC Bioinformatics. 2019; 20: 514. PubMed Abstract | Publisher Full Text\n\nOppenheim D, Shani G, Erlich O, et al.: Using Deep Learning for Image-Based Potato Tuber Disease Detection. Phytopathology. 2019; 109: 1083–1087. Publisher Full Text\n\nKaundal R, Kapoor AS, Raghava GPS: Machine learning techniques in disease forecasting: a case study on rice blast prediction. BMC Bioinformatics. 2006; 7: 485. PubMed Abstract | Publisher Full Text\n\nKuska MT, Behmann J, Großkinsky DK, et al.: Screening of Barley Resistance Against Powdery Mildew by Simultaneous High-Throughput Enzyme Activity Signature Profiling and Multispectral Imaging. Front. Plant Sci. 2018; 9: 1074. Publisher Full Text\n\nSperschneider J, Dodds PN, Singh KB, et al.: ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning. New Phytol. 2018; 217: 1764–1778. PubMed Abstract | Publisher Full Text\n\nMontesinos-López OA, Montesinos-López A, Pérez-Rodríguez P, et al.: A review of deep learning applications for genomic selection. BMC Genomics. 2021; 22: 19. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "205805",
"date": "29 Sep 2023",
"name": "Aalt-Jan van Dijk",
"expertise": [
"Reviewer Expertise Machin learning",
"plant systems biology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nA variety of reviews on omics data analysis and machine learning (ML) in the fields of plant science and plant breeding have recently been published. It is unclear where exactly this manuscript positions itself with respect to these existing reviews. In particular, the title seems to indicate a strong focus on ML; however, the introduction makes clear that there is a broader view, including review on data sources, “bioinformatics software, tools and packages”, in addition to reviewing the application of ML. This seems like a very broad topic to review, and maybe as a result, various sections of the manuscript are not satisfactory in my opinion:\n\nThe description of genomic information in 1.1. seems limited as well as somewhat confusing (“cis-elements, gene expression data, protein interactome, transcriptional and post-transcriptional data“). How can protein interactome be described as “genomic information”?\n\nOn the other hand, how about e.g. DNA methylation, histone modifications, transcription factor binding sites etc?\n\nSimilarly, the information in Table 1 seems unorganized as well as incomplete. It would help to provide some sub-division with headers of subsections; moreover, it is unclear what criteria are used to include/exclude databases. E.g. what about https://bar.utoronto.ca/thalemine/begin.do, http://plantismash.secondarymetabolites.org/, http://cisbp.ccbr.utoronto.ca/, protein interaction databases, the jaspar database, and various others. Also note that when I tested urls from the table, not all seemed reachable (e.g. chromdb.org, http://mips.gsf.de/).\n\nSometimes very arbitrary examples are chosen to refer to; e.g. for QTL mapping ref 41 – why would that one specifically be relevant, there would be numerous other QTL mapping studies that could be mentioned?\n\nFigure 2, does not add much compared to figure 1 – it could well be removed or provided as a (SI) table\n\nSome sections in the part on ML are quite disappointing. For example, Table 2 is very brief – there are definitely more examples of ML tools for plant omics data analysis and in fact even some tools mentioned in the manuscript itself (e.g. apoplastp) are not mentioned in the table.\n\nThe explanation on ML in section 3.1 is not always to the point. E.g. the sentence “Machine learning algorithms are generally classified into the following categories; supervised, semi-supervised, unsupervised, reinforcement, and deep learning” suggests that deep learning is an alternative type of ML compared to supervised, semi-supervised learning etc, which is not correct. Also the statement “Unsupervised learning is a learning approach focused on statistics…” is unclear. Similarly, Reinforcement Learning is not well explained.\n\nSome of the examples mentioned in the text on ML are also not to the point. For example, ref 93 seems like a randomly chosen example of genomic prediction – there would be many studies that could be mentioned, why would this one be mentioned specifically as ML? Similarly for ref 67, this seems just like a straightforward analysis of omics data – it is again not clear why this is ML?\n\nRelevant other examples of application of ML are missing, including e.g. https://www.pnas.org/doi/10.1073/pnas.1814551116, https://www.nature.com/articles/s41467-021-25893-w, https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.13979\n\nVarious statements in the text are not clear (sometimes too strong worded), e.g.:\n\nIn the abstract “These threats are now being mitigated through the analyses of omics data like genomics, transcriptomics, proteomics, metabolomics, and phenomics. “ – I don’t think threats are mitigated by data analysis itself.\n\nSection 2.1 “Genome sequence availability has paved the way for identifying all genes and genetic variants associated with agronomics traits” – that seems too simple, just having genome sequence does not mean we known which genes/variatns are associated with traits of interest\n\nSection 3.6: “Finally, a comprehensive plant database must be constructed to facilitate comparative studies” – not clear what this would mean and why this has to be done.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? No\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? No",
"responses": []
},
{
"id": "220205",
"date": "24 Nov 2023",
"name": "Hao Tong",
"expertise": [
"Reviewer Expertise Artificial intelligence in genetics",
"Systems biology modelling",
"Quantitative genetics modelling",
"Multi-omics big data analysis"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe review paper prepared by Isewon et al. tried to summarize how machine learning models applied to agriculture. This manuscript is not well-structured, many sentences are unclear for me. There are many review papers on this topic in different particular focuses, I did not see the novelty this general review paper contributed to this topic.\nIt is better to begin with why we need to use machine learning models in agriculture in introduction section, instead of using nearly half of manuscripts to summarize the dataset.\n\nThe Table 1 needs to be better organized to include what species and omics data. Also, some links are not working when I click it, need to be double-checked for updates. The title is for plant genomics database, while some are not for genome but for proteomic data, for instance.\n\nIt would be more helpful that the authors summarize the database not only for genomic data, but also database have multiple omics data.\n\nJust given definitions of many omics data is not so useful. It would be great to see how to integrate multiple omics data in machine learning to solve agriculture questions.\n\nThe sentence “Quality traits encompass morphological features like plant height, seed weight” is incorrect. These traits are quantitative traits in the context of quantitative genetics.\n\nBy given the definition of supervised, unsupervised machine leaning models, you should also be mentioned in your following example studies, which are supervised or unsupervised.\n\nIn the context of genomic selection, the most common used models, rrBLUP or Bayes models should be mentioned and even compared with any machine learning models.\n\nIn the studies you mentioned, it would be better to state the predictability in the main text.\n\nMany statements are unclear for me. For instance, “the lack of robust phenotypic data limits the efficient utilization of available genomic information …”. Why the lack of robust phenotypic data, is it from the measurement error or environmental factors?\n\nMany statements need reference paper to support. For instance, “deep learning generated a robust prediction accuracy in grain yield compared to the conventional linear statistical methods…”. The authors need to carefully check the entire manuscripts.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? No\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? No",
"responses": []
},
{
"id": "220199",
"date": "15 Dec 2023",
"name": "Haixiao Hu",
"expertise": [
"Reviewer Expertise Bioinformatics",
"Quantitative Genetics",
"Statistics",
"Plant Breeding"
],
"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 endeavored to review the applications of machine learning algorithms in plant omics and agronomic trait improvement. In Section 1, the authors enumerated various genomics databases and identified five subfields within plant omics technologies. In Section 2, the utilization of plant omics technologies across four major research areas was discussed. Section 3, classifying machine learning algorithms into five categories, and highlighted their application across five research areas in sections 3.2 to 3.5.\nWhile acknowledging the importance of the four application research areas for omics technology and machine learning methods, I noted that the authors did not thoroughly describe how each omics technology, individually or collaboratively, contributes to enhancing agronomic traits in plant science. Similarly, regarding machine learning algorithms/methods, the authors omitted detailed discussions on theories, the gradual implementation of these computational technologies in each area, milestone works, and the most successful applications in major plant species. Therefore, in addition to merely listing the areas to which omics technologies and machine learning algorithms can be applied, it is strongly recommended that the authors delve extensively into each application area. This entails a thorough examination of a substantial number of high-quality papers to ensure a profound understanding of how omics and machine learning technologies have significantly impacted each research domain, who are the major contributors in each of these areas, etc. A comprehensive review should not only outline the application areas but also offer insights into how these technologies have reshaped the landscape of plant science within each specific area.\nMinor comments: Concerning Figure 1, it's recommended that the authors specify the source of the published plant genome sequences from 2000 to the present, indicating whether it comprises a full set or a subset of the total plant genomes released each year. Additionally, the inclusion of a y-axis is suggested for clarity.\nRegarding Table 1, clarification is sought on the criteria used for selecting the databases listed. Furthermore, the absence of certain important species-specific databases like TAIR, maizeGDB, SoyBase, etc., raises questions about the selection criteria.\nIn Section 3.2, the statement \"Genomic selection is a critical method used in selecting plant species with genetic gains of interest in plant breeding\" is deemed not entirely accurate. It is suggested to revise it to \"Genomic prediction is a critical method used to select the best individuals with the optimal combination of beneficial alleles in a breeding population.\"\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1256
|
https://f1000research.com/articles/11-1255/v1
|
04 Nov 22
|
{
"type": "Research Article",
"title": "Hand injuries in Kenya: a chaff cutter menace",
"authors": [
"Samuel Wanjara",
"Peter Oduor",
"Peter Oduor"
],
"abstract": "Introduction Hand injuries are a recognized occupational hazard from the use of chaff cutters. With increasing mechanization of farming in our region, the burden of hand injuries is poised to increase. Methods We conducted a descriptive study of 47 patients presenting with chaff cutter hand injuries at our center in one year. Results They were predominantly male (98%) and the majority (70%) were aged between 21 and 40 years. The majority of patients who had not resumed work were those with severe injuries and those who had had an amputation. There was a positive correlation between age category and severity of injury. Discussion Chaff cutter injuries contribute considerably to hand amputations at our center. The majority of patients with severe injuries and those undergoing amputations do not return to gainful activities one year after sustaining the injury, suggesting increased dependency. Further research is paramount to identify safety features of chaff cutters in this region.",
"keywords": [
"Hand injuries",
"chaff-cutter",
"Kenya",
"return-to-work"
],
"content": "Introduction\n\nAgriculture is among the most hazardous economic fields (Mucci et al., 2020) In dairy farming, the commonest site of injury are the extremities (Pratt et al., 1992). The hands are the most commonly affected, sustaining an injury in 20.5% of cases (Naseer et al., 2016; Mucci et al., 2020). The use of farm machinery such as hay bailers and chaff cutters has been implicated as the commonest cause of hand injury (Naseer et al., 2016) Chaff cutters are used in chopping of fodder in dairy farming. Whereas the traditional chaff cutters were manually operated and safe, current cutters in use are power driven and more unsafe (Naseer et al., 2016; Ali et al., 2021). Increasing mechanization predisposes workers to high risks for injuries, often with devastating outcomes (Angoules et al., 2007). Incidence of hand injuries sustained from chaff cutters vary with age and sex, with a preponderance for young male adults (Naseer et al., 2016; Das, 2014; Mucci et al., 2020; Patel et al., 2018).\n\nThe majority of the injuries from chaff cutters are non-fatal (Das, 2014; He et al., 2010; Patel et al., 2018); however, they can lead to limb loss and loss of function (Wairegi, 2019). They vary from simple lacerations, dislocations, fractures, crush injuries and amputations. Campbell and Kay proposed an objective grading system, the Hand Injury Severity Score (HISS), for the severity of the injuries to enhance assessment, communication and plan of management with consideration of the skin, motor, neural and skeletal components of the injury (Naseer et al., 2016; Campbell & Kay, 1996). The hand is an important organ, especially in low-income settings, where it is thought to create an identity for the individual in the society (Naseer et al., 2016). Moreover, hand injuries resulting from chaff cutters are more likely to involve the dominant hand thereby affecting the capabilities of the affected in participating in gainful activities and in integrating in the society (Naseer et al., 2016; Wairegi, 2019). This leads to social and economic losses until the individuals are fit to return to pre-injury activities (Ali et al., 2021). The return to gainful activities and social incorporation after injury is influenced by demographic, clinical and economic factors (He et al., 2010).\n\nOur region, and Kenya in particular, has a robust dairy industry that is experiencing rapid commercialization, mechanization and innovation (Bebe et al., 2015; Mutavi, 2017). With the increased mechanization of farming in the region, the burden of hand injuries is poised to increase. However, literature on characteristics and management of these injuries from our region is largely limited. We therefore aimed to study the characteristics of chaff cutter injuries from our center, including their management and impact on return to gainful activities.\n\n\nMethods\n\nWe conducted a retrospective descriptive study on patients presenting with chaff cutter hand injuries. The study was done in Nakuru County, in Kenya. We collected data for all patients who presented and were managed from Nakuru Level V Hospital during the period starting July 2019 through June 2020. Patients who did not give an informed written consent for participation were excluded. The case notes for the patients were retrieved from patients’ records and from the register of operations in the operating room. The patients’ biodata, type of injury and the surgical procedure performed were obtained. Self-reported sex category was obtained retrospectively from records of routine data in our unit. We included all injuries in the volar zones of the hand(s) distal to the wrist joint and assigned a severity score for the following categories; integument, skeletal, motor and neural. The individual category scores were aggregated into a summative Hand Injury Severity Score (HISS) score for every patient.\n\nSubsequently, an enquiry was then made through a telephone call to the patients or their caretakers, a year after the month of hospital discharge, collecting data on whether the patient had resumed gainful activity. Data was entered into Microsoft Excel (Microsoft Corp) and exported for analysis.\n\nThe data were analyzed using Stata Version 14, (StataCorp LLC Canada, US). Fischer’s exact test was used to assess the relationship of resumption to work and surgical procedure performed while Pairwise correlation was used to test for correlation between age and sex with severity of injury. A p-value of ≤0.05 was considered statistically significant where applicable.\n\nWe obtained ethical review exemption from Nakuru Level V Hospital ethical committee (Ref: ERC/NLV5/2021/9) in consideration of the observational design of our study. In addition, we only intended to utilize anonymized routine clinical data.\n\n\nResults\n\nForty-seven patients were included. The age varied from 14 to 69 years with the mean age being years 28.34 (SD 11.91) with a median of 25 years. They were predominantly male (98%) while the majority (70%) were aged between 21 and 40 years.\n\nHand injuries were assessed and graded with the HISS. Injuries with a HISS score of above 51 were grouped as severe/major injuries, while those with a HISS score of 21–50 were graded as moderate and HISS score below 20 as minor. 36.2% of the patients equally had minor and severe/major injuries while 27.7% had moderate injuries (Figure 1). The majority of patients with severe injuries were between 21 and 40 years (58.8%), and all of them underwent an amputation. Many of the patients with minor injuries underwent debridement alone (41.2%) while the rest had either debridement with repair (23.5%) or primary amputation (35.3%). Table 1 demonstrates the HISS scores.\n\nThe majority of patients who had not resumed work were those with severe injuries (60.0%) and those who had had an amputation (84.4%). Table 2 demonstrates the resumption to work. There was no statistically significant relationship between surgical procedure and resumption to work (p=0.120). There was a positive correlation between age category and severity of injury (r=0.2781, p>0.005). A negative correlation was observed for sex and severity of injury. (r=−0.1734, p>0.005) However, there was no significant association among age, sex and severity of injury.\n\n\nDiscussion\n\nThe findings from our study showed that male persons aged between 21 and 40 years were the commonest group of workers likely to sustain chaff cutter injuries involving the hand. In a study from Pakistan including 30 cases of tokka (chaff cutter) injuries, the male-to-female ratio of the victims was 3:1 (Ali et al., 2021). In contrast, in another retrospective study from Pakistan, Naseer et al. (2016) found that male persons were affected in only 43.8% of the cases. The likely explanation for this observation was that fodder chopping was considered a domestic chore in the study’s cultural background and likely to be performed by women and children (Naseer et al., 2016). Similarly in industrialized nations, machine injury accounts for the majority of injuries to the hand (Naseer et al., 2016; Cooper et al., 2006). A systematic review of upper limb injuries in agriculture by Mucci and colleagues found that the 20 to 45 year old age group was the most affected by chaff cutter injuries, agreeing with our findings. They observed that this could be explained by a workforce dominated by the young, in low- and high-income settings alike (Mucci et al., 2020).\n\nIn a study from Nepal on hand injuries caused by fodder cutters, Kishor and colleagues demonstrated that majority of the injuries were minor to moderate (Shrestha et al., 2018). In our study, no degree of injury predominated significantly. Wairegi further notes that in patients who underwent upper limb amputations from a tertiary hospital in Kenya, the majority of the injuries were from chaff cutters (Wairegi, 2019). The severity of hand injuries could be dependent on age, literacy levels and time of day (Angoules et al., 2007; Wairegi, 2019). We found a positive correlation between age and severity of injury. In addition, patients aged between 21 and 40 years were more likely to sustain a severe injury. This could also be explained by the fact that majority of those injured were young and that the workforce in agriculture in low income countries is also predominantly young (Mucci et al., 2020). Work by Mucci and colleagues suggested that individuals with low literacy levels had a higher risk of injury than their counterparts with higher educational status (Mucci et al., 2020). However, our study did not investigate the impact of educational status.\n\nThe return to gainful activities after injury is hugely affected by the severity of injury (He et al., 2010). At one year after the injury, majority of patients in our study had not returned to their pre-injury occupations with the majority being those with severe/major injuries. On the contrary, Savitsky et al. observed that the period to return to work among individuals injured in the work setting was independent of injury characteristics (Savitsky et al., 2020). However, their findings might have been affected by the incentive of occupational injury allowances given to participants in their study. Notably, in our setting injured patients do not receive any such allowances, which potentially impoverishes them further. In general, farm injuries lead to profound physical and emotional disability and economic loss (Angoules et al., 2007). The period taken to return to work might be an indicator of temporary or permanent disablement, suggesting inability of the affected individual to earn a livelihood during this period and to lose their social standing. This consequently makes them depend on other persons for sustenance (Naseer et al., 2016; Savitsky et al., 2020).\n\nPrevention of farmhand injuries is an key priority to avoid the economic loss, reduction of quality of life and emotional and social alterations resulting from such injuries (Angoules et al., 2007). Specific interventions, legislative or otherwise, ought to be designed to achieve practical safety standards (Voaklander et al., 2006). Das states that the majority of these injuries result from human factors (73%), with machine factors contributing to only 13% (Das, 2014). Imperatively, therefore, efforts by governments and/or employers should be concentrated on worker education especially on occupational health and safety (Naseer et al., 2016). In addition, a design change should be strongly considered to guarantee safety (Kumar et al., 2013; Paul, 2012).\n\nOur study had several limitations. First, we did not assess the handedness of the subjects. This would have enabled us to determine if there was any association between handedness with severity of injury or with the period taken to resume work. Secondly, our study had a relatively small sample size which weakens the strength of our findings and potentially affects the generalizability of our conclusions. Lastly, the design of our study limited the assessment of the possible effect of gender differences on the patterns of injury, treatment offered or on the period of return to gainful activities. The proportion of female sex was also low in our study - this might adversely affect the generalizability of our findings. Nevertheless, we are confident that the insights from our work will raise awareness on this problem, avail the much-needed literature from our region and hopefully inform interventions to curb the chaff cutter menace.\n\nIn conclusion, chaff cutter injuries contribute considerably to hand amputations at our center. The majority of patients with severe injuries and those undergoing amputations do not return to gainful activities one year after sustaining the injury. Further research is needed into the safety features of chaff cutters in use in Nakuru county to help reduce such injuries. The prolonged interval to return to work might also suggest increased dependency at a young age.",
"appendix": "Data availability\n\nFigshare: Chaff Cutter Hand Injuries from Nakuru Kenya. https://doi.org/10.6084/m9.figshare.21213293.v1 (Wanjara and Oduor, 2022).\n\nThis project contains the following underlying data:\n\n• Chaff Cutter Hand Injuries from Nakuru Kenya.xlsx. (Data on baseline characteristics, injury pattern and severity, and period to return to work)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 4.0 Public domain dedication).\n\n\nAcknowledgments\n\nWe would like to acknowledge the efforts of Moses O. Odhiambo who is a clinical data analyst at AIC Kijabe Hospital, Kenya, for assisting us with data analysis.\n\n\nReferences\n\nAli D, Kaiser MA, Khokhar MI, et al.: Fodder cutter (Tokka) injuries: A preventable morbidity. JPMA. The Journal of the Pakistan Medical Association. 2021; 71(3): 1022–1024. PubMed Abstract | Publisher Full Text\n\nAngoules AG, Lindner T, Vrentzos G, et al.: Prevalence and current concepts of management of farmyard injuries. Injury. 2007; 38(5): S26–S33. PubMed Abstract | Publisher Full Text\n\nBebe B, Rademaker C, Lee J, et al.: Executive summary Sustainable growth of the Kenyan dairy sector – A quick scan of robustness, reli- ability and resilience. Wageningen U R. 2015: 1–6.\n\nCampbell DA, Kay SP: The Hand Injury Severity Scoring System. Journal of Hand Surgery (Edinburgh, Scotland). 1996; 21(3): 295–298. PubMed Abstract | Publisher Full Text\n\nCooper SP, Burau KE, Frankowski R, et al.: A cohort study of injuries in migrant farm worker families in South Texas. Annals of Epidemiology. 2006; 16(4): 313–320. PubMed Abstract | Publisher Full Text\n\nDas B: Agricultural work related injuries among the farmers of West Bengal, India. International Journal of Injury Control and Safety Promotion. 2014; 21(3): 205–215. PubMed Abstract | Publisher Full Text\n\nHe Y, Hu J, Yu ITS, et al.: Determinants of Return to Work After Occupational Injury. Journal of Occupational Rehabilitation. 2010; 20: 378–386. PubMed Abstract | Publisher Full Text\n\nKumar A, Singh JK, Singh C: Prevention of chaff cutter injuries in rural India. International Journal of Injury Control and Safety Promotion. 2013; 20(1): 59–67. PubMed Abstract | Publisher Full Text\n\nMucci N, Traversini V, Lulli LG, et al.: Upper Limb’s Injuries in Agriculture: A Systematic Review. International Journal of Environmental Research and Public Health. 2020; 17(12): 4501. PubMed Abstract | Publisher Full Text\n\nMutavi K: Determinants Of Adoption Of Forage Technologies Among Peri-Urban Dairy Farmers In The Semi-Arid Region Of South Eastern Kenya. Afribary. 2021. Reference Source\n\nNaseer AC, Muhammad A, Muhammad ZI, et al.: Fodder Cutter Amputations-Evaluation of Risk Factors. Journal of Pakistan Orthopedic Association. 2016; 28(2): 46–49.Reference Source\n\nPatel T, Pranav PK, Biswas M: Nonfatal agricultural work-related injuries: A case study from Northeast India. Work (Reading, Mass.). 2018; 59(3): 367–374. PubMed Abstract | Publisher Full Text\n\nPaul NM: The outcomes of treatment of hand injuries at Moi Teaching & Referral Hospital, Eldoret, Kenya. Moi University;2012.Reference Source\n\nPratt DS, Marvel LH, Darrow D, et al.: The dangers of dairy farming: the injury experience of 600 workers followed for two years. American Journal of Industrial Medicine. 1992; 21(5): 637–650. PubMed Abstract | Publisher Full Text\n\nSavitsky B, Radomislensky I, Goldman S, et al.: Socio-economic disparities and returning to work following an injury. Israel Journal of Health Policy Research. 2020; 9(1): 35. PubMed Abstract | Publisher Full Text\n\nShrestha KM, Shrestha B, Kandel PR, et al.: FODDER CUTTER MACHINE INJURIES OF HAND. Journal of Universal College of Medical Sciences. 2018; 6(1 SE-Original Articles): 14–18. Publisher Full Text\n\nVoaklander DC, Kelly KD, Rowe BH, et al.: Pain, medication, and injury in older farmers. American Journal of Industrial Medicine. 2006; 49(5): 374–382. PubMed Abstract | Publisher Full Text\n\nWairegi A: Pattern of Hand Injury in Patients seen at kenyatta National Hospital. University of Nairobi;2019.Reference Source\n\nWanjara S, Oduor P:Chaff Cutter Hand Injuries from Nakuru Kenya. [DATASET].2022. Publisher Full Text"
}
|
[
{
"id": "157449",
"date": "20 Dec 2022",
"name": "Joseph Wanjeri",
"expertise": [
"Reviewer Expertise Plastic and Reconstructive Surgery",
"Research Methodology. Research interest: Burn injuries"
],
"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 good article based on the results of a descriptive retrospective study. The title is however misleading because the study was conducted at only one hospital/institution in Kenya and the results therefore may not apply to the whole country. In other words, the sample is not representative of the whole population of Kenya.\nThere are a few grammatical errors including two instances of incorrect word use: Instead of ‘poised’ the authors could have used ‘are likely’ and in place of ‘paramount’ they should have simply used ‘needed’. There are also instances where sentences needed to be merged to improve the grammar. I appreciate however that English is not the authors’ first language.\nThis was a descriptive retrospective study but the researchers took liberty to apply analytic statistics which I feel was inappropriate and as a result of it some of the inferences and conclusions can be challenged. However, in their discussion the researchers do acknowledge the study limitations which is a good thing.\nConcerning the recommendation, the authors cite other researchers who reported that human/user/operator factors were more important in chaff cutter injuries than machine/equipment factors. It would have been better to recommend that further research is needed to determine the risk factors for chaff cutter injuries seen at Nakuru Level 5 Hospital.\nAll in all this was a good seminal research for Nakuru county in Kenya and the report of which will facilitate future 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?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "216314",
"date": "31 Oct 2023",
"name": "Salah Fuad Issa",
"expertise": [
"Reviewer Expertise Agricultural safety",
"machine safety",
"grain 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\nThis paper evaluated chaff or fodder cutter injuries in a hospital in Kenya. It followed up with 47 individuals who received injuries due to fodder cutters and found that the majority where male between ages 20-40 years old and those who received severe injuries (amputations) were more likely not to return to work a year after the injury. This study builds on existing reports in Pakistan and other countries on the dangers of fodder cutters.\nDescribe the reasons you used different statistical methods to calculate correlation.\nIn figure 1, I would add what each injury represents in terms of HISS score. For example, figure A is graded with a HISS score below 20 and so on.\nTable 1 needs rework, you are using brackets as % for rows, but when you reach the total it becomes across category, it is a bit hard to follow. Also missing some values in the table (example total male incidents).\nFor surgical procedure and injury level in table 1, what method did you use to calculate p-value, not clear from methods.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "216316",
"date": "01 Nov 2023",
"name": "Mahmoud A Hifny",
"expertise": [
"Reviewer Expertise Plastic Surgery",
"Hand Surgery",
"Microsurgery",
"Burn",
"Reconstructive 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\nThank you so much for your kind invitation to review this article entitled “Hand Injuries in Kenya: a chaff cutter menace“\nIn this research, the authors conducted a descriptive study of 47 patients presenting with chaff cutter hand injuries at their center over a one year period. They found that the majority of patients with severe injuries according to the HISS score were between 21 and 40 years (58.8%), and all of them underwent an amputation and many of them had not resumed their work again. The authors claimed that chaff cutter injuries contribute considerably to hand amputations and it is paramount to identify the safety features of using chaff cutters in their region in order to reduce such injuries.\nThis article is well-written with a nice flow and relevant information. The topic is of great significance given the increased frequency of hand injuries following increasing mechanization of the chaff cutter which predisposes workers to high risks for injuries with devastating outcomes.\nAlthough the authors represent a good descriptive retrospective study with an excellent review of the previous literature in their discussion, I have a few minor issues with regard to this study.\nThe authors stated that “We found a positive correlation between age and severity of injury”. Could you describe an explanation of this correlation in your opinion?\nAlso the authors reported that “At one year after the injury, majority of patients in our study had not returned to their pre-injury occupations with the majority being those with severe/major injuries”. It would be better to add a percentage instead of the word ‘majority’\nI feel that it is appropriate to discuss the author’s recommendations, from their point of view, the safety measures that should be applied when using the chaff cutter in order to reduce the incidence of such injuries. Or it would be better that the authors cite other researchers who described the safety measures to minimize the hazards of using this machine but the researchers.\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": []
}
] | 1
|
https://f1000research.com/articles/11-1255
|
https://f1000research.com/articles/11-1253/v1
|
04 Nov 22
|
{
"type": "Review",
"title": "Role of RAS signaling in ovarian cancer",
"authors": [
"Lubna Therachiyil",
"Anjana Anand",
"Abdullah Azmi",
"Ajaz Bhat",
"Hesham M. Korashy",
"Shahab Uddin",
"Lubna Therachiyil",
"Anjana Anand",
"Abdullah Azmi",
"Ajaz Bhat",
"Hesham M. Korashy"
],
"abstract": "The RAS family of proteins is among the most frequently mutated genes in human malignancies. In ovarian cancer (OC), the most lethal gynecological malignancy, RAS, especially KRAS mutational status at codons 12, 13, and 61, ranges from 6–65% spanning different histo-types. Normally RAS regulates several signaling pathways involved in a myriad of cellular signaling cascades mediating numerous cellular processes like cell proliferation, differentiation, invasion, and death. Aberrant activation of RAS leads to uncontrolled induction of several downstream signaling pathways such as RAF-1/MAPK (mitogen-activated protein kinase), PI3K phosphoinositide-3 kinase (PI3K)/AKT, RalGEFs, Rac/Rho, BRAF (v-Raf murine sarcoma viral oncogene homolog B), MEK1 (mitogen-activated protein kinase kinase 1), ERK (extracellular signal-regulated kinase), PKB (protein kinase B) and PKC (protein kinase C) involved in cell proliferation as well as maintenance pathways thereby driving tumorigenesis and cancer cell propagation. KRAS mutation is also known to be a biomarker for poor outcome and chemoresistance in OC. As a malignancy with several histotypes showing varying histopathological characteristics, we focus on reviewing recent literature showcasing the involvement of oncogenic RAS in mediating carcinogenesis and chemoresistance in OC and its subtypes.",
"keywords": [
"Ovarian cancers",
"RAS",
"Oncogene",
"mutation",
"cell signaling"
],
"content": "Introduction\n\nGynecological malignancies in women’s reproductive organs seriously threaten female lives. Primarily classified based on the organ affected, gynecological cancers are of five major types, ovarian, cervical, uterine, vaginal, and vulvar.1,2 OC is the most lethal gynecological malignancy and the fifth prominent cause of death in females worldwide.3 Characterized by the poor outcome and relatively lower survival rate, OC is presented with several gene mutations.4 Until now, four major gene mutations are stated to have highly correlated to the occurrence of OC including TP53, KRAS, BRCA1/2 and PIK3CA, ultimately leading to several characteristics of the tumor cells, including abnormal DNA repair mechanisms, impaired tumor suppression, oncogene gain of function, and epigenetic inactivation.4,5 In OC, KRAS mutation is one of the most frequently observed abnormalities.6 Though typically considered to be a single disease, OC is classified into various sub types based on the origin of the tumor and the cellular histology.7\n\nRAS is a family of intrinsic GTP-binding proteins involved in various crucial cellular signal transduction pathways that fundamentally regulate cell growth, differentiation, cell adhesion and migration, and survival.8–10 Among the small G-proteins, the RAS subfamily is the most studied, due to their crucial involvement in human tumorigenesis.11 RAS is one of the major pathways found to be the most frequently mutated in several cancers, including pancreatic,12 lung,13 colorectal,14,15 ovarian,16 and hematopoietic malignancies.17,18\n\nEven though OC is majorly driven by several genetic mutations,19 the role and involvement of RAS mutation in this cancer have been scarcely reviewed before. In this review, we will discuss the significance of RAS, its mutational status, and its role in the pathogenesis of different histological types of OC.\n\nThe RAS superfamily comprises more than 170 members,20 which can be classified into five major protein subfamilies: RAS, Rho, Rab, Ran, and Arf.21–23 Primarily discovered as a viral component that initiated viral sarcoma in rats by Jennifer Harvey,24,25 the oncogenic role of RAS has been known since then. Canonically, RAS superfamily proteins exist in either the active GTP-bound or the inactive GDP-bound state, their transformation being dependent on GTPase activating protein (GAP) and guanine nucleotide exchange factors (GEFs).26,27\n\nUntil now, five isoforms of RAS proteins have been identified, namely HRAS, KRAS, NRAS, MRAS, and RRAS.8 The HRAS, KRAS, and NRAS proteins share around 85% amino acid sequence identity and are widely expressed in cells. However, despite their similarities, studies have shown that KRAS is a fundamental protein in mouse development.28 Upstream of RAS includes several signaling pathways like epidermal growth factor receptor (EGFR (ERBB1)), human epithelial growth factor receptor 2 (HER2 (ERBB2)), HER3 (ERBB3), and ERBB4, which mediates cellular proliferation and migratory actions.29,30\n\nRAS proteins require post-translational modification by farnesylation, adding a farnesyl isoprenoid moiety catalyzed by farnesyltransferase (FTase) to be biologically active.31 This ensures the exact localization of RAS proteins at the inner surface of the plasma membrane, thus enabling them to recruit their target enzymes and initiate the signaling.32,33 Upon activation, RAS induces numerous downstream proteins, such as Raf-1/mitogen-activated protein kinase pathway, phosphoinositide-3 kinase (PI3K), as well as the GEFs for the RAS-like (Ral) small GTPases (RalGEFs) and the Rac/Rho pathway.34 Aberrant activation of RAS could lead to irregular cellular events such as cell proliferation, differentiation, and cancer.35,36 Alteration of the RAS-MAPK pathway due to mutations in RAS or RAF genes has been very often reported.37 RAS also activates BRAF, MEK1, and ERK, which regulate the transcription of genes that promote cancer. Moreover, RAS can activate the phosphatidylinositol 3-kinase (PI3K)-3-phosphoinositide-dependent protein kinase 1 (PDK1)-AKT pathway that facilitates cell growth and survival. RAS also activates the enzyme phospholipase C (PLC), that mediate calcium signaling and the protein kinase C (PKC).38\n\nRAS serves as a cell signaling protein downstream of various receptor tyrosine kinases and upstream of many signaling pathways associated with cancer.39 When abnormally activated, RAS proteins initiate and collate many proliferative signaling pathways to exert a tumorigenic effect in tumor cells by significantly contributing to several aspects such as tumor growth, apoptosis, invasiveness, and angiogenesis.32,40 Among the various cancer types, the global disease burden associated with RAS mutations accounts for approximately 19% of all cancer types engaged in tumorigenesis and tumor progression.40,41 Single mutations at codon 12, 13 or 61 result in abnormal RAS functioning leading to hyperproliferative disorders such as cancer.42\n\nIn humans, around 20% of all tumors show a gain-of-function mutation in one of the RAS genes.43,44 Genomic sequencing analysis of human cancer specimens identified KRAS gene as the most frequently mutated gene, followed by NRAS and HRAS.45,46 The incidence of RAS mutations in various cancers includes 57% in pancreatic cancer, 35% in the large intestine, 28% in the biliary tract, 17% in the small intestine, 16% in lung cancer, 15% in the endometrium, and 14% in OC.47\n\nAn aberrant RAS signaling can be contributed by various mutations in closely related RAS proteins, importantly KRAS being most frequently mutated (about 85%), followed by N RAS (about 15%), and HRAS (less than 1%).9,41,48 All these mutations are associated with GTPase activity of RAS, which prevents GAPs (GTPase Activating Proteins) from stimulating the hydrolysis of GTP on RAS, which in turn leads to the accumulation of RAS in the GTP-bound active form.9 Moreover, mutations in the KRAS gene have been manifested to be involved in the pathogenesis of a variety of human tumors with pancreatic ductal adenocarcinoma (PDAC), colon cancer, and non-small cell lung cancer (NSCLC) showing the highest rate of RAS mutations.47,49\n\nA retrospective analysis by Zhu X. et al. reported a correlation between RAS mutational status and clinicopathological features among the colorectal cancer patients. Patients who foster mutant RAS has unique pathological characteristics, phenotypes, and staging.41,50 Several studies have portrayed a remarkable correlation of RAS mutation with overall survival (OS) and poor prognosis. A comprehensive analysis conducted on metastatic colorectal cancer patients presented that, patients with a mutation in codon 12 of the KRAS gene demonstrated significantly poor OS compared to those with a wild-type mutation. However, the difference was insignificant for patients with KRAS mutation at codon 13.51 Studies in pancreatic cancer cells highlight a novel approach to metabolic reprogramming created by combining glutamine inhibitors with chemotherapeutic drugs. This may be a potential therapeutic intervention to address the mutant KRAS that confers to chemoresistance in clinical studies.52\n\nDespite the enormous studies conducted, RAS, however, stood apart; it is allegedly termed “undruggable” and direct RAS inhibitor development proved exceedingly challenging.53 Direct drugging of RAS protein was considered paradoxical due to the absence of a drug-binding pocket; consequently, studies started focusing on the proteins upstream and downstream of RAS that could help suppress the oncogenic signal.41 Albeit drugging RAS had initial failures, tremendous efforts in understanding the complications of RAS have initiated new avenues for next-generation anti-RAS drug discovery by NCI (National Cancer Institute).\n\nOC, the uncontrolled division of malignant cells of ovaries,3 is a leading gynecologic malignancy characterized by high mortality rates and poor prognostic outcomes.54,55 In accordance with the American cancer society, in 2019, about 22,530 women were diagnosed with OC, and a mortality rate of 13,980 was reported.3 Debulking surgery followed by chemotherapy and targeted therapy are the mainstay treatment strategies; however, most patients relapse due to chemoresistance.56 There has been minimal progress in transitioning the remarkable strides in the multi-omics approach, including genomics, proteomics, and radiomics, into effective clinical administration of OC.3 Despite the advancements in the treatment of OC, several studies report a relative five-year survival rate of less than 45%, and there has been no significant improvement in increasing the OS. Chemoresistance with the subsequent relapse and the side effects of the chemotherapeutic drugs urges the need to identify a better and reliable diagnostic, prognostic and predictive biomarker that would enable early detection and better screening.3,57,58 Considering the heterogeneity, genetics, and molecular status of OC and the introduction of targeted therapies could significantly influence the management of OC.59 The potential therapeutic targets identified for OC includes anti-VEGF/VEGFR angiogenic inhibitors, WNT inhibitors, non-VEGF angiogenic inhibitors, SONIC Hedgehog (SHH) inhibitors, NOTCH inhibitors, PARP inhibitors, EGFR inhibitors, folate receptor inhibitor, IGFR inhibitors, PI3K/PTEN inhibitors, and NF-kB inhibitor.60,61\n\nIn a study involving 72 Japanese OC patients, RAS was found to be the third most commonly mutated gene with a frequency of 3.9% regardless of the histological subtypes, observed as mutually exclusive. Moreover, KRAS was more frequently found to be mutated in clear cell carcinoma patients (25.9%).62\n\nThe KRAS mutations are the most commonly observed RAS isoforms, including KRAS4A and KRAS4B, wherein the mutations occur in exons 1 or 2.63,64 Furthermore, the variant located in the 3′UTR of the KRAS gene (rs61764370 T > G), is associated with higher risks of several cancers such as OC.65 However, it is noticed that KRAS mutations occur mostly in tissues with FIGO I and II than in FIGO III and IV stages, indicating KRAS mutation to be happening at an earlier part of cancer development.66,67\n\nIntriguingly, in OC, the most commonly mutated genes include TP53, PIK3CA, ARID1A, and KRAS disproportionately among the different histological subtypes with respect to their frequency of occurrence.68,69 Moreover, KRAS mutation has been a common event in many histotypes of OC.70,71\n\nReports from previous studies confirm that the mutational status of KRAS shows an increasing trend from normal ovaries (0%) to benign mucinous ovarian tumors (BMOT) (57%), mucinous borderline ovarian tumors (MBOT) (90%), and mucinous OC (MOC) (76%) signifying its key involvement in the succession of benign tumors to aggressive OC.72\n\nIn OC, KRAS mutations are observed in codons 12, 13, and 61, leading to a constitutively active RAS protein paving its way to an aberrant increase in tumor growth and malignant transformation.43 KRAS mutation is also found to be a biomarker for poor outcomes and chemoresistance in OC.73,74 In a comprehensive study, Mayr et al., assessed KRAS and BRAF mutations in a series of ovarian tumors and found that mutations usually occur at codons 12 and 13 of the KRAS gene with an occurrence rate of 3–11%.71 Another study showed that KRAS mutations at codon 12 were more prevalent in borderline tumors than malignant ones.75 Furthermore, a higher expression of Rab23, a member of RAS subfamily, is evidenced in OC tissues and is associated with the advanced FIGO stage. It is also known for its pivotal part in the malignant characteristic of OC and can be considered a potential therapeutic target for OC.76\n\nGenetically, OC represents a distinct subset of cancers with extensive genomic variations.77 Broadly classified into epithelial OC (EOC), sex cord-stromal tumors (SCSTs), ovarian germ cell tumors (OGCTs), and small cell carcinoma of the ovary (SCCO), based on the origin of cancer,78 EOC accounts for 90% of malignant ovarian neoplasms.79 Currently, five major types of EOC is characterized: high-grade serous (HGSOC 70%), low-grade serous (LGSOC 10%), mucinous (MOC, 3%), endometrioid (EnOC, 10%), and clear-cell (OCCC,10%) carcinomas.77,80,81 In addition, borderline ovarian tumors (BOT), also known as semi-malignant ovarian tumors, account for around 15% of EOC.82 A broad classification of OC is represented in Figure 1.\n\nOC is broadly classified into epithelial, germ cell, sex cord stromal and mixed cell types based on cellular origin, and subclassified based on the site of tumor occurrence and mutational status (created with biorender.com).\n\nIn the next section, we briefly discuss about the frequency (Table 1) of RAS mutations in different types of OC and their clinical relevance (Table 2).\n\nLGSOC is a morphologically discrete subtype of OC, accounting for ~10% of serous carcinomas.110 LGSOC is a distinct histological subtype that accounts for only 3% of EOC. It’s clinical characteristics include the diagnosis at a young age, prolonged OS, and chemoresistance.104,111 In a previous study, up to 70% of LGSOCs were found to have KRAS mutation.105 The LGSOCs have more frequent mutations in KRAS, BRAF, ERBB2, and NRAS, which are the signature genes involved in the MAPK signaling pathway.77,104,111,112 LGSOC affects younger women aged between 43 and 47 years.113 KRAS mutations are common (>70%) in recurrent LGSOC,105 which usually occurs in SBOTs with LGSOC recurrence. In low-grade serous ovarian carcinoma, along with the BRAF and KRAS mutations, studies have also reported an NRAS mutation only in serous ovarian carcinoma, suggesting NRAS to be an oncogenic driver in serous OC.107 Another study reported that NRAS mutations were present in 26.3% of LGSOC and were anticipated to be a potent initiator of tumorigenesis.83 On the contrary, studies also suggest that the low mutation rates of NRAS alone may play only a minor role in the LGSOC development.109 Somatic mutations in MAPK signaling pathway genes such as KRAS, BRAF, and NRAS are highly prevalent in LGSOC.110 In the comprehensive genomic profiling study, Zhong et al. reported that KRAS mutation was a characteristic feature of LGSOC.108 A report from Zuo et al. suggests that KRAS mutations are significantly associated with invasive implants of borderline serous tumor. They found that KRAS mutation is a significant prognostic indicator for tumor recurrence as higher recurrence rate of 71% was observed with patients carrying KRAS mutation wherein it was as low as 21% in patients without KRAS mutation.114\n\nIn a study initiated by Xing et al., the mutational status of NRAS was determined at the hotspot region of exon 3 in 98 cases, and they detected NRAS Q61R mutations in 7.4% of LGSOC cases and 3.6% of non-invasive LGSOCs. This further suggests a lesser role of NRAS mutations in the occurrence of LGSOC.109 These findings are also in accordance with previous studies where NRAS mutation was not observed in either SBT/APSTs or non-invasive LGSOCs.83,107\n\nMoreover, the co-existence of NRAS and BRAF mutations in LGSOC contradicts the type of mutations among MAPK pathway proteins. This further indicates that NRAS mutations might have a functional role in mediating other tumorigenic functions, such as invasion or tumor advancement115–117; however, this warrants further investigation.\n\nChemoresistance is a challenging issue in the treatment of OC.118 About 70% of the patients at the advanced stage are most refractory to platinum-based chemotherapy.68,119 Previous reports suggest that LGSOCs are refractory to chemotherapy compared to the HGSOC.120 The association of RAS with STAT3 has been proved to contribute to tumor growth, metastasis, and resistance to cisplatin treatment. This has also been known for the differential regulation of MAPK- and PI3K/AKT-mediated ERS and autophagy.118 Moreover, platinum resistance was plausibly significant among the postmenopausal women with EOC among KRAS variant-positive patients than in the non-KRAS variant patients, making KRAS variant a prominent predictor of platinum resistance. Given the correlation between the KRAS variant and the resistance to platinum-based chemotherapy, the KRAS variant is considered as a biomarker of poor outcome.74 Reports from Kato et al. showed that combination therapy using MEK inhibitor trametinib and aromatase inhibitor letrozole resulted in a better remarkable response in a woman with aggressive ER-positive, KRAS-mutated LGSOC. However, this effect was not observed when used as monotherapies.121 Regardless of the enormous research, the chemoresistance due to RAS mutation still prevails as a major cause of concern and could be a promising approach to focus on the RAS initiated resistance to instigate a better treatment regimen for OC.\n\nThe high-grade serous ovarian carcinoma (HGSOC) is the most common form of EOC, accounting for more than 70% of its frequency of occurrence and accounts for 70–80% of death in OC patients.122,123 They portray a high degree of invasiveness and are mostly diagnosed at the later stage of development. They harbor some notable mutations that include: somatic TP53 mutation, germline BRCA1 and BRCA2 defects, and lower frequencies of RB1, PTEN, and NF1 mutations112,124; scarcely they carry KRAS and BRAF mutations.5\n\nMOC, which is characterized by larger cells filled with fluid, is a rare subtype of EOC.125 MOC are the histological subtype rarely reported in western countries and more commonly reported in Thailand.102 The majority of the cases are presented as borderline tumors or at the early disease stage (FIGO I-II).77,89 They have a better prognosis in case of early diagnosis but worse if diagnosed at the advanced stage. They have also been known for their poor response rates to platinum-based chemotherapy.126 The most significant genetic alteration observed in mucinous carcinoma is the KRAS (71%) and TP53 (57%) mutations.125 Other mutations such as PIK3CA (8%) and BRAF (2%) have also been reported as an event of occurrence in MOC.102 A higher amplification rate and overexpression of ERBB2 and ERBB3 mutation were also reported in mucinous ovarian tumors.90 Mutations in codon 61 are rare in OC; moreover, it was found to frequently occur in mucinous adenocarcinomas and rarely in other common EOC. KRAS mutations are common in mucinous ovarian tumors and are identified in 40–50% of MOC cases.127–129\n\nIn a study aimed at identifying the mutations in KRAS that were analyzed by direct genomic sequencing, the group determined that the overall frequency of RAS gene mutations was 27% found in most of the mucinous tumors.130 The study portrayed about 11% of the cases with KRAS mutation at codon 12 and one with a mutation at codon 13 in ovarian tumors. They also demonstrated a noteworthy prognostic effect of KRAS mutation in EnOCs compared to the other histological subtypes.103 A case study also reported the existence of the same KRAS mutation in the carcinoma cells and the functioning stromal cells, suggesting some regions possibly having a common origin.131\n\nMackenzie et al. performed next-generation sequencing analysis with two MOC cases, previously established to have ERBB2 over expression heterogeneity to identify sub-clonal populations containing either KRAS mutation or ERBB2 amplification in order to establish if they were expressed independently or simultaneously. This study shows that KRAS mutations were the most frequently observed, with an incidence rate of 64.9% in MOC. However, concurrent ERBB2 amplification and KRAS mutation were observed in many cases.89\n\nPanyavaranant et al.'s report using 50 cases of primary mucinous ovarian carcinoma cases evaluated the relationship between genetic mutation and patients’ prognosis. Among the studied samples, 54% of the cases showed KRAS mutation; however, these cases had excellent prognoses.102 A cohort study by Nodin et al. demonstrates an important correlation between KRAS mutations, mucinous histological subtype and progesterone receptor expression in OC patients.103\n\nEnOC is associated with endometriosis and has a genetic resemblance to the endometrial tissue.112 They account for about 10–20% of all OCs diagnosed at the early stage and are sensitive to platinum-based chemotherapy.77 They are further classified as high- and low-grade endometrioid carcinoma, in which the high-grade closely resembles HGSOC clinically and molecularly.77,112 The genes that are frequently mutated are CTNNB1 ~50%, PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α) ~40%, PTEN ~25%, KRAS ~35%, and ARID1A (AT-rich interaction domain 1A) ~30%. Very few also harbor mutant PPP2R1A.77,111,112,132 An elevated frequency of KRAS mutation in the human tissue specimens was hypothesized as the rationale for the chemoresistance and aggressiveness of EnOC.133 A previous study also demonstrated the significant prevalence of the overexpression and amplification of KRAS gene in the aggressive phenotypes compared to the primary lesions.134 Reports also suggest that the inflammatory, NF-κB, RAS, and TGF-β signaling pathways play a pivotal role in the pathogenesis of EnOC.135 A retrospective analysis of the mouse model illustrates that the activation of the oncogenic KRAS allele provoked the epithelial component of the endometriosis to develop into benign epithelial lesions. They also reported that either the expression of the KRAS allele or conditional PTEN deletion in the ovarian epithelial surface resulted in preneoplastic ovarian lesions that showed an endometrioid glandular morphology.136\n\nSimilar to endometrioid cancer, OCCC is also associated with the endometriosis and is most frequently observed in Asian countries, accounting for ~30% of cases in Japan and less than 10% of cases reported in Europe and the USA.111,112 They are normally diagnosed at an earlier stage and are generally associated with resistance to platinum-based chemotherapy and poor prognosis. The most frequently observed mutations at the genomic level are ARID1A of ~50%, PIK3CA of ~50%, KRAS of ~14%, and PTEN at ~5%.77,91–93 KRAS mutation in codon 12 exon 2 is observed in about 14% of OCCC, and an absence of NRAS and BRAF mutation. KRAS mutation was observed only in codon 12 and not in codon 13, validating the heterogeneity of EOC characterized by distinct molecular signatures.92 Reports also suggest that, along with KRAS, the other gene components of MAPK pathway PPP2R1A and ERBB2 were also frequently mutated in OCCCs and EnOCs.137 The ovarian tumor tissue samples and their corresponding blood sample analysis from a group of Japanese women diagnosed with OCCC illustrated the alterations in genes involved in the RTK/RAS signaling cascade in 29% of cases. This includes the amplification of ERBB2 (11%) and ERBB3 (5%), and mutations of ERBB2 (4%), ERBB3 (7%), KRAS (9%), and BRAF (2%).97 A whole genome sequencing of serum samples from the Korean patients diagnosed with OCCC revealed somatic mutation observed in genes that include PIK3CA (40%), ARID1A (40%), and KRAS (20%) in about 15 patients that correlates with PI3K/AKT, TP53, and ERBB2 pathways.138 In a retrospective analysis, KRAS mutations were detected among the Japanese patients in cells isolated from the regions of endometriosis adjacent to the site of carcinoma. Their DNA analysis of regions of endometriosis, atypical endometriosis and OCCC cells also displayed that KRAS mutation was observed only in the OCCC cells but not in endometriosis and atypical endometriosis. Their study hypothesized a correlation between KRAS mutation with malignant transformation of atypical endometriosis to OCCC.139 A pyrosequencing analysis conducted on 63 patients diagnosed with OCCC revealed a higher prevalence of PI3KCA mutations of about 32% compared to the KRAS mutation, which existed at only about 13%. They also displayed a total absence of BRAF mutation and involvement of the PI3K/AKT pathway as an important event in carcinogenesis and progression, suggesting that OCCC harbor distinct molecular signatures with respect to other EnOC.140\n\nBOT are epithelial tumors characterized by variable nuclear atypia.141 As first described by Taylor in 1929, this cancer was first described as a semi-malignant disease142 characterized by a lack of stromal invasion.143 Dobrzycka et al. analyzed the mutation at codon 12 of the KRAS gene in 78 women with ovarian tumors, including 64 invasive OCs and 14 BOTs, using an RFLP-PCR technique. KRAS codon 12 gene mutations were observed in 6.2% of OC tissue and 14.3% of BOTs. KRAS mutations were found to have a significantly higher frequency in MOC and BOT than serous tumors (p<0.01). They also found that mutation frequency was correlated with the histological type of tumor but not with stage, grade, or patient age.144\n\nStudies show that 88% of serous BOTs are presented with KRAS or BRAF mutations, suggesting their importance in developing SBOTs.71,100 In mucinous BOT (MBOT), KRAS mutations are reported to be at a higher incidence level of 92.3%.89 RAS mutation, along with ERBB2 and BRAF mutations, can activate the MAPK pathway, ultimately leading to cell proliferation and cancer progression.145 Ohnishi and his group have identified KRAS mutations in 43.8% of MOC cases. Specifically, the most predominant mutations were observed at G12D and G13D. In their study, the KRAS, BRAF, TP53, and PIK3CA mutational status in mucinous tumors of the ovary were identified using direct sequence analysis on 38 tumor specimens, including 16 MOCs, 10 MBOTs, and 12 MCAs. KRAS mutations were detected in MOC (43.8%) and MBOT (20%) cases and not in MCA cases. Moreover, the frequency of occurrence was higher in MBOT. These findings indicates that, KRAS mutations in MBOT might have a role in progression to MOC.101\n\nRAS is found to crosstalk with many other tumor-inducing and tumor-suppressing pathways to regulate several physiological and pathological characteristics in OC. Mutant RAS interaction with p53, a tumor suppressor gene, is observed to regulate cisplatin resistance in OC via HDAC4- and HIF-1α-mediated regulation of apoptosis and autophagy. The group also found that ERK and AKT active RAS mutants are mutually suppressive, demonstrating that a crosstalk between RAS/p53 signaling and STAT3 regulates metastasis and chemoresistance in OC cells via the slug/MAPK and PI3K/AKT/mTOR- mediated regulation of epithelial to mesenchymal transition (EMT) and autophagy.118 Downregulation of beclin 1, an important protein involved in autophagy, by RAS via PI3K/AKT and MEK/ERK pathway has been proved to inhibit autophagy.146 Furthermore, loss of beclin1 activity is evidenced to be associated with several cancers including breast, ovarian and prostate cancer.147\n\nIsoprenyl cysteine carboxyl methyltransferase (Icmt), is an enzyme that catalyzes the final step of oncoproteins' prenylation,148 and is known to have a role in growth and survival of various cancer cells.149 Icmt expression is found to be upregulated in EOC patients irrespective of age and tumor stage. However, this upregulation is observed both at mRNA and protein levels. Moreover, OC cell lines with higher Icmt levels have been shown to express chemoresistance to drugs. Liu et al. showed RAS activation as a crucial effector for Icmt in OC cells. Using in vitro and in vivo studies, this group demonstrated that Icmt modulates RAS activation in OC cells and imparts chemoresistance in these cells.150\n\nFSH receptor binding inhibitor (FRBI) is an FSH antagonist that blocks FSH binding to its receptor.151 FRBI is believed to suppress the tumorigenesis of OC by reducing cMyc, KRAS, and FSHR levels in the presence of FSH. Wei and his group reported that FRBI inhibited carcinogenesis and progression of OC by suppressing KRAS.152\n\nAs reported earlier, RAS is activated by the son of sevenless (SOS1), whose expression is mediated by ligands that activate the aryl hydrocarbon receptor (AhR). This DRE-dependent activation of SOS is found to hasten cell proliferation in HepG2 hepatoma cells.153 Though our group has already reported the involvement of AhR in inducing tumor proliferation in OC, the cross-talk between AhR and the RAS pathway still needs to be investigated thoroughly.154 TCDD, an AhR activator, is found to induce RAS activity in hepatoma cells; however, studies contradict each other in terms of tissue specificity of this cross-talk.155–157 Moreover, a microarray global expression analysis report has shown that RAS MAP kinase pathway activation observed in TCDD-treated human hepatoma cells to be AhR-dependent.158\n\nA recent study by Li et al. examined the effects of dysregulated micro-RNA expression in the progression of OC. The group tried to unveil the mechanism by which reduced expression of miR-324-3p could suppress OC proliferation. They found that WNK2, a cytoplasmic protein involved in ion transport,159 is upregulated and promotes the growth and invasion of OC cells SKOV3 and CAOV3 by activating the RAS pathway. Moreover, phosphorylation modification levels of most proteins, most significantly RAS was observed when WNK2 was knocked down in SKOV3 and CAOV3 cell lines as analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis.160\n\nReports from a recent study reveal that tumor progression was abolished upon the inhibition of RAS GTPase-activating protein SH3 domain-binding protein 1 (G3BP1)161 involved in the RAS signaling pathway which is also involved in the development of several cancers such as breast, colon, and gastric cancer.162 Figure 2. depicts the effect of oncogenic activation of RAS in OC and its pathological outcome.\n\nRAS mutation leads to aberrant activation of the RAS pathway leading to a cluster of other pathway activations involved in tumorigenesis (created with biorender.com).\n\nAs a crucial gene mutated, the effects correlating with increased tumorigenesis, aggressiveness, and invasiveness in OC indicate RAS as a potential candidate for targeted therapy. RAS proteins are considered merely undruggable owing to their lack of drug binding pockets and to the very low binding affinity of GTP for RAS, which also makes GTP-competitive inhibitors inefficient.163–165 Inhibiting RAS directly has proven challenging and has diverted researchers to consider alternate approaches targeting RAS downstream effectors.164 Salirasib is a RAS inhibitor that interferes with the localization of RAS protein by removing the protein from the cellular membrane, resulting in reduced intracellular RAS, thereby affecting its downstream effectors.166 Due to the extensive crosstalk of RAS with other pathways such as PI3K, the early attempt to inhibit a single pathway usually ended in promoting cellular resistance to chemotherapeutic drugs via a feedback loop. In the study conducted by Kim et al., when GDC, a pan inhibitor of PI3K, was administered to OC cells with KRAS mutation, the subsequent reduction in PI3K signaling resulted in over-expression of KRAS. However, when the inhibitor was combined with si-KRAS, this resulted in a synergistic anti-cancer effect in both ovarian OSE cell lines and allograft OC model impeding cell proliferation and migration and also inducing apoptosis in tumors in vivo.167\n\nMost studies published until now have confirmed that rather than targeting RAS itself, many targeted therapies use inhibitors of proteins involved in mutated RAS-activated downstream signaling pathways such as the RAF-MEK-ERK pathway.168 Desai et al. evaluated the effect of Lifirafenib, primarily an RAF family kinase inhibitor, in tumors with KRAS mutations via dose escalation and observed antitumor activity in KRAS mutated endometrial cancer.169\n\nEven though profusely known to be undruggable, certain drugs that selectively target KRASG12C, not wild type or other KRAS mutants, have been discovered170,171 AMG510, which potentially keeps RAS in an inactive GDP binding state,172 MRTX849 (adagrasib), an oral selective inhibitor of RASG12C that targets the mutant cysteine 12 of KRAS, ultimately keeping RAS in an inactive state,173 and MRTX1133, a potent non-covalent inhibitor174 are selective inhibitors of KRAS mutants, in which MRTX849 is currently in Phase I/II clinical studies.175 Though these drugs are effective in attenuating RAS activity,176,177 their effect on the cancer cells remains questionable due to some reports showing cell lines expressing KRASG12C, capable of sustaining the proliferating properties of cells despite the use of inhibitors, through adaptive feedback via wild-type RAS proteins.178\n\nDespite all the targeted therapy approaches defined, resistance to these inhibitors is developed. This includes mutations within the drug binding pockets, new KRASG12C protein production, feedback activations of the KRAS pathway, activation of both upstream and downstream mediators, etc.179 KRAS mutation is a predictive marker of poor response to anti-EGFR monoclonal antibody therapies.180–183\n\nIn a molecular profiling study with 55 patients with EOC, 35% were found to have ≥1 somatic mutation, including 23 KRAS and six NRAS. Out of this, 14 patients with KRAS/NRAS mutations treated with MEK inhibitor targeted combinations were subsequently enrolled in genotype-matched phase I or II trials. They observed that, in patients with KRAS mutation, a higher sensitivity to MEK inhibitors was observed, with seven patients showing a partial response, seven showing stable disease, and one showing disease progression.184 The synthetic lethality therapeutic approach aims to inhibit both downstream pathway activation and feedback regulation of KRAS to ensure efficient therapy outcomes. One such drug is AZDD5483, a cyclin-dependent kinase effective on KRAS mutant tumor inhibition at G0/G1 phase, as confirmed in colorectal and pancreatic cancer.185 In OC, this effect is achieved by combining MEK inhibitor (pimasertib) and PI3K/mTOR inhibitor (SAR245409, voxtalisib), identified by fluorescence resonance energy transfer imaging.186\n\nCancer stem cells (CSCs) are small subpopulation of cells within tumors with the potency for self-renewal, differentiation and tumorigenicity.187 Accumulated pieces of evidence suggest a role of OC stem cells (OCSCs) in facilitating metastatic cascade, in frequent disease recurrence and increased resistance.188,189 Few CSC markers, including ALDH1, CD44, CD117, and CD133 are considered to be useful predictive or prognostic biomarkers of OC.190 The platinum-based chemotherapy resistance and tumor cell stemness is associated with the recurrence in HGSOC. In an aggressive murine model of OC, the stem phenotypes with a gain of KRAS, MYC, and FAK genes were found to be associated with intrinsic platinum resistance and tumorsphere formation.191 Cisplatin-resistant EOC cell lines were found to significantly express OCSC markers and EMT activation triggered by activated PI3K/Akt/mTOR signaling indicating its correlation with chemoresistance in EOC. Moreover, treatment with an inhibitor BEZ235 in combination with cisplatin increased chemosensitivity in cisplatin-resistant EOC by inhibiting PI3K/Akt/mTOR signaling.192 A gene expression analysis revealed OC patients with a significantly higher expression of ROR1 having gene expression signatures associated with CSCs and shorter OS. ROR1 was also involved in promoting tumor-cell growth, metastasis, and tumor initiation, making ROR1 a potential target for therapies directed against OCSCs.193 A recent analysis conducted by Zhang et al. to identify potential core signaling pathways of OCSCs using integrated transcriptome data of OCSCs isolated ALDH and side population, two distinctive stem cell surface markers.194 A recent study by Shokouhifar et al. highlights the protocol for the generation of natural killer cells from umbilical cord blood hematopoietic stem cells by manipulating RAS/MAPK, IGF-1R and TGF-β signaling pathways that can be used for cancer immunotherapy.195 RAS associated acquisition of chemoresistance in OC is depicted in Figure 3. Though the mechanism underlying chemoresistance in OC is still ambiguous, numerous such reports suggests the integral role of CSCs in chemoresistance and recurrence. Hence, OCSCs are a plausible therapeutic target in overcoming therapeutic resistance and recurrence.\n\nActive RAS mutants initiates CSC properties in OC resulting in chemoresistance, tumor recurrence and poor patient outcome (created with biorender.com).\n\n\nConclusion\n\nOC is a crucial disease characterized by chemoresistance, higher recurrence, and lower survival rates. A vast plethora of studies has already demonstrated the involvement and influence of several genes and their specific mutational statuses to be a major cause of OC, from the early development towards progression to invasion and metastasis. Studies confirm that RAS is one of the most mutated genes in OC, specifically, KRAS at codons 12,13 and 61. As a significant protein that has shown to be both downstream effector of several signaling pathways such as EGFR (ERBB1), HER2 (ERBB2), HER3 (ERBB3), and ERBB4, and upstream effector of RAF-1/MAPK, PI3K, RalGEFs, Rac/Rho, BRAF, MEK1, ERK, AKT, PLC and PKC, a mutation in RAS thereby causing hyperactivation of proteins could result in dysregulation ultimately leading to cancer initiation and proliferation. KRAS mutation, one of the majorly observed mutation in OC, is a predicted biomarker for poor clinical outcomes and chemoresistance. Involvement of genetic mutations, however, demanded targeted therapy initiation in OC in addition to the conservative therapeutic method of cytoreductive surgery followed by platinum-based chemotherapy. RAS was primarily believed to be undruggable due to the lack of drug binding pockets. Most publications confirm that targeting the downstream effectors of RAS paved more effect.\n\nMoreover, as of its involvement in many other pathways such as cell proliferation, targeted therapy also had its disadvantages owing to the feedback loop, wherein inhibition of a single pathway ended up promoting chemoresistance. Recent advancements in targeting RAS utilize highly specific inhibitors that selectively target KRASG12C, not wild-type or other KRAS mutants. Targeting RAS, however, is much less explored in different histotypes of ovarian carcinoma and warrants further investigation.",
"appendix": "Data availability\n\nThere are no data associated with this article.\n\n\nReferences\n\nRahimian N, Razavi ZS, Aslanbeigi F, et al.: Non-coding RNAs related to angiogenesis in gynecological cancer. Gynecol. Oncol. 2021; 161: 896–912. PubMed Abstract | Publisher Full Text\n\nManzoor H, Naheed H, Ahmad K, et al.: Pattern of gynaecological malignancies in south western region of Pakistan: An overview of 12 years. Biomed Reports. 2017; 7(5): 487–491. PubMed Abstract | Publisher Full Text\n\nShaik B, Zafar T, Balasubramanian K, et al.: An Overview of Ovarian Cancer: Molecular Processes Involved and Development of Target-based Chemotherapeutics. Curr. Top. Med. Chem. 2020; 21(4): 329–346.\n\nGuo T, Dong X, Xie S, et al.: Cellular mechanism of gene mutations and potential therapeutic targets in ovarian cancer. Cancer Manag. Res. 2021; 13: 3081–3100. PubMed Abstract | Publisher Full Text\n\nTesta U, Petrucci E, Pasquini L, et al.: Ovarian Cancers: Genetic Abnormalities, Tumor Heterogeneity and Progression, Clonal Evolution and Cancer Stem Cells. Medicines. 2018; 5(1). PubMed Abstract | Publisher Full Text\n\nNakayama N, Nakayama K, Yeasmin S, et al.: KRAS or BRAF mutation status is a useful predictor of sensitivity to MEK inhibition in ovarian cancer. Br. J. Cancer. 2008; 99(12): 2020–2028. PubMed Abstract | Publisher Full Text\n\nHatano Y, Hatano K, Tamada M, et al.: A comprehensive review of ovarian serous carcinoma. Adv. Anat. Pathol. 2019; 26: 329–339. PubMed Abstract | Publisher Full Text\n\nRajasekharan SK, Raman T: Ras and Ras mutations in cancer. Cent. Eur. J. Biol. 2013; 8.\n\nDownward J: Targeting RAS signalling pathways in cancer therapy. Nat. Rev. Cancer. 2003 31. 2003 Jan [cited 2022 Aug 16]; 3(1): 11–22. Publisher Full Text Reference Source\n\nMalumbres M, Barbacid M: RAS oncogenes: The first 30 years. Nat. Rev. Cancer. 2003; 3.\n\nRepasky GA, Chenette EJ, Der CJ: Renewing the conspiracy theory debate: Does Raf function alone to mediate Ras oncogenesis? Trends Cell Biol. 2004; 14: 639–647. PubMed Abstract | Publisher Full Text\n\nForbes SA, Bindal N, Bamford S, et al.: COSMIC: Mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2011; 39(SUPPL. 1): D945–D950. PubMed Abstract | Publisher Full Text\n\nLohinai Z, Klikovits T, Moldvay J, et al.: KRas-mutation incidence and prognostic value are metastatic site-specific in lung adenocarcinoma: Poor prognosis in patients with KRAS mutation and bone metastasis. Sci. Rep. 2017; 7.\n\nDe Luca A, Maiello MR, D’Alessio A, et al.: The RAS/RAF/MEK/ERK and the PI3K/AKT signalling pathways: Role in cancer pathogenesis and implications for therapeutic approaches. Expert Opin. Ther. Targets. 2012; 16: S17–S27. Publisher Full Text\n\nBoutin AT, Liao WT, Wang M, et al.: Oncogenic Kras drives invasion and maintains metastases in colorectal cancer. Genes Dev. 2017; 31(4): 370–382. PubMed Abstract | Publisher Full Text\n\nRechsteiner M, Zimmermann AK, Wild PJ, et al.: TP53 mutations are common in all subtypes of epithelial ovarian cancer and occur concomitantly with KRAS mutations in the mucinous type. Exp. Mol. Pathol. 2013; 95(2): 235–241. PubMed Abstract | Publisher Full Text\n\nZhou JD, Yao DM, Li XX, et al.: KRAS overexpression independent of RAS mutations confers an adverse prognosis in cytogenetically normal acute myeloid leukemia. Oncotarget. 2017; 8(39).\n\nChen S, Li F, Xu D, et al.: The Function of RAS Mutation in Cancer and Advances in its Drug Research. Curr. Pharm. Des. 2019; 25(10): 1105–1114. Publisher Full Text\n\nDella Pepa C, Tonini G, Santini D, et al.: Low Grade Serous Ovarian Carcinoma: From the molecular characterization to the best therapeutic strategy. Cancer Treat. Rev. 2015; 41: 136–143. PubMed Abstract | Publisher Full Text\n\nColicelli J: Human RAS superfamily proteins and related GTPases. Science’s STKE: signal transduction knowledge environment. 2004; 2004: 2004. Publisher Full Text\n\nEtienne-Manneville S, Hall A: Rho GTPases in cell biology. Nature. 2002; 420: 629–635. Publisher Full Text\n\nVega FM, Ridley AJ: Rho GTPases in cancer cell biology. FEBS Lett. 2008; 582: 2093–2101. Publisher Full Text\n\nCheng KW, Agarwal R, Mills GB: Ras-Superfamily GTP-ases in Ovarian Cancer. Cancer Treat. Res. 2009; 149. PubMed Abstract | Publisher Full Text\n\nHarvey JJ: An unidentified virus which causes the rapid production of tumours in mice [33]. Nature. 1964; 204: 1104–1105. PubMed Abstract | Publisher Full Text\n\nKirsten WH, Schauf V, McCoy J: Properties of a murine sarcoma virus. Bibl. Haematol. 1970; 36.\n\nChen FY, Li X, Zhu HP, et al.: Regulation of the Ras-Related Signaling Pathway by Small Molecules Containing an Indole Core Scaffold: A Potential Antitumor Therapy. Front. Pharmacol. 2020; 11.\n\nYe X, Carew TJ: Small G Protein Signaling in Neuronal Plasticity and Memory Formation: The Specific Role of Ras Family Proteins. Neuron. 2010; 68: 340–361. PubMed Abstract | Publisher Full Text\n\nJohnson L, Greenbaum D, Cichowski K, et al.: K-ras is an essential gene in the mouse with partial functional overlap with N-ras. Genes Dev. 1997; 11(19): 2468–2481. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMangiapane LR, Nicotra A, Turdo A, et al.: PI3K-driven HER2 expression is a potential therapeutic target in colorectal cancer stem cells. Gut. 2022; 71(1): 119–128. PubMed Abstract | Publisher Full Text\n\nPao W, Girard N: New driver mutations in non-small-cell lung cancer. Lancet Oncol. 2011; 12: 175–180. Publisher Full Text\n\nDownward J: Targeting RAS signalling pathways in cancer therapy. Nat. Rev. Cancer. 2003; 3: 11–22. Publisher Full Text\n\nShields JM, Pruitt K, McFall A, et al.: Understanding Ras: ‘It ain’t over “til it’s over.”. Trends Cell Biol. 2000; 10: 147–154. PubMed Abstract | Publisher Full Text\n\nRubio I, Wittig U, Meyer C, et al.: Farnesylation of Ras is important for the interaction with phosphoinositide 3-kinase γ. Eur. J. Biochem. 1999; 266(1): 70–82. PubMed Abstract | Publisher Full Text\n\nRowinsky EK, Windle JJ, Von Hoff DD: Ras protein farnesyltransferase: A strategic target for anticancer therapeutic development. J. Clin. Oncol. 1999; 17(11): 3631–3652. PubMed Abstract | Publisher Full Text\n\nMcKay MM, Morrison DK: Integrating signals from RTKs to ERK/MAPK. Oncogene. 2007; 26: 3113–3121. PubMed Abstract | Publisher Full Text\n\nMcCubrey JA, Steelman LS, Chappell WH, et al.: Roles of the Raf/MEK/ERK pathway in cell growth, malignant transformation and drug resistance. Biochimica et Biophysica Acta - Molecular Cell Research. 2007; 1773.\n\nSantarpia LL, Lippman S, El-Naggar A: Targeting the Mitogen-Activated Protein Kinase RAS-RAF Signaling Pathway in Cancer Therapy. Expert Opin. Ther. Targets. 2012; 16(1): 103–119. PubMed Abstract | Publisher Full Text\n\nKhan AQ, Kuttikrishnan S, Siveen KS, et al.: RAS-mediated oncogenic signaling pathways in human malignancies. Semin. Cancer Biol. 2019; 54: 1–13. PubMed Abstract | Publisher Full Text\n\nStites EC, Ravichandran KS: A Systems Perspective of Ras Signaling in Cancer.[cited 2022 Aug 16].Reference Source\n\nPrior IA, Hood FE, Hartley JL: The frequency of Ras mutations in cancer.\n\nChen K, Zhang Y, Qian L, et al.: Emerging strategies to target RAS signaling in human cancer therapy. J. Hematol. Oncol. 2021; 14(1): 116–123. PubMed Abstract | Publisher Full Text\n\nPrior IA, Lewis PD, Mattos C: A comprehensive survey of Ras mutations in cancer.\n\nBos JL: Ras Oncogenes in Human Cancer: A Review. Cancer Res. 1989; 49(17): 4682–4689. PubMed Abstract\n\nMoon A: Differential functions of ras for malignant phenotypic conversion. Arch. Pharm. Res. 2006; 29(2): 113–122. PubMed Abstract | Publisher Full Text\n\nBaines AT, Xu D, Der CJ: Inhibition of Ras for cancer treatment: The search continues. Future Med. Chem. 2011; 3: 1787–1808. PubMed Abstract | Publisher Full Text\n\nPylayeva-Gupta Y, Grabocka E, Bar-Sagi D: RAS oncogenes: Weaving a tumorigenic web. Nat. Rev. Cancer. 2011; 11: 761–774. PubMed Abstract | Publisher Full Text\n\nKannan Murugan A, Grieco M, Tsuchida N: RAS mutations in human cancers: Roles in precision medicine.2020 [cited 2022 Aug 16]. Publisher Full Text\n\nGurung AB, Bhattacharjee A: Significance of Ras Signaling in Cancer and Strategies for its Control. Oncol. Hematol. Rev. 2015; 11(02): 147.\n\nSerna-Blasco R, Sanz-Álvarez M, Aguilera Ó, et al.: Targeting the RAS-dependent chemoresistance: The Warburg connection. Semin. Cancer Biol. 2019 [cited 2022 Aug 31]; 54: 80–90. www.elsevier.com/locate/semcancer . PubMed Abstract | Publisher Full Text\n\nZhu X, Meng X, Xiang W, et al.: Correlation between clinicopathological features and KRAS, NRAS, and BRAF mutation status in Chinese colorectal cancer patients. Int. J. Clin. Exp. Pathol. 2018; 11(5): 2839–45. PubMed Abstract Reference Source\n\nDolatkhah R, Dastgiri S, Taher Eftekhar Sadat A, et al.: Impact of RAS/RAF mutations on clinical and prognostic outcomes in metastatic colorectal cancer. Tabriz Univ. Med. Sci. 2021 [cited 2022 Aug 17]; 11(1): 5–14.Reference Source\n\nMukhopadhyay S, Goswami D, Adiseshaiah PP, et al.: Undermining glutaminolysis bolsters chemotherapy while NRF2 promotes chemoresistance in KRAS-driven pancreatic cancers Graphical Abstract HHS Public Access. Cancer Res. 2020; 80(8): 1630–1643. PubMed Abstract | Publisher Full Text\n\nConroy M, Cowzer D, Kolch W, et al.: Emerging RAS-directed therapies for cancer. Cancer Drug Resist. 2021 [cited 2022 Aug 16]; 4(3): 543–558. PubMed Abstract | Publisher Full Text\n\nKossaï M, Leary A, Scoazec J-Y, et al.: E-Mail Tumour Heterogeneity Ovarian Cancer: A Heterogeneous Disease. Pathobiology. 2018 [cited 2022 Aug 23]; 85: 41–49. www.karger.com/pat . Publisher Full Text\n\nMenon U, Karpinskyj C, Gentry-Maharaj A: Ovarian Cancer Prevention and Screening. Obstet. Gynecol. 2018; 131(5): 909–927. Publisher Full Text\n\nLi SS, Ma J, Wong AST; Chemoresistance in ovarian cancer: exploiting cancer stem cell metabolism. J. Gynecol. Oncol. 2018 Mar 1 [cited 2022 Aug 24]; 29(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nWebb PM, Leader G; Cancers Group G et al.: Epidemiology of epithelial ovarian cancer. Best Pract. Res. Clin. Obstet. Gynaecol. 2017 [cited 2022 Aug 24]; 41: 3–14. Publisher Full Text\n\nMak VCY, Siu MKY, Wong OGW, et al.: Dysregulated stemness-related genes in gynecological malignancies. Histol. Histopathol. 2012; 27.\n\nLim HJ, Ledger W: Targeted Therapy in Ovarian Cancer. Women’s Heal. 2016 Jun 1 [cited 2022 Sep 13]; 12(3): 363. Free Full Text\n\nKeyvani V, Farshchian M, Esmaeili SA, et al.: Ovarian cancer stem cells and targeted therapy. J. Ovarian Res. 2019 Dec 6 [cited 2022 Sep 13]; 12(1): 120. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLim HJ, Ledger W: Targeted Therapy in Ovarian Cancer. Women’s Heal. 2016 Jun; 12(3): 363–378. Publisher Full Text\n\nTakenaka M, Saito M, Iwakawa R, et al.: Profiling of actionable gene alterations in ovarian cancer by targeted deep sequencing. Int. J. Oncol. 2015; 46(6): 2389–2398. PubMed Abstract | Publisher Full Text\n\nTsuchida N, Murugan AK, Grieco M: Kirsten Ras* oncogene: Significance of its discovery in human cancer research. Oncotarget. 2016; 7: 46717–46733. Publisher Full Text\n\nTsai FD, Lopes MS, Zhou M, et al.: K-RAS4A splice variant is widely expressed in cancer and uses a hybrid membrane-targeting motif. Proc. Natl. Acad. Sci. U. S. A. 2015; 112(3).\n\nHollestelle A, Pelletier C, Hooning M, et al.: Prevalence of the variant allele rs61764370 T>G in the 3′UTR of KRAS among Dutch BRCA1, BRCA2 and non-BRCA1/BRCA2 breast cancer families. Breast Cancer Res. Treat. 2011; 128(1): 79–84. PubMed Abstract | Publisher Full Text\n\nSadlecki P, Grzanka D, Grabiec M: Testing for NRAS mutations in serous borderline ovarian tumors and low-grade serous ovarian carcinomas. Dis. Markers. 2018; 2018: 1–7. PubMed Abstract | Publisher Full Text\n\nCarvalho PD, Guimarães CF, Cardoso AP, et al.: KRAS oncogenic signaling extends beyond cancer cells to orchestrate the microenvironment. Cancer Res. 2018; 78.\n\nKim S, Han Y, Kim I, et al.: Tumor evolution and chemoresistance in ovarian cancer. npj Precis. Oncol. 2018 [cited 2022 Sep 1]; 2: 20. PubMed Abstract | Publisher Full Text Reference Source\n\nBulun SE, Wan Y, Matei D: Epithelial Mutations in Endometriosis: Link to Ovarian. Cancer. 2019.Reference Source\n\nAuner V, Kriegshäuser G, Tong D, et al.: KRAS mutation analysis in ovarian samples using a high sensitivity biochip assay. BMC Cancer. 2009 Apr 9 [cited 2022 Aug 28]; 9(1): 1–8. PubMed Abstract | Publisher Full Text\n\nMayr D, Hirschmann A, Löhrs U, et al.: KRAS and BRAF mutations in ovarian tumors: A comprehensive study of invasive carcinomas, borderline tumors and extraovarian implants. Gynecol. Oncol. 2006 Dec; 103(3): 883–887. PubMed Abstract | Publisher Full Text\n\nLee YJ, Lee MY, Ruan A, et al.: Multipoint Kras oncogene mutations potentially indicate mucinous carcinoma on the entire spectrum of mucinous ovarian neoplasms. Oncotarget. 2016; 7(50): 82097–82103. PubMed Abstract | Publisher Full Text\n\nWang Y, Niu XL, Qu Y, et al.: Autocrine production of interleukin-6 confers cisplatin and paclitaxel resistance in ovarian cancer cells. Cancer Lett. 2010; 295(1): 110–123. PubMed Abstract | Publisher Full Text\n\nRatner E, Keane F, Lindner R, et al.: A KRAS variant is a biomarker of poor outcome, platinum chemotherapy resistance and a potential target for therapy in ovarian cancer. Oncogene. 2012 [cited 2022 Aug 24]; 31: 4559–4566. PubMed Abstract | Publisher Full Text Reference Source\n\nCaduff RF, Svoboda-Newman SM, Ferguson AW, et al.: Comparison of mutations of Ki-RAS and p53 immunoreactivity in borderline and malignant epithelial ovarian tumors. Am. J. Surg. Pathol. 1999; 23(3): 323–328. PubMed Abstract | Publisher Full Text\n\nGao L, Zheng M, Guo Q, et al.: Downregulation of Rab23 inhibits proliferation, invasion, and metastasis of human ovarian cancer. Int. J. Biochem. Cell Biol. 2019 Nov 1; 116: 105617. Publisher Full Text\n\nHirst J, Crow J, Godwin A: Ovarian Cancer Genetics: Subtypes and Risk Factors. Ovarian Cancer - From Pathog to Treat. 2018 Jan 26 [cited 2022 Sep 6]. undefined/state.item.id. Publisher Full Text\n\nRavindran F, Choudhary B: Ovarian Cancer: Molecular Classification and Targeted Therapy. In: Ovarian Cancer - Updates in Tumour Biology and Therapeutics [Working Title].2021.\n\nMorgan RJ, Armstrong DK, Alvarez RD, et al.: Ovarian cancer, version 1.2016: Clinical practice guidelines in oncology. JNCCN J. Natl. Compr. Cancer Netw. 2016; 14(9).\n\nPrat J, D’Angelo E, Espinosa I: Ovarian carcinomas: at least five different diseases with distinct histological features and molecular genetics. Hum. Pathol. 2018; 80: 11–27. PubMed Abstract | Publisher Full Text\n\nMorphologic, Immunophenotypic, and Molecular Features of Epithelial Ovarian Cancer.[cited 2022 Sep 6].Reference Source\n\nSilverberg SG, Bell DA, Kurman RJ, et al.: Borderline ovarian tumors: Key points and workshop summary. Hum. Pathol. 2004; 35: 910–917. PubMed Abstract | Publisher Full Text\n\nHunter SM, Anglesio MS, Ryland GL, et al.: Molecular profiling of low grade serous ovarian tumours identifies novel candidate driver genes. Oncotarget. 2015; 6(35): 37663–37677. PubMed Abstract | Publisher Full Text\n\nJones S, Wang TL, Kurman RJ, et al.: Low-grade serous carcinomas of the ovary contain very few point mutations. J. Pathol. 2012; 226(3): 413–420. PubMed Abstract | Publisher Full Text\n\nEtemadmoghadam D, Azar WJ, Lei Y, et al.: EIF1AX and NRAS mutations co-occur and cooperate in low-grade serous ovarian carcinomas. Cancer Res. 2017; 77(16): 4268–4278. PubMed Abstract | Publisher Full Text\n\nNakamura K, Nakayama K, Ishikawa N, et al.: Reconstitution of high-grade serous ovarian carcinoma from primary fallopian tube secretory epithelial cells. Oncotarget. 2018; 9(16): 12609–12619. PubMed Abstract | Publisher Full Text\n\nVoutsadakis IA: Further understanding of high-grade serous ovarian carcinogenesis: Potential therapeutic targets. Cancer Manag. Res. 2020; 12: 10423–10437. PubMed Abstract | Publisher Full Text\n\nTeer JK, Yoder S, Gjyshi A, et al.: Mutational heterogeneity in non-serous ovarian cancers OPEN.[cited 2022 Sep 9].Reference Source\n\nMackenzie R, Kommoss S, Winterhoff BJ, et al.: Targeted deep sequencing of mucinous ovarian tumors reveals multiple overlapping RAS-pathway activating mutations in borderline and cancerous neoplasms. BMC Cancer. 2015; 15(1): 415. PubMed Abstract | Publisher Full Text\n\nRyland GL, Hunter SM, Doyle MA, et al.; Mutational landscape of mucinous ovarian carcinoma and its neoplastic precursors.2015.\n\nIida Y, Okamoto A, Hollis RL, et al.: Clear cell carcinoma of the ovary: a clinical and molecular perspective. Int. J. Gynecol. Cancer. 2021 [cited 2022 Sep 7]; 31: 605–616. Publisher Full Text Reference Source\n\nFranco Zannoni G, Improta G, Chiarello G, et al.: Mutational status of KRAS, NRAS, and BRAF in primary clear cell ovarian carcinoma.\n\nFan C, Zhao C, Shugen Li FW, et al.: Significance of PTEN Mutation in Cellular Process, Prognosis, and Drug Selection in Clear Cell Renal Cell Carcinoma. Front. Oncol. 2019 [cited 2022 Sep 8]; 9(MAY). PubMed Abstract | Publisher Full Text | Free Full Text\n\nFriedlander ML, Russell K, Millis S, et al.: Molecular Profiling of Clear Cell Ovarian Cancers Identifying Potential Treatment Targets for Clinical Trials.[cited 2022 Sep 8].Reference Source\n\nBagherlou N, Farajnia S, Zahri S, et al.: Original Article Prevalence of K-RAS mutations and CA125 tumor marker in patients with ovarian carcinoma. Casp. J. Intern. Med. 2020; 11(1): 75–82.\n\nHollis RL, Thomson JP, Stanley B, et al.: Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome. Nat. Commun. 2020. 2020 Oct 5 [cited 2022 Sep 12]; 11(1): 1–10.Reference Source\n\nItamochi H, Oishi T, Oumi N, et al.: Whole-genome sequencing revealed novel prognostic biomarkers and promising targets for therapy of ovarian clear cell carcinoma. Br. J. Cancer. 2017; 117(5): 717–724. PubMed Abstract | Publisher Full Text\n\nKim I, Lee JW, Lee M, et al.: Genomic landscape of ovarian clear cell carcinoma via whole exome sequencing. Gynecol. Oncol. 2018 Feb; 148(2): 375–382. PubMed Abstract | Publisher Full Text\n\nZannoni GF, Improta G, Pettinato A, et al.: Molecular status of PI3KCA, KRAS and BRAF in ovarian clear cell carcinoma: an analysis of 63 patients. J. Clin. Pathol. 2016; 69: 1088–1092. PubMed Abstract | Publisher Full Text\n\nHo CL, Kurman RJ, Dehari R, et al.: Mutations of BRAF and KRAS precede the development of ovarian serous borderline tumors. Cancer Res. 2004; 64(19): 6915–6918. PubMed Abstract | Publisher Full Text\n\nOhnishi K, Nakayama K, Ishikawa M, et al.: Mucinous borderline ovarian tumors with BRAF V600E mutation may have low risk for progression to invasive carcinomas. Arch. Gynecol. Obstet. 2020; 302(2): 487–495. PubMed Abstract | Publisher Full Text\n\nPanyavaranant P, Teerapakpinyo C, Pohthipornthawat N, et al.: RAS mutation in mucinous carcinoma of the ovary. Asian Pacific. J Cancer Prev. 2019; 20(4): 1127–1132. Publisher Full Text\n\nNodin B, Zendehrokh N, Sundström M, et al.: Clinicopathological correlates and prognostic significance of KRAS mutation status in a pooled prospective cohort of epithelial ovarian cancer. Diagn. Pathol. 2013 [cited 2022 Aug 24]; 8: 1.Reference Source\n\nGershenson DM, Sun CC, Wong K-K: Impact of mutational status on survival in low-grade serous carcinoma of the ovary or peritoneum.2015 [cited 2022 Sep 6].Reference Source\n\nTsang YT, Deavers MT, Sun CC, et al.: KRAS (but not BRAF) mutations in ovarian serous borderline tumour are associated with recurrent low-grade serous carcinoma. J. Pathol. 2013; 231(4): 449–456. PubMed Abstract | Publisher Full Text\n\nGemignani ML, Schlaerth AC, Bogomolniy F, et al.: Role of KRAS and BRAF gene mutations in mucinous ovarian carcinoma. Gynecol. Oncol. 2003; 90(2): 378–381. PubMed Abstract | Publisher Full Text\n\nEmmanuel C, Chiew Y-E, George J, et al.: Genomic Classification of Serous Ovarian Cancer with Adjacent Borderline Differentiates RAS Pathway and TP53-Mutant Tumors and Identifies NRAS as an Oncogenic Driver; current address for. Clin. Cancer Res. Clin. Cancer Res. 2014 [cited 2022 Aug 25]; 20(24).Reference Source\n\nZhong F, Zhu T, Pan X, et al.: Comprehensive genomic profiling of high-grade serous ovarian carcinoma from Chinese patients identifies co-occurring mutations in the Ras/Raf pathway with TP53. Cancer Med. 2019; 8(8).\n\nXing D, Rahmanto YS, Zeppernick F, et al.: Mutation of NRAS is a Rare Genetic Event in Ovarian Low-Grade Serous Carcinoma HHS Public Access. Hum. Pathol. 2017; 68: 87–91. PubMed Abstract | Publisher Full Text\n\nMoujaber T, Balleine RL, Gao B, et al.: New therapeutic opportunities for women with low-grade serous ovarian cancer. Endocr. Relat. Cancer. 2022; 29(1): R1–R16. Publisher Full Text\n\nBarnes BM, Nelson L, Tighe A, et al.: Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes.[cited 2022 Sep 6]. Publisher Full Text\n\nHollis RL, Gourley C: Genetic and molecular changes in ovarian cancer.2016 [cited 2022 Sep 6].Reference Source\n\nGershenson DM, Bodurka DC, Lu KH, et al.: Impact of age and primary disease site on outcome in women with low-grade serous carcinoma of the ovary or peritoneum: Results of a large single-institution registry of a rare tumor. J. Clin. Oncol. 2015; 33(24): 2675–2682. PubMed Abstract | Publisher Full Text\n\nZuo T, Wong S, Buza N, et al.: KRAS mutation of extraovarian implants of serous borderline tumor: Prognostic indicator for adverse clinical outcome. Mod. Pathol. 2018; 31(2): 350–357. PubMed Abstract | Publisher Full Text\n\nMatulonis UA, Hirsch M, Palescandolo E, et al.: High throughput interrogation of somatic mutations in high grade serous cancer of the ovary. PLoS One. 2011; 6(9): e24433. PubMed Abstract | Publisher Full Text\n\nAnglesio MS, Wiegand KC, Melnyk N, et al.: Type-Specific Cell Line Models for Type-Specific Ovarian Cancer Research. PLoS One. 2013; 8(9). Publisher Full Text\n\nDokianakis DN, Varras MN, Papaefthimiou M, et al.: Ras gene activation in malignant cells of human ovarian carcinoma peritoneal fluids. Clin. Exp. Metastasis. 1999; 17(4): 293–297. Publisher Full Text\n\nLiang F, Ren C, Wang J, et al.: The crosstalk between STAT3 and p53/RAS signaling controls cancer cell metastasis and cisplatin resistance via the Slug/MAPK/PI3K/AKT-mediated regulation of EMT and autophagy. Oncog. 2019. 2019 Oct 9 [cited 2022 Aug 25]; 8(10): 1–15.Reference Source\n\nMai J, Yang L, Xie HJ, et al.: Molecular mechanisms of platinum-based chemotherapy resistance in ovarian cancer (Review). Oncol. Rep. 2022; 47(4). Publisher Full Text\n\nGershenson DM, Sun CC, Bodurka D, et al.: Recurrent low-grade serous ovarian carcinoma is relatively chemoresistant.2009.\n\nKato S, McFall T, Takahashi K, et al.: KRAS-Mutated, Estrogen Receptor-Positive Low-Grade Serous Ovarian Cancer: Unraveling an Exceptional Response Mystery. Oncologist. 2021 Apr 1; 26(4): e530–e536. PubMed Abstract | Publisher Full Text\n\nKurman RJ, Shih IM: The dualistic model of ovarian carcinogenesis revisited, revised, and expanded. Am. J. Pathol. 2016; 186: 733–747. PubMed Abstract | Publisher Full Text\n\nBowtell DD, Böhm S, Ahmed AA, et al.: Rethinking ovarian cancer II: Reducing mortality from high-grade serous ovarian cancer. Nat. Rev. Cancer. 2015; 15: 668–679. PubMed Abstract | Publisher Full Text | Free Full Text\n\nContributions Conceptualization A, Methodology RJY, -N.; Formal Analysis AF, Investigation RJY: Most Commonly Mutated Genes in High-Grade Serous Ovarian Carcinoma Are Nonessential for Ovarian Surface Epithelial Stem Cell Transformation Graphical Abstract In Brief.2020.\n\nBabaier A, Ghatage P: Mucinous cancer of the ovary: Overview and current status. Diagnostics. 2020; 10. PubMed Abstract | Publisher Full Text\n\nBabaier A, Ghatage P: diagnostics Mucinous Cancer of the Ovary: Overview and Current Status.[cited 2022 Sep 9].Reference Source\n\nLiddell C, Droy-Dupré L, Métairie S, et al.: Mapping clinicopathological entities within colorectal mucinous adenocarcinomas: A hierarchical clustering approach. Mod. Pathol. 2017; 30(8): 1177–1189. PubMed Abstract | Publisher Full Text\n\nPrat J: New insights into ovarian cancer pathology. Ann. Oncol. 2012; 23: x111–x117. Publisher Full Text\n\nLuo C, Cen S, Ding G, et al.: Mucinous colorectal adenocarcinoma: Clinical pathology and treatment options. Cancer Commun. 2019; 39: 13. PubMed Abstract | Publisher Full Text\n\nEnomoto T, Weghorst CM, Inoue M, et al.: K-ras activation occurs frequently in mucinous adenocarcinomas and rarely in other common epithelial tumors of the human ovary. Am. J. Pathol. 1991; 139(4): 777–785. PubMed Abstract\n\nNarikiyo M, Yano M, Kamada K, et al.: Molecular association of functioning stroma with carcinoma cells in the ovary: A preliminary study. Oncol. Lett. 2019; 17(3): 3562–3568. PubMed Abstract | Publisher Full Text\n\nWatanabe T, Nanamiya H, Endo Y, et al.: Identification and clinical significance of somatic oncogenic mutations in epithelial ovarian cancer. J Ovarian Res. 2021 [cited 2022 Sep 6]; 14: 129. PubMed Abstract | Publisher Full Text\n\nPierson WE, Peters PN, Chang MT, et al.: may, Quigley DA, Ashworth A, et al. An integrated molecular profile of endometrioid ovarian cancer. Gynecol. Oncol. 2020 Apr 1; 157(1): 55–61. PubMed Abstract | Publisher Full Text\n\nBirkeland E, Wik E, Mjos S, et al.: KRAS gene amplification and overexpression but not mutation associates with aggressive and metastatic endometrial cancer. Br. J. Cancer. 2012 [cited 2022 Sep 12]; 107(12): 1997–2004. PubMed Abstract | Publisher Full Text Reference Source\n\nZhang C, Wang X, Anaya Y, et al.: Distinct molecular pathways in ovarian endometrioid adenocarcinoma with concurrent endometriosis. Int. J. Cancer. 2018 Nov 15 [cited 2022 Sep 12]; 143(10): 2505–2515. PubMed Abstract | Publisher Full Text\n\nDinulescu DM, Ince TA, Quade BJ, et al.: Role of K-ras and Pten in the development of mouse models of endometriosis and endometrioid ovarian cancer. Nat. Med. 2005; 11(1): 63–70. Publisher Full Text\n\nYachida N, Yoshihara K, Yamaguchi M, et al.: How does endometriosis lead to ovarian cancer? The molecular mechanism of endometriosis-associated ovarian cancer development. Cancers (Basel). 2021; 13(6): 1–14. Publisher Full Text\n\nKim I, Lee JW, Lee M, et al.: Genomic landscape of ovarian clear cell carcinoma via whole exome sequencing. Gynecol. Oncol. 2018 Feb 1 [cited 2022 Sep 12]; 148(2): 375–382. PubMed Abstract | Publisher Full Text Reference Source\n\nOtsuka J, Okuda T, Sekizawa A, et al.: Kras mutation may promote carcinogenesis of endometriosis leading to ovarian clear cell carcinoma. Med. Electron Microsc. 2004; 37: 188–192.\n\nZannoni GF, Improta G, Pettinato A, et al.: Molecular status of PI3KCA, KRAS and BRAF in ovarian clear cell carcinoma: an analysis of 63 patients. J. Clin. Pathol. 2016 [cited 2022 Sep 13]; 69: 1088–1092. PubMed Abstract | Publisher Full Text\n\nMaramai M, Barra F, Menada MV, et al.: Borderline ovarian tumours: Management in the era of fertility-sparing surgery. ecancermedicalscience. 2020; 14. PubMed Abstract | Publisher Full Text\n\nTaylor HC: Malignant and semimalignant tumors of the ovary. Surg. Gynecol. Obs. 1929; 48(2).\n\nPrat J: Pathology of borderline and invasive cancers. Best Pract. Res. Clin. Obstet. Gynaecol. 2017; 41.\n\nDobrzycka B, Terlikowski SJ, Kowalczuk O, et al.: Mutations in the KRAS gene in ovarian tumors. Folia Histochem. Cytobiol. 2009; 47(2). Publisher Full Text\n\nAnglesio MS, Arnold JM, George J, et al.: Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors. Mol. Cancer Res. 2008; 6(11): 1678–1690. Publisher Full Text\n\nWu SY, Lan SH, Cheng DE, et al.: Ras-related tumorigenesis is suppressed by BNIP3-mediated autophagy through inhibition of cell proliferation. Neoplasia. 2011; 13(12): 1171–IN28. PubMed Abstract | Publisher Full Text\n\nMiracco C, Cosci E, Oliveri G, et al.: Protein and mRNA expression of autophagy gene Beclin 1 in human brain tumours. Int. J. Oncol. 2007; 30(2): 429–436. PubMed Abstract\n\nWinter-Vann AM, Casey PJ: Post-prenylation-processing enzymes as new targets in oncogenesis. Nat. Rev. Cancer. 2005; 5: 405–412. PubMed Abstract | Publisher Full Text\n\nLau HY, Tang J, Casey PJ, et al.: Isoprenylcysteine carboxylmethyltransferase is critical for malignant transformation and tumor maintenance by all RAS isoforms. Oncogene. 2017; 36(27): 3934–3942. PubMed Abstract | Publisher Full Text\n\nLiu Q, Chen J, Fu B, et al.: Isoprenylcysteine carboxylmethyltransferase regulates ovarian cancer cell response to chemotherapy and RAS activation. Biochem. Biophys. Res. Commun. 2018; 501(2): 556–562. PubMed Abstract | Publisher Full Text\n\nChitnis SS, Selvaakumar C, Jagtap DD, et al.: Interaction of follicle-stimulating hormone (FSH) receptor binding inhibitor-8: A novel FSH-binding inhibitor, with FSH and its receptor. Chem. Biol. Drug Des. 2009; 73(6): 637–643. PubMed Abstract | Publisher Full Text\n\nWei S, Shen X, Lai L, et al.: FSH receptor binding inhibitor impacts K-Ras and c-Myc of ovarian cancer and signal pathway. Oncotarget. 2018; 9(32): 22498–22508. PubMed Abstract | Publisher Full Text\n\nPierre S, Bats AS, Chevallier A, et al.: Induction of the Ras activator Son of Sevenless 1 by environmental pollutants mediates their effects on cellular proliferation. Biochem. Pharmacol. 2011; 81(2): 304–313. PubMed Abstract | Publisher Full Text\n\nTherachiyil L, Krishnankutty R, Ahmad F, et al.: Aryl Hydrocarbon Receptor Promotes Cell Growth, Stemness Like Characteristics, and Metastasis in Human Ovarian Cancer via Activation of PI3K/Akt, β-Catenin, and Epithelial to Mesenchymal Transition Pathways.2022. Publisher Full Text\n\nParrish AR, Fisher R, Bral CM, et al.: Benzo(a)pyrene-induced alterations in growth-related gene expression and signaling in precision-cut adult rat liver and kidney slices. Toxicol. Appl. Pharmacol. 1998; 152(2): 302–308. PubMed Abstract | Publisher Full Text\n\nBral CM, Ramos KS: Identification of benzo [a]pyrene-inducible cis-acting elements within c- Ha-ras transcriptional regulatory sequences. Mol. Pharmacol. 1997; 52(6): 974–982. PubMed Abstract | Publisher Full Text\n\nEnan E, Matsumura F: Significance of TCDD-induced changes in protein phosphorylation in the adipocyte of male guinea pigs. J. Biochem. Toxicol. 1994; 9(3): 159–170. PubMed Abstract | Publisher Full Text\n\nPuga A, Maier A, Medvedovic M: The transcriptional signature of dioxin in human hepatoma HepG2 cells. Biochem. Pharmacol. 2000; 60(8): 1129–1142. PubMed Abstract | Publisher Full Text\n\nBhuiyan MIH, Song S, Yuan H, et al.: WNK-Cab39-NKCC1 signaling increases the susceptibility to ischemic brain damage in hypertensive rats. J. Cereb. Blood Flow Metab. 2017; 37(8): 2780–2794. PubMed Abstract | Publisher Full Text\n\nLi F, Liang Z, Jia Y, et al.: microRNA-324-3p suppresses the aggressive ovarian cancer by targeting WNK2/RAS pathway. Bioengineered. 2022; 13(5): 12030–12044. PubMed Abstract | Publisher Full Text\n\nParker F, Maurier F, Delumeau I, et al.: A Ras-GTPase-activating protein SH3-domain-binding protein. Mol. Cell. Biol. 1996; 16(6): 2561–2569. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang H, Zhang S, He H, et al.: RasGAP-derived peptide 38GAP potentiates the cytotoxicity of cisplatin through inhibitions of Akt, ERK and NF-κB in colon carcinoma HCT116 cells. Cancer Lett. 2011; 308(1): 62–70. PubMed Abstract | Publisher Full Text\n\nGoody RS, Frech M, Wittinghofer A: Affinity of guanine nucleotide binding proteins for their ligands: facts and artefacts. Trends Biochem. Sci. 1991; 16(C): 327–328. PubMed Abstract | Publisher Full Text\n\nRyan MB, Corcoran RB: Therapeutic strategies to target RAS-mutant cancers. Nat. Rev. Clin. Oncol. 2018; 15: 709–720. PubMed Abstract | Publisher Full Text\n\nCox AD, Fesik SW, Kimmelman AC, et al.: Drugging the undruggable RAS: Mission Possible? Nat. Rev. Drug Discov. 2014; 13: 828–851. PubMed Abstract | Publisher Full Text\n\nKiessling MK, Rogler G: Targeting the RAS pathway by mitogen-activated protein kinase inhibitors. Swiss Med. Wkly. 2015; 145.\n\nKim MJ, Lee SJ, Ryu JH, et al.: Combination of KRAS gene silencing and PI3K inhibition for ovarian cancer treatment. J. Control. Release. 2020; 318: 98–108. PubMed Abstract | Publisher Full Text\n\nLito P, Rosen N, Solit DB: Tumor adaptation and resistance to RAF inhibitors. Nat. Med. 2013; 19: 1401–1409. Publisher Full Text\n\nDesai J, Gan H, Barrow C, et al.: Phase I, open-label, dose-escalation/dose-expansion study of lifirafenib (BGB-283), an RAF family kinase inhibitor, in patients with solid tumors. J. Clin. Oncol. 2020; 38(19): 2140–2150. PubMed Abstract | Publisher Full Text\n\nThein KZ, Biter AB, Hong DS: Therapeutics Targeting Mutant KRAS. Annu. Rev. Med. 2021; 72: 349–364. Publisher Full Text\n\nKessler D, Gmachl M, Mantoulidis A, et al.: Drugging an undruggable pocket on KRAS. Proc. Natl. Acad. Sci. U. S. A. 2019; 116(32): 15823–15829. Publisher Full Text\n\nNagasaka M, Li Y, Sukari A, et al.: KRAS G12C Game of Thrones, which direct KRAS inhibitor will claim the iron throne? Cancer Treat. Rev. 2020; 84: 101974. PubMed Abstract | Publisher Full Text\n\nHallin J, Engstrom LD, Hargi L, et al.: The KRASG12C inhibitor MRTX849 provides insight toward therapeutic susceptibility of KRAS-mutant cancers in mouse models and patients. Cancer Discov. 2020; 10(1): 54–71. PubMed Abstract | Publisher Full Text\n\nWang X, Allen S, Blake JF, et al.: Identification of MRTX1133, a Noncovalent, Potent, and Selective KRASG12DInhibitor. J. Med. Chem. 2022; 65(4): 3123–3133. Publisher Full Text\n\nJänne PA, Rybkin II, Spira AI, et al.: KRYSTAL-1: Activity and Safety of Adagrasib (MRTX849) in Advanced/Metastatic Non–Small-Cell Lung Cancer (NSCLC) Harboring KRAS G12C Mutation. Eur. J. Cancer. 2020; 138.\n\nLito P, Solomon M, Li LS, et al.: Cancer therapeutics: Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism. Science (80-). 2016; 351(6273): 604–608. PubMed Abstract | Publisher Full Text\n\nMuzumdar MD, Chen PY, Dorans KJ, et al.: Survival of pancreatic cancer cells lacking KRAS function. Nat. Commun. 2017; 8(1): 1090. PubMed Abstract | Publisher Full Text\n\nRyan MB, de la Cruz FF , Phat S, et al.: Vertical pathway inhibition overcomes adaptive feedback resistance to KrasG12C inhibition. Clin. Cancer Res. 2020; 26(7): 1633–1643. PubMed Abstract | Publisher Full Text\n\nZhu C, Guan X, Zhang X, et al.: Targeting KRAS mutant cancers: from druggable therapy to drug resistance. Mol. Cancer. 2022; 21(1): 159. PubMed Abstract | Publisher Full Text\n\nShroff GS, de Groot PM , Papadimitrakopoulou VA, et al.: Targeted Therapy and Immunotherapy in the Treatment of Non–Small Cell Lung Cancer. Radiol. Clin. N. Am. 2018; 56: 485–495. Publisher Full Text\n\nGuo F, Gong H, Zhao H, et al.: Mutation status and prognostic values of KRAS, NRAS, BRAF and PIK3CA in 353 Chinese colorectal cancer patients. Sci. Rep. 2018; 8(1). Publisher Full Text\n\nTherkildsen C, Bergmann TK, Henrichsen-Schnack T, et al.: The predictive value of KRAS, NRAS, BRAF, PIK3CA and PTEN for anti-EGFR treatment in metastatic colorectal cancer: A systematic review and meta-analysis. Acta Oncol. 2014; 53: 852–864. PubMed Abstract | Publisher Full Text\n\nSideris M, Emin EI, Abdullah Z, et al.: The role of KRAS in endometrial cancer: A mini-review. Anticancer Res. 2019; 39(2): 533–539. PubMed Abstract | Publisher Full Text\n\nSpreafico A, Oza AM, Clarke BA, et al.: Genotype-matched treatment for patients with advanced type I epithelial ovarian cancer (EOC). Gynecol. Oncol. 2017; 144(2): 250–255. PubMed Abstract | Publisher Full Text\n\nCosta-Cabral S, Brough R, Konde A, et al.: CDK1 Is a synthetic lethal target for KRAS mutant tumours. PLoS One. 2016; 11(2).\n\nInaba K, Oda K, Aoki K, et al.: Synergistic antitumor effects of combination PI3K/mTOR and MEK inhibition (SAR245409 and pimasertib) in mucinous ovarian carcinoma cells by fluorescence resonance energy transfer imaging. Oncotarget. 2016; 7(20): 29577–29591. PubMed Abstract | Publisher Full Text\n\nYu Z, Pestell TG, Lisanti MP, et al.: Cancer Stem Cells.2012.\n\nZong X, Nephew KP: cancers Ovarian Cancer Stem Cells: Role in Metastasis and Opportunity for Therapeutic Targeting.[cited 2022 Sep 26].Reference Source\n\nTerraneo N, Jacob F, Dubrovska A, et al.: Novel Therapeutic Strategies for Ovarian Cancer Stem Cells. Front. Oncol. 2020; 10(March): 1–17. Publisher Full Text\n\nTakahashi A, Hong L, Chefetz I: Review Open Access Cancer Drug Resistance How to win the ovarian cancer stem cell battle: destroying the roots. Cancer Drug Resist. 2020 [cited 2022 Sep 29]; 3: 1021–1033. PubMed Abstract | Publisher Full Text Reference Source\n\nDiaz Osterman CJ, Ozmadenci D, Kleinschmidt EG, et al.: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy.2019 [cited 2022 Sep 26]. Publisher Full Text\n\nDeng J, Bai X, Feng X, et al.: Inhibition of PI3K/Akt/mTOR signaling pathway alleviates ovarian cancer chemoresistance through reversing epithelial-mesenchymal transition and decreasing cancer stem cell marker expression.[cited 2022 Sep 29]. Publisher Full Text\n\nZhang S, Cui B, Lai H, et al.: Ovarian cancer stem cells express ROR1, which can be targeted for anti-cancer-stem-cell therapy.[cited 2022 Sep 29]. Publisher Full Text\n\nZhang T, Xu J, Deng S, et al.: Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data.2018 [cited 2022 Sep 27]. Publisher Full Text\n\nShokouhifar A, Sarab GA, Yazdanifar M, et al.: Overcoming the UCB HSCs-Derived NK cells Dysfunction through Harnessing RAS/MAPK, IGF-1R and TGF-β Signaling Pathways. Cancer Cell Int. 2021 [cited 2022 Sep 27]; 21: 298. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "155266",
"date": "14 Nov 2022",
"name": "Shams Tabrez",
"expertise": [
"Reviewer Expertise Cancer Biology",
"Molecular Signalling",
"Chemoprevention"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article the authors have highlighted the role of the RAS family of proteins in the pathogenesis of ovarian cancers. The article has covered a wide range of functional aspects of RAS including mutational aspects of RAS and its association with various signaling pathways such as RAF-1/MAPK (mitogen-activated protein kinase), PI3K phosphoinositide-3 kinase (PI3K)/AKT, RalGEFs, Rac/Rho, BRAF (v-Raf murine sarcoma viral oncogene homolog B), MEK1 (mitogen-activated protein kinase kinase 1), ERK (extracellular signal-regulated kinase), PKB (protein kinase B), and PKC (protein kinase C) involved in cell proliferation as well as maintenance pathways thereby driving tumorigenesis and cancer cell propagation.\n\nIt is an important addition to the current state of literature and a very timely one too. The manuscript is well written, and literature extensively reviewed. There are just a few minor issues to take care of before possible indexing:\nMinor comments:\nIt is will important to add a graphic abstract.\n\nThe full form of OC should be provided for use in the introduction section.\n\nEditing/spelling checks in a few sections is required.\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": "155264",
"date": "16 Nov 2022",
"name": "Haider Raza",
"expertise": [
"Reviewer Expertise Biochemical and molecular bases of diseases",
"diabetes and cancer signalling. Molecular toxicology",
"oxidative stress",
"inflammation and mitochondrial dysfunction."
],
"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 comprehensive and interesting review on RAS family mutations in cancer focusing on ovarian cancer. In this review, the authors have described the role of RAS, which regulates several signaling pathways involved in cell proliferation, differentiation, and cell death/survival. The authors have focused on the mutational status of RAS, especially KRAS in mediating carcinogenesis and chemoresistance in ovarian cancer (OC).\nThe authors have reviewed the subtypes of ovarian cancer, mutations in RAS, especially KRAS, the frequency of incidence, and the clinical relevance of the mutations on signaling pathways. They have also favorably tackled the problems involved in KRAS-targeted therapy and resistance in OC.\nHowever, a few minor issues need to be addressed:\nThe authors have schematically presented the classification of OC very well, based on cellular origin, with the various sub-types. Though the frequency of the other carcinomas is minimal compared to that of the epithelial, it would be a good idea to include at least some basic information regarding the tumors from other cellular origins.\n\nIn Table 2, the authors have given the mutational status and clinical relevance of RAS mutations. In the column, showing ‘Specimen’, the authors have given arbitrary descriptions like patient specimens or human tissue specimens etc. It would be good if the authors could identify and specify the specimen/tissues referred to in the given references.\n\nThe authors have mentioned the disadvantages of targeted therapy due to the feedback loop leading to chemoresistance. An elaboration on this would help the readers better understand the mechanism.\n\nThe discussion on the role of AhR and RAS activation is limited and referred to the author’s previous review which is not published yet (Ref #154?). An expansion on this subject (or access to the previous published review) may be beneficial to the readers owing to the wide range of AhR involvement in carcinogenesis, inflammation and hormonal signaling, including in OC.\n\nA brief description on the pathophysiology and hormonal sensitivity of OC progression/regression, metastasis and chemoresistance/sensitivity would also improve the quality of the present review. Only cisplatin/platinum based-drug resistance has been discussed in this review. This can also be expanded by including other specific/precision-based therapies (e.g. in Figure 2 on radio-or other chemo-based therapies).\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/11-1253
|
https://f1000research.com/articles/11-955/v1
|
18 Aug 22
|
{
"type": "Research Article",
"title": "Does online mindfulness-based intervention help college students succeed in their job search during the COVID-19 pandemic?",
"authors": [
"Rajalakshmi S.A.",
"Sowndaram C.S.",
"Preetham Ganesh",
"Harsha Vardhini Vasu",
"Sowndaram C.S.",
"Preetham Ganesh",
"Harsha Vardhini Vasu"
],
"abstract": "Background: Immediately after graduation from university, college students need to make significant decisions about starting their careers or pursuing higher studies. They are also pressured to meet the expectations and demands of self, others, and the environment. Owing to the impact of the COVID-19 pandemic, the aforementioned challenging decisions may become hazardous stressors for college students. Hence, the researchers intended to assist and assess the college students involved in student placements. The research goal was to investigate the impact of mindfulness-based intervention (MBI) on the stress and self-esteem of college students involved in student placements. Methods: One hundred college students participating in the campus placements were selected using purposive sampling from Amrita Vishwa Vidyapeetham University in Coimbatore, India. For evaluation purposes, college students were administered the perceived stress, Rosenberg self-esteem, and Kuppuswamy socio-economic scales. Seventy-five college students were selected for the MBI process and were administered with a pre-intervention and post-intervention without a control group research design. Results: Statistical analysis including analysis of variance (ANOVA) and the Bonferroni post hoc test showed a significant increase in self-esteem and a decrease in the stress of the college students involved in placements. Conclusions: Thus, the researchers recommend that policymakers create awareness, include MBI in the curriculum, and allocate funds for training ventures in educational institutions to assist college students in their challenging life journeys",
"keywords": [
"COVID-19",
"placements",
"college students",
"mindfulness",
"stress",
"self-esteem"
],
"content": "Introduction\n\nUnemployment is one of the critical problems many people face across the globe. Some of them are new graduates, employees who have been laid off, and individuals who try for better options than their current employment. Students can find employment either by attending interviews with companies or by attending job fairs. Labour market opportunities are open to individuals with higher degrees and more experience1. Indeed, the global pandemic COVID-19 has impacted all the spheres of human lives, and the job market has also been affected. European countries were significantly impacted due to the COVID-19 pandemic. The countries had imposed multiple lockdowns, due to a high number of cases and deaths, which led to economic decline, and resulted in companies reducing their budget for hiring new employees2. During COVID-19, in Sweden, job seekers did not show much interest in applying for high profile careers, which reduced the new job announcements from the recruiter’s side3. India’s urban and rural areas suffered because of COVID cases, lockdown, and economic decline, and all these issues contributed to the rise in unemployment4.\n\nIn general, students who try to find a placement in established corporate companies have high stress and low self-esteem as they do not have pre-exposure to corporate companies5. Research on Israel’s younger population showed a connection between unemployment, COVID-19, and mental distress. This mental distress increased due to financial insecurity and aloofness6.\n\nStress takes time to build and does not come overnight. Likewise, self-esteem lowers gradually due to a sequence of events and not just one event in an individual’s life. Stress can be of two types: acute and chronic7. The chronic stress caused by unemployment may lead to low self-esteem, and with the help of mindfulness training it can be handled well8. Factors like gender and college students’ perception of parenting style can also impact their self-esteem9. Introverted college students showed more association with low self-esteem10.\n\nBefore the COVID-19 pandemic outbreak, institutions opted for placement coaching to solve placement-related mental health issues. In addition, there are choices for stress reduction like yoga meditation11, self-reiki12, progressive muscle relaxation13, and many more. Likewise, self-esteem may improve in several ways, such as self-uncertainty salience14, Yoga Nidra15, materialism16. The process of bringing awareness of the outer and inner occurrences in the current moment is called mindfulness17.\n\nBefore everything else, the impact of the pandemic on college students needs special consideration. As an after-effect of the pandemic, college students may experience anxiety and depression due to a decline in family income, loss of housing, infection with the coronavirus; hence, they require a psychological support system. Ultimately, college students have to be handled with a method that addresses multidimensional issues18. College students were isolated inside their homes because of COVID-19, which caused severe mental health issues due to problems such as separation from other people, increased psychiatric symptoms, and non-availability of the necessary information related to the pandemic19. Owing to the pandemic, college students’ took less time for important tasks such as sleeping, eating, and communicating with their peers. They also started spending more time using electronic gadgets. Severance of one’s routine results in depression and other mental health issues20. The adverse effects of COVID-19 made some college students endure psychological distress and other symptoms. Despite these issues, they were able to adapt and learn new technology and survive amidst the crisis21.\n\nMindfulness-based intervention is a gentle method of treatment that can harmonize the mind and the body. Mindfulness techniques have been researched by many, and some of these methods include: using the functional near-infrared spectroscopy to identify the dissimilarity of the hemodynamics of participants22; examining enhancements of brain indexes of consciousness process using event-related potentials after giving school-based mindfulness23; using voxel-based morphometry to identify the neural relationship of solitary differences in trait mindfulness16; using electroencephalogram and electrocardiogram to record the brain and heart activities and study the relationship between the signals during their reaction to mindfulness-based stress reduction24; using mindfulness on stroke and motor neuron disease patients and comparing the performance with music training while using electroencephalogram-based brain-computer interface devices25, and many more.\n\nMindfulness has various applications among students, but the needs of college students are different to school students. Researchers have performed mindfulness-based studies with college students in many ways, some of which are listed as follows: mindfulness has been applied to improve self-compassion and regulation of emotion in college students by using yoga-based meditation techniques26; examining the influence of protective behavioural strategies as a mediator on the impact of mindfulness on repercussions related to effects of alcohol consumption27; evaluating the role of therapeutic groups like mindfulness, relaxation, and control on outputs like drinking urge, negative and positive effects among students prone to alcohol consumption28; assessing the effects of mindfulness and behavioural activation on a waitlist control group29.\n\nHowever, mindfulness studies conducted with school students focused on different aspects. It has been applied to increase the focus of school students and it resulted in a positive outcome30. For example, digital game-based creativity learning has been used to identify the relationship between goal, self-determination, mastery experience, and mindfulness31. The influence of mindfulness has also been used to estimate the creativity level in graphics in a group of Latin American teenagers32, decreasing illness linked with corpulence and psychology disorders33.\n\nStudies indicate that mindfulness has extreme benefits with problems such as chronic disease34 including heart disease35, bowel disease36, lung disease37, insomnia38 and leukaemia39.\n\nCollege students who received online mindfulness training showed a reduction in anxiety and depression levels caused by COVID-1940. The repercussions of the COVID-19 pandemic impacted both teachers and students. Students showed a decline in their learning performance but mindfulness practices could address these issues41.\n\nAlthough the COVID-19 pandemic did not offer us many options, the efficacy of online mindfulness interventions raised concerns among practitioners. Mindfulness intervention was offered through a smartphone application, Headspace42 to employers, and the results showed that consistent practice aided in the reduction of stress and enhancement of psychological well-being43. The competence of mindfulness training in a video-based streaming service named Spectiv was found to facilitate mindfulness and well-being effectively44. Mindfulness-based interventions may assist the student placement process and the impact caused by COVID-19. Kam et al.45 found that even brief 10-minute mindfulness meditation practice on a daily basis will mitigate the negative effect caused by the constant exposure to COVID-19 news.\n\nIn this experimental study, we analyzed the impact of mindfulness-based interventions on college students involved in placement training. We hypothesised that mindfulness-based interventions would reduce stress and enhance self-esteem that both the placement and COVID-19 would likely impact. Therefore, we assume that consistent mindfulness meditation practices by college students will bring positive changes in stress, self-esteem, and the after-effects of the COVID-19 pandemic.\n\nTo assess the level of self-esteem among college students involved in a placement.\n\nTo evaluate the stress levels among college students involved in a placement.\n\nTo estimate the effect of mindfulness-based interventions among the college students involved in a placement.\n\nTo assess the significant difference between mindfulness-based interventions in the pre, post, and follow-up phases of the study.\n\nOur hypotheses in the following study were:\n\nThere will be a significant change in the self-esteem of the college students involved in the placements during the COVID-19 pandemic pre, post and follow-up phases of mindfulness-based interventions.\n\nThere will be a significant change in the stress of the college students involved in the placements during the COVID-19 pandemic pre, post and follow-up phases of mindfulness-based interventions.\n\nMindfulness-based interventions will enhance self-esteem and mitigate stress among college students involved in the placements during the COVID-19 pandemic pre, post and follow-up phases.\n\n\nMethods\n\nThe researchers initiated a focused group discussion among the researchers, teachers, and counselors to discuss the methods and procedures required. The members approved purposive sampling, online data collection, and intervention owing to the COVID-19 and convenience factors. Although members suggested different questionnaires, the unanimous consensus was to use the perceived stress scale, Rosenberg’s self-esteem scale, and the Kuppuswamy socio-economic scale. The researchers decided on questionnaires after carefully validating the objectives and suitability of the questionnaires to the Indian culture. The discussions led to checking the reliability and validity of the questionnaires to ensure the quality of the research. The members also suggested a pilot study to confirm the proposed intervention plan.\n\nThe focused group members are all from the Amrita School of Engineering, Coimbatore and devised the research strategy from first-hand experience with the potential participants. Thus immediately after the focused group discussion, researchers framed the research outline and sought ethical clearance.\n\nThis research gained approval and ethical clearance (AMRITA/SOE/ADMN/DOE/01/2021/01) from the Ethics Committee, Amrita School of Engineering, Amrita Vishwa Vidhyapeetham, Coimbatore, India. Written informed consent was obtained from the participants on the Google form. Participants were also given the necessary details about the intervention outcomes and assured that they had full rights to withdraw at any point of the research. The data collection and analysis were done based on the ethics committee, Amrita Vishwa Vidhyapeetham, India, and the personal identification details of the participants were removed. The tools (Perceived stress scale, Rosenberg self-esteem scale & Kuppuswamy socio-economic scale)46,47 were added to a Google Form, and a total of 100 students completed the form. Then every student’s stress and self-esteem were calculated. Although the Google form had data from 100 students, not all had high stress and low self-esteem. Hence, a threshold value was chosen for both the variables, where the value for stress was 22 and self-esteem was 31. A total of eighty students fell into this category, upon which they were sent emails regarding their scores and the option to attend the mindfulness-based intervention. Out of the 80 students, 75 responded positively and attended the intervention. Figure 1 indicates the process flow of the study.\n\nThe stress and self-esteem scores before the intervention were taken from the Google form, and after the intervention, the students were asked to fill out a new Google form containing the same questionnaires. A follow-up was conducted using the same set of procedures one month after the intervention. The results were analyzed using SPSS 23.0 (IBM SPSS Statistics: RRID: SCR_016479)48.\n\nPurposive sampling was used to select college students involved in the placement process at Amrita Vishwa Vidyapeetham University in Coimbatore, India. The inclusion criteria were: (1) Students with high stress and low self-esteem or either of the above. (2) Students who were in their final year of college, preparing for their placements. (3) Students with a grade point average of more than 6.5 out of 10 (University placement eligibility policy). The exclusion criteria were: (1) Students who were preparing to pursue higher studies inside or outside India. (2) Students who were planning start-ups. One hundred students who fit the criteria mentioned above, completed a demographic survey shared with them through Google Forms.\n\nIn this research, self-esteem is the perception of the sense of worth of the college student involved in placement possess. This self-esteem may have varied due to the adverse situations produced by placements during COVID-19. Stress is the perception of burden and negative feeling due to a problem, person or thing caused by the self-evaluation that they lack the specific skills required to handle that situation. This stress may lead to physical disturbances also. However, physical disturbances were not included in the scope of the study. Henceforth, stress was defined as an overtaxing, and heavy feeling and thinking in college students caused by the placements during COVID-19.\n\nA demographic survey was used to collect participants’ data such as name, age, class, gender, and consent to participate in the intervention. The students were informed about confidentiality and that their details would not be revealed to anyone under any circumstances. At the end of the intervention, the students were asked to provide feedback (if any). The following tools were used to collect data:\n\nThe perceived stress scale (PSS) was designed by Cohen et al.49,50 to measure the perceived stress in individuals. It is a five-point Likert scale ranging from zero to four with the options of never to not very often. It is a 10 item instrument where the total score is summed, and the higher the score, the higher the perceived stress. Some of the items are, \"In the last month, how often have you been upset because of something that happened unexpectedly?\", \"In the last month, how often have you felt that you were on top of things?\". This scale’s reliability was assessed by pre-testing it to one hundred and six college students participating in campus placements. The Cronbach’s alpha value of 10-item PSS indicates moderate internal consistency of 0.79, and test-retest reliability for a week showed, Intra-class correlation (ICC) of 0.83. During focused group discussion, the expert team authorized the face validity and content validity of the same.\n\nThe Rosenberg self-esteem scale is a 10 item scale for estimating the value of an individual’s self-esteem, it has a four-point Likert scale ranging from strongly agree to disagree strongly50,51. Some of the statements are: \"I certainly feel useless at times\" and \"I take a positive attitude towards myself\". While conducting the focused group discussion, face validity and content validity were discussed: a pre-testing of this 10-item scale was carried out on 106 college students involved in campus placements. Results showed that Cronbach’s value for internal consistency was 0.85 and ICC value for test-retest reliability was 0.86.\n\nThe Kuppuswamy’s socio-economic scale50,52 is mainly used to measure the status of a person in society by considering parameters such as education, occupation, and salary earned by the head of the family. The parameters, as mentioned earlier, have further subgroups where each has individual scores, the total of which ranges from 3–29. Based on the total score, the students were grouped into the following five classes: upper class, upper-middle class, lower-middle class, upper-lower class, and lower class.\n\nThe mindfulness-based intervention used in this research was inspired by Kabat-Zinn17,50. The intervention used in this experiment combined five mindfulness meditation techniques and mindfulness-based activities. The outline of the interventions used is tabulated in Table 1. The sessions were conducted online using Google meet, and each session was for two hours. Thus, the students attended one session weekly and, overall, eight sessions. In addition, the college students were asked to practice at least 30 minutes of mindfulness meditation on their own and report to the researchers. The college students were eager to oblige, and they completed the practice for eight weeks and reported their progress weekly once a month.\n\nThe quantitative measures were analyzed using SPSS 23.0, segregating the research process into pre, post, and follow-up phases. The demographic variables, namely age, gender and socio-economic status, were analyzed using percentage analysis. Researchers calculated the mean and standard deviation to understand the changes in the variables during pre, post and follow-up phases. One-way ANOVA portrayed the significant difference caused in the variables because of mindfulness-based intervention. Post hoc analysis was employed to identify the significant changes during the pre, post and follow-up phases of mindfulness-based interventions.\n\nThe researchers conducted a pilot study to ensure the feasibility of the design and outcome. Out of fifty involved in the placements, thirty had high stress and low self-esteem and among them, a few dropped out due to personal and academic difficulties. The pilot study started by pre-testing the twenty-one college students with the Perceived stress scale and the Rosenberg self-esteem scale followed by a mindfulness-based intervention: eating meditation, breathing meditation and body scan meditation for two weeks (two sessions, total four hours). It was found that the pre-phase mean value of stress was 28.05, and the post was 24.33. Similarly, the pre-phase self-esteem value was 23.80, and the post was 25.85. A one-way ANOVA test showed that there was a significant difference in the stress scores during the pre- and post phases of the mindfulness-based intervention (F (1,40)) = 11.69, p = 0.00). However, for self-esteem the one-way ANOVA indicated that there was no statistically significant difference between the pre- and post phases (F (1,40)) = 2.47, p = 0.12). Although there was a rise in the mean score, it was not statistically significant. In the focused group, discussion members suggested the following inclusions and those were carried out in the study. Expanding the intervention time from two weeks to eight weeks and including the meditation methods such as mountain meditation and loving-kindness meditation A session was devoted solely to connecting with meditation, self-reflection on its benefits and committing to understand and practice MBI.\n\n\nResults\n\nAlthough 80 students needed the mindfulness-based intervention, five members opted out due to conflict with college practical lab sessions and personal reasons. Thus, the mindfulness-based intervention commenced with 75 members, and all of them attended all three phases: pre, post and follow-up.\n\nTable 2 shows the demographic variables of the college students. The college students involved in the study were from 19 to 21 years of age, of which 48% of the population were 20-years-old, while 12% were 21-years-old. Twentynine percent of the students were female, and 71% were male. The absence of the socio-economic classes upper-lower and lower among the college students was noted. The majority of the college students were from upper-middle class (50.67%) and upper class (46.67%) backgrounds, while a few were lower-middle class (0.02%).\n\nTable 3, shows the pre-phase mean value of stress was 22.57, which is higher than the post-phase mean value 18.25, indicating that the intervention has reduced the stress levels in the participants. Similarly, the pre-phase mean value of self-esteem was 25.92, which is lower than the post-phase mean value 28.90, indicating that the intervention increased self-esteem among the participants. During the follow-up phase, the mean values for stress and self-esteem were 18.04 and 29.09, respectively, and these scores show that the impact of the intervention was sustained.\n\nN = 75\n\nS. D: Standard Deviation\n\nTable 4 shows the approximate F calculation of the pre-, post-, and follow-up phases for both the variables (self-esteem and stress). The output of analysis shows that for self-esteem, there was a statistically significant difference between pre-, post-, and follow-up phases as determined by one-way ANOVA, (F (2,222)) = 23.21, p = 0.00). There was also a statistically significant difference between the pre-, post- and follow-up phases for stress as determined by one-way ANOVA (F (2,222)) = 18.15, p = 0.00). The results indicated that mindfulness-based interventions helped college students during the placements.\n\n** Significance at 0.01 level\n\nDf: Degree of Freedom\n\nFigure 2 and Figure 3 show the changes in the mean stress and self-esteem scores across the pre-, post-, and follow-up phases of the intervention. It can be observed from Figure 2 that there is a significant difference in stress during pre- and post- phases of the intervention. However, it can also be observed that the difference tends to decrease between the post- and follow-up phases of the intervention. A similar pattern can also be observed with self-esteem in Figure 3. More specifically, the mean value of stress and self-esteem improved throughout the study.\n\nTable 5 shows the Post hoc analysis for the pre-, post-, and follow-up phases of intervention for stress and self-esteem. The mean stress scores of the college students during pre- and post-phases changed with a significant difference, 4.32 ± 0.75, p = 0.00. Pre- and follow-up phases also significantly differed, 4.53 ± 0.75, p = 0.00. There was no statistically significant difference between the follow-up and post-phases, 0.21 ± 0.75, p = 1.00. This analysis showed a significant decline in the stress scores of the pre- and post-phases because of the intervention. Self-esteem mean score pre- and post-phases (2.97 ± 0.75, p = 0.00.) and pre- and follow-up phases (3.17 ± 0.75, p = 0.00.) were statistically significant. Though there was an increase in the mean score of the post- and follow-up phases, the post hoc analysis revealed that (0.18 ± 0.75, p = 0.00.) were not statistically significant. Thus, we can conclude that the mindfulness intervention raised the self-esteem scores of the college students involved in placements.\n\n* Significance at 0.05 level\n\n\nDiscussion\n\nThis interventional study commenced with a focused group discussion, approved by the institutional ethical review board, using an online platform. Google docs helped collect the data from a hundred college students involved in the placements, and eighty out of a hundred had high stress and low self-esteem. Among eighty, seventy-five benefited from the mindfulness-based intervention. The study’s findings confirmed the existence of high stress and low self-esteem and the impact of mindfulness-based interventions in handling them. Although the post hoc analysis did not reveal a statistically significant change in reducing the participants’ stress, the enhancement of self-esteem and reduction of stress were implied by the mean scores.\n\nThe after-effects of COVID-19 on humans are fathomable, and people are now mitigating the negatives and focusing on development and improving their lives. However, college students who need to start new endeavours in the arena of life might feel stagnant because of the added stress of COVID-19 during placements. Furthermore, the consistent stress due to placements and COVID-19 might make the students doubt their ability. It was found in this experimental study that mindfulness-based intervention could serve as a support system throughout these challenging situations. Similarly, Coffey et al.53 showed that mindfulness-based intervention improves individuals’ mental health.\n\nOn the other hand, self-esteem is a personalised evaluation of one’s confidence. It serves as a powerful tool capable of estimating specific outcomes such as academic success46, happiness in relationships54, and much more. Guidetti et al.55 found that mindfulness as a trait mitigates stress levels and enhances meaning in a person’s career. This serves as a protective mechanism against burnout.\n\nMindfulness has the potential to serve as a protective mechanism throughout a college student’s life, and its impact need not be limited to scenarios such as placements and COVID-19. Buddhism and other spiritual practices across the globe suggest mindfulness as a way of living. These various ideologies found in spiritual practices include the main elements of non-discrimination of psychological distress and positive emotional experiences56. This ideology thereby reduces the partiality to contemplate these kinds of experiences as highs and lows and instead considers acceptance of all human experience as a whole. It was proposed in 47 that the lifelong learning concept will become practical and applicable if the under-estimated domain of learning is placed at the core of the whole structure. For the above scenario to happen, mindfulness has to be incorporated into the curriculum.\n\nCollege students need to take up new roles and make tough decisions in life. In addition, they have to meet the demands, pressure, and expectations from society and the after effects of the pandemic. Thus, mindfulness-based interventions will aid their focus and set a path for a bright future. Frontline workers like psychologists, psychiatric nurses, and psychiatric social workers can teach mindfulness to college students. The awareness and impact of mindfulness-based interventions should be made mandatory to all colleges and universities. In addition, the government could allocate funds and grants to researchers and trainers who conduct research and training programs on mindfulness.\n\nPurposive sampling was used to conduct this research in a single university. Future research should cover a diverse population, including more colleges in different districts/counties. The same experiment could also be conducted for alumni who are yet to find employment. Focusing on a diverse population and including parameters covering different areas of psychological health will open up new scope for research. Although the post hoc analysis revealed statistically significant results, the mean scores of stress and self-esteem did not continue in the follow-up phase. This could be rectified by assisting the participants to engage more in mindfulness meditation interim sessions. In addition, mindfulness meditation could be introduced as a life skill by creating an online presence on platforms like websites, apps, and courses. This will encourage students to habituate mindfulness meditation as a lifelong learning process.\n\n\nConclusions\n\nThe COVID-19 pandemic has made us reflect on all our endeavours. College students devote three-quarters of their time to educational purposes until they graduate and are expected by society to find a suitable placement. Although COVID-19 has impacted and challenged college students’ placements, the psychological problems it has caused can be handled using mindfulness-based intervention. It can also serve as an efficient tool that benefits students preparing for placements, job fairs, or interviews by making them focus on the task at hand and mitigating the impact of COVID-19.\n\n\nData availability\n\nFigshare: Underlying data for ’Does online mindfulness-based intervention help college students succeed in their job search during the COVID-19 pandemic?’ https://doi.org/10.6084/m9.figshare.19360955.v450\n\nThis project contains the following underlying data:\n\nData file: Complete data containing Socio-Economic Scale information for each participant.xlsx\n\nFigshare: Extended data for ’Does online mindfulness-based intervention help college students succeed in their job search during the COVID-19 pandemic?’ https://doi.org/10.6084/m9.figshare.19360955.v450\n\nThis project contains the following extended data:\n\nQuestionnaire: Demographic questions.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nConsent\n\nWritten informed consent for publication of the participants’ details was obtained from the participants.",
"appendix": "References\n\nLavrinovicha I, Lavrinenko O, Teivans-Treinovskis J: Influence of education on unemployment rate and incomes of residents. Procedia Soc Behav Sci. International Conference on New Horizons in Education, INTE, 2014, 25-27 June 2014, Paris, France, 2015; 174: 3824–3831. Publisher Full Text\n\nSu CW, Dai K, Ullah S, et al.: Covid-19 pandemic and unemployment dynamics in european economies. Economic Research-Ekonomska Istraživanja. 2021; 1–13. Publisher Full Text\n\nHensvik L, Le Barbanchon T, Rathelot R: Job search during the covid-19 crisis. J Public Econ. 2021; 194: 104349. Publisher Full Text\n\nAli MA, Kamraju M: A STUDY ON IMPACT OF COVID-19 PANDEMIC ON UNEMPLOYMENT IN INDIA. 2020; 50–61. Reference Source\n\nPeláez-Fernández MA, Rey L, Extremera N: Psychological distress among the unemployed: Do core self-evaluations and emotional intelligence help to minimize the psychological costs of unemployment? J Affect Disord. 2019; 256: 627–632. PubMed Abstract | Publisher Full Text\n\nAschdut N, Refaeli T: Unemployment and psychological distress among young people during the covid-19 pandemic: Psychological resources and risk factors. Int J Environ Res Public Health. 2020; 17(19): 7163. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRohleder N: Stress and inflammation - the need to address the gap in the transition between acute and chronic stress effects. Psychoneuroendocrinology. 2019; 105: 164–171. PubMed Abstract | Publisher Full Text\n\nAránega AY, Sánchez RC, Pérez CG: Mindfulness' effects on undergraduates' perception of self-knowledge and stress levels. J Bus Res. 2019; 101: 441–446. Publisher Full Text\n\nReshma K, Mathew JA: Self-esteem and adolescents’ perception regarding maternal parenting style. Indian J Public Health Res Dev. 2018; 9(8): 215. Reference Source\n\nSreedevi PA, Aswathy BL, Roy N: A correlational study on assertiveness and self esteem of undergraduate students of a selected college of nursing, ernakulam. Indian J Public Health Res Dev. 2018; 9(6): 49–55. Reference Source\n\nPascoe MC, Thompson DR, Ski CF: Yoga, mindfulness-based stress reduction and stress-related physiological measures: A meta-analysis. Psychoneuroendocrinology. 2017; 86: 152–168. PubMed Abstract | Publisher Full Text\n\nBukowski EL: The use of self-reiki for stress reduction and relaxation. J Integr Med. 2015; 13(5): 336–340. PubMed Abstract | Publisher Full Text\n\nCorbett C, Egan J, Pilch M: A randomised comparison of two 'stress control' programmes: Progressive muscle relaxation versus mindfulness body scan Ment Health Prev. 2019; 15: 200163. Publisher Full Text\n\nYang Q, Ybarra O, Van den Bos K, et al.: Neurophysiological and behavioral evidence that self-uncertainty salience increases self-esteem striving. Biol Psychol. 2019; 143: 62–73. PubMed Abstract | Publisher Full Text\n\nDol KS: Effects of a yoga nidra on the life stress and self-esteem in university students. Complement Ther Clin Pract. 2019; 35: 232–236. PubMed Abstract | Publisher Full Text\n\nLi J, Lu M, Xia T, et al.: Materialism as compensation for self-esteem among lower-class students. Pers Individ Dif. 2018; 131: 191–196. Publisher Full Text\n\nKabat-Zinn J: Wherever you go, there you are: Mindfulness meditation in everyday life. Hachette Books, 2009. Reference Source\n\nJones HE, Manze M, Ngo V, et al.: The impact of the covid-19 pandemic on college students' health and financial stability in new york city: Findings from a population-based sample of city university of new york (cuny) students. J Urban Health. 2021; 98(2): 187–196. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWathelet M, Duhem S, Vaiva G, et al.: Factors associated with mental health disorders among university students in france confined during the covid-19 pandemic. JAMA Netw Open. 2020; 3(10): e2025591. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGiuntella O, Hyde K, Saccardo S, et al.: Lifestyle and mental health disruptions during covid-19. Proc Natl Acad Sci U S A. 2021; 118(9): e2016632118. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorris ME, Kuehn KS, Brown J, et al.: College from home during covid-19: A mixed-methods study of heterogeneous experiences. PLoS One. 2021; 16(6): e0251580. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGundel F, von Spee J, Schneider S, et al.: Meditation and the brain-neuronal correlates of mindfulness as assessed with near-infrared spectroscopy. Psychiatry Res Neuroimaging. 2018; 271: 24–33. PubMed Abstract | Publisher Full Text\n\nSanger KL, Dorjee D: Mindfulness training with adolescents enhances metacognition and the inhibition of irrelevant stimuli: Evidence from event-related brain potentials. Trends Neurosci Educ. 2016; 5(1): 1–11. Publisher Full Text\n\nGao J, Fan J, Wu BW, et al.: Entrainment of chaotic activities in brain and heart during mbsr mindfulness training. Neurosci Lett. 2016; 616: 218–223. PubMed Abstract | Publisher Full Text\n\nTan LF, Dienes Z, Jansari A, et al.: Effect of mindfulness meditation on brain-computer interface performance. Conscious Cogn. 2014; 23: 12–21. PubMed Abstract | Publisher Full Text\n\nPatel NK, Nivethitha L, Mooventhan A: Effect of a yoga based meditation technique on emotional regulation, self-compassion and mindfulness in college students. Explore (NY). 2018; 14(6): 443–447. PubMed Abstract | Publisher Full Text\n\nBrett EI, Leffingwell TR, Leavens EL: Trait mindfulness and protective strategies for alcohol use: Implications for college student drinking. Addict Behav. 2017; 73: 16–21. PubMed Abstract | Publisher Full Text\n\nVinci C, Peltier M, Waldo K, et al.: Examination of trait impulsivity on the response to a brief mindfulness intervention among college student drinkers. Psychiatry Res. 2016; 242: 365–374. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcIndoo CC, File AA, Preddy T, et al.: Mindfulness-based therapy and behavioral activation: a randomized controlled trial with depressed college students. Behav Res Ther. 2016; 77: 118–128. PubMed Abstract | Publisher Full Text\n\nReindl D, Hamm A, Lewis R, et al.: Elementary student and teacher perceptions of a mindfulness and yoga-based program in school: A qualitative evaluation. Explore (NY). 2020; 16(2): 90–93. PubMed Abstract | Publisher Full Text\n\nYeh YC, Chang HL, Chen SY: Mindful learning: A mediator of mastery experience during digital creativity game-based learning among elementary school students. Comput Educ. 2019; 132: 63–75. Publisher Full Text\n\nJusto CF, Mañas IM, Ayala ES: Improving the graphic creativity levels of latin american high school students currently living in spain by means of a mindfulness program. Procedia Soc Behav Sci. 2014; 132: 229–234. Publisher Full Text\n\nSoleimaninanadegani M, Shahmohammadi N: The impact of mindfulness-based cognitive therapy on anthropometric indices balance in high-school obese girls' students in iran. Procedia Soc Behav Sci. 2013; 84: 542–548. Publisher Full Text\n\nHarrison SL, Lee A, Goldstein RS, et al.: Perspectives of healthcare professionals and patients on the application of mindfulness in individuals with chronic obstructive pulmonary disease. Patient Educ Couns. 2017; 100(2): 337–342. PubMed Abstract | Publisher Full Text\n\nJalali D, Abdolazimi M, Alaei Z, et al.: Effectiveness of mindfulness-based stress reduction program on quality of life in cardiovascular disease patients. Int J Cardiol Heart Vasc. 2019; 23: 100356. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHood MM, Jedel S: Mindfulness-based interventions in inflammatory bowel disease. Gastroenterol Clin North Am. 2017; 46(4): 859–874. PubMed Abstract | Publisher Full Text\n\nTan SB, Liam CK, Pang YK, et al.: The effect of 20-minute mindful breathing on the rapid reduction of dyspnea at rest in patients with lung diseases: a randomized controlled trial. J Pain Symptom Manage. 2019; 57(4): 802–808. PubMed Abstract | Publisher Full Text\n\nZhang H, Li Y, Li M, et al.: A randomized controlled trial of mindfulness-based stress reduction for insomnia secondary to cervical cancer: Sleep effects. Appl Nurs Res. 2019; 48: 52–57. PubMed Abstract | Publisher Full Text\n\nZhang R, Yin J, Zhou Y: Effects of mindfulness-based psychological care on mood and sleep of leukemia patients in chemotherapy. Int J Nurs Sci. 2017; 4(4): 357–361. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu JL, Schülke R, Vatansever D, et al.: Mindfulness practice for protecting mental health during the covid-19 pandemic. Transl Psychiatry. 2021; 11(1): 329. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTortella GR, Seabra AB, Padrão J, et al.: Mindfulness and other simple neuroscience-based proposals to promote the learning performance and mental health of students during the covid-19 pandemic. Brain Sci. 2021; 11(5): 552. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaliwa I, Ford CG, Wilson JM, et al.: A mixed-method assessment of a 10-day mobile mindfulness intervention. Front Psychol. 2021; 12: 722995. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBostock S, Crosswell AD, Prather AA, et al.: Mindfulness on-the-go: Effects of a mindfulness meditation app on work stress and well-being. J Occup Health Psychol. 2019; 24(1): 127–138. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaylor G, Alpert J, Waddell TF, et al.: Streaming mindfulness: Well-being and mindfulness among subscribers to a video streaming service. Internet Interv. 2021; 25: 100419. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKam JWY, Javed J, Hart CM, et al.: Daily mindfulness training reduces negative impact of covid-19 news exposure on affective well-being. Psychol Res. 2022; 86(4): 1203–1214. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarsh HW: Causal ordering of academic self-concept and academic achievement: a multiwave, longitudinal panel analysis. J Educ Psychol. 1990; 82(4): 646–656. Publisher Full Text\n\nHyland T: Lifelong learning, mindfulness and the affective domain of education, In: Second international handbook of lifelong learning. Springer, 2012; 26: 209–226. Publisher Full Text\n\nIBM Corp: Ibm spss statistics for windows. Reference Source\n\nCohen S, Kamarck T, Mermelstein R: A global measure of perceived stress. J Health Soc Behav. 1983; 24(4): 385–396. PubMed Abstract\n\nRajalakshmi SA, Sowndaram CS, Ganesh G, et al.: COVID-19 and Placement Impact on College Students. 2022. http://www.doi.org/10.6084/m9.figshare.19360955\n\nRosenberg m: Rosenberg self-esteem scale (rse). Acceptance and commitment therapy. Measures package. 1965; 61(52): 18. Reference Source\n\nSaleem SM: Modified kuppuswamy socioeconomic scale updated for the year 2019. Indian J Forensic Community Med. 2019; 6(1): 1–3. Publisher Full Text\n\nCoffey KA, Hartman M, Fredrickson BL: Deconstructing mindfulness and constructing mental health: Understanding mindfulness and its mechanisms of action. Mindfulness. 2010; 1(4): 235–253. Publisher Full Text\n\nOrth U, Robins RW: The development of self-esteem. Curr Dir Psychol Sci. 2014; 23(5): 381–387. Publisher Full Text\n\nGuidetti G, Viotti S, Badagliacca R, et al.: Can mindfulness mitigate the energy-depleting process and increase job resources to prevent burnout? a study on the mindfulness trait in the school context. PLoS One. 2019; 14(4): e0214935. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKeng SL, Smoski MJ, Robins CJ: Effects of mindfulness on psychological health: A review of empirical studies. Clin Psychol Rev. 2011; 31(6): 1041–56. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "148093",
"date": "08 Sep 2022",
"name": "Nanchatsan Sakunpong",
"expertise": [
"Reviewer Expertise Positive psychology",
"Psychology of gender and sexual orientation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study is interesting in how to apply mindfulness with an online intervention which might be appropriate for the digital technology era. However, this study still has some points that can be developed and need to be explained with the following details:\nThe title of the study told us that the program would help in job search success, which was inconsistent with the variables studied by the researcher. Therefore, perhaps changing the title by adding the dependent variable of this research instead of succeed in job search would be more appropriate.\n\nIn the introduction section, it may be necessary to explain the knowledge gap and how this research can help fill the missing knowledge gap.\n\nThis study seems to use a quasi-experimental research design but was not specified in the research design section. Instead, it was written to be focus group discussion, which was inconsistent with the actual research methodology used in the study.\n\nBecause this study wants to present a new intervention. So, it's important to write a detailed description of each activity (e.g. eating meditation, body scan, mountain meditation - short how-to) that will be helpful to anyone interested in implementing or re-testing the program in the future.\n\nShould add the effect size of the program in the results section.\n\nBecause this study appears to be a quasi-experimental study where confounding variables can arise. So, the recommendation for research in the future can be conducted with additional control groups to be more clearly describe the influence of independent variables on dependent variables.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8878",
"date": "04 Nov 2022",
"name": "Rajalakshmi S.A.",
"role": "Author Response",
"response": "We are happy to see your review of our paper, and we are grateful for your time and suggestions. We have incorporated your comments into our work, and please continue to guide and support us."
}
]
}
] | 1
|
https://f1000research.com/articles/11-955
|
https://f1000research.com/articles/10-402/v1
|
19 May 21
|
{
"type": "Research Article",
"title": "Regular antenatal care visits were associated with low risk of low birth weight among newborns in Rwanda: Evidence from the 2014/2015 Rwanda Demographic Health Survey (RDHS) Data",
"authors": [
"Emmanuel Biracyaza",
"Samuel Habimana",
"Donat Rusengamihigo",
"Heather Evans",
"Samuel Habimana",
"Donat Rusengamihigo",
"Heather Evans"
],
"abstract": "Background: Low birth weight (LBW) remains the global unfinished agenda in most countries of the world especially in low- and middle-income countries. LBW subsequently has harmful effects on the lifestyle, psychosocial and physiological development of the child. Although it is known that antenatal care (ANC) visits are important interventions contributing to prediction of newborn birth weight, little has been conducted on effect of ANC visits on birth weight in Rwanda. This study aimed at determining the association between regular ANC visits and risk of LBW among newborns in Rwanda. Methods: A cross-sectional study design was conducted to analyse the effects of ANC on LBW using the 2014/2015 Rwanda Demographic Health Survey. Associations of socio-demographic, socio-economic, and individual factors of the mother with LBW newborns were performed using bivariate and multiple logistic regression analyses. Results: Prevalences of LBW and macrosomia were 5.8% and 17.6%, respectively. Newborns delivered from mothers attending fewer than four ANC visits were at almost three-times greater risk of having LBW [aOR=2.8; 95%CI (1.5–5.4), p=0.002] compared to those whose mothers attending four or more ANC visits. Residing in a rural area for pregnant women was significantly associated with LBW [aOR=1.1; 95%CI (0.7–1.6), p=0.008]. Maternal characteristics, such as anemia, predicted an increase in LBW [aOR=3.5; 95%CI (1.5–5.4), p<0.001]. Those who received no nutritional counseling [aOR=2.5; 95%CI (2–8.5), p<0.001] and who were not told about maternal complications [aOR=3.3; 95%CI (1.5–6.6), p=0.003] were more prone to deliver newborns with LBW than those who received them. Pregnant women who received iron and folic acid were less likely to have LBW newborns [aOR=0.5; 95%CI (0.3–0.9), p=0.015]. Conclusion: ANC visits significantly contributed to reducing the incidence of LBW. This study underscores the need for early, comprehensive, and high-quality ANC services to prevent LBW in Rwanda.",
"keywords": [
"Antenatal care",
"Birth weight",
"newborn",
"Maternal factors",
"Sustainable Development Goals",
"Pregnancy"
],
"content": "Introduction\n\nAntenatal care (ANC) globally is an important health strategy that has been considered as an essential intervention to contribute to the health of newborns and their mothers. This health intervention reduces low birth weight (LBW) which is a foremost public health burden that weakens the development of families and nations due to its harmful effects on quality of life.1 LBW is defined when a baby weighs less than 2.5 kilograms at birth. This health burden particularly, in low- and middle-income countries (LMICs) may cause multiple effects, such as birth asphyxia, amniotic fluid aspiration, hypoglycemia and hyponatremia.2–4 The estimate of 15.5% to 15.9% of LBW worldwide was reported5,6 and the high prevalence (95.6%) of LBW newborns occurred in LMICs.7,8 ANC visits were found to play a great role in the health promotion of mothers and children before, during and after delivery. It specifically contributes to the reduction of morbidity and mortality of mothers and children.9,10 Epidemiological studies have shown that the children weighing less than 2.5 kilograms are nearly 20-times more likely to die than those who weigh 2.5 kilograms and more.11 Other studies have stated that newborns with LBW were 5–10-times more likely to die than those who weighed 2.5 kilograms and more.2,3 Prior studies have indicated that the newborn may develop macrosomia, defined as birth weight more than 4 kilograms. These newborns are considered to have an excessive birth weight. Its prevalence varies globally between 3 and 15% depending on the region, due to various factors where it remains higher in the developing world.12,13\n\nPrior studies indicated that maternal and environmental factors are major factors with regard to LBW.14,15 The number of ANC visits attended by the pregnant women and the amount of recommended packages of the interventions provided during ANC are the main factors contributing to LBW.14,16 A low socio-economic status and limited access to qualified health services related to pregnancy are risk factors for LBW.16 Multiple studies established that accessibility to poor food consumption behaviors, problems of health status for pregnant women, low caloric intake, hypertension, urinary infections, smoking behaviors, genital infections and psychological distress were found to be risk factors of LBW.4,17,18 Earlier studies conveyed that consumption of iron, birth order, and calcium supplementation reduces the risk to develop LBW.18–20\n\nANC refers to the routine health management of presumed healthy pregnant women without the symptomatology or screening so as to diagnose and detect the diseases or complicating symptoms.16,21,22 The World Health Organization (WHO) recommended pregnant women attend a minimum of four ANC visits for obtaining the basic health education and interventions that promote health of babies. The more they attend ANC services, the more they receive the maximum health package that plays a crucial role in their health and the health of their newborn.23 Prior studies have documented that two-thirds of all pregnant women worldwide attended at least one ANC service during pregnancy. They also documented that ANC is the significant predictor of birth weight where attending the required ANC increases the probability of achieving full life-saving potential and having a newborn with more than 2,500 grams.24–27 In ANC visits, pregnant women are offered health education, such as adequate nutrients to be consumed during and after delivery, vitamin intake, proper vaccination, changing risk behaviors such as smoking, and place of delivery.28,29 The package provided to pregnant women consists of many interventions like the identification and management of the obstetric complications including pre-eclampsia, tetanus toxoid immunization, de-worming, iron, folic acid, and interventions related to infectious diseases, such as malaria prevention, during pregnant period and insecticide-treated nets (ITNs). The fundamental rudiments of a focused approach to ANC are surveillance of health issues among pregnant woman and their babies, management of complications occurring in the pregnancy period, such as hypertension, treatment of underlying or concurrent illness, screening for health conditions and diseases, mental health problems and intra-partner violence or domestic violence.25,29,30 ANC visits are obviously the opportunities for promoting the use of skilled attendance at birth, injury prevention, adherence support for preventive interventions, healthy lifestyle safety, and healthy behaviors such as breastfeeding, early postnatal, and planning for the optimal pregnancy spacing.24,31,32 Pregnant women are provided supplementary nutrients for enhancing the baby’s and mother’s health, screening for genetic and congenital disorders, and offered folic acid supplementation to reduce the risk of neural tube defects.1,8,28,33,34\n\nEarlier researchers documented that through ANC services, pregnant women and their newborns develop physiological and psychosocial wellbeing. It also reduces risk to have a LBW newborn. ANC visits contributed to development of healthy behaviors and compromise of the emergency preparedness plan to intensify the maternal awareness, improving the newborn needs and self-care.29 Other studies indicated that ANC visits contribute to weight gain and weight regulation of women. They confirmed that ANC services increase the weight of pregnant women and contribute to the growth of the fetal and maternal tissues and fluids.21,35 This health intervention plays a great role in the provision of information about lifestyle, pregnancy, and delivery. They prevent the potential determinants associated with morbidity and mortality of mothers and children. ANC services not only contribute to pregnant women and their fetus, but also foster a virtuous social and family cohesion and resilience. It was found that more than 80% of pregnant women who attended at least four ANC visits reported showed effectively controlled pregnancy complications.33,36,37 ANC services contribute to preparing women for delivery and understanding warning signs during the pregnancy and childbirth.38 It was scientifically found that the ANC interventions attended early become the best opportunity for appropriate screening and medical testing for health problems in which pregnant women are exposed to have during and after pregnancy.39 ANC coverage was an important indicator for reducing the risks to neonatal, infant mortality, maternal mortality and stunting issues to the child.37\n\nPrevious studies indicated that there is a substantial influence of ANC on increase of birth weight for the children and their development of a good life characterized by prevention and management of pregnancy-related or concurrent diseases and psychosocial development.37,40 Maternal health production function explained that early onset of ANC, prenatal care and have a minimum number of ANC and prenatal care visits.41,42\n\nThe rationale of this study was to increase the accessibility to ANC services that were documented to be practiced, but there was no scientific evidence that was conducted to indicate its effect on neither LBW nor contributing determinants to the reduction of children and maternal morbidity and deaths in Rwanda. Through the findings from this research, the investigators indicated how pregnant women achieve the third goal of Sustainable Development Goal (SDG-III) related to the reduction of infant and maternal mortality and morbidity by completing four ANC visits and more. Although it is known that ANC visits are an important intervention that contributes to prediction of the newborn birth weight, little has been conducted on effect of ANC visits on birth weight in developing countries, including Rwanda. This research, therefore, aimed to determine the effect of antenatal care visits on the LBW of children in Rwanda using the secondary data analysis of Rwanda Demographic and Health Survey (RDHS) 2014-2015. We hypothesize that ANC visits result in reducing the high incidence of LBW among newborns of Rwanda.\n\n\nMethods\n\nThe fifth RDHS 2015 was utilized as a nationally representative sample implemented by the National Institute of Statistics of Rwanda (NISR) and Ministry of Health of Rwanda.\n\nThe study design was a secondary analysis of cross-sectional survey data from RDHS 2014/2015 that was retrospectively carried out for investigating the effects of antenatal care visits on birth weight of the newborn in Rwanda. The RDHS data collection fieldwork was conducted from November 9, 2014, to April 8, 2015. The data entry, editing, and cleaning was completed by May 15, 2015, and the final survey report was completed in March 2016. A total of 8,004 pregnant women who were to receive antenatal care interventions before delivery were recruited. The interviewed women were of reproductive age (15–49 years). This study was conducted in Rwanda, a small country located in the Central and Eastern Africa bordered by the Republic Democratic of Congo to the West, Uganda to the North, Tanzania to the East and Burundi to the South. This country lies a few degrees south of the equator and is landlocked. Concerning ANC visits, accessibility to ANC services is increasing due to the improvement of the health system and health financing.1 This health system contributes to the achievement of SDG-III those targets reducing morbidity and mortality of mothers and children worldwide specifically in LMICs. The total area of Rwanda is approximately 26,338 km2, the Rwandan population density around 416 people per km2 and the total population is roughly 10.8 million. The majority (43%) of the Rwandan population is aged 15 years or less. Women accounted for about 52.6% of the population, 84% of Rwandans resided in the rural setting, and 71% participant in agricultural activities.43\n\nRDHS was a national survey conducted to assess the birth weight of newborns. To collect the data of this household-based survey, mothers who had the youngest children, age five years or less, were interviewed to provide data related to birth weight for their children. The data for this survey were collected using a two-stage sampling strategy for enrolling participants. These stages were cluster sampling design and the sampling frame. The sampling frame was composed of the list of the enumerators’ areas (EAs) that covered the entire country. All residents in selected households were eligible to be interviewed. At the first stage of this study, 492 clusters were randomly selected (113 in urban and 379 in rural areas). At the second stage of this study, the systematic sampling technique that focused on selecting the households was applied. Then, a fixed number of 26 households were selected randomly from each cluster and a total of 12,792 households were selected for the final sample for this study.\n\nAdditionally, the proportional sampling technique was used in the survey where the sample for each cluster was equal. The study included women aged 15–49 years who were permanent residents of the households or visitors who stayed in the recruited household the night before the survey. For this epidemiological research, this fifth demographic survey presented that although the weight of the newborns at birth is an important predictor of their probability of surviving, current birth weights were not available for the most children. Instead, the mothers were interviewed about the size of their children at birth because this determinant was found to be a proxy for the weight of the newborn. Therefore, 8,004 mothers with 15–49 years of reproductive age were interviewed for reporting the actual weight in kilograms using the written information about birth weight or recalling the weight at birth for their newborns. It was found that 92% of newborns had a birth weight reported while 8% did not.\n\nRDHS 2014/2015 collected data at the national level using household-based survey data on birth weight retrospectively collected from the mothers. The data collection was completed by trained data collectors who used face-to-face interviews, asking mothers eligible for this study to provide a detailed birth history for children born in the preceding five years. Recruitment included stratified sampling, two stages of cluster sampling designs. The first stage was characterized by selecting the participants from the samples frame constructed from enumeration whereas the second stage involved the systematic sampling of the households. These were listed from each cluster to ensure that an adequate number of the completed individuals were obtained.44 Participants were interviewed based on the measurement of the DHS program. Birth weight was recorded in the RDHS using metric measurement (in kilograms) for all participants from the entire stratum of the country. Data from mothers with stillbirths were excluded from this study.\n\nBias refers to any tendency or deviation from the truth in study design, data collection, recruiting participants, data analysis, and results interpretation. Generally, bias may occur at any stage of the research. To manage the bias for the data from RDHS, the authors systematically did data cleaning and removed the missing variables. All authors checked several times the selected variables to include in the analysis for minimizing all possible systematic errors that could occur in the study.\n\nDependent variable\n\nThe outcome variable of the current study was birth weight of the newborns. As per World Health Organization (WHO) classification, newborns weighing <2,500 grams were categorized as LBW while newborns weigh >2,500 grams were categorized as not having LBW.45\n\nExplanatory variables\n\nBased on the literature review and the structure of the RDHS 2014/2015 dataset, the independent variables were found. The main explanatory variable was the number of the antenatal care visits for the pregnant women. Pregnant women who attend none or one ANC visit were considered to have inadequate number of visits, those who attended two or three ANC visits were considered to have intermediate, and those who attended four to seven were taken as adequate number of visits. As recommended by WHO, the pregnant women who attended four ANC visits were considered to have obtained extremely adequate healthcare that effectively contributes to the health of the mother and unborn.46–48 This study used different covariate variables selected based on the previous epidemiological studies, reviewing the suitable published demographic and epidemiological studies and the available information provided in the demographic health survey (DHS) datasets with the consideration of the potential confounders. Based on the insights from the literature and availability in the datasets, the following variables were included as potential confounders: maternal age (<19 years, 20–34 years and 35–49 years); maternal height (1: <160 cm; 2: ≥160 cm), parity (i.e. birth order), maternal weight (1: <80 kg; 2: 80-89 kg; and 3: ≥90 kg), body mass index (BMI), residence (0: urban; 1: rural); educational attainment (0: illiterate; 1: primary; 2: secondary and higher); household wealth status (0: poor, 1: middle and rich); place of delivery, marital status, maternal occupation, tetanus injection during the pregnancy (0: yes; 1: no), intake iron during the pregnancy (0: yes; 1: no), sex of the child (0: female; 1: male), sex of household head (0: female; 1: male), wanted pregnancy when became pregnant (0: yes; 1: no), blood pressure taken during pregnancy (0: yes; 1: no) provided anti-malaria drugs during pregnancy (0: yes; 1: no), urine sample taken during pregnancy (0: yes; 1: no), received counseling or health education related to nutrients (0: yes; 1: no).\n\nBefore analysis, the observations with missing data were dropped. Statistical analysis was performed using descriptive (such as frequency, percentage, standard deviation, and mean) and analytical analyses. In the analytical analysis, bivariate logistic regression and multiple logistic regression models were computed to determine the association between LBW and the explanatory variables. The factors that were significantly associated with LBW at 0.05 or 0.01 in bivariate logistic regression were analyzed using multiple logistic regression models for identifying the association between ANC visits and birth weight when controlling for other covariates, presenting adjusted odds ratio, 95% confidence intervals. Therefore, we adjusted sampling based on the RDHS data that were widely used and consistent data for assessing maternal and child health statistics at the national level using STATA software version 13 (RRID:SCR_012763).49 In this cross-sectional study design, we respected the guidelines outlined in the Strengthening the Reporting of Observational Studies in Epidemiology statement in writing the manuscript.50\n\nData used were electronically accessed. To get full access, the first registration was completed on the DHS website. The permission to use the 2014/2015 RDHS data was granted by DHS using its website and the prior approval was maintained. In the prior approval, the women of reproductive age who were age 18–49 years provided oral and written informed consent forms to take part in the survey. In the cases on the minor participants (those women aged 15–17 years); the assent form was obtained from them while written informed consent were simultaneously provided by their guardians or parents who were adults.\n\n\nResults\n\nThe results indicated the average birth weight was 3846.1 grams with a standard deviation of 1840.5 grams. The results indicated that the average family size was 5.7 (SD=2). The majority [6012 (76.6%)] weighed 2,500–4,000grams. The majority (61.3%) of pregnant women were aged 35–39 years. For the occupation of the pregnant women, it was found that the majority (86.1%) were involved in agricultural activities (self-employed). About the participants’ religious beliefs, the majority (96.8%) were Christians. Regarding the information about the households, the results indicated that the majority (21.6%) were the poorest. The majority of them (57.9%) were from the families consisting of four to seven family members and 77.3% resided in rural setting. 92% of the pregnant women attended ANC at health centers. Moreover, the prevalence of LBW and macrosomia was 5.8% and 17.6%, respectively, whereas 76.6% of pregnant women delivered newborns who weighed between 2.5 kg and 4 kg. The number of pregnant women who attended four or more ANC visits was 44.1%, those who attended fewer than four ANC was 55.1%, and only 0.8% attended no ANC visits. This indicated that Rwanda did not yet achieve the SDG-III. Besides, the findings showed that during pregnancy, these women are provided different health education and measurement for improving the health of the children including normalizing the birth weight for both mother and their children. Within this period, the results indicated that the majority of the pregnant women (80.5%) were provided at least one tetanus injection before birth, but 19.5% were not. Before pregnancy, the results indicated that the majority was not given any tetanus injection. This means that the tetanus injection is mostly attended by the women when they were pregnant during the ANC visits. The results indicated that more than 70.7% of the pregnant women were provided counseling and education related to nutrients. Indeed, the findings showed that 79.9% of pregnant women were given iron tablet during the pregnant period. The majority (83.4%) of pregnant women were measured blood pressure (Table 1).\n\nNotice: SD: Standard Deviaton.\n\nIn the bivariate logistic regression, we indicated how low birth weight is associated with ANC services, socio-demographic characteristics, maternal influences and behaviors. Therefore, we found that LBW is significantly associated with the ANC visits, BMI, maternal height, maternal weight, residence, place of delivery, sex of child, HWI, maternal parity, maternal, anemia for pregnant women, family size, age, maternal education, provision of tetanus injection during the pregnancy, health education about pregnant complications, provision of counseling about nutrients during pregnancy, provision of malaria drugs, use of health card, and attendance of ANC visits at health center (Table 2).\n\nNotice: (*) Indicates the statistical significance level at 0.05; (**) Estimates the statistical significance level at 0.01; Unmarked p-values were not fond to be the significant risk factors of LBW in Rwanda.\n\nMultiple logistic regression analyses indicated that ANC check-ups are the risk factor of LBW among the pregnant women. Mother attending fewer than four ANC visits are almost three-times more likely to give birth to LBW children [aOR=2.8; 95%CI (1.5–5.4), p=.002] when compared with mothers attending four or more ANC visits. Besides, newborns who were delivered at the health center [aOR=0.3; 95%CI (0.2–0.7), p=.002] and private health institutions [aOR=0.3; 95%CI (0.2–0.6), p<0.001] were less likely to weigh less than 2.5 kg than who were delivered in their households. The findings demonstrated that pregnant women who were not provided Coartem for malaria treatment [aOR=0.6; 95%CI (0.4–0.8), p<0.001] or who received other malaria drugs [aOR=4.1;95CI (1.7–10), p=0.02] were more likely to have LBW newborns. The pregnant women who attended the ANC visits at the health center [aOR=0.5; 95%CI (0.3–0.9), p=0.02] were less likely to have newborns with less than 2.5 kg. For marital status, married and cohabiting pregnant women were 1.86-times at greater risk to have LBW children [aOR=1.9; 95%CI (1.3–2.8), p=0.002] compared with single pregnant women. Mothers who were widowed, divorced and separated from their husbands were more likely to have LBW children compared with the women who were single during pregnancy. The results indicated that the widowed, separated and divorced pregnant women had 1.7-times greater risk of having LBW babies [aOR=1.7; 95%CI (1.1–2.5), p=0.015] than women who were single during pregnancy. Results found that being provided maternal iron and folic acid supplementation during pregnancy [aOR=0.5, 95%CI (0.3–0.9), p=0.015], not being given nutrients during pregnancy [aOR=2.5, 95%CI (2-8.4), p<0.001], being told about maternal complications during pregnancy [aOR=0.7, 95%CI (0.5–1), p=0.05], pregnant women with anemia [aOR=3.5, 95%CI (1.5–9), p<0.001] were positively associated with LBW. Through the number of the pregnant women who smoked during pregnancy, it was found that birth weight is significantly associated with smoking, as pregnant women who did not smoke were less likely [aOR=0.3; 95%CI (0.1–0.6), p=0.002] to deliver LBW babies (Table 3).\n\nNotice: * Indicates statistical significance at p-value <0.05; ** Indicates significance at 0.01, Unmarked p-values were not fond to be the significant risk factors of LBW in Rwanda.\n\n\nDiscussion\n\nThis study revealed that LBW remains a public health burden at the national level and it remains higher in Rwanda. The results found that the prevalence of LBW and macrosomia was 5.8% and 17.6%, respectively; however, the newborns weighing more than 2.5kg were 94.2%. These results were coincided with the previous studies that documented an improvement of ANC services contributing to birth weight of the newborns.34 Similarly, the prevalence of LBW is low compared with other counties in the same region such as Zambia, Uganda and Nigeria.51–53 It is also less than the prevalence of some countries in Asia such as in China where the accessibility to ANC visits remains challenging.54 The present prevalence of LBW is less than the previous document which was 7.1% and low access of four recommended ANC visits was 35.4%.55 There is a significant reduction of the prevalence of LMICs compared with the prevalence (15.9%) found in developing countries.6 Among the women with the newborns who weigh less than 2.5kg, only 44.1% of pregnant women attended four recommended ANC visits. Within this study, a strong correlation between ANC and LBW was discovered and the results of inadequate ANC visit for pregnant women. However, almost all pregnant women (99%) attended ANC visits and only 44.1% obtained 4 recommended ANC packages, there is a need to increase attendance of ANC visits for reducing the number of newborns with LBW. These results corroborated preceding studies.54,56\n\nWe observed that pregnant women who attended four and more ANC visits had less risk of having LBW children than those who attended fewer than four recommended ANC visits. This finding is consistent with previous data that indicated that the more pregnant women attend ANC visits, especially more than four, the more their children do not have LBW.57,58 Pregnant women who attended fewer than four ANC check-ups had 2.8-times greater odds of LBW than those who attended four and more ANC visits. These findings are relevant with the previous studies that indicated that ANC visits are significant maternal factors contributing to birth weight babies, since it normalizes the birth weight of the child and their mother due to the prevention, intervention and health education that are effectively provided in each visit.54,59,60 They are also relevant to prior studies conducted in central African counties that indicated that the attendance of ANC visits and being provided the recommended packages for pregnant women reduce the risk for delivering LBW outcome.27,61–63 Results revealed that the pregnant women who were not provided Coartem for malaria treatment were 0.6-times likely to have LBW children compared with the pregnant women who were provided Coartem for malaria treatment.57,64 It was found that the pregnant women who received no drug for malaria treatment had 0.3-times greater risk of having LBW children than the women who received the drugs for malaria.21 These results were similar to the previous studies that documented that children born to educated pregnant women and pregnant women with high wealth index who attend are less likely to weigh less than 2.5kg than other pregnant women.32,65 Prominently, in this research, the results are robust to adjustment for the socio-demographic characteristics of the recruited pregnant women. They revealed that marital status increased the odds of LBW. It was found that pregnant women who were married or living with the cohabitants were 1.9-times likely to have LBW compared with pregnant women who were single. They also revealed that the pregnant women who divorced or separated had 1.7-greater risks to have newborns who weigh less than 2.5 kg. These results challenged the previous studies that indicated that pregnant women who were single had a greater risk of having LBW children than others.52,66,67\n\nNewborns whose mothers were had normal BMI (18.5–24.9 kg/m2) and mothers who were overweight (or obese;) were less likely to have new-born with LBW when compared to those mothers who were underweight. This result is consistent with the earlier research carried out in Uganda.68 Newborns of women who smoke during pregnancy had low birth weight when compared with babies whose mothers did not smoke during pregnancies. Our findings are in congruence with the studies conducted in Tanzania.69 Mothers from rural areas had 1.1 times greater risks of having an LBW newborn than those residing in urban settings. Mothers with secondary and higher education were less likely to have an LBW newborn than those who were illiterate. Our results concur with the earlier studies that established that the residence of pregnant women, HWI, family size, maternal age, utilization of tetanus injections and iron tablets consumption are factors of LBW.42,69\n\nMaternal anemia was identified as a risk factor, where we found that pregnant women with anemia had 3.5- times greater odds of delivering a newborn who weighed less than 2.5 kg than those who are not anemic. This result is in line with the prior studies conducted in Nigeria.52 The mothers who were not provided health counseling and education about nutrients were 2.5-times more likely to have LBW newborns than those who received nutritional counseling and education during ANC visits. The mothers who were not informed about maternal complications had 3.3-times greater risks of having newborns who weighed less than 2.5 kg than those who received information about health complications during pregnancy. Mothers with a weight at delivery greater than 80 kg were more likely to deliver newborn with LBW than the mothers who weighed less than 80 kg. This result is not in line with the previous studies carried out in Ethiopia.70 The findings of this study did not reveal a significant association between maternal age, parity, HWI, sex of child, family size and LBW, however, the prior studies conducted in sub-Saharan African countries confirmed a significant association between maternal age, parity, sex of child, HWI, and LBW.52,70\n\n\nStrengths and limitations\n\nThe present research has numerous prominent strengths. The first strength is that the RDHS 2014/2015 used the validated and standardized tools for interviewing the eligible participants. Second, the research data about birth weight that we used were obviously verified through records and recall bias was prevented. However, several limitations also warrant discussion. First, it was limited to a study design that did not actually explore for modifiable factors of ANC visits, such as HIV status of pregnant women, maternal gestational age, prenatal depression, receiving the supplementary vitamins (like vitamin A) during the pregnant period, maternal weight gain during pregnancy, eclampsia, gestational diabetes, high blood glucose level during pregnancy, antiretroviral (ART) for HIV-positive women and reducing transmission of HIV from pregnant mother to child. Second, birth weight data was available for only babies whose weight was measured at birth. This limited us for estimating the real prevalence. Third, the selection bias resulted in the underestimation of the association between ANC and birth weight. This was because not all babies’ weight was measured. The other limitation was that the qualitative aspects data from the participants was not included for exploring some factors and to triangulate the findings of the quantitative methods used. Additionally, as the methods used for measuring birth weight were not validated by the survey team, the misclassification could occur in this research. As we do not know the exact timing of the birth weight measurement, this causes misclassification.\n\n\nConclusion\n\nIn conclusion, this study found several risk factors of LBW in Rwanda that remains a national public health concern. However, ANC services for pregnant women are a fundamental intervention for reducing LBW. This integral part of primary health care, ANC services, is the population-based intervention that reduces the risk to deliver the newborn with LBW. Therefore, there is a need of a multifaceted approach for addressing the factors of LBW through reinforcing ANC coverage and quality of ANC services for pregnant women. Information on anthropometric measurement and increased awareness of the importance of regular ANC visits is also desirable. Attending four or more ANC visits is a step toward improving maternal health by providing maximum required packages and this strategy reduces the risk to LBW. The policy makers and researchers should prioritize maternal education and families with low socio-economic status for preventing LBW in Rwanda.\n\nWe recommend further research be conducted on the risk factors of macrosomia in Rwanda. Additionally, further study to explore the barriers to access ANC visits effectively for pregnant women from the rural settings is recommended. In the meantime, pregnant women in Rwanda are required to attend ANC visits appropriately and regularly for benefiting from the required packages that increase the probability to attenuate the LBW among the newborns. We recommend to measure birth weight immediately after birth for reducing the recall bias and misclassification.\n\n\nData availability\n\nUnderlying data for ‘Regular antenatal care visits were associated with low risk of low birth weight among newborn in Rwanda: Evidence from the 2014/2015 Rwanda Demographic Health Survey (RDHS) Data was owned by the DHS program that can be obtained from https://dhsprogram.com/methodology/survey/survey-display-468.cfm.\n\nThe electronic data is available from the DHS program under its terms of use. Before downloading the data, the main author of this study registered as DHS user for reasons laid out on the DHS program website and dataset access was only granted for legitimate purpose of this research.\n\n\nAuthors’ contributions\n\nEB conceptualized the study, did study design, formal analysis, wrote the protocol, requested the permission from the DHS website, drafted the manuscript and coordinated the study. SH contributed to data analysis, data curation and methodology. DR substantially contributed to the conceptualization. He also wrote the original draft preparation. He revised and reviewed the manuscript, and searched the relevant journal to which the study is submitted. HE reviewed and edited the study. All investigators approved the final manuscript. They also agreed to take responsibility and be accountable for the content of the manuscript. All of them agreed on all versions of the manuscript before submitting it in the international journal. They also agreed on the final version accepted for publication.\n\n\nEthics and consent to participate\n\nThe present study was exempt from searching the ethical approval because the RDHS 2014/15 obtained the ethical approval from the Institutional Review Board (IRB) of the Rwanda National Ethics Committee (RNEC).",
"appendix": "Acknowledgments\n\nWe are thankful to DHS program for providing for us the permission to use the dataset. We sincerely acknowledge the substantial help of RDHS for provision of the datasets.\n\n\nReferences\n\nAtaguba JE-O: A reassessment of global antenatal care coverage for improving maternal health using sub-Saharan Africa as a case study. PLoS One. 2018; 13(10): e0204822. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbdullah A, Hort K, Butu Y, et al.: Risk factors associated with neonatal deaths: a matched case control study in Indonesia. Glob Heal Action. 2016; 1(3): 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGardner H, Green K, Gardner AS, et al.: Observations on the health of infants at a time of rapid societal change: a longitudinal study from birth to fifteen months in Abu Dhabi. BMC Pediatr. 2018; 18(32): 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTshotetsi L, Dzikiti L, Hajison P, et al.: Maternal factors contributing to low birth weight deliveries in Tshwane District, South Africa. PLoS One. 2014; 14(3): e0213058. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHe Z, Bishwajit G, Yaya S, et al.: Prevalence of low birth weight and its association with maternal body weight status in selected countries in Africa: a cross-sectional study. BMJ Open. 2018; 8(8): 2020410. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahumud RA, Sultana M, Sarker AR: Distribution and determinants of low birth weight in developing countries. J Prev Med Public Heal. 2017; 50(1): 18–28. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO) & United Nations Children’s Fund (UNICEF): Low Birth Weight Country, Regional and Global Estimates. World Health Organization; 2004. Reference Source\n\nBasinga P, Gertler PJ, Binagwaho A, et al.: Effect on maternal and child health services in Rwanda of payment to primary health-care providers for performance: an impact evaluation. Lancet. 2006; 377(9775): 1421–1428. PubMed Abstract | Publisher Full Text\n\nBalarajan Y, Subramanian S, Fawzi W: Maternal iron and folic acid supplementation is associated with lower risk of low birth weight in India. J Nutr. 2013; 143(8): 1309–1315. PubMed Abstract | Publisher Full Text\n\nWagura P, Wasunna A, Laving A, et al.: Prevalence and factors associated with preterm birth at Kenyatta National Hospital.2018; 18(107). Reference Source\n\nChukwudi NK, Nwokeukwu HI, Adimorah GN: Use of a Simple Anthropometric Measurement to Identify Low-Birth- Weight Infants in Enugu, Nigeria. Glob Pediatr Heal. 2018; 5: 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO):Sustainable Development and Healthy Environments. International Statistics Classification of Diseases and Related Health Problems. 1999. Reference Source\n\nHenriksen T: The macrosomic fetus: a challenge in current obstetrics. Acta Obs Gynecol Scand. 2008; 87: 134–135. PubMed Abstract | Publisher Full Text\n\nMuchie KF: Quality of antenatal care services and completion of four or more antenatal care visits in Ethiopia: A finding based on a demographic and health survey. BMC Pregnancy Childbirth. 2017; 17(1): 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHayat H, Khan PS: A study of epidemiological factors affecting low birth weight. East J Med. 2014; 18(2013): 13–15.\n\nOulay L, Laohasiriwong W, Phajan T, et al.: Effect of antenatal care on low birth weight prevention in Lao PDR: A case control study [version 1; peer review: 1 approved with reservations, 1 not approved]. F1000Res. 2018; 7: 1–12. Publisher Full Text\n\nLaohasiriwong W, Phajan T, Assana S, et al.: Effect of antenatal care on low birth weight prevention in Lao PDR: A case control study [version 1; referees : 1 approved with reservations, 1 not approved] Latsamy Oulay Referee Status. F1000Res. 2019; 7(1138): 1–12. Publisher Full Text\n\nJayant DD, Phalke D, Bangal V, et al.: Maternal risk factors for low birth weight neonates: a hospital based casecontrol study in rural area of western maharashtra, India. Natl J Community Med. 2011; 2(3): 394–398.\n\nMatin A, Azimul S, Matiur A, et al.: Maternal socioeconomic and nutritional determinants of low birth weight in urban area of Bangladesh. J Dhaka Med Coll. 2008; 17: 83–87.\n\nCelik Y, Younis MZ: Effects of Antenatal Care Services on Birthweight: Importance of Model Specification and Empirical Procedure Used in Estimating the Marginal Productivity of Health Inputs. J Med Syst. 2007; 31: 197–204. PubMed Abstract | Publisher Full Text\n\nGebrearegay F, Id T, Bezabih AM, et al.: Effect of pregnancy weight gain on infant birth weight among mothers attending antenatal care from private clinics in Mekelle City, Northern Ethiopia: A facility based follow-up study. PLoS One. 2019; 14(3): e0212424. 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMetgud C, Naik V, Mallapur M: Factors affecting birth weight of a newborn a community based community based study in rural Karnataka, India. PLoS One. 2012; 7: e40040. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization:WHO Recommendations on Antenatal Care for a Positive Pregnancy Experience.Printed in.; 2016.\n\nLincetto O, Mothebesoane-anoh S, Gomez P, et al.: Opportunities for Africa’s Newborns. World Health Organization; 2015; 51–62.\n\nTunçalp Ö, Pena-Rosas J, Lawrie T, et al.: WHO recommendations on antenatal care for a positive pregnancy experience - going beyond survival. An Int J Obstet Gynaecol. 2017; 124(6): 860–862. Publisher Full Text\n\nWHO: WHO Recommendations on Antenatal Care for a Positive Pregnancy Experience. 2016. Reference Source\n\nTafere TE, Afework MF, Yalew AW: Providers adherence to essential contents of antenatal care services increases birth weight in Bahir Dar City Administration, north West Ethiopia: a prospective follow up study. Reprod Health. 2018; 15(163): 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: Low Birth Weight. Country:Regional and Global Estimates; 2004.\n\nLassi ZS, Kumar R, Mansoor T, et al.: Essential interventions: implementation strategies and proposed packages of care. Reprod Health. 2014; 11(Suppl 1): S5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaddad GS, Dejong J, Terreri N, et al.: Patterns and determinants of antenatal care utilization: analysis of national survey data in seven countdown countries. J Glob Health. 2016; 6(1): 1309–1315. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnthony J, Damasceno A, Ojjii D: Hypertensive disorders of pregnancy: what the physician needs to know. Cardiovasc J Afr. 2016; 27(2): 104–110. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMishra V, Thapa S, Retherford RD, et al.: Effect of iron supplementation during pregnancy on birthweight: Evidence from Zimbabwe. Food Nutr Bull. 2005; 26(4): 338–347. PubMed Abstract | Publisher Full Text\n\nRooney CW: Maternal Health and Safe Motherhood Programme. Antenatal care and maternal health: how effective is it? a review of the evidence/by Cleone Rooney.Geneva:World Health Organization. Published online; 1992.\n\nKanyangarara M, Melinda K, Walker N: Quality of antenatal care service provision in health facilities across sub – Saharan Africa: Evidence from nationally representative health facility assessments. J Glob Health. 2017; 7(2): 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTela F, Bezabih A, Adhanu A: Effect of pregnancy weight gain on infant birth weight among mothers attending antenatal care from private clinics in Mekelle City, Northern Ethiopia: A facility based follow-up study. PLoS One. 2019; 14(3): e0212424. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCumber SN, Diale DC, Stanly EM, et al.: Importance of Antenatal Care Services to Pregnant Women at the Buea Regional Hospital Cameroon Email address. J Fam Med Heal Care. 2016; 2(4): 23–29. Publisher Full Text\n\nLaohasiriwong W, Phajan T, Assana S, et al.: Effect of antenatal care on low birth weight prevention in Lao PDR: A case control study [version 1; peer review:1 approved with reservations, 1 not approved]. F1000Res. 2019; 7(1138): 1–12. Publisher Full Text\n\nPeter K, AkiiBua D, Aleni C, et al.: Utilization of Antenatal Care (ANC) Services: Multi-Center Study in Upcountry Areas of Uganda. Am J Prev Med. 2009; 5(3): 132–142. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoller A, Petzold M, Chou D, et al.: Articles Early antenatal care visit: a systematic analysis of regional and global levels and trends of coverage from 1990 to 2013. Lancet Glob Heal. 2013; 5(10): e977–e983. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTakahashi K, Nomura M, Horiuchi S, et al.: Global policy directions for maternal and child health in the SDG era SDGs Review Global policy directions for maternal and child health in the SDG era. J Natl Inst Public Heal. 2017; 66(September 4): 401–395. Publisher Full Text\n\nAwiti JO: A multilevel analysis of prenatal care and birth weight in Kenya. Health Econ Rev. 2014; 4(33): 1–16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRosenzweig MR, Schultz T: Estimating a household production function: Heterogeneity, the demand for health inputs, and their effects on birth weight. J Polit Econ. 1983; 9(5): 723–46. Publisher Full Text\n\nNISR:Rwanda Demographic and Health Survey 2014-15: Final Report.National Institute of Statistics of Rwanda; 2015. doi: March, 2016\n\nHabimana S, Biracyaza E: Risk Factors Of Stunting Among Children Under 5 Years Of Age In The Eastern And Western Provinces Of Rwanda: Analysis Of Rwanda Demographic And Health Survey 2014/2015. Pediatr Heal Med Ther. 2019; 10: 115–130. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHughes MM, Black RE, Katz J: 2500-g Low Birth Weight Cutoff: History and Implications for Future Research and Policy. Matern Child Health J. 2017; 21(2): 283–289. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO): WHO Recommendations on Antenatal Care for a Positive Pregnancy Experience.2016.\n\nNoh J, Kim Y, Lee LJ, et al.: Factors associated with the use of antenatal care in Sindh province, Pakistan: A population- based study. PLoS One. 2019; 14(4): 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nManzi A, Nyirazinyoye L, Ntaganira J, et al.: Beyond coverage: improving the quality of antenatal care delivery through integrated mentorship and quality improvement at health centers in rural Rwanda. BMC Health Serv Res. 2018; 18(1): 136. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStataCorp. Stata Statistical Software: Release 2014; vol. 13. StataCorp LP.: College Station.\n\nVandenbroucke JP, Von Elm E, Altman DG, et al.: Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and elaboration. PLoS Med. 2007; 4(10): 1628–1654. PubMed Abstract | Publisher Full Text\n\nChibwesha CJ, Zanolinib A, Smida M, et al.: Predictors and outcomes of low birth weight in Lusaka, Zambia. Int J Gynaecol Obs. 2016; 134(3): 309–314. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOladeinde HB, Oladeinde OB, Omoregie R, et al.: Prevalence and determinants of low birth weight: the situation in a traditional birth home in Benin City, Nigeria. Afr Heal Sci. 2015; 15(4): 1123–1129. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArunda MO, Agardh A, Asamoah BO: Survival of low birthweight neonates in Uganda: Analysis of progress between 1995 and 2011. BMC Pregnancy Childbirth. 2018; 18(1): 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou H, Wang A, Huang X, et al.: Quality antenatal care protects against low birth weight in 42 poor counties of Western China. PLoS One. 2019; 14(1): 1–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNISR: Rwanda Demographic and Health Survey 2010. 2010. Reference Source\n\nRurangirwa AA, Mogren I, Ntaganira J, et al.: Quality of antenatal care services in Rwanda: assessing practices of health care providers. BMC Heal Serv Res Res. 2018; 5: 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAcharya D, Singh JK, Kade R, et al.: Maternal Factors and Utilization of the Antenatal Care Services during Pregnancy Associated with Low Birth Weight in Rural Nepal: Analyses of the Antenatal Care and Birth Weight Records of the MATRI-SUMAN Trial. Int J Env Res Public Heal. 2018; 15(11). PubMed Abstract | Publisher Full Text | Free Full Text\n\nTekelab T, Chojenta C, Smith R, et al.: Factors affecting utilization of antenatal care in Ethiopia: A systematic review and meta-analysis. PLoS One. 2019; 14(4): e0214848. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnant P, Durgesh K: Maternal factors associated with low birth weight: a case control study in rural Kerala. Int J Community Med Public Heal. 2017; 4(10): 3793–3795. Publisher Full Text\n\nMumbare S, Maindarkar G, Darade R: Maternal risk factors associated with term low birth weight neonates: A matched-pair case control study. Indian Pediatr. 2012; 49(1): 25–28. PubMed Abstract | Publisher Full Text\n\nChuku SN: Low Birth Weight in Nigeria: Does Antenatal Care Matter? Published online. 2008.\n\nGupta S, Yamada G, Mpembeni R, et al.: Factors Associated with Four or More Antenatal Care Visits and Its Decline among Pregnant Women in Tanzania between 1999 and 2010. PLoS One. 2014; 9(7): 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSiza JE: Risk factors associated with low birth weight of neonates among pregnant women attending a referral hospital in northern Tanzania. Tanzan J Health Res. 2008; 10(1): 1–8. PubMed Abstract | Publisher Full Text\n\nBayo L, Buyungo S, Margret N, et al.: Prevalence and Factors Associated with Low Birth Weight among Teenage Mothers in New Mulago Hospital: A Cross Sectional Study. J Heal Sci. 2016; 4(4): 192–199. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRode SJ: Effect of Complete Antenatal Care on Birth Weight of Children in India: Evidence from National Family Health Survey (NFHS) Data. J Women’s Heal Care. 2018; 7(1): 1–12. Publisher Full Text\n\nAgbor VN, Ditah C, Tochie JN, et al.: Low birthweight in rural Cameroon: an analysis of a cut-off value. BMC Pregnancy Childbirth. 2018; 18(30): 1–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSebayang SK, Dibley MJ, Kelly PJ, et al.: Determinants of low birthweight, small forgestational age and preterm birth in Lombok, Indonesia: analyses of the birthweight cohort of the SUMMIT trial. Trop Med Int Heal. 2012; 17(8): 938–950. PubMed Abstract | Publisher Full Text\n\nLouis B, Steven B, Margret N, et al.: Traffic and Transportation Improvement Plans for Trivandrum. Indian Highw. 2016; 14(2): 22–29. Publisher Full Text\n\nMvunta MH, Mboya IB, Msuya SE, et al.: Incidence and recurrence risk of low birth weight in Northern Tanzania: A registry based study. PLoS One. 2019; 14(4): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMengesha H, Wuneh A, Weldearegawi B: Low birth weight and macrosomia in Tigray, Northern Ethiopia: who are the mothers at risk? BMC Pediatr. Published online 2017: 17: 144. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "98487",
"date": "22 Nov 2021",
"name": "M. Mazharul Islam",
"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 paper addressed a very important issue of public health. The findings of the paper are likely to contribute in literature of the impact of antenatal care on birth weight. However, I have some observations, which are given below.\nIn the Introduction section, page 3, the authors stated that WHO recommended four or more ANC visits during pregnancy, which is a dated recommendation. Perhaps, the authors are referencing 2001 WHO recommended schedule of 4 ANC visits (Villar et al., 2001). However, in 2016 WHO revised its recommendation and prescribed 8 or more visit schedules (see WHO (2016). WHO recommendations on antenatal care for a positive pregnancy experience. https://apps.who.int/iris/bitstream/handle/10665/250796/9789241549912-eng.pdf). The authors defined the main explanatory variable (no or less than 4 ANC and ≥ 4 ANC) based on the old schedule of ANC. Considering the low average frequency of ANC visits in Rwanda, I am not claiming that the analysis is wrong, but not mentioning the latest development is a clear oversight. The authors should discuss the compliance of 8 or more ANC visits in Rwanda.\n\nUnder sampling design, page 4, the authors wrote:\n\n……. “current birth weights were not available for the most children”, which contradicts the last line of the paragraph stating that “It was found that 92% of newborns had a birth weight reported while 8% did not.”\n\nThe authors should provide clear information about the total number of births considered in the study, of whom birth weights were available for how many or what proportion of births. Among the children with birth weights, what proportion of birth weights was obtained from mothers' recall and what proportion from written information. What was meant by written information? Is it birth certificates or health cards?\n\nThe most important information which is missing in this study is the total sample size of the study population. In one place, the authors mentioned about 8,004 mothers of reproductive age, but the distribution of the mothers provided in column 2 of Table 1 does not reflect that. What are these numbers in column 2 of Table 1 and why there is a wide variation in number across the variables?\n\nIn page 6, under the Results section of Multiple logistic regression analysis: There are a lot of mistakes. Most of the aORs and the 95%CIs given within parenthesis do not correspond with the results presented in Table 3.\n\nThe discussion section has been written very poorly, as it is mostly a repetition of the description of the findings without providing any explanations or possible implications of their findings. To validate their results, the authors just wrote “the results are consistent or similar or corroborate with findings of other study” without providing any numerical evidence how their findings are consistent with other studies.\n\nThere is a methodological problem in the application of multiple logistic regression analysis to the real data considered in this study. One of the basic assumptions of the regression model is that the explanatory variables are independent. However, in this study, all the selected explanatory variables are not independent. For example, maternal height and weight are linearly dependent, and they are also related to body mass index (BMI) because BMI = weight/height2. Violation of the assumption of independence creates a serious problem in statistical analysis, which is known as multicollinearity problem, resulting in biased results. While applying regression model, the researchers should be careful about multicollinerity problem. The authors did not provide any information about the goodness of fit of the model and adequacy of the fitted model. The author should redo the multiple regression analysis by removing the suspected inter-correlated variables.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8881",
"date": "10 Oct 2022",
"name": "Emmanuel Biracyaza",
"role": "Author Response",
"response": "The paper addressed a very important issue of public health. The findings of the paper are likely to contribute in literature of the impact of antenatal care on birth weight. However, I have some observations, which are given below. In the Introduction section, page 3, the authors stated that WHO recommended four or more ANC visits during pregnancy, which is a dated recommendation. Perhaps, the authors are referencing 2001 WHO recommended schedule of 4 ANC visits (Villar et al., 2001). However, in 2016 WHO revised its recommendation and prescribed 8 or more visit schedules (see WHO (2016). WHO recommendations on antenatal care for a positive pregnancy experience. https://apps.who.int/iris/bitstream/handle/10665/250796/9789241549912-eng.pdf). Responses: Thank you very much; we found that there was an typing error since in our study, we used expected to use the recent recommendations of the WHO that recommend 8 ANC visits for the pregnant women. But when we realised that it could not be possible to assess it because the prevalence of using 8 recommended ANC contacts was low in Rwanda (less than 1%). So, in the study limitations and conclusions we tried to mention it and then recommend the policy makers to encourage pregnant women to respect the respected ANC contacts. The authors defined the main explanatory variable (no or less than 4 ANC and ≥ 4 ANC) based on the old schedule of ANC. Considering the low average frequency of ANC visits in Rwanda, I am not claiming that the analysis is wrong, but not mentioning the latest development is a clear oversight. The authors should discuss the compliance of 8 or more ANC visits in Rwanda. Responses: Thank you very much. As indicated in the work, we considered the 8 ANC visits as recommended by 2016 WHO. So, the problem was in the first table where we shared the wrong table, but we effectively corrected it and then provided the appropriate table. Notice. For the case of 2016 WHO recommendations, you can also refer to the following publications to indicate you how the ANC remains very low: 1. Sserwanja, Q., Nuwabaine, L., Gatasi, G. et al. Factors associated with utilization of quality antenatal care: a secondary data analysis of Rwandan Demographic Health Survey 2020. BMC Health Serv Res 22, 812 (2022). https://doi.org/10.1186/s12913-022-08169-x 2. Rurangirwa, A.A., Mogren, I., Ntaganira, J. et al. Quality of antenatal care services in Rwanda: assessing practices of health care providers. BMC Health Serv Res 18, 865 (2018). https://doi.org/10.1186/s12913-018-3694-5 Under sampling design, page 4, the authors wrote: ……. “current birth weights were not available for the most children”, which contradicts the last line of the paragraph stating that “It was found that 92% of newborns had a birth weight reported while 8% did not.” Responses: We edited the sentence after noticing that what you have observed. We decided to remove it because we found it was not necessary. Thus, the last line of the paragraph was really enough. The authors should provide clear information about the total number of births considered in the study, of whom birth weights were available for how many or what proportion of births. Among the children with birth weights, what proportion of birth weights was obtained from mothers' recall and what proportion from written information. What was meant by written information? Is it birth certificates or health cards? Responses: We thank you very much for this suggestion. Normally, after we recheck our dataset and remove missing variables, we also tried to indicate the corrected number of the births and pregnant women. Please, note that we only used the data of the women who provided the number weight of their newborns at birth. the women who were of out of this major inclusion criteria were removed from the analyses (therefore, our study was conducted among 7381 women). The most important information, which is missing in this study, is the total sample size of the study population. In one place, the authors mentioned about 8,004 mothers of reproductive age, but the distribution of the mothers provided in column 2 of Table 1 does not reflect that. What are these numbers in column 2 of Table 1 and why there is a wide variation in number across the variables? Responses: Thank you very much for this observation about mismatching of the totals for the table 1. We included the corrected table. In addition to that, the sample size was 7381 women who provided the weight of their babies. They were recruited from 8004 women who delivered and 30058 individuals for the participants of this dataset in which we used. In page 6, under the Results section of Multiple logistic regression analysis: There are a lot of mistakes. Most of the aORs and the 95%CIs given within parenthesis do not correspond with the results presented in Table 3. Responses: We thank you or this observation. We have corrected the interpretations since the information provided in the table was correct. Improved interpretations of the results were also made. The discussion section has been written very poorly, as it is mostly a repetition of the description of the findings without providing any explanations or possible implications of their findings. To validate their results, the authors just wrote “the results are consistent or similar or corroborate with findings of other study” without providing any numerical evidence how their findings are consistent with other studies. Responses: Regarding the discussion, we have importantly made the revisions and changes based on the major results from the section results. There is a methodological problem in the application of multiple logistic regression analysis to the real data considered in this study. One of the basic assumptions of the regression model is that the explanatory variables are independent. However, in this study, all the selected explanatory variables are not independent. For example, maternal height and weight are linearly dependent, and they are also related to body mass index (BMI) because BMI = weight/height2. Violation of the assumption of independence creates a serious problem in statistical analysis, which is known as multicollinearity problem, resulting in biased results. While applying regression model, the researchers should be careful about multicollinerity problem. The authors did not provide any information about the goodness of fit of the model and adequacy of the fitted model. The author should redo the multiple regression analysis by removing the suspected inter-correlated variables. Responses: Thank you for these recommendations. To manage the issues of methods, we did again the analysis part and we found the new results with some differences. So, we really have computed the goodness of fit for the multivariate logistical model. Multicolinearity was assessed using VIF and as a result several variables that inflacted were directly removed from models for avoiding overestimation or underestimations. We really found that the removed variables negatively impacted some variables because some of the remaining variables became significantly associated while others were not. But we observed crucial improvements."
}
]
},
{
"id": "144427",
"date": "04 Aug 2022",
"name": "Manoja Das",
"expertise": [
"Reviewer Expertise Child health",
"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\nThe article presents the prevalence of LBW and the risk factors for the same in Rwanda using the RDHS 2014/15 data.\nThe manuscript needs attention in some sections: 1. Methods 1.1 Macrosomia definitions should be mentioned\n\n2. Results 2.1 The following statements need review and clarification. \"For marital status, married and cohabiting pregnant women were 1.86-times at greater risk to have LBW children [aOR=1.9; 95%CI (1.3–2.8), p=0.002] compared with single pregnant women.\" \"The results indicated that the widowed, separated and divorced pregnant women had 1.7-times greater risk of having LBW babies [aOR=1.7; 95%CI (1.1–2.5), p=0.015] than women who were single during pregnancy.\" The two statements are in conflict. Please check.\n2.2. The statement \"Results found that being provided maternal iron and folic acid supplementation during pregnancy [aOR=0.5, 95%CI (0.3–0.9), p=0.015], not being given nutrients during pregnancy [aOR=2.5, 95%CI (2-8.4), p<0.001], being told about maternal complications during pregnancy [aOR=0.7....\" How was the nutrient given assessed?\n3. Discussion 3.1. Please check the statements and discuss \"They revealed that marital status increased the odds of LBW. It was found that pregnant women who were married or living with the cohabitants were 1.9-times likely to have LBW compared with pregnant women who were single. They also revealed that the pregnant women who divorced or separated had 1.7-greater risks to have new-borns who weigh less than 2.5 kg.\" This statement needs to be examined carefully, whether the factor responsible was crowding, low SES and undernutrition or hunger.\n4. Limitations 4.1 The limitations should mention the qualitative nature of the risk factors captured in the RDHS, like iron intake and duration, nutrition intake, maternal anemia and malnutrition status, which influence the birth weight.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8882",
"date": "10 Oct 2022",
"name": "Emmanuel Biracyaza",
"role": "Author Response",
"response": "Reviewer 2 First of all, I thank you for the valuable points you raised for us. They have of course and prominently helped us to strengthen our study. The article presents the prevalence of LBW and the risk factors for the same in Rwanda using the RDHS 2014/15 data. Response: Thank you very much for this appreciation. The manuscript needs attention in some sections: 1. Methods 1.1 Macrosomia definitions should be mentioned Responses: Thank you very much for the recommendations. The concept macrosomia was also defined in the first paragraph of the background of the study. It was defined as when a baby is born with more than 4 kilograms (or 4000 grams). 2. Results 2.1 The following statements need review and clarification. \"For marital status, married and cohabiting pregnant women were 1.86-times at greater risk to have LBW children [aOR=1.9; 95%CI (1.3–2.8), p=0.002] compared with single pregnant women.\" Response: This sentence was rephrased and improved. \"The results indicated that the widowed, separated and divorced pregnant women had 1.7-times greater risk of having LBW babies [aOR=1.7; 95%CI (1.1–2.5), p=0.015] than women who were single during pregnancy.\" The two statements are in conflict. Please check. Responses: This sentence was rephrased and improved 2.2. The statement \"Results found that being provided maternal iron and folic acid supplementation during pregnancy [aOR=0.5, 95%CI (0.3–0.9), p=0.015], not being given nutrients during pregnancy [aOR=2.5, 95%CI (2-8.4), p<0.001], being told about maternal complications during pregnancy [aOR=0.7....\" How was the nutrient given assessed? Responses: This statement was also improved after adjusting some analyes due to the required analysis from the other reviewers. 3. Discussion 3.1. Please check the statements and discuss \"They revealed that marital status increased the odds of LBW. It was found that pregnant women who were married or living with the cohabitants were 1.9-times likely to have LBW compared with pregnant women who were single. They also revealed that the pregnant women who divorced or separated had 1.7-greater risks to have new-borns who weigh less than 2.5 kg.\" Responses: In discussion section, we improved this part, and we changed the statement as recommended by the reviewer. This statement needs to be examined carefully, whether the factor responsible was crowding, low SES and undernutrition or hunger. Responses: Thank you very much the factors such as SES and undernutrition (based on wasting, underweight, stunting and obesity) were also explored. 4. Limitations 4.1 The limitations should mention the qualitative nature of the risk factors captured in the RDHS, like iron intake and duration, nutrition intake, maternal anemia and malnutrition status, which influence the birth weight. Responses: Thank you very much for these recommendations; and we included the recommendation that further studies could also be conducted using qualitative methods for exploring the perspectives from the pregnant women about the factors that influence their attendance of ANC and the benefits from attending ANC services on child weight at birth. So, we believe that the women can be experts in this qualitative exploration. Thank you very much for your prominent recommendations that have helped us to improve our study."
}
]
},
{
"id": "142748",
"date": "12 Aug 2022",
"name": "Sarmila Mazumder",
"expertise": [
"Reviewer Expertise Maternal and child health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an important domain and the paper reiterates the importance of antenatal care. However, this a rather simplistic view of a complex issue. Few points to consider:\n\nThe focus of the manuscript is on the number of ANC visits and not on the quality, content, examination, investigations, ultrasound, or respectful care, ability to identify/manage or refer high risk pregnancies, etc. The underlying assumption is that these are optimum at the the ANC sources. In that case, information on the same needs to be provided.\n\nAdditionally, just the number of ANC visits is not enough, gestational age when the pregnant women was first registered, the timeliness of the ANC visits going by the 4 ANC norm, that is, one in the first trimester, 1 in the second trimester and 2 in the third trimester, are equally important.\n\nThe ANC standard needs mention, there are women with 7 ANCs. Is the 2016 WHO ANC guideline being implemented at the study site? In that case is the rationale of 4 ANC as a cut-off based on minimum ANC visits? Need clarity.\n\nSpecific issues: How were the 8004 women selected? It is mentioned that that women who had documented birth weight were interviewed. The sampling method says 2 stage cluster sampling and random selection. In that case the selection of women seems purposive, this needs clarity.\n\nThis is a retrospective data collection, where women with youngest child less than 5 years were interviewed. It will be important to mention that all records on birth weight, number of ANC visits, measurement of BP, administration of antimalarial drug, height, weight and BMI, etc were available. Recall bias cannot be ruled out unless good documentation was available.\n\nAt which stage was BMI measured? Pre-pregnancy or early first trimester? This will be important to document.\n\nGestational weight gain is an essential component of ANC, this is not specified.\n\nIt is not clear why BP measurement and antimalarials are considered as confounders.\n\nTables do not have N (total number, denominators). Table 1 needs explanation. The sample size was 8004 women but in table 1, the numbers do not add up to 8004. it varies with each variable. There is no information on the number of births. It would be informative to know about preterms, SGA, AGA as well.\n\nThe information on availability of birth weight is a little confusing. 92% reported birth weight, were these documented on discharge reports or verbally reported. Additionally, the low birth weight does not seem to be a major issue, with only 5.8% low birth weight while 18% macrosomia.\n\nSome information would be useful to present. 99% women attended ANC clinic but 44% had 4 ANCs. A qualitative component would have been helpful to understand the barriers to low utilization.\n\nThe discussion section needs strengthening, it is repetition of the previous section. Some of the findings could have been analyzed, for eg., explore further how was home delivery associated with LBW. The places of ANC, pros and cons, etc. have not been discussed.\n\nTypographical error, table 2, 7th row, last column. 0.0.3.\n\nThe authors need to match the numbers in the tables and text.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": [
{
"c_id": "8883",
"date": "10 Oct 2022",
"name": "Emmanuel Biracyaza",
"role": "Author Response",
"response": "This is an important domain, and the paper reiterates the importance of antenatal care. However, this a rather simplistic view of a complex issue. Few points to consider: Response: Dear reviewer, thank you very much for these kind words and crucial suggestions and recommendations for improving our study that was submitted in the f1000research.com. All the point you raised so that we can improve our study have been relevant and they helped us to continue looking our further investigation. Frankly, the ANC contacts remains at a very low level (less than 1%) which represents pregnant women who attended 8 ANC contacts. This is similar to the other countries of the same region (SSA) or LMICs. The focus of the manuscript is on the number of ANC visits and not on the quality, content, examination, investigations, ultrasound, or respectful care, ability to identify/manage or refer high risk pregnancies, etc. The underlying assumption is that these are optimum at the ANC sources. In that case, information on the same needs to be provided. Responses: Thank you for the recommendations that are important. We totally agree with you about the focus of this work. But these variables about ultrasound, respectful care and risk pregnancies etc. were not found in the RDHS and we cannot change the dataset. But we recommend that the further studies can investigate and include such variables. In our data analysis, we included socio-demographic, nutritional variables, maternal and individual variables. But we did not find that the information about ultrasound or respectful care etc., however, we know how they are important in the ANC contacts. Additionally, just the number of ANC visits is not enough, gestational age when the pregnant women was first registered, the timeliness of the ANC visits going by the 4 ANC norm, that is, one in the first trimester, 1 in the second trimester and 2 in the third trimester, are equally important. Responses: We thank you for this essential observation and suggestion. We have checked and corrected according to the suggestions provided. Variables such as gestational age were added. But about the ANC visits, we found that majority of the attended 4-7 ANCs while only 1% attended 8 recommended ANC contacts by the 2016 WHO but we have recommended the decision makers to encourage the pregnant women to attend the ANC visits as recommended by WHO. The main challenge was that the utilisation of 8 ANC visits is at low level and this could limit us in the data analysis. The ANC standard needs mention, there are women with 7 ANCs. Is the 2016 WHO ANC guideline being implemented at the study site? In that case is the rationale of 4 ANC as a cut-off based on minimum ANC visits? Need clarity. Responses: The cut-off of used is the 4 ANC visits as recommended by the WHO due to the evidence provided above. We wrote an unintentional in our previous version and this created the mismatch in the first version. We notice that the attendance of the ANC as required remains a public health concern in Rwanda as one of SSA countries which remain with such concern that has to be solved through multidisciplinary team. Specific issues: How were the 8004 women selected? It is mentioned that that women who had documented birth weight were interviewed. The sampling method says 2 stage cluster sampling and random selection. In that case the selection of women seems purposive, this needs clarity. Responses: Thank you as the study used secondary study (dataset from DHS), we did not conduct the data collection with direct contact with the women. But the RDHS indicates that the women were interviewed. The sample size was clearly indicated (7381 women who fit the inclusion criteria). We only included the women who provided information about the birth weight (they were only 7381) while 8004 was for the women who gave birth. Of course, if we take 8004-7381, we directly find the number of those who did not provide birth weight for their babies. This is a retrospective data collection, where women with youngest child less than 5 years were interviewed. It will be important to mention that all records on birth weight, number of ANC visits, measurement of BP, administration of antimalarial drug, height, weight and BMI, etc were available. Recall bias cannot be ruled out unless good documentation was available. Response: Thank you for this recommendation that has helped us to improve our study. We included your recommendations and clarified the above-mentioned part. At which stage was BMI measured? Pre-pregnancy or early first trimester? This will be important to document. Response: This was documented in the study. BMI as an important anthropometric indicator for pregnant women and can have a crucial effect on weight of child was measured at early first trimester (when the pregnant women attended the 1st ANC contact). Gestational weight gain is an essential component of ANC, this is not specified. Responses: Thank you. The gestational age was added in the analysis; however, gestational diabetes was not included because of having several missing information. It is not clear why BP measurement and antimalarials are considered as confounders. Responses: We have corrected according to your recommendations. By analysing the multicollinerality, we found that the variables such as variables related to malaria and BP inflacted with the birth weight. As results, we removed them from the analysis and we remained with the good variables that presented the variables, which seemed to be equal (near to 1). But the removed ones had more than 3 values of VIF. Tables do not have N (total number, denominators). Table 1 needs explanation. The sample size was 8004 women but in table 1, the numbers do not add up to 8004. it varies with each variable. There is no information on the number of births. It would be informative to know about preterms, SGA, AGA as well. Responses: All the tables were appropriately corrected. The mismatching was because we shared the wrong table. This impact in the interpretations. About the above variables such as AGA, preterms, and SGA; they had several missing variables. So, that is why we did not include them in the analysis. The information on availability of birth weight is a little confusing. 92% reported birth weight, were these documented on discharge reports or verbally reported. Additionally, the low birth weight does not seem to be a major issue, with only 5.8% low birth weight while 18% macrosomia. Responses: Thank you very much for this but for the developing country like Rwanda, the prevalence of about 6% for LBW may be a public health burden if the further strategies to promote health for the pregnant woman and the newborns. Some information would be useful to present. 99% women attended ANC clinic but 44% had 4 ANCs. A qualitative component would have been helpful to understand the barriers to low utilization. Responses: Thank you for these important recommendations. The qualitative study design was recommended based on our results. This can be found in the strengths and further directions. The discussion section needs strengthening, it is repetition of the previous section. Some of the findings could have been analyzed, for e.g., explore further how was home delivery associated with LBW. The places of ANC, pros and cons, etc. have not been discussed. Responses: The discussion was also modified and of course improved due to your recommendations. Typographical error, table 2, 7th row, last column. 0.0.3. Responses: This typo error and grammatical errors were corrected. The authors need to match the numbers in the tables and text. Responses: We kindly thank you for these recommendations. We have matched the results from the tables and texts. Thank you very much."
}
]
}
] | 1
|
https://f1000research.com/articles/10-402
|
https://f1000research.com/articles/11-1250/v1
|
03 Nov 22
|
{
"type": "Research Article",
"title": "Multidisciplinary digital methodologies for documentation and preservation of immovable Archaeological heritage in the Khovd River Valley, Western Mongolia",
"authors": [
"Michael T. Fisher",
"Dovydas Jurkenas",
"Amina Jambajantsan",
"Bayarsaikhan Jamsranjav",
"Eredene-Ochir Nasan-Ochir",
"Eregzen Gelegdorj",
"Munkhbayar Chuluunbat",
"Michael Petraglia",
"Nicole Boivin",
"Dovydas Jurkenas",
"Amina Jambajantsan",
"Bayarsaikhan Jamsranjav",
"Eredene-Ochir Nasan-Ochir",
"Eregzen Gelegdorj",
"Munkhbayar Chuluunbat",
"Michael Petraglia",
"Nicole Boivin"
],
"abstract": "Background: The archaeological and ethnographic heritages of Mongolia reflect a multi-millennial continuity of typically mobile-pastoral occupations across sparsely populated, environmentally diverse landscapes, but the threats of modernisation and industrialisation to those heritages are nevertheless present and substantial. The construction of the Erdeneburen Hydroelectric Dam on the Khovd River in western Mongolia is planned to submerge hundreds of archaeological features and jeopardise at least another thousand. Methods: The Mongolian Archaeology Project: Surveying the Steppes, in collaboration with the Mongolian Institute of Archaeology, integrates a variety of digital techniques including GIS (geographic information systems), Machine Learning automated site detection, drone mapping, and Structure-from-Motion LiDAR scanning to document the endangered archaeology. This paper presents the resulting dataset of archaeological features across three different impact zones associated with the dam construction and evaluates the degree of efficacy of the initial data integration strategy through informal partner feedback and self-assessment. Results: While only approximately 20% of the documented sites fall within the planned flood zone, the remaining sites will be subjected to collateral threats such as industrial and infrastructural development that will necessitate extended monitoring, both temporally and spatially. In consideration of these results, this paper argues that a ‘responsive’ mode of heritage disaster intervention can bridge the gap between ‘reactive’ and ‘proactive’ modes, but requires development of an integrated (digital) methodology. Conclusions: The paper concludes by offering a new, more interconnected ‘transmethodology’ that addresses spatiality, sub-sampling, data reuse, and community input across multiple disciplines such as cultural heritage preservation, salvage archaeology, computer vision, and community archaeology. The authors developed this ‘transmethodology’ and the resulting workflows out of a theoretical framework that considers principles of Symmetrical Archaeology, Resilience Humanitarianism, and the CARE standard for inclusive data management (Collective benefit, Authority to control, Responsibility, and Ethics).",
"keywords": [
"Mongolian archaeology",
"digital cultural heritage preservation",
"Machine Learning",
"remote sensing",
"landscape archaeology",
"GIS",
"semantic data modelling",
"transmethodology",
"Erdeneburen Dam",
"endangered archaeology"
],
"content": "Introduction\n\nDigital archaeology is a rapidly emerging sub-discipline that draws on a wide range of methodologies, theoretical dispositions, and techniques to integrate traditional archaeological methods with computer applications, digital recording equipment, and, ideally, processes of digitalisation (Richards-Rissetto & Landau 2019; Huggett 2017, 2015; Zubrow 2006). Increasingly, digital archaeology approaches are advancing the methodologies of adjacent disciplines such as cultural heritage preservation (Lukas et al. 2018; MacFarland & Vokes 2016; Clarke 2015; Esteva et al. 2010; Hadjimitsis et al. 2009; Witcher 2008; Reichel 2005), expanding the potential for breadth of coverage and depth of recorded information. This is especially evident in the practices of remote survey (VanValkenburgh & Dufton 2020; Luo et al. 2019; Bradley 2006), particularly for documenting archaeological sites and monitoring their threats and disturbances (e.g., Breen et al. 2022; Tews et al. 2022; Hammer et al. 2018; Fradley & Sheldrick 2017; Casana & Laugier 2017; Parcak et al. 2016; Casana & Panahipour 2014; Parcak 2007; Box 1999). This paper demonstrates an approach to integrating various digital-archaeology methods for cultural heritage preservation in Mongolia, focusing on archaeological sites affected by the planned flooding to result from the Erdeneburen Hydroelectric Dam Construction Project in the Khovd River Valley, Khovd aimag/province (Figure 1).\n\nMap sources (open access): Esri, Maxar, GeoEye Earthstar Geographics, cNEs/Airbus Ds, UsDA, UsGs, AeroGRID, IGN, and the GIS User Community (left); US National Park Service (right).\n\nThe Mongolian Archaeology Project: Surveying the Steppes (MAPSS) is a cultural heritage preservation and archaeological research endeavour that draws on digital methodologies to detect, interpret, and assess archaeological and ethnographic sites across Mongolia, generating a large body of primarily ‘born-digital’ (Scott et al. 2021) data. Similar to other large-scale heritage documentation projects (e.g., Westley et al. 2021; Stein 2020; Green et al. 2019; Bewley et al. 2016), MAPSS deploys remote sensing methods such as interpretation of high-resolution satellite imagery to rapidly identify surficial archaeological remains, confirming and complementing those data with targeted pedestrian surveys. As a digital archaeology project, it integrates its various digital techniques through a strategic aggregational methodology and integrates its datasets in a geospatial semantic database. Its aim is to avail those data to other researchers, the general public, and, especially, Mongolian heritage professionals. These categories describe overlapping, non-exclusive group memberships, but represent different modes of data dissemination. Moreover, the theoretical bases of this research incorporate elements of Symmetrical Archaeology and Resilience Humanitarianism to essentialise both the FAIR1 and CARE2 data management principles by incorporating local input into the workflows and feedback systems.\n\nMongolia presents unique challenges to cultural heritage preservation, as it is the least densely populated nation on earth (Cui et al. 2019). The rural economy predominantly comprises mobile pastoralism, with little agriculture, industry, or sedentarism to disturb its archaeological remains (Honeychurch 2010). But sustainable, traditional economies are shifting toward more destructive, modern industrial practices nevertheless (ibid.), and the rapid growth of the capital city of Ulaanbaatar, at the expense of the rural population count (Cui et al. 2019), appears to be initiating a transformation of the pastoral countryside and its perdurance of pre-modern social praxis into an industrialised hinterland supporting the urban capital.\n\nSome of the most readily identifiable threats to archaeology across the Asian and African cultural landscapes include human activities such as industrial development and agricultural and urban expansion (e.g., Ekblom et al. 2019; Zerbini & Sheldrick 2017; Williams 2016). Using remote sensing methods, the MAPSS project’s risk analysis of archaeological remains in Mongolia indicates that environmental processes such as wind and water activity have posed the most glaring threats there, contrastingly (Figure 2).\n\nWith such low population density levels, this is an unsurprising observation. Threats from development and economic activities such as mining (both legal and illegal) to archaeological remains are nevertheless present, but are less visibly prominent—and so harder to detect remotely—due to their nascence. However, these practices are poised to become highly destructive to Mongolian cultural heritage in the near future. The Erdeneburen Hydroelectric Dam Construction Project illustrates this with great urgency, as it is planned to flood an approximately 3,500 km2 section of the Khovd River Valley by 2027, submerging and endangering hundreds of archaeological sites alongside traditional lifeways. The national government has funded the Mongolian Institute of Archaeology to conduct emergency pedestrian survey and salvage excavation operations as the dam construction begins. The MAPSS project offered to assist with the site documentation process using digital methods in order to generate complementary datasets.\n\nThe working hypothesis of this research is that an integrative, inclusive, and attentive digital archaeology program—which features data sharing, local input in data modelling, and methodological training—can have a net positive impact on archaeological recording systems and cultural heritage conservation in Mongolia, and support ‘proactive’ heritage preservation, rather than ‘reactive’ interventions (Faizi et al. 2017: 31-35). In many instances, such as the construction of the Erdeneburen Dam, a ‘responsive’ mode of intervention is warranted. In these cases, the threat event triggers the response, which should then itself pre-empt establishment of proactive heritage preservation practices going forward, rather than deploying successive ‘reactive’ interventions (Fisher, in press). The MAPSS project realises both ‘responsive’ and ‘proactive’ modes of heritage preservation through its data and digitalisation integration strategies.\n\n‘Responsive’ and ‘proactive’ digital solutions should adhere to both the FAIR and CARE principles, not simply because they have become universal standards in data management, but because, we suggest, an interrelationship exists between reusability, inclusivity, and sustainability. Toward these ends, the MAPSS data collection and management systems are designed to consider modelling uncertainty at scale, multilinguality, multivocality, and interpretive multiplicity. Thus, the project balances capture of metadata, paradata, resource relationships, site conditions, and archaeological interpretation with the scope, ambition, and inclusivity of populating a national cultural heritage database.\n\nThe outcomes of MAPSS’ involvement with the Erdeneburen Dam Project are both empirical and methodological. The opportunity to form a collaboration between MAPSS and the Mongolian Institute of Archaeology served as a means of using digitally integrated methods to document endangered heritage and as a test case for the project’s data transmission pipelines and integration strategies. Thus, the results of this research are presented here in terms of both the data generated and, more generally, the utility of the system design and its impact. Based on informal reporting by partners in the Mongolian Institute of Archaeology, the overall impact of the MAPSS data integration program was positive, but the reporting included constructive feedback as well, which has led to MAPSS redefining its methodology and reformulating some of its techniques and workflows. This paper will start by describing the initial MAPSS methodology and the methods it comprises, before presenting the datasets, analyses, and outcomes, which include a reimagined, pyramidal, and vertically integrated MAPSS methodology or ‘transmethodology’ (Khwaja & Kousholt 2021; see below).\n\n\nMethods\n\nThe primary function of the MAPSS project is to document the archaeological landscapes of Mongolia through manual remote sensing (MRS) of archaeological sites and features (together called “heritage resources”) by interpreting landscape features seen on high-resolution satellite imagery, as well as through automated detection of certain heritage resource types using a specialised subset of machine learning (ML) methods called deep learning (DL). MAPSS also relies on utilising data furnished by partner institutions in Mongolia such as the National Centre for Cultural Heritage, the Institute of Archaeology, and Khovd University, and digitally integrates the resulting outputs (Fisher 2022).\n\nMRS of archaeological features is at the core of the project’s methodology, working at a pace of approximately 25,000 sq. km per year to identify heritage resources using freely available, open-access imagery from Google Earth, Bing, Esri, HERE WeGo, and Maxar Technologies. MAPSS analysts follow now-standard methods for satellite imagery interpretation (e.g., Fowler 2010; Hritz 2010; Ur 2006; Wilkinson et al. 2006; Richards 2005), marking the locations of archaeological and ethnographic features such as funerary monuments, ritual monuments, and campsites, as well as assessing disturbances and threats to heritage resources in accordance with ICCROM (International Centre for the Study of the Preservation and Restoration of Cultural Property) guidelines (see Jigyasu 2019). MAPSS employs a condition/threat assessment model based on the three-tier system for interpreting effects (disturbances), threats, and threat drivers (see Zaina 2019), previously implemented by the Endangered Archaeology in the Middle East and North Africa (EAMENA) project (Ten Harkel & Fisher 2021) but modified further for purposes of localisation, semantic efficiency, and data reusability.\n\nIn parallel, the MAPSS project developed DL techniques using ‘supervised learning’ functions in order to identify potential archaeological features such as funerary and habitation sites in the Khovd River Valley region, akin to ‘pure prediction’ of archaeological remains (Bevan 2015: 1478). This approach automates remote site discovery by using ArcGIS Pro’s dedicated Deep Learning Toolset, which features a third-party DL Python application programming interface (API) (TensorFlow, PyTorch, or Keras) to detect pixel clusters (‘objects’) in an image, deploying a specified Python raster function to process each object. By training the system using known datasets of heritage resources and ready-made DL models such as Mask Region-based Convolutional Neural Network (R-CNN), You Only Look Once v3 (YOLOv3), or Single Shot Detector (SSD), analysts run the selected model against an input raster image to produce results according to each object class (such as ‘burial mound’ or ‘winter-camp habitation site’). The input raster images are high resolution and freely accessible, with a typical spatial resolution of 0.6 m.\n\nDL models rely on ‘neural networks’, or series of algorithms that work together to mirror human brain function using weights and biases for decision making (Casini et al. 2021; Shrestha & Mahmood 2019). For automated object detection across large images (in geographic terms, landscapes), convolutional neural networks (CNNs) aggregate constituent networks through a sequence of typically four layers that first sort pixel values (input layer), then filter pixels to identify edges (convolutional layer), then pool values (pooling layer), and finally connect all layers and assign a unique value to each object (fully-connected layer; Shrestha & Mahmood 2019: 53044). Supervised learning is a function of DL in which a human operator uses image data to label objects in a training dataset composed of business data (ibid.: 11). It is useful for extrapolating outward from known business data to unknown business data, identifying all objects that fall within the range of pixel-value signatures per object class according to the algorithms of the DL model.\n\nOperationally, the first steps of supervised learning are typically to obtain the open-access imagery data and normalise them by modifying each tensor so that the mean is 0 and the standard deviation is 1, allowing the neurons in the network to “learn” faster (MAPSS uses Anaconda Jupyter Notebook for normalisation). To then create training data, one makes a visual assessment of the geographical area, imports the business dataset (if available), draws bounding boxes or polygons around the known objects, and exports the polygons into a folder containing images, their labels, an ESRI-accumulated statistical JSON file, and an ESRI model-definition file. Then one chooses a DL model for training.\n\nMAPSS tested five DL models (SSD, RetinaNet, YOLOv3, Faster R-CNN, and Mask R-CNN) using a geographically constrained subset of its geospatial dataset from western Mongolia. SSD is a model that runs once over the input image and is designed for both speed and accuracy (Liu et al. 2015). The backbone of this model is typically a network such as ResNet, and the SSD head comprises one or more overlying convolutional layers. The model divides the image according to a grid and within each grid cell detects objects, predicting their class and location. RetinaNet is a one-stage object detection model (Alhasanat et al. 2021), often applied to aerial and satellite imagery, and has a high true-positive rate for small-scale objects. RetinaNet also uses a ResNet as a backbone network, but uses Focal Loss as an enhancement over Cross-Entropy Loss to handle the class imbalance problem. YOLOv3 has a different backbone than the previous two as it uses Darknet-53, which employs 53 convolutional layers and so is generally faster than the ResNet family (Redmon & Farhadi 2018). It integrates upsampling and concatenation of feature layers with earlier layers, detecting at three different scales, and so can be effective for sensing objects of varying size. Faster R-CNN relies on a convolutional algorithm called the Region Proposal Network (RPN) and a CNN backbone. RPN algorithms use low-cost region proposals to predict object boundaries and “objectness” scores for each pixel cluster (Shaoqing et al. 2015).\n\nMask R-CNN is a variant of the Faster R-CNN model, also utilising the RPN convolutional algorithm, but it can additionally predict a segmentation mask that marks the individual pixels composing each object. Mask R-CNN has so far been the most successful model applied to MAPSS data, with a 63% success rate against the training dataset, making it the best choice for automated remote sensing detection in the Khovd River Valley region. MAPSS ran it in ArcGIS against the selected raster input and then manually evaluated the initial output, deleting false positives and adding false negatives. Finally, analysts exported the output as a.CSV file, deployable as a layer in any geographic information systems (GIS) application.\n\nThe initial strategy to integrate the data resulting from these methodologies featured approximately parallel workflows for each of the three data types–external/archival datasets, MRS data, and DL-generated data–with integration between them achieved firstly in ArcGIS and then the Arches database via.CSV import (Figure 3). MAPSS analysts use these geospatial data management applications to visualise and calculate convergences between the methods, achieving data integration through both applications but using each toward different ends.\n\nThe Arches database will be the main access point to MAPSS data for the public and is the semantic heart of the recording system that integrates and informs the other components. Arches is a web-based geospatial semantic graph database platform that allows users to design fully customised, triple-store (RDF3) graphs to structure data, and is CIDOC-CRM4 compatible to ensure semantic interoperability (Meyers 2016). The basic design of the MAPSS database comprises multiple resource models, each custom designed for specific purposes (Figure 4), which are integrated through ‘resource-instance’ data-type nodes that are semantically embedded within and distributed throughout each graph.\n\nThe graph of each resource model utilises hierarchical data structures to capture multiplicity of interpretations, each one replete with its own metadata (including date, assessor name, and assessor affiliation) and paradata (including interpretation method and information resources used; see Matskevich & Sharon 2015: 107 ff.). The MAPSS graphs additionally model interpretive uncertainty throughout the graph design, allowing for greater reusability (the ‘R’ in the FAIR principles; Figure 5). Overall, this design follows the principles of ‘relativistic recording’, as opposed to determinist, positivistic recording (ibid.: 108).\n\nSpeaking further to the issue of reusability and sustainability of datasets, MAPSS has collaborated with developers and cultural heritage colleagues to redevelop the export and import functionalities of the Arches platform so as to improve interoperability across the divide between graph-structured databases and flat files. Most graph-based data do not fit flat-file formats such as.CSV or.SHP due, primarily, to their potential for N-cardinality both horizontally and vertically (i.e., N-children each with N-children). This type of cardinality flexibility, natively deployable in graph structures, is essential for modelling complex concepts such as interpretive plurality and uncertainty at scale. But because Arches at its core is, uniquely, a graph interfacing layer overlying a PostgreSQL relational-database backend (Barton et al. 2017), it enables both importing data from and exporting data into SQL-like shapes across spreadsheets, accurately capturing the semantic logic and graph structure in spreadsheet format with zero data loss or ambiguity.\n\nUpon learning of the plans for the construction of the Erdeneburen Dam and the accompanying archaeological and cultural surveys, MAPSS analysts processed archival datasets containing the field survey data that had already been generated by local entities such as the Khovd University Department of Archaeology. They then investigated the area using high-resolution satellite imagery, to confirm and further identify visible archaeological features and their condition states. Although threats and disturbances are less relevant for long-term heritage management of sites facing imminent inundation, as is the case within the Erdeneburen Dam Project flood zone, MAPSS documents all visible condition states and risks, for scientific purposes.\n\nFor local professionals in Mongolia, MAPSS is planning future training workshops to transfer the skills required to extract meaningful datasets from the Arches database. Due to the urgency of the Erdeneburen Dam Survey, in this case the project plotted the geospatial data over maps in ArcGIS to integrate the various datasets. The output was a printable portfolio, each page of which displayed a localised grid square illustrating feature locations (Figure 6), that accompanied a.SHP file transferred to the Institute of Archaeology in advance of their survey season. Upon arrival at the Institute of Archaeology camp in Khovd, MAPSS personnel transferred the coordinates of archaeological features to partners’ GPS devices directly.\n\nBackground satellite imagery source (open access): Maxar Technologies.\n\nAs the Mongolian government funded the Institute of Archaeology salvage expedition to target the flood and surrounding development zones exclusively, the MAPSS team focused on adjacent areas as well, in order to capture field data for assessment and monitoring of the archaeological sites that would remain above water. Simultaneously, MAPSS collected field data to evaluate remote sensing accuracy. In order to target certain high-density heritage areas, and expand the extent of the survey beyond the flood and development zones, the MAPSS pedestrian survey focused on all visible archaeological remains, mainly detecting four different feature types: funerary monuments such as kurgans, ritual monuments such as standing stones and pavements, ethnoarchaeological settlements such as prolonged-used winter camps, and rock art/cave sites.\n\nThe two aims were to ground-truth remotely sensed archaeological features and to record features unrecognisable in the open-acceess satellite imagery available for remote sensing. The survey participants included MAPSS team members based at the Max Planck Institute in Jena, Germany, and two partners based in Ulaanbaatar, Mongolia, Dr. Khurelsukh Sosorbaram and Batchuluun Oyundelger. Participants used a digital recording system for pedestrian survey that is designed to generate Arches data directly in the field, in addition to 2D visual recording with digital cameras and 3D visual recording using iPad LiDAR sensors (for a subset of archaeological features; Figure 7). Project members recorded survey data directly into spreadsheets on computer tablets, which can then be uploaded into Arches with minimal transformation and cleaning.\n\nAn essential component of the MAPSS field methodology is using programmable, rotary-wing unmanned aerial vehicle (UAV) photography to generate Very-High-Resolution orthomosaics of the landscape, beneficial for remote survey of mountainous regions poorly covered by high-resolution satellite imagery (Rouse & Krumnow 2020). The process begins by creating a flight plan in Map Pilot Pro, flying the drone over the selected area (Figure 8), and then processing the images in either ArcGIS Pro or Agisoft Metashape. Georectification of the resulting image files enables the production of orthomosaics, Digital Surface Models (DSM), and other outputs.\n\nThe resulting Very-High-Resolution imagery of the research areas allows MAPSS analysts to “drone truth” remote sensing data on a much broader scale than is possible through pedestrian survey alone, but with better spatial resolution than available commercial imagery (Figure 9). For example, the MAPSS pedestrian survey covered approximately 1 km2 in the Khovd River Valley research area, compared with 7 km2 covered by drone mapping. With a typically 0.3m spatial resolution, the orthomosaics allow for effective reanalysis of targeted areas, clearly showing details unrecognisable in 1m-resolution imagery, including sub-3m objects such as standing stones as well as nearly flat-lying features such as stone pavements.\n\nA main function of the MAPSS field survey activities (as opposed to the Institute of Archaeology survey) in the Khovd River Valley was to evaluate the efficacy of project methods such as remote-sensing site detection, as well as overall methodology. The testing targeted verification of the remote sensing results using pedestrian and drone mapping surveys, assessing confidence rates and reliability of the remotely sensed data. MAPSS randomly chose three sampling areas to survey across environmentally varied zones within the area of interest. The evaluation of the data is still ongoing, and so this paper will present the results of two sampling areas, Khovd Gol 1 and Khovd Gol 2. Simultaneously, the Erdeneburen Dam project provided MAPSS the opportunity to evaluate and test the broader methodological and theoretical frameworks in which it generates and curates its datasets.\n\n\nResults\n\nSatellite imagery of the flood zone and the broader area surrounding it suggests that the impact of the flooding will affect various areas of the valley differently, depending on proximity and topography. After georectifying the government maps that delineate the two impact zones, we then added a proposed extended monitoring zone of approximately 2 km (Figure 10). The case study presented here includes two clusters of archaeological features that the project documented and analysed, one in the flood zone and the other in the extended monitoring zone.\n\nThe site of Khovd Gol 1, located inside of the flood zone, is situated on the slope or low cliff of the river valley (Figure 10). The surrounding plain is steppe or semi-desert, presently containing almost no vegetation. All of the archaeological features documented have been exposed to natural depositional processes and many are at least partially covered by sand, rendering them unrecognisable in most types of remotely captured imagery.\n\nThe pedestrian survey of Khovd Gol 1 recorded 22 features in total. Remote sensing had already identified eight features, while MAPSS identified only 14 (63.6%) in the field (Figure 11). This indicates an approximate remote-sensing rate of 36%. The MAPSS survey achieved similar results at the Khovd Gol 2 site, which is situated in a rocky environment outside of the highest-risk areas. The pedestrian survey there recorded 43 features in total, including 15 (~35%) that analysts had already captured through remote sensing and 24 (~56%) discovered only through ground truthing (the remaining four were unverified by ground truthing).\n\nA more complex evaluation comparing the total MRS data from the Khovd River Valley with external survey datasets addresses the different levels of detail recorded in each. Both the Khovd University (KU) dataset and the NCCH dataset mainly consist of “site” records, meaning one record represents multiple archaeological features, rather than representing individual features as MAPSS records do. Comparing MAPSS MRS with the more detailed, ground-based KU survey data, and considering only funerary monuments, 27% of the 199 sites appear in both datasets. This relatively low percentage of overlapping site identification is largely due to the KU pedestrian-survey recording of features too small to detect using freely available, open-access imagery. Alternatively, comparing the singular records within the surveyed area, the numbers approach parity: 300 funerary monuments recorded by the KU survey compare against 196 records generated remotely by MAPSS. According to our interpretation of the KU survey extent, 70 MRS records do not appear in the KU dataset. The divergences in each case suggest that both MRS and pedestrian survey have the potential to identify archaeological features that the other method might miss.\n\nA different picture emerges by comparing MRS records with NCCH data. In the Khovd River Valley research area it is possible to correlate seven out of eight MRS sites with NCCH records. In other words, using remote sensing techniques, MAPSS identified 87% of the sites recorded by NCCH during pedestrian survey. Transposing these data to individual feature records, MRS identified 252 features compared with 168 features (from eight sites) that the NCCH had already recorded. MRS enabled MAPSS analysts to assign precise locations to most of the NCCH records, while also complementing the existing records with new discoveries. Comparison across all datasets shows a 63.3% overlap (660 records) between pedestrian survey in general and MRS data.\n\nTo summarise, MAPSS analysts identified approximately one-third of known features using MRS techniques. The majority of the features (56-65%) were field discoveries (i.e., not detected by remote sensing methods), due primarily to their small size. According to a preliminary assessment, the average approximate diameter of features unrecognised through remote-sensing methods is 3m, and does not exceed 8m, or otherwise are shallow/paved features. Though the evaluation of the results is ongoing, the ground-truthing based confidence in the features identified through MRS in Khovd Gol 1 and 2 is preliminarily at 90%.\n\nWe also compare ML/DL outcomes to MRS (Figure 12). Approximately 10% (126/1262) of the records are exclusive to DL automated site detection. Based on raw numbers, DL detects 25.4% (777/1042) fewer archaeological features (e.g., individual burials or monuments) than MRS detection of features. However, DL detects a similar rate of the major clusters and sites, and so MAPSS ultimately factored this aspect of the different methods into its revised workflow and data integration strategy (see below).\n\nFor condition state, threat, and risk analyses, project members identified the threats and disturbances impacting heritage resources in the development and extended monitoring zones, including infrastructure, looting, and erosion. It is unfortunately a near inevitability that sites within the flood zone face complete submersion. The government-use zone represents an area subject to industrial and administrative activities necessary for constructing and operating the dam, and so has the potential for a very high rate of disturbance. The proposed extended monitoring zone will presumably incur a significant amount of population displacement from the other zones, although redefining this zone using demographic data and geographic analysis would be beneficial. Nevertheless, the simply defined area shown here will include not only potentially higher population density in places, but more destructively, new infrastructural development.\n\nAccording to the zonal distribution (Figure 13), 21.6% of the recorded sites fall within the flood zone, although nearly two-thirds of those are campsites. Recording occurrences of seasonal habitation sites is primarily ethnographic in nature, although in many cases campsites evidence occupations dating to mediaeval (Wright 2016) and prehistoric (Houle 2016) periods. Clearly, the largest impact of the dam construction will be on the lives of the valley inhabitants, who will at some point be unable to return to their riparian spring-season camp locales. Over 600 ancient funerary monuments, however, will be subjected to potentially destructive activities carried out in the government-use zone, indicating that authorities and cultural heritage institutions should pay close attention to changing condition states of the archaeological features located there. Furthermore, the extended ‘possible high-risk’ zone contains hundreds of archaeological features as well as nearly one hundred campsites whose inhabitants will likely witness added population pressure and increased infrastructural development in their seasonal habitation areas.\n\nThe concentration of 610 (likely) ancient funerary sites in the government-use zone (out of 1,126 total) indicates that the destruction of access to cultural heritage effected by the dam construction can either expand–if sites are not monitored and protected–or be stemmed, through ongoing intervention efforts. A responsive/proactive mode of intervention would include measures that Mongolian authorities and their partners have already taken such as documentation and development of monitoring techniques. It would also require, of course, use of the resulting datasets and techniques to regularly assess the impact of dam-related processes on cultural heritage features and possibly deteriorating feature conditions.\n\nMAPSS Khovd River datasets provide a basic foundation of information about the number and type of features that the dam construction will submerge and what will survive but be exposed to increased threats from associated development activities. This can facilitate strategic decision making for damage mitigation, rescue survey, and monitoring of heritage resources. Remote sensing methodology has an advantage over classical survey in cases such as these in terms of coverage area, time requirement, and human resource expenditure. Additionally, this case study provides the preliminary statistical evaluation of the MAPSS data and their confidence values, and so the methods complement one another. For example, areas with high occurrences of complex khirigsuur burials (Figure 14) also feature higher (ground) detection rates of objects that are “invisible” to remote sensing, such as paved ritual features, than the areas featuring primarily simple stone mounds, which show higher rates of other object types such as standings stones. Enabled by the pedestrian and drone-based ground-truthing surveys, future analysis can evaluate whether there is any statistical correlation between set types of archaeological features.\n\nDrone image of a khirigsuur burial, typical of the 2nd millennium BCE, to be submerged.\n\n\nDiscussion\n\nThe major outcomes of this case study have been: 1) the expansion of the surveyed zone, extending the monitoring capabilities beyond the government’s originally funded plan and demonstrating the benefits of cooperation between local and non-local entities; and 2) the feedback received on the shared dataset in combination with a self-evaluation of the MAPSS methodology, integration strategy, and data transmission pipeline.\n\nInformal partner feedback (through unsolicited conversation) and project self-assessment, identifying a lower DL object-detection rate than MRS, both indicated that the MAPSS project needed to devise a stronger, more integrational methodology across the various fields of practice, which include cultural heritage preservation, field archaeology, geography, and computer science. In order to theorise such a strategy, this paper borrows the term ‘transmethodology’ from Khwaja and Kousholt, who describe it as a\n\n… focus on phenomena through multiple theoretical perspectives and multiple interacting/connected empirical methods. This may also indicate a combination of qualitative and quantitative elements of inquiry and the creation of new onto-epistemological approaches and ethics (Khwaja & Kousholt 2021: 3).\n\nWe consider this in conjunction with Symmetrical Archaeology, which Shanks (2007) defines as an “attitude” that removes the assumptive distinction between people, processes, and material remains. In a sense, this dovetails with the supposition that digital archaeology dematerialises the past (Brouwer & Mulder 2003: 4; cf. Sluis 2017: 28). However, within a Symmetrical Archaeology rubric, the degree of materiality is less germane than the resulting impact of identifying, structuring, generating, and using those data (Fisher et al. 2021). Finally, within this framework, the MAPSS project seeks to help develop communities of local digital archaeology and heritage specialists in order to practise ‘responsive’ and ‘proactive’ heritage interventions through Resilience Humanitarianism (Hilhorst 2018), which identifies local communities as the primary heritage practitioners and the first emergency responders to heritage disasters.\n\nSo how does one operationalise these theoretical frameworks, thereby reifying them (Shanks & Tilley 1992: 49)? As a digital documentation project tasked with identifying and recording as much of the immovable cultural heritage of Mongolia as possible, any methodology that MAPSS applies has to remain focused on productivity and quantifiable results, while still realising that there is more to productivity than the technical processes.\n\nThe first step is to integrate the various areas of practice into a single, principled methodology in which recording moves from higher-volume/lower-resolution sensing capabilities to lower-volume/higher-resolution sensing capabilities, with each scalar informing the next (Figure 15). DL-automated remote sensing now provides the project’s baseline of sites, from which it is then possible to decide on areas for further investigation through MRS. This adds a higher degree of certainty, greater number of feature detections, and richer interpretations and assessments, but over a more limited spatial extent. From the MRS dataset, the MAPSS project can select research areas for field-based drone mapping (Hritz 2010), from which analysts generate very-high-resolution orthomosaic imagery. Within each UAV fly zone, the project can then choose smaller areas for pedestrian survey, including investigation of potential rock-art sites, based on local guidance. Within each of those pedestrian survey zones, survey participants then select a subset of monuments for 3D scanning, primarily using hand-held LiDAR sensors equipped on iPad devices.\n\nEach scalar in the pyramid requires not only internal evaluation for informing the next scalar, but in order to adhere to principles of Symmetrical Archaeology, Resilience Humanitarianism, and the CARE principles, external input from local archaeological and cultural heritage communities as well (Figure 16). A revised workflow diagram illustrates this, demonstrating how the new MAPSS ‘transmethodology’ functions in practice (Figure 17). The colours of each action node correspond to their scalar in the methodology pyramid.\n\nIn conclusion, the MAPSS project, in collaboration with the Institute of Archaeology, assisted with a ‘responsive intervention’ approach to the Khovd River Dam emergency. It is ‘responsive’ rather than ‘reactive’ because, although triggered by a punctuated emergency, it in-builds the potential for not only better monitoring of affected (but above-water) sites, but also a broader methodology that improves both input feedback and output data. This provides more optimal conditions for ‘proactive’ heritage preservation efforts, both in relation to the Erdeneburen Dam construction zone and across Mongolia more broadly. The MAPSS component of this international, trans-institutional collaboration has also produced statistical analysis of its remote discovery methods, identified an expanded set of endangered archaeological sites, and incorporated local partner feedback to re-evaluate how it integrates the various methodologies into a single, productive, and principled transmethdology that balances output with impact.\n\n\nSoftware availability\n\nSoftware available from: https://github.com/orgs/MPI-MAPSS/repositories\n\nSource code available from: https://github.com/MPI-MAPSS/, https://github.com/MPI-MAPSS/MAPSSdb\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.7188788 (Fisher 2022).\n\nLicense: Creative Commons Zero v1.0 Universal, GNU Affero General Public License v3.0",
"appendix": "Data availability\n\nAll archaeological business data is deposited at https://mapss.server.shh.mpg.de/ and will be made available to the public as of 01.12.2022. Due to the sensitive nature of geospatial data (i.e., site locations), and ethical considerations such as local authority to control, data access requests will have to be approved upon submission of name, valid email address, intent of use, and professional affiliation(s). Before 01.12.2022, data is available upon request via email to mapps@shh.mpg.de.\n\n\nAcknowledgements\n\nThe authors are grateful for the cooperation of and collaboration with Mongolian partners including the Institute of Archaeology, the National Centre for Cultural Heritage, the Academy of Sciences, and Khovd University. We must thank Dr. Khurelsukh Sosorbaram and Batchuluun Oyundelger for participating in the fieldwork component of this research, Byambadorj Batsuren for translating and cleaning the archival datasets, and Graeme Richardson for facilitating the MAPSS project. We must finally thank our project liaison at Arcadia, Dr. Mike Heyworth, for all of his assistance with MAPSS.\n\n\nReferences\n\nAlhasanat MN, Alsafasfeh MH, Alhasanat AE, et al.: RetinaNet-based Approach for Object Detection and DistanceEstimation in an Image. International Journal on Communications Antenna and Propagation (IRECAP). 2021; 11(1): 1–9.\n\nBarton C, Cox A, Delgadillo Cruz S, et al.: Cultural-heritage inventory implementations: the versatility of the Arches system. APT Bulletin: The Journal of Preservation Technology. 2017; 48(4): 19–28.\n\nBevan A: The Data Deluge. Antiquity. 2015; 89(348): 1473–1484. Publisher Full Text\n\nBewley R, Wilson AI, Kennedy D, et al.: Endangered Archaeology in the Middle East and North Africa: Introducing the EAMENA Project.2016; CAA2015: 919–932.\n\nBox P: GIS and Cultural Resource Management: A Manual for Heritage Managers. Bangkok:PROAP;1999.\n\nBradley M:Archaeological Survey in a Digital World.Daly P, Evans TL, editors. Digital Archaeology - Bridging Method and Theory. New York:Routledge;2006; 35–49.\n\nBreen C, Blue L, Andreou GM: Documenting, Protecting and Managing Endangered Maritime Cultural Heritage in the Middle East and North Africa (MENA) Region. J. Marit. Archaeol. 2022. [accessed Sep 24 2022]. Publisher Full Text\n\nBrouwer J, Mulder A: Information is Alive. Information is Alive: Art and Theory on Archiving and Retrieving Data v2. Brouwer J, Mulder A, editors.Rotterdam:Nai Publishers;2003; 4–6.\n\nCasana J, Laugier EJ: Satellite Imagery-based Monitoring of Archaeological Site Damage in the Syrian Civil War. PLoS One. 2017; 12(11): e0188589. PubMed Abstract | Publisher Full Text\n\nCasana J, Panahipour M: Satellite-Based Monitoring of Looting and Damage to Archaeological Sites in Syria. Journal of Eastern Mediterranean Archaeology and Heritage Studies. 2014; 2(2): 128–151. Publisher Full Text\n\nCasini L, Roccetti M, Delnevo G, et al.: The Barrier of Meaning in Archaeological Data Science. Proceedings SCIFI-IT'2020-4th Annual Science Fiction Prototyping Conference, Ghent, Eurosis.2021; 61–65.\n\nCui D, Liu H, Ye X, et al.: Spatiotemporal Evolution and the Driving Forces of the Coupling Coordination Degree between Urbanization and Urban Residents’ Livelihood Level in Mongolia. Sustainability. 2019; 11(781): 1–22. Publisher Full Text\n\nClarke M: The Digital Dilemma: Preservation and the Digital Archaeological Record. Advances in Archaeological Practice. 2015; 3(4): 313–330. Publisher Full Text\n\nEkblom A, Shoemaker A, Gillson L, et al.: Conservation through Biocultural Heritage—Examples from Sub-Saharan Africa. Land. 2019; 8(1): 5. Publisher Full Text\n\nEsteva M, Trelogan J, Rabinowitz A, et al.: From Site to Long-term Preservation: A Reflexive System to Manage and Archive Digital Archaeological Data. Archiving 2010 – Preservation Strategies and Imaging Technologies for Cultural Heritage Institutions and Memory Organizations Final Program and Proceedings (Den Haag, Netherlands 1-4 June 2010). Springfield, VA:Society for Imaging Science & Technology;2010; 1–6.\n\nFaizi KK, Kolb CC, Maiwandi A, et al.: Discussion: Organizational Frameworks for Cultural Heritage Preservation. Preserving the Cultural Heritage of Afghanistan. Stein G, Fisher MT, Latify H, Popal N, et al., Editors.Chicago:Oriental Institute of the University of Chicago;2017; 29–35. SAOC 73.\n\nFisher MT: Stability of Cultural Information in Unstable Environments: Data Management for Immovable Cultural Heritage in Times of Disaster. Routledge Handbook for Cultural Heritage Preservation in Times of Disaster, B. Rouhani & X. Romão, eds. Accepted 3 May, 2022.In press.\n\nFisher MT: MPI-MAPSS/MAPSSdb: MAPSS-Oct-2022 (MAPSS-Oct-2022). [Software]. Zenodo.2022. Publisher Full Text\n\nFisher MT, Fradley M, Flohr P, et al.: Ethical Considerations for Remote Sensing and Open Data in Relation to the Endangered Archaeology in the Middle East and North Africa Project. Archaeological Prospection. 2021; 28: 279–292. Publisher Full Text\n\nFradley M, Sheldrick N: Satellite Imagery and Heritage Damage in Egypt: A Response to ‘Satellite Evidence of Archaeological Site Looting in Egypt: 2002–2013’ (Parcak et al. 2016). Antiquity: A Quarterly Review of Archaeology. 2017; 91(357): 784–792. Publisher Full Text\n\nFowler MJF: Satellite Imagery and Archaeology. Landscapes through the Lens: Aerial Photographs and Historic Environment. Cowley DC, Standring RA, Abicht MJ, editors.Oxford:Oxbow Books;2010; 99–110.\n\nGreen AS, Orengo HA, Alam A, et al.: Re-Discovering Ancient Landscapes: Archaeological Survey of Mound Features from Historical Maps in Northwest India and Implications for Investigating the Large-Scale Distribution of Cultural Heritage Sites in South Asia. Remote Sensing. 2019; 11(2089): 1–26.\n\nGupta N, Nicholas R, Blair S:Postcolonial and Indigenous Perspectives in Digital Archaeology.Watrall E, Goldstein L, editors. Digital Heritage and Archaeology in Practice. Tallahassee:University Press Florida2022; 241–274.\n\nHadjimitsis DG, Themistocleous K, Agapiou A, et al.: Monitoring Archaeological Site Landscapes in Cyprus Using Multi-Temporal Atmospheric Corrected Image Data. International Journal of Architectural Computing. 2009; 7(1): 121–138. Publisher Full Text\n\nHammer E, Seifried R, Franklin K, et al.: Remote Assessments of the Archaeological Heritage Situation in Afghanistan. Journal of Cultural Heritage. 2018; 33: 125–144. 1296-2074. Publisher Full Text\n\nHilhorst D: Classical Humanitarianism and Resilience Humanitarianism: Making Sense of Two Brands of Humanitarian Action. Journal of International Humanitarian Action. 2018; 3(15). [accessed 20.03.2022]. Publisher Full Text\n\nHoneychurch W: Pastoral Nomadic Voices: A Mongolian Archaeology for the Future. World Archaeology. 2010; 42(3): 405–417. Publisher Full Text\n\nHoule J-L: Long-Term Occupation and Seasonal Mobility in Mongolia: A Comparative Study of Two Mobile Pastoralist Communities. Fitful Histories and Unruly Publics: Rethinking Temporality and Community in Eurasian Archaeology. Weber KO, Hite E, Khatchadourian L, et al., editors.Leiden:Brill;2016; 155–174. Publisher Full Text\n\nHritz C: Tracing Settlement Pattern and Channel Systems in Southern Mesopotamia Using Remote Sensing. Journal of Field Archaeology. 2010; 35(2): 184–203. Publisher Full Text\n\nHuggett J: Challenging Digital Archaeology. Open Archaeology. 2015; 1(1): 79–85.\n\nHuggett J: The Apparatus of Digital Archaeology. Internet Archaeology. 2017; 44. Publisher Full Text\n\nJigyasu R: Managing Cultural Heritage in the Face of Climate Change. Journal of International Affairs. 2019; 73(1): 87–100.\n\nKhwaja I, Kousholt D: Transmethodology: Creating spaces for transgressive and transformative inquiry. Outlines - Critical Practice Studies. 2021; 22(1): 1–21.\n\nLetellier R, Schmid W, LeBlanc F: Guiding Principles. Recording, Documentation, and Information Management for the Conservation of Heritage Places. Los Angeles:Getty Conservation Institute;2007.\n\nLiu W, Anguelov D, Erhan D, et al.: SSD: Single Shot MultiBox Detector. arXiv:1512.02325.2015.\n\nLukas D, Engel C, Mazzucato C: Towards a Living Archive: Making Multi Layered Research Data and Knowledge Generation Transparent. Journal of Field Archaeology. 2018; 43: S19–S30. Publisher Full Text\n\nLuo L, Wang X, Guo H, et al.: Airborne and Spaceborne Remote Sensing for Archaeological and Cultural Heritage Applications: A Review of the Century (1907–2017). Remote Sensing of Environment. 2019; 232: 1–34. Publisher Full Text\n\nMacFarland K, Vokes AW: Dusting Off the Data: Curating and Rehabilitating Archaeological Legacy and Orphaned Collections. Advances in Archaeological Practice. 2016; 4(2): 161–175. Publisher Full Text\n\nMatskevich S, Sharon I: Modelling the Archaeological Record: A Look from the Levant: Past and Future Approaches.2015; CAA2015: 103–115.\n\nMeyers D: Heritage Inventories: Promoting Effectiveness as a vital tool for Sustainable Heritage Management. Journal of Cultural Heritage Management and Sustainable Development. 2016; 6(2): 102–112. Publisher Full Text\n\nParcak S: Satellite Remote Sensing Methods for Monitoring Archaeological Tells in the Middle East. Journal of Field Archaeology. 2007; 32: 65–81. Publisher Full Text\n\nParcak S, Gathings D, Childs C, et al.: Satellite Evidence of Archaeological Site Looting in Egypt: 2002–2013. Antiquity. 2016; 90: 188–205. Publisher Full Text\n\nQuintero S, Awad R, Barazzetti L: Harnessing digital workflows for the understanding, promotion and participation in the conservation of heritage sites by meeting both ethical and technical challenges. Built Heritage. 2020; 4(6). [accessed 23.03.2022]. Publisher Full Text\n\nRedmon J, Farhadi A: YOLOv3: An Incremental Improvement. Tech Report, Computer Vision and Pattern Recognition. 2018; 2–3. Publisher Full Text\n\nReichel CD: Beyond Cataloguing Losses: The Iraq Museum Database Project at the Oriental Institute, University of Chicago. Visual Resources. 2005; XXI(1): 93–113.\n\nRichards JA: Remote Sensing Digital Image Analysis: An Introduction. Berlin:Springler-Verlag;2005.\n\nRichards-Rissetto H, Landau K: Digitally-Mediated Practices of Geospatial Archaeological Data: Transformation, Integration, & Interpretation. Journal of Computer Applications in Archaeology. 2019; 2(1): 120–135. Publisher Full Text\n\nRouse LM, Krumnow J: On the Fly: Strategies for UAV-based Archaeological Survey in Mountainous Areas of Central Asia and their Implications for Landscape Research. Journal of Archaeological Science: Reports. 2020; 30: 1–14.\n\nScott CB, Roosevelt CH, Nobles GR, et al.: Born-Digital Logistics: Impacts of 3D Recording on Archaeological Workflow, Training, and Interpretation. Open Archaeology. 7(1): 574–588. Publisher Full Text\n\nShanks M: Symmetrical Archaeology. World Archaeology. 2007; 39(4): 589–596. Publisher Full Text\n\nShanks M, Tilley C: Re-constructing Archaeology: Theory and Practice. 2nd ed.London:Routledge;1992.\n\nShaoqing R, He K, Girshick R, et al.: Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks. Extended Technical Report. 2015; 1–14. Publisher Full Text\n\nShrestha A, Mahmood A: Review of Deep Learning Algorithms and Architectures. IEEE Access. 2019; 7: 53040–53065. Publisher Full Text\n\nSluis K: Accumulate, Aggregate, Destroy. Database Fever and the Archival Web. Lost and Living (in) Archives Collectively Shaping New Memories. Dekker A, editor.Rotterdam:Zwart Institute;2017; 27–40.\n\nStein GJ: Cultural Heritage Preservation Work in Afghanistan and Central Asia. Oriental Institute Annual Report 2019-2020.2020; 21–31.\n\nten Harkel L, Fisher MT: The EAMENA Database and Its Potential Impact on Research and Heritage Management: A Case Study of Crusader Heritage in Lebanon. Levant. 2021; 53(3): 282–301. Publisher Full Text\n\nTews S, ten Harkel L, Shams A: From the Coast to the High Mountains: A Remote Sensing Survey of Disturbances and Threats to the Archaeology and Heritage of South Sinai. Journal of Maritime Archaeology. 2022. [accessed Sep 24 2022]. Publisher Full Text\n\nUr J: Google Earth and Archaeology. The SAA Archaeological Record. 2006; 6: 35–38.\n\nVanValkenburgh P, Dufton JA: Big Archaeology: Horizons and Blindspots. Journal of Field Archaeology. 2020; 45(1): S1–S7. Publisher Full Text\n\nWestley K, Andreou G, el Safadi C , et al.: Climate Change and Coastal Archaeology in the Middle East and North Africa: Assessing Past Impacts and Future Threats. The Journal of Island Coastal Archaeology. 2021; 1–33. [accessed Sep 19 2022]. Publisher Full Text\n\nWilkinson KN, Beck AR, Philip G: Satellite imagery as a resource in the prospection for archaeological sites in central Syria. Geoarchaeology. 2006; 21: 735–750. Publisher Full Text\n\nWilkinson MD, Dumontier M, Aalbersberg JJ, et al.: The FAIR Guiding Principles for Scientific Data Management and Stewardship. Scientific Data. 2016; 3: 160018. PubMed Abstract | Publisher Full Text\n\nWilliams T: Silk Roads in the Kingdom of Bhutan and the Development of a National Heritage Inventory. Archaeology International. 2016; 19: 122–133. Publisher Full Text\n\nWitcher R: (Re) surveying Mediterranean Rural Landscapes: GIS and Legacy Survey Data. Internet Archaeology. 2008; 24. Publisher Full Text\n\nWright J: Households without Houses. Journal of Anthropological Research. 2016; 72(2): 133–157. Publisher Full Text\n\nZaina F: A Risk Assessment for Cultural Heritage in Southern Iraq: Framing Drivers, Threats and Actions Affecting Archaeological Sites. In Conservation and Management of Archaeological Sites. 2019; 2(3): 184–206.\n\nZerbini A: Developing a Heritage Database for Endangered Archaeology in the Middle East and North Africa. Journal of Field Archaeology. 2018; 43sup1: S9–S18.\n\nZerbini A, Sheldrick N: A Heritage Inventory for Documenting Endangered Archaeology in the Middle East and North Africa. ISPRS Annals of the Photogrammetry, Remote Sensing and Spatial Information Sciences. 2017; IV-2(W2): 237–241.\n\nZubrow EBW: Digital Archaeology - A Historical Context. Digital Archaeology - Bridging Method and Theory. Daly P, Evans TL, editors.New York:Routledge;2006; 10–31.\n\n\nFootnotes\n\n1 The FAIR principles state that data should be Findable, Accessible, Interoperable, and Reusable (Wilkinson et al. 2016; Letellier et al. 2007; Quintero et al. 2020).\n\n2 The CARE principles state that data should prioritise Collective benefit, Authority to control, Responsibility, and Ethics.\n\n3 A Resource Description Framework (RDF) is a semantic protocol that structures variables (fields) into “triple-stores” always featuring two nodes (variables) and an edge (relationship property) between them.\n\n4 CIDOC-CRM is the Comité International pour la Documentation de l'ICOM Conceptual Reference Model\n\n."
}
|
[
{
"id": "177077",
"date": "23 Jun 2023",
"name": "Georgia Andreou",
"expertise": [
"Reviewer Expertise Cultural heritage",
"heritage big data",
"Mediterranean Archaeology",
"Near Eastern 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 paper presents the results of a cultural heritage documentation project in Mongolia. The results are the collaborative effort of the MASS project and the Mongolian Institute of Archaeology to document sites directly and indirectly impacted by an upcoming dam construction. The authors focus on interdisciplinary and multiscalar data collection methodologies, highlight the conceptual model of the used database, and demonstrate the importance of data quality control. Overall it is a well-written paper that employs a thoughtful, robust and technically sound methodology to document archaeological sites. The clear presentation of their ground- and drone-verification methods are to be commented.\n\nThe work builds on appropriately cited extensive research on big geospatial datasets. The method and analyses are presented in sufficient detail, allowing for their replication.\nThough the paper provides a link for the source data (https://mapss.server.shh.mpg.de/), which are mentioned to be available to the public as of 01/12/2022, that link is not functioning. This review was thus unable to assess the quality of the source data.\nSeveral aspects of the paper require either clarification or further detail. Specifically:\nA brief description of the terms \"ethnographic\" and \"ethnoarchaeological\" sites. Are they distinguished from other archaeological sites due to their chronology?\n\nThe concept of symmetrical archaeology is mentioned briefly in the introduction, while further detail is provided in the discussion section. It would appear more useful if further detail on the meaning and deductive capacity of symmetrical archaeology was introduced earlier in the text.\n\nExplanation of \"attentive digital archaeology program\".\n\nFigure 2 presents deterioration as a major factor impacting cultural heritage in Mongolia. Assuming that there are no archaeological sites not experiencing deterioration, it would be useful (perhaps in the caption) to clarify if deterioration is particularly rapid or acute in Mongolia.\n\nProvide further detail for a clearer distinction between proactive and responsive action.\n\nThe paper mentions that the authors received constructive feedback from the Mongolian Institute of Archaeology. It would be interesting to see what that feedback was about, as it is coming from the perspective of those working on the ground.\n\nThe workflow figures are detailed and very useful. They would be easier to digest if they were more simplified (e.g. figure 3), perhaps with the removal of specific file names in the diagrams.\n\nThe paper identifies possible risks to heritage related to potential population increase and associated infrastructure. Considering the very low population density in Mongolia, is there evidence that the area under examination will experience population pressures in the foreseeable future?\n\nProvide further detail for a clearer distinction between transmethodology and interdisciplinary methodology.\nAll these are minor issues and providing further detail/clarification would improve the already high quality 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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "177079",
"date": "04 Jul 2023",
"name": "Cinzia Bettineschi",
"expertise": [
"Reviewer Expertise Archaeological Remote Sensing"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper titled \"Multidisciplinary digital methodologies for documentation and preservation of immovable Archaeological heritage in the Khovd River Valley, Western Mongolia\" presents a relevant contribution to the disciplines of archaeology, RS, and heritage science. The authors have successfully documented and evaluated the (ethno)archaeological remains in different impact zones associated with the construction of the Erdeneburen Hydroelectric Dam in western Mongolia. Their work showcases how invaluable is the integration of various methodological approaches and emphasizes the urgent need for a 'responsive' mode of heritage disaster intervention.\nOne of the strengths of this paper lies in its comprehensive methodology. By employing GIS, Machine Learning automated site detection, drone mapping, and Structure-from-Motion, the authors have compiled a rich dataset that provides crucial insights into the threatened archaeological heritage of Mongolia.\nThe results presented in the paper are both informative and thought-provoking. It is commendable that approximately 20% of the documented sites fall within the planned flood zone, highlighting the immediate threats posed by the construction of the dam. Equally important is the acknowledgment of collateral threats, such as industrial and infrastructural development, which necessitate extended monitoring. This recognition underscores the authors' commitment to preserving not only the sites directly affected but also the broader archaeological landscape.\nI have particularly appreciated the relevance given to fieldwork as an irreplaceable mean for data acquisition, and the efforts in balancing remote (and sometimes automated) methods for fast landscape screenings with detailed ground surveys on well-selected areas.\nThe theoretical framework adopted by the authors, the high ethical standards of the cooperation, and the specific attention to metadata and paradata, add depth to their work. By intertwining these principles, the authors establish a solid foundation for this methodology, emphasizing the collective benefit and responsibility of mapping, monitoring, managing and preserving cultural heritage. This inclusive approach ensures that multiple perspectives are considered, thus enhancing the overall effectiveness of heritage preservation efforts.\nThe literature is abundant and well-selected. It reflects a comprehensive understanding of the subject matter, incorporating a wide range of scholarly sources from various disciplines relevant to the study.\nWhile the paper presents a comprehensive analysis, there are areas that could benefit from further improvement and clarification. Specifically, more information is needed regarding the implementation of the case study itself and certain points require clarification.\nFirstly, in the abstract, the authors mention “SfM Lidar scanning”. However, it is important to note that SfM (Structure-from-Motion) and Lidar (Light Detection and Ranging) are two distinct methods with different interpretative potential, especially in forested areas, and they require different processing strategies, even if they both produce point clouds. The authors should provide clarification on whether they used SfM, Lidar, or both in different contexts.\nAdditionally, while the paper delves into the details of the software and algorithms used for their neural network (NN), it would be valuable to have more practical information related to the case study. Specifically, the paper mentions classes of mounds and winter-camps, but it appears that there may be additional features that could be discussed. Furthermore, details about the quality and quantity of training data used for each class, their homogeneity, and the validation strategy should be provided. It is crucial to explain how the confidence rate for the results was calculated. Moreover, the potential and limitations of the method, as well as its accuracy compared to traditional survey methods like MRS (Manual Remote Sensing) and pedestrian surveys, should be clearly described. This is because remote archaeological objects suffer from issues of equifinality and multifinality (see Magnini and Bettineschi, 20191) which can create important bias in the results of the automated predictions, if not carefully taken into account.\nRegarding UAV surveys, it would be beneficial to clarify whether RTK (Real-Time Kinematic), PPK (Post-Processed Kinematic), or GCPs (Ground Control Points) were utilized and to provide information about the accuracy of the measurements.\nMoving on to some minor points:\nFigure 1: It would be helpful to add a scale bar to the figure on the left side to provide a clearer understanding of the sub-area's extent. Figure 6 (left): The grid in the figure does not indicate the location of the area, and it should be addressed. Figure 7: It would be advantageous to include an orthophoto or plan of the area to provide scale and context. Figure 8: Please add a scale and north arrow to aid in interpretation. Figure 9: Please include a north arrow for reference.\nLastly, it is stated that the data should already be available to the public as of 01.12.2022, but the provided website (https://mapss.server.shh.mpg.de/) is currently inaccessible. Please correct.\nIn conclusion, while the paper offers a comprehensive analysis, addressing the points mentioned above and ensuring clarity in the practical details of the case study would enhance the overall quality and impact of the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "174172",
"date": "10 Sep 2024",
"name": "Fanar Mansour Abed",
"expertise": [
"Reviewer Expertise Geospatial Engineering",
"CV Photogrammetry",
"Lidar"
],
"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 presents an approach to integrate noninvasive techniques using MRS methodologies with the field invasive discoveries to improve CH preservation in Mongolia. It also demonstrates the potential of the CV and DL algorithms to speed the digital process based on multiple training DL Modules.\nThe article is well written and presented. The literature included are up to date, however it should include more studies regarding the discussion of DL module effectiveness in CH. The technical contents are valued and the methodology presented is well illustrated but further suggestions for future improvements are required including results outcomes and analysis. However, some details are missing regarding the integration of the recorded data from Apple Lidar and what outcomes has delivered from integrating range-based data with image-based data.\nFuture insights:\nPrevious studies have claimed that standalone data are vital for prospecting archaeological features. However, combining multi-datasets derived from different RS sources is more effective in digital archaeology to reveal uncovered remains. For example, digital hybrid raster images can be extracted from the RS data combination approaches in order explore buried archaeology and not only confirm detected features through the RS standalone raster products, see (https://www.mdpi.com/2072-4292/15/4/1057). These rasters can derive from SfM photogrammetry, LiDAR data, multispectral images, etc. those have different specifications (e.g., different cameras, sensors, spatial resolutions, and GSD).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1250
|
https://f1000research.com/articles/11-1249/v1
|
03 Nov 22
|
{
"type": "Research Article",
"title": "Machine learning model to predict endophytic colonisation of rice cultivar plant tissues by Beauveria bassiana isolates and their potential as bio-control agents against rice stem borer using existing knowledge",
"authors": [
"Mireille Merlise Megnidio-Tchoukouegno",
"Evariste Bosco Gueguim Kana",
"Wonroo B.A. Bancole"
],
"abstract": "Background: Finding well-known Beauveria bassiana isolates that could preserve rice crops from Sesamia calamistis (stem borer) is problematic. Another difficult task is the development of precise inoculation methods, which have been employed for their establishment as endophytes in cereal crops. This study proposed machine learning models to predict the best entomopathogenic fungi, Beauveria bassiana that could directly protect rice crops against Sesamia calamistis. Methods: Data driven machine learning decisions were implemented and assessed from 60 experimental runs with nine different feature/input variables and three target/output variables following foliar spray and seed treatment inoculation method. The feature variables consisted of rice plant tissue, such as Nerica-L19, Nerica1, Nerica8, the time, and the five promising isolates Beauveria bassiana (Bb3, Bb4, Bb10, Bb21, Bb35). The target variable consisted of the number of colonised roots, stems and leaves, expressed as a percentage depending on the degree of protection after each inoculation. A data driven decision by the extreme gradient boosting regression algorithm was used to proficiently abstract the situation where there is no direct relationship between features and target variables. Results: The foliar spray inoculation method exhibited high coefficient of determination (R2) of 0.99, 0.98 and 0.94 depending on the number of colonised stems, roots and leaves, respectively, while the seed treatment approach exhibited the coefficient of determination (R2) of 0.91, 0.87 and 0.75, respectively. Conclusions: These results demonstrated that the Extreme Gradient Boosting algorithm effectively abstracted the nonlinear relationship between the attribute variables that were taken into consideration and predicted Beauveria bassiana as a bio-pesticide for rice and perhaps other cereal stem borers. Thus, this XGBoost regression model could be used to navigate the optimization domain and reduce the development time of the biocontrol process.",
"keywords": [
"Endophytic Colonisation",
"Beauveria bassiana",
"Sesamia calamistis",
"Entomopathogenic Fungi",
"Machine Learning",
"XGBoost",
"Bio-pesticide"
],
"content": "1. Introduction\n\nThe agricultural industries continued success is problematic to our future due to global climate changes. However, enhanced pest attacks on crops have decreased productivity in agriculture, which is severely affected by global climate changes. Numerous cereal crops, particularly rice, are crucial for human nourishment and are farmed all over the world especially in West Africa where it has become the primary source of employment and subsistence for destitute households (Bancole et al., 2020; Nguyen and Ferrero, 2006). Its consumption in Africa has significantly increased, making it the continent’s second-largest source of carbohydrates. However, about 140 insect pests attack rice, maize, wheat, sorghum, particularly Lepidopteran stem borers are the most commercially significant insect pests that influence its production, and their management depends on the use of pesticide chemicals that have harmful consequences on people and biodiversity. Other issues brought on by the use of chemical pesticides include environmental issues, residues in food, water and soil, the possibility of harmful effects on humans and non target creatures, as well as their prohibitive cost for small scale farmers (Goulson, 2013; Togola et al., 2018). The use of chemical pesticides has been a major component of the pest management measures against this borer pest. However, because of their elusive feeding habits, negative impacts on the environment, and danger to human health, borer pests are very difficult to manage with chemical insecticides. It has also been demonstrated that many stem borers such as S. calamistis have developed resistance to chemicals. Hence there is a need for the development of an alternate, safe control measure using entomopathogenic fungus like Beauveria bassiana (Balsamo) Vuillemin. Studies and research have shown that B. bassiana is endophytic in a number of crops and have established its function in defending plants against diseases and pest arthropods (Ownley et al., 2008; Ownley et al., 2010; Gurulingappa et al., 2011; Dara, 2013; Hollingsworth et al., 2020; Rai and Ingle, 2012; Silva et al., 2020; Wagner and Lewis, 2000) with many making it a potential mycopesticide (Wei et al., 2020; Zhang et al., 2012; Barra-Bucarei et al., 2020). Endophytic colonisation of entomopathogenic fungi like B. bassiana within the plant system provides more benefits than external application due to its various traits, including parasitism of a wide range of pests, different mechanisms of pathogenicity, environmental safety, endophytic colonisation, and ease of production (Azevedo et al., 2000; Vega et al., 2009; Cherry et al., 1999; Kikuchi et al., 2015). In order to manage different insects, some strains have been injected into different plant species utilising a variety of inoculation techniques, including seed treatments, soil drenches, foliar and flower sprays, and stem injections. Numerous investigations have been conducted to identify the Beauveria bassiana endophytic strains that are most effective in cereal crops. Numerous experimental research have also been conducted to determine the most effective inoculation technique and to identify a safe protection technology using endophytic entomofungal infections.\n\nThe creation of machine learning algorithms, which are a group of analytical techniques that automate the process of creating models and iteratively learn from data to gain insights without explicitly programming, has made it possible to use more effective and powerful tools to not only determine the best inoculation technique for protecting cereal crops from insects and other crop infections but also to assess the potential of various promising indigenous isolates of Beauveria bassiana.\n\nAdvancement in technology has driven many researchers to apply machine learning approaches to various agricultural sector. For example finding the crop succession and stamp behavior (Hazard et al., 2018; Johnson and Zhang, 2014), using environmental data as training data to determine the ideal future weather conditions for growing good crops (Kamilaris and Prenafeta-Boldú, 2018). Various algorithms, including swarm intelligence optimisation, artificial neural networks, k-nearest neighbour, and genetic algorithms that were also expanded with the aid of pesticides control in the field of plant pathology, have been used in other studies to evaluate crop yield time prediction and crop pest prediction (Teeda et al., 2018; Cai and Sharma, 2021). Furthermore, 26 diseases and 14 crop species have been categorised using deep convolutional neural networks (Mohanty et al., 2016).\n\nMachine learning algorithm has also been used to correctly identify 13 different plant diseases as well as identify bacteria with high prediction accuracy (Schikora et al., 2010; Sladojevic et al., 2016). However, due to the implications for precision agriculture, prediction and quantification of the best biological control agent, and the best inoculation method may be more crucial in the future than disease categorisation and identification. Such studies might result in early insect prevention for cereal crops and lower pesticide costs.\n\nThe research’s objective is to use machine learning algorithm to investigate, study and analyse the entomopathogenic fungi, Beauveria bassiana, one of the biological control agent that directly protect rice crops against S. calamistis, the most common rice arthropod in West Africa. Additionally, the inoculation technique highly affects how well rice crops are protected from pests and other crop infections. As a result, the proposed algorithm will also aid in predicting the most effective crop pest inoculation method.\n\n\n2. Methods\n\nThis section follows machine learning workflow to explore and prepare our dataset for modelling purposes. The process consists of learning about the data, cleaning it by removing outliers, converting categorical variables to numerical variables, training the model using various machine learning algorithms, and evaluating the model’s performance using existing regression metrics. This procedure has several phases, which are as follows:\n\nData collection and description\n\nThe experimental data used for this research were obtained from (Bancole et al., 2020) previous studies. The original tabulated dataset contains 63 data points for each targeted rice plant tissues. Each variable in the dataset was classified as categorical or numerical based on its nature. The selected features variables in the original dataset consisted of African rice cultivar such as NERICA-L19, NERICA1, and NERICA8, the five Beauveria bassiana such as Bb3, Bb4, Bb10, Bb21 and Bb35, and the time. The target variables were the percentage of roots, stems, and leaves sections colonised based on their degree of protection after inoculation.\n\nData preparation\n\nBefore developing each model, a pre-processing phase was carried out to enhance the model’s predictive power in order to assess the potential of five promising indigenous isolated Beauveria bassiana as endophytes in rice sections. The least significant data points (controls 1, 2, and 3) were also manually removed from the original dataset because they had no bearing on the colonisation of rice tissue following each inoculation method. Furthermore, the time was normalised in accordance to Equation 1 (Sewsynker and Kana, 2016) by translating the data into the range [0,1].\n\nwhere Emin and Emax stand for the minimum and maximum values and ei represents the normalised data. Rice plant tissues and Beauveria bassiana strain features were classified in the original dataset as categorical values. But due to the fact that machine learning did not work directly with categorical values, Sklearn library (RRID:SCR_019053) (Pedregosa et al., 2011) was used to automatically encode the features into numerical values. To map categorical values to integer values, OneHotEncoder, a method for converting categorical values to numerical values, was used. Each integer value was represented as a binary vector, with all zero values except the integer’s index marked as one (Seger, 2018). In addition, the target variable was taken as a percentage of roots, or stem, or leaves colonised depending on the inoculation method with the highest number considered as a 100% protection. Finally, a high-level interface for creating appealing and instructive statistical visualisations was provided by seaborn (Waskom, 2021), a Python data visualisation library.\n\nFeature selection\n\nThe most important characteristics influencing the rice plant tissue were identified using a process called feature selection. This was achieved by measuring the linear relationship between two or more variables. The rationale for utilising correlation to choose features is that the attributes have a strong connection with the target variable. A further requirement is that attributes should be uncorrelated among themselves while being correlated with the target variable. Due to the potential impact that strongly correlated feature variables may have on an algorithm’s performance, this procedure is crucial to machine learning.\n\nIn order to analyse the prediction of the entomopathogenic fungi, computational intelligence techniques including Linear regression (LR) (Pedregosa et al., 2011), least absolute shrinkage and selection operator (LaSSO) (RRID:SCR_003418), support vector regression (SVR), k-nearest neighbor (KNN), ensemble learning (EN), and Extreme Gradient Boosting (XGBoost) (RRID:SCR_021361) were used, with an emphasis on accuracy and efficiency as well as their ability to handle experimental data. Following a thorough analysis and application of the various machine learning prediction techniques, it was discovered that the scalable, adaptable, precise, and reasonably quick XGBoost regression approach offered a more regularised model formalisation and improved over-fitting management.\n\nXGBoost regression is a type of ensemble machine learning algorithm that can be used to solve problems involving classification and regression predictive modelling. In this algorithm, Decision tree models are used to build ensembles and trees are added to the ensemble one at a time and fitted to fix the prediction errors caused by prior models.\n\nSuppose we have K trees as explicitly described in Wang et al. (2019), mathematical prediction output of XGBoost can be written as\n\nIn this situation, it minimises the following objective:\n\nSecond-order Taylor approximation can be utilised in the general scenario as follows to optimise the objective:\n\nThe goal of creating a predictive model is to create a model that is accurate on previously unseen data. This can be accomplished using statistical techniques in which the training dataset is carefully used to estimate the model’s performance on new and unknown data. The most basic technique of model validation is to perform a train/test split on the dataset. A typical ratio for this varies depending on the amount of data, but it is critical to have enough training data. After training the model with the hyper-parameters provided by the algorithms, predictions on test data must be made and compared to the expected results.\n\nIn the current study, the datasets were split into training sets, which comprised 80% of the datasets, and testing sets, which comprised 20% of the datasets. The hyper-parameters were supplied as arguments while creating an instance of an XGBoost regressor from the XGBoost library. This stage is crucial for controlling how effectively the machine learning techniques are being used. The training section of the datasets was used to train the adopted algorithms with tuning parameters, and the testing portion of the datasets was used to demonstrate the developed model’s response to new data being processed for the first time.\n\nRandom-state was also assigned to maintain reproducibility of the results. Root mean squared error and the coefficient of determination R2 were computed on validation data and used to assess the accuracy of the model. Parameters tuning was conducted to avoid over-fitting and under-fitting. This was achieved by varying some XGBoost parameters between its minimum and maximum value while all other parameters were maintained at their default values.\n\nOur main focus were on the four main parameters such as number of estimators, learning rate, colsample-bytree, max-depth, and the regularisation parameters. As for other parameters, default values set in XGBoost package were considered. When training a deep tree, XGBoost rapidly consumes memory, thus we should be cautious when choosing big values of max-depth (Tianqi, 2016). In order to achieve this, suitable hyper-parameter values can be determined through systematic testing, such as grid searching across a range of values, or by trial and error for a given dataset. It is important to emphasise that cross-validation was used to choose the optimum parameters and decrease the weight of each step in order to strengthen the model.\n\n\n3. Results\n\nIt is critical to identify the most influential features via correlation in order to speed up the prediction process and avoid potential over-fitting by reducing the number of attributes considered. This was accomplished by examining the data to determine how features variables affect the colonisation of roots, stems, and leaves following the two inoculation methods. Furthermore, a model performance evaluation was presented, in which the accuracy of the prediction results was verified and the competency of the four algorithms was compared for different k-fold cross-validations.\n\nFor correlation analysis with regard to feature engineering results, the most predominate attributes are taken into account. Correlation values closer to 1 signify a strong and direct correlation between the two features since attributes can be thought of as the Pearson Coefficient. A high yet inverse correlation, however, is indicated by correlation values that are closer to -1. For instance, the seaborn library was used to plot the correlation plot between variables.\n\nFigure 1 (Kana et al., 2022) presents a one to one relationship between variable. Every variable shows a relationship with another variable regardless of the inoculation method. We can see a strong positive correlation between number of colonised stem sections and the passage of time (30-60 days). This shows that the degree of stems protection increases with an increase number of days following foliar spray treatment. Also, Beauveria bassiana isolates Bb10 and Bb3 have a 0.26 and 0.19 correlation values with the number of stem section colonised value, respectively, indicating that Bb10 and Bb3 are the most effective strain regarding the rice stem tissue. Nerica1 has a 0.2 correlation value with the rice stems specie, indicating that the level of colonisation of the rice stems favor the rice cultivar, Nerica1. On the other hand, Nerica8 and the rice stems tissue have a -0.26 correlation value, indicating that the colonisation of rice stem specie do not favour the rice cultivar, Nerica8. There is also a moderate negative correlation between number of stems section colonised, Bb21 and Bb35, indicating similar levels of pathogenicity of the Beauveria bassiana isolates.\n\nThe colour represents the correlation coefficient’s value. The intensity of the colour is proportional to the correlation coefficient, with both positive and negative correlations displayed. Reduced colour intensity denotes lower correlations.\n\nAfter foliar spray treatment, a weak but favourable connection between the level of roots colonised over time was observed between Nerica1, Bb10 and Bb4 as presented in Figure 2. This shows that the level of colonisation of the roots increases with an increase number of days, and the Beauveria bassiana isolates Bb10 and Bb4 are the most effective strain killing most of S. calamistis larvae. Furthermore, we noticed a weak negative correlation in the level of colonisation of the roots between Nerica8, Beauveria bassiana isolates Bb21 and Bb3.\n\nThe colour represents the correlation coefficient’s value. The intensity of the colour is proportional to the correlation coefficient, with both positive and negative correlations displayed. Reduced colour intensity denotes lower correlations.\n\nPositive weak correlation was also observed in the level of colonisation of the leaves between Nerica-L19, Nerica1, Bb3, Bb4 and Bb10 as shown in Figure 3, indicating that Bb3 and Bb10 were the most effective strain in the colonisation of leaves. Additionally, Nerica-L19 and Nerica1 had a 0.2 and 0.15 correlation value, respectively, with the rice leaves species, indicating that the level of colonisation of the rice leaves favoured the two rice cultivar species as reported in Figure 3. There is also a moderate negative correlation in the level of colonisation of leaves between Nerica8, Bb21, and Bb35.\n\nThe colour represents the correlation coefficient’s value. The intensity of the colour is proportional to the correlation coefficient, with both positive and negative correlations displayed. Reduced colour intensity denotes lower correlations.\n\nThese correlations are useful for understanding the data in depth because they show how one variable affects the other.\n\nFollowing seed treatment, a favourable connection between Beauveria bassiana isolates and a particular rice cultivar was seen in the colonisation of stems. Figure 4 presents a moderate positive correlation of the colonisation of stem between Nerica1. This shows that the level of colonisation of the rice stem favoured the rice cultivar species. Moreover, Beauveria bassiana isolates Bb10 seemed to be the most effective strain in the colonisation of stem with the correlation value of 0.13. It can be seen that Nerica8, Bb3 and Bb4 represent the other three factors influencing the stem rice plant tissue. Strong negative correlation occurred in the level of colonisation of stem between NericaL-19, indicating that the level of colonisation of the rice stem do not favour the rice cultivar species. In addition, time (in days), Bb21 and Bb35 affect the stem rice plant tissue with a weak negative correlation.\n\nThe colour represents the correlation coefficient’s value. The intensity of the colour is proportional to the correlation coefficient, with both positive and negative correlations displayed. Reduced colour intensity denotes lower correlations.\n\nAs displayed in Figure 5, a weak positive correlation was also observed in the colonisation of roots between Beauveria bassiana isolates and rice cultivar. Furthermore, a moderate positive correlation in the colonisation of roots between Nerica1 was observed. This shows that the level of colonisation of the rice roots favoured the rice cultivar species. Additionally, Beauveria bassiana isolates Bb10 seemed to be the most effective strain in the colonisation of roots with the correlation value of 0.18. There was also a negative correlation between the number of root sections colonised, Nerica-L19, Bb21 and Bb35 with the Nerica-L19 being the rice cultivar that does not favour the colonisation of roots.\n\nThe colour represents the correlation coefficient’s value. The intensity of the colour is proportional to the correlation coefficient, with both positive and negative correlations displayed. Reduced colour intensity denotes lower correlations.\n\nFigure 6 shows a weak positive correlation in the colonisation of leaves between Nerica1, Nerica8 and Beauveria bassiana isolates Bb10. This demonstrates that the level of colonisation of the rice leaves favour the two rice cultivar species. On the other hand, there was a moderate negative correlation in the level of colonisation of leaves between NericaL-19, indicating that the level of colonisation of rice leaves do not favour the rice cultivar species. Time (in days), Bb3, Bb4, Bb21 and Bb35 were the other factor influencing the stem rice plant tissue with a weak negative correlation.\n\nThe colour represents the correlation coefficient’s value. The intensity of the colour is proportional to the correlation coefficient, with both positive and negative correlations displayed. Reduced colour intensity denotes lower correlations.\n\nModel’s evaluation\n\nThe experimental data that were gathered were divided into a training set and a testing set. The training set was used to generate the final strong learner, while the testing set was used to demonstrate the model’s accuracy in predicting the best biological control agent that directly protects rice crops from stem borer. For the model’s training, 80% of the datasets were randomly chosen, while the remaining 20% were utilised to gauge the model’s effectiveness. A range of assessment metrics, including root mean squared error (RMSE) and coefficient of determination (R2) were calculated according to Equation 7 and Equation 8.\n\nwhere SSE is the sum of residuals, which equal to ∑i=1nyi−yî2, and SST the total sum of square, which equal to ∑i=1nyi−yi¯2. During the training process, the RMSE between the predicted and the observed data reduced to 12.24 and 4.58 following seed treatment and foliar spray method for the colonisation of roots, and to 10.97 and 0.28 following seed treatment and foliar spray method for the colonisation of stems, also to 19.68 and 7.96 following seed treatment and foliar spray method for the colonisation of leaves. The XGBoost model accurately predicted the residual value of the colonisation of roots, stems and leaves, with the highest accuracy of 0.87, 0.91 and 0.75, respectively, following seed treatment method and 0.98, 0.99, and 0.94, respectively, following foliar spray method. This study shows that the foliar spray treatment method has excellent prediction accuracy on the colonisation of roots, stems and leaves.\n\nA trend or correlation between the predicted variables and the observed variables is depicted visually using the line of best fit. Figure 7 depicts a plot of predicted versus observed values of colonisation of rice plant tissues following foliar spray (left) and seed treatment (right) methods. The coefficient of determination R2 for both methods was also shown in the figures. The left panel of Figure 7 revealed that the large majority of the data points of colonisation of roots plant rice following foliar spray are congregated along the predictive trend with R2 = 0.93, thus demonstrating the closeness between the predicted and observed values. On the other hand, the right panel of Figure 7 following seed treatment method showed that the data points are dispersed on either side of the prediction trend with R2 = 0.81, thereby demonstrating a fragile relationship between the predicted and the observed values.\n\nThe best-fit regression line depicts expectations under a one-to-one relationship between predicted and observed values.\n\nThe left and right panel of Figure 8 presents the relationship between the predicted and the observed values of colonisation of stem plant rice following foliar spray and seed treatment method, respectively. The coefficient of determination R2 are also displayed on the two plots. Results from the left and right panel of Figure 8 revealed that the large majority of the data points of colonisation of stem plant rice following both methods are congregated along the predictive trend with R2 = 0.95 and R2 = 0.93, respectively, thereby demonstrating how closely the predicted and observed values match up.\n\nThe best-fit regression line depicts expectations under a one-to-one relationship between predicted and observed values.\n\nThe graph in Figure 9 compares predicted and observed values for the colonisation of rice plant tissues after foliar spraying (left) and seed treatment (right). The figures also included the R2 coefficients for both approaches. The left panel of Figure 9 revealed that the large majority of the data points of colonisation of leaves plant rice following foliar spray are congregated along the predictive trend with R2 = 0.88, thus highlighting the similarity between the predicted and observed values. Furthermore, the right panel of Figure 9 following the seed treatment method revealed that the data points are dispersed on the predictive trend with R2 = 0.75, thereby indicating a weak relationship between the predicted and the observed values.\n\nThe best-fit regression line represents expectations under a one-to-one connection between predicted and observed values.\n\nThe left and right plot displayed in Figure 10 compared the distribution plot of the observed values (orange curve) and the predicted values (blue curve) of colonisation of roots plant rice following foliar spray and seed treatment method of train data. The sharp block like structures are histograms and the smoothed curves are called probability density function. It’s observed from the left panel of Figure 10 that the probability density function of both observed and predicted curves are filled for foliar spray method. Moreover, there is an overlap between the probability density function of both observed and predicted curves for the seed treatment method as shown at the right panel of Figure 10.\n\nThe left and right plots depicted in Figure 11 compared the distribution plot of the observed values (orange curve) and the predicted value (blue curve) of colonisation of stem plant rice following the foliar spray and the seed treatment method of train data. The sharp block like structures are histograms and the smoothed curves are called probability density function. It’s observed from the left panel of Figure 11 that, the probability density function of the observed and predicted curves are filled for foliar spray method. Furthermore, there is an overlap between the probability density function of the observed and predicted curves for the seed treatment method as shown on the right panel of Figure 11.\n\nThe left and the right panel of Figure 12 compared the distribution plot of the observed values (orange curve) and the predicted values (blue curve) of colonisation of leaves plant rice following foliar spray and seed treatment method of train data. The left panel of Figure 12 showed that the probability density function of observed and predicted values are filled for foliar spray method. Moreover, there is an overlap between the probability density function of the observed and predicted curves for the seed treatment method as shown on the right panel of Figure 12.\n\n\n4. Conclusions\n\nFinding the biological control agent that would directly defend rice crops and other cereal crops against the stem borer, which is common in West Africa, is made possible by the specialised, powerful, adaptable, and intelligible predictive machine learning algorithms. Researchers can tremendously benefit from coherent, accurate, and integrated prognostic models for biological control agent prediction. Farmers can also choose the best inoculation technique to apply pest control on cereal crops.\n\nModels for predicting biological control agents were created and the residual value estimates made by the support vector regression, LaSSO, and KNN regression models were noticeably inaccurate. This led to the proposal of a novel method for creating a single classification model from multi-dimensional class data.\n\nThe XGBoost is a novel ensemble-based prediction model built using decision tree models. In order to repair the prediction mistakes caused by earlier models, trees are added one at a time to the ensemble and fitted. Any arbitrary differentiable loss function and the gradient descent optimisation procedure are used to fit the models. In order to evaluate the model’s proficiency, two evaluation metrics such as RMSE and R2 were used.\n\nRegarding the coefficient of determination result, the colonisation of rice cultivar plant tissues following foliar spray method had the highest prediction accuracy of 0.99 for the stem, followed by 0.98 for the roots and 0.94 for the leaves. The seed treatment method obtain a prediction accuracy of 0.91 for the stem, followed by 0.87 for the roots and 0.75 for the leaves. A significant discrepancy was observed in the coefficient of determination of leaves following foliar spray method (0.94) and the one following seed treatment (0.75). Evaluation of these models revealed that they effectively captured the extremely non-linear relationships between the feature variables and related target variables within the given data. Foliar spray method showed the highest colonisation of predictive accuracy on various plant tissues used to investigate the bio-control proficiency.\n\nFor future research, more sophisticated methods such as deep learning algorithms will be applied in finding a better method to handle insect in cereal crops and discover the most appropriate plant tissues. Additionally, better data collection and assortment techniques can be applied, allowing acquired datasets to be archived, organised, analysed, and regenerated for results that are more accurate. Furthermore, the suggested modelling methods can be refined and further developed for greater performance and more precise prediction outcomes.\n\n\nAuthor contributions\n\nM.T selected the algorithms, collected, gathered and processed the data, and wrote the manuscript. E. K supervised the project. B. B conceptualised the experiment and provided the data used for this research. All the authors discussed and revised the manuscript.",
"appendix": "Data availability\n\nFigshare: Machine Learning Model to Predict Endophytic Colonisation of Rice Cultivar Plant Tissues by B. bassiana Isolates and their Potential as Bio-control Agents Against Rice Stem Borer using Existing Knowledge. https://doi.org/10.6084/m9.figshare.20934613 (Kana et al., 2022).\n\nThis project contains the following underlying data:\n\n• seed_inoculation.csv\n\n• foliarSpray_inoculation.csv\n\n• foliarsprayleaves.ipynb\n\n• foliarspraystem.ipynb\n\n• foliarSprayroot.ipynb\n\n• Seedleaves.ipynb\n\n• Seedroot.ipynb\n\n• Seedstem.ipynb\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 everyone who took part in the study for their hard work and contributions. We’d also like to thank the open-source Python community for providing free tools (Python Programming Language (RRID:SCR_008394)). We thank Google Colaboratory (Google CoLab (RRID:SCR_018009)), Anaconda (Conda (RRID:SCR_018317)), scikit-learn (RRID:SCR_002577), Pandas (RRID:SCR_018214), NumPy (RRID:SCR_008633), and Jupyter Notebook (RRID:SCR_018315).\n\n\nReferences\n\nAzevedo J, Maccheroni JW, Pereira JO, et al.: Endophytic microorganisms: a review on insect control and recent advances on tropical plants. Electron. J. Biotechnol. 2000; 3(1): 15–16.\n\nBancole WBA, Laing MD, Yobo KS, et al.: Establishment of Beauveria Bassiana Isolates as Endophytes in Rice Cultivars and their Biocontrol Efficacy Against Rice Stem Borer, Sesamia Calamistis. S. Afr. J. Sci. 2020; 116: 12. Publisher Full Text\n\nBarra-Bucarei L, Iglesias AF, González MG, et al.: Antifungal activity of beauveria bassiana endophyte against botrytis cinerea in two solanaceae crops. Microorganisms. 2020; 8(1): 65.\n\nCai Y, Sharma A: Swarm intelligence optimization: An exploration and application of machine learning technology. J. Intell. Syst. 2021; 30: 460–469. Publisher Full Text\n\nCherry AY, Lomer c J, Djegui D, et al.: Pathogen incidence and their potential as microbial control agents in ipm of maize stem borers in west africa. BioControl. 1999; 44: 301–327. Publisher Full Text\n\nDara SK: Entomopathogenic fungus beauveria bassiana promotes strawberry plant growth and health. UCANR eJournal Strawberries and Vegetables. 2013; 30.\n\nFriedman JH: Greedy function approximation: A gradient boosting machine. Ann. Stat. 2001; 29(5): 1189–1232.\n\nGoulson D: Review: an overview of the environmental risks posed by neonicotinoid insecticides. J. Appl. Ecol. 2013; 50(4): 977–987. Publisher Full Text\n\nGurulingappa P, McGee PA, Sword G: Endophytic lecanicillium lecanii and beauveria bassiana reduce the survival and fecundity of aphis gossypii following contact with conidia and secondary metabolites. Crop. Prot. 2011; 30(3): 349–353. Publisher Full Text\n\nHazard L, Steyaert P, Martin G, et al.: Mutual learning between researchers and farmers during implementation of scientific principles for sustainable development: the case of biodiversity-based agriculture. Sustain. Sci. 2018; 13: 517–530. Publisher Full Text\n\nHollingsworth RG, Aristizábal LF, Shriner S, et al.: Incorporating beauveria bassiana into an integrated pest management plan for coffee berry borer in hawaii. Front. Sustain. Sys. 2020; 4. Publisher Full Text\n\nJohnson R, Zhang T: Learning nonlinear functions using regularized greedy forest. IEEE Trans. Pattern Anal. Mach. Intell. 2014; 36: 942–954. Publisher Full Text\n\nKamilaris A, Prenafeta-Boldú FX: Deep learning in agriculture: A survey. Comput. Electron. Agric. 2018; 147: 70–90. Publisher Full Text\n\nKikuchi M, Haneishi Y, Tokida K, et al.: The structure of rice retail markets in sub-saharan africa. Trop. Agric. Development. 2015; 59: 127–139.\n\nMegnidio MM, Kana EBG, Bancole WBA:Machine Learning Model to Predict Endophytic Colonisation of Rice Cultivar Plant Tissues by Beauveria Bassiana Isolates and their Potential as Bio-control Agents Against Rice Stem Borer using Existing Knowledge. figshare. [Dataset].2022. Publisher Full Text\n\nMohanty SP, Hughes DP, Salathé M: Using deep learning for image-based plant disease detection. Front. Plant Sci. 2016; 7. Publisher Full Text\n\nNguyen NV, Ferrero A: Meeting the challenges of global rice production. Paddy Water Environ. 2006; 4: 1–9. Publisher Full Text\n\nOwnley BH, Grifn MR, Klingeman WE, et al.: Beauveria bassiana: endophytic colonization and plant disease control. J. Invertebr. Pathol. 2008; 98: 267–270. PubMed Abstract | Publisher Full Text\n\nOwnley BH, Gwinn KD, Vega FE: Endophytic fungal entomopathogens with activity against plant pathogens: ecology and evolution. BioControl. 2010; 55: 113–128. Publisher Full Text\n\nPedregosa F, Varoquaux G, Gramfort A, et al.: Scikit-learn: Machine learning in python. J. Mach. Learn. Res. 2011; 12(Oct): 2825–2830.\n\nRai M, Ingle A: Role of nanotechnology in agriculture with special reference to management of insect pests. Appl. Microbiol. Biotechnol. 2012; 94: 287–293. Publisher Full Text\n\nRaskutti G, Wainwright MJ, Yu B: Early stopping for non-parametric regression: An optimal data-dependent stopping rule.2011 49th Annual Allerton Conference on Communication, Control, and Computing (Allerton).2011; pp. 1318–1325. Publisher Full Text\n\nSchikora M, Schikora A, Kogel KH, et al.:Probabilistic classification of disease symptoms caused by salmonella on arabidopsis plants.Fähnrich K-P, Franczyk B, editors. INFORMATIK 2010. Service Science – Neue Perspektiven für die Informatik. Band. Bonn:Gesellschaft für Informatik e.V;2010; 2. : pages 874–879.\n\nSeger C: An investigation of categorical variable encoding techniques in machine learning: binary versus one-hot and feature hashing. Student thesis, School of Electrical Engineering and Computer Science.2018.\n\nSewsynker Y, Kana EBG: Intelligent models to predict hydrogen yield in dark microbial fermentations using existing knowledge. Int. J. Hydrog. Energy. 2016; 41: 12929–12940. Publisher Full Text\n\nSilva A, Silva GA, Abib P, et al.: Endophytic colonization of tomato plants by the entomopathogenic fungus beauveria bassiana for controlling the south american tomato pinworm, tuta absolu. CABI Agric. Biosci. 2020; 1(3): 1–9.\n\nSladojevic S, Arsenovic M, Anderla A, et al.: Deep neural networks based recognition of plant diseases by leaf image classification. Comput. Intell. Neurosci. 2016; 6: 1–11.\n\nTeeda K, Vallabhaneni N, Sridevi T: Comparative analysis of data mining models for crop yield by using rainfall and soil attributes. 2018 Second International Conference on Inventive Communication and Computational Technologies (ICICCT). 2018; pages 1176–1180.\n\nTogola A, Meseka S, Menkir A, et al.: Measurement of pesticide residues from chemical control of the invasive spodoptera frugiperda (lepidoptera: Noctuidae) in a maize experimental feld in mokwa, nigeria. Int. J. Environ. Res. Public Health. 2018; 15(5): 849. PubMed Abstract | Publisher Full Text\n\nTianqi C:KDD 16: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining.Association for Computing Machinery, New York, NY, USA, San Francisco, California, USA.2016.\n\nVega FE, Goettel MS, Blackwell M, et al.: Fungal entomopathogens: new insights on their ecology. Fungal Ecol. 2009; 2: 149–159. Publisher Full Text\n\nWagner BL, Lewis LC: Colonization of corn, zea mays, by the entomopathogenic fungus beauveria bassiana. Appl. Environ. Microbiol. 2000; 66: 3468–3473. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang Y, Pan Z, Zheng J, et al.: A hybrid ensemble method for pulsar candidate classification. Astrophys. Space Sci. 2019; 364. Publisher Full Text\n\nWaskom ML: seaborn: statistical data visualization. J. Open Source Softw. 2021; 6(60): 3021. Publisher Full Text\n\nWei Q, Li Y, Xu C, et al.: Endophytic colonization by beauveria bassiana increases the resistance of tomatoes against bemisia tabaci. Arthropod Plant Interact. 2020; 14(3): 289–300. Publisher Full Text\n\nZhang S, Widemann E, Bernard G, et al.: Cyp52x1 representing new cytochrome p450 subfamily displays fatty acid hydroxylase activity and contributes to virulence and growth on insect cuticular substrates in entomopathogenic fungus beauveria bassian. J. Biol. Chem. 2012; 287: 1347–1348."
}
|
[
{
"id": "211682",
"date": "16 Oct 2023",
"name": "Luis Carlos Ramos Aguila",
"expertise": [
"Reviewer Expertise entomopathogens",
"endophytes"
],
"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 described here is worthy, however I included some minor comments:\nThe section of Introduction is lacking reference, add the beneficial options that Beauveria bassina offer once stabilized as endophyte. Such as boots gene expression and promote plant growth, induce gene expression in pest that feed on endophytically colonize plants (cite following papers1,2).\n\nInclude statistical analysis section in the methodology.\n\nBriefly describe the method use to keep B. bassiana, which media were used?\n\nWhat’s the concentration used for foliar spray inoculation? And for seed treatment inoculation method ? This info has to be clearly explained in the methodology .\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "225543",
"date": "30 Nov 2023",
"name": "Yordanys Ramos",
"expertise": [
"Reviewer Expertise Biological Control",
"Insect Pathology",
"Microbiology",
"Entomology",
"Integrated Pest 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\nThe results of the study are very valuable and interesting. The model under study allows predicting the best inoculation method and the best Beauveria bassiana candidate to establish itself as an endophyte in rice plants.\nHowever, in the introduction, there are many statements that are not supported by any bibliographic citation. In other cases, there are too many citations. It is necessary for the authors to seek a balance in this aspect.\nThe classification of Beauveria bassiana should be amended to Beauveria bassiana (Balsamo-Crivelli) Vuillemin.\nThe full name of the entomopathogenic fungus should be written, but later abbreviated as B. bassiana when mentioned throughout the article.\nThe methods should include a section explaining details of the fungal isolates, such as:\nWhere were the isolates of Beauveria bassiana obtained? and where were these five isolates taken?\n\nWhat was the concentration at which the isolates were applied, and how was this calculated?\n\nWhat volume per plant and seed of the fungal formulation was applied?\n\nHow were the fungi formulated?\n\nUnder what climatic conditions were the plants maintained for endophytic establishment (temperature, relative humidity, photoperiod)?\n\nAt what growth stage of the plant were the B. bassiana isolates sprayed?\n\nHow many days after inoculation were the evaluations performed?\n\nHow was the endophytic establishment of different plant tissues (root, stem, and leaf) confirmed?\n\nAdditionally, the methods should include the statistical analyses that were conducted.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1249
|
https://f1000research.com/articles/11-205/v1
|
17 Feb 22
|
{
"type": "Research Article",
"title": "Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020 and molecular characterization of the spike protein, in Gabon",
"authors": [
"Sonia Etenna LEKANA-DOUKI",
"Nadine N'DILIMABAKA",
"Elvire MBONGO-KAMA",
"Marisca KANDET YATTARA",
"Armel MINTSA NDONG",
"Audrey Michel NGONGA DIKONGO",
"Julia Cyrielle ANDEKO",
"Ornella ZONG MINKO",
"Danielle Styvie KOUMBA MAVOUNGOU",
"Abdoulaye DIANE",
"Arsene MABIKA MABIKA",
"Telstar NDONG MEBALEY",
"Nal Kennedy NDJANGANGOYE",
"Octavie BANGA MVE-ELLA",
"Linda BOHOU KOMBILA",
"Joa Braithe MANGOMBI PAMBOU",
"Jeordy Dimitri ENGONE ONDO",
"Gael Darren MAGANGA",
"Jean-Bernard LEKANA-DOUKI",
"Nadine N'DILIMABAKA",
"Elvire MBONGO-KAMA",
"Marisca KANDET YATTARA",
"Armel MINTSA NDONG",
"Audrey Michel NGONGA DIKONGO",
"Julia Cyrielle ANDEKO",
"Ornella ZONG MINKO",
"Danielle Styvie KOUMBA MAVOUNGOU",
"Abdoulaye DIANE",
"Arsene MABIKA MABIKA",
"Telstar NDONG MEBALEY",
"Nal Kennedy NDJANGANGOYE",
"Octavie BANGA MVE-ELLA",
"Linda BOHOU KOMBILA",
"Joa Braithe MANGOMBI PAMBOU",
"Jeordy Dimitri ENGONE ONDO",
"Gael Darren MAGANGA",
"Jean-Bernard LEKANA-DOUKI"
],
"abstract": "Background After the first cases of coronaviruses disease 2019 (COVID-19) in China in January 2020, we conducted an epidemiological surveillance of COVID-19 in Gabon. Methods We led molecular investigations on nasopharyngeal and oropharyngeal samples from the 1161 first suspected cases of COVID-19. We diagnosed the first case of COVID-19 on March, 12 2020. Results Among those suspected cases, 83 were confirmed cases. There was no significant difference in prevalence of SARS-CoV-2 between age groups (p=0.14). 73% were asymptomatic. The viral loads were significantly higher in the nasopharyngeal samples than in the oropharyngeal samples (p=0.03). There was no significant difference in viral loads between age groups (p=0.9895) and no correlation between clinical symptoms and viral loads (p=0.06042). A phylogenetic analysis performed with five sequences of the spike S gene showed that two sequences had the D614G mutation. Conclusion In conclusion, this study provides the first molecular data from Gabon concerning the COVID-19 pandemic. The data showed that most of the infected people were asymptomatic. The viral load was higher in the nasopharyngeal samples. The S gene analyzed suggested both introduction of the D614 and G614 variant in Gabon.",
"keywords": [
"COVID-19",
"Diagnostic",
"Epidemiology",
"Viral load",
"S gene",
"Gabon"
],
"content": "Introduction\n\nIn December 2019, an atypical pneumonia emerged in China. A total of 44 case-patients were reported from December 31, 2019, to January 4, 2020, with an unknown etiology (https://apps.who.int/iris/handle/10665/330760). In January 2020, a 2019 novel coronavirus was identified, and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 caused an outbreak in China and rapidly spread in the whole world.1 From January 20, 2020, the first cases were reported in North America.2 In Europe on January 24, 2020, the first cases were reported by the World Health Organization (WHO).3 On March 11, the WHO declared COVID-19 a pandemic disease4 and reported 118,319 confirmed cases and 4292 deaths (https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200311-sitrep-51-covid-19.pdf). In Central Africa, Gabon reported its first case of COVID-19 on March 12, 2020. On December 15, 2020, nearly a year after its discovery, this disease continues to rise in the world with 70 million cumulative cases and 1.6 million deaths globally since the beginning of the pandemic (https://www.who.int/publications/m/item/weekly-epidemiological-update---15-december-2020).\n\nThe literature reports that COVID-19 has an incubation period of 1–14 days and it affects both children and adults. Symptoms present in children are similar to those found in adults with an incubation period of 1–14 days; however, over 90% of affected children are asymptomatic or have no severe form of the disease.4 The SARS-CoV-2 virus is detected in several clinical samples, such as nasopharyngeal samples, oropharyngeal samples, sputum, saliva, serum, urine and stool.5,6 The viral load can vary between the different clinical samples, throughout the infection after the onset of the first symptoms or could depend on the severity of the disease.5,6 The study of the infectivity of SARS-CoV-2 includes the analysis of viral loads, the host’s immune response but also the genomic analysis of the strains circulating in order to provide a response to the pandemic and develop a vaccine candidate.7–9\n\n15 first mutations have been identified in the genome, particularly in the main sequence, in the genes encoding non-structural protein, the polymerase, the spike glycoprotein (S), the membrane glycoprotein, and the nucleocapsid phosphoprotein.10 The mutation D614G in the gene coding S protein could be associated with a more virulent variant leading to a higher mortality rate (http://dx.doi.org/10.1038/s10038-020-0808-9). More recently, several mutations were identified in the spike region gene in a new variant of SARS-CoV-2 in the United Kingdom and South Africa (https://www.who.int/csr/don/21-december-2020-sars-cov2-variant-united-kingdom/en/).\n\nThe first cases of COVID-19 have been widely documented in many countries. However few data are available from sub-Saharan Africa, and more particularly from Central Africa. The aim of this study is to report epidemiological and molecular data on the SARS-CoV-2 virus. Phylogenetic analysis of the S gene will identify the mutations in this genomic region and therefore the strains circulating in Gabon.\n\n\nMethods\n\nWhen the worldwide coronavirus pandemic began in January 2020, the “Centre Interdisciplinaire de Recherches Médicales de Franceville” (CIRMF) set up a surveillance of COVID-19 in Gabon, according to the guidelines of the Gabonese Ministry of Health, the WHO Region Office for Africa and the Africa Center for Disease Control (Africa CDC). Patients who were enrolled in this study visited health centers for respiratory syndrome comprising fever (≥38°C) and runny nose, or fever and cough, or fever and sore throat. Epidemiological data, including the name, age, sex, and travel history during the month before onset and clinical data were collected. Other people were asymptomatic but had been in contact with people who tested positive for COVID-19. So, from February 2020, nasopharyngeal and oropharyngeal samples were collected from suspected cases in hospitals: the “Hôpital d’instruction des Armées Omar Bongo Onbimba” (HIAOBO), the “Hôpital d’instruction des Armées d’Akanda” (HIA A) in Libreville, mobile health centers which collected samples, and health centers in the Haut-Ogooue province. From February 15 to April 30, 2020, 1161 first suspected cases were enrolled in Libreville, Franceville, Port-Gentil and Bitam for the confirmation of SARS-CoV-2 infection with molecular test diagnostics. The size of the study had correlated with samples collected for a month and a half after the first positive case. After collection, samples were stored in transport medium at 4°C until they were sent to the CIRMF along with the patient’s medical history mentioned demographical and clinical data such as symptoms and signs of the disease, comorbidities and travel history. The lack of information about age on some files constituted a bias.\n\nThe confirmation of SARS-CoV-2 was done by real-time reverse transcriptase polymerase chain reaction (RT-PCR) according to Africa CDC guidelines. Swabs samples processed in a biosafety level-3 laboratory with personal protection equipment were placed in saline (0.9%). RNA extraction was done with the QIAamp® Viral RNA mini Kit (Qiagen) according to the manufacturer’s instructions. An extraction control was introduced during this step allowing the validation of the diagnosis by amplifying a gene fragment from Equine Arteritis Virus according to the instructions of the “TIB MOLBIOL” kit. An extraction control was introduced during this step. RT-PCR was performed using Superscript III RT-PCR kit Invitrogen in simplex, primers and probes targeted the E gene coding envelope and the RdRP gene coding RNA-dependent RNA polymerase (kit Tib-Molbiol), in a 7500 Real Time PCR System (Applied Biosystems).11 The samples were considered negative if the cycle threshold (Ct value) exceeded 36 cycles for the E gene and 40 cycles for the RdRP gene. A person was confirmed as positive case if both nasopharyngeal and oropharyngeal sample were positive or if one of the two was positive for SARS-CoV-2. Viral load was calculated from the Ct value using the standard curve generated by dilution of RNA positive control.\n\nThe 3822 nucleotides coding for the 1274 amino acid homotrimeric spike glycoprotein of SARS-CoV-2 (article) were sequenced by the Sanger method with a 3500 Genetic Analyzer (Applied Biosystem) with the BigDye terminator V1.1 kit. The amplification of S gene was made by the technique of walking the genome using overlapping S gene fragments. Ten pairs of forward and reverse primers were designed in order to amplify ten genes fragments from 505 to 753 bp using a conventional RT-PCR method (Supplemental Materials). The fragments were assembled by Chromas Pro and phylogenetic analyses were performed using a multiple sequence alignment with the SARS-CoV-2 isolate Wuhan-Hu-1 reference strain (GenBank Accession number NC_0445512 and MN908947) and twenty five others strains from several countries available in the GenBank database. Sequences were aligned using ClustalX (version 1.81). The phylogenetic tree was built with the PhyML algorithm using the maximum-likelihood method and drawn using FigTree v.1.4.0.12,13\n\nPatient records were used as the data sources. Data were analyzed using the Statview version 5.0 software. Pearson’s Chi-squared test and Fisher’s exact test were used to compare variables and to assess the relation between demographical data such as sex, age and clinical data. The R software package (version 4.0.3) was also used to compare the viral load between nasopharyngeal and oropharyngeal clinical samples, the viral load among asymptomatic patients and those with symptoms and the viral load across age groups. Data analysis revealed that the distribution did not follow a normal distribution. So a non-parametric analysis with with the Mann–Whitney U test. A p-value less than 0.05 was considered statistically significant.\n\n\nResults\n\nThis study took place between February 15, 2020, and April 30, 2020. The first cases of COVID-19 were detected on March 12, 2020, in Gabon. Among the 1161 suspected cases sampled, 517 (48.0%) were male, 560 (52.0%) were female. The sex ratio was 0.92, the median age was 36.0 years (range, 15 days to 82 years) and the mean age was 35.9±12.2 years (Table 1). Information on gender and age was unavailable for 84 and 282 people, respectively, because some data were confidential at the beginning of the pandemic. The most represented age groups were 25–35 and 35–45 years, 32.4% and 34.4%, respectively, while the least represented group was composed of patients aged over 65 years (1.4%) (Table 1). 96% of nasopharyngeal and oropharyngeal samples from the 1161 suspected cases were collected in the capital Libreville, and 19 (1.6%), 10 (0.9%), 16 (1.4%) were collected in Franceville, Port-Gentil and Bitam respectively (Table 1).\n\nAmong the 1161 suspected cases, 83 (7.15%) were confirmed cases of COVID-19. There was no significant difference between males (48.2%) and females (51.8%) according to prevalence, 7.74 and 7.68, respectively (X2=0.001, p=0.97). The median age was 37.5 years (range, 3 years to 68 years) and the mean age was 37.1±12.9 years (Table 1). Regarding to the age group distribution, the highest percentages were in the 25–35 (24.1%) and 35–45 years (32.5%) age groups. However, there was no significant difference in prevalence of SARS-CoV-2 between age groups (X2=9.58, p=0.14). No confirmed cases were found in the 47 suspected cases of the 15-25 years age group (Table 1). All the positive samples were collected in Libreville, except, one which came from Bitam.\n\n73% of the confirmed cases were asymptomatic (Table 2). However the prevalence of COVID-19 in patients with a respiratory syndrome (18.9%) was higher than in asymptomatic cases (5.8%), (X2=25.17, p<0.0001). Among the 22 symptomatic cases, 20 (90.9%) had an influenza-like illness (ILI) defined as fever (≥38°C) and a runny nose, cough, or sore throat while two (9.1%) patients had respiratory distress. ILI symptoms were accompanied by anosmia and ageusia for two patients, one patient suffered from diarrhea and another had asthenia (Table 2). 94% of people infected with the coronavirus did not have comorbidity. One confirmed case had asthma, two had sinusitis, one had diabetes and another had hypertension (Table 2). The positive rate in people with chronic disease and no chronic disease was 6.3% and 7.2%, respectively. So, no association was found between comorbidities and SARS-CoV-2 infection (X2=0.004, p=0.95).\n\nThe surveillance of COVID-19 in Gabon revealed that more than three-quarters of positive cases (87.9%) had no recent travel history, 67 (80.7%) were in contact with confirmed cases, and 6 (7.2%) persons participated in voluntary screening (Figure 1A). The 10 (12.1%) people who had traveled from affected areas came from France (n=9) and Senegal (n=1) (Figure 1B).\n\nA. Causes of COVID-19 screening. B. Travel history of confirmed cases.\n\nThe prevalence was similar in the three categories of confirmed cases, the contact cases (6.7%), the voluntary screening cases (6.3%) and people who reported having traveled recently (13.7%), (X2=5.07, p=0.08). All positive cases who presented themselves for voluntary screening were asymptomatic, whereas all the confirmed cases who had a recent travel history abroad had respiratory symptoms. Among the 67 contacts cases 55 were asymptomatic.\n\nThe viral loads in oropharyngeal samples ranged from 2.86 log10 copies/mL (7.25×103 copies/mL) to 7.51 log10 copies/mL (3.21×107 copies/mL) with a median of 3.96 log10 copies/mL (9.13×103 copies/mL) (Figure 2A). In the nasopharyngeal samples the viral load ranged from 2.50 log10 copies/mL (3.16×103 copies/mL) to 7.70 log10 copies/mL (4.98×107 copies/mL) with a median of 4.68 log10 copies/mL (47.67×103 copies/mL). The viral loads were significantly higher in the nasopharyngeal samples than in the oropharyngeal samples (p=0.03) (Figure 2A).\n\nA: Viral load from oropharyngeal and nasopharyngeal samples. B: Comparison of viral loads in two age groups. C: Comparison of viral loads in symptomatic and asymptomatic people.\n\nThere was no significant difference in viral loads between children under 15 years old and people over 15 years old (p=0.9895) (Figure 2B). Likewise, there was no correlation between clinical symptoms and viral loads (p=0.06042) (Figure 2C).\n\nThe phylogenetic analysis was performed with five sequences of 3822 nucleotides of the spike S gene obtained from the collected samples in five patients. Among the patients, two had symptoms and came from France (62GAB_S, accession number MW512913), including the first case diagnosed in Gabon (34GAB_S, accession number MW512911), one had symptoms and a travel history in Senegal (121GAB_S, accession number MW512914), and finally, the other two were contact cases without travel history, one of which had symptoms (56GAB_S, accession number MW512912) and the other was asymptomatic (297GAB_S, accession number MW512915). We compared these sequences with 27 sequences of SARS-CoV-2 of the GenBank database which were diagnosed in several countries of the five continents (China, South Korea, Malaysia, Russia, Sweden, France, Italy, USA, Brazil, Guatemala, Tunisia, Egypt, Morocco, South Africa and Benin) (Figure 3). The five sequences were distributed in two clusters. The sequences 56GAB_S and 121GAB_S clustered with the sequences of the reference strain (NC_045512, MN908947) and ten sequences registered in the GenBank database (Figure 3). Six sequences including, 56GAB_S, displayed 100% identity at the nucleotide level with the sequences of the reference strain in this cluster. On the other hand, three sequences MT499216-Tunisia, MT093571-Sweeden and 121GAB_S displayed 99.97% identity with the reference strain. The alignment of SARS-CoV-2 sequences showed that the nucleotide substitution (G906T) on the S gene of the 121GAB_S sequence did not generate an amino-acid substitution (Threonine). The alignment of the 18 sequences of the second cluster, including the three others sequences of Gabon (34GAB_S, 62GAB_S and 297GAB_S), showed a nucleotide substitution (A1841G) generated a synonymous D614G mutation, with an amino-acid substitution of aspartic acid Asp (D) with glycine Gly (G), at position 614 (Figure 3). Furthermore, there was a nucleotide substitution (G3621T) in the 34GAB_S sequence which displayed 99.95% identity with the reference sequence strain. This substitution generated a mutation at the amino-acid sequence position 1207, glutamic acid Glu (E) was substituted by aspartic acid Asp (D) (Figure 3).\n\nLegend: The red rectangles indicates the sequences of SARS-CoV-2 strain circulating in Gabon.\n\n\nDiscussion\n\nBetween, March 12, 2020, and April 30, 2020, 83 confirmed cases of COVID-19 were detected in Gabon. During the 50-day period, the progression of the disease was slow and comparable to the spread of COVID-19 in Nigeria during the first 45 days. However, in several countries in Africa, such as Cameroon, South Africa, Tunisia, Morocco, the burden of COVID-19 was higher, with more than 500 confirmed cases reported 35 days after the first case.14 This difference could probably due to the population density which would be higher in these countries. Several studies which described more confirmed cases showed that more than three quarters of patients were found in the [30–79] age group.15,16 Despite the fact that all ages were susceptible, others studies showed that the majority of cases were over 30 and more specifically between 30 and 60 years old.16,17 The 30-years-olds in our study were one of the most represented age groups (32.4%).\n\nMore than 70% of the cases were asymptomatic in our study. Two studies which reported the first cases of COVID-19 in China and Europe mentioned that 5% of case were asymptomatic.3,18 The proportion of asymptomatic cases varied according to the studies, values ranged from 1% to 78%7,19,20 (http://dx.doi.org/doi:10.1136/bmj.m1375). The percentage of asymptomatic cases (73.5%) in Gabon during this period was within the range of the value reported worldwide meaning that asymptomatic carrier transmission was effective in Gabon. Moreover, there may have been presymptomatic transmission in Gabon such as the one described in Gernamy where an asymptomatic businessman from China transmitted the virus to a healthy German businessman. The Chinese visitor reportedly had symptoms of COVID-19 upon his return.21 Several reports cases have recorded similar facts and shown asymptomatic and presymptomatic transmission.22,23 Approximately 98% of patients would had an incubation period of 5 days on average ranging from 2 to 14 days, although this period could be up to 24 days.4 These data could explain the spread of the virus in Gabon despite the high number of asymptomatic cases (73%).\n\nReview authors described symptoms of COVID-19 as predominantly flu-like symptoms such as fever (80–90%), cough (50%), lethargy (20–40%) and in some cases diarrhea.4 In some more vulnerable patients including the elderly and people with chronic diseases, the symptoms progress to pneumonia and respiratory distress, requiring in 20% of cases hospital treatment.4 In addition, 80% of COVID-19 infections in China were mild flu-like symptoms.4 Our data corroborated those of this study. Indeed, a large number of symptomatic patients developed mild flu-like symptoms (90% of symptomatic patients) (Table 2). Only two patients had respiratory distress and 78 (94%) had no chronic disease (Table 2). However, since our data only considered the first cases in Gabon, the number of cases was low and probably underestimated.\n\nIn the 50 days following the report of the first case of COVID-19 on March 12, 2020, 87% of confirmed cases declared that they had not made a recent trip (Figure 1A), which would suggest that the virus was introduced in Gabon before March. The WHO declared the COVID-19 pandemic on March 11, 2020 meaning that a large number of countries across the African continent were affected by this period. The flow of travelers and international trade between Gabon and various affected countries would explain the introduction of the virus in Gabon. The slow spread is said to be linked to the fact that the government acted by closing borders, closing schools, quarantine of all suspected and confirmed cases and restricting movement as early as the end of March.\n\nSome studies report a very high SARS-CoV-2 viral load in nasal swabs and others in throat swabs.8 We found that the viral loads were significantly higher in the nasopharyngeal samples than in the oropharyngeal samples (p=0.03) (Figure 2A). Our data is similar to a study which compared the viral load in different clinical samples (saliva, spectrum, urine, nasopharyngeal and oropharyngeal samples) and showed that the viral load was the highest in the nasopharynx.5 One review based on seven studies measured and compared the viral load in pre-symptomatic, asymptomatic and symptomatic patients. It reported little to no difference between the SARS-CoV-2 viral load in the three categories of patients.8 Our results which showed no correlation between the viral load and the clinical symptom of patients are in accordance with these studies. Some studies compared the SARS-CoV-2 viral loads in patients of different age groups in order to establish a possible link between the viral load, the duration of symptoms and the age of the patients. They concluded that there was no significant difference with regard to viral load or the duration of virus detection between adults and children.8 The number of patients in each age group and the relationship between viral load and infectivity should be considered. Our study shows that there is no difference between patients under 15 and patients over 15 (Figure 2).\n\nIt is important to characterize the virus SAR-CoV-2 by identifying the genotype circulating in Gabon in order to set up an efficient response to this pandemic. The first SARS-CoV-2 genome of the isolate Wuhan-Hu-1 was sequenced in China (accession number NC_045512 or MN908947) in January 2020. The 1273 amino acid spike glycoprotein (S) located on the virion surface is essential for the entry of the virus in host cells. Thus, we compared the 3822 nucleotide fragments of the S gene with sequences published in the GenBank database. The alignment of the sequences and the phylogenetic tree showed that the sequences were distributed in two clusters. One cluster was composed of the SARS-CoV-2 reference strain sequences without the D614G mutation, including two sequences of Gabon, 56GAB_S and 121GAB_S. The second cluster included sequences without the D614G mutation. The three others sequences 34GAB_S, 62GAB_S and 297GAB_S were in the second cluster (Figure 3). The literature reported a frequent mutation in the S gene (position 23403A>G) coding the variant of S protein D614G10 (http://dx.doi.org/10.1038/s10038-020-0808-9). This mutation emerged in Europe and North America on January 29 and February 28, 2020 respectively.24 Initially, the D614 and G614 variants reached an equal ratio in Europe and North America at the end of February, then in March, the G614 variant started to circulate predominantly in both continents from March.24 The sequence 34GAB_S isolated from the sample of the first case of SARS-CoV-2 diagnosed in Gabon on March 12, 2020, had the D614G mutation. Among the five samples collected at the beginning of the pandemic in Gabon, three had a SARS-CoV-2 strain with the D614G mutation. These results corroborated that of a study which reported the emergence of the G614 variant in Africa on March 13, 2020.24 At this time, the circulation of both the D614 and G614 variants in Europe and the world suggested a simultaneous introduction of the two strains in Gabon. A Japanese study showed a significant positive correlation between the S protein 614G variant and fatality rates (http://dx.doi.org/10.1038/s10038-020-0808-9). They analyzed the frequency of mutations in the SARS-CoV-2 genome in 28 countries which they grouped into three clusters in which they show a correlation between the mutations and the fatality rate (http://dx.doi.org/10.1038/s10038-020-0808-9). The full genome of a large number of our Gabonese strains would provide more information on the multiple mutations and their impact on the COVID-19 disease in Gabon.\n\nIn conclusion, this study reported the first data on the COVID-19 pandemic in Gabon. The data showed that most of the infected people were asymptomatic. The viral load was higher in the nasopharyngeal samples. The S gene analyzed suggested both introduction of the D614 and G614 variant in Gabon. However analysis of the full genome in order to identify possible mutations, as well as immunological investigations would provide additional data and increase knowledge about the circulation and the impact of the virus in Gabon and more generally in Africa.\n\n\nData availability\n\nBioStudies: “Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020 and molecular characterization of the spike protein, in Gabon”. Accession number S-BSST800: https://identifiers.org/biostudies:S-BSST800\n\nNCBI Gene: Accession numbers:\n\nMW512911: https://www.ncbi.nlm.nih.gov/nuccore/MW512911\n\nMW512912: https://www.ncbi.nlm.nih.gov/nuccore/MW512912\n\nMW512913: https://www.ncbi.nlm.nih.gov/nuccore/MW512913\n\nMW512914: https://www.ncbi.nlm.nih.gov/nuccore/MW512914\n\nMW512915: https://www.ncbi.nlm.nih.gov/nuccore/MW512915\n\n\nConsent\n\nInformed consent for publication of the participants/patients’ details was obtained from the participants/patients/parents/guardian/relative of the participant/patient.’",
"appendix": "Acknowledgments\n\nWe would like to thank the staffs of all the health centers. We also wish to thank the members of the CIRMF’s public health emergencies group, Kumulungui Brice, Yala Jean Fabrice, Mouinga Ondeme Augustin, Ngoubangoye Barthelemy, Onanga Richard, Kengne Pierre, Oyegue Lydie Sandrine, Kassa Kassa Roland Fabrice, for their suggestions concerning the management of the pandemic. We also thank Lekouna Lady Charlène and Mombo Illich Mandred for their participation in the meeting.\n\nWe acknowledge Heïdi Lançon for the English revision of the manuscript.\n\n\nReferences\n\nGorbalenya AE, Baker SC, Baric RS, et al.: The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 2020; 5(4): 536–544.\n\nKujawski SA, Wong KK, Collins JP, et al.: Clinical and virologic characteristics of the first 12 patients with coronavirus disease 2019 (COVID-19) in the United States. Nat. Med. 2020; 26(6): 861–868.\n\nSpiteri G, Fielding J, Diercke M, et al.: First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020. Eurosurveillance. 2020; 25(9) PubMed Abstract | Publisher Full Text\n\nOrtiz-Prado E, Simbaña-Rivera K, Gómez- Barreno L, et al.: Clinical, molecular, and epidemiological characterization of the SARS-CoV-2 virus and the Coronavirus Disease 2019 (COVID-19), a comprehensive literature review. Vol. 98, Diagnostic Microbiology and Infectious Disease. Elsevier Inc.; 2020.\n\nYoon JG, Yoon J, Song JY, et al.: Clinical significance of a high SARS-CoV-2 viral load in the Saliva. J. Korean Med. Sci. 2020; 35(20): 1–6.\n\nZheng S, Fan J, Yu F, et al.: Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China, January-March 2020: Retrospective cohort study. BMJ. 2020; 369(March): 1–8. Publisher Full Text\n\nWidders A, Alex Broom JB: SARS-CoV-2:The viral shedding vs infectivity dilemma. Infect Dis Heal. 2020; 25: 210–215. PubMed Abstract | Publisher Full Text\n\nWalsh KA, Jordan K, Clyne B, et al.: SARS-CoV-2 detection, viral load and infectivity over the course of an infection. J. Infect. 2020; 81: 357–371. PubMed Abstract | Publisher Full Text\n\nRabi FA, Al Zoubi MS, Al-Nasser AD, et al.: Sars-cov-2 and coronavirus disease 2019: What we know so far. Vol. 9, Pathogens. MDPI AG; 2020.\n\nChangchuan Y: Genotyping coronavirus SARS-CoV-2: methods and implications. Genomics. 2020; 14(4)(January): 337–9.\n\nCorman VM, Landt O, Kaiser M, et al.: Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance. 2020; 25(3): 1–8. Publisher Full Text\n\nAnisimova M, Gascuel O: Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 2006; 55(4): 539–552. PubMed Abstract | Publisher Full Text\n\nGuindon S, Dufayard JF, Lefort V, et al.: New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst. Biol. 2010; 59(3): 307–321. PubMed Abstract | Publisher Full Text\n\nAdegboye OA, Adekunle AI, Gayawan E: Early transmission dynamics of novel coronavirus (Covid-19) in Nigeria. Int. J. Environ. Res. Public Health. 2020; 17(9). PubMed Abstract | Publisher Full Text\n\nJin Y, Yang H, Ji W, et al.: Virology, epidemiology, pathogenesis, and control of covid-19. Viruses. 2020; 12: 1–17. Publisher Full Text\n\nXing B, Xue Za Z, Liu Z: The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China. Chinese Center for Disease Control and Prevention. 2020; 41: 145–151.\n\nDiseases KS of I: Report on the epidemiological features of coronavirus disease 2019 (covid-19) outbreak in the republic of korea from january 19 to march 2, 2020. J. Korean Med. Sci. 2020; 35(10): 1–11. Publisher Full Text\n\nTian S, Hu N, Lou J, et al.: Characteristics of COVID-19 infection in Beijing. J. Infect. 2020; 80(4): 401–406. PubMed Abstract | Publisher Full Text\n\nWu Z, McGoogan JM: Characteristics of and Important Lessons from the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases from the Chinese Center for Disease Control and Prevention. JAMA - J. Am. Med. Assoc. 2020; 323(13): 1239–1242. PubMed Abstract | Publisher Full Text\n\nNishiura H, Kobayashi T, Miyama T, et al.: Estimation of the asymptomatic ratio of novel coronavirus infections (COVID-19). Int. J. Infect. Dis. 2020; 94: 154–155. PubMed Abstract | Publisher Full Text\n\nRothe C, Schunk M, Sothmann P, et al.: Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany. N. Engl. J. Med. 2020; 382(10): 970–971. PubMed Abstract | Publisher Full Text\n\nTong ZD, Tang A, Li KF, et al.: Potential presymptomatic transmission of SARS-CoV-2, Zhejiang Province, China, 2020. Emerg. Infect. Dis. 2020; 26(5): 1052–1054. PubMed Abstract | Publisher Full Text\n\nYu P, Zhu J, Zhang Z, et al.: A familial cluster of infection associated with the 2019 novel coronavirus indicating possible person-to-person transmission during the incubation period. J. Infect. Dis. 2020; 221(11): 1757–1761. PubMed Abstract | Publisher Full Text\n\nHuang SW, Miller SO, Yen CH, et al.: Impact of genetic variability in ace2 expression on the evolutionary dynamics of SARS-CoV-2 spike D614G mutation. Genes (Basel). 2021; 12(1): 1–9."
}
|
[
{
"id": "141590",
"date": "18 Jul 2022",
"name": "Babatunde Motayo",
"expertise": [
"Reviewer Expertise Virology",
"Molecular Epidemiology",
"Evolutionary 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\nI thank the handling Editor of the F1000research for selecting me as a reviewer for the paper titled “Epidemiology of the first cases of SARSCoV-2 infection from March to April 2020 and molecular characterization of the Spike protein in Gabon”. I have gone through the paper and have made a decision of major revision. My comments and suggested revision are outlined below.\nMAJOR COMMENTS\nABSTRACT: The background section of the Abstract needs to be re-written to summarize actual events that led to the study. The method section is not explicit enough nothing was mentioned about how the study was carried out or actual techniques used such as RT-PCR and sequencing, please re-cast to reflect the actual techniques used to carry out the study.\nMETHODS; The authors did not mention anything about ethical approval and consent, this should be stated clearly if it was sought. The authors did not apply the generally acceptable classification system to properly genotype the Gabonese isolates identified, that is the PANGO-lineage and Nexclade classification. These two genotyping tools should be done and reported appropriately. Also, the associated genomic data that was generated to generate sequence alignments and the phylogenetic tree is not enough to conclusively derive any significant phylogenetic relationship, considering the enormity of data already available in databases such as GenBank and GISAID, at least a reasonable number of sequences from each sub-region of Africa and major continents, including China should be included. The authors should update with more sequences from diverse SARSCoV Lineages including major variants of concerns, variants of interest, and relevant global sequences and re-do the alignment and ML tree construction. The authors are also advised to improve on the tree visualization the labels should be bolder and more informative, I suggest the authors make use of tree visualization tools such as FigTree, or ggTree for better representation, authors are also advised to construct an MCC time tree showing lineage assignments of the Gabonese isolates along with relevant circulating lineages in Africa and their dates of introduction.\nRESULTS: The results in the first two sub-sections should be merged since they both report the same thing in different sub-populations. The sub-heading of the last sub-section SARSCoV-2 sequences should be re-casted e.g Molecular characterization of S-gene of SARSCoV-2. The molecular data from the suggested analysis such as PANGO-lineage should be included also; results of phylogenetic analysis should reflect lineage clustering, geographic diversification from previous/more recent related isolates, e.t.c. A time tree will also show introductions of same lineage, or multiple lineages within the time frame under study.\nDISCUSSION: The discussion aspect has to be re-written to include the data generated from the suggested additional analysis particularly the genotype and potential implications. Also, the sample size of the sequences is too small and should be included as a limitation to the study. Also, other limitations should be clearly stated such as the inability to sequence the complete genome of the Gabonese SARSCoV-2 strains.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8964",
"date": "03 Nov 2022",
"name": "Sonia LEKANA-DOUKI",
"role": "Author Response",
"response": "Responses to reviewer 1 Manuscript title: Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020 and molecular characterization of the spike protein, in Gabon Manuscript ID : Sonia Etenna Lekana-Doukia, Nadine N’dilimabakaa,b, Elvire Mbongo-Kamac, Marisca Kandet Yattarad, Armel Mintsa Ndonge, Audrey Michel Ngonga Dikongoa, Julia Cyrielle Andekoa, Ornella Zong Minkoa, Danielle Styvie Koumba Mavoungoua, Abdoulaye Dianéf, Arsène Mabika Mabikag, Telstar Ndong Mebaleya, Nal Kennedy Ndjangangoyea,h, Octavie Banga Mve-Ellaa, Linda Bohou Kombilaa, Joa Braithe Mangombia, Jeordy Dimitri Engone Ondof, Gaël Darren Magangaa,i, Jean-Bernard Lekana-Douki h,j Reviewer 1 APPROVED WITH RESERVATIONS I thank the handling Editor of the F1000research for selecting me as a reviewer for the paper titled “Epidemiology of the first cases of SARSCoV-2 infection from March to April 2020 and molecular characterization of the Spike protein in Gabon”. I have gone through the paper and have made a decision of major revision. My comments and suggested revision are outlined below. MAJOR COMMENTS ABSTRACT: The background section of the Abstract needs to be re-written to summarize actual events that led to the study. The method section is not explicit enough nothing was mentioned about how the study was carried out or actual techniques used such as RT-PCR and sequencing, please re-cast to reflect the actual techniques used to carry out the study. We have re-written the section “ABSTRACT” with information about events that led to the study and information about le PCR and the sequencing (line 31 to 40). METHODS; The authors did not mention anything about ethical approval and consent, this should be stated clearly if it was sought. We added the following information about ethical approved and consent in the section Ethics declaration: “This study was approved by the national ethics committee (N°0003/2020/CNER/SG/P) and was performed in accordance with the ethical standards of the Declaration of Helsinki of 1964. Consent was obtained before sampling.” (line 305). The authors did not apply the generally acceptable classification system to properly genotype the Gabonese isolates identified, that is the PANGO-lineage and Nexclade classification. These two genotyping tools should be done and reported appropriately. Also, the associated genomic data that was generated to generate sequence alignments and the phylogenetic tree is not enough to conclusively derive any significant phylogenetic relationship, considering the enormity of data already available in databases such as GenBank and GISAID, at least a reasonable number of sequences from each sub-region of Africa and major continents, including China should be included. The authors should update with more sequences from diverse SARSCoV Lineages including major variants of concerns, variants of interest, and relevant global sequences and re-do the alignment and ML tree construction. The authors are also advised to improve on the tree visualization the labels should be bolder and more informative, I suggest the authors make use of tree visualization tools such as FigTree, or ggTree for better representation, authors are also advised to construct an MCC time tree showing lineage assignments of the Gabonese isolates along with relevant circulating lineages in Africa and their dates of introduction. Since the first data presented in this study, we have carried out another study on the complete genomes of samples from the first wave of the pandemic in Gabon (line 273, 286). Thus, we have deleted the paragraph on Sanger's method in the methods section as well as the paragraph SARS-CoV-2 sequences in the results. We have modified the discussion in this way. Three samples for which we had done sequencing by the Sanger method were selected in this other study to obtain the complete genome. These were samples 34, 56 and 62. We have therefore added information on their lineage to the discussion (line 273). We deleted the Figure 3. As a result, the title of the study has been modified because the data concerning the characterization of the strains by the genotyping of the S gene are no longer provided in this study but constitute a comment in the discussion which provided additional information on the first cases of COVID-19 in Gabon : “Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020” (line 26). The keywords have been modified: “COVID-19, Diagnostic, Epidemiology, Viral load, Gabon” (line 52). RESULTS: The results in the first two sub-sections should be merged since they both report the same thing in different sub-populations. The sub-heading of the last sub-section SARSCoV-2 sequences should be re-casted e.g Molecular characterization of S-gene of SARSCoV-2. The molecular data from the suggested analysis such as PANGO-lineage should be included also; results of phylogenetic analysis should reflect lineage clustering, geographic diversification from previous/more recent related isolates, e.t.c. A time tree will also show introductions of same lineage, or multiple lineages within the time frame under study. We merged the first two sub-sections and changed the title of the sub-section: Epidemiological data of suspected and confirmed cases (line 146). We deleted the sub-section SARS-CoV-2 sequences for the reasons previously mentioned. DISCUSSION: The discussion aspect has to be re-written to include the data generated from the suggested additional analysis particularly the genotype and potential implications. Also, the sample size of the sequences is too small and should be included as a limitation to the study. Also, other limitations should be clearly stated such as the inability to sequence the complete genome of the Gabonese SARSCoV-2 strains. We have re-written the discussion by mentioning the whole genomes made in another study which provides information on the lineages that circulated at the beginning of the pandemic (line 273, 286)."
}
]
},
{
"id": "140050",
"date": "08 Aug 2022",
"name": "Anggraini Dwi Sensusiati",
"expertise": [
"Reviewer Expertise COVID-19",
"Radiology",
"Laboratory Findings",
"Neuroradiology",
"and Head & Neck Imaging",
"Artificial Intelligence for COVID-19."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is about the epidemiological data of the first SARS-Cov-2 infection case in Gabon and the molecular characteristics data of the spike protein. Based on the results of the study, it was explained that the first COVID-19 case in Gabon was found on March 12, 2020. The characteristics of confirmed COVID-19 patients are mostly asymptomatic. While symptomatic patients mostly have influenza-like symptoms (ILI symptoms), namely fever; runny nose; cough; sore throat; and some of them experience respiratory distress. Some patients with ILI symptoms are also accompanied by anosmia, ageusia, diarrhea, or asthenia. The results of the study also stated that there was no relationship between comorbidities and SARS-Cov-2 infection. Based on travel history, all samples confirmed to have COVID-19 who traveled abroad had respiratory symptoms.\nIn the results of the study related to the molecular characteristics of spike proteins, it was explained that the viral load was higher in nasopharyngeal samples than in oropharynx; there was no significant difference in the viral load of children under 15 years of age with people aged 15 years and over; and there is no correlation between the clinical symptoms of confirmed COVID-19 patients and viral loads.\nPhylogenetic analysis in this study was carried out with five sequences of 3822 spike S gene nucleotides, obtained from 5 patients (2 symptomatic patients originally from Paris; the first case in Gabon; and 2 contact cases without travel history). The S genes that have been analyzed suggest the introduction of the D614 and G614 variants in Gabon.\nIn general, this research is good. The results of the study are important to enrich data and literature related to the epidemiology of COVID-19 in all countries around the world, including Gabon. The results of molecular research of the virus are also useful to enrich the genome database of the COVID-19 virus, which can be used for other molecular research in the future.\nThe systematic of writing this article has also been good. The writing of research methods is good and complete. Especially in the study design section and patient information. The number of samples used is also sufficient. The writing of the results and discussion have also answered the purpose of the study.\nTo make the discussion section more comprehensive, it would be better if the authors add more information related to the profession and the activities of the sample. It is also necessary to add more detailed information related to comorbidities such as the level of blood sugar in diabetic patients.\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": "8965",
"date": "03 Nov 2022",
"name": "Sonia LEKANA-DOUKI",
"role": "Author Response",
"response": "Responses to reviewer 2 Manuscript title: Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020 and molecular characterization of the spike protein, in Gabon We were unable to obtain some detailed data such as sugar levels in diabetic patients because some data were missed during the implementation of monitoring at the begining of the pandemic. We changed the title and removed the sequencing section to better accommodate the other reviewer's suggestions. Title: “Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020” (line 26). The keywords have been modified: “COVID-19, Diagnostic, Epidemiology, Viral load, Gabon” (line 52). Since the first data presented in this study, we have carried out another study on the complete genomes of samples from the first wave of the pandemic in Gabon (line 273, 286). Thus, we have deleted the paragraph on Sanger's method in the methods section as well as the paragraph SARS-CoV-2 sequences in the results. We have modified the discussion in this way Three samples for which we had done sequencing by the Sanger method were selected in this other study to obtain the complete genome. These were samples 34, 56 and 62. We have therefore added information on their lineage to the discussion (line 273). We deleted the Figure 3. As a result, the title of the study has been modified because the data concerning the characterization of the strains by the genotyping of the S gene are no longer provided in this study but constitute a comment in the discussion which provided additional information on the lineage of the first cases of COVID-19 in Gabon."
}
]
}
] | 1
|
https://f1000research.com/articles/11-205
|
https://f1000research.com/articles/11-259/v1
|
02 Mar 22
|
{
"type": "Systematic Review",
"title": "Analysis of the safety and immunogenicity profile of an azoximer bromide polymer-adjuvanted subunit influenza vaccine.",
"authors": [
"Ronald Kompier",
"Pieter Neels",
"Walter Beyer",
"Tim Hardman",
"Dmitry Lioznov",
"Susanna Kharit",
"Michail Kostinov",
"Ronald Kompier",
"Pieter Neels",
"Walter Beyer",
"Dmitry Lioznov",
"Susanna Kharit",
"Michail Kostinov"
],
"abstract": "A systematic review of clinical trials conducted with a low-dose inactivated influenza vaccine adjuvanted by azoximer bromide (AZB, Polyoxidonium), was performed to compare vaccine reactogenicity against non-adjuvant vaccines. We also assessed whether lower amounts of antigen per viral strain in AZB-adjuvanted vaccines affected antibody responses. A robust search strategy identified scientific publications reporting 30 clinical trials, comprising data on 11,736 participants and 86 trial arms, for inclusion in the analysis. Local reaction rates (Rlr) appeared to be lower in AZB-adjuvanted vaccine treatment arms versus comparator vaccine treatment arms. Meta‑regression analysis revealed that AZB did not contribute to vaccine reactogenicity. Post-vaccination geometric mean titres in those exposed to AZB-adjuvanted vaccine and comparator vaccine treatment arms were similar in both children and adults aged 18–60 years, implying an antigen-sparing effect by AZB.",
"keywords": [
"influenza vaccine",
"vaccine adjuvant",
"azoximer bromide",
"vaccine safety",
"immunogenicity",
"review",
"meta-analysis"
],
"content": "Introduction\n\nInfluenza virus infections cause seasonal epidemics worldwide and continue to be a major health and economic burden.1–3 Despite ongoing research, understanding of the precise pathogenesis of disease and appropriate specific treatments remain elusive, leaving vaccination as the most effective means of prevention. Current licenced influenza vaccines involve either inactivated, live-attenuated or recombinant formulations and contain either the whole virion, split virion or viral subunits as the antigen. In particular, inactivated subunit (SU) vaccines possess a favourable tolerability and safety profile and are relatively simple to produce. Influenza vaccines aim to induce antibodies against viral hemagglutinin (HA) proteins which undergo steady antigenic drift and therefore require regular vaccine reformulation.4–8 Furthermore, HA antigens insufficiently induce long-term immunity and may require large doses and/or more than one vaccination to guarantee robust protection.9–12 Adjuvants can be added to inactivated vaccines to increase their immunogenicity13; this is particularly relevant when considering vaccines for the elderly and immunocompromised people, as well as during pandemics, when a rapid antibody response is required.14 Well-established adjuvants include alum15 and MF5910,11; however, efficacy on antibody induction is impacted by age and may vary considerably9,16,17\n\nAn adjuvanted, inactivated subunit influenza vaccine for subcutaneous and intramuscular injection (Grippol, NPO Petrovax Pharm, Moscow, Russia) has been used in the Russian Federation and other countries of the Commonwealth of Independent States for over two decades. The vaccine contains influenza virus HA and neuraminidase subunits18 adjuvanted by 500 μg azoximer bromide (AZB, Polyoxidonium), an immune-modulating polymer from a class of synthetic heterochain polyamines. There are three formulations of Grippol, or azoximer-adjuvanted subunit vaccine (AZB-SU): Two trivalent formulations contain HAs of two strains of influenza A (from A/H3N2 and A/H1N1 subtypes) and one of two B strains (from B/Victoria or B/Yamagata lineage). The third formulation contains HAs of all four strains (quadrivalent). All formulations of AZB-SU contain 5 μg HA per strain, a third less than the standard amount of 15 μg HA.19\n\nThe addition of AZB to influenza SU vaccine enhances antibody production, even in immunosuppressed mice.20–22 In the Grippol formulations, AZB allows a reduction in the amount of HA antigen required per dose.23 This antigen-sparing strategy raises two questions:\n\n1. Does AZB itself increase vaccine reactogenicity compared with non-adjuvant vaccines, i.e., does it have an impact on vaccine safety and tolerability?\n\n2. Does AZB-SU induce antibody levels comparable to non-adjuvant vaccines, despite its lower HA dose?\n\nThe present study investigated these questions by interrogating the clinical data reported for clinical trials with AZB-SU (published and unpublished) over the past 20 years.\n\n\nMethods\n\nThis study was conducted according to the principles of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA).24 A literature search was performed in English- and Russian-language databases (United States National Library of Medicine at the National Institutes of Health PubMed database, Cochrane Database of Systematic Reviews, Russian National Medical Library) to identify any public records or reports of clinical trials conducted with AZB-SU between 1998 and 2018. Relevant articles were identified by searching the terms: ‘influenza’ AND ‘vaccin*’ AND ‘[‘azoximer bromide’ OR ‘polyoxidonium’ OR ‘Grippol’]. The online search was performed in January 2019 and updated in August 2019.\n\nManual search of existing lists of references, provided by the manufacturer, NPO Petrovax Pharm (Moscow, Russia), was performed, and assessments included original trial reports and trial compilations produced by the manufacturer. Study reports were rejected if a full text was not openly available or in case of pre-clinical studies, field studies or post-marketing reports on rare events or individual cases.\n\nReports from studies with at least one of the following assessments were included:\n\n- Reactogenicity: Participants were followed for at least 5–6 days after intervention (vaccine or placebo), and local and systemic vaccine reactions were recorded.\n\n- Safety: Serious adverse events (SAEs) were recorded within at least 3–4 weeks after intervention.\n\n- Immunogenicity: Antibody titres against vaccine strains were determined with a standard hemagglutination inhibition assay, in sera drawn before and 3–4 weeks after intervention.\n\nA data extraction form was used based on the PRISMA recommendations. Titles and abstracts identified from searches were screened by two independent reviewers. They also independently reviewed full-text versions of marked articles that met the predefined criteria. Each study was provided with a unique identifier number (Study reference number). All extracted data were independently reviewed by two researchers and finalised after consultation and agreement on inclusion and exclusion assignment was unanimous. Data extracted from included studies comprised: authors and date of study, population characteristics (including age, medical history and previous vaccinations), trial design and intervention arms, vaccines used (formulations, virus strains, amount of HA per strain and per dose), numbers or percentages of participants with post-vaccination local or systemic reactions and the numbers of participants who experienced SAEs. Immunogenicity data, i.e. pre- and post-vaccination geometric mean titre (GMT) and variance (e.g., confidence interval [CI]) and serologic Committee for Proprietary Medicinal Products (CPMP) variables (see below), were collected for efficacy analyses. All entry data were critically assessed for eligibility by the reviewers.\n\nReactogenicity outcomes per treatment arm were the rate (proportion) of participants with any local (Rlr) or systemic (Rsr) reactions up to 6 days post-vaccination. Safety outcomes per treatment arm were the number of SAEs within 4 weeks following vaccination. Only data on SAE widely recognised to be related to vaccination were extracted, such as allergic reactions, Guillain-Barré syndrome and narcolepsy. The primary immunogenicity outcome was pre- and post-vaccination GMT. Post-vaccination HA antibody titre correlates well with protection against influenza infection, and could act as a predictor of actual vaccine efficacy in the wider population using an evidence-based clinical protection curve.25 Secondary efficacy outcomes were: seroprotection rate (SPR, proportion of participants with a post-vaccination titre of at least 40); seroconversion rate (SCR, proportion of participants with at least a 4-fold increase from baseline); mean fold increase (MFI) (post-vaccination GMT: pre-vaccination GMT ratio). For annual re-licensing of inactivated influenza vaccines in the European Union, age-defined criteria for SPR, SCR and MFI in groups of at least 50 vaccinees, had been set by the CPMP in 1992,19 but were withdrawn in 2016. These variables are considered here for the purpose of completeness.\n\nIn trials with randomized allocation of different treatments, the following measures of distance between two treatments, and their 95% CIs, were calculated:\n\n- The local and systemic rate difference (RDlr and RDsr), derived from local and systemic reaction rates, respectively. Two treatments were regarded as having similar reactogenicity when the 95% CI of their RD value included zero.\n\n- The GMT ratio (GMTR), derived from post-vaccination GMTs. Two treatments were regarded as having similar immunogenicity when the 95% CI of their GMTR value included 1.0. In trials designed and powered to assess non-inferiority or superiority, one treatment was regarded non-inferior to another one when the lower limit of the 95% CI of their GMTR value exceeded 0.67, and superior when it exceeded 1.5.\n\nAll participants assessed for efficacy had three or four anti-HA titre values (one titre for each vaccine strain; A-H3N2 and A-H1N1, and one or two B strains), therefore trial arms were subdivided into sub-arms, one sub-arm per vaccine strain. Any sub-arms that were further subdivided into groups with low and high pre-vaccinations titres in original publications were pooled to increase statistical power. When two comparator vaccines were given within a trial, they were pooled into one treatment arm due to their similarity in terms of safety and immunogenicity.26 An additional analysis was performed for one trial with AZB-SU and comparator vaccine whereby GMT and standard deviation (SD) values were transformed into post-vaccination antibody-predicted protection rates (post-PRab).27,28 The post-PRab ratio between treatment arms was calculated. The post-PRab values were regarded similar if the 95% CI of their ratio included 1.0.\n\nA linear meta-regression analysis was performed to adjust local and systemic reaction rates for several variables: total HA amount per vaccine dose, mean age and health status. Adjusted reaction rates were tested with a dummy binary variable representing AZB content (0: placebo and comparator vaccines [no AZB]; 1: AZB-SU) to determine whether there was any intrinsic reactogenicity associated with AZB. Funnel plots were constructed from logarithmic local and systemic rate ratios and their standard errors to assess potential publication bias,29 which would be represented by asymmetry in the funnel plot.\n\nOutcome variables from several trials were combined using the inverse-variance weighted method or were subjected to least-squares linear meta-regression using the software package ‘Comprehensive Meta-Analysis’,30 [version 3.3.070/20140 (Biostat, Englewood, NJ, USA)]. Other analyses were performed using IBM SPSS Statistics for Windows version 25/2017 (Armonk, NY, USA).\n\n\nResults\n\nThe selection process of clinical trials is summarised in Table 1. One hundred and forty-eight reports were identified, of which 30 were found to be duplicates, and 118 records were screened. Forty-seven reports were found not to include clinical trial data and were therefore excluded. Seventy-one records were assessed further for eligibility. Nineteen records were excluded because they did not focus on the topic of interest, 20 records were excluded because they did not include data on the outcome of interest, and two records were excluded because the study arm population was considered to be too small (<10 participants). Data from the remaining 30 publications or reports were included in the analyses (Figure 1).\n\nLegend: (none).\n\nThe trials were performed between 1993 and 2016 and comprised 11,736 participants aged between six months and 99 years (Table 1). The majority of participants (7,392 [63.0%]) were reported as healthy (no reported chronic disease). The remaining 4,344 participants (37.0%) were reported as having allergies, chronic obstructive pulmonary disease, cardiovascular disease, diabetes mellitus type 1, HIV infection or age-related chronic conditions. A breakdown of study population characteristics by trial is presented in Extended data, Figure C. Eleven of the trials were uncontrolled or placebo-controlled standalone trials, 12 were randomised bridging trials (between AZB-SU formulations), and seven were randomised non-inferiority trials conducted with non-adjuvanted comparator vaccines. A total of 14 trials (46.7%) assessed both safety and immunogenicity, 15 (50.0%) assessed safety only, and one (3.3%) assessed immunogenicity only. A total of 7,037 participants (60.0%) in 56 treatment arms received the AZB-SU vaccine and 1,391 (11.9%) participants in 15 treatment arms received comparator vaccines, which were either whole virus (Immunopreparation), split (Begrivac, Vaxigrip, Fluarix), or subunit formulation (Influvac, Agrippal). Participants in trivalent AZB-SU arms received 15 μg HA per dose in most cases, except in dose-finding trials where some participants received lower (7.5 μg HA) or higher (30 μg HA) doses. The HA amount of the influenza B component was increased from 5 μg to 11 μg (21 μg HA per dose) in two trials (T14 and T16, Supplemental Materials Figure D). Participants in quadrivalent AZB-SU arms all received 5 μg HA per vaccine strain (20 μg HA per dose). All comparator vaccines contained 15 μg HA per vaccine strain; participants in comparator treatment arms received 45 μg HA per dose as all comparator vaccines were trivalent. A total of 2,242 participants (19.1%) in 10 trial arms received a placebo (saline) and 1,066 participants (9.1%) received no intervention. No data were reported for two no-intervention treatment arms, which were therefore excluded from the analysis. Other placebo or no-intervention arms that contained eligible data were included in the safety analysis and excluded from the immunogenicity analysis. Further details on study design and trial arms in each trial are presented in the Supplementary Materials, Figure D (Extended data).\n\nNo SAEs or deaths were reported in any of the trials. Overall, local reactions (at least one) occurred in 646 of 10,405 participants (6.2%), and at least one systemic reaction occurred in 495 of 10,348 participants (4.8%). The difference in number of total participants was a consequence of exclusion of what trial authors identified as intercurrent trivial events that were reported in some of the original papers. Single Rlr and Rsr values were grouped according to treatment type, and their distributions were plotted against total HA per vaccine dose (Figure 2) reaching from no HA (placebo and no-intervention arms) to 45 μg HA (comparator vaccines). Reaction rate values (Rlr and Rsr) were <6.0% for most treatment arms. Notably, the largest Rlr value (35.5%) occurred in a comparator vaccine treatment arm, and the largest Rsr value (24.3%) in a placebo arm.\n\nLegend: Symbols represent local and systemic reaction rate estimates from single intervention arms, arranged according to increasing total vaccine dose.\n\nIn randomised trials, rate differences (RD) between reaction rates of AZB-SU vaccines and other treatment types (placebo or comparator vaccines) could be calculated (Figure 3). For local reactions, most 95% CIs included 0. However, AZB-SU tended to have lower Rlr compared with comparator vaccines and higher Rlr compared with placebo. In the meta-analysis, pooled RDlr values differed significantly between AZB-SU and comparator vaccines (-2.3%; 95% CI: -3.8 to -0.7). For systemic reactions, no such trend was observed, and pooled RDsr values were not significantly different between treatment types. Meta-regression analysis revealed a positive correlation between reaction rate and total amount (μg) HA per vaccine dose for local reactions (P=0.03), but not for systemic reactions. There was a positive correlation between both Rlr and Rsr with mean age up to a mean of 60 years; reaction rates dropped sharply at higher mean ages. There was no correlation between AZB-SU Rlr or Rsr and health status. Other possible modulators of reactogenicity were not analysed as they were reported in only a few trials. None of the various meta-regression models involving a dummy variable representing AZB content showed evidence of reactogenicity associated with AZB: Reaction rates were similar when adjusted for total HA per dose and mean age (Extended data, Figure E). Funnel plots constructed from logarithmic local and systemic rate ratios were largely symmetrical.\n\nReaction rate difference values.\n\nLegend: Minuend: AZB-SU1996 in trials T01, T03, T06, T07, T08, T10, T14 and T16; AZB-SU2008 in T13, T18, T19, T21, T23, T27 and T28; AZB-SU2018 (20 μg HA) in T29 and T30. Subtrahend bridging studies: AZB-SU1996 2 times 2.5 μg HA in T08; AZB-SU2008 in T14, T29 and T30; PO- SUTC in T16 and T19. Subtrahend non-adjuvanted IIV: whole virus in T01; subunit in T10, T18, T21, T23, T27 and T28; subunit and split combined in T07. For trial numbers, see Supplementary Materials, Figure B and C. T06 was divided into two age groups. MA RD, meta-analysed (pooled) rate difference.\n\nThe immunogenicity analysis included data from 3,311 participants and 9,408 pre- and post-vaccination GMT pairs gathered from 28 intervention arms and 80 antibody sub-arms from 15 trials. A non-inferiority analysis comparing post-vaccination GMT values of AZB-SU and non-adjuvant comparator vaccines was performed using data from five trials (Figure 4, middle panel). In three trials (Trial 01, Trial 23 and Trial 27), the 95% CIs of GMTR (AZB-SU: comparator) included 1, which indicated that the GMT values were not significantly different between treatment types. In Trial 10, the GMTR of all three viral strains had 95% CIs much higher than 1.0; AZB-SU vaccine GMT values were eight– to nine–fold higher than that of the comparator vaccine (AZB-SU: 239–448; comparator: 30–48). In Trial 07, the only trial performed in elderly participants (>60 years), 95% CIs were lower than 1.0 for all three strains. Comparator GMT values were one to two-fold higher than those of AZB-SU (Table 2). This result was explored further by evaluating whether the difference in antibody titer was associated with lower antibody-predicted clinical protection for AZB-SU vaccines. The post-PRab values ranged from 81.0% to 94.7% in AZB-SU treatment arms and from 87.5% to 97.8% in comparator arms. The respective ratios included 1.0, which indicated that protection was similar between AZB-SU and non-adjuvant comparator.\n\nGeometric mean titre ratios.\n\nLegend: AZB-SU mutual: T14A: AZB-SU2008 vs. AZB-SU1996; T16A: AZB-SUTC vs. AZB-SU1996; T19: AZB-SUTC vs. PO- SU2008; T14B: AZB-SU2008 10 μg HA vs. AZB-SU1996 5 μg; T16B: AZB-SUTC 10 μg HA vs. AZB-SU1996; T20: AZB-SU2008 10 μg HA vs AZB-SU2008. AZB-SU vs. non-adjuvanted inactivated influenza vaccine (IIV): T01, T07, T10: AZB-SU1996; T23, T27: AZB-SU2008. QIV vs. TIV: QIV, quadrivalent influenza vaccine; TIV: trivalent influenza vaccine; Y, B/Yamagata; V: B/Victoria. Non-inferiority is demonstrated if the lower limit of the 95% confidence interval around the GMTR value (QIV versus TIV) is larger than the pre-defined non-inferiority margin of 0.67. Superiority is demonstrated if the lower limit of the 95% CI around the GMTR is larger than the pre-defined superiority margin of 1.5.\n\n* atypical influenza B component in 2008.\n\nA non-inferiority trial in adults aged 18–60 years compared the quadrivalent AZB-SU formulation with two trivalent non-adjuvant comparators (Trial 30), of which one contained B/Yamagata and the other contained B/Victoria. Non-inferiority of quadrivalent AZB-SU to trivalent AZB-SU was demonstrated for all three common strains (Figure 4, right panel), and superiority of quadrivalent AZB-SU to trivalent AZB-SU for the B strain not included in the trivalent formulation.\n\nThe former re-licensing criteria of the CPMP needed to be evaluated in groups of 50 adult participants or more.19 This requirement was met in 29 trial sub-arms from seven trials. Seroconversion rates, seroprotection rates and mean geometric increase after AZB-SU vaccination were higher than the CPMP thresholds set for adults aged 18–60 years and elderly adults in the majority of sub-arms; all 29 arms met at least one of these criteria (Extended data, Figure H).\n\n\nDiscussion\n\nThe current work analysing the available clinical evidence supports the hypothesis that across all age groups, the inclusion of azoximer bromide as an adjuvant to influenza subunit vaccine does not cause any increase in reported local or systemic reactions following vaccination. This conclusion particularly holds in elderly and vulnerable populations, the main target groups for yearly influenza vaccinations. Similarly, we noted that the antigen-sparing approach of including AZB and reducing total antigen (5 μg versus 15 μg HA per strain), resulted in similar antibody responses to non-adjuvanted vaccines in non-elderly patients; however, more data is necessary to make this conclusion for older populations.\n\nReview of the available safety data suggests that AZB-SU vaccines are associated with fewer local reactions compared with vaccines that contained higher amounts of HA antigen; the incidence of systemic reactions, however, appears to be similar for AS-SU and other vaccines. This finding is congruent with observations made in large clinical trials, which showed an overall higher average rate of local reactions with higher HA per dose but little or no difference in the rate of systemic reactions.31,32 The similarity in the systemic reaction rates between AZB-SU, placebo and comparator vaccines, suggests that the reporting of such systemic reactions was most likely to have been attributable to the act of intramuscular injection, or reflects little more than the everyday incidence of trivial symptoms that people experience; indeed, treatment arms in two trials (Trial 02 and Trial 08) had elevated Rsr values even though participants received no treatment. A symptomatic complex of systemic reactions following vaccination during pregnancy has been described, which was most often associated with psychological state and anxiety of the development of AEs in response to vaccination.33\n\nThe intrinsic reactogenicity of AZB could not be determined directly, in the absence of randomised clinical trials comparing SU vaccines with identical amounts of HA, but with or without AZB. However, meta-regression analysis of the available data detected no difference in reaction rates after adjustment for mean age and the amount of HA administered, and predicted that AZB was not associated with intrinsic reactogenicity.\n\nNo SAEs of an allergic or neurological nature were reported in any of the trials selected for review, covering a total population of 11,736 participants. While this suggests a low risk of SAEs, a formal conclusion cannot be drawn as it exceeds the power of clinical trials to detect very rare events. However, favourable safety data come from a previous mass vaccination trial with AZB-SU that reviewed vaccination in nearly 420,000 paediatric participants and reported no more than 33 allergic SAEs (incidence: 0.008%; one event per 12,700 participants vaccinated) and no SAEs that were neurological in nature.34\n\nThe immunogenicity data collected on more than 3,000 participants across 15 studies generally supported the antigen-sparing effect of AZB, maintaining efficacy although the amount of HA in AZB-SU was only a third of the standard dose in comparable non-adjuvanted influenza vaccines. It was clear that AZB-SU vaccines induced antibody production in both children and adults up to 60 years at levels similar to those noted with comparator vaccines. This observation was seen for all comparisons except for one study in favour of AZB-SU (Trial 10; see Figure 4, middle panel) which remains unexplained but may result from a data artefact. The data from older adults (>60 years) were less robust, based on only three sub-arms. Analysis on post-PRab showed that clinical protection was not compromised in the AZB-SU vaccinees. Seroprotection and seroconversion data in AZB-SU treatment arms revealed that AZB-SU would have met CPMP criteria for annual re-licensing of vaccines in the European Union in both adults aged 18–60 years and adults >60 years.\n\nA possible limitation of this study is its partial reliance on reports provided by the manufacturer. The sponsor’s clinical study reports had not undergone peer review, although the data from many of them were published in peer-reviewed journals. However, it is expected that these reports were prepared in line with good clinical practice, with a view to submission to regulatory agencies, and were therefore conducted robustly, countering the potential for any selection or interpretation bias. Review of the funnel plot data for reactogenicity variables showed no evidence of bias. In addition, during the preparation of this article, two new studies assessed the safety and immunogenicity of the quadrivalent vaccine. Their findings are in line with those reported here, and they also provide supportive information on the practical use of quadrivalent AZB-SU vaccines.35,36\n\nIn conclusion, the favourable safety profile and immunogenicity of AZB-SU vaccines, along with the reduced amount of antigen per dose and sparing effect of AZB, make AZB-SU vaccines good candidates for use not only during a pandemic or limited national capacity of vaccine production, but in general for seasonal influenza vaccination. Future research will be directed towards evaluating whether AZB also shows an antigen-sparing effect in elderly patients undergoing vaccination.\n\n\nData availability\n\nZenodo: Grippol Supplementary Files, https://doi.org/10.5281/zenodo.622194237\n\nThis project contains the following underlying data:\n\n- Grippol_Paper_Supplementary_Material.docx (Figure B; list of eligible publications)\n\nZenodo: Grippol Supplementary Files, https://doi.org/10.5281/zenodo.622194237\n\nThis project contains the following extended data:\n\n- Grippol_Paper_Supplementary_Material.docx\n\n- README_file.txt.docx\n\nZenodo: PRISMA checklist for “Analysis of the safety and immunogenicity profile of an azoximer bromide polymer-adjuvanted subunit influenza vaccine”, https://doi.org/10.5281/zenodo.622194237\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThis is an updated and extended version of a Clinical Expert Report to Petrovax Pharm (2017). RK presented parts of this investigation at the symposium ‘100 years of the Spanish Flu pandemic. New opportunities of influenza vaccination’ within the Fifth Russian Scientific Conference ‘Infectious Diseases - Current Problems, Treatment and Prevention’ in Moscow, Russia on May 24, 2018, and the conference ‘Influenza Vaccines for the World’, Edinburgh, Scotland, UK, April 4, 2019.\n\nThe authors wish to thank Mimoun Boulfich, BSc University of Amsterdam, The Netherlands, for acting as second reviewer during data extraction, assemblage and review of the working databases, and the colleagues of NPO Petrovax Pharm for supporting the literature search and providing unpublished documents.\n\n\nReferences\n\nWorld Health Organisation: Influenza fact sheet.2018. Accessed November 6, 2018. Reference Source\n\nCenters for Disease Control and Prevention, Seasonal influenza vaccine effectiveness, 2005–2018. Accessed 26 July 2018. Reference Source\n\nOzawa S, et al.: Modeling the economic burden of adult vaccine-preventable diseases in the United States. Health Aff. (Millwood). 2016; 35: 2124–2132. PubMed Abstract | Publisher Full Text\n\nEsposito S, Principi N; European Society of Clinical Microbiology Infectious Diseases (ESCMID) Vaccine Study Group (EVASG). Influenza vaccination and prevention of antimicrobial resistance. Expert Rev. Vaccines. 2018 Oct; 17(10): 881–888. Publisher Full Text\n\nde Vries RD , Altenburg AF, Rimmelzwaan GF: Universal influenza vaccines, science fiction or soon reality?. Expert Rev. Vaccines. 2015; 14(10): 1299–1301. Publisher Full Text\n\nKostinov MP, Akhmatova NK, Khromova EA, et al.: The impact of adjuvanted and non-adjuvanted influenza vaccines on the innate and adaptive immunity effectors. IntechOpen Book Series. Infectious Diseases, Vol. 1. Influenza. Therapeutics and Challenges. Saxena SK, editor. 2018; p. 83–109. Publisher Full Text\n\nAltenburg AF, Rimmelzwaan GF, de Vries RD : Virus-specific T cells as correlate of (cross-) protective immunity against influenza. Vaccine. 2015 Jan 15; 33(4): 500–506. PubMed Abstract | Publisher Full Text\n\nSubbarao K, Murphy BR, Fauci AS: Development of effective vac- cines against pandemic influenza. Immunity. 2006; 24(1): 5–9. Publisher Full Text\n\nTreanor JJ, Wilkinson BE, Masseoud F, et al.: Safety and immunogenicity of a recombinant hemagglutinin vaccine for H5 influenza in humans. Vaccine. 2001; 19: 1732–1737. PubMed Abstract | Publisher Full Text\n\nNicholson KG, Colegate AE, Podda A, et al.: Safety and antigenicity of non- adjuvanted and MF59-adjuvanted influenza A/duck/Singapore/97 (H5N3) vaccine: a randomised trial of two potential vaccines against H5N1 influenza. Lancet. 2001; 357: 1937–1943. PubMed Abstract | Publisher Full Text\n\nTreanor JJ, Campbell JD, Zangwill KM, et al.: Safety and immunogenicity of an inactivated subvirion influenza A (H5N1) vaccine. N. Engl. J. Med. 2006; 354: 1343–1351. PubMed Abstract | Publisher Full Text\n\nAtmar RL, Keitel WA, Patel SM, et al.: Safety and immunogenicity of nonadjuvanted and MF59-adjuvanted influenza A/H9N2 vaccine preparations. Clin Infect Dis: Off Publ Infect Dis Soc Am. 2006; 43: 1135–1142. PubMed Abstract | Publisher Full Text\n\nKhalaj-Hedayati A, Chua CLL, Smooker P, et al.: Nanoparticles in influenza subunit vaccine development: Immunogenicity enhancement. Influenza Other Respir. Viruses. 2020; 14(1): 92–101. PubMed Abstract | Publisher Full Text\n\nTregoning JS, Russell RF, Kinnear E: Adjuvanted influenza vac- cines. Hum. Vaccin. Immunother. 2018; 14(3): 550–564. PubMed Abstract | Publisher Full Text\n\nHehme N, Engelmann H, Kunzel W, et al.: Pandemic preparedness: lessons learnt from H2N2 and H9N2 candidate vaccines. Med Microbiol Immunol (Berl). 2002; 191: 203–208. PubMed Abstract | Publisher Full Text\n\nBresson JL, Perronne C, Launay O, et al.: Safety and immunogenicity of an inactivated split-virion influenza A/Vietnam/1194/2004(H5N1) vaccine: phase I randomised trial. Lancet. 2006; 367: 1657–1664. PubMed Abstract | Publisher Full Text\n\nBeyer WEP, Palache AM, Reperant LA, et al.: Association between vaccine adjuvant effect and pre-seasonal immunity. Systematic review and meta-analysis of randomised immunogenicity trials comparing squalene-adjuvanted and aqueous inactivated influenza vaccines. Vaccine. 2020; 38: 1614–1622. PubMed Abstract | Publisher Full Text\n\nBachmayer H, Schmidt G, Liehl E: Preparation and properties of a novel influenza subunit vaccine. Postgrad. Med. J. 1976; 52: 360–367. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCommittee for Proprietary Medicinal Products (CPMP), CPMP: Note for guidance on preclinical pharmacological and toxicological testing of vaccines (CPMP/SWP/565/95 adopted December 97).1997. Reference Source\n\nGrivtsova LY, Falaleeva NA, Tupitsyn NN: Azoximer bromide: mystery, serendipity and promise. Front. Oncol. 2021; 11. Publisher Full Text\n\nKabanov VA: From synthetic polyelectrolytes to polymer-subunit vaccines. Pure Appl. Chem. 2004; 76: 1659–1677. Publisher Full Text\n\nIvanova AS, Puchkova NG, Nekrasov AV, et al.: Polyoxidonium adjuvant effect mechanisms. Hæmatopoïesis Immunol. 2015; 13: 30–92.\n\nTalayev V, Zaichenko I, Svetlova M, et al.: Low-dose influenza vaccine Grippol Quadrivalent with adjuvant Polyoxidonium induces a T helper-2 mediated humoral immune response and increases NK cell activity. Vaccine. 2020; 38: 6645–6655. PubMed Abstract | Publisher Full Text\n\nMoher D, Liberati A, Tetzlaff J, et al.: PRISMA Group: Preferred reporting items for systematic reviews and meta-analyses: the PRISMA Statement. BMJ. 2009; 339: b2535. PubMed Abstract | Publisher Full Text\n\nCoudeville L, Bailleux F, Riche B, et al.: Relationship between haemagglutination-inhibiting antibody titres and clinical protection against influenza: development and application of a bayesian random-effects model. BMC Med Res Methol. 2010; 10: 18. PubMed Abstract | Publisher Full Text\n\nBeyer WEP, Nauta JJP, Palache AM, et al.: Immunogenicity and safety of inactivated influenza vaccines in primed populations: A systematic literature review and meta-analysis. Vaccine. 2011; 29: 5785–5792. PubMed Abstract | Publisher Full Text\n\nCoudeville L, Andre P, Bailleux F, et al.: A new approach to estimate vaccine efficacy based on immunogenicity data applied to influenza vaccines administered by the intradermal or intramuscular routes. Hum. Vaccin. 2010; 6: 841–848. PubMed Abstract | Publisher Full Text\n\nNauta JJP, Beyer WEP, Osterhaus ADME: On the relationship between antibody response to influenza vaccination, seroprotection and clinical protection from influenza. Biologicals. 2009; 37: 216–221. PubMed Abstract | Publisher Full Text\n\nSterne JAC, Egger M: Funnel plots for detecting bias in meta-analysis: Guidelines on choice of axis. J. Clin. Epidemiol. 2001; 54: 1046–1055. Publisher Full Text\n\nBorenstein M, Hedges L, Higgins J, Rothstein H: Comprehensive Meta Analysis software programme (Version 3).2014.\n\nBeyer WEP, Palache AM, Kerstens R, et al.: Gender differences in local and systemic reactions to inactivated influenza vaccine, established by a meta- analysis of fourteen independent studies. Eur. J. Clin. Microbiol. Infect. Dis. 1996; 15: 65–70. PubMed Abstract | Publisher Full Text\n\nNichol KL, Margolis KL, Lind A, et al.: Side effects associated with influenza vaccination in healthy working adults. A randomized, placebo-controlled trial. Arch. Intern. Med. 1996; 156: 1546–1550. PubMed Abstract | Publisher Full Text\n\nKostinov MP, Cherdantsev AP, Akhmatova NK, et al.: Immunogencity and safety of subunit influenza vaccines in pregnant women. ERJ Open research. 2018; 4: 00060–02017. Publisher Full Text\n\nLuss AS, Kostinov MP, Bakhmatova OB, et al.: Results of post- vaccination reactions in children of Perm Krai after influenza vaccination. Vaccination. 2007; 50: 8–10. (Russian).\n\nKostinova AM, Akhmatova NK, Latysheva EA, et al.: Assessment of immunogenicity of adjuvanted influenza vaccine in healthy people and patients with common variable immune deficiency. Front. Immunol. 1876; 2020: 11.\n\nKostinov MP, Latysheva EA, Rjstinova AM, et al.: Immunogenicity and Safety of the Quadrivalent Adjuvant Subunit Influenza Vaccine in Seropositive and Seronegative Healthy People and Patients with Common Variable Immunodeficiency. Vaccine. 2020; 8: 640. PubMed Abstract | Publisher Full Text\n\nKompier R, Neels P, Beyer W, et al.: Grippol Supplementary Files [Data set]. Zenodo. 2022. Publisher Full Text"
}
|
[
{
"id": "123089",
"date": "15 Mar 2022",
"name": "Marek Petra",
"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\n1) Abstract The main results were obtained by quantitative meta-analysis. It would be appropriate to state it also in the abstract.\n2) Introduction It will be suitable to better describe azoximer bromide, i.e. if it is used in some medical products, if it is a pharmacopoeial substance, etc.\n3) Materials and methods A meta-analysis was conducted, therefore the MOOSE assessment (Meta-analysis of Observational Studies in Epidemiology) is missing. In addition, the authors omitted the bias risk assessment according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) guidelines. It is not clear if the study outcome can be burdened by this risk of bias.\nThe fixed-effects method is applied in the case of studies' homogeneity. There is no explanation of the I-V method, i.e. the selection criteria. Furthermore, the random-effects method helps to evaluate the literary bias. Therefore, both results are required.\n4) Results Page 13, line 268: \"The respective ratios included 1.0...\", this should read: \"The confidence interval of appropriate ratios included…\".\n5) Discussion Influenza vaccine is a specific vaccine depending on seasonal influenza strains changing every year. Therefore, it should be discussed whether this specific feature of influenza seasons had an effect on the immunogenicity and, possibly, the safety of the adjuvanted influenza vaccine being evaluated.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "8961",
"date": "31 Oct 2022",
"name": "Tim Hardman",
"role": "Author Response",
"response": "1) Abstract Comment: The main results were obtained by quantitative meta-analysis. It would be appropriate to state it also in the abstract. Response: The initial wording of the abstract was unintentionally misleading and placed undue emphasis on the term ‘meta-analysis’. The main results of this study were obtained through systematic review and consisted of various point estimates from single trials/trial arms. The pooled rate differences discussed, and incorporated in Figure 3, are averages of the rate difference estimates from the involved trials, weighted by their inverse variance. This method was adopted over other techniques, such as unweighted average, and overall median, due to its superior accuracy. The results of this method are purely descriptive in nature, offering no particular conclusion beyond the expected result that the PO vaccine and comparators are similar in reactogenicity. The wording has been altered to more accurately portray the importance of anything related to meta-analysis. 2) Introduction Comment: It will be suitable to better describe azoximer bromide, i.e. if it is used in some medical products, if it is a pharmacopoeial substance, etc. Response: Additional information has been added to the Introduction to briefly expand upon the usages of azoximer bromide. 3) Materials and methods Comment 1: A meta-analysis was conducted, therefore the MOOSE assessment (Meta-analysis of Observational Studies in Epidemiology) is missing. Response: As mentioned in the earlier response, the term ‘meta-analysis’ was afforded undue importance. Originally the manuscript incorporated both a systemic review and meta-analysis, with the latter becoming less important and ultimately relegated into a hypothesis-creating tool as opposed to a central component of the study, as the significance of the data identified by the systematic review became more apparent. As such, the full MOOSE assessment was determined to be extraneous to the study in the context of the data from which the manuscript’s conclusions are drawn. Comment 2: In addition, the authors omitted the bias risk assessment according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) guidelines. It is not clear if the study outcome can be burdened by this risk of bias. Response: As mentioned earlier, the importance of the meta-analysis in this manuscript was over-stated, with the results being generated by a systematic review. As such the bias risk assessment was not determined to be necessary for the finished manuscript. Comment 3: The fixed-effects method is applied in the case of studies' homogeneity. There is no explanation of the I-V method, i.e. the selection criteria. Furthermore, the random-effects method helps to evaluate the literary bias. Therefore, both results are required. Response: The I-V method, and random effects methods were both part of the meta-analysis, which, as mentioned, was relegated to a hypothesis-creating tool only. 4) Results Comment: Page 13, line 268: \"The respective ratios included 1.0...\", this should read: \"The confidence interval of appropriate ratios included…\". Response: Thank you for pointing out this oversight, a more accurate phrasing of the sentence that is closer to its original intent, has been drafted. 5) Discussion Comment: Influenza vaccine is a specific vaccine depending on seasonal influenza strains changing every year. Therefore, it should be discussed whether this specific feature of influenza seasons had an effect on the immunogenicity and, possibly, the safety of the adjuvanted influenza vaccine being evaluated. Response: This is an excellent point to raise and has been added to the potential limitations of this study. Members of the authorship have conducted some investigations into the impact of these features of influenza in the context of a different adjuvant, but the level of data available in this study was insufficient to investigate it here."
}
]
},
{
"id": "149675",
"date": "21 Sep 2022",
"name": "Lyazzat Yeraliyeva",
"expertise": [
"Reviewer Expertise infection diseases",
"vaccination",
"epidemiology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe relevance of the research topic is beyond doubt. Influenza is a serious disease causing various complications and deaths in infants, elderly people, and patients with chronic diseases. Vaccination is still the most effective method of influenza prevention.\nToday, there are 5 generations of influenza vaccines, and the authors carried out a systematic review and analysis of 30 clinical trials of various study designs, including 11,736 participants aged 6 months to over 60 years; the study was aimed at the reactogenicity, safety, and immunogenicity comparison of an inactivated adjuvanted influenza vaccine (AZB-SU vaccines) containing low antigen 5 µg HA per strain (with addition of azoximer bromide 500 µg) and non-adjuvanted vaccines containing antigen 15 µg HA.\n1. Abstract It is advisable to indicate in the abstract the meta-analysis period\n2. Introduction Provide a detailed information on the azoximer bromide adjuvant (Polyoxidonium), specifically its pharmacological properties.\n3. Methods In the \"Definitions and outcomes\" and \"Statistical analyses\" subsections, authors indicate the treatment outcomes, but the vaccination outcomes are required. To be clarified.\n4. Results It is necessary to clarify the period of meta-analysis carried out by the authors, since the period from 1993 to 2016 is indicated in the \"Characteristics of studies\" section, and 1998-2018 in the \"Methods\" section.\n5. Discussion It is necessary to discuss whether the presence of chronic diseases affected immunogenicity depending on the vaccine type used with different antigens and adjuvants content. Besides, it is necessary to discuss the immunogenicity issues\nReviewing this article, I would like to note that the systematic review is of undoubted scientific and practical importance and will be of interest both among a wide range of medical workers, immunologists, epidemiologists, and among public health professionals.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "8962",
"date": "31 Oct 2022",
"name": "Tim Hardman",
"role": "Author Response",
"response": "1) Abstract Comment: It is advisable to indicate in the abstract the meta-analysis period Response: The meta-analysis period has been included in the draft of the manuscript, as recommended. 2) Introduction Comment 2: Provide a detailed information on the azoximer bromide adjuvant (Polyoxidonium), specifically its pharmacological properties. Response: Thank you for your comment. A lot of the pharmacological information about azoximer bromide, including mechanism(s) of action and target(s) are still under investigation. However, the authorship believes all the relevant information has been included in the revised manuscript. 3) Materials and methods Comment: In the \"Definitions and outcomes\" and \"Statistical analyses\" subsections, authors indicate the treatment outcomes, but the vaccination outcomes are required. To be clarified. Response: The vaccination outcomes are the treatment outcomes described. In this context ‘treatment outcome’ was used in a statistical sense, as opposed to the strict medical definition of the term, as this includes both the placebo and no-intervention arms. 4) Results Comment: It is necessary to clarify the period of meta-analysis carried out by the authors, since the period from 1993 to 2016 is indicated in the \"Characteristics of studies\" section, and 1998-2018 in the \"Methods\" section. Response: The period of meta-analysis has been clarified in both the abstract and the results section. 5) Discussion Comment: It is necessary to discuss whether the presence of chronic diseases affected immunogenicity depending on the vaccine type used with different antigens and adjuvants content. Besides, it is necessary to discuss the immunogenicity issues Response: This is another great, relevant point to raise and has also been added to the potential limitations of this study. The presence of chronic diseases and their impact on immunogenicity in the context of different antigens and adjuvants, are areas the authorship have involvement in, but again, the level of data available in this study was insufficient to investigate it here."
}
]
}
] | 1
|
https://f1000research.com/articles/11-259
|
https://f1000research.com/articles/11-1247/v1
|
02 Nov 22
|
{
"type": "Research Article",
"title": "Psychosocial- and disclosure-related challenges among HIV-serodiscordant couples: an interpretative phenomenological analysis study",
"authors": [
"Constance Matshidiso Lelaka",
"Livhuwani Tshivhase",
"Idah Moyo",
"Nthomeni Dorah Ndou",
"Azwihangwizi Hellen Mavhandu-Mudzusi",
"Livhuwani Tshivhase",
"Idah Moyo",
"Nthomeni Dorah Ndou",
"Azwihangwizi Hellen Mavhandu-Mudzusi"
],
"abstract": "Background: Serodiscordant refers to a couple where one has human immunodeficiency virus (HIV), and the other partner is HIV negative. HIV-serodiscordancy often results in diverse psychological and emotional challenges. Evidence demonstrates that the dynamics of living in an HIV-serodiscordant relationship are often stressful. This study explored the psychosocial- and disclosure-related challenges faced by couples in HIV-serodiscordant relationships in South Africa. Methods: An interpretative phenomenological analysis (IPA) design was followed. A total of 13 HIV-serodiscordant partners were purposively sampled. Data were collected through individual face-to-face interviews and analysed using the IPA framework. Results: The findings indicated that HIV-serodiscordant couples experienced diverse psychosocial challenges such as shock, sadness, hurt, denial and disbelief. Participants also experienced challenges such as selective disclosure and fear of further disclosure. Conclusions: The findings have implications for public health and are critical in programming and designing couple-based HIV care interventions. Couples in HIV-serodiscordant relationships would benefit more from differentiated, client-centred psychosocial support. To contribute to the HIV epidemic control and reduction of new HIV infections, specific interventions such as couples counselling, disclosure counselling, support groups, health education and safer conception risk reduction strategies need to be implemented.",
"keywords": [
"HIV-serodiscordant couples",
"serodiscordancy",
"psychosocial",
"disclosure",
"challenges"
],
"content": "Introduction\n\nSerodiscordant couples are a major source of human immunodeficiency virus (HIV) transmission in the sub-Saharan Africa region and evidence estimates their contribution to be about 30% of all new infections occurring in this region (Chihana, Ellman, Poulet, Garone, Ortuno, Wanjala, Masiku, Etard, Davies & Maman, 2021). HIV serodiscordancy often results in diverse psychological and emotional challenges. Evidence demonstrates that the dynamics of living in an HIV-serodiscordant relationship are often stressful (Martins, Canavarro & Pereira, 2021). HIV-serodiscordant couples experience psychological, social and sexual challenges. The challenges determine decision-making in all aspects of the couple’s lives. Challenges such as disease acquisition, transfer of HIV to the uninfected partner and fertility decisions are all sources of conflict (Mendelsohn, Calzavara, Daftary, Mitra, Pidutti, Allman & Myers, 2015).\n\nAccording to the Joint United Nations Programme on HIV/AIDS (UNAIDS, 2019), in 2018, 37.9 million people were living with HIV (PLHIV) worldwide, 1.7 million had new HIV infections with 61% of these being in sub-Saharan Africa and there were 770,000 AIDS-related deaths globally. According to (Statistics SA, 2021), South Africa has been reported to have the highest HIV epidemic in the world compared to other countries, and a total of approximately 7.7 million people are living with HIV in the continent. The prevalence of HIV among the general population has been reported to as high as 20.4%. Thus, such prevalence is also higher in the following population groups e.g., people who inject themselves with drugs, transgender women, men who have sex with men and sex workers.\n\nMen living in a serodiscordant relationship often have reproductive goals that can increase the HIV-transmission risk to their partners (Mathenjwa, Khidir, Milford, Mosery, Greener, Pratt, O’Neil, Harrison, Bangsberg, Safren & Smit, 2022). Transmission of HIV may be reduced by earlier initiation of antiretroviral therapy (ART), medical male circumcision and the use of Pre-Exposure Prophylaxis (PrEP). However, for these strategies to be effectively implemented, couples counselling that is tailored to the needs of this group is of paramount importance. Additionally, the Joint United Nations Programme on HIV/AIDS (UNAIDS, 2019) indicates that the effective expansion of PrEP provision requires attracting people who are at high risk of HIV infection, serodiscordant couples being one example, and supporting its proper use and adherence.\n\nSerodiscordant couples experience diverse psychological challenges resulting in shock, sadness, hurt, denial and disbelief. Their relationship also revolves around challenges related to trust between partners, communication issues, HIV-related stigma, HIV risk perceptions, partner support and decision-making processes between relationships (Larki, Latifnejad-Roudsari, Bahri & Moghri, 2020). Challenges may lead to an impaired ability to maintain therapeutic marriage relationships.\n\nAfter receiving HIV-serodiscordant results, couples are shocked and stressed. Shock and stress occur out of the fear of the risk of the increased spread of HIV. Seronegative partners in a serodiscordant relationship are at higher risk of HIV transmission in comparison with the negative serodiscordant one (Mavhandu-Mudzusi, Lelaka & Sandy, 2014). Living within an HIV-serodiscordant relationship has been recognised as a stressful experience for both HIV-infected and HIV-uninfected partners (Martins et al., 2021). Shock and stress are manifested by sadness, hurt, denial and disbelief. Evidence has demonstrated that living in an HIV-serodiscordant relationship results in diverse psychological and emotional challenges (Kumwenda, Corbett, Choko, Chikovore, Kaswaswa, Mwapasa, Sambakunsi, Gutteberg, Gordon, Munthali & Desmond, 2019; Martins et al., 2021). Additionally, the non-disclosure by such partners makes it difficult for the family members to provide additional social support to the couple (Dessalegn, Hailemichael, Shewa-Amare, Sawleshwarkar, Lodebo, Amberbir & Hillman, 2019; Siegel, Meunier & Lekas, 2018). According to Mashaphu (2018), a significant challenge when it comes to infected individuals disclosing their status, is mainly due to the fear of stigma or the feeling of guilt after contracting the virus. Mashaphu (2018) also reported on instances of intimate partner violence among couples in HIV serodiscordancy. Additionally, the HIV seronegative spouses of People Living with HIV AIDS suffered from instances of stigma (Siegel, Meunier & Lekas, 2018). The study explored the psychosocial- and disclosure-related challenges faced by couples in HIV-serodiscordant relationships in South Africa.\n\n\nMethods\n\nAn interpretative phenomenological approach was chosen as an appropriate design for this study. The design is praised for its ability to delve deeply into the participants’ lived experiences (Qutoshi, 2018; Creswell & Creswell, 2018). The design was used to explore and describe the psychosocial- and disclosure-related challenges as “lived experiences” of HIV-serodiscordant couples from the point of view of those who have lived it (Qutoshi, 2018; Ellis, 2016). The approach was chosen to understand the event at a deeper level of consciousness; to help explore our own nature as researchers and to bring transformation at a personal level (Qutoshi, 2018, Smith & Osborn, 2015; Creswell & Creswell, 2018). The researchers selected this approach as the best to explore and describe the psychosocial- and disclosure-related challenges of the HIV-serodiscordant couples as experienced by them. This study followed the COREQ checklist (Lelaka, 2022).\n\nEthical approval of the study was received from the Ethics Committee of University of South Africa (HSHDC/608/2017) on 15/02/2017. Permission to conduct the research study was also received from the Department of Health Gauteng Province and the Chief Executive Officer (CEO) of the hospital. Written informed consent was sought before the interviews were conducted, participants were informed prior about the upcoming study that would take place. Confidentiality and anonymity were ensured through the use of pseudo names and age ranges, instead of exact ages. The hospital name was also not mentioned to protect the hospital’s identity. Ethical principles such as voluntary participation, withdrawal, respect for autonomy, privacy, confidentiality, justice and informed consent were adhered to (Babbie, 2020; Polit & Beck, 2021).\n\nThe research was conducted in an urban public regional hospital situated in South Africa under the Johannesburg district and is affiliated to the University of Witwatersrand. The hospital is a level three institution and offers diverse healthcare services to adolescent children and adults. The hospital collaborates closely with various non-governmental organisations (NGO) both within the hospital and those outside the hospital. It also has specialised clinics that treat mostly patients presenting with tuberculosis (TB)-related and HIV-related diseases. The hospital as such, provides diverse and comprehensive healthcare services to in-patients and out-patients including discordant couples.\n\nThe population for the study was all HIV-serodiscordant couples receiving their treatment at an HIV unit within the regional specialist hospital in Gauteng. A purposively selected study sample comprising of 13 participants, who were in an HIV-serodiscordant relationship at the study site, were recruited with the assistance of the facility counsellor. The researchers received the participants who met the inclusion criteria from the facility counsellor. Both the HIV negative and positive participants took part in the study. All the study participants were interviewed in the counselling room. A total sample size of 13 participants were interviewed and was deemed adequate as supported by Alase (2017) who indicated that in interpretative phenomenological analysis (IPA), two to 25 participants could suffice. Additionally, Kvale (2018) asserted that a sample of six participants or more could be adequate for an interpretative phenomenological design. However, the sample size for this study was determined by data saturation. Data saturation was reached at the stage where no new data emerged and there was redundancy of data already collected (Polit & Beck, 2021).\n\nThe researchers used own judgement in selecting those participants that met the inclusion criteria as follows: heterosexual HIV-serodiscordant couples who have been in stable relationships for at least six months, disclosed their HIV status to either a partner or a family member, aged 18 years old and above, living in Soweto and willing to participate in the study (Polit & Beck, 2021).\n\nThe study excluded heterosexual HIV-serodiscordant couples who had been in stable relationships for less than six months, aged below 18 years old, living outside of Soweto, those who had not disclosed their HIV status and those not willing to participate in the study.\n\nThe researchers developed a semi-structured interview guide for the study and data collection was conducted from October 2017 to December 2018. The guide had several questions that were framed to explore the psychosocial- and disclosure-related challenges experienced by HIV-serodiscordant couples. The development of the interview guide was based on a literature review and the aim of the study guided the questions. The guide can be found as Extended data (Lelaka, 2022).\n\nThe pilot process was helpful since it enabled the researchers to check the feasibility of the approach before embarking on the interviews with the rest of the participants (Brink, van der Walt & van Rensburg, 2012; Babbie, 2020; Ellis, 2016). The researchers were, therefore, able to revise the data collection tool in relation to the demographic section as well as the probes to get more in-depth answers. The data collection tool was initially piloted on two participants and refined post-interview; the data obtained during these sessions was not included in the findings of the study, to prevent contamination of the study results. The purpose of the study was explained and written informed consent was obtained from study participants before proceeding with the data collection and audio-recording of the sessions.\n\nThe semi-structured interview guide questions comprised of one central question posed as: “May you describe the challenges of being in an HIV serodiscordancy relationship?”. Other questions were comprised of open-ended questions with follow-up questions for further clarification (Creswell & Creswell, 2018). Probes followed as directed by what the participants said. The semi-structured interview was chosen for facilitation of rapport, which is vital when the phenomenon of the study is a sensitive matter such as HIV serodiscodancy (DeJonckheere & Vaughn, 2019; De Vos, Strydom, Fouche & Delport, 2016). The guide gave flexibility of coverage and allowed the participants to introduce an issue that the researchers had not thought of. The researchers were directed by the participants on the flow of questions, as the questions were not sequentially followed. The semi-structured interview guide was a good instrument as it allowed the researchers to explore novel areas to get rich data. Participants could tell their stories. An audio tape recorder was used to record all interviews, as consented to by participants deidentified, and stored safely for privacy and confidentiality purposes. Field notes were used to capture notes on physical expressions and gestures (De Vos, Strydom, Fouche & Delport, 2016). Data were collected through in-depth face-to-face interviews in the hospital private counselling rooms. The duration of each interview was about 30 to 45 minutes, and the sessions were conducted in English, Sesotho, or Zulu, depending on the participants’ preferences.\n\nAnalysis of data was done immediately following data collection. The recorded data were transcribed verbatim. The researchers first bracketed their personal experiences related to HIV serodiscordancy to avoid interjecting personal experiences into the lived experiences of the research participants. The four researchers analysed the transcripts independently using an IPA framework (Smith & Osborn, 2015; Alase, 2017). No software was utilised, however, line by line coding analysis was adopted to understand the narratives reported by participants. One experienced researcher was a co-coder who assisted code further with the interview transcripts. For coding to be successful, transcripts were read, this was followed by listening to the audios several times to verify participants interviews. The researcher adopted the following steps by Smith and Osborn (2015): (1) the first step was reading and re-reading transcripts; (2) taking notes to develop themes, taking and developing emergent themes; (3) clustering of the themes; (4) drafting a table of themes, subthemes and other categories identified from the data; (5) checking and identifying the similar related themes; and (6) compiling a single master list composed of the themes and sub-themes. Following this process, all researchers discussed the list of themes and subthemes that emerged from the transcripts and finally agreed to develop a finalised master table describing themes and subthemes. All the subthemes were supported by the excepts from the transcripts of participants (Smith & Osborn, 2015; Creswell & Creswell, 2018).\n\nThe researcher who collected data at the time of the study was a PhD student with interest in doing research to explore serodiscordant couples. The researchers have knowledge of the study location, however – only one researcher (PhD student) used to work at the study location a few years ago as a social worker and was able to access the setting easily since she was familiar with the place. This enabled the researcher to establish a safe, healthy, and professional rapport with participants. However, the researcher did not have any relationship with participants as they did not know each other at the time of the study.\n\nWhile collecting data, in addition to observing research ethics, the researcher also respected social work principles to accept participants for whom they are, understand where they come from and what they are going through. This enabled the researcher to have an open mind and allowed participants to freely share their experiences but ensured she needed to be fair, not impose any personal beliefs, bias, nor allow prejudice or negative perceptions while collecting and analysing data with the team. The narratives of participants were accepted as they shared their own experiences and the researcher was challenged to observe that discordant couples indeed experience a lot of challenges and need further support like other people experiencing HIV challenges. All authors who took part in this paper have research experience and PhD qualification.\n\n\nResults\n\nA total of 13 participants aged 30 to 62 years old who met the inclusion criteria participated in the study (see Table 1). Out of the 13 participants, nine were female and the remaining four were male. With reference to the HIV status, seven female and two male participants were HIV positive. The marital status revealed that the majority (nine) of participants were unmarried with only four being married. Table 1 below presents the demographic data of the study participants.\n\nTable 2 below presents the themes, subthemes and related excepts from the participants of the study.\n\nFollowing the data analysis, two superordinate themes emerged: reactions to HIV serodiscordancy and disclosure issues. Reactions to serodiscordancy emerged as emotional and psychological reactions. Three sub-themes on the emotional reactions and two sub-themes on the psychological reactions emerged. Disclosure-related challenges emerged as selective disclosure and fear of further disclosure. Table 2 provides the summary of the superordinate themes, themes and sub-themes.\n\nEmotional reactions\n\nParticipants reported having reacted differently to the news and the reactions, such as feelings of shock and sadness, were evident in their partners. In nearly all the circumstances, interviewed couples expressed how shocked they were after receiving the news of their status for the first time. This is supported by the following excerpts:\n\nShock\n\n“I was shocked. I felt like dying. This was although I had symptoms that were pointing to that result”. (Nomzamo)\n\nRelated to this, another participant had this to say:\n\n“This has affected me so much as I was shocked when I found out about my status”. (Dumisani)\n\nThe HIV diagnosis shocked not only the infected but also the affected partners, as shown in the following extract:\n\n“This had scared and shocked my partner too. We were not open about it. I guess we were both embarrassed and too scared to talk about it. But we took things very slowly. I thought of my children so much during the first few weeks. Then after 2 to 3 months, things were much better between my partner and I. We were able to talk freely about HIV, and she was there to support me”. (Dudu)\n\nSadness\n\nIn addition to the shock, the participants further admitted that the discovering of their status was a turning point in their relationships. The participants indicated that they felt disturbed and saddened by the apparent betrayal. The extracts illustrate that:\n\n“My partner did not tell me as I had to find out by myself, and that disturbed me so much and I was hurt”. (Lerato)\n\nOther participants recall how they took longer to become composed enough to deliver news of their status to their respective partners:\n\n“After discovering that I was HIV positive, I felt so sad and pained, it took long for me to compose myself and eventually disclose the test results to my partner”. (Khumbu)\n\nParticipants experienced different reactions after finding out the HIV diagnosis and felt hurt after the discovery.\n\nHurt\n\nHurt was also one of the identified emotional experiences highlighted by participants following the HIV test results associated with blame apportioning. A reaction of hurt on hearing about HIV-serodiscordant diagnosis was displayed by participants. This is supported by the following excerpt:\n\n“How was it possible that the results would come out differently for both of us? I believed I was the innocent party”. (Dumisani)\n\nIt was evident that participants reacted differently upon receiving the HIV results after testing, as some were in denial of their HIV status despite being given the test results by healthcare providers.\n\nPsychological reactions\n\nParticipants reacted with denial and disbelief when they first discovered that they were in a serodiscordant relationship.\n\nDenial\n\nSome participants reported that their partners reacted with denial to their HIV status results. Regardless of the results, there were still some challenges related to accepting HIV discordant results by some couples. Some participants’ partners stayed in denial as shown by the excerpt below:\n\n“He thinks it is not true even though he is HIV negative”. (Keneilwe)\n\nDisbelief\n\nHIV positive participants and their partners found themselves in disbelief after receiving their results. Some went to the extent of insisting on having retests. The following extracts show that:\n\n“I could not believe it and was saddened and very stressed about the results. I had to go for a retest”. (Dumisani)\n\nDespite witnessing their partners taking medication daily as evidence that they are infected with HIV, some participants were still in denial and disbelief. This is shown in the following extract:\n\n“I told my partner about my HIV status when I was six months into the current relationship. I tried to explain to him, but he does not believe me even though he could see that I am taking medication. Even now, he does not believe that I am HIV infected. You see, some people are ignorant”. (Khumbu)\n\n“My partner was in disbelief and surprised at the beginning that I have HIV, and he doesn’t have it since we met one year ago”. (Winnie)\n\nThe findings from this study emerged as disclosure and psychosocial challenges experienced by HIV-serodiscordant couples.\n\nParticipants disclosed their HIV status to their preferred and trusted family members. However, not all family members were aware of their HIV status, as they did not inform other family members due to personal reasons. A significant number of interviewed individuals from the couples had not disclosed their status to close family members and relatives at all. Participants had selective disclosure as well as a fear of further disclosure, which was influenced by the stigma attached to the phenomenon.\n\nSelective disclosure\n\nWhen asked about how they view disclosing their HIV status to other people later, most couples promised that they would do so in due time, while others vowed to keep it a secret. Couples’ account that from their understanding of their family members, a message of living with HIV or being married to a person with HIV would not be well received. Just as much as wide shock, disbelief and denial would be expected, there is also a real chance that family members may seek to break the relationships. Furthermore, signs of social stigma were greatly feared by couples who have chosen not to disclose their status. Society around interviewed couples seems to possess a negative opinion, especially since the understanding of HIV-serodiscordant couples is limited. A general social view, today, suggests that if two individuals are sexually involved with each other and one is positive, then the negative one is going to contract the virus as well. Worse still, couples feared workplace stigma arising from disclosure, as workmates begin to look at them differently and probably become reluctant to associate with them. The responses quoted below show selective disclosure:\n\n“I am not comfortable about it; I think it is better if it’s only my parent and sister only who know that. I am scared; I am also scared of the stigma. I can’t do that. We kept this a secret for many years; my sister as well has not told anyone. Even my mom’s status, other family members don’t know about it”. (Khumbu)\n\n“They do not know at all; it’s only my mom that knows. We decided to keep it between us as a couple”. (Khethiwe)\n\nWhile some have felt comfortable to disclose to friends and neighbours, some participants, unfortunately, were not comfortable to share their status and did not disclose it, specifically to their children. Dudu supports this:\n\n“My few friends and neighbours know, but my children do not know at all”. (Dudu)\n\nWhen asked about their reasons for selective disclosure, couples had this to say on why they only allow a select few to know their status:\n\n“Truth is that the other ones are talkative; I do not know how they will take it, but for now my mom and sister know, but people talk too much like I said, I do not want them to know. I do not think they know much about discordant, and I believe they do not understand it so much, I do not think they believe me as well. I told my friend who is my neighbour one day about my HIV status, I also told her that my partner is HIV negative, and she went to tell other people about that”. (Nomzamo)\n\n“From his family, nobody knows only from my family. And from my family, it’s only my mom who knows as the rest don’t know anything. If my family knows they will look at her with bad eyes and treat her badly. So, I don’t want them to know as they will stigmatise her, so I don’t want them to know. It fine for me not to know”. (Khethiwe)\n\nIn other instances, HIV positive partners delayed or completely withheld disclosure of their status from their partners. One HIV negative female participant attested to the following quote:\n\n“When he got the results, he thought I would dump him and was scared to attend at the government clinic because he didn’t want people to see him due to stigma and discrimination”. (Lindiwe)\n\nFear of further disclosure\n\nAfter finding the bravery to at least disclose to select family members, participants indicated that they found it difficult to disclose to other family members.\n\n“No one knows about my HIV status from the family, and I do not want them to know so far. It’s only from my partner’s side”. (Dumisani)\n\n“Part of me does not care if others know, but also part of me does not want. I do not want them to treat me differently, and I am scared they will be hurt. I know my family; they will get hurt. My partner does not want people to know; he does not want that at all”. (Keneilwe)\n\nParticipants showed that they felt more comfortable with those family members they had already disclosed to and could not see any other reason to disclose to other family members as shown below:\n\n“Those who know about my HIV status are fine. I do not want others to know”. (Nomzamo)\n\nParticipants as couples were completely aware of the serodiscordancy status and had accepted their conditions as couples. They experienced challenges when trying to explain serodiscordancy to friends, family and other people. Participants expressed their challenges of disclosure in the following quotes:\n\n“I need to go through this process and explain to people how it is so, which is difficult for me. I struggle to explain as I do not have the right answers, I do not have the right words to explain when they ask me how and why so, it is difficult really”. (Winnie)\n\nThe limited understanding may be a key to explain the likely stigma arising from disclosure, thus the decision to keep quiet as Partner Nine recollects:\n\n“From my experience, people are still ignorant. They do not know anything related to that (serodiscordancy); they do not even know much about general HIV, and they do not know other ways of how one can contract it. They think that even when one uses my cup, they can still get it (HIV)”. (Dudu)\n\n\nDiscussion\n\nHIV serodiscordancy often results in diverse psychological and emotional challenges. Evidence demonstrates that the dynamics of living in an HIV-serodiscordant relationship are often stressful (Martins et al., 2021). The following themes emerged from the study: shock, sadness, hurt, denial and disbelief. This study found that couples reacted with shock on receipt of the HIV positive results for the infected partner. The common thread across studies on HIV serodiscordancy is that, for many couples, the HIV positive diagnosis is stressful, and feelings of shock, hopelessness and fear emerge (Yang, Lewis & Wojnar, 2016). The related findings by Kumwenda, Corbett, Choko, Chikovore, Kaswaswa, Mwapasa, Sambakunsi, Gutteberg, Gordon, Munthali and Desmond (2019) found that the couples reacted with shock on learning that they were in an HIV-serodiscordant relationship. However, the same author highlighted the fact that although there were a few who had developed coping mechanisms, because they already knew from the symptoms, usually, the immediate response was one of immense distress. This was also the finding of this study where some participants already had suspicions about being HIV positive because of the symptoms they had. It also emerged that being aware of the HIV symptoms did not cushion the individual against the shock.\n\nAnother adverse psychological effect after getting an HIV positive result was hurt. This concurs with study findings in Malawi, where these feelings of hurt included crying and blaming oneself (Kasenga, Hurtig, & Emmelin, 2010). Meanwhile, Kumwenda, Corbett, Choko, Chikovore, Kaswaswa, Mwapasa, Sambakunsi, Gutteberg, Gordon, Munthali and Desmond (2019) found that the feelings of hurt also included blame directed at the infected partner, especially if the partner had a previous record of infidelity. These feelings were often accompanied by feelings of betrayal by the partner who was being blamed for introducing HIV into the relationship. Similarly, in this study, the uninfected partners felt not only hurt, but betrayed as well. This study also found that the couples reacted to knowing the dire affliction of their HIV status with sadness. Similar findings were established by Thapa and Yang (2018) in Cambodia, where couples reported feeling sad due to the HIV serodiscordancy. The sadness in women often bordered on anxiety disorders (Darak, Pawar, Phadke, & Kulkarni, 2021). Other findings noted that sadness was accompanied by fear of social disgrace and depression (Pence et al., 2012; Simms et al., 2011).\n\nIn some instances, partners reacted with disbelief of the HIV test results, particularly where one partner was HIV negative and the other was HIV positive. Reconciling the apparent contradictions was difficult. Similar findings were noted in a study in Uganda by King et al., (2012) and in South Africa by Rispel (2011). Both studies reported shock and disbelief concerning the HIV serodiscordancy. The findings of this study showed that some participants reacted with denial to the serodiscordancy. Denial was also associated with fear. A study in Ethiopia by Jibat, Nigussie, & Tesfaye (2014) noted that serodiscordant relationships were characterised by disbelief, denial and fear of HIV transmission, leading to a shift in patterns of sexuality and emotional intimacy. This was despite the fact that the HIV tests were conducted in their presence. Whilst in our study, fear was associated with contracting or spreading HIV, in other studies, fear in serodiscordant couples was linked to intimate partner violence, stigma and discrimination, rejection and loss of intimacy (Maeri et al., 2016; Nannozi et al., 2017). Some studies have shown that the denial about HIV positive diagnosis in serodiscordant couple acts as a barrier to antiretroviral or PrEP initiations (Patel, Anand, Stanford-Moore, Wakhungu, Bukusi, Baeten, Brown, 2016). Evidence has shown that HIV-serodiscordant relationships are challenging and result in unique stressors that negatively affect the mental well-being of these couples (Lua, Mustapha, Abdullah & Abdul Rahman, 2014; Jibat, Nigussie, & Tesfaye 2014). According to Ondenge et al. (2018), HIV-discordant couples can also experience non-specific psychological distress after discovering their HIV positive status or that of their partner. A study in India by Darak et al. (2021) found that women in HIV-serodiscordant relationships experienced anxiety disorders and suicidal ideations, following the disclosure of the HIV status of their husbands.\n\nDisclosure remains a dilemma in most serodiscordant couples. Participants of this study indicated different ways of disclosing and not disclosing their serodiscordancy to other people. It was indicated that participants either disclose to their partner only, some family members or chose not to disclose at all. A pattern followed for disclosing differed with individual couples. Some of the couples chose to disclose their status to select people. Others chose some family members over others, for reasons ranging from fear of being stigmatised to fear of being discriminated against. Some participants chose not to disclose as a way of avoiding the stigmatisation. Others even voiced that out of the two families from which the couples came, one family would have members who were disclosed to and some to whom disclosure had not been made. Participants even agreed to the fact that the stigma around serodiscordancy is still rife, as most people were still in shock of whether a condition such as serodiscordancy exists. There was also fear of talkative family members who would then let the status of the couple reach others outside the circle of confidentiality.\n\nParticipants also noted that disclosure may predispose them to being treated differently by those who knew their HIV status. A number of participants were not comfortable to disclose their status to certain members, even if they were family, as they could further disclose to other people. Most participants wanted to keep their status undisclosed, whilst some were saying they could disclose and were not concerned about the consequences. The participants in this study believed that stigma is the main reason for not disclosing their status. Selective disclosure of HIV-serodiscordant status to family, friends and community members is not unique to this study. Similar findings were established in studies on serodiscordant couples in South Africa, Tanzania and the Ukraine (Rispel et al., 2015). Non-disclosure of such partners can lead some family members to not know the status of such couples, denying them additional social support (Dessalegn et al., 2019). However, there is a significant challenge when it comes to infected individuals disclosing their status, mainly due to the fear of stigma or the feeling of guilt after contracting the virus. Some individuals even failed to disclose their status to their partners, who in turn would find out through other means with the resultant fallout including fights, feelings of anger and regret. However, disclosure challenges do not end here; uninfected partners in the relationship often find it hard to disclose to their own families for fear that their family members would become hostile towards the infected partner for “bringing the disease into the house”.\n\nUpon disclosing to a select few confidants, fear of further disclosure was common as couples were unsure of the possible reactions, including fear of stigma and discrimination. Norman, Chopra and Kadiyala (2007) assert that people living with HIV find it daunting to disclose their status, for reasons ranging from fear of disclosing a secret to fear of rejection and breaking up of relationships. Other reasons, as noted by Daftary, Padayatchi and Padilla (2007), are fear of losing economic support, blame, abandonment, physical and emotional abuse, discrimination and disruption of family relationships. Mashaphu (2018) reported on intimate partner violence among couples with HIV serodiscordancy and disclosing the discordancy results to a partner as predisposing to family or sexual violence.\n\nOnly one public hospital HIV unit was the setting for this study and, therefore, the results cannot be generalised to the whole Gauteng Province or all the provinces of South Africa. The topic of the study is a sensitive matter and could have caused emotional harm to the participants, however, all participants were given the contact number of a psychologist and social worker in case they needed further counselling following the interviews. Further research could be done focusing on counsellors, HIV-serodiscordant couples and their family members.\n\nThis paper has explored the psychosocial- and disclosure-related challenges of being in an HIV-serodiscordant relationship. What emerged from this study was how HIV-serodiscordant couples experienced adverse psychological feelings of fear, sadness, disbelief and hurt on discovering that they were in a serodiscordant relationship, including disclosure challenges. Our findings suggest that couples in serodiscordant relationships would benefit more from differentiated, client-centred psychosocial support, directed at the management of dynamic challenges in such relationships and disclosure counselling. It is recommended that the HIV-serodiscordant couple go through extensive on-going counselling to improve their mental well-being and strengthen their resilience.",
"appendix": "Data availability\n\nThe underlying data cannot be provided as the authors have an existing agreement with participants that their responses/data will not be shared without their consent. Due to the privacy, confidentiality, sensitivity and nature of the study on HIV, data cannot be openly shared with the public and the researcher did not receive consent from participants to do so. For more information on the research study, the researcher can be reached at lelakatshidi@gmail.com/lekalcm@unisa.ac.za.\n\nFigshare: INTERVIEW GUIDE FOR HIV-SERODISCORDANT COUPLES.docx. https://doi.org/10.6084/m9.figshare.21437943 (Lelaka, 2022).\n\nFigshare: COREQ checklist for ‘Psychosocial- and disclosure-related challenges among HIV-serodiscordant couples: an interpretative phenomenological analysis study’. https://doi.org/10.6084/m9.figshare.21408489 (Lelaka, 2022).\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 thank University of South Africa for providing one of the researchers (a PhD candidate) with a bursary to pursue the study. In addition, we thank participants who took part in the study, as well as the Hospital Chief Executive Manager for giving permission for the study to be conducted among its counsellors.\n\n\nReferences\n\nAlase A: The interpretative phenomenological analysis (IPA): a guide to a good qualitative research approach. Int. J. Educ. Literacy Stud. 2017; 5(2): 9–19. Publisher Full Text\n\nBabbie E: The practice of social research. 15th ed.United States of America:Cengage Learning Inc.;2020.\n\nBrink H, van der Walt C , van Rensburg G : Fundamentals of research methodology for health professionals. 3rd ed.Cape Town:Juta;2012.\n\nChihana ML, Conan N, Ellman T, et al.: The HIV cascade of care among serodiscordant couples in four high HIV prevalence settings in sub-Saharan Africa. SAMJ: S. Afr. Med. J. 111(8): 768–776. PubMed Abstract | Publisher Full Text\n\nCreswell JW, Creswell JD: Research design: qualitative, quantitative, and mixed methods approaches. 5th ed.Chicago, Thousand Oaks:SAGE;2018.\n\nDaftary A, Padayatchi N, Padilla M: HIV testing and disclosure: a qualitative analysis of TB patients in South Africa. AIDS Care. 2007; 19: 572–577. PubMed Abstract | Publisher Full Text\n\nDarak SS, Pawar SR, Phadke SS, et al.: Common mental disorders among HIV-uninfected women living in HIV serodiscordant setting: a clinic-based study in Pune, Maharashtra, India. Indian J. Public Health. 2021; 63: 44–50.Reference Source\n\nDeJonckheere M, Vaughn LM: Semistructured interviewing in primary care research: a balance of relationship and rigour. Fam. Med. Community Health. 2019; 7(2): e000057. PubMed Abstract | Publisher Full Text\n\nDessalegn NG, Hailemichael RG, Shewa-Amare A, et al.: HIV disclosure: HIV-positive status disclosure to sexual partners among individuals receiving HIV care in Addis Ababa, Ethiopia. PLoS One. 2019; 14(2): e0211967. PubMed Abstract | Publisher Full Text\n\nDe Vos AS, Strydom H, Fouche CB, et al.: Research at grass roots. Pretoria:Van Schaik;2016.\n\nEllis P: Evidence-based practice in nursing. 3rd ed.London:SAGE Publishers;2016.\n\nJibat N, Nigussie B, Tesfaye S: Socioeconomic challenges and coping mechanisms of HIV serodiscordant couples in Jimma Town, Oromia/Ethiopia. Eur. Sci. J. 2014; 10(23): 158–175.\n\nJoint United Nations Programme on HIV/AIDS: UNAIDS data, 2018. Geneva:UNAIDS;2019.Reference Source\n\nKasenga F, Hurtig A, Emmelin M: HIV-positive women’s experiences of a PMTCT programme in rural Malawi. Midwifery. 2010; 26(1): 27–37. PubMed Abstract | Publisher Full Text PubMedCrossRefGoogle Scholar\n\nKing R, Wamai N, Khana K, et al.: “Maybe his blood is still strong”: a qualitative study among HIV-sero-discordant couples on ART in rural Uganda. BMC Public Health. 2012; 12: 801. PubMed Abstract | Publisher Full Text\n\nKvale S: Interviews: An Introduction to Qualitative. Research Interviewing. London:SAGE;2018.\n\nKumwenda MK, Corbett EL, Choko AT, et al.: Post-test adverse psychological effects and coping mechanisms amongst HIV self-tested individuals living in couples in urban Blantyre, Malawi. PLoS One. 2019; 14(6): e0217534. PubMed Abstract | Publisher Full Text\n\nLarki M, Latifnejad-Roudsari R, Bahri N, et al.: Home-based care: a modern approach to fight against acquired immune deficiency syndrome in Iran. Iran. J. Nurs. Midwifery Res. 2020; 25(3): 263. PubMed Abstract | Publisher Full Text\n\nLelaka CM:INTERVIEW GUIDE FOR HIV-SERODISCORDANT COUPLES.docx. figshare. [Dataset]. 2022. Publisher Full Text\n\nLelaka CM:Tshidi Lelaka - COREQ_checklist.pdf. figshare. [Dataset]. 2022. Publisher Full Text\n\nLua PL, Mustapha N, Abdullah R, et al.: The experiences and challenges in caring for HIV/AIDS patients: a qualitative exploration among Muslim family caregivers in Terengganu, Malaysia. ASEAN J. Psychiatry Ment. Health. 2014; 15(2): 120–130.\n\nMaeri I, El Ayadi A, Getahun M, et al.: “How can I tell?” Consequences of HIV status disclosure among couples in eastern African communities in the context of an ongoing HIV “test-and-treat” trial. AIDS care. 2016; 28 Suppl 3(Suppl 3): 59–66. PubMed Abstract | Publisher Full Text\n\nMashaphu S, Wyatt GE, Gomo E, et al.: Intimate partner violence among HIV-serodiscordant couples in Durban, South Africa. South African Medical Journal = Suid-Afrikaanse tydskrif vir geneeskunde. 2018; 108(11): 960–964. PubMed Abstract | Publisher Full Text\n\nMartins A, Canavarro MC, Pereira M: The relationship between dyadic coping and dyadic adjustment among HIV-serodiscordant couples. AIDS Care. 2021; 33(4): 413–422. PubMed Abstract | Publisher Full Text\n\nMathenjwa M, Khidir H, Milford C, et al.: Acceptability of an Intervention to Promote Viral Suppression and Serostatus Disclosure for Men Living with HIV in South Africa: Qualitative Findings. AIDS Behav. 2022; 26(1): 1–12. PubMed Abstract | Publisher Full Text\n\nMavhandu-Mudzusi AH, Lelaka MC, Sandy PT: The experiences of HIV-serodiscordant couples at the perinatal HIV research unit in Soweto, South Africa. Stud. Ethno-Med. 2014; 8(2): 119–125. Publisher Full Text\n\nMendelsohn JB, Calzavara L, Daftary A, et al.: A scoping review and thematic analysis of social and behavioural research among HIV-serodiscordant couples in high-income settings. BMC Public Health. 2015; 15(1): 1–18. Publisher Full Text\n\nNannozi V, Wobudeya E, Gahagan J: Fear of an HIV positive test result: an exploration of the low uptake of couples HIV counselling and testing (CHCT) in a rural setting in Mukono district, Uganda. Glob. Health Promot. 2017; 24(4): 33–42. PubMed Abstract | Publisher Full Text Google Scholar\n\nNorman A, Chopra M, Kadiyala S: Factors related to HIV disclosure in 2 South African communities. Am. J. Public Health. 2007; 97(10): 1775–1781. PubMed Abstract | Publisher Full Text\n\nOndenge K, Khalil G, Odero I, et al.: Factors associated with psychological distress among members of HIV discordant couples in western Kenya: the role of adverse childhood experiences. J. Glob. Health Rep. 2018; 2: e2018018. Publisher Full Text\n\nPatel RC, Odoyo J, Anand K, et al.: Facilitators and barriers of antiretroviral therapy initiation among HIV discordant couples in Kenya: qualitative insights from a pre-exposure prophylaxis implementation study. PLoS One. 2016; 11(12): e0168057. PubMed Abstract | Publisher Full Text\n\nPence BW, Shirey K, Whetten K, et al.: Prevalence of psychological trauma and association with current health and functioning in a sample of HIV-infected and HIV-uninfected Tanzanian adults. PLoS One. 2012; 7(5): e36304. PubMed Abstract | Publisher Full Text | Free Full Text Google Scholar\n\nPolit DF, Beck CT: Nursing research: generating and assessing evidence for nursing practice. 10th ed.Philadelphia:Wolters Kluwer Health/Lippincott Williams & Wilkins;2021.\n\nQutoshi SB: Phenomenology: a philosophy and method of inquiry. J. Educ. Dev. 2018; 5(1): 215–222. Publisher Full Text\n\nRispel LC, Cloete A, Metcalf CA, et al.: ‘It [HIV] is part of the relationship’: exploring communication among HIV-serodiscordant couples in South Africa and Tanzania. Cult. Health Sex. 2011; 14(3): 257–268. PubMed Abstract | Publisher Full Text\n\nRispel LC, Cloete A, Metcalf CA: 'We keep her status to ourselves': experiences of stigma and discrimination among HIV-discordant couples in South Africa, Tanzania and Ukraine. SAHARA J: journal of Social Aspects of HIV/AIDS Research Alliance. 2015; 12(1): 10–17. PubMed Abstract | Publisher Full Text\n\nSiegel K, Meunier É, Lekas HM: The experience and management of HIV stigma among HIV-negative adults in heterosexual serodiscordant relationships in New York City. AIDS Care. 2018; 30(7): 871–878. PubMed Abstract | Publisher Full Text\n\nSimms VM, Higginson IJ, Harding R: What palliative care-related problems do patients experience at HIV diagnosis? A systematic review of the evidence. J. Pain Symptom Manag. 2011; 42(5): 734–753. PubMed Abstract | Publisher Full Text Google Scholar\n\nSmith JA, Osborn M: Interpretative phenomenological analysis as a useful methodology for research on the lived experience of pain. Br. J. Pain. 2015; 9(1): 41–42. PubMed Abstract | Publisher Full Text\n\nStatistics South Africa: Mid-year population estimate P0302. Pretoria;2021.Reference Source\n\nThapa R, Yang Y: Experiences, Emotions, and Adjustments of HIV-Infected Men in HIV-Concordant Marital Relationship in Cambodia. Am. J. Mens Health. 2018; 12(5): 1215–1225. PubMed Abstract | Publisher Full Text\n\nYang Y, Lewis FM, Wojnar D: Culturally embedded risk factors for Cambodian husband-wife HIV transmission: from women’s point of view. J. Nurs. Scholarsh. 2016; 48(2): 154–162. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "187737",
"date": "29 Nov 2023",
"name": "Jennifer M. Belus",
"expertise": [
"Reviewer Expertise psychosocial experiences of people with HIV",
"HIV disclosure",
"couples",
"mental health"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the authors’ focus on investigating the psychosocial and disclosure related challenges of individuals in serodiscordant relationships, particularly by using an interpretive phenomenological analysis as this should provide rich, in-depth understanding of participants’ experiences. Unfortunately, there are some major limitations in the current version of the manuscript that minimize the study’s contribution. I outline my two major concerns below, which are related, followed by minor considerations.\nMajor\n1. Greater justification for the study is needed. The authors use the introduction to describe some of the challenges and experiences of serodiscordant couples, including the fact that these couples experience psychosocial challenges and disclosure-related issues. The introduction then ends with the goal of the current study, but no gap in the literature is identified.\nA small point but in the fourth paragraph of the introduction, the authors describe past research on psychological impact using the exact same words that are used to describe their own study findings in the abstract. Not sure if this was an oversight but it speaks to the need to differentiate the current study’s purpose (and findings) from prior research.\n2. The analyses and findings missed the mark for me in terms of uncovering in-depth experiences of individuals living in serodiscordant relationships. A few related points.\nThe findings on psychosocial experiences focused exclusively on the reactions to serodiscordancy, though it wasn’t clear if that was the study aim per se. This relates back to the justification for the study, as it seems that most of what is already known about serodiscordant couples actually relates to the disclosure experience. What were the authors’ aims of the study—what new things were they trying to learn?\n\nGiven the in-depth approach of IPA, I would expect more in-depth unpacking and diving into the lived experiences of the study participants. However, the findings stayed at the surface level. I would expect the authors to analyze their findings by examining how certain relevant characteristics (like age, relationship length/type, HIV status) affects the experiences of participants (i.e., the themes), as this would provide more nuanced and in-depth information about participant lived experiences.\n\nThe findings could be much improved by providing an overall summary and synthesis of each broader theme and then having a few illustrative quotes to support the statements. At the moment, the findings are broken down too much and it’s hard to clearly see the bigger picture of the findings.\n\nIt was a bit striking that there wasn’t more in the findings/analyses specifically on relationship dynamics, how the couple was coping, etc. What can the authors say about how the relationship was affected after the couple learned they were in a serodiscordant relationship? How has their relationship changed over time as a serodiscordant couple?\n\nMinor\n3. The title and abstract is slightly misleading, as the study only interviews one member of the couple in the serodiscordant relationship. I suggest changing the term “HIV serodiscordant couples” to “individuals in serodiscordant relationships”.\n4. Conclusions in the abstract and the manuscript should stay closer to the findings of the study. Rather than focusing on implications for public health based on a small qualitative study or statements that couples in serodiscordant relationships would benefit more from differentiated care (this was not tested), the authors should make sense of their specific findings. What in-depth information was learned in this study?\n5. More detail on study sampling and recruitment are needed. For example, it’s not clear how HIV-negative partners were recruited—were they also receiving care at this clinic? Were both members of a given couple recruited to participate? What did the researchers mean when they said “researchers used their own judgment in selecting those participants that met the inclusion criteria”? I suggest the researchers also ensure they are referring to individuals in this section, not couples, as that is who they interviewed.\n6. For each quote, the authors should provide the relevant demographic information (age, sex/gender, HIV status at a minimum).\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?\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": "172793",
"date": "29 Nov 2023",
"name": "Bhadra Subhasis",
"expertise": [
"Reviewer Expertise Psychosocial Support",
"Mental Health",
"Gender and development",
"Life skills education",
"Mental Health issues in Disaster and Conflict"
],
"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 is very much relevant and most needed.\n\nThere are some scientific development with the concept of UU status with the Discordant couple and medical development to stop the transmission. These issues are not reflected enough to highlight the availability of the medical treatment facilities. What are counselling facilities are available for them can be mentioned, and how that helped or did not help also should be highlighted.\n\nIn the research method, the inclusion criteria for the sample selection are fine, but the exclusion criteria mentioned are natural exclusion. It should mention the aspect of excluding a sample who is eligible to be included based on certain criteria, like, mental illness, comorbidity, bed-ridden, etc.\n\nThe sample size is small but enough to justify a qualitative study. But, as a whole, analysis of the qualitative information needs to have a more detailed understanding of the theme and sub-themes. The quotes are not analyzed adequately.\n\nDiscussion can bring specific psychosocial issues other than the common problems of HIV-positive persons. This would justify the purpose of working with discordant couples.\n\nRecommendations need to be formulated based on the study findings. Those are very general as of now.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1247
|
https://f1000research.com/articles/8-1030/v1
|
09 Jul 19
|
{
"type": "Research Article",
"title": "Comparison of sleep and health behaviors among diabetic patients and non-diabetics in Phitsanulok, Thailand: a cross-sectional study",
"authors": [
"Chudchawal Juntarawijit",
"Yuwayong Juntarawijit",
"Yuwayong Juntarawijit"
],
"abstract": "Background: Type 2 diabetes mellitus (T2DM) is a global public health problem. To avoid disease complications, diabetic patients have to control their blood glucose and maintain a healthy lifestyle including a healthy diet, weight control, moderate exercise and smoking cessation. Methods: This study aimed to survey sleep, eating and exercise behaviors of diabetic patients in Bang Rakam district, a rural community in Phitsanulok province, Thailand. The data on sleep and other health behaviors were taken from 1,385 T2DM patients and 1,394 non-T2DM controls, who were aged 30 - 85 years and were free from other chronic diseases. The data were collected using a structured questionnaire. Results: Compared to the control group, the diabetic group had a significantly higher body mass index (BMI). However, fewer of them were found to smoke cigarettes and drink alcohol. Most of the participants were ‘morning people’ who slept 7-9 hours per day. It was found that sleep ≥8 hours increased the risk of diabetes among women (OR = 1.27, 95% CI 1.03 - 1.56). The diabetic group reported eating chicken and vegetables more than the control group. They also avoided eating beef and eating more than a cup of rice per meal. However, the T2DM group did fewer physical activities, such as walking, biking or playing sports, during their leisure time. Conclusions: Compared to the control group, diabetic patients in a rural community of Thailand had healthier sleep, lifestyle and eating behaviors but not healthier exercise behaviors, especially among obese women. Diabetic prevention programs should emphasize and promote weight control and increasing levels of exercise.",
"keywords": [
"Diabetes mellitus",
"Diabetic care",
"Health behavior",
"Sleep duration",
"Sleep deprivation"
],
"content": "Introduction\n\nType 2 diabetes mellitus (T2DM) is a global public health problem. It has been estimated that by the year 2030, there will be 439 million people with T2DM (Olokoba et al., 2012). The well-established risk factors for this disease are genetic factors, eating behaviors and exercise (Zheng et al., 2018). Recent studies also related T2DM to sleep and lifestyle. In a large population study in Korea, it was found that ‘evening people’ (those who go to bed late, being alert and prefer to work at night) had an increased diabetic risk (odds ratio, OR = 1.73, 95% CI 1.01-2.95) compared to ‘morning people’ (those who usually go to bed early and like to work or being active during the day) (Yu et al., 2015).\n\nIn meta-analysis studies, there a strong U-shaped dose-response association between T2DM and sleep quality and quantity has been observed (Cappuccio et al., 2010; Lee et al., 2017). Compared to men with seven hours of sleep, the risk of T2DM was about twice among for a short sleeper (under or equal to five or six hours of sleep per night) and three times among for a long sleeper (over eight hours) (Heianza et al. (2014); Yaggi et al., 2006). reported a similar result among ≤45 year-olds but not for those ≥60 years of age. In experimental studies, sleep deprivation increased insulin resistance, hunger hormone levels, appetite and food intake but reduced glucose metabolism, leading to obesity, a common predictive factor for diabetes (Beccuti & Pannain, 2011; Reutrakul & Van Cauter, 2018) .\n\nOn the other hand, T2DM itself can interfere with sleep and cause sleep apnea among diabetic patients (Barone & Menna-Barreto, 2011; Resnick et al., 2003). Poor sleep is often found among T2DM patients as compared to healthy control groups (Trento et al., 2008). A study among elderly Iranian women with T2DM found that being a poor sleeper is associated with: being middle-aged (OR = 2.03, 95% CI 1.01-4.08); having a longer duration of diabetes (OR = 1.77, 95% CI 0.98-3.13); and having high cholesterol levels ≥240 mg/dL (OR = 1.99, 95% CI 1.01-3.94) (Shamshirgaran et al., 2017). This was consistent with a previous study, which also reported a higher prevalence of sleep disorders (33.7%) among T2DM patients than in a non-diabetic control group (8.2%) (Sridhar & Madhu, 1994). A study in the United States reported that 55% of T2DM patients have poor sleep (Luyster & Dunbar-Jacob, 2011). Sleep problems among diabetic people might be caused by the disease itself, which affects neurobehavioral and endocrine functions, or due to complications of the disease, such as peripheral neuropathy, restless legs syndrome, polyuria and associated depression (Khandelwal et al., 2017). In an experimental study, sleep restriction (five hours per night) for a week can reduce insulin sensitivity and increase blood glucose; these changes affected kidney function and increased urination, which interfered with sleep (Buxton et al., 2010; Reutrakul & Van Cauter, 2018).\n\nTo avoid disease complications, diabetic patients have to control their blood glucose and maintain a healthy lifestyle through, for example, a healthy diet, weight control, moderate exercise and smoking cessation (Stolar, 2010; Tang et al., 2008). Optimal control of sleep duration and quality was also proposed as an intervention to improve blood glucose levels in patients with T2DM (Trento et al., 2008). However, studies about the health behaviors of diabetic patients is surprisingly rare. A population based survey in Australia reported that there was a minimal change in lifestyle among people after being diagnosed with T2DM. Compared to the healthy control group, the recently diagnosed T2DM group had a minimal weight loss of 1.38 kg (95% CI -1.85 to -0.89), and were more likely to stop smoking (OR of quitting = 2.71, 95% CI 1.59-4.63). However, there was no positive improvement in other lifestyle behaviors such as sitting, walking, moderate to vigorous physical activity (MVPA) and vegetable and fruit consumption (Chong et al., 2017).\n\nThis study aimed to survey the sleep, eating and exercise behaviors of diabetic patients in a rural community in Phitsanulok province, Thailand. The predictive factors of sleep and other health behaviors were also investigated. The results will be useful for local diabetic care programs and comparative studies worldwide.\n\n\nObjectives\n\n1. To explore sleep, eating and exercise behaviors among T2DM and non-T2DM groups.\n\n2. To identify factors that affect sleep and exercise among diabetic patients.\n\n3. To determine the association between diabetes and sleep duration.\n\n\nMethods\n\nThis study is an analytical cross-sectional design with a comparison group.\n\nThis study utilized data from a previous case-control study on diabetes and pesticide exposure (Juntarawijit & Juntarawijit, 2018). The data on health behaviors were collected from February to May 2016 from diabetic patients (T2DM) and a non-T2DM control group living in the rural community of Bang Rakam, a district with 95,098 people (in the year 2018) in Phitsanulok province, Thailand. The district is located in the lower northern part of Thailand, about 400 km from Bangkok.\n\nThe diabetic patients were those who had come to receive follow-up services at seven health promoting hospitals, which were randomly selected, using random number tables, from all 21 local hospitals in the target area. All diabetic patients who met the inclusion criteria were approached at their home by village health volunteers to take part in the study. In this study, the T2DM group was limited to those aged 30–85 years and free from other chronic diseases, such as heart disease, allergies, chronic pulmonary disease, and cancer. For each diabetic case, one healthy control (non-T2DM) who was free from diabetic disease and met the same inclusion criteria as the case was also approached by the same health volunteer based on the convenience sampling method. The control group were neighbors of the diabetic patients matched for gender and age (± five years.).\n\nIn addition to demographic information, data on sleep duration and other health behaviors were collected using an interviewer-administered questionnaire during a face-to-face interview, which was written in the Thai language (Juntarawijit, 2019b). Before use, the questionnaire was tested for question sequencing and understanding. An interview took place at home of each participant. The participants’ self-reported sleep duration was collected using the question “How many hours do you usually sleep per day?”. Participants were classified as ‘current smoker’ if they had smoked 100 cigarettes or more in their lifetime and they currently smoke cigarettes. Those who drank alcohol 2-4 times a week were classified as ‘alcohol use’. Data on food consumption, including consumption of meat, sausage, vegetable, fruit, sweets, rice and sweet soft drinks, were also collected using ‘yes or no’ questions. Information on personal lifestyle (whether they are a morning person or an evening person) was collected using the question “What is the lifestyle that best describes you, morning people or evening people: “morning people” refer to those who usually go to bed early and like to work or being active during the day; “evening people” are those who go to bed late, being alert and prefer to work at night?”. Participants were also asked to report how frequently they did certain physical activities (walking, biking, playing sports or sweating excessively from exercise or physical activity but not from hot climate or health problems) and watched television during their leisure time using two categories: absent (never, rarely) and present (sometimes, often, almost always). Body mass index (BMI) was calculated by dividing body weight (in kg) by height (in meters squared). The high BMI group was those with BMI ≥25.00. For waist to hip ratio (WHR), a high WHR referred to men with WHR ≥0.90 or women with WHR ≥85. For waist circumstance (WC), a high WC referred to men with WC ≥90.0 or women with WC ≥80. All of these measurements were assessed by the health volunteers. Data were collected by 50 village health volunteers who were trained on how to use questionnaires and how to interview study participants.\n\nDemographic and health behaviors were analyzed using descriptive statistics and Chi-square test for comparison of categorical data. To identify predictive factors of sleep duration, logistic regression was performed, adjusted for gender, age (continuous), waist to hip ratio (WHR) and lifestyle (evening person vs morning person). The predictive factors of physical activity were also analyzed using ordinal regression, with physical activity categorized as never, rarely, sometimes, often and almost always. All analyses were performed using IBM SPSS statistics (version 19). Confidence intervals of 95% were used to determine significant statistics and all p-values are two two-sided. In this study, listwise or case deletion was used to handling of missing data.\n\nThis study was approved by the Ethics Board of Naresuan University (project number 402/59). Written informed consent for an interview and participation in the study was obtained from each of the subjects before the interview process.\n\n\nResults\n\nFrom a dataset of 2,936, 157 (3.4%) were discarded as they were missing important information, such as age (17 cases) and sleep data (140 cases). In total, data from 2,779 participants (1,385 cases and 1,394 controls), with a 92.6% response rate, were included in data analysis.\n\nMost of the participants were female (74.4% for T2DM and 72.8% for non-T2DM) with a comparable mean age between the T2DM (61.1 ± 10.0 years) and non-T2DM groups (60.2 ± 9.8 years) (Table 1) (Juntarawijit, 2019a). However, the T2DM group had significantly higher obesity indices, with an average BMI of 24.9 ± 4.7 vs. 23.8 ± 4.3 (T2DM to non-T2DM group), waist to hip ratio (WHR) of 0.91 ± 0.14 vs. 0.90 ± 0.11 and waist circumference (WC) of 36.8 ± 11.8 vs. 35.6 ± 11.9. In comparison to the control group, there were more participants in the T2DM group who classified themselves as being in retirement or housewives (41.8% vs. 31.6%) and fewer as being a farmer (32.0% vs. 40.2%). A lower percentage of the T2DM group were current cigarette smokers (10.8% vs. 14.3%) and alcohol users (6.6% vs. 9.7%).\n\n* Significant with p <0.05 (two-sided).\n\n** Sweating refers to an excessive sweat from exercise or physical activity but not from hot climate or health problems.\n\nMost of the participants (81.9% of T2DM and 82.3% of non-T2DM) slept 7–9 hours per day (Table 2). However, in comparison to control group, there was a significantly higher proportion of diabetics whose sleep hours were ≤5 h, and ≥8 h (Table 2). Nearly all of the participants (93.1% for T2DM and 93.8% for non-T2DM) classified themselves to be morning people.\n\n* Significant with p <0.05 (2-sided).\n\nLogistic regression analysis found a significant association between diabetes and a sleeping time of ≥8 hours (OR = 1.21, 95% CI 1.02-1.43) after being adjusted for gender and age (Table 3). This association did not change much after being adjusted for WHR (OR = 1.20, 95% CI 1.00-1.43) and lifestyle (OR = 1.20, 95% CI 1.00-1.44).\n\na Model1: adjusted for gender and age (continuous).\n\nModel2: added waist-hip ratio (continuous).\n\nModel3: added lifestyle (evening person, morning person).\n\nb Adjusted for gender, age, waist-hip ratio and style.\n\n* Significant with p <0.05 (two-sided).\n\nStratified analysis found that a sleeping time of ≥8 hours was associated with women (OR = 1.27, 95% CI 1.03-1.56) and a high WHR (OR = 1.28, 95% CI 1.04-1.59) (Table 4). A sleeping time of ≤5 hours was significantly associated with a high WC (OR = 3.14, 95% CI 1.13-8.75) and women with a high WC (OR = 3.47, 95% CI 1.21-9.97). A short sleep (≤5 hours) is also strongly associated with being an evening person (OR = 5.92, 95% CI 3.46-10.13) and being a woman who is an evening person (OR = 7.55, 95% CI 4.17-13.66).\n\nAll tested used 6–7 hours as a reference, with 95% confidence intervals (p-value <0.05).\n\na Adjusted for gender, age, waist-hip ratio and lifestyle.\n\nb Adjusted for age, waist-hip ratio and lifestyle.\n\nNA = data not available.\n\nCompared with the control group, there were more participants in the T2DM group who eat chicken (16.8% vs. 13.5%, p=0.03) and vegetables (91.5% vs. 89.0%, p=0.03) (Table 1). However, the opposite was true for those who eat beef (34.7% vs. 40.6%) and eat more than a cup of rice per meal (37.4% vs. 42.6%, p<0.01). For sausage, fruit, desert and rice, the two groups had a similar percentage of consumption.\n\nFor exercise and physical activity, participants in the T2DM group were less active than those in the control group. There was a higher percentage of T2DM who classified themselves being ‘far less’ or ‘less than’ active during their leisure time (40.7% vs. 27.2%) (Table 1). Moreover, there were fewer of them who reported excessive sweating (36.9% vs. 38.4%) during their free time. The diabetic group also had lower percentage of those who play sports or do exercise (35.0% vs. 43.1%), walking (70.1% vs. 78.1%) and cycling (32.8% vs. 47.1%) during their leisure time.\n\nThe behavior of the T2DM that was healthier compared to the control group was in watching television. There was a slightly lower percentage of the T2DM group who reported watching television during their leisure time compared to the control group (76.1% vs. 78.7%). Further analysis using ordinal regression found BMI to be associated with walking, riding a bicycle and exercise (Table 5).\n\nNote: Data was analyzed using ordinal regression. Physical activity categorized as: never, rarely, sometimes, often, almost always.\n\n* Statistically significant (p <0.05).\n\n\nDiscussion\n\nMost of the participants in this study had a healthy sleep pattern and lifestyle. Over 80% of the participants usually sleep 7–9 hours per day, which is considered to be a healthy amount of sleep (Ip & Mokhlesi, 2007). However, a closer look revealed that there was a higher percentage of the T2DM group compared to the control group who sleep less than six hours per day (3.2% vs. 2.4%) or more than nine hours per day (9.3%% vs. 7.5%) (Table 1) than the control group. Comparing these results to the literature, these participants had a better sleep pattern. The National Sleep Foundation in the United Sates reported that about 30% of middle-aged men and women slept less than six hours per night (Ip & Mokhlesi, 2007). Another study in the United States reported about half of diabetics had sleep problems (Shamshirgaran et al., 2017).\n\nFurther analysis revealed that sleep ≥8 hours was significantly associated with being women (OR = 1.27, 95% CI 1.03-1.56) and having a high WHR (OR = 1.28, 95% CI 1.04-1.59). A short sleep duration (≤5 hours) was significantly associated with a high WC (OR = 3.14, 95% CI 1.13-8.75) and women with a high WC (OR = 3.47, 95% CI 1.21-9.97) and being an evening person (OR = 5.92, 95% CI 3.46-10.13) and women who are evening people (OR = 7.55, 95% CI 4.17-13.66). These results were supported by a study that reported that sleep disturbance increases metabolic disorders and obesity (Chattu et al., 2019).\n\nCompared to the control group, the T2DM group were more overweight and had a higher BMI, (24.9 ± 4.7 vs. 23.8 ± 4.3), higher WHR (0.91 ± 0.14 vs. 0.90 ± 0.11) and higher WC (36.8 ± 11.8 vs. 35.6 ± 11.9) (Table 1). This was not surprising since obesity is a well-established risk factor of diabetes. In an epidemiological study, a short sleep was associated with BMI and weight gain (Leproult & Van Cauter, 2010). In laboratory studies, sleep deprivation affected sympathovagal balance, evening concentrations of cortisol and ghrelin hormones or hunger hormones, but decreased glucose tolerance, insulin sensitivity and leptin, a hormone controlling body weight (Van Cauter & Knutson, 2008). These changes increase blood glucose (Nedeltcheva & Scheer, 2014) and appetite for carbohydrate-rich food (Ip & Mokhlesi, 2007).\n\nCompared with other studies, the number of cigarette smokers (10.8% of T2DM and 14.3% of non-T2DM) and alcohol users (6.6% of T2DM and 9.7% of non-T2DM) in this study were relatively small. In the United States, the prevalence of cigarette smoking among adults with diabetes was about 23.6% (Ford et al., 2004). A study in California, United States, reported that 50% of participants in the diabetic group consumed alcohol (Ahmed et al., 2006).\n\nCompared to the control group, the prevalence of smoking and alcohol consumption among the T2DM group was significantly lower (p<0.01). A recent study in Australia also reported a higher rate of smoking cessation (OR for quitting smoking = 2.71, 95% CI 1.59-4.63) among recently diagnosed T2DM as compared to a healthy control group (Chong et al., 2017). This behavior change was often claimed to be a result of diabetic care programs and global trends of cigarette and alcohol consumption (Shi et al., 2013).\n\nConcerning eating behaviors and choice of food, the diabetic group trended to be healthier than the control group and were more likely to eat foods that are believed to be good for health. Compared to non-T2DM, there was a significantly higher percentage of the T2DM group who reported eating vegetables (91.5% vs. 89.0%, p=0.03) and chicken (16.8% vs. 13.5%; p=0.03) and the opposite was true for beef (34.7% vs. 40.6%, p<0.01) and eating more than a cup of rice per meal (37.4% vs. 42.6%, p<0.01). A similar study in Australia also found a lifestyle change among newly diagnosed diabetic patients (Chong et al., 2017).\n\nHowever, it must be noted that there were a large portion of participants in both T2DM and non-T2DM groups who reported eating fruit (63.6% vs. 61.7%), sweets (40.6% vs. 38.5%), and drinking sweet soft drinks (46.4% vs. 50.7%). Eating these foods might affect blood sugar and sleep pattern.\n\nComparing the frequency of several physical activities performed during their leisure time, participants in the T2DM group were less active than the control group. A significantly higher number of T2DM participants admitted to being less active compared with people of the same age and not doing exercise or playing sports as often as the control group (Table 1). There were also fewer T2DM participants who reported doing walking (41.5% vs. 51.1%) and riding a bicycle (17.4% vs. 26.7%) during their leisure time. These results are supported by other studies. In a study in rural communities of Missouri, Tennessee, and Arkansas, it was reported that 37% of T2DM patients had no leisure-time physical activity (Deshpande et al., 2005). Hays and Clark (1999) also found that over half of T2DM (54.6%) patients, mostly elderly females, had no weekly physical activity. However, a study in Nepal reported that 52% of diabetic patients were moderately active and 28% were highly active (Kadariya & Aro, 2018). This discrepancy in physical activity might be related to the culture and lifestyle of the patients. It was expected that study participants in this study would be more active because they are rural people who mainly work in agriculture.\n\nFurther ordinal regression analysis revealed that physical activities were associated with obesity (BMI). Those with a lower BMI trended to have a higher rate of walking, biking and exercising (Table 5). This result is well consistent with literature. A study on outpatients with T2DM and their matched controls found that the total energy expenditure (<300 kcal/day), number of steps (<1500 /day), physical activity duration (<130 min/day) and active energy expenditure/day (<300 kcal) were all lower in the diabetic group (p<0.05) (Fagour et al., 2013; Hamasaki, 2016). This lower physical activity might be partially due to a fear of joint or leg pain (Dutton et al., 2005) or hypoglycemia (Brazeau et al., 2008).\n\nAfter applying several grouping methods, the association was found to be significant only when sleep duration was grouped to ≤5 hours, 6–7 hours and ≥8 hours. In comparison to the 6–7 hours group, further analysis using logistic regression found that a significant association between diabetes and sleep was only among women with ≥8 hours of sleep (OR = 1.27, 95% CI 1.03-1.56) after being adjusted for age, gender, WHR and lifestyle (Table 3). A similar result was also reported in a study in Finland, which found that sleep of ≥8 hours increased the risk of diabetes among middle aged women (Tuomilehto et al., 2008). The effect of oversleeping on the risk of developing diabetes is well established, but most of the previous studies use 7-8 hours of sleep as a reference and defined oversleep to be 10–12 hours per day (Chattu et al., 2019). It was also noticed that the relative risk of diabetes in this study (OR = 1.27) was rather low compared with those reported in previous studies, which mostly reported sleep to increase diabetic risk by 2–3 times (Heianza et al., 2014; Yaggi et al., 2006). These results might be explained by the fact that sufficient sleep depends on both quantity and quality of sleep (Chattu et al., 2019). Since most participants in this study are rural villagers with a healthier lifestyle, they were more likely to have a good sleep and thus, require a shorter sleep duration. This was supported by the fact that only approximately 7% of the participants (T2DM and non-T2DM) who classified themselves to be evening people that like to stay up late at night (Table 1).\n\nIt was found that less than 7% of the study participants are evening people and the association between diabetes and lifestyle was not statistically significant. These results were in contrast to previous studies. In a large study in Korea, there was a large proportion of people who were evening people, and this group was at risk of diabetes (OR = 1.73, 95% CI 1.01-2.95). (Yu et al., 2015). The differences in workload, lifestyle, social activities and technology might affect sleep patterns of the two groups. Most of the participants in this study were rural villagers, while those in the Korean study were urban people with a modern lifestyle. In Thailand, most villagers usually go to bed early after being exhausted from hard, physical work on the farm during the day and they usually wake up early in the morning to have enough time to prepare food for their family members and the Buddhist monks.\n\nOne of the main limitations of this study was that it used a cross-sectional design and there was a lack of data on diabetes onset. Since the relationship between diabetes and sleep is double-sided, it therefore cannot be determined whether sleep causes diabetes or the disease interferes with the sleep pattern of the patient (Chattu et al., 2019). This bias will cause a positive effect and overestimate the association of diabetes and sleep. Without data on diabetic onset, behavior change and disease duration cannot be analyzed. This is also true of the effect of sleep duration on glucose control. These two issues are often reported in literature (Chong et al., 2017).\n\n\nConclusion\n\nIn conclusion, this study revealed that diabetic patients in a rural community in Thailand had healthy behaviors regarding sleep, lifestyle, eating, cigarette smoking and alcohol consumption. However, they tended to play sports, walk or ride a bicycle during their leisure time less often than the control group with a similar gender and age. This study also found that sleep of ≥8 hours increases the risk of diabetes as compared to sleep of 6–7 hours. Sleep was significantly related to gender, lifestyle and obesity. Those with high BMIs tended to have low levels of physical activity during their leisure time. In addition to weight control, diabetic prevention programs should emphasize and promote healthy sleep patterns and exercise, especially among women. More research on different societies and lifestyles are required before the effect of oversleeping on diabetes risk can be clearly understood.\n\n\nData availability\n\nFigshare: Sleep and health behaviors among diabetic and non-diabetic groups. 10.6084/m9.figshare.8246780 (Juntarawijit, 2019a)\n\nThis project contains the following underlying data:\n\n- Diabete-dataset.sav (dataset containing demographic characteristics, medical information and questionnaire responses for all participants)\n\n- Data Dictionary.docx\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\nFigshare: Questionnaire-sleep and health behavior among diabetes. 10.6084/m9.figshare.8298689 (Juntarawijit, 2019b)\n\nThis project contains the following extended data:\n\n- Questionnaire-English.docx\n\n- Questionnaire-Thai.docx\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Grant information\n\nThis study was supported by Naresuan University [R2560C031].\n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\n\nAcknowledgments\n\nOur great appreciation go to the village health volunteers in the district of Bang Rakam for data collection. We must also thank the Health Promoting Hospitals in Bang Rakam for the coordination and data support. We also thank Mr. Kenje Baris Gunda for language assistance.\n\n\nReferences\n\nAhmed AT, Karter AJ, Liu J: Alcohol consumption is inversely associated with adherence to diabetes self-care behaviours. Diabet Med. 2006; 23(7): 795–802. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarone MT, Menna-Barreto L: Diabetes and sleep: a complex cause-and-effect relationship. Diabetes Res Clin Pract. 2011; 91(2): 129–137. PubMed Abstract | Publisher Full Text\n\nBeccuti G, Pannain S: Sleep and obesity. Curr Opin Clin Nutr Metab Care. 2011; 14(4): 402–412. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrazeau AS, Rabasa-Lhoret R, Strychar I, et al.: Barriers to physical activity among patients with type 1 diabetes. Diabetes Care. 2008; 31(11): 2108–2109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBuxton OM, Pavlova M, Reid EW, et al.: Sleep restriction for 1 week reduces insulin sensitivity in healthy men. Diabetes. 2010; 59(9): 2126–2133. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCappuccio FP, D’Elia L, Strazzullo P, et al.: Quantity and quality of sleep and incidence of type 2 diabetes: a systematic review and meta-analysis. Diabetes Care. 2010; 33(2): 414–420. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChattu VK, Chattu SK, Burman D, et al.: The Interlinked Rising Epidemic of Insufficient Sleep and Diabetes Mellitus. Healthcare (Basel). 2019; 7(1): pii: E37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChong S, Ding D, Byun R, et al.: Lifestyle Changes After a Diagnosis of Type 2 Diabetes. Diabetes Spectr. 2017; 30(1): 43–50. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeshpande AD, Baker EA, Lovegreen SL, et al.: Environmental correlates of physical activity among individuals with diabetes in the rural midwest. Diabetes Care. 2005; 28(5): 1012–1018. PubMed Abstract | Publisher Full Text\n\nDutton GR, Johnson J, Whitehead D, et al.: Barriers to physical activity among predominantly low-income African-American patients with type 2 diabetes. Diabetes Care. 2005; 28(5): 1209–1210. PubMed Abstract | Publisher Full Text\n\nFagour C, Gonzalez C, Pezzino S, et al.: Low physical activity in patients with type 2 diabetes: the role of obesity. Diabetes Metab. 2013; 39(1): 85–87. PubMed Abstract | Publisher Full Text\n\nFord ES, Mokdad AH, Gregg EW: Trends in cigarette smoking among US adults with diabetes: findings from the Behavioral Risk Factor Surveillance System. Prev Med. 2004; 39(6): 1238–1242. PubMed Abstract | Publisher Full Text\n\nHamasaki H: Daily physical activity and type 2 diabetes: A review. World J Diabetes. 2016; 7(12): 243–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHays LM, Clark DO: Correlates of physical activity in a sample of older adults with type 2 diabetes. Diabetes Care. 1999; 22(5): 706–712. PubMed Abstract | Publisher Full Text\n\nHeianza Y, Kato K, Fujihara K, et al.: Role of sleep duration as a risk factor for Type 2 diabetes among adults of different ages in Japan: the Niigata Wellness Study. Diabet Med. 2014; 31(11): 1363–1615. PubMed Abstract | Publisher Full Text\n\nIp M, Mokhlesi B: Sleep and Glucose Intolerance/Diabetes Mellitus. Sleep Med Clin. NIH Public Access. 2007; 2(1): 19–29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJuntarawijit C: Sleep and health behaviors among diabetic and non-diabetic groups. 2019a. http://www.doi.org/10.6084/m9.figshare.8246780\n\nJuntarawijit C: Questionnaire-sleep and health behavior among diabetes. 2019b. http://www.doi.org/10.6084/m9.figshare.8298689.v1\n\nJuntarawijit C, Juntarawijit Y: Association between diabetes and pesticides: a case-control study among Thai farmers. Environ Health Prev Med. 2018; 23(1): 3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKadariya S, Aro AR: Barriers and facilitators to physical activity among urban residents with diabetes in Nepal. PLoS One. 2018; 13(6): e0199329. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhandelwal D, Dutta D, Chittawar S, et al.: Sleep Disorders in Type 2 Diabetes. Indian J Endocrinol Metab. 2017; 21(5): 758–761. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee SWH, Ng KY, Chin WK: The impact of sleep amount and sleep quality on glycemic control in type 2 diabetes: A systematic review and meta-analysis. Sleep Med Rev. 2017; 31: 91–101. PubMed Abstract | Publisher Full Text\n\nLeproult R, Van Cauter E: Role of Sleep and Sleep Loss in Hormonal Release and Metabolism. Endocr Dev. Basel: KARGER. 2010; 17: 11–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuyster FS, Dunbar-Jacob J: Sleep quality and quality of life in adults with type 2 diabetes. Diabetes Educ. 2011; 37(3): 347–355. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShamshirgaran SM, Ataei J, Malek A, et al.: Quality of sleep and its determinants among people with type 2 diabetes mellitus in Northwest of Iran. World J Diabetes. 2017; 8(7): 358–364. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNedeltcheva AV, Scheer FA: Metabolic effects of sleep disruption, links to obesity and diabetes. Curr Opin Endocrinol Diabetes Obes. 2014; 21(4): 293–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOlokoba AB, Obateru OA, Olokoba LB: Type 2 diabetes mellitus: a review of current trends. Oman Med J. Oman Medical Specialty Board. 2012; 27(4): 269–73. PubMed Abstract | Publisher Full Text | Free Full Text\n\nResnick HE, Redline S, Shahar E, et al.: Diabetes and sleep disturbances: findings from the Sleep Heart Health Study. Diabetes Care. 2003; 26(3): 702–709. PubMed Abstract | Publisher Full Text\n\nReutrakul S, Van Cauter E: Sleep influences on obesity, insulin resistance, and risk of type 2 diabetes. Metabolism. 2018; 84: 56–66. PubMed Abstract | Publisher Full Text\n\nShi L, Shu XO, Li H, et al.: Physical activity, smoking, and alcohol consumption in association with incidence of type 2 diabetes among middle-aged and elderly Chinese men. PLoS One. 2013; 8(11): e77919. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSridhar GR, Madhu K: Prevalence of sleep disturbances in diabetes mellitus. Diabetes Res Clin Pract. 1994; 23(3): 183–186. PubMed Abstract | Publisher Full Text\n\nStolar M: Glycemic control and complications in type 2 diabetes mellitus. Am J Med. 2010; 123(3 Suppl): S3–S11. PubMed Abstract | Publisher Full Text\n\nTang YH, Pang SMC, Chan MF, et al.: Health literacy, complication awareness, and diabetic control in patients with type 2 diabetes mellitus. J Adv Nurs. 2008; 62(1): 74–83. PubMed Abstract | Publisher Full Text\n\nTrento M, Broglio F, Riganti F, et al.: Sleep abnormalities in type 2 diabetes may be associated with glycemic control. Acta Diabetol. 2008; 45(4): 225–229. PubMed Abstract | Publisher Full Text\n\nTuomilehto H, Peltonen M, Partinen M, et al.: Sleep duration is associated with an increased risk for the prevalence of type 2 diabetes in middle-aged women - The FIN-D2D survey. Sleep Med. 2008; 9(3): 221–227. PubMed Abstract | Publisher Full Text\n\nVan Cauter E, Knutson KL: Sleep and the epidemic of obesity in children and adults. Eur J Endocrinol. 2008; 159 Suppl 1: S59–66. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYaggi HK, Araujo AB, McKinlay JB: Sleep duration as a risk factor for the development of type 2 diabetes. Diabetes Care. 2006; 29(3): 657–661. PubMed Abstract | Publisher Full Text\n\nYu JH, Yun CH, Ahn JH, et al.: Evening chronotype is associated with metabolic disorders and body composition in middle-aged adults. J Clin Endocrinol Metab. 2015; 100(4): 1494–1502. PubMed Abstract | Publisher Full Text\n\nZheng Y, Ley SH, Hu FB: Global aetiology and epidemiology of type 2 diabetes mellitus and its complications. Nat Rev Endocrinol. Nature Publishing Group. 2018; 14(2): 88–98. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "62203",
"date": "11 May 2020",
"name": "Anastasia Thanopoulou",
"expertise": [
"Reviewer Expertise Diabetes Mellitus",
"Nutrition",
"Diabetes Comorbidities"
],
"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 compares cross-sectionally sleep and health behaviors among diabetic patients and non-diabetics in a single area in Thailand. The subject is of importance, since Type 2 diabetes mellitus (T2DM) prevention and treatment lie a lot on lifestyle habits. It is well conducted and written. The results show that exercise behaviors should be ameliorated in the diabetic patients' population.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "98032",
"date": "26 Nov 2021",
"name": "Ahmad Alkhatib",
"expertise": [
"Reviewer Expertise Lifestyle prevention of 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\nThis a very good article, which is needed to demonstrate the exercise and nutritional prevention of diabetes by understanding those behaviours in a group of individuals with or without diabetes in Thailand.\nThe article is well written in many parts. However, its significance is not clear in the way it has been written, so I suggest a major revision to incorporate some amendments in order to be accepted for indexing. Once done, I am happy to look over it again.\n\nGeneric:\nPlease check the English and grammar throughout.\n\nSpecific: Abstract:\n\n“Diabetic prevention programmes”, should be “diabetes prevention programs”.\n\nTerminology use “people with diabetes” rather than “diabetic”.\n\nIntroduction:\nExpand a little on eating behaviour and diabetes and try make a link on why/why not such factors may be important for communities with a similar lifestyle to those tested here.\n\nExpand a little with statements showing some mechanisms linking the sleep/eating/exercise habits with the physiology of diabetes and its development.\n\nAdd a paragraph to justify why and what is special about why the rural communities in Thailand have been tested here. The reader needs to understand the link between these.\n\nThe last paragraph needs to have a statement about what is not known and how this study is adding to such knowledge.\n\nMethods:\nQuestionnaire: Specify what type of interview in the 1st paragraph.\n\nSleep questions, is there a valid sleep questionnaire used here? Why only one question? How do you differentiate between deep sleep/etc.? Did the interview cover more than the one question asked? Details are needed.\n\nData on food consumption requires justification, what type of questionnaire has been used or developed for this purpose? Why was there a focus on selected foods?\n\nFrequency of certain physical activities. What physical activity questionnaire was used? Was it IPAQ recall? Any validated questionnaire or justification of the questions selected?\n\nResults:\nIt is not clear why Table 3 has many gaps. Is it to do with insufficient number?\n\nDiscussion:\nPlease add a paragraph to start with, which should clearly state the most important findings and discuss what is novel.\n\nMany paragraphs seem to repeat what is in the results. All paragraphs should have concluding statements stating what is new and how it is relevant for the field.\n\nConclusion:\nAvoid repetitions “in conclusion” or “this study reveals”. It needs to go straight to the point and concise.\n\nAgain: the conclusion seems to repeat the findings. Please state the significance of your findings rather than repeating them.\n\nThe findings here contrast with the common perception that people with diabetes have bad lifestyle patterns, instead it showed that a healthy lifestyle pattern based on dietary patterns alone may not be sufficient and that lifestyle prevention of diabetes (esp. T2D) should always include physical activity as an integral part.\n\nThe authors could also make specific suggestions for how to implement physical activity in the rural community they tested based on the finding that some have better physical activity than others.\n\nA conclusion about the sleep patterns finding is missing and should be added.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "7545",
"date": "13 Dec 2021",
"name": "Chudchawal Juntarawijit",
"role": "Author Response",
"response": "Responses to the reviewer: Comment: This a very good article, which is needed to demonstrate the exercise and nutritional prevention of diabetes by understanding those behaviours in a group of individuals with or without diabetes in Thailand. The article is well written in many parts. However, its significance is not clear in the way it has been written, so I suggest a major revision to incorporate some amendments in order to be accepted for indexing. Once done, I am happy to look over it again. Generic: Please check the English and grammar throughout. Response: Thank you very much for reviewing this manuscript and providing valuable and encouraging feedbacks. The English and grammar was edited by Mr. Kenje Baris Gunda. Specific: Abstract: Comment: “Diabetic prevention programmes”, should be “diabetes prevention programs”. Terminology use “people with diabetes” rather than “diabetic”. Response: The errors about the terminology use have been corrected. Introduction: Comment: Expand a little on eating behaviour and diabetes and try make a link on why/why not such factors may be important for communities with a similar lifestyle to those tested here. Response: More information on eating behaviors and diabetes have been added as suggested. Comment: Expand a little with statements showing some mechanisms linking the sleep/eating/exercise habits with the physiology of diabetes and its development. Response: A statement on the mechanism linking eating, exercise and diabetes has been added. For sleep and diabetes, it was reported that sleep deprivation increases insulin resistance and indirectly affect diabetes by increasing appetite and body weight. This information has already been presented in the second paragraph. Comment: Add a paragraph to justify why and what is special about why the rural communities in Thailand have been tested here. The reader needs to understand the link between these. Response: Actually, there were no special characteristics, the community was selected because it has a high number of people with diabetes, and it was in a convenient location. Comment: The last paragraph needs to have a statement about what is not known and how this study is adding to such knowledge. Response: Introduction has been revised as suggested (see the manuscript). In the last paragraph, a statement about what is not known has been added. Methods: Comment: Questionnaire: Specify what type of interview in the 1st paragraph. Response: Information on the types of interviews are specified in the first paragraph. Comment: Sleep questions, is there a valid sleep questionnaire used here? Why only one question? How do you differentiate between deep sleep/etc.? Did the interview cover more than the one question asked? Details are needed. Response: Yes, we only asked the participants how long they usually slept each day. For information regarding quality of sleep, we believed that it was rather subjective and hard to justify, therefore, it was not included in the survey. The questionnaire method has been widely used to collect information on sleep duration (Yaggi, Araujo, and McKinlay, 2006) Chong et al., 2017) (Yu et al., 2015). However, we accept that this will be another important limitation of the study and the issue has been further discussed in study limitations. Comment: Data on food consumption requires justification, what type of questionnaire has been used or developed for this purpose? Why was there a focus on selected foods? The questionnaire was used in previous studies Response: In this study, a modified Food Frequency Questionnaire (FFQ) was used. The questionnaire was validated and used in previous studies, e.g. Barrat et al. (2012). Due to different cultures and eating habits, only foods found to relate to diabetes and those often found in Thailand were selected. This information has been added to the method section. Comment: Frequency of certain physical activities. What physical activity questionnaire was used? Was it IPAQ recall? Any validated questionnaire or justification of the questions selected? Response: In this study, a modified Baecke Habitual Physical Activity Questionnaire (BHPAQ) was used and the questionnaire has been validated in previous studies (Florindo and Latorre, 2003). Yes, the questionnaire method might cause recall bias. However, if the problem occurs, it should equally affect both the study and comparison group and thus, not seriously affect the results. The issue has been added in study limitations. Results: Comment: It is not clear why Table 3 has many gaps. Is it to do with insufficient number? Response: In the first row of the table, the association (ORs) between sleep hours and diabetes in different models were presented. The association was then further analyzed using only data from model 3 (adjusted for all potential confounding factors) in regard to gender, by carrying out a comparison between males and females. Discussion: Comment: Please add a paragraph to start with, which should clearly state the most important findings and discuss what is novel. Response: A new paragraph which states the most important findings, has been added to the discussion section as suggested. Comment: Many paragraphs seem to repeat what is in the results. All paragraphs should have concluding statements stating what is new and how it is relevant for the field. Response: Every paragraph has been reviewed to make sure they do not repeat the results and now contain conclusions of statements. Conclusion: Comment: Avoid repetitions “in conclusion” or “this study reveals”. It needs to go straight to the point and concise. Response: The repetition terms have been deleted. Comment: Again: the conclusion seems to repeat the findings. Please state the significance of your findings rather than repeating them. Response: The conclusion statement has been completely revised. Comment: The findings here contrast with the common perception that people with diabetes have bad lifestyle patterns, instead it showed that a healthy lifestyle pattern based on dietary patterns alone may not be sufficient and that lifestyle prevention of diabetes (esp. T2D) should always include physical activity as an integral part. Response: Thank you for helping us to clarify this important point. The idea has been added to manuscript. Comment: The authors could also make specific suggestions for how to implement physical activity in the rural community they tested based on the finding that some have better physical activity than others. Response: In this study, we found that women with high BMIs did the least physical activities and exercise, therefore, we recommend that exercise programs are designed for this specific group. Comment: A conclusion about the sleep patterns finding is missing and should be added. Response: A conclusion statement regarding sleep patterns has been added. References Barrat et al. (2012). Repeatability and relative validity of a quantitative food-frequency questionnaire among French adults. Food & Nutrition Research, 56: 18472. 10.3402/fnr.v56i0.18472 Chong S, Ding D, Byun R, et al. (2017). Lifestyle Changes After a Diagnosis of Type 2 Diabetes. Diabetes Spectr, 30(1):43–50. 28270714 10.2337/ds15-0044 5309903 Colberg SR, Sigal R, Yardley JE, et al. (2016). Physical Activity/Exercise and Diabetes: A Position Statement of the American Diabetes Association. Diabetes Care, 39(11): 2065-2079. 10.2337/dc16-1728 Florindo AA, and Latorre MRDO. (2003). Validation and reliability of the Baecke questionnaire for the evaluation of habitual physical activity in adult men. Rev Bras Med Esporte, 9(3):129-135.10.1590/S1517-86922003000300002 Yaggi HK, Araujo AB, McKinlay JB. (2006). Sleep duration as a risk factor for the development of type 2 diabetes. Diabetes Care, 29(3):657–661. 16505522 10.2337/diacare.29.03.06.dc05-0879 Yu JH, Yun CH, and Ahn JH, et al. (2015). Evening chronotype is associated with metabolic disorders and body composition in middle-aged adults. J Clin Endocrinol Metab, 100(4):1494–1502. 25831477 10.1210/jc.2014-3754"
},
{
"c_id": "8935",
"date": "17 Nov 2022",
"name": "Chudchawal Juntarawijit",
"role": "Author Response",
"response": "Comments This a very good article, which is needed to demonstrate the exercise and nutritional prevention of diabetes by understanding those behaviours in a group of individuals with or without diabetes in Thailand. Response: Thank you very much for your time and effort in reviewing the manuscript and providing valuable suggestions to improve the paper. All the comments are accepted, and we have tried to revise the paper as such. Generic: Comment: Please check the English and grammar throughout. Response: English has been rechecked by Mr. Kevin Mark Roebl, a native English speaker. Specific: Abstract: Comment: “Diabetic prevention programmes”, should be “diabetes prevention programs”. Response: The terminology has been revised as suggested. Comment: Terminology use “people with diabetes” rather than “diabetic”. Response: The terminology “diabetic” has been replaced by “people with diabetes”. Introduction: Comment: Expand a little on eating behaviour and diabetes and try make a link on why/why not such factors may be important for communities with a similar lifestyle to those tested here. Response: More information on eating and diabetes has been added. Food choice depends not only on behaviour but also socio-economic status. Comment: Expand a little with statements showing some mechanisms linking the sleep/eating/exercise habits with the physiology of diabetes and its development. Response: More information on the association between sleep, eating, and exercise has been added as suggested. Comment: Add a paragraph to justify why and what is special about why the rural communities in Thailand have been tested here. The reader needs to understand the link between these. Response: The information has been added. Information concerning diabetes in Thailand, especially those in small communities, is limited. The selected community may not have special characteristics but has sufficient diabetes cases and convenience for data collection. It can represent a rural community of the province. Comment: The last paragraph needs to have a statement about what is not known and how this study is adding to such knowledge. Response: Yes, we totally agree. What is not known is the health behaviours, sleep, and other aspects of the lifestyle of people with diabetes in Thailand. In this, we try to study those factors and among various groups. This information was presented in the study objective. Methods Comment: Questionnaire: Specify what type of interview in the 1st paragraph. Response: The information on the type of interview has been added as suggested. Comment: Sleep questions, is there a valid sleep questionnaire used here? Why only one question? How do you differentiate between deep sleep/etc.? Did the interview cover more than the one question asked? Details are needed. Response: In this study, only duration of sleep and lifestyle (moringness or eveningness) was selected as target information. For sleep quality, we believe it was rather subjective and hard to collect data. We accepted that this was a study limitation and clearly mentioned in the study limitation section. Comment: Data on food consumption requires justification, what type of questionnaire has been used or developed for this purpose? Why was there a focus on selected foods? Response: In this study, data on food consumption were collected using a modified Food Frequency Questionnaire (FFQ). The questionnaire was tested against a 7-day diet record and found to have high repeatability and good validity score (repeatability for intake was 0.62-0.90 (median 0.81), relative validity was 0.36-0.80 (0.64). Yes, we focused on only types of foods found to be related to diabetes and those often found in Thailand. This information was already presented in the study questionnaire section. Comment: Frequency of certain physical activities. What physical activity questionnaire was used? Was it IPAQ recall? Any validated questionnaire or justification of the questions selected? Response: In this study, we used a Baecke Habitual Physical Activity Questionnaire (BHPAQ) which has been adopted by several countries as a reliable tool to measure habitual physical activity in adult men. Results: Comment: It is not clear why Table 3 has many gaps. Is it to do with insufficient number? Response: Table 3 presented results OR of different models. Further analysis was conducted among men and women. However, this analysis was done only on model3, the best model which included all related variables. This left data on Model 1 and Model2 blank. Discussion: Comment: Please add a paragraph to start with, which should clearly state the most important findings and discuss what is novel. Response: In this study, the most important issues were health behaviours of T2DM. Thus, we began with this finding. Comment: Many paragraphs seem to repeat what is in the results. All paragraphs should have concluding statements stating what is new and how it is relevant for the field. Response: In each paragraph, we have summarized the most important finding before discussing it. Conclusion: Comment: Avoid repetitions “in conclusion” or “this study reveals”. It needs to go straight to the point and concise. Response: Thanks for the reminder. We try to avoid those wordy statements. Comment: Again: the conclusion seems to repeat the findings. Please state the significance of your findings rather than repeating them. Response: The concluding statement has been revised and those repetitions were deleted. Comment: The findings here contrast with the common perception that people with diabetes have bad lifestyle patterns, instead it showed that a healthy lifestyle pattern based on dietary patterns alone may not be sufficient and that lifestyle prevention of diabetes (esp. T2D) should always include physical activity as an integral part. Response: Yes, we agree and thank you for your affirmative. Comment: The authors could also make specific suggestions for how to implement physical activity in the rural community they tested based on the finding that some have better physical activity than others. Response: Thank you for your suggestion. We recommend those activities with low impact, e.g. walking, swimming, biking or doing yoga. This information has been added. Designing a good physical plan is not easy and many of them often fail within a short period of time. A good physical program should be based on research from the specific group and getting the public involved at an early stage. Comment: A conclusion about the sleep patterns finding is missing and should be added. Response: The concluding statement has been added as suggested."
}
]
}
] | 1
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https://f1000research.com/articles/8-1030
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https://f1000research.com/articles/11-1246/v1
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02 Nov 22
|
{
"type": "Brief Report",
"title": "Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation",
"authors": [
"Julien Do Vale",
"Damien Roux",
"Antoine Bridier Nahmias",
"Maud Salmona",
"Séverine Mercier-Delarue",
"Noémie Ranger",
"Jean-Damien Ricard",
"Jérôme Le Goff",
"Mélanie Fromentin",
"Julien Do Vale",
"Damien Roux",
"Antoine Bridier Nahmias",
"Maud Salmona",
"Séverine Mercier-Delarue",
"Noémie Ranger",
"Jean-Damien Ricard",
"Jérôme Le Goff"
],
"abstract": "Background: The lung microbiome is composed of bacteria, viruses and fungi that interplay with each other and participate in mucosal defense protecting the lungs from colonization and infection by pathogenic microorganisms. In intensive care, a change in the composition of the lung microbiome, called dysbiosis, could be associated to the occurrence of ventilator-associated pneumonia. The objective of the study was to test a method to assess the lung virome. Methods: We applied a protocol including the same nucleic acid extraction methods as used for bacterial lung microbiome and a metagenomic next-generation sequencing (mNGS) to detect eukaryotic RNA, DNA viruses and bacteriophages. Results: Our method was able to detect all viruses identified with multiplex polymerase chain reaction (PCR), other eukaryotic viruses not included in the multiplex PCR panel, and bacteriophages. Notably persistent viruses, mainly Herpesviridae, associated with opportunistic infections and those showing immunodepression such as Anellovirus have been identified. Conclusions: A better description of the global composition and evolution of the lung microbiome, including viruses, could help to better understand ventilator-associated pneumonia occurrence and outcomes.",
"keywords": [
"lung microbiome",
"lung virome",
"metagenomic shotgun sequencing",
"metagenomic next-generation sequencing",
"clinical metagenomics",
"ventilator-associated pneumonia",
"mechanical ventilation"
],
"content": "List of abbreviations\n\nBAL bronchoalveolar lavage\n\nCMV: cytomegalovirus\n\nCOPD: chronic obstructive pulmonary disease\n\nETA endotracheal aspirate\n\nHSV: Herpes simplex virus\n\nICU: intensive care unit\n\nmNGS metagenomic shotgun sequencing\n\nPCR: polymerase chain reaction\n\nVAP: ventilator associated pneumonia\n\n\nIntroduction\n\nThe respiratory microbiota is composed of bacteria, viruses, fungi and archaea that interact and constitute a barrier protecting the lungs from colonization by pathogenic microorganisms.1 A dysbiosis of the respiratory microbiota (change in composition or functioning) may be associated with a pathological state and promote infection, as suggested in asthma, chronic obstructive pulmonary disease (COPD) or cystic fibrosis.2 In intensive care units (ICU), some studies have also described an association between a decrease in lung microbiota diversity and the occurrence of ventilator-associated pneumonia (VAP).3 The lung microbiota is indeed deeply affected by different therapies in critically ill patients such as antibiotics or mechanical ventilation.4 A better understanding of its evolution could thus help manage VAP.5 To date, outside lung transplant recipients, studies in ventilated patients have mainly focused on bacterial microbiota. Very few have studied the viral populations besides Papazian et al 10 years ago.6 However, analysis of bacterial fungal and viral communities simultaneously seems essential to obtain a comprehensive view of the potential dysbiosis.7 The human lung virome integrates all viruses present in the lungs, both eukaryotic and prokaryotic viruses (also called phages), and plays a fundamental role in the development and regulation of the innate and adaptive immune system.7,8 For instance, a respiratory syncytial virus (RSV) infection leads to a deregulation of the immune system that persists for several weeks.9 Identification of influenza virus or rhinovirus in the airways has also been associated with the occurrence of bacterial infections.10 Specific analysis of the lung virome in ICU is thus essential to improve our understanding of the VAP pathophysiology.\n\n\nMethods\n\nIn a pilot study based on a prospective observational cohort study (January 2015 to June 2016, Paris, France, in press) (ethical authorization CE SRLF 15-41), we aimed to evaluate the feasibility of studying the lung virome in patients under mechanical ventilation in ICU by metagenomic shotgun sequencing (mNGS) using an extraction method of nucleic acids allowing an analysis of the bacterial microbiota on the same samples.\n\nAll samples were provided from patients initially included in a cohort study titled “Lung microbiota of ventilated ICU patients: towards a new understanding of nosocomial pneumonia” (in press). The ethics committee of the French intensive care society approved the cohort study, authorizing the use of the samples for the study of bacterial microbiota and of the virome each as a part of this cohort study (reference CE SRLF 15-41, date of acceptance October 1st 2015).\n\nInformed consent was sought on admission to the intensive care unit in mechanically ventilated patients placed under general anaesthesia or in patients who presented signs of acute respiratory failure and required orotracheal intubation. As a result, oral consent was systematically obtained from patient’s next of kin. After patient’s extubation, verbal informed consent was systematically confirmed by the patients themselves except in cases of altered mental status or delirium. According to French regulations on non-interventional studies, the ethics committee of the French Intensive Care Society considered oral consent to be sufficient.\n\nFor each patient, when informed consent was confirmed by the patient themselves after extubation, verbal consent for publication was also obtained.\n\nInclusion criteria in the cohort study were age over 18 years, intubation at admission or within the six hours before, expected duration of mechanical ventilation above 72 hours. Exclusion criteria were a known chronic lung disease (severe chronic obstructive pulmonary disease, emphysema, bronchiectasis, cystic fibrosis, lung transplant or a restrictive lung disease), an invasive ventilation for more than 72 hours in the last six months, an immunosuppression (HIV with less than 200 CD4 lymphocytes/mm3, neutropenia below 500/mm3, treatment by immunosuppressive agents), and absence of consent to participate. Overall, 86 patients were included in the cohort study.\n\nFor this feasibility study, we selected nine patients, in order to represent all subgroups of patients (patients who were hospitalized for a bacterial or viral community-acquired pneumonia, and/or patients who developed VAP). The respiratory virome of 24 samples (endotracheal aspirate (ETA) or bronchoalveolar lavage (BAL)) in these 9 representative patients was evaluated.\n\nSamples were removed from -80°C storage and were put in 2 ml lysis matrix tube Y (MP Biomedicals®, catalogue number SGD135.55) for bead beating. For ETA only, 500 microliters of PBS EDTA free with Ca2+ and Mg2+ (Invitrogen®) were added to the lysis matrix tube. Samples were homogenized for 30 seconds two times at 6000 rpm using PlexIDbb instrument (Precellys Bertin technologies®). After centrifugation (one min at 8000 rpm), viral nucleic acid of samples was extracted from each sample using the nucleic extraction platform based on magnetic silica technology NucliSENS® easyMAG® (Biomerieux®). For each nucleic acid extraction, negative controls (NC) (600 μL of PBS EDTA free) were used. For each sample and NC, after Qubit fluorometer quantification® of the nucleic acid amount (Qubit dsDNA Hs Assay Invitrogen®, catalogue number Q32851), DNA and RNA libraries were generated in order to analyze the entire viral population.\n\nDNA libraries were generated using the Nextera DNA XT Kit (Illumina®, San Diego, CA, USA, catalogue number FC-131-1096) in a five steps procedure: i) a methylated DNA removal step using MBD2-Fc beads in order to eliminate human DNA ii) a DNA concentration by Zymo DNA clean concentrator iii) a 5 minute ATM enzyme tagmentation step performed at 55°C with a final enzyme inhibition iv) a final 16 cycles PCR reaction with Illumina® sequencing primer (Nextera XT Index Kit v2 Set D, 96 indexes, catalogue number FC-131-2004).\n\nRNA libraries were performed using RNA Seq Trio kit (Nugen®, San Carlos, California, USA, catalogue number M01440) as per manufacturer’s instructions. This kit is notably used for small amounts of RNA (between 500 picogram and 50 nanogram).11 After DNase incubation (37°C 10 min, 60°C 5 min, hold at 4°C) double strand cDNA was synthetized performing two successive PCR reaction containing 25 μL of eluate after nucleic acid extraction, and PCR products were purified using AMpure magnetic bead-based purification system (Beckman Coulter, Inc, Atlanta, Georgia) as per manufacturer’s instructions.\n\nAfter single primer isothermal amplification (SPIA), indexed Illumina libraries were prepared as per manufacturer’s instructions. First, cDNA strands fragmentation was performed to obtain homogenous 300 pb PCR products (25°C-30 min, 70°C-10 min, hold at 4°C). Then library amplification of the 300 pb based long cDNA with Illumina® sequencing primer, consisted in two PCR reactions separated by a targeted depletion with Anydeplete® (60°C-30 min, 95°C-5 min, hold at 4°C).\n\nAfter each library preparation, PCR products were purified using a 0.9 volume of AMpure® magnetic bead-based purification system (Beckman Coulter, Inc, Atlanta, Georgia, catalogue number A63881) as per manufacturer’s instructions and eluted in low Tris-EDTA buffer. Successful amplifications were verified in 4200 Tape Station Agilent bioanalyzer (Agilent Technologies®) as per manufacturer’s instructions, with DNA 5000 screen tape (catalogue number 5067-5588) and reagents (catalogue number 5067-5589) and indexed-DNA sequences quantified in purified samples using a quantitative PCR performed with KAPA Library quantification kit for Illumina platforms (Kappabiosystems®, catalogue number KK4854 – 07960298001) as per manufacturer’s instructions. After sample preparation following the Illumina’s protocol instructions, 24 samples for final DNA library and 24 samples for final RNA library were loaded at 1.8 pM and sequenced in two sequencing runs on NextSeq 500 platform (Illumina®, San Diego, California, USA), using the indexing strategy and 150-bp paired-end reads (V2 300 cycle kit, Illumina® catalogue number MS-102-2002) as per manufacturer’s instructions.\n\nThe bioinformatics analysis was performed using the SURPI (Sequence based ultra rapid pathogen identification) computational pipeline12 available at https://chiulab.ucsf.edu/?s=surpi. All the sequences were deposited in the European nucleotide archive: ENA: Analysis of the lung virome under mechanical ventilation by high-throughput sequencing accession number PRJEB56382 (second accession number ERP141316).18\n\nViruses identified in negative controls were then excluded from the analysis of other samples.\n\nIn order to evaluate accuracy and sensitivity of metagenomic shotgun sequencing method, we used conventional targeted polymerase chain reaction (PCR) to identify respiratory viruses in each sample. A respiratory panel of 17 pathogenic viruses (including rhinovirus, influenza and parainfluenza virus and syncytial respiratory virus) was investigated using FilmArray® Respiratory Panel 2 (bioMérieux, France) as per manufacturer’s instructions, on the first sample collected for each patient.13 Herpes simplex viruses and cytomegalovirus were also tested by quantitative PCR (RealStar® HSV PCR Kit CE - Altona-Diagnostics catalogue number 061013, CMV RealTime Abbott, Abbott Molecular® catalogue number 05N23-090) in BAL samples as per manufacturer’s instructions.\n\nThe analysis code used in this study has been deposited in Zenodo.20\n\n\nResults\n\nIn total, nine patients were included in this study, all males with a median age of 72 years [66;72], 33% active smokers, with a median duration of mechanical ventilation of 18 days [16;20]. The patient’s characteristics are presented in Table 1.19\n\nOverall, eight of these patients presented a community acquired pneumonia (CAP) or an aspiration pneumonia on ICU admission, two presented a viral pneumonia and three of them developed a VAP during their ICU stay (patients 1, 2 and 3). Data from conventional microbiology for all subtypes of bacterial pneumonia are presented in Table 2 with five out of eight having documented CAP (Table 2).\n\nFour viral species were identified by conventional PCR methods among six patients: patient 1 with influenza virus B (Orthomyxoviridae), patients 2 and 3 with cytomegalovirus (Herpesviridae), patients 4 and 5 with respiratory syncytial virus (Paramyxoviridae), and patient 9 with influenza virus A (Orthomyxoviridae). No viral species were identified by PCR in patients 6, 7 and 8.\n\nMetagenomic shotgun sequencing generated a total of about 1 billion reads, a majority of them corresponding to human reads (83%) for RNA and DNA libraries (Figure 1a and b). Nevertheless, SURPI identified a total of 196,580 viral reads. After family assignation and consideration of positive detection in samples with at least five reads of the same species, eleven viral families were detected, including seven families of eukaryotic viruses and four families of phages (Figure 2).\n\nAssignation of reads obtained after high throughput sequencing are represented in (a) for RNA libraries and (b) for DNA libraries. For RNA library, 75% were human RNA sequences and 25% were classified as “other”. For DNA library, 94% were human DNA sequences and 6% were classified as “other”. For both types of libraries, the remaining sequences corresponded to bacterial, viral, or unassigned sequences expressed as a percentage of non human sequences. Viral sequences represented only 0.12% of the other non-human RNA sequences and 0.05% of the other non-human DNA sequences.\n\nOverall, 11 virus families have been identified after high throughput sequencing. The number of reads assigned to each family are shown on the diagrams. The three main families are Orthomyxoviridae, Herpesviridae and Paramyxoviridae. Only 2314 reads belonged to other families. Families of eukaryotic viruses are represented in grey or brown tones. Families of phages are represented in green tones and in bold.\n\nVirus detection per patient is given in Table 3. All viruses detected by conventional targeted PCR were identified by mNGS. In addition, a large number of viruses not detected by PCR were detected by metagenomic shotgun sequencing. For patients 1 and 9, the multiplex PCR identified influenza virus and mNGS identified nine different viral families including influenza virus, Herpesviridae and Anelloviridae, and phages. The same observation was made for patients 2 and 3 in whom cytomegalovirus (CMV) was detected by specific PCR and by mNGS in addition to many families of bacteriophages. For patients 4 and 5, while respiratory syncytial virus was detected by both PCR and mNGS, the latter method also identified a significant number of other viruses such as Herpesviridae (mostly represented by Herpes simplex virus 1 (HSV1)) and Anelloviridae. For patients 6, 7 and 8, while no virus was identified by PCR, numerous viral families were identified by mNGS.\n\n\nDiscussion\n\nThe presented method enabled to determine the respiratory virome profile with a good accuracy compared to multiplex PCR. Interestingly we were able to describe the bacterial microbiota on the same samples, as shown in our previous pilot study on respiratory bacterial microbiota, using the same nucleic acid extraction before 16s rRNA high-throughput sequencing.14 Overall, these results demonstrated the opportunity to study both bacterial and viral microbiota in respiratory samples of ventilated patients, providing a more comprehensive view of the respiratory microbiome and thus allowing a better understanding of VAP pathophysiology.15 The small number of samples and patients do not allow generalization at this stage. As previously observed in other studies, the number of viral reads is lower than those related to human or bacterial genomes by suing global metagenomics without a dedicated approach to enrich in viral particles.16,17 However this did not hamper the overall sensitivity as all respiratory viruses identified by targeted multiplex PCR were also detected by metagenomics.\n\nThis feasibility study thus validates the strategy of a unique metagenomics protocol with the final aim of studying not only the lung bacterial microbiota but also the lung virome.15 Adding the ITS2 high-throughput sequencing, it will allow investigating global respiratory microbiota profiles and coevolution including bacteria, fungi and viruses in ventilated patients. Larger cohort studies are needed to fully characterize pulmonary dysbiosis in ventilated patients who have developed a VAP to understand whether pulmonary dysbiosis is a cause, a consequence or both.\n\nVAP prevention is a crucial challenge for the management of ICU patients. Obviously in case of causal pulmonary dysbiosis, a better understanding of infectious steps leading to VAP development can help to define targeted interventions on the bacterial microbiota, the mycobiota and the virome.",
"appendix": "Data availability\n\nEuropean nucleotide archive: All sequences from this study. Accession number PRJEB56382; https://identifiers.org/ena.embl:PRJEB56382. 18\n\nZenodo: Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation. https://doi.org/10.5281/zenodo.7046988. 19\n\nThis project contains the following underlying data:\n\n- Electrophoresis from DNA and RNA libraries control performed using 4200 Tape Station Agilent bioanalyzer (Agilent Technologies®)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAll the script of the analysis is available in chuilab: https://chiulab.ucsf.edu/?s=surpi\n\nArchived analysis code at time of publication: https://doi.org/10.5281/zenodo.7040994. 20\n\nLicense: Creative Commons Attribution 4.0 International\n\n\nAcknowledgments\n\nWe thank the PTechnologic Plateform IRSL for hosting this work. We thank the European Society of Intensive Care Medicine for funding. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.\n\n\nReferences\n\nMan WH, de Steenhuijsen Piters WAA , Bogaert D: The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat. Rev. Microbiol. 2017; 15(5): 259–270. PubMed Abstract | Publisher Full Text Reference Source\n\nBudden KF, Shukla SD, Rehman SF, et al.: Functional effects of the microbiota in chronic respiratory disease. Lancet Respir. Med. 2019; 7(10): 907–920. Publisher Full Text Reference Source\n\nZakharkina T, Martin-Loeches I, Matamoros S, et al.: The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia. Thorax. 2017; 72(9): 803–810. PubMed Abstract | Publisher Full Text\n\nDickson RP: The microbiome and critical illness. Lancet Respir. Med. 2016; 4(1): 59–72. PubMed Abstract | Publisher Full Text Reference Source\n\nKitsios GD, Morowitz MJ, Dickson RP, et al.: Dysbiosis in the intensive care unit: Microbiome science coming to the bedside. J. Crit. Care. 2017; 38: 84–91. PubMed Abstract | Publisher Full Text Reference Source\n\nPapazian L, Doddoli C, Chetaille B, et al.: A contributive result of open-lung biopsy improves survival in acute respiratory distress syndrome patients. Crit. Care Med. 2007; 35(3): 755–762. PubMed Abstract | Publisher Full Text Reference Source\n\nZou S, Caler L, Colombini-Hatch S, et al.: Research on the human virome: where are we and what is next. Microbiome. 2016; 4(1): 32. PubMed Abstract | Publisher Full Text\n\nCadwell K: The Virome in Host Health and Disease. Immunity. 2015; 42(5): 805–813. PubMed Abstract | Publisher Full Text Reference Source\n\nMolyneaux PL, Mallia P, Cox MJ, et al.: Outgrowth of the Bacterial Airway Microbiome after Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease. Am. J. Respir. Crit. Care Med. 2013; 188(10): 1224–1231. Publisher Full Text\n\nBellinghausen C, Rohde GGU, Savelkoul PHM, et al.: Viral–bacterial interactions in the respiratory tract. J. Gen. Virol. 2016; 97(12): 3089–3102. Publisher Full Text\n\nAdiconis X, Borges-Rivera D, Satija R, et al.: Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods. 2013; 10(7): 623–629. PubMed Abstract | Publisher Full Text Reference Source\n\nNaccache SN, Federman S, Veeraraghavan N, et al.: A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res. 2014; 24(7): 1180–1192. PubMed Abstract | Publisher Full Text\n\nLeber AL, Everhart K, Daly JA, et al.: Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples. Tang YW, editor. J. Clin. Microbiol. 2018; 56(6): e01945–17.Reference Source\n\nFromentin M, Bridier-Nahmias A, Legoff J, et al.: The 16S rRNA lung microbiome in mechanically ventilated patients: a methodological study. Exp. Lung Res. 2022; 48(1): 23–34. PubMed Abstract | Publisher Full Text\n\nFromentin M, Ricard JD, Roux D: Respiratory microbiome in mechanically ventilated patients: a narrative review. Intensive Care Med. 2021; 47(3): 292–306. PubMed Abstract | Publisher Full Text\n\nZoll J, Rahamat-Langendoen J, Ahout I, et al.: Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information. J. Clin. Virol. 2015; 66: 6–11. PubMed Abstract | Publisher Full Text Reference Source\n\nZhang D, Lou X, Yan H, et al.: Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples. BMC Genomics. 2018; 19(1): 773. PubMed Abstract | Publisher Full Text\n\nINSERM Paris nord Bichat, Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation. [Dataset]. European Nucleotide Archive. (8-Oct-2022).hReference Source\n\nDo Vale J, Roux D, Bridier-Nahmias A, et al.:Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation. [Dataset]. Zenodo. 2022. Publisher Full Text\n\nVale D, Julien B-N, Antoine R, et al.:Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation. [Dataset]. Zenodo. 2022. Publisher Full Text"
}
|
[
{
"id": "154867",
"date": "28 Nov 2022",
"name": "Allan Glanville",
"expertise": [
"Reviewer Expertise Thoracic medicine",
"lung transplantation",
"CLAD and the pulmonary virome in particular"
],
"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 a small prospective study of ventilated patients the authors describe a novel technique to permit determination of both bacterial and viral components of the pulmonary microbiome, which is a major advance in applied thinking given that most studies to date have focussed solely on the bacterial components. The working hypothesis was that dysbiosis may be associated with ventilator associated pneumonia (VAP) but as the authors acknowledge, the study was not powered to demonstrate causality or designed to inform the time sequence as to which came first. Nevertheless, as an observational study, the work adds important knowledge regarding how to consider and analyse components of the pulmonary microbiome, allowing that details of richness and diversity of species detected were not presented, which may be valuable in future studies.\nMAJOR\nThe authors should use precise terminology throughout the manuscript. The microbiome refers to the microorganisms and their genes whereas the microbiota only refers to the microbes themselves, so the terms should not be used interchangeably.\n\nAgain, precise terminology should be used when referring to sequencing technique. The authors report that ” 24 samples for final DNA library and 24 samples for final RNA library were loaded at 1.8 pM and sequenced in two sequencing runs on NextSeq 500 platform (Illumina®, San Diego, California, USA)”, hence the comparison of PCR testing was made versus mNGS, as correctly described in Table 3, not with “shotgun sequencing” as mentioned in the text describing Table 3, which is a different technique. Please correct the text accordingly throughout the manuscript.\n\nNormal controls are mentioned and the viruses found were excluded from clinical sample analysis, presumably as “contaminants”. Could the authors please describe how many normal control samples were analysed, what comprised a normal control, whether the analysis performed was identical and what viruses were found?\n\nCould the authors please describe details of the ETA and BAL technique and handling? Were cell filters used?\n\nReference is made to their prior study showing the bacterial components found (Ref 14). This aspect is worthy of greater explanation as it is a key finding that the same techniques can be used to amplify the breadth of knowledge about the microbiome.\n\nHow long were samples stored before processing and did this lead to any degradation of samples or inability to detect viruses given their low biomass?\n\nCould the authors comment on the sensitivity of their multiplex PCR to detect respiratory viruses viz a vis uniplex PCR studies?\n\nMINOR\nList of Abbreviations: mNGS “metagenomic shotgun sequencing”, should be “metagenomic next generation sequencing” as correctly abbreviated in the Abstract\n\nVAP is “ventilator associated pneumonia” as correctly noted in List of Abbreviations, not “ventilated” so this should be corrected throughout the manuscript and figures / tables.\n\nDiscussion: the meaning of the following sentence is unclear, “the number of viral reads is lower than those related to human or bacterial genomes by suing global metagenomics without a dedicated approach to enrich in viral particles”. The term “suing” does not make sense, do you mean “pursuing”?\n\nTable 2: D0 should be defined.\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? 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": []
},
{
"id": "154866",
"date": "02 Dec 2022",
"name": "Sophie Vallet",
"expertise": [
"Reviewer Expertise Virology",
"virome",
"diversity of RNA viruses"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary The manuscript written by Do Vale et al entitled “Analysis by metagenomic next-generation sequencing of the lung virome during mechanical ventilation » is a brief report. The authors report an analysis of the lung microbiome of 9 ICU mechanically ventilated patients. They state the importance of dysbiosis in respiratory microbiota, which potentially promotes pneumonia. Differently from the description of bacterial microbiota in patients under mechanical ventilation, there is a lack of generalized methodological approach to the lung virome, it drastically misses viral data in this compartment. In order to address this, the objective of this French research team was to test the feasibility of a deeply metagenomic next generation sequencing (mNGS) of respiratory virome. The methodology used by the research team combines an already improved bacterial DNA extraction and an extraction of eukaryotic RNA plus DNA viruses. The accuracy and sensitivity of the mNGS methodology were assessed by compared results obtained in multiplex viral respiratory PCR in the same samples. Results retrieved one billion reads only 0.12 % and 0.05% of non-human RNA and DNA sequences respectively were viral. Among them, some mNGS identified Orthomyxoviridae, Herpesviridae, Paramyxoviridae as did Multiplex PCR but also numerous viruses not targeted by PCR. The authors, aware of its limits, finally comforted the feasibility of their mNGS protocol, describing both bacterial and viral microbiota on a single sample.\nComments The manuscript is well-written and respects the criteria defined by F1000Research for a brief report. The introduction is structured, it states the field and the essential aim to analyse lung virome in ICU to improve the understanding of the ventilator-associated pneumonia pathophysiology. In that sense, the main question is the evaluation of the feasibility of studying pulmonary virome in ventilated patients. In their recent “narrative review”1, authors have largely argued the necessity of a global approach to the human respiratory microbiome, including, not only the bacterial, but also the fungal microbiota and the virome.\nMethodology/Results This is a feasibility study of virome analysis conducted on 24 samples from 9 patients, 3 of whom had developed VAP (Ventilator Associated Pneumonia), using the same extraction technique for viral and bacterial nucleic acids and the Illumina NextSeq 500 platform to sequence libraries. This high throughput sequencing implemented by the authors has identified 11 viral families combining eukaryotic viruses and bacteriophages. We understand that the methodology has been improved in a previous cohort study, for bacterial microbiota exploration only.\n\nPositive points: - It’s one of the first studies that states mNGS virome data in deep pulmonary airways of ventilated ICU patients. The authors have reviewed the until now poor existing state of knowledge on respiratory virome in ICU ventilated patients. Effectively very few descriptive studies conducted in ventilated ICU patients have focused on the viral microbiota. Which strongly justifies this study. This feasibility study gives viral data not evaluated until now in mechanically ventilated patients with pneumonia. Even if the exploration has been made to a few subjects (9), it constitutes a first step essential in the approach to the viral part linked to ICU pneumonia.\n- The methodology is described in detail for all steps, from nucleic acids extraction, quantification and preparation of RNA and DNA libraries, with the precaution to circumvent bias of small amounts of RNA by the use of kits which can be used with RNA input as few as 500 pg to 50 ng. Recently a new commercial kit has been designed to detect as few as 250 pg to 10 ng.\n- The viral data reported by the authors are coherent with previously described data in various virome mNGS from different diseased associated human compartments such as respiratory airways but also digestive, cutaneous or genital areas. In most of them like in the present study, bacteriophages represent most of the viruses identified.\n- Due to a good visualization of metagenomic results, tables and figures allow the reader to see the importance of the weak numerical proportion of identified viruses. Numerous viruses non identified in multiplex PCR were detected by mNGS.\n- The results obtained, although improvable are encouraging and need to be verified in terms of reproducibility with the aim implementing this metagenomic method in lab structures. After the improvement of their mNGS methodology it will constitute an accurate tool to drive the longitudinal microbiota approach in ICU. The authors have succeeded in using a common automated extraction for the exploration of both the virome and the bacteriome in the same and single sample. Which could give a global vision of the microbiome and its evolution over time (through its use in longitudinal cohort studies).\n- One important point in the design of the study is the availability of kinetic detection for viral pathogens on iterative samples (ETA or BAL) with the number of days from intubation. The kinetic results are however not commented. The viral kinetic tends to show viral presence as soon as 3 or 6 days from intubation and later (9 to 11 days ) for “persistent” or reactivated viruses like CMV (table 3). A few number of reads were reported in two BAL samples, in relation to the patient’s clinical status. They might be associated with increased length of stay or mortality.\n- The researchers of the present study had shared their libraries’ RNA and DNA datas and quality controls performed. All the source data underlying the results had been made available to ensure full reproducibility.\nAreas for improvement: - As with any pilot study, a low number of patients/samples were included. It may not allow the generalization of results because of a lack of representativeness of the population of patients ventilated in the ICU - That number of reads of the same species used for the assignation of viral pathogens detected appears to be quite low, with only at least five reads. - The dynamics performed were carried out over a short period of time to show a modification in the diversity of the pulmonary microbiota during mechanical ventilation. - The strategy for human DNA depletion is apparently insufficient; this is a strong usually met problem that affects the results sensitivity and difficult to overcome completely. - Table 2: D0 should be defined - CAP: Community acquired pneumonia may be added in the list of abbreviations - I have requested for further details about microbial analyses:\nIn this study, nine patients were selected from a French prospective observational cohort study; their respiratory virome was evaluated either on endotracheal aspirate (for CAP) or bronchoalveolar lavage (for VAP). Microbial analyses were conducted on samples from the lower respiratory tract, endotracheal or bronchoalveolar lavage, is there a justified advantage for either one of them? The point that some viruses were identified in negative controls concerns me. No more is specified, just that these sequences have been excluded from the analysis of other samples. Could you make light on this? To which viruses corresponded these sequences? Bacteriophages? Reagent contaminants? Are DNA or RNA more concerned? The authors haven’t reported tests or results of reproducibility (no number of replicates specified) nor statistical analyses data in mNGS assays. One might consider that it is in relation to the limited numbers of samples of the pilot studies... For non-discussed data one could easily imagine that the small number of patients, couldn’t allow concluding. That is one of the weaknesses of the study, but let’s recall that the principal aim of the study is the technical aspect of the virome exploration, more than clinical discussion. Evidence is that the authors have given a short place for that in the discussion. To overcome the weak detection of viral genomes, some enrichment methodologies may be implemented before the extraction process like filtration, sonication… Had these enrichment procedures been performed? The reference of the pipeline used is also mentioned; it has the capacity, amongst other functions, to subtract human DNA sequences (software SNAP) but it is not a recent one (2014). Some pipelines more adapted could also be experimented (VirSorter2, Guo et al 2021 Microbiome).\nConclusion: In conclusion, in the context where the impact of mechanical ventilation on the respiratory virome remains rarely studied, the authors have validated in their pilot study the feasibility of their mNGS methodology. This feasibility study gives viral data not evaluated until now in mechanically ventilated patients with pneumonia. Even if the exploration has been made to a few subjects (9), it constitutes a first step in the approach to the viral part linked to ICU pneumonia. Their work could contribute to the understanding of the viral dysbiosis in ventilated associated pneumonia development.\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? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1246
|
https://f1000research.com/articles/11-781/v1
|
12 Jul 22
|
{
"type": "Case Report",
"title": "Case Report: Caecal volvulus management from diagnosis to treatment in a young patient",
"authors": [
"Imed Abbassi",
"Wissem Triki",
"Racem Trigui",
"Ahmed Itaimi",
"Karim Ayed",
"Hajer Sebri",
"Oussema Baraket",
"Sami Bouchoucha",
"Wissem Triki",
"Racem Trigui",
"Ahmed Itaimi",
"Karim Ayed",
"Hajer Sebri",
"Oussema Baraket",
"Sami Bouchoucha"
],
"abstract": "Caecal volvulus (CV) is a rare cause of intestinal obstruction, defined by an axial torsion of the caecum, ascending colon, and terminal ileum around the mesenteric vascular pedicles, leading to ischemia and bowel necrosis. A 20-year-old woman, with no significant medical history, was admitted for generalized abdominal pain evolving for three days, along with constipation and abdominal distension, but with no vomiting. Physical examination showed a generalized abdominal tenderness with no rigidity or rebound tenderness, associated with abdominal distension and tympanic upon percussion. Laboratory findings were within normal limits. An abdominal computed tomography scan revealed distension of a loop of the large bowel with its long axis extending from the right lower quadrant to the epigastrium or left upper quadrant. Colonic haustral pattern was absent. An abdominal computed tomography scan showed a rounded focal collection of air-distended bowel with haustral creases in the upper left quadrant. In addition, spiraled loops of the collapsed cecum (giving a whirl sign) were noted, along with low-attenuating fatty mesentery from the twisted bowel. The patient underwent an emergency laparotomy and caecectomy using GEA 80 charges. The patient had no complaints post-operation. CV is a rare cause of bowel obstruction, mainly caused by an exceedingly mobile caecum. Despite its rareness, CV represents the second most common cause of large bowel volvulus, behind sigmoid volvulus. For acute obstruction by CV, it is hard to differentiate it clinically from obstruction of the small bowel; therefore, radiological exams are needed. Surgery is the gold standard treatment for CV. We report a rare case of CV to highlight the rarity of this pathology, specify its diagnostic and therapeutic means, and its clinical and biological evolution.",
"keywords": [
"caecal volvulus",
"whirl sign",
"caecopexy",
"caecectomy"
],
"content": "Introduction\n\nVolvulus is commonly defined as a twisted loop of the intestinal bowel and associated mesentery around a fixed point at its base. Caecal volvulus (CV) is a rare cause of intestinal obstruction, defined by an axial torsion of the caecum, ascending colon, and terminal ileum around the mesenteric vascular pedicles.1\n\nPreoperative diagnosis can be difficult due to its unspecific symptoms. As a result, CV is a surgical emergency and any delay in management can be associated with complications mainly bowel ischemia eventually leading to perforation and peritonitis.\n\nWe report this case of CV to highlight the rarity of this pathology, the difficulty of clinical diagnosis, and to report the success of caecostomy as a surgical option against right colectomy.\n\n\nCase presentation\n\nA 20-year-old Tunisian woman, unemployed, with no significant medical history, was admitted for generalized abdominal pain evolving for three days, along with constipation and abdominal distension, but with no vomiting. Physical examination showed a generalized abdominal tenderness with no rigidity or rebound tenderness, associated with abdominal distension and tympanic upon percussion. Laboratory findings were within normal limits.\n\nAbdominal X-rays were taken, and they revealed distension of a loop of the large bowel, with its long axis extending from the right lower quadrant to the epigastrium or left upper quadrant. Colonic haustral pattern was absent (Figure 1).\n\nAn abdominal computed tomography (CT) scan showed a rounded focal collection of air-distended bowel with haustral creases in the upper left quadrant. In addition, spiralled loops of collapsed cecum (giving a whirl sign) were noted, with low-attenuating fatty mesentery from the twisted bowel (Figure 2).\n\nThe patient was kept for six hours under observation, with nothing by mouth, nasogastric tube suction, and IV fluids. At the end of the evaluation period (six hours post suction), the patient underwent an emergency laparotomy.\n\nDuring the operation, the caecum in the left hypochondrium was hugely distended and contained signs of pre-perforation, such as bowel deperitonization lesions (Figure 3). CV was seen, and clockwise de-rotation of volvulus was performed. After CV was diagnosed, a caecectomy was performed using GEA 80 charges.\n\nThe patient had an adequate postoperative evolution. Antibiotics prophylaxis was given for 48 hours post-operatively with amoxicillin (Ac. Clavulanique intravenously at the dosage of 1gr three times a day). Venous thromboembolism prophylaxis was given using enoxaparin subcutaneously at a dosage of 4000 UI once a day. A liquid diet was initiated 48 h after surgery. The patient had no clinical signs of leakage. On day 5, the patient was discharged. After two weeks, the final histopathological examination was performed, reporting caecal necrosis without underlying lesions.\n\nIn the postoperative assessment after two months, the patient was found to be tolerating oral intake, was asymptomatic, and did not have any signs of weight loss.\n\n\nDiscussion\n\nCV is an infrequent cause of colon obstruction.2 It is the second most frequent location of colonic volvulus and accounts for up to 60% of cases according to several studies.3 To be diagnosed with CV, two conditions must be met: an abnormal mobile caecum associated with the lack of attachment of the mesenterium, caecum, or right colon to the posterior peritoneum3–5; and a fixed point around which the caecum can twist.6\n\nA mobile caecum is an anatomical variant, present in 25% of the general population according to some studies.7 It is believed that a mobile caecum is caused by deficient colonic fixation to the peritoneum or colon elongation resulting from over-rotation during embryologic development.8 Clinical presentation is exceedingly variable, but the most common symptoms are abdominal, accompanied by nausea, vomiting, and abdominal distension.9\n\nIn general, CV can be presented in three clinical syndromes: recurring intermittent pain, acute abdominal obstruction, and devastating acute obstruction.2 In recurring intermittent volvulus, patients experience pain in their lower right quadrant associated with abdominal dilation partially relived by gas release, such as the case of our patient.10,11 For acute obstruction by caecal volvulus, it is hard to differentiate it clinically from obstruction of the small bowel; therefore, radiological exams are needed.3 If not treated on time, an acute obstruction may progress into a devastating acute obstruction associated with severe abdominal pain, sepsis, and peritoneal irritation caused by necrosis and intestinal perforation due to obstruction and twisted mesenteric vessels.12,13\n\nIn terms of diagnosis, CT is the imaging technique of choice, allowing not only confirmation of the diagnosis, but also ruling out other causes of acute obstruction. Coffee bean, bride beak, and whirl signs are the most common observations identified during CT.14\n\nSurgery is the main course of treatment for CV, ranging from simple detorsion to right colectomy.7 If gangrene, necrosis, or perforation are identified, resection is mandatory, and the current method of choice is right colectomy with primary anastomosis or ileostomy depending on perioperative factors.12 Three main procedures are described in the literature following caecum detorsion with no suspicion regarding its viability: isolated detorsion, caecopexy, and caecostomy.8 Isolated detorsion without caecopexy or cecostomy is associated with a high risk of recurrence; therefore, it should not be used anymore.15 Caecopexy is obtained by attaching the right colon to the parietal peritoneum with a recurrence rate of up to 40%. Cecostomy is associated with a higher risk of complications, including caecum gangrene, fistula, and leakage. In this case, our patient was young with signs of caecal pre perforation and not prepared for a right colectomy; as a result, we choose to perform a caecostomy. Compared to caecopexy, caecostomy has a higher rate of morbidity and mortality. As a result, caecopexy is recommended for patients with viable intestines not tolerating right colectomy and those suffering from mobile caecum syndrome.8,11,16 This, in conjunction with modern-day laparoscopic evolution, has decreased mortality, and post-operative results have markedly improved.3\n\n\nConclusion\n\nCaecal volvulus is a rare cause of bowel obstruction, mainly caused by an exceedingly mobile caecum. Early diagnosis can be difficult due to its unspecific symptoms. Computed tomography plays a major role in a positive diagnosis. The main course of treatment is surgical, and modalities depend on various factors such as patient status and perioperative findings. Nowadays laparoscopic evolution continues to reduce postoperative morbidity.\n\n\nConsent\n\nWritten informed consent to publish this case report and any associated images was obtained from the patient.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
"appendix": "References\n\nMajeski J: Operative therapy for cecal volvulus combining resection with colopexy. Am. J. Surg. févr. 2005; 189(2): 211–213. PubMed Abstract | Publisher Full Text\n\nConsorti E, Liu T: Diagnosis and treatment of caecal volvulus. Postgrad. Med. J. déc. 2005; 81(962): 772–776. PubMed Abstract | Publisher Full Text\n\nHasbahceci M, Basak F, Alimoglu O: Cecal Volvulus. Indian J. Surg. déc. 2012; 74(6): 476–479. PubMed Abstract | Publisher Full Text\n\nDelabrousse E, Sarliève P, Sailley N, et al.: Cecal volvulus: CT findings and correlation with pathophysiology. Emerg. Radiol. nov. 2007; 14(6): 411–415. PubMed Abstract | Publisher Full Text\n\nValsdottir E, Marks JH: Volvulus: small bowel and colon. Clin. Colon Rectal Surg. mai 2008; 21(2): 091–093. PubMed Abstract | Publisher Full Text\n\nHaskin PH, Teplick SK, Teplick JG, et al.: Volvulus of the Cecum and Right Colon. JAMA. juin 1981; 245(23): 2433–2435. Publisher Full Text\n\nDeSilva SG: Cecal volvulus case report. Imaging in Medicine. mai 2017; 9(2): 31–32.\n\nRamírez-Ramírez MM, Villanueva-Sáenz E, Ramírez-Wiella-Schwuchow G: Elective laparoscopic right colectomy for caecal volvulus: Case report and literature review. Cirugía y Cirujanos (English Edition). janv. 2017; 85(1): 87–92. PubMed Abstract | Publisher Full Text\n\nYohannes B, Muleta MB: Cecal Volvulus: A Case Report and Review of the Literature. OAS. sept. 2021; 14: 55–58. Publisher Full Text\n\nWest JEM: Cecal Volvulus In Adolescence Presenting As Recurring Visits For Abdominal Pain. West. J. Emerg. Med. 30 mai 2010; 11: 257–263. (consulté le 26 janvier 2022). PubMed Abstract Reference Source\n\nTsushimi T, et al.: Laparoscopic cecopexy for mobile cecum syndrome manifesting as cecal volvulus: report of a case. Surg. Today. 2008; 38(4): 359–362. PubMed Abstract | Publisher Full Text\n\nKatoh T, Shigemori T, Fukaya R, et al.: Cecal volvulus: report of a case and review of Japanese literature. World J. Gastroenterol. mai 2009; 15(20): 2547–2549. PubMed Abstract | Publisher Full Text\n\nRabinovici R, Simansky DA, Kaplan O, et al.: Cecal volvulus. Dis. Colon Rectum. sept. 1990; 33(9): 765–769. Publisher Full Text\n\nDane B, Hindman N, Johnson E, et al.: Utility of CT Findings in the Diagnosis of Cecal Volvulus. Am. J. Roentgenol. oct. 2017; 209(4): 762–766. PubMed Abstract | Publisher Full Text\n\nMadiba TE, Thomson SR: The management of cecal volvulus. Dis. Colon Rectum. févr. 2002; 45(2): 264–267. Publisher Full Text\n\nBerger JA, van Leersum M , Plaisier PW: Cecal volvulus: Case report and overview of the literature. Eur. J. Radiol. sept. 2005; 55(3): 101–103. Publisher Full Text"
}
|
[
{
"id": "144137",
"date": "04 Aug 2022",
"name": "Sardar Hassan Arif",
"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 was a good case report written in a proper manner.\nSome few comments for the authors in the management of case:\nBetter to mention in the history that there was no history of previous abdominal operation.\n\nWhy was the case kept on observation for 6 hours while it is very clear case of intestinal obstruction, only resuscitation for 1-2 hours enough?\n\nDuring the operation it is better to put clamps on proximal and distal before de-rotation to prevent endotoxins being liberated into circulation.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "146154",
"date": "08 Aug 2022",
"name": "Houcine Magherbi",
"expertise": [
"Reviewer Expertise surgery"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting paper which describes a case of cecal volvulus (CV).\nCV is an uncommon cause of colonic obstruction. Diagnosis is difficult and, if delayed, the results may be intestinal ischemia, perforation, sepsis, and even death.\nFirst-line treatment for cecal volvulus is surgery, as nonoperative management is rarely achievable.\nThat Is why I want to ask the authors why they perform an evaluation period of six hours? They must insist that Caecum Volvulus requires immediate surgery because the delay in diagnosis is responsible of high rate of mortality. They should also mention if there was previous abdominal surgery, history of chronic colicky abdominal pain or intermittent bowel subocclusion.\nPlease correct those sentences: “After CV was diagnosed, a caecectomy was performed using GEA 80 charges. -> After CV was diagnosed, a caecectomy was performed using GIA 80 surgical staplers”\n“A mobile caecum is an anatomical variant, present in 25% of the general population according to some studies.\" This is overestimated because mobility of the cecum and ascending colon has been estimated to occur in 10–20 % of population.\nYou can mention that several authors have reported successful colonoscopic reduction of cecal volvulus. The manuscript is well described and all the other parts are well described with adequate diagnostic steps.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "146450",
"date": "19 Aug 2022",
"name": "DANIEL WAISBERG",
"expertise": [
"Reviewer Expertise Gastrointestinal 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\nComments to the Authors Abbassi et al performed an interesting case report of caecal volvulus. Some issues with this manuscript are detailed below.\nAbstract\nThe findings of the abdominal X-rays are described as they were from the abdominal CT scan The correct term is “GIA 80 stapler” instead of “GEA 80 charges”\n\nIntroduction\n\nIt is mentioned that the objective of this report is to address the success of caecostomy, but in the case presentation it is stated that the patient underwent caecectomy (resection). Which treatment was perfomed? Please clarify We suggest using the sentence: “We report A case of (…)\n\nCase Presentation\nWe suggest using the term: “fasted” instead of “nothing by mouth” The correct term is “GIA 80 stapler” instead of “GEA 80 charges” Please specify which treatment was performed: caecostomy or caecectomy (resection). If it was a resection, was primary anastomosis performed? “Clavulanique” is a French word If the diagnosis of CV was already made by abdominal CT scan, why was the patient kept under observation for 6 hours? Why was emergency laparotomy or laparoscopic not performed after diagnosis?\n\nDiscussion\n\nThe authors state that CV is an infrequent cause of colon obstruction, but then the mention it is responsible for 60% of colonic volvulus. Is this data correct? We suggest using the sentence: “its use is not currently advocated” instead of “it should not be used anymore? The authors stated they performed a caecostomy. Is this correct? Why not resect the caecum? Please clarify which surgery was performed and justify its choice in the discussion\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? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-781
|
https://f1000research.com/articles/11-1245/v1
|
02 Nov 22
|
{
"type": "Research Article",
"title": "Early detection of biliary atresia in primary health care: still a problem",
"authors": [
"Bagus Setyoboedi",
"Rendi Aji Prihaningtyas",
"Martono Tri Utomo",
"Sjamsul Arief",
"Rendi Aji Prihaningtyas",
"Martono Tri Utomo",
"Sjamsul Arief"
],
"abstract": "Background: Biliary atresia is the leading cause of liver transplantation in children. Early detection of biliary atresia is crucial for diagnosis and disease progression. The purpose of this study was to analyze knowledge about biliary atresia and the effectiveness of health education in increasing the knowledge of primary health care providers. Methods: A quasi-experimental study with pretest and posttest designs was carried out in Sidoarjo, East Java using a self-administered questionnaire. The intervention using health education was delivered by pediatrician and consultant of pediatric gastro hepatology. There were 13 questions on the questionnaire, question numbers 1 to 6 were about normal and abnormal neonatal jaundice, question numbers 7 to 13 were about biliary atresia. Results: A total of 252 participants were involved, the mean age of the participants was 40.7 ± 9.4 years old. Most of the participants were midwives (61.9%) and 77.8% of participants have years of service in primary health care > 5 years. A total of 40.5% participants stated that newborns may have physiological jaundice, which was characterized by icteric sclera, pale stools, and dark urine. A total of 27,4% and 24,2% participants said that all jaundice in newborn will always improve on their own and newborn with prolonged jaundice does not need further examination, respectively. There was an increase in the median value in the pretest and posttest knowledge scores after interventional health education (p < 0,05). Conclusions: The primary health care provider understands about biliary atresia, however, the initial knowledge about early detection of biliary atresia is not evenly distributed in all primary health care providers. These findings suggest that improving knowledge to early detection of biliary atresia is needed. Health education can be used effectively in increasing knowledge about biliary atresia.",
"keywords": [
"Biliary atresia",
"knowledge",
"primary health care provider",
"early detection"
],
"content": "Introduction\n\nBiliary atresia (BA) is the most common cause of pediatric end-stage liver disease and is the leading cause of liver transplantation in children. It remains a challenge for clinicians.1 BA is found worldwide, with incidence rates of 1 in 10-19,000 in Europe and North America, and higher incidence rates of 1 in every 3,000 infants in East Asia.2–4\n\nBiliary atresia is manifested with abnormal narrowing of the bile ducts, blockage of the bile ducts to the absence of bile ducts in the liver.2 Early detection of biliary atresia is crucial for diagnosis and the rate of disease progression. Currently, increasing evidence has shown that the development of BA is associated with infections, such as perinatal viral infections. The presence of infection can trigger neonatal cholestasis which begins with progressive inflammation of the intrahepatic and extrahepatic bile ducts.2 Biliary obstruction can happen within the first few weeks after birth.1 The best prognosis of BA remains dependent on early diagnosis and surgical treatment.5\n\nThere are two clinical forms of BA, perinatal and congenital. In the perinatal form of BA, the infant has no congenital abnormalities and the onset of jaundice begins during or after the second week of life. This contrasts to the congenital form, in which signs of cholestasis appear soon after birth and associated with non-hepatic congenital anomalies.5 Most cases (80%) are considered perinatal form.3\n\nClinically, in infants with biliary atresia, cholestatic jaundice develops in the first few weeks of life followed by acholic stools, dark urine, hepatomegaly, poor growth, progressing to cirrhosis, portal hypertension, and liver failure.2,5 The symptoms of BA continue to worsen two weeks after birth. It is different with physiological jaundice. Physiological jaundice will improve within two weeks and get better. Meanwhile, in cholestasis that occurs due to biliary atresia, jaundice will worsen.3 Unfortunately, identification of infants with cholestatic jaundice is quite difficult because it appears similar to the physiological jaundice that is very common in early infancy.1 Currently, the Stool Color Card has been introduced as an early detection tool for biliary atresia in infants which can diagnose earlier, shorten surgical treatment time, and improve the long-term prognosis of children with biliary atresia.5\n\nUnfortunately, early diagnosis of biliary atresia is still challenging. The delay in diagnosing BA is the main problem, especially in Indonesia. The lack of knowledge and awareness about early detection of BA among primary healthcare providers is the important cause of delayed diagnosis of BA.6 This study aims to analyses the knowledge about BA and evaluate the effectiveness of health education to increase knowledge of primary health care providers in early detection of BA in infants. Increasing primary health care awareness by conducting an educational seminar on early detection of BA was expected in this study.\n\n\nMethods\n\nA quasi-experimental study with a pretest and posttest design was performed to analyses the knowledge about BA and evaluate the effectiveness of health education to increase the knowledge of primary healthcare providers about early detection of BA in infants. An educational seminar on early detection of BA was performed. A total of 252 health care providers at seven primary healthcare centers in Sidoarjo, East Java during the period from April to August 2022 were involved in this study. The inclusion criteria in this study were healthcare providers who provided health services and were willing to participate in the study. Exclusion criteria in this study were healthcare providers who were not involved in patient health care.\n\nThe evaluation of knowledge about BA was performed using a self-administered questionnaire. The intervention using health education of BA in this study was performed by a pediatrician and a consultant of pediatric gastro hepatology who already has more than 10 years of experience in treating patients with biliary atresia in a teaching center hospital. The interventional health education was delivered by a face-to-face meeting with health care provider in primary healthcare centers. A pretest questionnaire was first delivered to evaluate the participant’s initial level of knowledge about BA ten minutes before conducting the health education seminar. The health education was then performed followed by an interactive discussion, including the basics of jaundice, BA, early detection of BA, and how to use the stool color card as a screening tool of BA. The health education was delivered within a total duration of two hours. Afterward, the posttest questionnaire was given to evaluate post educational health intervention. There were 13 questions on the questionnaire, question numbers 1 to 6 were about normal and abnormal neonatal jaundice, question numbers 7 to 13 were about BA (symptoms, early detection, management and complications of BA).\n\nThis study was carried out in accordance with the Declaration of the Helsinki World Medical Association. This study was undertaken with the understanding and written consent of respondents. Before the study, a permit was obtained from the Sidoarjo District Health Office and all primary healthcare centers agreed to participate in the study. This study was previously reviewed and independently approved by an ethical board of Faculty of Medicine, Airlangga University, Surabaya (No. 60/EC/KEPK/FKUA/2022).\n\nPre- and post-test questionnaire results were obtained to evaluate the initial knowledge of BA and effect of health education on the participants. Normality test was conducted to evaluate the normality of data distribution. If the data was not normally distributed, non-parametric test analysis was performed such as using the Wilcoxon Signed Ranks Test. The difference in pre-test and post-test scores was obtained by analysis using chi Square (Fisher's Exact Test) with a significant p < 0.05. The data analysis was done using SPSS version 21.0.\n\n\nResults\n\nIn this study, there were 252 participants involved and the majority (92.9%) were female. The mean age of the participants was 40.7 ± 9.4 years old (Min-Max: 22-71 years old). Most of the participants were midwives (61.9%) with a diploma graduate (82.5%). A total of 77.8% of participants have years of service in primary health care > 5 years as described in Table 1.\n\nQuestion (1): Newborns < 28 days old may have normal (physiological) jaundice, which is characterized by icteric sclera, pale stools, and dark urine.\n\nThere were 18.7% of participants who consistently answered correctly, although 21.8% answered incorrectly on the post test. Overall, there were 40.5% of the pre-test who answered correctly, down to only 28.6% who answered correctly. There was a difference in pre and post values for question 1, using chi Square (Fisher's Exact Test) obtained a p-value of 0.000 (Table 2).\n\n* Chi square test.\n\nQuestion (2): All jaundice that occurs in babies aged < 28 days will always improve on its own.\n\nThere were 10.7% of participants who consistently answered correctly, although 16.7% answered incorrectly on the post test. Overall, there were 27.4% pre-test who answered correctly, down to only 14.7% who answered correctly. There was a difference in pre and post values for question 2 obtained a p-value of 0.000 (Table 3).\n\n* Chi square test.\n\nQuestion (3): A yellow baby > 2 weeks old does not need further examination, it is enough to just expose to the sun.\n\nThere were 6.7% of participants who consistently answered correctly, although 17.5% answered incorrectly on the post test. Overall, the pre-test was 24.2% who answered correctly, down to only 10.7% who answered correctly. Therewas a difference in pre- and post-values for question 3 obtained a p-value of 0.000 (Table 4).\n\n* Chi square test.\n\nThere were 77.4% of participants who consistently answered correctly in question 9, although 0.8% answered incorrectly on the post test. Overall, the pre-test there were 78.2% who answered correctly, increasing to 96.8% who answered correctly. There is a difference in pre and post values for question 9, using chi Square (Fisher's Exact Test) obtained a p-value of 0.000 (Table 5). There were 67.1% of participants who consistently answered correctly in question 11, although 1.6% answered incorrectly on the post test. Overall, the pre-test there were 69.0% who answered correctly, increasing to 94.0% who answered correctly. There was a difference in pre and post scores for question 11, using chi Square (Fisher's Exact Test) the p-value is 0.004 (Table 5).\n\nThere is no difference in pre and post scores for questions 10,12,13, using chi Square (Fisher's Exact Test) p-values are 0.0116, 1.000, and 1.000 (Table 5). There was a significant difference between the posttest and pretest scores (p value 0.000). The post test score (median 17) was higher than the pretest score (median 15) (Table 6).\n\n* Wilcoxon sign ranks test.\n\nThere was no significant difference between the participants' pre and post test scores based on gender, education, age, and years of service (Table 7). This is indicated by p value > 0.05.\n\n1 Mann-Whitney test.\n\n2 Kruskal-Wallis test.\n\n\nDiscussion\n\nBiliary atresia is present with findings: (1) the occurrence of total extrahepatic bile duct obstruction (2) the presence of proliferation of the intrahepatic bile ducts, and (3) the discovery of intrahepatic fibrosis that occurs at an early age.7 BA is found worldwide, and incidence rate is 1 in 10-19,000 infant in Europe and North America, up to 6.5 to 7.5 in 100 000 infant in the US mainland until high incidence rate to 1 in 3,000 infants in East Asia.1–4 But no official data on the incidence of BA has been published in Indonesia.8\n\nAlthough BA is a rare disease, BA is the leading cause of liver transplantation in children and the most common cause of death from liver disease in infants.9 The prognosis of BA in infants is influenced by several factors, including age at the time of surgical intervention and the anatomy of the bile duct remnant. Nearly half of all infant with BA survive into adolescence if Kasai surgery is carried out early.10\n\nUnfortunately, the challenge remains in recognizing that infants with jaundice may have BA, not a common physiologic jaundice. Delayed diagnosis is still a problem worldwide.11 Delayed diagnosis and Kasai procedure performed after three months of age have a significantly poor prognosis for survival of the original liver.12 Kasai surgery can improve long-term liver survival and reduce the need for a liver transplant if performed before 60 days of age.13,14 Liver cirrhosis is major morbidity resulting from untreated BA, requires very costly liver transplantation that Indonesia has limited facilities. Not all centers in Indonesia can perform liver transplants. Therefore, the most likely thing to do is to carry out the Kasai procedure as early as possible.15\n\nAn early diagnosis of biliary atresia is difficult. Delay in diagnosing BA is also a major source of problems in therapy, especially in Indonesia. Global efforts are urgently needed to increase the rate of BA diagnosis as early as possible.15 The lack of knowledge and awareness about early detection of BA among primary healthcare providers is the important cause of delayed diagnosis of BA.6\n\nIn this study, there were 40.5% of the primary health care provider stated that newborns < 28 days old may have normal (physiological) jaundice, which is characterized by icteric sclera, pale stools, and dark urine. Infants suffering from BA generally appear as healthy as any other infant when they are neonates.1,2 Clinically, in the early condition of BA, infants with BA are indistinguishable from infants with non-conjugated hyperbilirubinemia, such as physiologic jaundice and breast milk-associated jaundice. Then, making the diagnosis of infant jaundice other than physiologic or breast milk-related jaundice is still a challenge today.1 However, in BA jaundice will extend beyond two weeks of age and infants will experience other complaints, such as pale stools, dark urine, poor growth, increased abdominal circumference due to ascites and splenomegaly, and other complications due to liver damage.2,9\n\nOverall, there were 27.4% health care provider showed that all jaundice that occurs in newborn will always improve on their own in this study. A total of 24.2% primary health care provider stated that newborn with prolonged jaundice does not need further examination, it is enough to just expose to the sun. The evaluation of bilirubin serum should be done in infant with prolonged jaundice. Then the presence of BA should be considered for any jaundiced infant with acholic stools and accompanied by an increase in the serum conjugated bilirubin concentration.1\n\nThere was no difference in pre- and post- test scores for questions about complication of biliary atresia in this study and the need for liver transplantation. The primary health care provider understands about biliary atresia and its complications, however, in this study it was found that only 69.0% of participants understood that jaundice due to biliary atresia must be detected as early as possible and surgery performed before the age of two months.\n\nEarly diagnosis and treatment are necessary in infants with BA.1 There was a significant difference between the pretest and posttest scores (p value 0.000). The post test score (median 17) was higher than the pretest score (median 15) after interventional health education. Improving knowledge to early detection of biliary atresia using screening with stool color cards is a promising and economically feasible strategy.11,16 It is necessary to increase the awareness of primary healthcare providers to early detection of BA for improving the outcomes of the Kasai procedure and reduce the need for liver transplantation.10 Therefore, it is very important to socialize how to early detection BA in Indonesia, especially in the regions to reduce the delay rate in the referral of infants with BA using interventional health education.\n\nSerum conjugated bilirubin concentrations and stool color cards are the two BA screening methods currently in use.1 A study in the United Kingdom stated that baby with conjugated bilirubin more than 20% of total bilirubin was followed up in a community setting, from this study several liver diseases such as neonatal hepatitis, extra-hepatic biliary atresia, Alagille syndrome, hypopituitarism, and alpha-1-antitrypsin deficiency were detected.17 Another study showed that at 24 to 48 hours of life, subjects with BA had mean conjugated bilirubin levels significantly higher than those of controls, and it can happen shortly after birth.18 Thus, serum conjugated bilirubin levels can be a valuable screening test for BA.1\n\nScreening with stool color cards is currently an important strategy because it requires lower costs and better results.16 Stool Color Cards have been used in China, Taiwan, and Japan to shorten the age at diagnosis and shorten the time between diagnosis and the Kasai procedure.19,20 A 19-year cohort study in Japan showed that the sensitivity and specificity of stool color card screening at one-month evaluation were 76.5% and 99.9%, respectively.21 In Taiwan, the stool color card screening had a sensitivity and specificity of 89.7% and 99.9%, respectively.22 However, in this study, it was found that 78.2% of health workers in primary health facilities understood the stool color card used as a screening tool for biliary atresia in infants. The optimization of biliary atresia screening is still needed using the health intervention to primary health care provider to reduce the need for liver transplantations.13\n\nThis study was the first research conducted and provides new information that one of the failures of early detection of biliary atresia is the uneven level of knowledge about jaundice and biliary atresia in primary health facilities which is the main milestone in public health services. The results of this study can be used as the basis for policies to carry out more massive socialization to health workers in primary health facilities about biliary atresia. The weakness of this study is the limited number of subjects. Further research with a larger number of subjects and a wider area is needed to determine the level of knowledge of early detection of biliary atresia in Indonesia.\n\n\nConclusion\n\nThe natural history of biliary atresia has been described. Early diagnosis provides a better prognosis for infants with biliary atresia. These findings suggest that improving knowledge to early detection of biliary atresia is needed to primary healthcare providers, including information about prolonged jaundice and screening with the stool color card for improving outcomes in BA in Indonesia. Health education interventions has significantly increased the knowledge of primary healthcare providers about early detection of BA. Further studies with larger subjects and area are needed to evaluate the effectiveness and feasibility of potential education for early identification of infants with biliary atresia in Indonesia.",
"appendix": "Data availability\n\nFigshare: Knowledge of Biliary Atresia, https://doi.org/10.6084/m9.figshare.20579820.v2. 23\n\nThis project contains the following underlying data:\n\n- knowledge of biliary atresia F1000.xlsx\n\nFigshare: Knowledge of Biliary Atresia, https://doi.org/10.6084/m9.figshare.20579820.v2. 23\n\nThis project contains the following extended data:\n\n- kuesioner pengetahuan atresia bilier_Indonesia.pdf (questionnaire in Indonesian)\n\n- kuesioner pengetahuan atresia bilier_English.pdf (questionnaire in English)\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 would like to give thanks to all staff of Sidoarjo District Health Office and Primary Health Care Centers involved.\n\n\nReferences\n\nWang KS, Moss RL, Caty MG, et al.: Newborn Screening for Biliary Atresia. Pediatrics. 2015 Dec 1; 136(6): e1663–e1669. PubMed Abstract | Publisher Full Text\n\nAverbukh LD, Wu GY: Evidence for Viral Induction of Biliary Atresia: A Review. J. Clin. Transl. Hepatol. 2018 Dec 28; 6(4): 1–10. Publisher Full Text\n\nKobayashi H, Stringer MD: Biliary atresia. Semin. Neonatol. 2003 Oct; 8(5): 383–391. Publisher Full Text\n\nVerkade HJ, Bezerra JA, Davenport M, et al.: Biliary atresia and other cholestatic childhood diseases: Advances and future challenges. J. Hepatol. 2016 Sep; 65(3): 631–642. PubMed Abstract | Publisher Full Text\n\nSantos JL, Carvalho E, Bezerra JA: Advances in biliary atresia: from patient care to research. Braz. J. Med. Biol. Res. 2010 Jun; 43(6): 522–527. PubMed Abstract | Publisher Full Text\n\nCampion A, Guimber D, Michaud L, et al.: Analyse du retard au diagnostic de l’atrésie des voies biliaires. Arch. Pediatr. 2001 May; 8(5): 493–498. PubMed Abstract | Publisher Full Text\n\nSokol RJ, Mack C, Narkewicz MR, et al.: Pathogenesis and outcome of biliary atresia: current concepts. J. Pediatr. Gastroenterol. Nutr. 2003 Jul; 37(1): 4–21. PubMed Abstract | Publisher Full Text\n\nKurnia N, Rinaldhy K, Aji AS, et al.: Analysis of knowledge regarding Biliary Atresia among healthcare providers and laypersons in East Jakarta after educational intervention. ASEAN J. Community Engagement. 2020 Jul 31 [cited 2022 Aug 19]; 4(1). Publisher Full Text Reference Source\n\nSanchez-Valle A, Kassira N, Varela VC, et al.: Biliary Atresia. Adv. Pediatr. 2017 Aug; 64(1): 285–305. Publisher Full Text\n\nRamachandran P, Safwan M, Reddy MS, et al.: Recent trends in the diagnosis and management of biliary atresia in developing countries. Indian Pediatr. 2015 Oct; 52(10): 871–879. PubMed Abstract | Publisher Full Text\n\nSchreiber RA, Masucci L, Kaczorowski J, et al.: Home-based screening for biliary atresia using infant stool colour cards: a large-scale prospective cohort study and cost-effectiveness analysis. J. Med. Screen. 2014 Sep; 21(3): 126–132. PubMed Abstract | Publisher Full Text\n\nMorinville V, Ahmed N, Ibberson C, et al.: Home-Based Screening for Biliary Atresia Using Infant Stool Color Cards in Canada: Quebec Feasibility Study. J. Pediatr. Gastroenterol. Nutr. 2016 Apr; 62(4): 536–541. PubMed Abstract | Publisher Full Text\n\nSerinet MO, Wildhaber BE, Broué P, et al.: Impact of Age at Kasai Operation on Its Results in Late Childhood and Adolescence: A Rational Basis for Biliary Atresia Screening. Pediatrics. 2009 May 1; 123(5): 1280–1286. PubMed Abstract | Publisher Full Text\n\nNio M, Sasaki H, Wada M, et al.: Impact of age at Kasai operation on short- and long–term outcomes of type III biliary atresia at a single institution. J. Pediatr. Surg. 2010 Dec; 45(12): 2361–2363. PubMed Abstract | Publisher Full Text\n\nNio M, Wada M, Sasaki H, et al.: Effects of age at Kasai portoenterostomy on the surgical outcome: a review of the literature. Surg. Today. 2015 Jul; 45(7): 813–818. PubMed Abstract | Publisher Full Text\n\nMogul D, Zhou M, Intihar P, et al.: Cost-Effective Analysis of Screening for Biliary Atresia With the Stool Color Card. J. Pediatr. Gastroenterol. Nutr. 2015 Jan; 60(1): 91–98. PubMed Abstract | Publisher Full Text\n\nPowell JE, Keffler S, Kelly DA, et al.: Population screening for neonatal liver disease: potential for a community-based programme. J. Med. Screen. 2003; 10(3): 112–116. PubMed Abstract | Publisher Full Text\n\nHarpavat S, Finegold MJ, Karpen SJ: Patients with biliary atresia have elevated direct/conjugated bilirubin levels shortly after birth. Pediatrics. 2011 Dec; 128(6): e1428–e1433. PubMed Abstract | Publisher Full Text\n\nGoodhue C, Fenlon M, Wang KS: Newborn screening for biliary atresia in the United States. Pediatr. Surg. Int. 2017 Dec; 33(12): 1315–1318. PubMed Abstract | Publisher Full Text\n\nKong YY, Zhao JQ, Wang J, et al.: Modified stool color card with digital images was efficient and feasible for early detection of biliary atresia—a pilot study in Beijing. China. World J. Pediatr. 2016 Nov; 12(4): 415–420. PubMed Abstract | Publisher Full Text\n\nGu YH, Yokoyama K, Mizuta K, et al.: Stool color card screening for early detection of biliary atresia and long-term native liver survival: a 19-year cohort study in Japan. J. Pediatr. 2015 Apr; 166(4): 897–902.e1. PubMed Abstract | Publisher Full Text\n\nChen SM, Chang MH, Du JC, et al.: Screening for biliary atresia by infant stool color card in Taiwan. Pediatrics. 2006 Apr; 117(4): 1147–1154. PubMed Abstract | Publisher Full Text\n\nSetyoboedi B:Knowledge of Biliary Atresia. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "157245",
"date": "05 Apr 2024",
"name": "Tina M. Slusher",
"expertise": [
"Reviewer Expertise Neonatal hyperbilirubinemia and pediatric/neonatal global 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\nI like this study. The results are important and could lead to earlier diagnosis of BA using a combination of education and screening using the card. But it is hard to read and needs to be rewritten with someone whose first language it English. Addition, clarity about what the tables and data actually say is critical. With these edits this paper could be a good addition to tool. Kits in LMICS and educate about the importance of early detection of BA and how to actually diagnosis BA. I hope the authors will revise it.\nIntroduction paragraph 3: The symptoms of BA continue to worsen two weeks after birth. I think you mean generally begin to worsen about 2 weeks after birth.\nCurrently, the Stool Color Card has been introduced as an early detection tool for biliary atresia in infants which can diagnose earlier, shorten surgical treatment time, and improve the long-term prognosis of children with biliary atresia. This whole paragraph could be shortened but this sentence is awkwardly worded—think you mean SCD……in infants. This can lead to earlier diagnosis, shorten……..\nI do not understand what you are saying in your interpretation of your results in each of the questions in the tables. Are you comparing pre and post test results? Are you telling us the number who correctly answered each question.\n\nBiliary atresia is present with findings: (1) the occurrence of total extrahepatic bile duct obstruction (2) the presence of proliferation of the intrahepatic bile ducts, and (3) the discovery of intrahepatic fibrosis that occurs at an early age.\nThis sentence belongs in the introduction\nLiver cirrhosis is major morbidity resulting from untreated BA, requires very costly liver transplantation that Indonesia has limited facilities. Not all centers in Indonesia can perform liver transplants. Therefore, the most likely thing to do is to carry out the Kasai procedure as early as possible.\nPlease reword.\nClinically, in the early condition of BA, infants with BA are indistinguishable from infants with non-conjugated hyperbilirubinemia, such as physiologic jaundice and breast milk-associated jaundice. Then, making the diagnosis of infant jaundice other than physiologic or breast milk-related jaundice is still a challenge today.\nPlease reword.\nTherefore, it is very important to socialize how to early detection BA in Indonesia, especially in the regions to reduce the delay rate in the referral of infants with BA using interventional health education. Think you mean is it important to educate about how to detect BA early in Indonesia…… A study in the United Kingdom stated that baby with conjugated bilirubin more than 20% of total bilirubin was followed up in a community setting, from this study several liver diseases such as neonatal hepatitis, extra-hepatic biliary atresia, Alagille syndrome, hypopituitarism, and alpha-1-antitrypsin deficiency were detected. Would be better worded if you said “ In a study in the United Kingdom they follow baby’s with a conjugated total bilirubin of more than 20% and found several liver diseases…… because it requires lower costs and better results Less costly than what??? Better working because it costs less and …….\n\nHowever, in this study, it was found that 78.2% of health workers in primary health facilities understood the stool color card used as a screening tool for biliary atresia in infants. The optimization of biliary atresia screening is still needed using the health intervention to primary health care provider to reduce the need for liver transplantations. Please reword.\nHealth education interventions has significantly increased the knowledge of primary healthcare providers about early detection of BA.\nBetter wording might be Health education interventions have significantly increased….\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1245
|
https://f1000research.com/articles/10-1057/v1
|
18 Oct 21
|
{
"type": "Research Article",
"title": "Pancreatic cancer grading in pathological images using deep learning convolutional neural networks",
"authors": [
"Muhammad Nurmahir Mohamad Sehmi",
"Mohammad Faizal Ahmad Fauzi",
"Wan Siti Halimatul Munirah Wan Ahmad",
"Elaine Wan Ling Chan",
"Muhammad Nurmahir Mohamad Sehmi",
"Wan Siti Halimatul Munirah Wan Ahmad",
"Elaine Wan Ling Chan"
],
"abstract": "Background: Pancreatic cancer is one of the deadliest forms of cancer. The cancer grades define how aggressively the cancer will spread and give indication for doctors to make proper prognosis and treatment. The current method of pancreatic cancer grading, by means of manual examination of the cancerous tissue following a biopsy, is time consuming and often results in misdiagnosis and thus incorrect treatment. This paper presents an automated grading system for pancreatic cancer from pathology images developed by comparing deep learning models on two different pathological stains. Methods: A transfer-learning technique was adopted by testing the method on 14 different ImageNet pre-trained models. The models were fine-tuned to be trained with our dataset. Results: From the experiment, DenseNet models appeared to be the best at classifying the validation set with up to 95.61% accuracy in grading pancreatic cancer despite the small sample set. Conclusions: To the best of our knowledge, this is the first work in grading pancreatic cancer based on pathology images. Previous works have either focused only on detection (benign or malignant), or on radiology images (computerized tomography [CT], magnetic resonance imaging [MRI] etc.). The proposed system can be very useful to pathologists in facilitating an automated or semi-automated cancer grading system, which can address the problems found in manual grading.",
"keywords": [
"digital pathology",
"pancreatic cancer",
"cancer grading",
"deep learning",
"image classification"
],
"content": "Introduction\n\nPancreatic cancer is one of the most lethal malignant neoplasms in the world,1 developed when cells multiply and grow out of control in the pancreas,2 forming cancer cells caused by cells mutation in their genes.3 Doctors commonly perform a biopsy to diagnose cancer when physical examination or imaging tests like magnetic resonance imaging (MRI) and computerized tomography (CT) scans are insufficient. In pancreatic cancer, grading is essential for planning treatment but is currently done using a meticulous microscopic examination.4 Up to now, there has been no successful implementation of artificial intelligence (AI) for classifying pancreatic cancer grade. The absence of such AI work motivates this paper to use transfer-learning to grade pathological pancreatic cancer images using 14 deep learning (DL) models. This work can facilitate an automated cancer grading system to address the exhaustive work of manual grading.\n\nPancreatic cancer is considered to be under-studied, and improvements in the diagnosis and prognosis of pancreatic cancer have therefore been minor.5 Digital pathology is an image-based environment obtained by scanning tissue samples from glass slides. Staining, usually using May-Grünwald-Giemsa (MGG) and haematoxylin and eosin (H&E) stains, is carried out on the tissue samples before digitization into whole-slide images. The cancer grade is identified by the degree of differentiation of the tumour cells6 ranging from well to poorly differentiated as described in Table 1.\n\nMGG = May-Grünwald-Giemsa; H&E = haematoxylin and eosin.\n\nConvolutional neural network (CNN) is a widely used deep learning (DL) algorithm in medical image-based classification and prediction.7 Several methods use CNN in cancer detection and diagnosis8 such as the Gleason grading of prostate cancer,9–11 colon cancer grading,12 breast cancer detection,13,14 and pancreatic cancer detection15–18 and classification.19 However, grading of pancreatic cancer with DL still needs comprehensive study.\n\n\nMethodology\n\nThe methodology of this work was done at Multimedia University, Cyberjaya, from June 2020 to May 2021. The overall methodology of this research is as illustrated in Figure 1, with two major stages. In the data preparation stage, pathology images of pancreas tissue samples were obtained from our collaborator and the images were pre-classified by a pathologist into four classes. In the DL model development stage, the images were trained on the DL model and evaluated accordingly. All stages were carried out using Jupyter notebook in Google Colab. The source code is available from GitHub and archived with Zenodo.24\n\nThis work was approved by the Research Ethics Committee of Multimedia University with approval number EA2102021. This article does not contain any studies with human participants or animals performed by any of the authors. Only pathology images were used, and the patients’ personal data were anonymized.\n\nPathology image procurement\n\nA total of 138 high-resolution images with varying dimensions (1600 × 1200, 1807 × 835 and 1807 × 896) were obtained and pre-classified by the collaborators (see Acknowledgements). Four classes were identified (as shown in Table 2): Normal, Grade-I, Grade-II and Grade-III. Each image consisted of a tissue-sample stained with MGG and H&E. The image distribution in each class was unequal with Grade-II having 58 images and Normal with only 20 images. To better capture the cells characteristics which is paramount in determining their grade and to match the lower-resolution setting of the network’s input, the images were pre-processed into small non-overlapping patches.\n\nMGG = May-Grünwald-Giemsa; H&E = haematoxylin and eosin.\n\nImage pre-processing\n\nThe pre-trained models require a low dimension and square image for training and making predictions. The squared slicing method is used where smaller patches with approximately 200 × 200 pixels of non-overlapping regions are sampled from the original images. Further processing was done to remove unwanted patches, as shown in Figure 2.\n\nImage dataset\n\nA total of 6468 patches were generated from the slicing process of the 138 original images which is an increase of 468% in number of images. Overall, 50.5% (3267) of the patches with background and non-tissue information were discarded, and the remaining are listed in Table 3. Examples of MGG stain and H&E stain pathology images are shown in Table 1, with the mixed dataset combining all images from MGG and H&E stains. From the numbers in Table 3, these datasets still had an imbalanced number of patch images in each class but this can be mitigated by employing a weighted average to evaluate the model.\n\nMGG = May-Grünwald-Giemsa; H&E = haematoxylin and eosin.\n\nTraining-validation splitting and K-fold cross-validation\n\nTo evaluate the DL model, images in each dataset were split into training and validation set with 80-20 ratio. K-fold cross-validation with K = 5 was used by splitting all MGG, H&E and the mixed dataset into five parts, producing cross-validation sets with five new copies of MGG, H&E and mixed datasets and labelled (e.g. MGG Set 1 to MGG Set 5 for MGG). Each set had a different set of images used for training (80%) and validation (20%). The average value was calculated from the five-training iterations to evaluate the performance.\n\nImage data augmentation and normalisation\n\nImage data augmentation was implemented to virtually expand the training set, but not on the validation set. The transformation parameter involved was horizontal flip, vertical flip and -90° to 90° rotation range. Image data normalisation was used to rescale image pixels from a range of [0,255] to [0,1] so the input pixels will have similar data distribution.\n\nDeep CNN algorithm was used for developing a model for classifying pancreatic cancer grading from pathology images.\n\nTransfer-learning\n\nA total of 14 CNN pre-trained models from recognizing 1000 classes in ImageNet was selected from Keras API20 to get the best model for classifying the 4-grade classes of pancreatic cancer. The proposed pre-trained models are listed in Table 4 along with their original model’s image input shape, and its respective top-1 accuracy on the ImageNet validation set.\n\nFine-tuning\n\nAll 14 models were fine-tuned with four newly added layers to extract the features from pathology images: a flatten-layer to form a 1D fully connected layer; a dense-layer with 256 nodes and ReLu activation-function; a dropout-layer with a rate of 0.4 to regularise the network; and lastly another dense-layer with 4-nodes and SoftMax activation-function to normalize the probability of prediction.\n\nSetup and evaluation parameters\n\nBatch size of 64 was chosen to allow the computer to train and validate 64-patch-samples at the same time. Adam optimizer with default initial learning rate of α = 0.01 and moment decay rate of β1 = 0.9 and β2 = 0.999 was used. The loss function is calculated using categorical cross-entropy for the 4-class classification task. With this setup, the models are compiled and trained for 100-epochs.\n\nThe confusion matrix, precision, recall, f1-score and weighted-average were used to evaluate the model's performance. Weighted-average was used to calculate the performance of individual cross-validation set and suitable for imbalanced dataset. The equation for the weighted-average is:\n\n\nResults and discussion\n\nThis experiment was done with the first cross-validation set of the mixed dataset, to observe how data augmentation impacts a model training performance.23 Table 5 and Table 6 display the final accuracy and loss of training and validation set after 100 epochs. Without data augmentation in Table 5, it is evident that overfitting has occurred, because the model is doing very well on the training set but not on the validation set. With data augmentation, the validation accuracy improved, specifically on VGG19 model (54.83% to 77.22%). The training accuracy of other models are slightly reduced with data augmentation (except for VGG19) but it is normal as the model is learning newly transformed images. The validation loss also shows a reduction, as in Table 6, such as on NASNetLarge model from 3.36376 to 0.68587. Overall, these results show that data augmentation may reduce overfitting and improve model performance as reported in.10,13,14\n\nThe overall performance results of all 14 different transfer-learning models proposed for this experiment are presented. Each model was trained with the 3 datasets and 5-fold cross-validation. Figure 3 illustrates the overall performance in terms of mean f1-score.\n\nComparison between MGG, H&E and the mixed dataset\n\nThis comparison shows how a DL model learns from single coloured stain. In Figure 3, all models trained with the H&E obtained the highest f1-score compared to MGG and mixed. Most models scored above 0.9 except for VGG19 (0.87). When trained with the MGG, models other than VGG16 and VGG19 performed the lowest compared to H&E and Mixed. The performance of mixed is as expected because it contains a mixture of both datasets. The VGG16 and VGG19 model, however, performed better on MGG than Mixed, due to the small VGG network architecture and small fully-connected layers making it unable to learn complex features and patterns in pathology image. The trend described in Figure 3 indicates that image patches in the H&E are easier to learn with better prediction than MGG.\n\nComparison between pre-trained models\n\nFrom the result, DenseNet network architecture was the best at classifying pathology images where all three variations trained on MGG, H&E and mixed take the top spot among the 14 models. The ResNet on mixed dataset were ranked ascendingly from ResNet101V2, ResNet50V2 and ResNet152V2 before the three DenseNet models. This supports the work of Huang et al. in21 where DenseNet was designed to improve the ResNet architecture. DenseNet201 which is a much deeper layer than the other two DenseNet models managed to achieve the highest f1-score of 0.88, 0.96 and 0.89 for MGG, H&E and mixed, respectively. The DenseNet121 and DenseNet169 performance on the three dataset scores were marginally lower at 0.87, 0.95, 0.89 and 0.87, 0.95, 0.88, respectively. This shows that a deeper DenseNet layer can perform more accurate prediction.\n\nThe Xception21 and InceptionResNetV222 are improvements of InceptionV3, which performs better than their ancestor. The f1-scores for Xception trained by MGG, H&E and Mixed are 0.85, 0.94 and 0.86, as compared to InceptionV3, 0.80, 0.92 and 0.83, respectively. However, InceptionResNetV2 are just slightly higher than InceptionV3 (0.93 and 0.83 for H&E and mixed) but lower for MGG (0.80). VGG models did not perform quite well when compared to its earlier models. VGG19, which is supposed to be an improvement to VGG16, failed to achieve a greater f1-score, with 0.74, 0.87 and 0.65 for the MGG, H&E and mixed, respectively, while VGG16 was higher at 0.80, 0.93 and 0.78. The results concluded that VGG19 was the worst performing model for our datasets.\n\nThis experiment applied transfer-learning on 14 ImageNet pre-trained models to classify pancreatic cancer grades. From the comparisons, DenseNet201 model is suggested for practical application of pancreatic grading system of MGG or H&E stains.\n\nComparison between the best and the worst performing model\n\nTable 7 and Table 8 shows the precision and recall of VGG19 (the worst) and DenseNet201 (the best) for the three datasets. VGG19 struggles to make prediction for Grade-I patches in MGG where the precision and recall are 0.00 for CV sets 3, 4, and 5. A similar pattern is noticed in Grade-III patches, and from our observation, this is because most of the Grade-I and Grade-III patches were wrongly predicted as Grade-II. This is due to the imbalance classes in MGG where Grade-II patches account for 52.9% of the total images whereas Grade-I consist of only 5% and Grade-III 19.7%. This class imbalance has caused the VGG19 model to struggle a lot at recalling class with fewer data.\n\nFor H&E images, the effect of class imbalance however did not affect the performance of VGG19. The recall and precision for Normal class are ranked among the highest despite its smallest number (10%) of patches. Looking back at Table 1, the H&E Normal images have a quite different stain colour compared to other classes, which explains the good prediction for both models. This could be seen as a problem where limited image variation can cause biasness. The precision of Normal class would score poorly if it were tested to predict different variation of H&E stain image even with the same set of ground truth, but can be assuaged if the class have many different variations of stain colour.\n\nFor the mixed dataset, VGG19 also struggled to predict Grade-III class, especially on CV 4 and 5 where it scored 0.00 for both metrics. The reason could be that the Grade-III patches are difficult for the VGG19 model to learn. This is the reason why cross-validation should be performed to rigorously evaluate a DL model. DenseNet201 managed to get good recall for Grade-III patches for both CV sets, confirming its ability to learn complex features on the pathology image.\n\n\nConclusion\n\nThis paper presents development of several deep learning models through transfer-learning for classifying pancreatic cancer grade from pathology images. The datasets were trained on a total of 14 ImageNet pre-trained models. Image data augmentation was performed to counter the low number of images and has proven to improve the validation accuracies of all pre-trained models up to 40%. The evaluation on 14 pre-trained models shows that the DenseNet models performed best compared to the other models. Most of the models trained by H&E managed to achieve f1-score above 0.9. The MGG dataset scores lower f1-score compared to the mixed dataset. The highest f1-scores were achieved by DenseNet201, with 0.8786, 0.9561 and 0.8915 for MGG, H&E and Mixed, respectively. To the best of our knowledge, no similar work on pancreatic cancer grading has been reported in the literature. With these promising early results, this work can aid pathologists in facilitating an automated pancreatic cancer grading system for better cancer diagnosis and prognosis. This study has not been tested with whole slide images (WSI), but similar approaches can be applied. Further improvements to the system can potentially be achieved by using future state-of-the-art DL models.\n\n\nData availability\n\nOpen Science Framework: Dataset for Pancreatic Cancer Grading in Pathological Images using Deep Learning Convolutional Neural Networks. https://doi.org/10.17605/OSF.IO/WC4U9.23\n\nThis project contains the following underlying data:\n\n- Dataset PCGIPI-Original.zip (pancreatic pathological image patches used for our analysis. The stain types are May-Grünwald-Giemsa (MGG) and Haematoxylin and Eosin (H&E)).\n\n- Dataset PCGIPI-sliced.zip\n\n- PCGIPI Results.xlsx\n\n- Slicing Process for Table 3.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nAnalysis code available from: https://github.com/mnmahir/FYProject-PCGIPI\n\nArchived analysis code as at time of publication: https://doi.org/10.5281/zenodo.5532663.24\n\nLicense: MIT",
"appendix": "Acknowledgements\n\nWe would like to thank our collaborators Clinipath (Malaysia) Sdn. Bhd. for providing the image dataset and their ground truth for evaluation.\n\n\nReferences\n\nRawla P, Sunkara T, Gaduputi V: Epidemiology of Pancreatic Cancer: Global Trends, Etiology and Risk Factors. World J. Onco. 2019; 10(1): 10–27. Publisher Full Text | Free Full Text PubMed Abstract |\n\nA. C. Society: What Is a Pancreatic Neuroendocrine Tumor?. 2020, 17th September.Reference Source\n\nA. C. Society: Changes in genes. 2014, 17th September.Reference Source\n\nHaeberle L, Esposito I: Pathology of pancreatic cancer. Translational gastroenterology and hepatology. 2019; 4: 50–50. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcGuigan A, Kelly P, Turkington RC, et al.: Pancreatic cancer: A review of clinical diagnosis, epidemiology, treatment and outcomes. World J. Gastroenterol. Nov 21 2018; 24(43): 4846–4861. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWasif N, et al.: Impact of tumor grade on prognosis in pancreatic cancer: should we include grade in AJCC staging?. Ann. Surg. Oncol. Sep 2010; 17(9): 2312–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLatif J, Xiao C, Imran A, et al.: Medical Imaging using Machine Learning and Deep Learning Algorithms: A Review. 2019 2nd International Conference on Computing, Mathematics and Engineering Technologies (iCoMET). 2019. pp. 1–5.\n\nAcs B, Rantalainen M, Hartman J: Artificial intelligence as the next step towards precision pathology. J. Intern. Med. Jul 2020; 288(1): 62–81. PubMed Abstract | Publisher Full Text\n\nArvaniti E, et al.: Automated Gleason grading of prostate cancer tissue microarrays via deep learning. Sci. Rep. Aug 13 2018; 8(1): 12054. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKarimi D, Nir G, Fazli L, et al.: Deep Learning-Based Gleason Grading of Prostate Cancer From Histopathology Images-Role of Multiscale Decision Aggregation and Data Augmentation. IEEE J. Biomed. Health Inform. May 2020; 24(5): 1413–1426. Publisher Full Text\n\nLi Y, et al.: Automated Gleason Grading and Gleason Pattern Region Segmentation Based on Deep Learning for Pathological Images of Prostate Cancer. IEEE Access. 2020; 8: 117714–117725. Publisher Full Text\n\nVuong TLT, Lee D, Kwak JT, et al.: Multi-task Deep Learning for Colon Cancer Grading. 2020 International Conference on Electronics, Information, and Communication (ICEIC). 2020; pp. 1–2.\n\nAlom MZ, Yakopcic C, Nasrin MS, et al.: Breast Cancer Classification from Histopathological Images with Inception Recurrent Residual Convolutional Neural Network. J. Digit. Imaging. 2019/08/01 2019; 32(4): 605–617. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShahidi F, Daud SM, Abas H, et al.: Breast Cancer Classification Using Deep Learning Approaches and Histopathology Image: A Comparison Study. IEEE Access. 2020; 8: 187531–187552. Publisher Full Text\n\nChu LC, Fishman EK: Deep learning for pancreatic cancer detection: current challenges and future strategies. The Lancet Digital Health. 2020; 2(6): e271–e272. PubMed Abstract | Publisher Full Text\n\nChu LC, Park S, Kawamoto S, et al.: Pancreatic Cancer Imaging: A New Look at an Old Problem. Curr. Probl. Diagn. Radiol. 2021/07/01/2021; 50(4): 540–550. PubMed Abstract | Publisher Full Text\n\nLiu KL, et al.: Deep learning to distinguish pancreatic cancer tissue from non-cancerous pancreatic tissue: a retrospective study with cross-racial external validation. Lancet Digit Health. Jun 2020; 2(6): e303–e313. PubMed Abstract | Publisher Full Text\n\nSekaran K, Chandana P, Krishna NM, et al.: Deep learning convolutional neural network (CNN) With Gaussian mixture model for predicting pancreatic cancer. Multimed. Tools Appl. 2020/04/01 2020; 79(15): 10233–10247. Publisher Full Text\n\nNaito Y, et al.: A deep learning model to detect pancreatic ductal adenocarcinoma on endoscopic ultrasound-guided fine-needle biopsy. Sci. Rep. 2021/04/19 2021; 11(1): 8454. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKeras: Keras Applications. 15th December.Reference Source\n\nChollet F: Xception: Deep learning with depthwise separable convolutions. Proceedings of the IEEE conference on computer vision and pattern recognition. 2017; pp. 1251–1258.\n\nSzegedy C, Ioffe S, Vanhoucke V, et al.: Inception-v4, inception-resnet and the impact of residual connections on learning. Thirty-first AAAI conference on artificial intelligence. 2017.\n\nAhmad WSHMW, Sehmi MNM, Fauzi MFA, et al.: Dataset for Pancreatic Cancer Grading in Pathological Images using Deep Learning Convolutional Neural Networks.2021, October 5. Publisher Full Text\n\nSehmi M: mnmahir/FYProject-PCGIPI: First release (v1.0.0). Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "142618",
"date": "18 Jul 2022",
"name": "Francisco Maria Calisto",
"expertise": [
"Reviewer Expertise Human-Computer Interaction",
"Health Informatics",
"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\nIn this manuscript, the authors are presenting the development of several DL (deep learning) models through transfer-learning for classifying pancreatic cancer grade from pathology images. Specifically, the authors performed data augmentation across a dataset of images to counter the low number of images and improve the validation accuracies of all pre-trained models. Overall, this is an exciting line of work, but the current draft of this manuscript has some minor concerns that must be addressed first before publication. Contributions, if so, must be described clearly. Additionally, the findings are also important attributes of such significant research work. As follows, further comments are detailing improvements for the next iterations of the manuscript.\nStrengths\n1.1. The manuscript addresses key concerns about transfer-learning for classifying pancreatic cancer; 1.2. The manuscript brings forward novel perspectives for DL developments in a specific medical domain;\nWeaknesses\n2.1. Contributions and impact for this scientific community are not clear; 2.2. Findings and implications of the work are merely discussed;\nRequested Changes\nThere is much to appreciate in this manuscript, as it investigates several DL models for classifying pancreatic cancer. However, the provided findings and work implications are not enough, and the discussion section would need to be considerably strengthened by a more robust engagement with the cited literature. I would encourage the authors to think about how their findings extend or add to both DL and medical literatures in this space in order to refine their contribution to both fields. For instance, it would be interesting to understand the application of these DL models to a real scenario [1, 4]. At least, a small discussion on how could these techniques help real problems, such as different medical domains [2, 3, 5].\nThe paper needs a brief proofreading. Be aware of tenses also. It would be wise to proofread the paper and correct these, as well as other spelling errors.\nThe related work seems scarce for a work around the healthcare domain. The paper must discuss recent work in a methodological sense and base their work on the proposed approach. A lot of work is already available into this topic [1, 3, 5]. Specifically, the scientific community has numerous works on this topic [1, 5, 7], but authors could also map some literature around other domains [5, 6, 8], where these level of approaches are essential.\nTo conclude, the paper is almost ready for indexing and the authors did a splendid work. However, I strongly recommend the authors improve the manuscript for the next iterations of the work, as this is a chief importance domain.\nMissing References\n[1] https://doi.org/10.1259/bjr.20220072\n[2] https://doi.org/10.1016/j.artmed.2022.102285\n[3] https://doi.org/10.1007/s00521-022-07183-8\n[4] https://doi.org/10.1016/j.ijhcs.2021.102607\n[5] https://doi.org/10.1007/978-981-15-9735-0_2\n[6] https://doi.org/10.1145/3399715.3399744\n[7] https://doi.org/10.1371/journal.pone.0195621\n[8] https://doi.org/10.1145/3132272.3134111\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": "8741",
"date": "01 Nov 2022",
"name": "Wan Siti Halimatul Munirah Wan Ahmad",
"role": "Author Response",
"response": "Thank you Prof. F.M.Calisto for the encouraging comments for improving our article. We have noted the following changes (new texts are emphasized in Bold): Revised Introduction: Pancreatic cancer is one of the most lethal malignant neoplasms in the world,1 developed when cells multiply and grow out of control in the pancreas,2 forming cancer cells caused by cells mutation in their genes.3 Doctors commonly perform a biopsy to diagnose cancer when physical examination or imaging tests like magnetic resonance imaging (MRI) and computerized tomography (CT) scans are insufficient. In pancreatic cancer, grading is essential for planning treatment but is currently done using a meticulous microscopic examination.4 Limited work found on analysis of pathological images for pancreatic cancer. Niazi et al. [Suggested Reference 7] presented a deep learning method to differentiate between pancreatic neuroendocrine tumor and non-tumor regions based on Ki67 stained biopsies. The purpose is for the quantification of positive tumor cells in a hotspot. Up to now, there has been no successful implementation of artificial intelligence (AI) for classifying pancreatic cancer grade. The absence of such AI work motivates this paper to use transfer-learning to grade pathological pancreatic cancer images using 14 deep learning (DL) models. This work can facilitate an automated cancer grading system to address the exhaustive work of manual grading. Revised Deep learning and related works section: Convolutional neural network (CNN) is a widely used deep learning (DL) algorithm in medical image-based classification and prediction.7 Several methods use CNN in cancer detection and diagnosis8 such as the Gleason grading of prostate cancer,9–11 colon cancer grading,12 breast cancer detection,13,14 and pancreatic cancer detection15–18 and classification.19 AI has been proven to assist clinicians with better prediction and faster diagnosis for breast cancer screening [Suggested Reference 2]. However, the grading of pancreatic cancer with DL still needs comprehensive study. New subsection at the end of Introduction: Contributions: This work presents an automated grading system focusing on pancreatic cancer from pathology images, which has not been done before to the best of our knowledge. The work also contributes a comparison of performance for 14 DL models on two different pathological stains, namely the May-Grünwald-Giemsa and haematoxylin and eosin. Revised Effect of data augmentation section: This experiment was done with the first cross-validation set of the mixed dataset, to observe how data augmentation impacts a model training performance.23 Table 5 and Table 6 display the final accuracy and loss of training and validation set after 100 epochs. Without data augmentation in Table 5, it is evident that overfitting has occurred, because the model is doing very well on the training set but not on the validation set. With data augmentation, the validation accuracy improved, specifically on VGG19 model (54.83% to 77.22%). The training accuracies of other models are slightly reduced with data augmentation (except for VGG19) but it is normal as the model is learning newly transformed images. The validation loss also shows a reduction, as in Table 6, such as on NASNetLarge model from 3.36376 to 0.68587. Overall, these results show that data augmentation may reduce overfitting and improve model performance as reported in.10,13,14The reason behind this is the model is becoming more robust with data augmentation for getting to learn various transformed images of the limited size dataset. These kind of images are high-likely to exist in real-world applications, especially when it comes to unique human cells. Added last paragraph before Conclusion section: From the study, we can see that integrating AI into the diagnosis system can assist the pathologist in getting the suggestive grading based on the prediction. It is however meant to assist and not on decision-making. The future aim of this study is to have a platform for screening of pancreatic cancer biopsies. We look forward to getting this article indexed. Thank you very much."
}
]
},
{
"id": "142271",
"date": "19 Jul 2022",
"name": "Rajasvaran Logeswaran",
"expertise": [
"Reviewer Expertise Medical image processing"
],
"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: The paper reports on novel work undertaken in automated grading of pancreatic cancer using pathology images and deep learning. The classification is based on the grade of the cancer, instead of just detecting the presence or type of cancer, and uses pathology images as opposed to the conventional radiology images prevalent in most prior research efforts. The main advantage of the proposed system is that it overcomes the very tedious and error prone conventional pancreatic cancer grading method that requires manual microscopic examination of the cancerous tissues after biopsy. The reduced misdiagnosis promotes providing correct treatment planning for patients. Although using only a limited size training set, the proposed system was tested using 14 different ImageNet pre-trained models and achieved high accuracies of up to 95.61% for two different pathological stains.\n\nComments: The paper is well written and the flow is both logical and guides the reader through the work in an easy to understand manner. The technical content is good with appropriate use of vocabulary and terminology. The subject matter is of current interest and the publication is a worthwhile contribution to the body of knowledge.\nRecommendations for Improvement: Some points of consideration for improvement of the paper are listed below:\nAbstract - Results: It would be advisable to change \"small sample set\" to \"small training set\", to better represent the effectiveness even when training was limited. This is especially so as deep learning is employed for the grading system.\n\nIntroduction: Consider changing \"paper\" in \"The absence of such AI work motivates this paper to\" to \"project\" or \"research\".\n\nReferences: Although the references are fairly recent, the paper would benefit by additionally citing the most recent relevant publications from the current year. It should also be checked if \"et al.\" can be used in the References or the names of all authors should be listed in the References section.\n\nMethodology: In terms of language, better to change \"The methodology of this work was done at\" to \"The research work was undertaken at\".\n\nFigure 1: Do use consistent style of verbs in the flowchart, e.g. change \"Fine tuning\" to \"Fine tune\" and \"Training\" to \"Train\".\n\nPathology image procurement: Consider changing \"which is\" to \"that are\".\n\nImage dataset: Consider adding a comma before \"which\" in \"images which is\".\n\nImage data augmentation and normalization: It is stated that the images were rescaled from [0,255] to [0,1]. However, was this as a grayscale intensity image or for each of the RGB (or other colour space) components? Do clarify as there are no further images shown, making it difficult to infer.\n\nEquation numbering could be added.\n\nEffect of data augmentation: Citation 23 appears to be out of place. Consider changing \"is doing very well on the training set\" to \"performed well on the training set\". The citations at he end of the last sentence should be moved to before the full-stop.\n\nTable 5: Consider simplifying the caption to \"Model accuracy after 100 epochs\" or removing \"for\". Similarly for the Table 6 caption.\n\nFigure 3: The names of the dataset do not tally with the description given earlier in the text. For consistency, \"Blue\" and \"Purple\" should be changed to \"MGG\" and \"H&E\", respectively. The y-axis of the graph should be labelled (\"Mean f1-score\"). Also ensure consistency of spelling for \"f1-score\" in the caption and text. Similarly, ensure consistency of the spelling \"Mixed\" dataset (cf. \"mixed\").\n\nComparison between pre-trained models: Consider deleting \", which performs better than their ancestor.\"\n\nComparison between the best and the worst performing model: Consider changing \"imbalance classes\" to \"imbalanced classes\". Also, \"recalling class with fewer data\" to \"recalling classes with less data\".\n\nData availability: The authors have made their data and results available for other researchers. This is useful as it allows for verification of the findings, should the need be, and can propagates further research in this area by helping overcome the scarcity of labelled data. The code used is also provided to assist other researchers.\nConclusion: The paper presents useful findings that would be beneficial in quick and accurate pancreatic cancer grading for correct timely treatment planning. The finding may also open avenues of research and implementation in for other types of cancers and tissue analysis. This work is a useful contribution to the body of knowledge in this domain.\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/10-1057
|
https://f1000research.com/articles/11-716/v1
|
29 Jun 22
|
{
"type": "Review",
"title": "Tourette syndrome research highlights from 2021",
"authors": [
"Andreas Hartmann",
"Per Andrén",
"Cyril Atkinson-Clément",
"Virginie Czernecki",
"Cécile Delorme",
"Nanette Marinette Debes",
"Natalia Szejko",
"Keisuke Ueda",
"Kevin Black",
"Per Andrén",
"Cyril Atkinson-Clément",
"Virginie Czernecki",
"Cécile Delorme",
"Nanette Marinette Debes",
"Natalia Szejko",
"Keisuke Ueda",
"Kevin Black"
],
"abstract": "We summarize selected research reports from 2021 relevant to Tourette syndrome that the authors consider most important or interesting. The authors welcome article suggestions and thoughtful feedback from readers.",
"keywords": [
"Tics",
"Tourette syndrome",
"2021"
],
"content": "Introduction\n\nThis article is meant to disseminate recent scientific progress on Gilles de la Tourette Syndrome (TS). This is the eighth annual update for the Tics collection on F1000Research (https://f1000research.com/collections/tics). The authors eagerly invite article suggestions for the 2022 highlights article at https://www.authorea.com/554771/.\n\n\nMethods\n\nWe searched PubMed using the search strategy (“Tic Disorders”[MeSH] OR Tourette NOT Tourette [AU]) AND 2021[PDAT] NOT 1950:2020[PDAT]. On 10 January 2022 this search returned 306 citations, available at this link. Colleagues also recommended articles, and we attended selected medical conferences. We selected material for this review subjectively, guided by our judgment of possible future impact on the field.\n\n\nResults\n\nDefinition\n\nA very compelling data analysis and review argues for the conclusion that persistent (chronic) motor or vocal tic disorder (PMVT) and Tourette Disorder (TS) are the same illness, or at least that “PMVT and TS occur along a clinical spectrum in which TS is a more severe and PMVT a less severe manifestation of a continuous neurodevelopmental tic spectrum disorder.”1\n\nThe European clinical guidelines for Tourette syndrome were updated (version 2.0) with regard to assessment of tic disorders.2 As an introduction to these updated guidelines, it is well worth reading the summary statement3 and the patients’ perspectives.4\n\nEpidemiology\n\nWhen it comes to sex differences, a review by Garris and Quigg described that although TS is more common in boys, tics in girls tend to be more persistent.5 Also, comorbidity differed, with ADHD being more common in boys and mood and anxiety disorders more common in girls. This topic was also explored by the European Multicentre Tics in Children Studies (EMTICS) group who showed that males, in general, had more severe symptoms than females with the exception of emotional problems. Since male symptoms seem more predominant at a younger age, their diagnosis might be facilitated compared to females.6\n\nAs for the course of tics, another EMTICS study assessed clinical precursors of tics by comparing 61 high-risk children who did develop tics in a seven-year follow-up period with 126 high-risk children who did not develop tics. Male sex, severity of conduct problems, autism spectrum disorder (ASD), compulsions, and emotional problems were shown to be precursors to tic occurrence.7\n\nA study by Gromark and colleagues also tackled the topic of disease prognosis and course, but in a cohort of individuals with Pediatric Acute-onset Neuropsychiatric Syndrome (PANS).8 Over a median of 3.3 years after the diagnosis, most symptoms improved substantially and only 35% of children had a chronic, non-remitting course. These results suggest a generally positive outcome for children diagnosed with PANS, and interestingly may not differ substantially from the outcome in recent studies in non-PANS children, including the population of Provisional Tic Disorder.9,10\n\nAnother important report regarding treatment of tics comes from China.11 Demographic and prescription data regarding tic disorder were extracted from the electronic medical records database of Beijing Children’s Hospital from 2018 to 2020. The authors paid special attention to treatment choices. All in all, 20,417 patients were included and 28.1% (n=5028) of them were treatment-free. In contrast, 70% received anti-tic medication. In line with reports from other countries, in children less than six years of age, clonidine was the most frequently employed medication (in particular, clonidine adhesive patches, CAP). Another treatment option commonly used in this group was traditional Chinese medication (TCM). As patients were older, the use of antipsychotics was growing. As for the number of medications prescribed, 22% (n=3389) were treated with at least two compounds, with the most common combination being tiapride and TCM (33.7%), followed by CAP and TCM (22.1%).\n\nRegarding reports on particular types of tics, Kaczyńska and Janik reported their experience with tonic (isometric) tics in 241 consecutive TS patients (including 153 children).12 Tensing of the abdomen was the most common localization, followed by the neck and upper extremities. Tonic tics were common, occurred early in the course of the disease, and were associated with greater number, severity and complexity of tics. The same authors covered the topic of blocking tics in the setting of a one-time registration study including 195 consecutive TS patients. Blocking tics were found frequently (37.4%) and were early associated with more severe disease phenotype.13\n\nThe controversial topic of cognitive tic-like phenomena was studied by Janik and colleagues.14 They included 227 consecutive TS patients. Cognitive tic-like phenomena were defined as brief and sudden involuntary thoughts. These phenomena occurred in 15% of patients and were correlated with older age, increased tic severity and anxiety disorder.\n\nDavid Mataix-Cols’s lab reported a national registry study of cervical spine injuries in TS. Risk of vascular and nonvascular C-spine injuries were 38% to 57% higher compared to controls, without a significant difference by sex. This epidemiological study confirms previous case reports and suggests that, although most TS patients do not injure their spine, doctors should carefully monitor patients with severe disease or nuchal symptoms, and have a low threshold for intervention, since these injuries can be serious and persistent.\n\nAn interesting case series described six patients whose driving capacity was impaired by their tics. This is a highly relevant and rather frequent topic of discussion in TS clinics, and relies more on common sense than established guidelines, as in epilepsy. On the same topic, a survey study with 228 adult participants with self-reported chronic tic disorder (CTD) or TS showed that tics in most individuals did not influence driving.15 However, reported tic severity was significantly higher among those without a driver’s license compared to those with a driver’s license, and tic severity was indicated as cause of not having a driver’s license in 60.7%.\n\nComorbidity\n\nZinna and colleagues performed a retrospective, naturalistic study of all children with CTD and TS admitted to an inpatient mental health unit during a 10-year period. 19.7% of the children needing inpatient treatment had comorbid CTD/TS, especially with obsessive compulsive disorder (OCD), intellectual disability, and autism spectrum disorder.16 Moreover, presence of these co-existing disorders was associated with longer admissions. Interestingly, no association with CTD/TS and attention deficit hyperactivity disorder (ADHD) was found. Park and colleagues performed a retrospective review of medical records of 119 pediatric patients diagnosed with TS. The mean age at onset of tics was 6.9 years and mean age at diagnosis was 8 years. 31.1% had at least one comorbid neuropsychiatric disorder.17 Tic severity was associated with shorter time to diagnosis and greater functional impairment.\n\nVermilion and colleagues compared anxiety symptom profile in youth with tic disorders with a community control group and a group of youths with clinically significant anxiety who were seeking anxiety treatment.18 A weak, but significant, association between severity of tics and anxiety was found. Youths with tic disorders had similar anxiety severity as youths with clinically significant anxiety, and significantly higher anxiety severity than healthy controls. Separation anxiety severity in youths with tic disorders was significantly higher than in the group with anxiety.\n\nAnother Swedish registry study of over 10 million people found a 6.7-fold increased prevalence of insomnia in the 5,877 who had a recorded diagnosis of TS/CTD, after adjusting for demographics and somatic illness.19 Excluding people with ADHD, ASD, or a sibling with TS/CTD reduced the odds ratio somewhat, suggesting that part of the risk is attributable to familial factors or these two comorbid diagnoses. Medication for ADHD also increased the likelihood of insomnia. These results suggest that assessment for sleep quality is important in managing TS. The association could be partly explained by ADHD, ADHD medication, familial factors, and neurodevelopmental comorbidities. This was confirmed by the findings in the meta-analysis by Keenan and colleagues, which included polysomnography studies in three groups of patients: CTD-only, ADHD-only, and CTD+ADHD. The CTD+ADHD group had most sleep difficulties, but both in CTD-only and CTD+ADHD group lower sleep efficiency and higher sleep onset latency were seen.20\n\nThe etiology of anger outbursts and aggressive symptoms in patients with TS may be multifactorial and influenced by severity of illness and psychosocial factors.21 In relation to this topic, it is also worth mentioning a small case series published by Kurvits and colleagues that explored the topic of allo-aggression and presented helpful tips to distinguish between allo-aggressive behaviors and tics.22 The authors present cases of three patients with variety of complex repetitive behaviors and allo-aggression (e.g., sudden kicking, hitting, slapping and biting others, or pushing someone off a bike) which were mistaken for tics. An exhaustive clinical examination revealed the presence of red flag psychiatric symptomatology atypical for TS, such as blackouts or feeling of being possessed by different personalities.\n\nA very interesting study by Vicario and colleagues23 explored the topic of moral reasoning (MR) in TS. The hypothesis about altered MR in TS is based on altered social cognition and reduced cognitive empathy that has been found in TS. Comparing the results of variety of tests assessing MR between 21 TS patients and 21 healthy controls, the authors documented a greater tolerance of unethical behaviors in TS adolescents.\n\nAs for other, non-psychiatric comorbidities, in a cohort of 201 patients with TS, 33.3% turned out to have comorbid non-tic movement disorders, particularly piano-playing movements (11%) and stereotypies (8%).24 The most common etiology was drug-induced movements (6.0%) but in most cases no etiology was found and no association with severity of tics was found. The presence of connective tissue-altered conditions, like joint hypermobility, was shown to be associated with tic disorders.25\n\nPremonitory urge and tic suppression\n\nSeveral studies have explored the topic of premonitory urge (PU) in TS. Ramsey and colleagues26 investigated the nature of relationship between PU and disease severity in TS using structural equation modeling. This analysis revealed that higher levels of urge intolerance predicted greater levels of tic-related disability. Moreover, the association between urge intolerance and tic-related disability was more pronounced in adolescents with internalizing symptoms. Another study, by He and colleagues,27 used magnetic resonance spectroscopy to examine the pattern of alterations in γ-aminobutyric acid (GABA) and glutamate neurotransmission in the following regions of the brain: the right primary sensorimotor cortex (SM1), supplementary motor area (SMA), and insular cortex. Interestingly, neither GABA+ nor glutamine levels were associated with tic diagnosis or severity. However, in children with TS, lower levels of SMA GABA+ were associated with more severe and more frequent premonitory urges. The authors concluded that GABAergic neurotransmission in the SMA area is involved in the development of PU. Schubert and colleagues28 explored inter-individual differences in PU and urge-tic associations in 21 adult patients with TS. They demonstrated that, as expected, at the group level there was a positive association between PU and tic frequency and intensity. In addition, they demonstrated inter-individual differences in associations between urges and tics. The majority of participants (57-66%, depending on the measure that was used) demonstrated positive associations between tic severity and PU, but this was not the case for all patients and in two cases there was a negative association with tic occurrence and PU.\n\nAs for studies focused on tic suppression, Morand-Beaulieu and colleagues29 investigated brain correlates of tic suppression. They applied high-density electroencephalography at rest and during tic suppression. Graph theoretical analyses showed a distinctive global network topology during tic suppression in comparison to rest. The authors complemented their analysis with network-based statistics and found a subnetwork of increased connectivity during tic suppression. The main regions of the brain involved in this network were right superior frontal gyrus and the left precuneus. Interestingly, there was a condition-by-age interaction, suggesting that with age brain circuits responsible for tic inhibition mature.\n\nOther\n\nDisease-related quality of life (QOL) in adults with TS at a subspecialty neurology movement disorders center did significantly correlate with current tic severity.30 However, QOL was explained primarily by current non-tic symptom severity (in decreasing order of correlation strength: anxiety, ADHD, and OCD, followed by the Yale Global Tic Severity Scale [YGTSS] total tic score [TTS]). In a hierarchical regression analysis, the association of TTS with QOL was statistically significant only after removing the other variables.\n\nAdults with TS (n=53, compared to 53 tic-free controls) had higher levels of food sensitivity and avoidance, and food neophobia was predicted by greater sensitivity to taste (gustatory hypersensitivity) in a study by Smith and colleagues.31\n\nGenetics\n\nA genome-wide pathway analysis conducted by the TS/OCD working group of the Psychiatric Genomics Consortium used 1,285 cases with TS and 4,964 ancestry-matched controls. The study identified three gene sets as differing in TS: (i) ligand-gated ion channel signaling, (ii) lymphocytic (driven by variants in FLT3), and (iii) cell adhesion and trans-synaptic signaling sets.32 These gene sets are in line with and reinforce previous hypotheses regarding the potential roles of neuroinflammation, GABA, and cell adhesion in the pathophysiology of TS.\n\nA cross-disorder genome-wide association study (GWAS) on 93,294 individuals revealed genes that contribute shared genetic risk for TS in combination with ADHD, ASD, and OCD.33 Regarding the TS-ADHD-ASD association, tissue specific analysis implicated the hypothalamus-pituitary-adrenal gland axis, in accordance with previous clinical studies implicating this system in multiple childhood-onset psychiatric traits, including TS and ADHD.\n\nIn a large (n=122) and densely-affected pedigree of individuals with TS, 66 DNA samples were available and analyzed using different methods.34 Overall, this family had a high load of common risk alleles for TS, suggesting that multiple common variants contribute more to risk than a few variants of strong effect.\n\nJones and collegues35 prospectively recruited 200 sequentially referred children with tic disorders/OCD, 100 autoimmune neurological controls, and 100 age-matched healthy controls. Using a structured interview, the maternal and family history of autoimmune diseases and other pro-inflammatory states was captured. Maternal blood and published Tourette brain transcriptomes were analyzed for overlapping enriched pathways. Overall, this fascinating study suggested that innate immune signaling may link maternal inflammation and childhood tics/OCD, and that targeting inflammation may represent a plausible therapeutic target in neurodevelopmental disorders, including TS. This line of argument was developed and expanded in two reviews on this topic by the same group.36,37\n\nIn an analysis of genome-wide DNA methylation patterns in whole blood samples from 16 monozygotic twin pairs (eight discordant and six concordant for TS, plus two asymptomatic pairs), no site reached statistical significance, but a strong association was suggested with genes belonging to the mTOR pathway, previously implicated in a variety of neuropsychiatric disorders.38\n\nEnvironmental risk factors\n\nThe EMTICS study published its results testing the pediatric autoimmune neuropsychiatric disorders associated with streptococcal infection (PANDAS) hypothesis.39 This study followed 715 children with TS/CTD for an average of 16 months. Tic severity was measured thrice annually, and infection with group A beta-hemolytic streptococcus (GAS) was monitored carefully using pharyngeal swabs and serologic testing. The study identified 405 tic exacerbations in 308 participants, but these exacerbations did not correspond temporally to GAS exposure. The authors conclude that their “study does not support GAS exposures as contributing factors for tic exacerbations in children with CTD. Specific work-up or active management of GAS infections is unlikely to help modifying the course of tics in CTD and is therefore not recommended.”39 These results and conclusion support those of previous studies.40\n\nAyubi and colleagues reviewed data from previously published epidemiological studies and concluded that maternal smoking during pregnancy raised the risk of TS in their children by 35%.41\n\nThis year brought widespread attention to social contagion as a possible cause of sudden-onset tic-like symptoms in adolescents. Such a phenomenon had been described previously, for instance ten years ago in a group of high school students in the Rochester, New York, area,42,43 but in 2020, Müller-Vahl and German colleagues reported a rush of cases among patients who did not know each other in person but had watched videos from the same social media personality and showed his same symptoms.44 A report from London45 reported a similar phenomenon and was picked up by numerous media outlets (a Google search on 13 November 2021 for “functional tic-like behaviors, TikTok, social media” returned about 100 relevant results). Zea Vera and colleagues carefully examined popular ‘Tourette’ TikTok videos with unusual symptoms and described a number of features of these videos that are highly unusual for TS.46 These features include aggression (in 19% of these videos), self-injurious behaviors (28%), coprophenomena (over half), long phrases (more than three words, 46%), throwing objects (22%), and very strong influence by the environment (over half). Senior clinicians viewing these videos rated them on a Likert scale of one (“All the tics are typical of TS”) to five (“None of the tics are typical of TS”). The median rating was five (interquartile range 4-5), meaning that almost none of these patients’ presentations even slightly resembled TS to these clinicians. A group from Lübeck and Dresden directly compared demographic and clinical variables of 13 cases starting dramatically after social media exposure to 13 TS patients similar in age and sex.47 A number of features were seen only in the post-social-media patients (i.e., 100% specific), including abrupt symptom onset, first symptom being complex, primarily slow and tonic movements, mostly trunk or extremities, a rapidly varying repertoire of symptoms, symptom deterioration in the presence of others, lack of spontaneous symptom fluctuations over the course of weeks to months, a symptom involving goal-directed movement (e.g., directed at another person), and dramatic context dependence. Symptoms continuing unabated throughout the examination was nearly as specific (13 of 13, vs. 1 of 10 with TS). Copropraxia was present in over half, as was echolalia, and symptom onset was significantly later (mean 15.3 years, vs. 5.2 years for TS). For all these reasons, most experts concluded that these presentations comprised a functional movement disorder rather than a variant expression of TS.\n\nOne concern raised early in this FND epidemic was that If the very features clinicians used to define FND patients turned out to be more common in their FND patients, one has not proved anything. Pringsheim et al authored one of the first prospective studies that fully addresses that concern.48 They reported on a prospective cohort of 290 children with tic-like phenomenology seen at Calgary. Twenty of these had rapid onset of clinically problematic tics. Crucially, these patients were not defined by clinical judgment of FND, so the results cannot be circular. These 20 rapid-onset patients differed substantially from the remaining 270 children with a (typical) primary tic disorder. They were an average of 7.5 years older at onset, 3.8 years older at the first visit to the center, had more severe tics (YGTSS total tic score 14.9 points higher and impairment score 12.8 points higher, on average), and had more severe anxiety and depression scores (all of these p < .0001). Several dichotomous features were significantly more common in the rapid-onset group, though specificity for rapid-onset group membership was variable: 56% for ADHD, 84% for female sex, 81% for an anxiety disorder, and 96% for a depression diagnosis.The Tourette Association of America convened an international working group that provided a summary and recommendations for assessment and care49; another helpful resource for patients is available at NeuroSymptoms.org.50\n\nAnimal models\n\nBenzodiazepines and ethanol are among the well-known positive allosteric modulators (PAMs) of GABA-A receptors. A PAM highly selective for GABA-A receptors containing α6 subunits showed efficacy in the D1CT-7 transgenic mouse model of tics.51 Dopamine antagonists showed similar effects but induced catalepsy, whereas this PAM did not. These results suggest a strategy for future human studies, including for treatment of tic disorders; benzodiazepines are widely prescribed for TS but there is a paucity of controlled data supporting their efficacy for tics.\n\nLikely the most relevant and best established rodent models for tics have been developed by the group of Izhar Bar-Gad. In this paper, they provide a comprehensive overview of their work so far.52\n\nElectroencephalography\n\nSeveral studies using electroencephalography (EEG) to elucidate the pathophysiology of tic disorders were published in 2021. An EEG study of lateral readiness potentials, a measure of activation and preparation of responses occurring in motor cortical areas, showed that action integration per se was normal in patients with TS, suggesting that TS is not only a movement disorder.53 EEG studies characterizing oscillatory activity and functional connectivity revealed that children with tics exhibited abnormal activation and communication patterns within the frontal-parietal lobe network during cognitive inhibition54 and that children with TS suppressed tics through a distributed brain circuit of cortical regions.29 In an EEG study of TS patients and controls, movement-related EEG (i.e., mu- and beta-band oscillations) was examined just before voluntary movements and tics were performed.55 Mu and beta oscillations were not observed before tics, suggesting that a network of large brain regions (insular cortex, cingulate cortex, basal ganglia, cerebellum, etc.) is involved in the development of tics. In the same study, beta-band desynchronization occurred when TS patients initiated voluntary movements and, in contrast to healthy controls, no desynchronization of mu-band oscillations was observed during the execution of voluntary movements, which was interpreted as a physiological inhibition impairment in TS. Another study using EEG was conducted to calculate scale-free activity (1/f neural noise) based on the theory that tics are behavioral surplus, or “motor noise”.56 Although task-related 1/f noise and high-frequency band aperiodic activity were found to be increased in patients with TS during sensory-motor processing, there was no evidence that scale-free and aperiodic activity was related to the process of tic development. The authors suggested that increased 1/f noise and aperiodic activity are not directly related to tics, but more likely related to a new aspect of TS. Systematic review and meta-analysis investigating the electrophysiological correlates of performance monitoring showed that error-related negativity on EEG showed significantly increased amplitude in TS patients.57 However, this was based on only five studies and there was a high degree of heterogeneity between studies.\n\nNeuroimaging studies\n\nIn 2021, two voxel-based morphometry (VBM) meta-analyses were published.58,59 Their objectives were the same (i.e., comparing TS patients to healthy controls), but they used different approaches and found different results. The first59 selected 10 studies and used a voxel-wise meta-analysis called seed-based d mapping. The second58 selected six studies and used the more classical Activation Likelihood Estimation (ALE) method. They both reported increased gray matter (GM) volume in the thalamus and the putamen and decreased GM in the postcentral gyrus. Surprisingly, their remaining results differed and can therefore be considered more controversial: increased GM volume in the cerebellum (vermis III), in limbic areas (striatum, insula, and hypothalamus) and in sensorimotor regions (pre- and post-central gyri); decreased GM volume in frontal (inferior and medial parts and rolandic operculum), temporal (superior temporal gyrus) and parietal cortices (supramarginal gyrus) as well as cingulate gyrus (anterior and posterior parts).\n\nThe anterior cingulate cortex (ACC) is largely suspected to play an important role in TS. A study using both VBM and structural covariance network mapping focused on this region.60 This study found, first, decreased GM volume within the ACC and, second, increased structural covariance between the ACC and the motor parts of the cerebellum, the inferior frontal cortex and the posterior cingulate cortex.\n\nInteresting functional magnetic resonance imaging (fMRI) studies in TS were also published last year. One used multivariate analysis with a support vector machine (SVM) to distinguish TD patients from healthy controls.61 This classification algorithm reached a correct general accuracy of 67% to distinguish the two groups, especially on the basis of resting-state fMRI data within the striatum, the fronto-parietal cortex, and the cerebellum. In addition, the authors distinguished medicated and unmedicated patients with an accuracy of 69% based on the activity of the striatum, the insular and cerebellar networks. These results and previous similar work62 show that resting state functional imaging contains information relevant to distinguishing diagnosis and other clinical features in TS.\n\nFrom a cognitive standpoint, the neural networks that underlie urge inhibition were assessed in TS patients with obsessive-compulsive symptoms during a task involving blink suppression while viewing emotional (angry and neutral) faces.63 The authors found that, compared to healthy controls, patients had higher activity in the superior temporal gyrus and the middle cingulate cortex. In addition, by decomposing the task, they found that (1) tic severity was related to higher activity during angry faces trials in comparison to neutral faces; (2) premonitory urge severity was related to higher activity in the hippocampus, middle temporal gyrus, thalamus and caudate nucleus; and that (3) blink inhibition was associated with decreased activity in both the thalamus and the insular cortex.\n\nAnother fMRI study focused on decisional impulsivity by using a delay-discounting task involving choosing between a small immediate reward or a larger delayed reward.64 While they found no abnormal decisions in patients in comparison to a group of healthy controls, the authors identified a subgroup of patients with higher impulsivity. This group was also characterized by a higher burden of impulse-control disorders and a higher level of general impulsivity. In this group, reward discounting was related to brain activity in a network comprising the orbito-frontal, cingulate, pre-supplementary motor area, temporal and insular cortices, as well as ventral striatum and hippocampus. However, the most interesting result was that a greater connectivity of pre-supplementary motor area with anterior insular cortex predicted both steeper reward discounting and more severe tics. This suggests a relation between cognitive (decision-making) and motor (tics) impulsivity in this subgroup of patients.\n\nPharmacological studies\n\nSturm and colleagues investigated inhibitory control abilities in 24 TS patients, 139 ADHD patients, 19 TD+ADHD patients, and 59 typically developing controls aged nine to 14 years.65 Inhibitory control was measured using common neurocognitive tasks [Attentional Network Task (ANT), Stop Signal Task (SST), Delis-Kaplan Stroop task, and Go-Nogo task]. Surprisingly, their results did not confirm the inhibitory control deficit that had previously been found in TS or TS+ADHD patients (reviewed by Morand-Beaulieu et al.66). But the originality of this paper was to evaluate how inhibitory control deficit, tic severity (YGTSS), ADHD symptoms severity (by the Strengths and Weaknesses of Attention-Deficit/Hyperactivity symptoms and Normal behaviors scale, SWAN), and subjective tic suppressibility (item 10 on the Premonitory Urge for Tics scale, PUTS), contribute to objective tic suppressibility (tic suppression paradigm67). The authors found that the only predictor of performance in the tic suppression paradigm was subjective tic suppressibility, and that inhibitory control deficit, tics, and ADHD severity had no effect. As objective tic suppression is known to be a potential mechanism of behavioral treatment response for TS patients, these findings have interesting clinical implications.\n\nTic assessment\n\nAn important study by Haas and colleagues evaluated the psychometric properties of the gold standard for tic assessment, namely the Yale Global Tic Severity Scale (YGTSS). The authors used a subsample of the EMTICS including 706 children and adolescents with a chronic tic disorder, and investigated convergent, discriminant, and factorial validity, as well as internal consistency, of the YGTSS. The YGTSS demonstrated acceptable psychometric quality. Nevertheless, they also showed that there is a need for further improvement of some items, for example, the global severity (total) score, indicating that separate use of the total tic score and the impairment rating is more beneficial.68\n\nPsychometric properties of the Chinese version of the YGTSS were explored by Wen and colleagues.69 The authors included 367 children and adolescents with tic disorders and tested both reliability and validity. Overall, the Chinese version of YGTSS showed good psychometric properties. Similarly, Li and colleagues70 tested the psychometric properties of another gold standard scale used in tic research, the Premonitory Urge for Tics scale (PUTS), in the Chinese population. No differences regarding PU manifestation were found in diverse age groups. The exploratory factor analysis of PUTS demonstrated the emergence of four primary factors. Finally, reliability and validity analyses indicated that the Chinese version of PUTS had good psychometric properties.\n\nMany studies have focused on the development of new assessment tools for tic assessment, especially using new technologies. In one study by Eriguchi and colleagues, the authors tested a new method used to quantify the angular movements of neck tics using a compact gyroscope. The authors also investigated the clinical course of neck tics during a follow-up period of two years. Although the authors did not detect any changes in intensity and frequency of neck tics during the follow-up period, the gyroscope proved to be a valuable solution to monitor severe, healthy, or even life-threatening neck tics.71 Another approach using new technologies was proposed by Cernera and colleagues who tested a sensor-based technology called ‘the human tic detector’ to detect and classify tics.72 The authors recorded both surface electromyogram and acceleration data from 17 patients with TS when performing voluntary and involuntary movements (tics) using the modified Rush Video Tic Rating Scale (mRVTRS). In addition, they evaluated spectral properties of voluntary and tic movements with a sensor capturing the dominant tic and used a support vector machine (SVM) to detect and classify movements. It was demonstrated that wearable sensors can be used to distinguish between tics and voluntary movements and are comparable to expert consensus. Paulus and colleagues analyzed videos of 101 patients with TS and 109 healthy controls according to the Modified Rush Videotape Rating using a machine learning-based analysis. Severity of motor tics was shown to be the best predictor of a diagnosis of TS. Interestingly, vocal tics did not predict TS diagnosis, which might challenge the validity of the current diagnostic criteria for TS.\n\nOne important analytical avenue used both for data analysis as well as development of tic assessment algorithms is artificial intelligence. This approach was used by Wu and colleagues, who attempted to find an automatic method for detecting tics to assist in diagnosis and evaluation.73 Based on clinical data, the authors proposed a deep learning algorithm using both unsupervised and supervised learning and learning features from videos for tic motion detection. Taken together, the proposed models demonstrated satisfactory recognition between tics and non-tic movements, and the authors concluded that this methodology could be potentially useful in clinical care.\n\nPsychological interventions\n\nTreatment guidelines published by the American Academy of Neurology (AAN) in 201974 and the European Society for the Study of Tourette Syndrome (ESSTS) in 202175 recommend behavior therapy (BT) as the first-line intervention for TS/CTD. Out of several types of BT, recommendations are primarily for Habit Reversal Training (HRT) and its extended package Comprehensive Behavioral Intervention for Tics (CBIT), and secondarily for Exposure and Response Prevention (ERP).\n\nSeveral research groups are currently investigating ways to make BT more accessible to healthcare seeking TS/CTD individuals, including various remote formats. In a British randomized controlled trial (RCT) by Hollis and colleagues,76 referred to as the ORBIT study, 224 young TS/CTD individuals were randomized to therapist-supported, internet-delivered ERP (the previously piloted Swedish BIP TIC ERP program77) or a therapist-supported, internet-delivered psychoeducation comparator. Participants in the ERP group improved on average 4.5 points (16%) on the primary outcome (tic severity as measured by the YGTSS-TTSS) from baseline to post-treatment, compared to 1.6 points (6%) in the comparator group, a significant interaction of group and time showing superiority for the BIP TIC ERP intervention. The ORBIT study is a significant contribution to the field, being the largest study of BT for TS/CTD to date and the first study to show ERP to be superior to an active control intervention. An ongoing similar Swedish RCT will further add to the evaluation of the BIP TIC ERP program.78 Time will tell whether BIP TIC ERP will be implemented into regular healthcare.\n\nThe internet-delivered format has also recently been evaluated among adults. In a German RCT by Haas and colleagues,79 161 adult TS/CTD individuals were randomized to unsupported internet-delivered CBIT (n=67), unsupported internet-delivered psychoeducation (n=70), or face-to-face CBIT (n=24). The primary comparison between the two internet-delivered interventions showed a trend towards superiority of internet-delivered CBIT in reducing tic severity (as measured by the YGTSS-TTSS) at the primary endpoint (post-treatment). This trend later evolved to a statistically significant superiority of internet-delivered CBIT at follow-ups three and six months post-treatment. Even though the tic severity improvements were lower than in RCTs of face-to-face CBIT, and the study experienced relatively high dropout rates, internet-delivered CBIT may be a cost-effective (i.e., no therapist support is required) and helpful treatment option for some TS/CTD individuals.\n\nA few smaller studies have also investigated remote treatment formats. Viefhaus and colleagues80 piloted a blended approach, where online therapist support via videoconferencing was added to a regular face-to-face HRT intervention. The aim was two-fold: to provide therapist support for homework directly and to reduce the need for travel to the clinic. The format was shown feasible in a case series of children and adolescents (N=5). Reese and colleagues81 conducted a pilot study (N=8) of an online mindfulness-based intervention (self-help mixed with therapist-supported group sessions via videoconferencing) for adults with TS/CTD. The authors concluded that the intervention was feasible and acceptable, but that participant adherence to the mindfulness homework assignments was lower than expected. Individual improvements in YGTSS-TTSS were also modest. Further refinement and evaluation of this intervention is needed.\n\nA traditional group format, without the online component, may also be an efficient way to save therapist resources and promote the dissemination of BT. Zimmerman-Brenner and colleagues82 randomized 61 young TS/CTD individuals to group CBIT or group psychoeducation. The study showed somewhat mixed findings, with no significant between-group effect on the YGTSS-TTSS at the primary endpoint. Unexpectedly, tic severity increased in both groups between baseline and post-treatment, to later decrease at three-month follow-up. The temporary increase in symptoms seems to have been driven by an increase in vocal tic severity, potentially a side effect of the group format. Limitations included not including a power calculation nor performing intention-to-treat analyses.\n\nDuring 2021, a few variations and extensions of previous studies of face-to-face CBIT were also conducted. In a small pilot study (N=6), Peterson and colleagues83 investigated the specific effect of relaxation training as part of the CBIT package (alongside HRT and function-based interventions). The study concluded that relaxation training alone was not effective in reducing tic severity; rather, it should be included in conjunction with other CBIT elements.\n\nEspil and colleagues84 followed up young participants 11 years after receiving CBIT or supportive therapy and education (comparator) in the Piacentini and colleagues RCT from 2010.85 This is the longest published prospective follow-up to date of TS/CTD individuals having received BT. The results showed a significant tic severity decrease across the sample during the follow-up period. Further, treatment responders to both interventions in the original study achieved at least partial tic remission during the follow-up period (a YGTSS-TTSS score <14), of which treatment responders in the CBIT group were more likely to achieve remission than treatment responders in the comparator. Despite limitations such as confounding TS/CTD interventions during the follow-up period and data loss, the study indicated good durability of the effects of BT.\n\nAlso based on previous RCTs of CBIT,86 Essoe and colleagues87 investigated the relation between homework adherence and treatment outcomes. The results showed that greater overall homework adherence predicted tic severity reductions and treatment response. Essoe and colleagues separately reviewed literature on the working mechanism of BT for TS/CTD.88 This review showed that mechanisms appear to differ between youth and adults. Data primarily supported associative learning (e.g., positive reinforcement) and cognitive control (e.g., active tic inhibition) as mechanisms, while habituation may be a mechanism for adults only. Interpretation is made difficult by a mixture of laboratory and clinical studies, overall small sample sizes, and different ways to measure phenomena such as premonitory urge intensity.\n\nMedication\n\nThe European clinical guidelines for Tourette syndrome were updated (version 2.0) with regard to pharmacological treatments.89\n\nA number of randomized controlled studies have investigated the potential efficacy of new (extended release) VMAT2 inhibitors for the treatment of tics. To date, the mother compound, tetrabenazine, has been used largely off label for tic treatment in the absence of evidence derived from high quality clinical studies. Alas, both deutetrabenazine90,91 and valbenazine failed to meet primary endpoints in their respective studies.92\n\nAn interesting case series described six children or adolescents with aggressive behaviors in whom lurasidone, a novel antipsychotic, was added to either aripiprazole or risperidone; the addition of lurasidone appeared to diminish these symptoms with good tolerability.93\n\nInterest in cannabis (and, more generally, the cannabinoid system) in the treatment of tics is ongoing. Monoacylglycerol lipase inhibition to increase levels of 2-arachidonoylglycerol (2-AG), an endocannabinoid, was tested in a 12-week, multicenter, randomized, placebo-controlled, double-blind clinical trial using a compound called Lu AG06466 (formerly known as ABX-1431). This was a phase two trial in adult patients with TS. There were no significant differences on the YGTSS between groups, nor for other endpoints assessing tic severity, premonitory urges, quality of life, and common psychiatric comorbidities. Further development of the compound for tics/TS was abandoned.94 In contrast, encouraging results were obtained by Bloch and colleagues for THX-110, a combination of Δ9-tetrahydracannabinol (Δ9-THC) and palmitoylethanolamide (PEA) in a 12-week uncontrolled trial in 16 adults patients with TS.95 Tic symptoms improved on average by more than 20% (=7-point decrease in the YGTSS score), and 12 of the 16 participants elected to continue to the extension phase. However, tolerability was slightly tricky and, of course, these results now require validation in randomized double-blind placebo-controlled trials.\n\nFinally, another treatment target in TS might be the serotonergic system. Pimavanserin, a serotonin 2A receptor inverse agonist and antagonist, was tested in an open label trial over eight weeks in 10 adult patients with TS. A small but noteworthy decrease in tic severity (-12%) was noted on the YGTSS-TTS, as well as improvements on scales assessing global clinical impression and quality of life. Here too, larger, placebo-controlled trials are warranted.96\n\nNeurosurgery\n\nSeveral important papers have been published in 2021, which provide interesting insights for clinical management of these patients and also for the better understanding of the neural bases and brain targets involved in deep brain stimulation (DBS) effects.\n\nTwo important guidelines papers were published this year, which may be useful to refine inclusion criteria for DBS in TS patients. Szejko and colleagues published a revised version of the ESSTS guidelines on DBS based on data from the literature and the International Tourette DBS registry and database. Important takeaways from these guidelines include: i) the importance of excluding ‘tic-like’ functional movement disorders before considering DBS; ii) the fact that reduction of tics should be the main objective of DBS aimed at tics, and thus the importance of ensuring that tics are the primary source of impairment; iii) the inclusion of patients who are refractory to pharmacologic and behavioral therapies; iv) the fact that DBS should be very cautiously considered in children and teenagers due to the frequent improvement of tics in adulthood; and v) the importance of performing DBS following a specified protocol within the context of controlled trials, cohort studies or registry databases.97 These recommendations are in line with the opinion paper by Martino and colleagues, about the ‘five pillars’ for considering TS patients for DBS: i) high tic severity; ii) tic-related impact on quality of life; iii) treatment refractoriness; iv) stability of comorbid psychiatric disorders for six months; and v) multidisciplinary and particularly careful assessment of indications for patients under 18.98\n\nTwo RCTs have been published which add to the data on efficacy of DBS in TS. Baldermann and colleagues published a trial involving eight patients with stimulation of the Cm-Voi nuclei of the thalamus with an interesting design of combined naturalistic open label with brief randomized, sham-controlled assessments.99 They showed an improvement of tics with stimulation ON compared to sham stimulation, and an improvement in quality of life. Another study by Müller-Vahl and colleagues provided mixed findings. Their study involved 10 patients randomized to either sham, GPi, or thalamic stimulation. They found an improvement of tics with GPi stimulation and a superiority to GPi over thalamic and sham stimulation, with no overall improvement in quality of life, and with an important variability across patients. Importantly, four patients out of 10 had to be re-operated due to cable dysfunctions, and six years after surgery, five out of 10 patients had their stimulation turned off due to infections, technical problems, or lack of efficacy.100 In an interesting clinical paper, MacLean et al., report the complete resolution of GTS symptoms after the placement of stereo-EEG electrodes in the GPi and nucleus accumbens and suggest that stimulation at multiple patient-specific targets could provide effective control of GTS symptoms.This approach warrants further study.101\n\nRegarding the neural bases of DBS in GTS and the question of optimal stimulation target, several novel findings are worthy of attention. In a retrospective study involving 35 patients, Johnson and colleagues highlighted the important variability in pathway activation across patients and stimulation settings.102 They showed a correlation between tic improvement and predicted activation of the associative pallido-subthalamic pathway, the ansa lenticularis, and the internal capsule tracts projecting to the prefrontal cortex. Anterior GPi stimulation may act via associative and limbic pathways modulation, whereas posterior GPi stimulation may have an effect on sensorimotor networks. Interestingly, Aminzade and colleagues reported the case of a patient with improvement of OCD, without improvement of tics, after anteromedial GPi stimulation.103\n\nA systematic review on clinical responses to several DBS targets in patients with TS showed fiber connectivity to be important in target selection because the effects of DBS on tics seem to occur through different networks at different stimulation sites.104 Finally, an interesting case report described a patient with major depressive disorder who developed voltage-dependent coprolalia and tic-like movements along with changes in emotion, mood, and memory after DBS of bilateral ventral internal capsule and ventral striatum.105\n\nTranscranial magnetic stimulation\n\nFocusing on the benefits of noninvasive brain stimulation as a potential treatment for TS, methodological (e.g., transcranial magnetic stimulation (TMS), transcranial direct current stimulation) and theoretical issues,106 and TMS as a potential marker for TS107 were discussed. Dual-site TMS and diffusion tensor imaging showed reduced prefrontal (pre-SMA) inhibition in children with TS/CTD compared to controls and the decreased inhibition correlated with impairment of tic suppressibility.108 In addition, increased fractional anisotropy was observed in several white matter pathways in patients with TS/CTD, supporting a plausible pathophysiological mechanism associated with tic persistence.\n\nDyke et al., present an exhaustive review of non-invasive brain stimulation in the treatment of TS.106 One original study on low-frequency repetitive transcranial stimulation (rTMS) that stands out uses the bilateral parietal cortex as the target zone for the treatment of tics. The results, in 30 adult patients with TS, were very encouraging on all measures (YGTSS, MRVBTS and PUTS scores). Importantly, the beneficial effects lasted for up to a month after the last rTMS session.109 This approach warrants replication and extension in larger cohorts. In children (n=10), bilateral rTMS of the supplementary motor area was well tolerated and decreased tic severity post-treatment.110 However, this was an open label trial and requires confirmation in a blinded setting, and preferably over longer time periods.\n\nOther treatments\n\nThe Movement Disorders Society Tourette Syndrome Study Group performed a Delphi survey amongst 36 international experts in 14 countries to better define the concept of treatment failure in persistent tic disorders, both with regard to pharmacological and behavioral therapy.111 An operational definition was proposed and its feasibility now needs to be assessed in clinical decision making, for instance in choosing candidates for DBS. The Movement Disorders Society Tourette Syndrome Study Group also published a survey on clinical practice patterns in tic disorders and concluded that tic disorders remain understudied beyond a scope of dedicated experts, and that diagnosis and treatment still requires improvement across the globe.112\n\nSeveral tic experts argued that, although TS is not a rare disease according to international classifications, it remains understudied and should therefore qualify for public health regulations that direct funding to treatment research for orphan or neglected diseases.113 This is also reflected by an excellent review highlighting the scarcity of specialized TS clinics and dedicated experts.114 This international group investigated health service delivery and care practices by clinicians in different geographical settings (Canada, US, Europe, and the United Kingdom). The results suggested that there is a scarcity of specialized TS clinical care in all investigated regions. Similarly, a study from the Tourette OCD Alberta Network reported on pitfalls and solutions for development of systemic care networks for tic detection.115 In this mixed-methods study, 10 parents were interviewed in person and 140 parents responded to a survey. Qualitative data showed there was often an absence of a clear pathway to access healthcare for people with TS and OCD. Importantly, several solutions to tackle this problem were identified, such as: preparation of school-based training webinars, educational outreach in schools, and peer support.\n\nQuality of life\n\nLee and colleagues116 explored the role of self-esteem in mediating the relationship between psychosocial stress and social adjustment among adolescents with TS. Self-esteem of adolescents with TS fully mediated the relationship between psychosocial stress and social adjustment, while comorbidities moderated the relationship between self-esteem and social adjustment.\n\nSolis-Garcia et al.,117 studied quality of life and psychiatric comorbidities in pediatric patients with TS. In accordance with previous reports, higher severity of tics and ADHD were associated with poorer quality of life.\n\n\nConclusions\n\nThe year 2021 saw publication of important work on a variety of fronts. Larger and collaborative studies produced ever more frequent, important contributions. On the other hand, the flexibility of the TS clinical and research community was demonstrated by its response to the explosion of rapid-onset Tourette-like cases, beginning with rapid publication of case series but progressing quickly over the past one to two years to include international collaborations, controlled investigations, and prospective follow-up studies. Of perhaps greatest interest to our patients, new and actionable information appeared regarding numerous approaches to treatment of TS. These included the full range from psychological interventions to pharmaceuticals to non-invasive and invasive brain stimulation, and several clinical trials examined approaches that increased the availability of care at lower cost and to patients for whom frequent visits to a specialty center are difficult or impossible.\n\nKeeping up with the relevant literature on TS has become increasingly difficult. Over the eight years since we began this yearly review, PubMed has indexed almost 2,000 new publications dealing with Tourette syndrome and other tic disorders, with a record 300 publications in 2021 (see Figure 1). Despite the length of this review, the authors suspect that we have omitted some important work or may have overstated the relevance of a publication mentioned above. To improve these reviews, we warmly invite readers both to comment on this article after publication and to nominate important articles from 2022 (including their own best work) by commenting on the draft for next year’s highlights article.\n\nNational Library of Medicine. Image created by authors.",
"appendix": "References\n\nClaudio-Campos K, Stevens D, Koo SW, et al.: Is Persistent Motor or Vocal Tic Disorder a Milder Form of Tourette Syndrome? Mov. Disord. 2021; 36: 1899–1910. PubMed Abstract | Publisher Full Text\n\nSzejko N, Robinson S, Hartmann A, et al.: European clinical guidelines for Tourette syndrome and other tic disorders-version 2.0. Part I: assessment. Eur. Child Adolesc. Psychiatry. 2022; 31: 383–402. Publisher Full Text\n\nMüller-Vahl KR, Szejko N, Verdellen C, et al.: European clinical guidelines for Tourette syndrome and other tic disorders: summary statement. Eur. Child Adolesc. Psychiatry. 2022; 31: 377–382. Publisher Full Text\n\nAnderson SM: European clinical guidelines for Tourette Syndrome and other tic disorders: patients’ perspectives on research and treatment. Eur. Child Adolesc. Psychiatry. 2022; 31: 463–469. Publisher Full Text\n\nGarris J, Quigg M: The female Tourette patient: Sex differences in Tourette Disorder. Neurosci. Biobehav. Rev. 2021; 129: 261–268. Publisher Full Text\n\nGarcia-Delgar B, Servera M, Coffey BJ, et al.: Tic disorders in children and adolescents: does the clinical presentation differ in males and females? A report by the EMTICS group. Eur. Child Adolesc. Psychiatry. 2021. PubMed Abstract | Publisher Full Text\n\nOpenneer TJC, Huyser C, Martino D, et al.: Clinical precursors of tics: an EMTICS study. J. Child Psychol. Psychiatry. 2022; 63: 305–314. PubMed Abstract | Publisher Full Text\n\nGromark C, Hesselmark E, Djupedal IG, et al.: A Two-to-Five Year Follow-Up of a Pediatric Acute-Onset Neuropsychiatric Syndrome Cohort. Child Psychiatry Hum. Dev. 2022; 53: 354–364. Publisher Full Text\n\nBlack KJ, Kim S, Schlaggar BL, et al.: The New Tics study: A Novel Approach to Pathophysiology and Cause of Tic Disorders. J. Psychiatr. Brain Sci. 2020; 5.\n\nKim S, Greene DJ, Bihun EC, et al.: Provisional Tic Disorder is not so transient. Sci. Rep. 2019; 9: 3951. PubMed Abstract | Publisher Full Text\n\nWang N, Qin DD, Xie YH, et al.: Traditional Chinese Medicine Strategy for Patients with Tourette Syndrome Based on Clinical Efficacy and Safety: A Meta-Analysis of 47 Randomized Controlled Trials. Biomed. Res. Int. 2021; 2021: 6630598.\n\nKaczyńska J, Janik P: Tonic Tics in Gilles de la Tourette Syndrome. Neuropediatrics. 2021; 52: 370–376. PubMed Abstract | Publisher Full Text\n\nKaczyńska J, Janik P: Blocking Tics in Gilles de la Tourette Syndrome. Front. Neurol. 2021; 12: 686785. PubMed Abstract | Publisher Full Text\n\nJanik P, Dunalska A, Szejko N, et al.: Cognitive Tic-Like Phenomena in Gilles de la Tourette Syndrome. J. Clin. Med. 2021; 10. PubMed Abstract | Publisher Full Text\n\nFernández de la CL, Ringberg H, Anderson S, et al.: Driving with Tic Disorders: An International Survey of Lived Experiences. Mov. Disord. Clin. Pract. 2021; 8: 412–419. PubMed Abstract | Publisher Full Text\n\nZinna S, Luxton R, Papachristou E, et al.: Comorbid chronic tic disorder and tourette syndrome in children requiring inpatient mental health treatment. Clin. Child Psychol. Psychiatry. 2021; 26: 894–905. PubMed Abstract | Publisher Full Text\n\nPark EG, Kim YH: Clinical features and neuropsychiatric comorbidities in pediatric patients with tic disorders: a retrospective chart review study from South Korea. BMC Psychiatry. 2021; 21: 14. PubMed Abstract | Publisher Full Text\n\nVermilion J, Pedraza C, Augustine EF, et al.: Anxiety Symptoms Differ in Youth With and Without Tic Disorders. Child Psychiatry Hum. Dev. 2021; 52: 301–310. PubMed Abstract | Publisher Full Text\n\nIsomura K, Sidorchuk A, Sevilla-Cermeño L, et al.: Insomnia in Tourette Syndrome and Chronic Tic Disorder. Mov. Disord. 2022; 37: 392–400. Publisher Full Text\n\nKeenan L, Sherlock C, Bramham J, et al.: Overlapping sleep disturbances in persistent tic disorders and attention-deficit hyperactivity disorder: A systematic review and meta-analysis of polysomnographic findings. Neurosci. Biobehav. Rev. 2021; 126: 194–212. Publisher Full Text\n\nAshurova M, Budman C, Coffey BJ: Ticked Off: Anger Outbursts and Aggressive Symptoms in Tourette Disorder. Child Adolesc. Psychiatr. Clin. N. Am. 2021; 30: 361–373. PubMed Abstract | Publisher Full Text\n\nKurvits L, Mainka T, Cavanna AE, et al.: Aggression Toward Others Misdiagnosed as Primary Tics. Mov. Disord. Clin. Pract. 2021; 8: 769–771. PubMed Abstract | Publisher Full Text\n\nVicario CM, Gulisano M, Maugeri N, et al.: Moral Decision-Making in Adolescents with Tourette Syndrome. Mov. Disord. 2021; 36: 2205–2206. PubMed Abstract | Publisher Full Text\n\nBaizabal-Carvallo JF, Jankovic J: Beyond tics: movement disorders in patients with Tourette syndrome. J. Neural Transm. (Vienna). 2021; 128: 1177–1183. PubMed Abstract | Publisher Full Text\n\nBaeza-Velasco C: Neurodevelopmental atypisms in the context of joint hypermobility, hypermobility spectrum disorders, and Ehlers-Danlos syndromes. Am. J. Med. Genet. C Semin. Med. Genet. 2021; 187: 491–499. PubMed Abstract | Publisher Full Text\n\nRamsey KA, Essoe JK, Storch EA, et al.: Urge Intolerance and Impairment Among Youth with Tourette’s and Chronic Tic Disorders. Child Psychiatry Hum. Dev. 2021; 52: 761–771. PubMed Abstract | Publisher Full Text\n\nHe JL, Mikkelsen M, Huddleston DA, et al.: Frequency and Intensity of Premonitory Urges-to-Tic in Tourette Syndrome Is Associated With Supplementary Motor Area GABA+ Levels. Mov. Disord. 2021.\n\nSchubert L, Verrel J, Behm A, et al.: Inter-individual differences in urge-tic associations in Tourette syndrome. Cortex. 2021; 143: 80–91. Publisher Full Text\n\nMorand-Beaulieu S, Wu J, Mayes LC, et al.: Increased Alpha-Band Connectivity During Tic Suppression in Children With Tourette Syndrome Revealed by Source Electroencephalography Analyses. Biol. Psychiatry Cogn. Neurosci. Neuroimaging. 2021. Publisher Full Text\n\nIsaacs DA, Riordan HR, Claassen DO: Clinical Correlates of Health-Related Quality of Life in Adults With Chronic Tic Disorder. Front. Psychiatry. 2021; 12: 619854. PubMed Abstract | Publisher Full Text\n\nSmith BL, Gutierrez R, Ludlow AK: A comparison of food avoidant behaviours and sensory sensitivity in adults with and without Tourette syndrome. Appetite. 2022; 16: 105713. Publisher Full Text\n\nTsetsos F, Yu D, Sul JH, et al.: Synaptic processes and immune-related pathways implicated in Tourette syndrome. Transl. Psychiatry. 2021; 11: 56. PubMed Abstract | Publisher Full Text\n\nYang Z, Wu H, Lee PH, et al.: Investigating Shared Genetic Basis Across Tourette Syndrome and Comorbid Neurodevelopmental Disorders Along the Impulsivity-Compulsivity Spectrum. Biol. Psychiatry. 2021; 90: 317–327. PubMed Abstract | Publisher Full Text\n\nHalvorsen M, Szatkiewicz J, Mudgal P, et al.: Elevated common variant genetic risk for Tourette syndrome in a densely-affected pedigree. Mol. Psychiatry. 2021; 26: 7522–7529. PubMed Abstract | Publisher Full Text\n\nJones HF, Han VX, Patel S, et al.: Maternal autoimmunity and inflammation are associated with childhood tics and obsessive-compulsive disorder: Transcriptomic data show common enriched innate immune pathways. Brain Behav. Immun. 2021; 94: 308–317. PubMed Abstract | Publisher Full Text\n\nHan VX, Patel S, Jones HF, et al.: Maternal immune activation and neuroinflammation in human neurodevelopmental disorders. Nat. Rev. Neurol. 2021; 17: 564–579. PubMed Abstract | Publisher Full Text\n\nHan VX, Patel S, Jones HF, et al.: Maternal acute and chronic inflammation in pregnancy is associated with common neurodevelopmental disorders: a systematic review. Transl. Psychiatry. 2021; 11: 71. PubMed Abstract | Publisher Full Text\n\nHildonen M, Levy AM, Hansen CS, et al.: EWAS of Monozygotic Twins Implicate a Role of mTOR Pathway in Pathogenesis of Tic Spectrum Disorder. Genes (Basel). 2021; 12. PubMed Abstract | Publisher Full Text\n\nMartino D, Schrag A, Anastasiou Z, et al.: Association of Group A Streptococcus Exposure and Exacerbations of Chronic Tic Disorders: A Multinational Prospective Cohort Study. Neurology. 2021; 96: e1680–e1693. PubMed Abstract | Publisher Full Text\n\nGilbert DL: Inflammation in Tic Disorders and Obsessive-Compulsive Disorder: Are PANS and PANDAS a Path Forward?. J. Child Neurol. 2019; 34: 598–611. PubMed Abstract | Publisher Full Text\n\nAyubi E, Mansori K, Doosti-Irani A: Effect of maternal smoking during pregnancy on Tourette syndrome and chronic tic disorders among offspring: a systematic review and meta-analysis. Obstet Gynecol Sci. 2021; 64: 1–12. Publisher Full Text\n\nMcVige JW, Fritz CL, Mechtler LL: Mass psychogenic illness in Leroy High School, New York. Ann. Neurol. 2012; 72: S192.\n\nMink JW: Conversion disorder and mass psychogenic illness in child neurology. Ann. N. Y. Acad. Sci. 2013; 1304: 40–44. PubMed Abstract | Publisher Full Text\n\nMüller-Vahl KR, Roessner V, Münchau A: Tourette-Syndrom: Häufig eine Fehldiagnose [Tourette Syndrome: Often a misdiagnosis]. Dtsch Arztebl. 2020; 117: A332–A333.Reference Source\n\nHeyman I, Liang H, Hedderly T: COVID-19 related increase in childhood tics and tic-like attacks. Arch. Dis. Child. 2021; 106: 420–421. PubMed Abstract | Publisher Full Text\n\nZea Vera A, Bruce A, Garris J, et al.: The phenomenology of tics and tic-like behavior in TikTok. medRxiv. 2021; 2021.09.08.21263218. Publisher Full Text\n\nPaulus T, Bäumer T, Verrel J, et al.: Pandemic Tic-like Behaviors Following Social Media Consumption. Mov. Disord. 2021; 36: 2932–2935. PubMed Abstract | Publisher Full Text\n\nPringsheim T, Ganos C, McGuire JF, et al.: Rapid Onset Functional Tic-Like Behaviors in Young Females During the COVID-19 Pandemic. Mov. Disord. 2021; 36: 2707–2713. Publisher Full Text\n\nAnderson S, Bennett S, Black KJ, et al.: Rising incidence of functional tic-like behaviors: What’s happening? Why now? 2021.Reference Source\n\nHedderly T, Heyman I, Ganos C, et al.: Functional tics.2021.Reference Source\n\nCadeddu R, Knutson DE, Mosher LJ, et al.: The α6 GABA_A Receptor Positive Allosteric Modulator DK-I-56-1 Reduces Tic-Related Behaviors in Mouse Models of Tourette Syndrome. Biomolecules. 2021; 11. PubMed Abstract | Publisher Full Text\n\nVinner E, Belelovsky K, Bar-Gad I: Generating Acute and Chronic Experimental Models of Motor Tic Expression in Rats. J. Vis. Exp. 2021. PubMed Abstract | Publisher Full Text\n\nMielke E, Takacs A, Kleimaker M, et al.: Tourette syndrome as a motor disorder revisited - Evidence from action coding. Neuroimage Clin. 2021; 30: 102611. PubMed Abstract | Publisher Full Text\n\nJurgiel J, Miyakoshi M, Dillon A, et al.: Inhibitory control in children with tic disorder: aberrant fronto-parietal network activity and connectivity. Brain Commun. 2021; 3: fcab067. PubMed Abstract | Publisher Full Text\n\nMorera MB, Jackson GM, Jackson SR: Examining the neural antecedents of tics in Tourette syndrome using electroencephalography. J. Neuropsychol. 2021.\n\nAdelhöfer N, Paulus T, Mückschel M, et al.: Increased scale-free and aperiodic neural activity during sensorimotor integration-a novel facet in Tourette syndrome. Brain Commun. 2021; 3: fcab250. PubMed Abstract | Publisher Full Text\n\nBellato A, Norman L, Idrees I, et al.: A systematic review and meta-analysis of altered electrophysiological markers of performance monitoring in Obsessive-Compulsive Disorder (OCD), Gilles de la Tourette Syndrome (GTS), Attention-Deficit/Hyperactivity disorder (ADHD) and Autism. Neurosci. Biobehav. Rev. 2021; 131: 964–987. PubMed Abstract | Publisher Full Text\n\nWen F, Yan J, Yu L, et al.: Grey matter abnormalities in Tourette syndrome: an activation likelihood estimation meta-analysis. BMC Psychiatry. 2021; 21: 184. PubMed Abstract | Publisher Full Text\n\nWan X, Zhang S, Wang W, et al.: Gray matter abnormalities in Tourette Syndrome: a meta-analysis of voxel-based morphometry studies. Transl. Psychiatry. 2021; 11: 287. PubMed Abstract | Publisher Full Text\n\nJackson SR, Sigurdsson HP, Dyke K, et al.: The role of the cingulate cortex in the generation of motor tics and the experience of the premonitory urge-to-tic in Tourette syndrome. J. Neuropsychol. 2021; 15: 340–362. PubMed Abstract | Publisher Full Text\n\nZito GA, Hartmann A, Béranger B, et al.: Multivariate classification provides a neural signature of Tourette disorder. Psychol. Med. 2021: 1–9. PubMed Abstract | Publisher Full Text\n\nNielsen AN, Gratton C, Church JA, et al.: Atypical functional connectivity in Tourette syndrome differs between children and adults. Biol. Psychiatry. 2020; 87: 164–173. PubMed Abstract | Publisher Full Text\n\nBhikram T, Crawley A, Arnold P, et al.: Neuroimaging the emotional modulation of urge inhibition in Tourette Syndrome. Cortex. 2021; 135: 341–351. PubMed Abstract | Publisher Full Text\n\nAtkinson-Clement C, de LA, Klein Y, et al.: The sooner the better: clinical and neural correlates of impulsive choice in Tourette disorder. Transl. Psychiatry. 2021; 11: 560. PubMed Abstract | Publisher Full Text\n\nSturm A, Ricketts EJ, McGuire JF, et al.: Inhibitory control in youth with Tourette’s Disorder, attention-deficit/hyperactivity disorder and their combination and predictors of objective tic suppressibility. Psychiatry Res. 2021; 304: 114163. PubMed Abstract | Publisher Full Text\n\nMorand-Beaulieu S, Grot S, Lavoie J, et al.: The puzzling question of inhibitory control in Tourette syndrome: A meta-analysis. Neurosci. Biobehav. Rev. 2017; 80: 240–262. PubMed Abstract | Publisher Full Text\n\nHimle MB, Woods DW: An experimental evaluation of tic suppression and the tic rebound effect. Behav. Res. Ther. 2005; 43: 1443–1451. PubMed Abstract | Publisher Full Text\n\nHaas M, Jakubovski E, Fremer C, et al.: Yale Global Tic Severity Scale (YGTSS): Psychometric Quality of the Gold Standard for Tic Assessment Based on the Large-Scale EMTICS Study. Front Psychiatry. 2021; 12: 626459. PubMed Abstract | Publisher Full Text\n\nWen F, Gu Y, Yan J, et al.: Revisiting the structure of the Yale Global Tic Severity Scale (YGTSS) in a sample of Chinese children with tic disorders. BMC Psychiatry. 2021; 21. Publisher Full Text\n\nLi Y, Woods DW, Gu Y, et al.: Psychometric Properties of the Chinese Version of the Premonitory Urge for Tics Scale: A Preliminary Report. Front. Psychol. 2021; 12: 573803. PubMed Abstract | Publisher Full Text\n\nEriguchi Y, Aoki N, Kano Y, et al.: Rotational plane-wise analysis of angular movement of neck motor tics in Tourette’s syndrome. Prog. Neuro-Psychopharmacol. Biol. Psychiatry. 2021; 108: 110092. PubMed Abstract | Publisher Full Text\n\nCernera S, Pramanik L, Boogaart Z, et al.: The Human Tic Detector: An automatic approach to tic characterization using wearable sensors. Clin. Neurophysiol. 2022; 134: 102–110. PubMed Abstract | Publisher Full Text\n\nWu J, Zhou T, Guo Y, et al.: Tic Detection in Tourette Syndrome Patients Based on Unsupervised Visual Feature Learning. J. Healthc. Eng. 2021; 2021: 1–10. Publisher Full Text\n\nPringsheim T, Okun MS, Müller-Vahl K, et al.: Practice guideline recommendations summary: Treatment of tics in people with Tourette syndrome and chronic tic disorders. Neurology. 2019; 92: 896–906. PubMed Abstract | Publisher Full Text\n\nAndrén P, Jakubovski E, Murphy TL, et al.: European clinical guidelines for Tourette syndrome and other tic disorders-version 2.0. Part II: psychological interventions. Eur. Child Adolesc. Psychiatry. 2022; 31: 403–423. Publisher Full Text\n\nHollis C, Hall CL, Jones R, et al.: Therapist-supported online remote behavioural intervention for tics in children and adolescents in England (ORBIT): a multicentre, parallel group, single-blind, randomised controlled trial. Lancet Psychiatry. 2021; 8: 871–882. PubMed Abstract | Publisher Full Text\n\nAndrén P, Aspvall K, Fernández de la CL, et al.: Therapist-guided and parent-guided internet-delivered behaviour therapy for paediatric Tourette’s disorder: a pilot randomised controlled trial with long-term follow-up. BMJ Open. 2019; 9: e024685. PubMed Abstract | Publisher Full Text\n\nAndrén P, de la CLF, Isomura K, et al.: Efficacy and cost-effectiveness of therapist-guided internet-delivered behaviour therapy for children and adolescents with Tourette syndrome: study protocol for a single-blind randomised controlled trial. Trials. 2021; 22: 669. PubMed Abstract | Publisher Full Text\n\nHaas M, Jakubovski E, Kunert K, et al.: ONLINE-TICS: Internet-Delivered Behavioral Treatment for Patients with Chronic Tic Disorders. J. Clin. Med. 2022; 11. PubMed Abstract | Publisher Full Text\n\nViefhaus P, Adam J, Goletz H, et al.: Implementation and Evaluation of Therapeutic Online Coaching Using Habit Reversal Training in Children With Tourette’s Disorder - A Pilot Study. Front. Psychol. 2021; 12: 780539. PubMed Abstract | Publisher Full Text\n\nReese HE, Brown WA, Summers BJ, et al.: Feasibility and acceptability of an online mindfulness-based group intervention for adults with tic disorders. Pilot Feasibility Stud. 2021; 7: 82. PubMed Abstract | Publisher Full Text\n\nZimmerman-Brenner S, Pilowsky-Peleg T, Rachamim L, et al.: Group behavioral interventions for tics and comorbid symptoms in children with chronic tic disorders. Eur. Child Adolesc. Psychiatry. 2022; 31: 637–648. Publisher Full Text\n\nPeterson AL, Blount TH, Villarreal R, et al.: Relaxation training with and without Comprehensive Behavioral Intervention for Tics for Tourette’s disorder: A multiple baseline across participants consecutive case series. J. Behav. Ther. Exp. Psychiatry. 2022; 74: 101692. PubMed Abstract | Publisher Full Text\n\nEspil FM, Woods DW, Specht MW, et al.: Long-term Outcomes of Behavior Therapy for Youth With Tourette Disorder. J. Am. Acad. Child Adolesc. Psychiatry. 2022; 61: 764–771. Publisher Full Text\n\nPiacentini J, Woods DW, Scahill L, et al.: Behavior therapy for children with Tourette disorder: a randomized controlled trial. JAMA. 2010; 303: 1929–1937. PubMed Abstract | Publisher Full Text\n\nWilhelm S, Peterson AL, Piacentini J, et al.: Randomized trial of behavior therapy for adults with Tourette syndrome. Arch. Gen. Psychiatry. 2012; 69: 795–803. PubMed Abstract | Publisher Full Text\n\nEssoe JK, Ricketts EJ, Ramsey KA, et al.: Homework adherence predicts therapeutic improvement from behavior therapy in Tourette’s disorder. Behav. Res. Ther. 2021; 140: 103844. PubMed Abstract | Publisher Full Text\n\nEssoe JK-Y, Ramsey KA, Singer HS, et al.: Mechanisms Underlying Behavior Therapy for Tourette’s Disorder. Curr. Dev. Disord. Rep. 2021; 8: 161–174. Publisher Full Text\n\nRoessner V, Eichele H, Stern JS, et al.: European clinical guidelines for Tourette syndrome and other tic disorders-version 2.0. Part III: pharmacological treatment. Eur. Child Adolesc. Psychiatry. 2022; 31: 425–441. Publisher Full Text\n\nCoffey B, Jankovic J, Claassen DO, et al.: Efficacy and Safety of Fixed-Dose Deutetrabenazine in Children and Adolescents for Tics Associated With Tourette Syndrome: A Randomized Clinical Trial. JAMA Netw. Open. 2021; 4: e2129397. PubMed Abstract | Publisher Full Text\n\nJankovic J, Coffey B, Claassen DO, et al.: Safety and Efficacy of Flexible-Dose Deutetrabenazine in Children and Adolescents With Tourette Syndrome: A Randomized Clinical Trial. JAMA Netw. Open. 2021; 4: e2128204. PubMed Abstract | Publisher Full Text\n\nFarber RH, Angelov A, Kim K, et al.: Clinical development of valbenazine for tics associated with Tourette syndrome. Expert. Rev. Neurother. 2021; 21: 393–404. PubMed Abstract | Publisher Full Text\n\nColizzi M, Bortoletto R, Zoccante L: The Effectiveness of Lurasidone Add-On for Residual Aggressive Behavior and Obsessive Symptoms in Antipsychotic-Treated Children and Adolescents with Tourette Syndrome: Preliminary Evidence from a Case Series. Children (Basel). 2021; 8. Publisher Full Text\n\nMüller-Vahl KR, Fremer C, Beals C, et al.: Monoacylglycerol Lipase Inhibition in Tourette Syndrome: A 12-Week, Randomized. Mov. Disord. Clin. Pract. 2021; 36: 2413–2418. PubMed Abstract | Publisher Full Text\n\nBloch MH, Landeros-Weisenberger A, Johnson JA, et al.: A Phase-2 Pilot Study of a Therapeutic Combination of Δ9-Tetrahydracannabinol and Palmitoylethanolamide for Adults With Tourette’s Syndrome. J. Neuropsychiatry Clin. Neurosci. 2021; 33: 328–336. PubMed Abstract | Publisher Full Text\n\nBillnitzer A, Jankovic J: Pilot Study to Evaluate Pimavanserin for the Treatment of Motor and Behavioral Symptoms of Tourette Syndrome. Mov. Disord. Clin. Pract. 2021; 8: 694–700. PubMed Abstract | Publisher Full Text\n\nSzejko N, Worbe Y, Hartmann A, et al.: European clinical guidelines for Tourette syndrome and other tic disorders-version 2.0. Part IV: deep brain stimulation. Eur. Child Adolesc. Psychiatry. 2022; 31: 443–461. Publisher Full Text\n\nMartino D, Deeb W, Jimenez-Shahed J, et al.: The 5 Pillars in Tourette Syndrome Deep Brain Stimulation Patient Selection: Present and Future. Neurology. 2021; 96: 664–676. PubMed Abstract | Publisher Full Text\n\nBaldermann JC, Kuhn J, Schüller T, et al.: Thalamic deep brain stimulation for Tourette Syndrome: A naturalistic trial with brief randomized, double-blinded sham-controlled periods. Brain Stimul. 2021; 14: 1059–1067. PubMed Abstract | Publisher Full Text\n\nMüller-Vahl KR, Szejko N, Saryyeva A, et al.: Randomized double-blind sham-controlled trial of thalamic versus GPi stimulation in patients with severe medically refractory Gilles de la Tourette syndrome. Brain Stimul. 2021; 14: 662–675. PubMed Abstract | Publisher Full Text\n\nMacLean JA, Ferman D, Chu JK, et al.: Transient Complete Resolution of Tourette Syndrome Symptoms Following Personalized Depth Electrode Placement. Brain Sci. 2021; 11. PubMed Abstract | Publisher Full Text\n\nJohnson KA, Duffley G, Foltynie T, et al.: Basal Ganglia Pathways Associated With Therapeutic Pallidal Deep Brain Stimulation for Tourette Syndrome. Biol. Psychiatry Cogn. Neurosci. Neuroimaging. 2021; 6: 961–972. PubMed Abstract | Publisher Full Text\n\nAminzade Z, Fateh ST, Khoshnoud RJ, et al.: Deep brain stimulation of anteromedial globus pallidus internus improved OCD rather than tics in a Gilles de la Tourette syndrome patient. Clinical Case Reports. 2021; 9: e05204. PubMed Abstract | Publisher Full Text\n\nAcevedo N, Bosanac P, Pikoos T, et al.: Therapeutic Neurostimulation in Obsessive-Compulsive and Related Disorders. Brain Sci. 2021; 11. Publisher Full Text\n\nCamprodon JA, Chou T, Testo AA, et al.: Case Report: Deep Brain Stimulation to the Ventral Internal Capsule/Ventral Striatum Induces Repeated Transient Episodes of Voltage-Dependent Tourette-Like Behaviors. Front. Hum. Neurosci. 2021; 14: 590379. PubMed Abstract | Publisher Full Text\n\nDyke K, Jackson G, Jackson S: Non-invasive brain stimulation as therapy: systematic review and recommendations with a focus on the treatment of Tourette syndrome. Exp. Brain Res. 2022; 240: 341–363. Publisher Full Text\n\nJannati A, Ryan MA, Kaye HL, et al.: Biomarkers Obtained by Transcranial Magnetic Stimulation in Neurodevelopmental Disorders. J. Clin. Neurophysiol. 2022; 39: 135–148. Publisher Full Text\n\nBruce AB, Yuan W, Gilbert DL, et al.: Altered frontal-mediated inhibition and white matter connectivity in pediatric chronic tic disorders. Exp. Brain Res. 2021; 239: 955–965. PubMed Abstract | Publisher Full Text\n\nFu M, Wei H, Meng X, et al.: Effects of Low-Frequency Repetitive Transcranial Magnetic Stimulation of the Bilateral Parietal Cortex in Patients With Tourette Syndrome. Front. Neurol. 2021; 12: 602830. PubMed Abstract | Publisher Full Text\n\nKahl CK, Kirton A, Pringsheim T, et al.: Bilateral transcranial magnetic stimulation of the supplementary motor area in children with Tourette syndrome. Dev. Med. Child Neurol. 2021; 63: 808–815. PubMed Abstract | Publisher Full Text\n\nMartino D, Malaty I, Müller-Vahl K, et al.: Treatment failure in persistent tic disorders: an expert clinicians’ consensus-based definition. Eur. Child Adolesc. Psychiatry. 2021. PubMed Abstract | Publisher Full Text\n\nGanos C, Sarva H, Kurvits L, et al.: Clinical Practice Patterns in Tic Disorders Among Movement Disorder Society Members. Tremor Other Hyperkinet Mov. (N Y). 2021; 11: 43. PubMed Abstract | Publisher Full Text\n\nHartmann A, Szejko N, Mol DN, et al.: Is Tourette syndrome a rare condition? F1000Res. 2021; 10: 434. Publisher Full Text\n\nBhikram T, Elmaghraby R, Abi-Jaoude E, et al.: An International Survey of Health Care Services Available to Patients With Tourette Syndrome. Front Psychiatry. 2021; 12: 621874. PubMed Abstract | Publisher Full Text\n\nFletcher J, Dimitropoulos G, Martino D, et al.: Developing a provincial patient support network for children and families affected by Tourette syndrome and/or obsessive-compulsive disorder: results of a stakeholder consultation. Child Adolesc. Psychiatry Ment. Health. 2021; 15: 29. PubMed Abstract | Publisher Full Text\n\nLee MY, Wang HS, Lee TY: Psychosocial stress, self-esteem, and social adjustment: A moderated mediation analysis in Taiwanese adolescents with Tourette syndrome. J. Pediatr. Nurs. 2022; 62: e84–e90. PubMed Abstract | Publisher Full Text\n\nSolís-García G, Jové-Blanco A, Chacón-Pascual A, et al.: Quality of life and psychiatric comorbidities in pediatric patients with Gilles de la Tourette syndrome. Rev. Neurol. 2021; 73: 339–344. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "142613",
"date": "18 Jul 2022",
"name": "Daniel Alvarez-Fischer",
"expertise": [
"Reviewer Expertise Tourette's",
"Autism",
"and ADHD"
],
"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 provide a good overview of the current literature. This annual summary of the current scientific literature is an important milestone for people active in Tourette's research and treatment to keep themselves informed.\nThe selection of literature is presented clearly and understandably. Perhaps the categories into which the selected literature is placed could also be presented in an overview at the beginning. Such a list would make reading even more straightforward. The authors mention that they have also integrated congress contributions. A list of the selected congresses would be desirable.\nThere is an interesting graph at the end of the review about the increasing number of annual publications in the field. Probably the number of publications is still too small; if not, a map from which countries how many publications come, and from which countries how many publications are taken into account (e.g., by the size and color of dots on a map) would be an interesting, but not necessary information for the publication.\nThe present manuscript is a very successful work that merits indexing in this form.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "8696",
"date": "01 Nov 2022",
"name": "Andreas Hartmann",
"role": "Author Response",
"response": "We thank Dr Alvarez-Fischer for his kind comments on our manuscript. The figure was a labor of love by Dr Black and adding geographic information is beyond what we can offer, at least this year. We agree, however, that this information might be of interest!"
}
]
},
{
"id": "142616",
"date": "25 Jul 2022",
"name": "Erica L. Greenberg",
"expertise": [
"Reviewer Expertise Tourette syndrome and co-occurring related disorders",
"including OCD. Child and adolescent psychiatry."
],
"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 comprehensive review of the 2021 literature covering Tourette syndrome (TS) and related disorders. The authors did a wonderful job presenting a thorough, detailed, yet succinct summary of an enormous number of new, important articles in the field. I appreciated that they showed the growth of research in TS over the last forty years, and are open to creative ways to make sure they have access to the likely even larger 2022 literature base. They covered a range of topics, broken down in effective sections, including Phenomenology and Natural History, Pathophysiology, Electrophysiology, Treatment, each with its own appropriate subsections. The authors presented the brief summaries of the literature clearly, and without bias.\n\nI only have a few comments/recommended adjustments that I would suggest the authors consider following up on.\nUnder Epidemiology, starting \"The controversial topic of cognitive...\" - it would help if the authors add a sentence clarifying why that phenomena is not considered OCD/intrusive thoughts.\n\nUnder Comorbidity, starting \"A very interesting study...\" - I would recommend either eliminating that or expanding on it, as the findings are quite provocative, and given the sample size was so small, I worry about it being given more attention than warranted without further studies to validate (and/or without commenting on co-occurring conditions that may also influence moral reasoning).\n\nUnder Premonitory Urge and Tic Suppression, starting \"Another study, by He...\" - I would make that a new paragraph\n\nUnder Environmental Risk Factors, starting \"This year brought,\" I would recommend condensing the paragraph to make it more in line with the other summaries, particularly related to citations 46 and 47. Given that they were small studies, particularly 47, I would recommend not listing all the findings/differences (particularly as I wonder about multiple comparisons in that study..). Related, I would soften the sentence saying \"meaning that almost none of these patients' presentations even slightly resembled TS to these clinicians\" as it sounds more subjective/intense than the rest of the paper. And I would soften the language in the paragraph starting \"One concern...\" as again, it read as more subjective/opinion-driven than the rest of the manuscript.\n\nIn the paragraph starting, \"Sturm and colleagues...\" I believe the heading above it is incorrect.\n\nUnder Tic Assessment, starting \"Many studies have focused...\" it would help to clarify the last sentence starting, \"Interesting vocal tics...\" Without more context, it is difficult to understand why vocal tics not predicting TS diagnosis might challenge the validity of diagnostic TS criteria vs challenge the validity of the SVM (support vector machine)?\n\nUnder Treatment Psychological interventions, starting \"Several research groups...\" - it would help to spell out what the acronym BIP means\n\nIn the figure depicting the increase in TS related literature over time, it looks like the legend is flipped\n\nIn Conclusions, I wonder if the authors mean to say \"Additionally\" rather than \"On the other hand.\"\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "8697",
"date": "01 Nov 2022",
"name": "Andreas Hartmann",
"role": "Author Response",
"response": "We thank Dr Greenberg for her positive evaluation of our manuscript and her helpful comments. We have incorporated nearly all comments except the passages on FND which we did shorten only marginally. Because many readers will not be familiar with the clinical presentation of these patients, a bit more detail seemed appropriate to us even if the case numbers were small. However, we agree that in the absence of larger studies and harder data (coming up in 2022, hopefully!), much is opinion-driven at this stage. Also, we do not know what the BIP in BIP TIC stands for, it is an abbreviation that has been used by the Karolinska group from the beginning and might actually be Swedish. Finally, we believe the figure legend to be adequate."
}
]
}
] | 1
|
https://f1000research.com/articles/11-716
|
https://f1000research.com/articles/11-1240/v1
|
01 Nov 22
|
{
"type": "Research Article",
"title": "Effect of problem-based learning on students’ attitude towards learning physics: a cohort study",
"authors": [
"Stella T. Kanyesigye",
"Jean Uwamahoro",
"Imelda Kemeza",
"Jean Uwamahoro",
"Imelda Kemeza"
],
"abstract": "Background: Attitude is a learning scale that informs which approach should be used to call students to school. It can be seen a supporting tool that informs teachers, policymakers, and researchers of the needs for raising interest in learning a certain subject, such as physics. This study aimed at determining the effect of problem-based learning on students’ attitude towards learning physics. Methods: The study followed a quantitative approach with a quasi-experimental design employing cross-sectional survey techniques. The participants of the study were 419 13th-grade physics students of the 2020/2021 school year in both Ugandan government and private secondary schools. Among these students, one group was taught using problem-based learning instruction while another group was taught using traditional instruction for 12 weeks. Data were collected using a standardized tool called Views About Science Survey. Using Microsoft Excel 2016 and Statistical Package for Social Scientist version 23.0, descriptive and inferential statistics were used to determine a significant difference between experiment and control groups. Results: It was found that both problem-based learning and traditional instructions caused a statistically significant positive effect on students’ attitudes towards physics. However, the experimental group gained more positive attitude than the control group as they were more inclined towards the expert-like attitude (thinking like a scientist in a domain) than their counterparts due to the problem-based learning approach they learned in. Conclusions: Therefore, it was concluded that problem-based learning is a more effective method of teaching physics than traditional methods. Hence, we suggest that secondary school teachers need to adopt the use of problem-based learning in the teaching of science concepts, especially physics.",
"keywords": [
"problem-based learning",
"teaching instruction",
"attitude",
"physics",
"expert-like attitude"
],
"content": "Introduction\n\nThe world is presently faced with the challenge of getting graduates who possess the knowledge and skills required to solve difficult problems, gather and evaluate evidence, and interpret information received from various sources (U.S. Department of Education Office of Innovation and Improvement, 2016). Learning and practicing science, technology, engineering, and mathematics (STEM) helps students gain these skills, which they use to understand the world around them and be curious in nature (Andiema, 2016). STEM education enables students to gain knowledge and skills through solving problems from a multidisciplinary point of view and provides them with opportunities to obtain 21st-century skills to specialize in related fields (Saraç, 2018) for their career endeavors. However, these graduates are reluctant to follow STEM subjects; others cannot deliver what is expected from their expertise due to the low interest they possess (Gunel et al., 2007; Ndihokubwayo et al., 2021; Nyirahabimana, 2022).\n\nWe need to encourage our students to think scientifically or become expert physicists (Madsen et al., 2020). Scientific thinking is a type of information seeking that involves purposeful information seeking, including asking questions, testing hypotheses, making observations, recognizing patterns, and drawing conclusions. Various researchers (Halloun & Hestenes, 1996b; Madsen et al., 2020; Phillips & O’donnell, 2021; Stephens & Clement, 2010) involved in physics education research (PER) have undertaken studies of expert-like and novice-like problem-solving and attitude strategies. For instance, Phillips and O’donnell (2021) identified “expert approaches” as those possessed by physics PhDs and “novices” as introductory physics students. Thus, expert-like attitude is to perceive and think systematically and like a physicist. On other hand, folks-like attitudes are possessed by people with general and insufficient knowledge of physics. One of the earliest documenting instruments of such attitudes is the Views About Science Survey (VASS), which sought to distinguish between “expert” and “folk” views of physics (Halloun, 1996; Phillips & O’donnell, 2021). The relative importance of the scientific thinking of experts and students is debatable because some teachers prefer to stress the importance of propositional thinking, while others believe that pictorial processes using the imagination are just as important as propositional knowledge (Stephens & Clement, 2010).\n\nTeacher-centered methods, commonly referred to as traditional or conventional instruction, allow the teacher to retain full control of the classroom and its activities (Mpho, 2018) while students remain passive recipients of knowledge (Karamustafaoglu, 2009). According to Hill (2002), an example of traditional instruction includes direct instruction/chalk and talk, which describes various whole-class expository teaching techniques. In this instruction, the teacher is an information provider, decides the content to be taught, does not motivate or encourage learners, and gives low facilitation; the learners, on the other hand, are lowly participating, have insignificant initiatives, are passive in the classroom interaction, and only respond to the teachers’ questions (Nzeyimana & Ndihokubwayo, 2019). Teachers who employ this approach concentrate on the content of teaching and what they do in teaching by focusing on organizing, structuring, and presenting the course content in a way that is easier for the students to understand (Sari et al., 2006).\n\nOne of the most targeted practices in STEM education has been to improve the social aspects of learners, including attitude (Nite et al., 2015). Attitude is someone’s feeling, opinion, or behavior towards something. According to Arman (2018), attitude is a tendency to behave in a particular way; it is an internal state that influences students’ choices or decisions to act under certain conditions. Thus, in this study, we define attitude towards physics as the feeling, beliefs, and values possessed by students towards the subject conveyed in the form of like or dislike; and positive or negative reactions towards physics concepts. A positive attitude creates a positive identity, improves one’s health, creates possibilities, and makes one win friends; people with a positive attitude tend to be goal achievers, enjoy success, and seem to be happy by choice despite their circumstances; while people with negative attitude tend to drift through life complaining that nothing good ever happens; everything looks bad to them, and it becomes terrible (Toler, 2016).\n\nHowever, enrollment of science students into higher institutions has been low partly due to few students opting for science subjects at an advanced level of secondary education (Nannyonjo et al., 2009). Physics knowledge is thought to facilitate students in developing logical skills needed for problem-solving in various dimensions of life they encounter (Eijkelhof & Kortland, 1998). However, students tend to have difficulty understanding physics concepts and solving related problems (Kanyesigye et al., 2022a; Sirait et al., 2017). They look at physics as a challenging subject (Ibrahim, 2019) and as a problematic one (Ryan, 2013; Selçuk, 2010). They also consider the contents of physics to be mere facts and composed of formulas that need memorization, making them possess a negative attitude towards the subject (Mbonyiryivuze, et al., 2021).\n\nReferring to previous research, according to Nite et al. (2015), students’ attitude was found to influence their performance significantly and consequently their decision to major in a STEM field. Olusola and Rotimi (2012) noted that students who have a negative attitude towards sciences, including physics, also tend not to like the subject teachers (Olusola & Rotimi, 2012). Previous researchers such as Mbonyiryivuze et al. (2021); Andiema (2016), and Selçuk (2010) recommended the adoption of interactive pedagogical approaches in the teaching-learning process, including problem-based learning (PBL) instruction (Kanyesigye & Kemeza, 2021) as a way of bringing about a desirable positive change in students’ attitude towards science and physics in particular.\n\nToday’s education system focuses on training students to develop skills that enable them to work in a variety of situations (Ndihokubwayo et al., 2021). Like pragmatists, philosophers of education suggest that people learn by solving and learning from real problems they face in everyday life (Richardson, 2003). Based on these philosophies, PBL was developed from the constructivism school of thought, where learners work themselves to generate new knowledge. PBL is defined as a method of inquiry where students solve difficulties, oddities, qualms, and problems in real life (Dorimana et al., 2021). PBL is one of the powerful teaching methods in reforming science education (Allchin, 2013). The method acknowledges the importance of actively engaging students in their learning. It contextualizes the learning, which contributes both to student motivation and the making of meaning. According to Orozco and Yangco (2016), most of the students involved in PBL can share their opinions with others, use different approaches to analyze situations, and explore ways of solving problems. Therefore, the present study employs the extended constructivism theory of Albert Bandura’s social learning theory (Bandura, 1985). This theory proposes that new behaviors can be acquired by observing and imitating others (Bandura, 1985). Social learning theory fits our study because, through PBL, students interact with each other to reach a positive outcome. Students cooperatively share ideas (Sibomana et al., 2021) and then find the probable solution from a combined effort.\n\nStudents’ attitude towards learning can affect their success (Sirait et al., 2017). According to Ibrahim (2019), students’ negative attitude towards physics positively corresponds to low student achievement in the subject. Assessing students’ attitude is crucial for adapting to appropriate instruction. Madsen et al., (2020) advised teachers and researchers that improving your students’ attitudes and beliefs about physics helps them more successfully learn physics content and helps develop their ability to think like a physicist. In this regard, research by Nteere, et al., pointed out that the method of instruction employed by a teacher influences students’ attitude towards physics as a subject. However, research on how methods of instruction such as PBL effect the attitudes of students are limited. This study aimed to determine the effect of PBL on students’ attitudes towards physics. Two basic questions guided this study:\n\n1. Does PBL instruction cause a statistically significant effect on students’ attitudes towards physics?\n\n2. How does students’ attitude correlate with their performance scores?\n\n\nMethods\n\nThis study aimed at determining the effect of PBL instruction on students’ attitude towards physics. The study followed a quantitative approach with a quasi-experimental design employing, specifically, a pre-test–post-test control group experimental design following a randomized solomon four group design (Dimitrov & Rumrill, 2003) in which PBL as an intervention was applied on the experimental group while the control group was instructed using traditional instructions as elaborated in the literature review section.\n\nThe study was conducted from January to April 2021 with 419 physics students of the 13th grade (aged between 16 and 21) in Mitooma District-Southwestern Uganda. Selection of participating schools and allocation to the treatment and comparison groups were based on simple random sampling. Cluster sampling technique (Creswell, 2014) was employed in this study where intact classes were used as units of analysis. 19 classes from 19 schools were employed. The number of students in each school can be found in our data article (Kanyesigye et al., 2022b). For instance, the sample of female students in the pre- and post-test groups was 53, while the sample of male students in the experimental group was 79. In the control group, there were 39 female students and 68 male students. Similarly, the sample of public-school students was 39 in the pre-test and post-test, while the sample of private school students was 92 in the experimental group. There were also 55 students in public school and 51 students in private school included in the control group. The population and sample sizes used in this study were taken at a 95% confidence interval in accordance with Morgan (2006). All secondary schools in Mitooma district are both day and boarding, with only two single girls’ schools. Thus, all schools included are day and boarding schools. Note that there was no exclusion criteria.\n\nA two-day, six-hour professional training was organized on 10th and 11th January 2021 at Ruhinda Secondary School-Mitooma district and was attended by 30 physics teachers from Mitooma district in Southwestern Uganda. This training was designed as part of the study (Kanyesigye et al., 2022d). The participants were invited to the training depending on their teaching subject (physics) in Mitooma district. The main purpose of the professional training was to enhance secondary school in-service physics teachers’ knowledge of PBL and was guided by the following objectives:\n\n1. To provide background information on the origin and importance of PBL\n\n2. To provide skills on generating PBL questions\n\n3. To provide skills on the presentation of a PBL lesson\n\n4. To provide knowledge on the assessment of a PBL lesson\n\nParticipants were split into groups of five. The trainer for the Secondary Science and Mathematics (SESEMAT) program in the western region of Uganda and the first author served as facilitators for the formed groups. The SESEMAT trainer is one of the experts in Uganda that were first trained in the implementation of competence-based curriculum and appointed at the regional level by the government to train other teachers. As such, during the proposal development and development of the training content, this expert played a big role. So, inviting him to facilitate the training was based on his expertise and the fact that he had participated in the material development and validation of this study research instrument. The first author is a national examiner of physics. During proposal development, the author consulted the physics teachers (participants of this study) on which topics in physics generally posed greater challenges to students. Among other topics, the topic of waves was pointed out based on the generally poor performance of students in wave concepts and the fact that questions on wave concepts are also mostly dodged. So, the author took up the topic of waves for the PhD project. The roles for the participants and the training leader were defined at the start of the training. In formulating PBL questions, the topic of waves was selected as agreed prior to the course upon by majority of the participants, using direct messaging (WhatsApp) with the first author, in the training based on possession of prior knowledge. The aim of the training, was to provide the participants with the ability to draft real-life-based problems on the concepts of waves using online resources and textbooks.\n\nAll activities were carried out throughout the study during normal class hours (four hours per week for four weeks). Before starting the experimentation, a pre-test was administered to both experimental and control groups in the first week — 10 physics teachers who handled the experimentation group first trained students about PBL strategies before starting the experiment. Experimental-1 (pre- and post-test design) accommodated 132 students, experimental-2 (post-test only design) accommodated 99 students, control-1 (pre- and post-test design) accommodated 107 students, and control-2 (post-test only design) accommodated 81 students. During the implementation, the teachers of the experimental groups in each lesson would purposively divide students into five to six-member groups, and each group would be presented a problem to research and after make a presentation to the whole class under the guidance of their respective teachers. This implementation was monitored at all levels by the researchers. Each group member, in one way or the other, had a responsibility to fulfill. The members were required to participate during the group discussions actively. Members in their groups were required to share their knowledge, ideas, and experiences about the solution of the given problem. Before group discussion, each member was expected to make individual study and be able to represent, communicate and evaluate and assess their learning either individually or at group level. In case of need for guidance, the teacher would pose open-ended general questions for students to think about critically. Students would, at the end of each activity, evaluate each other in relation to participation, preparation, interpersonal skills contribution to the progress of the group.\n\nOn the other hand, students in the control group were instructed (under supervision from the researchers) using traditional approaches where the teachers copied notes either from textbooks or from their notebooks and dictated them to students to write down in their notebooks. A few teachers would write about one or two problems on the chalkboard and again solve them as students watched. They would thereafter be referring the students to either textbooks and/past-papers for trial questions, and students’ solutions were hardly harmonized. The exercise lasted for twelve weeks, after which a post-test similar to the pre-test was administered to the participating students. Note that a researcher was present for all lessons across all groups. This was possible because different schools taught the topic of waves at different periods in the term. So, throughout the whole period of data collection, the authors were in the field. The notes from these observations can be found at Kanyesigye et al. (2022c).\n\nData was collected using the Views About Science Survey (VASS) developed by Ibrahim Halloun (Halloun, 1996; Halloun & Hestenes, 1996a, 1996b) focused on attitude. “Attitudes and beliefs surveys that are commonly used in physics courses (such as VASS) are about how students perceive the discipline of physics or their particular physics course” (Madsen et al., 2020, p.90). This tool is a valid and reliable tool to fit our research objectives and has two versions, P20, and P05.07 (Halloun & Hestenes, 1996b). We used the current P05.07 version accessible from the PhysPort website. This version contains 33 items that measure students learning outcome before and after covering a certain content. VASS is not multiple-choice1, items are formulated based on Halloun’s Contrasting Alternatives rating scale (Cars) and done in 40 minutes. Items are rated on a 5-point scale and each scale an ‘a’ revealing negative attitude and a ‘b’ statement revealing a positive attitude (see Figure 1). The first scale (a) >> (b) means mostly (a), rarely (b); the second scale (a) > (b) means more (a) than (b); the third scale (a) = (b) means equally (a) and (b); the fourth scale (b) > (a) means more (b) than (a); and the fifth scale (b) >> (a) means mostly (b), rarely (a).\n\nTo ensure content validity of the study instruments, the instrument was presented to four research experts before its adoption to ensure that it matched the problem under investigation as recommended by scores (Gay, Mills & Airasian, 2012; Samsudin et al., 2019). The experts were selected from Secondary Science and Mathematics Teachers (SESEMAT) association in Uganda, and from the department of science education in the University of Rwanda College of Education and Mbarara University of Science and Technology and were requested to indicate whether the items were relevant to the problem under investigation. After collecting their opinions on every item, the content validity ratio (C.V.R) for each item was calculated based on the formula by Lawshe (1975):\n\nIn this study (N = 4 and ne = 3), when the C.V.R. values for all items were averaged, the items with the CVR bigger than 0.49 remained, and the Content Validity Index (C.V.I.) was obtained as 0.98. Comparing this value with the critical value of 0.99 (Lawshe, 1975), the difference was considered good hence the instrument was considered valid.\n\nSuppose a research instrument is to be considered reliable. In that case, it must prove that if it were to be used on a similar group of participants under the same conditions, it would still result in similar results (Cohen et al., 2007). Achievement of consistency gives the researcher assurance that the results obtained represent the achievement of the individual participants (Fraenkel et al., 2012). After the survey was accepted for adoption, a pilot study was administered to 42 randomly selected students among the study participants. The internal consistency of the study instrument was determined by computing the Cronbach’s Alpha which gave a 0.73 coefficient, and this value rendered it reliable according to Gliem and Gliem (2003). We have also employed and administered the mechanical waves concept survey (Tongchai et al., 2008), a valid and standard tool available at physport.com for triangulation purpose.\n\nAfter the approval of the proposal, an ethical clearance (Ref: 03/DRI-CE/067/EN/gi/2020) was obtained from research and innovation office, University of Rwanda, College of Education and thereafter an authorisation letter to conduct research in Uganda was given by the permanent secretary, Ministry of Education and Sports – Uganda. A week before the start of data collection, participants first signed written informed consent letters. Participants who were below 18 years were asked to consult their parents and in turn, their parents consented on their behalf. Each participant was given a code and was referred to only by that code. No monetary compensation was given to participants. Participants were free to withdraw from the study at any time without penalty and were also free not to answer any questions or respond to any research situations if they chose so.\n\nIn VASS development, Halloun (1996) classified students’ views or attitude in three profiles; expert, transitional, and folk. We have based our analysis on these distinct categories. The most common way to score these surveys is to collapse students’ responses into two categories depending on whether they are the same as an expert physicist would give (called “percent expert like response” or “percent favorable response”) (Madsen et al., 2020). We used both MS Excel 2016 (Microsoft, 2016) (RRID:SCR_016137) and SPSS 23.0 (IBM Corp, 2015) (RRID:SCR_016479) to analyze data. We computed frequencies of students in each of the VASS categories (1-5) using “countif” function in Excel 2016. We then merged these five categories into three categories. Thus, we averaged the first two categories into folks-like attitude, last two categories into physics expert-like attitude, and the third (middle) category remained as it is and named transitional attitude. We averaged these frequencies across 33 VASS items to make displayable percentages along with the Solomon four groups. We then followed this procedure to compute frequencies across gender and school type. The “shift” in percent favorable responses is calculated by subtracting the pre-test class average percent favorable from the post-test class average percent favorable. This metric tells you how students’ expert-like or favorable beliefs about physics changed from the start to the end of their physics course (Madsen et al., 2020). To measure the correlation between students’ attitude and performance, we computed and compared the average scores of mechanical waves conceptual survey (MWCS) correct answers and average scores of VASS for each student. To measure the statistical significance between test groups and gender or school factors, we employed nonparametric tests in SPSS and computed Mann-Whitney U or Kruskal-Wallis tests where appropriate.\n\n\nResults\n\nFigure 2 displays the overall results of learning physics. By considering only the groups of students who sat for both pre-and post-tests, it is seen that most of the students (66%), within the experimental group, display high and similar attitude (folks-like attitude) before learning via PBL approach. However, after learning about mechanical waves, there was a great shift from attitude in both students in control and experimental groups. The difference between these two groups was 19% more students (79% of students in experimental and 60% of students in control group) changed their attitude towards physics expert-like due to PBL. It is also noted that in the second stream of students who did not sit for pre-test, only 3% of students taught using PBL, alongside 13% of those who were taught in traditional methods, had a folk-like attitude after completing the lessons.\n\nTable 1 presents the statistical significances of the groups discussed in Figure 3 above. The students’ attitude from either control or experimental groups was similar before learning mechanical waves. However, it diverged after learning, and a physics expert-like attitude was developed more in the experimental group. Therefore, we retained the hypothesis that assumed that the distribution of mean scores of all students was the same at the pre-test stage and rejected the hypothesis that assumed the distribution of mean scores of all students was the same at the post-test stage. Nevertheless, there was no statistically significant difference (p > 0.05) between female and male students and between public and private schools both at pre- and post-test stages.\n\n* Statistically significant difference at.05 significance level and rejecting the null hypothesis, N: Sample size, df: degrees of freedom.\n\nNote: y-axis shows average scores and x-axis shows number of students in %.\n\nFigure 2 displays the VASS mean scores of students in control and experimental groups at pre- and post-test stages. It can be visualized that students’ attitudes shifted to higher scores in the experimental group than the control group after learning mechanical waves (at the pre-test stage). Note that higher scores refer to a more “expert” like attitude.\n\nFigure 4 displays box and whisker plots across Solomon’s four-group design. It is seen that the experimental group (those who learned with PBL) either performed both pre- and post-test or those who performed only post-test had similar high VASS average scores compared to their counterparts in the control group (those who learned with chalk and board).\n\nWe have investigated two factors (students’ gender and school type/ownership) that could influence students’ attitude toward learning physics when learned with or without PBL.\n\nCase 1.Gender difference\n\nSince gender showed no statistical (p > 0.05) effect (see Table 1), Figure 5 displays the classification of students’ attitude about learning physics before and after learning through PBL according to gender. Thus, both male and female students were able to shift from folks-like to physics expert-like attitude after learning mechanical waves. The sample for female students at both pre- and post-test was 53 while that of male was 79 in experimental group. Likewise, there wre 39 female and 68 male students in control group.\n\nIt can be seen that 65% female students had folk-like views in pre-test that shifted to 83% expert-like in post-test due to the PBL intervention. A similar shift in male students was observed from 66% to 77%, from folk to expert-like views. However, such big shift was not observed in a control group. For instance, the shift in expert-like views was from 8% to 60% and from 8% to 61% among females and males respectively.\n\nCase 2. Public versus private school\n\nSince public and private schools did not show any statistical (p > 0.05) effect (see Table 1), Figure 6 displays the classification of students’ attitude about learning physics before and after learning through PBL across the type of schools. Thus, students in public or private were able to shift from folks-like to physics expert-like attitude after learning mechanical waves. The sample for students from government school at both pre- and post-test was 39 while that of those from private was 92 in experimental group. Likewise, there were 55 students in government school and 51 students in private school.\n\nIt can be seen that 66% government students had folk-like views in pre-test, that shifted to 80% expert-like in post-test due to the PBL intervention. A similar shift in private students was observed from 66% to 78%, from folk to expert-like views. However, such big shift was not observed in a control group. For instance, there was only 60% students from government school and 60% students from private school shifted to expert-like views.\n\nAfter measuring the effect of PBL on students’ attitude, we went further and correlated the scores from the MWCS and VASS scores. Figure 7 presents these results. Surprisingly, a positive attitude, such as physics expert-like, was found to not significantly correlate with students’ performance scores. A small correlation coefficient of 0.35 was found in overall students at the post-test stage. This was large compared with a very small correlation coefficient of 0.02 found in overall students at the pre- test stage. Note that a correlation between 0.00 and 0.49 is considered low, 0.50 and 0.69 is considered medium, while 0.70 and 1.00 is considered as high.\n\nSpecifically, a negative correlation (but very small) coefficient (-0.03) was found in a control group (in a post-test only design), while a positive correlation (but small) coefficient (0.10) was found in a control group (in a pre- and post-test design) at pre-test stage (Table 2).\n\nLikewise, a series of negative correlation coefficients (such as -0.19 found in Experim group of pre- and post-test design) were found at the post-test stage with only a positive correlation (but a small) coefficient (.08) in a control group that performed only post-test.\n\n\nDiscussion\n\nAttitude is one of the best behavior characteristics that can show the orientation of the course during teaching and learning. We have investigated the effect of PBL on improving the attitude in learning physics among Ugandan students. We found that PBL raises students toward learning physics more than traditional methods do (N = 419, p > 0.05). Students shifted from folks-like attitudes before learning mechanical waves to physics expert-like after learning mechanical waves. These results our study tend to agree with those of Laforce and Noble (2017) who found that significantly enhanced students’ motivation and beliefs about STEM careers. In a similar way, PBL method of teaching was found to have a stronger positive impact in the general perception of Pharmacy students towards the study of anatomy as compared to the traditional methods in the study by Azu and Osinubi (2011). However, Sahin (2010) did not find a significant difference in students’ beliefs about learning physics between those instructed under PBL and those instructed under traditional lecture method. The expert-like attitude are attitudes we believe are shared by scientists and educators at large (Halloun, 1996). This author argued that students with an expert profile are chiefly scientific realists and critical learners. Students with a folk profile are primarily naive realists and passive learners (Madsen et al., 2020). Students with transitional profiles hold mixtures of this attitude.\n\nIn a study done in Uganda, Kwarikunda et al. (2021) investigated motivation pertains of high school students toward learning physics and found that low-quantity and grade-introjected motivated students mostly used surface learning strategies whilst the high-quantity and primarily intrinsically motivated students used deep learning strategies. This is related to our findings in a way that the PBL strategy has raised motivation of students to learn physics. The shift towards physicist-like attitude were also realized during examining the attitude of physics experts, physics educationists in the incorporation of history and philosophy of science-based materials in physics instruction (Galili & Hazan, 2001). The authors of that study realized that such knowledge could guide those who devote their efforts to constructing and implementing learning materials in science education. These findings indicate that not only students but also teachers may experience such folks-like beliefs as pointed out by Zhukova (2017) in his study findings which suggested that some teachers especially the beginners tend to hold traditional beliefs or feel incompetent in relation to using learner-centered methods although they tend to hind their fears due to student expectations among other factors.\n\nWith reference to Figure 2, although students’ views in the post test were more of expert-like especially with the experimental group, some students still possessed folk-like and transitional views despite being instructed with PBL method. I this regard, the VASS study (Halloun, 1996), also found that college physics students have attitude about physics that often diverge from physicists’ attitude, with the majority of students evincing a transitional profile. Such results may persist due to the fact that some students may naturally have low interest rate, expectation or success towards physics as a subject according to Boyuk (2011).\n\nIn our study, gender and type of school did not show any effect of changing attitude or supporting PBL to change students’ attitude toward physics expert-like thinking. Thus, attitude changes with instruction rather than on gender or school factors. Other studies such as Argaw et al. (2017) did not find any gender difference in motivation to learn physics across groups, thus, there was no domination of gender existed in the results obtained in both the experimental and comparison groups. However, a comparison study done in Turkey about PBL and traditional lecture students’ expectations in an introductory physics classroom showed that there was a sense that the attitude towards physics may change with gender (Sahin & Yorek, 2009). Likewise, Mbonyiryivuze et al. (2021) found a statistically relevant gender gap in favor of female students about the use of learning physics in helping to understand situations in students’ everyday life.\n\nOne of the findings in our study that builds the gap in the current literature is that we found a non-significant difference between public and private schools in attitude when high school students experience PBL instruction. Existing literature (Maison et al., 2021) has shown that public junior high school students have slightly more positive attitudes than private students when learning science in general. Likewise, in relation to school levels, Mukagihana et al. (2021) found an increased motivation of learning biology at a public university than at a private university when animation and lab instructions are administered. We have also measured the correlation between students’ attitude and performance. Sometimes students’ attitude may significantly affect what they learn in science courses (Halloun & Hestenes, 1996a); however, our results show no such correlation (r < 0.50). This is surprising because everyone would predict the positive correction with performance after seeing the increase in students’ attitude as our study revealed. Note that more results about students’ achievement are reported in our study (Kanyesigye et al., 2022a). Contrariwise, other studies have seen a significant correlation between attitude and scores. For instance, Halloun and Hestenes (1996a) study, student profiles correlated significantly with physics achievement (r > 0.441). Students with an expert profile were the most likely to earn an “A” in their physics courses, while those with a folk profile are the most likely to do poorly or fail in these courses (Halloun, 1996).\n\n\nConclusions\n\nIn this study, we aimed to investigate whether problem-based learning instruction causes a statistically significant effect in students’ attitudes towards physics, whether there is a statistically significant difference by gender in students’ attitude towards physics, whether there is a statistically significant difference by school type in students’ attitude towards physics, and whether students’ attitude correlates with their performance scores. We found that students’ attitudes increase drastically after learning mechanical waves, developing physics expert-like profiles. There was no significant effect on the attitudes of students based on gender and school type. However, the correlation between positive attitudes did not highly correlate with their performance. We recommend teachers keep using problem-based learning techniques to develop students who possess a scientific profile. When attitude shifts are negative, teachers can change their teaching techniques to help develop students’ beliefs to be more expert-like. When differences in attitudes and beliefs scores are found in demographics, teachers should look for ways to support students in a more equitable manner.\n\n\nData availability\n\nWe have previously published a data article in Data in Brief (Kanyesigye et al., 2022b) and full description of the data can be found in this study.\n\nMendeley Data: Data for measuring impact of problem-based learning during learning mechanical waves: MWCS, VASS, RTOP. https://doi.org/10.17632/rdtcgstmps.3 (Kanyesigye et al., 2022c)\n\nThis project contains the following underlying data:\n\n- Ugandan Secondary Form 6 Students Views About Sciences Survey [Feb-Apr 2021].xlsx\n\n- Ugandan Secondary Form 6 Responses on Mechanical Wave Conceptual Survey [Feb-Apr 2021].xlsx\n\nMendeley Data: Teacher Training in Implementing Problem-Based Learning. https://doi.org/10.17632/b28d3p7kf8.1 (Kanyesigye, 2022)\n\nThis project contains the following extended data.\n\n- Training of Teachers in Problem-Based Learning.pptx\n\nMendeley Data: Data for measuring impact of problem-based learning during learning mechanical waves: MWCS, VASS, RTOP. https://doi.org/10.17632/rdtcgstmps.3 (Kanyesigye et al., 2022c)\n\nThis project contains the following extended data.\n\n- Reformed teaching observation classroom practices in Ugandan Secondary Form 6 [Feb-Apr 2021].xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nStudies related to this current study\n\nThe current study is a portion of the first author doctoral research project. There are other studies by the authors related to this one that may overlap the methods or data. These are:\n\nPublished:\n\nKanyesigye, S. T., & Kemeza, I. (2021). Effect Of Problem-Based Learning Instruction On Secondary School Physics Students In Understanding Of Electromagnetic Waves. Voice of Research, 10(1), 1–17. http://www.voiceofresearch.org/Doc/Jun-2021/Jun-2021_1.pdf\n\nKanyesigye, S. T., Uwamahoro, J., & Kemeza, I. (2022a). Difficulties in understanding mechanical waves: Remediated by problem-based instruction. Physical Review Physics Education Research. https://journals.aps.org/prper/accepted/99074L91A641480370857b82c918eea0b009ef16e\n\nKanyesigye, T. S., Uwamahoro, J., & Kemeza, I. (2022b). Data collected to measure the impact of problem-based learning and document physics classroom practices among Ugandan secondary schools. Data in Brief, 44(108534 Contents), 1–9. https://doi.org/10.1016/j.dib.2022.108534\n\nAccepted manuscript:\n\nKanyesigye, S. T., Uwamahoro, J., & Kemeza, I. (2022). The effect of Professional Training on In-service Secondary School Physics Teachers’ Motivation to Use Problem-Based Learning. International Journal of Learning, Teaching and Educational Research (IJLTER)\n\nUnder review:\n\nKanyesigye, S. T., Uwamahoro, J., & Kemeza, I. (2022). The Impact of Problem-Based Learning on Students’ Achievement in Mechanical Waves in Secondary Schools. Research in Science Education (RISE).\n\nManuscript in preparation:\n\nKanyesigye, S. T., Uwamahoro, J., & Kemeza, I. (2022). Ugandan physics classroom observation practices documented using reformed teaching observation protocol.",
"appendix": "References\n\nAka EI, Ezgi G, Aydoğdu M: Effect of Problem Solving Method on Science Process Skills and Academic Achievement. J. Turk. Sci. Educ. 2010; 7(4): 13–25.Reference Source\n\nAllchin D: Problem- and Case-Based Learning in Science: An Introduction to Distinctions, Values, and Outcomes. CBE Life Sci. Educ. 2013; 12: 364–372. PubMed Abstract | Publisher Full Text\n\nAndiema NC: Effect of Child Centred Methods on Teaching and Learning of Science Activities in Pre-Schools in Kenya. J. Educ. Pract. 2016; 7(27): 1–9. ISSN 2222-1735 (Paper) ISSN 2222-288X (Online).\n\nArgaw AS, Haile BB, Ayalew BT, et al.: The effect of problem based learning (PBL) instruction on students’ motivation and problem solving skills of physics. Eurasia J. Math. Sci. Technol. Educ. 2017; 13(3): 857–871. Publisher Full Text\n\nArman AM: Students’ Attitudes toward Problem Based Learning – Analog Electronic Course in the Electrical Engineering Programs in PPU Case Study. Journal of E-Learning and Higher Education. 2018; 2018: 1–9. Publisher Full Text\n\nAzu OO, Osinubi AA: A survey of problem-based learning and traditional methods of teaching anatomy to 200 level pharmacy students of the university of lagos, Nigeria. Afr. J. Pharm. Pharmacol. 2011; 5(2): 219–224. Publisher Full Text\n\nBandura A:Model of causality in social learning theory. Cognition and psychotherapy. Springer;1985; pp. 81–99.\n\nBoyuk HK v U: Attitude Towards Physics Lessons And Physical Experiments Of The High School Students. Eur. J. Phys. Educ. 2011; 2(1): 23–31.\n\nCohen L, Manion L, Morrison K:Research Methods in Education. Professional Development in Education. 6th ed.Routledge;2007; Vol. 38(Issue 3). Publisher Full Text Reference Source\n\nCreswell JW: Research Design: Qualitative, Quantitative, and Mixed Methods Approaches. 4th ed.SAGE Publications, Inc.;2014.Reference SourceReference Source\n\nDeWitt J, Archer L, Moote J: 15/16-Year-Old Students’ Reasons for Choosing and Not Choosing Physics at a Level. Int. J. Sci. Math. Educ. 2019; 17(6): 1071–1087. Publisher Full Text\n\nDimitrov DM, Rumrill PD: Pretest-posttest designs and measurement of change. Work. 2003; 20(2): 159–165. PubMed Abstract Reference Source\n\nDorimana A, Uworwabayeho A, Nizeyimana G: Examining Mathematical Problem-Solving Beliefs among Rwandan Secondary School Teachers. Int. J. Learn. Teach. Educ. Res. 2021; 20(7): 227–240. Publisher Full Text\n\nEijkelhof HM, Kortland J: Broadening the Aims of Physics Education. Falmer Press;1998.Reference Source\n\nFraenkel JR, Wallen NE, Hyun HH: How to Design and Evaluate Research in Education. 8th ed.McGraw-Hill;2012.Reference Source\n\nGalili I, Hazan A: Experts’ views on using history and philosophy of science in the practice of physics instruction. Sci. Educ. 2001; 10(4): 345–367. Publisher Full Text\n\nGay LR, Mills GE, Airasian P: Educational Research. Pearson Education, Inc;2012.Reference Source\n\nGliem JA, Gliem RR: Calculating, Interpreting, and Reporting Cronbach’s Alpha Reliability Coefficient for Likert-Type Scales. Midwest Research to Practice Conference in Adult, Continuing, and Community Education. 2003. Reference Source\n\nGunel M, Hand B, Gunduz S: Comparing Student Understanding of Quantum Physics When Embedding Multimodal Representations into Two Different Writing Formats: Presentation Format Versus Summary Report Format. Sci. Educ. 2007; 91: 1093–1112. Publisher Full Text\n\nHalloun I: Views About Science and Physics Achievement: The VASS Story. ICUPE;1996.\n\nHalloun IA, Hestenes D: Views About Sciences Survey: VASS. NARST Annual Meeting. 1996a; 266–276.\n\nHalloun I, Hestenes D: Interpreting VASS Dimensions and Profiles. Sci. & Educ. 1996b; 7(6): 553–577. Publisher Full Text\n\nHerman BC, Owens DC, Oertli RT, et al.: Exploring the Complexity of Students’ Scientific Explanations and Associated Nature of Science Views Within a Place-Based Socioscientific Issue Context. Sci. Educ. 2019; 28(3–5): 329–366. Publisher Full Text\n\nHill L: Teaching Methodology.In Professional Development Strand. Australian Agency for International Development (AusAID).2002.Reference Source\n\nIbrahim N: Attitude in Learning Physics among Form Four Students. Soc. Manag. Res. J. 2019; 16(2): 19–40. Publisher Full Text\n\nKanyesigye S: Teacher Training in Implementing Problem-Based Learning. Mendeley Data. 2022; V1. [Dataset]. Publisher Full Text\n\nKanyesigye ST, Kemeza I: Effect Of Problem-Based Learning Instruction On Secondary School Physics Students In Understanding Of Electromagnetic Waves. Voice Res. 2021; 10(1): 1–17.\n\nKanyesigye ST, Uwamahoro J, Kemeza I: Difficulties in understanding mechanical waves: Remediated by problem-based instruction. Phys. Rev. Phys. Educ. Res. 2022a; 18. Publisher Full Text Reference Source\n\nKanyesigye TS, Uwamahoro J, Kemeza I: Data collected to measure the impact of problem-based learning and document physics classroom practices among Ugandan secondary schools. Data Brief. 2022b; 44(108534 Contents): 108534–108539. PubMed Abstract | Publisher Full Text\n\nKanyesigye ST, Uwamahoro J, Kemeza I: Data for measuring impact of problem-based learning during learning mechanical waves: MWCS, VASS, RTOP. Mendeley Data. 2022c; V3. [Dataset]. Publisher Full Text\n\nKanyesigye ST, Uwamahoro J, Kemeza I: The Effect of Professional Training on In-service Secondary School Physics’ Teachers’ Motivation to Use Problem-Based Learning. Int. J. Learn. Teach. Educ. Res. 2022d; 21(8): 271–287. Publisher Full Text\n\nKaramustafaoglu O: Active learning strategies in physics teaching. Energy Education Science and Technology Part B: Social and Educational Studies. 2009; 1(1): 27–50.Reference Source\n\nKwarikunda D, Schiefele U, Ssenyonga J, et al.: Secondary School Students’ Motivation Profiles for Physics Learning: Relations with Cognitive Learning Strategies, Gender, Attitudes and Individual Interest. African Journal of Research in Mathematics, Science and Technology Education. 2021; 25: 197–210. Publisher Full Text\n\nLaforce M, Noble E: Problem-Based Learning (PBL) and Student Interest in STEM Careers: The Roles of Motivation and Ability Beliefs. Educ. Sci. 2017; 7. Publisher Full Text\n\nLawshe CH: A Quantitative Approach To Content Validity. Pers. Psychol. 1975; 28(4): 563–575. Publisher Full Text\n\nMadsen A, McKagan SB, Sayre EC: Best Practices for Administering Attitudes and Beliefs Surveys in Physics. Phys. Teach. 2020; 58(2): 90–93. Publisher Full Text\n\nMaison M, Kurniawan DA, Zain MS: Students’ Attitudes in Science Learning: Comparison Between Public and Private Junior High Schools. J. Educ. Res. Eval. 2021; 5(4): 568. Publisher Full Text\n\nMbonyiryivuze A, Yadav LL, Amadalo MM: Students’ attitudes towards physics in Nine Years Basic Education in Rwanda. Int. J. Eval. Res. Educ. 2021; 10(2): 648–659. Publisher Full Text\n\nMorgan: MORGAN’S TABLE FOR SAMPLE SIZE. The Research Advisors;2006.Reference Source\n\nMpho O: Teacher centered dominated approaches: Their implications for today’ s inclusive classrooms.2018; 10(February): 11–21. Publisher Full Text\n\nMukagihana J, Nsanganwimana F, Aurah CM: Effect of resource-based instructions on pre-service biology teachers’ motivation toward learning biology. LUMAT: International Journal on Math, Science and Technology Education. 2021; 9(8): 262–277. Publisher Full Text\n\nNannyonjo H, Mulindwa IN, Usher A: Funding Higher Education in Uganda in an Era of Growth.2009.Reference Source\n\nNdihokubwayo K, Nyirahabimana P, Musengimana T: Teaching and Learning Bucket Model: Experimented with Mechanics Baseline Test. European. J. Educ. Res. 2021; 10(2): 525–536. Publisher Full Text\n\nNite SB, Margaret M, Capraro RM, et al.: Science, technology, engineering and mathematics (STEM) education: A longitudinal examination of secondary school intervention. 2014 IEEE Frontiers in Education Conference. 2015. Publisher Full Text\n\nNteere NM, Kwaria JM, Kirimi NK: Influence of Selected Factors on Students’ Attitude towards Physics in Public Secondary Schools. American. J. Educ. Res. 2017; 5(9): 939–943. Publisher Full Text\n\nNyirahabimana P: An Investigation of prime indicators of current teaching methodologies and students’ perceptions in Quantum physics for quality knowledge delivery system at the University of Rwanda College of Education. International Journal of Evaluation and Research in Education (IJERE). 2022; 11(3): 1134. Publisher Full Text\n\nNzeyimana JC, Ndihokubwayo K: Teachers’ Role and Learners’ Responsibility in Teaching and Learning Science and Elementary Technology in Rwanda. Afr. J. Educ. Studies Math. Sci. 2019; 15(2): 1–16. Publisher Full Text\n\nOlusola OO, Rotimi CO: Attitudes of Students towards the Study of Physics in College of Education Ikere. Am. Int. J. Contemp. Res. 2012; 2(12): 86–89.Reference Source\n\nPhillips AM, O’donnell, C.: A critical examination of “expert-like” in physics education research. Physics Education Research Conference Proceedings. 2021; 339–346. Publisher Full Text\n\nRichardson L: Writing: A method of inquiry. Turning points in qualitative research.In books.google.com: Tying knots in a handkerchief. 2003; 2: 379.Reference Source\n\nRyan G: Attitude and Motivation towards Learning Physics. International Journal of Engineering Research & Technology (IJERT). 2013; 2(11): 2087–2094.Reference Source\n\nSahin M: Effects of problem-based learning on university students’ epistemological beliefs about physics and physics learning and conceptual understanding of Newtonian Mechanics. J. Sci. Educ. Technol. 2010; 19(3): 266–275. Publisher Full Text\n\nSahin M, Yorek N: A comparison of problem-based learning and traditional lecture students’ expectations and course grades in an introductory physics classroom. Sci. Res. Essays. 2009; 4(8): 753–762.\n\nSamsudin A, Suhandi A, Rusdiana D, et al.: Optimizing Students’ Conceptual Understanding on Electricity and Magnetism through Cognitive Conflict-Based Multimode Teaching (CC- BMT). J. Phys. Conf. Ser. 2019; 1204(1204): 012027. Publisher Full Text\n\nSaraç H: The Effect of Science, Technology, Engineering and Mathematics-Stem Educational Practices on Students’ Learning Outcomes: A Meta-Analysis Study. Turk. Online J. Educ. Technol. 2018; 17(2): 125–142.Reference Source\n\nSari L, Keith T, Anne N, et al.: How approaches to teaching are affected by discipline and teaching context. Stud. High. Educ. 2006; 31(3): 285–298. Publisher Full Text\n\nSelçuk GS: The effects of problem-based learning on pre-service teachers’ achievement, approaches and attitudes towards learning physics.2010; 5(June): 711–723.Reference Source\n\nSibomana A, Karegeya C, Sentongo J: Effect of Cooperative Learning on Chemistry Students’ Achievement in Rwandan Day-upper Secondary Schools. Eur. J. Educ. Res. 2021; 10(4): 2079–2088. Publisher Full Text\n\nSirait J, Balta N, Mason A: The Development of Questionnaire to Investigate Students’ Attitudes and Approaches in Physics Problem solving. Jurnal Pendidikan Fisika Indonesia. 2017; 13(2): 79–87. Publisher Full Text\n\nStephens AL, Clement JJ: Documenting the use of expert scientific reasoning processes by high school physics students. Physical Review Special Topics - Physics Education Research. 2010; 6(2): 1–15. Publisher Full Text\n\nTeddy S, Uwamahoro J, Kemeza I: Data collected to measure the impact of problem-based learning and document physics classroom practices among Ugandan secondary schools. Data Brief. 2022; 44: 108534. PubMed Abstract | Publisher Full Text\n\nToler S: The Power of Your Attitude. Harvest House Publishers;2016. Publisher Full Text\n\nTongchai A, Sharma M, Johnston I, et al.: Students’ conceptual knowledge of mechanical waves across different backgrounds and cultures. UniServe Science Proceedings Visualisation. 2008; 121–126.Reference Source\n\nU.S. Department of Education Office of Innovation and Improvement, A: STEM 2026: A Vision for Innonation in STEM Education. Education Week. 2016.Reference Source\n\nZhukova O: Novice Teachers’ Beliefs about Problem-Based Learning Approach, and Teaching Practices. CBU Int. Conf. Proc. 2017; 901–909. Publisher Full Text\n\n\nFootnotes\n\n1 The overall score on the attitudes and beliefs questionnaire is a measure of how well students agree with physicists, while the overall score on the multiple-choice conceptual test measures how well students understand physics content (Madsen et al., 2020, p.91)."
}
|
[
{
"id": "165348",
"date": "22 Mar 2023",
"name": "Edy Shahali",
"expertise": [
"Reviewer Expertise Science education",
"STEM education",
"teacher professional 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\nThe manuscript describes the effect of problem-based learning (PBL) instruction on students’ attitudes towards physics, and how students’ attitudes towards physics correlate with students' performance in physics.\n\nLiterature review: Literature related to how attitudes effect student performance should be described. The writing is found to tend to focus on how attitudes effect interest towards science/physics rather that how attitudes effect performance (which is the second objective of this study).\nThe need or justification for the importance of conducting this study needs to be highlighted by presenting the relevant gaps in past studies. Researchers were found to use the words \"STEM\", \"science\" and \"physics\" interchangeably throughout the writing. It is necessary to examine the appropriateness of its use because it may give different interpretations to the reader. It is recommended that the writing be focused on learning physics which is the context of this study.\nObjective: There are no objectives related to differences in attitudes based on gender and type of school stated in this section. However, in the Results section, there are findings related to differences in attitudes towards gender and type of school were reported. Therefore, it is necessary to revise the writing of the objective to be in line with the reported research findings.\nMethodology: The appropriateness of this sentence needs to be reviewed. \"So, the author took up the topic of waves for the PhD project \".What does this statement have to do with this study need to be checked.\nImplementation: The number of physics teachers reported in the Implementation section (10) does not match the number of physics teachers trained (30) as stated in the Methodology section. It is necessary to explain why there is such a difference.\nThe researchers stated that \"10 physics teachers who handled the experimentation group first trained students about PBL strategies before starting the experiment.\" - How the students were trained needs to be explained.\nThe researchers stated that \"each member was expected to make individual study\" - What is meant by \"individual study' and how it is carried out need to be explained.\nResult: The researchers were found to report an analysis related to students' attitudes towards physics (when learned with or without PBL) based on gender and school type/ownership. However, objective of the study does not state this. Therefore, it is necessary to revise the writing of the objective to be in line with the reported research findings.\nDiscussion: Writing in the discussion section needs to be re-examined and needs to be written more comprehensively by presenting possible reasons for the reported findings. Researchers are found to only report the findings of past studies that are parallel and not parallel to their research findings. No arguments are presented to explain the findings.\n\nThe researchers was also found to be comparing the findings of their study with the findings of previous studies that involved factors such as belief, motivation, and perceptions, rather than comparing past studies related to attitudes. Therefore, it is necessary to check its appropriateness.\nThe researchers stated that \"This is related to our findings in a way that the PBL strategy has raised motivation of students to learn physics\". However, this study is related to the attitude towards physics and no data related to the level of motivation was obtained in this study.\nThe researchers stated that \"our results show no such correlation between attitudes and achievement\". However, no possible reason to explain this was discussed.\n\nConclusion - There are some statements that are not consistent with the findings of the study and need to be revised. Among them, the researchers were found to draw conclusions about beliefs, whereas this study only identified the level of students' attitudes towards physics.\nThank you.\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": [
{
"c_id": "10804",
"date": "13 Apr 2024",
"name": "Stella Kanyesigye",
"role": "Author Response",
"response": "Authors’ responses: Thank you very much for taking your valuable time to read our manuscript! We fully understand your concerns, and your advice has helped us to revise it. The literature on how attitudes affect performance was enhanced in the following paragraph. “Referring to previous research, according to Nite et al. (2015), students’ attitude was found to influence their performance significantly. Olusola and Rotimi (2012) noted that students who have a negative attitude towards sciences, including physics, also tend not to like the subject teachers ( Olusola & Rotimi, 2012). Previous researchers such as Mbonyiryivuze et al. (2021); Andiema (2016), and Selçuk (2010) recommended the adoption of interactive pedagogical approaches in the teaching-learning process, including problem-based learning (PBL) instruction ( Kanyesigye & Kemeza, 2021) as a way of bringing about a desirable positive change in students’ attitude towards science and physics in particular. Expanding on this narrative, the existing body of literature has dedicated considerable attention to unraveling the intricate relationship between students’ attitudes and their academic performance. Studies by (Cahill et al., 2018) and (Martinko & Vorkapić, 2017) emphasize the central role of positive attitudes in creating a conducive learning environment and enhancing overall academic achievement. (Mao et al., 2021) comprehensive review delves into how attitudes can impact cognitive processes, motivation, and academic success. The need or justification for the importance of conducting was revised as follows: “Identified gaps in past research underscore the significance of this study. While numerous studies have explored the influence of instructional methods on academic outcomes, there remains a notable void in understanding how specific instructional approaches, such as PBL, affect students’ attitudes toward physics. This study seeks to address this gap by providing nuanced insights into the relationship between PBL instruction and attitudes, thereby contributing to a more comprehensive understanding of effective pedagogical strategies in physics education. Additionally, existing literature has acknowledged the importance of attitudes in shaping academic performance. However, the specific nuances of this relationship, particularly concerning gender and type of school, have not been extensively explored. This study aims to bridge this gap by examining how attitudes may vary across diverse student groups and how these variations may impact academic achievement.” In the context of this study, we deleted the STEM context to allow writing to be focused on learning physics. We revised the research objectives by incorporating gender and type of school variables: Determine if PBL instruction causes a statistically significant effect on students’ attitudes towards physics, with a specific focus on exploring variations based on gender and type of school. Investigate the correlation between students’ attitudes and their performance scores. By “So, the author took up the topic of waves for the PhD project” sentence, we were referring to a large project of the first author’s doctoral program. Anyway, we deleted this sentence to avoid confusion. There is no contradiction between 30achers trained and ten teachers who delivered PBL intervention. We trained 30 teachers to implement PBL professionally, as we published in Kanyesigye et al. (2022d), but some of them (10) were assigned to teach PBL classes while others taught control classes. By training students, there was no such formal training; teachers just explained how PBL is done, which is different from how they used to learn. Steps of PBL and what they are expected to do in introducing the problem, group work, collecting ideas and research, and presenting the findings stages. The phrase’ individual study’ refers to a specific phase in the PBL process where each member of the group is expected to independently explore and understand the relevant concepts related to the given problem. During this phase, students engage in self-directed learning, which involves conducting research, reviewing course materials, and seeking additional resources to deepen their understanding. We revised the objective’s writing to align with the reported research findings. We recognize the need to improve the comprehensiveness of our writing by providing a more detailed exploration of possible reasons for our findings and by aligning our comparisons with studies specifically focused on attitudes toward physics. In the revised discussion, we refrain from making unsupported claims about the correlation between the PBL strategy and motivation, ensuring a more accurate representation of our study’s scope. We also acknowledge the importance of explaining the lack of correlation between attitudes and achievement, and we addressed this omission in our discussion. For other terms related to attitude, such as belief and motivation, VASS was not limited to attitude alone, and we provided an operational definition of attitude in our study in the fourth paragraph of the introduction. “Thus, in this study, we define attitude towards physics as the feeling, beliefs, and values possessed by students towards the subject conveyed in the form of like or dislike; and positive or negative reactions towards physics concepts.” Anyway, we tried to stick to the same attitude in the discussion. We acknowledge the need for clarity in our conclusions, particularly concerning beliefs, given that our study specifically focused on identifying the level of students’ attitudes toward physics. Thank you!"
}
]
},
{
"id": "210936",
"date": "29 Nov 2023",
"name": "Hasan Şahin Kızılcık",
"expertise": [
"Reviewer Expertise Physics education",
"Problem-based laearning"
],
"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 discusses how problem-based learning (PBL) education affected students' attitudes toward physics, as well as how those attitudes and physics performance are related.\n\nAbstract:\nYou should clearly write which method you mean by traditional instruction.\nLiterature review:\nLow relevance to the main problem. I did not understand the link between this study and STEM. STEM is an interdisciplinary approach, but only physics was analysed here. In addition, while there is rich literature on PBL and attitudes, these are barely mentioned. A focused review of the literature would increase the comprehensibility and impact of the study.\nObjectives:\nIn the study, comparisons were made according to school type and gender. However, there is no objective for these.\nSampling:\nThe sample contains the phrase \"13th grade (aged between 16 and 21)\". Is this not a very wide age range for a grade level? Is there a specific reason for this? There are significant differences between the cognitive and developmental characteristics of a 21-year-old student and a 16-year-old student.\nImplementation of the intervention:\nDuring the intervention, I understood that PBL sessions about waves were carried out with the students. However, I could not find any information about what kind of problem they were trying to solve. The content of the problem, its level and what exactly was expected from the students were not explained.\nData collection methods:\nThe structure of the survey is presented quite complex. It could have been presented more simply. Validity and reliability studies are adequately explained. However, I did not see information about the construct validity of the survey. Is the survey a single factor?\nData analysis:\nThe first and third categories are worth two points each and the middle category is worth one point. What is the reason for not keeping the category range equal when dividing the pentad structure into three categories?\nWhy did you use nonparametric methods? Did your data not fulfill the prerequisites of parametric methods?\nResults:\nThe presentation of the results is very clear.\nDiscussion:\nThe discussion section is organised to cover all aspects of the study. However, the literature used in the discussion and the educational level of the study are different. In the discussion, studies on university students were generally mentioned. However, the study was conducted with high school students. Studies at similar educational levels should also be included.\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": "10806",
"date": "13 Apr 2024",
"name": "Stella Kanyesigye",
"role": "Author Response",
"response": "Authors’ responses: Thank you very much for reviewing our manuscript and offering insightful suggestions to reframe it! We explicitly mentioned the “lecture-based method” in the abstract for a clearer understanding of what is considered traditional instruction in the context of our study. We removed STEM from the literature that omitted the context of physics to increase the comprehensibility and impact of the study. The literature on PBL and attitudes was enhanced in the following paragraph: “Today’s education system focuses on training students to develop skills that enable them to work in a variety of situations ( Ndihokubwayo et al., 2021). Like pragmatists, philosophers of education suggest that people learn by solving and learning from real problems they face in everyday life ( Richardson, 2003). Based on these philosophies, PBL was developed from the constructivism school of thought, where learners work themselves to generate new knowledge. PBL is defined as a method of inquiry where students solve difficulties, oddities, qualms, and problems in real life ( Dorimana et al., 2021). PBL is one of the powerful teaching methods in reforming science education ( Allchin, 2013). The method acknowledges the importance of actively engaging students in their learning. It contextualizes the learning, which contributes both to student motivation and the making of meaning. According to Orozco and Yangco (2016), most of the students involved in PBL can share their opinions with others, use different approaches to analyze situations, and explore ways of solving problems. Therefore, the present study employs the extended constructivism theory of Albert Bandura’s social learning theory ( Bandura, 1985). This theory proposes that new behaviors can be acquired by observing and imitating others ( Bandura, 1985). Social learning theory fits our study because, through PBL, students interact with each other to reach a positive outcome. Students cooperatively share ideas ( Sibomana et al., 2021) and then find the probable solution from a combined effort. Implementing PBL in physics education has significantly influenced students’ attitudes. Research studies ( such as those by Fidan & Tuncel, 2019 and Selçuk, 2010), have demonstrated a positive correlation between using PBL instructional methods and favorable student attitude shifts. These studies suggest that the interactive and collaborative nature of PBL enhances the learning experience and contributes to cultivating a more positive and engaged attitude among students in physics education.” We revised the research objectives by incorporating gender and type of school variables: Determine if PBL instruction causes a statistically significant effect on students’ attitudes towards physics, with a specific focus on exploring variations based on gender and type of school. Investigate the correlation between students’ attitudes and their performance scores. For the sampling, there is no particular age for starting or ending school, meaning one can start at a later age than the other, hence the age difference. Also, some learners may have repeated a class or classes, hence making them older than their classmates. Additionally, one may study and then drop out and rejoin later. But assume a child who starts grade one at four years will finish primary seven at 11 years and will be in grade 13 when still at the age of 16 years and some months. To avoid duplication, we cited our previously published article that contains more detailed information about the problem students were trying to solve ( Kanyesigye et al., 2022a, p.3). The Views About Science Survey (VASS) is not a traditional multiple-choice survey. It utilizes Halloun’s Contrasting Alternatives rating scale (Cars), where respondents rate items on a 5-point scale. Each point is associated with a statement (‘a’ for negative attitude and ‘b’ for positive attitude). The scale is interpreted based on the relative positioning of ‘a’ and ‘b’ statements. This unique scaling system is designed to nuancedly capture the intensity and direction of respondents’ attitudes. VASS is not intended to measure multiple constructs but rather focuses on eliciting detailed and nuanced information about individuals’ views on science. This aligns with the survey’s distinctive approach, and the scale’s structure reflects the complexity of attitudes toward science as intended by Ibrahim Halloun. By dividing the pentad structure into three categories, the categorization is based on a nuanced scoring system, where the first two scales represent one category, the third scale stands alone, and the last two scales form another category. This approach was chosen to facilitate a more straightforward interpretation of participants’ views while acknowledging the nuances in the original scales. Thus, we have combined the first two scales into “Folks-like views,” the third scale remains as “Transitional views,” and the last two scales have been averaged into “Physics expert-like views.” This categorization allows for a simplified representation of participants’ views. Typically, nonparametric tests do not rely on assumptions about the underlying data distribution and are considered more robust in certain situations. Choosing nonparametric tests is common when dealing with Likert scale data, which is often the case in surveys like VASS. Your observation regarding the discrepancy between the literature cited in the discussion and the educational level of our study is duly noted. In the revised version, we ensured a more congruent alignment between the studies referenced in the discussion and the educational level of our participants, who are high school students."
}
]
},
{
"id": "191679",
"date": "14 Dec 2023",
"name": "KINGSLEY T. ONAH",
"expertise": [
"Reviewer Expertise Science Education/Physics",
"students achievement in physics",
"self-efficacy",
"interest",
"motivation",
"procrastination",
"teachers support",
"innovative teaching approach."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract: state the problem of the study before purpose as done. introduction: Present as thus: Physics and its relevance attitude level of the students; if there is any poor attitude amongst students, link it with any kind of instructions that had led to these abysmal attainment in the students attitude. then, introduce problem based learning strategy. gender if necessary. substantiate the choice of the study area. what problem existed in the area as regard the students level of attitude that occasioned the study. use analytical tool of mean and standard deviation to answer the research questions and ANCOVA to test the hypotheses.\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?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1240
|
https://f1000research.com/articles/11-970/v1
|
23 Aug 22
|
{
"type": "Research Article",
"title": "Assessment of medication-related burden among a sample of Iraqi patients with systemic lupus erythematosus and its relationship with disease activity: a cross-sectional study",
"authors": [
"Hawraa Kadhim Abbas",
"Dheyaa Jabbar Kadhim",
"Faiq Isho Gorial",
"Laith G. Shareef",
"Hawraa Kadhim Abbas",
"Dheyaa Jabbar Kadhim",
"Faiq Isho Gorial"
],
"abstract": "Background: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with high morbidity and disability. The routines involved in taking medications, side effects, the nature of medicines, difficulties with the healthcare system, and disruptions to social activities all contribute to patients frequently experiencing medication-related burdens (MRB). The current study aimed to assess the perceived MRB among a sample of SLE patients from Iraq and to look for any possible relationship between MRB and disease activity.\nMethods: The current study was cross-sectional on diagnosed SLE patients who arrived at Baghdad Teaching Hospital/Medical City/Rheumatology department from September 2021 to January 2022. MRB was measured using the Living with Medicines Questionnaire (LMQ). Results: The study recruited 156 SLE patients. The patients were 35.8 ±11.7 years old on average. Great majority of them were women (96.8 %). The average LMQ score was 117.30± 18.37. The results showed that most patients (69.87%) experienced a moderate level of burden, followed by a low level (19.87%), high level (7.69%), and no burden at all (2.56%). No patients experienced an extremely high level of burden (0.0%). The mean burden scores for two LMQ domains—relationships with health care professionals (HCPs) and effectiveness of prescription medications—were the lowest (below average). Conclusions: Many of the SLE patients in this study reported experiencing MRB. Healthcare professionals should implement strategies to reduce this burden, particularly for low-income patients.",
"keywords": [
"Systemic lupus erythematosus",
"medication-related burden",
"Living with Medicines Questionnaire",
"SELENA-SLEDAI",
"Iraq."
],
"content": "Introduction\n\nSystemic lupus erythematosus (SLE) is a chronic, heterogeneous autoimmune disease associated with complex and varied immunological dysregulation.1 Regardless of age or race, women of childbearing age are 10 times more likely than men to be affected by SLE. Globally, SLE prevalence and incidence vary considerably with sex, age, ethnicity, and time.2 In Iraq, the prevalence of SLE is about 1/1867 of the general population, and the first case of SLE was reported in 1971.3 Genetic factors, environmental factors, and hormonal factors are believed to contribute to the occurrence of SLE.4 Systemic lupus erythematosus is an autoimmune disease with a chronic-relapsing course in which periods of remission alternate with periods of activity of the disease.5 Multiple organ systems, including the musculoskeletal, mucocutaneous, cardiopulmonary, renal, and hematologic systems, are clinically involved in SLE.1 The short-term goals of SLE treatment are to reduce or control disease activity, alleviate clinical symptoms, and achieve clinical remission. The long-term objectives are to achieve long-term sustained remission of the disease, lower mortality, enhance the quality of life, avoid and reduce recurrence, reduce adverse drug responses, prevent and control organ damage carried on by the disease, and prevent and control certain organ damage events.6 The US Food and Drug Administration currently approved corticosteroids, antimalarials like hydroxychloroquine, and belimumab for treating SLE. Nonsteroidal anti-inflammatory drugs (NSAIDs), immunosuppressive and immunomodulatory drugs and rituximab are further treatments for the management of SLE.7 The idea of “medication-related burden” (MRB) or “treatment burden” succinctly describes the entire workload that patients are subject to as a result of using healthcare, with several harmful effects on their lives.8 Because medications are the primary method of managing most disorders, MRB is a significant portion of the overall treatment burden and is commonly mentioned in qualitative studies.9 The treatment burden includes financial, temporal, physical, and psychosocial time demands on patients to adhere to the recommended treatment plan.10 Adherence to the prescribed regimen may be difficult for patients who experience high MRB. As a result, patients stop taking their medications as prescribed, which raises morbidity and mortality, the frequency of hospital admissions, and the expenditure on healthcare.9 Systemic lupus erythematosus is associated with high unmet needs and a considerable patient burden.11 The current study aimed to measure MRB among a sample of Iraqi patients with SLE and to determine the possible association between MRB and disease activity.\n\n\nMethods\n\nThe scientific and ethical committee examined and gave its approval to the research proposal that was submitted to the College of Pharmacy, the University of Baghdad, which describes the goals of the current study as well as the expected methods for data collection (ethics board approval code: 2014 on 15th February 2021). Additionally, approval was obtained from the Iraqi Ministry of Health (ethics board approval code: 6325) on 25th February 2021. The investigator explained the purpose of the study to each participant and obtained verbal consent. Written informed consent was then gained before administering the questionnaire. No incentives were offered to the patients.\n\nThe current study was an observational, cross-sectional study on already diagnosed SLE patients.\n\nThis research was conducted in a single center and recruited patients who attended Baghdad Teaching Hospital/Medical City/Rheumatology Department from September 2021 to January 2022.\n\nG*Power (RRID:SCR_013726) version 3.1.9.7 software was used to figure out the number of participants. With a 95% confidence interval, 90% power, a two-tailed alpha of 0.05, and an effect size of 0.30, and the output parameters were as the following: noncentrally parameter δ= 3.6404323, critical t =1.9780988, Df= 132 the sample size had to be at least 134 patients (f).\n\nThe inclusion criteria of the study were: (1) SLE patients who were eligible to participate in the study and were ≥ 18 years of age and either sex, (2) Had the disease for ≥ 6 months.\n\nThe exclusion criteria of the study were: (1) Patients didn’t consent to participate, (2) Patients with hearing, speech, or cognitive deficits (physical or mental state) impairing understanding of the questions.\n\nDuring sample selection, selection bias may occur. This is particularly apparent in retrospective cohort studies when exposure and outcome have already happened. As a matter of fact, in this study, sampling error is less probable. The ideal study population is well-defined, accessible, highly dependable, and reasonable in order to get the intended outcome. To remove prejudice, participants were chosen in such a manner that individuals with hearing, speech, or cognitive issues that limit subject understanding were not given included. We also utilized common terms to prevent misinterpretation.\n\nThe Arabic version8 of the living with medicine questionnaire (LMQ) was used to assess MRB in SLE patients. The LMQ consisted of 41 items to which participants responded on a five-point Likert-type scale (from strongly disagree to agree strongly). Furthermore, a free text (open-ended) question permitted the participant to add any additional topics not addressed in the questionnaire. Relationships with health professionals, Practicalities, Information, Efficacy, Side effects, Attitudes, Impact, and Control were the 8 domains covered by the questionnaire. The total LMQ score is the sum of all 41 questionnaire questions and ranges from 41 to 205, with higher scores suggesting more MRB.8 In addition, SLE disease activity was evaluated using the Systemic Lupus Erythematosus Disease Activity Index score with the Safety of Estrogens in Lupus Erythematosus National Assessment (SELENA-SLEDAI).12\n\nWhen the patients presented at the Rheumatology Department, they were asked whether they would accept to participate in the study. If they would, each patient was explained the questionnaire and given 20 to 30 minutes to complete it.\n\nIBM SPSS Statistics (RRID: SCR_016479) version 27 software for Microsoft Windows was used throughout the statistical analysis process. The participants and disease were calculated by descriptive statistics (means, standards deviations, frequencies and percentages). Because the continuous variables were not normally distributed, non-parametric tests were used for the differential analyses. Spearman correlation was used to measure the correlations of LMQ domains with the SELENA-SLEDAI Score. The impact of a patient’s demographic on MRB was evaluated using the Mann-Whitney and Kruskal-Wallis tests. P-values below 0.05 were regarded as statistically significant.\n\n\nResults\n\nThe study recruited 156 SLE patients Figure 1.62 95.5% of the study participants living in urban cities. The patient’s age was 35.8 ±11.7 years old on average. 96.8% of the population were women, and 71.8% of them were married. More than two-thirds (68%) had primary or secondary school degrees, and 66.7% had a middle income, as shown in Table 1.\n\nThe mean SELENA-SLEDAI value was 15.26 ± 10.199, the mean disease duration was 6.248 ± 5.44 years, no. of chronic medications was 4.6 ± 2.23, no. of other chronic diseases was 0.62 ± 0.85 as shown in (Table 2).\n\nThe mean LMQ score was 117.30 ± 18.37 (Range: 52-163). The findings showed that the majority of the SLE patients experienced a moderate degree of medication burden (69.87%), followed by minimum burden (19.87%) and high burden (7.69%). Finally, no burden at all (2.56%), with no patient experiencing an extremely high burden (0.0 %), as illustrated in Table 3.\n\nTwo LMQ domains had the lowest mean of burden scores (below the average): domain-1 [relationships with health care professionals (HCPs)] and domain-5 (effectiveness of prescribed medications). In other words, the patients had good relationships with their HCPs and reasonable belief in their medication effectiveness, reducing their MRB in these two domains. On the other hand, three domains had the highest mean of burden scores: Domain-2 (practical difficulties in using medicines), Domain-6 (concerns about medicine use), and Domain-7 (impact of using medications on daily life). In other words, the patients had relatively great difficulties in using medicines and had concerns about medicine use and their prescriptions impact their everyday life, as illustrated in Table 4.\n\nSix domains of LMQ (domains 2, 3, 4, 5, 6, and 7) had significant (P-value <0.05) positive correlations with the SELENA-SLEDAI score. In other words, when the scores of these six LMQ domains increase, the scores of SELENA-SLEDAI increase. In contrast, Domain-1 (relationships with HCPs) and Domain-8 (autonomy to vary regimen) had non-significant (P-value ˃0.05) correlations with the SELENA-SLEDAI score as illustrated in (Table 5).\n\nAccording to Mann-Whitney test, there were no significant differences in MRB (total LMQ score) according to eight demographic and clinical characteristics (Table 6A). However, according to Kruskal-Wallis test, there was a significant difference in the total LMQ score according to the patient’s income. The higher-income patient had significantly lower MRB (total LMQ score) compared to low-income patients (Table 6B).\n\n* Significant (P-value <0.05) according to Kruskal-Wallis Test.\n\nLMQ: Living with Medicine Questionnaire.\n\n\nDiscussion\n\nSystemic lupus erythematosus is a chronic, prototypic autoimmune disorder that may affect almost any organ or system.13 SLE continues to carry an unacceptably high morbidity burden.14 However, over the past 50 years, patient survival has drastically increased, probably due to earlier diagnosis and more effective treatment plans.15 This study measured MRB and assessed any associations between the MRB and various patient-related factors. As shown in sociodemographic data of the patients, about (96.8%) of patients were female. Nearly 80% of autoimmune disease patients are female, which brings attention to the gender disparity.16\n\nAccording to our study, a significant number of the participants (97.44%) had varying degrees of MRB. For patients and their families, chronic rheumatic diseases such as rheumatoid arthritis (RA), ankylosing spondylitis (AS), and SLE are very burdensome.17–21 In addition, patients who had organ failure (such as lupus nephritis), disease flare-ups, high disease activity, and chronic disease are more burdened.22\n\nThe current study showed that the mean LMQ score was 117.30 ± 18.37 with the majority of the participants reporting experiencing minimum (19.87%) to moderate (69.87%) MRB. According to the recent increase of interest in understanding and quantifying MRB, there is currently no study measuring MRB among SLE patients to compare our results. Most of the available studies included patients with chronic diseases in general. The results of the current study differ from those in Qatar,8 where the MRB ranged from minimal (66.8%) to moderate (24.1%) degrees of burden while being comparable to those in England23: minimal (33.1%) to moderate (54.6%); and in Kuwait9 that ranged from minimal (35.4%) to moderate (62.0%) degrees of burden.\n\nThe three domains with the highest mean burden scores were (practical difficulties in using medications), (concerns about the use of drugs), and (the impact of using medicines on daily life). The results are consistent with recent qualitative research that examined patient perceptions on treatment and MRB and showed that medication use could impair relationships, work, and social relationships and have adverse physiological effects.24,25 In addition, patients are burdened more by dealing with their drugs’ harmful effects and adjusting their daily routines to meet the requirements of their therapeutic regimens.26–28\n\nIn the current study, two LMQ domains had the lowest mean of burden scores: (relationships with HCPs) and (the effectiveness of prescribed medications). In other words, the patients had good relationships with their HCPs and reasonable belief in their medication effectiveness, reducing their MRB in these two domains. To make appropriate therapy decisions, developing a connection between the patient and the HCP can allow collaborative discussions29,30 to assist practitioners in identifying the specific MRB observed and understanding the actual lived experiences of the patient. Improvements in patient knowledge, satisfaction, and therapeutic and health outcomes were made possible by the value of two-way patient-provider interactions where patients’ experiences are discussed and shared decisions.29,31 Across studies, people’s good attitude toward medications could be seen.32–34 Positive attitudes were primarily associated with trust in healthcare professionals, positive drug experiences, and achieving anticipated therapeutic goals.32–36\n\nSix domains of LMQ (practical difficulties, cost, side effects, effectiveness of prescribed medications, concerns regarding medication use, and the effect of medication use on daily life) correlated positively with the SELENA-SLEDAI score. In addition, treatment burden was associated with several adverse health outcomes, including specific symptoms,37,38 recurrence of disease,39–41 decline in health,38,40 reduced survival,41 decreased treatment satisfaction42 and reduced quality of life.43,44\n\nAge, gender, marital status, place of residence, smoking, the number of drugs one takes, comorbidities, the length of the disease, and level of education were unrelated to MRB (P> 0.05 for all comparisons). The results of the current study do not match the results of many previous studies. Age and treatment burden showed a significant relationship. Given the likelihood of illness and various disorders, older persons appeared to have a higher treatment burden than younger people.37,44,45 Chronic conditions such as diabetes46 were associated with a more significant treatment burden. Longer illness duration in diabetic patients was linked to lower burden.47 Using many medications38,48–52 emerged as the most common predictor of commitment. In addition, the low education level was associated with a higher medication burden.53\n\nPatients with higher income had significantly lower MRB (total LMQ score) compared to low-income patients. Rheumatic diseases are frequently treated with many drug combinations, contributing to the patient’s burden of high medical costs.54 As a result, patients on the border of poverty are more likely to stop taking their drugs due to financial difficulties.55–61\n\nWhen interpreting the findings of this study, a few potential limitations should be considered. The first thing to remember was the limited patient population, partially due to rheumatic disorders’ rarity. Second, self-selection and recall bias was probably present in the results obtained from self-report questionnaires. Third, all participants were recruited from one center. Finally, it is crucial to replicate this study with a larger sample size because our patients might not be representative of Iraqi patients overall. Another limitation is the cross-sectional nature of the data, which was presented at a specific time and does not account for changes in participants’ lived experiences regarding medication usage and adherence over time.\n\n\nConclusions\n\nA significant number of the SLE patients in this research had MRB, with the majority of participants reporting a medium level of burden. According to the present research results, HCPs should be aware of the influence of treatment strategies on the lives of SLE patients. Furthermore, healthcare professionals must develop initiatives to reduce this burden, particularly amongst low-income populations.\n\n\nData availability\n\nZenodo: Demographic data along with questionnaires responses. https://doi.org/10.5281/zenodo.6941308.62\n\nThis project contains the following underlying data:\n\n- Article’s data.xlsx (Demographic data along with questionnaires responses)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThe authors thank the participants and the Baghdad Teaching Hospital/Consultation Clinic team for their continuous support during data collection and patient interviews.\n\n\nReferences\n\nThanou A, Jupe E, Purushothaman M, et al.: Clinical disease activity and flare in SLE: Current concepts and novel biomarkers. J. Autoimmun. 2021; 119: 102615. PubMed Abstract | Publisher Full Text\n\nBongomin F, Sekimpi M, Kaddumukasa M: Clinical and immunological characteristics of 56 patients with systemic lupus erythematosus in Uganda. Rheumatology Advances in Practice. 2020; 4(1): rkaa011. PubMed Abstract | Publisher Full Text\n\nAl-Qubaeissy KYC, Abdulsamad T, Al-Rawi Z, et al.: Does Rheumatoid Factor have any Protective Role in Patients with Lupus Nephritis. Editorial Board. 2020.\n\nPan L, Lu M-P, Wang J-H, et al.: Immunological pathogenesis and treatment of systemic lupus erythematosus. World J. Pediatr. 2020; 16(1): 19–30. PubMed Abstract | Publisher Full Text\n\nFilotico R, Mastrandrea V: Cutaneous lupus erythematosus: clinico-pathologic correlation. Giornale italiano di dermatologia e venereologia: organo ufficiale, Societa italiana di dermatologia e sifilografia. 2018; 153(2): 216–229. PubMed Abstract | Publisher Full Text\n\nLi M, Zhao Y, Zhang Z, et al.: 2020 Chinese guidelines for the diagnosis and treatment of systemic lupus erythematosus. Rheumatology and Immunology Research. 2020; 1(1): 5–23. Publisher Full Text\n\nJiang M, Near AM, Desta B, et al.: Disease and economic burden increase with systemic lupus erythematosus severity 1 year before and after diagnosis: a real-world cohort study, United States, 2004–2015. Lupus science & medicine. 2021; 8(1): e000503. PubMed Abstract | Publisher Full Text\n\nZidan A, Awaisu A, El-Hajj MS, et al.: Medication-related burden among patients with chronic disease conditions: perspectives of patients attending non-communicable disease clinics in a primary healthcare setting in Qatar. Pharmacy. 2018; 6(3): 85. PubMed Abstract | Publisher Full Text\n\nAwad A, Alhadab A, Albassam A: Medication-related burden and medication adherence among geriatric patients in Kuwait: a cross-sectional study. Front. Pharmacol. 2020; 11: 1296. PubMed Abstract | Publisher Full Text\n\nGiven BA, Given CW, Sikorskii A, et al.: Medication burden of treatment using oral cancer medications. Asia Pac. J. Oncol. Nurs. 2017; 4(4): 275–282. PubMed Abstract | Publisher Full Text\n\nGaballah NM, El-Najjar AR: Clinical characteristics and health related quality of life (HRQoL) in Egyptian patients with systemic lupus erythematosus. The Egyptian Rheumatologist. 2019; 41(2): 117–121. Publisher Full Text\n\nImmunology Pathways Weight Descriptor SLEDAI-2K Definition SLEDAI-2K Score* SELENA-SLEDAI Definition SELENA- SLEDAI Score*\n\nFan Y, Hao Y-J, Zhang Z-L: Systemic lupus erythematosus: year in review 2019. Chin. Med. J. 2020; 133(18): 2189–2196. PubMed Abstract | Publisher Full Text\n\nGolder V, Ooi JJY, Antony AS, et al.: Discordance of patient and physician health status concerns in systemic lupus erythematosus. Lupus. 2018; 27(3): 501–506. PubMed Abstract | Publisher Full Text\n\nMohamed A, Chen Y, Wu H, et al.: Therapeutic advances in the treatment of SLE. Int. Immunopharmacol. 2019; 72: 218–223. Publisher Full Text\n\nLiu K, Kurien BT, Zimmerman SL, et al.: X chromosome dose and sex bias in autoimmune diseases: increased prevalence of 47, XXX in systemic lupus erythematosus and Sjögren’s syndrome. Arthritis Rheum. 2016; 68(5): 1290–1300.\n\nJönsen A, Bengtsson AA, Hjalte F, et al.: Total cost and cost predictors in systemic lupus erythematosus–8-years follow-up of a Swedish inception cohort. Lupus. 2015; 24(12): 1248–1256. PubMed Abstract | Publisher Full Text\n\nBexelius C, Wachtmeister K, Skare P, et al.: Drivers of cost and health-related quality of life in patients with systemic lupus erythematosus (SLE): a Swedish nationwide study based on patient reports. Lupus. 2013; 22(8): 793–801. PubMed Abstract | Publisher Full Text\n\nDoria A, Amoura Z, Cervera R, et al.: Annual direct medical cost of active systemic lupus erythematosus in five European countries. Ann. Rheum. Dis. 2014; 73(1): 154–160. PubMed Abstract | Publisher Full Text\n\nCho JH, Chang SH, Shin NH, et al.: Costs of illness and quality of life in patients with systemic lupus erythematosus in South Korea. Lupus. 2014; 23(9): 949–957. PubMed Abstract | Publisher Full Text\n\nPierotti F, Palla I, Pippo L, et al.: Budget impact analysis of belimumab in treating systemic lupus erythematosus. Int. J. Technol. Assess. Health Care. 2016; 32(5): 348–354. PubMed Abstract | Publisher Full Text\n\nGarris C, Jhingran P, Bass D, et al.: Healthcare utilization and cost of systemic lupus erythematosus in a US managed care health plan. J. Med. Econ. 2013; 16(5): 667–677. PubMed Abstract | Publisher Full Text\n\nKrska J, Corlett SA, Katusiime B: Complexity of medicine regimens and patient perception of medicine burden. Pharmacy. 2019; 7(1): 18. PubMed Abstract | Publisher Full Text\n\nDemain S, Goncalves A-C, Areia C, et al.: Living with, managing and minimising treatment burden in long term conditions: a systematic review of qualitative research. PLoS One. 2015; 10(5): e0125457. PubMed Abstract | Publisher Full Text\n\nMohammed MA, Moles RJ, Chen TF: Medication-related burden and patients’ lived experience with medicine: a systematic review and metasynthesis of qualitative studies. BMJ Open. 2016; 6(2): e010035. PubMed Abstract | Publisher Full Text\n\nTran V-T, Montori VM, Eton DT, et al.: Development and description of measurement properties of an instrument to assess treatment burden among patients with multiple chronic conditions. BMC Med. 2012; 10(1): 1–10.\n\nTran V-T, Barnes C, Montori VM, et al.: Taxonomy of the burden of treatment: a multi-country web-based qualitative study of patients with chronic conditions. BMC Med. 2015; 13(1): 1–15.\n\nTran V-T, Harrington M, Montori VM, et al.: Adaptation and validation of the Treatment Burden Questionnaire (TBQ) in English using an internet platform. BMC Med. 2014; 12(1): 1–9.\n\nStevenson FA, Cox K, Britten N, et al.: A systematic review of the research on communication between patients and health care professionals about medicines: the consequences for concordance. Health Expect. 2004; 7(3): 235–245. PubMed Abstract | Publisher Full Text\n\nSav A, King MA, Whitty JA, et al.: Burden of treatment for chronic illness: a concept analysis and review of the literature. Health Expect. 2015; 18(3): 312–324. PubMed Abstract | Publisher Full Text\n\nShay LA, Lafata JE: Where is the evidence? A systematic review of shared decision making and patient outcomes. Med. Decis. Mak. 2015; 35(1): 114–131. PubMed Abstract | Publisher Full Text\n\nRidgeway JL, Egginton JS, Tiedje K, et al.: Factors that lessen the burden of treatment in complex patients with chronic conditions: a qualitative study. Patient Prefer. Adherence. 2014; 8: 339. Publisher Full Text\n\nSav A, Kendall E, McMillan SS, et al.: ‘You say treatment, I say hard work’: treatment burden among people with chronic illness and their carers in Australia. Health Soc. Care Community. 2013; 21(6): 665–674. PubMed Abstract | Publisher Full Text\n\nLorem GF, Frafjord JS, Steffensen M, et al.: Medication and participation: A qualitative study of patient experiences with antipsychotic drugs. Nurs. Ethics. 2014; 21(3): 347–358. Publisher Full Text\n\nAbdulridha SH, Kadhim DJ, Razzak SAA: Beliefs about Medicines among a Sample of Iraqi patients with Psoriasis. Innovations in Pharmacy. 2021; 12(1). Publisher Full Text\n\nFaiq MK, Kadhim DJ, Gorial FI: The Belief about Medicines among a Sample of Iraqi Patients with Rheumatoid Arthritis. Iraqi Journal of Pharmaceutical Sciences (IJPS). 2019; 28(2): 134–141. Publisher Full Text\n\nRibi K, Bernhard J, Rufibach K, et al.: Endocrine symptom assessment in women with breast cancer: what a simple “yes” means. Support. Care Cancer. 2007; 15(12): 1349–1356. PubMed Abstract | Publisher Full Text\n\nMoss L, Crane PB: Exploring polypharmacy in elderly women after myocardial infarction. J. Women Aging. 2010; 22(1): 22–33. PubMed Abstract | Publisher Full Text\n\nGutiérrez-Maldonado J, Caqueo-Urízar A: Effectiveness of a psycho-educational intervention for reducing burden in Latin American families of patients with schizophrenia. Qual. Life Res. 2007; 16(5): 739–747. PubMed Abstract | Publisher Full Text\n\nNicholl D, Akhras KS, Diels J, et al.: Burden of schizophrenia in recently diagnosed patients: healthcare utilisation and cost perspective. Curr. Med. Res. Opin. 2010; 26(4): 943–955. PubMed Abstract | Publisher Full Text\n\nDe Kraker J, Graf N, Van Tinteren H, et al.: Reduction of postoperative chemotherapy in children with stage I intermediate-risk and anaplastic Wilms’ tumour (SIOP 93-01 trial): a randomised controlled trial. Lancet. 2004; 364(9441): 1229–1235. Publisher Full Text\n\nBrod M, Christensen T, Bushnell D: Maximizing the value of validation findings to better understand treatment satisfaction issues for diabetes. Qual. Life Res. 2007; 16(6): 1053–1063. PubMed Abstract | Publisher Full Text\n\nFiese BH, Wamboldt FS, Anbar RD: Family asthma management routines: Connections to medical adherence and quality of life. J. Pediatr. 2005; 146(2): 171–176. PubMed Abstract | Publisher Full Text\n\nOlinder AL, Kernell A, Smide B: Missed bolus doses: devastating for metabolic control in CSII-treated adolescents with type 1 diabetes. Pediatr. Diabetes. 2009; 10(2): 142–148. PubMed Abstract | Publisher Full Text\n\nYoon J, Malin JL, Tao ML, et al.: Symptoms after breast cancer treatment: are they influenced by patient characteristics? Breast Cancer Res. Treat. 2008; 108(2): 153–165. Publisher Full Text\n\nVijan S, Hayward RA, Ronis DL, et al.: Brief report: the burden of diabetes therapy. J. Gen. Intern. Med. 2005; 20(5): 479–482. PubMed Abstract | Publisher Full Text\n\nBrod M, Valensi P, Shaban JA, et al.: Patient treatment satisfaction after switching to NovoMix® 30 (BIAsp 30) in the IMPROVE™ study: an analysis of the influence of prior and current treatment factors. Qual. Life Res. 2010; 19(9): 1285–1293. PubMed Abstract | Publisher Full Text\n\nGallacher K, May CR, Montori VM, et al.: Understanding patients’ experiences of treatment burden in chronic heart failure using normalization process theory. The Annals of Family Medicine. 2011; 9(3): 235–243. PubMed Abstract | Publisher Full Text\n\nGraves MM, Adams CD, Bender JA, et al.: Volitional nonadherence in pediatric asthma: parental report of motivating factors. Curr Allergy Asthma Rep. 2007; 7(6): 427–432. PubMed Abstract | Publisher Full Text\n\nTjia J, Micco E, Armstrong K: Interest in breast cancer chemoprevention among older women. Breast Cancer Res. Treat. 2008; 108(3): 435–453. PubMed Abstract | Publisher Full Text\n\nBenner JS, Chapman RH, Petrilla AA, et al.: Association between prescription burden and medication adherence in patients initiating antihypertensive and lipid-lowering therapy. Am. J. Health Syst. Pharm. 2009; 66(16): 1471–1477. PubMed Abstract | Publisher Full Text\n\nRobertson TA, Cooke CE, Wang J, et al.: Effect of medication burden on persistent use of lipid-lowering drugs among patients with hypertension. Am. J. Manag. Care. 2008; 14(11): 710–716. PubMed Abstract\n\nWang Y, Li X, Jia D, et al.: Exploring polypharmacy burden among elderly patients with chronic diseases in Chinese community: a cross-sectional study. BMC Geriatr. 2021; 21(1): 308. PubMed Abstract | Publisher Full Text\n\nCarter EE, Barr SG, Clarke AE: The global burden of SLE: prevalence, health disparities and socioeconomic impact. Nat. Rev. Rheumatol. 2016; 12(10): 605–620. PubMed Abstract | Publisher Full Text\n\nTrindade VC, Carneiro-Sampaio M, Bonfa E, et al.: An Update on the Management of Childhood-Onset Systemic Lupus Erythematosus. Paediatr. Drugs. 2021; 23(4): 331–347. PubMed Abstract | Publisher Full Text\n\nGross R, Graybill J, Wahezi D, et al.: Increased Education is Associated with Decreased Compliance in an Urban Multi-Ethnic Lupus Cohort. Journal of clinical & cellular immunology. 2014; 5(3).\n\nAbdul-Sattar AB, Abou El Magd SA: Determinants of medication non-adherence in Egyptian patients with systemic lupus erythematosus: Sharkia Governorate. Rheumatol. Int. 2015; 35(6): 1045–1051. PubMed Abstract | Publisher Full Text\n\nPascual-Ramos V, Contreras-Yáñez I: Motivations for inadequate persistence with disease modifying anti-rheumatic drugs in early rheumatoid arthritis: the patient’s perspective. BMC Musculoskelet. Disord. 2013; 14: 336. PubMed Abstract | Publisher Full Text\n\nBonafede M, Johnson BH, Princic N, et al.: Cost per patient-year in response using a claims-based algorithm for the 2 years following biologic initiation in patients with rheumatoid arthritis. J. Med. Econ. 2015; 18(5): 376–389. PubMed Abstract | Publisher Full Text\n\nNasser-Ghodsi N, Harrold LR: Overcoming adherence issues and other barriers to optimal care in gout. Curr. Opin. Rheumatol. 2015; 27(2): 134–138. PubMed Abstract | Publisher Full Text\n\nSolomon DH, Tonner C, Lu B, et al.: Predictors of stopping and starting disease-modifying antirheumatic drugs for rheumatoid arthritis. Arthritis Care Res. 2014; 66(8): 1152–1158. PubMed Abstract | Publisher Full Text\n\nShareef LG: Demographic data along with questionnaires responses [Data set]. Zenodo. 2022. Publisher Full Text"
}
|
[
{
"id": "149919",
"date": "27 Sep 2022",
"name": "Bridget Hodkinson",
"expertise": [
"Reviewer Expertise Rheumatology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper measured medication-related burden amongst Iraqi SLE patients and showed moderate burden, particularly in areas of practical difficulties in using medications, concerns about the use of drugs, and the impact of using medicines on daily life. This is an important study, and useful information to allow better care of patients.\nPlease address the following questions:\nHow did “illiterate” patients complete the questionnaire? Almost 20% of your patients are illiterate according to your data.\n\nTable 6B shows that patients with a lower monthly income had significantly higher MRB scores. In the discussion, you assume this is due to financial constraints causing pts to stop meds. Do you have evidence for this? Suggest looking at individual domains affected by income to defend your interpretation. Other reasons may be true also.\n\nAre you able to comment on SLE organ involvement (e.g. nephritis, NPSLE) effects on MRB rather than just the summation score? See your ref 22. If not mention this as a limitation.\nThere are a few grammatical/style errors that need addressing:\nThe use of brackets midsentence, e.g. pg 7 - \"…(practical difficulties in using medications), (concerns about the use of drugs), and (the impact of using medicines on daily life).\"\n\nAlso, paragraph 1 of the discussion needs refining – avoid words like “unacceptably” and “drastically – these are not used in scientific writing.\n\nRevise “about (96.8%) of patients”, say over 96% were female or the vast majority (96.8%) were female.\n\nClean up the repetitive headings of Table 6A and B, make another column for p-value in Table 5 and delete the rows of the p-value. Remove column 1 from Table 6.\n\nCombine Tables 3 and 4.\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? Partly",
"responses": [
{
"c_id": "8903",
"date": "01 Nov 2022",
"name": "Laith G. Shareef",
"role": "Author Response",
"response": "1. How did “illiterate” patients complete the questionnaire? Almost 20% of your patients are illiterate according to your data. Answer: After obtaining the patient's permission to participate in the research, we interviewed them in a dedicated room in the rheumatology unit, explained each item in the questionnaire, acquired the patient's degree of reaction, and noted it in the questionnaire. 2. Table 6B shows that patients with a lower monthly income had significantly higher MRB scores. In the discussion, you assume this is due to financial constraints causing pts to stop meds. Do you have evidence for this? Suggest looking at individual domains affected by income to defend your interpretation. Other reasons may be true also. Answer: Because rheumatic diseases are frequently treated with many drug combinations, which contributes to the patient's burden of high medical costs, when we looked at two items of cost-related burden domain: \"I worry about paying for my medicines. I have to pay more than I can afford for my medicines\", in these items the mean of burden score higher than the average, in other words, those patients were more worried about paying for their medicines, and they paid for their medicines more than they can afford, leading to increase the burden of medicines on patients with low monthly income and contribute to an inadequate level of adherence. 3. Are you able to comment on SLE organ involvement (e.g., nephritis, NPSLE) effects on MRB rather than just the summation score? See your ref 22. If not mention this as a limitation. Answer: We cannot comment on the effects of SLE organ involvement (e.g., nephritis, NPSLE) on MRB; this needs further study; we can determine it as a limitation in the current study. There are a few grammatical/style errors that need addressing: 1- The use of brackets midsentence, e.g. pg 7 - \"(practical difficulties in using medications), (concerns about the use of drugs), and (the impact of using medicines on daily life).\" Answer: The new version includes the requested adjustments. 2- Also, paragraph 1 of the discussion needs refining – avoid words like “unacceptably” and “drastically – these are not used in scientific writing. Answer: The new version includes the requested adjustments. 3- Revise “about (96.8%) of patients”, say over 96% were female or the vast majority (96.8%) were female. Answer: The new version includes the requested adjustments. 4- Clean up the repetitive headings of Table 6A and B, make another column for p-value in Table 5 and delete the rows of the p-value. Remove column 1 from Table 6. Answer: The new version includes the requested adjustments. 5- Combine Tables 3 and 4. Answer: The new version includes the requested adjustments."
}
]
}
] | 1
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https://f1000research.com/articles/11-970
|
https://f1000research.com/articles/11-118/v1
|
28 Jan 22
|
{
"type": "Research Article",
"title": "Research Software vs. Research Data I: Towards a Research Data definition in the Open Science context",
"authors": [
"Teresa Gomez-Diaz",
"Tomas Recio"
],
"abstract": "Background: Research Software is a concept that has been only recently clarified. In this paper we address the need for a similar enlightenment concerning the Research Data concept. Methods: Our contribution begins by reviewing the Research Software definition, which includes the analysis of software as a legal concept, followed by the study of its production in the research environment and within the Open Science framework. Then we explore the challenges of a data definition and some of the Research Data definitions proposed in the literature. Results: We propose a Research Data concept featuring three characteristics: the data should be produced (collected, processed, analyzed, shared & disseminated) to answer a scientific question, by a scientific team, and has yield a result published or disseminated in some article or scientific contribution of any kind. Conclusions: The analysis of this definition and the context in which it is proposed provides some answers to the Borgman’s conundrum challenges, that is, which Research Data might be shared, by whom, with whom, under what conditions, why, and to what effects. They are completed with answers to the questions: how? and where?",
"keywords": [
"Research Data",
"Research Software",
"Open Science."
],
"content": "1. Introduction\n\nEach particle of the Universe, known or unknown by what is widely accepted as Science, is information. Different datasets can be associated to each particle to convey information, as, for example: where has this particle been discovered? By whom? At what time? Is this particle a constituent element of a rock, or a plant, or…? Indeed, as living entities of the Earth planet, …we are all part of this Universe and every atom in our bodies came from a star that exploded…, therefore …we are all stardust….1\n\nSo long ago that we have never been able to give a precise date, information started to be fixed in cave paintings, figurines, and bone cravings, which have been found in caves like Altamira2 or Lascaux3. That is, some human beings intentionally fixed information on a support. Much more recently, languages have been developed to deal with information, fixing and exchanging it in clay bricks, papyrus, monument walls, and paper books. Even more recently, information has been fixed in films, photographs, and has finally adopted digital formats.\n\nScientists study all kinds of subjects and objects: persons, animals, trees and plants and other living beings, philosophies and philosophers, artists and artworks, mathematical theories, music, languages, societies, cities, Earth and many other planets and exoplanets, clouds, weather and climate, stars and galaxies, as well as other animate or inanimate objects, molecules, particles, nanoparticles and viruses, nowadays including digital objects such as computer programs. Some of these items, like images, texts, and music etc. may have associated intellectual property rights; but others, like statistics or geographical data, may not. Yet, they may be affected by other legal contexts, such as, for example, the one given by the EU INSPIRE Directive 1 for spatial data, concerning any data with a direct or indirect reference to a specific location or geographical area.\n\nNow, in our digital era, most of the above subjects under consideration are handled by humans using computers, through numerical data. Scientists present new theories and results built and produced with numerical simulations and through the analysis of numerical datasets. They are usually stored in databases, manipulated or produced in digital environments using existing software, either Free/Open Source Software (FLOSS)4 or commercial, or by means of software developed by research teams to address specific problems 2,3.\n\nIn this specific scientific context, the aims and developments of Open Science practices are particularly relevant. Indeed, as remarked by 4: \"We must all accept that science is data and that data are science…\". Therefore, in this article we take into consideration the following definition of Open Science, in which the open access to Research Data (RD) and to Research Software (RS) is part of the core pillars 5:\n\nOpen Science is the political and legal framework where research outputs are shared and disseminated in order to be rendered visible, accessible and reusable.\n\nA more transversal and global vision can be found in the ongoing work for the UNESCO Recommendation on Open Science5 6. See also 7 for another relevant example of ongoing work on the Open Science concept.\n\nAmong the most important kinds of research outputs of any scientific work, we focus on the trio formed by articles, software and data. Actually, among all the possible duos, the couple RS and RD present more similarities. For instance, unlike the dissemination of published articles, usually at the hands of scientific editors, the dissemination of software and data that have been produced in the research process is mostly at the hands of their producers, the research team. More generally, as sketched in 8, the release of RD and RS raises the same questions, at the same time, in the production context. As a direct consequence, it seems suitable to propose a similar dissemination procedure 9.\n\nAs mentioned in the last reference, both RS and RD can be disseminated using licenses to set their sharing conditions. RS licenses and licensing information can be found at the Free Software Foundation (FSF)6, the Open Source Initiative (OSI)7, and the Software Package Data Exchange (SPDX)8. The SPDX licenses list also includes licenses that can be used for databases, like the Creative Commons licenses9 or the Open Data Commons Licenses10. On the other hand, let us remark that Data Management Plans are nowadays required by several research funders (see for example 10,11) and that Software Management Plans are also available 12. Finally, concerning evaluation, as observed in 3, a similar evaluation protocol can be proposed for both RS and RD. These two subjects, RD dissemination and evaluation, are more closely analyzed in the article 13 that follows the present work.\n\nInspired by this collection of analogies, we will argue in the next sections that a definition for RD can be proposed following the main features of the RS definition given in our recent work 3,14. However, it remains a challenging issue. In fact, although one of the most widely accepted RD definitions is the one proposed by the OECD (2007) 15, other works have shown the difficulties to fix such a definition 16,17.\n\nIndeed, this concept has important and not well settled consequences, for example, in the context of data sharing, as highlighted by C. Borgman in 18:\n\nData sharing is thus a conundrum. […]\n\nThe challenges are to understand which data might be shared, by whom, with whom, under what conditions, why, and to what effects. Answers will inform data policy and practice.\n\nIt is the intention of our present work to bring some answers to these questions.\n\nThe plan of this article is as follows. The next section introduces the concept of RS after a summary presentation of the key points involved in the notion of software as a legal object. Section 3 is devoted to discuss the different issues involved in the challenge towards a precise data definition. Section 4 describes partially the landscape of existing work addressing the RD definition, enumerating some difficulties to settle such a concept. Then we propose our RD definition based in three characteristics: the data should be produced (collected, processed, analyzed, shared & disseminated) to answer a scientific question, by a scientific team, and has yield a result published or disseminated in some article or scientific contribution of any kind. Comparisons with other RD definitions are examined. The last and final section concludes with the proposition of some specific answers to Borgman’s conundrum challenges 18. Let us remark that these conundrum challenges involve as well RD dissemination issues that are studied in detail in the article that follows this work 13, which also includes the analysis of RD evaluation issues.\n\nThe reader of the current work should be aware that its authors are not legal experts. Thus, in order to complete this article, we have analyzed legal documents and articles written by law experts 1,16,17,19–31, but from the scientist’s point of view. Yet, a deeper understanding of legal issues may require the intervention of legal specialists.\n\nFollowing the standard scientific behavior (the authors of this work are mathematicians), we have detected a problem – the need to provide a more suitable RD definition – and have observed the involved landscape and studied the related literature; we have focused on and structured different components of the problem; finally, we have proposed what we think can be a solution for the challenge under consideration. As in any other research work, we believe that our proposal should be examined by the scientific community in order to evaluate its correctness, and to help improving it, if needed, advancing towards a better solution.\n\n\n2. Research Software\n\nIn this section we bring together some of the existing definitions of software as a legal object (see references below). We also recall our definition of RS coming from 3,14.\n\nIn what follows we refer to the documents 22–25 dealing with a definition of software as a legal object. Note that the terms computer program, software, logiciel (in French), programa de ordenador (in Spanish) are synonyms in this work. The terms source code (or código fuente in Spanish), compiled code (or code compilé, código compilado) correspond to subsets of a computer program.\n\nThe first definition that we would like to consider comes from the Directive 2009/24/EC of the European Parliament 22, that states:\n\nFor the purpose of this Directive, the term “computer program” shall include programs in any form, including those which are incorporated into hardware. This term also includes preparatory design work leading to the development of a computer program provided that the nature of the preparatory work is such that a computer program can result from it at a later stage.\n\nMoreover, in the Spanish Boletn Oficial del Estado n. 97 (1996) 23 we can find11:\n\nA los efectos de la presente Ley se entenderá por programa de ordenador toda secuencia de instrucciones o indicaciones destinadas a ser utilizadas, directa o indirectamente, en un sistema informático para realizar una función o una tarea o para obtener un resultado determinado, cualquiera que fuere su forma de expresión y fijación. […] comprenderá también su documentación preparatoria.12\n\nLikewise, in the French Journal officiel de la République française (1982) 25 we can read:\n\nLogiciel: Ensemble des programmes, procédés et règles, et éventuellement de la documentation, relatifs au fonctionnement d’un ensemble de traitement de données (en anglais: software)13.\n\nAnd in the French Code de la propriété intellectuelle (current regulation) 24, Article L112-2, we can find:\n\nLes logiciels, y compris le matériel de conception préparatoire, sont considérés notamment comme œ uvres de l’esprit au sens du présent code.14\n\nWe observe that, in the above mentioned documents, the concept of software or computer program, logiciel or programa de ordenador refers to the set of instructions, of any kind, that are to be used in a computer system (including hardware). It is a work protected by the author rights. It can include the source code, the compiled code, and, eventually, the associated documentation and the preparatory material. It can be related to some data processing or to other tasks to be implemented in a computer system.\n\nIn order to complete this legal vision of the software concept we refer to item (11) of 22:\n\nFor the avoidance of doubt, it has to be made clear that only the expression of a computer program is protected and that ideas and principles which underlie any element of a program, including those which underlie its interfaces, are not protected by copyright under this Directive. In accordance with this principle of copyright, to the extent that logic, algorithms and programming languages comprise ideas and principles, those ideas and principles are not protected under this Directive. In accordance with the legislation and case-law of the Member States and the international copyright conventions, the expression of those ideas and principles is to be protected by copyright.\n\nIndeed, there is a difference between the concepts of algorithm and software from the legal point of view, as there is a difference between the mere idea for the plot of a novel and the final written work. Several persons could have the same idea for the plot, but its realization in a final document will deliver different novels by different writers, as the novel will reflect the personality of its author. Similarly, an algorithm remains on the side of ideas, and as such, it is not protected by copyright laws. On the other side, poetry, novels and software are protected under copyright laws. Moreover, a computer program can implement several algorithms, and the same algorithm can be implemented in several programs.\n\nFinally, note the nature of software as a digital object underlying all the above considerations.\n\nBeyond the vision of software as a legal object, we will focus here on the concept of software as a scientific production. In particular, we consider the following definition of RS 3,14:\n\nResearch Software is a well identified set of code that has been written by a (again, well identified) research team. It is software that has been built and used to produce a result published or disseminated in some article or scientific contribution. Each research software encloses a set (of files) that contains the source code and the compiled code. It can also include other elements as the documentation, specifications, use cases, a test suite, examples of input data and corresponding output data, and even preparatory material.\n\nSection 2.1 of 3 introduces several definitions regarding the notions of scientific and research software as found in the literature, as a way to support the above definition, while 14 provides complementary analysis on this concept. Note that this definition does not take into consideration if the RS status is “ongoing” or “finalized”, and does not regard if the RS has been disseminated, its quality or scope, its size, or if it is documented, maintained, used only by the development team for the production of an article, or it is currently used in several labs… 2. Another example of recent work on the RS concept can be found on the RDA FAIR for Research Software (FAIR4RS) working group.15\n\nWe observe, following the above definition, that RS has three main characteristics:\n\n• the goal of the RS development is to do research. As stated by D. Kelly: it is developed to answer a scientific question 32,\n\n• it has been written by a research team,\n\n• the RS is involved in the obtention of the results presented in scientific articles (as the most important means for scientific exchange are still articles published in scientific journals).\n\nNote that documentation, licenses, examples, data, tests, Software Management Plans and other related information and materials can also be part of the set of files that constitutes a specific RS. Remark that the data we refer to in this list will qualify as RD (as defined in Section 4) if they have been produced by a research team, that can be the same team that has produced the RS, but not necessarily.\n\nBesides, we do not include in this RS category neither commercial software nor existing Free/Open Source Software (FLOSS) software developed outside Academia. As a matter of fact, a research team can use RS produced by other teams for their scientific work, as well as FLOSS or other software developed outside the scientific community, but the present work is centered in the making-of aspects which are pertinent for the proposed definition. Obviously, a RS that has been initially developed in a research lab can evolve to become commercial software or just evolve outside its initial academic context. The above definition concerns its early, academic life.\n\nMoreover, a RS development team may not just use software produced by other teams, but also include external software as a component inside the ongoing development, which is facilitated by the FLOSS licenses. This external component will qualify here as RS if it complies with the three characteristics given in the above definition, and the producers of the resulting work should clearly identify the included external components, their licenses, as well as highlight other used or included RS components by means of the citation of a paper or the different RS 3,9,33–35.\n\nLet us observe that a RS may involve other software components that can remain external, and that are not included in the RS development. It is then left to the users the task to recover and install them, and assemble these external components in order to get a running environment. On the other hand, in another example that we have analyzed in 14, the GeoGebra code developed by T. Recio and collaborators16 does not disseminate the whole GeoGebra software17, but only the part that they have developed. Users are well aware of the need to have a running GeoGebra environment in order to launch the new software developed by the above mentioned research team.\n\nSee 2,3,14 for more discussions and references that have motivated the RS definition we have sketched in this section.\n\n\n3. The challenges of a data definition\n\nAs stated in 36:\n\n“Data” is a difficult concept to define, as data may take many forms, both physical and digital.\n\nUnlike software, data is, as a legal object, much more difficult to grasp. In fact, according to 30, data is not a legal concept, as it does not fall into a specific legal regime. For example, data can be either mere information or une œuvre, a work with associated intellectual property, when it involves creative choices in its production that reflect the author’s personality 29. The Knowledge Exchange report 17 provide guidelines that can be used to assess the legal status of research data, and mentions:\n\nIt is important to know the legal status of the data to be shared. […] not all data are protected by law, and not every use of protected research data requires the author’s consent. […] Whether data are in fact protected must be determined on a case-by-case basis.\n\nIn relation with this legal context of data sharing and reuse, a very complete framework is introduced in 19:\n\nLes problématiques liées à la réutilisation nécessitent une matrise parfaite du droit de la propriété intellectuelle, du droit à l’image, du droit des données personnelles, du respect à la vie privée et du secret de la statistique, du droit des affaires, du droit de la concurrence, du droit de la culture, du droit européen et des règles de l’économie publique.18\n\nAnother list of legal issues related to data is provided by 30, similar but not equal to the one in the previous quote.\n\nYet, it is also necessary to consider other legal contexts concerning, for example, les données couvertes par le secret médical ou le secret industriel et commercial 19. Let us remark that the section Applicable Laws and Regulations of 11 provides a broad overview of regulatory aspects that need to be taken into consideration when developing disciplinary RD management protocols.\n\nThe problem is that data can refer to many different subjects or objects and they may be protected under different laws. It is not our intention to consider here these legal aspects. We need to simplify the context to help us to set a manageable concept of research data in the scientific framework. For this purpose we present here two relevant data definitions found in the data scientific literature.\n\nThe OECD data definition in its Glossary of Statistical Terms20 states that:\n\nDATA\n\nDefinition: Characteristics or information, usually numerical, that are collected through observation.\n\nContext: Data is the physical representation of information in a manner suitable for communication, interpretation, or processing by human beings or by automatic means (Economic Commission for Europe of the United Nations (UNECE)), “Terminology on Statistical Metadata”, Conference of European Statisticians Statistical Standards and Studies, No. 53, Geneva, 2000.\n\nAlso, as a relevant precedent, let us quote here the data definition of the Committee for a Study on Promoting Access to Scientific and Technical Data for the Public Interest, as mentioned in 37:\n\nA data set is a collection of related data and information – generally numeric, word oriented, sound, and/or image – organized to permit search and retrieval or processing and reorganizing. Many data sets are resources from which specific data points, facts, or textual information is extracted for use in building a derivative data set or data product. A derivative data set, also called a value-added or transformative data set, is built from one or more preexisting data set(s) and frequently includes extractions from multiple data sets as well as original data (Committee for a Study on Promoting Access to Scientific and Technical Data for the Public Interest, 1999, p. 15).\n\nTo better grasp the connection between the concepts of data and information we have consulted several sources of different natures, as for example: the definition of dato21 and the definition of información22 in the Diccionario de la lengua española of the Real Academia Española, the definition of donnée23 and the definition of information24 in the Dictionnaire Larousse de français, and the data definition25 in Wikipedia. Note that we can find information among the data synonyms in the Larousse dictionary, but data is not among the information synonyms. On the other hand, Wikipedia mentions that both terms can be used interchangeably, but that they have different meanings. These sources bring to us an eclectic panorama on the ingredients that could form a data definition and their relation with the concept of information. Some extracts of the texts in the links mentioned in the previous footnotes have been included in Box 1.\n\nI.1 Diccionario de la lengua española of the Real Academia Española\n\n• Definition of dato (https://dle.rae.es/dato)\n\n– Del latín datum ‘lo que se da’.\n\n– 1. m. Información sobre algo concreto que permite su conocimiento exacto o sirve para deducir las consecuencias derivadas de un hecho. A este problema le faltan datos numéricos.\n\n– 2. m. Documento, testimonio, fundamento.\n\n– 3. m. Inform. Información dispuesta de manera adecuada para su tratamiento por una computadora.\n\n• Definition of información (https://dle.rae.es/informaci%C3%B3n)\n\n– Del latín informatio, -o¯nis ‘concepto’, ‘explicación de una palabra’.\n\n– 1. f. Acción y efecto de informar.\n\n– 2. f. Oficina donde se informa sobre algo.\n\n– 3. f. Averiguación jurídica y legal de un hecho o delito.\n\n– 4. f. Pruebas que se hacen de la calidad y circunstancias necesarias en una persona para un empleo u honor. U. m. en pl.\n\n– 5. f. Comunicación o adquisición de conocimientos que permiten ampliar o precisar los que se poseen sobre una materia determinada.\n\n– 6. f. Conocimientos comunicados o adquiridos mediante una información.\n\n– 7. f. Biol. Propiedad intrínseca de ciertos biopolímeros, como los ácidos nucleicos, originada por la secuencia de las unidades componentes.\n\n– 8. f. desus. Educación, instrucción.\n\nI.2 Diccionnaire Larousse de la langue française\n\n• Definition of donnée (https://www.larousse.fr/dictionnaires/francais/donn%c3%a9e/26436)\n\n– Ce qui est connu ou admis comme tel, sur lequel on peut fonder un raisonnement, qui sert de point de départ pour une recherche (ex. Les données actuelles de la biologie).\n\n– Idée fondamentale qui sert de point de départ, élément essentiel sur lequel est construit un ouvrage (ex. Les données d’une comédie).\n\n– Renseignement qui sert de point d’appui (ex. Manquer de données pour faire une analyse approfondie).\n\n– Représentation conventionnelle d’une information en vue de son traitement informatique.\n\n– Dans un problème de mathématiques, hypothèse figurant dans l’énoncé.\n\n– Résultats d’observations ou d’expériences faites délibérément ou à l’occasion d’autres tâches et soumis aux méthodes statistiques.\n\n• Definition of information (https://www.larousse.fr/dictionnaires/francais/information/42993)\n\n– Action d’informer quelqu’un, un groupe, de le tenir au courant des événements : La presse est un moyen d’information.\n\n– Indication, renseignement, précision que l’on donne ou que l’on obtient sur quelqu’un ou quelque chose: Manquer d’informations sur les causes d’un accident. (Abréviation familière : info.)\n\n– Tout événement, tout fait, tout jugement porté à la connaissance d’un public plus ou moins large, sous forme d’images, de textes, de discours, de sons. (Abréviation familière : info.)\n\n– Nouvelle communiquée par une agence de presse, un journal, la radio, la télévision. (Abréviation familière : info.)\n\n– Cybernétique. Mesure de la diversité des choix dans un répertoire de messages possibles.\n\n– Droit. Instruction préparatoire, diligentée par le juge d’instruction en vue de rechercher et de rassembler les preuves d’une infraction, de découvrir l’auteur, de constituer à charge et à décharge le dossier du procès pénal. (Elle est close par un non-lieu ou par un renvoi devant une juridiction répressive. En matière criminelle, l’instruction est à double degré [juge d’instruction, chambre d’accusation].)\n\n– Informatique. Élément de connaissance susceptible d’être représenté à l’aide de conventions pour être conservé, traité ou communiqué.\n\nI.3 Wikipedia\n\nExtract from the Data page of Wikipedia (https://en.wikipedia.org/wiki/Data):\n\nData are characteristics or information, usually numeric, that are collected through observation. In a more technical sense, data are a set of values of qualitative or quantitative variables about one or more persons or objects, while a datum (singular of data) is a single value of a single variable.\n\n[…]\n\nAlthough the terms “data” and “information” are often used interchangeably, these terms have distinct meanings. […] data are sometimes said to be transformed into information when they are viewed in context or in post-analysis. However, […] data are simply units of information.\n\nYet, the above considerations only provide a light panorama of the complexity that is hiding behind the concepts of data and information. To illustrate this complexity in full terms we can refer to the French Code de l’environnement 26. In its Article L-124-226 we can appreciate the subtleties of the definition of environmental data in the following description:\n\nEst considérée comme information relative à l’environnement au sens du présent chapitre toute information disponible, quel qu’en soit le support, qui a pour objet :\n\n1. L’état des éléments de l’environnement, notamment l’air, l’atmosphère, l’eau, le sol, les terres, les paysages, les sites naturels, les zones côtières ou marines et la diversité biologique, ainsi que les interactions entre ces éléments ;\n\n2. Les décisions, les activités et les facteurs, notamment les substances, l’énergie, le bruit, les rayonnements, les déchets, les émissions, les déversements et autres rejets, susceptibles d’avoir des incidences sur l’état des éléments visés au point 1 ;\n\n3. L’état de la santé humaine, la sécurité et les conditions de vie des personnes, les constructions et le patrimoine culturel, dans la mesure où ils sont ou peuvent être altérés par des éléments de l’environnement, des décisions, des activités ou des facteurs mentionnés ci-dessus ;\n\n4. Les analyses des coûts et avantages ainsi que les hypothèses économiques utilisées dans le cadre des décisions et activités visées au point 2 ;\n\n5. Les rapports établis par les autorités publiques ou pour leur compte sur l’application des dispositions législatives et réglementaires relatives à l’environnement.27\n\nTo be compared with the much more easier to understand concept of geographical data as introduced by the Article L127-128 of the same Code de l’environnement 26:\n\nDonnée géographique, toute donnée faisant directement ou indirectement référence à un lieu spécifique ou une zone géographique ;29\n\nAnother example to show the complexity of the representation and manipulation of data and information that we would like to mention here corresponds to the linguistic research work developed at the Laboratoire d’informatique Gaspard-Monge, where one of the authors of the present work resides, see for example the doctoral thesis 38,39.\n\nAn additional factor that adds complexity to the concept of scientific data has to do with the potential use(s) and sharing of these data. As remarked by the OECD Glossary of Statistical Terms30:\n\nThe context provides detailed background information about the definition, its relevance, and in the case of data element definitions, the appropriate use(s) of the element described.\n\nThe importance of the context is also noted in 18:\n\n…research data take many forms, are handled in many ways, using many approaches, and often are difficult to interpret once removed from their initial context.\n\nThis opens the door to a series of complex issues. For example, to the need for complementary, technical information associated to a given dataset in order to facilitate its reuse. See 40 (p.16) (and also 36) that highlights the difficulties raised by the concept of temperature related data, as explained by a CENS biologist:\n\nThere are hundreds of ways to measure temperature. “The temperature is 98” is low-value compared to, “the temperature of the surface, measured by the infrared thermopile, model number XYZ, is 98.” That means it is measuring a proxy for a temperature, rather than being in contact with a probe, and it is measuring from a distance. The accuracy is plus or minus.05 of a degree. I [also] want to know that it was taken outside versus inside a controlled environment, how long it had been in place, and the last time it was calibrated, which might tell me whether it has drifted.\n\nAnother instance to further illustrate the complexity of technical information associated to a data set in the STRENDA Guidelines that have been developed to assist authors to provide data describing their investigations of enzyme activities.31 Other examples from the collection of complex issues associated to data use(s) and sharing conditions are:\n\n• 19 (p.11) The concept of right of access, involving the meaning of public information, requiring three characteristics: the existence of a document, of administrative nature, and in the possession of the Public Administration.\n\n• 19 (p.13) The idea of reuse:\n\n…l’utilisation d’une information publique par toute personne qui le souhaite à d’autres fins que celles de la mission de service public pour les besoins de laquelle les documents ont été élaborés ou détenus.32\n\nfinds a strong formulation for scientific data in 41:\n\nThe value of data lies in their use. Full and open access to scientific data should be adopted as the international norm for the exchange of scientific data derived from publicly funded research. The public-good interests in the full and open access to and use of scientific data need to be balanced against legitimate concerns for the protection of national security, individual privacy, and intellectual property.\n\nFor more information on ‘re-use’ see, for example, 16,21,29,40.\n\n• 19 (p.10) The evolution from the right of access to documents from the Public Administration to the right of reuse of public information.\n\n• 19 (section II) The meaning of free/libre reuse of public information, under three circumstances:\n\n1 public information derived from a document produced or hold by the Administration,\n\n2 there are no other intellectual property rights owners,\n\n3 data do not affect personal or private issues of people.\n\n• 18 (p. 1060) The concept of data sharing in a scientific context:\n\nFor the purposes of this article, data sharing is the release of research data for use by others. Release may take many forms, from private exchange upon request to deposit in a public data collection. Posting datasets on a public website or providing them to a journal as supplementary materials also qualifies as sharing.\n\n\n\n• The importance of licenses to set the sharing and re-use conditions as highlighted in 42,28,5.\n\n• The concepts of Open Data33 and Open access to data, see for example 21,29,43,44.\n\n• The recent and relevant introduction of the term Big Data34, that refers to the exploitation of larger amounts of data. They can appear in medical research, meteorology, genomics, astronomy, demographic studies … and in real life, as we live all in a digital world where we generate large amounts of data every day by the use of phones and computers to do work, traveling, e-mail, business, shopping etc.\n\nBig data is associated mainly to four “V” characteristics: Volume, Variety, Velocity, Veracity, and others can be found for example in the mentioned Wikipedia page and in the references mentioned there. See also 45.\n\nLet us remark again that legal aspects arise quite naturally in the above list of items. Among others, some aspects are related to the fact that the datasets are usually organized in databases, where data is arranged in a systematic or methodical way and is individually accessible by electronic or other means 16,17,20,24,28. The intellectual property rights can apply to the content of a database, the disposition of its elements and to the tools that make it working (for example software). The sui generis database rights primarily protects the producer of the database and may prohibit, for instance, the extraction and/or reuse of all or a substantial part of its content 20.\n\nFinally, let us quote here this paragraph from the OpenAIRE project report 16 (p.19) that highlights the difficulties to set a research data definition in the context of legal studies:\n\nFrom a legal point of view, one of the very basic questions of this study is which kind of potentially protected data we are dealing with in the context of e-infrastructures for publications and research data such as OpenAIREplus. The term “research data” in this context does not seem to be very helpful, since there is no common definition of what research data basically is.\n\nIt seems rather that every author or research study in this context uses its own definition of the term. Therefore, the term “research data” will not be strictly defined, but will include any kind of data produced in the course of scientific research, such as databases of raw data, tables, graphics, pictures or whatever else.\n\n\n4. Data as a research output: towards a definition for Research Data\n\nAfter a partial description of the current difficulties involved in the RD concept, we propose here a RD definition, directly derived from the RS definition presented in Section 2.2. To this aim we start by gathering some previous definitions that are particularly relevant for our proposal.\n\nThe first one is the White House document 31, and in particular the Intangible property section where we can find the following definition.\n\nResearch data is defined as the recorded factual material commonly accepted in the scientific community as necessary to validate research findings, but not any of the following: preliminary analyses, drafts of scientific papers, plans for future research, peer reviews, or communications with colleagues.\n\nLet us remark that, according to31 this definition explicitly excludes:\n\n(A) Trade secrets, commercial information, materials necessary to be held confidential by a researcher until they are published, or similar information which is protected under law; and\n\n(B) Personnel and medical information and similar information the disclosure of which would constitute a clearly unwarranted invasion of personal privacy, such as information that could be used to identify a particular person in a research study.\n\nThe above RD definition has been extended in 46, emphasizing, among other aspects, the scientific purpose of the recorded factual material and the link with the scientific community.\n\nA second basic inspiration for our proposal is the Directive for Open Data 21 that states:\n\n(27) The volume of research data generated is growing exponentially and has potential for re-use beyond the scientific community. […] Research data includes statistics, results of experiments, measurements, observations resulting from fieldwork, survey results, interview recordings and images. It also includes meta-data, specifications and other digital objects. Research data is different from scientific articles reporting and commenting on findings resulting from their scientific research.\n\n[…]\n\n(Article 2 (9)) ‘research data’ means documents in a digital form, other than scientific publications, which are collected or produced in the course of scientific research activities and are used as evidence in the research process, or are commonly accepted in the research community as necessary to validate research findings and results;\n\nThe third pillar that we consider essential to support our proposal is the OECD report 15 (p.13) where we can find one of the most largely accepted and adopted definitions of RD:\n\nResearch data are defined as factual records (numerical scores, textual records, images and sounds) used as primary sources for scientific research, and that are commonly accepted in the scientific community as necessary to validate research findings. A research data set constitutes a systematic, partial representation of the subject being investigated.\n\nThis term does not cover the following: laboratory notebooks, pre-liminary analyses, and drafts of scientific papers, plans for future research, peer reviews, or personal communications with colleagues or physical objects (e.g. laboratory samples, strains of bacteria and test animals such as mice). Access to all of these products or outcomes of research is governed by different considerations than those dealt with here.\n\nA remarkable “positive” aspect of these three definitions is that they separate the data from the subject under study, and set what is, or is not, RD. This is relevant, as the legal context of the subjects under study sets up the legal (and ethical) context of the RD.\n\nWe don’t agree completely with (for example) the exclusion of the laboratory notebooks as RD elements, as they can be used as input data for other studies (how a laboratory works, which is the information that appears in some notebooks depending on the scientific matter). We think that these information and data can be of interest for other researchers.\n\nSome “negative” aspects: the role of the data producers does not appear in the definitions although it is more or less hidden under the connection with the scientific community. But their role is very important as observed in 40 (p.6):\n\nData creators usually have the most intimate knowledge about a given dataset, gained while designing, collecting, processing, analyzing and interpreting the data. Many individuals may participate in data creation, hence knowledge may be distributed among multiple parties over time.\n\nIndeed, as for each research output, the producer team is the guarantor of the data quality, in particular to ensure that the data are not outdated, erroneous, falsified, irrelevant, and unusable. Note that this is particularly relevant in the case of RD, as a consequence of the lack of a widely accepted publication procedure as the one existing for articles in scientific journals, where the responsibility of the quality of the publication is somehow shared by the authors, the journal editors, and the reviewers. This is also confirmed by 47 (p. 73):\n\nThe concept of data quality is determined by multiple factors. The first is trust. This factor is complex in itself. […] Giarlo (2013) also mentions trust in first place, stating that it depends on subjective judgments on authenticity, acceptability or applicability of the data. Trust is also influenced by the given subject discipline, the reputation of those responsible for the creation of the data, and the biases of the persons who are evaluating the data.\n\nMoreover, note that, as remarked in 19 the quality of the producer legal entity defines the cultural quality of the data in legal terms, and thus we have cultural data.\n\nLet us observe that the central role of the scientific team as the producer of the research output is missing in the preceding definitions, but it is distinctly highlighted in our RS definition (see Section 2.2), which implies that the quality of the producer research team reflects over the quality of the software.\n\nOn the other hand, in these three definitions, the RD scientific purpose is focused in its role to validate research findings, although RD can be reused for many other finalities in the scientific context as, for instance, to generate new knowledge, i.e. as primary sources for new scientific findings. These are two of the four rationales for data sharing examined in 18.\n\nBearing all this in mind, we propose the following RD definition.\n\nResearch data is a well identified set of data that has been produced (collected, processed, analyzed, shared & disseminated) by a (again, well identified) research team. The data has been collected, processed and analyzed to produce a result published or disseminated in some article or scientific contribution. Each research data encloses a set (of files) that contains the dataset maybe organized as a database, and it can also include other elements as the documentation, specifications, use cases, and any other useful material as provenance information, instrument information, etc. It can include the research software that has been developed to manipulate the dataset (from short scripts to research software of larger size) or give the references to the software that is necessary to manipulate the data (developed or not in an academic context).\n\nAs previously declared, we have followed closely the RS definition in Section 2.2, translating, as a consequence, the digital nature of RS to RD. This does not mean that we do not consider physical samples as possible RD, but rather we assume that the information extracted from the physical samples has been already treated as digital information to be manipulated in a computer system, which simplifies the manipulation of physical data and its inclusion in the proposed RD definition.\n\nThus, RD has three main characteristics:\n\n• the goal of the collection and analysis is to do research, that is, to answer a scientific question (which includes the validation of research findings),\n\n• it has been produced by a research team,\n\n• the RD is involved in the obtention of the results presented in scientific articles (as the most important means for scientific exchange are still articles published in scientific journals).\n\nLet us observe that the first one agrees with 36 (p. 508): … data from scientific sensors are a means and not an end for their own research.\n\nNote that, according to our definition, documentation, licenses, Data Management Plans and other documents can also be part of the set of files that constitutes the RD. Moreover, as explained in Section 2.2, a RS can also include data in the list of included materials that could also be qualified as RD. There are here a broad spectrum of possibilities, according to the size, the importance given by the research team and the chosen strategy in the dissemination stage. If the RD is considered of little size and less importance than the RS, it can be just included and disseminated as part of the software, and also the other way around, when the RS is considered less important than the RD, as for example when the software development effort is much less important than the time and effort invested in the data collection and analysis. It can also happen that both outputs are considered as of equal value, and can be disseminated separately. In this case it is important that both outputs are linked in order to allow other researchers to find easily the other output.\n\nIn a similar manner as for RS, RD can include other data components, and the RD producer team should explain how these components have been selected, mixed and analyzed, and highlight the reuse of other RD components (with citations, see for example 33,35,37,48).\n\nMoreover, software and data can have several versions and releases, and they can be manipulated alike and with similar tools (forges, etc…) 34,49,50. One of the differences that we have detected between RS and RD is that while some research teams can decide to give access to early stages of the software development, what we observe in the consulted work is that RD is expected in its final form, ready for reuse, as mentioned in 18:\n\nIf the rewards of the data deluge are to be reaped, then researchers who produce those data must share them, and do so in such a way that the data are interpretable and reusable by others.\n\nThis difference is a consequence of the distinct nature of the building process of both objects. In the FLOSS community, we find the release early, release often principle associated to the development of the Linux kernel 51 and to Agile developments.35 This principle may not have the same sense in the building of a dataset for which a research team collects, processes and analyzes data with a very particular research purpose, maybe difficult to share with a large or external community in the early stages of the RD production.\n\nNote also that, in this work, we do not consider production issues like best software development practices or data curation. In here, the research outputs have reach a status in which the research team is happy enough for its dissemination. Neither we do enter in the different roles (see 18) that may appear in the RD team, taking care of actions involving: collection, cleaning, selection, documentation, analysis, curation, preservation, or the role of Data Officer proposed in.11\n\n\n5. Conclusion\n\nRS and RD present many similarities. Analysing the different aspects of what means to define software and to define RS has driven us to the proposition of a RD definition in an independent way of a data definition. As a side effect, the fact that we can adopt easily the RS definition formulation for RD confirms and validates the RS definition.\n\nIn the introduction we have mentioned Borgman’s conundrum challenges related to RD 18:\n\nThe challenges are to understand which data might be shared, by whom, with whom, under what conditions, why, and to what effects. Answers will inform data policy and practice.\n\nWe think that the proposed RD definition provides some answers to these queries, as well as to two extra ones that we consider equally relevant, namely how and where to share RD:\n\nWhich data might be shared? Following the arguments supporting our RD definition, we think that it is a decision of the research team: similarly to the stage in which the team decides to present some research work in the form of a document for its dissemination as a preprint, or a journal article, a conference paper, a book… the team decides which data might be shared, in which form and when (following maybe funder or institutional Open Science requirements).\n\nBy Whom? The research team that has collected, processed, analyzed the RD, and decides to share & disseminate it, that is the RD producer team. Data ownership issues have been discussed for example in 16,17,29,52-54.\n\nHow? By following some kind of dissemination procedure like the one proposed in 9 in order to identify correctly the RD set of files, to set a title and the list of persons in the producer team (that can be completed with their different roles), to determine the important versions and associated dates, to give a documentation, to verify the legal 17,30 (and ethical) context of the RD and give the license to settle the sharing conditions 28, etc. which can include the publication of a data paper. In order to increase the return on public investments in scientific research, RD dissemination could respect principles and follow guidelines as described in 15,55. Further analysis on RD dissemination issues can be found in 13.\n\nWhere? There are different places to disseminate a RD, including the web pages of the producer team, of the funded project, or in a existing data repository. The Registry of Research Data Repository36 is a global registry of RD repositories that covers repositories from different academic disciplines. It is funded by the German Research Foundation (DFG)37 and it can help to find the right repository. Note that the Science Europe report 56 provides criteria for the selection of trustworthy repositories to deposit RD.\n\nWith whom? Each act of scholar communication has its own target public, and initially, the RD dissemination strategy can target the same public as the one that could be interested by the associated research article. But it can happen that the RD is of interdisciplinary value, larger than the initial discipline targeted by the publication, and this public can be difficult to assess at first glance.\n\nAs observed by 18:\n\nAn investigator may be part of multiple, overlapping communities of interest, each of which may have different notions of what are data and different data practices. The boundaries of communities of interest are neither clear nor stable.\n\nSo, it can be difficult to assess the target community of interest for a particular RD, but this also happens for articles, and it seems to us that this has never been an obstacle for sharing a publication. Thus 18:\n\n…the intended users may vary from researchers within a narrow specialty to the general public.\n\nUnder what conditions? The sharing conditions are to be found in the licence that goes with the RD, it can be for example a Creative Commons licence38 or other licenses to settle the attribution, re-use, mining… conditions 28. For example in France, the law of 2016 for a Digital Republic Act sets in a Décret the list of licenses that can be used for RS or RD release 29,27.\n\nWhy and to what effects? There maybe different reasons to release some RD, from the contribution to build more solid and easy to validate science to simply answer to the recommendations or requirements of the funder of a project, of the institutions supporting the research team, or those of a scientific journal, including Open Science issues 5. The works 41,18 give a thorough analysis on this subject. As documented there and already mentioned in Section 3:\n\n“The value of data lies in their use. Full and open access to scientific data should be adopted as the international norm for the exchange of scientific data derived from publicly funded research.”\n\nAs remarked in 5 and in the work analyzed there, the evaluation step is an important enabler in order to improve the adoption of Open Science best practices and to increase RD sharing and open access. To disseminate high quality RD outputs asks for time, work and hands willing to verify the quality of the data, write a documentation, etc. Incentives are needed to motivate the teams. It also asks for the establishment of best citation practices and evolution in the protocols of research evaluation. In particular, the CDUR protocol 3 proposed for RS evaluation can be proposed for RD as presented in the article that follows the present work 13.\n\n\nData availability\n\nData underlying the arguments presented in this article can be found in the references, footnotes and Box 1.",
"appendix": "References\n\nEuropean Parliament and the Council: Directive 2007/2/EC of 14 March 2007 establishing an Infrastructure for Spatial Information in the European Community (INSPIRE).Reference Source\n\nGomez-Diaz T: Article vs. Logiciel: questions juridiques et de politique scientifique dans la production de logiciels. 1024 - Bulletin de la société informatique de France. 2015; 5. First version initially published in the platform of the PLUME project, October 2011. First version initially published in the platform of the PLUME project, October 2011. Reference SourcePublisher Full TextReference Source\n\nGomez-Diaz T, Recio T: On the evaluation of research software: the CDUR procedure [version 2; peer review: 2 approved]. F1000Res. 2019; 8: 1353. First published: 05 Aug 2019. PubMed Abstract | Publisher Full Text\n\nHanson B, Sugden A, Alberts B: Making data maximally available. Science 2011; 331(6018): 649–649. PubMed Abstract | Publisher Full Text Reference Source\n\nGomez-Diaz T, Recio T: Towards an Open Science definition as a political and legal framework: on the sharing and dissemination of research outputs. POLIS N. 2020; 19. Last Version dated 28/02/2021. Publisher Full TextReference Source (Last Version)\n\nUNESCO: Recommendation on Open Science 2021.Reference Source\n\nMéndez E: Open Science por defecto. La nueva normalidad para la investigación. Open science by default. The “new normal” for research. ARBOR Ciencia, Pensamiento y Cultura, Vol. 197-799, enero-marzo 2021, a587, ISSN-L: 0210-1963.Publisher Full Text\n\nGomez-Diaz T: Articles, software, data: a study of the (French) scientic production. Presented at the Poster session of the EUDAT 3rd conference, Bringing data infrastructures to Horizon 2020, Amsterdam, 2014. Reference Source\n\nGomez-Diaz T: Free software, Open source software, licenses. A short presentation including a procedure for research software and data dissemination. 2014. Presented at the Workshop on open licenses: Data licencing and policies, EGI Conference 2015, Lisbon, May 2015. Spanish version: Software libre, software de código abierto, licencias. Donde se propone un procedimiento de distribución de software y datos de investigación, Septembre 2015.Reference SourceReference SourceReference Source\n\nEuropean Commission: Commission Recommendation (EU) 2018/790 of 25 April 2018 on access to and preservation of scientific information.Reference Source\n\nScience Europe: Presenting a framework for discipline-specific research data management. Science Europe Guidance Document D/2018/13.324/12018. Reference Source\n\nGomez-Diaz T, Romier G: Research Software management Plan Template V3.2. Projet PRESOFT, Bilingual document (FR/EN).2018. Reference Source\n\nGomez-Diaz T, Recio T: Research Software vs. Research Data II: protocols for Research Data dissemination and evaluation in the Open Science context. F1000Res. Publisher Full Text\n\nGomez-Diaz T, Recio T: Open comments on the Task Force SIRS report: Scholarly Infrastructures for Research Software (EOSC Executive Board, EOSCArchitecture). Research Ideas and Outcomes. 7: e63872. Publisher Full Text\n\nOECD: OECD Principles and Guidelines for Access to Research Data from Public Funding.Paris: OECD Publishing; 2007. Publisher Full Text\n\nGuibault L, Wiebe A, editors. Safe to Be Open: Study on the Protection of Research Data and Recommendations for Access and Usage.Universitätsverlag Göttingen; 2014. Publisher Full Text Reference Source\n\nde Cock BM , van Dinther B , Jeppersende Boer CG, et al.: The Legal Status of Research Data in the Knowledge Exchange Partner Countries, Knowledge Exchange report.2011. Reference Source\n\nBorgman CL: The conundrum of sharing research data. J. Am. Soc. Inf. Sci. Technol. 2012; 63: 1059–1078. Publisher Full Text\n\nDomange C (Rapporteur): Guide Data Culture. Pour une stratégie numérique de diffusion et de réutilisation des données publiques numériques du secteur culturel. Ministére de la Culture et de la Communication, Sécretariat Général N. 2013-01, Mars 2013. Reference Source\n\nEuropean Parliament and the Council: Directive 96/9/EC of 11 March 1996 on the 1248 legal protection of databases.Reference Source\n\nEuropean Parliament and the Council: Directive (EU) 2019/1024 of 20 June 2019 on open data and the re-use of public sector information.Reference Source\n\nEuropean Parliament and the Council: Directive 2009/24/EC of 23 April 2009 on the legal protection of computer programs.Reference Source\n\nBoletín Oficial del Estado: lunes 22 de abril de 1996, Número 97. http\n\nJournal officiel de la République française, Lois et décrets: Code de la propriété intellectuelle, Version en vigueur au 23 juin 2021. http\n\nJournal officiel de la République française, Lois et décrets: Arrêté du 22 décembre 1981, Enrichissement du vocabulaire de l’informatique, Numéro complémentaire n. 0014 du 17 janvier 1982. http\n\nJournal officiel de la République française, Lois et décrets: Code de l’environnement, Version en vigueur au 21 juillet 2021. http\n\nJournal officiel de la République française, Lois et décrets: Décret n. 2017-638 du 27 avril 2017 relatif aux licences de réutilisation à titre gratuit des informations publiques et aux modalités de leur homologation. http\n\nLabastida I, Margoni T: Licensing FAIR Data for Reuse Data Intelligence 2020; 2(1-2): 199–207. Publisher Full Text\n\nMaurel L: La réutilisation des données de la recherche après la loi pour une République numérique. La diffusion numérique des données en SHS - Guide de bonnes pratiques éthiques et juridiques. Presses Universitaires de Provence; 2018. Reference Source\n\nStérin A-L: Diffuser des données de la recherche dans le respect du droit et de l’éthique: Comment faire lorsqu’on n’est pas juriste? Guide de bonnes pratiques éthiques et juridiques. Presses Universitaires de Provence; 2018. Reference Source\n\nWhite House: Circular A-110 Revised 11/19/93, As Further Amended 9/30/99.1999. Reference Source\n\nKelly D: An Analysis of Process Characteristics for Developing Scientific Software. J Organ End User Com. 2011; 23(4): 64–79. Publisher Full Text\n\nKatz DS, Niemeyer KE, Smith AM, et al.: Software vs. data in the context of citation. PeerJ Preprints 2016; 4: e2630v1. Publisher Full Text\n\nRios F: Preserving and Sharing Software for Transparent and Reproducible Research: A Review v1.4August 18th 2016. Reference Source\n\nSmith AM, Katz DS, Niemeyer KE, et al.: Software citation principles. PeerJ Computer Science 2016; 2: e86. Publisher Full Text\n\nBorgman CL, Wallis JC, Mayernik MS: Who’s Got the Data? Interdependencies in Science and Technology Collaborations. Comput. Supported Coop. Work 2012; 21: 485–523. Publisher Full Text\n\nTask Group on Data Citation Standards and Practices, C.-I: Out of Cite, Out of Mind: The Current State of Practice, Policy, and Technology for the Citation of Data. Data Sci. J. 2013; 12: CIDCR1–CIDCR7. Publisher Full Text\n\nKyriakopoulou A: Elaboration de ressources électroniques pour les noms composés de type N (E+DET=G) N=G du grec moderne.Linguistique: Université Paris-Est; 2011. Reference Source\n\nTolone E: Analyse syntaxique `a l’aide des tables du Lexique-Grammaire du français.Linguistique: Université Paris-Est; 2011. Reference Source\n\nPasquetto IV, Borgman CL, Wofford MF: Uses and Reuses of Scientific Data: The Data Creators Advantage. Harvard Data Science Review 2019; 1(2). Publisher Full Text\n\nNational Research Council: Bits of Power: Issues in Global Access to Scientific Data.Washington, DC: The National Academies Press; 1997. Publisher Full Text\n\nSwan A: Policy Guidelines for the Development and Promotion of Open Access.Paris: UNESCO; 2012. Reference Source\n\nNational Research Council: On the Full and Open Exchange of Scientific Data.Washington, DC: The National Academies Press; 1995. Publisher Full Text\n\nSá C, Grieco J: Open Data for Science, Policy, and the Public Good. Rev. Policy Res. 2016; 33: 526–543. Publisher Full Text\n\nAbiteboul S, Senellart P: Un déluge de données. Interstices.INRIA, 2014. Reference Source\n\nSchöpfel J, Kergosien E, Prost H: Pour commencer, pourriez-vous définir ‘données de la recherche’ ? Une tentative de réponse. Atelier VADOR: Valorisation et Analyse des Données de la Recherche; INFORSID 2017, May 2017, Toulouse, France.Reference Source\n\nKoltay T: Digital research data. Baker D, Evans W, editors. Digital Information Strategies Oxford: Chandos Publishing; 2015; pp. 71–84. Available in Google Books.\n\nCallaghan S: Preserving the integrity of the scientific record: data citation and linking.Learned Publishing; 2014; 27. : S15–S24. Publisher Full Text\n\nKlump J, Wyborn L, Wu M, et al.: Versioning Data Is About More than Revisions: A Conceptual Framework and Proposed Principles. Data Sci. J. 2021; 20(1): 12. Publisher Full Text\n\nRam K: Git can facilitate greater reproducibility and increased transparency in science. Source Code Biol. Med. 2013; 8(1). PubMed Abstract | Publisher Full Text\n\nRaymond E: The cathedral and the bazaar - musings on Linux and Open Source by an accidental revolutionary. Knowledge, Technology, & Policy Fall 1999; 12(3): 23–49. Publisher Full Text Reference Source\n\nAmiel P, Frontini F, Lacour PY, et al.: Pratiques de gestion des données de la recherche: une nécessaire acculturation des chercheurs aux enjeux de la science ouverte ? Cahiers Droit, Sciences & Technologies 2020; 10: 147–168. Publisher Full Text\n\nHampton SE, Anderson SS, Bagby SC, et al.: The Tao of open science for ecology. Ecosphere 2015; 6(7): art120. Publisher Full Text\n\nParry O, Mauthner NS: Whose Data are They Anyway?: Practical, Legal and Ethical Issues in Archiving Qualitative Research Data. Sociology 2004; 38(1): 139–152. Publisher Full Text\n\nWilkinson M, Dumontier M, Aalbersberg I, et al.: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 2016; 3: 160018. PubMed Abstract | Publisher Full Text\n\nScience Europe: Practical Guide to the International Alignment of Research Data Management (Extended Edition).2021. Reference Source\n\n\nFootnotes\n\n1 “We Are Star Dust” - Symphony of Science, https://www.youtube.com/watch?v=8g4d-rnhuSg\n\n2 Cave of Altamira and Paleolithic Cave Art of Northern Spain, https://whc.unesco.org/en/list/310/\n\n3 Prehistoric Sites and Decorated Caves of the Vézère Valley, https://whc.unesco.org/en/list/85/\n\n4 https://en.wikipedia.org/wiki/Free_and_open-source_software\n\n5 https://en.unesco.org/science-sustainable-future/open-science/recommendation\n\n6 https://www.fsf.org/licensing/\n\n7 https://opensource.org/licenses\n\n8 https://spdx.org/licenses/\n\n9 https://creativecommons.org/licenses/?lang=en\n\n10 https://opendatacommons.org/licenses/\n\n11 Note that the authors of this article provide their own translations. Authors prefer to keep the original text for two reasons. First, because of the legal nature of the involved quotations. Second, for French or Spanish speaking readers to enjoy it, very much in line with the Helsinki Initiative on Multilingualism in Scholarly Communication (2019), see https://doi.org/10.6084/m9.figshare.7887059. These translations have been helped by Google Translate, https://translate.google.com/ and Linguee, https://www.linguee.fr/.\n\n12 For the purpose of this Law, a computer program shall be understood as any sequence of instructions or indications intended to be used, directly or indirectly, in a computer system to perform a function or a task or to obtain a certain result, whatever expression and fixation form it can take. […] it can also include its preparatory documentation.\n\n13 Software: All programs, procedures and rules, and possibly documentation, related to the performance of some data processing (in English: software).\n\n14 Software, including the preparatory material, is considered as works protected by the present code.\n\n15 https://www.rd-alliance.org/groups/fair-research-software-fair4rs-wg\n\n16 https://matek.hu/zoltan/issac-2021.php\n\n17 https://swmath.org/software/4203\n\n18 The issues related to reuse require a perfect mastership of intellectual property rights, image rights, personal data rights, respect for private life and statistical confidentiality, business law, competition law, cultural law, European law and the rules of the public economy.\n\n19 Data covered by medical secret or by the industrial and commercial secret. See, for example, https://www.senat.fr/dossier-legislatif/pjl16-504.html\n\n20 https://stats.oecd.org/glossary/detail.asp?ID=532\n\n21 https://dle.rae.es/dato\n\n22 https://dle.rae.es/informaci%C3%B3n\n\n23 https://www.larousse.fr/dictionnaires/francais/donn%c3%a9e/26436\n\n24 https://www.larousse.fr/dictionnaires/francais/information/42993\n\n25 https://en.wikipedia.org/wiki/Data\n\n26 https://www.legifrance.gouv.fr/codes/article_lc/LEGIARTI000006832922/\n\n27 For the purposes of this chapter, information relating to the environment is considered to be any information available, whatever the medium, the purpose of which is:\n\n1. The state of the elements of the environment, namely the air, atmosphere, water, soil, land, landscapes, natural sites, coastal or marine areas and biological diversity, as well as the interactions between these elements;\n\n2. Decisions, activities and factors, namely substances, energy, noise, radiation, waste, emissions, spills and other discharges, likely to have an impact on the state of the elements concerned in point 1;\n\n3. The state of human health, safety and living conditions of people, buildings and cultural heritage, insofar as they are or may be altered by elements of the environment, decisions, activities or the factors mentioned above;\n\n4. The analyses of costs and advantages as well as the economic assumptions used in the context of the decisions and activities referred to in point 2;\n\n5. Reports drawn up by public authorities or on their behalf on the application of legislative and regulatory provisions related to the environment.\n\n28 https://www.legifrance.gouv.fr/codes/section_lc/LEGITEXT000006074220/LEGISCTA000022936254/\n\n29 Geographic data, any data that refers directly or indirectly to a specific place or geographic area;\n\n30 The entries of the glossary https://stats.oecd.org/glossary/ have several parts including Definition and Context as shown in the Data definition included in Section 3. This quotation appears when placing the pointer over the Context part of the Data entry.\n\n31 https://www.beilstein-institut.de/en/projects/strenda/guidelines/\n\n32 …the use of public information by anyone who wishes it for other purposes than those of the original needs for which the documents were prepared or held by the public service mission.\n\n33 https://en.wikipedia.org/wiki/Open_data\n\n34 https://en.wikipedia.org/wiki/Big_data\n\n35 https://en.wikipedia.org/wiki/Agile_software_development\n\n36 https://www.re3data.org/\n\n37 http://www.dfg.de/\n\n38 https://creativecommons.org/"
}
|
[
{
"id": "121519",
"date": "08 Feb 2022",
"name": "Tibor Koltay",
"expertise": [
"Reviewer Expertise Information 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\nThe content of the first two paragraphs of the paper (especially the first one) seems to be less appropriate, compared to the purpose of your paper. I would thus advise you to consider rewriting these paragraphs.\nYour practice of providing the cited texts in the original language (French or Spanish) and providing the translations of these passages only in the footnotes is unusual and may be not appropriate for a readership that probably reads and writes only in English, or is not familiar with Spanish and/or French texts. As I see it, if you would want to make a favour to your readers, who prefer French or Spanish, the solution could be reverse this order, i.e. putting the original texts into the footnotes.\nOther remarks I think that it would be better if the following sentence would be changed as follows:\n“Indeed, as remarked by Hanson et al., we must all accept that science is data and that data are science…4”\nThis regards not only the form of citing, but content, because this remark comes from Borgman’s Conundrum, cited in your paper a couple of times.\nYou describe three main characteristics of RS:\n“the goal of the RS development is to do research. As stated by D. Kelly: it is developed to answer a scientific question32, it has been written by a research team, the RS is involved in the obtention of the results presented in scientific articles (as the most important means for scientific exchange are still articles published in scientific journals).”\nIn general, these three claims are correct. However, the first one of them is a little awkward. I would thus change it to anything like “the goal of the RS development is to support research. As stated by Kelly, it is developed to answer a general, or a specific scientific question. Writing the software requires close involvement of someone with deep domain knowledge in the application area related to the question.32”. Theses sentences however may prove redundant, because you provide a more complete definition:\n“Research Software is a well identified set of code that has been written by a (again, well identified) research team…If take this, linger definition only, the expression “(again, well identified)” should be deleted.\nYou write that “Indeed, there is a difference between the concepts of algorithm and software from the legal point of view, as there is a difference between the mere idea for the plot of a novel and the final written work.” This is a brilliant idea, although I believe that it should not be restricted to the legal point of view.\nIn my view, it seems to be dangerous to write about copyright issues without being legal experts. Personally, I have only basic knowledge of copyright laws, so I cannot judge the correctness of all your argument. Fortunately, what you describe is also related to different issues.\nI do not see any further problems. Therefore, I will not enumerate passages that are correct and rather straightforward. My suggestion is however, that you carefully review you text in order to reach clarity of your argument.\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\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": [
{
"c_id": "7893",
"date": "28 Feb 2022",
"name": "Teresa Gomez-Diaz",
"role": "Author Response",
"response": "Many thanks to you, Tibor Koltay, for these very interesting comments. We are preparing a new version of this article and we will include several of the proposed corrections. Meanwhile, we would like to provide in here some preliminary comments. 1. [first two paragraphs] We have chosen to start in a ''light'' manner an article that can ask for some effort to be understood, this is our author’s choice. It is the reader’s choice to skip these two first paragraphs or to enjoy them, as this does not have any consequence for the understanding of the content of the article. 2. [translations to English] We agree with you, the translations to English in the footnotes may hinder the fluent reading of this work, we will modify the presentation. 3. [Hanson et al. Reference] You are right, we have found this reference in Borgman’s work, but we have consulted the original article and we have chosen to do this reference in a slightly different manner. 4. [RS definition characteristics] We will modify the phrase to include your proposition as follows: “the goal of the RS development is to do or to support research’’. Please note that the composition of a research team involved in the development of a RS has been thoroughly studied in section 2.2 of [Reference 3]. We will include this reference to clarify this point as you ask. Please, also note that long developments may involve many different contributions from developers with different status. As copyright issues enter into play, it is important that the RS developers and contributors are correctly listed. 5. [Algorithms and software] Comparisons between algorithms and software can be done in several contexts, for example in mathematics, or in computer science, among others. We have highlighted the legal aspects as we detect regularly the confusion between these two concepts, and the [Reference 22] providers a pretty clear explanation. 6. [Copyright issues] Please note that one of the authors has study copyright issues in order to write [Reference 2], work that has been validated by several experts, including legal experts. On the other hand, we are regularly in contact and follow the work of legal experts, in such a manner as to provide us with the necessary confidence to deal with copyright issues in the way we propose in this article. The remark included at the end of the Introduction gives the necessary warning to our readers on this point. Teresa Gomez-Diaz, Tomas Recio"
}
]
},
{
"id": "121511",
"date": "23 Feb 2022",
"name": "Remedios Melero",
"expertise": [
"Reviewer Expertise Open science",
"open research data",
"scholarly publications",
"open access policies"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors proposed a Research Data (RD) definition \"based in three characteristics: the data should be produced (collected, processed, analyzed, shared & disseminated) to answer a scientific question, by a scientific team, and has yield a result published or disseminated in some article or scientific contribution of any kind.\" From my point of view this definition restricts RD to those that are published by a scientific team, however what about the citizen science, or data produced by non-scientist staff? What about any other data that do not deserve be published but help to further research?\nAuthors say: \"the RS is involved in the obtention of the results presented in scientific articles\" - This is not necessarily true. RS is not always involved in the obtention of results because it can be developed for any other purpose, again the authors make a very strict definition.\nAuthors say: \"As a matter of fact, a research team can use RS produced by other teams for their scientific work, as well as FLOSS or other software developed outside the scientific community, but the present work is centered in the making-of aspects which are pertinent for the proposed definition.\" - This restricts the definition of Research Software (RS) a lot by excluding all FLOSS produced by non-academic members.\nThe authors have missed any mention to the Directive (EU) 2019/1024 of the European Parliament and of the Council of 20 June 2019 on open data and the re-use of public sector information, in which RD are defined and included as part of the public sector. In fact, the authors have cited it but they have not commented/mentioned the fact that RD has a wider meaning and that according to this Directive are considered public sector information, and they need not necessarily be published in a scientific journal but shared.\nDefinitions given by dictionaries are not particularly relevant to the scientific context/environment. I think this part should be omitted, it only adds some definitions in the authors' own languages.\n\"For example, to the need for complementary, technical information associated to a given dataset in order to facilitate its reuse.\" - This is part of the FAIR principles which are not mentioned/linked to this comment. Obviously, a dataset without any information about how data have been produced/obtained, etc. are not valuable.\nAuthors write: \"In here, the research outputs have reach a status in which the research team is happy enough for its dissemination.\" - This seems a very naïve assertion. Because the authors \"do not consider production issues like best software development practices or data curation\", it seems they do not care about these important issues.\nConclusions again repeat the proposal of a RD definition. Concepts like linked data, FAR data, and open data have not been treated in the article. Their definition of RD is very strict and narrow, and they have not considered any semantic issues about data and the benefits and implications of being a 5star open data. Their definition is far from the 4th or 5th step of the stars.\nIn general, from my point of view, the article does not add any new ideas about RD definition and restricts it to data produced by scientific teams.\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?\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": [
{
"c_id": "7894",
"date": "28 Feb 2022",
"name": "Teresa Gomez-Diaz",
"role": "Author Response",
"response": "Many thanks to you, Remedios Melero, for these very interesting comments. We are preparing a new version of this article and we will include several of the proposed corrections. Meanwhile, we would like to provide in here some preliminary comments. 1. [this definition restricts RD to those that are published by a scientific team, however what about the citizen science, or data produced by non-scientist staff?] [the article does not add any new ideas about RD definition and restricts it to data produced by scientific teams.] It would be strange to consider any article published in a newspaper as a scientific publication. On the other hand, scientists may read the newspapers and many other documents, including tweets, and may use these documents as input information for a research work. As already explained in our answer to Rob Hooft’s comment, yes, we have chosen a restricted definition for RD. It allows us to provide the answers to the Borgman’s conundrum challenges that are in the Conclusion section. As far as we know, we have not found in the consulted literature the proposition of such kind of answers in this complete view. Moreover, as the RD definition finds a similar formulation as the RS one, we can also translate RS dissemination and evaluation protocols to RD [Reference 13]. Once we understand well the restricted context, it can be studied its extension and then see which are the answers to Borgman’s conundrum challenges and the dissemination and evaluation protocols that can be proposed in the extended context. The fact that we do not include e.g. public sector data as RD is different from the claim that these data cannot be used as input for a research work. As explained in section 3.2 of [Reference 13], these external data components should be correctly presented and referenced, and some can also fall in the category of RD. 2. [RS is not always involved in the obtention of results because it can be developed for any other purpose, again the authors make a very strict definition.] [This restricts the definition of Research Software (RS) a lot by excluding all FLOSS produced by non-academic members.] You are right, this point should be explained better. To obtain a research result may involve the use of software (FLOSS or not FLOSS), the development of software to support some work or service, and the development of RS by the research team as explained in [References 3, 14]. Note that RS can be also disseminated as FLOSS, which is the usual practice in the work of T. Recio and in the research lab of T. Gomez-Diaz. This is also similar for data and RD, that can be disseminated as open data, as well as for publications and research articles as seen in the previous point. 3. [Research data defined in the Directive (EU) 2019/1024 ] This definition was included in the preparation versions of the present article, and it will be included again in the new version in preparation, following your advice. 4. [Definitions given by dictionaries] In the difficulties to explain easily the concepts of data and information we have ended in the consultation of several dictionaries, including some in English. Some of the found definitions, mainly in Spanish and French have attracted our attention and we have decided to included them in Box 1. This box can be easily skipped by readers not interested in these definitions. We prefer to leave the reading of the content of this box at the choice of readers. 5. [FAIR and \"For example, to the need for complementary, technical information associated to a given dataset in order to facilitate its reuse.\"] Please note that FAIR principles appear in the [Reference 55] dated 2016, while [Reference 36] that we have chosen to illustrate the need for complementary, technical information is dated 2012. Moreover, this is also related to the importance of context, that is explained in the OECD Glossary of Statistical Terms, with PDF and WORD download versions dated 2007 [https://stats.oecd.org/glossary/download.asp]. On the other hand, FAIR principles are considered in the second part of this work [Reference 13], as they are related to dissemination issues. We will also mention them in the second version of this first part. 6. [\"In here, the research outputs have reached a status in which the research team is happy enough for its dissemination.\"] [authors \"do not consider production issues like best software development practices or data curation\", it seems they do not care about these important issues.] You are right, this point should be better explained in the new version of the article. It is not that we do not care about these important issues, as they are part of the 3rd step of the proposed CDUR evaluation protocol for RS and RD, see sections 2.3 and 3.3 of [Reference 13]. 7. [Concepts like linked data, FAIR data, and open data have not been treated in the article. Their definition of RD is very strict and narrow, and they have not considered any semantic issues about data and the benefits and implications of being a 5star open data. Their definition is far from the 4th or 5th step of the stars.] Please note that FAIR data and open data are treated in [Reference 13]. We will include in the second version the mention of the 5star open data, many thanks for this reference. Teresa Gomez-Diaz, Tomas Recio"
}
]
},
{
"id": "121514",
"date": "19 Apr 2022",
"name": "Joachim Schopfel",
"expertise": [
"Reviewer Expertise Information 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\nThe research data management is a central dimension of the development of scientific research and related infrastructures. Also, any original attempt to define research data is welcome and helpful for the understanding of this field. This conceptual paper will be a valuable contribution to the discussion on the research but. Yet, it should be improved, and a couple of more or less minor issues should be fixed.\nFirst, all cited text should be systematically translated into English.\n\nThe main concepts (such as data, information, knowledge...) should be defined from the beginning on and not only later (section 3). The definitions should not be based on Wikipedia, Larrousse etc but on academic works in the field of information science (eg ISKO).\n\nOpen science is a fuzzy concept, an umbrella term or even a \"boundary object\" (as Samuel Moore put it). But it should be made clear that open science is more than \"sharing and dissemination of research outputs\" (as in the [5] citation).\n\nThe former comment is important because the approach of the paper is in some kind limited or reduced to the aspect of \"research output\". Generally, in the research process, research software and research data are not only output but also tools (software) and input (data). This needs clarification.\n\nIn the same context, the paper cites Wikipedia with \"We must all accept that science is data and that data are science\". I have two problems with this: nobody must accept anything in science, all is matter of discussion; and this sentence is either trivial or it makes no sense. My advice would be to avoid these kind of sentences.\n\nLater on, the paper presents \"analogies\" between RS and RD. Analogy, even if it exists, does not mean \"similarity\", and I think that this comparison is somehow misleading because the underlying assumption is not entirely correct (\"a definition for RD can be proposed following the main features of the RS definition\"). Software and data are different objects, with different issues (IP protection, communities etc.); the analysis of RS may be helpful for a better understanding of RD but this does not mean that both are more or less similar or even \"fungible\".\n\nIn section 3, I would suggest that the paper tries to describe the relationship between RS and RD, perhaps with \"use cases\".\n\nI admit that the authors are not legal experts but section 3 should be more explicit (and perhaps shorter and more restrictive) about the different laws and legal frameworks. Are you speaking about French laws? Or about the EU regulation?\n\nAnother, related issue is the data typology. The paper is about research data but section 3 mentions (and apparently does not differentiate) environmental data, cultural data and public sector information.\n\nMy suggestion would be to improve the structure of section 3 and to distinguish between concepts, typology, legal status and reuse/policy (subsections).\n\nSection 4: I already mentioned it above - RD is not only output but also input, with different issues (third party rights etc). This requires clarification.\n\nAt the end of section 4, the paper states that \"documentation, licenses, Data Management Plans and other documents can also be part of the set of files that constitutes the RD\". The meaning of this statement requires attention, as well as its implications. Does this mean that \"RDM and other documents\" are data? Or that they may be part of a RD deposit? But again (see above, comment 5), a statement that \"all is data\" is not helpful; it may make sense as a political catchword but not in an academic paper.\n\nLast comment: I like very much Borgman's assessment of RD and her \"conundrum challenges\" but I have a somewhat different understanding of the meaning of this - for me, these \"challenges\" are questions that require attention and evaluation in a given situation, not for all RD in a general way. For me, they provide a kind of \"reading grid\" to analyse a specific data community, or a specific instrument or infrastructure or workflow; but they don't require or demand a comprehensive response as such provided by the paper.\n\nAnyway, the paper is an interesting contribution to the academic research on RD, and I am looking forward to read a revised and improved version. Thank you!\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?\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": [
{
"c_id": "8144",
"date": "25 Apr 2022",
"name": "Teresa Gomez-Diaz",
"role": "Author Response",
"response": "Many thanks to you, Joachim Schopfel, for your interesting comments that give us the opportunity to improve this work. A new version is in preparation, but we provide here some answers to your comments. 1. [translations into English] Translations are included as footnotes, they will be moved to the main text. 2. [information science (eg ISKO).] Many thanks for this reference, we are looking into it. 3. [Open science is a fuzzy concept…] As indicated in the introduction: A more transversal and global vision can be found in the ongoing work for the UNESCO Recommendation on Open Science [Reference 6]. See also [Reference 7]. We will explain better this point. 4. [the paper is in some kind limited or reduced to the aspect of \"research output\". Generally, in the research process, research software and research data are not only output but also tools (software) and input (data). This needs clarification.] In our view, each \"research output\" is a potential input for new research work. For example a RS can be a tool to manipulate data or an input for a new RS, this can be in the form of a component, or in the form of a new version done by the initial research team or another one. A RD can be used by other teams (as a tool) to understand some problem, it can be modified to produce a new RD, or it can be included as part of a larger data set, that can be as well a new RD. To better understand the production context is not, in our view, a limitation. But you are right, this point needs clarification. 5. [cites Wikipedia with \"We must all accept that science is data and that data are science\".] Please note that this cited phrase comes from [Reference 4], and as indicated to Referee T. Koltay, we have chosen to do this reference in a slightly different manner as done in the Borgman’s work, where we have found it. 6.1. [similarity/analogy] When consulting Cambridge English Learner’s Dictionary dictionary we find: analogy: a comparison that shows how two things are similar 6.2. [Software and data are different objects, with different issues (IP protection, communities etc.); the analysis of RS may be helpful for a better understanding of RD but this does not mean that both are more or less similar or even \"fungible\".] It is one of the intentions of the present work to show the differences between data and software form the legal point of view. While software finds a somehow clear and simple presentation (Section 2.1), data is much more difficult to grasp, as studied in Section 3. But this is not an obstacle to present an unified vision of RS and RD as research outputs, as we can see in the RS and RD proposed definitions. The fact that we can propose a similar formulation for both definitions allows us to propose similar dissemination and evaluation protocols as you can find in the article that follows this work [Reference 13]. The fact that we can deal with RS and RD in a similar way does not mean that they are similar. 7. [describe the relationship between RS and RD, perhaps with \"use cases\".] It seems to us that it is quite usual for the targeted research audience to use and/or produce RS and/or RD as part of their everyday research practices, and that this point does not require further explanation. Examples can be found easily in the literature, as for example in the bibliography included at the end of this work. 8. [I admit that the authors are not legal experts but section 3 should be more explicit (and perhaps shorter and more restrictive) about the different laws and legal frameworks. Are you speaking about French laws? Or about the EU regulation?] As indicated in the introduction, we have consulted legal texts and legal experts’ work in order to understand and explain the legal context in which we place this work. We have consulted French, European and USA texts, and selected the parts that we have used to document the article. We consider that our role is restricted to this intention, due to the lack or further expertise in legal matters, which does not hide the efforts we have put in to understand and to explain some legal issues. But we are unable to give more information on the regulations that can be taken into consideration, as this is the role of legal experts in the light of a well defined setting. 9. [Another, related issue is the data typology. The paper is about research data but section 3 mentions (and apparently does not differentiate) environmental data, cultural data and public sector information.] The goal of Section 3 is to show the difficulties existing to set a data definition from the legal point of view, which is a very different context as the one existing for software, as shown in Section 2.1. The case of cultural data is very interesting, as legally speaking [Reference 19] the quality of the producer legal entity defines the cultural quality of the data. Then we can establish the parallel with the quality of research for some data set, as the consequence of the research quality of the producer team. Data typology could be the object of future work. 10. [My suggestion would be to improve the structure of section 3 and to distinguish between concepts, typology, legal status and reuse/policy (subsections).] We will consider this suggestion 11. [Section 4: I already mentioned it above - RD is not only output but also input, with different issues (third party rights etc). This requires clarification.] As already explained, we study in here the production aspects, and other aspects are presented in [Reference 13]. But you are right, this needs better explanation. 12. [At the end of section 4, the paper states that \"documentation, licenses, Data Management Plans and other documents can also be part of the set of files that constitutes the RD\". ] Section 2.1 shows that the preparatory design work and documentation are part of the software, and these are documents that can be included in the released version of a RS, following the choice of the RS producer team. There can be other elements as for example tests, input and output files to illustrate how to use the RS, licenses, etc. To include these elements in the released RS correspond to best practices that facilitate RS reuse. In our view, to release a RD can follow similar practices, that is, to include a documentation, some use examples, a license, a data management plan…this is to be decided by the producer team. 13. [Last comment: I like very much Borgman's assessment of RD and her \"conundrum challenges\" but I have a somewhat different understanding of the meaning of this - for me, these \"challenges\" are questions that require attention and evaluation in a given situation, not for all RD in a general way. For me, they provide a kind of \"reading grid\" to analyse a specific data community, or a specific instrument or infrastructure or workflow; but they don't require or demand a comprehensive response as such provided by the paper.] In our experience, Borgman's conundrum challenges correspond to questions that appear regularly at different stages of the RD production. We think that to provide such vision as the one exposed in Section 4 could be of help to deal with these questions, and, as you said, as a first step to tackle some problems in a well determined situation. Moreover, this view proposed in Section 4 is extended and completed with the dissemination and evaluation protocols proposed in [Reference 13]. Our experience of many years confirms the need of these protocols for RS, and we think that they will be appropriated, useful and relevant for RD as well. Teresa Gomez-Diaz and Tomas Recio"
}
]
}
] | 1
|
https://f1000research.com/articles/11-118
|
https://f1000research.com/articles/11-1235/v1
|
31 Oct 22
|
{
"type": "Research Article",
"title": "Anti-ischemic effect of Tamarindus indica L. seed extract against myocardial hypoxic injury",
"authors": [
"Sirirat Surinkaew",
"Podsawee Mongkolpathumrat",
"Veeranoot Nissapatorn",
"Sarawut Kumphune",
"Sirirat Surinkaew",
"Podsawee Mongkolpathumrat",
"Veeranoot Nissapatorn"
],
"abstract": "Background: Ischemic heart disease is a leading cause of death in patients with cardiovascular disease. Natural products containing high antioxidant activity have been used as an alternative therapy to improve the living conditions of patients. In this study, we examine the protective effect of tamarind seed (TS) on myocardial hypoxic injury. Methods: The hypoxia model was mimicked by mineral oil overlayed on H9c2 cardiomyoblasts for 4 h. TS extract was pretreated and administered during the hypoxic condition. Radical scavenging activity of TS extract was measured and exhibited very potent antioxidant activities on 2,2-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assays. Results: TS extract at a concentration of 10 µg/ml significantly reversed the effect of hypoxia-induced cell death and intracellular reactive oxygen species (ROS) production. We also observed hypoxia-induced over-expression of both inflammatory cytokine mRNA and activation of cellular apoptosis. Pretreatment of TS extract significantly reduced hypoxia-induced HIF-1α and pro-inflammatory cytokine production, IL-1β and IL-6. The Western blot analysis for apoptotic regulatory molecules, caspase 3, caspase 8 and Bax proteins, also showed hypoxic injury reversal by TS extract treatment. Conclusions: The results suggest that the anti-ischemic effect of TS extract protects against hypoxia-induced injury and has potential to be an effective alternative therapy for ischemic heart disease and oxidative-damage related disease.",
"keywords": [
"tamarind seed",
"hypoxia",
"antioxidant",
"anti-inflammatory",
"anti-apoptosis",
"H9c2"
],
"content": "Introduction\n\nIschemic heart disease (IHD) is a heart condition response to deprivation of oxygen and blood supply, ultimately causing heart attack or acute myocardial infarction (AMI). IHD is considered the most prevalent cardiovascular disease and continues to rise.1,2 Epidemiological data from 2016 to 2019 shows a rise in the number of patients suffering from IHD, which was the leading cause of death in the global population.3 The pathological cause that leads to IHD is the development of atherosclerosis.4 and metabolic risk factors, particularly high BMI, diabetes mellitus, hypertension and high cholesterol,1 leading to plaque buildup, narrowing of arteries and blood flow blockage. The impairment of mitochondrial respiratory chain and oxidation of ferrous heme in the oxymyoglobin complex are the potential sources of reactive oxygen species (ROS) formation upon the onset of ischemia.5,6 Excessive ROS production with an imbalance of the antioxidant defense system increases inflammation and oxidative stress in IHD patients.7 ROS can also directly injure cell membranes, causing cell death.8 An effective treatment of IHD will thus lead to significant alleviation of strain on the healthcare system and a profound improvement in the quality of life.\n\nAlthough several kinds of treatment for IHD have been developing,9 the paradigm shift in medical care tends to focus on preventive care. Therefore, early prevention with antioxidant-based therapy is prone to lower the risk of complications from ischemia injury and continues to be an alternative treatment approach.10,11 A growing number of studies have demonstrated that herbal medication rich in antioxidant properties attenuates oxidative stress, preserves mitochondrial function and exhibits cardioprotective effects.12,13\n\nTamarindus indica L., commonly known as tamarind, is abundant in India and tropical regions. It has long been used as a spice, snack, food component and traditional medicine.14 As a traditional medicine, tamarind pulp has been used as a laxative, digestive, antioxidant, carminative and antipyretic.15 Tamarind seed (TS) is consequently a commonly discarded and undervalued component of tamarind products. Interestingly, the seeds also exhibit biological and pharmacological effects, as do the other parts of tamarind. The previous reports showed that TS could enhance wound healing and anti-aging, as well as function as an immunomodulatory, renoprotective and anti-diabetic treatment.16–20 Ethanolic extract of TS exhibits antioxidant properties due to its high content of flavonoid, tannin, polyphenol, anthocyanin and oligomeric proanthocyanidins.19,21 Ground TS could lower blood glucose, serum cholesterol level, and enhance the storage of glycogen in a hypertensive rat model.22 The possible explainable mechanisms could be its free radical-scavenging activity, antioxidant system homeostasis balancing, and attenuating inflammatory mediators.23,24\n\nThere are intensive bioactivity studies on many parts of Tamarind indica; however, the direct effects of TS on cardiomyocytes subjected to ischemic injury have not been reported. Therefore, in the present study, we determine an in vitro anti-ischemic effect of TS on cardiac cells subjected to hypoxic injury. Moreover, we examined the effects of TS on Hypoxia-inducible factor-1 alpha (HIF-1α) expression, inflammatory cytokine expression, intracellular ROS production, and cellular apoptosis under hypoxic injury.\n\n\nMethods\n\nEthical approval for plant use in this study was waived by the Research Institute for Health Sciences, Walailak University, which also approved the research protocol.\n\nTamarindus indica L. fruits were collected in the southern part of Thailand during the peak harvest season from December, 2020 to January, 2021. The seeds were removed and thoroughly washed with tap water, dried in a hot air oven overnight and ground with an electric blender. Then, 50 g of the dried seed powder was extracted in 200 ml of 95% ethanol for seven days at room temperature. The extract solution was filtered and then concentrated under reduced pressure at 40°C using a rotary evaporator, Rotavapor® R-100 (Buchi Labortechnik AG, Flawil, Switzerland). The sample was air-dried at room temperature to eliminate the remainder of the solvent.25 Crude extract of Tamarindus indica L. seeds (TS) was dissolved in 100% dimethyl sulfoxide (DMSO) and stored at 4°C for further experiments.\n\nAn in vitro free radical scavenging activity was performed by 2,2-diphenyl-2-picrylhydrazyl (DPPH) (Sigma-Aldrich) scavenging assay.26 Ten millimolar DPPH solution was diluted in absolute methanol and the working reagent of DPPH was adjusted to an optical density of 0.07 ± 0.02 at 517 nm. Ten microliters of different concentrations (0.125–0.4 mg/ml) of the TS extracts and ascorbic acid (used as standard) were thoroughly mixed with 90 μl of freshly prepared DPPH reagent in a 96-well plate. The reaction mixture was incubated in the dark for 30 mins at room temperature. The absorbance was measured at 517 nm with EonTM Microplate Spectrophotometer (BioTek Instruments, Inc. Vermont, USA). The measurement was repeated with three individual experiments. The decrease of absorbance determined scavenging activity. The percentage of DPPH radical scavenging activity was calculated from [(A517 of control – A517 of sample)/A517 of control] × 100. IC50 value was determined from the percentage inhibition graph, obtained using the y = mx + c formula from the slope of the graph.\n\nThe 2,2′-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assay is based on decolorization occurring when blue/green ABTS•+ is reduced by antioxidants to ABTS• (2,2′-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (Sigma-Aldrich). ABTS was dissolved to a concentration of 7 mM in water.27 The radicals of ABTS •+ were generated by reaction of 7 mM ABTS• and 2.45 mM potassium persulfate at a 1:1 ratio. The mixture was incubated in the dark for 16 to 18 h at room temperature. Then, the ABTS•+ solution was further diluted in absolute methanol until an absorbance value of 734 nm was reached at 0.07 ± 0.02 optical density. The different concentrations (0.125–0.4 mg/ml) of TS extract and ascorbic acid standard were mixed with 90 μl of ABTS•+ working solution in a 96-well plate. The reactions were incubated for 45 mins at room temperature and the absorbance was measured at 734 nm. The experiment was performed in triplicate. The percentage of ABTS•+ scavenging activity was calculated as [(A734 of control – A734 of sample)/A734 of control] × 100. IC50 value was determined from the percentage inhibition graph obtained using the y = mx + c formula from the slope of the graph.\n\nThe rat cardiomyoblast cell line (H9c2) was obtained from ATCC® CRL-1446 (RRID:CVCL_0286). The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) with 10% fetal bovine serum and 1% penicillin/streptomycin (Thermo Fisher Scientific). Cells were cultured for 5 to 7 days and maintained in 5% CO2/95%-humidified air at 37°C.\n\nAfter cells reached 80% confluence, cells were trypsinized with 0.05% trypsin and plated with a density of 5 × 103 cells/well in 96-well plates for 48 h. Cell culture media was replaced with serum free medium before being subjected to hypoxia for 4 h. Hypoxic condition was induced by overlayed mineral oil on the culture media to mimic hypoxic conditions.28,29 In some experiments, cells were pretreated with TS extract for a 48-h period before and during hypoxic induction.\n\nCell viability was determined by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay. The medium was replaced with 0.5 mg/ml MTT (Invitrogen, Thermo Fisher Scientific) in phosphate buffer saline (PBS) and incubated in the dark for 4 h at 37 °C. The medium was then removed and 100 μl dimethyl sulfoxide (DMSO) was added into each well. The absorbance values were measured at 570 nm using the EonTM Microplate Spectrophotometer (BioTek Instruments, Inc., VT, USA). The relative percentage of cell viability was compared with the control group.\n\nCells were seeded in a black-wall 96-well plate at a density of 5 × 103 cells/well and maintained in completed DMEM overnight in 5% CO2/95%-humidified air at 37°C. The medium was discarded and replaced with condition media containing 25 μM 2′,7′-dichlorofluorescin diacetate (DCFH-DA, Sigma-Aldrich). In the hypoxia group, mineral oil was overlayed on condition media and incubated in 5% CO2/95%-humidified air at 37°C for 4 h. In the presence of ROS, the DCHF-DA was rapidly oxidized to highly fluorescent 2′,7′-dichlorofluorescine (DCF). After removing the leftover dye, PBS was added and the intracellular production of ROS was measured by fluorescence intensity with excitation and emission wavelengths of 498 and 522 nm, respectively, with Synergy Mx Microplate Reader (BioTek Instruments Inc., VT, USA).\n\nTo measure hypoxic condition, HIF-1α was determined. GENEzolTM Reagent (Geneaid, Taiwan) was added directly to 7 × 104 cultured cells in a 12-well plate. The cells were lysed by pipetting several times and the sample mixture was incubated for 5 mins at room temperature (RT). Total RNA from the cells was extracted with a GF-1 extraction kit (catalog #GF-TR-100, Vivantis Technologies, Malaysia). The sample was transferred into an RNA Binding Column assembled in a collection tube and centrifuged at 10,000 × g for 1 min then the flow-through was discarded. Wash buffer provided by the kit was then added and centrifuged at 10,000 × g for 1 min. DNase I Digestion Mix provided by the kit was subsequently added into the RNA Binding Column and incubated at RT for 15 mins. Inhibitor Removal Buffer was then added, centrifuged and the flow-through was discarded. The membrane was washed twice with Wash Buffer before the column was placed into a new microcentrifuge tube. Forty microliters of RNase-free water were added directly into the membrane and incubated for 1 min before being centrifuged at 10,000 × g for 1 min. The RNA concentration was determined by NanoDrop OneC (Thermo Fisher Scientific, MA, USA). Complementary DNA synthesis was performed using 0.1 μg of RNA with Viva cDNA Synthesis Kit (catalog #cDSK01-050, Vivantis Technologies, Selangor, Malaysia) following the manufacturer’s protocol.\n\nQuantitative PCR (qPCR) reaction mix was prepared using iTaq™ Universal SYBR® Green Supermix kit (catalog #1725121, Bio-Rad Laboratories, CA, USA). Ten microliters of iTaq™ Universal SYBR Green Supermix (2X) was mixed with 100 ng of cDNA and 1 μl of 200 mM F + R primers. The total reaction mix volume was adjusted to 20 μl with diethyl pyrocarbonate (DEPC) water. The software StepOnePlus™ Real-Time PCR system (Applied Biosystems, Waltham, MA, USA) was set with a thermal cycle as follows: holding stage 95 °C for 30 s; cycling stage at 95 °C for 15 s; 60 °C for 60 s for 40 cycles; and then melting curve stage at 95 °C for 15 s, 60 °C for 60 s, and 95 °C for 15 s with a temperature increase of 0.3 °C. SYBR Green primers were HIF-1α (Forward primer: 5′ ACACAGAAATGGCCCAGTGAG; Reverse primer: 5′ CACCTTCCACGTTGCTGACTT),30 IL-1β (Forward primer: 5′ CACCTCTCAAGCAGAGCACAG; Reverse primer: GGGTTCCATGGTGAAGTCAAC) and IL-6 (Forward primer: 5′ TCCTACCCCAACTTCCAATGCTC; Reverse primer: TTGGATGGTCTTGGTCCTTAGCC).31 Measurements were performed in triplicates and relative gene expression levels were normalized to endogenous reference gene, GAPDH (Forward primer: 5′ TTCCTACCCCCAATGTATCCG; Reverse primer: 5′ CATGAGGTCCACCACCCTGTT).32 Relative fold change in expression was calculated using the 2-∆∆Ct method.\n\nCells were seeded in a six-well plate at a density of 1 × 105 cells/well. At the end of each experiment, the culture plate was placed on ice and then the media was removed. Cells were washed with ice-cold PBS and proteins were collected with 2X Laemmli Sample Buffer (catalog #161-0737, Bio-Rad Laboratories, CA, USA) containing 2-mercaptoethanol and homogenized with insulin syringes. The lysates in 2X Laemmli buffer were denatured at 95°C for 5 mins in a heating box. The cellular protein was separated on 12% SDS-polyacrylamide gel at 90 V for 10 mins followed by 100 V for ~90 mins and then was transferred to polyvinylidene fluoride (PVDF) membranes (100 V; 100 mins). The membranes were blocked with 5% nonfat dry milk in Tris-buffered saline (pH 7.4) containing 0.1% Tween-20 (TBST) for 1 h, followed by incubation with primary antibodies, at the dilution of 1:1,000, cleaved caspase-3 rabbit polyclonal antibody (catalog #9661, RRID:AB_2341188, Cell Signaling Technology, MA, USA), cleaved caspase-8 rabbit monoclonal antibody (catalog #9496, RRID:AB_561381, Cell Signaling Technology, MA, USA), Bax rabbit polyclonal antibody (catalog #sc-493, RRID:AB_2227995, Santa Cruz Biotechnology, Inc., TX, USA) and Bcl-2 rabbit polyclonal antibody (catalog #sc-492, RRID:AB_2064290, Santa Cruz Biotechnology, Inc., TX, USA) in 1% nonfat dry milk in TBST at 4°C overnight. Membranes were washed and incubated with 1:5,000 dilution goat anti-rabbit IgG secondary antibody, horseradish peroxidase (HRP)-conjugated (catalog #AP132P, Merck & Co., NJ, USA) at room temperature for 1 h. Signals were visualized by Affinity® Western blot ECL kit (Affinity Biosciences, OH, USA). The digital images of chemiluminescent Western blots were obtained from ImageQuantTM LAS 500 (GE Healthcare, Life Sciences, NJ, USA). Results were expressed relative to β-actin (Santa Cruz Biotechnology) expression bands on the same samples. The protein quantifications were performed using ImageJ (Version 1.53) (RRID:SCR_003070).\n\nAll data are expressed in mean ± SEM. Statistical comparisons between each time point and a single control group were performed with one-way ANOVA followed by Tukey’s multiple comparisons test. The comparisons between two groups of studies were performed with unpaired Student’s t tests. Statistical analyses were performed using GraphPad Prism (Version 9.0). All data analyses performed using this software have been included in the manuscript.33 A p-value of <0.05 was considered statistically significant. R programming language is an open-access alternative that can perform functions equivalent to GraphPad Prism software.\n\n\nResults\n\nTo optimize timing of hypoxia-induced cell injury, H9c2 cells were subjected to hypoxic conditions for 30 min, 1 h, 4 h or 6 h. Cell viability was determined by MTT assay. Under hypoxic condition, cell viability was significantly decreased to 54 ± 0.6%, 50 ± 0.7%, 49 ± 1.2% and 54 ± 2.7% at 30 min, 1 h, 4 h or 6 h, respectively, compared with the control (Figure 1: see also Underlying data Fig 133).\n\n* p < 0.0001 vs. CTL, one-way ANOVA followed by Tukey’s multiple comparisons test.\n\nAntioxidant activity of TS extract was performed by DPPH and ABTS assays. The crude extract of TS showed potent antioxidant activities obtained from both assays. The DPPH scavenging activity of TS extract displayed 79 ± 5.8% at 0.4 mg/ml and 24 ± 6.1% at 0.1 mg/ml. Similarly, the DPPH radical scavenging activity of ascorbic acid was 89 ± 1.8% at 0.4 mg/ml and 24 ± 3.6% at 0.1 mg/ml (Figure 2A: see also Underlying data Fig 2A33). Moreover, the scavenging activity of ABTS+ radicals of TS extract was observed as a potential antioxidant property; TS extract displayed 100 ± 0.1% scavenging activity at 0.4 mg/ml and 63 ± 2.3% at 0.1 mg/ml, while ascorbic acid served as the standard antioxidant, showing maximum scavenging activity of 100 ± 0.1% at 0.4 mg/ml and 54 ± 2.0% at 0.1 mg/ml (Figure 2B: see also Underlying data Fig 2B33). The IC50 values of DPPH free radical scavenging and ABTS radical scavenging were 236 μg/ml and 82 μg/ml, respectively, for TS extract.\n\nDifferent concentrations (0.125 – 0.4 mg/ml) of TS extract or ascorbic acid were performed by DPPH (A) and ABTS (B) assay.\n\nTo determine the optimal concentration of TS on H9c2 cells that does not cause cellular injury, H9c2 was treated with different concentrations of TS crude extract, varying from 10 μg/ml to 200 μg/ml, for 48 h. The cytotoxicity of TS was measured with MTT assay. The results showed that TS extract at concentrations of 10 μg/ml, 20 μg/ml and 50 μg/ml did not affect cell viability when compared with the untreated control group, 101.3 ± 3.6%, 100.9 ± 8.8% and 83.5 ± 4.3%, respectively. However, TS extract at 100 μg/ml and 200 μg/ml significantly reduced cell viability by 76.8 ± 6.4% (p = 0.0272) and 26.2 ± 2.1% (p <0.0001), respectively, compared with the untreated control group (Figure 3A: see also Underlying data Fig 3A33).\n\n(A) The H9c2 cells were incubated with TS crude extract at different concentrations (10 μg/ml to 200 μg/ml) for 48 h, * p = 0.0272, ** p < 0.0001 vs. control (CTL); (B) TS extract at a concentration of 10 μg/ml increased cell viable in 4 h hypoxia-induced cell death. * p = 0.008 vs. CTL, # p = 0.0151 vs. hypoxia (H).\n\nTo examine the effect of TS extract treatment on cell viability under hypoxia, H9c2 cells were pretreated with TS extract at a concentration of 10 μg/ml for 48 h before being subjected to hypoxia for 4 h. The results showed that hypoxic condition significantly reduced cell viability by MTT assay to 60 ± 4.2%, compared with control (p = 0.0008). Pretreatment with 10 μg/ml of TS extract increased cell viability to 72 ± 2.5%, compared with CTL (p = 0.0151). Therefore, TS extract increased cell viability by 21% compared with hypoxia-induced cell injury (Figure 3B: see also Underlying data Fig 3B33).\n\nIn order to investigate whether TS extract could reduce intracellular ROS production, H9c2 cells were cultured under hypoxic condition for 4 h and measured with DCFH-DA. It was shown that hypoxic condition significantly increased relative ROS production to 29.7 ± 3.4%, compared with CTL (p <0.0001, Figure 4). Pretreatment of 10 μg/ml of TS extract with an additional treatment during hypoxia significantly reduced relative intracellular ROS production to 18.9 ± 2.0 compared with hypoxic group (p = 0.0136, Figure 4: see also Underlying data Fig 433).\n\nPretreatment with 10 μg/ml TS extract significantly decreased ROS production. * p < 0.0001 vs. control (CTL), # p = 0.0136 vs. hypoxia (H).\n\nThe key transcription factor, HIF-1α, is a response to hypoxic injury. The effects of TS extract-mediated cellular inflammation under hypoxic stimulation on HIF-1α mRNA expression were measured. The effects are shown as fold-changes relative to the control (see also Underlying data Fig 5A–C33). The results showed that hypoxic condition significantly increased HIF-1α expression by 2.5 ± 0.37 when compared with control (p = 0.0421, Figure 5A), confirming a hypoxic response in H9c2 cells. Treatment with TS extract significantly reduced HIF-1α expression by 3.7-fold, compared with hypoxia group (p = 0.0160, Figure 5A).\n\n(A) TS extract attenuated HIF-1α mRNA expression and (B) reversed mRNA levels of inflammatory cytokines IL-1β and (C) IL-6 under hypoxic condition. n = 4/group. HIF-1α, * p = 0.0421; IL-1β, * p = 0.0144 vs. control (CTL). HIF-1α, # p = 0.0160; IL-1β, # p = 0.0081; IL-6, # p = 0.0330 vs. hypoxia (H).\n\nTo determine whether TS extract mediates inflammation, the mRNA expression of inflammatory cytokines, IL-1β and IL-6, were measured. Under hypoxic condition, the mRNA expressions of IL-1β and IL-6 increased by 3.7 ± 0.89 and 1.6 ± 0.23, respectively, compared with the control (Figure 5B, C). Most importantly, pretreatment with TS extract significantly attenuated mRNA expression of IL-1β and IL-6 by 5.2- and 3.1-fold, compared with hypoxia, with nearly complete reversal of changes (Figure 5B, C: see also Underlying data Fig 5A–C and supplementary file S1–S733). Overall, these results indicate that TS extract protected against hypoxia-induced cytokine production.\n\nTo assess the effect of TS extract on H9c2 cells apoptosis under hypoxic condition, TS extract at a concentration of 10 μg/ml was pretreated for 48 h prior to hypoxia. The levels of apoptotic regulatory protein cleaved-caspase 3, cleaved-caspase 8 and Bax were assessed by Western blot. The representative immunoblots were normalized to actin. The results showed that hypoxic condition significantly increased the level of cleaved-caspase 3, cleaved-caspase 8 and Bax to 0.34 ± 0.04, 0.40 ± 0.08 and 1.35 ± 0.19, respectively, compared with the control (Figure 6A–C: see also Underlying data Fig 6A–6C33). Interestingly, TS extract was markedly decreased in cleaved-caspase 3, cleaved-caspase 8 and Bax levels by 1.4-fold, 4.3-fold and 1.8-fold, respectively, compared with hypoxic condition. However, the level of Bcl-2 protein expression was not different between groups (Figure 6D–E: see also Underlying data Fig 6D–6E and supplementary file S833). Our results suggest that TS extract plays an important role in inhibiting cellular apoptosis associated with hypoxic-promoted cell death.\n\n(A-D) Quantitative protein expressions of cleaved-caspase 3, cleaved-caspase 8, Bax and Bcl-2 from H9c2 stimulated with hypoxic condition with or without TS extract (10 μg/ml). n = 4-6/group. Caspase3, * p = 0.0080; Caspase 8, * p = 0.0374; Bax, * p = 0.0003 vs. control (CTL). Caspase3, # p = 0.0206; Caspase 8, # p = 0.0024; Bax, # p = 0.0140 vs. hypoxia (H). (E) Representative immunoblot of cleaved-caspase 3, cleaved-caspase 8, Bax, Bcl-2 and β-actin from H9c2 stimulated with hypoxic condition.\n\n\nDiscussion\n\nIn the present study, we demonstrated for the first time an in vitro anti-ischemic effect of tamarind seed (TS) extract on hypoxia-induced cardiac injury by increasing cell viability, reducing ROS accumulation, and lowering HIF-1α mRNA expression. Furthermore, TS extract could reduce inflammatory cytokine IL-1β and IL-6 expression and reduce apoptotic regulatory protein level by decreasing caspase 3, caspase 8 and Bax expression.\n\nHydroalcoholic TS extract showed a higher amount of antioxidant activity compared with acetone or water-based extraction.23 In the present study, ethanolic extraction of TS showed strong antioxidant activity, similar to ascorbic acid, which was used as a standard, measured by DPPH (2,2-diphenyl-1-picrylhydrazyl) and ABTS free radical scavenging assay. The antioxidant property of TS ethanol extract was confirmed by Luengthanaphol et al, 2004.34 The quantitative analysis of phenolic compounds of Tamarindus indica seed by HPLC analytical method displayed a high content of antioxidant capacity.21 It was observed that methanolic extracts of TS consist of oligomeric procyanidin tetramer, procyanidin hexamer, procyanidin trimer, procyanidin pentamer, procyanidin B2 and (-)-epicatechin.21 TS-coated extract has also been reported to contain other phenolic antioxidants, such as 2-hydroxy-3’,4’-dihydroxyacetophenone, methyl 3,4-dihydroxybenzoate, 3,4-dihydroxyphenyl acetate, catechin, caffeic acid, ferulic acid, chloramphenicol, myricetin, morin, quercetin, apigenin and kaempferol.35,36 The polyphenolic compound with the highest content in the methanal seed extract was procyanidin B2, followed by caffeic acid and myricetin.36 As an antioxidant, procyanidin B2 displayed antioxidant properties by inhibiting DNA damage.37 Direct evidence of TS extract protecting cardiomyocytes under oxidative condition has not been previously reported. However, the procyanidin profiles detected in TS are similar to those found in berry, cocoa and dark chocolate and can thus be utilized as an alternative therapy for various cardiovascular diseases, such as angina, hypertension, hyperlipidemia, arrhythmia and congestive heart failure.38–42\n\nDuring hypoxia, mitochondria play a role as an O2 sensor by increasing the production of ROS,43 which could induce mitochondrial damage, release of cytochrome c, modulate downstream apoptotic cascade through pro-apoptotic factors and subsequently lead to cellular apoptosis. ROS generated from mitochondria can also regulate downstream signaling pathways, including HIF-1α. In cardiac disease, HIF-1α plays a key role in the regulation of multiple genes involved in the maintenance of oxygen homeostasis at a low oxygen level, regulating cell survival and differentiation. The increase of HIF-1α expression is an adaptive response of the body to myocardial ischemia and hypoxia. HIF-1α can increase blood oxygen capacity by regulating angiogenesis, vascular remodeling, regulation glucose metabolism and redox balance and improving oxygen utilization.44 On the other hand, a previous study found that hypoxia can induce inflammation and apoptosis via the nitric oxide (NO)-mediated pathway in cardiomyoblast cells.45 NO is a potent mediator of cellular damage, which can react with superoxide anion to produce peroxynitrite, which, in turn, can interact with DNA, proteins and lipids, leading to oxidative injury and cellular apoptosis.46 Antioxidant effects of TS have been shown to reduce lipid peroxidation47 and inhibit NO production,48 which may result from nitric oxide radical scavenging activity, superoxide anion and hydroxyl ion scavenging activity.17 Here, we showed that hypoxia increased cellular injury involved in the regulation of HIF-1α gene expression, which was attenuated by the scavenging activity of TS extract. TS extract may also decrease metabolic stress induced by hypoxia and ultimately attenuate cellular apoptosis. The direct effect of TS extract on preserving mitochondria metabolism and functions should be further investigated.\n\nIt has been reported that TS extract administered in experimental arthritic rat model efficiently maintained the homeostasis of the antioxidant system and significantly reduced serum levels of tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, IL-6, IL-23 and cyclooxygenase-2.24 In this study’s results, we demonstrated that phenolic flavonoids from seed extract reduced ROS levels, and in turn, reduced the production of pro-inflammatory cytokine mediators, IL-1β and IL-6, following exposure to acute hypoxia compared with the control group. The overexpression of caspase 3, caspase 8 and Bax protein expression was reversed by TS extract, which indicated that TS extract can protect against inflammation induced by hypoxia, subsequently preventing apoptosis. The cardioprotective effects of TS may directly scavenge ROS under oxidative stress, thereby protecting from inflammatory response and cell death. Overall, TS was observed as a great potential extract to directly reverse myocardial hypoxia-mediated inflammation and cellular apoptosis. TS extract may also reduce inflammation in other diseases, such as inflammatory cardiomyopathy, etc., which should be further studied as an alternative choice.\n\nThere are some limitations on the anti-ischemic effect of TS against hypoxic injury, which need to be clarified. During hypoxia, the imbalance between free radical production and elimination can occur.49 According to this study, we showed that TS extract has potential antioxidant activity similar to ascorbic acid, which was supported by other studies.19,50 Radical scavenging activities of TS extract could directly reduce intracellular ROS accumulation under hypoxic condition in an in vitro model. However, antioxidant defense systems, such as glutathione peroxidase, peroxiredoxin, total antioxidant activities, as well as associated transcriptional factors, should be further investigated. We also demonstrated strong evidence of pretreatment of TS extract attenuating the effects of hypoxia induced-inflammatory cytokines and apoptosis, which is likely due to its anti-oxidant and anti-inflammatory properties, as previously reported.48,50,51 The underlying mechanism of TS in preventing hypoxic injury remains to be clarified. The p38 MAPK, involving cell differentiation, survival and apoptosis, plays a crucial role in cardiac ischemic response and is known to be regulated by HIF-1α.52,53 However, the signaling pathway of p38 MAPK regulating HIF-1α through ROS scavenging of TS extract needs to be further elucidated. Furthermore, in order to study the systemic effects of TS extract, including long term treatment, different time point of administration (such as at the onset of ischemia or at the beginning of reperfusion), and the effect of isolated TS compounds, as well as their combinations, a myocardial infarction experimental animal model, should be further performed and its associated mechanisms (such as p38 MAPK) need to be further investigated.\n\n\nConclusions\n\nIn the present study, we demonstrated that the anti-inflammatory and anti-apoptotic activity of TS extract protects against hypoxia-induced cardiac cell injury. These beneficial effects may come from the potent antioxidant activity of TS extract, which may be utilized as a natural antioxidant product to reduce the risk of myocardial ischemia.",
"appendix": "Data availability\n\nFigshare: Underlying data for ‘Anti-ischemic effect of Tamarindus indica L. seed extract against myocardial hypoxic injury’, https://doi.org/10.6084/m9.figshare.21066028. 33\n\nThis project contains the following underlying data:\n\n• Data file 1: Fig 1_Absorbance value of duration of hypoxia.csv\n\n• Data file 2: Fig 2A_Absorbance value of DPPH.csv\n\n• Data file 3: Fig 2B_Absorbance value of ABTS.csv\n\n• Data file 4: Fig 3A_Absorbance value of cytotoxicity.csv\n\n• Data file 5: Fig 3B_Absorbance value of cell viability.csv\n\n• Data file 6: Fig 4_Fluorescent intensity of ROS production.csv\n\n• Data file 7: Fig 5A-C_Relative mRNA expression of HIF-1alpha, IL-1B and IL-6.csv\n\n• Data file 8: Fig 6A_Relative protein expression of Caspase3_actin.csv\n\n• Data file 9: Fig 6B_Relative protein expression of Caspase8_actin.csv\n\n• Data file 10: Fig 6C_Relative protein expression of Bax_actin.csv\n\n• Data file 11: Fig 6D_Relative protein expression of Bcl-2_actin.csv\n\n• Supplementary file 1: S1_RNA measurement.csv\n\n• Supplementary file 2: S2_Raw Ct_GAPDH_HIF-1alpha.csv\n\n• Supplementary file 3: S3_Raw Ct_IL1B_IL-6.csv\n\n• Supplementary file 4: S4_Raw data quantification_GAPDH_HIF-1alpha.csv\n\n• Supplementary file 5: S5_Raw data quantification_IL-1B_IL-6.csv\n\n• Supplementary file 6: S6_Amplification data_GAPDH_HIF-1alpha.csv\n\n• Supplementary file 7: S7_Amplification data_IL-1B_IL-6.csv\n\n• Supplementary file 8: S8_Fig 6E_Original blot.pptx\n\n• Supplementary file 9: S9_GraphPad Prism of all data and statistical analysis\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 gratefully acknowledge the Research Institute for Health Sciences, Walailak University, for their support in the laboratory facility.\n\n\nReferences\n\nNowbar AN, Gitto M, Howard JP, et al.: Mortality From Ischemic Heart Disease. Circ. Cardiovasc. Qual. Outcomes. 2019; 12: e005375. 2019/06/06. PubMed Abstract | Publisher Full Text\n\nMortality GBD and Causes of Death C: Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet. 2015; 385: 117–171. 2014/12/23. Publisher Full Text\n\nDiseases GBD and Injuries C: Global burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2020; 396: 1204–1222. 2020/10/19. PubMed Abstract | Publisher Full Text\n\nKhan MA, Hashim MJ, Mustafa H, et al.: Global Epidemiology of Ischemic Heart Disease: Results from the Global Burden of Disease Study. Cureus. 2020; 12: e9349. 2020/08/04. PubMed Abstract | Publisher Full Text\n\nZhu X, Zuo L: Characterization of oxygen radical formation mechanism at early cardiac ischemia. Cell Death Dis. 2013; 4(e787): e787. PubMed Abstract | Publisher Full Text\n\nZhou T, Chuang CC, Zuo L: Molecular Characterization of Reactive Oxygen Species in Myocardial Ischemia-Reperfusion Injury. Biomed. Res. Int. 2015; 2015: 864946–9. 20151005. PubMed Abstract | Publisher Full Text\n\nPatil N, Chavan V, Karnik ND: Antioxidant status in patients with acute myocardial infarction. Indian J. Clin. Biochem. 2007; 22: 45–51. Publisher Full Text\n\nHori M, Nishida K: Oxidative stress and left ventricular remodelling after myocardial infarction. Cardiovasc. Res. 2008; 81: 457–464. Publisher Full Text\n\nZhou T, Prather ER, Garrison DE, et al.: Interplay between ROS and Antioxidants during Ischemia-Reperfusion Injuries in Cardiac and Skeletal Muscle. Int. J. Mol. Sci. 2018; 19: 417. PubMed Abstract | Publisher Full Text\n\nWang W, Kang PM: Oxidative Stress and Antioxidant Treatments in Cardiovascular Diseases. Antioxidants (Basel). 2020; 9: 20201217. PubMed Abstract | Publisher Full Text\n\nGasparetto C, Malinverno A, Culacciati D, et al.: Antioxidant Vitamins Reduce Oxidative Stress and Ventricular Remodeling in Patients with Acute Myocardial Infarction. Int. J. Immunopathol. Pharmacol. 2005; 18: 487–496. PubMed Abstract | Publisher Full Text\n\nYu H, Guan Q, Guo L, et al.: Gypenosides alleviate myocardial ischemia-reperfusion injury via attenuation of oxidative stress and preservation of mitochondrial function in rat heart. Cell Stress Chaperones. 2016; 21(429-437): 429–437. PubMed Abstract | Publisher Full Text\n\nShaito A, Thuan DTB, Phu HT, et al.: Herbal Medicine for Cardiovascular Diseases: Efficacy, Mechanisms, and Safety. Front. Pharmacol. 2020; 11: 422–422. PubMed Abstract | Publisher Full Text\n\nBhadoriya SS, Ganeshpurkar A, Narwaria J, et al.: Tamarindus indica: Extent of explored potential. Pharmacogn. Rev. 2011; 5: 73–81. 2011/11/19. PubMed Abstract | Publisher Full Text\n\nKuru P: Tamarindus indica and its health related effects. Asian Pac. J. Trop. Biomed. 2014; 4: 676–681. Publisher Full Text\n\nBurgalassi S, Raimondi L, Pirisino R, et al.: Effect of xyloglucan (tamarind seed polysaccharide) on conjunctival cell adhesion to laminin and on corneal epithelium wound healing. Eur. J. Ophthalmol. 2000; 10: 71–76. 2000/04/01. PubMed Abstract | Publisher Full Text\n\nWaqas MK, Khan BA, Akhtar N, et al.: Fabrication of Tamarindus indica seeds extract loaded-cream for photo-aged skin: Visioscan((R)) studies. Postepy. Dermatol. Alergol. 2017; 34: 339–345. 2017/09/28. PubMed Abstract | Publisher Full Text\n\nSreelekha TT, Vijayakumar T, Ankanthil R, et al.: Immunomodulatory effects of a polysaccharide from Tamarindus indica. Anti-Cancer Drugs. 1993; 4: 209–212. 1993/04/01. PubMed Abstract | Publisher Full Text\n\nVargas-Olvera CY, Sánchez-González DJ, Solano JD, et al.: Characterization of N-diethylnitrosamine-initiated and ferric nitrilotriacetate-promoted renal cell carcinoma experimental model and effect of a tamarind seed extract against acute nephrotoxicity and carcinogenesis. Mol. Cell. Biochem. 2012; 369: 105–117. 20120704. PubMed Abstract | Publisher Full Text\n\nMaiti R, Jana D, Das UK, et al.: Antidiabetic effect of aqueous extract of seed of Tamarindus indica in streptozotocin-induced diabetic rats. J. Ethnopharmacol. 2004; 92: 85–91. 2004/04/22. PubMed Abstract | Publisher Full Text\n\nSudjaroen Y, Haubner R, Wurtele G, et al.: Isolation and structure elucidation of phenolic antioxidants from Tamarind (Tamarindus indica L.) seeds and pericarp. Food Chem. Toxicol. 2005; 43: 1673–1682. 2005/07/08. PubMed Abstract | Publisher Full Text\n\nUchenna UE, Shori AB, Baba AS: Tamarindus indica seeds improve carbohydrate and lipid metabolism: An in vivo study. J. Ayurveda Integr. Med. 2018; 9: 258–265. 2017/12/06. PubMed Abstract | Publisher Full Text\n\nSandesh P, Velu V, Singh RP: Antioxidant activities of tamarind (Tamarindus Indica) seed coat extracts using in vitro and in vivo models. J. Food Sci. Technol. 2014; 51: 1965–1973. 2014/09/06. PubMed Abstract | Publisher Full Text\n\nSundaram MS, Hemshekhar M, Santhosh MS, et al.: Tamarind Seed (Tamarindus indica) Extract Ameliorates Adjuvant-Induced Arthritis via Regulating the Mediators of Cartilage/Bone Degeneration, Inflammation and Oxidative Stress. Sci. Rep. 2015; 5: 11117. PubMed Abstract | Publisher Full Text\n\nUshanandini S, Nagaraju S, Harish Kumar K, et al.: The anti-snake venom properties of Tamarindus indica (leguminosae) seed extract. Phytother. Res. 2006; 20: 851–858. PubMed Abstract | Publisher Full Text\n\nChatatikun M, Chiabchalard A: Thai plants with high antioxidant levels, free radical scavenging activity, anti-tyrosinase and anti-collagenase activity. BMC Complement. Altern. Med. 2017; 17: 487. 2017/11/11. PubMed Abstract | Publisher Full Text\n\nRe R, Pellegrini N, Proteggente A, et al.: Antioxidant activity applying an improved ABTS radical cation decolorization assay. Free Radic. Biol. Med. 1999; 26: 1231–1237. 1999/06/25. PubMed Abstract | Publisher Full Text\n\nKongpol K, Nernpermpisooth N, Prompunt E, et al.: Endothelial-Cell-Derived Human Secretory Leukocyte Protease Inhibitor (SLPI) Protects Cardiomyocytes against Ischemia/Reperfusion Injury. Biomolecules. 2019; 9: 678. PubMed Abstract | Publisher Full Text\n\nStrijdom H, Jacobs S, Hattingh S, et al.: Nitric oxide production is higher in rat cardiac microvessel endothelial cells than ventricular cardiomyocytes in baseline and hypoxic conditions: a comparative study. FASEB J. 2006; 20: 314–316. 20051214. PubMed Abstract | Publisher Full Text\n\nPu J, Zhu S, Zhou D, et al.: Propofol Alleviates Apoptosis Induced by Chronic High Glucose Exposure via Regulation of HIF-1alpha in H9c2 Cells. Oxidative Med. Cell. Longev. 2019; 2019: 4824035. 2019/05/17. PubMed Abstract | Publisher Full Text\n\nPeinnequin A, Mouret C, Birot O, et al.: Rat pro-inflammatory cytokine and cytokine related mRNA quantification by real-time polymerase chain reaction using SYBR green. BMC Immunol. 2004; 5: 3. 2004/03/26. PubMed Abstract | Publisher Full Text\n\nPu J, Zhu S, Zhou D, et al.: Propofol Alleviates Apoptosis Induced by Chronic High Glucose Exposure via Regulation of HIF-1α in H9c2 Cells. Oxidative Med. Cell. Longev. 2019; 2019: 4824035. PubMed Abstract | Publisher Full Text\n\nSurinkaew S: Spreadsheet data of anti-ischemic effect of TS extract in cardiomyocyte. figshare.2022.\n\nLuengthanaphol S, Mongkholkhajornsilp D, Douglas S, et al.: Extraction of antioxidants from sweet Thai tamarind seed coat––preliminary experiments. J. Food Eng. 2004; 63: 247–252. Publisher Full Text\n\nTsuda TW, Ohshima M, Yamamoto K, et al.: Antioxidative components isolated from the seed of tamarind (Tamarindus indica L.). J. Agric. Food Chem. 1994; 42: 2671–2674. Publisher Full Text\n\nRazali N, Mat Junit S, Ariffin A, et al.: Polyphenols from the extract and fraction of T. indica seeds protected HepG2 cells against oxidative stress. BMC Complement. Altern. Med. 2015; 15: 438. 2015/12/20. PubMed Abstract | Publisher Full Text\n\nSakano K, Mizutani M, Murata M, et al.: Procyanidin B2 has anti- and pro-oxidant effects on metal-mediated DNA damage. Free Radic. Biol. Med. 2005; 39: 1041–1049. 2005/10/04. PubMed Abstract | Publisher Full Text\n\nWang J, Xiong X, Feng B: Effect of crataegus usage in cardiovascular disease prevention: an evidence-based approach. Evid. Based Complement. Alternat. Med. 2013; 2013: 149363. 2014/01/25. PubMed Abstract | Publisher Full Text\n\nChang WT, Dao J, Shao ZH: Hawthorn: potential roles in cardiovascular disease. Am. J. Chin. Med. 2005; 33: 1–10. 2005/04/23. PubMed Abstract | Publisher Full Text\n\nOttaviani JI, Heiss C, Spencer JPE, et al.: Recommending flavanols and procyanidins for cardiovascular health: Revisited. Mol. Asp. Med. 2018; 61: 63–75. 2018/02/11. PubMed Abstract | Publisher Full Text\n\nKatz DL, Doughty K, Ali A: Cocoa and chocolate in human health and disease. Antioxid. Redox Signal. 2011; 15: 2779–2811. 2011/04/08. Publisher Full Text\n\nCho ES, Jang YJ, Kang NJ, et al.: Cocoa procyanidins attenuate 4-hydroxynonenal-induced apoptosis of PC12 cells by directly inhibiting mitogen-activated protein kinase kinase 4 activity. Free Radic. Biol. Med. 2009; 46: 1319–1327. 2009/03/03. PubMed Abstract | Publisher Full Text\n\nChandel NS, Maltepe E, Goldwasser E, et al.: Mitochondrial reactive oxygen species trigger hypoxia-induced transcription. Proc. Natl. Acad. Sci. U. S. A. 1998; 95: 11715–11720. 1998/09/30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSemenza GL: Hypoxia-inducible factor 1 and cardiovascular disease. Annu. Rev. Physiol. 2014; 76: 39–56. 2013/08/31. Publisher Full Text\n\nDuan L, Lei H, Zhang Y, et al.: Calcitonin Gene-Related Peptide Improves Hypoxia-Induced Inflammation and Apoptosis via Nitric Oxide in H9c2 Cardiomyoblast Cells. Cardiology. 2016; 133: 44–53. 2015/10/03. PubMed Abstract | Publisher Full Text\n\nPacher P, Beckman JS, Liaudet L: Nitric oxide and peroxynitrite in health and disease. Physiol. Rev. 2007; 87: 315–424. 2007/01/24. Publisher Full Text\n\nTsuda TW, Ohshima M, Yamamoto K, et al.: Screening for Antioxidative Activity of Edible Pulses. Biosci. Biotechnol. Biochem. 1993; 57: 1606–1608. Publisher Full Text\n\nKomutarin T, Azadi S, Butterworth L, et al.: Extract of the seed coat of Tamarindus indica inhibits nitric oxide production by murine macrophages in vitro and in vivo. Food Chem. Toxicol. 2004; 42: 649–658. PubMed Abstract | Publisher Full Text\n\nMcGarry T, Biniecka M, Veale DJ, et al.: Hypoxia, oxidative stress and inflammation. Free Radic. Biol. Med. 2018; 125: 15–24. Publisher Full Text\n\nSuksomtip M, Ukrisdawithid S, Bhusawang P, et al.: Phenolic Compound Content, Antioxidant And Radical-Scavenging Properties Of Methanolic Extracts From The Seed Coat Of Certain Thai Tamarind Cultivars. J. Food Biochem. 2010; 34: 916–931. Publisher Full Text\n\nSiddhuraju P: Antioxidant activity of polyphenolic compounds extracted from defatted raw and dry heated Tamarindus indica seed coat. LWT Food Sci. Technol. 2007; 40: 982–990. Publisher Full Text\n\nRomero-Becerra R, Santamans AM, Folgueira C, et al.: p38 MAPK Pathway in the Heart: New Insights in Health and Disease. Int. J. Mol. Sci. 2020; 21: 7412. PubMed Abstract | Publisher Full Text\n\nEmerling BM, Platanias LC, Black E, et al.: Mitochondrial reactive oxygen species activation of p38 mitogen-activated protein kinase is required for hypoxia signaling. Mol. Cell. Biol. 2005; 25: 4853–4862. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "253348",
"date": "25 Apr 2024",
"name": "Christophe Wiart",
"expertise": [
"Reviewer Expertise Natural products",
"ethnopharmacology",
"pharmacy"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a well-written paper. The topic is timely. Protocol and methods are okay. The results are okay. I feel that the authors need to explain why no positive standard was used for the cytotoxicity test as well as the hypoxia test. I also feel that the authors could write a lot more about the traditional use of the plant in Thailand and why they chose the seeds only and why not the whole fruit or the pulp. Editing is excellent.\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": "253353",
"date": "25 Apr 2024",
"name": "Siva Ramamoorthy",
"expertise": [
"Reviewer Expertise Natural Products",
"pigments",
"cancer 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\nHere are the limitations that I have seen in the paper.\nTS extract has a potential antioxidant activity similar to ascorbic acid. Radical scavenging activities of TS extract could directly reduce intracellular ROS accumulation under hypoxic conditions in an in vitro model. However, antioxidant defense systems, such as glutathione peroxidase, peroxiredoxin, total antioxidant activities, as well as associated transcriptional factors, should be further investigated.\n\nThe authors have demonstrated strong evidence of pretreatment of TS extract attenuating the effects of hypoxia-induced-inflammatory cytokines and apoptosis, which is likely due to its antioxidant and anti-inflammatory properties. The underlying mechanism of TS in preventing hypoxic injury remains to be clarified.\n\nThe p38 MAPK, involving cell differentiation, survival, and apoptosis, plays a crucial role in cardiac ischemic response and is known to be regulated by HIF-1α. However, the signaling pathway of p38 MAPK regulating HIF-1α through ROS scavenging of TS extract needs to be further elucidated.\n\nThe systemic effects of TS extract, including long-term treatment, different time points of administration (such as at the onset of ischemia or the beginning of reperfusion), and the effect of isolated TS compounds, as well as their combinations in a myocardial infarction experimental animal model should be further performed and its associated mechanisms (such as p38 MAPK) need to be further investigated.\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/11-1235
|
https://f1000research.com/articles/11-1234/v1
|
31 Oct 22
|
{
"type": "Data Note",
"title": "The computationally predicted drug-likeness, pharmacokinetics properties, medicinal chemistry parameters, and toxicity properties of Cucurbita maxima compounds.",
"authors": [
"Ryman Shoko"
],
"abstract": "Natural compounds are increasingly becoming an important source of drug leads for computer-aided drug design approaches. Cucurbita maxima has been observed to have medicinal properties and can, therefore, be a potential source of novel drug leads. However, before compounds can be synthesized in the lab for tests, modern approaches require that the candidate compounds be screened for drug-likeness characteristics and toxicity, among others. In this work, the computational tools, SwissADME and DataWarrior were used to screen C. maxima compounds for their potential consideration as drug leads. A total of 130 compounds, downloaded from the LOTUS natural products database, were computationally analysed. The data set presented in this work will be useful to researchers searching for novel drug leads based on natural compounds.",
"keywords": [
"Cucurbita maxima",
"medicinal plants",
"druglikeness",
"natural products",
"pharmacoinformatics"
],
"content": "Introduction\n\nNatural products (NP), such as plants and their extracts, have been used to cure diseases in humans and livestock since ancient times (Daina et al., 2017; Greenwell & Rahman, 2015). In modern computer-aided drug design approaches, NPs are considered to be a significant foundation for drug discovery due to their diverse chemical components and their often-unique biomedical properties (Süntar, 2020). Among their unique properties, the NPs are often rich in stereogenic centres and occupy portions of the chemical space that is usually not covered by most synthetic drugs (Marxer et al., 2012).\n\nCucurbita maxima (commonly known as giant pumpkin) is rich in phenolics, tannins, flavonoids, alkaloids, saponins, terpenoids, carbohydrates and proteins (Salehi et al., 2019; Sorescu et al., 2020). For centuries, extracts from different parts of the plant have been used to treat various diseases such as intestinal infections, renal failure, hyperplasia, constipation, and parasite infestation (Menendez-Baceta et al., 2014; Kujawska & Pieroni, 2015; Mahomoodally et al., 2016; Mtemeli et al. 2021). Thus, CADD approaches can be applied to investigate the potential of some compounds from this plant to act as drug leads. Before synthesising a compound in the laboratory for testing, modern computational approaches require that the compounds be computationally screened for drug-likeness and potential toxicity.\n\nThe standard method to evaluate drug-likeness of a compound is to assess compliance to Lipinski's Rule of Five (Lipinski et al., 1997), which covers the molecular weight, numbers of hydrophilic groups and hydrophobicity. This data note presents a list of C. maxima natural compounds and their computationally calculated data on drug-likeness characteristics, pharmacokinetics, medicinal chemistry parameters and predicted toxicity. Toxicity predictions are important because substructures with known toxic, teratogenic or mutagenic properties negatively affects the usefulness of a designed drug. With data produced in this work, researchers can better predict which C. maxima compounds have a better chance of succeeding throughout all stages of clinical trials, through to drug approval.\n\n\nMaterials and methods\n\nTo create a library of C. maxima natural compounds, the term 'Cucurbita maxima' was entered into the search box of the Lotus Natural Compounds Database (https://lotus.naturalproducts.net/). The search returned 130 natural products. A file containing the 130 compounds in the structure-data file (SDF) format was downloaded and then fed into BIOVIA Discovery Studio v21.1.0.20298, RRID:SCR_015651 to get the molecular structures in the corresponding simplified molecular-input line-entry system (SMILE) format. The SMILEs were then used to calculate the various properties of the compounds using the SwissADME (Daina et al., 2017) web tool and the DataWarrior v5.5.0 (Sander et al., 2015) software.\n\n\nDataset validation and limitations\n\nAn inherent limitation of computational prediction of drug-likeness is the lack of validated datasets of drugs and non-drugs. Therefore, the classification presented here is solely based on the similarity of structure of the compounds to known drugs. Also compounds from completely new classes are likely to be wrongly classified. Another important limitation of computationally predicted drug-likeness is that it does not predict the biological/pharmacological activity of a compound. Wet bench methods are required to validate the biological/pharmacological activity.\n\nIn summary, the dataset presented here will probably be most useful in lead discovery where they could be used for prioritizing compounds for synthesis or for purchasing from external suppliers.",
"appendix": "Data availability\n\nHarvard Dataverse: Underlying data for ‘The Computationally predicted drug-likeness, pharmacokinetics properties, medicinal chemistry parameters, and toxicity properties of Cucurbita maxima compounds’. https://doi.org/10.7910/DVN/4ISBWI (Shoko, 2022).\n\nThis project contains the following underlying data:\n\n• Data file 1. (Druglikeness Properties of C. maxima natural compounds.)\n\n• Data file 2. (Medicinal Chemistry Properties of C. maxima natural compounds.)\n\n• Data file 3. (Pharmacokinetics Properties of C. maxima compounds.)\n\n• Data file 4. (Toxicity Properties of C. maxima compounds.)\n\nData are available under the terms of the CC0 1.0 Universal (CC0 1.0)\n\nPublic Domain Dedication.\n\n\nReferences\n\nDaina A, Michielin O, Zoete V: SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 2017; 7(1): Article 1. PubMed Abstract | Publisher Full Text\n\nGreenwell M, Rahman PKSM: Medicinal Plants: Their Use in Anticancer Treatment. Int. J. Pharm. Sci. Res. 2015; 6(10): 4103–4112. PubMed Abstract | Publisher Full Text\n\nKujawska M, Pieroni A: Plants used as food and medicine by Polish migrants in Misiones, Argentina. Ecol. Food Nutr. 2015; 54(3): 255–279. PubMed Abstract | Publisher Full Text\n\nLipinski CA, Lombardo F, Dominy BW, et al.: Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997; 23(1): 3–25. Publisher Full Text\n\nMahomoodally MF, Mootoosamy A, Wambugu S: Traditional Therapies Used to Manage Diabetes and Related Complications in Mauritius: A Comparative Ethnoreligious Study. Evid. Based Complement. Alternat. Med. 2016; 2016: 4523825–4523828. PubMed Abstract | Publisher Full Text\n\nMarxer M, Ingram K, Keiser J: Development of an in vitro drug screening assay using Schistosoma haematobium schistosomula. Parasit. Vectors. 2012; 5(1): 165. PubMed Abstract | Publisher Full Text\n\nMenendez-Baceta G, Aceituno-Mata L, Molina M, et al.: Medicinal plants traditionally used in the northwest of the Basque Country (Biscay and Alava), Iberian Peninsula. J. Ethnopharmacol. 2014; 152(1): 113–134. PubMed Abstract | Publisher Full Text\n\nMtemeli FL, Walter I, Tinago T, et al.: An assessment of the molluscicidal potential of Cucurbita maxima seed extracts on Biomphalaria pfeifferi and Bulinus globosus snails. All Life. 2021; 14(1): 244–255. Publisher Full Text\n\nSalehi B, Sharifi-Rad J, Capanoglu E, et al.: Cucurbita Plants: From Farm to Industry. Appl. Sci. 2019; 9(16): Article 16. Publisher Full Text\n\nSander T, Freyss J, von Korff M , et al.: DataWarrior: An Open-Source Program For Chemistry Aware Data Visualization And Analysis. J. Chem. Inf. Model. 2015; 55(2): 460–473. PubMed Abstract | Publisher Full Text\n\nShoko R: Computationally predicted drug-likeness, pharmacokinetics properties, medicinal chemistry parameters, and toxicity properties of Cucurbita maxima compounds. Harvard Dataverse, V1. 2022. Publisher Full Text\n\nSorescu A-A, Nuţă A, Ion R-M: Qualitative Screening of Phytocompounds and Spectrophotometric Investigations of Two Pumpkin Species. Biol. Life Sci. Forum. 2020; 4(1). Article 1. Publisher Full Text\n\nSüntar I: Importance of ethnopharmacological studies in drug discovery: Role of medicinal plants. Phytochem. Rev. 2020; 19(5): 1199–1209. Publisher Full Text"
}
|
[
{
"id": "230597",
"date": "21 Feb 2024",
"name": "Edgar López-López",
"expertise": [
"Reviewer Expertise Cheminformatics",
"Natural products",
"Drug design",
"Drug development",
"Computer-aided drug design."
],
"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 author,\nI consider this \"data note\" to be interesting and transcendent. This work presents a dataset of properties of pharmaceutical interest of molecules present in Curcubita maxima, which could be of interest to those research groups that plan to isolate, synthesize, or acquire any of these molecules for subsequent trials. However, I consider that some minor comments should be resolved :\n1. Introduction section: About the sentence \"... occupy portions of the chemical space that is usually not covered by most synthetic drugs\". I suggest adding most recent references that support it. I share with you examples that could be useful: (Saldívar-G et al, 2019)[Ref 1] ,(Sorokina M et al, 2021) [Ref 2], (Medina-Franco JL et al, 2022) [Ref 3], (López-Pérez K et al, 2023) [Ref 4]\n2. Introduction section: The abbreviation \"CADD\" could be unclear for \"non-expert readers\", I suggest adding the explicit significance of this.\n3. Please change \"SMILE\" to \"SMILES\".\n4. I suggest citing this \"technology evaluation\" article that complements the original Data Warrior reference: (López-López et al, 2019) [Ref 5] 5. Please, add a reference that supports the sentence \"Another important limitation of computationally predicted drug-likeness is that it does not predict the biological/pharmacological activity of a compound. \"\n6. Scientific names (e.g. Curcubita maxima) must be written using italic style.\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": []
},
{
"id": "262625",
"date": "29 Apr 2024",
"name": "Gurudutt Dubey",
"expertise": [
"Reviewer Expertise Drug Discovery",
"Medicinal Chemistry",
"Computer-aided drug design",
"computational chemistry",
"RNA 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\nThis data not summaries the computationally predicted ADME and toxicity parameters of Cucurbita maxima. Author has used SwissADME and DataWarrior tools to generate the database. Introduction is well written but incorporation of some latest references is recommended. At some places, full form of the abbreviations are missing for e.g. CADD. I will suggest to incorporate ADME and toxicity parameters calculated using other tools than SwissADME as well. It will be helpful to understand the variability in the parameters calculated using various tools.\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/11-1234
|
https://f1000research.com/articles/11-1233/v1
|
31 Oct 22
|
{
"type": "Case Report",
"title": "Case Report: A rare case of symptomatic bradycardia secondary to aripiprazole in a patient with bipolar disorder type I",
"authors": [
"Mailing Flores Chang",
"Nehemias Guevara",
"Marlon Argueta",
"Yomary Jimenez",
"Adler Vitaly",
"Salim Baghdadi",
"Marlon Argueta",
"Yomary Jimenez",
"Adler Vitaly",
"Salim Baghdadi"
],
"abstract": "It is well known that typical antipsychotic drugs have been implicated as a cause of ventricular arrhythmias and cardiac arrest; studies have shown that conventional antipsychotics increase the risk of hospitalization for ventricular arrhythmias or cardiac arrest nearly 2-fold. However, atypical antipsychotics are not associated with an increased risk of hospitalization for ventricular arrhythmias or cardiac arrest. The use of atypical antipsychotics increased since they were first discovered and now are the mainstay of treatment, but with their broad use, heart effects have been documented, such as prolonged QT interval. Clozapine has been linked to severe cardiac problems, and risperidone has been linked to an increased risk of ventricular arrhythmias and cardiac arrest. We present a case of a patient with bipolar disorder who presented with symptomatic bradycardia secondary to aripiprazole.",
"keywords": [
"Bradycardia",
"atypical antipsychotic",
"Aripiprazole",
"Bipolar disorder."
],
"content": "Introduction\n\nSeveral medication classes benefit psychotic disorders, such as schizophrenia and bipolar disorder. Over the years, atypical antipsychotics have been deemed first-line treatment due to their beneficial effects on overall mood and cognition. However, their detrimental effects, such as obesity, diabetes mellitus, and dyslipidemia, should not be ignored.1 These medications also have increased cardiovascular side effects, including QTc prolongation, torsade de Pointes (TdP), sudden cardiac death, myocarditis, and cardiomyopathy.2,3 In addition, patients with psychotic disorders already have an increased risk of cardiovascular mortality.4\n\nThe complexity of the mechanism of action of atypical antipsychotics is broad and still under active investigation5,6; however, direct cardiovascular risks overweight their benefits.7\n\nAlthough there is extensive evidence of the detrimental effects of atypical antipsychotics on cardiovascular health, there is not enough evidence of the effect of aripiprazole on heart rate (HR) and how it causes bradycardia. To the best of our knowledge, there are only two cases of aripiprazole related to bradycardia/syncope.4,8\n\nWe present a case of a patient with bipolar disorder with aripiprazole-induced symptomatic bradycardia that did not respond to standard treatment such as atropine and resolved with medication discontinuation.\n\n\nCase report\n\nA 61-year-old Latin male, unemployed at the moment, with a medical history of bipolar disorder type I diagnosed one year ago, recently started on aripiprazole. The patient did not have any further relevant family or social history. He presented to the emergency department (ED) complaining of intermittent episodes of dizziness initiated after his second dose of intramuscular (IM) aripiprazole which had worsened three days prior to admission. He denied any use of drugs or other medications. His last aripiprazole dose was two weeks before admission.\n\nUpon arrival at the ED, the patient was found to be bradycardic (44 beats/minute), normotensive, and had pulse oximetry of 98% on room oxygen. An electrocardiogram showed sinus bradycardia of 44 bpm with QT of 410 msec (Figure 1). Emergent management with atropine 0.5 mg IV was started which increased the heart rate to 50 beats/minute; however, the patient’s intermittent dizziness persisted.\n\nInitial hematologic and chemistry blood work was unremarkable (Table 1). The COVID-19 antigen test was negative. Cardiology evaluation was unremarkable. The stress test showed a peak heart rate of 144 (90 % of the maximum predicted for his age) and was negative for any ischemia. A 24-hour Holter and echocardiogram were within normal limits (Figure 2). At this point, after ruling out the most frequent causes of bradycardia, such as ischemia, medication reconciliation showed a possible association between atypical antipsychotics and previous cases reported of bradycardia. Therefore, a psychiatric evaluation was requested; psychiatry saw the patient 4 days after admission and suggested discontinuation of aripiprazole. Naranjo score calculations showed a score of 9, which put the patient as probable his symptoms were caused by an adverse effect of aripiprazole. After 4 days of discontinuation of aripiprazole, patient’s heart rate improved to 55 beats per minute, therefore, a resolution of symptoms. The patient was discharged on risperidone 1 mg twice a day and sodium valproate 500 mg twice a day. After discharge, patient was seen for the first time as an outpatient 4 months later at the cardiology clinic and he has not reported similar symptoms; furthermore, a follow-up EKG showed a complete resolution of bradycardia (Figure 3). Although aripiprazole was suspected to be the cause at the time of hospitalization and discharge due to the patient’s improvement, this was not confirmed until the subsequent follow-ups which showed a complete resolution of symptoms.\n\n\nDiscussion\n\nAtypical antipsychotic drugs came out in the 1990s; we currently have clozapine, risperidone, olanzapine, quetiapine, ziprasidone, and aripiprazole.\n\nThey have been associated with multiple side effects, such as obesity, diabetes mellitus, and dyslipidemia; therefore, cardiovascular risk increases when taking these medications.2,3\n\nSpecific cardiovascular side effects include orthostatic hypotension and reflex tachycardia; these have been linked to the antagonization of α1 receptors.\n\nHowever, more serious cardiac side effects also have been reported, such as sudden cardiac death due to anticholinergic activity; ventricular tachycardia, torsades de pointes (TdP), delayed cardiac repolarization, myocarditis, myocardial infarction, and cardiomyopathy.9–11\n\nAripiprazole was approved in 2002 for schizophrenia and shortly after for bipolar disorder I; benefits such as less propensity for weight gain, favorable metabolic profile, and no association with hyperprolactinemia make it a good option.8 Furthermore, multiple clinical trials have shown safety profiles in acute and chronic symptoms of schizophrenia and bipolar disorder I. The most common share adverse events were headache, agitation, insomnia, anxiety, akathisia, and somnolence. An increased level of prolactin was also reported.5,7,12–14\n\nPotkin et al. (2003) reported small changes in QTc but these were not significant; however, there is evidence that atypical antipsychotics can cause prolongation of the QT, therefore, inducing ventricular tachycardia and torsades de pointes.5\n\nBradycardia has been reported after the initiation of atypical antipsychotics,15,16 but we found only two cases where aripiprazole was associated as the causative drug of symptomatic bradycardia.4,8\n\nThe mechanism of action for which atypical antipsychotics could cause bradycardia has been related to the effects on 5-HT1A (5-beta hydroxytryptamine receptor 1) activation with upregulation of α2-adrenoreceptors in the brainstem.8,15,17,18\n\nThe complex signaling and the role played by the sympathetic and parasympathetic nervous systems, as well as serotonin pathways in the heart, is complex and is the reason behind this type of medication can have an effect on the heart.18–20\n\nAripiprazole is a partial dopamine agonist with substantial binding affinity for the serotonin 5HT2A (short for 5-hydroxy-tryptamine subtype 2 A) receptor; it has a broad spectrum receptors interaction as mentioned by Shapiro et al.6 with high affinity for h5-HT(2B) (5-hydroxytryptamine receptors), hD(2L)-, and hD(3)-dopamine receptors. Furthermore, an affinity for several other 5-HT receptors such as (5-HT(1A), 5-HT(2A), 5-HT(7)), as well as alpha(1A)-adrenergic and hH(1)-histamine receptors.\n\nAripiprazole has less affinity (30-200 nM) for other G protein-coupled receptors, including the 5-HT(1D), 5-HT(2C), alpha(1B)-, alpha(2A)-, alpha(2B)-, alpha(2C)-, beta(1)-, and beta (2)-adrenergic, and H(3)-histamine receptors.6,21\n\nOur patient arrived with symptomatic bradycardia negative normal thyroid gland function test (TSH: 2.36). An echocardiogram showed borderline left ventricular hypertrophy and normal left ventricular wall motion and ejection fraction, with a normal stress test.\n\nTypical medications that are associated with bradycardia were ruled out, such as beta-blockers.\n\nAripiprazole 400 mg IM monthly injections and 5 mg oral daily two months prior to his hospitalization, with the last dose two weeks prior to admission, make this association possible. Furthermore, Naranjo Adverse Drug Reaction Probability Scale was calculated and was 9.22\n\nAs per the literature review, in all the cases reported where the bradycardia cause was atypical antipsychotics6,23 all symptoms were reversible after stopping the medication, and our case was not the exception.\n\nHe has been following up in our clinic without the persistence of his symptoms and normal EKGs.\n\n\nConclusion\n\nMultiple cardiovascular risk factors have been associated with the use of antipsychotic medications, such as ventricular tachycardia, TdP, delayed cardiac repolarization, myocarditis, myocardial infarction, and cardiomyopathy. However, there is limited evidence regarding antipsychotic-induced bradycardia, specifically aripiprazole-related. As observed in our case, the patient with bipolar disorder treated who was with aripiprazole developed symptomatic bradycardia which was induced by the use of this medication. This was proven after extensive cardiac workup that resulted in negatives for other common causes such as ischemia; furthermore, symptoms resolved after discontinuation of the medication.\n\nAlthough we could prove with our case that aripiprazole can cause bradycardia, further studies with more data are needed to establish a clear relationship between this medication and bradycardia.\n\n\nPatient perspective\n\nThe patient states he started to feel unwell after initiating the new treatment but never associated his symptoms with the new medication. Upon discharge, he understood what symptom management he had received and received a full explanation of the new treatment's side effects.\n\n\nConsent for publication\n\nInformed written consent was obtained from the patient for the publication of this case report and the accompanying images.\n\n\nAuthors' contributions\n\n\n\n• All authors have contributed equally to this case report.",
"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\nWu CS, Tsai YT, Tsai HJ: Antipsychotic drugs and the risk of ventricular arrhythmia and/or sudden cardiac death: a nation-wide case-crossover study. J. Am. Heart Assoc. 2015 Feb 23; 4(2): e001568. PubMed Abstract | Publisher Full Text\n\nStoner SC: Management of serious cardiac adverse effects of antipsychotic medications. Ment Health Clin. 2017 Nov; 7(6): 246–254. PubMed Abstract | Publisher Full Text\n\nAtypical antipsychotics, schizophrenia, and cardiovascular risk: What family physicians need to know. British Columbia Med. J. [cited 2022 Sep 21].Reference Source\n\nFletke K, Blanchard J, Kuo S: 23-year-old woman • syncopal episode • sinus bradycardia • history of bipolar disorder • Dx? J. Fam. Pract. 2021 Apr; 70(3): 150–151. PubMed Abstract | Publisher Full Text\n\nPotkin SG, Saha AR, Kujawa MJ, et al.: Aripiprazole, an antipsychotic with a novel mechanism of action, and risperidone vs placebo in patients with schizophrenia and schizoaffective disorder. Arch. Gen. Psychiatry. 2003 Jul; 60(7): 681–690. PubMed Abstract | Publisher Full Text\n\nShapiro DA, Renock S, Arrington E, et al.: Aripiprazole, A Novel Atypical Antipsychotic Drug with a Unique and Robust Pharmacology. Neuropsychopharmacology. 2003 Aug; 28(8): 1400–1411. PubMed Abstract | Publisher Full Text\n\nPigott TA, Carson WH, Saha AR, et al.: Aripiprazole for the prevention of relapse in stabilized patients with chronic schizophrenia: a placebo-controlled 26-week study. J. Clin. Psychiatry. 2003 Sep; 64(9): 1048–1056. PubMed Abstract | Publisher Full Text\n\nSnarr BS, Phan SV, Garner A, et al.: Symptomatic bradycardia with oral aripiprazole and oral ziprasidone. Ann. Pharmacother. 2010 Apr; 44(4): 760–763. PubMed Abstract | Publisher Full Text\n\nHonkola J, Hookana E, Malinen S, et al.: Psychotropic medications and the risk of sudden cardiac death during an acute coronary event. Eur. Heart J. 2012 Mar 1; 33(6): 745–751. PubMed Abstract | Publisher Full Text\n\nRay WA, Chung CP, Murray KT, et al.: Atypical Antipsychotic Drugs and the Risk of Sudden Cardiac Death. N. Engl. J. Med. 2009 Jan 15; 360(3): 225–235. PubMed Abstract | Publisher Full Text\n\nWu C, Tsai Y, Tsai H: Antipsychotic Drugs and the Risk of Ventricular Arrhythmia and/or Sudden Cardiac Death: A Nation-wide Case-Crossover Study. J. Am. Heart. Assoc. Cardiovasc. Cerebrovasc. Dis. 2015 Feb 23; 4(2): e001568. PubMed Abstract | Publisher Full Text\n\nKane J, Meltzer H, Carson W, et al.: Aripiprazole for Treatment-Resistant Schizophrenia: Results of a Multicenter, Randomized, Double-Blind, Comparison Study Versus Perphenazine. J. Clin. Psychiatry. 2007 Feb 1; 68: 213–223. Publisher Full Text\n\nKasper S, Lerman MN, McQuade RD, et al.: Efficacy and safety of aripiprazole vs. haloperidol for long-term maintenance treatment following acute relapse of schizophrenia. Int. J. Neuropsychopharmacol. 2003 Dec 1; 6(4): 325–337. PubMed Abstract | Publisher Full Text\n\nMarder SR, McQuade RD, Stock E, et al.: Aripiprazole in the treatment of schizophrenia: safety and tolerability in short-term, placebo-controlled trials. Schizophr. Res. 2003 Jun; 61(2–3): 123–136. PubMed Abstract | Publisher Full Text\n\nLee TW, Tsai SJ, Hwang JP: Severe cardiovascular side effects of olanzapine in an elderly patient: case report. Int. J. Psychiatry Med. 2003; 33(4): 399–401. PubMed Abstract | Publisher Full Text\n\nPedrosa Gil F, Grohmann R, Rüther E: Asymptomatic bradycardia associated with amisulpride. Pharmacopsychiatry. 2001 Nov; 34(6): 259–261. PubMed Abstract | Publisher Full Text\n\nGoyal RS, Goyal SB: Symptomatic Bradyarrhythmia Secondary to Risperidone. Am. J. Psychiatry. 2003 Dec; 160(12): 2243–2243. PubMed Abstract | Publisher Full Text\n\nRazakarivony O, Newman-Tancredi A, Zimmer L: Towards in vivo imaging of functionally active 5-HT1A receptors in schizophrenia: concepts and challenges. Transl. Psychiatry. 2021 Jan 7; 11: 22. PubMed Abstract | Publisher Full Text\n\nBrodde OE, Bruck H, Leineweber K, et al.: Presence, distribution and physiological function of adrenergic and muscarinic receptor subtypes in the human heart. Basic Res. Cardiol. 2001 Nov; 96(6): 528–538. PubMed Abstract | Publisher Full Text\n\nWoo AYH, Xiao R, ping.: β-Adrenergic receptor subtype signaling in heart: from bench to bedside. Acta Pharmacol. Sin. 2012 Mar; 33(3): 335–341. PubMed Abstract | Publisher Full Text\n\nPotkin SG, Saha AR, Kujawa MJ, et al.: Aripiprazole, an antipsychotic with a novel mechanism of action, and risperidone vs placebo in patients with schizophrenia and schizoaffective disorder. Arch. Gen. Psychiatry. 2003 Jul; 60(7): 681–690. PubMed Abstract | Publisher Full Text\n\nNaranjo CA, Busto U, Sellers EM, et al.: A method for estimating the probability of adverse drug reactions. Clin. Pharmacol. Ther. 1981 Aug; 30(2): 239–245. Publisher Full Text\n\nPitner JK, Mintzer JE, Pennypacker LC, et al.: Efficacy and adverse effects of clozapine in four elderly psychotic patients. J. Clin. Psychiatry. 1995 May; 56(5): 180–185. PubMed Abstract"
}
|
[
{
"id": "154570",
"date": "06 Dec 2022",
"name": "Juan Manuel Muñoz Moreno",
"expertise": [
"Reviewer Expertise Bradyarrhythmias",
"antiarrhythmic",
"heart disease"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFlores Chang, et al., describe an interesting case of symptomatic bradycardia associated with the use of the atypical antipsychotic, aripiprazole.\nI would like to add a few minor observations:\nAn electrocardiogram showed sinus bradycardia of 44 bpm with QT of 410 msec: describe the QT interval corrected for HR, and note that it was in the normal range.\n\nOur patient arrived with symptomatic bradycardia negative normal thyroid gland function test (TSH: 2.36). An echocardiogram showed borderline left ventricular hypertrophy and normal left ventricular wall motion and ejection fraction, with a normal stress test. Typical medications that are associated with bradycardia were ruled out, such as beta-blockers.\n-- > It could be written as: Our patient arrived with symptomatic bradycardia, and alternative causes such as the use of beta-blockers, alterations in thyroid hormones and myocardial ischemia were ruled out.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "227264",
"date": "18 Dec 2023",
"name": "Liliang Li",
"expertise": [
"Reviewer Expertise Antipsychotics cardiotoxicity"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors described a rare case who presented symptomatic bradycardia secondary to aripiprazole, but recovered after replacement with risperidone treatment. This is an interesting case that would arouse attention to clinical treatment. I have the following suggestions: 1. Authors need to state the metabolic parameters and BMI since these are very important risk factors for cardiovascular changes. 2. Discussion section is not well-organized and did not cover the recent research progress. First, authors should delete some redundant and repeated statements. Second, since aripiprazole also belongs to atypical antipsychotics, authors may need to discuss whether the bradycardia is drug-dependent? I suggest authors refer to two recent literatures (PMID:34733639 and 35739093). 3. Authors may revise their language.\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? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
},
{
"id": "227261",
"date": "26 Jan 2024",
"name": "Barun Kumar",
"expertise": [
"Reviewer Expertise Cardiology",
"coronary artery disease",
"Angioplasty & Stenting."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWell-written case report. Although a rare side effect, timely recognition is important as at this age one may confuse this with sick sinus syndrome and may implant a pacemaker. As the patient recovered and didn't show bradycardia, it proves that the drug was the culprit. A longer follow up will further support the authors' observations. Congratulations.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1233
|
https://f1000research.com/articles/11-1232/v1
|
31 Oct 22
|
{
"type": "Genome Note",
"title": "Identification of the exuviae of larva from Teinopalpus aureus Mell, 1923 using the complete mitochondrial genome",
"authors": [
"Lei-Lei Liu",
"Li-Hua Zhang",
"Guo-Hang Weng",
"Wei-Qin Wang",
"Xi-Cheng Gong",
"Shan-Biao Wang",
"Shu-Sheng Zhang",
"Lei-Lei Liu",
"Li-Hua Zhang",
"Guo-Hang Weng",
"Wei-Qin Wang",
"Xi-Cheng Gong",
"Shan-Biao Wang"
],
"abstract": "Teinopalpus aureus Mell (Lepidoptera: Papilionidae) is distributed throughout China, Vietnam and Laos, and is listed as a Class I species in China. To identify whether the exuviae of larva is belonging to Teinopalpus aureus Mell, 1923 or not, and to compare the gene structure and genetic differences among the known populations, ten mitogenomes of T. aureus from the exuviae of larva collected in the Michelia maudiae were sequenced. This method of sequencing the mitogenomes of exuviae of larva can give us the chance to monitor the conservation of rare butterflies. Ten mitogenomes of T. aureus showed typical gene arrangements and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). The two haplotypes with one base different in T. aureus were found. We also conducted phylogenetic analyses including all different populations of T. aureus to assess the phylogenetic relationship of T. aureus. The lengths of the 12S rRNA and 16S rRNA genes from both haplotypes were 776 base pairs (bp) and 1,334 bp, respectively. The genetic distance of the ten samples was calculated as 0-0.000065 on the basis of the whole mitogenomes. T. aureus found in Taishun, Zhejiang province, China had a close phylogenetic relationship with the clade of T. aureus found in Pingshan, Jiangxi province, China, which was supported by neighbour-joining analysis.",
"keywords": [
"Golden Kaiserihind",
"Mitogenome",
"Phylogeny"
],
"content": "Introduction\n\nBecause of its beautiful appearance and relative rarity in China, Teinopalpus aureus Mell, 1923 (Lepidoptera: Papilionidae) distributed in China, Vietnam and Laos is listed as a Class I species in China (Morita 1998; Masui 1999; Xing et al. 2019; Huang et al. 2015), which is one of three highest classifications for protection of endangered insect species in China. If we can identify the larva of T. aureus and obtain the mitochondrial genome using the exuviae of larva, we can determine its habitat sites and compare the genetic diversity of T. aureus using non-damage sampling to protect it in the larva stage.\n\nNo ethical approval was obtained for this study as we used wild exuviate gathered from the Wuyanling National Nature Reserve.\n\n\nMethods\n\nTen exuviae of larva of T. aureus (No. ZJWYL20200601TP01- ZJWYL20200601TP10) were collected from wild host plants, Michelia maudiae, in Zhejiang Wuyanling National Nature Reserve, Taishun, Zhejiang province, China and stored in 100% absolute ethyl alcohol in the Natural Museum of Wuyanling National Nature Reserve, China.\n\nA total of ten genomic DNAs from exuviae of larva (No. ZJWYL20200601TP01- ZJWYL20200601TP10) were extracted from partial exuviae using QIAGEN DNeasy Blood and Tissue Kit (QIAGEN, Valencia, CA) according to the manufacturer instructions, and stored at -20 °C refrigerator in Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province.\n\nThe mitochondrial genome was obtained by the Sanger method. Ten mt genomes were amplified by polymerase chain reaction (PCR) by using the normal primers (Zhang et al. 2018; Guan et al. 2021; Xu et al. 2021; Yu et al. 2021) and six specific primers according to the reported mitochondrial genomes of T. aureus (Huang et al. 2015). This study used both normal polymerase chain reaction (PCR) and long-and-accurate PCR (LA PCR) methods with Takara Taq or Takara LA Taq DNA polymerase (Takara, Dalian, China). Normal PCR (or Long PCR) was performed in a 50 μL reaction mixture consisting of 32.5 μL (or 26.5 μL) of sterilized distilled water; 5 μL MgCl2, 25 mM; 5 μL 10 × PCR Buffer (or 5 μL 10 × LA PCR Buffer); 4 μL (or 8 μL) dNTP, 2.5 mM; 1 μL (or 2 μL) of each primer, 5 μmol; 1 μL DNA template; 0.5 μL Takara Taq enzyme (or Takara LA Taq enzyme) DNA polymerase (Takara Biomedical, Japan). Fragments were amplified using Takara Taq enzyme via normal PCR or Takara LA Tag enzyme: initial denaturation for 3 min at 95 °C, followed by 35 cycles of 40 s at 95 °C, 1 min or 3 min at 46–58 °C, and 50–90 s at 72 °C, and a subsequent 10 min final extension step at 72 °C. All PCR reactions were used in Applied Biosystems Veriti instrument (Singapore). PCR products were purified using the Axygen agarose-out kit (Axygen, Hangzhou, China), and sequenced using ABI 3730 system by primer walking with two-directions.\n\nTo further discuss the phylogenetic relationship of T. aureus found in Zhejiang Wuyanling National Nature Reserve, a total of 13 mitogenomes were analyzed, including 11 mt genomes of T. aureus downloaded from NCBI (Qin et al. 2012; Huang et al. 2015; Zou et al. 2021) and two mt genomes of T. imperialis (Huang et al. 2016) as outgroups (Figure 1). To align the all complete mt genomes, we used Clustal W in Mega 7.0 (Kumar et al. 2016). We constructed a Neighbour-Joining phylogenetic tree with the parameters as below: bootstrap replications (1000), substitution model (Kimura 2-parameter model), Rates among sites (Gamma distributed), other parameters used default parameters.\n\nNumbers around the nodes are the the bootstrap values of NJ. The GenBank numbers and the abbreviations of location information of all species are shown in the figure. JXPS: Pingshan, Jiangxi province; ZJMHS: Meihuashan, Zhejiang province; WYL: Wuyanling, Zhejiang province; JXJLS: Jiulianshan, Jiangxi province; GXDYS: Dayaoshan, Guangxi Zhuang Autonomous Region; WZ: Zhuang Autonomous Region.\n\n\nResults\n\nThe two haplotypes with one base different in control region were found. The two obtained whole mt genome haplotypes were deposited in the National Center for Biotechnology Information with accession numbers OL449691 and OL449692.\n\nThe two mt genome haplotypes of T. aureus in majority-strand was 15,243 base pairs (bp) in length with negative AT-skew and GC-skew, which were -0.0025 and -0.2376, respectively, which showed typical lepidopterous gene structure and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and one control region (D-loop). One base T replaced C in control region between two haplotypes was found. The start codons of PCGs were ATG (in COX2, COX3, ATP6, ATP8, ND1, ND4, ND4L, and Cytb), ATT (in ND2, ND3, ND5, and ND6), and CGA (in COX1). The stop codons of PCGs were TAA (in ND2, ATP6, ATP8, COX3, ND1, ND5, ND6, and Cytb), TAG (in ND4L), and the incomplete stop codon T- (in COX1, COX2, ND3, and ND4). The gene arrangement was identical to the reported mt genome of T. aureus wuyiensis from Lee (Zou et al. 2021). The overall nucleotide composition of A, T, C and G in majority-strand was 39.8%, 40.0%, 12.5%, 7.7%, respectively. The lengths of the 12S rRNA and 16S rRNA genes from two haplotypes were 776 bp and 1,334 bp, respectively. The genetic distance of between two haplotypes and other reported population of T. aureus based on Kimura 2-parameter model was calculated as 0.00007-0.01013 on the basis of the whole mitogenomes. According to genetic distance, we can identify that ten exuviae of larva is belonging to the exuviae from T. aureus. This method using the exuviae to identify species can help us to monitor and protect T. aureus.\n\nIn NJ tree, two haplotypes from Taishun, Zhejiang province and the sample from Wuyishan, Fujian province were formed one clade 1. Then this clade is closed to the clade 2 from Pingshan and Meihuashan. Clade 1 and clade 2 are sister clade to the clade 3 from Jiulianshan and Dayaoshan. The clade 4 is sister clade to other clade and formed the phylogenetic relationship of (Clade 4 + (Clade 3 + (Clade 1+ Clade 2).\n\nIn this study, the monophyly of T. aureus was well supported. The samples collected in Taishun, Zhejiang province can be identified as T. aureus wuyiensis because the genetic distance is below 0.00013 and the phylogenetic relationship of the samples collected in Taishun are clustered together with T. aureus wuyiensis. The new mitochondrial genomes obtained from the exuviae of larva of T. aureus can give us a further understanding of phylogenetic relationships of T. aureus to protect it.\n\n\nAuthor contributions\n\nAll authors were involved in the conception and design, or analysis and interpretation of the data; LL Liu, LH Zhang, GH Weng, WQ Wang, and SS Zhang were involved in the drafting of the paper; all authors were involved in revising it critically for intellectual content; and all authors were involved in the final approval of the version to be published; and that all authors agree to be accountable for all aspects of the work.",
"appendix": "Data availability\n\nThe mitochondrial genome data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov/nuccore/OL449691 and https://www.ncbi.nlm.nih.gov/nuccore/OL449692] under the accession no. OL449691 and OL449692. The mt genome was obtained by the Sanger method, so no associated “BioProject”, “SRA” and “Bio-Sample” numbers should be shown.\n\n\nReferences\n\nGuan JY, Zhang ZY, Cao YR, et al.: The complete mitochondrial genome of Choroterpes (Euthralus) yixingensis (Ephemeroptera: Leptophlebiidae) and its mitochondrial protein-coding gene expression under imidacloprid stress. Gene. 2021; 800: 145833–145844. PubMed Abstract | Publisher Full Text\n\nHuang CB, Zeng JP, Zhou SY: Complete mitochondrial genomes of Teinopalpus imperialis (Lepidoptera: Papilionidae) and phylogenetic relationships analyses. Mitochondrial DNA A. 2016; 27(4): 2903–2904. PubMed Abstract | Publisher Full Text\n\nHuang Y, Zhou S, Huang C, et al.: Geophylogenetic analysis of Teinopalpus aureus Mell based on re-sequencing of the whole mitochondrial genome. Issues Biol. Sci. Pharm. Res. 2015; 3(5): 47–56.\n\nKumar S, Stecher G, Tamura K: Mega 7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016; 33(7): 1870–1874. PubMed Abstract | Publisher Full Text\n\nMasui A: Butterflies recently collected from Laos PDR. Gekkan-Mushi. 1999; 338: 18–23.\n\nMorita S: A new subspecies of Teinopalpus aureus Mell, 1923 from Vietnam (Lepidoptera: Papilionidae). Wallace. 1998; 4(2): 13–15.\n\nQin F, Jiang G, Zhou S: Complete mitochondrial genome of the Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mitochondrial DNA. 2012; 23(2): 123–125. PubMed Abstract | Publisher Full Text\n\nXing S, Au TF, Dufour PC, et al.: Conservation of data deficient species under multiple threats: Lessons from an iconic tropical butterfly (Teinopalpus aureus). Biol. Conserv. 2019; 234: 154–164. Publisher Full Text\n\nXu XD, Guan JY, Zhang ZY, et al.: Insight into the phylogenetic relationships among three subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with low-temperature selection pressure analyses using mitogenomes. Insects. 2021; 12: 656–674. PubMed Abstract | Publisher Full Text\n\nYu DN, Yu PP, Zhang LP, et al.: Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations. PeerJ. 2021; 9(1): e11402. PubMed Abstract | Publisher Full Text\n\nZhang LP, Yu DN, Storey KB, et al.: Higher tRNA gene duplication in mitogenomes of praying mantises (Dictyoptera, Mantodea) and the phylogeny within Mantodea. Int. J. Biol. Macromol. 2018; 111: 787–795. PubMed Abstract | Publisher Full Text\n\nZou W, Huang CB, Wang L, et al.: The validity of the subspecies, Teinopalpus aureus wuyiensis Lee, from complete mitochondrial genome. Mitochondrial DNA B. 2021; 6(9): 2589–2591. Publisher Full Text"
}
|
[
{
"id": "156619",
"date": "09 Dec 2022",
"name": "Chang-Bae Kim",
"expertise": [
"Reviewer Expertise Genomics and bioinformatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript sequenced and analyzed the complete mitogenomes for identification of the exuviae of larva from Teinopalpus aureus. However, the authors did not explain why mitogenomes are necessary for this aim.\nIn the manuscript, the authors focus on describing mitogenome structure but this work was done 10 years ago by Qin et al. (2012): “Complete mitochondrial genome of the Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae) and related phylogenetic analyses”1 and some following studies, compare your data to previous studies.\nMoreover, all 10 samples for analyses in this study were collected in one region so there was almost no variation among mitogenome sequences. The authors describe these limitations and further studies.\n\nAre the rationale for sequencing the genome and the species significance clearly described? No\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": "163936",
"date": "27 Mar 2023",
"name": "Xue-yan Li",
"expertise": [
"Reviewer Expertise Insect genome"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript investigated a method to use exuviae of butterfly larva for species identification, which is useful especially for protected species. Nevertheless, the authors should describe more details of methods and explain some following points.\n1. What does 'Class I species in China' mean?\n2. The authors got ten mt genomes of T. aureus by the Sanger methods. Are all these sequences submitted to a public database? GenBank or other database?\n3. Figure 1 include 11 mt genomes of Teinopalpus aureus and two mt genomes of Teinopalpus imperialis. For 11 mt genomes of Teinopalpus aureus, which one(s) are from this study? Which ones from published database? The authors said “including 11 mt genomes of T. aureus downloaded from NCBI”, please make the figure legend to be readable by itself.\n\nAre the rationale for sequencing the genome and the species significance clearly described? Partly\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? Partly\n\nAre the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/11-1232
|
https://f1000research.com/articles/10-1236/v1
|
03 Dec 21
|
{
"type": "Software Tool Article",
"title": "PDBrt: A free database of complexes with measured drug-target residence time",
"authors": [
"Magdalena Ługowska",
"Marcin Pacholczyk",
"Magdalena Ługowska"
],
"abstract": "Background: Difficulties in translating the in vitro potency determined by cellular assays into in vivo efficacy in living organisms complicates the design and development of drugs. However, the residence time of a drug in its molecular target is becoming a key parameter in the design and optimization of new drugs, as recent studies show that residence time can reliably predict drug efficacy in vivo. Experimental approaches to binding kinetics and target ligand complex solutions are currently available, but known bioinformatics databases do not usually report information about the ligand residence time in its molecular target. Methods: To extend existing databases we developed the Protein Data Bank (PDB) residence time database (PDBrt) which reports drug residence time. The database is implemented as an open access web-based tool. The front end uses Bootstrap with Hypertext Markup Language (HTML), jQuery for the interface and 3Dmol.js to visualize the complexes. The server-side code uses Python web application framework, Django Rest Framework and backend database PostgreSQL. Results: The PDBrt database is a free, non-commercial repository for 3D protein-ligand complex data, including the measured ligand residence time inside the binding pocket of the specific biological macromolecules as deposited in The Protein Data Bank. The PDBrt database contains information about both the protein and the ligand separately, as well as the protein-ligand complex, binding kinetics, and time of the ligand residence inside the protein binding site. Availability: https://pdbrt.polsl.pl",
"keywords": [
"protein-ligand binding",
"residence time",
"binding kinetics",
"web services",
"database"
],
"content": "Introduction\n\nCurrent knowledge allowing for the determination of the effectiveness of small molecules in vivo is limited. It is known that the leading reason for drug candidate failure is the lack of efficacy caused by a poor translation of in vitro potency assays into in vivo activity in humans (Copeland, 2016a, 2016b; Swinney, 2009). In vitro experimentation refers to closed system conditions in which the drug molecule and its target are present at unchanging concentrations throughout the experiment (Tummino & Copeland, 2008). However, in living organisms, processes run under open, non-equilibrium conditions where the drug is constantly interacting with various molecules during many physiological processes in addition to its native target. To improve prediction of in vivo drug efficacy measurements of drug-target complexes, the residence time, defined as the reciprocal of the dissociation rate constant (koff), should be considered. Drug-target residence time is crucial because pharmacological activity depends on the drug being bound to its molecular target. When the drug dissociates from the binding site, the target molecule is free to continue its pathophysiological function. Within 10 years of the development of the drug-target residence time concept, the parameter has become an extremely important factor in the process of optimizing lead structures in computer-aided drug design (Copeland et al., 2006; Copeland, 2016a, 2016b). Traditional computational approaches (such as molecular docking) take into account only the equilibrium affinity of the drug for its molecular target (e.g., Ki); however, the concept of residence time also takes into account conformational dynamics of molecules, which can have a significant effect on the binding and dissociation of the drug (Copeland et al., 2006; Tummino & Copeland, 2008). Existing free and commercial software does not include a residence time model that is able to estimate this quantity, and thus the effects of ligand modification relevant to the design and optimization of drug candidates is not available.\n\nTo enable further studies and the development of useful drug-target residence time models, we created a database of experimentally measured residence times for biomolecular complexes deposited in the Protein Data Bank (PDB). These data represent a link between structural and kinetic information of the complexes which may be helpful for various computational and machine learning studies on drug-like molecules in biological systems. The current version of our database, called PDBrt, contains 59 complexes with experimentally measured residence time including seven protein families, and 56 small molecules. Summary statistics are available in Figure 1 and Table 1.\n\n\nMethods\n\nPDBrt database design and structure\n\nThe PDBrt database has been designed as an interactive web interface where the user can browse and extract information about the ligand residence time in its molecular target. The RESTful application programming interface (API) with the Django Rest Framework (v2.2.20) and a backend PostgreSQL (v12) database running on a Nginx (v1.21.3) web server has been developed to represent the output of a query as a user-friendly web page generated in Bootstrap (v3.3.7) with Hypertext Markup Language (HTML), Cascading Style Sheets (CSS) and jQuery (v3.5.1) to report the results. Search, query, and data extraction and visualization systems were developed for searching ligand residence time and binding kinetics coefficients. The PDBrt database facilitates access to information about the ligand residence time in its molecular target.\n\nPDBrt database management system\n\nThe Database Management System (DBMS) allows users and programmers to manipulate the data in a systematic way. The DBMS serves as an interface between the database and end users, ensuring consistent data organization and easy accessibility. The PDBrt database is a type of relational DBMS using Structured Query Language (SQL) as the standard programming language for data manipulation.\n\nDevelopment of the PDBrt database was a multi-step process consisting of a systematic literature search, abstract and report screening, and article review. Several sequential steps involved in data management ensure that the processed data is accessible, reliable and current for its users (Figure 2).\n\nBinding kinetics data acquisition and extraction\n\nData acquisition starts with collection of protein-ligand binding kinetics data from available literature by reviewing the primary reference of each pdb file in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) to retrieve the experimentally measured ligand-target residence time or dissociation rate (koff). The references were downloaded and carefully studied to manually extract the data. Only complexes with known ligand-target residence time or dissociation rate were added into the final dataset. Additionally, major binding kinetics coefficients were collected (if available): inhibition constant (Ki) and association rate (kon). Currently the PDBrt database includes 59 protein-ligand complexes with known ligand-target residence time. Structures will be added on a regular basis as respective data becomes available.\n\nStructural data acquisition\n\nComplexes with particular PDB identifiers are downloaded from the RCSB PDB database into the internal PDBrt database core. The protein molecule along with other components such as water molecules and metal ions were saved in the pdb format, while the ligand (drug) in Structure Data Format (sdf). Neither the protein nor the ligand was subjected to any structural optimization or modification after being downloaded from the RCSB PDB.\n\nPDBrt data content\n\nPDBrt database data contain, in addition to the coordinates and general information required for all deposited structures in the RCSB PDB database, target residence time and other binding kinetics coefficients, structure files mentioned above, basic ligand properties like simplified molecular-input line-entry system (SMILES) or International Chemical Identifier (InChI) string, as well as links to external databases: RCSB PDB, PDBj, PDBe, PDBsum, and the reference literature in PubMed. The database includes citations to the original sources (publications) that contain information about the experimentally measured residence time or dissociation rate. For each complex, a web-based three-dimensional rendering is provided using the free, openly available object-oriented JavaScript library 3Dmol.js, which is used for visualizing molecular data.\n\nPDBrt database availability and updates\n\nPDBrt is available to the community through its web-based interface. Since the PDB database is growing rapidly and drug–target residence time is a parameter of great interest for drug design and optimization, the PDBrt will be updated on a regular basis with major versions issued annually. New data can be added by the authors (database administrators) either by uploading an xlsx (MS Excel) file or manually.\n\nPDBrt database architecture\n\nPDBrt is a three-tier architecture:\n\n1. Data tier comprises database and data access layer;\n\n2. Application tier controls application functionality by performing detailed processing;\n\n3. Presentation tier is accessible for end-users and displays information on the website.\n\nCore relational database managed by PostgreSQL server provides information storage for the deposited data. Back end (data access layer) was implemented in Python (v3.6) and the front end of the database (presentation layer) in HTML/CSS.\n\nPDBrt database model\n\nIn PDBrt data is presented as a collection of relations - tables. Each column (also called attribute or field) in the table has a distinct name and a specific data type assigned to it. All the information related to a particular type is stored in a row (also called record) of that table. PDBrt database has three main columns (‘Complex’, ‘Protein’, ‘Ligand’) and 59 records with one-to-one type of relationship. This means that one protein or ligand could only belong to one complex and one complex consists of only one specific protein and ligand molecule (Figure 3).\n\nPDBrt is available to the community through its web-based interface and is freely available to non-commercial users. The PDBrt database runs on all modern web browsers. See Software availability (Ługowska & Pacholczyk, 2021) for access to the database and code.\n\nUse case\n\nTo show the usage of the PDBrt database, the Unified Modelling Language (UML) use case diagram was adopted. Figure 4 shows five use cases of PDBrt as well as three actors: system administrator, end user and the database. The database is an actor for all use cases, system administrator for two and end user for three of these. The database actor is involved in all five use cases because it stores the data and enables operations by which advanced data handling functions are created. In the ‘complex management’ use case the system administrator is able to perform basic Create, Read, Update and Delete (CRUD) actions on the ‘Complex’ table: add, delete, update as well as upload new data as Microsoft Excel (xlsx) file format. In the ‘user management’ use case the system administrator can add, edit and delete a regular user. In the ‘view’, ‘search’ and ‘download’ use case a user actor is involved. In the ‘view’ use case a list of complexes is displayed to the user who can choose a single complex and view its details as well as its 3D visualization. In the ‘search’ use case the user is able to filter from the whole database by PDB code, residence time, and protein or ligand name. The ‘download’ use case allows users to either download the data stored in the database as plain text file or pdb/sdf file formats.\n\nDiagram shows a subset of functions available to the regular user and website administrator.\n\n‘Rectangle’ represents a user, ‘rounded rectangle’ represents a use case and ‘arrow’ represents a relationship.\n\nQuery interface has been implemented for the query of data within PDBrt. Figure 5 shows how the query options are organised. The search engine provides one form field for keyword search and allows retrieval by PDB code, protein name and residence time.\n\nDiagram presents the structure of the PDBrt website. Each symbol (shape or arrow) presents PDBrt web page (single web view), page content, group of related content on a single page, relationship between web pages and group of similar web pages as described in the legend.\n\nTwo user interfaces provide extensive information for result sets obtained for particular search query. The ‘homepage’ interface allows access to some general information in tabular format, and offers the possibility to download whole sets of data files for result sets consisting of multiple PDBrt entries. The ‘complex detail’ interface provides information about individual structures as well as cross-links to many external resources for macromolecular structure data.\n\n\nDiscussion\n\nDrug-target residence time has been shown to play an important role in the prediction of in vivo efficacy of the drug. Since the parameter is independent of drug and enzyme concentration, it is important in the drug design process and should be taken into account at an early stage. The availability of information about drug-target complexes with known (measured) residence times is becoming more and more significant. Several databases containing information about protein – ligand complexes are available, for example PDB-bind (Liu et al., 2015), BindingDB (Gilson et al., 2016), and Binding MOAD (Smith et al., 2019). However, these databases (except for BindingDB) do not store detailed information about binding rates, and none of these contain direct information about ligand (drug) residence time in its target macromolecule. The PDBrt database is dedicated to reporting the structure of protein - small molecule complexes, along with their target residence time and additional binding parameters (Ki, kon, koff). Currently a total of 59 protein–ligand complexes are deposited in the web – based PDBrt database and this data will be updated frequently as more data is made available. The information associated with the existing 59 protein–ligand complexes is available in Underlying data (Ługowska, 2021).\n\n\nData availability\n\nZenodo: Drug-target residence time data. https://doi.org/10.5281/zenodo.5647983 (Ługowska, 2021).\n\nThis project contains the following underlying data:\n\n‐ Residence_time_data.xlsx (information about target residence time and other binding kinetics coefficients, basic ligand properties like simplified molecular-input line-entry system (SMILES) or International Chemical Identifier (InChI) string, as well as the reference literature in PubMed).\n\n‐ Structures.zip (the protein molecule along with other components such as water molecules and metal ions in the pdb format, the protein-ligand structure in the pdb format, and the ligand (drug) in both pdb and Structure Data Format (sdf)).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nSoftware availability\n\nDatabase available from: https://pdbrt.polsl.pl/\n\nSource code available from: https://github.com/mlugowska/residence_time\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.5583543 (Ługowska & Pacholczyk, 2021)\n\nLicense: MIT",
"appendix": "References\n\nCopeland RA: Drug-target interaction kinetics: underutilized in drug optimization? Future Med. Chem. 2016a; 8(18): 2173–2175. PubMed Abstract | Publisher Full Text\n\nCopeland RA: The drug-target residence time model: A 10-year retrospective. Nat. Rev. Drug Discov. 2016b; 15(2): 87–95. PubMed Abstract | Publisher Full Text\n\nCopeland RA, Pompliano DL, Meek TD: Drug-target residence time and its implications for lead optimization. Nat. Rev. Drug Discov. 2006; 5(2): 730–739. PubMed Abstract | Publisher Full Text\n\nGilson MK, Liu T, Baitaluk M, et al.: BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 2016; 44: D1045–D1053. PubMed Abstract | Publisher Full Text\n\nLiu Z, Li Y, Han L, et al.: PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics. 2015; 31(3): 405–412. PubMed Abstract | Publisher Full Text\n\nŁugowska M: Drug-target residence time data [Data set]. Zenodo. 2021. Publisher Full Text\n\nŁugowska M, Pacholczyk M: PDBrt: a free database of complexes with measured drug - target residence time. Zenodo. 2021. Publisher Full Text\n\nSmith RD, Clark JJ, Ahmed A, et al.: Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. J. Mol. Biol. 2019; 431: 2423–2433. PubMed Abstract | Publisher Full Text\n\nSwinney DC: The role of binding kinetics in therapeutically useful drug action. Curr. Opin. Drug Discov. Devel. 2009; 12(1): 31–39. PubMed Abstract\n\nTummino PJ, Copeland RA: Residence time of receptor–ligand complexes and its effect on biological function. Biochemistry. 2008; 47: 5481–5492. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "102208",
"date": "20 Jan 2022",
"name": "Wiesław Nowak",
"expertise": [
"Reviewer Expertise biophysics",
"bioinformatics",
"computer modeling of proteins",
"single molecule nanomechanics",
"atomic and molecular physics"
],
"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\nMankind needs new, effective medicines, and science should provide them.\n\nFor many years expectations with respect to molecular modeling were high: medicinal chemists looked for substantial help from the computer modeling community, and computational chemists provided hundreds of methods, including high-throughput virtual docking, aimed at selecting best drug leads. There are some success stories of such approach (Śledź & Caflish, 2018) but, given the human effort and money, the outcome measured by a number of new effective drugs is, in my opinion, at most \"moderate\", and some other more critical medical specialist may say \"mediocre\". The problem of rational, structure based drug design is too complex that it may be solved by, for example, a simple ligand-protein docking. Fortunately, there is a hope in this field. My optimism is based on a recent success of AlphaFold2 computer method that won CASP14 competition in protein folding (Jumper at al, 2021). The Artificial Intelligence (AI) based algorithm outperformed all the best research groups in a series of tasks that seemed to be too complex to be solved in reasonable time: how to predict a true 3D protein structures from the known 1-D sequences. So, one may expect that AI/Machine Learning (ML) based methods will be developed to a similar level of efficacy in drug-design field as well. However, ML needs good quality training data, and for that a ligand residence time seems to be very serious factor in estimation of biological effect of a tested molecule on a metabolic pathway of interest.\nThe manuscript \"PDBrt: A free database of complexes with measured drug-target residence time \" by M Ługowska and M. Pacholczyk addresses an important drawback in the computational drug design: lack of a database collecting in one place measured drugs’ residence times. The authors prepared the first version of a database containing some 50 ligand-protein complexes with known kinetic characteristics. This is a highly desirable tool that may contribute to improving rational computational pharmacology.\nThe idea of creating such database is in my opinion very good and just in time.\nPresentation of the software project is correct and contains the majority of required information. The depositories indicated by the authors are active and apparently contain relevant data. The information content of the database may be always better, for example, I would appreciate having in it pictures (just in jpg format) showing structural 2D formulas of the scrutinized ligands. Biological essays to get residence time numerical data are very different, perhaps a separate field with comments on that and adequate error bars extracted from the original papers could also contribute to more critical usage of the data. So, the effort is ranked high, but, for the current version of the manuscript, I have two main objections/postulates:\nThe web version of the PDBrt did not work for me, neither from Windows, Firefox, nor Ipad Safari. Authors do not precise in the manuscript how actually the user can work with the on-line version of the PDBrt. In the main www page there is no Help or Readme button. I do not know: shall I register to use it or not? From that main page an unexperienced user simply does not know how to get records with the sought ligand residence time for a particular protein (keyword search works only if a perfect match is indicated). One can reasonably expect that the residence time should be presented in some time units (seconds/minutes/hours) or, if it is not the case (depending on a definition adopted), an explanation should be somewhere given (at least in the manuscript).\n\nGitHub depository contains a source code of the database, but again, for me it was not so clear what do I need to install all software locally (what are hardware requirements, under what system?) to make full use of it.\n\nA minor point: In the literature there is some criticism against residence time concept, and this should be mentioned in the paper, see for example: (Folmer 2018). R.A. Copeland, the main author of the idea of drug residency time, published recently an interesting review and update of this topic, it should be referenced in the corrected manuscript as well (Copeland 2018).\nAfter adding more instructions to less experienced potential users of the database the manuscript should be promoted to \"abstracted\" status and certainly will attract some users. Sure enough, the number of records should grow and real users will customize the created software to their local needs.\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": "8790",
"date": "31 Oct 2022",
"name": "Magdalena Ługowska",
"role": "Author Response",
"response": "Thank you very much for taking the time to review our software tool article. We are happy to address your comments. The information content of the database may be always better, for example, I would appreciate having in it pictures (just in jpg format) showing structural 2D formulas of the scrutinized ligands. Biological essays to get residence time numerical data are very different, perhaps a separate field with comments on that and adequate error bars extracted from the original papers could also contribute to more critical usage of the data. The PDBrt was created for its practical use by users, so every comment on the presentation, as well as the type of data, is extremely important to us. It is possible that in the next update of the database we will introduce the proposed solutions. The web version of the PDBrt did not work for me, neither from Windows, Firefox, nor Ipad Safari. Authors do not precise in the manuscript how actually the user can work with the on-line version of the PDBrt. In the main www page there is no Help or Readme button. I do not know: shall I register to use it or not? The PDBrt is available for all users through its web-based interface only (https://pdbrt.polsl.pl). The manuscript includes use case descriptions as well as a diagram showing the possibilities offered by the database’s interface (Figure 4, 5). Indeed, that can be insufficient and it is right to note the lack of clear information about how the user can work with the on-line version of the PDBrt. “Help” button was added to the PDBrt interface where the user can find the following information: “Getting started” with a general description of the PDBrt. \"How to search?” with a description of search options and query results (how the user can obtain desired information about drug-target residence time or other parameters). “Explore PDBrt entry” with a description of a single protein-ligand details and how the user can work with it. From that main page an inexperienced user simply does not know how to get records with the sought ligand residence time for a particular protein (keyword search works only if a perfect match is indicated). To search the database, please enter one of the following in the field: PDB ID, protein or ligand name, residence time. Unfortunately, the current version does not allow advanced search, including combining individual features of the searched complex. One can reasonably expect that the residence time should be presented in some time units (seconds/minutes/hours) or, if it is not the case (depending on a definition adopted), an explanation should be somewhere given (at least in the manuscript). Information about the unit of time in which the residence time is presented has been added to the main table on the homepage. Such information can also be found in the table with detailed information about a single complex on the Structure Detail Page. GitHub depository contains a source code of the database, but again, for me it was not so clear what do I need to install all software locally (what are hardware requirements, under what system?) to make full use of it. The README file was added to the Github repository with basic description how to work with the PDBrt locally. In the literature there is some criticism against residence time concept, and this should be mentioned in the paper, see for example: (Folmer 2018). R.A. Copeland, the main author of the idea of drug residency time, recently published an interesting review and update of this topic; it should be referenced in the corrected manuscript as well (Copeland 2018). Thank you for bringing these 2 references to our attention. These have, of course, been included in the revised manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/10-1236
|
https://f1000research.com/articles/11-1073/v1
|
20 Sep 22
|
{
"type": "Research Article",
"title": "Genetic and environmental perturbations alter the rhythmic expression pattern of a circadian long non-coding RNA, Per2AS, in mouse liver",
"authors": [
"Lin Miao",
"Kyle R. Batty",
"Ayana N. Jackson",
"Heather A. Pieno",
"Maisy W. Rhoades",
"Shihoko Kojima",
"Lin Miao",
"Kyle R. Batty",
"Ayana N. Jackson",
"Heather A. Pieno",
"Maisy W. Rhoades"
],
"abstract": "Background: Long non-coding RNAs (lncRNAs) play a wide variety of biological roles without encoding a protein. Although the functions of many lncRNAs have been uncovered in recent years, the regulatory mechanism of lncRNA expression is still poorly understood despite that the expression patterns of lncRNAs are much more specific compared to mRNAs. Here, we investigated the rhythmic expression of Per2AS, a novel lncRNA that regulates circadian rhythms. Given that Per2AS expression is antiphasic to Period2 (Per2), a core circadian clock gene, and transcribed from the antisense strand of Per2, we hypothesized that the rhythmic Per2AS expression is driven either by its own promoter or by the rhythmic Per2 transcription via transcriptional interference. Methods: We leveraged existing circadian RNA-seq datasets and analyzed the expression patterns of Per2AS and Per2 in response to the genetic or environmental disruption of the circadian rhythm in mouse liver. We tested our hypotheses by comparing the changes in the expression patterns of Per2AS and Per2. Conclusions: We found that, in some cases, Per2AS expression is independently controlled by other circadian transcription factors. In other cases, the pattern of expression change is consistent with both transcriptional interference and independent regulation hypotheses. Although additional experiments will be necessary to distinguish these possibilities, findings from this work contribute to a deeper understanding of the mechanism of how the expression of lncRNA is regulated.",
"keywords": [
"LncRNAs",
"circadian rhythm",
"antisense",
"rhythmicity",
"feeding regimen"
],
"content": "Introduction\n\nLong non-coding RNAs (lncRNAs) are a subgroup of RNAs longer than 200 nucleotides that do not produce proteins and play a variety of roles in a number of biological processes, including innate immune response,1 cell cycle control,2 cell differentiation,3,4 X-inactivation,5,6 and neuronal activity.7,8 Because lncRNAs do not produce proteins, it is important for lncRNAs to interact with other molecules, such as other nucleic acids and RNA-binding proteins, to exert their functions. For example, nuclear lncRNAs interact with DNA, chromatin, and proteins and modulate nuclear processes, like chromatin organization, RNA transcription, splicing, and lncRNA nuclear export and retention. In contrast, cytoplasmic lncRNAs interact with proteins, other RNAs, or different organelles to alter mRNA stability and localization, protein translation, post-translational modification, mitochondrial functions, or protein trafficking.9–15 In some cases, the act of transcription, rather than the lncRNA transcripts, is the functional entity to regulate target gene expression locally.16\n\nAlthough significant progress has been made in understanding the functions of lncRNAs in recent years, their transcription regulatory mechanism has been poorly understood. Similar to mRNAs which are transcribed by RNA Polymerase II, a considerable number of lncRNAs are also transcribed by RNA Polymerase II, 5′ capped, 3′ polyadenylated, and multi-exonic.17 Interestingly, however, lncRNAs exhibit more cell type-, tissue-, developmental stage- or disease state-specific expression patterns compared to mRNAs.18–21 This has raised many interesting questions: What are the regulatory mechanisms of lncRNA transcription to achieve highly specific expression patterns? Is the transcription of lncRNAs also regulated by transcription factors which bind to its promoter/enhancer, similar to mRNAs? If so, why is lncRNA expression more specific? Is there a universal mechanism to regulate the transcription of all lncRNAs, or is the transcription of different lncRNAs regulated by different mechanisms? Does the expression of lncRNAs respond to external inputs similar to mRNAs?\n\nWe have recently shown that Per2AS, a lncRNA, plays an important role in regulating circadian rhythms,22 an internal timing mechanism to anticipate and respond to daily environmental rhythms driven by the rotation of the Earth. Interestingly, Per2AS is transcribed from the antisense strand of Period 2 (Per2), one of the core clock genes essential for generating circadian rhythmicity, and its expression is rhythmic and antiphasic to Per2 mRNA.23–26 Most strikingly, we further demonstrated that the transcription of Per2AS, rather than its transcripts, is important for regulating circadian rhythms.22 These data prompted us to interrogate how rhythmic Per2AS transcription is regulated.\n\nIn this study, we analyzed the expression patterns of Per2AS under conditions in which the circadian clock was perturbed either genetically or environmentally. We used publicly available circadian transcriptomic datasets from mouse liver, where Per2AS is abundantly and rhythmically expressed.23–26 Our first hypothesis is that the rhythmic Per2AS transcription is regulated by rhythmic antiphasic transcription of Per2 by means of transcriptional interference.27–29 Our alternative hypothesis is that rhythmic Per2AS expression is driven by its own promoter, similar to mRNAs.30–33 If the former is true, we anticipate that changes in Per2 and Per2AS expression would always be antiphasic. If the latter, then we anticipate that a change in Per2AS expression would be independent of that of Per2. We also take into account the possibility that the two hypotheses are not mutually exclusive. Results from this study contribute to our mechanistic understanding of how circadian rhythm is regulated by Per2AS and, more broadly, how the transcription of antisense lncRNAs is regulated.\n\n\nMethods\n\nAll the fastq files were obtained from NCBI SRA (GSE135898, GSE135875, GSE107787, GSE102072, GSE143528,34–37 except for PRJDB7789, which was obtained from DDBJ DRA (PRJDB7789).38 Fastq reads were mapped to the Ensembl mouse genome release 38 (mm10) using STAR 2.7.7a39 with outFilterScoreMinOverLRead = 0.3 and outFilterMatchNMinOverLRead = 0.3 options. The ‘condenseGenes’ option was also used to select the most abundant isoform of each gene. The mapped reads were quantified by HOMER (v 4.11.1)40 and normalized by the transcripts per million (TPM) option. We used the -sspe option for paired-end reads and the -strand – or -strand + option to quantify mapped reads in a strand-specific manner. The option -bp10 was used for GSE102072 and PRJDB7789 to filter alignments with mapQ smaller than 10. Per2AS expression was calculated from the antisense strand of the Per2 genomic region as it is not annotated in Mus musculus GRCm38.95 GTF or NCBI RefSeq mm10 GTF files.\n\nWe used the two-way analysis of variance (ANOVA) in Microsoft Excel to test for differences in RNA levels between the experimental groups (i.e., genotype, diet), except for the dataset GSE102072 in which some samples had only one biological replica. The rhythmicity of each RNA expression was assessed by MetaCycle,41 which integrates three algorithms, ARSER, JTK CYCLE, and Lomb-Scargle, to determine the p-value, Benjamini-Hochberg q-value (BH.Q value), period, phase, baseline value, amplitude (AMP), and relative amplitude (rAMP). We defined the expression of an RNA as rhythmic when meta2d p<0.05.\n\n\nResults\n\nTo test whether any of the core clock genes have an effect on the expression of Per2AS and Per2, we analyzed the circadian transcriptomic datasets from mice livers lacking one or more “core” clock genes (Figure 1). Circadian rhythms in each cell are driven by a cell-autonomous molecular clock, composed of a group of core clock genes that form a network of transcriptional–translational feedback loops (TTFLs)42 and regulate daily rhythms in biochemistry, physiology, and behavior. In the first loop, transcription activators BMAL1 (gene name: Arntl) and CLOCK form a heterodimeric complex and bind to the E-box sequence in the promoter regions to regulate the rhythmic expression of their target genes, including Per1-3 and Cryptochrome (Cry)1-2. High levels of PER and CRY proteins form a protein complex in the cytoplasm, then translocate back to the nucleus to inhibit its own transcription by interacting with CLOCK/BMAL1. This cycle takes approximately 24 hours, and this is the molecular basis of generating circadian rhythms. The secondary feedback loop is comprised of the transcriptional repressors REV-ERBs (gene name: Nr1d) and the activator RORs that are regulated by BMAL1/CLOCK. REV-ERB and ROR proteins both recognize and bind to the RORE sequence in the promoter region and compete with each other to drive the rhythmicity of the target gene expression, including Bmal1. The last loop consists of transcription activators of proline and acidic amino acid-rich basic leucine zipper (PAR bZip) proteins: DBP, TEF, and HLF, and the repressor NFIL3, all of which target genes containing D-box element within their promoters, including Rev-erbs, Rors, and Pers.42\n\nMice were kept under an L:D=12:12 cycle and fed ad libitum. Liver RNAs were extracted every four hours in (A) Bmal1, (B) Nfil3, (C) Cry1/2 double, and (E) Dbp/Tef/Hlf triple knockout mice (n=2), or every three hours in (D) Nr1d1/2 double knockout mice (n=3). Y-axis represents strand-specific TPM. Points and error bars represent mean±SE. (**) p<0.01, (***), p<0.001, N.S. indicates no significant difference between genotypes (two-way ANOVA). Data derived from Weger et al., Proc Natl Acad Sci U S A, 202034; Yoshitane et al., Commun Biol., 201938; Guan et al., Science, 2020.37\n\nRemoval of Bmal1 from the TTFL results in arrhythmic locomotor activity and disrupts circadian expression of hepatic core clock genes.43,44 Similarly, removal of both Cry1 and 2 also results in the loss of the rhythm in locomotor activities and core clock gene expression.45,46 In both Bmal1 knock-out (KO) and Cry1/2 double knock-out (DKO) animals, our analysis demonstrated that the rhythmicity of Per2 was abolished but expression was maintained at intermediate levels, as was reported previously34,47,48 (Figure 1A, C, Table S184). Whereas the expression of Per2AS was markedly low and arrhythmic, indicating that Bmal1 and Cry1/2 activate the expression of Per2AS (Figure 1A, C, Table S184).\n\nIn contrast, the removal of Nfil3 or PAR bZip genes (Dbp/Tef/Hlf) did not change the expression pattern of Per2 (Figure 1B, E). This is in line with previous findings that the rhythmic expression of core clock genes was nearly identical between wild-type (WT) and Nfil3 or PAR bZip-deficient mice in liver.38,49 Interestingly, however, the amplitude of Per2AS increased in both Nfil3 KO and Dbp/Tef/Hlf triple knock-out (TKO) mice, indicating that the NFIL3 and PAR bZip proteins repress the expression of Per2AS without affecting Per2 (Figure 1B, E, Table S184).\n\nRemoval of both Nr1d1 and Nr1d2 abolishes rhythmic locomotor activity and interferes with the circadian expression of many hepatic core clock genes, including dampening the rhythm of Per2.50 Consistent with this, the amplitude of Per2 expression was decreased in Nr1d1/2 DKO mice while the relative amplitude of Per2AS expression was increased (Figure 1D, Table S184). These data suggest that Nr1d1/2 have an opposing effect on Per2 and Per2AS, activating Per2 while repressing Per2AS. We also confirmed the genotypes of each dataset by checking the mRNA levels of the knock-out genes, all of which were significantly decreased (Figures 1, 3, 4).\n\nWe next tested the effect of environmental perturbation on the expression patterns of Per2AS and Per2. In mammals, light is the most potent environmental cue that entrains the circadian clock through the suprachiasmatic nucleus (SCN) of the hypothalamus. However, food intake also serves as a strong ‘Zeitgeber’ (time giver) to entrain the circadian clock of peripheral organs in an SCN-independent manner.51–54 Previous studies have demonstrated that fasting directly affects a large number of physiological parameters, such as body temperature,55,56 body weight,57,58 hormone levels,59,60 and hepatic glucose levels,61,62 in addition to the expression patterns of the core clock genes in mouse liver.\n\nIn particular, the expression levels of BMAL1-target genes, including Per2, are lower in the liver of fasting mice.35,63–67 In line with this, the amplitude of Per2 expression was considerably lower in the fasted mice (Figure 2, Table S184) whose liver samples were collected after 24 hours of fasting for each time point, compared to the mice fed under the ad libitum (ad lib) condition. In contrast, the expression patterns of Per2AS show little or no difference between the ad lib fed and 24-hr fasting conditions (Figure 2, Table S184). These data indicate that the 24-hr fasting alters the expression pattern of Per2, but not that of Per2AS.\n\nMice were kept under an L:D=12:12 cycle and either fed ad libitum or food was removed 24 hours prior to tissue sampling for the fasting group of mice. Liver RNAs were extracted every four hours. Points and error bars represent mean±SE (n=3). (***) p<0.001, N.S. indicates no significant difference between feeding conditions (two-way ANOVA). Data derived from Kinouchi et al., Cell Rep., 2018.35\n\nTime-restricted feeding (TRF) is a form of intermittent fasting in which food consumption is restricted to a certain time window of the day. The TRF regimen can protect mice from excessive body weight gain and liver damage depending on the timing of the food availability, and also improve metabolic and physiological rhythms when food access is restricted to the active phase.68–71 Here, we also looked at the differences in Per2AS and Per2 expression patterns when food access was restricted to nighttime (i.e., the active phase of mice) to understand whether core clock genes still have the same effect on the expression of Per2AS and Per2. Similar to what was observed with the ad lib feeding condition (Figure 1A, C), the expression of Per2AS was very low and arrhythmic in Bmal1 KO and Cry1/2 DKO animals experiencing TRF compared to WT (Figure 3, Table S184). The expression of Per2 was also arrhythmic but still maintained intermediate levels both in Bmal1 KO and Cry1/2 DKO animals even under TRF (Figure 3, Table S184). Compared to ad lib feeding, TRF did not affect the expression patterns of Per2AS and Per2, showing that the core clock gene KO is the primary factor to alter the expressions of Per2AS and Per2. Additionally, these findings further support that BMAL1 and CRY are crucial transcription factors to activate Per2AS expression, regardless of the feeding patterns.\n\nMice were kept under an L:D=12:12 cycle and access to food were restricted between ZT12 to ZT24. Liver RNAs were extracted every four hours in (A) Bmal1 and (B) Cry1/2 double knockout mice. Y-axis represents strand-specific TPM. Points and error bars represent mean±SE (n=2). (**) p<0.01, (***) p<0.001, N.S. indicates no significant difference between genotypes (two-way ANOVA). Data derived from Weger et al., Proc Natl Acad Sci U S A, 2020.34\n\nIn addition to the timing of diet, the composition of the diet, such as high-fat or ketogenic, also affects circadian rhythms and alters core clock gene expression.68,72–75 To understand whether different diet compositions affect the expression of Per2AS and Per2 differently, we also examined the expression levels of Per2AS and Per2 when mice were fed with a 60% high-fat diet (HFD) either ad lib or TRF during the active phase (ZT13-22 or 23).36\n\nThe expression of Per2 was arrhythmic in WT fed with HFD under the ad lib condition (Figure 4A, Table S184), as was reported previously.73 However, it was rhythmic under the TRF condition (Figure 4D, Table S184), supporting the idea that TRF restores peripheral oscillations of core clock gene expressions.76,77 Similar to the results observed with a regular chow diet under the ad lib condition (Figure 1), Per2 expression was arrhythmic but maintained intermediate expression in both ad lib and TRF conditions in Bmal1 KO and Cry1/2 DKO (Figure 4, Table S184), but not in Nr1d1/2 DKO mice with HFD (Figure 4C, F, Table S184). In contrast, Per2AS levels were low and arrhythmic in both ad lib and TRF conditions in Bmal1 KO and Cry1/2 DKO mice compared to WT mice with HFD (Figure 4A-B, D-E), similar to what was observed in regular chow mice under both ad lib and TRF conditions (Figure 1A, C; Figure 3). This further supports the idea that Per2AS expression is regulated by Bmal1 and Cry1/2, regardless of the composition of the diet. On the other hand, Per2AS expression was arrhythmic in Nr1d1/2 DKO mice with HFD in contrast to the regular chow diet under ad lib condition (Figure 1D), suggesting that the effect of Nr1d1/2 on Per2AS is different between regular chow and HFD (Figure 4C, F; Table S184).\n\nMice were kept under an L:D=12:12 cycle and fed with a 60% high-fat diet either ad lib (A-C) or with TRF (D-F) condition. Liver RNAs were extracted every four hours in wild type and (A) Bmal1 knockout mice, or every three hours in (B) Cry1/2 double and (C) Nr1d1/2 double knockout mice. Y-axis represents strand-specific TPM. The same WT mice were used in each group. Points and error bars represent mean±SE (n=2). Two-way ANOVA analysis was not performed for this dataset, because the KO samples consisted of a single biological replicate. Data derived from Chaix et al., Cell Metab., 2019.36\n\n\nDiscussion\n\nIn this study, we focused on the circadian antisense lncRNA, Per2AS, and asked whether the rhythmic expression of Per2AS is regulated independently by its own promoter like many other circadian mRNAs, or transcriptional interference driven by the antiphasic expression of its sense-strand gene Per2. By using circadian transcriptomic datasets from mouse liver, in which the molecular clock machinery was genetically and environmentally disrupted, we examined how these perturbations affect the expression patterns of Per2AS and Per2. Our data demonstrated that the expression of Per2AS can be altered by both genetic and environmental perturbations of the circadian clock.\n\nWe were able to test the effect of Bmal1, Nfil3, Cry1/2, Nr1d1/2, and Dbp/Tef/Hlf, but not that of Rora/b/c as the circadian transcriptome dataset for Rora/c KO mouse liver is only available with a microarray platform and this does not allow us to quantify Per2AS levels.78 We also tested the effect of fasting, TRF, and an HFD on the expression patterns of Per2AS and Per2. Even though the expression of many core clock genes, including Per2, is affected by fasting (Figure 2) or HFD (Figure 4),35,36,63–67 Per2AS appears to be less sensitive to these changes and its expression remained rhythmic under fasting, TRF, or HFD conditions (Figures 2-4). These data suggest that the timing of food intake, the composition of the diet, and fasting are not the primary factor that regulates the rhythmic expression of Per2AS. By contrast, the effect of genetic perturbation within the circadian rhythm system is stronger than environmental perturbation on the expression Per2AS.\n\nWe tested our hypotheses for Per2AS transcription regulation by comparing the changes in the expression pattern between Per2AS and Per2. We found that, in some cases, the Per2AS expression pattern was altered even when that of Per2 was unaltered (Figure 1B, E). We also found, in other cases, that the Per2AS expression pattern was unaltered even when that of Per2 was altered (Figure 2). These data strongly support the independent hypothesis that the expression of Per2AS is regulated by its own promoter, and its transcription is independent from that of Per2. Indeed, the expression of many lncRNAs is controlled by their promoter or other DNA elements, such as enhancers.30,79 The majority of lncRNAs also contain highly conserved core promoter sequences and can be regulated by different transcription factors.80,81 In addition, the promoters of lncRNAs are evolutionarily conserved as much as that of mRNAs at least between humans and mice, even though their nucleotide sequences are less conserved than mRNAs. These data support the significance of promoter sequences in regulating lncRNA expression patterns.82 Our data also indicate that BMAL1 and CRY1/2 are the activators, and NFIL3 and PAR bZip proteins are the repressors of Per2AS (Figure 1, 3). However, the removal of one particular core clock gene may alter the expression of other core clock genes or their downstream genes.34,83 Thus, we cannot eliminate the possibility that the Per2AS expression is indirectly impacted by the change of the core clock gene circuit.\n\nAlthough these data strongly support the independent hypothesis, we cannot completely reject the alternative hypothesis that Per2AS expression is regulated by transcriptional interference from Per2, since there are some instances where the changes in the expression pattern of Per2AS and Per2 can still be explained by the transcriptional interference hypothesis. For example, in Bmal1 KO and Cry1/2 DKO animals under any dietary conditions (i.e., ad lib, TRF, and HFD feeding), the Per2AS expression was completely abolished, and the Per2 expression pattern was also arrhythmic but stayed at the intermediate levels (Figures 1A, C, 3, 4D, E, Table S184). It is possible that the constant Per2 expression prevents the transcription of Per2AS on the other strand, leading to the decreased and arhythmic Per2AS expression. Additionally, in Nr1d1/2 DKO mice, Per2AS expression increased and its rhythmicity became more robust, while Per2 expression decreased and its rhythmicity was dampened (Figure 1D). This could be due to decreased Per2 transcription leading to the increased Per2AS transcription on the other strand. Therefore, the two alternative hypotheses can both be viable and coordinated together to regulate the rhythmic transcription of Per2AS. At the same time, these data can also be explained solely by the independent hypothesis, and additional experimental evidence will be required to distinguish these possibilities. For example, it would be helpful to understand whether these core clock proteins are indeed recruited to the Per2AS promoter or enhancer sequences. We can also modify the transcription of Per2 directly and test whether this would lead to changes in Per2AS expression patterns.\n\nRegardless, these results help us better understand not only how the transcription of Per2AS is regulated, but also how Per2AS interacts with other core clock proteins in transcriptional-translational feedback loops to regulate circadian rhythms because the rhythmic transcription of Per2AS is important for its functions in regulating circadian rhythms. More broadly, our results also help us understand the transcription regulation mechanism of antisense lncRNAs.\n\n\nData availability\n\nNCBI GEO: Temporal profiles of gene expression in Cry1/2 KO, Bmal1 KO under night restricted feeding and ad libitum feeding regimen. Accession number: GSE135898, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135898.\n\nNCBI GEO: Temporal profiles of hepatic gene expression in PAR bZip triple knockout mice. Accession number: GSE135875, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135875.\n\nNCBI GEO: Fasting Imparts a Switch to Alternative Circadian Transcriptional Pathways in Liver and Muscle. Accession number: GSE107787, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107787.\n\nNCBI GEO: Hepatic transcriptome by Next Generation Sequencing of WT and clock mutant mice fed a HFD ad libitum or time-restricted feeding. Accession number: GSE102072, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102072.\n\nNCBI GEO: The Hepatocyte Clock and Feeding Interdependently Control Chrono-Homeostasis of Multiple Liver Cell Types (RNA-seq). Accession number: GSE143524, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143524.\n\nNCBI BioProject: Transcriptome of mouse liver in Per2::Luc KI and E4bp4 KO/Per2::Luc KI mice. Accession number: PRJDB7789, https://www.ncbi.nlm.nih.gov/bioproject?term=PRJDB7789&cmd=DetailsSearch.\n\nfigshare: Table_S1.xlsx. https://doi.org/10.6084/m9.figshare.21067537.84\n\nThis project contains the following underlying data:\n\n‐ Table S1. xlsx (Metacycle analysis to determine whether the gene expression is rhythmic)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThe authors thank Dr. Nobuya Koike from the Kyoto Prefectural University of Medicine for technical assistance and the members of the Kojima laboratory for critical proofreading of the manuscript.\n\n\nReferences\n\nOuyang J, Hu J, Chen JL: lncRNAs regulate the innate immune response to viral infection. Wiley Interdiscip. Rev. RNA. 2016 Jan-Feb; 7(1): 129–143. Epub 20151215. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou Z, Tan F, Pei Q, et al.: lncRNA SNHG4 modulates colorectal cancer cell cycle and cell proliferation through regulating miR-590-3p/CDK1 axis. Aging (Albany NY). 2021 Mar 19; 13(7): 9838–9858. Epub 20210319. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFeng J, Bi C, Clark BS, et al.: The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev. 2006 Jun 1; 20(11): 1470–1484. Epub 20060516. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOmote N, Sakamoto K, Li Q, et al.: Long noncoding RNA TINCR is a novel regulator of human bronchial epithelial cell differentiation state. Physiol. Rep. 2021 Feb; 9(3): e14727. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPlath K, Fang J, Mlynarczyk-Evans SK, et al.: Role of histone H3 lysine 27 methylation in X inactivation. Science. 2003 Apr 4; 300(5616): 131–135. Epub 20030320. eng. PubMed Abstract | Publisher Full Text\n\nOhhata T, Hoki Y, Sasaki H, et al.: Crucial role of antisense transcription across the Xist promoter in Tsix-mediated Xist chromatin modification. Development. 2008 Jan; 135(2): 227–235. Epub 20071205. eng. PubMed Abstract | Publisher Full Text\n\nBarry G, Briggs JA, Hwang DW, et al.: The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states. Sci. Rep. 2017 Jan 5; 7: 40127. Epub 20170105. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMercer TR, Qureshi IA, Gokhan S, et al.: Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci. 2010 Feb 5; 11: 14. Epub 20100205. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBridges MC, Daulagala AC, Kourtidis A: LNCcation: lncRNA localization and function. J. Cell Biol. 2021 Feb 1; 220(2). eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCarlevaro-Fita J, Polidori T, Das M, et al.: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs. Genome Res. 2019 Feb; 29(2): 208–222. Epub 20181226. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFazal FM, Han S, Parker KR, et al.: Atlas of Subcellular RNA Localization Revealed by APEX-Seq. Cell. 2019 Jul 11; 178(2): 473–90.e26. Epub 20190620. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHerman AB, Tsitsipatis D, Gorospe M: Integrated lncRNA function upon genomic and epigenomic regulation. Mol. Cell. 2022 Jun 16; 82(12): 2252–2266. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRackham O, Shearwood AM, Mercer TR, et al.: Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA. 2011 Dec; 17(12): 2085–2093. Epub 20111025. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Li B, Bai Q, et al.: The lncRNA Snhg1-Vps13D vesicle trafficking system promotes memory CD8 T cell establishment via regulating the dual effects of IL-7 signaling. Signal Transduct. Target. Ther. 2021 Mar 24; 6(1): 126. Epub 20210324. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLyu Q, Xu S, Lyu Y, et al.: SENCR stabilizes vascular endothelial cell adherens junctions through interaction with CKAP4. Proc. Natl. Acad. Sci. U. S. A. 2019 Jan 8; 116(2): 546–555. Epub 20181224. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStatello L, Guo CJ, Chen LL, et al.: Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 2021 Feb; 22(2): 96–118. Epub 20201222. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuttman M, Amit I, Garber M, et al.: Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009 Mar 12; 458(7235): 223–227. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuinn JJ, Chang HY: Unique features of long non-coding RNA biogenesis and function. Nat. Rev. Genet. 2016 Jan; 17(1): 47–62. PubMed Abstract | eng Publisher Full Text\n\nDerrien T, Johnson R, Bussotti G, et al.: The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep; 22(9): 1775–1789. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCabili MN, Trapnell C, Goff L, et al.: Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15; 25(18): 1915–1927. Epub 20110902. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMercer TR, Dinger ME, Sunkin SM, et al.: Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl. Acad. Sci. U. S. A. 2008 Jan 15; 105(2): 716–721. Epub 20080109. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMosig RA, Castaneda AN, Deslauriers JC, et al.: Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the mouse circadian clock. Genes Dev. 2021 Jun; 35(11-12): 899–913. Epub 20210520. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoike N, Yoo SH, Huang HC, et al.: Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science. 2012 Oct 19; 338(6105): 349–354. Epub 20120830. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVollmers C, Schmitz RJ, Nathanson J, et al.: Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab. 2012 Dec 5; 16(6): 833–845. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMenet JS, Rodriguez J, Abruzzi KC, et al.: Nascent-Seq reveals novel features of mouse circadian transcriptional regulation. elife. 2012 Nov 13; 1: e00011. Epub 20121113. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang R, Lahens NF, Ballance HI, et al.: A circadian gene expression atlas in mammals: implications for biology and medicine. Proc. Natl. Acad. Sci. U. S. A. 2014 Nov 11; 111(45): 16219–16224. Epub 20141027. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShearwin KE, Callen BP, Egan JB: Transcriptional interference--a crash course. Trends Genet. 2005 Jun; 21(6): 339–345. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXue Z, Ye Q, Anson SR, et al.: Transcriptional interference by antisense RNA is required for circadian clock function. Nature. 2014 Oct 30; 514(7524): 650–653. Epub 20140817. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGeorg J, Hess WR: cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev. 2011 Jun; 75(2): 286–300. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMattioli K, Volders PJ, Gerhardinger C, et al.: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Res. 2019 Mar; 29(3): 344–355. Epub 20190125. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrantl S, Wagner EG: An antisense RNA-mediated transcriptional attenuation mechanism functions in Escherichia coli. J. Bacteriol. 2002 May; 184(10): 2740–2747. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrantl S: Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr. Opin. Microbiol. 2007 Apr; 10(2): 102–109. Epub 20070326. eng. PubMed Abstract | Publisher Full Text\n\nBrophy JA, Voigt CA: Antisense transcription as a tool to tune gene expression. Mol. Syst. Biol. 2016 Jan 14; 12(1): 854. Epub 20160114. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeger BD, Gobet C, David FPA, et al.: Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. Proc. Natl. Acad. Sci. U. S. A. 2021 Jan 19; 118(3). pii: e2015803118. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKinouchi K, Magnan C, Ceglia N, et al.: Fasting Imparts a Switch to Alternative Daily Pathways in Liver and Muscle. Cell Rep. 2018 Dec 18; 25(12): 3299–314.e6. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChaix A, Lin T, Le HD, et al.: Time-Restricted Feeding Prevents Obesity and Metabolic Syndrome in Mice Lacking a Circadian Clock. Cell Metab. 2019 Feb 5; 29(2): 303–19.e4. Epub 20180830. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuan D, Xiong Y, Trinh TM, et al.: The hepatocyte clock and feeding control chronophysiology of multiple liver cell types. Science. 2020 Sep 11; 369(6509): 1388–1394. Epub 20200730. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYoshitane H, Asano Y, Sagami A, et al.: Functional D-box sequences reset the circadian clock and drive mRNA rhythms. Commun. Biol. 2019; 2: 300. Epub 20190808. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDobin A, Davis CA, Schlesinger F, et al.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1; 29(1): 15–21. Epub 20121025. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHeinz S, Benner C, Spann N, et al.: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell. 2010 May 28; 38(4): 576–589. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu YW, Simmons BA, Singer SW: MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. (1367-4811 (Electronic)). eng.\n\nTakahashi JS: Transcriptional architecture of the mammalian circadian clock. Nat. Rev. Genet. 2017 Mar; 18(3): 164–179. Epub 20161219. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBunger MK, Wilsbacher LD, Moran SM, et al.: Mop3 is an essential component of the master circadian pacemaker in mammals. Cell. 2000 Dec 22; 103(7): 1009–1017. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKondratov RV, Shamanna RK, Kondratova AA, et al.: Dual role of the CLOCK/BMAL1 circadian complex in transcriptional regulation. FASEB J. 2006 Mar; 20(3): 530–532. Epub 20060125. eng. PubMed Abstract | Publisher Full Text\n\nvan der Horst GT , Muijtjens M, Kobayashi K, et al.: Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature. 1999 Apr 15; 398(6728): 627–630. eng. PubMed Abstract | Publisher Full Text\n\nOishi K, Miyazaki K, Kadota K, et al.: Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes. J. Biol. Chem. 2003 Oct 17; 278(42): 41519–41527. Epub 20030715. eng. PubMed Abstract | Publisher Full Text\n\nZhou B, Zhang Y, Zhang F, et al.: CLOCK/BMAL1 regulates circadian change of mouse hepatic insulin sensitivity by SIRT1. Hepatology. 2014 Jun; 59(6): 2196–2206. Epub 20140425. eng. PubMed Abstract | Publisher Full Text\n\nKoronowski KB, Kinouchi K, Welz PS, et al.: Defining the Independence of the Liver Circadian Clock. Cell. 2019 May 30; 177(6): 1448–62.e14. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGachon F, Fonjallaz P, Damiola F, et al.: The loss of circadian PAR bZip transcription factors results in epilepsy. Genes Dev. 2004 Jun 15; 18(12): 1397–1412. Epub 20040602. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCho H, Zhao X, Hatori M, et al.: Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β. Nature. 2012 Mar 29; 485(7396): 123–127. Epub 20120329. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStokkan KA, Yamazaki S, Tei H, et al.: Entrainment of the circadian clock in the liver by feeding. Science. 2001 Jan 19; 291(5503): 490–493. eng. PubMed Abstract | Publisher Full Text\n\nChallet E, Caldelas I, Graff C, et al.: Synchronization of the molecular clockwork by light- and food-related cues in mammals. Biol. Chem. 2003 May; 384(5): 711–719. eng. PubMed Abstract | Publisher Full Text\n\nDamiola F, Le Minh N, Preitner N, et al.: Restricted feeding uncouples circadian oscillators in peripheral tissues from the central pacemaker in the suprachiasmatic nucleus. Genes Dev. 2000 Dec 1; 14(23): 2950–2961. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHonma S: The mammalian circadian system: a hierarchical multi-oscillator structure for generating circadian rhythm. J. Physiol. Sci. 2018 May; 68(3): 207–219. Epub 20180219. eng. PubMed Abstract | Publisher Full Text\n\nWankhade UD, Vella KR, Fox DL, et al.: Deletion of Nhlh2 results in a defective torpor response and reduced Beta adrenergic receptor expression in adipose tissue. PLoS One. 2010 Aug 23; 5(8): e12324. Epub 20100823. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKanizsai P, Garami A, Solymár M, et al.: Energetics of fasting heterothermia in TRPV1-KO and wild type mice. Physiol. Behav. 2009 Jan 8; 96(1): 149–154. Epub 20081008. eng. PubMed Abstract | Publisher Full Text\n\nHeijboer AC, Donga E, Voshol PJ, et al.: Sixteen hours of fasting differentially affects hepatic and muscle insulin sensitivity in mice. J. Lipid Res. 2005 Mar; 46(3): 582–588. Epub 20041201. eng PubMed Abstract | Publisher Full Text\n\nFurner RL, Feller DD: The influence of starvation upon hepatic drug metabolism in rats, mice, and guinea pigs. Proc. Soc. Exp. Biol. Med. 1971 Jul; 137(3): 816–819. eng. PubMed Abstract | Publisher Full Text\n\nMoitra J, Mason MM, Olive M, et al.: Life without white fat: a transgenic mouse. Genes Dev. 1998 Oct 15; 12(20): 3168–3181. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGavrilova O, Leon LR, Marcus-Samuels B, et al.: Torpor in mice is induced by both leptin-dependent and -independent mechanisms. Proc. Natl. Acad. Sci. U. S. A. 1999 Dec 7; 96(25): 14623–14628. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAyala JE, Bracy DP, McGuinness OP, et al.: Considerations in the design of hyperinsulinemic-euglycemic clamps in the conscious mouse. Diabetes. 2006 Feb; 55(2): 390–397. eng. PubMed Abstract | Publisher Full Text\n\nStrubelt O, Dost-Kempf E, Siegers CP, et al.: The influence of fasting on the susceptibility of mice to hepatotoxic injury. Toxicol. Appl. Pharmacol. 1981 Aug; 60(1): 66–77. eng. PubMed Abstract | Publisher Full Text\n\nKawamoto T, Noshiro M, Furukawa M, et al.: Effects of fasting and re-feeding on the expression of Dec1, Per1, and other clock-related genes. J. Biochem. 2006 Sep; 140(3): 401–408. Epub 20060727. eng. PubMed Abstract | Publisher Full Text\n\nShavlakadze T, Anwari T, Soffe Z, et al.: Impact of fasting on the rhythmic expression of myogenic and metabolic factors in skeletal muscle of adult mice. Am. J. Physiol. Cell Physiol. 2013 Jul 1; 305(1): C26–C35. Epub 20130417. eng. PubMed Abstract | Publisher Full Text\n\nSun X, Dang F, Zhang D, et al.: Glucagon-CREB/CRTC2 signaling cascade regulates hepatic BMAL1 protein. J. Biol. Chem. 2015 Jan 23; 290(4): 2189–2197. Epub 20141205. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXie Z, Zhang D, Chung D, et al.: Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. Mol. Cell. 2016 Apr 21; 62(2): 194–206. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPickel L, Lee JH, Maughan H, et al.: Circadian rhythms in metabolic organs and the microbiota during acute fasting in mice. Physiol. Rep. 2022 Jul; 10(14): e15393. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHatori M, Vollmers C, Zarrinpar A, et al.: Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metab. 2012 Jun 6; 15(6): 848–860. Epub 20120517. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLongo VD, Panda S: Fasting, Circadian Rhythms, and Time-Restricted Feeding in Healthy Lifespan. Cell Metab. 2016 Jun 14; 23(6): 1048–1059. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDuncan MJ, Smith JT, Narbaiza J, et al.: Restricting feeding to the active phase in middle-aged mice attenuates adverse metabolic effects of a high-fat diet. Physiol. Behav. 2016 Dec; 167(167): 1–9. Epub 20160830. eng. PubMed Abstract | Publisher Full Text\n\nJamshed H, Beyl RA, Della Manna DL, et al.: Early Time-Restricted Feeding Improves 24-Hour Glucose Levels and Affects Markers of the Circadian Clock, Aging, and Autophagy in Humans. Nutrients. 2019 May 30; 11(6). Epub 20190530. eng. pii: E1234. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYanagihara H, Ando H, Hayashi Y, et al.: High-fat feeding exerts minimal effects on rhythmic mRNA expression of clock genes in mouse peripheral tissues. Chronobiol. Int. 2006; 23(5): 905–914. eng. PubMed Abstract | Publisher Full Text\n\nKohsaka A, Laposky AD, Ramsey KM, et al.: High-fat diet disrupts behavioral and molecular circadian rhythms in mice. Cell Metab. 2007 Nov; 6(5): 414–421. eng. PubMed Abstract | Publisher Full Text\n\nEckel-Mahan KL, Patel VR, de Mateo S , et al.: Reprogramming of the circadian clock by nutritional challenge. Cell. 2013 Dec 19; 155(7): 1464–1478. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLizier M, Bomba L, Minuti A, et al.: The nutrigenomic investigation of C57BL/6N mice fed a short-term high-fat diet highlights early changes in clock genes expression. Genes Nutr. 2013 Sep; 8(5): 465–474. Epub 20130416. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSherman H, Genzer Y, Cohen R, et al.: Timed high-fat diet resets circadian metabolism and prevents obesity. FASEB J. 2012 Aug; 26(8): 3493–3502. Epub 20120516. eng. PubMed Abstract | Publisher Full Text\n\nVollmers C, Gill S, DiTacchio L, et al.: Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression. Proc. Natl. Acad. Sci. U. S. A. 2009 Dec 15; 106(50): 21453–21458. Epub 20091125. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Papazyan R, Damle M, et al.: The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORα/γ. Genes Dev. 2017 Jun 15; 31(12): 1202–1211. Epub 20170726. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBatut PJ, Gingeras TR: Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. elife. 2017 Dec 20; 6. Epub 20171220. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAli T, Grote P: Beyond the RNA-dependent function of LncRNA genes. elife. 2020 Oct 23; 9. Epub 20201023. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRansohoff JD, Wei Y, Khavari PA: The functions and unique features of long intergenic non-coding RNA. Nat. Rev. Mol. Cell Biol. 2018 Mar; 19(3): 143–157. Epub 20171115. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPonjavic J, Ponting CP, Lunter G: Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 2007 May; 17(5): 556–565. Epub 20070326. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang G, Chen L, Grant GR, et al.: Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Sci. Transl. Med. 2016 Feb 3; 8(324): 324ra16. Epub 20160203. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMiao L, Batty K, Jackson A, et al.: Table_S1.xlsx. figshare. [Dataset].2022. Publisher Full Text"
}
|
[
{
"id": "150976",
"date": "21 Sep 2022",
"name": "Hikari Yoshitane",
"expertise": [
"Reviewer Expertise Circadian clock",
"post-translational modifications",
"phosphorylation",
"LC-MS/MS"
],
"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\nDr. Shihoko Kojima and their colleagues focused on the molecular basis of the rhythmic expression pattern of a circadian long non-coding RNA, PerAS, in the mouse liver. PerAS gene is located in the genomic locus of one of the core clock gene, Per2, and is transcribed as an antisense strand RNA. Intriguingly, PerAS shows a clear circadian rhythm of its RNA expression in the mouse liver, and the rhythmic pattern is almost anti-phasic to that of Per2 mRNA. Many chronobiologists, including me, predict that these genes probably repress each other's transcription, resulting in their anti-phasic RNA rhythms. In this study, however, the authors clearly demonstrated that Per2AS expression and Per2 mRNA expression are independently controlled by unknown mechanisms that will be revealed in the near future. They obtained a series of RNA-Seq datasets in this field to analyze RNA expression patterns of Per2AS in the mouse livers that lack core clock genes or under altered food conditions. The results are clear and the conclusion is so simple, and I strongly encourage to Approve this research in F1000Research paper with the following minor modifications.\nThe authors cite Cho et al., (2012) in which conditional DKO mice of Nr1d1/2 (REV-ERBs) genes did not show clear circadian rhythms in the locomotor activity. However, this arrhythmic phenotype was probably due to the severe unhealthiness of the mutant mice, because canonical DKO mice are lethal. In Adlanmerini et al., (2021)1 (from the same Dr. Lazar Lab), they showed clear locomotor rhythms with significant short period in the SCN-specific DKO of REV-ERBs. Therefore, REV-ERBs are not essential genes for the circadian oscillation. This will be informative for the readers to understand the results in this paper.\n\nThe authors re-analyzed a series of RNA-Seq datasets in this field to analyze RNA expression patterns of Per2AS in the mouse livers. Since the bioinformatic methods for analyzing RNA-Seq data are advancing day by day and the obtained results will change depending on the method, the results analyzed by the same authors using the same method are very useful for many chronobiologists. For example in Figure 1, they showed only expression patterns of Per2AS, Per2, and the deleted genes in a series of KO mice, but I suggest them to show expression patterns of core clock genes in all the case probably in supplemental figures; especially E-box genes (Dbp and Rev-erb) expression in Bmal1-KO and Cry-DKO mice and RRE genes (Bmal1 and E4bp4) expression in Rev-erb-DKO. These results will support the quality of their bioinformatic method in this paper and also will show the quality of the raw data in the previous studies.\nMinor:\nI find it easier to compare the gene expression patterns if panels are displayed in the same size even between different figures. For example, panels in figure 2 is too big and figure 4 is too small.\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": "8936",
"date": "31 Oct 2022",
"name": "Shihoko Kojima",
"role": "Author Response",
"response": "1. We thank the reviewer for the suggestion. We have added the paper that the reviewer mentioned, and edited the last paragraph of the section “Core clock genes Bmal1, Cry1/2, and Nr1d1/2 affect the expression patterns of Per2AS and Per2”. 2. We agree with the reviewer. We have now provided an additional extended data file as Table S2, which includes RNA expression levels (i.e., strand-specific TPM) of the core clock genes as well as the rhythmicity analysis of the expression patterns with MetaCycle (doi: 10.6084/m9.figshare.21375783). We also mentioned this extended data by the end of the session “Core clock genes Bmal1, Cry1/2, and Nr1d1/2 affect the expression patterns of Per2AS and Per2”. 3. Unfortunately, we, the authors, have no control over the size of the figures and are not able to change their sizes."
}
]
},
{
"id": "151597",
"date": "10 Oct 2022",
"name": "Yao Cai",
"expertise": [
"Reviewer Expertise Circadian clock",
"phosphorylation",
"Drosophila genetics"
],
"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\nMiao et al. investigated how genetic and environmental manipulations influence the expression of Per2AS, a circadian long non-coding RNA. Despite the identification of Per2AS in several circadian transcriptome studies and publication of a functional studies (Mosig et al., 2021, G&D), how Per2AS transcription is regulated remains a major gap in knowledge. A lncRNA transcription can be regulated via transcriptional interference. Alternatively, the promoter of a lncRNA is regulated independent of its sense RNA transcript. To gain insights on the transcriptional regulation of Per2AS, the authors analyzed the expression pattern of Per2AS and Per2 in response to genetic and/or environmental manipulation from publicly available RNA-seq database. Per2AS expression is altered in most core clock gene mutant mice. Whereas Per2AS expression is less sensitive to environmental manipulations including fasting, time-restricted feeding and high-fat diet. They authors suggest both models regarding transcription of the Per2AS lncRNA may be true. (1) In some conditions (e.g. Cry1/2 double knock-out) where Per2 expression is in intermediate level throughout the day, Per2AS level remains in a trough level, supporting the transcriptional interference hypothesis. (2) When Per2 expression remains in the trough level under 24-hour fasting condition, Per2AS level is unaltered, favoring the independent regulation hypothesis. Taken together, this manuscript provides new insights on the transcriptional regulation of Per2AS. Below are some minor suggestions for the authors to improve the manuscript.\nClarify what transcriptional interference (TI) means in the introduction section. Is there a specific TI mechanism you refer to, such as promoter competition, RNAPII collision? I believe this helps readers who are unfamiliar with TI to understand the TI hypothesis.\n\nTranscripts of Per2AS seems to be a few fold higher than Per2 in any given conditions (e.g., Figure 1A). Is this relevant to the two hypotheses? Can the authors comment on this phenomenon?\n\nCan the authors speculate whether Per2AS is more sensitive to signals from the central clock than the peripheral liver clock? It is interesting that Per2AS is unaltered under 24-hour fasting condition (Figure 2), despite the dampening of Per2 transcripts. Maybe analyzing Per2AS level in the liver of SCN lesioned mice or mice kept under constant light will be informative.\n\nTo date, there are no data that can solidly differentiate whether BMAL1 and CRY1/2 activates or depresses Per2AS transcription. For this reason, I think the word “promote” is better than “activate” when describing upregulation of Per2AS expression (e.g., the sentence that cites Figure 1A, C, Table S1). This will include both possibilities.\n\nI have difficulty understanding the first sentence of the last paragraph in the Discussion section. What do the authors mean by “interacts with other core clock proteins”? To my understanding, this manuscript investigates how Per2AS transcription is influenced upon genetic manipulation on core clock genes, instead of how Per2AS regulates core clock proteins.\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": "8937",
"date": "31 Oct 2022",
"name": "Shihoko Kojima",
"role": "Author Response",
"response": "1. We agree that the explanation of transcriptional interference (TI) will help readers better understand our hypothesis. We supplemented this information, and it now reads: “Our first hypothesis is that the rhythmic Per2AS transcription is regulated by rhythmic antiphasic transcription of Per2 by means of transcriptional interference, in which the transcription process on one strand suppresses the transcription process of the other strand. 27-29” We currently do not have any specific mechanism in mind and did not mention any. 2. The reviewer is correct that the strand-specific TPM (transcripts per million) for Per2AS is generally higher than that of Per2. This is because we had to separately calculate the strand-specific TPM on each strand. Since the total number of raw read counts is different in each strand, the expression level of Per2 and Per2AS cannot be directly compared with each other. This is not relevant to the two hypotheses. 3. We have shown that Per2AS is sensitive to the local liver clock as well as environmental perturbation triggered by changes in diet (Figs 1-4). It is unclear whether Per2AS is sensitive to the central clock (i.e., SCN). To our knowledge, there is no circadian transcriptome dataset in liver from SCN-lesioned mice. 4. We agree with the reviewer that the word “promote” is more accurate than “activate”. We have now changed these, as suggested. 1) “Whereas the expression of Per2AS was markedly low and arrhythmic, indicating that Bmal1 and Cry1/2 promote the expression of Per2AS (Figure 1A, C, Table S1 84).” 2) “Additionally, these findings further support that BMAL1 and CRY are crucial transcription factors to promote Per2AS expression, regardless of the feeding patterns. ” 5. We apologize for the confusion. We revised this sentence, which now reads: “Regardless, these results help us better understand not only how the transcription of Per2AS is regulated, but also how Per2AS is wired with other core clock proteins in transcriptional-translational feedback loops to regulate circadian rhythms because the rhythmic transcription of Per2AS is important for its functions in regulating circadian rhythms.”"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1073
|
https://f1000research.com/articles/11-1016/v1
|
07 Sep 22
|
{
"type": "Research Article",
"title": "A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins",
"authors": [
"Moeri Yagi",
"Simon Miller",
"Yoshiko Nagai",
"Shinsuke Inuki",
"Ayato Sato",
"Tsuyoshi Hirota",
"Moeri Yagi",
"Simon Miller",
"Yoshiko Nagai",
"Shinsuke Inuki",
"Ayato Sato"
],
"abstract": "Background: Impairment of the circadian clock has been associated with numerous diseases, including sleep disorders and metabolic disease. Although small-molecules that modulate clock function may form the basis of drug discovery of clock-related diseases, only a few compounds that selectively target core clock proteins have been identified. Three scaffolds were previously discovered as small-molecule activators of the clock protein Cryptochrome (CRY), and they have been providing powerful tools to understand and control the circadian clock system. Identifying new scaffolds will expand the possibilities of drug discovery. Methods: A methylbenzimidazole derivative TH401 identified from cell-based circadian screens was characterized. Effects of TH401 on circadian rhythms were evaluated in cellular assays. Functional assays and X-ray crystallography were used to elucidate the effects of the compound on CRY1 and CRY2 isoforms. Results: TH401 lengthened the period of circadian rhythms and stabilized both CRY1 and CRY2. The compound repressed Per2 reporter activity, which was reduced by Cry1 or Cry2 knockout and abolished by Cry1/Cry2 double knockout, indicating the dependence on CRY isoforms. Thermal shift assays showed slightly higher interaction of TH401 with CRY2 over CRY1. The crystal structure of CRY1 in complex with TH401 revealed a conformational change of the gatekeeper W399, which is involved in isoform-selectivity determination. Conclusions: The present study identified a new small-molecule TH401 that targets both CRY isoforms. This compound has expanded the chemical diversity of CRY activators, and will ultimately aid in the development of therapeutics against circadian clock-related disorders.",
"keywords": [
"Circadian clock",
"Cryptochrome",
"Small-molecule compound"
],
"content": "Introduction\n\nLiving organisms have a molecular clock, called the circadian clock, which drives the ~24-hour circadian rhythm. The circadian clock regulates daily rhythms of various physiological processes, such as sleep-wake behavior, body temperature, and metabolism.1 This clock is composed of a transcriptional regulatory network of clock genes, Period (Per1 and Per2), Cryptochrome (Cry1 and Cry2), Clock and Bmal1. In the core feedback loop of the mammalian circadian clock, transcription factors CLOCK and BMAL1 activate transcription of Per and Cry genes by forming a heterodimer. The translated PER and CRY proteins then repress the transcriptional activity of CLOCK-BMAL1 to close the loop, followed by the degradation of PER and CRY through the ubiquitin-proteasome pathway reactivating CLOCK-BMAL1.2\n\nImpairment of clock functions due to genetic mutations of clock genes or environmental factors, including shift work or chronic jet lag, has been shown to cause sleep disorders and increase the risk of numerous diseases, such as obesity and cancer.3 Thus, elucidating the circadian clock system is important for understanding how circadian clock dysfunction results in circadian-related diseases. Small-molecule compounds that control clock function provide a powerful and useful tool in the drug discovery of such diseases.4–6 Cell-based chemical screening has identified several synthetic small-molecule compounds that selectively target the core clock protein CRY. A carbazole-containing compound KL001 targets both CRY1 and CRY2 to inhibit their ubiquitin-dependent degradation, thus lengthening the circadian period.7 Several KL001 derivatives have been developed, including KL044 which is 10 times more potent than KL001,8 and a period-shortening compound GO044.9 Several other KL001 derivatives have shown potential application in the treatment of diabetes and glioblastoma. Compound 41 and compound 50 improved glucose clearance in diet-induced obese mice and db/db mice, respectively, indicating their antidiabetic efficacy.10,11 Treatment with KL001 and its derivative SHP656 inhibited proliferation and survival of patient-derived glioblastoma stem cells (GSCs), which cause a highly malignant primary brain tumor, and SHP656 prolonged the survival of mice implanted with GSCs.12 Furthermore, a new series of CRY activators that target either CRY1 or CRY2 in an isoform-selective manner were recently identified: phenylpyrazole-containing compounds KL101, TH301, and TH129,13,14 and a thienopyrimidine derivative KL201.15 In addition to these three scaffolds, the identification of novel scaffolds will expand the chemical diversity of CRY activators, as well as the possibility of drug discovery for the treatment of circadian clock-related diseases.\n\nIn this study, we revealed the effects of a new circadian clock modulator TH401, which contains a methylbenzimidazole moiety, on CRY isoforms by taking a target-based approach. TH401 showed stabilization and activation of CRY1 and CRY2. The repression of Per2 reporter by TH401 was dependent on both CRY isoforms, indicating CRY-specific activity of the compound. TH401 directly interacted with CRY1 and CRY2, albeit with a slight preference to CRY2, and the X-ray crystal structure of a CRY1-TH401 complex revealed the binding mode of TH401.\n\n\nMethods\n\nTH401 powder was purchased from Vitas-M Laboratory (STK095604). TH403-TH411 were obtained from a 10 mM original stock of a compound library containing 20,000 small molecules used for primary screening of circadian clock modulators.\n\nU2OS cells expressing a Bmal1-dLuc and Per2-dLuc reporter16,17 were plated onto a white, solid-bottom 384-well plate at 30 μl (3,000 cells) per well as previously described.18 After 2 days, 40 μl of explant medium [DMEM (12800-017, Gibco) supplemented with 2% B27 (17504-001, Gibco), 10 mM HEPES, 0.38 mg/ml sodium bicarbonate, 0.29 mg/ml L-glutamine, 100 units/ml penicillin, 100 μg/ml streptomycin, and 1 mM luciferin; pH 7.2] was dispensed into each well, and 500 nl of compounds (final 0.7% dimethyl sulfoxide (DMSO)) were applied. The luminescence was recorded every 100 min for 5 days in a microplate reader (Infinite M200Pro, Tecan).\n\nBmal1-dLuc and Per2-dLuc U2OS cells were plated by following the cell-based circadian assay protocol as described above and cultured for 5 days. Then, CellTiter-Glo Reagent (G9242, Promega) was applied to each well, and luminescence corresponding to cellular ATP levels was recorded in a multi-mode reader (Cytation3, BioTek).\n\nThe effect of compounds on casein kinase Iδ (CKIδ) activity in vitro was analyzed as previously described.19 The reaction mixture containing 2 ng/μl CKIδ (14-520, Eurofins), 50 μM peptide substrate RKKKAEpSVASLTSQCSYSS corresponding to human PER2 Lys659-Ser674 (custom made), CKI buffer (40 mM Tris, 10 mM MgCl2, 0.5 mM DTT, 0.1 mg/ml BSA, pH7.5), compound (final 5% DMSO), and 5 μM ATP was incubation at 30°C for 3 h. Kinase-Glo Luminescent Kinase Assay reagent (V6713, Promega) was used to determine the amount of remaining ATP.\n\nStable HEK293 cells expressing a C-terminally luciferase-fused CRY1 (CRY1-LUC), CRY2-LUC or LUC reporter were plated onto a white, solid-bottom 96-well plate (30,000 cells per well) and treated with TH401 for 24 h as previously described.7 After 24 h treatment with compounds, luciferin (final 0.1 mM) and HEPES-NaOH (pH 7.2; final 10 mM) were added to the medium. After 1 h, it was further supplemented with cycloheximide (final 20 μg/ml), and luminescence was recorded every 10 min for 18 h in a microplate reader (Infinite M200Pro, Tecan).\n\nWild type, Cry1/Cry2 double knockout, Cry1 knockout, and Cry2 knockout fibroblasts expressing a Per2::Luc knock-in reporter20 were plated on a white, solid-bottom 384-well plate. They were cultured for 2 days to reach confluency, and 500 nl of compounds (final 0.7% DMSO) were applied. After 2 days of treatment with the compounds, the medium was replaced with BrightGlo (E2620, Promega), and luminescence was recorded in a multi-mode reader (Cytation3, BioTek).\n\nFunctional rescue of Cry1/Cry2 double knockout mouse embryonic fibroblasts with CRY expression vectors21 was performed as previously described13 with modifications: 15,000 cells were plated onto a white, solid-bottom 96-well plate, and after 24 h, transfected with 0.1 or 0.2 ng of CRY1 and CRY2 expression vectors and 100 ng of a Bmal1-Eluc reporter vector by Fugene 6 (E2691, Promega). After treatment with forskolin (final 10 μM) for 2 h, the medium was replaced with explant medium containing 0.2 mM luciferin, and 500 nl of compounds (final 0.4% DMSO) were applied. Luminescence was recorded every 36 min in a microplate reader (Infinite M200Pro, Tecan) for 5 days.\n\nHEK293T cells were co-transfected with Flag-tagged CRY1 and HA-tagged CRY2 expression vectors as previously described.13 After 2 days, the cell pellet was suspended in serum-free DMEM with cOmplete EDTA-free Protease Inhibitor Cocktail (04693132001, Roche), treated with 0, 8, and 24 μM of compounds (final 0.7% DMSO) on a 96-well PCR plate, and incubated at 37°C for 1 h, followed by heat treatment for 3 min. The optimized temperatures for heat treatment of CRY1 and CRY2 were 55°C and 49°C, respectively. The cells were lysed by 2 cycles of freeze-thawing and centrifuged at 18,000 x g for 20 min at 4°C. The supernatants were analyzed by Western blotting with mouse monoclonal anti-Flag-HRP (A8592, Sigma; RRID: AB_439702) and rat monoclonal anti-HA-HRP (12013819001, Roche; RRID: AB_390917) antibodies.\n\nHis6-MBP-CRY1(PHR) and His6-MBP-CRY2(PHR) were expressed in Sf9 (Spodoptera frugiperda) insect cells (Invitrogen) via baculovirus infection as previously described.13 Cell pellets were resuspended in lysis buffer (1x PBS, 50 mM NaNO3, 1% (v/v) glycerol, 0.1% Triton X-100, and Complete Protease Inhibitor Cocktail (Roche); pH 7.4) and purified according to our previously determined method.14 Briefly, cells were sonicated on ice, centrifuged at 19,000 × g for 90 min at 4°C, and the supernatant, containing target CRY proteins, was purified via a high-performance liquid chromatography (HPLC) system using a HisTrap 5 ml column (GE Healthcare). After tobacco etch virus (TEV) protease cleavage of the His6-MBP tag, further purification was performed via a HiTrap Heparin HP column (GE Healthcare), amylose resin (E8021, New England Biolabs), and a gel filtration chromatography Superdex 75 16/60 column (GE Healthcare). Purified proteins were buffer-exchanged (see Protein crystallization and structure determination section) and concentrated using an Amicon Ultra (Merck) concentrator.\n\nCRY1(PHR) or CRY2(PHR) were diluted to 2 μM with differential scanning fluorimetry (DSF) buffer (20 mM HEPES-NaOH, 150 mM NaCl, 2 mM DTT; pH 7.5) and dispensed into a 384-well white PCR plate (Bio-Rad) at 17 μl per well. After the application of 1 μl of compounds (final 5% DMSO), the mixtures were incubated at room temperature with gentle shaking for 60 min. 2 μl of SYPRO Orange (S6650, Invitrogen) diluted with DSF buffer (final 5x SYPRO Orange) was added, and thermal denaturation was performed using a real-time PCR detection system (CFX384 Touch, Bio-Rad).\n\nCRY1(PHR) was buffer-exchanged into 100 mM Bis-Tris propane (B6755, Sigma), 100 mM NaCl, and 2 mM tris(2-carboxyethyl) phosphine (209-19861, Wako Pure Chemical Industries); pH 7.5, concentrated to 6 mg/ml, and crystallized via hanging-drop vapor diffusion at 20°C. CRY1(PHR) (1 μl) was mixed with 1 μl of precipitant solution containing 250 mM NH4Cl, 21% (w/v) PEG 3350, 3% (v/v) ethylene glycol. Apo crystals grew over several days and were soaked overnight with 0.5 mM TH401 dissolved in mother liquor. The crystals were cryoprotected in mother liquor plus 30% (v/v) PEG 400, and flash-cooled in liquid nitrogen. In contrast, we were unable to obtain protein crystals of a CRY2-TH401 complex.\n\nX-ray diffraction data for CRY1-TH401 was collected at the SPring-8 synchrotron radiation facility (beamline BL41XU) at a wavelength of 1.0 Å and a temperature of 100 K. The dataset was processed with DIALS/xia222 and SCALA23 in the CCP4 suite.24 The CRY1-TH401 structure was determined in space group P212121 (1 molecule per asymmetric unit) by Phaser25 using CRY1-apo (PDB ID: 6KX4) as a molecular replacement (MR) template. Density modification was performed with PARROT.26 Model building was performed iteratively using Coot27 and refinement in REFMAC5.28 Final refinement was performed with PHENIX refine.29\n\nA curve fitting program MultiCycle (Actimetrics) was utilized to determine the circadian period, and the luminescence intensity was calculated by averaging the intensity during the entire experiment. Due to transient changes in luminescence upon medium exchange, data from the first day was excluded from analysis. In degradation assays, half-life was obtained by one phase exponential decay fitting with Prism software (version 7.04, GraphPad Software; any open-access software can be used as an alternative, including the freely available R). In cellular thermal shift assays, band intensity was analyzed by ImageQuant TL software (version 8.1, GE Healthcare). In thermal shift assays, the highest peak of the dF/dT curve (the first derivative of the fluorescence intensity against temperature) was defined as the melting temperature.\n\n\nResults and discussion\n\nWe discovered new small-molecule modulators of the circadian clock from cell-based screens of a library of ~20,000 uncharacterized compounds.13,14,18 In this study, we characterized a methylbenzimidazole derivative TH401 (Figure 1A). Treatment of human U2OS cells expressing either a Bmal1 promoter-luciferase (Bmal1-dLuc) reporter or a Per2-dLuc reporter with TH401 caused lengthening of the circadian period in a dose-dependent manner (Figure 1B and C).30 Furthermore, increasing the concentrations of TH401 suppressed the intensity of the Per2-dLuc reporter more than that of Bmal1-dLuc (Figure 1B and D),30 without affecting cellular viability (Figure 1E).30 These results indicate that TH401 is a new clock-modulating compound.\n\n(A) The chemical structure of TH401. (B-D) Effects on circadian rhythms in Bmal1-dLuc and Per2-dLuc U2OS cells. Luminescence rhythms in the presence of various concentrations of TH401 (B, mean of n = 2) and changes in period (C) and luminescence intensity (D) compared to a dimethyl sulfoxide (DMSO) control are shown (n = 6 biologically independent samples). When arrhythmic, the period is not plotted. (E) Effect on cell viability in Bmal1-dLuc and Per2-dLuc U2OS cells. Cellular ATP levels after treatment with various concentrations of TH401 are plotted by setting a DMSO control to 1 (n = 4 biologically independent samples).\n\nWe took a target-based approach to reveal how TH401 modulates circadian rhythms. Longdaysin is known to induce period lengthening by targeting the protein kinase CKIδ,19 but TH401 did not affect CKIδ activity in an in vitro kinase assay (Figure 2A),30 suggesting an alternative mechanism of action other than CKI. We next analyzed the effect of TH401 on CRY stability in a cell-based degradation assay. HEK293 cells expressing a CRY1-luciferase (CRY1-LUC) or CRY2-LUC fusion protein reporter were treated with the compound at various concentrations, and the half-life of luminescence signals were measured. TH401 stabilized both CRY1 and CRY2 (Figure 2B),30 suggesting that the compound targets CRY proteins.\n\n(A) Effect of TH401 on casein kinase Iδ (CKIδ) activity in vitro. Kinase activity was analyzed in the presence of various concentrations of compounds (n = 1). Longdaysin is an inhibitor of CKIδ. (B) Effect of TH401 on Cryptochrome (CRY) degradation in HEK293 cells. The half-lives of CRY-luciferase fusion proteins (CRY1-LUC and CRY2-LUC) relative to LUC are plotted by setting a DMSO control to 1 (n = 2 biologically independent samples). (C) Effect on Per2::Luc knock-in reporter activity in wild type, Cry1/Cry2 double knockout, Cry1 knockout, and Cry2 knockout fibroblasts. Changes in luminescence intensity compared to a DMSO control are shown (n = 4–8 biologically independent samples). (D) Effect on cellular circadian period of Bmal1-Eluc reporter rhythms in Cry1/Cry2 double knockout fibroblasts rescued with CRY. Changes in period compared to a DMSO control are shown (n = 3–6 biologically independent samples). (E) Interaction with CRY proteins in HEK293T cells. The band intensities of Flag-tagged CRY1 and HA-tagged CRY2 proteins protected from thermal denaturation in cells are plotted by setting a DMSO control to 1 (mean of n = 4 biologically independent samples). Compound interaction induced thermal stabilization. (F) Interaction with CRY1(PHR) and CRY2(PHR) in vitro. Changes in denaturing temperatures of recombinant CRY(PHR) proteins in the presence of various concentrations of TH401, compared to a DMSO control are shown (n = 2 biologically independent samples).\n\nThe effect of TH401 on endogenous CRY1 and CRY2 activity was analyzed by using Cry knock-out fibroblasts from mice carrying a Per2::Luc knock-in reporter.31 CRY is a repressor of CLOCK-BMAL1, and CRY stabilization reduces the expression of CLOCK-BMAL1-target genes such as Per2.2 TH401 repressed the intensity of the Per2::Luc reporter in a dose-dependent manner in wild type cells with both CRY1 and CRY2 present (Figure 2C).30 Per2 repression was not observed in Cry1/Cry2 double knockout fibroblasts, indicating that the effect of TH401 was CRY-dependent. In Cry1 and Cry2 single knockout cells, Per2 repression by TH401 was reduced compared to wild type, which supports that TH401 targets both CRY1 and CRY2. We further evaluated its effect on the circadian period of a Bmal1-Eluc reporter in Cry1/Cry2 double knockout mouse fibroblasts rescued with CRY1 and CRY2. Period-lengthening by TH401 was enhanced when the dose of CRY1 or CRY2 was increased (Figure 2D).30\n\nTo assess the interaction of TH401 with CRY proteins, a cellular thermal shift assay was conducted using HEK293T cells expressing CRY1-Flag and CRY2-HA. Exposing proteins to a high temperature causes them to lose their tertiary structure. However, the binding of a ligand increases resistance to unfolding, leading to thermal stabilization of the bound protein.32 TH401 stabilized CRY1 and CRY2 against thermal denaturation in a dose-dependent manner (Figure 2E),30 suggesting that TH401 interacts with both CRY isoforms. The direct interaction of TH401 with recombinant CRY1 photolyase homology region (PHR) and CRY2(PHR) was further evaluated by performing an in vitro thermal shift assay. We found that TH401 interacted with both recombinant CRY(PHR) proteins with a slightly higher preference against CRY2 over CRY1 (Figure 2F).30 Together, these data indicate that TH401 induces circadian period lengthening by targeting and interacting with both CRY1 and CRY2 proteins.\n\nTo obtain insights into the regulatory effects of TH401 on CRY proteins, we determined the crystal structure of CRY1(PHR) in complex with TH401 at a resolution of 2.05 Å (Table 1) (PDB ID: 7WVA). The overall protein fold was highly similar to previously published CRY1 structures.13–15,33–35 With regard to the binding mode of TH401, the 1-methylbenzimidazole moiety formed hydrophobic interactions with W292, R293 and W399, as well as additional offset π-stacking with W292 (Figure 3A). The trimethoxyphenyl moiety formed multiple hydrophobic interactions with residues R358, A362, F381, L385, A388, W397 and L400. Oxygen atoms in two methoxy groups (ortho and meta) formed hydrogen bonds with the guanidinium group of R358, while methyl groups in two methoxy groups (ortho and meta) formed C–H hydrogen bonds with N393 and S396 (Figure 3A). One notable difference in the binding mode of TH401, compared to almost all other CRY-interacting compounds, was the absence of a canonical H-bond between the linker (connecting the methylbenzimidazole and trimethoxyphenyl moieties) and S396. Instead, H359 interacted with the sulfanylacetohydrazide linker by forming two hydrogen bonds, one with the hydrazide carbonyl and the other with a hydrazide nitrogen (Figure 3A).\n\nValues in parentheses are for the highest resolution shell. Root mean square (R,m.s.); correlation coefficient (CC).\n\n(A) The binding mode of TH401 in CRY1. Flavin adenine dinucleotide (FAD) pocket residues (white) that interact with TH401 (cyan) are shown. Hydrogen bonds and C–H hydrogen bonds are represented by red and yellow dashes, respectively. (B) TH401 induced conformational changes in the FAD pocket of CRY1. Superposition of CRY1-TH401 (white-cyan) onto CRY1-PG4 (brown) (PDB: 7D0M; PG4, a non-biological tetraethylene glycol cryoprotectant, is not shown) and CRY2-apo (green) (PDB: 7D0N). Only the gatekeeper–lid loop interface is shown in CRY2-apo for simplicity. The binding of TH401 resulted in the repositioning of the gatekeeper W399 from an intrinsic “out” conformation in CRY1-PG4 (apo-like structure) to a “middle” conformation in CRY1-TH401. The W399 “middle” conformation resulted in the loss of an NH–aryl interaction between W399 and Q407 at the gatekeeper–lid loop interface in CRY1-PG4. Additional flexibility in the lid loop of CRY1 with bound TH401 meant the lid loop was not built into the crystal structure and its predicted structure is represented as dashed lines as modeled by Pymol. The intrinsic “in” conformation of the gatekeeper W417 in CRY2 would require a smaller conformational change to adopt a “middle” position than the intrinsic “out” conformation of W399 in CRY1. (C) Superposition of CRY1-TH401 (white-cyan) onto CRY1-PER2 (yellow) (PDB: 4CT0) and CRY2-PER2 (orange) (PDB: 4U8H). PER2 is not shown for simplicity. The binding mode of TH401 looks compatible with the key FAD pocket residues H355 and W399 in CRY1-PER2, corresponding to CRY2-PER2 residues H373 and W417, respectively.\n\nTH401 binding was compatible with the intrinsic conformations of most FAD (flavin adenine dinucleotide) pocket residues of CRY1; however, a notable difference was observed in the conformation of the gatekeeper W399, and steric restraint was imposed on the possible rotamer positions of H355 (Figure 3B). W399 underwent a sizeable conformational change from an intrinsic “out” position to a “middle” conformation to form a hydrophobic interaction with the methyl group of the 1-methylbenzimidazole moiety, and H355 adopted a forward-facing rotamer, similar to an alternate conformer that was observed in the CRY1-apo structure13 (PDB ID: 6KX4). The lid loop was disordered in CRY1-TH401, most likely because the intrinsic W399–Q407 gatekeeper–lid loop interface was disrupted by TH401-induced repositioning of W399 (Figure 3B). Overall, the binding mode of TH401 appears less compatible with the FAD pocket in CRY1 than CRY2, which supports the slightly lower interaction of CRY1 over CRY2 in thermal shift assays (Figure 2E and F).\n\nOur structural data showed that TH401 binding to CRY1 induced a sizeable conformational change in the gatekeeper W399. Isoform-specific gatekeeper conformations that mediate distinct gatekeeper–lid loop interfaces in CRY1 and CRY2 have been implicated in the potential regulation of compound isoform-selectivity.35,36 Interestingly, the TH401-induced “middle” gatekeeper conformation in the CRY1-TH401 structure would appear to be more energetically favorable in CRY2, because only a small conformational change (W417 from “in” to “middle”; CRY2 W417 corresponds to CRY1 W399) would be required (Figure 3B). In contrast, CRY1 W399 would need to rotate much further from an “out” to a “middle” conformation. Furthermore, the NH–aryl interaction between W399 and Q407 in CRY1 has more favorable free binding energy than the stacking interaction of W417 and F424 in CRY2,35 which may result in CRY1 W399 being less flexible than CRY2 W417. These structural observations correlate to the slightly lower preferential interaction of TH401 with CRY1 compared to CRY2 in thermal shift assays. In contrast, however, TH401 displayed a very low level of isoform preference in functional assays (Figure 2C and D). This disparity may be due to higher repressor activity of CRY1 over CRY2,37–40 resulting in the similar functional effects of TH401 on both isoforms, despite its preferential interaction with CRY2. In addition to the gatekeeper and lid loop, a flexible region downstream of the PHR known as the CRY C-terminal tail (CCT) has been associated with compound selectivity.13 In Drosophila CRY, the residue H378, corresponding to mouse CRY1 H355, has been shown to regulate CCT interaction with the FAD pocket via a conformational change.41–43 Both W399 and H355 in CRY1-TH401 underwent large conformational changes, compared to CRY1-apo structures35 (Figure 3B), and the lid loop was disordered as a result of W399-repositioning. These changes could affect CCT interaction for functional changes.\n\nCRYs form large complexes in both the cytoplasm and nucleus, and PER2, a primary CRY-interacting protein, changes the conformations of key FAD pocket residues, including the gatekeeper W399, as well as the lid loop44 (PDB ID: 4CT0). Interestingly, the conformations of the gatekeeper W399 and H355 in the CRY1-TH401 crystal structure are very similar to those in CRY1/2-PER2 complex structures44,45 (Figure 3C) (PDB IDs: 4CT0; and 4U8H). The conformation of W292 in CRY1-PER2 would form a steric clash with the methylbenzimidazole of TH401; however, W292 is very flexible and can accommodate compounds by easily adopting a different rotamer.35 Therefore, TH401 may be able to bind to CRY1 and CRY2 equally when they are complexed with PER2, resulting in similar potency against both isoforms.\n\nTo further characterize the CRY2-TH401 interaction, we searched for TH401 derivatives in the compound library used for primary screening of circadian clock modulators and checked their activity in the screen (Figure 4, blue).30 Because the derivatives TH403-TH411 showed almost no effect on circadian period in the screen at 7 μM (using 1 mM working stock compounds), we obtained these compounds from the original 10 mM stock of the library and analyzed their activity in a circadian assay using human Bmal1-dLuc U2OS cells at 24 or 8 μM (Figure 4, purple).30 Extension of the methyl group of 1-methylbenzimidazole together with replacement of the ortho-methoxy group of trimethoxyphenyl to meta (TH403) caused a loss of activity, consistent with the interactions of the methyl group with W399, and the ortho-methoxy group with R358 and S396 (Figure 3A). Modifications to the trimethoxy groups of the trimethoxyphenyl resulted in either weak activity (TH404-TH406) or inactivity (TH407-TH411), supporting their interactions with R358, S396, and N393, as well as A362, F381, L385, A388, W397, and L400. The weak activities of TH404-TH406 suggested that an interaction of the ortho-hydroxy group with R358 can support activity. Therefore, CRY2-TH401 interactions in the crystal structure are consistent with activity in cells.\n\nChanges in the circadian period of Bmal1-dLuc U2OS cells compared to a dimethyl sulfoxide (DMSO) control in primary screening (tested at 7 μM; n = 1) and a secondary assay (tested at 24 μM; mean±SD, n = 3 biologically independent samples) are shown in blue and purple, respectively, with chemical structures. TH406 caused low amplitude with unreliable period estimation (ND, not determined) in primary screening and the secondary assay at 24 μM, and were therefore tested at 8 μM (shown in italics). Modified part of the compound is shown in red.\n\n\nConclusion\n\nWe have discovered that TH401 provides a new chemical scaffold, methylbenzimidazole, for CRY regulation by targeting both CRY1 and CRY2. Cell-based phenotypic screens of circadian clock modulators resulted in the identification of small-molecule activators of CRY proteins. In addition to this approach, CRY inhibitors have been identified through a cell-based screen of E-box-mediated transcription. 2-ethoxypropanoic acid derivatives target both CRY isoforms and inhibit their repressive function, enhancing E-box-mediated transcription.46,47 Furthermore, a recent study showed that structure-based drug design could be another useful approach to find CRY1 modulators.48 In order to obtain further insights into the mechanisms of action of these small-molecules, it is necessary to determine the crystal structures in complex with CRY proteins. Identification of new CRY modulators and their characterization will facilitate the understanding and regulation of CRY protein functions in gene expression,49 metabolism,7,10,11,13,50,51 cancer,12,52–54 and sleep-wake rhythms,55–57 ultimately leading to the discovery of therapeutic agents for circadian clock-related diseases.\n\n\nData availability\n\nThe X-ray crystal structure of CRY1-TH401 was deposited into the Protein Data Bank with the accession number 7WVA.\n\nFigshare: Yagi et al. Figure data. https://doi.org/10.6084/m9.figshare.20431692.30\n\nThis project contains the following underlying data:\n\n• Figure 1B. csv (Luminescence rhythms of Bmal1-dLuc and Per2-dLuc U2OS cells in the presence of various concentrations of TH401 (n = 2))\n\n• Figure 1C. csv (Changes in period (n = 6))\n\n• Figure 1D. csv (Changes in luminescence intensity (n = 6))\n\n• Figure 1E. csv (Changes in cellular ATP levels after treatment with various concentrations of TH401 (n = 4))\n\n• Figure 2A. csv (Inhibitory effect of Longdaysin and TH401 on CKIδ activity in vitro (n = 1))\n\n• Figure 2B. csv (Changes in the half-lives of CRY-luciferase fusion proteins (CRY1-LUC and CRY2-LUC) relative to LUC in the presence of various concentrations of TH401 (n = 2))\n\n• Figure 2C. csv (Changes in Per2::Luc knock-in reporter activity in wild type, Cry1/Cry2 double knockout, Cry1 knockout, and Cry2 knockout fibroblasts (n = 4–8))\n\n• Figure 2D. csv (Changes in the cellular circadian period of Bmal1-Eluc reporter rhythms in Cry1/Cry2 double knockout fibroblasts rescued with CRY1 and CRY2 (n = 3–6))\n\n• Figure 2E. csv (Changes in the protection of CRY1 and CRY2 proteins from thermal denaturation in HEK293T cells (n = 4))\n\n• Figure 2F. csv (Changes in denaturing temperatures of recombinant CRY1(PHR) and CRY2(PHR) in vitro (n = 2))\n\n• Figure 4. csv (Changes in the circadian period in primary screening (tested at 7 μM; n = 1) and a secondary assay (tested at 24 or 8 μM; n = 3))\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\nAccession numbers\n\nProtein Data Bank:\n\n• Crystal structure of mouse Cryptochrome 1 in complex with TH401 compound. Accession number: 7WVA. https://doi.org/10.2210/pdb7WVA/pdb.\n\n• Crystal structure of mouse CRY1 with bound cryoprotectant. Accession number: 7D0M. https://doi.org/10.2210/pdb7D0M/pdb.\n\n• Crystal structure of mouse CRY2 apo form. Accession number: 7D0N. https://doi.org/10.2210/pdb7D0N/pdb.\n\n• Crystal Structure of Mouse Cryptochrome1 in Complex with Period2. Accession number: 4CT0. https://doi.org/10.2210/pdb4CT0/pdb.\n\n• Crystal Structure of Mammalian Period-Cryptochrome Complex. Accession number: 4U8H. https://doi.org/10.2210/pdb4U8H/pdb.\n\n• Crystal structure of mouse Cryptochrome 1 apo form. Accession number: 6KX4. https://doi.org/10.2210/pdb6KX4/pdb.",
"appendix": "Acknowledgements\n\nWe thank Natsuko Ono, Dr. Kaori Goto, Naoya Kadofusa, and Dr. Kazuya Hasegawa for technical assistance, Dr. Shinya Oishi for technical assistance and helpful discussion, and Dr. Hiroki R. Ueda for Cry1/Cry2 double knockout cells and pMU2-P (Cry1)-FLAG-I/RRE-Cry1 plasmid. X-ray diffraction data collection and preliminary experiments were carried out at beamlines BL41XU and BL44XU of SPring-8 synchrotron facility (proposals 2019A6942 and 2019B6942) and BL-17A of Photon Factory (proposal 2019G024). Recombinant CRY expression, beamline experiments, and supply of library compounds were supported in part by Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS) from Japan Agency for Medical Research and Development support numbers JP20am0101074-0055, JP20am0101071-0529, and JP22ama121034.\n\n\nReferences\n\nGreen CB, Takahashi JS, Bass J: The meter of metabolism. Cell 2008; 134: 728–742. PubMed Abstract | Publisher Full Text\n\nTakahashi JS: Transcriptional architecture of the mammalian circadian clock. Nat. Rev. Genet. 2017; 18: 164–179. PubMed Abstract | Publisher Full Text\n\nTakahashi JS, et al.: The genetics of mammalian circadian order and disorder: implications for physiology and disease. Nat. Rev. Genet. 2008; 9: 764–775. PubMed Abstract | Publisher Full Text\n\nChen Z, Yoo SH, Takahashi JS: Development and Therapeutic Potential of Small-Molecule Modulators of Circadian Systems. Annu. Rev. Pharmacol. Toxicol. 2018; 58: 231–252. PubMed Abstract | Publisher Full Text\n\nMiller S, Hirota T: Pharmacological Interventions to Circadian Clocks and Their Molecular Bases. J. Mol. Biol. 2020; 432: 3498–3514. PubMed Abstract | Publisher Full Text\n\nRasmussen ES, Takahashi JS, Green CB: Time to target the circadian clock for drug discovery. Trends Biochem. Sci. 2022; 47: 745–758. PubMed Abstract | Publisher Full Text\n\nHirota T, et al.: Identification of small molecule activators of cryptochrome. Science 2012; 337: 1094–1097. PubMed Abstract | Publisher Full Text\n\nLee JW, et al.: Development of Small-Molecule Cryptochrome Stabilizer Derivatives as Modulators of the Circadian Clock. ChemMedChem 2015; 10: 1489–1497. PubMed Abstract | Publisher Full Text\n\nOshima T, et al.: C-H activation generates period-shortening molecules that target cryptochrome in the mammalian circadian clock. Angew. Chem. Int. Ed. Engl. 2015; 54: 7193–7197. PubMed Abstract | Publisher Full Text\n\nHumphries PS, et al.: Carbazole-containing sulfonamides and sulfamides: Discovery of cryptochrome modulators as antidiabetic agents. Bioorg. Med. Chem. Lett. 2016; 26: 757–760. Publisher Full Text\n\nHumphries PS, et al.: Carbazole-containing amides and ureas: Discovery of cryptochrome modulators as antihyperglycemic agents. Bioorg. Med. Chem. Lett. 2018; 28: 293–297. PubMed Abstract | Publisher Full Text\n\nDong Z, et al.: Targeting Glioblastoma Stem Cells through Disruption of the Circadian Clock. Cancer Discov. 2019; 9: 1556–1573. PubMed Abstract | Publisher Full Text\n\nMiller S, et al.: Isoform-selective regulation of mammalian cryptochromes. Nat. Chem. Biol. 2020; 16: 676–685. PubMed Abstract | Publisher Full Text\n\nKolarski D, et al.: Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock. J. Am. Chem. Soc. 2021; 143: 2078–2087. PubMed Abstract | Publisher Full Text\n\nMiller S, et al.: An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals. Cell Chem. Biol. 2020; 27: 1192–1198.e5. PubMed Abstract | Publisher Full Text\n\nHirota T, et al.: A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3beta. Proc. Natl. Acad. Sci. U. S. A. 2008; 105: 20746–20751. PubMed Abstract | Publisher Full Text\n\nZhang EE, et al.: A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 2009; 139: 199–210. Publisher Full Text\n\nHatori M, Hirota T: Cell-Based Phenotypic Screens to Discover Circadian Clock-Modulating Compounds. Methods Mol. Biol. 2022; 2482: 95–104. PubMed Abstract | Publisher Full Text\n\nHirota T, et al.: High-throughput chemical screen identifies a novel potent modulator of cellular circadian rhythms and reveals CKIα as a clock regulatory kinase. PLoS Biol. 2010; 8: e1000559. PubMed Abstract | Publisher Full Text\n\nLiu AC, et al.: Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell 2007; 129: 605–616. PubMed Abstract | Publisher Full Text\n\nOde KL, et al.: Knockout-Rescue Embryonic Stem Cell-Derived Mouse Reveals Circadian-Period Control by Quality and Quantity of CRY1. Mol. Cell 2017; 65: 176–190. Publisher Full Text\n\nWinter G: xia2: an expert system for macromolecular crystallography data reduction. J. Appl. Crystallogr. 2010; 43: 186–190. Publisher Full Text\n\nEvans P: Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 2006; 62: 72–82. Publisher Full Text\n\nWinn MD, et al.: Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 2011; 67: 235–242. PubMed Abstract | Publisher Full Text\n\nMcCoy AJ, et al.: Phaser crystallographic software. J. Appl. Crystallogr. 2007; 40: 658–674. PubMed Abstract | Publisher Full Text\n\nCowtan K: Recent developments in classical density modification. Acta Crystallogr. D Biol. Crystallogr. 2010; 66: 470–478. PubMed Abstract | Publisher Full Text\n\nEmsley P, et al.: Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 2010; 66: 486–501. PubMed Abstract | Publisher Full Text\n\nMurshudov GN, et al.: REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 2011; 67: 355–367. PubMed Abstract | Publisher Full Text\n\nAfonine PV, et al.: Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr. 2012; 68: 352–367. PubMed Abstract | Publisher Full Text\n\nYagi M, et al.: Yagi et al. Figure data. Figshare 2022. Publisher Full Text\n\nYoo SH, et al.: PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues. Proc. Natl. Acad. Sci. U. S. A. 2004; 101: 5339–5346. PubMed Abstract | Publisher Full Text\n\nMartinez Molina D, et al.: Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay. Science 2013; 341: 84–87. PubMed Abstract | Publisher Full Text\n\nCzarna A, et al.: Structures of Drosophila cryptochrome and mouse cryptochrome1 provide insight into circadian function. Cell 2013; 153: 1394–1405. PubMed Abstract | Publisher Full Text\n\nMichael AK, et al.: Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proc. Natl. Acad. Sci. U. S. A. 2017; 114: 1560–1565. PubMed Abstract | Publisher Full Text\n\nMiller S, et al.: Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation. Proc. Natl. Acad. Sci. U. S. A. 2021; 118: e2026191118. PubMed Abstract | Publisher Full Text\n\nMiller S, Hirota T: Structural and Chemical Biology Approaches Reveal Isoform-Selective Mechanisms of Ligand Interactions in Mammalian Cryptochromes. Front. Physiol. 2022; 13: 837280. PubMed Abstract | Publisher Full Text\n\nGriffin EA Jr, Staknis D, Weitz CJ: Light-independent role of CRY1 and CRY2 in the mammalian circadian clock. Science 1999; 286: 768–771. PubMed Abstract | Publisher Full Text\n\nKhan SK, et al.: Identification of a novel cryptochrome differentiating domain required for feedback repression in circadian clock function. J. Biol. Chem. 2012; 287: 25917–25926. PubMed Abstract | Publisher Full Text\n\nRosensweig C, et al.: An evolutionary hotspot defines functional differences between CRYPTOCHROMES. Nat. Commun. 2018; 9: 1138. PubMed Abstract | Publisher Full Text\n\nFribourgh JL, et al.: Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. elife 2020; 9: e55275. PubMed Abstract | Publisher Full Text\n\nGanguly A, et al.: Changes in active site histidine hydrogen bonding trigger cryptochrome activation. Proc. Natl. Acad. Sci. U. S. A. 2016; 113: 10073–10078. Publisher Full Text\n\nChandrasekaran S, et al.: Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome. Commun. Biol. 2021; 4: 249. PubMed Abstract | Publisher Full Text\n\nLin C, et al.: Mechanistic insight into light-dependent recognition of Timeless by Drosophila Cryptochrome. Structure 2022; 30: 851–861.e5. PubMed Abstract | Publisher Full Text\n\nSchmalen I, et al.: Interaction of circadian clock proteins CRY1 and PER2 is modulated by zinc binding and disulfide bond formation. Cell 2014; 157: 1203–1215. PubMed Abstract | Publisher Full Text\n\nNangle SN, et al.: Molecular assembly of the period-cryptochrome circadian transcriptional repressor complex. elife 2014; 3: e03674. PubMed Abstract | Publisher Full Text\n\nChun SK, et al.: Identification and validation of cryptochrome inhibitors that modulate the molecular circadian clock. ACS Chem. Biol. 2014; 9: 703–710. PubMed Abstract | Publisher Full Text\n\nJeong YU, et al.: Development of Non-Ethoxypropanoic Acid Type Cryptochrome Inhibitors with Circadian Molecular Clock-Enhancing Activity by Bioisosteric Replacement. Pharmaceuticals (Basel) 2021; 14: 496. PubMed Abstract | Publisher Full Text\n\nGul S, et al.: Structure-based design and classifications of small molecules regulating the circadian rhythm period. Sci. Rep. 2021; 11: 18510. PubMed Abstract | Publisher Full Text\n\nKoike N, et al.: Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 2012; 338: 349–354. PubMed Abstract | Publisher Full Text\n\nZhang EE, et al.: Cryptochrome mediates circadian regulation of cAMP signaling and hepatic gluconeogenesis. Nat. Med. 2010; 16: 1152–1156. PubMed Abstract | Publisher Full Text\n\nLamia KA, et al.: Cryptochromes mediate rhythmic repression of the glucocorticoid receptor. Nature 2011; 480: 552–556. PubMed Abstract | Publisher Full Text\n\nHuber AL, et al.: CRY2 and FBXL3 Cooperatively Degrade c-MYC. Mol. Cell 2016; 64: 774–789. PubMed Abstract | Publisher Full Text\n\nChan AB, et al.: CRY2 missense mutations suppress P53 and enhance cell growth. Proc. Natl. Acad. Sci. U. S. A. 2021; 118: e2101416118. PubMed Abstract | Publisher Full Text\n\nShafi AA, et al.: The circadian cryptochrome, CRY1, is a pro-tumorigenic factor that rhythmically modulates DNA repair. Nat. Commun. 2021; 12: 401. PubMed Abstract | Publisher Full Text\n\nHirano A, et al.: A Cryptochrome 2 mutation yields advanced sleep phase in humans. elife 2016; 5: e16695. PubMed Abstract | Publisher Full Text\n\nPatke A, et al.: Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder. Cell 2017; 169: 203–215.e13. PubMed Abstract | Publisher Full Text\n\nIida M, et al.: Effects of cryptochrome-modulating compounds on circadian behavioural rhythms in zebrafish. J. Biochem. 2022; 171: 501–507. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "149802",
"date": "21 Sep 2022",
"name": "Eric Zhang",
"expertise": [
"Reviewer Expertise Circadian clock"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, Moeri Yagi and co-authors describe the characterization of a small molecule TH401 which stabilizes both isoforms of the clock protein Cryptochrome (CRY1 and CRY2) and lengthens the period of circadian rhythms in cellular models. The co-crystal structure of CRY1 in complex with TH401 was obtained and compared with the structure of CRY1 and CRY2, explaining the slight preference of TH401 to CRY2. Several TH401 derivatives were further tested for their period-lengthening activities, confirming the proposed mechanism of CRY-TH401 interaction. As a methylbenzimidazole derivative, TH401 provides a new scaffold for CRY modulators, which will not only enable a better understanding of the structure of CRY, but also contribute to the discovery of therapeutics against circadian clock-related diseases. In general, this manuscript is well-written, and I recommend its publication after a minor revision.\nSpecific comments:\nIn the first paragraph on page 9, the conclusion “the binding mode of TH401 appears less compatible with the FAD pocket in CRY1 than CRY2” is drawn before the structure of FAD pocket in CRY2 is elucidated, which is somehow confusing.\n\nIn the third paragraph on page 10, the authors state “To further characterize the CRY2-TH401 interaction…” at the beginning and “CRY2-TH401 interactions in the crystal structure are consistent with activity in cells” in the end. However, the experiments using Bmal1-dLuc U2OS cells can not reflect the interaction of TH401 derivatives with CRY1 and CRY2 separately. It might be better to change “CRY2-TH401” into “CRY-TH401”.\n\nAlthough several TH401 derivatives have been tested for their period-lengthening activities, no mutants of CRY1 or CRY2 were tested for their interactions with TH401. Rescue assay in Cry1/Cry2double knockout fibroblasts with CRY mutants carrying point mutations in TH401 binding residues may further confirm the proposed mechanism of CRY-TH401 interaction and is therefore recommended.\n\nThe hyphen should not be added between “small molecule” when it is used as a noun. This has appeared three times: “Although small-molecules that…” in Abstract, “…identified a new small-molecule TH401 that…” in Abstract and “…action of these small-molecules” in Conclusion.\n\nTable 1 legend: “R,m.s.” should be “R.m.s.”\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": "8840",
"date": "30 Sep 2022",
"name": "Tsuyoshi Hirota",
"role": "Author Response",
"response": "Reviewer #1: In this article, Moeri Yagi and co-authors describe the characterization of a small molecule TH401 which stabilizes both isoforms of the clock protein Cryptochrome (CRY1 and CRY2) and lengthens the period of circadian rhythms in cellular models. The co-crystal structure of CRY1 in complex with TH401 was obtained and compared with the structure of CRY1 and CRY2, explaining the slight preference of TH401 to CRY2. Several TH401 derivatives were further tested for their period-lengthening activities, confirming the proposed mechanism of CRY-TH401 interaction. As a methylbenzimidazole derivative, TH401 provides a new scaffold for CRY modulators, which will not only enable a better understanding of the structure of CRY, but also contribute to the discovery of therapeutics against circadian clock-related diseases. In general, this manuscript is well-written, and I recommend its publication after a minor revision. We thank the reviewer for the insightful comments. We are very pleased to hear that the reviewer recommends the publication of this manuscript. Our point-by-point responses are listed below. We believe that the changes have clarified our manuscript. Comment 1: In the first paragraph on page 9, the conclusion “the binding mode of TH401 appears less compatible with the FAD pocket in CRY1 than CRY2” is drawn before the structure of FAD pocket in CRY2 is elucidated, which is somehow confusing. We agree with the reviewer and modified the sentence to \"Overall, the binding mode of TH401 is not fully compatible with the intrinsic FAD pocket in CRY1-apo and induces conformational rearrangement of key pocket residues for a favorable interaction.\" Comment 2: In the third paragraph on page 10, the authors state “To further characterize the CRY2-TH401 interaction…” at the beginning and “CRY2-TH401 interactions in the crystal structure are consistent with activity in cells” in the end. However, the experiments using Bmal1-dLuc U2OS cells can not reflect the interaction of TH401 derivatives with CRY1 and CRY2 separately. It might be better to change “CRY2-TH401” into “CRY-TH401”. Thank you for raising this point. We changed “CRY2-TH401” to “CRY-TH401”. Comment 3: Although several TH401 derivatives have been tested for their period-lengthening activities, no mutants of CRY1 or CRY2 were tested for their interactions with TH401. Rescue assay in Cry1/Cry2double knockout fibroblasts with CRY mutants carrying point mutations in TH401 binding residues may further confirm the proposed mechanism of CRY-TH401 interaction and is therefore recommended. This is an interesting point that we would like to address in our future studies. Thank you for your suggestion. Comment 4: The hyphen should not be added between “small molecule” when it is used as a noun. This has appeared three times: “Although small-molecules that…” in Abstract, “…identified a new small-molecule TH401 that…” in Abstract and “…action of these small-molecules” in Conclusion. Thank you for pointing this out. We removed the hyphen. Comment 5: Table 1 legend: “R,m.s.” should be “R.m.s.” Thank you for pointing this out. It was fixed."
}
]
},
{
"id": "149801",
"date": "29 Sep 2022",
"name": "Katja A. Lamia",
"expertise": [
"Reviewer Expertise circadian biology",
"cryptochrome proteins"
],
"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\nMoeri Yagi and colleagues report the identification of a chemical stabilizer of CRY1 and CRY2 based on a methylbenzimidazole scaffold, which is different from the scaffolds of previously reported CRY-stabilizing compounds. They present well designed experiments that persuasively show that this compound, TH401, interacts directly with both CRY1 and CRY2 at their FAD-binding pockets and thereby leads to their stabilization and lengthening of circadian period in cells.\nI have one minor suggestions to improve clarity: In the introduction, the sentence “…compounds that control clock function provide a powerful and useful tool in the drug discovery of such diseases” is unclear. Do the authors mean “… compounds that control clock function provide a powerful and useful tool in drug discovery related to diseases that are impacted by circadian disruption”?\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": "8841",
"date": "30 Sep 2022",
"name": "Tsuyoshi Hirota",
"role": "Author Response",
"response": "Reviewer #2: Moeri Yagi and colleagues report the identification of a chemical stabilizer of CRY1 and CRY2 based on a methylbenzimidazole scaffold, which is different from the scaffolds of previously reported CRY-stabilizing compounds. They present well designed experiments that persuasively show that this compound, TH401, interacts directly with both CRY1 and CRY2 at their FAD-binding pockets and thereby leads to their stabilization and lengthening of circadian period in cells. I have one minor suggestions to improve clarity: In the introduction, the sentence “…compounds that control clock function provide a powerful and useful tool in the drug discovery of such diseases” is unclear. Do the authors mean “… compounds that control clock function provide a powerful and useful tool in drug discovery related to diseases that are impacted by circadian disruption”? We thank the reviewer for the insightful comment. We are very pleased to hear that the reviewer approved the publication of this manuscript. We agree with the reviewer and modified the sentence accordingly."
}
]
}
] | 1
|
https://f1000research.com/articles/11-1016
|
https://f1000research.com/articles/11-1012/v1
|
07 Sep 22
|
{
"type": "Research Article",
"title": "Study of the protective effects of cyanocobalamin on methotrexate induced nephrotoxicity in rats",
"authors": [
"Rana Q. Abdulwahhab",
"Samara Muwafaq Ali Alabdali",
"Samara Muwafaq Ali Alabdali"
],
"abstract": "Background: Methotrexate (MTX) is a chemotherapeutic drug, used mainly in many cancerous stages, inflammatory and auto-immune diseases, but its use has been limited by its nephrotoxicity. Cyanocobalamin is a water-soluble vitamin possessing nephro-protective properties. The aim of this study was to investigate the effect of cyanocobalamin on the nephrotoxicity of methotrexate. Methods: In the study 42 albino adult female rats were used, divided into six groups each containing seven rats (n=7). 1st group: Control group (Negative control), 7 rats were injected intraperitoneally with 0.5ml/kg/day NS. Second group: 7 rats were injected intraperitoneally with a single dose of methotrexate (20 mg/kg) for 4 days. Third Group: 7 rats were given intraperitoneally cyanocobalamin at a dose (1.5 mg/kg/day) for two weeks, fourth, fifth, sixth group: 7 rats from each group were injected intraperitoneally with different concentrations of cyanocobalamin (0.5, 1, 1.5 mg/kg /day), respectively, for two weeks and MTX (20 mg/kg), which was injected only on day 11. On day 15, rats from all groups were euthanized, and blood samples were taken for biochemical tests, including evaluating serum urea and creatinine. The kidneys were extracted for histological investigation and evaluation of antioxidant (GSH) and oxidative stress (MDA) by using kidney tissue homogenates. Results: This study revealed that kidney damage, produced by the MTX (group II), is manifested by significantly elevated (P<0.05) urea and creatinine. On the contrary, the cyanocobalamin groups (IV, V, VI) significantly (P<0.05) reduced urea and creatinine. Renal antioxidant defense systems, such as reduced glutathione depleted by MTX therapy, were restored to normal levels by cyanocobalamin. Furthermore, cyanocobalamin reduced oxidative stress (MDA) and histologically reduced renal tissue injury induced by MTX. Conclusions: In conclusion, the study revealed that cyanocobalamin has a nephroprotective action upon MTX-induced renal damage in rats; cyanocobalamin may offer a protective effect, such as antioxidant action.",
"keywords": [
"Methotrexate",
"nephrotoxicity",
"cyanocobalamin",
"antioxidants",
"rat",
"histopathology"
],
"content": "Introduction\n\nMethotrexate (MTX) is known as an antifolate drug and has been prescribed for over 60 years to treat different auto-immune disorders1 and numerous types of cancers, used in combination with other anticancer drugs2 and remains of great interest for researchers all over the world.2\n\nHowever, some adverse effects including nephrotoxicity triggered by MTX are severe, thus, assessment of effective drugs to overcome this problem are necessary.3\n\nMTX is one of the most common drugs induced nephrotoxicity, when used at high doses, having molecular features that favor crystal precipitation in the tubular lumens in a manner of slowing urine flow and decreasing urine pH.4,5\n\nResearchers reported that the mechanism of MTX inducing nephrotoxicity is as a result of oxidative damage by the formation of reactive oxygen species (ROS), then creating an imbalance between oxidants and antioxidants that are responsible for the adverse effect of MTX, such as nephrotoxicity.6\n\nHistologically in MTX–treated rats, kidneys showed: enlargement of Bowman capsule cavity, infiltration of lymphocytes, diminish of glomeruli size, an increase in blood cells count, and degeneration of tubules.7,8\n\nLike other drugs with nephrotoxic effects, MTX-induced renal function declination is clinically tested by observation of hematuria and deterioration in serum urea and creatinine level. Reproduction of such effects is done in research studies in animals after a single dose of MTX.9\n\nMany studies show that dietary antioxidants play a role in the protection of the kidney against MTX-induced nephrotoxicity.6\n\nCyanocobalamin is considered a synthetic compound of vitamin B12. Vitamin B12 is known as a water-soluble vitamin which is synthesized by microorganisms in nature, and in the chemical aspect it is related to a class known as corrinoids. This name is derived from the cyanide group that is attached to molecule.10\n\nVitamin B12 has several functions in methylation reactions in the body, acts as a cofactor in the form of methylcoblamin by the conversion of homocysteine to methionine and in the form of adenosylcobalamin in the transformation of methylmalonyl-CoA to succinyl-CoA. Both of these chemical reactions are important for cell division and growth,11 Vitamin B12 plays a role in erythropoiesis and healthy neurological functions,12 and it proved useful in the treatment of many diseases associated with inflammatory and oxidative stress.13\n\nThe FDA have stated that cyanocobalamin is safe, there is no toxicity reported when cyanocobalamin given to animals, even at several thousand times their nutritional requirements.14\n\nThe objective of this study is to determine the protective effects of cyanocobalamin administration on methotrexate-induced nephrotoxicity in rats using biochemical and histopathological studies in renal tissue of rats.\n\n\nMethods\n\nWe have received ethical approval for work on experimental animals from the Researcher Ethics Committees at Department of Pharmacology and College of Medicine/University of Baghdad. On 7 November 2021 via ethical letter (approval number 1455). This study is reported in line with the ARRIVE guidelines.40\n\nAll chemicals used in this experimental study were of the highest available purity, and no purification was necessary. Vitamin B12 GERDA (1000 mcg/4 ml) (GERDA®1000, batch: H060) was purchased from GERDA, France. Methotrexate ampule (50 mg/2 ml) Methotrexate Mylan 50 mg/2 ml (batch/LOT 5103) was purchased from Mylan – Merck generiques, Italy, pellet food patch number 3218 from Mazuri ® food pellets (Mazuri Primate Diet, Special Diet Foods Ltd., UK).\n\nThe study was carried out on 42 adult female albino rats. The sample size of n=7 per group was calculated based on previous research, inclusion criteria include (ages ranged from 2-3 months, sex: female and body weight ranged from 150-250 grams. In this study there were no exclusion criteria, the animals used were were obtained from the same source, at the same time, there is no previous procedure performed on these rats before the experimental study.\n\nThe rats were obtained from the Animal House of the Iraqi center of cancer and genetic research/Almustansria University. They remained for one week, to be adapted without intervention in a climate-controlled environment with appropriate temperature (22-25 c) and synthetic 12:12 hours in the light-dark cycle, rats received pellet food and tap water/ad libitum.\n\nThe human care of the animals was according to international guidelines for the care and use of laboratory animals, All of these efforts were made to reduce the number of rats and their suffering, These efforts included: 1. constant checking of animal house air conditioning with a standard free access to tap water/ad libitum; 2. cleaning the animal house and cages; 3. During the experimental careful handling and when given the dose of drug injection as quickly as possible and given the dose to each rat separated from other; 4. used the effective anesthetic dose.\n\nWhen the period of adaptation was over, the weight of the rats was recorded and they were randomly divided and placed in one cage per group, the name of the group was then recorded in each cage.\n\nIn total, 42 rats were randomly (simple randomization) divided into six group (n=7) All groups of animal, treated in the same house under same environment. The experimental procedure was done blindly, daily between 8 am -12 pm for 15 days.\n\nSix animal groups were made in this study (7 animals/each group) as follows:\n\nGroup I (control): 7 rats were treated with 0.5 ml normal saline once daily by intraperitoneal (I.P.) injection for 14 days and it was served as negative control.\n\nGroup II (MTX): 7 rats were treated with a single I.P. dose of methotrexate (MTX) (20 mg/kg) afterward, a single I.P. injection of 0.5 ml was administered. normal saline for 4 days. This group served as positive control.15\n\nGroup III (1.5 mg of vit b12): 7 rats were treated with vitamin B12 (1.5 mg/kg/rat/day) once daily by I.P. for two weeks.\n\nGroup IV (0.5 mg vit b12 +MTX): 7 rats were treated with vitamin B12 (0.5 mg/kg/rat/day)) once daily by I.P. for two weeks + 20 mg/kg I.P. of MTX injected only at day 11.16\n\nGroup V (1 mg vit b12 +MTX): 7 rats were treated with vitamin B12 (1 mg/kg/rat/day) once daily by I.P. for for two week + 20 mg/kg I.P. of MTX injected only at day 11.\n\nGroup VI (1.5 mg vit b12 +MTX): 7 rats were treated with vitamin B12 (1.5 mg/kg/rat/day) once daily by I.P.for two week + 20 mg/kg by I.P. of MTX injected only at day 11.16\n\nAt the end of this experiment on day 15 the rats were euthanized by the use of xylazine (10 mg/kg) and ketamine (75 mg/kg)17 both are commonly used for this purpose (this is following the ethical standards and ARRIVE guidelines and this type of euthanization is normally performed in most acute toxicity tests). Kidney tissue samples were taken for biochemical37 and histopathological studies.38\n\nAfter euthanasia of the animals, blood was collected by intracardiac puncture. The clot was isolated with a glass rod and then centrifuged (CGOLDENWALL 80-2 Electric Lab Centrifuge) at 3000 rpm for 15 minutes, and the supernatant was used to evaluate urea and creatinine as parameters of kidney function.37 The abdomen was cut with a scalpel blade, then the kidney was extracted and then stored in 10% formalin (Pan Reac APPliChem, Cat NO:A0877.100).\n\nA small portion of the kidney was cut and weighed on an electrical weighing scale (Redwag, model: AS220.R1). A sample of almost 0.4 gram weight was converted to homogenizer (Omni TH, Cat NO, 51-001) and mixed with 1 ml of ice cold phosphate buffered saline and centrifuged for 15 minutes at 5000 rpm. Subsequently, the resulting supernatant was isolated and stored at -20° C until used for the determination of the MDA and GSH biomarkers.37\n\nHistological examination of the kidneys\n\nHistopathological studies were performed, kidney tissue samples were fixed in 10% formalin, then graded in ethanol, dehydrated, and embedded in paraffin. Kidney sections were cut with a microtome (HHQ-1508R Rotary Microtome, China) set at a thickness of 3-4 μm; mounted on clear glass, then the kidney tissue was stained with Hematoxylin and Eosin (H&E). Then the kidney tissue sections were examined and evaluated by the histopathologist using light microscopy at 10× and 40× (Viola Mc 20i, Micros® Austria).18 An overall score of the severity of damage to kidney tissue was assessed in stained tissue sections by scoring each of the following histopathological observations as shown in Figure 1A. Congestion of glomeruli B. Congestion of interstitial C. Cast and degeneration D. Inflammatory cell infiltrate E. Increased urinary space F. Inflammation of the Pelvicalyceal area.\n\nWhere, 0=none (no damage); 1=mild; 2=moderate; 3=severe. A total of field of section was examined for all animals in each group19,38\n\nDetermination of serum creatinine and urea level\n\nThe quantitative assay of creatinine using the jaffe method was used. The quantitative assay of creatinine by the jaffe method is based on the reaction of creatinine with sodium picrate, and creatinine reacts with alkaline picrate forming a red-color complex. The intensity of the formed color is proportional to the creatinine concentration within the sample and the creatinine level can be calculated by measuring the absorbance at 490 nm.20 This method was performed using a creatinine kit (Cat. NO D500, Spinreact, Espana), while urea was measured quantitatively using the enzyme method described below,21 using a urea kit (Cat.NO p406, Spinreact, Espana).\n\nEnzymatic method\n\nQuantitative determination of serum urea by depend on enzymatic reaction in which the urea within the sample is hydrolyzed enzymatically into ammonia (NH4 +) and carbon dioxide (CO2). Ammonia ions formed reacts with α-ketoglutarate in a reaction catalyzed by glutamate dehydrogenase (GLDH) with simultaneous oxidation of NADH to NAD+:\n\nThe decrease in NADH concentration is proportional to the concentration of urea within the samples, and the level of urea can be calculated by measuring the absorbance at 340 nm. Calculation of urea (mg/dl) within serum samples = (∆A) Sample × 50 (Standard conc.) = mg/dL urea in the sample.\n\n\nDetermination of malondialdehyde (MDA) and reduced glutathione (GSH) within the kidney homogenate of the rat\n\nMalondialdehyde and reduced glutathione levels were measured by the enzyme-linked immunosorbent assay (ELISA) sandwich technique.22\n\nThe MDA content in the kidney tissue homogenate was quantitatively estimated by the MDA kit based on the ELISA method according to the manufacturer's instructions (Cat. No. E0156Ra, Bioassay Technology Laboratory, China) and Rat reduced glutathione ELISA kit (Cat. No E1443Ra, Bioassay technology laboratory, China), as written on the manufacturing protocol.\n\nThe content of MDA and GSH in kidney tissue homogenate samples can be measured by comparing the optical density of the samples, with the standard curve. Level of MDA is expressed as nmol/mL, and level of GSH is expressed in Ng/ml.\n\nWe prepared all reagents and chemicals tokit in the kit box (and stored at room temperature, then we were Add 40 μl sample to sample wells and then add 10 μl anti-MDA antibody to sample wells, then 50 μl streptavidin-HRP to sample wells. Then we mixed them well and Incubated 60 minutes at 37°C. We removed the sealer and cleaned the plate 5 times with wash buffer. Then the product was placed in automated washing (biotek® ELX 600-biotek Co. – USA), then we determined the absorption of the plate using Elisa reader equipment (biotek® ELX 600-biotek Co. – USA) the absorption is directly proportional to the concentration, which is then estimated by comparing the reading with the control group.\n\nThis was the same as the MDA procedure.\n\nData was expressed statistically as the mean±SEM, (standard error of mean) and the significance of the differences among various groups was decided by one-way analysis of variance (ANОVA), then by least significant difference (LSD) test. The statistical package for the social sciences (SPSS) version 26 was used. Differences were deemed statistically significant at the P-value less than 0.05 level.23\n\n\nResults\n\nA nonsignificant difference was observed between the cyanocobalamin (group III) and control groups (group I).37\n\nWhile the level of GSH in the renal tissue homogenate decreased significantly decreased (P<0.05) in both groups IV and V, it was highly significantly decreased in group VI compared to the group treated with MTX treated group (P<0.01) as shown in Figure 2.\n\nTable 1 and Figure 3 show that, compared to the control and cobalamin groups (I, III), the MDA level was significantly (P<0.05) elevated in the methotrexate group (II).\n\n* Highly significant difference from MTX P<0.01.\n\nNon-significant differences were detected among the cyanocobalamin (group III) and control groups (group I).\n\nAlthough MDA levels in renal tissue homogenate (P<0.05) significantly in the IV & V groups, and decreased significantly in group VI compared to the the MTX treated group (P<0.01).\n\nTable 2 and Figures 4 & 5 showed that the methotrexate-treated rat group (II) produced a significant elevation (p <0.05) of the plasma level of urea and creatinine, compared to the corresponding levels of the control group (I) and the cobalamin group (II).\n\n* Highly significant difference from MTX P<0.01.\n\nNon-significant difference (P>0.05) of the serum of urea and creatinine was found between the control group (I) and cobalamin group (III).\n\nRats treated with different concentrations of cyanocobalamins in group IV and group V produced significantly decreased serum urea and creatinine levels levels (P<0.05), while group VI produces highly significantly decreased serum urea levels compared to MTX-treated group II (P<0.01).\n\nHistopathological changes were examined to assist the finding of biochemical markers.38,39\n\nThe MTX –treated group (II) kidneys revealed obvious variations and injuries, characterized by severe congestion of both interstitial and glomeruli, moderate increased urinary space causing shrinkage in the glomerular size as shown in Figure 6B and a high number of hyaline casts in the medullary region with degeneration of tubules as shown in Figure 6C, severe inflammation of inflammatory cell infiltrate as shown in Figure 6D and pelvicalycial system as shown in the as shown in Figure 6E in the Extended data.39\n\nFurthermore, the cobalamins group (group III) show a normal glomerular cellularity (no congestion) and the urinary space is within normal limits. The interstitial does not show congestion; the tubule does not show degeneration and no inflammatory infiltrate as shown in Figure 7, similar to the control group (group I), which shows a normal looking cortex; the glomeruli have normal cellularity, no capillary congestion, the urinary space is not dilated; the interstitial does not show congestion, no inflammatory infiltrate, there is no tubular cell degeneration, and no casts. The pelvicalyceal system is not shown here, as shown in Figure 6A.\n\nGroup IV showed a moderate increase in urinary space, moderate congestion of the glomeruli and interstitial as shown in Figure 8A, a moderate amount of hyaline cast formation and degeneration as shown in Figure 8B, moderate inflammation of the pelvicalycial system Figure 8c, moderate infiltrate of inflammatory cells of the interstitial Figure 8d as shown in the Extended data.39\n\nGroup V showed a moderate increase in urinary space, moderate congestion of glomeruli and interstitial as shown in Figure 9A, moderate amount of hyaline cast in the tubular lumen and degeneration as shown in Figure 9B, moderate inflammation of the pelvicalycial system 9C, moderate inflammatory cell infiltrate of interstitial as shown in Figure 9D as shown in the Extended data.39\n\nFurthermore, in group VI there was a significant decrease in damage in all histopathological parameters compared to other groups (II, IV, and V), There is mild glomerular congestion and increased cellularity, the interstitial space also shows mild congestion and degeneration, mild increased urinary space as shown in Figure 10A, Few casts are seen within tubular lumens as shown in Figure 10B, mild inflammatory infiltrate in the pelvicalycial system as shown in Figure 10c, mild inflammatory cell infiltrate of the interstitial as shown in Figure 10d in the Extended data.39\n\n\nDiscussion\n\nThe renal system plays a vital role in maintaining extracellular environment homeostasis, mainly detoxification and elimination of toxic drugs and their metabolites. Nephrotoxicity related to toxic medications, especially chemotherapeutic drugs, is common and represents approximately 20% of all renal failure cases.24\n\nThis study focused on the protective effect of cyanocobalamin on MTX-induced renal damage in rats by reducing Cr and urea levels and repairing histopathological damage to the kidney.\n\nThe present data established that the activities of vit B12 against MTX-induced renal damage in rats could be successful by suppressing oxidative stress by reducing MDA levels and increasing GSH levels.\n\nThere were significant elevations in creatinine and urea levels in the MTX treated group (group II), compared to the levels in the the control rats (group I) and the the cyanocobalamin treated group (group III) (P<0.05).\n\nResearchers indicated the main pathway for MTX elimination by kidney. Furthermore, the administration of high doses of MTX causes higher drug concentrations in plasma and urine, at an acute and extremely toxic dose the elimination of MTX is delayed execution, then increases the serum creatinine level, and thus is one of the biomarkers of renal failure, this is consistent with the present study.25,26\n\nGroup IV, V, and VI resulted in a significant (P<0.05) reduction (P <0.05) in plasma urea and creatinine levels, compared to those levels in group II. That is consistent with the finding of Alshanwani et al.,24 which showed that vitamin B12 improved creatinine clearance levels and renal blood flow, thus, this can reduce creatinine and blood urea nitrogen.24\n\nIn the current study, a non-significant difference was found (p >0.05) within the content of MDA of kidney tissue homogenate among the control (group I) and cyanocobalamin (group III), which is in line with a previous animal study.13\n\nMTX treated rats (group II) demonstrated significant increases in MDA levels in group II, compared to control (group I) and cyanocobalamin (group III) which is consistent with previous studies.27,28\n\nIncreased levels of MDA in the methotrexate group might be related to oxidative stress, which likely stores the leukocyte in tissues by increased the level of ROS.29 Active leukocytes release many chemical enzymes, such as protease, elastase, and myeloperoxidase, resulting in more free radicals.\n\nIn addition, reactive oxygen species produce changes in permeability of both endothelial and epithelial cells. It can produce tissue injury, caused by MTX-prompted OS, by interfering with unsaturated form fatty acids of cell membranes, nucleic acid and sulfhydryl bonds. MTX therapy can indirectly secrete mitochondrial enzymes that lead to damaged mitochondria, and a decrease in antioxidant action.8\n\nIn this study, groups IV, V and VI produced a significant (P<0.05) reduction (P <0.05) in the level of MDA, compared to the group II treated with MTX.\n\nThese results are due to the antioxidant function of Cyanocobalamin by inducing the activity of methionine synthase, interacting with ROS, and avoiding glutathione.13,30\n\nGlutathione (GSH) is a non-enzymatic antioxidant; preserving reduced glutathione in the cell is essential to improve the immune system and protect the body from diseases.31,32\n\nGSH act as reducing agents that are important for conserving enzymes and antioxidants in the form of an active state. This mechanism is important to provide protection from cytotoxic agents, free radicals, and oxidative damage.33\n\nIn this study, the MTX group (group II) produced a significant reduction in the level of GSH, compared to the control group (group I) which is in line with a previous study.3\n\nThis result may be related to the mechanism of OS generation by MTX by inhibiting cellular NADPH (nicotinamide adenine dinucleotide phosphate). Through the pentose phosphate cycle, the glutathione reductase enzyme NADPH is used as a reducing agent for cellular GSH (primary antioxidant). The reduction of cellular GSH by MTX decreased the systemic antioxidant action.34\n\nGroup IV, V, and VI produced a significant (P<0.05) raise in GSH levels compared to those levels in groups II, these effects could be explained by the fact that cyanocobalamin has antioxidant properties consistent with the findings of Padmanabhan et al., which showed that supplementation with cyanocobalamin was confirmed by increased GSH, this institutes the main intracellular antioxidant and reduces oxidative stress.33\n\nHowever, histological analysis revealed that, unlike the control group (group I), the methotrexate group (group II) had destructive effects, where kidney sections of such rats showed moderate increased urinary space causing shrinkage in the glomerular size, forming a high number of hyaline casts in the medullary region, with degeneration of tubules, congestion of both interstitial and glomeruli. The glomerular show reduced cellularity, severe inflammation of the inflammatory cell infiltrate, and pelvicalyceal system. This is similar to the findings of other previous studies.7,8\n\nThe exact mechanism of MTX nephrotoxicity was unclear. However, some studies found that the main factor in MTX-related tissue injury was oxidative damage, with successive generation of more free radicals, the role of oxidative stress has been reported in MTX-induced nephrotoxicity.35\n\nMoreover, in groups IV, V and VI, there was a significant decrease in damage in all histological parameters (Expansion of bowman space, Congestion of glomeruli, Congestion of interstitial, Cast and degeneration, Inflammatory cell infiltrate, Inflammation of pelvicalycial system) (P<0.05), as compared to group II. These findings are similar to those of Saeed et al36; where the protective effect of vitamin B12 against nephrotoxicity was observed by histopathological examination.36\n\nThese results were considered an index of the defensive effect of cyanocobalamin on the kidney damaged by the methotrexate drug, the protective action of vitamin b12 has been previously reported in experimental studies.24\n\n\nConclusion\n\nThis study demonstrates the beneficial effects of cyanocobalamin on MTX-induced nephrotoxicity. Data suggest that the protective effect of cyanocobalamin is through the amelioration of oxidative markers (MDA) in kidney homogenate; the improvement of antioxidants (GSH), compensating for the increase in urea, creatinine, and the improvement of histopathological lesions of the kidney of rats. These results will make a new technique of protection from nephrotoxicity by MTX therapy, by administration of cyanocobalamin.\n\n\nData availability\n\nZenodo: Study in the protective effects of cyanocobalamin on Methotrexate induced Nephrotoxicity in rats. https://doi.org/10.5281/zenodo.6842130.37\n\nThis project contains the following underlying data:\n\n- Z.xlsx (biochemical test plasma of urea and creatinine, antioxidant enzyme (GHS) and oxidative stress marker (MDA))\n\nZenodo: Study in the protective effects of cyanocobalamin on Methotrexate induced Nephrotoxicity in rats. https://doi.org/10.5281/zenodo.6970347.38\n\nThis project contains the following underlying data:\n\n- Histopathological score.xlsx\n\nZenodo: Study in the protective effects of Cyanocobalamin on Methotrexate induced Nephrotoxcity in rats. https://doi.org/10.5281/zenodo.7008082.39\n\nThis project contains the following extended data:\n\n‐ Supplementary data.docx (histopathological images of kidney section of all six group (n=7))\n\n\nReporting guidelines\n\nZenodo: ARRIVE checklist for ‘Study in the protective effects of cyanocobalamin on Methotrexate induced nephrotoxicity in rats’. https://doi.org/10.5281/zenodo.6982116.40\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThe authors would like to thanks department of pharmacology/college of medicine, to providing facilities to bring this study and doctor Ban A. Abdul Majeed, consultant pathologist and PhD pharmacist Farah kais for assistance during the study.\n\n\nReferences\n\nKhudhair DH, Al-Gareeb AI, Al-Kuraishy HM, et al.: Combination of Vitamin C and Curcumin Safeguards against Methotrexate-Induced Acute Liver Injury in Mice by Synergistic Antioxidant Effects. Front. Med. 2022; 9. Publisher Full Text\n\nKoźmiński P, et al.: Overview of dual-acting drug methotrexate in different neurological diseases, autoimmune pathologies and cancers. Int. J. Mol. Sci. 2020; 21(10): 3483. PubMed Abstract | Publisher Full Text\n\nLi Y, et al.: Dioscin ameliorates methotrexate-induced liver and kidney damages via adjusting miRNA-145-5p-mediated oxidative stress. Free Radic. Biol. Med. 2021; 169: 99–109. PubMed Abstract | Publisher Full Text\n\nIzzedine H, Perazella MA: Anticancer drug-induced acute kidney injury. Kidney Int. Rep. 2017; 2(4): 504–514. PubMed Abstract | Publisher Full Text\n\nValade S, et al.: High-dose methotrexate in ICU patients: a retrospective study. Ann. Intensive Care. 2020; 10(1): 1–5. Publisher Full Text\n\nYuksel Y, et al.: Effects of quercetin on methotrexate-induced nephrotoxicity in rats. Hum. Exp. Toxicol. 2017; 36(1): 51–61. PubMed Abstract | Publisher Full Text\n\nAl-Rashidy AH, et al.: Role of erythropoietin in methotrexate-induced nephrotoxicity in adult male albino rats. J. Nephropharmacol. 2018; 7(2): 156–163. Publisher Full Text\n\nJalili C, et al.: Toxic effects of methotrexate on rat kidney recovered by crocin as a consequence of antioxidant activity and lipid peroxidation prevention. Iran. Biomed. J. 2020; 24(1): 39–46. PubMed Abstract | Publisher Full Text\n\nStojiljkovic N, et al.: The encapsulation of lycopene in nanoliposomes enhances its protective potential in methotrexate-induced kidney injury model. Oxidative Med. Cell. Longev. 2018; 2018: 1–11. PubMed Abstract | Publisher Full Text\n\nDerya K, Nurhan K, Emin K, et al.: Vitamin B12 Regulates the Expression of Methotrexate-Induced Increased Markers of Autophagy: An Immunohistochemical Study. Open Acc. J. Toxicol. 2021; 4(5): 555648.\n\nSinbad OO, et al.: Vitamins as antioxidants. J. Food Sci. Nutr. Res. 2019; 2(3): 214–235.\n\nGreibe E, et al.: Dietary intake of vitamin B12 is better for restoring a low B12 status than a daily high-dose vitamin pill: An experimental study in rats. Nutrients. 2018; 10(8): 1096. PubMed Abstract | Publisher Full Text\n\nHajihashemi S, et al.: Effects of cobalamin (Vitamin B12) on gentamicin induced nephrotoxicity in rat. Drug Res. 2017; 67(12): 710–718. PubMed Abstract | Publisher Full Text\n\nGabriele A, Alex B, Vasileios B, et al.: Scientific Opinion on safety and efficacy of vitamin B12 (cyanocobalamin) produced by Ensiferadhaerens when used as a feed additive for all animal species. EFSA J. 2015; 13: 1–21.\n\nYucel Y, Tabur S, Gozeneli O, et al.: The effects of lycopene on intestinal injury due to methotrexate in rats. Redox Rep. 2016; 21: 113–118. PubMed Abstract | Publisher Full Text\n\nSalah R, Salama MF, Mahgoub HA, et al.: Antitumor activity of sitagliptin and vitamin B12 on Ehrlich ascites carcinoma solid tumor in mice. J. Biochem. Mol. Toxicol. 2021; 35(2): e22645. PubMed Abstract | Publisher Full Text\n\nDabak DO, Kocaman N: Effects of silymarin on methotrexate-induced nephrotoxicity in rats. Ren. Fail. 2015; 37(4): 734–739. PubMed Abstract | Publisher Full Text\n\nAbd MR, Hassan AF: The Ameliorative Effect of Fimasartan against Methotrexate-Induced Nephrotoxicity in Rats. Iraqi J. Pharm. Sci. 2022; 31(1): 87–94.\n\nAbdul-Wahab FK, Al-Shawi NN: Effects of Vitamin D3 on Methotrexate-Induced Jejunum Damage in Rats. Iraqi J. Pharm. Sci. 2020; 29(1): 260–267. Publisher Full Text\n\nYoung DS: Effects of disease on clinical Lab. Tests. 4th ed.AACC;2001.\n\nUrea KA, Kaplan A, et al.: Clin Chem the C.V. Mosby Co. St Louis. Toronto. Princeton 1984; 1257-1260 and 437 and 418.\n\nDahniar S A’a, et al.: Effect of Brown Algae Extract Sargassum sp on Malondialdehyde Levels in White Rats (Rattus Norvegicus) Pregnant Wistar Strains. Medico Legal Update. 2020; 20(3): 822–827.\n\nRidha DK, Al-Shawi NN: The Impacts of Graded Doses of Pyridoxine on the Biomarkers, Aspartate Aminotransferase, lactate Dehydrogenase and Total Antioxidant Capacity in Doxorubicin-Induced Cardiotoxicity in Female Rats. Iraqi J. Pharm. Sci. 2017; 25: 12–21.\n\nAlshanwani AR, et al.: Cyanocobalamin and/or calcitriol mitigate renal damage-mediated by tamoxifen in rats: Implication of caspase-3/NF-κB signaling pathways. Life Sci. 2021; 277: 119512. Publisher Full Text\n\nOsman AT, et al.: Empagliflozin and neohesperidin protect against methotrexate-induced renal toxicity via suppression of oxidative stress and inflammation in male rats. Food Chem. Toxicol. 2021; 155: 112406. PubMed Abstract | Publisher Full Text\n\nPatel NN, et al.: Subacute toxicopathological studies of methotrexate in Wistar rats. Vet. World. 2014; 7(7): 489–495. Publisher Full Text\n\nAl-Abdaly YZ, et al.: Effect of methotrexate and aspirin interaction and its relationship to oxidative stress in rats. Iraqi J. Vet. Sci. 2021; 35(1): 151–156. Publisher Full Text\n\nMoodi H, et al.: Ethanolic extract of Iris songarica rhizome attenuates methotrexate-induced liver and kidney damages in rats. Avicenna J. Phytomed. 2020; 10(4): 372–383. PubMed Abstract\n\nSener G, Eksioğlu-Demiralp E, Cetiner M, et al.: Beta-glucan ameliorates methotrexate-induced oxidative organ injury via its antioxidant and immunomodulatory effects. Eur. J. Pharmacol. 2006; 542(1-3): 170–178. PubMed Abstract | Publisher Full Text\n\nSalah R, et al.: Antitumor activity of sitagliptin and vitamin B12 on Ehrlich ascites carcinoma solid tumor in mice. J. Biochem. Mol. Toxicol. 2021; 35(2): e22645. PubMed Abstract | Publisher Full Text\n\nBas Z: Inhibition effect of nicotinamide (vitamin B3) and reduced glutathione (GSH) peptide on angiotensin-converting enzyme activity purified from sheep kidney. Int. J. Biol. Macromol. 2021; 189: 65–71. PubMed Abstract | Publisher Full Text\n\nLucio C d F, et al.: Effect of reduced glutathione (GSH) in canine sperm cryopreservation: in vitro and in vivo evaluation. Cryobiology. 2016; 72(2): 135–140. PubMed Abstract | Publisher Full Text\n\nPadmanabhan S, et al.: Folate/vitamin B12 supplementation combats oxidative stress-associated carcinogenesis in a rat model of colon cancer. Nutr. Cancer. 2019; 71(1): 100–110. PubMed Abstract | Publisher Full Text\n\nGarcía-Sánchez A, Miranda-Díaz AG, Cardona-Muñoz EG: The role of oxidative stress in physiopathology and pharmacological treatment with pro-and antioxidant properties in chronic diseases. Oxidative Med. Cell. Longev. 2020; 2020: 1–16. PubMed Abstract | Publisher Full Text\n\nÇetin ES, et al.: Methotrexate-induced nephrotoxicity in rats: protective effect of mistletoe (Viscum album L.) extract. Complement. Med. Res. 2017; 24(6): 364–370. Publisher Full Text\n\nSaeed H, Zeinab H, Ali R, et al.: Effects of Cobalamin: 672017; Drug Res) on Gentamicin Induced Nephrotoxicity in Rat. 12(Vitamin B710-718.\n\nAbdulwahab RQ, Ali SM: Study in the protective effects of cyanocobalamin on Methotrexate induced Nephrotoxicity in rats. [Dataset].2022. Publisher Full Text\n\nAbdulwahab RQ, Ali SM: Study in the protective effects of cyanocobalamin on Methotrexate induced Nephrotoxicity in rats. [Dataset].2022.Reference Source\n\nAbdulwahab RQ: Study in the protective effects of Cyanocobalamin on Methotrexate induced Nephrotoxcity in rats.2022. Publisher Full Text\n\nAbdulwahab RQ: Study in the protective effects of cyanocobalamin on Methotrexate induced Nephrotoxicity in rats.2022. Publisher Full Text"
}
|
[
{
"id": "149805",
"date": "20 Sep 2022",
"name": "Hasan Alhaddad",
"expertise": [
"Reviewer Expertise Neuropharmacology and oncology."
],
"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 interesting manuscript studies the possible effect of cyanocobalamin to protect from methotrexate induced nephrotoxicity. Authors showed that cyanocobalamin protected rat kidneys from methotrexate toxicity through reduction of oxidative stress, increase GSH and reduction in lesions. This paper would be more valuable and interesting for readers if the authors revise the manuscript and address the following issues:\n1. The overall writing style of the paper needs more attention. I would recommend to improve the writing and correct some grammar and punctuation errors.\n2. The rationale for use of cyanocobalamin as a protective agent is not clear in the introduction. Is it utilized due to its antioxidant action? Please add some justification for why you chose this drug, i.e. add some previous studies that support its value as a possible protective agent.\n3. In the methods, group II treatment is not clear. Please rephrase the treatment paradigm for this group.\n4. The figures need more attention. Please make sure to have a unified x axis title. Please mention what the letters a, b, c, and d on the bars represent. Try to expand the figure legends to accurately describe the figure contents in details. Also, make sure to not cut part of the axis titles.\n5. Again, revise all the writing. Please make sure to not miss words, for example: Although MDA levels in renal tissue homogenate (P<0.05) significantly in the IV & V groups, and decreased significantly in group VI compared to the the MTX treated group (P<0.01); In this case, is the MDA levels in renal tissue is higher or lower compared to IV and V groups. Please revise all.\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": "8888",
"date": "13 Oct 2022",
"name": "rana qais",
"role": "Author Response",
"response": "Thank you Dr. Hasan for review of article, I made some change in the new version according to your notes. The answers to your notes: 1. I made changes to these issues. 2.In this study, vit B12 was selected due to antioxidant action, according to previous animal studies, in which vitamin B12 can lower oxidative stress when used with different drugs such as tamoxifen and gentamycin. Vit B12 act as antioxidant by different mechanism: as a direct superoxide scavenger; in addition, may indirectly enhance ROS scavenging by protecting glutathione, which probably involves a complex network of processes that is not yet fully understood 3. I rephrased (7 rats were treated with a single IP dose of methotrexate (MTX) (20 mg/kg) followed by single IP injection of 0.5ml normal saline for 4 days. This group was served as positive control). 4. I added this explanation (Values expressed in non-identical letters (a, b, c, d) are significantly difference (p<0.05). 5. The MDA significant decrease (P<0.05) in group IV, V and highly significant decreased in group VI compared to MTX treaded group II(P<0.01). I changed in the article (Although MDA levels in renal tissue homogenate (P<0.05) significantly decrease in the IV & V groups, and highly significant decrease in group VI compared to the MTX treated group (P<0.01)."
}
]
},
{
"id": "150890",
"date": "03 Oct 2022",
"name": "Israa Albanaa",
"expertise": [
"Reviewer Expertise Pharmacology and toxicology"
],
"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 did good lab work, but lack clarity and consistency of the work.\nThe citation is not accurate; the authors are citing the same paper which is under review.\nIn the results section, the presentation of the data is not clear, in particular the comparison between different groups. It would be better if the authors specify the compared group in the graphs so the reader can easily follow the results.\nThe discussion is not thorough; it would be more beneficial if they indicate the significance of the GSH and MDA so the reader could relate to the subject. I would recommend accepting the article after major corrections.\nPlease refer to the annotated pdf for additional notes, located here.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "8890",
"date": "12 Oct 2022",
"name": "rana qais",
"role": "Author Response",
"response": "Thank you Dr. Israa for review my article, I made changes according to the notes that you sent on pdf and made a new version of the article. About the (enzymatic method) section I wrote the procedure according to the journal instructions include the detail of the method used of the laboratory analysis. I moved the figure (1) to the result section. I changed the wrong references but the reference no 37,38,39 remain because these references include the data of result (data of GSH, MDA, urea and creatinine also the data of histopathological score and the other histological images) and refer to this data according to the journal instruction of and put this data on repository such as zenodo. I can’t change the method of comparing in the result section, I made it according to my supervisor in the study. I added some explanation on the MDA and GSH in the discussion section"
}
]
}
] | 1
|
https://f1000research.com/articles/11-1012
|
https://f1000research.com/articles/11-559/v1
|
23 May 22
|
{
"type": "Research Article",
"title": "Modelling computer assisted audit techniques (CAATs) in enhancing the Indonesian public sector",
"authors": [
"Pupung Purnamasari",
"Noor Afza Amran",
"Rudy Hartanto",
"Noor Afza Amran",
"Rudy Hartanto"
],
"abstract": "Background: This study aims to examine public sector auditors' tendency to use somputer assisted audit techniques (CAATs) in managing their audit works. Methods: A total of 400 questionnaires were distributed to auditors working in the public sectors in Central Java, West Java, and East Java. From the total, 225 questionnaires were returned and completed. The Structural Equation Modelling (SEM) and Partial Least Square (PLS) were used to analyze the data. Results: The empirical findings reveal that performance expectation and facilitating conditions have encouraged auditors to use CAATs in their works. Further, there is a positive influence between the intention to use and CAATs audit. This implies that auditors with an intention will be more open to using the CAATs optimally in achieving effective and efficient work. The utilization of CAATs in public services needs to have strong support from the government and positive attitudes from the auditors as the users of the system. Conclusion: This study covers broad areas of Central Java, West Java, and East Java. Further, the findings add to the literature on emerging markets specifically for Indonesian government auditors' intention and appropriateness of using CAATs. The use of CAATs help to provide auditors information on the highest number of auditees involved in corruption.",
"keywords": [
"Audit support",
"Effectiveness",
"Efficiency",
"Computer-assisted audit techniques (CAATs)",
"Public sector"
],
"content": "Introduction\n\nMany organizations prefer to use information technology to effectively develop and enhance their business.1 The use of information technology has also been an effective tool in increasing the quality of public services.2 In addition to its positive impact, such effective information technology in business, public, and private sectors can bring risks and new vulnerabilities in a fully automatic setting. With the use of a novel auditing method, such risk and vulnerability can be recognized, mitigated, and controlled.3 As a result, the development of the audit profession must keep abreast with the evolution of its surroundings.4 A new audit technique includes the use of computer-assisted tools and technologies.5 Examining auditors’ acceptance of the use of computer-assisted audit tools (CAATs) is significant because researchers and practitioners believe that using CAATs will improve an audit’s efficiency, effectiveness, and functionality.5–8\n\nCAATs are used by auditors in various nations, both internally and externally, in public and commercial sectors. CAATs have been used in the private sector to keep up with technological advancements in large corporations.5,9,10 The adoption of CAATs by public-sector auditors has coincided with the shift to information technology-based public-sector auditing, or what is known as e-government. The use of CAATs by auditors in public sectors has been in parallel with the change of information technology-based public service. E-Government refers to any government or institution’s use of information technology to modify how they communicate and interact with citizens, businesses, and other government entities.11\n\nCAATs is a model in inspecting as a course of study/discipline. In contrast to the old-style auditing in medium-sized practices, auditing in the information systems is yet in its primary stages.12 Nevertheless, the International Federation of Accountants (IFAC) has established the International Standards on Auditing (ISA).13 In most scenarios, the auditors are organized to assure the appropriateness and effectiveness of the inner controls executed in the information systems. Moreover, it can be concluded that the speedy variations in the technology have familiarized novel approaches on the required ways the assessment should conduct. Consequently, the former-style audit functions have been challenged by the information system’s usage.13\n\nMoreover, the constantly developing technology has made implementing the audit functions through typical auditing techniques complicated for the assessors.14 The audit’s focus must be shifted from manual recognition to technology-based prevention.15 Many well-established devices have been designed to help the auditors in accomplishing the auditing purposes. Such as the CAATs were proposed for assisting the auditors with the auditing tasks on screening accountancy data. The auditors employed Generalized Audit Software (GAS) for scrutinizing and auditing live or mined info from an extensive stream of applications.16 The software further involves multiple tools allowing the data mining from a customer’s system and examining that data; arithmetical examination, and audit practiced organizations.16,17\n\nThe situation is definite that to empower auditors to subject best accounting data and make simultaneous decisions, have and depend on quality information and exist on the web. Analysts in this area ensure that continuous information is fundamental for precision results in the inspecting space. At the point when reviewers acquire electronic information, they can deal with it all the more deftly.16 This information is without a doubt open; adaptable; it is saved, consolidated, and coordinated in a way better compared to paper-based bookkeeping information. Journalists in the inspecting area proposed that information advancements drive firms to do their exchanges electronically. They will actually want to give their budget reports electronically and online through the ongoing framework. At the latest occasions and under the umbrella of the constant bookkeeping real-time auditing (RTA) frameworks, monetary information might be handled electronically just as having review proof accessible in an electric structure. This necessary organizations to supplant their term paper and customary archives with automatic ones, including orders for buying; solicitations; and checks.18 Evaluating Practice Regulation 1009 “PC Assisted Audit Techniques” (CAATs) is created dependent on the International Auditing Practice Regulation “PC Assisted Audit Techniques” was endorsed by the International Federation of Accountants (IFAC) in the 2001 version.19 Evaluating companies and inspecting experts have presented various CAATs. These methods have been better-quality to help evaluators, completing their inspecting drives relying upon mechanized bookkeeping data. The idea of modernized bookkeeping data frameworks has discovered its direction into the universe of bookkeeping accordingly. The most critical and broadly utilized CAATs in electronic evaluation is Generalized Audit Software, truncated as (GAS) (Singleton and CISA, 2006). Inspectors use GAS to investigate and review live or separate information from an extensive scope of utilizations.16\n\nThe CAATs systems offer multiple possibilities. It has employed the computer in place of an auditing tool to increase the auditing method’s usefulness and productivity.20 The purpose of the following research is to observe the effects of computer-assisted audit tools on the establishment of auditing approaches by the auditor’s performance expectations. The study gives an overview of the CAATs technology usage and implications. The possible reason that the auditors started considering CAATs might be the determining resource issue and the distinctive operator perceptions. Previous information system studies signify that even after the availability of enough resources for purchasing IT, the users might not use the new one.21 Information system studies have established multiple samples for predicting the auditor’s IT consideration.\n\nThe utilization of CAATs by inward reviewers is not new; however it has developed after some time as the expansion of data innovation utilization has created in organizations.22 The unavoidable idea of data innovation, the ideal monetary and functional adaptability of present-day figuring innovation, and the internationally open and cutthroat a publicise influences that drive the pace of innovative development are together making a period of significant change in the commercial center for review robotization.23–25 While reviewers have been somewhat effective in utilizing existing advances to robotize components of their capacities, the organizations they work with are likewise going through critical change themselves.26 Numerous associations have picked to use refined data advances for fostering their business cycle support, just as working on their data handling exercises.22 This expands the requirement for CAATs in such organizations to permit examiners to keep on having the option to play out their audit and observing assignments successfully, just as to assume essential parts during the time spent developing in these organizations all the more by and large.\n\nA large number of these commercial environment alterations are having a solid effect on the advancement of the inner and outer review and affirmation trade.27,28 Inspectors’ strategies must keep up with the auditee business’s administration, and detailing variations to guarantee the viability and efficiencies of the review capacity can be kept up. More extensive utilization of CAATs has been generally promoted as a significant reaction to these changes.16,29 A large number of scholarly investigations have been led that expression to aid more vast conception of the problems of CAATs reception – less still that especially center around their reception by interior evaluators.18,30 Accordingly, there is the circumstance for additional investigations to be embraced to give a superior the inspirational comprehension and requirements on the utilization of CAATs in inner review offices. This exploration endeavors to deliver further knowledge on these issuers by and large.\n\nCAATs are thought to minimize audit expenses, improve audit characteristics and efficiency, support suitable reports of the auditing, and increase audit efficiency for auditors and firms that use them.6,31,32 Despite its merits, auditors do not use it regularly or constantly for either external auditors5,16,33,34 or public sector auditors.35 This is owing to the fact that there are only a few advantages of adopting CAATs for a small number of clients.33\n\nThe International Organization of Supreme Audit Institutions (INTOSAI) began to produce a guidance book on using audit information technology in 2014 for the government audit board in the context of the use of CAATs in public or governmental sectors. After that, INTOSAI, of which Indonesia is a member, has developed the CAATs. As the government audit board in Indonesia is known as the Indonesian Audit Board (BPK), has established four types of CAATs systems for the audit process, which are: Audit Management System (SMP), Audit Application System (SIAP), E-audit, and Follow-up Monitoring Information System (SIPTL).\n\nAn established system’s availability has encouraged Indonesian government auditors to adopt the newest or most recent audit technique known as CAATs. However, several studies have found the inclination in the acceptance of CAATs,12,36,37 as well as a low level of the use of CAATs by auditors.33,38,39 In light of these circumstances, the objective of this study is to examine how effective CAATs are in assisting BPK auditors in doing their audit works in Indonesian public services. This study employed a model for predicting information technology adoption, namely, the use of technology acceptance and use of technology (UTAUT).40 A novel technology, Unified Theory of Acceptance and Use of Technology (UTAUT) combines numerous formerly accepted samples to measure the acceptance probability of novel technologies. Acknowledging the factors responsible for the acceptance enables the examiners and audit firm administration to perceptively develop involvements aimed at the auditors who are unlikely to accept and employ novel systems. As per the UTAUT, four aspects effects user acceptance: (1) the user’s expectancy of a system to enhance their performance, (2) the efforts required to function the new structure, (3) the feedback of the structure by the worker’s trusted sources (e.g., societal impact), and lastly (4) the user’s expectancy about the presence of a technical and organizational set-up, supporting the system’s use (e.g., service settings).\n\nUTAUT combines many formerly established models for determining the probability of success when implementing fresh technologies. The adoption trigger allows researchers and audit firm management to plan proactive interventions (such as training and marketing) for auditors who are less inclined to embrace and use a new system.40 The CAATs involve technologies like electronic audit-working papers, applications of the dataset, as well as business intelligence audit software.5,29,41 Despite the CAATs significance in decreasing the cost of an audit, enhancing the value and efficiency of audit,42,43 and their broad use in advanced states,43 the CAATs is yet not used commonly in the evolving countries.44,45 The reason for such limited acceptance of CAATs is the audits that are conducted unproductively, or even worst, requiring quality. An investigation on the limitation of CAATs acceptance in such framework is required. Even though the study on CAATs and further technology’s acceptance have concentrated on the organizational aspects (i.e., size of the firms, IT capability of employees, and top administration commitment) and atmospheric aspects (i.e., competitive burdens), however, such elements exclude crucial atmospheric variables which are exclusive for CAATs acceptance.46,47 The CAATs acceptance is diverse compared to the other technological acceptance typically seen in specific businesses such as industrial and marketing. Three aspects are exclusive for the outer auditing atmosphere: customer’s AISb environment’s complication, the competence pressure from the other auditing firms for CAATs acceptance, and lastly, the degree of support from the qualified accounting organizations for CAATs acceptance. Primarily, customers having the complicated AIS are more expected to appoint bigger audit firms with the ability and enough investments in IT resources and knowledge.48 The competitive pressure for CAATs acceptance is even complicated as compared to other industries. Audit firms confront increased pressure for meeting their financial plans, the need to collect enough verifications, and offer a competitive audit within their assigned budget and time.48 Finally, Professional Accounting Bodies (PABs) control the audit industry, which performs a key part to impact audit firms for the acceptance of CAATs. As per the previous studies on technological acceptance, the central purpose of the following study is to analyze within an evolving state context if the organizational and atmospheric aspects exclusive to CAATs have any impact on the CAATs acceptance across audit firms.\n\n\nLiterature review\n\nThe use of information technology (IT) has gained much attention in many organizations in recent years. This enlightened that computers and information systems become a necessity for business to complete their daily tasks. With the use of technology, businesses have evolved to collect and disclose their financial data. This helps organizations spend less time in paper-based presentation of their financial data and spend more time on their firms’ performance.49 Consequently, many businesses are now attentive towards e-business (electronic business) and investing in complex IT software.50 Various researches emphasize explicitly PC-based audit support networks. For instance, Mansour50 recorded the effect of innovation on review arranging in five huge audit firms and stated that innovation could be utilized to give customers direct internal controls that help the inspector recognize the defects in the client’s frameworks. He additionally found that innovation is helpful for breaking down the client’s business measures, decide and survey the degree of controls, and prescribe tests that should be performed. Moreover, innovation ensures consistency with review principles and other review-related guidelines. Bierstaker, Burnaby51 portrayed the utilization of innovation on the review cycle by talking to IT experts from four of the five biggest US bookkeeping firms. Bierstaker, Burnaby51 studies were graphic in nature and zeroed in on a particular audit application from one audit firm; consequently, the two examinations are not generalizable to the external auditor’s actual utilization of innovation. The examined auditors’ view of the significance of CAATs and the degree of CAATs use. They additionally analyzed how the apparent significance and degree of IT use vary by firm size and over the long run. They discovered firm size had been displayed to be critical in deciding CAATs utilization. Auditors from Big 4 firms (the leading players in the accountancy industry, with their services spanning advisory, audit and assurance, tax, risk consulting and management consulting, and capital and transaction management) were almost certain that more modest firms to utilize IT review applications. The investigation likewise discovered that the hole between IT use for Big 4 and Non-Big 4 firms has been shutting contrasted with the 2004 information. The Non-Big 4 firms’ CAATs utilization nearly looked like that of the Big 4 firms.43 Earlier CAATs learns at the singular level utilized the Technology Acceptance Model (TAM) and Unified Theory of Acceptance, furthermore, Use of Technology (UTAUT) hypothesis. These hypotheses center around innovation trademark factors like performance expectancy, social impact, working with conditions, and perceived usefulness.28,52\n\nStudies have analyzed the aspects affecting the acceptance of CAATs. The previous studies on CAATs discover its acceptance from the specific level of auditors but not among the audit firms from the organizational perspective. The adoption of CAATs should initiate from an organization’s choice to obtain the technology, invest fundamentally, and offer the services for acceptance for individual auditor’s use. Hence, the firm’s degree of audit technology investment might adequately denote audit technology adoption instead of the individual auditor’s viewpoints.5 Just few studies have examined CAATs’ acceptance from the organizational point. Ismail and Abidin53 described the outcomes of the descriptive analysis regarding IT knowledge and the significance of audit technology across Malaysian audit firms. Ramen, Jugurnath1 postulated several aspects influencing the CAATs acceptance and analyzed the association and the major differences among the individual and organizational-standard aspects. A qualitative study was conducted to discuss the elements capable of influencing the CAATs and recognized Prescribed Accountancy Body (PAB) support as one of them. The auditor’s identification of the CAATs significance and the degree of CAATs usage was investigated by.43 It was also inspected that in which ways the recognized cruciality and scope of IT usage differs from the size of the firm and time. The observation revealed that it was the firm’s size that is vital in considering CAATs use. The auditors from the Big 4 firms were most likely to employ the IT audit applications. The research also revealed that the gap between IT usage for the Big 4 and Non-Big 4 firms was filling, as per the former information. The earlier individual-level CAATs studies have utilized TAM and the UTAUT model. The theories concentrate on the technology features, such as performance expectations, societal impacts, service-providing situations, and recognized practicality.53,54 The majority of the studies analyzed if the variables in the present UTAUT theoretical context might be implemented to CAATs acceptance in the exterior assessment settings.5,55\n\nUTAUT is a basic theory that can be used to determine e-audit or electornic audit acceptance by individual auditors, which can impact an organization’s technological acceptance. Venkatesh, Morris40 initially proposed UTAUT, which contains four essential predictors of intention and usage: performance expectancy, effort expectancy, social influence, and facilitating condition. Furthermore, UTAUT is a theory that takes genders, age, and experiences into account.40 The use of information technology in the form of an application would be more readily accepted by its users, even if the UTAUT model assumes that auditors, particularly those who have received training on the use of information technology, will be more likely to use Computer Assisted Audit Techniques (CAATs) if it is simple to use.34,56\n\nE-Audit is a technology-based information system that allows auditors to commit to their auditing tasks easily. The usage of E-Audit or CAATs has been widely used in the private sector in several nations. CAATs are used to combat and detect fraudulent activity and dangers.57 The e-Audit system model can be applied through a specific electronic audit program and information technology tools. According to Liang, Lin,58 the Internet’s massive rise has prompted the development of various modern information technologies, including object-oriented middlewares, Internet security technology, and smart agents. Computer-Assisted Audit Techniques (CAAT) can be employed more successfully with information technology that emerges from a new approach to Electronic Data Processing (EDP) audits. Shaikh59 proposed using CAAT, which is built on an electronic audit framework that incorporates most of the present capabilities of audit software but can be designed and distributed independently of the EDP auditors. CAAT, according to Zhao, Yen,6 is required to conduct ongoing audits in the electronic audit process. Because the auditor is a significant actor who has access to the party’s database being audited, the auditor’s capacity and competency are required.\n\nThe usage of e-audit was included in BPK’s strategic planning (Renstra) for 2011 to 2014 as the first step in establishing CAATs. The four major components of the e-audit implementation are BPK’s internal information system (e-BPK), BPK’s data warehouse (BPK data warehouse), BPK’s center of access and analysis (BPK Command Centre), and BPK’s internal information system (e-BPK). For BPK, e-audit can be utilized as an early warning system in the event of fraud in public finance management, which will eventually inspire accountability in managing state finances.60 Auditors should keep pace electronically with their customers. Customers need help in introducing and overhauling their endeavour-wide registering stages. Respondents show that it takes a few years for an organization to totally move their old programming to big business-wide figuring stages regularly. In these circumstances, examiners should work with their customers to guarantee that all controls and execution measures expected to assess every business interaction are set up.51 As examining programming is coordinated into the review interaction, evaluators will have more opportunities to resolve their customers’ perplexing issues in the worldwide commercial center. Customer, the board, should foster techniques that fuse the organization’s targets and objectives into execution estimates that can rapidly feature when an interaction is not performing up to norms. Evaluators can utilize CAATs in creating quantifiable targets and execution markers that enterprise wide processing frameworks can serve to electronically screen.\n\nHow much somebody accepts that taking on a specific apparatus would assist him with accomplishing more prominent importance is referred to as Performance expectancy.40,61 Execution hope insinuates the degrees to which an individual acknowledges that using the device can accomplish work execution gains.40 According to Jakšić62 and Saygili,63 commentators who acknowledge that the gathering of CAATs might overhaul their audit convenience and the idea of survey work ought to have uplifting objectives to take on the advancement. They moreover found that the audit specialists’ dynamic communication was updated by electronic demonstration of accounting information.64 Plus, analysts’ conviction that using CAATs will chip away at coordinating audit preliminaries of controls and impressive testing will likely have significant standards to accept CAATs as shown by Bedard, Jackson65 and Loraas and Wolfe.66 Withstanding these benefits, the researcher acknowledges that analysts’ perspective on the support and productivity they desire to gain from using CAATs in their assessing space will quite affect the assumption to embrace and use them. Execution anticipation alludes to the degree to which an individual accepts that utilizing the device can support accomplish gains in work execution.40 Banker, Chang64 found that utilizing CAATs in large review firms diminishes the review time required for working paper arrangement. They likewise tracked down that the review experts’ dynamic interaction was upgraded by the electronic show of bookkeeping data.64 Besides, examiners’ conviction that utilizing CAATs will work on the productivity of leading review trial of controls and meaningful testing is probably going to have high aims to embrace CAATs as indicated by65 and Loraas and Wolfe.66 Withstanding these advantages, the specialist accepts that examiners’ impression of the convenience and usefulness they hope to acquire from utilizing CAATs in their reviewing area will certainly impact the expectation to take on and use them. In summation, the past research demonstrates that the effect of IT on the review cycle has been huge in numerous ways. This adds to the improvement of the audit interaction.31,41\n\nFor example, an auditor might feel that utilizing CAATs will help him fulfill his audit time budget because it minimizes the number of hours spent on substantive testing and controlling, which will lead to an increase in audit time efficiency.5 Many studies show that the use of General Audit Software (GAS) by internal auditors,29,67 external auditors,9,50 and legal auditors68 is influenced by performance expectancy. Based on the following studies, it is hypothesized that:\n\nH1=Performance expectancy influences the intention to use CAATs.\n\nEffort expectancy refers to ‘the ease level related to the use of tools’.40 Janvrin, Bierstaker5 illustrated how comfortable those auditors who have received training are using CAATs. Hoque, Saif56 also found that users can accept an application if it is easy to use. Research by68 showed that effort expectancy influences the use of CAATs by legal auditors. Venkatesh, Morris40 contend that effort expectancy is relied upon to be more notable in the beginning phases of another conduct when interaction issues address obstacles to survive and later become superseded by instrumentality concerns. Payne and Curtis34 note that since inspectors may settle on the choice to take on innovation and be answerable for carrying out the innovation, the work associated with innovation reception might be more notable to evaluators than to other IT experts. Hence, Payne and Curtis34 contend that work hope will be related to a social goal. Furthermore, a study by67 revealed that the expectation of work also influences the use of CAATs by internal auditors. The second hypothesis presumed that:\n\nH2=The effort expectancy influences the intention of using CAAT’s.\n\nSocial influence can be defined as ‘the extent to which someone perceives the importance of others to use the new tool.40 In the context of an audit, this study expects the extent to which auditors perceive their direct managers’ support the use of CAATs can influence whether they adopt CAATs or not.5 The earlier examination has demonstrated that social influence affects the client’s aim to acknowledge and use an innovation.69,70 In a review setting, we expect that the more noteworthy examiners see that their immediate administrators support CAATs utilization, the more certain inspectors are to take on CAATs. Loraas and Wolfe66 find that help from companions and support from managers decidedly impacts social aim. Hence, we foresee that social impact will positively influence CAATs use. Several studies have reported that the use of General Auditing Software (GAS) by external auditors is influenced by social influence.1 Based on past studies, this study hypothesized that:\n\nH3=Social influence affects the intention of using CAATs.\n\nFacilitating condition is defined as ‘the extent to which people believe that the existing organizations have infrastructure and technique to support the use of tools’.40 In the context of the Indonesian public sector of auditing, infrastructures may involve Kantor Akuntan Publik (KAP) providing services based on human resources of CAATs and the support of computers for staff such as special instructions, support center, hotline, and the use of guidance.71 Many studies have demonstrated that the use of General Auditing Software by internal auditors,29 external auditors,1,9,50 and legal auditors68 are influenced by the facilitating condition. Therefore, based on the above arguments, this study hypothesized that:\n\nH4=Facilitating condition influences the appropriate use of CAATs.\n\nThe intention of usage\n\nIndividual motivation to do an activity is captured by intention.72 Despite the fact that various circumstances influence how auditors want to utilize auditing support systems, the theory of planned behavior suggests that auditors who want to use the system properly will be more likely to do so.72 Ajzen72 showed that business intelligence (BI) is the most general indicator of conduct and is proposed to be a predecessor of genuine use. UTAUT’s goal to embrace and utilize CAATs is the reliant variable in the exploration model and is an element of execution anticipation, exertion, hope, social impact, and working with conditions.21,73 This build puts the first ‘goal to utilize’ develop in the CAATs’ setting. Furthermore,74 found that purpose and external factors influence the optimal usage of supporting auditing systems. Thus, the following hypothesis presumed that:\n\nH5=Intention of using CAATs influences the use of appropriate use of CAATs.\n\nModeration model of CAATs acceptance\n\nAdditionally, Curtis and Payne32 discovered that the budget period’s variables and the risk priorities of auditors substantially impact the intention of using CAATs in the UTAUT. The majority of the following researches were conducted in technologically advanced states, whose assessment set-up might be distinct from the evolving states (Greenstein-Prosch et al., 2008). Such as the US setting, where the audit firms are parted among the Big 4, national, local, and regional firms. Whereas in Malaysia, apart from the Big-4 and middle-sized regional and national firms, the majority of the audit firms are individual administrators or contains fewer than five local-based associates.75 Hence, the audit firms of Malaysia are likely to be partitioned into the ones focusing on the national or local extent.\n\nBesides, the former studies have limitations since just the technologically featuring aspects were determined there, leaving the atmospheric and organizational impacts untouched. The Technology-Organization-Environment (TOE) context was utilized to remove those limitations, allowing the investigators to scrutinize multiple elements associated with technology, organizations, and the environment.76 Tornatzky, Fleischer76 established the TOE, an acceptance context at the firms-level. The TOE projected the significance of several relevant aspects in adopting novel technologies. The TOE context is largely used in the IT or IS works and is utilized in considering the acceptance characteristics in many IT frameworks. This context is also suitable for studying CAATs acceptance as it ranges over the technological models for involving the standpoints of organizations and the environment.77 However, a query about the range over which the variables might impact CAATs acceptance rises here. Therefore, a CAATs acceptance paradigm was proposed to combine the technical aspects of Diffusion of Innovation (DOI) theory to involve the elements of organization and environment.\n\nThe profile of auditees has an impact on auditors’ acceptance of audits. Age, gender, and experience are the elements contained in the profile of an auditee. The term “age” refers to a person’s chronological age as measured in years. A Bachelor’s degree was found to have a direct, significant, and moderate effect on age on user behavior and adoption.40,73,78 The sexual classifications of users, both males, and females are referred to as gender. Gender was found to substantially impact technology adoption in businesses in previous research by Venkatesh, Morris.40 Gender moderates the effect of believed benefits on behavioral intention. The number of years that an auditing firm has been in operation is referred to as experience. Previous behavior is influenced by previous experiences.72 Evidence has revealed that prior familiarity or experience with an existing system can assist employees in adjusting to a new similar approach in the workplace.79,80 Thus, the auditor’s information technology experience is taken into account in this study. Like Bierstaker, Janvrin9 and Mahzan and Lymer,29 we discover proof supporting the thought that working with condition emphatically impacts the inward evaluators’ expectations to utilize and acknowledge CAATs. The outcome recommends that organizations ought to put sufficient cash in cutting edge foundation to relieve the hindrance of inspectors from tolerating and using CAATs. Besides, firms might expand CAATs use however growing new arrangements in regards to recruiting and advancement of examiners. These arrangements ought to devote more weight to inspector’s capacity to utilize information examination in their everyday review exercises.\n\n\nMethods\n\nThis study was approved by Universitas Islam Bandung Ethical Clearance Commite (Protocol Number 718/B.04/Bak-k/XII/2020) after due consultation, consent letter had been provided by the researchers to all respondents. Respondents had provided their consent without any force from anyone. Subsequently, in order to protect the rights and privacy of the respondents, all forms of data were acquired will remain confidential. Written, informed consent was obtained from participants.\n\nA quantitative study using a survey method94 has been utilized in this study. Questionnaires were distributed from Juny 2021 to September 2021 to the targeted respondents, BPK personnel, who worked as auditors in the Indonesian public sectors using an online survey. There were 3600 auditors located in the central and regional offices of Indonesia. The criteria used to select the location sites were based on those offices with a significant number of corruption cases and auditees. A total of 400 questionnaires model e-audit were distributed to the targeted respondents. From the 400, 225 surveys were returned and completed. This study combines both studies by Venkatesh, Morris40 on technology adoption and Dowling74 on the use of the system to help do audit works.\n\nThe UTAUT model usage from Venkatesh, Morris40 was adopted in this study because it combines several models that predict technology usage, including TAM,21 planned behavior theory,72,81 the idea of innovation diffusion,82 and the theory of social cognitive learning.82,83 Furthermore, the UTAUT model has explained 70 percent of the intention variants to use technology and outperform each high-level model.40 The definition for each of the constructs is listed in Table 1. Table 1 is a summary table made by researchers based on several previous studies.\n\nThe criteria for respondents in this study were auditors who work at the central and regional offices with a high number of auditees and a high level of corruption cases. BPK’s regional offices or representations include BPK’s Central Java, West Java, and East Java. Regional office with low cases and with a low number of auditees not include the criteria of respondents. The final sample consists of 225 respondents who were the auditors working in the public sector of Indonesia. The distribution of respondents are depicted in Table 2, with the majority of the respondents being men (67.1 percent), aged 36 to 40 (30.2 percent), and having Bachelor’s educational backgrounds (54.7 percent).\n\nThis study has adopted Structural Equation Modelling (SEM) to examine the correlations between factors influencing intention and behavior of using CAATs. Respondents’ profile (gender, age, and experience) has been used as a moderator in this study. The Partial Least Squares (PLS) method was used to analyze the data. The SmartPLS 3 was used to analyze the data for correlations between factors influencing intention and behavior of using CAATs.\n\n\nResults\n\nThe purpose of the reliability and validity tests was to determine whether the construct matched the structural model domain analysis. Cronbach Alpha (CA) was used to measure the reliability test, and the Fornell-Larcker measure was calculated from the composite reliability score (CR). The mean-variance extracted was used to conduct a validity test (AVE). The recommended score of the CA and CR for each construct is above 0.70,84,85 and the AVE score of all factors should meet the recommended cutting-of point of 0.5 and above.86 Table 3 shows the results of the CA, CR, and AVE tests. The value of CA and CR scores for each construct is more significant than 0.70, and it is within the allowable reliability range. All factors in the AVE satisfy the recommended cutting-off point of 0.5 and higher.\n\nThe variance inflation factor (VIF) was used to test for multicollinearity problems. It is used to identifies the correlation between independent variables and the strength of that correlation. Because the value of VIF for the constructs is less than the maximum cutting-off point of 10, the structural study model is not negatively affected by the issue of collinearity.87 The results are depicted in Table 3. As the results indicates, the value of variance inflation factor for all varibales is higher than 1, which demonstrates the moderate correlation between variables.\n\nThe square root of the AVE score is used to determine the validity of this model. A factor must be higher than the factors’ cross-correlation.84 Figure 1 shows the results of the discriminant validity test, which shows that discriminant validity is reliable because the AVE scores for those factors are higher than the square cross-correlation for those factors.\n\nThe structural model was carried out after testing the constructs for reliability test, validity, discriminant, and multicollinearity tests. Next, the hypotheses were tested using the Bootstrap Smart-PLS technique. As shown in Figure 2 and Table 4, the structural model results indicate the correlation between exogenous and endogenous factors using an algorithm of PLS.\n\n(Source: the results of the author’s analysis using the SmartPLS software).\n\nGender, education, and audit experience do not play a role in moderating the links between effort expectancy, performance expectancy, and social influence in facilitating behavior intention and usage intention (p>0.05). Interestingly, there is a favorable association between the intention of using CAATs and using CAATs appropriately.93\n\nPerformance expectancy is positively related to the intention to use CAATs, and facilitating conditions are positively associated with the appropriate use of CAATs. The coefficient determinant (R2) is used to assess the model quality test.86 The estimated R2 for correctly using CAATs is 0.447 (44.7 percent), indicating that exogenous factors are 0.447 (44.7 percent) in the endogenous variables of appropriately using CAATs. Meanwhile, the calculated R2 for the intention of using CAATs is 0.507 (50.7 percent), indicating that exogenous factors are 0.507 (50.7 percent) in the endogenous variables of “Intention to use CAATs.” A good model is where the fit model test employs cross-validated redundancy (Q2), more significant than zero.86,88 In sum, this model is fit or has a predictive interest based on the results of Q2AU, which is 0.377, and Q2BI, which is 0.353 (Table 4).\n\n\nDiscussion\n\nPerformance expectancy has a positive and significant influence on the intention to use CAATs. Thus H1 is accepted. Auditors believe that employing CAATs in auditing will help them execute tasks more efficiently. This also indicates that BPK’s auditors believe and agree that CAATs help assists their auditing works. The positive association between performance expectations and the intention to use CAATs has also been observed in previous studies.9,29,50,68\n\nHowever, the results of different tests for the variable constructs of effort expectancy (H2) on the use of CAATs indicate no statistically significant association. This finding differs from past studies.1,68 The existence of four CAATs applications given by BPK still requires more intense training to the staff, which may explain why effort expectancy does not stimulate the intention to utilize CAATs. Another possibility is that evaluated entities (auditees) are considered sufficient to audit without CAATs, which is more likely to occur. However, these are not found in this study, implying that more research and exploration are required to uncover relevant essential elements. The finding reveals that effort expectancy is unrelated to using CAATs is consistent with previous research by Mahzan and Lymer.29\n\nThe significance of the job of CAATs in the review interaction is generally perceived. However, notwithstanding their normal advantages and ideas from researchers and controllers, various inward reviewers do not right now embrace these instruments when directing different inward review capacities.34 Acquiring from data frameworks research, we utilize the UTAUT model to analyze the determinants of CAATs reception by inward examiners in Jordan. After reviewing 105 inward examiners, this investigation discovers that the significant variables which might influence inside inspectors’ goals to utilize CAATs are working with conditions and execution anticipation. Be that as it may, both exertion hope and social impact are observed to be inconsequential.\n\nAs discussed before, firms can grow CAATs utilization by instructing inside evaluators concerning the advantages of utilizing these automated devices, by devoting more response to put resources into the specialized foundation, by working on their abilities through expanded CAATs preparing programs, and by creating reward frameworks that urge reviewers to utilize CAATs. Second, considering that the choice to acknowledge and use CAATs is willful, firms ought to perceive the results of their strategies and culture on inner reviewers’ aim to take on CAATs.34 In conclusion, our review proposes the putting resources into review programming without thinking about the hindrances to the reception of CAATs, may restrict the ideal impacts of these robotized devices.\n\nThe result of variable construct testing of social influence on the intention of CAATs usage (H3) is not significant, consistent with previous studies.9,29,67 In BPK, social influence on the intention of CAATs usage is insignificant because their location is far from each entity, and they have low access to an internet connection. According to the Speedtest Global Index, Indonesia is among the Asia Pacific countries with a standard internet connection.89\n\nIn particular, the relapse investigations show that the impact of execution hope, as predicted by H1, was genuinely huge in clarifying the expectation of internal auditors to adopt on CAATs. This outcome is predictable.9,29,32 This outcome recommends that internal evaluators be more ready to use CAATs when they know that the advantages acquired from utilizing these mechanized apparatuses would further develop their work productivity. Accordingly, the board that looks to expand CAATs utilization ought to prepare projects to instruct inward reviewers about the advantages of using such devices and assist them with staying current with evolving innovation.9\n\nThe variable construct of the facilitating condition (H4) was found to be significant and has a positive influence on the appropriate use of CAATs.1,9,29,50,68 Additionally, the construct of the intention of using audit (H5) has a positive association with the appropriate use of CAATs.74 This implies that the facility of information technology is available to support the proper use of CAATs.\n\nAs per past research,29,32 we find that work expectancy is irrelevant. The reasons behind the irrelevant outcome might be that the more significant part of inward inspectors in our example are youthful and have an undeniable degree of capability in data innovation. Hence, interior evaluators might see that the level of straightforwardness with the utilization of CAATs is generally irrelevant to their choice. One more translation for the irrelevant outcome is that in an examining setting, the viability of review strategies is given a high need by inside evaluators when settling on innovation use choices instead of the individual inclinations concerning the endeavors needed to utilize the innovation.9 Despite our assumption, the discovering shows that social impact is inconsequential, implying that that choice to utilize CAATs is not influenced by the prevailing difficulty emerging from the head of the inside review division, their friends inside the organizations, or from the expert bookkeeping bodies. In this specific situation, Venkatesh, Morris40 state that the social impact factor is huge in an acute setting, though it is not huge in an intentional setting. In Jordan, CAAT’s use is willful, despite various researchers and expert guidelines urging reviewers to utilize CAATs.\n\nWhat is more, Mahzan and Lymer29 noticed that the level of requirement and checking of consistency with CAATs utilization is powerless, thus making internal auditors allowed to perform setting explicit choices on reception. Therefore, the willfulness of utilization has no impact on the goal to utilize CAATs. Generally speaking, the proof is conflicting with Curtis and Payne32 and Gonzalez, Sharma,90 yet is in accordance with previous studies.9,29,32\n\nAlso, multiple studies concentrate significantly on computer-based audit support systems. Thompson, Higgins71 recognized the technology’s influence on audit preparation in five big audit firms and stated that technology might offer consumer-specific interior controls that help the auditor identify the customer’s system lacking. Additionally, it was also revealed that technology helps to examine the business procedures of clients, for considering and measuring the degree of control, as well as suggests trials being required to conduct. Moreover, the technology assures concurrence with audit standards and further guidelines associated with the audit. Bierstaker, Burnaby51 explained the technology used in the audit procedure by interviewing IT experts from four of the five biggest accounting firms in the US. The studies of Bierstaker, Burnaby51 were descriptive by nature and concentrated on an individual audit application from an audit firm; therefore, both studies cannot be generalized to the exterior auditor’s proper technology usage.91\n\nLike Bierstaker, Janvrin9 and Mahzan and Lymer,29 we discover proof supporting the thought that working with conditions definitely impacts the inward evaluators’ expectations to utilize and acknowledge CAATs. The outcome recommends that organizations ought to put sufficient cash in a cutting-edge foundation to relieve the hindrance of inspectors from tolerating and using CAATs. Besides, firms might expand CAATs use, however, growing new arrangements regarding recruiting and advancement of examiners. These arrangements ought to devote more weight to inspector’s capacity to utilize information examination in their everyday review exercises.\n\nBoth scholars and practitioners will benefit from these discoveries. The audit profession is “developing rapidly as a result of innovation in its environment,” according to Solomon and Trotman.4 As a result, the audit profession is under pressure to increase audit efficiency and effectiveness.92 Because both researchers and practitioners contend that CAATs will improve audit efficiency and effectiveness, our findings may aid both researchers and practitioners in their efforts to boost CAATs acceptability. Furthermore, previous research only looked at a small number of CAATs with small sample sizes and an emphasis on the prevalence of CAATs rather than the underlying reasons for their usage.41\n\nIn contrast, our study aims to examine public sector auditors’ tendency to use Computer Assisted Audit Techniques (CAATs). This study covers broad areas of Central Java, West Java, and East Java. Further, the findings add to the literature on emerging markets specifically for Indonesian government auditors’ intention and appropriateness of using CAATs. The use of CAATs help to provide auditors information on the highest number of auditees involved in corruption. The empirical findings reveal that performance expectation and facilitating conditions have encouraged auditors to use CAATs in their works. Further, there is a positive influence between the intention to use and CAATs audit. This implies that auditors with an intention will be more open to use the CAATs optimally in achieving effective and efficient work. The utilization of CAATs in public services need to have strong support from the government and positive attitudes from the auditors as the users of the system.\n\n\nConclusion\n\nThe use of CAATs in today’s audits has become a critical issue in achieving efficiency and effectiveness. Therefore, this study examines the use of CAATs by auditors in the public sector of Indonesia. The UTAUT model measures the performance expectancy, effort expectancy, social influence, facilitating conditions, the intention of CAAT usage, and the appropriate use of CAATs. Findings evidence that the performance expectations and the facilitating conditions have shown a positive association with the use of CAATs in doing audits. Further, the result reveals that a positive influence between the intention to use and CAATs audit. This shows that an individual with a strong intention will be more inclined and excited to utilize the CAATs to be used appropriately and optimally based on its goal. The readiness of the CAATs system and the support of both facilitating conditions will increase an auditor’s desire to use CAATs. Furthermore, a detailed and extensive audit will improve performance expectancy by examining the role of CAATs. It can improve audit performance by being faster, more effective, and efficient.\n\nThere are some limitations identified in this study. The CAATs in the BPK are still new and are undergoing the process; thus, the impact may not be stable and cannot be justified at large. Next, no in-depth interview is conducted to gain a better insight into the CAATs employed at BPK. Supposedly, the interview can provide a better view of the respondents’ perceptions on the effectiveness of CAATs implementation. Thus, the future study may consider all these factors to be researched in detail.\n\n\nData availability\n\nFigshare: Dataset of Questionnaire Result from the respondents of Modelling Computer Assisted Audit Techniques (CAATs) in Enhancing Indonesian Public Sector, https://doi.org/10.6084/m9.figshare.19642374.v2.93\n\nThis project contains the following underlying data:\n\n- Response from 225 respondents in Model E-audit Indonesia.csv\n\nFigshare: List of of questions and descriptions of questionnaire of the Modelling Computer Assisted Audit Techniques (CAATs) in Enhancing Indonesian Public Sector, https://doi.org/10.6084/m9.figshare.19642437.v1.94\n\nThis project contains the following extended data:\n\n- List of of questions.csv\n\nFigshare: The Respondent characteristics of the Modelling Computer Assisted Audit Techniques (CAATs) in Enhancing Indonesian Public Sector, https://doi.org/10.6084/m9.figshare.19642425.v2.95\n\nThis project contains the following extended data:\n\n- The Respondent characteristics.csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe researchers would like to thank Kementerian Riset dan Teknologi for providing research funding and the opportunity for researchers to research to continue the existing research roadmap.\n\n\nReferences\n\nRamen M, Jugurnath B, Ramhit P: UTR-CTOE: a new paradigm explaining CAATs adoption. Journal of Modern Accounting and Auditing. 2015; 11(12): 615–631.\n\nMahzan N, Veerankutty F: IT auditing activities of public sector auditors in Malaysia. Afr. J. Bus. Manag. 2011; 5(5): 1551–1563.\n\nINCOSAI: WGITA – Idi Handbook on It Audit for Supreme Audit Institutions. Beijing, China: International Standards for Supreme Audit Institutions (ISSAI); 2014.\n\nSolomon I, Trotman KT: Experimental judgment and decision research in auditing: The first 25 years of AOS. Acc. Organ. Soc. 2003; 28(4): 395–412. Publisher Full Text\n\nJanvrin D, Bierstaker J, Lowe DJ: An examination of audit information technology use and perceived importance. Account. Horiz. 2008; 22(1): 1–21. Publisher Full Text\n\nZhao N, Yen DC, Chang IC: Auditing in the e-commerce era. Inf. Manag. Comput. Secur. 2004; 12(5): 389–400. Publisher Full Text\n\nAICPA, A: Audit risk exposure standards Statements of Auditing Standards. New York: AICPA; 2006.\n\nIFAC: Technology and e-business In Guide to practice management for small- and medium-sized practices. 2nd ed.New York: International Federation of Accountants; 2011.\n\nBierstaker J, Janvrin D, Lowe DJ: What factors influence auditors’ use of computer-assisted audit techniques?. Adv. Account. 2014; 30(1): 67–74. Publisher Full Text\n\nBrooks D, Lanza R: Why companies are not implementing Audit, Antifraud and Assurance Software and how to fix it. Information Systems Control Journal. 2006; 1: 30.\n\nBank, W: e-Government. 2015 [cited 2021 21 Mey]. Reference Source\n\nThnaibat A: Use and Usefulness of Information Technology in the Audit Process in Jordan. Derassat, Business Administration, University of Jordan; 2003; vol. 30. : 253–268.\n\nWinograd BN, Gerson JS, Berlin BL: Audit practices of PricewaterhouseCoopers. Audit. J. Pract. Theory. 2000; 19(2): 176–182. Publisher Full Text\n\nMancuso AJ: Auditing Standards Board issues SAS Nos. 80 and 81. CPA J. 1997; 67(3): 74.\n\nBierstaker J, Houston R, Wright A: The impact of competition on audit planning, review, and performance. J. Account. Lit. 2006; 25: 1–58.\n\nDebreceny R, et al.: Employing generalized audit software in the financial services sector: Challenges and opportunities. Manag. Audit. J. 2005; 20(6): 605–618. Publisher Full Text\n\nSiew E-G, Rosli K, Yeow PH: Organizational and environmental influences in the adoption of computer-assisted audit tools and techniques (CAATTs) by audit firms in Malaysia. Int. J. Account. Inf. Syst. 2020; 36(100445): 100419–100445. Publisher Full Text\n\nRezaee Z, et al.: Continuous auditing: Building automated auditing capability. Audit. J. Pract. Theory. 2002; 21(1): 147–163. Publisher Full Text\n\nCiprian-Costel M: Arguments on using computer-assisted audit techniques (Caat) and business intelligence to improve the work of the financial auditor. Strateg. Manag. J. 2014; 26(4): 212–220.\n\nWang H-I, Yang H-L: The role of personality traits in UTAUT model under online stocking. Contemp. Manag. Res. 2005; 1(1): 69–82. Publisher Full Text\n\nDavis FD: Perceived usefulness, perceived ease of use, and user acceptance of information technology. MIS Q. 1989; 13: 319–340. Publisher Full Text\n\nRosli K, Siew E-G, Yeow PH: Technological, organisational and environmental aspects of audit technology acceptance. Int. J. Bus. Manag. 2016; 11(5): 140–145. Publisher Full Text\n\nBhimani A: Securing the commercial Internet. Commun. ACM. 1996; 39(6): 29–35. Publisher Full Text\n\nAbdel-Hamid TK, Sengupta K, Swett C: The impact of goals on software project management: An experimental investigation. MIS Q. 1999; 23: 531–555. Publisher Full Text\n\nBerry J: Assume nothing, audit instead. Computerworld. 2003; 37(14): 43.\n\nElliott RK: Twenty-first century assurance. Audit. J. Pract. Theory. 2002; 21(1): 139–146. Publisher Full Text\n\nGhosh S: Making business sense of the Internet. Harv. Bus. Rev. 1998; 76(2): 126–136.\n\nMahzan N, Lymer A: Adoption of computer assisted audit tools and techniques (CAATTs) by internal auditors: current issues in the UK. BAA Annual Conference. 2008.\n\nMahzan N, Lymer A: Examining the adoption of computer-assisted audit tools and techniques: Cases of generalized audit software use by internal auditors. Manag. Audit. J. 2014; 29(4): 327–349. Publisher Full Text\n\nDebreceny R, et al.: The development of embedded audit modules to support continuous monitoring in the electronic commerce environment. Int. J. Audit. 2003; 7(2): 169–185. Publisher Full Text\n\nDowling C, Leech S: Audit support systems and decision aids: Current practice and opportunities for future research. Int. J. Account. Inf. Syst. 2007; 8(2): 92–116. Publisher Full Text\n\nCurtis MB, Payne EA: Modeling voluntary CAAT utilization decisions in auditing. Manag. Audit. J. 2014.\n\nAhmi A, Kent S: The utilisation of generalized audit software (GAS) by external auditors. Manag. Audit. J. 2013; 28(2): 88–113.\n\nPayne E, Curtis MB: Can the unified theory of acceptance and use of technology help us understand the adoption of computer-aided audit techniques by auditors. Working Paper. 2008.\n\nDharma DPB, et al.: Antecedents of intention-to-use of e-audit system: a case of the Audit Board of the Republic of Indonesia. Int. J. Bus. Inf. Syst. 2017; 26(2): 185–204. Publisher Full Text\n\nKhaddash H, Siam W: The Extent of Auditors’ Acceptance to the Use of Information Technology in Auditing, in Derassat, Business Administration. Jordan: University of Jordan; 2003.\n\nFarah ARA: Audit Technology Gap in Developing Countries - the Jordanian CPA Firms: Towards enhancing the corporate governance credibility in developing countries, the case of Jordan. Germany: VDM Publishing; 2011.\n\nAhmi A, et al.: State of information technology adoption by internal audit department in Malaysian public sector. Int. J. Econ. Financ. Issues. 2016; 6: S7.\n\nAhmi A, Saidin SZ, Abdullah A: Examining CAATTs Implementation by Internal Auditors in the Public Sector. Indian-Pacific Journal of Accounting and Finance. 2017; 1(2): 50–56. Publisher Full Text\n\nVenkatesh V, et al.: User acceptance of information technology: Toward a unified view. MIS Q. 2003; 27(3): 425–478. Publisher Full Text\n\nBraun RL, Davis HE: Computer-assisted audit tools and techniques: analysis and perspectives. Manag. Audit. J. 2003; 18(9): 725–731. Publisher Full Text\n\nPincus KV, Bernardi RA, Ludwig SE: Audit effectiveness versus audit efficiency: Are the two in conflict?. Int. J. Audit. 1999; 3(2): 121–133. Publisher Full Text\n\nLowe DJ, et al.: Information technology in an audit context: Have the Big 4 lost their advantage?. J. Inf. Syst. 2018; 32(1): 87–107. Publisher Full Text\n\nOni AA: Computer assisted audit techniques and audit quality in developing countries: Evidence from Nigeria. J. Internet Bank. Commer. 2015; 20(2): 1–17.\n\nWiduri R, O’Connell B, Yapa PW: Adopting generalized audit software: an Indonesian perspective. Manag. Audit. J. 2016; 31(8/9): 821–847. Publisher Full Text\n\nThong JY: An integrated model of information systems adoption in small businesses. J. Manag. Inf. Syst. 1999; 15(4): 187–214. Publisher Full Text\n\nBradford M, Florin J: Examining the role of innovation diffusion factors on the implementation success of enterprise resource planning systems. Int. J. Account. Inf. Syst. 2003; 4(3): 205–225. Publisher Full Text\n\nAxelsen M, Green P, Ridley G: Explaining the information systems auditor role in the public sector financial audit. Int. J. Account. Inf. Syst. 2017; 24(1): 15–31. Publisher Full Text\n\nByrnes PE, et al.: Evolution of Auditing: From the Traditional Approach to the Future Audit1 Continuous auditing. Emerald Publishing Limited; 2018; p. 285–297.\n\nMansour EM: Factors affecting the adoption of computer assisted audit techniques in audit process: Findings from Jordan. Business and Economic Research. 2016; 6(1): 248–271. Publisher Full Text\n\nBierstaker JL, Burnaby P, Thibodeau J: The impact of information technology on the audit process: an assessment of the state of the art and implications for the future. Manag. Audit. J. 2001; 16(3): 159–164. Publisher Full Text\n\nKim H-J, Mannino M, Nieschwietz RJ: Information technology acceptance in the internal audit profession: Impact of technology features and complexity. Int. J. Account. Inf. Syst. 2009; 10(4): 214–228. Publisher Full Text\n\nIsmail NA, Abidin AZ: Perception towards the importance and knowledge of information technology among auditors in Malaysia. J. Account. Taxation. 2009; 1(4): 61–69.\n\nHuang S-M, Hung Y-C, Tsao H-H: Examining the determinants of computer-assisted audit techniques acceptance from internal auditors’ viewpoints. International Journal of Services and Standards. 2008; 4(4): 377–392. Publisher Full Text\n\nZainol S, et al.: Determinants of computer assisted audit techniques (Caats) adoption. A study in small and medium practices in Malaysia. European Journal of Business and Social Sciences. 2017; 6(2): 135–150.\n\nHoque MR, et al.: Adoption of information and communication technology for development: A case study of small and medium enterprises in Bangladesh. Inf. Dev. 2016; 32(4): 986–1000. Publisher Full Text\n\nOlasanmi OO: Computer aided audit techniques and fraud detection. Research Journal of Finance and Accounting. 2013; 4(5): 67–80.\n\nLiang D, Lin F, Wu S: Electronically auditing EDP systems: With the support of emerging information technologies. Int. J. Account. Inf. Syst. 2001; 2(2): 130–147. Publisher Full Text\n\nShaikh JM: E-commerce impact: emerging technology–electronic auditing. Manag. Audit. J. 2005; 20(4): 408–421. Publisher Full Text\n\nBPK: Implementasi E-Audit Untuk Mencegah Korupsi. 2012 [cited 2021 1 May]. Reference Source\n\nWilliams M, et al.: Is UTAUT really used or just cited for the sake of it? A systematic review of citations of UTAUT’s originating article. ECIS 2011 Proceedings. 2011.\n\nJakšić D: Implementation of computer assisted audit techniques in application controls testing. Manag. Inf. Syst. 2009; 4(1): 9–12.\n\nSaygili AT: Taking advantage of computer assisted audit tools and techniques during testing phase in financial audits: An empirical study in a food processing company in Turkey. Global Journal of Management and Business Research. 2010; 10(2): 113–119.\n\nBanker RD, Chang H, Kao Y: Impact of information technology on public accounting firm productivity. J. Inf. Syst. 2002; 16(2): 209–222. Publisher Full Text\n\nBedard JC, et al.: The effect of training on auditors’ acceptance of an electronic work system. Int. J. Account. Inf. Syst. 2003; 4(4): 227–250. Publisher Full Text\n\nLoraas T, Wolfe CJ: Why wait? Modeling factors that influence the decision of when to learn a new use of technology. J. Inf. Syst. 2006; 20(2): 1–23. Publisher Full Text\n\nAl-Hiyari A, Al Said N, Hattab E: Factors that influence the use of computer assisted audit techniques (CAATs) by internal auditors in Jordan. Acad. Account. Financ. Stud. J. 2019; 23(3): 1–15.\n\nPedrosa I, Costa CJ, Aparicio M: Determinants adoption of computer-assisted auditing tools (CAATs). Cogn. Tech. Work. 2020; 22(3): 565–583. Publisher Full Text\n\nKesharwani A, Bisht SS: The impact of trust and perceived risk on internet banking adoption in India: An extension of technology acceptance model. Int. J. Bank Mark. 2012; 30(4): 303–322. Publisher Full Text\n\nZuiderwijk A, Janssen M, Dwivedi YK: Acceptance and use predictors of open data technologies: Drawing upon the unified theory of acceptance and use of technology. Gov. Inf. Q. 2015; 32(4): 429–440. Publisher Full Text\n\nThompson RL, Higgins CA, Howell JM: Personal computing: Toward a conceptual model of utilization. MIS Q. 1991; 15: 125–143. Publisher Full Text\n\nAjzen I: The theory of planned behavior. Organ. Behav. Hum. Decis. Process. 1991; 50(2): 179–211. Publisher Full Text\n\nMorris MG, Venkatesh V: Age differences in technology adoption decisions: Implications for a changing work force. Pers. Psychol. 2000; 53(2): 375–403.\n\nDowling C: Appropriate audit support system use: The influence of auditor, audit team, and firm factors. Account. Rev. 2009; 84(3): 771–810. Publisher Full Text\n\nBoard AO: Sectorial Dialogue with Audit Firms. Regulatory Updates and Sharing of Best Practices. 2014; 10.\n\nTornatzky LG, Fleischer M, Chakrabarti AK: Processes of technological innovation. Lexington Books; 1990.\n\nMcKinnie M: Cloud computing: TOE adoption factors by service model in manufacturing.2016.\n\nVenkatesh V, Davis FD: A theoretical extension of the technology acceptance model: Four longitudinal field studies. Manag. Sci. 2000; 46(2): 186–204. Publisher Full Text\n\nKuan KK, Chau PY: A perception-based model for EDI adoption in small businesses using a technology–organization–environment framework. Inf. Manag. 2001; 38(8): 507–521. Publisher Full Text\n\nDholakia RR, Kshetri N: Factors impacting the adoption of the Internet among SMEs. Small Bus. Econ. 2004; 23(4): 311–322. Publisher Full Text\n\nTaylor S, Todd P: Assessing IT usage: The role of prior experience. MIS Q. 1995; 19: 561–570. Publisher Full Text\n\nMoore GC, Benbasat I: Development of an instrument to measure the perceptions of adopting an information technology innovation. Inf. Syst. Res. 1991; 2(3): 192–222. Publisher Full Text\n\nCompeau DR, Higgins CA: Computer self-efficacy: Development of a measure and initial test. MIS Q. 1995; 19: 189–211. Publisher Full Text\n\nFornell C, Larcker DF: Structural equation models with unobservable variables and measurement error: Algebra and statistics. Los Angeles, CA: Sage Publications Sage CA; 1981.\n\nNunnally JC: Psychometric theory—25 years ago and now. Educ. Res. 1975; 4(10): 7–21.\n\nHair JF Jr, et al.: Partial least squares structural equation modeling (PLS-SEM): An emerging tool in business research. Eur. Bus. Rev. 2014.\n\nO’brien RM: A caution regarding rules of thumb for variance inflation factors. Qual. Quant. 2007; 41(5): 673–690. Publisher Full Text\n\nOwusu GMY, et al.: Temptation and the propensity to engage in unethical behaviour. Int. J. Ethics Syst. 2019; 35(1): 43–58. Publisher Full Text\n\nthejakartapost: Indonesia among Asia Pacific countries with slowest internet connection.2017 [cited 2021 1 May 2021]. Reference Source\n\nGonzalez GC, Sharma PN, Galletta DF: The antecedents of the use of continuous auditing in the internal auditing context. Int. J. Account. Inf. Syst. 2012; 13(3): 248–262. Publisher Full Text\n\nMarei A, Iskandar E: The impact of Computer Assisted Auditing Techniques (CAATs) on develop-ment of audit process: an assessment of Performance Expectancy of by the auditors. Int. J. Manag. Commerce Innov. 2019; 7(2): 1199–1205.\n\nChaney PK, Jeter DC, Shaw PE: The impact on the market for audit services of aggressive competition by auditors. J. Account. Public Policy. 2003; 22(6): 487–516. Publisher Full Text\n\nPurnamasari P, Amran NA, Hartanto R: Response from 225 respondents in Model E-audit Indonesia.csv. figshare. Dataset. Indonesia; 2022.\n\nPurnamasari P, Amran NA, Hartanto R; List of of questions and descriptions of questionnaire. figshare. Dataset. Indonesia; 2022.\n\nPurnamasari P, Amran NA, Hartanto R: The Respondent characteristics of the Modelling Computer Assisted Audit Techniques (CAATs) in Enhancing Indonesian Public Sector. figshare. Dataset. Indonesia; 2022."
}
|
[
{
"id": "145799",
"date": "02 Aug 2022",
"name": "Agung Nur Probohudono",
"expertise": [
"Reviewer Expertise Public sector",
"Financial reporting",
"Financial statement analysis",
"Internal control",
"Corporate governance"
],
"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 have read this paper and I believe it deserves to be published. This is intended to provide further information to all parties related to reporting in the public sector to improve their performance in terms of strengthening audits.\nThe problems that arise are in accordance with the real conditions and the given background is logical. The author has described that many organizations have used information technology to develop and improve the effectiveness of their performance. Utilization of information technology is also an effective means of improving the quality of public services. However, its utilization in Indonesia is still minimal, so it needs encouragement from various parties, especially from the government.\nIn the future, it is necessary to provide data on how much or the current level of usage in Indonesia.\nThe method offered is good although it can still be enforced by sensitivity analysis. Respondents have covered the minimum needs of data analysis and are able to represent the desired conditions in this study.\nThe sensitivity analysis we mean is to be able to find out more about the difference between the results obtained with the analysis carried out by analysis with other methods, whether it will show the same results.\nThe results of the analysis are presented completely and clearly, and show that there are still many factors that have no effect. This is the reason that this research is important to be developed again in the future so that the implementation of CAATs can be optimized.\nThe conclusions that have been drawn are good for reference by various interested parties, where the use of CAATs in today's audits has become an important issue in achieving efficiency and effectiveness, especially in the public sector. The conclusions in this study have also provided a clear direction for future 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": []
},
{
"id": "147101",
"date": "28 Sep 2022",
"name": "Ellis Kofi Akwaa-Sekyi",
"expertise": [
"Reviewer Expertise Corporate governance",
"Internal controls",
"Venture capital finance",
"Bank risk"
],
"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 examines how computer assisted audit techniques enhances the auditor’s work in the Indonesian public sector. This is a trending subject in modern day auditing and financial reporting. The introduction of ICT into the auditing profession calls for studies of this nature to unearth the intricacies involved in this transformation agenda. In spite of the effort exerted in the writing of this manuscript, it is believed that if the authors pay attention to these suggestions, the quality of the paper will improve tremendously:\nRewrite the conclusion section of the abstract. It is only the last sentence which looks like a conclusion.\n\nThe introduction is too long. It should specifically cover the purpose of study, research gaps, problem statement, motivation for the study, brief methodology and results (optional), the contribution of the study and structure of the paper. What is it that is missing in research that is necessitating this paper?\n\nThe authors should use the literature review section to amplify the research gaps. Show from the literature review that there is still a missing link in spite of the plentiful research on the topic. This will strengthen the significance of the study. Otherwise, an impression is created that that there is nothing more to research about.\n\nThe voice of the literature review section should not sound like a recommendation.\n\nWhy do you have only one question on the actual use of CAATs? It gives the impression that the study is focused on intention more than behavior.\n\nThe authors fail to show a scientific approach to the determination and selection of the respondents.\n\nThe discussion component should not be mixed with the limitations, implications and conclusions. It is good practice to use the discussion to relate the findings to existing literature and proposed underlying theories. The authors should strengthen why most of their hypotheses were rejected. Is that not a cause for concern?\n\nThe authors should use the conclusion section to answer the research questions. After a brief summary of the work, the key research questions should be answered. How were the limitations addressed such that they did not affect the results of the study?\n\nThe work heavily relies on literature that is a bit old. Even though the topic is a current issue, a significant number of the references are old. The authors may consider beefing up the references with current ones.\n\nThe manuscript requires thorough proofreading and 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? 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": [
{
"c_id": "8902",
"date": "17 Oct 2022",
"name": "Pupung Purnamasari",
"role": "Author Response",
"response": "Dear reviewers, We have made revisions according to your suggestions."
}
]
}
] | 1
|
https://f1000research.com/articles/11-559
|
https://f1000research.com/articles/9-1317/v1
|
12 Nov 20
|
{
"type": "Research Article",
"title": "Creating and sustaining collaborative multi-institutional industry site visit programs: a toolkit",
"authors": [
"Tammy R.L. Collins",
"Kiri Hoff",
"Molly Starback",
"Patrick D. Brandt",
"Christopher E. Holmquist",
"Rebekah L. Layton",
"Kiri Hoff",
"Patrick D. Brandt",
"Christopher E. Holmquist"
],
"abstract": "Background: As more early career scientists enter into diverse career pathways, visiting local companies or organizations can support their exploration of these paths. As an efficient way to facilitate this, we developed a collaborative regional site visit program: the Enhancing Local Industry Transitions through Exploration (ELITE) Consortium. Consortium members arrange half-day visits to local industry sites, thus providing companies and trainees the opportunity to meet and identify potential professional and career opportunities. Three different training institutions worked cooperatively in the development and maintenance of the program. The ELITE Consortium was developed with eight phased steps; guidelines and operating procedures were created for each of these steps and are provided along with sample materials for institutions interested in building similar programs. Methods: Prior to fully developing the program, trainee interests were evaluated via questionnaire. During program implementation and thereafter, program directors tracked attendance and collected career outcome data from publicly available sources to identify first job positions after training. Regression analyses and chi-squared analyses were used to examine site visit matches and career outcome data. Results: Analyses suggest a positive impact of site visits on postdoctoral and graduate trainees’ career outcomes at companies or institutions that match a similar sector (e.g., for-profit) and type (e.g., biotech, pharmaceutical, contract research organization). Despite a small sample size, evidence suggests an especially positive impact on trainees who organize site visits to companies compared with those who simply participate. Conclusions: The ELITE Consortium was successful in helping trainees explore and identify a multitude of career paths. Trainees attained employment either directly or in related companies and institutions visited by ELITE participants. The joint, three-institution, flexible nature of the ELITE Consortium positively impacts the program’s sustainability and reach. The toolkit provided here will help other institutions to replicate and adapt the program with minimal effort.",
"keywords": [
"graduate and postdoctoral professional development",
"experiential learning",
"industry site visit program",
"biomedical workforce",
"career outcomes"
],
"content": "Introduction\n\nIt is widely known that the number of tenure-track positions remains relatively flat while the number of PhD-holders increases (National Institutes of Health [NIH], 2012)—meaning many individuals will enter into other types of careers beyond faculty positions (Stayart et al., 2020). Therefore, institutions should be preparing their graduate students and postdoctoral scholars for these other types of careers (Sinche et al., 2017)—and this idea finally seems to be gaining traction in academe (Lenzi et al., 2020). Preparing students and postdocs for such careers can take on many forms, and one example is through company site visits. While this has long been common practice in the professional degree-seeking communities and for undergraduate students (e.g., business, engineering; see Velez & Giner, 2015 and Carbone et al., 2020 for reviews), PhD-level trainees in the scientific research training community (particularly in STEM and the biosciences) have had limited applications of this learning model until recently.\n\nTo address this gap in career preparation, experiential learning has recently been applied more broadly in graduate education (Schnoes et al., 2018; Van Wart et al., 2020). The NIH Broadening Experiences in Scientific Training (BEST) Consortium has deployed career development training across four major types of experiential learning: job simulation, site visits, job shadowing, and internships (Van Wart et al., 2020). Each of these variations of experiential learning activities has varying levels of engagement and skill acquisition, but also can require very intensive resource and time commitments (e.g., high dose of experiential learning potential in resource-intensive internship). However, not all trainees are at a place in their professional development where they are ready to invest the time and resources needed to take advantage of these intensive experiences; furthermore, not all institutions have resources or staff available to coordinate such time-intensive options. Fortunately, lower-dose and less time-intensive options may also provide benefits to trainee-participants. The current work explores the effectiveness of delivering career development experiential learning though site visits organized across a multi-institutional collaboration, creating an efficient method to deliver potentially valuable professional development experiences.\n\nThe focus of this manuscript is a company site visit program termed the Enhancing Local Industry Transitions through Exploration (ELITE) Consortium. The mission of the ELITE Consortium is to connect companies that hire PhDs with PhD students and postdocs from the National Institute of Environmental Health Sciences (NIEHS), the University of North Carolina: Chapel Hill (UNC), and Duke University (Duke). ELITE helps trainees explore industry career options through site visits to leading Research Triangle Park, NC, life-science companies, and to other employers beyond the traditional tenure-track (e.g., University-operated contract research organizations, (https://factor.niehs.nih.gov/2016/11/science-highlights/elite/index.htm). Site visits allow trainees to learn about the different types of industry jobs open to PhDs and how best to prepare for them. These visits also provide an excellent opportunity to network with industry professionals, and to experience company culture first-hand. ELITE also benefits participating companies, who can gain positive exposure among PhD trainees and identify talent for future hiring.\n\nThe concept of having trainees visit local companies and industries has previously been established as good practice at several other institutions. The industry site visit program developed by postdoctoral scholars at Massachusetts General Hospital in 2010 (Abu-Yousif et al., 2010), and the Postdoc Industry Exploration Program (PIEP) developed by postdocs at the University of California, Berkeley (Nature, 2011; Tsang & Fisher, 2011) are examples of well-designed programs that directly expose postdocs to the type of research conducted and career paths available at a particular company, while at the same time giving them a glimpse of the company’s culture and providing networking opportunities. Since the inception of these innovative programs, a number of other institutions have followed suit to create their own, such as the Exploration Program for Industry Careers (EPIC) program at the Fred Hutchinson Cancer Research Center (https://www.fredhutch.org/en/research/education-training/office-of-scientific-career-development.html); the Explore On Site (ExPOSE) program at the National Cancer Institute (https://events.cancer.gov/cct/expose); the Bridges to Biotech multi-institutional partnership program in Maryland (https://open.maryland.gov/blog/bridges-to-biotech-preparing-tomorrows-workforce-today/); and others. This sharp rise in new experiential site visit programs is a testament to the growing interest of training institutes and academic institutions in programs of this type.\n\nBuilding directly upon the Massachusetts and Berkeley industry site visit program models, here we describe a variation on an industry site visit program that is a joint effort between three institutions: the NIEHS’ Office of Fellows’ Career Development (OFCD), the Duke University Office of Postdoctoral Services, and the Training Initiatives in Biomedical & Biological Sciences (TIBBS) at UNC. The unique three-institution ELITE site visit Consortium (https://www.niehs.nih.gov/careers/research/fellows/involvement/committees/elite/index.cfm) was created to enhance the synergy from each of our three institutions’ pre-existing site visit programs and efforts, and was structured around the single-institution-based ELITE program that NIEHS initiated and formed in 2015.\n\nHere, we provide a toolkit for running a joint multi-institutional industry site visit program. Our main aim is to remove barriers and administrative burdens of running such a program for other institutions by providing detailed standard operating procedures (SOPs), guidelines, and sample materials that other institutions could directly adapt and use. We also describe the preliminary career outcomes of ELITE consortium participants in an effort to determine whether the program impacted their career decisions and outcomes.\n\n\nProgram development\n\nThe ELITE program at NIEHS was originally modeled after successful programs in San Francisco, Boston, and Seattle. Briefly, attendees completed a biosketch and indicated interest in a site visit, the NIEHS Program Director selected attendees, attendees were required to attend a preparatory meeting, and NIEHS provided transportation to the site visit. UNC TIBBS also piloted a \"Program for Industry Exploration\" (PIE) prior to joining ELITE, and Duke was informally visiting companies about once per year. While these parallel institutional site visit programs were either modeled after others’ programs or developed in-house, we found that key adaptations were needed for continued success in our local environment. One of the most impactful adaptations involved inter-institutional collaboration. With this adaptation, all three institutions (NIEHS, UNC, & Duke) joined together to form the ELITE Consortium; we share the work of organizing visits, and an equal number of trainees from all three institutions may attend each site visit, regardless of the organizer that month. Besides decreasing the burden on any particular institution to plan all of the site visits, it enabled us to have a critical mass of attendees, which made better use of the company’s time, and thus increased their interest in hosting such an event since they could reach a more diverse audience—in short, because the program was explicitly a joint effort, companies were quicker to say “yes” to hosting a visit.\n\nAnother key adaptation involved the way in which trainees apply to attend a site visit. NIEHS began the original ELITE program in a manner similar to UC Berkeley’s Postdoc Industry Exploration Program (Nature, 2011; Tsang & Fisher, 2011) which involved having those interested in the program submit a detailed biosketch to keep on file. The idea was that for each site visit, all biosketches would be reviewed and those with the closest match would be chosen to attend a visit. This biosketch model did not work well at NIEHS—likely due to its smaller postdoctoral population—and the decision was therefore made to switch to a new system. Interested attendees applied to attend each site visit by submitting a tailored cover letter as if they were applying to a job within the company. This adaptation has several benefits—1) it creates ‘up-front’ effort on the part of the trainee, thus selecting for those most interested and most likely to keep their commitment to attend a site visit; 2) it gives the trainee experience in writing a tailored cover letter; 3) it requires that the trainee conduct research on the company prior to attending; 4) companies may choose to receive these letters if they wish, and it could provide them with a potential talent pool. Institutions with related site visit programs (Van Wart et al., 2020) that involve extensive travel (e.g., Vanderbilt’s ASPIRE On the Road (https://medschool.vanderbilt.edu/career-development/aspire-on-the-road/#:~:text=ASPIRE%20on%20the%20Road%20is,make%20well%2Dinformed%20career%20decisions) and the University of Chicago’s Trek Program (https://careeradvancement.uchicago.edu/student-opportunities/treks) have also adopted cover letters as part of their application process.\n\nThus far, we have described some basics of the ELITE Consortium site visit program, as well as key adaptations that have made this joint program successful. Next, we describe the finer details of how the program works—including program variations at each member institution. Our goal is to provide a detailed framework that other institutions can use in order to seamlessly replicate, adapt, and/or expand this program for their trainees.\n\nPrior to beginning the site visit program in earnest, trainees were asked to provide input on the types of companies they would like to visit. Hence, pre-interest questionnaires were administered in some cases prior to establishment of the ELITE Consortium in order to gauge interest in site visits, help prioritize types of companies to visit, and to obtain a snapshot of career interests prior to ELITE program opportunities. A brief questionnaire was developed and employed (see representative sample results from one institution’s pre-program interest questionnaire, Underlying Data S1 (Collins et al., 2020)). These results showed that the top three interests identified in this sample were to learn more about: research & development, pharmaceutical companies, and contract research organizations (CROs).\n\nSteps. There are a number of steps involved in organizing a site visit (see Figure 1), ranging from identifying host companies all the way to follow-up. Here, we describe an overview of these steps; a detailed example Standard Operating Procedure (SOP) is also provided (see Extended Data: S2 (Collins et al., 2020)) as a step-by-step guide that lays out many of the small details to consider when organizing a visit.\n\nThere are eight main steps involved in organizing an ELITE site visit, ranging all the way from identifying and contacting companies through to attending the site visit and following-up with the hosts.\n\nIdentifying and contacting companies. Based on the pre-program-development interest questionnaire, initial efforts were focused on attempting to organize site visits to company types that were of greatest interest, such as pharmaceutical companies and CROs. Cold-emailing company representatives met with some success (see Extended Data: S3 (Collins et al., 2020)). Some connections were also made with potential host companies at conferences or events while networking or tabling (see example industry-geared flyer Extended Data: S4 (Collins et al., 2020)). In addition, we found that connecting to alumni working within a company was often a reliable way to gain initial buy-in for a company to host a visit. In our sample SOP (see Extended Data: S3), we provide a detailed framework for how to identify contacts within a company, and we recommend doing so approximately 4–6 months prior to an anticipated site visit date.\n\nInstitutional variations: NIEHS’ program was originally designed by trainees, and the organizing committee consists of staff within the Office of Fellows’ Career Development as well as a committee of trainees. For any particular site visit, an individual trainee can volunteer to be the lead organizer of a site visit; the SOP was originally written for trainees since their time at an institution is limited. The SOP helps to consolidate knowledge and best-practices, and it simplifies, streamlines and de-mystifies the process for trainee volunteers. Trainee volunteers also receive a sample ‘first contact’ letter template (see Extended Data: S2) to assist them in communicating with company representatives. Sample Agendas (see Extended Data: 5 (Collins et al., 2020)) are also available as templates to share with companies in subsequent communications in order to help the company better understand what a site visit might entail (for common site visit activity ideas, see Figure 2). In lieu of trainee volunteers, institutional program staff at UNC and Duke within either UNC's Training Initiatives in Biomedical and Biological Sciences (TIBBS), or Duke’s Office of Postdoctoral Services serve as the lead organizers of site visits at their respective institutions, and they can utilize/adapt the SOPs for their institutions when planning a visit.\n\nThere are six key activities that may take place during a site visit, ranging from an overview of the company’s activities to networking with individual scientists at the company.\n\nRegardless of the specific individual—whether trainee or program staff—organizing a given site visit, it is important to have some degree of institutional program support in order to provide continuity. Institutional program contacts typically convene annually to divide up the organizing load, and to determine which institution will organize a site visit for a given month. However, because organizing site visits can be an organic process, close communication between each institution is vital so that everyone is aware of potential site visits in the pipeline.\n\nMarketing/call for applicants. Once the lead organizer has identified a company and date for a site visit, the event is marketed at each institution via flyers and emails sent out to each institution’s trainee listserv (see Figure 3 for program branding logo). The lead organizer typically uses an SOP template for creating an email and/or flyer (for template email and flyer sample, see Extended Data: S6 and S7 (Collins et al., 2020)) to market the event and call for applicants, who apply by writing a cover letter as if it were to be submitted to the company. In this initial announcement, we explicitly define the scope of the application and mention whether or not the company has requested to see the cover letters. In the vast majority of cases, the cover letter is not seen by the company, and is used solely for selecting site visit participants. The marketing materials are typically sent out approximately one month prior to the site visit, and they also include the date by which applications are due as well as the date of the mandatory preparatory meeting selectees are required to attend. Each institution may set their own application deadlines and preparatory meeting dates, and we collectively aim for application deadlines to be approximately two weeks prior to the site visit date.\n\nWe developed a unique logo for the program to ensure consistency in messaging, and to make the program easily recognizable when distributing marketing materials.\n\nApplicants write and submit cover letter. Trainees apply for each site visit by writing a cover letter addressed to the company being visited. The letter must outline trainees’ background, fit, and interest in the company. As mentioned earlier, this gives trainees practice in writing cover letters; it ensures that they conduct research on the company ahead of time; it creates up-front ‘buy-in’ and increases chances that they will attend if selected; and it provides a potential talent pool for companies, as they are given the option to view the cover letters. However, many companies opt to not receive the letters, and they most often serve the intended purpose of preparing trainees. Trainees email their cover letter application to their respective institutional training office.\n\nSelection of participants. Participants are selected by institutional program directors; companies are not involved in the selection process. However, companies may view the cover letters if they request them during the initial planning phase. It is important to note for the institution with a trainee organizing committee (NIEHS), that trainees are not involved in the selection process and do not see the letters submitted. Before the selection process begins, institutions take note of the number of spots available for the site visit in question. Depending on what a company can accommodate, site visits typically include 15–50 participants, with the vast majority of visits hosting 20–25 participants. Keeping these numbers small allows for a smaller attendee-to-company-scientist ratio which could provide a more engaging learning and networking environment. The available spots are divided evenly among Duke, UNC, and NIEHS, regardless of the institution that is planning that particular site visit. As part of the selection process, cover letters are evaluated on the degree to which they are tailored to the company being visited. Typically, the number of cover letters submitted per institution allows us to accommodate all applicants by sharing open, extra spots across institutions if there are more applicants at one institution versus another. Once we begin to reach capacity, program directors make every attempt to accommodate all applicants—they often release their own designated spots to trainees, and they may contact the company host to ask whether the company can accommodate additional participants. In the rare instances in which capacity is reached, we may prioritize trainees who are more senior in their training fellowship (or nearing graduation). We may also prioritize attendance for those who have participated in the NIEHS ELITE organizing committee or those who have demonstrated other leadership involvement. Another point to note—since a trainee organizes the site visits at NIEHS, the organizer automatically reserves a spot to attend.\n\nAfter participants are formally notified of their selection, we may request that they each submit 2–3 questions they would like answered during the site visit. An example of questions submitted for one of the site visits is included (see example questions, Extended Data: S8 (Collins et al., 2020)). These questions may be shared with the company ahead of time to help prepare their scientists for the types of questions that attendees may have. The purpose of this is to also encourage attendees to think more deeply about the company in advance, which will enhance their overall experience.\n\nMandatory preparatory meeting. Once accepted to a site visit, trainees must attend a mandatory, though brief (30 minute), preparatory meeting (see sample preparatory meeting slides, Extended Data: S9 (Collins et al., 2020)) that is organized and presented by each institutional program director. The preparatory meeting occurs anywhere from one week to a few days in advance of the site visit. At the preparatory meeting, program directors begin by discussing general site visit etiquette (e.g., networking tips, what to wear, and how to follow up with contacts using email or LinkedIn). In some instances, an institution may assist trainees in creating business cards and attendees are encouraged to exchange them during the site visit. After discussing general etiquette, directors present background research on the company found from sources including company annual reports, news articles, BioSpace, Google Patents, etc. Program directors then lead a discussion among trainees—many of whom have conducted their own research into the company. The meeting ends with a discussion about the site visit agenda and any confirmed company representatives that participants will meet. If any of the company representatives are institutional alumni, program directors try to point this out to participants in advance.\n\nTransportation. Transportation to a site visit varies by institution. NIEHS provides group transportation to all site visits. NIEHS identifies a location and time where participants gather well in advance of the site visit time. Institutional program directors reserve a van or multiple cars from the government motor pool. If a single vehicle can be taken that accommodates all participants, the institutional program director drives the participants to the site visit; if more than one vehicle is needed, a trainee volunteer may also drive. In rare situations, individuals may choose to drive their own personal vehicles depending on their personal circumstances.\n\nUNC has a mixed model in which participants may either ride in a van provided by the UNC program office for group transportation to site visits, or participants may instead choose to drive their personal vehicles and/or coordinate carpooling among themselves as needed. For those who opt to ride with the group (most of the participants), UNC identifies a location and time where participants gather well in advance of the site visit time. Trainees may volunteer to drive the program office’s van. For those who choose to drive individually or arrange carpooling among themselves, UNC instructs individuals to arrive to the site visit no later than 15 minutes before the site visit start time.\n\nBecause Duke does not have institutional vehicles available to reserve, participants drive their personal vehicles and are encouraged to carpool. Carpooling is often discussed at the prep meeting. As at UNC, the option for personal vehicle use or carpooling is necessitated by the fact that many participants are spread out across large campuses. Trainees are encouraged to arrive at least 10 minutes early.\n\nThe fact that each of our three institutions have varied transportation models ranging from group-to-individual-transportation demonstrates that a site visit program can be successful with any of these models, and institutions should adopt the one that best suits trainees in their institutional environment.\n\nSite visit day. A site visit typically lasts three hours, and may involve a variety of activities (for sample agendas, see Figure 2 and Extended Data: S5), which differ based on the type of company visited—for example, whether bench- or office-based. A site visit frequently begins with a company overview presentation in order to provide participants with a basic understanding of what a company does. Site visits also often include a panel discussion with scientists working in a variety of positions across the company so that participants can learn about the different types of positions. Participants have found it informative to learn from both those in more senior roles as well as those who recently made the transition from academia to industry. Site visits may also include presentations from Human Resources representatives, and they may include an informal networking session to give participants a chance to mingle with company representatives. If the visit is to a company that primarily conducts bench research, participants are often provided a detailed tour of the company’s facilities.\n\nFollow-up. After a site visit, institutions follow-up in various ways. Participants are encouraged to immediately send an email thanking the company host and any company representatives that they connected with during the site visit. Participants are also encouraged to connect with company representatives on LinkedIn using a tailored invitation. Trainees may further follow-up via informational interviews with company representatives over coffee, lunch, or the phone. Some institutional program staff maintain a collection of thank-you cards; trainees are encouraged to sign and send a group snail-mail card to the company host. Some institutions may choose to send a gift basket or other token of appreciation to the company host (government funds are not used for these purposes).\n\n\nMethods\n\nOnce we organized the site visits, we identified key metrics to record each site visit in order to assess the program’s success. To maximize sample size, data from all three institution’s attendees were pooled and we standardized data collection criteria. Program participants’ career outcomes were evaluated by collecting publicly available career outcomes from the internet.\n\nCareer outcome data were then grouped into taxonomic tiers jointly agreed upon by the authors, particularly those corresponding to Tier 1 of the commonly used PhD Career Outcomes Taxonomies (Lenzi et al., 2020; Stayart et al., 2020; Xu et al., 2018). Furthermore, due to the specific types of companies that hosted site visits, we further categorized each company into either Contract Service Organization (CSO), Biotech, or Pharma to reflect the Research Triangle Park’s primary markets. Some CSOs are also referred to as Contract Research Organizations or Clinical Research Associations, but for consistency as an umbrella term, CSO will be used hereafter. CSOs were identified by each company’s personal online description, as were biotechs and pharmaceutical companies. When biotech and pharma companies’ descriptions were confounded (for example, a Pharma Biotech company, or a Biotech company that made pharmaceuticals), we used an employee cutoff of 20,000 or less employees for Biotech, and 20,000+ for Pharma. This was recorded in a common spreadsheet and then recoded for each participant’s career outcome.\n\nFurthermore, attendance data was collected and collated for each site visit, and the number and type of site visits were coded by attendance and by whether a person was hired at the host company. Data was then coded to match the visit and career outcome on a number of criteria including: being hired at site visit company, being hired at a company of the same type (CSO, Biotech, or Pharma), and being hired at a company sharing the same Tier 1 coding (academia, for profit, government, etc.). MS Excel logic functions were used to create variables that quantified matching pairs (e.g., site visit job sector corresponding with hired job sector). We recorded if the participants attended a site visit, if they were hired at the visited company, if they were hired at a company of the same type (CSO, etc.), and if they were hired at a Tier 1 match (government, non-profit, etc.) by checkmark. We converted the Boolean checkmarks to binary 1’s and 0’s, and applied IF ELSE statements to the columns to simplify analysis. We compared the visited categories to the hired categories for each attendee. For example, IF attendee visit equals 1 (true), check the hire location to see if it matches the visit location and record 1 (true) for hired at site visit, ELSE record 0 (false). The same logic was applied to the type of company and tier one category of company. Due to not offering governmental site or teaching-intensive university site visits, the Sector (Tier 1) match analysis specifically compared For-Profit matches, but did not count other matches (Government, Non-Profit, Academic) because there were few site visits that fell into any of the latter three categories; hence only for-profit matches were included in the match count.\n\nProgram summaries. 30 total site visits included 24 unique sites/companies total (https://www.niehs.nih.gov/careers/research/fellows/involvement/committees/elite/index.cfm contains full list), with 250 unique ELITE participants. We limited our career outcomes data analyses to those that graduated or were hired since attending an ELITE site visit (n=126) through January 2020. Among those who participated and are now in their first position post-training, postdoctoral trainees (n=79) constituted 63% of the sample while doctoral students (n = 46) constituted the other 37%.\n\nParticipants. On average, ELITE participants who have since been hired into a first position attended 1–2 visits total (M=1.81, SD=1.38; min = 1, max =9; see Table 1 for attendance summary info) with 90% attending between 1–3 visits, which lasted approximately 3–4 hours per visit. Hence, our data suggests that positive benefits can arise with as little as 4–12 hours of time invested in professional development, networking, and experiential immersion during site visit activities.\n\nThe majority of participant alumni attended only one site visit (76, 60%). Some participants attended as many as seven (two individuals) or nine (one individual) ELITE site visits.\n\nCompanies. Company sites visited included Contract Service Organizations (CSO; 46%, n=11), Biotech (25%, n=6), and Pharma (21%, n=5); a small percent were affiliated with academic institutions and did not clearly fit into any of these categories and were hence coded as “not applicable” N/A (8%, n=2).\n\nPlanned analyses. Summary statistics are provided to represent program participation for trainees and companies/organizations. Differences in career outcomes for graduate vs. postdoctoral trainees were tested using Chi-Squared analyses (e.g., company hiring match, sector hiring match). Logistic regression was used to test the hypothesis that attending more site visits was associated with a greater chance of being hired at a site visit company (or in that sector). IBM SPSS v26 was used to run analyses.\n\n\nResults\n\nStated goals of the program included experiencing company culture, learning and practicing professional etiquette, and learning how to network and develop professional contacts. While getting hired at the company was explicitly not the stated goal of these site visits (and this is repeatedly emphasized to trainees in the mandatory prep visits), when hiring opportunities arose organically, they were a beneficial outcome for both the trainee and the company. While only 8% (n=10) were hired at a specific company they visited (see Figure 4), 65% (n=82) were hired at a type of company they visited (e.g., CSO) (see Figure 4). In addition, a majority of trainees (64%, n=81) were hired in the sector of a company they visited (e.g., for-profit). Thus, while site visits did not necessarily act as direct career pipelines, they did allow for attendees to gain a sense of the culture within a particular company type and sector, allowing for them to have a more confident match in their future careers.\n\nThe majority of ELITE attendee alumni were hired at a company type that matched those they visited (N=82). Ten were hired at the specific company visited, and 3 of those 10 were trainee site visit organizers.\n\nA small number of trainees who organized a site visit had a much stronger likelihood of being hired at the company whose site visit they organized: 60% were hired by the company they organized the visit with (n=3/5). Furthermore, by definition, all of these were also company-type matches. This may indicate that an in-depth, meaningful interaction with company representatives while organizing site visits results in a stronger personal connection; it provides trainees an ability to demonstrate planning/organizational skills and professionalism; and it also offers an extended opportunity to connect and network beyond introductory levels. Furthermore, a person’s character and passion for the company may better shine through during prolonged planning interactions.\n\nThe large number (n=82) of participants hired into a similar company type (and even a few into the specific companies) suggests that attending site visits is helping the trainee find and/or display a good fit with the company, type, or industry. While we can’t isolate a single mechanism, it seems likely that trainees may have been able to confirm or deny their interest in a particular type and sector of company/organization, and perhaps these visits impact their interest and confidence in applying; knowledge of the roles and responsibilities of different positions; ability to create competitive application materials using appropriate industry terms; and networking connections within the industry. Further research is needed to tease apart the specific route(s) by which the site visits made a difference in trainee job searches and application processes.\n\nOf ELITE participants hired at a matching company type, 57% (n=47) were hired at CSOs, 23% (n=19) at Biotech, and 20% (n=16) at Pharma. Participants from our sample were hired into CSOs at a high rate (at about twice the number compared with each of the other categories), which is not surprising given that the local job market is highly saturated with this type of organization. In fact, North Carolina has the greatest concentration of Contract Research Organizations in the world (https://www.ncbiotech.org/about/history-of-biotechnology-north-carolina#panel6).\n\nOverall, there were no differences in being hired into a specific company type when comparing postdoctoral and graduate trainees (Chi-squared test, X2(1, N=126)=.26, p=.88). Although more postdocs were hired into positions across all three categories, there were more postdoc participants in the sample, so this did not differ from variations expected by chance based on the sampling distribution.\n\nTier 1 sector hires (For Profit as compared with Other – including Government, Non-Profit, or Academic) were compared between doctoral and postdoctoral trainees. For-profit vs. other (Chi-squared test, X2(2,126)=10.29, p=.001) favored postdocs in for-profit positions, with a split roughly equally for grads in for-profit and other sectors compared with postdocs in other sectors (Chi-squared test, X2(2,126)= 9.18, p=.002); however, the 2×2 Chi-Squared did not indicate a proportional difference from chance for the combined effect of postdoc vs. graduate student into for-profit vs. other sectors (X2(1,126)= 1.90, p=0.17, NS). Hence, while a slightly greater proportion of postdocs entered for-profit directly compared with graduate students, the combined effect was not significant. This could partially be explained by the higher incidence of grad students entering into postdoctoral training whereas a natural next step for a postdoc is full-time employment (see Figure 5).\n\nAs expected, more graduate students entered into trainee positions as their next position (24%), whereas far fewer postdoctoral scholars entered into another training position (4%).\n\nTo better understand if there was any effect for postdocs or grad students transitioning into for-profit roles, we ran a further post-hoc analysis and removed trainees who entered into training positions as their next step (n=11 grad students entered into postdoctoral training positions, and n=3 postdocs entered into further postdoctoral training in a new role or at another institution). When trainees who entered into a subsequent training role were removed from the sample, 67% of graduate students vs. 69% of postdoctoral trainees constituted matches on tier 1 sector for-profit hires (X2(1, 112) = .03, p= 0.87, NS). Hence, any differences in postdoctoral versus graduate hiring rates seem to be accounted for by rates of continued training being more prevalent in graduate student populations than for postdoctoral trainees (which makes sense since they are chronologically further along in training by definition).\n\nIn total, 75% (n=18/24, see Figure 6) of company partner organizations who have participated to date have hired a candidate who was an ELITE participant. The majority of companies have held one site visit to date, although a few have held more (in the current dataset, the site visit per company mode = 1, with 25% holding a second visit). Top hiring companies have hired up to 4 and 5 ELITE participants per company (range 0–5 hires, mode = 1 hire).\n\nA large majority (75%) of ELITE host companies have hired individuals who participated in the ELITE program.\n\nThe number of site visits attended predict being hired at a company, with attendees’ hiring chances being about 1.5 times greater per site visit attended (OR = 1.58, p < .01, Wald = 6.90, B = .46, SEb= .17). Site visit participation continues to show a significant positive impact when controlling for grad/postdoc status (OR = 1.53, p=.02); there was no significant difference between graduate or postdoctoral status (OR = .59, p=.54). In other words, attending more site visits made one more competitive as a future hire, regardless of whether one was a grad student or postdoc.\n\nSome of this effect could be driven by the fact that site visit organizers tended to attend more than others (see Figure 7); nonetheless we see a positive relationship between attendance and being hired at a similar company. When the three trainee organizers were removed from the analysis (10 minus 3; n=7 hired), attendance rates were no longer a significant predictor (OR = 1.16, p=0.58; grad/postdoc remained non-significant, OR=.71, p=.69) of being hired, although the directionality of the effect was still positive. While this could be an artifact of lower power to detect an effect as the number hired at a company was previously already low (n=10), this suggests that being an organizer for a company site visit (which was also associated with attending more visits) may be a stronger predictor of later hiring success than simply attending.\n\nThe ten individuals hired directly by the ELITE companies they visited attended more site visits overall on average. Those not hired into a visited company attended less visits on average (mean indicated by red bar).\n\n\nDiscussion\n\nOverall, the ELITE program was successful in its mission: to help trainees explore industry career options through site visits in Research Triangle Park, NC and to other employers beyond the traditional tenure-track. We saw significant numbers of both graduate students and postdocs hired at companies that match the type of company they visited, and several successful hires at the same sites visited. The visits were succinct and effective, even under the time constraints of a half-day visit. The program identified trainees looking for a variety of career options and companies looking for new talent, and coordinated the two fairly and representatively. Not all effects achieved significance which may be in part due to the limited sample size; nonetheless, emergent trends were identified.\n\nIn summary, there are different institutional models for a site visit program’s operation, and they can each work to meet the needs of the institution while still allowing for collaboration and serving to benefit the overall ELITE Consortium. It is important to figure out the optimal attendance capacity for visits and optimal frequency for each set of institutions and partners in your area, but it is also common to have trial and error while working out the ideal size.\n\nThe benefits and challenges of collaboration are varied. Benefits include less time per institution for planning; companies are more interested in hosting because they can reach multiple institutions simultaneously; and hosts have a guaranteed critical mass to make it worth the company’s time with higher attendance. Challenges include the additional complexity of coordination across multiple sites (requires more time, but happens less frequently per institution) such as establishing common date decisions, number of trainee acceptances, etc. While collaboration means there is the drawback of fewer overall spots per institution, a benefit is that when a particular host company is less popular at one institution, critical mass can still easily be reached. However, on occasion a host company may be popular across all three institutions, in which case less attendees per institution can be accommodated than if each had arranged separately. One other potential pitfall for institutions with trainees organizing the visits is that program leadership may need to educate trainee committee members on business etiquette in order to avoid any potentially negative interactions that could damage either the image of the Consortium or an individual’s professional image. To date, we have not experienced this pitfall, but it is a potential risk to consider – especially if early-stage trainees are involved in planning a site visit. In our experience, trainee involvement in planning has been a tremendous benefit, and having planners across sites has balanced-out responsibilities for planning well. However, it does require close interactions and real-time communication during the trainee site selection/ organization process, so working closely with colleagues across all institutions is important.\n\nTo better understand the time-associated benefits and/or challenges of collaborating with trainees and other institutions to organize a site visit, we estimated the amount of time it would take a program director to organize a site visit in different scenarios. Organized independently, it requires ~12.5 hours for a program director to organize a single site visit from start to finish—including all steps from identifying and contacting companies through attending the site visit itself and following-up afterwards. If a program director alone were to organize and attend one site visit per month for a year (12 visits/year), this would amount to an average of ~150 hours spent in a year. Collaborating with a trainee at one’s institution would reduce a program director’s hours by 20%. Extending this further to collaborate with two other institutions in the model described here reduces the total time spent per year to about 96 hours, which amounts to ~2.5 weeks of FTE time. These estimated hours all suppose that a program director is also attending each site visit, which takes up a significant portion of the time. If they choose not to attend the site visits, then the amount of time spent organizing in the collaborative model is further reduced to 36 hours per year. As illustrated, depending on the time constraints of the program director and needs of the institution, one can adjust their level of time commitment by using a program model that best fits their needs—whether by collaborating with more institutions and/or adjusting the number of site visits planned in a year.\n\nWe have also observed a multitude of benefits for trainees. For the institution with trainee-organized visits especially, the postdoc leadership experience, professional communication experience, and networking opportunities have provided valued benefits. In addition to our data that suggests benefits to trainees who may be future applicants in the for-profit sector or to a particular company type, we learned anecdotally that some trainees were hired specifically because they demonstrated outstanding communication skills while organizing an ELITE site visit on behalf of the Consortium. We surmise that the trainee/company interactions may allow company representatives to observe trainees in action, thus allowing employers to unofficially evaluate them as potential future colleagues. Other benefits include cover letter practice writing, learning about a variety of companies, and networking between postdocs and graduate students across all three institutions in the Consortium—besides the obvious benefit of networking with company professionals. This benefit was manifest in a number of ways, one of which included the fact that some company HR representatives voluntarily offered to prioritize ELITE participant job applications for review. Furthermore, a larger pool of program alumni from the Consortium has created contacts for future site visits, resulting in a synergistic effect which can then lead to future trainees being hired and/or learning more about company types through informational interviews, etc.\n\nAnecdotally, some representative comments about participation benefits included the following:\n\n“Thank you for selecting me as one of the applicants to attend the [Company] site visit. It was a great experience, and I enjoyed learning about the company culture and what it is like to work for a contract development/manufacturing organization. I think the ELITE program is a great way to help us postdocs make local industry contacts, and I hope to be able to participate in future site visits.” – ELITE Participant\n\n“The site visit to [Company] was awesome. Such exposure to industry is invaluable to Postdocs like me. Thanks for helping coordinate that visit.” – ELITE Participant\n\n“I love the environment of [the organization]. Thank you very much for your time and the previous chance of visiting [the organization]! Hopefully, I can naturally transfer to the clinical research field as you.” – ELITE Participant\n\n“The cover letter application is a good technique for applications and the actual site visit was excellent!” – ELITE Participant\n\n“[What I most liked about the [Company] visit was] the ability to hear from employees at varying stages of their career. The mix of hearing from early/newer employees all the way up to the VP and CEO was really great. Really enjoying the small group discussion/networking session opportunities to ask more questions!” – ELITE Participant\n\nOf ELITE participants questioned on the inaugural site visit (prior to the Consortium formation), 100% (n=4) indicated that the site visit met their expectations; other benefits were also mentioned—such as seeing what the company does, how the company works, and what it is like to work for them (Kristin Gabor, personal communication). A follow-up to one of the tri-institutional ELITE Consortium site visits indicated that 100% (n=12) thought it met their expectations and 100% (n=12) thought it was a positive use of their time. Though preliminary, these results suggest that trainees felt that they were getting what they wanted out of the site visit program; however, regular, comprehensive programmatic post-questionnaires would provide more robust evaluations of trainee satisfaction.\n\nWhile we do not have conclusive data, it seems likely that at least some of the many trainees who did not match into a career outcome of a site they visited may have still gained perspective, experience, and information that impacted their decision-making in helping them make a confident choice away from those specific career paths. Data from one institution’s annual survey (n=82) indicated that trainees were both able to connect with other scientists and experience a career path. The survey also showed that ELITE Consortium visits helped trainees identify which career options were not a good fit (Layton, unpublished data). Trainees referred to ELITE site visits by name in an open text-response answer; this data was provided in response to the question, “In your time [here], have you changed your mind about the career path you plan to take?” (47 yes); “If YES, asked “Please explain the factors that contributed to your change in career interest.”\n\nFurthermore, in response to the question: “Please list any suggestions for additional events or workshops that [we] should offer:” one respondent indicated that “[they] wish[ed] there were more options for ELITE site visits- the past few have seemed like they're all geared towards bench science careers in industry that are very specific to a certain area of research that I feel like only a few grad students would be qualified for... So maybe something a little more generalized.” Hence, a future direction would be to create site visits to a broader range of companies, perhaps even outside the scope of science-specific companies.\n\nAnother possible benefit may be reducing the number of graduate students who continue for additional postdoctoral training versus moving directly to a permanent position after graduation. In one institution’s sample of ELITE participants (n=46 graduate students), only 24% (n=10) continued on to postdoctoral positions whereas 76% (n=36) continued to permanent employment. In comparison, national results from the NSF Survey of Earned Doctorates between 1998–2018 (https://www.nsf.gov/statistics/srvydoctorates/#tabs-2), show that the percentage of life scientists that report entering postdoctoral training ranged from 59–65%. While this data is not conclusive, it at least suggests that there may be merit for further investigation. This is an issue that has long been a concern of the biomedical workforce (NIH, 2012; NPA, 2012), and hence may provide a valuable tool to help trainees move into permanent positions more quickly and enhance the biomedical workforce with their talents.\n\nIn addition, we see evidence that employers found value in participating in the ELITE site visit as well, with some anecdotal unsolicited comments including:\n\n“Thank you again for all of your work recruiting and connecting the [Institution] participants for the ELITE site visit on Tuesday. We enjoyed having you here and meeting your participants. I connected with a few [Institution] students including at the [Institution] Career Symposium and he has shown great interest in positions at [our company] so this was a great opportunity for him and others to come meet some of our R&D employees. Thanks again for taking the time to help set up this site visit and we look forward to continuing this partnership with [Institution]!”- Employer\n\n“It was really great to meet … the attendees. Everyone asked really wonderful questions and the energy during the networking was electric. So kudos to you guys for setting up such a successful program. We were happy to be a part of it!” – Employer\n\n“I wanted to let you know that one of the students you brought with you to the site visit interviewed with [our company] and we made an offer, which was accepted! This is a big win! We would love for you to use this to promote other students to apply to roles they are interested in and qualified for.”- Employer\n\n“We really enjoyed hosting, and I always enjoy talking with folks about the company! I spoke with a number of attendees, and was very impressed by their questions about the technology and how we are using it. I hope to continue discussions with several of them, and we certainly look forward to hosting again in the future.” - Employer\n\nBeyond these unsolicited anecdotal comments, several employers have taken the initiative to invite the ELITE Consortium back on a yearly basis—even taking the lead in organizing subsequent site visits. In one particular case, an employer created a flyer with “ELITE Program Alumni” to showcase all of the hires they had made through this site visit program, complete with quotes by hires. Taken together, this suggests that companies and organizations that host ELITE site visits find some value in doing so. Nonetheless, a limitation of the current study is that it does not allow for granular data regarding host company benefits. Additional data should be systematically collected from companies during future site visit programs to explore what benefits are most impactful to host organizations, what features of the program convinced them to participate, and what data they would want to demonstrate return on investment of their company’s time and resources. This data could help inform program development to ensure that it provides mutual value and benefit to the hosts, organizers, and participants alike.\n\nAlumni engagement is also a benefit, and we heard from alumni that reflecting back on their own career training and transitions from graduate or postdoctoral research, it was fulfilling to be part of setting up opportunities though ELITE for current trainees. Another benefit is that over time, site visit participants themselves may be hired at those or other companies and become the new points of contact to plan visits. This benefits the company to be able to tailor the visits to best create a PhD-trainee-centric experience. Furthermore, the alumni perspective allows the site visit host to better anticipate, plan for, and directly address common trainee questions.\n\n“It was a pleasure to have you all visit yesterday. It was only a few short months ago that I was taking advantage of opportunities like this (thanks for those, by the way!) so I’m happy to be able to pay it forward now.” - Alumni/Employer\n\nAnecdotally, the ELITE program has resulted in additional employer engagement opportunities outside of site visits. In one example, a site visit resulted in a company representative volunteering to present a separate session at one of the ELITE Consortium member institutions, in which the representative explained the company’s career path options and trajectories to a broader audience. Fellows really appreciated the company representative explaining what the position titles meant, and explaining the career ladder progression at the company.\n\n“It was great to see you here at [Company] and to interact with the fellows who came with you. I’m happy to help out as much as I can with answering questions and providing advice, so please feel free to keep using me as a resource for fellows who are interested in patent law. And if anyone sees something here at [our company] that they are interested in applying for, or if they want to speak with someone here about work in a particular field (immunotherapy, gene therapy, etc.), you can certainly reach out to me and I can put them in touch with the right person.” - Employer\n\n“It was a pleasure meeting all of you – there are so many opportunities available, whether you stay in academia or go to industry or government. Kudos for seeking out information to make the best decision for you (and extra kudos for the follow-up e-mail – it matters more than you might think). Happy to connect on LinkedIn, or chat further if you have additional questions.” - Employer\n\n\nConclusions and future directions\n\nOur data suggests that a minimal amount of professional development time has shown significant positive impacts on career outcomes. Because this program has the potential to help many other graduate students and postdoctoral scholars, we wanted to reduce the barriers for other institutions to replicate such a program. Therefore, we have included a toolkit for developing a site visit program with local industry that can be adapted for single- or multi-institutional programs. The SOPs contain sample communications, marketing materials, policies, presentations, and program structure recommendations. We share lessons learned to create a robust, sustainable program. Furthermore, given resource scarcity, site visits can provide exceptionally effective professional development programming with minimal cost. In our experience, however, there is still a demonstrated necessity for including staff oversight and coordination time to develop a program that can run efficiently and consistently while ensuring professional business etiquette with industry – whether or not the staff take the role of the primary planners or as coordinators with a trainee planning committee. While the program results and accompanying data is encouraging, especially from the participant benefit vantage point, future research should explore the intersecting needs and potential benefits for other stakeholder benefits in greater detail. Comprehensive survey evaluations and focus groups of industry hosts, program alumni, site visit organizers, and program staff would allow for a more robust understanding of how each of these groups benefits from participating.\n\nGiven the potential need for virtual visits now and into the future, we are currently exploring opportunities to pivot these types of programs into a virtual space, as it seems likely that this will be an area of future growth. In fact, leaders in graduate education have issued calls for a greater focus on preparing trainees for broader career options especially due to the implications of COVID-19 on a global economy (Mathur, 2020). Answering these calls, we have initiated conversations with a company about hosting the first virtual site visit. It seems feasible that the company overview and panel discussions or mini-presentations may be the easiest to replicate in a virtual space. A virtual tour of the company may be feasible as well, since we learned that the company was already developing this capacity to host virtual tours; attendees may be able to view either a live or pre-recorded virtual company tour with the opportunity to ask questions at the end. While we also believe it is important to provide the opportunity for open networking, that may be an aspect of a site visit that is most challenging to replicate virtually; nonetheless, we are hopeful that the virtual networking options being explored will still provide an impactful and educational experience for attendees. Organizations such as the academic-industry collaborative non-profit organization University-Industry Demonstration Partnership (UIDP) have proposed exploring virtual site visit best practices as well (https://uidp.org/projects/; in the development phase of project at this writing). We believe virtual site visits will become increasingly pivotal for creating experiential learning opportunities for trainees interested in exploring industry, especially given the need for alternative options created by the global pandemic. Future directions should continue to explore the efficacy of virtual visits and other types of digital collaborations and connections between universities and companies.\n\n\nEthical considerations\n\nThis activity was determined to constitute Non-Human Subjects Research (NHSR) as part of the NIH BEST Consortium under the auspices of the University of North Carolina IRB (IRB Number 14-0544). For the student surveys referenced herein, information sheets were provided to trainees, along with additional consent information for any who elected to complete surveys in which case they consented by continuing the voluntary survey.\n\n\nData availability\n\nIRB approval for public data-sharing is limited to de-identified and aggregated data only, due to concerns of sharing personally identifiable information, which could be traced back to identify individuals included in the data set. Hence, personally-identifying information collected by individual institutions for their own alumni and used for coding purposes has been removed (job title, employer, LinkedIn profile or other job-related URL). Limited data-sharing for publication was approved by the respective IRBs as noted above.\n\nOpen Science Framework: Creating and Sustaining Collaborative Multi-Institutional Industry Site Visit Programs: A Toolkit - Extended Data S1-S10, https://doi.org/10.17605/OSF.IO/RNSX3 (Collins et al., 2020).\n\nThis project contains the following underlying data (information about each variable is embedded within the SPSS data files):\n\nExtended Data File – S1. UNC TIBBS Site Visit Interest Survey_DEID (SPSS)\n\nExtended Data File – S10. ELITE_DEID_coded (SPSS)\n\nOpen Science Framework: Creating and Sustaining Collaborative Multi-Institutional Industry Site Visit Programs: A Toolkit - Extended Data S1-S10, https://doi.org/10.17605/OSF.IO/RNSX3 (Collins et al., 2020).\n\nThis project contains the following extended data:\n\nExtended Data File – S2. ELITE Sample SOP Final\n\nExtended Data File – S3. ELITE First Contact Template Invitation\n\nExtended Data File – S4. ELITE Program Flyer for Industry\n\nExtended Data File – S5. ELITE Sample Agendas\n\nExtended Data File – S6. ELITE Template Email Announcement to Fellowslist\n\nExtended Data File – S7. ELITE Flyer Sample\n\nExtended Data File – S8. Sample Questions to ask Company at Site Visit\n\nExtended Data File – S9. ELITE Sample Prep Meeting Slides\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 would like to thank members of the original ELITE organizing committee, especially Tracy Clement (founder & program brander) and the founding committee Kristin Gabor, Neal Englert, Chad Osterlund, and Gabe Knudsen. We also thank subsequent NIEHS ELITE committee members Erin Romes, Prashant Rai, David Scoville, Alicia Wellman, Dierdre Tucker and Seda Kocaman. We thank NIEHS OFCD team members Katy Hamilton and Hong Xu. We would also like to acknowledge student leaders and founders of the Program in Industry Exploration (PIE) at UNC, Andrew Lerner and Justin Black. We thank the Graduate Career Consortium Graduate Education Research and Practice Committee and Dahea You for helpful comments on the manuscript. The conclusions, views, and opinions expressed in this study are those of the authors and do not necessarily reflect the official policy or position of NIH or of the institutions employing the authors.\n\n\nReferences\n\nAbu-Yousif AO, Hett EC, Skoczenski AM, et al.: The ABC's of industry: a postdoc program provides a sneak peek into industry careers. Nat Biotechnol. 2010; 28(6): 625–626. PubMed Abstract | Publisher Full Text\n\nCarbone A, Rayner GM, Ye J, et al.: Connecting curricula content with career context: the value of engineering industry site visits to students, academics and industry. European Journal of Engineering Education. 2020; 1–14. Publisher Full Text\n\nCollins TR, Hoff K, Starback M, et al.: Creating and Sustaining Collaborative Multi-Institutional Industry Site Visit Programs: A Toolkit - Extended Data S1-S10. 2020. http://www.doi.org/10.17605/OSF.IO/RNSX3\n\nLenzi RN, Korn SJ, Wallace M, et al.: The NIH \"BEST\" programs: Institutional programs, the program evaluation, and early data. FASEB J. 2020; 34(3): 3570–3582. PubMed Abstract | Publisher Full Text\n\nMathur A: Meeting the Moment. Inside Higher Ed. 2020. Retrieved September 3, 2020. Reference Source\n\nNational Institutes of Health (NIH): Biomedical Research Workforce Working Group Report. Bethesda, MD, 2012. Retrieved September 3, 2020. Reference Source\n\nNational Postdoctoral Association (NPA) 10TH ANNUAL MEETING: Ymaws.com. 2012. Retrieved July 31, 2020. Reference Source\n\nNature: Postdocs probe industry. Nature Careers. 2011; 478(277). Retrieved September 3, 2020. Reference Source\n\nSchnoes AM, Caliendo A, Morand J, et al.: Internship experiences contribute to confident career decision making for doctoral students in the life sciences. CBE Life Sci Educ. 2018; 17(1): ar16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSinche M, Layton RL, Brandt PD, et al.: An evidence-based evaluation of transferrable skills and job satisfaction for science PhDs. PLoS One. 2017; 12(9): e0185023. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStayart CA, Brandt PD, Brown AM, et al.: Applying inter-rater reliability to improve consistency in classifying PhD career outcomes [version 2; peer review: 2 approved]. F1000Res. 2020; 9: 8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTsang C, Fisher M: Testing the waters. Nature. 2011; 480(576): 576–576. Publisher Full Text\n\nUniversity Industry Demonstration Partnerships (UIDP). UIDP Active Projects. Accessed August 25, 2020. Reference Source\n\nVan Wart A, O’Brien TC, Varvayanis S, et al.: Applying Experiential Learning to Career Development Training for Biomedical Graduate Students and Postdocs: Perspectives on Program Development and Design. CBE Life Sci Educ. 2020; 19(3): es7. PubMed Abstract | Publisher Full Text\n\nVelez GS, Giner GR: Effects of business internships on students, employers, and higher education institutions: A systematic review. J Employ Couns. 2015; 52(3): 121–130. Publisher Full Text\n\nXu H, Gilliam RST, Peddada SD, et al.: Visualizing detailed postdoctoral employment trends using a new career outcome taxonomy. Nat Biotechnol. 2018; 36(2): 197–202. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "74735",
"date": "27 Nov 2020",
"name": "Nana Lee",
"expertise": [
"Reviewer Expertise Graduate professional development",
"industry collaborations",
"graduate curriculum",
"site visits",
"mentorshp",
"career outcomes of graduate students."
],
"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\nMethods were thoroughly written and a great idea for SOPs to involve multiple-institutional collaboration. Here are some points which should be addressed.\n1) Site visits are valuable, but the authors should address other variables which could have contributed to the hiring of these graduates, such as their professional development before or after these site visits. What other factors may have contributed to the hiring of these graduates? The authors should state these in their discussion - as just having a site visit is not the only factor in the hiring of these graduates.\na) Selection of attendees was by cover letters which already skews the pool of attendees who are deeply invested in their own career development, who had already perhaps attended cover letter-writing training.\nb) The selection process also used \"leadership involvement\" which selects for students who are driven in their career development already.\n2) Under joint program development: students were asked for their interests in R & D, pharma and CROs - some of these overlap, as all of these categories can contain R & D. This is related to point 5.\n3) Site visits - were there any liability waivers which the trainees had to sign? Just a question which could be a supplemental form in the future.\n4) Methods - data collection to \"assess the program's success\" - what defines success here? Career outcomes of participants? The proper negative control would be to collect employment data from a group of graduates who did not attend site visits, or even better, if the control group did not attend site visits, but had simliar interests, academic productivity and similar leadership experience. If this control was not collected, this has to be addressed in the discussion, as being a limitation of this study.\n5) The cutoff of 20,000 or less employees for biotech and 20,000+ for Pharma seems random - the type of career which the graduate enters should be assessed by their specific role. i.e. R & D, Medical Affairs, Business Development - regardless of the title/type of organization. Both biotech and pharma hold all of these roles. A more detailed analysis would be to see if the graduate obtained a job in the area of interest they had expressed prior/during site visit. Most students who are interested in R&D go into R&D, regardless if it is in biotech, pharma, non-profit government, CRO. This would affect the statement in the Results \"Thus, while site visits did not necessarily act as direct career pipelines, they did allow for attendees to gain a sense of the culture within a particular company type and sector, allowing for them to have a more confident match in their future careers.\" If authors do not have this data (I could not tell from the supplemental information), this should be addressed in the discussion.\n6) Under program summaries, the authors state n=126 but the total number in figure 4 is 141.\n7) \"Hence, our data suggests that positive benefits can arise with as little as 4–12 hours of time invested in professional development, networking, and experiential immersion during site visit activities.\" With the caveat that a negative control group does not exist here.\n8) The sample number of organizing trainees (n=5) is too small to make any conclusion. Although yes, the numbers who were hired by the company 3/5 is 60% - probably best to leave it as just the number and not a percentage.\n9) Fig 6: What are the numbers of graduates these companies hired who did not participate in the ELITE program? This would be a control group. If authors cannot obtain this data, this would be a discussion point.\n10) \"In one institution’s sample of ELITE participants (n=46 graduate students), only 24% (n=10) continued on to postdoctoral positions whereas 76% (n=36) continued to permanent employment.\" Trainees attending these site visits are more likely to be the ones who have decided to not pursue a postdoc. Maybe an intake question for the next site visit.\n11) Another factor which could have been discussed is geography. Research Triangle Park is a research hub - how many of these graduates are employed by these institutations because they live here? How many of these ELITE students left NC area with what type of career outcome?\nThese points should be addressed in the discussion and/or future directions to make this publication a more thorough report and study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8677",
"date": "28 Oct 2022",
"name": "Tammy Collins",
"role": "Author Response",
"response": "Response to 1-a & b: We made every effort to accommodate nearly all applicants for each site visit--including asking the companies if they could accommodate a few extra people when the applicant pool was high, and including giving up ‘program director’ seats to trainees. We acknowledge that writing a cover letter requires effort and planning, and at the same time we do not expect that this creates an insurmountable barrier for graduate and postdoctoral trainees. While we acknowledge that some self-selection bias may occur, the process of practicing cover-letter writing and thus researching the company will help strengthen their job application skills and thus competitiveness on the job market. In addition, we acknowledge that many factors may influence the hiring of graduates into these companies. Self-selection bias has now been acknowledged in a new limitations and future directions section added to the manuscript. Response to 2: We agree that there is some overlap between R&D, pharma, and CRO; the pre-interest questionnaire allowed respondents to select from a wide variety of career categories and they could select interest in more than one. These distinctions were based on a convenience sample representative of the type of industries most common in our area, and we recognize that this could differ in other regions. Response to 3: Regarding legal liabilities, such as if an accident were to happen--this is an important consideration for organizing a site visit. In our experience, trainees participating in an institutionally-organized site visit would typically be covered by the institution’s existing worker’s compensation policy. Site visit organizers should refer to their own institutions’ worker’s compensation policies to determine accident liability. In addition to accident liabilities, another common question that arises concerns confidentiality agreements. Companies occasionally requested that attendees sign confidentiality agreements stating that they would not divulge proprietary information learned during the visit. We have added the following text to the “Identifying and contacting companies” section: “Additional considerations include confidentiality and liability. While rare, companies have occasionally requested that attendees sign non-disclosure agreements; thus we suggest that organizers coordinate with the company and check with institutional subject matter experts (e.g. ethics officer, legal counsel) to ensure compliance with institutional guidelines. In case of questions from the company about liability, it is also important for institutions to clarify the extent of their coverage (e.g. liability coverage, workers’ compensation). Each of our institutions’ coverage extended to trainees while off campus and one should check their own institutions’ local policy.” Response to 4: The purpose of this study was to assess initial program outcomes and to provide a toolkit to help facilitate the adoption of site visits by other institutions. We agree that obtaining a negative control would be a cleaner test of the hypothesis. At the same time, we also acknowledge that there is always some element of self-selection bias in career development participation; hence, it is difficult to define a true negative control. One approach could be to compare these results to national or institutional career outcome averages, yet there are inherent difficulties in obtaining a representative sample that is truly comparable to a site visit participant comparison sample. Nonetheless, future studies could attempt to establish a baseline measurement of career outcomes pre- and post- introduction of site visit programs, while acknowledging that this method could also be confounded by economic and programmatic changes over time. This is beyond the scope of the current study but we agree that this is an interesting question which merits further attention across the career development field as a whole in identifying promising practices for effectively evaluating programs. We have acknowledged this limitation in the new limitations and future directions section of the manuscript. Response to 5: Regarding company type, we searched the company website, LinkedIn, or the NC Biotechnology company directory to determine how to categorize a company based on their own self-identification. In rare cases where the self-identification was not made, company size was used as a factor in determining biotech versus pharma. The definition of these two has morphed over time, with size now being a commonly used factor toward distinguishing between the two (e.g., https://biotechhealth.com/biotech-vs-pharma/) and we used LinkedIn’s automatic company size designations as a cutoff which is now indicated in the manuscript. Regarding specific roles, thank you for pointing out that R & D may be a common career interest. It will be interesting to note for future analysis how company size and type factors into career choices relative to roles within a company. We also would like to point out the nuance that company cultures can vary quite a bit between large and small companies, and also between those that identify as contract research organizations relative to biotech or pharma, even across common R & D roles. We have acknowledged this in the new limitations and future direction section of the manuscript by adding the following text: “Future directions could look at different binnings of company type as well as how interest, exposure, and first job match is related to specific roles (e.g., R &D). Our site visits covered a multitude of roles within each company type and hence career outcomes for specific roles could not be matched at this level of granularity.” Response to 6: We understand that the figure may be confusing. The total number hired at a different company type (44) plus the number hired at a matching company type (82) is equal to 126. The number hired at a specific company visited (10, of which 3 were site visit organizers) is still part of the 82 hired at a company type; extra description was added to clarify the relative proportion of the 82 company type matches that involved being hired at a specific company visited. To clarify these distinctions, we have modified the figure legend. The following text modified to say the following: “The majority of ELITE attendee alumni were hired at a company type that matched those they visited (N=82, green icons (all shades)). Of those 82, ten were hired at the specific company visited, and 3 of those 10 were trainee site visit organizers.” Response to 7: Thank you for pointing this out. We have addressed this in our response to point 4 above. Response to 8: We agree that results should be interpreted with caution because in some cases the “N” is small. Because of that, we chose to include both the “N”s as well as the percentages so that it would be informative for the reader and also allow for comparisons of differing proportions in order to highlight patterns. Response to 9: This is a great area for future discussion and outside the scope of the current study. We have added a paragraph on limitations and future directions in which we address the need for a control group, including non-participant career outcomes (second paragraph). We acknowledge that this is an important area of future consideration. Response to 10: We agree that this is a key area of consideration, and it will be important to examine whether site visits are simply selecting for those who otherwise would not do a postdoc, or whether they are facilitating quicker transitions into permanent employment. It will be interesting to further pursue these questions and adjust our intake questionnaires accordingly in future studies. The following has been added to limitations and future directions section: “Furthermore, intent to pursue additional training (e.g., postdoc) may influence immediate career decisions and could impact first-destination outcomes. The current study did not account for intent to pursue additional training and future studies should account for this intent versus intent to directly enter the workforce.” Response to 11: A large percentage of ELITE attendees are employed in NC; as more institutions are reporting their career outcomes, it is becoming apparent that geography indeed plays a role--increasing evidence demonstrates a strong correlation between the location in which someone trained and the location in which they became employed. For instance, the top job location for all ELITE institutions with publicly available location information was North Carolina (e.g., Xu et al 2018, https://www.niehs.nih.gov/careers/research/fellows/alumni-outcomes/index.cfm, https://bbsp.unc.edu/professional-development/career-outcomes/, https://gradschool.duke.edu/about/statistics/all-departments-phd-career-outcomes-statistics, https://postdoc.duke.edu/statistics-coalition-next-generation-life-science-0 The correlation between training and subsequent close proximity of employment is further supported when examining outcomes of graduate students and postdocs around the United States (Mathur et al 2016). Examples of collated institutional career outcome information can be found by exploring the Graduate Career Consortium’s database of member institution outcomes ( https://osf.io/28dn6/), or the Coalition of Next Generation of Life Sciences’ member institution outcomes (https://nglscoalition.org/). The following has been added to the article in the Limitations and Future Directions Section: “Third, we acknowledge that geographic location may influence concentration of available companies for site visits, especially given that Research Triangle Park is a major life science hub. However, future directions could explore virtual options as well as TREKs (Van Wart et al, 2020) for those institutions with fewer companies in close proximity.” Response to last statement: We have addressed these points by adding a Limitations section in the manuscript and have expanded upon the Future Directions section. Thank you for thoughtful feedback; we believe that this has significantly strengthened the manuscript."
}
]
},
{
"id": "74733",
"date": "03 Dec 2020",
"name": "Linda Louie",
"expertise": [
"Reviewer Expertise career counseling",
"career development",
"program development and evaluation",
"career education 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\nIn this article, the authors describe the development, implementation, and results of their “Enhancing Local Industry Transitions through Exploration (ELITE) Consortium,” a multi-institution industry site visit program designed to provide career exploration, company culture exposure, professional etiquette practice, and networking for biomedical graduate students and postdoctoral scholars in the Research Triangle region of North Carolina. They provide a detailed toolkit for other institutions to use in order to implement and execute their own site visit programs, and they discuss benefits for both the program participants and the employers visited. Additionally, the authors convey the career outcomes of program alumni in terms of their employment at contract research organizations, biotech companies, or pharmaceutical companies – the types of companies visited in this program. Specifically, the authors state that trainee site visit participation is positively correlated with being hired to the company visited, or to one of these three company types. In their cohort, this effect was significant for those who attended more than one site visit, namely trainees who organized the industry site visits, but not significant when these individuals were excluded from the analysis.\nThe strength of this article is it provides a toolkit to establish this type of collaboration and program. The article, and the included toolkit, is a facilitators guide that includes timelines, standard operating procedures, communications, agendas, and data collection tools. Historically, a limitation of these types of programs is that their feasibility relies on geographic location – a university located in or near a pharmaceutical and biotechnology hub, like Research Triangle Park, will have a greater ability to form the partnerships required for such a program, simply due to proximity. However, as the authors note in their discussion of future directions, these programs can be adapted from a physical to a virtual space, utilizing technologies that are now more commonplace due to the COVID-19 pandemic, such as Zoom or Remo.\nDespite this strength, we are concerned that the two conclusions stated by the authors – that site visit participation is correlated positively with being hired at one of these company types, and that site visit participation helped trainees explore industry culture and careers – are not supported conclusively by the data provided in the article.\nPrimarily, we feel it is overreaching for the authors to claim a causal relationship, significant or otherwise, between site visit participation and career outcome, given the data provided. We’re specifically concerned about the following:\n\nThere is a lack of a control group for comparison. Inclusion of a local control, or comparison to national career outcome data for biomedical trainees, would help indicate whether the outcomes for this cohort differ from those who did not attend a site visit, or from national trends.\n\nSelection biases and equity are not addressed. For example, is there a self-selection bias of program participants among trainees who may have already intended to apply for roles at a contract research organization, biotech company, or pharmaceutical company? Is the application process itself a barrier to entry for people in earlier stages of career exploration? Is there a selection bias for applicants who were more skilled at writing a mock cover letter, opposed to selection based on whether their intended goals aligned with those of the program? Since exclusion criteria are not detailed in the article, we wonder what criteria were used to evaluate how well a cover letter was tailored.\nSecondarily, the authors include only anecdotal evidence for several claims pertaining to the success of their program. Statements, such as those below, seem overreaching given the limited data.\n\n“…our data suggests that positive benefits can arise with as little as 4–12 hours of time invested in professional development, networking, and experiential immersion during site visit activities.”\n\n“Thus, while site visits did not necessarily act as direct career pipelines, they did allow for attendees to gain a sense of the culture within a particular company type and sector, allowing for them to have a more confident match in their future careers.”\n\nThese statements would be strengthened by inclusion of data pertaining to how these variables (time invested, understanding of company culture, etc.) were evaluated, and how the success of the program was evaluated overall.\n\nTo improve the authors’ conclusions with the data they have, we think a stronger case could be made by separating the program description, toolkit, and benefits from the story about career outcomes, allowing each to stand on their own.\n\nFor the program, toolkit and benefits story, addition of program evaluation criteria would benefit not only the toolkit for someone who wishes to emulate the program, but also strengthen the conclusions made about the benefits and impacts to the cohort studied here. Additionally, we suggest the authors investigate more the qualitative data from their program. It seems that they have quite a few written testimonials from both employers and participants; perhaps these responses could be coded, and further conclusions drawn that would flesh out the program benefits and could support the quantitative career outcomes data. It would also allow for a more in-depth analysis of their program in context of the current literature. For example, how does the ELITE program compare with other research into internships, job simulations, and other kinds of career exploration activities, and can you draw some conclusions about how site visits provide some of the same benefits in a shorter amount of time? Or do they provide additional benefits, such as employer engagement, not offered by traditional career exploration activities?\n\nFor the career outcomes story, we feel that, aside from addressing our concerns stated above, studying a larger cohort is necessary in order to strengthen evidence that a positive correlation exists between site visit attendance and being hired at a company. To do so, the authors might consider partnering with another entity who runs a similar program. For example, the Society of Fellows, the postdoctoral association at The Scripps Research Institute, runs a long-standing industry site visit program, much like that at NIEHS. Not only would this increase the size of the cohort, but would also strengthen the authors’ most compelling evidence that being a site visit organizer significantly increases the likelihood of being hired in industry, as Scripps’ organizers are postdoctoral scholars.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "8678",
"date": "28 Oct 2022",
"name": "Tammy Collins",
"role": "Author Response",
"response": "Response to 1: We agree that this is a methodological limitation; more detail is addressed in our response to Reviewer 1Q4 who raised the same concern. Please note that we also address this concern in the newly added \"Limitations and future directions\" section of the manuscript. Response to 2: Minimizing biases and ensuring equity during the selection process are important considerations for any program. We address a similar concern about selection criteria in our response to Reviewer 1Q1, and note that we also included discussion in the newly added \"Limitations and future directions\" section to address this. Equity and access issues have also been acknowledged and the following sentence has been added to the \"Limitations and future directions\" section of the manuscript: “We also recognize that preparation and understanding of career development processes may not be equitably accessed, which could influence site visit participation.” We also acknowledge that additional inequities exist (e.g., between Black job seekers’ networks and white job seekers’ networks). The ELITE program could help to explicitly overcome this by expanding networks and connecting to individuals primed to take action to assist in job seeking at the company. Response to 3: Thank you for raising these issues. Reviewer 1 had the same concerns which we address in our response to R1Q4 and R1Q7. Additionally, we added text to the new Limitations and future directions section of the manuscript as indicated above. Response to next statement about separating the manuscript: The purpose of this study was to assess initial program outcomes and to provide a toolkit to help facilitate the adoption of site visits by other institutions. We feel that it is important to include initial program outcomes alongside the toolkit in order to provide an initial preview of the potential benefits of such a program. In the future, it will be interesting to conduct additional studies to better ascertain the mechanism(s) and the degree to which site visits may help trainees make more informed career decisions. We have modified text in the Introduction to include the following statement: “Our purpose in providing a toolkit along with preliminary outcomes is to demonstrate initial program effectiveness and lessons learned in order to inspire development of experiential opportunities at other institutions.” Furthermore, to acknowledge the importance of replicating the toolkit, we included the following statement in the new Limitations and Future Directions section: “It will be important for future work to replicate this program using the toolkit at other institutions and evaluate its effectiveness.” Response to the next statement about evaluation: We thank the reviewer for their feedback and agree that further research would allow us to better assess all of the benefits of conducting site visits. These will be important topics to pursue in future directions; we should note that all of the testimonials from employers resulted from unsolicited feedback and subsets of trainee self-report survey data (e.g., select cohort comparisons). We did not systematically collect qualitative data for a comprehensive evaluation and we agree this would provide a rich data source for future studies. The following statement has been added to the new Limitations and future directions section of the manuscript: “Furthermore, to complement quantitative analysis of career outcome matches, a comprehensive qualitative evaluation could provide more robust insight about the benefits of participating in the ELITE program.” Response to next statement about cohort size: This is a fantastic idea and we agree it would provide not only a greater sample size but allow for additional multi-site comparisons of program success. Examples of great potential collaboration opportunities include but are not limited to the variety of program examples we included in the manuscript. We also modified the article to include Scripps’ Society of Fellows Industry Bridge Program. Thank you for bringing this to our attention. We also modified the text within the Limitations and future directions section to include the cross-site evaluation recommendation: “...to collaboratively conduct cross-site evaluations with similar existing programs.”"
}
]
},
{
"id": "74731",
"date": "07 Dec 2020",
"name": "Subu Subramanian",
"expertise": [
"Reviewer Expertise Neuroscience"
],
"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: The article describes the conceptualization, implementation and preliminary evaluation of a career development program termed Enhancing Local Industry Transitions through Exploration (ELITE) that is aimed at postdoctoral researchers and senior graduate students in three research institutions (Duke University, NIEHS and UNC) in and around the Research Triangle Park, North Carolina. As the number of PhD holders keeps increasing while the number of tenure-track positions remains constant, there is an increasing need for trainees at research centers to explore industry opportunities. The ELITE program was established to facilitate site-visits to local industries that provide networking opportunities between the candidate and the company. Unlike other student/trainee driven career programs, at ELITE the institutional staff of the participating institutes serve as lead organizers. The authors provide (i) a detailed toolkit, including standard operating procedures (SOP) for initiating first contact with company partners, selecting appropriate candidates from the application pool, organizing transportation and logistics for travel as well as fostering, and maintaining future relationships with the company partner organizations after the site visit. (ii) an analysis of how successful the ELITE trainees are in finding jobs in the industry.\nThe toolkit illustrates a framework with a detailed standard operating processes (SOP) for initiating first contact with company partners, selecting appropriate candidates from the application pool, organizing transportation and logistics for travel as well as fostering, and maintaining future relationships with the company partner organizations after the site visit. The toolkit and SOP are bound to be a useful resource for trainees at various research institutions wanting to organize site visits to local industries. The framework is beneficial for all stake-holders, for the trainees, it provides a platform to learn writing cover-letters, business etiquette and conducting background research on companies before the site-visit. For the company partners it provides activity templates for conducting a successful site-visit. The article reports that several of the trainees successfully transitioned to the industry of their choice and that many ex-alumni of the program have anecdotally praised it. In conclusion, considering the limited opportunities to find an academic position, the article supports an important point about the necessity of career development avenues for postdoctoral researchers.\nGeneral Comments: Minor comments:\nFor the data collected for the manuscript, mention the years or months for which the ELITE program was operational, and comment on how representative the data is across the different years / institutions.\n\nFigure 3 is unnecessary.\n\nFigure 4, 5 and 6 can be condensed to panels of a single figure, or a table.\n\nUse “graduate students” in place of the colloquial “grad students”. Pages 10,13.\n\nMinor clarification:\nIf possible, is there data available on how many candidates of the ELITE program that successfully transitioned to the industry were international candidates? And how many industrial partners were willing to sponsor work visas?\n\nDoes the program only focus on life sciences related industries? Do other non-life science candidates benefit from the ELITE program?\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": "8679",
"date": "28 Oct 2022",
"name": "Tammy Collins",
"role": "Author Response",
"response": "Response to 1: Thank you for this suggestion, we have now included additional information to clarify this. Data includes all site visits from program inception (2015) through December 2019 and accepted job offers and/or start dates reflecting the same period. Excluding 2015, in which the program was just beginning to be formed, approximately 6 site visits per year were conducted. Participants were split approximately equally from all three institutions (Duke n=47; NIEHS n=38; UNC n=41). Please refer to the “Program summaries” section under “Methods” where we have modified the text to include this additional information. Response to 2: Thank you for noting this; while Figure 3 doesn’t present data, it was provided as an example of program branding for institutions who may want to replicate their own site visits so we have chosen to retain it. Response to 3: Thank you for pointing out that these figures could be consolidated. However, they were developed to help convey information through individual visualizations in order to highlight specific findings and better engage the reader. Because of the distinct purpose of each figure, we have elected to have them remain separate. Response to 4: Thank you for pointing that out; we have modified the article and changed all incidents of “grad” to “graduate.” Response to minor clarification 1: We acknowledge that this information would be especially informative for international students considering their career possibilities. While we do not have access to that data in the current sample, we agree that this is an interesting area to consider in future studies. We have now added a comment in the new limitations and future directions section: “Additional limitations included the inability to limit career outcomes by demographics, such as gender, race/ethnicity, international status, etc. It will be important for these variables to be examined in future research in order to identify who is participating as well as whether there are career outcome differences across groups.” Response to minor clarification 2. For the ELITE program, site visit participation was not explicitly limited to those in the life sciences, but we acknowledge that there is a strong representation of life science trainee participants based on the composition of those that program directors marketed the program to via listservs. Likewise, the ELITE program site visits were not strictly limited to life sciences by design--nonetheless, life sciences companies are very common in the Research Triangle Park area. We have added additional text within the new limitations and future directions section: “Second, our sample of trainees and companies were both life-science heavy by virtue of the population of participants served by the founding program directors and the high concentration of life science companies in this area.”"
}
]
}
] | 1
|
https://f1000research.com/articles/9-1317
|
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